@article {pmid39357284, year = {2024}, author = {Fuchs, J and García-Tabernero, A and Rosas, A and Camus, H and Metz, L and Slimak, L and Zanolli, C}, title = {The dentition of a new adult Neanderthal individual from Grotte Mandrin, France.}, journal = {Journal of human evolution}, volume = {196}, number = {}, pages = {103599}, doi = {10.1016/j.jhevol.2024.103599}, pmid = {39357284}, issn = {1095-8606}, abstract = {Grotte Mandrin is located in the middle Rhône River Valley, in Mediterranean France, and has yielded 11 Pleistocene archeological and paleoanthropological layers (ranging from the oldest layer J to the youngest layer B) dating from Marine Isotope Stage (MIS) 5 to MIS 3. We report here the nearly complete dentition of an adult Neanderthal individual, nicknamed 'Thorin,' associated to the last phase of the Post-Neronian II, in layer B2 (∼44.50-42.25 ka). A previous paleogenetic analysis revealed that Thorin is a male individual and that he shows a deep genetic divergence with other penecontemporaneous Neanderthals from western Europe that possibly occurred ∼105 ka. The 31 teeth of Thorin (including two distomolars) are described and analyzed using microcomputed tomography imaging and are compared with other Neanderthals and modern humans. Based on direct observation and measurements on the fossil remains, and using microtomographic imaging, tooth wear, nonmetric characters, crown dimensions, and dental tissue proportions were investigated, and the shape of the enamel-dentine junction of the M[2], M2, and M3 was analyzed by geometric morphometrics. Our results indicate that Thorin's teeth show dental characteristics typical of MIS 5-3 Neanderthals. It is also the first time that the presence of two distomolars is reported in a Neanderthal individual, a trait that is rare among modern human populations. Combined with the genetic peculiarities of this individual, the results of the present study imply either a process of morphological convergence among the latest Neanderthal groups or an underestimation of the genetic variability of recent Neanderthal groups.}, }
@article {pmid39333171, year = {2024}, author = {Sánchez-Yustos, P and Marín-Arroyo, AB and Arnold, LJ and Luque, L and Kehl, M and López-Sáez, JA and Carrancho Alonso, Á and Demuro, M and Sanz-Royo, A and Buckley, M and Maíllo-Fernández, JM and Cuartero-Monteagudo, F and Llamazares-González, J and Ruiz-Alonso, M and Luelmo-Lautenschlaeger, R and García-Soto, E and Alcaraz-Castaño, M}, title = {Initial Upper Palaeolithic lithic industry at Cueva Millán in the hinterlands of Iberia.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21705}, pmid = {39333171}, issn = {2045-2322}, support = {818299//the European Research Council/ ; 805478/ERC_/European Research Council/International ; }, mesh = {*Archaeology ; Animals ; Humans ; *Neanderthals ; Spain ; Fossils/history ; Industry/history ; History, Ancient ; }, abstract = {The extended period of coexistence between Neanderthals and Homo sapiens in Europe coincided with the emergence of regionally distinctive lithic industries, signalling the onset of the Upper Palaeolithic. The Iberian Peninsula was on the periphery of pioneering Upper Palaeolithic developments, with archaeological remains primarily found in northern territories. We report the discovery of an initial Upper Palaeolithic lithic industry at Cueva Millán in the hinterlands of Iberia. This industry, termed here Arlanzian, not only represents the earliest and southernmost evidence of such industries in Iberia but also lacks a direct counterpart. However, it exhibits chronological and technological parallels with the lithic industries associated with the earliest expansion of Homo sapiens throughout Eurasia. We interpret this as potential evidence of its intrusive nature, but not necessarily associated with a migration event, as more complex scenarios derived from inter-population connectivity must be also considered. The biological identity of the Arlanzian makers remains unknown, but they coexisted with declining Neanderthal groups from neighbouring territories.}, }
@article {pmid39288002, year = {2024}, author = {Relethford, JH}, title = {Craniometric variation and the ancestry of modern humans.}, journal = {American journal of biological anthropology}, volume = {}, number = {}, pages = {e25028}, doi = {10.1002/ajpa.25028}, pmid = {39288002}, issn = {2692-7691}, abstract = {OBJECTIVES: Ancient and contemporary DNA provide information about geographic variation in the ancestry of present-day humans. All living populations have ancestry from early Homo sapiens originating in sub-Saharan Africa. Populations of Eurasian descent also have a small amount of Neandertal ancestry. This study examines whether craniometric distances between recent modern human samples reflect this geographic variation in ancestry. Among recent modern humans, Eurasians are expected to be more similar to Neandertals, whereas both sub-Saharan Africans and Eurasians are expected to be equidistant from early H. sapiens.<br><br>MATERIALS AND METHODS: Data on 33 craniometric traits from 2524 recent modern humans were compared with data from the literature for Neandertals and early H. sapiens. Mahalanobis distances were computed for each modern specimen to both the Neandertal and early H. sapiens means. These distances were examined for differences between recent humans from sub-Saharan Africa (N&#x2009;=&#x2009;373) and those of Eurasian descent (N&#x2009;=&#x2009;2151).<br><br>RESULTS: Eurasians as a group are significantly closer than sub-Saharan Africans to Neandertals. There is no significant difference between the distances of sub-Saharan Africans and Eurasians to early H. sapiens.<br><br>DISCUSSION: The differences between sub-Saharan Africans and Eurasians for both Neandertals and early H. sapiens are as expected. Although there has been geographic differentiation among recent modern humans, including differences in Neandertal admixture, these differences have not affected overall similarity of recent modern sub-Saharan Africans and Eurasians to the earliest samples of H. sapiens.}, }
@article {pmid39271648, year = {2024}, author = {Higham, T and Frouin, M and Douka, K and Ronchitelli, A and Boscato, P and Benazzi, S and Crezzini, J and Spagnolo, V and McCarty, M and Marciani, G and Falcucci, A and Rossini, M and Arrighi, S and Dominici, C and Devièse, T and Schwenninger, JL and Martini, I and Moroni, A and Boschin, F}, title = {Chronometric data and stratigraphic evidence support discontinuity between Neanderthals and early Homo sapiens in the Italian Peninsula.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8016}, pmid = {39271648}, issn = {2041-1723}, support = {324139//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science-European Research Council)/ ; }, mesh = {*Neanderthals ; Italy ; Animals ; Humans ; *Bayes Theorem ; *Fossils ; Radiometric Dating/methods ; Archaeology/methods ; History, Ancient ; }, abstract = {The process by which Palaeolithic Europe was transformed from a Neanderthal-dominated region to one occupied exclusively by Homo sapiens has proven challenging to diagnose. A blurred chronology has made it difficult to determine when Neanderthals disappeared and whether modern humans overlapped with them. Italy is a crucial region because here we can identify not only Late Mousterian industries, assumed to be associated with Neanderthals, but also early Upper Palaeolithic industries linked with the appearance of early H. sapiens, such as the Uluzzian and the Aurignacian. Here, we present a chronometric dataset of 105 new determinations (74 radiocarbon and 31 luminescence ages) from four key southern Italian sites: Cavallo, Castelcivita, Cala, and Oscurusciuto. We built Bayesian-based chronometric models incorporating these results alongside the relative stratigraphic sequences at each site. The results suggest; 1) that the disappearance of Neanderthals probably pre-dated the appearance of early modern humans in the region and; 2) that there was a partial overlap in the chronology of the Uluzzian and Protoaurignacian, suggesting that these industries may have been produced by different human groups in Europe.}, }
@article {pmid39265525, year = {2024}, author = {Slimak, L and Vimala, T and Seguin-Orlando, A and Metz, L and Zanolli, C and Joannes-Boyau, R and Frouin, M and Arnold, LJ and Demuro, M and Devièse, T and Comeskey, D and Buckley, M and Camus, H and Muth, X and Lewis, JE and Bocherens, H and Yvorra, P and Tenailleau, C and Duployer, B and Coqueugniot, H and Dutour, O and Higham, T and Sikora, M}, title = {Long genetic and social isolation in Neanderthals before their extinction.}, journal = {Cell genomics}, volume = {4}, number = {9}, pages = {100593}, doi = {10.1016/j.xgen.2024.100593}, pmid = {39265525}, issn = {2666-979X}, mesh = {*Neanderthals/genetics ; Animals ; *Fossils ; Social Isolation ; Humans ; Genome ; Extinction, Biological ; France ; }, abstract = {Neanderthal genomes have been recovered from sites across Eurasia, painting an increasingly complex picture of their populations' structure that mostly indicates that late European Neanderthals belonged to a single metapopulation with no significant evidence of population structure. Here, we report the discovery of a late Neanderthal individual, nicknamed "Thorin," from Grotte Mandrin in Mediterranean France, and his genome. These dentognathic fossils, including a rare example of distomolars, are associated with a rich archeological record of Neanderthal final technological traditions in this region ∼50-42 thousand years ago. Thorin's genome reveals a relatively early divergence of ∼105 ka with other late Neanderthals. Thorin belonged to a population with a small group size that showed no genetic introgression with other known late European Neanderthals, revealing some 50 ka of genetic isolation of his lineage despite them living in neighboring regions. These results have important implications for resolving competing hypotheses about causes of the disappearance of the Neanderthals.}, }
@article {pmid39261722, year = {2024}, author = {Sun, W and Yang, T and Sun, F and Liu, P and Gao, J and Lan, X and Xu, W and Pang, Y and Li, T and Li, C and Liang, Q and Chen, H and Liu, X and Tan, W and Zhu, H and Wang, F and Cheng, F and Zhai, W and Kim, HN and Zhang, J and Zhang, L and Lu, L and Xi, Q and Deng, G and Huang, Y and Jin, X and Chen, X and Liu, W}, title = {An IGHG1 variant exhibits polarized prevalence and confers enhanced IgG1 antibody responses against life-threatening organisms.}, journal = {Nature immunology}, volume = {}, number = {}, pages = {}, pmid = {39261722}, issn = {1529-2916}, support = {2021YFC2300503//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 2021YFC2302403//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 32141004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81825010//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81930061//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Evolutionary pressures sculpt population genetics, whereas immune adaptation fortifies humans against life-threatening organisms. How the evolution of selective genetic variation in adaptive immune receptors orchestrates the adaptation of human populations to contextual perturbations remains elusive. Here, we show that the G396R coding variant within the human immunoglobulin G1 (IgG1) heavy chain presents a concentrated prevalence in Southeast Asian populations. We uncovered a 190-kb genomic linkage disequilibrium block peaked in close proximity to this variant, suggestive of potential Darwinian selection. This variant confers heightened immune resilience against various pathogens and viper toxins in mice. Mechanistic studies involving severe acute respiratory syndrome coronavirus 2 infection and vaccinated individuals reveal that this variant enhances pathogen-specific IgG1[+] memory B cell activation and antibody production. This G396R variant may have arisen on a Neanderthal haplotype background. These findings underscore the importance of an IGHG1 variant in reinforcing IgG1 antibody responses against life-threatening organisms, unraveling the intricate interplay between human evolution and immune adaptation.}, }
@article {pmid39227658, year = {2024}, author = {Richard, M and Del Val, M and Fewlass, H and Sinet-Mathiot, V and Lanos, P and Pons-Branchu, E and Puaud, S and Hublin, JJ and Moncel, MH}, title = {Multi-method dating reveals 200 ka of Middle Palaeolithic occupation at Maras rock shelter, Rhône Valley, France.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {20474}, pmid = {39227658}, issn = {2045-2322}, mesh = {*Neanderthals ; *Archaeology ; Animals ; *Radiometric Dating/methods ; France ; Humans ; Fossils ; Tooth/anatomy &amp; histology ; Geologic Sediments/analysis ; Bayes Theorem ; Bone and Bones/anatomy &amp; histology ; Electron Spin Resonance Spectroscopy/methods ; Uranium/analysis ; History, Ancient ; }, abstract = {The emergence of the Middle Palaeolithic, and its variability over time and space are key questions in the field of prehistoric archaeology. Many sites have been documented in the south-eastern margins of the Massif central and the middle Rhône valley, a migration path that connects Northern Europe with the Mediterranean. Well-dated, long stratigraphic sequences are essential to understand Neanderthals dynamics and demise, and potential interactions with Homo sapiens in the area, such as the one displayed at the Maras rock shelter ("Abri du Maras"). The site is characterised by exceptional preservation of archaeological remains, including bones dated using radiocarbon ([14]C) and teeth using electron spin resonance combined with uranium series (ESR/U-series). Optically stimulated luminescence was used to date the sedimentary deposits. By combining the new ages with previous ones using Bayesian modelling, we are able to clarify the occupation time over a period spanning 200,000 years. Between ca. 250 and 40 ka, the site has been used as a long-term residence by Neanderthals, specifically during three interglacial periods: first during marine isotopic stage (MIS) 7, between 247 ± 34 and 223 ± 33 ka, and then recurrently during MIS 5 (between 127 ± 17 and 90 ± 9 ka) and MIS 3 (up to 39,280 cal BP).}, }
@article {pmid39227643, year = {2024}, author = {Guran, SH and Yousefi, M and Kafash, A and Ghasidian, E}, title = {Reconstructing contact and a potential interbreeding geographical zone between Neanderthals and anatomically modern humans.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {20475}, pmid = {39227643}, issn = {2045-2322}, support = {402379177//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Neanderthals ; Animals ; Humans ; *Fossils ; Archaeology ; Geography ; }, abstract = {While the interbreeding of Homo neanderthalensis (hereafter Neanderthal) and Anatomically modern human (AMH) has been proven, owing to the shortage of fossils and absence of appropriate DNA, the timing and geography of their interbreeding are not clearly known. In this study, we applied ecological niche modelling (maximum entropy approach) and GIS to reconstruct the palaeodistribution of Neanderthals and AMHs in Southwest Asia and Southeast Europe and identify their contact and potential interbreeding zone during marine isotope stage 5 (MIS 5), when the second wave of interbreeding occurred. We used climatic variables characterizing the environmental conditions of MIS 5 ca. 120 to 80 kyr (averaged value) along with the topography and coordinates of Neanderthal and modern human archaeological sites to characterize the palaeodistribution of each species. Overlapping the models revealed that the Zagros Mountains were a contact and potential interbreeding zone for the two human species. We believe that the Zagros Mountains acted as a corridor connecting the Palearctic/Afrotropical realms, facilitating northwards dispersal of AMHs and southwards dispersal of Neanderthals during MIS 5. Our analyses are comparable with archaeological and genetic evidence collected during recent decades.}, }
@article {pmid39160167, year = {2024}, author = {Mateo-Lomba, P and Ollé, A and Fernández-Marchena, JL and Saladié, P and Marín, J and Chacón, MG and Vallverdú, J and Cáceres, I}, title = {First identification of a Neanderthal bone spear point through an interdisciplinary analysis at Abric Romaní (NE Iberian Peninsula).}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {19160}, pmid = {39160167}, issn = {2045-2322}, support = {CEX2019-000945-M//Spanish Ministry of Science and Innovation/ ; PID2021-122355NB-C32//MCIN/AEI/10.13039/501100011033 and by ERDF A way of making Europe/ ; PID2022-138590NB-C41//MCIN/AEI/10.13039/501100011033 and by ERDF A way of making Europe/ ; SGR 2021 01239//AGAUR/ ; SGR 2021 01237//AGAUR/ ; SGR 2021 01238//AGAUR/ ; 2023PFR-URV-01239//URV/ ; URV, 2023PFR-URV-0127//URV/ ; 2022PFR-URV- 64//URV/ ; 2023PFR-URV-01238//URV/ ; PRE2019-087734//MICINN/ ; ARQ001SOL-201-2022//Departament de Cultura of the Generalitat de Catalunya/ ; CIAPOS/2022/022//Generalitat Valenciana/ ; }, mesh = {Animals ; *Neanderthals/anatomy &amp; histology ; Spain ; *Fossils ; *Bone and Bones/anatomy &amp; histology ; *Archaeology ; Humans ; History, Ancient ; }, abstract = {Osseous industry has been observed at an increasing number of Neanderthal sites. Bone fragments were used for practical purposes, and a range of bone shaping techniques were employed. The variability of bone tools observed in different assemblages reflects considerable functional diversity. However, no bone spear points have been reported from these contexts. A comprehensive analysis of a bone spear point from the Middle Palaeolithic site of Abric Romaní (Barcelona, Spain) is presented. Through an interdisciplinary, multi-technique, and multi-scale approach combining technology, taphonomy, and functional analysis, compelling evidence for manufacture, use, and hafting was uncovered. The specimen exhibits clear signs of intentional knapping. The presence of microscopic linear impact marks, an impact fracture at the tip and potential internal stress fractures indicate its use as a spear. Furthermore, the observed wear pattern and a morphological adjustment of the trabecular tissue support the hafting hypothesis. Abric Romaní contributes to our understanding of Neanderthal hunting behaviour and the significance of composite bone tools in their technological repertoire 50,000 years ago. This discovery highlights the flexibility and adaptability of Neanderthal technology, providing evidence of bone technology that is sometimes obscured in the archaeological record and offering valuable insights into their hunting strategies during the Middle Palaeolithic.}, }
@article {pmid39144742, year = {2024}, author = {Zhao, W}, title = {Reconstructing human history from ancient genomes: an interview with Nobel laureate Svante Pääbo.}, journal = {National science review}, volume = {11}, number = {9}, pages = {nwae120}, doi = {10.1093/nsr/nwae120}, pmid = {39144742}, issn = {2053-714X}, abstract = {Professor Svante Pääbo, Director of the Max Planck Institute for Evolutionary Anthropology, won the Nobel Prize in Physiology or Medicine in 2022 for his discoveries in ancient hominine genomes and human evolution. His pioneering work in sequencing and interpreting the paleo genomes of Neanderthals and Denisovans, as well as their relationship with the modern human genome, was groundbreaking in terms of our understanding of human origins. Nowadays, we can even use commercial kits to easily detect the proportion of Neanderthal genes in our own genomes. Recently, NSR conducted an interview with Professor Pääbo to learn about his interesting work chasing the ancient genomes and reconstructing human evolutionary and migration history from the DNA evidence, as well as his perspective on paleo genome studies and his advice to young researchers: follow your interests and be ready to try some crazy things.}, }
@article {pmid39132848, year = {2024}, author = {Richards, GD and Jabbour, RS and Guipert, G and Defleur, A}, title = {Early Neanderthal mandibular remains from Baume Moula-Guercy (Soyons, Ardèche).}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {}, number = {}, pages = {}, doi = {10.1002/ar.25550}, pmid = {39132848}, issn = {1932-8494}, support = {03-Activity-059//Arthur A. Dugoni/ ; }, abstract = {We provide an ontogenetically-based comparative description of mandibular remains from Last Interglacial deposits (MIS 5e) at Baume Moula-Guercy and examine their affinities to European and Middle Eastern Middle-to-Late Pleistocene (≈MIS 14-MIS 1) Homo. Description of the M-G2-419 right partial mandibular corpus with M1-3 (15-16.0 years ±0.5 years) and mandibular fragments M-F4-77 and M-S-TNN1 is with reference to original fossils, casts, CT scans, literature descriptions, and virtual reconstructions. Our comparative sample is ontogenetically based and divided into a Preneanderthal-Neanderthal group and a Homo sapiens group. These groups are subdivided into (1) Preneanderthals (≈MIS 14-9), Early Neanderthals (MIS 7-5e), and Late Neanderthals (MIS 5d-3), and (2) Middle (MIS 5) and Upper (MIS 3-Pre-MIS 1) Paleolithic and recent H. sapiens. Standard techniques were employed for developmental age and sex determinations and measurements. The M-G2-419 mandible possesses corpus features that link it most closely with the Sima de los Huesos Preneanderthal and Early Neanderthal groups. These include mental foramen position, number, and height on the corpus, anterior marginal tubercle position, and mylohyoid line orientation. Metrically, the M-G2-419 mandibular corpus is small relative to adults in all groups, but the thickness/height relationship is like the adult condition. The thickness of the corpus is more like Neanderthal children than adolescents. Molar crown features suggest affinities with the Preneanderthal-Neanderthal group. The Moula-Guercy mandibles possess a combination of Neanderthal-associated features that provides insights into MIS 7-5e paleodeme variation and the timing of appearance of MIS 5d-3 Neanderthal facial features.}, }
@article {pmid39091830, year = {2024}, author = {Pfennig, A and Lachance, J}, title = {The evolutionary fate of Neanderthal DNA in 30,780 admixed genomes with recent African-like ancestry.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.07.25.605203}, pmid = {39091830}, issn = {2692-8205}, abstract = {Following introgression, Neanderthal DNA was initially purged from non-African genomes, but the evolutionary fate of remaining introgressed DNA has not been explored yet. To fill this gap, we analyzed 30,780 admixed genomes with African-like ancestry from the All of Us research program, in which Neanderthal alleles encountered novel genetic backgrounds during the last 15 generations. Observed amounts of Neanderthal DNA approximately match expectations based on ancestry proportions, suggesting neutral evolution. Nevertheless, we identified genomic regions that have significantly less or more Neanderthal ancestry than expected and are associated with spermatogenesis, innate immunity, and other biological processes. We also identified three novel introgression desert-like regions in recently admixed genomes, whose genetic features are compatible with hybrid incompatibilities and intrinsic negative selection. Overall, we find that much of the remaining Neanderthal DNA in human genomes is not under strong selection, and complex evolutionary dynamics have shaped introgression landscapes in our species.}, }
@article {pmid39032165, year = {2024}, author = {Seghi, F and Sorrentino, R and Bailey, SE and Piccirilli, E and Vazzana, A and Bortolini, E and Higgins, OA and Marciani, G and Orlando, MA and Spinapolice, EE and Moroni, A and Benazzi, S}, title = {Morphological and morphometric study of the hominin dental casts from Grotta-Riparo di Uluzzo C (Apulia, southern Italy).}, journal = {American journal of biological anthropology}, volume = {}, number = {}, pages = {e24998}, doi = {10.1002/ajpa.24998}, pmid = {39032165}, issn = {2692-7691}, support = {European Union - Next Generation EU PRIN 2022 TRAC//European Commission/ ; PNRR PE5 - CHANGES - SPOKE 5//European Commission/ ; }, abstract = {OBJECTIVES: Grotta-Riparo di Uluzzo C (Apulia, southern Italy) is a pivotal site for investigating the evolution of the Middle Paleolithic and the earliest phases of the Upper Paleolithic in southern Italy, as the extensive stratigraphic record of this site includes a thick Mousterian sequence followed by the Uluzzian. Here, we investigate the taxonomic affinity of seven unpublished deciduous human teeth retrieved from the site of Uluzzo C in 1960.<br><br>MATERIALS AND METHODS: The teeth are represented by seven plaster dental casts, which are housed at the Museo Civico di Paleontologia e Paletnologia in Maglie (Lecce, Apulia). The location of the original specimens remains unknown, rendering these casts the only human remains evidence yielded by Uluzzo C to date. Based on occlusal-view photographs and digital models of the casts, we examined the external morphology and morphometry of the teeth, comparing them to Homo sapiens and H. neanderthalensis samples. Through geometric morphometric methods and statistical analyses, we analyzed the crown outline of the deciduous molars.<br><br>RESULTS: The teeth show morphological and morphometric features that are variably found in H. neanderthalensis, H. sapiens, or both. Specifically, crown outline analysis shows that all molars fall within H. neanderthalensis variability, except for Uluzzo 853 (lower right deciduous first molar), which falls within H. sapiens variability.<br><br>DISCUSSION: This study provides the first taxonomic assessment of the hominin teeth from Uluzzo C. The results contribute additional insights into the Paleolithic peopling of southern Italy during a crucial period marked by the persistence of post-Tyrrhenian Neanderthal techno-complexes and the arrival of H. sapiens.}, }
@article {pmid39029412, year = {2024}, author = {Dodat, PJ and Albalat, E and Balter, V and Couture-Veschambre, C and Hardy, M and Henrion, J and Holliday, T and Maureille, B}, title = {Diverse bone-calcium isotope compositions in Neandertals suggest different dietary strategies.}, journal = {Journal of human evolution}, volume = {193}, number = {}, pages = {103566}, doi = {10.1016/j.jhevol.2024.103566}, pmid = {39029412}, issn = {1095-8606}, mesh = {Animals ; *Neanderthals ; *Diet ; *Bone and Bones/chemistry ; *Calcium Isotopes/analysis ; France ; Fossils ; }, abstract = {Zooarcheological and geochemical evidence suggests Neanderthals were top predators, but their adherence to a strictly carnivorous diet has been questioned. Recent studies have demonstrated the potential of calcium-stable isotopes to evaluate trophic and ecological relationships. Here, we measure the δ[44/42]Ca values in bone samples from Mousterian contexts at Grotte du Bison (Marine Isotope Stage 3, Yonne, France) and Regourdou (Marine Isotope Stage 5, Dordogne, France) in two new Neanderthal individuals, associated fauna, and living local plants. We use a Bayesian mixing model to estimate the dietary composition of these Neanderthal individuals, plus a third one already analyzed. The results reveal three distinct diets: a diet including accidental or voluntary consumption of bone-based food, an intermediate diet, and a diet without consumption of bone-based food. This finding is the first demonstration of diverse subsistence strategies among Neanderthals and as such, reconciles archaeological and geochemical dietary evidence.}, }
@article {pmid39011558, year = {2024}, author = {Ma, X and Lu, Y and Xu, S}, title = {Adaptive Evolution of Two Distinct Adaptive Haplotypes of Neanderthal Origin at the Immunoglobulin Heavy-chain Locus in East Asian and European Populations.}, journal = {Molecular biology and evolution}, volume = {41}, number = {7}, pages = {}, pmid = {39011558}, issn = {1537-1719}, support = {2023YFC2605400//National Key Research and Development Program of China/ ; 32030020//National Natural Science Foundation of China/ ; //Office of Global Partnerships/ ; //Human Phenome Data Center of Fudan University/ ; }, mesh = {*Neanderthals/genetics ; Animals ; *Haplotypes ; Humans ; Europe ; Asia, Eastern ; Asian People/genetics ; Immunoglobulin Heavy Chains/genetics ; White People/genetics ; Evolution, Molecular ; Genetic Introgression ; Selection, Genetic ; East Asian People ; }, abstract = {Immunoglobulins (Igs) have a crucial role in humoral immunity. Two recent studies have reported a high-frequency Neanderthal-introgressed haplotype throughout Eurasia and a high-frequency Neanderthal-introgressed haplotype specific to southern East Asia at the immunoglobulin heavy-chain (IGH) gene locus on chromosome 14q32.33. Surprisingly, we found the previously reported high-frequency Neanderthal-introgressed haplotype does not exist throughout Eurasia. Instead, our study identified two distinct high-frequency haplotypes of putative Neanderthal origin in East Asia and Europe, although they shared introgressed alleles. Notably, the alleles of putative Neanderthal origin reduced the expression of IGHG1 and increased the expression of IGHG2 and IGHG3 in various tissues. These putatively introgressed alleles also affected the production of IgG1 upon antigen stimulation and increased the risk of systemic lupus erythematosus. Additionally, the greatest genetic differentiation across the whole genome between southern and northern East Asians was observed for the East Asian haplotype of putative Neanderthal origin. The frequency decreased from southern to northern East Asia and correlated positively with the genome-wide proportion of southern East Asian ancestry, indicating that this putative positive selection likely occurred in the common ancestor of southern East Asian populations before the admixture with northern East Asian populations.}, }
@article {pmid38997559, year = {2024}, author = {Eisenstein, M}, title = {Neanderthal-human baby-making was recent - and brief.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41586-024-01452-3}, pmid = {38997559}, issn = {1476-4687}, }
@article {pmid38991054, year = {2024}, author = {Li, L and Comi, TJ and Bierman, RF and Akey, JM}, title = {Recurrent gene flow between Neanderthals and modern humans over the past 200,000 years.}, journal = {Science (New York, N.Y.)}, volume = {385}, number = {6705}, pages = {eadi1768}, doi = {10.1126/science.adi1768}, pmid = {38991054}, issn = {1095-9203}, mesh = {Animals ; Humans ; *Gene Flow ; Genetic Introgression ; *Genome, Human ; *Neanderthals/genetics ; Population Density ; Whole Genome Sequencing ; Extinction, Biological ; }, abstract = {Although it is well known that the ancestors of modern humans and Neanderthals admixed, the effects of gene flow on the Neanderthal genome are not well understood. We develop methods to estimate the amount of human-introgressed sequences in Neanderthals and apply it to whole-genome sequence data from 2000 modern humans and three Neanderthals. We estimate that Neanderthals have 2.5 to 3.7% human ancestry, and we leverage human-introgressed sequences in Neanderthals to revise estimates of Neanderthal ancestry in modern humans, show that Neanderthal population sizes were significantly smaller than previously estimated, and identify two distinct waves of modern human gene flow into Neanderthals. Our data provide insights into the genetic legacy of recurrent gene flow between modern humans and Neanderthals.}, }
@article {pmid38956433, year = {2024}, author = {Yaghmouri, M and Safdari Lord, J and Amini, M and Yekaninejad, MS and Izadi, P}, title = {The association of rs17713054 with Neanderthal origin at 3p21.31 locus with the severity of COVID-19 in Iranian patients.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {15058}, pmid = {38956433}, issn = {2045-2322}, support = {58558//Tehran University of Medical Sciences/ ; }, mesh = {Humans ; *COVID-19/genetics/virology/epidemiology ; Iran/epidemiology ; *Neanderthals/genetics ; Male ; Female ; *Polymorphism, Single Nucleotide ; Middle Aged ; *Severity of Illness Index ; *Genetic Predisposition to Disease ; Animals ; *SARS-CoV-2/genetics/isolation &amp; purification ; Adult ; Haplotypes ; Chromosomes, Human, Pair 3/genetics ; Alleles ; Genome-Wide Association Study ; Genotype ; Aged ; }, abstract = {Since the COVID-19 pandemic, the diversity of clinical manifestations in patients has been a tremendous challenge. It seems that genetic variations, as one of the players, contribute to the variety of symptoms. Genome-wide association studies have demonstrated the influence of certain genomic regions on the disease prognosis. Particularly, a haplotype at 3p21.31 locus, inherited from Neanderthals, showed an association with COVID-19 severity. Despite several studies regarding this haplotype, some key variants are not sufficiently addressed. In the present study, we investigated the association of rs17713054 at 3p21.31 with COVID-19 severity. We analyzed the genotype of 251 Iranian COVID-19 patients (151 patients with asymptomatic to mild form as control and 100 patients with severe to critical symptoms without any comorbidities as case group) using the ARMS-PCR method. Results demonstrated that the A allele confers an almost twofold increased risk for COVID-19 severity (P value = 0.008). The AA genotype also raises the risk by more than 11 times following the recessive model (P value = 0.013). In conclusion, the A allele in rs17713054 was a risk allele in Iranian patients and was independently associated with COVID-19 severity. More studies are beneficial to confirm these findings in other populations and to develop strategies for risk assessment, prevention, and personalized medicine.}, }
@article {pmid38932149, year = {2024}, author = {Ferreira, RC and Alves, GV and Ramon, M and Antoneli, F and Briones, MRS}, title = {Reconstructing Prehistoric Viral Genomes from Neanderthal Sequencing Data.}, journal = {Viruses}, volume = {16}, number = {6}, pages = {}, pmid = {38932149}, issn = {1999-4915}, support = {20/08943-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 311154/2021-2//National Council for Scientific and Technological Development/ ; }, mesh = {Animals ; *Neanderthals/genetics/virology ; *Genome, Viral ; *DNA, Ancient/analysis ; Evolution, Molecular ; DNA, Viral/genetics ; Sequence Analysis, DNA/methods ; Humans ; Phylogeny ; DNA Viruses/genetics/classification/isolation &amp; purification ; Fossils/virology ; }, abstract = {DNA viruses that produce persistent infections have been proposed as potential causes for the extinction of Neanderthals, and, therefore, the identification of viral genome remnants in Neanderthal sequence reads is an initial step to address this hypothesis. Here, as proof of concept, we searched for viral remnants in sequence reads of Neanderthal genome data by mapping to adenovirus, herpesvirus and papillomavirus, which are double-stranded DNA viruses that may establish lifelong latency and can produce persistent infections. The reconstructed ancient viral genomes of adenovirus, herpesvirus and papillomavirus revealed conserved segments, with nucleotide identity to extant viral genomes and variable regions in coding regions with substantial divergence to extant close relatives. Sequence reads mapped to extant viral genomes showed deamination patterns of ancient DNA, and these ancient viral genomes showed divergence consistent with the age of these samples (≈50,000 years) and viral evolutionary rates (10[-5] to 10[-8] substitutions/site/year). Analysis of random effects showed that the Neanderthal mapping to genomes of extant persistent viruses is above what is expected by random similarities of short reads. Also, negative control with a nonpersistent DNA virus does not yield statistically significant assemblies. This work demonstrates the feasibility of identifying viral genome remnants in archaeological samples with signal-to-noise assessment.}, }
@article {pmid38924400, year = {2024}, author = {Conde-Valverde, M and Quirós-Sánchez, A and Diez-Valero, J and Mata-Castro, N and García-Fernández, A and Quam, R and Carretero, JM and García-González, R and Rodríguez, L and Sánchez-Andrés, &#xc1; and Arsuaga, JL and Martínez, I and Villaverde, V}, title = {The child who lived: Down syndrome among Neanderthals?.}, journal = {Science advances}, volume = {10}, number = {26}, pages = {eadn9310}, pmid = {38924400}, issn = {2375-2548}, mesh = {*Down Syndrome/psychology ; Humans ; Animals ; *Neanderthals ; Child ; Female ; Male ; Child, Preschool ; }, abstract = {Caregiving for disabled individuals among Neanderthals has been known for a long time, and there is a debate about the implications of this behavior. Some authors believe that caregiving took place between individuals able to reciprocate the favor, while others argue that caregiving was produced by a feeling of compassion related to other highly adaptive prosocial behaviors. The study of children with severe pathologies is particularly interesting, as children have a very limited possibility to reciprocate the assistance. We present the case of a Neanderthal child who suffered from a congenital pathology of the inner ear, probably debilitating, and associated with Down syndrome. This child would have required care for at least 6 years, likely necessitating other group members to assist the mother in childcare.}, }
@article {pmid38916350, year = {2024}, author = {Sankaranarayanan, G and Kodiveri Muthukaliannan, G}, title = {Exploring antimicrobial resistance determinants in the Neanderthal microbiome.}, journal = {Microbiology spectrum}, volume = {12}, number = {8}, pages = {e0266223}, pmid = {38916350}, issn = {2165-0497}, abstract = {UNLABELLED: This study aimed to investigate the presence of antimicrobial resistance determinants (ARDs) in the Neanderthal microbiome through meticulous analysis of metagenomic data derived directly from dental calculus and fecal sediments across diverse Neanderthal sites in Europe. Employing a targeted locus mapping approach followed by a consensus strategy instead of an assembly-first approach, we aimed to identify and characterize ARDs within these ancient microbial communities. A comprehensive and redundant ARD database was constructed by amalgamating data from various antibiotic resistance gene repositories. Our results highlighted the efficacy of the KMA tool in providing a robust alignment of ancient metagenomic reads to the antibiotic resistance gene database. Notably, the KMA tool identified a limited number of ARDs, with only the 23S ribosomal gene from the dental calculus sample of Neanderthal remains at Goyet Troisieme Caverne exhibiting ancient DNA (aDNA) characteristics. Despite not identifying ARDs with typical ancient DNA damage patterns or negative distance proportions, our findings suggest a nuanced identification of putative antimicrobial resistance determinants in the Neanderthal microbiome's genetic repertoire based on the taxonomy-habitat correlation. Nevertheless, our findings are limited by factors such as environmental DNA contamination, DNA fragmentation, and cytosine deamination of aDNA. The study underscores the necessity for refined methodologies to unlock the genomic assets of prehistoric populations, fostering a comprehensive understanding of the intricate dynamics shaping the microbial landscape across history.<br><br>IMPORTANCE: The results of our analysis demonstrate the challenges in identifying determinants of antibiotic resistance within the endogenous microbiome of Neanderthals. Despite the comprehensive investigation of multiple studies and the utilization of advanced analytical techniques, the detection of antibiotic resistance determinants in the ancient microbial communities proved to be particularly difficult. However, our analysis did reveal the presence of some authentic ancient conservative genes, indicating the preservation of certain genetic elements over time. These findings raise intriguing questions about the factors influencing the presence or absence of antibiotic resistance in ancient microbial communities. It could be speculated that the spread of current antibiotic resistance, which has reached alarming levels in modern times, is primarily driven by anthropogenic factors such as the widespread use and misuse of antibiotics in medical and agricultural practices.}, }
@article {pmid38889149, year = {2024}, author = {Yermakovich, D and André, M and Brucato, N and Kariwiga, J and Leavesley, M and Pankratov, V and Mondal, M and Ricaut, FX and Dannemann, M}, title = {Denisovan admixture facilitated environmental adaptation in Papua New Guinean populations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {26}, pages = {e2405889121}, pmid = {38889149}, issn = {1091-6490}, support = {TK214//HM | Estonian Research Competency Council (Research Competency Council)/ ; 810645//EC | Horizon Europe | WPSERA | HORIZON EUROPE Reforming and enhancing the European Research and Innovation system (REERIS)/ ; MOBEC008//EC | European Regional Development Fund (ERDF)/ ; PAPUAEVOL 20-CE12-0003-01//Association Nationale de la Recherche et de la Technologie (ANRT)/ ; NA//French Ministry of Foreign and European Affairs/ ; NA//Laboratoire d'Excellence TULIP (Labex TULIP)/ ; NA//Leakey Foundation (The Leakey Foundation)/ ; }, mesh = {Papua New Guinea ; Humans ; Animals ; *Haplotypes ; *Neanderthals/genetics ; Adaptation, Physiological/genetics ; Genetics, Population ; }, abstract = {Neandertals and Denisovans, having inhabited distinct regions in Eurasia and possibly Oceania for over 200,000 y, experienced ample time to adapt to diverse environmental challenges these regions presented. Among present-day human populations, Papua New Guineans (PNG) stand out as one of the few carrying substantial amounts of both Neandertal and Denisovan DNA, a result of past admixture events with these archaic human groups. This study investigates the distribution of introgressed Denisovan and Neandertal DNA within two distinct PNG populations, residing in the highlands of Mt Wilhelm and the lowlands of Daru Island. These locations exhibit unique environmental features, some of which may parallel the challenges that archaic humans once confronted and adapted to. Our results show that PNG highlanders carry higher levels of Denisovan DNA compared to PNG lowlanders. Among the Denisovan-like haplotypes with higher frequencies in highlander populations, those exhibiting the greatest frequency difference compared to lowlander populations also demonstrate more pronounced differences in population frequencies than frequency-matched nonarchaic variants. Two of the five most highly differentiated of those haplotypes reside in genomic areas linked to brain development genes. Conversely, Denisovan-like haplotypes more frequent in lowlanders overlap with genes associated with immune response processes. Our findings suggest that Denisovan DNA has provided genetic variation associated with brain biology and immune response to PNG genomes, some of which might have facilitated adaptive processes to environmental challenges.}, }
@article {pmid38840007, year = {2024}, author = {Callaway, E}, title = {These Neanderthal fire pits offer an extraordinarily precise snapshot of ancient life.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {38840007}, issn = {1476-4687}, }
@article {pmid38802968, year = {2024}, author = {Roca-Ayats, N and Maceda, I and Bruque, CD and Martínez-Gil, N and Garcia-Giralt, N and Cozar, M and Mellibovsky, L and Van Hul, W and Lao, O and Grinberg, D and Balcells, S}, title = {Evolutionary and functional analyses of LRP5 in archaic and extant modern humans.}, journal = {Human genomics}, volume = {18}, number = {1}, pages = {53}, pmid = {38802968}, issn = {1479-7364}, support = {SAF 2016-75948R and PID2019-107188RB-C21//Ministerio de Ciencia e Innovaci&#xf3;n/ ; GRC 2017 SGR 937//Generalitat de Catalunya/ ; 2017SGR:00738//Catalan Government/ ; PGC2018-098574-B-I00//Ministerio de Econom&#xed;a y Competitividad/ ; }, mesh = {Humans ; *Low Density Lipoprotein Receptor-Related Protein-5/genetics ; *Evolution, Molecular ; Animals ; *Neanderthals/genetics ; Selection, Genetic/genetics ; Hominidae/genetics ; Haplotypes/genetics ; Bone Density/genetics ; Genome, Human/genetics ; }, abstract = {BACKGROUND: The human lineage has undergone a postcranial skeleton gracilization (i.e. lower bone mass and strength relative to body size) compared to other primates and archaic populations such as the Neanderthals. This gracilization has been traditionally explained by differences in the mechanical load that our ancestors exercised. However, there is growing evidence that gracilization could also be genetically influenced.<br><br>RESULTS: We have analyzed the LRP5 gene, which is known to be associated with high bone mineral density conditions, from an evolutionary and functional point of view. Taking advantage of the published genomes of archaic Homo populations, our results suggest that this gene has a complex evolutionary history both between archaic and living humans and within living human populations. In particular, we identified the presence of different selective pressures in archaics and extant modern humans, as well as evidence of positive selection in the African and South East Asian populations from the 1000 Genomes Project. Furthermore, we observed a very limited evidence of archaic introgression in this gene (only at three haplotypes of East Asian ancestry out of the 1000 Genomes), compatible with a general erasing of the fingerprint of archaic introgression due to functional differences in archaics compared to extant modern humans. In agreement with this hypothesis, we observed private mutations in the archaic genomes that we experimentally validated as putatively increasing bone mineral density. In particular, four of five archaic missense mutations affecting the first &#x3b2;-propeller of LRP5 displayed enhanced Wnt pathway activation, of which two also displayed reduced negative regulation.<br><br>CONCLUSIONS: In summary, these data suggest a genetic component contributing to the understanding of skeletal differences between extant&#xa0;modern humans and archaic Homo populations.}, }
@article {pmid38798350, year = {2024}, author = {Iasi, LNM and Chintalapati, M and Skov, L and Mesa, AB and Hajdinjak, M and Peter, BM and Moorjani, P}, title = {Neandertal ancestry through time: Insights from genomes of ancient and present-day humans.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38798350}, issn = {2692-8205}, support = {R35 GM142978/GM/NIGMS NIH HHS/United States ; }, abstract = {Gene flow from Neandertals has shaped the landscape of genetic and phenotypic variation in modern humans. We identify the location and size of introgressed Neandertal ancestry segments in more than 300 genomes spanning the last 50,000 years. We study how Neandertal ancestry is shared among individuals to infer the time and duration of the Neandertal gene flow. We find the correlation of Neandertal segment locations across individuals and their divergence to sequenced Neandertals, both support a model of single major Neandertal gene flow. Our catalog of introgressed segments through time confirms that most natural selection-positive and negative-on Neandertal ancestry variants occurred immediately after the gene flow, and provides new insights into how the contact with Neandertals shaped human origins and adaptation.}, }
@article {pmid38782948, year = {2024}, author = {Limmer, LS and Santon, M and McGrath, K and Harvati, K and El Zaatari, S}, title = {Differences in childhood stress between Neanderthals and early modern humans as reflected by dental enamel growth disruptions.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {11293}, pmid = {38782948}, issn = {2045-2322}, support = {353106138//Deutsche Forschungsgemeinschaft/ ; EP/X020819/1//Engineering and Physical Sciences Research Council/ ; State Research Award 2014//Ministerium f&#xfc;r Wissenschaft, Forschung und Kunst Baden-W&#xfc;rttemberg/ ; 101019659//H2020 European Research Council/ ; 101001889//H2020 European Research Council/ ; }, mesh = {Animals ; *Neanderthals ; Humans ; *Dental Enamel/growth &amp; development ; Child ; *Dental Enamel Hypoplasia ; Bayes Theorem ; Child, Preschool ; Male ; Fossils ; Female ; Stress, Physiological ; Infant ; }, abstract = {Neanderthals' lives were historically portrayed as highly stressful, shaped by constant pressures to survive in harsh ecological conditions, thus potentially contributing to their extinction. Recent work has challenged this interpretation, leaving the issue of stress among Paleolithic populations highly contested and warranting in-depth examination. Here, we analyze the frequency of dental enamel hypoplasia, a growth disruption indicator of early life stress, in the largest sample of Neanderthal and Upper Paleolithic dentitions investigated to date for these features. To track potential species-specific patterns in the ontogenetic distribution of childhood stress, we present the first comprehensive Bayesian modelling of the likelihood of occurrence of individual and matched enamel growth disruptions throughout ontogeny. Our findings support similar overall stress levels in both groups but reveal species-specific patterns in its ontogenetic distribution. While Neanderthal children faced increasing likelihoods of growth disruptions starting with the weaning process and culminating in intensity post-weaning, growth disruptions in Upper Paleolithic children were found to be limited around the period of weaning and substantially dropping after its expected completion. These results might, at least in part, reflect differences in childcare or other behavioral strategies between the two taxa, including those that were advantageous for modern humans' long-term survival.}, }
@article {pmid38782905, year = {2024}, author = {Yee, SW and Ferrández-Peral, L and Alentorn-Moron, P and Fontsere, C and Ceylan, M and Koleske, ML and Handin, N and Artegoitia, VM and Lara, G and Chien, HC and Zhou, X and Dainat, J and Zalevsky, A and Sali, A and Brand, CM and Wolfreys, FD and Yang, J and Gestwicki, JE and Capra, JA and Artursson, P and Newman, JW and Marquès-Bonet, T and Giacomini, KM}, title = {Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4380}, pmid = {38782905}, issn = {2041-1723}, support = {GM117163//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01 EY032161/EY/NEI NIH HHS/United States ; R01 GM139875/GM/NIGMS NIH HHS/United States ; GM139875//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01 GM117163/GM/NIGMS NIH HHS/United States ; EY032161//U.S. Department of Health &amp; Human Services | NIH | National Eye Institute (NEI)/ ; }, mesh = {Animals ; Humans ; Amino Acid Sequence ; Estradiol/metabolism ; HEK293 Cells ; Hominidae/genetics/metabolism ; Mutation, Missense ; Organic Cation Transport Proteins/metabolism/genetics ; *Primates/genetics ; Pseudogenes ; Substrate Specificity ; }, abstract = {SLC22A10 is an orphan transporter with unknown substrates and function. The goal of this study is to elucidate its substrate specificity and functional characteristics. In contrast to orthologs from great apes, human SLC22A10, tagged with green fluorescent protein, is not expressed on the plasma membrane. Cells expressing great ape SLC22A10 orthologs exhibit significant accumulation of estradiol-17β-glucuronide, unlike those expressing human SLC22A10. Sequence alignments reveal a proline at position 220 in humans, which is a leucine in great apes. Replacing proline with leucine in SLC22A10-P220L restores plasma membrane localization and uptake function. Neanderthal and Denisovan genomes show proline at position 220, akin to modern humans, indicating functional loss during hominin evolution. Human SLC22A10 is a unitary pseudogene due to a fixed missense mutation, P220, while in great apes, its orthologs transport sex steroid conjugates. Characterizing SLC22A10 across species sheds light on its biological role, influencing organism development and steroid homeostasis.}, }
@article {pmid38779339, year = {2024}, author = {Gennai, J}, title = {The Mousterian in North-Western Tuscany: publishing fieldwork documentation leads to a new stratigraphical interpretation of the Piano di Mommio sites.}, journal = {Open research Europe}, volume = {4}, number = {}, pages = {37}, pmid = {38779339}, issn = {2732-5121}, abstract = {BACKGROUND: The Mousterian technocomplex is commonly associated with Neanderthals and therefore serves as a proxy for their presence across Europe. Stratified archaeological sites are the most informative because they can yield information about artefacts' spatial distribution and dating. Only a few of the Mousterian sites in Tuscany (Italy) met these conditions and most of these sites are concentrated in the North-Western area, with three specific sites situated in proximity to the village of Piano di Mommio, on the slopes of a small river canyon. Nevertheless, research on the sites stopped early on due to their small extent and complete excavation, which does not allow for additional fieldwork.<br><br>METHODS: This article presents previously unpublished field notes, reports, and images, which are then correlated with recent archaeological surveys.<br><br>RESULTS: This combination of historical and contemporary data aims to provide a more detailed understanding of the context in which the assemblages at these sites were found. The insights gained from this research shed light on the arrangement and positioning of artefacts at these locations, offering valuable information to guide future investigations on the assemblages.<br><br>CONCLUSIONS: The proposed stratigraphical interpretation adheres to the available information and therefore contributes to a future baseline for new research on the sites and on Neanderthal presence in the area.}, }
@article {pmid38778167, year = {2024}, author = {Marinelli, F and Moncel, MH and Lemorini, C}, title = {The use of bones as tools in Late Lower Paleolithic of Central Italy.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {11666}, pmid = {38778167}, issn = {2045-2322}, support = {ANR-19-CE27-0011-01//Neandroots project/ ; }, mesh = {Italy ; Animals ; *Fossils ; *Bone and Bones ; *Archaeology ; Humans ; Neanderthals ; Hominidae ; History, Ancient ; Tool Use Behavior ; }, abstract = {The Latium area in Italy has yielded rich evidence of Lower Paleolithic sites with both faunal remains, artefacts, and human fossil remains, such as the Ceprano human skull. Many are the sites where lithic industry has been found in association with bone industry. Medium and large animals were a key resource because they provided an enormous amount of meat and fat. However, they were extensively exploited for their bones, rich in marrow, and as raw material for tool production. Bone tools are so far few documented for early period of time and especially for the Middle Pleistocene in Western Europe. We report here evidence of bone tools and their efficiency of use for hominin groups living in the Frosinone-Ceprano basin during the MIS 11/10, a key period which records behavioral innovations and onset of the Neanderthal behaviors. In three sites, Isoletta, Colle Avarone and Selvotta, several bone tools and bone flakes have been discovered (MIS 11/10). They were associated to stone artefacts part of the hominins tool-kit. Technological and use-wear analyses conducted on these bone industries, dated between 410 and 430 ka, yield relevant results to understand the effectiveness of the bones tools found associated with lithic series, including handaxes.}, }
@article {pmid38771659, year = {2024}, author = {Hubáček, JA and Šedová, L and Hellerová, V and Adámková, V and Tóthová, V}, title = {Increased prevalence of the COVID-19 associated Neanderthal mutations in the Central European Roma population.}, journal = {Annals of human biology}, volume = {51}, number = {1}, pages = {2341727}, doi = {10.1080/03014460.2024.2341727}, pmid = {38771659}, issn = {1464-5033}, mesh = {Humans ; *COVID-19/genetics/epidemiology ; *Roma/genetics ; Male ; *SARS-CoV-2 ; Female ; Animals ; *Neanderthals/genetics ; Mutation ; Middle Aged ; Czech Republic/epidemiology ; Adult ; Prevalence ; 2',5'-Oligoadenylate Synthetase/genetics ; Genetic Predisposition to Disease ; Polymorphism, Single Nucleotide ; Transcription Factors/genetics ; Aged ; }, abstract = {BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and subsequent COVID-19 has spread world-wide and become pandemic with about 7 million deaths reported so far. Interethnic variability of the disease has been described, but a significant part of the differences remain unexplained and may be attributable to genetic factors.<br><br>AIM: To analyse genetic factors potentially influencing COVID-19 susceptibility and severity in European Roma minority.<br><br>SUBJECTS AND METHODS: Two genetic determinants, within OAS-1 (2-prime,5-prime-oligoadenylate synthetase 1, a key protein in the defence against viral infection; it activates RNases that degrade viral RNAs; rs4767027 has been analysed) and LZTFL1 (leucine zipper transcription factor-like 1, expressed in the lung respiratory epithelium; rs35044562 has been analysed) genes were screened in a population-sample of Czech Roma (N&#x2009;=&#x2009;302) and majority population (N&#x2009;=&#x2009;2,559).<br><br>RESULTS: For both polymorphisms, Roma subjects were more likely carriers of at least one risky allele for both rs4767027-C (p&#x2009;<&#x2009;0.001) and rs35044562-G (p&#x2009;<&#x2009;0.00001) polymorphism. There were only 5.3% Roma subjects without at least one risky allele in comparison with 10.1% in the majority population (p&#x2009;<&#x2009;0.01).<br><br>CONCLUSIONS: It is possible that different genetic background plays an important role in increased prevalence of COVID-19 in the Roma minority.}, }
@article {pmid38760502, year = {2024}, author = {Pauly, R and Johnson, L and Feltus, FA and Casanova, EL}, title = {Enrichment of a subset of Neanderthal polymorphisms in autistic probands and siblings.}, journal = {Molecular psychiatry}, volume = {}, number = {}, pages = {}, pmid = {38760502}, issn = {1476-5578}, abstract = {Homo sapiens and Neanderthals underwent hybridization during the Middle/Upper Paleolithic age, culminating in retention of small amounts of Neanderthal-derived DNA in the modern human genome. In the current study, we address the potential roles Neanderthal single nucleotide polymorphisms (SNP) may be playing in autism susceptibility in samples of black non-Hispanic, white Hispanic, and white non-Hispanic people using data from the Simons Foundation Powering Autism Research (SPARK), Genotype-Tissue Expression (GTEx), and 1000 Genomes (1000G) databases. We have discovered that rare variants are significantly enriched in autistic probands compared to race-matched controls. In addition, we have identified 25 rare and common SNPs that are significantly enriched in autism on different ethnic backgrounds, some of which show significant clinical associations. We have also identified other SNPs that share more specific genotype-phenotype correlations but which are not necessarily enriched in autism and yet may nevertheless play roles in comorbid phenotype expression (e.g., intellectual disability, epilepsy, and language regression). These results strongly suggest Neanderthal-derived DNA is playing a significant role in autism susceptibility across major populations in the United States.}, }
@article {pmid38739836, year = {2024}, author = {Helmbrecht, N and Lackner, M and Maricic, T and Pääbo, S}, title = {The modern human aryl hydrocarbon receptor is more active when ancestralized by genome editing.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {22}, pages = {e2402159121}, pmid = {38739836}, issn = {1091-6490}, support = {PAABO//NOMIS Stiftung (NOMIS Foundation)/ ; }, mesh = {*Receptors, Aryl Hydrocarbon/genetics/metabolism ; Humans ; *Gene Editing/methods ; Animals ; *Basic Helix-Loop-Helix Transcription Factors/genetics/metabolism ; Evolution, Molecular ; Pan troglodytes/genetics ; Neanderthals/genetics ; Ligands ; }, abstract = {The aryl hydrocarbon receptor (AHR) is a transcription factor that has many functions in mammals. Its best known function is that it binds aromatic hydrocarbons and induces the expression of cytochrome P450 genes, which encode enzymes that metabolize aromatic hydrocarbons and other substrates. All present-day humans carry an amino acid substitution at position 381 in the AHR that occurred after the divergence of modern humans from Neandertals and Denisovans. Previous studies that have expressed the ancestral and modern versions of AHR from expression vectors have yielded conflicting results with regard to their activities. Here, we use genome editing to modify the endogenous AHR gene so that it encodes to the ancestral, Neandertal-like AHR protein in human cells. In the absence of exogenous ligands, the expression of AHR target genes is higher in cells expressing the ancestral AHR than in cells expressing the modern AHR, and similar to the expression in chimpanzee cells. Furthermore, the modern human AHR needs higher doses of three ligands than the ancestral AHR to induce the expression of target genes. Thus, the ability of AHR to induce the expression of many of its target genes is reduced in modern humans.}, }
@article {pmid38714790, year = {2024}, author = {Schmidt, P and Tennie, C}, title = {Problems with two recent Petri net analyses of Neanderthal adhesive technology.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {10481}, pmid = {38714790}, issn = {2045-2322}, }
@article {pmid38714734, year = {2024}, author = {Fajardo, S and Kozowyk, PRB and Langejans, GHJ}, title = {Reply to: Problems with two recent Petri net analyses of Neanderthal adhesive technology.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {10489}, pmid = {38714734}, issn = {2045-2322}, support = {804151//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, }
@article {pmid38683367, year = {2024}, author = {Mansueto, A and Good, DJ}, title = {Conservation of a Chromosome 8 Inversion and Exon Mutations Confirm Common Gulonolactone Oxidase Gene Evolution Among Primates, Including H. Neanderthalensis.}, journal = {Journal of molecular evolution}, volume = {92}, number = {3}, pages = {266-277}, pmid = {38683367}, issn = {1432-1432}, mesh = {Animals ; *Evolution, Molecular ; *Exons/genetics ; *Phylogeny ; *Primates/genetics ; *Mutation/genetics ; Humans ; *L-Gulonolactone Oxidase/genetics ; *Chromosome Inversion/genetics ; Pseudogenes/genetics ; Conserved Sequence/genetics ; }, abstract = {Ascorbic acid functions as an antioxidant and facilitates other biochemical processes such as collagen triple helix formation, and iron uptake by cells. Animals which endogenously produce ascorbic acid have a functional gulonolactone oxidase gene (GULO); however, humans have a GULO pseudogene (GULOP) and depend on dietary ascorbic acid. In this study, the conservation of GULOP sequences in the primate haplorhini suborder were investigated and compared to the GULO sequences belonging to the primates strepsirrhini suborder. Phylogenetic analysis suggested that the conserved GULOP exons in the haplorhini primates experienced a high rate of mutations following the haplorhini/strepsirrhini divergence. This high mutation rate has decreased during the evolution of the haplorhini primates. Additionally, indels of the haplorhini GULOP sequences were conserved across the suborder. A separate analysis for GULO sequences and well-conserved GULOP sequences focusing on placental mammals identified an in-frame GULO sequence in the Brazilian guinea pig, and a potential GULOP sequence in the pika. Similar to haplorhini primates, the guinea pig and lagomorph species have experienced a high substitution rate when compared to the mammals used in this study. A shared synteny to examine the conservation of local genes near GULO/GULOP identified a conserved inversion around the GULO/GULOP locus between the haplorhini and strepsirrhini primates. Fischer's exact test did not support an association between GULOP and the chromosomal inversion. Mauve alignment showed that the inversion of the length of the syntenic block that the GULO/GULOP genes belonged to was variable. However, there were frequent rearrangements around ~ 2 million base pairs adjacent to GULOP involving the KIF13B and MSRA genes. These data may suggest that genes acquiring deleterious mutations in the coding sequence may respond to these deleterious mutations with rapid substitution rates.}, }
@article {pmid38658463, year = {2024}, author = {Yousfi, FZE and Haroun, AE and Nebhani, C and Belayachi, J and Askander, O and Fahime, EE and Fares, H and Ennibi, K and Abouqal, R and Razine, R and Bouhouche, A}, title = {Prevalence of the protective OAS1 rs10774671-G allele against severe COVID-19 in Moroccans: implications for a North African Neanderthal connection.}, journal = {Archives of virology}, volume = {169}, number = {5}, pages = {109}, pmid = {38658463}, issn = {1432-8798}, mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; *2',5'-Oligoadenylate Synthetase/genetics ; Africa, Northern ; Alleles ; *COVID-19/genetics/virology/epidemiology ; Gene Frequency ; Genetic Predisposition to Disease ; Genotype ; Haplotypes ; North African People ; *Polymorphism, Single Nucleotide ; Prevalence ; }, abstract = {The clinical presentation of COVID-19 shows high variability among individuals, which is partly due to genetic factors. The OAS1/2/3 cluster has been found to be strongly associated with COVID-19 severity. We examined this locus in the Moroccan population for the occurrence of the critical variant rs10774671 and its respective haplotype blocks. The frequency of single-nucleotide polymorphisms (SNPs) in the cluster of OAS immunity genes in 157 unrelated individuals of Moroccan origin was determined using an in-house exome database. OAS1 exon 6 of 71 SARS-CoV-2-positive individuals with asymptomatic/mild disease and 74 with moderate/severe disease was sequenced by the Sanger method. The genotypic, allelic, and haplotype frequencies of three SNPs were compared between these two groups. Finally, males in our COVID-19 series were genotyped for the Berber-specific marker E-M81. The prevalence of the OAS1 rs10774671-G allele in present-day Moroccans was found to be 40.4%, which is similar to that found in Europeans. However, it was found equally in both the Neanderthal GGG haplotype and the African GAC haplotype, with a frequency of 20% each. These two haplotypes, and hence the rs10774671-G allele, were significantly associated with protection against severe COVID-19 (p = 0.034, p = 0.041, and p = 0.008, respectively). Surprisingly, in men with the Berber-specific uniparental markers, the African haplotype was absent, while the prevalence of the Neanderthal haplotype was similar to that in Europeans. The protective rs10774671-G allele of OAS1 was found only in the Neanderthal haplotype in Berbers, the indigenous people of North Africa, suggesting that this region may have served as a stepping-stone for the passage of hominids to other continents.}, }
@article {pmid38638564, year = {2024}, author = {Chen, S and Tang, D and Deng, L and Xu, S}, title = {Asian-European differentiation of schizophrenia-associated genes driven by admixture and natural selection.}, journal = {iScience}, volume = {27}, number = {5}, pages = {109560}, pmid = {38638564}, issn = {2589-0042}, abstract = {The European-centered genome-wide association studies of schizophrenia (SCZ) may not be well applied to non-European populations. We analyzed 1,592 reported SCZ-associated genes using the public genome data and found an overall higher Asian-European differentiation on the SCZ-associated variants than at the genome-wide level. Notable examples included 15 missense variants, a regulatory variant SLC5A10-rs1624825, and a damaging variant TSPAN18-rs1001292. Independent local adaptations in recent 25,000 years, after the Asian-European divergence, could have contributed to such genetic differentiation, as were identified at a missense mutation LTN1-rs57646126-A in Asians, and a non-risk allele ZSWIM6-rs72761442-G in Europeans. Altai-Neanderthal-derived alleles may have opposite effects on SCZ susceptibility between ancestries. Furthermore, adaptive introgression was detected on the non-risk haplotype at 1q21.2 in Europeans, while in Asians it was observed on the SCZ risk haplotype at 3p21.31 which is also potentially ultra-violet protective. This study emphasizes the importance of including more representative Asian samples in future SCZ studies.}, }
@article {pmid38612593, year = {2024}, author = {Ferreira, RC and Rodrigues, CR and Broach, JR and Briones, MRS}, title = {Convergent Mutations and Single Nucleotide Variants in Mitochondrial Genomes of Modern Humans and Neanderthals.}, journal = {International journal of molecular sciences}, volume = {25}, number = {7}, pages = {}, pmid = {38612593}, issn = {1422-0067}, support = {20/08943-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 311154/2021-2//National Council for Scientific and Technological Development/ ; }, mesh = {Humans ; Animals ; *Neanderthals/genetics ; *Genome, Mitochondrial ; Mutation ; *Alzheimer Disease ; Nucleotides ; }, abstract = {The genetic contributions of Neanderthals to the modern human genome have been evidenced by the comparison of present-day human genomes with paleogenomes. Neanderthal signatures in extant human genomes are attributed to intercrosses between Neanderthals and archaic anatomically modern humans (AMHs). Although Neanderthal signatures are well documented in the nuclear genome, it has been proposed that there is no contribution of Neanderthal mitochondrial DNA to contemporary human genomes. Here we show that modern human mitochondrial genomes contain 66 potential Neanderthal signatures, or Neanderthal single nucleotide variants (N-SNVs), of which 36 lie in coding regions and 7 result in nonsynonymous changes. Seven N-SNVs are associated with traits such as cycling vomiting syndrome, Alzheimer's disease and Parkinson's disease, and two N-SNVs are associated with intelligence quotient. Based on recombination tests, principal component analysis (PCA) and the complete absence of these N-SNVs in 41 archaic AMH mitogenomes, we conclude that convergent evolution, and not recombination, explains the presence of N-SNVs in present-day human mitogenomes.}, }
@article {pmid38565571, year = {2024}, author = {Yaworsky, PM and Nielsen, ES and Nielsen, TK}, title = {The Neanderthal niche space of Western Eurasia 145 ka to 30 ka ago.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {7788}, pmid = {38565571}, issn = {2045-2322}, support = {9062-00027B//Danmarks Frie Forskningsfond/ ; }, mesh = {Animals ; *Neanderthals ; Fossils ; }, abstract = {Neanderthals occupied Western Eurasia between 350 ka and 40 ka ago, during the climatically volatile Pleistocene. A key issue is to what extent Neanderthal populations expanded into areas of Western Eurasia and what conditions facilitated such range expansions. The range extent of Neanderthals is generally based on the distribution of Neanderthal material, but the land-altering nature of glacial periods has erased much of the already sparse material evidence of Neanderthals, particularly in the northern latitudes. To overcome this obstacle species distribution models can estimate past distributions of Neanderthals, however, most implementations are generally constrained spatially and temporally and may be artificially truncating the Neanderthal niche space. Using dated contexts from Neanderthal sites from across Western Eurasia, millennial-scale paleoclimate reconstructions, and a spatiotemporal species distribution model, we infer the fundamental climatic niche space of Neanderthals and estimate the extent of Neanderthal occupation. We find that (a.) despite the long timeframe, Neanderthals occupy a relatively narrow fundamental climatic niche space, (b.) the estimated projected potential Neanderthal niche space suggests a larger geographic range than the material record suggests, and (c.) that there was a general decline in the size of the projected potential Neanderthal niche from 145 ka ago onward, possibly contributing to their extinction.}, }
@article {pmid38558123, year = {2024}, author = {Aneli, S and Ceccatelli Berti, C and Gilea, AI and Birolo, G and Mutti, G and Pavesi, A and Baruffini, E and Goffrini, P and Capelli, C}, title = {Functional characterization of archaic-specific variants in mitonuclear genes: insights from comparative analysis in S. cerevisiae.}, journal = {Human molecular genetics}, volume = {33}, number = {13}, pages = {1152-1163}, doi = {10.1093/hmg/ddae057}, pmid = {38558123}, issn = {1460-2083}, support = {//Departments of Excellence/ ; //Italian Ministry for University and Research (MIUR, 2018-2022 and MUR, 2023-2027)/ ; //Programma Nazionale della Ricerca PNR 2021-2027 e PON "Ricerca e Innovazione" 2014-2020-progetti di ricerca su tematiche "Innovazione" e "Green"/ ; RF-2016-02361241//Italian Ministry of Health/ ; //University of Parma/ ; GGP19287A//Italian Telethon Foundation/ ; }, mesh = {Humans ; *Saccharomyces cerevisiae/genetics ; *Neanderthals/genetics ; Animals ; Genetic Variation ; Mitochondria/genetics/metabolism ; Alleles ; Genetic Introgression ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; }, abstract = {Neanderthal and Denisovan hybridisation with modern humans has generated a non-random genomic distribution of introgressed regions, the result of drift and selection dynamics. Cross-species genomic incompatibility and more efficient removal of slightly deleterious archaic variants have been proposed as selection-based processes involved in the post-hybridisation purge of archaic introgressed regions. Both scenarios require the presence of functionally different alleles across Homo species onto which selection operated differently according to which populations hosted them, but only a few of these variants have been pinpointed so far. In order to identify functionally divergent archaic variants removed in humans, we focused on mitonuclear genes, which are underrepresented in the genomic landscape of archaic humans. We searched for non-synonymous, fixed, archaic-derived variants present in mitonuclear genes, rare or absent in human populations. We then compared the functional impact of archaic and human variants in the model organism Saccharomyces cerevisiae. Notably, a variant within the mitochondrial tyrosyl-tRNA synthetase 2 (YARS2) gene exhibited a significant decrease in respiratory activity and a substantial reduction of Cox2 levels, a proxy for mitochondrial protein biosynthesis, coupled with the accumulation of the YARS2 protein precursor and a lower amount of mature enzyme. Our work suggests that this variant is associated with mitochondrial functionality impairment, thus contributing to the purging of archaic introgression in YARS2. While different molecular mechanisms may have impacted other mitonuclear genes, our approach can be extended to the functional screening of mitonuclear genetic variants present across species and populations.}, }
@article {pmid38552260, year = {2024}, author = {Rmoutilová, R and Brůžek, J and Gómez-Olivencia, A and Madelaine, S and Couture-Veschambre, C and Holliday, T and Maureille, B}, title = {Sex estimation of the adult Neandertal Regourdou 1 (Montignac, France): Implications for sexing human fossil remains.}, journal = {Journal of human evolution}, volume = {189}, number = {}, pages = {103470}, doi = {10.1016/j.jhevol.2023.103470}, pmid = {38552260}, issn = {1095-8606}, mesh = {Animals ; Humans ; Male ; *Neanderthals/anatomy &amp; histology ; Fossils ; Genomics ; Paleontology ; *Hominidae ; France ; }, abstract = {Sex is a biological trait fundamental to the study of hominin fossils. Among the many questions that can be addressed are those related to taxonomy, biological variability, sexual dimorphism, paleoobstetrics, funerary selection, and paleodemography. While new methodologies such as paleogenomics or paleoproteomics can be used to determine sex, they have not been systematically applied to Pleistocene human remains due to their destructive nature. Therefore, we estimated sex from the coxal bone of the newly discovered pelvic remains of the Regourdou 1 Neandertal (Southwest France, MIS 5) based on morphological and metric data employing two methods that have been recently revised and shown to be reliable in multiple studies. Both methods calculate posterior probabilities of the estimate. The right coxal bone of Regourdou 1 was partially reconstructed providing additional traits for sex estimation. These methods were cross validated on 14 sufficiently preserved coxal bones of specimens from the Neandertal lineage. Our results show that the Regourdou 1 individual, whose postcranial skeleton is not robust, is a male, and that previous sex attributions of comparative Neandertal specimens are largely in agreement with those obtained here. Our results encourage additional morphological research of fossil hominins in order to develop a set of methods that are applicable, reliable, and reproducible.}, }
@article {pmid38489387, year = {2024}, author = {Groh, JS and Coop, G}, title = {The temporal and genomic scale of selection following hybridization.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {12}, pages = {e2309168121}, pmid = {38489387}, issn = {1091-6490}, support = {R35 GM136290/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Genome/genetics ; Genomics ; Hybridization, Genetic ; Nucleic Acid Hybridization ; Haplotypes ; *Neanderthals/genetics ; Selection, Genetic ; }, abstract = {Genomic evidence supports an important role for selection in shaping patterns of introgression along the genome, but frameworks for understanding the evolutionary dynamics within hybrid populations that underlie these patterns have been lacking. Due to the clock-like effect of recombination in hybrids breaking up parental haplotypes, drift and selection produce predictable patterns of ancestry variation at varying spatial genomic scales through time. Here, we develop methods based on the Discrete Wavelet Transform to study the genomic scale of local ancestry variation and its association with recombination rates and show that these methods capture temporal dynamics of drift and genome-wide selection after hybridization. We apply these methods to published datasets from hybrid populations of swordtail fish (Xiphophorus) and baboons (Papio) and to inferred Neanderthal introgression in modern humans. Across systems, upward of 20% of variation in local ancestry at the broadest genomic scales can be attributed to systematic selection against introgressed alleles, consistent with strong selection acting on early-generation hybrids. Signatures of selection at fine genomic scales suggest selection over longer time scales; however, we suggest that our ability to confidently infer selection at fine scales is likely limited by inherent biases in current methods for estimating local ancestry from contiguous segments of genomic similarity. Wavelet approaches will become widely applicable as genomic data from systems with introgression become increasingly available and can help shed light on generalities of the genomic consequences of interspecific hybridization.}, }
@article {pmid38477186, year = {2024}, author = {Pablos, A and Arsuaga, JL}, title = {Tarsals from the Sima de los Huesos Middle Pleistocene site (Atapuerca, Burgos, Spain).}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {307}, number = {7}, pages = {2635-2664}, doi = {10.1002/ar.25425}, pmid = {38477186}, issn = {1932-8494}, support = {PGC2018-093925-B-C33//MCI/AEI/FEDER, UE/ ; PGC2018-093925-B-C31//MCI/AEI/FEDER, UE/ ; PID2021-122355NB-C31//MCIN/AEI/10.13039/501100011033/FEDER, UE/ ; 949330/ERC_/European Research Council/International ; EMERGIA20_00403//Junta de Andaluc&#xed;a, Spain/ ; //Junta de Castilla y Le&#xf3;n and Fundaci&#xf3;n Atapuerca/ ; }, mesh = {Animals ; *Fossils/anatomy &amp; histology ; Spain ; *Hominidae/anatomy &amp; histology ; *Biological Evolution ; Tarsal Bones/anatomy &amp; histology ; Neanderthals/anatomy &amp; histology ; Humans ; Male ; Female ; }, abstract = {Here, we provide a complete, updated, and illustrated inventory, as well as a comprehensive study, of the tarsals (rearfoot) recovered from the Middle Pleistocene site of Sima de los Huesos (SH, Atapuerca, Spain) in comparison to other Homo comparative samples, both extant and fossil. The minimum number of individuals (MNI) estimated from the tarsals has been established as 15, which represents 51.7% of the 29 dental individuals identified within the SH sample. Within the SH hominin foot sample, an exclusive combination of primitive or plesiomorphic and derived or autapomorphic traits can be observed when compared with other Homo individuals/populations. Other characters are shared among SH hominins and Neandertals that might represent shared derived or autapomorphic traits for this evolutionary line, and most are likely related to robusticity (e.g., rectangular-like trochlea of the talus, broad calcanei, broad naviculars, and short lateral cuneiforms). Additionally, we observed some exclusive autapomorphic traits in the SH tarsal sample (e.g., narrow head of the talus and short intermediate cuneiforms). A few exclusive traits in SH tarsal remains are even more robust than in Neandertals (e.g., broad lateral malleolar facet in talus, more projected sustentaculum tali, and broad medial cuneiform). These traits could suggest a slightly higher level of gracilization in the tarsal bones of Neandertals compared to the SH sample that is also supported by other anatomical postcranial skeleton elements. Additionally, some paleobiological inferences are made in relation to body size (stature and body mass) and some associations are proposed within the SH sample. In conclusion, the morphology of the SH tarsi confirms an evolutionary relationship of sister groups between this population and Neandertals, probably representing a morphotype similar to the Neandertal ancestors.}, }
@article {pmid38461589, year = {2024}, author = {Najafzadeh, A and Hernaiz-García, M and Benazzi, S and Chen, B and Hublin, JJ and Kullmer, O and Pokhojaev, A and Sarig, R and Sorrentino, R and Vazzana, A and Fiorenza, L}, title = {Finite element analysis of Neanderthal and early Homo sapiens maxillary central incisor.}, journal = {Journal of human evolution}, volume = {189}, number = {}, pages = {103512}, doi = {10.1016/j.jhevol.2024.103512}, pmid = {38461589}, issn = {1095-8606}, mesh = {Humans ; Adolescent ; Animals ; *Neanderthals ; Incisor ; Computer Simulation ; Finite Element Analysis ; Crowns ; Stress, Mechanical ; }, abstract = {Neanderthal anterior teeth are very large and have a distinctive morphology characterized by robust 'shovel-shaped' crowns. These features are frequently seen as adaptive responses in dissipating heavy mechanical loads resulting from masticatory and non-masticatory activities. Although the long-standing debate surrounding this hypothesis has played a central role in paleoanthropology, is still unclear if Neanderthal anterior teeth can resist high mechanical loads or not. A novel way to answer this question is to use a multidisciplinary approach that considers together tooth architecture, dental wear and jaw movements. The aim of this study is to functionally reposition the teeth of Le Moustier 1 (a Neanderthal adolescent) and Qafzeh 9 (an early Homo sapiens adolescent) derived from wear facet mapping, occlusal fingerprint analysis and physical dental restoration methods. The restored dental arches are then used to perform finite element analysis on the left central maxillary incisor during edge-to-edge occlusion. The results show stress distribution differences between Le Moustier 1 and Qafzeh 9, with the former displaying higher tensile stress in enamel around the lingual fossa but lower concentration of stress in the lingual aspect of the root surface. These results seem to suggest that the presence of labial convexity, lingual tubercle and of a large root surface in Le Moustier 1 incisor helps in dissipating mechanical stress. The absence of these dental features in Qafzeh 9 is compensated by the presence of a thicker enamel, which helps in reducing the stress in the tooth crown.}, }
@article {pmid38458749, year = {2024}, author = {Geier, A and Trost, J and Wang, K and Schmid, C and Krawczyk, M and Schiffels, S}, title = {PNPLA3 fatty liver allele was fixed in Neanderthals and segregates neutrally in humans.}, journal = {Gut}, volume = {73}, number = {6}, pages = {1008-1014}, doi = {10.1136/gutjnl-2023-331594}, pmid = {38458749}, issn = {1468-3288}, support = {851511/ERC_/European Research Council/International ; }, mesh = {Animals ; Humans ; *Acyltransferases/genetics ; *Alleles ; DNA, Ancient/analysis ; *Fatty Liver/genetics ; Gene Frequency ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Genotype ; *Neanderthals/genetics ; *Phospholipases A2, Calcium-Independent/genetics ; }, abstract = {OBJECTIVE: Fat deposition is modulated by environmental factors and genetic predisposition. Genome-wide association studies identified PNPLA3 p.I148M (rs738409) as a common variant that increases risk of developing liver steatosis. When and how this variant evolved in humans has not been studied to date.<br><br>DESIGN: Here we analyse ancient DNA to track the history of this allele throughout human history. In total, 6444 published ancient (modern humans, Neanderthal, Denisovan) and 3943 published present day genomes were used for analysis after extracting genotype calls for PNPLA3 p.I148M. To quantify changes through time, logistic and, by grouping individuals according to geography and age, linear regression analyses were performed.<br><br>RESULTS: We find that archaic human individuals (Neanderthal, Denisovan) exclusively carried a fixed PNPLA3 risk allele, whereas allele frequencies in modern human populations range from very low in Africa to >50% in Mesoamerica. Over the last 15&#x2009;000 years, distributions of ancestral and derived alleles roughly match the present day distribution. Logistic regression analyses did not yield signals of natural selection during the last 10&#x2009;000 years.<br><br>CONCLUSION: Archaic human individuals exclusively carried a fixed PNPLA3 allele associated with fatty liver, whereas allele frequencies in modern human populations are variable even in the oldest samples. Our observation might underscore the advantage of fat storage in cold climate and particularly for Neanderthal under ice age conditions. The absent signals of natural selection during modern human history does not support the thrifty gene hypothesis in case of PNPLA3 p.I148M.}, }
@article {pmid38454744, year = {2024}, author = {Pantoja-Pérez, A and Arsuaga, JL}, title = {The Cranium I: Neurocranium.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {307}, number = {7}, pages = {2278-2324}, doi = {10.1002/ar.25413}, pmid = {38454744}, issn = {1932-8494}, support = {PID2021-122355NB-C31//MCIN/AEI/10.13039/501100011033 and "ERDF A way of making Europe"/ ; PGC2018-093925-B-C31//MCIN/AEI/10.13039/501100011033 and "ERDF A way of making Europe"/ ; 949330//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program/ ; //CaixaBank-Fundaci&#xf3;n Atapuerca/ ; }, mesh = {Animals ; *Skull/anatomy &amp; histology ; *Neanderthals/anatomy &amp; histology ; Male ; Female ; *Fossils ; Humans ; *Biological Evolution ; }, abstract = {The Sima de los Huesos (SH) site has provided a significant collection of hominin remains, including numerous cranial fragments, which have contributed to our understanding of the MP human population. The taxonomic classification of the SH hominins remains a topic of debate, with some studies suggesting a close relationship to Neandertals based on nuclear DNA analysis. The cranial morphology of the SH specimens exhibits a mix of Neandertal-like features and primitive traits observed in earlier Homo populations, providing insights into the evolutionary pattern of the Neanderthal lineage. This study focuses on the neurocranial traits of the SH population and describes three previously undescribed cranial individuals. The SH cranial collection now comprises 20 nearly complete crania, representing approximately two-thirds of the estimated population size. The analysis of the SH population reveals variations in robustness, frontal torus development, sagittal keeling, and occipital torus morphology, which may be related to sexual dimorphism and ontogenetic factors. The suprainiac region exhibits notable ontogenetic changes, while suture obliteration patterns do not strictly correlate with dental age. Metric measurements, particularly cranial breadths, highlight significant intrapopulation variation within the SH sample. Compared with other Middle Pleistocene (MP) hominins, the SH cranial vault displays archaic characteristics but differs from Homo erectus and Neandertals. The SH individuals have relatively short and tall cranial vaults, distinguishing them from other MP fossils. These findings contribute to our understanding of the MP human populations and their evolutionary trajectories.}, }
@article {pmid38450997, year = {2024}, author = {Gómez-Olivencia, A and Arsuaga, JL}, title = {The Sima de los Huesos thorax and lumbar spine: Selected traits and state-of-the-art.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {307}, number = {7}, pages = {2465-2490}, doi = {10.1002/ar.25414}, pmid = {38450997}, issn = {1932-8494}, support = {PGC2018-093925-B-C33//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; PID2021-122355NB-C31//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; RYC-2017-22558//Ram&#xf3;n y Cajal fellowship/ ; //Fundaci&#xf3;n Atapuerca/ ; //Junta de Castilla y Le&#xf3;n/ ; }, mesh = {*Lumbar Vertebrae/anatomy &amp; histology ; Animals ; *Fossils/anatomy &amp; histology ; Humans ; *Thoracic Vertebrae/anatomy &amp; histology ; *Neanderthals/anatomy &amp; histology ; *Biological Evolution ; *Thorax/anatomy &amp; histology ; Ribs/anatomy &amp; histology ; Hominidae/anatomy &amp; histology ; }, abstract = {Information on the evolution of the thorax and lumbar spine in the genus Homo is hampered by a limited fossil record due to the inherent fragility of vertebrae and ribs. Neandertals show significant metric and morphological differences in these two anatomical regions, when compared to Homo sapiens. Thus, the important fossil record from the Middle Pleistocene site of Sima de los Huesos (SH) not only offers important information on the evolution of these anatomical regions within the Neandertal lineage but also provides important clues to understand the evolution of these regions at the genus level. We present the current knowledge of the costal skeleton, and the thoracic and lumbar spine anatomy of the hominins found in Sima de los Huesos compared to that of Neandertals and modern humans. The current SH fossil record comprises 738 vertebral specimens representing a minimum of 70 cervical, 95 thoracic and 47 lumbar vertebrae, 652 rib fragments representing a minimum of 118 ribs, and 26 sternal fragments representing 4 sterna. The SH hominins exhibit a morphological pattern in their thorax and lumbar spine more similar to that of Neandertals than to that of H. sapiens, which is consistent with the phylogenetic position of these hominins. However, there are some differences between the SH hominins and Neandertals in these anatomical regions, primarily in the orientation of the lumbar transverse processes and in the robusticity of the second ribs. The presence of some but not all of the suite of Neandertal-derived features is consistent with the pattern found in the cranium and other postcranial regions of this population.}, }
@article {pmid38422140, year = {2024}, author = {Nowell, A}, title = {Knowing the NeanderthalThe Naked Neanderthal: A New Understanding of the Human Creature Ludovic Slimak Pegasus, 2024. 208 pp.}, journal = {Science (New York, N.Y.)}, volume = {383}, number = {6686}, pages = {956}, doi = {10.1126/science.adn6093}, pmid = {38422140}, issn = {1095-9203}, abstract = {An archaeologist seeks to strip away modern misconceptions about our extinct relatives.}, }
@article {pmid38420653, year = {2024}, author = {Hernaiz-García, M and Zanolli, C and Martín-Francés, L and Mazurier, A and Benazzi, S and Sarig, R and Fu, J and Kullmer, O and Fiorenza, L}, title = {Masticatory habits of the adult Neanderthal individual BD 1 from La Chaise-de-Vouthon (France).}, journal = {American journal of biological anthropology}, volume = {184}, number = {1}, pages = {e24926}, doi = {10.1002/ajpa.24926}, pmid = {38420653}, issn = {2692-7691}, support = {//Biomedicine Discovery Scholarship from Monash University/ ; DP190100465//Australian Research Council/ ; }, mesh = {Adult ; Humans ; Animals ; *Neanderthals ; *Tooth ; *Tooth Wear ; France ; Habits ; }, abstract = {OBJECTIVES: The analysis of dental wear provides a useful approach for dietary and cultural habit reconstructions of past human populations. The analysis of macrowear patterns can also be used to better understand the individual chewing behavior and to investigate the biomechanical responses during different biting scenarios. The aim of this study is to evaluate the diet and chewing performance of the adult Neanderthal Bourgeois-Delaunay 1 (BD 1) and to investigate the relationship between wear and cementum deposition under mechanical demands.<br><br>MATERIALS AND METHODS: The macrowear pattern of BD 1 was analyzed using the occlusal fingerprint analysis method. We propose a new method for the bilateral measurement of the cementum volume along both buccal and lingual sides of the molar root.<br><br>RESULTS: BD 1's anterior dentition is more affected by wear compared to the posterior one. The macrowear pattern suggest a normal chewing behavior and a mixed-diet coming from temperate environments. The teeth on the left side of the mandible display greater levels of wear, as well as the buccal side of the molar crowns. The cementum analysis shows higher buccal volume along the molar roots.<br><br>DISCUSSION: BD1 could have been preferably chewing on the left side of the mandible. The exploitation of various food resources suggested by the macrowear analysis is compatible with the environmental reconstructions. Finally, the greater wear on the buccal side of the molar occlusal surface and the greater volume of cementum in that side of the molar roots offers a preliminary understanding about the potential correlation between dental wear and cementum deposition.}, }
@article {pmid38405782, year = {2024}, author = {Kerdoncuff, E and Skov, L and Patterson, N and Zhao, W and Lueng, YY and Schellenberg, GD and Smith, JA and Dey, S and Ganna, A and Dey, AB and Kardia, SLR and Lee, J and Moorjani, P}, title = {50,000 years of Evolutionary History of India: Insights from ~2,700 Whole Genome Sequences.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38405782}, issn = {2692-8205}, support = {R01 AG051125/AG/NIA NIH HHS/United States ; R35 GM142978/GM/NIGMS NIH HHS/United States ; RF1 AG055273/AG/NIA NIH HHS/United States ; }, abstract = {India has been underrepresented in whole genome sequencing studies. We generated 2,762 high coverage genomes from India-including individuals from most geographic regions, speakers of all major languages, and tribal and caste groups-providing a comprehensive survey of genetic variation in India. With these data, we reconstruct the evolutionary history of India through space and time at fine scales. We show that most Indians derive ancestry from three ancestral groups related to ancient Iranian farmers, Eurasian Steppe pastoralists and South Asian hunter-gatherers. We uncover a common source of Iranian-related ancestry from early Neolithic cultures of Central Asia into the ancestors of Ancestral South Indians (ASI), Ancestral North Indians (ANI), Austro-asiatic-related and East Asian-related groups in India. Following these admixtures, India experienced a major demographic shift towards endogamy, resulting in extensive homozygosity and identity-by-descent sharing among individuals. At deep time scales, Indians derive around 1-2% of their ancestry from gene flow from archaic hominins, Neanderthals and Denisovans. By assembling the surviving fragments of archaic ancestry in modern Indians, we recover ~1.5 Gb (or 50%) of the introgressing Neanderthal and ~0.6 Gb (or 20%) of the introgressing Denisovan genomes, more than any other previous archaic ancestry study. Moreover, Indians have the largest variation in Neanderthal ancestry, as well as the highest amount of population-specific Neanderthal segments among worldwide groups. Finally, we demonstrate that most of the genetic variation in Indians stems from a single major migration out of Africa that occurred around 50,000 years ago, with minimal contribution from earlier migration waves. Together, these analyses provide a detailed view of the population history of India and underscore the value of expanding genomic surveys to diverse groups outside Europe.}, }
@article {pmid38380556, year = {2024}, author = {Pablos, A and Arsuaga, JL}, title = {Metatarsals and foot phalanges from the Sima de los Huesos Middle Pleistocene site (Atapuerca, Burgos, Spain).}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {307}, number = {7}, pages = {2665-2707}, doi = {10.1002/ar.25412}, pmid = {38380556}, issn = {1932-8494}, support = {PGC2018-093925-B-C33//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PGC2018-093925-B-C31//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2021-122355NB-C31//MCIN/ ; 949330//H2020 European Research Council/ ; EMERGIA20_00403//EMERGIA/ ; //Junta de Castilla y Le&#xf3;n/ ; }, mesh = {Animals ; *Fossils/anatomy &amp; histology ; Spain ; *Metatarsal Bones/anatomy &amp; histology ; Humans ; *Hominidae/anatomy &amp; histology/physiology ; Biological Evolution ; Neanderthals/anatomy &amp; histology ; Toe Phalanges/anatomy &amp; histology ; }, abstract = {This study provides a complete, updated and illustrated inventory, as well as a comprehensive study, of the metatarsals and foot phalanges (forefoot) recovered from the Middle Pleistocene site of Sima de los Huesos (SH, Atapuerca, Spain) in comparison to other Homo comparative samples, both extant and fossils. This current updated review has established a minimum number of individuals (MNI) of 17, which represent 58.6% of the 29 dental individuals identified within the SH sample. An exclusive or autoapomorphic combination of traits can be recognized within the SH hominin foot sample. A few traits appear primitive or plesiomorphic when compared with earlier Homo individuals and other recent modern humans. There are other metrical and morphological traits that SH hominins and Neandertals have in common that sometimes represent shared derived traits in this evolutionary line, most of which are probably related to robusticity. Furthermore, some exclusive autoapomorphic traits are observed in the SH sample: a very broad first metatarsal, long and broad hallucal proximal foot phalanges and possibly extremely robust lateral distal foot phalanges compared to those of Neandertals and modern humans. In these last traits, the SH metatarsals and pedal phalanges are even more robust than in Neandertals. They are herein named as "hyper-Neandertal" traits, which could suggest a slight gracilization process in this evolutionary line, at least in the hallux toe. Finally, some paleobiological inferences are made in relation to body size (stature and body mass) and some associations are proposed within the SH sample.}, }
@article {pmid38379413, year = {2024}, author = {Cerrito, P and Nava, A and Radovčić, D and Borić, D and Cerrito, L and Basdeo, T and Ruggiero, G and Frayer, DW and Kao, AP and Bondioli, L and Mancini, L and Bromage, TG}, title = {Correction: 'Dental cementum virtual histology of Neanderthal teeth from Krapina (Croatia, 130-120 kyr): an informed estimate of age, sex and adult stressors' (2022), by Cerrito et al.}, journal = {Journal of the Royal Society, Interface}, volume = {21}, number = {211}, pages = {20240069}, doi = {10.1098/rsif.2024.0069}, pmid = {38379413}, issn = {1742-5662}, }
@article {pmid38377343, year = {2024}, author = {Liu, S and Luo, H and Zhang, P and Li, Y and Hao, D and Zhang, S and Song, T and Xu, T and He, S}, title = {Adaptive Selection of Cis-regulatory Elements in the Han Chinese.}, journal = {Molecular biology and evolution}, volume = {41}, number = {3}, pages = {}, pmid = {38377343}, issn = {1537-1719}, support = {XDB38040300//Chinese Academy of Sciences/ ; 2021YFF0703701//National Key R&amp;D Program of China/ ; 91940306//National Natural Science Foundation of China/ ; 2019FY100102//MOST, China/ ; 2022M713311//China Postdoctoral Science Foundation/ ; //National Genomics Data Center, China/ ; }, mesh = {Humans ; Animals ; *Diabetes Mellitus, Type 2/genetics ; Selection, Genetic ; Regulatory Sequences, Nucleic Acid ; Promoter Regions, Genetic ; *Neanderthals/genetics ; China ; Enhancer Elements, Genetic ; }, abstract = {Cis-regulatory elements have an important role in human adaptation to the living environment. However, the lag in population genomic cohort studies and epigenomic studies, hinders the research in the adaptive analysis of cis-regulatory elements in human populations. In this study, we collected 4,013 unrelated individuals and performed a comprehensive analysis of adaptive selection of genome-wide cis-regulatory elements in the Han Chinese. In total, 12.34% of genomic regions are under the influence of adaptive selection, where 1.00% of enhancers and 2.06% of promoters are under positive selection, and 0.06% of enhancers and 0.02% of promoters are under balancing selection. Gene ontology enrichment analysis of these cis-regulatory elements under adaptive selection reveals that many positive selections in the Han Chinese occur in pathways involved in cell-cell adhesion processes, and many balancing selections are related to immune processes. Two classes of adaptive cis-regulatory elements related to cell adhesion were in-depth analyzed, one is the adaptive enhancers derived from neanderthal introgression, leads to lower hyaluronidase level in skin, and brings better performance on UV-radiation resistance to the Han Chinese. Another one is the cis-regulatory elements regulating wound healing, and the results suggest the positive selection inhibits coagulation and promotes angiogenesis and wound healing in the Han Chinese. Finally, we found that many pathogenic alleles, such as risky alleles of type 2 diabetes or schizophrenia, remain in the population due to the hitchhiking effect of positive selections. Our findings will help deepen our understanding of the adaptive evolution of genome regulation in the Han Chinese.}, }
@article {pmid38367960, year = {2024}, author = {Voinescu, CD and Mozere, M and Genovese, G and Downie, ML and Gupta, S and Gale, DP and Bockenhauer, D and Kleta, R and Arcos-Burgos, M and Stanescu, HC}, title = {A Neanderthal haplotype introgressed into the human genome confers protection against membranous nephropathy.}, journal = {Kidney international}, volume = {105}, number = {4}, pages = {791-798}, doi = {10.1016/j.kint.2024.01.017}, pmid = {38367960}, issn = {1523-1755}, mesh = {Humans ; Animals ; *Neanderthals/genetics ; Haplotypes ; *Glomerulonephritis, Membranous/genetics ; Genome, Human ; Genome-Wide Association Study ; Receptors, Phospholipase A2/genetics ; }, abstract = {Class 2 HLA and PLA2R1 alleles are exceptionally strong genetic risk factors for membranous nephropathy (MN), leading, through an unknown mechanism, to a targeted autoimmune response. Introgressed archaic haplotypes (introduced from an archaic human genome into the modern human genome) might influence phenotypes through gene dysregulation. Here, we investigated the genomic region surrounding the PLA2R1 gene. We reconstructed the phylogeny of Neanderthal and modern haplotypes in this region and calculated the probability of the observed clustering being the result of introgression or common descent. We imputed variants for the participants in our previous genome-wide association study and we compared the distribution of Neanderthal variants between MN cases and controls. The region associated with the lead MN risk locus in the PLA2R1 gene was confirmed and showed that, within a 507 kb region enriched in introgressed sequence, a stringently defined 105 kb haplotype, intersecting the coding regions for PLA2R1 and ITGB6, is inherited from Neanderthals. Thus, introgressed Neanderthal haplotypes overlapping PLA2R1 are differentially represented in MN cases and controls, with enrichment In controls suggesting a protective effect.}, }
@article {pmid38345759, year = {2024}, author = {Yaghmouri, M and Izadi, P}, title = {Role of the Neanderthal Genome in Genetic Susceptibility to COVID-19: 3p21.31 Locus in the Spotlight.}, journal = {Biochemical genetics}, volume = {}, number = {}, pages = {}, pmid = {38345759}, issn = {1573-4927}, abstract = {Since the outbreak of COVID-19, genome-wide association studies have tried to discover the role of genetic predisposition in the clinical variability of this viral infection. The findings of various investigations have led to several loci for COVID-19 genetic susceptibility. Among candidate regions, the 3p21.31 locus has been in the spotlight among scientists, as it can increase the risk of severe COVID-19 by almost two fold. In addition to its substantial association with COVID-19 severity, this locus is related to some common diseases, such as diabetes, malignancies, and coronary artery disease. This locus also harbors evolutionary traces of Neanderthal genomes, which is believed to be the underlying reason for its association with COVID-19 severity. Additionally, the inheritance of this locus from Neanderthals seems to be under positive selection. This review aims to summarize a collection of evidence on the 3p21.31 locus and its impact on COVID-19 outcomes by focusing on the risk variants originated from the Neanderthal genome. Moreover, we discuss candidate genes at this locus and the possible mechanisms by which they influence the progression of COVID-19 symptoms. Better insights into human genetic susceptibility to newly emerging diseases such as COVID-19 and its evolutionary origin can provide fundamentals for risk assessment of different populations as well as the development of personalized prevention and treatments based on genomic medicine.}, }
@article {pmid38293167, year = {2024}, author = {Janivara, R and Hazra, U and Pfennig, A and Harlemon, M and Kim, MS and Eaaswarkhanth, M and Chen, WC and Ogunbiyi, A and Kachambwa, P and Petersen, LN and Jalloh, M and Mensah, JE and Adjei, AA and Adusei, B and Joffe, M and Gueye, SM and Aisuodionoe-Shadrach, OI and Fernandez, PW and Rohan, TE and Andrews, C and Rebbeck, TR and Adebiyi, AO and Agalliu, I and Lachance, J}, title = {Uncovering the genetic architecture and evolutionary roots of androgenetic alopecia in African men.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38293167}, issn = {2692-8205}, support = {R35 GM133727/GM/NIGMS NIH HHS/United States ; U01 CA184374/CA/NCI NIH HHS/United States ; U01 CA257328/CA/NCI NIH HHS/United States ; }, abstract = {Androgenetic alopecia is a highly heritable trait. However, much of our understanding about the genetics of male pattern baldness comes from individuals of European descent. Here, we examined a novel dataset comprising 2,136 men from Ghana, Nigeria, Senegal, and South Africa that were genotyped using a custom array. We first tested how genetic predictions of baldness generalize from Europe to Africa, finding that polygenic scores from European GWAS yielded AUC statistics that ranged from 0.513 to 0.546, indicating that genetic predictions of baldness in African populations performed notably worse than in European populations. Subsequently, we conducted the first African GWAS of androgenetic alopecia, focusing on self-reported baldness patterns at age 45. After correcting for present age, population structure, and study site, we identified 266 moderately significant associations, 51 of which were independent (p-value < 10[-5], r[2] < 0.2). Most baldness associations were autosomal, and the X chromosomes does not appear to have a large impact on baldness in African men. Finally, we examined the evolutionary causes of continental differences in genetic architecture. Although Neanderthal alleles have previously been associated with skin and hair phenotypes, we did not find evidence that European-ascertained baldness hits were enriched for signatures of ancient introgression. Most loci that are associated with androgenetic alopecia are evolving neutrally. However, multiple baldness-associated SNPs near the EDA2R and AR genes have large allele frequency differences between continents. Collectively, our findings illustrate how evolutionary history contributes to the limited portability of genetic predictions across ancestries.}, }
@article {pmid38269094, year = {2024}, author = {Jambrina-Enríquez, M and Mallol, C and Herrera Herrera, AV and Gonzalez-Urquijo, J and Lazuen, T}, title = {Microstratigraphic, lipid biomarker and stable isotope study of a middle Palaeolithic combustion feature from Axlor, Spain.}, journal = {iScience}, volume = {27}, number = {1}, pages = {108755}, pmid = {38269094}, issn = {2589-0042}, abstract = {Archaeological research has increasingly focused on studying combustion features as valuable sources of information regarding past technological and cultural aspects. The use of microstratigraphic and biomolecular techniques enables the identification of combustion residues and substrate components, and infer about past fire-related activities and the environments. Our study conducted on a combustion feature (Level N, ∼100 Ka) at the Axlor cave, a Middle Paleolithic site in northern Iberia, exemplifies the interdisciplinary approach to combustion features. Micromorphological features revealed depositional activities associated with occupations such as hearth rake-out and trampling. Through molecular (n-alkanes, n-alcohols, and n-fatty acids) and isotopic analysis (δ[13]C16:0 and δ[13]C18:0), we infer the good preservation of organic matter, the contributions of non-ruminant fats, and the dead-wood gathering strategies by Neanderthal groups. By combining microstratigraphic and biomolecular approaches, our study significantly contributes to the advancement of our current understanding of Neanderthal pyrotechnology.}, }
@article {pmid38262226, year = {2024}, author = {Bailey, SE and Davies, TW and Imbrasas, MD and Lazuen, T and Hublin, JJ and González-Urquijo, J}, title = {New Neanderthal remains from Axlor cave (Dima, Biscay, northern Iberian Peninsula).}, journal = {Journal of human evolution}, volume = {187}, number = {}, pages = {103483}, doi = {10.1016/j.jhevol.2023.103483}, pmid = {38262226}, issn = {1095-8606}, mesh = {Animals ; *Neanderthals ; Europe ; Fossils ; Caves ; Archaeology ; }, }
@article {pmid38213708, year = {2023}, author = {Borodko, DD and Zhenilo, SV and Sharko, FS}, title = {Search for differentially methylated regions in ancient and modern genomes.}, journal = {Vavilovskii zhurnal genetiki i selektsii}, volume = {27}, number = {7}, pages = {820-828}, doi = {10.18699/VJGB-23-95}, pmid = {38213708}, issn = {2500-0462}, abstract = {Currently, active research is focused on investigating the mechanisms that regulate the development of various pathologies and their evolutionary dynamics. Epigenetic mechanisms, such as DNA methylation, play a significant role in evolutionary processes, as their changes have a faster impact on the phenotype compared to mutagenesis. In this study, we attempted to develop an algorithm for identifying differentially methylated regions associated with metabolic syndrome, which have undergone methylation changes in humans during the transition from a hunter-gatherer to a sedentary lifestyle. The application of existing whole-genome bisulfite sequencing methods is limited for ancient samples due to their low quality and fragmentation, and the approach to obtaining DNA methylation profiles differs significantly between ancient hunter-gatherer samples and modern tissues. In this study, we validated DamMet, an algorithm for reconstructing ancient methylomes. Application of DamMet to Neanderthal and Denisovan genomes showed a moderate level of correlation with previously published methylation profiles and demonstrated an underestimation of methylation levels in the reconstructed profiles by an average of 15-20 %. Additionally, we developed a new Python-based algorithm that allows for the comparison of methylomes in ancient and modern samples, despite the absence of methylation profiles in modern bone tissue within the context of obesity. This analysis involves a two-step data processing approach, where the first step involves the identification and filtration of tissue-specific methylation regions, and the second step focuses on the direct search for differentially methylated regions in specific areas associated with the researcher's target condition. By applying this algorithm to test data, we identified 38 differentially methylated regions associated with obesity, the majority of which were located in promoter regions. The pipeline demonstrated sufficient efficiency in detecting these regions. These results confirm the feasibility of reconstructing DNA methylation profiles in ancient samples and comparing them with modern methylomes. Furthermore, possibilities for further methodological development and the implementation of a new step for studying differentially methylated positions associated with evolutionary processes are discussed.}, }
@article {pmid38166646, year = {2024}, author = {Levinstein Hallak, K and Rosset, S}, title = {Dating ancient splits in phylogenetic trees, with application to the human-Neanderthal split.}, journal = {BMC genomic data}, volume = {25}, number = {1}, pages = {4}, pmid = {38166646}, issn = {2730-6844}, support = {2180/20//Israeli Science Foundation grant/ ; }, mesh = {Animals ; Humans ; *Neanderthals/genetics ; Phylogeny ; Pan troglodytes/genetics ; Bayes Theorem ; *Hominidae/genetics ; DNA, Mitochondrial/genetics ; }, abstract = {BACKGROUND: We tackle the problem of estimating species TMRCAs (Time to Most Recent Common Ancestor), given a genome sequence from each species and a large known phylogenetic tree with a known structure (typically from one of the species). The number of transitions at each site from the first sequence to the other is assumed to be Poisson distributed, and only the parity of the number of transitions is observed. The detailed phylogenetic tree contains information about the transition rates in each site. We use this formulation to develop and analyze multiple estimators of the species' TMRCA. To test our methods, we use mtDNA substitution statistics from the well-established Phylotree as a baseline for data simulation such that the substitution rate per site mimics the real-world observed rates.<br><br>RESULTS: We evaluate our methods using simulated data and compare them to the Bayesian optimizing software BEAST2, showing that our proposed estimators are accurate for a wide range of TMRCAs and significantly outperform BEAST2. We then apply the proposed estimators on Neanderthal, Denisovan, and Chimpanzee mtDNA genomes to better estimate their TMRCA with modern humans and find that their TMRCA is substantially later, compared to values cited recently in the literature.<br><br>CONCLUSIONS: Our methods utilize the transition statistics from the entire known human mtDNA phylogenetic tree (Phylotree), eliminating the requirement to reconstruct a tree encompassing the specific sequences of interest. Moreover, they demonstrate notable improvement in both running speed and accuracy compared to BEAST2, particularly for earlier TMRCAs like the human-Chimpanzee split. Our results date the human - Neanderthal TMRCA to be [Formula: see text] years ago, considerably later than values cited in other recent studies.}, }
@article {pmid38113553, year = {2024}, author = {Palancar, CA and Bastir, M and Rosas, A and Dugailly, PM and Schlager, S and Beyer, B}, title = {Modern human atlas ranges of motion and Neanderthal estimations.}, journal = {Journal of human evolution}, volume = {187}, number = {}, pages = {103482}, doi = {10.1016/j.jhevol.2023.103482}, pmid = {38113553}, issn = {1095-8606}, mesh = {Humans ; Animals ; *Neanderthals ; Cervical Vertebrae ; Range of Motion, Articular ; Rotation ; Biomechanical Phenomena ; }, }
@article {pmid38110796, year = {2024}, author = {Zhao, H and Liu, LL and Sun, J and Jin, L and Xie, HB and Li, JB and Xu, H and Wu, DD and Zhuang, XL and Peng, MS and Guo, YJ and Qian, WZ and Otecko, NO and Sun, WJ and Qu, LH and He, J and Chen, ZL and Liu, R and Chen, CS and Zhang, YP}, title = {A human-specific insertion promotes cell proliferation and migration by enhancing TBC1D8B expression.}, journal = {Science China. Life sciences}, volume = {67}, number = {4}, pages = {765-777}, pmid = {38110796}, issn = {1869-1889}, mesh = {Humans ; Cell Line, Tumor ; Cell Movement/genetics ; Cell Proliferation/genetics ; *Gene Expression Regulation, Neoplastic ; Introns ; }, abstract = {Human-specific insertions play important roles in human phenotypes and diseases. Here we reported a 446-bp insertion (Insert-446) in intron 11 of the TBC1D8B gene, located on chromosome X, and traced its origin to a portion of intron 6 of the EBF1 gene on chromosome 5. Interestingly, Insert-446 was present in the human Neanderthal and Denisovans genomes, and was fixed in humans after human-chimpanzee divergence. We have demonstrated that Insert-446 acts as an enhancer through binding transcript factors that promotes a higher expression of human TBC1D8B gene as compared with orthologs in macaques. In addition, over-expression TBC1D8B promoted cell proliferation and migration through "a dual finger" catalytic mechanism (Arg538 and Gln573) in the TBC domain in vitro and knockdown of TBC1D8B attenuated tumorigenesis in vivo. Knockout of Insert-446 prevented cell proliferation and migration in cancer and normal cells. Our results reveal that the human-specific Insert-446 promotes cell proliferation and migration by upregulating the expression of TBC1D8B gene. These findings provide a significant insight into the effects of human-specific insertions on evolution.}, }
@article {pmid38051947, year = {2023}, author = {Wroblewski, TH and Witt, KE and Lee, SB and Malhi, RS and Peede, D and Huerta-Sánchez, E and Villanea, FA and Claw, KG}, title = {Pharmacogenetic Variation in Neanderthals and Denisovans and Implications for Human Health and Response to Medications.}, journal = {Genome biology and evolution}, volume = {15}, number = {12}, pages = {}, pmid = {38051947}, issn = {1759-6653}, support = {R35 GM128946/GM/NIGMS NIH HHS/United States ; R35 HG011319/HG/NHGRI NIH HHS/United States ; R35HG011319/HG/NHGRI NIH HHS/United States ; 1R35GM128946-01/NH/NIH HHS/United States ; T32 GM128596/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Neanderthals/genetics ; Pharmacogenetics ; Genome, Human ; *Hominidae/genetics ; Biological Evolution ; }, abstract = {Modern humans carry both Neanderthal and Denisovan (archaic) genome elements that are part of the human gene pool and affect the life and health of living individuals. The impact of archaic DNA may be particularly evident in pharmacogenes-genes responsible for the processing of exogenous substances such as food, pollutants, and medications-as these can relate to changing environmental effects, and beneficial variants may have been retained as modern humans encountered new environments. However, the health implications and contribution of archaic ancestry in pharmacogenes of modern humans remain understudied. Here, we explore 11 key cytochrome P450 genes (CYP450) involved in 75% of all drug metabolizing reactions in three Neanderthal and one Denisovan individuals and examine archaic introgression in modern human populations. We infer the metabolizing efficiency of these 11 CYP450 genes in archaic individuals and find important predicted phenotypic differences relative to modern human variants. We identify several single nucleotide variants shared between archaic and modern humans in each gene, including some potentially function-altering mutations in archaic CYP450 genes, which may result in altered metabolism in living people carrying these variants. We also identified several variants in the archaic CYP450 genes that are novel and unique to archaic humans as well as one gene, CYP2B6, that shows evidence for a gene duplication found only in Neanderthals and modern Africans. Finally, we highlight CYP2A6, CYP2C9, and CYP2J2, genes which show evidence for archaic introgression into modern humans and posit evolutionary hypotheses that explain their allele frequencies in modern populations.}, }
@article {pmid38048457, year = {2023}, author = {Gaudzinski-Windheuser, S and Kindler, L and Roebroeks, W}, title = {Widespread evidence for elephant exploitation by Last Interglacial Neanderthals on the North European plain.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {50}, pages = {e2309427120}, pmid = {38048457}, issn = {1091-6490}, support = {K283/2019//IPF | Leibniz-Gemeinschaft (LG)/ ; GA 683/7-1//Deutsche Forschungsgemeinschaft (DFG)/ ; Zielgerade//Gutenberg Forschungskolleg (GRC)/ ; 28-548//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; }, mesh = {Male ; Animals ; *Elephants ; *Neanderthals ; Mammals ; Germany ; *Tooth ; Fossils ; }, abstract = {Neanderthals hunted and butchered straight-tusked elephants, the largest terrestrial mammals of the Pleistocene, in a lake landscape on the North European plain, 125,000 years ago, as recently shown by a study of the Last Interglacial elephant assemblage from Neumark-Nord (Germany). With evidence for a remarkable focus on adult males and on their extended utilization, the data from this location are thus far without parallel in the archaeological record. Given their relevance for our knowledge of the Neanderthal niche, we investigated whether the Neumark-Nord subsistence practices were more than a local phenomenon, possibly determined by local characteristics. Analyzing elephant remains from two other Last Interglacial archaeological sites on the North European plain, Gröbern and Taubach, we identified in both assemblages similar butchering patterns as at Neumark-Nord, demonstrating that extended elephant exploitation was a widespread Neanderthal practice during the (early part of the) Last Interglacial. The substantial efforts needed to process these animals, weighing up to 13 metric tons, and the large amounts of food generated suggest that Neanderthals either had ways of storing vast amounts of meat and fat and/or temporarily aggregated in larger groups than commonly acknowledged. The data do not allow us to rule out one of the two explanations, and furthermore both factors, short-term larger group sizes as well as some form of food preservation, may have played a role. What the data do show is that exploitation of large straight-tusked elephants was a widespread and recurring phenomenon amongst Last Interglacial Neanderthals on the North European plain.}, }
@article {pmid38020913, year = {2023}, author = {Agata, A and Ohtsuka, S and Noji, R and Gotoh, H and Ono, K and Nomura, T}, title = {A Neanderthal/Denisovan GLI3 variant contributes to anatomical variations in mice.}, journal = {Frontiers in cell and developmental biology}, volume = {11}, number = {}, pages = {1247361}, pmid = {38020913}, issn = {2296-634X}, abstract = {Changes in genomic structures underlie phenotypic diversification in organisms. Amino acid-changing mutations affect pleiotropic functions of proteins, although little is known about how mutated proteins are adapted in existing developmental programs. Here we investigate the biological effects of a variant of the GLI3 transcription factor (GLI3[R1537C]) carried in Neanderthals and Denisovans, which are extinct hominins close to modern humans. R1537C does not compromise protein stability or GLI3 activator-dependent transcriptional activities. In contrast, R1537C affects the regulation of downstream target genes associated with developmental processes. Furthermore, genome-edited mice carrying the Neanderthal/Denisovan GLI3 mutation exhibited various alterations in skeletal morphology. Our data suggest that an extinct hominin-type GLI3 contributes to species-specific anatomical variations, which were tolerated by relaxed constraint in developmental programs during human evolution.}, }
@article {pmid38012927, year = {2023}, author = {Lee, OY and Wu, HHT and Besra, GS and Minnikin, DE and Jaeger, HY and Maixner, F and Zink, A and Gasparik, M and Pap, I and Bereczki, Z and Pálfi, G}, title = {Sensitive lipid biomarker detection for tuberculosis in late Neanderthal skeletons from Subalyuk Cave, Hungary.}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {143S}, number = {}, pages = {102420}, doi = {10.1016/j.tube.2023.102420}, pmid = {38012927}, issn = {1873-281X}, mesh = {Adult ; Child ; Humans ; Female ; Child, Preschool ; Animals ; *Neanderthals/genetics ; Hungary ; *Mycobacterium tuberculosis/genetics ; DNA, Bacterial/genetics ; *Tuberculosis/diagnosis ; Skeleton/chemistry ; Biomarkers/analysis ; Lipids/analysis ; }, abstract = {Skeletal remains of two Neanderthal individuals, a 25-35 year-old woman and a 3-4 year-old child, were discovered in a Subalyuk Cave in North-Eastern Hungary. Radiocarbon dating of the female and child remains revealed an age of 39,732-39,076 and 36,117-35,387 cal BP, respectively. Paleopathological studies of these Neanderthal remains revealed probable evidence of skeletal mycobacterial infection, including in the sacrum of the adult specimen and the endocranial surface of the child's skull. Application of PCR amplification to the juvenile cranium and a vertebra gave a positive result (IS6110) for tuberculosis, backed up by spoligotyping. Lipid biomarker analyses of the same two specimens revealed definitive signals for C32 mycoserosates, a very characteristic component of the Mycobacterium tuberculosis complex (MTBC). A vertebra from the adult provided weak evidence for mycocerosate biomarkers. The correlation of probable skeletal lesions with characteristic amplified DNA fragments and a proven lipid biomarker points to the presence of tuberculosis in these Neanderthals. In particular, the closely similar biomarker profiles, for two distinct juvenile cranial and vertebral bones, strengthen this diagnosis.}, }
@article {pmid38012926, year = {2023}, author = {Pálfi, G and Molnár, E and Bereczki, Z and Coqueugniot, H and Dutour, O and Tillier, AM and Rosendahl, W and Sklánitz, A and Mester, Z and Gasparik, M and Maixner, F and Zink, A and Minnikin, DE and Pap, I}, title = {Re-examination of the Subalyuk Neanderthal remains uncovers signs of probable TB infection (Subalyuk Cave, Hungary).}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {143S}, number = {}, pages = {102419}, doi = {10.1016/j.tube.2023.102419}, pmid = {38012926}, issn = {1873-281X}, mesh = {Young Adult ; Humans ; Female ; Child, Preschool ; Animals ; *Mycobacterium tuberculosis ; *Neanderthals ; Hungary ; *Tuberculosis ; Bone and Bones ; Paleopathology/methods ; }, abstract = {In 1932, skeletal remains of two Neanderthal individuals, a young adult female and a 3-4-year-old child, were discovered in Subalyuk Cave in Northern Hungary [1,2]. Results of the anthropological examination were published some years after this important discovery. Methodological progress encouraged re-examination of the material during the last few years. Radiocarbon dating revealed a chronological age of 39,732-39,076 cal. BP for the adult female and 36,117-35,387 cal. BP for the child [3]. Morphological paleopathological studies of these Neanderthal remains uncovered distinct evidence of skeletal infections. Alterations of the adult individual's sacrum suggest probable early-stage sacroiliitis, while several vertebral bodies indicate superficial osseous remodelling of infectious origin. Traces of pathological lesions were observed on the endocranial surface of the child's skull, reflecting a reaction of meningeal tissues, a consequence of a probable TB-related meningeal infectious process. Results of recent paleomicrobiological examinations - lipid biomarker and aDNA studies - support the morphological diagnosis of probable TB infections [4].}, }
@article {pmid37992125, year = {2023}, author = {Di Santo, LN and Quilodrán, CS and Currat, M}, title = {Temporal Variation in Introgressed Segments' Length Statistics Computed from a Limited Number of Ancient Genomes Sheds Light on Past Admixture Pulses.}, journal = {Molecular biology and evolution}, volume = {40}, number = {12}, pages = {}, pmid = {37992125}, issn = {1537-1719}, mesh = {Animals ; *Genomics ; Paleontology ; *Neanderthals/genetics ; Genome ; Biological Evolution ; }, abstract = {Hybridization is recognized as an important evolutionary force, but identifying and timing admixture events between divergent lineages remain a major aim of evolutionary biology. While this has traditionally been done using inferential tools on contemporary genomes, the latest advances in paleogenomics have provided a growing wealth of temporally distributed genomic data. Here, we used individual-based simulations to generate chromosome-level genomic data for a 2-population system and described temporal neutral introgression patterns under a single- and 2-pulse admixture model. We computed 6 summary statistics aiming to inform the timing and number of admixture pulses between interbreeding entities: lengths of introgressed sequences and their variance within genomes, as well as genome-wide introgression proportions and related measures. The first 2 statistics could confidently be used to infer interlineage hybridization history, peaking at the beginning and shortly after an admixture pulse. Temporal variation in introgression proportions and related statistics provided more limited insights, particularly when considering their application to ancient genomes still scant in number. Lastly, we computed these statistics on Homo sapiens paleogenomes and successfully inferred the hybridization pulse from Neanderthal that occurred approximately 40 to 60 kya. The scarce number of genomes dating from this period prevented more precise inferences, but the accumulation of paleogenomic data opens promising perspectives as our approach only requires a limited number of ancient genomes.}, }
@article {pmid37989099, year = {2023}, author = {Ragsdale, AP}, title = {Human evolution: Neanderthal footprints in African genomes.}, journal = {Current biology : CB}, volume = {33}, number = {22}, pages = {R1197-R1200}, doi = {10.1016/j.cub.2023.10.005}, pmid = {37989099}, issn = {1879-0445}, mesh = {Animals ; Humans ; Alleles ; *Evolution, Molecular ; Gene Flow ; *Genome, Human ; Genomics ; *Neanderthals/genetics ; Selection, Genetic ; African People ; }, abstract = {Human and Neanderthal populations met and mixed on multiple occasions over evolutionary time, resulting in the exchange of genetic material. New genomic analyses of diverse African populations reveal a history of bidirectional gene flow and selection acting on introgressed alleles.}, }
@article {pmid37977419, year = {2023}, author = {Urnikyte, A and Masiulyte, A and Pranckeniene, L and Kučinskas, V}, title = {Disentangling archaic introgression and genomic signatures of selection at human immunity genes.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {116}, number = {}, pages = {105528}, doi = {10.1016/j.meegid.2023.105528}, pmid = {37977419}, issn = {1567-7257}, mesh = {Humans ; Animals ; Evolution, Molecular ; *Neanderthals/genetics ; Genomics ; Genome, Human ; *Communicable Diseases/genetics ; Selection, Genetic ; }, abstract = {Pathogens and infectious diseases have imposed exceptionally strong selective pressure on ancient and modern human genomes and contributed to the current variation in many genes. There is evidence that modern humans acquired immune variants through interbreeding with ancient hominins, but the impact of such variants on human traits is not fully understood. The main objectives of this research were to infer the genetic signatures of positive selection that may be involved in adaptation to infectious diseases and to investigate the function of Neanderthal alleles identified within a set of 50 Lithuanian genomes. Introgressed regions were identified using the machine learning tool ArchIE. Recent positive selection signatures were analysed using iHS. We detected high-scoring signals of positive selection at innate immunity genes (EMB, PARP8, HLAC, and CDSN) and evaluated their interactions with the structural proteins of pathogens. Interactions with human immunodeficiency virus (HIV) 1 and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified. Overall, genomic regions introgressed from Neanderthals were shown to be enriched in genes related to immunity, keratinocyte differentiation, and sensory perception.}, }
@article {pmid37925533, year = {2023}, author = {Raja, A and Kuiper, JJW}, title = {Evolutionary immuno-genetics of endoplasmic reticulum aminopeptidase II (ERAP2).}, journal = {Genes and immunity}, volume = {24}, number = {6}, pages = {295-302}, pmid = {37925533}, issn = {1476-5470}, support = {954992//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; }, mesh = {Humans ; *Aminopeptidases/genetics/immunology ; Autoimmune Diseases/genetics/immunology ; *Endoplasmic Reticulum/enzymology ; Haplotypes ; Minor Histocompatibility Antigens/genetics ; *Evolution, Molecular ; *Adaptive Immunity/genetics ; }, abstract = {Endoplasmic reticulum aminopeptidase 2 (ERAP2) is a proteolytic enzyme involved in adaptive immunity. The ERAP2 gene is highly polymorphic and encodes haplotypes that confer resistance against lethal infectious diseases, but also increase the risk for autoimmune disorders. Identifying how ERAP2 influences susceptibility to these traits requires an understanding of the selective pressures that shaped and maintained allelic variation throughout human evolution. Our review discusses the genetic regulation of haplotypes and diversity in naturally occurring ERAP2 allotypes in the global population. We outline how these ERAP2 haplotypes evolved during human history and highlight the presence of Neanderthal DNA sequences in ERAP2 of modern humans. Recent evidence suggests that human adaptation during the last ~10,000 years and historic pandemics left a significant mark on the ERAP2 gene that determines susceptibility to infectious and inflammatory diseases today.}, }
@article {pmid37851812, year = {2023}, author = {Quilodrán, CS and Rio, J and Tsoupas, A and Currat, M}, title = {Past human expansions shaped the spatial pattern of Neanderthal ancestry.}, journal = {Science advances}, volume = {9}, number = {42}, pages = {eadg9817}, pmid = {37851812}, issn = {2375-2548}, mesh = {Animals ; Humans ; Africa ; Asian People ; Hominidae/genetics ; *Neanderthals/genetics ; *Phylogeography ; European People/genetics ; *Genetic Introgression/genetics ; }, abstract = {The worldwide expansion of modern humans (Homo sapiens) started before the extinction of Neanderthals (Homo neanderthalensis). Both species coexisted and interbred, leading to slightly higher introgression in East Asians than in Europeans. This distinct ancestry level has been argued to result from selection, but range expansions of modern humans could provide an alternative explanation. This hypothesis would lead to spatial introgression gradients, increasing with distance from the expansion source. We investigate the presence of Neanderthal introgression gradients after past human expansions by analyzing Eurasian paleogenomes. We show that the out-of-Africa expansion resulted in spatial gradients of Neanderthal ancestry that persisted through time. While keeping the same gradient orientation, the expansion of early Neolithic farmers contributed decisively to reducing the Neanderthal introgression in European populations compared to Asian populations. This is because Neolithic farmers carried less Neanderthal DNA than preceding Paleolithic hunter-gatherers. This study shows that inferences about past human population dynamics can be made from the spatiotemporal variation in archaic introgression.}, }
@article {pmid37846608, year = {2024}, author = {Chen, Y and Yu, XY and Xu, SJ and Shi, XQ and Zhang, XX and Sun, C}, title = {An indel introduced by Neanderthal introgression, rs3835124:ATTTATT &gt; ATT, might contribute to prostate cancer risk by regulating PDK1 expression.}, journal = {Annals of human genetics}, volume = {88}, number = {2}, pages = {126-137}, doi = {10.1111/ahg.12533}, pmid = {37846608}, issn = {1469-1809}, support = {//National Natural Science Foundation&#xa0;of China/ ; //Fundamental Research&#xa0;Funds for the Central Universities/ ; }, mesh = {Humans ; Animals ; *Neanderthals/genetics ; Genome-Wide Association Study ; Genetics, Population ; Phylogeny ; Haplotypes ; Genome, Human ; *Neoplasms/genetics ; }, abstract = {INTRODUCTION: Prostate cancer is one of the most common cancer types in males and rs12621278:A > G has been suggested to be associated with this disease by previous genome-wide association studies. One thousand genomes project data analysis indicated that rs12621278:A > G is within two long-core haplotypes. However, the origin, causal variant(s), and molecular function of these haplotypes were remaining unclear.<br><br>MATERIALS AND METHODS: Population genetics analysis and functional genomics work was performed for this locus.<br><br>RESULTS: Phylogeny analysis verified that the rare haplotype is derived from Neanderthal introgression. Genome annotation suggested that three genetic variants in the core haplotypes, rs116108611:G&#xa0;>&#xa0;A, rs139972066:AAAAAAAA&#xa0;>&#xa0;AAAAAAAAA, and rs3835124:ATTTATT&#xa0;>&#xa0;ATT, are located in functional regions. Luciferase assay indicated that rs139972066:AAAAAAAA&#xa0;>&#xa0;AAAAAAAAA and rs116108611:G&#xa0;>&#xa0;A are not able to alter ITGA6 (integrin alpha 6) and ITGA6 antisense RNA 1 expression, respectively. In contrast, rs3835124:ATTTATT&#xa0;>&#xa0;ATT can significantly influence PDK1 (pyruvate dehydrogenase kinase 1) expression, which was verified by expression quantitative trait locus analysis. This genetic variant can alter transcription factor cut like homeobox 1 interaction efficiency. The introgressed haplotype was observed to be subject to positive selection in East Asian populations. The molecular function of the haplotype suggested that Neanderthal should be with lower PDK1 expression and further different energy homeostasis from modern human.<br><br>CONCLUSION: This study provided new insight into the contribution of Neanderthal introgression to human phenotypes.}, }
@article {pmid37837965, year = {2023}, author = {Harris, DN and Platt, A and Hansen, MEB and Fan, S and McQuillan, MA and Nyambo, T and Mpoloka, SW and Mokone, GG and Belay, G and Fokunang, C and Njamnshi, AK and Tishkoff, SA}, title = {Diverse African genomes reveal selection on ancient modern human introgressions in Neanderthals.}, journal = {Current biology : CB}, volume = {33}, number = {22}, pages = {4905-4916.e5}, pmid = {37837965}, issn = {1879-0445}, support = {R01 AR076241/AR/NIAMS NIH HHS/United States ; R35 GM134957/GM/NIGMS NIH HHS/United States ; T32 DK007314/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Animals ; *Neanderthals/genetics ; Genome, Human ; Gene Flow ; Genomics ; Africa South of the Sahara ; }, abstract = {Comparisons of Neanderthal genomes to anatomically modern human (AMH) genomes show a history of Neanderthal-to-AMH introgression stemming from interbreeding after the migration of AMHs from Africa to Eurasia. All non-sub-Saharan African AMHs have genomic regions genetically similar to Neanderthals that descend from this introgression. Regions of the genome with Neanderthal similarities have also been identified in sub-Saharan African populations, but their origins have been unclear. To better understand how these regions are distributed across sub-Saharan Africa, the source of their origin, and what their distribution within the genome tells us about early AMH and Neanderthal evolution, we analyzed a dataset of high-coverage, whole-genome sequences from 180 individuals from 12 diverse sub-Saharan African populations. In sub-Saharan African populations with non-sub-Saharan African ancestry, as much as 1% of their genomes can be attributed to Neanderthal sequence introduced by recent migration, and subsequent admixture, of AMH populations originating from the Levant and North Africa. However, most Neanderthal homologous regions in sub-Saharan African populations originate from migration of AMH populations from Africa to Eurasia ∼250 kya, and subsequent admixture with Neanderthals, resulting in ∼6% AMH ancestry in Neanderthals. These results indicate that there have been multiple migration events of AMHs out of Africa and that Neanderthal and AMH gene flow has been bi-directional. Observing that genomic regions where AMHs show a depletion of Neanderthal introgression are also regions where Neanderthal genomes show a depletion of AMH introgression points to deleterious interactions between introgressed variants and background genomes in both groups-a hallmark of incipient speciation.}, }
@article {pmid37828055, year = {2023}, author = {Russo, G and Milks, A and Leder, D and Koddenberg, T and Starkovich, BM and Duval, M and Zhao, JX and Darga, R and Rosendahl, W and Terberger, T}, title = {First direct evidence of lion hunting and the early use of a lion pelt by Neanderthals.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {16405}, pmid = {37828055}, issn = {2045-2322}, mesh = {Animals ; Humans ; *Neanderthals ; *Lions ; Hunting ; Archaeology ; *Hominidae ; *Panthera ; Fossils ; }, abstract = {During the Upper Paleolithic, lions become an important theme in Paleolithic art and are more frequent in anthropogenic faunal assemblages. However, the relationship between hominins and lions in earlier periods is poorly known and primarily interpreted as interspecies competition. Here we present new evidence for Neanderthal-cave lion interactions during the Middle Paleolithic. We report new evidence of hunting lesions on the 48,000 old cave lion skeleton found at Siegsdorf (Germany) that attest to the earliest direct instance of a large predator kill in human history. A comparative analysis of a partial puncture to a rib suggests that the fatal stab was delivered with a wooden thrusting spear. We also present the discovery of distal lion phalanges at least 190,000 old from Einhornhöhle (Germany), representing the earliest example of the use of cave lion skin by Neanderthals in Central Europe. Our study provides novel evidence on a new dimension of Neanderthal behavioral complexity.}, }
@article {pmid37816865, year = {2023}, author = {Faux, P and Ding, L and Ramirez-Aristeguieta, LM and Chacón-Duque, JC and Comini, M and Mendoza-Revilla, J and Fuentes-Guajardo, M and Jaramillo, C and Arias, W and Hurtado, M and Villegas, V and Granja, V and Barquera, R and Everardo-Martínez, P and Quinto-Sánchez, M and Gómez-Valdés, J and Villamil-Ramírez, H and Silva de Cerqueira, CC and Hünemeier, T and Ramallo, V and Gonzalez-José, R and Schüler-Faccini, L and Bortolini, MC and Acuña-Alonzo, V and Canizales-Quinteros, S and Poletti, G and Gallo, C and Rothhammer, F and Rojas, W and Schmid, AB and Adhikari, K and Bennett, DL and Ruiz-Linares, A}, title = {Neanderthal introgression in SCN9A impacts mechanical pain sensitivity.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {958}, pmid = {37816865}, issn = {2399-3642}, support = {MR/W002388/1/MRC_/Medical Research Council/United Kingdom ; /DH_/Department of Health/United Kingdom ; 223149/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; 222101/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; MR/T020113/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; /VAC_/Versus Arthritis/United Kingdom ; BB/I021213/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; Animals ; *Pain Threshold ; *Neanderthals/genetics ; Pain/genetics ; NAV1.7 Voltage-Gated Sodium Channel/genetics ; Nociception ; }, abstract = {The Nav1.7 voltage-gated sodium channel plays a key role in nociception. Three functional variants in the SCN9A gene (encoding M932L, V991L, and D1908G in Nav1.7), have recently been identified as stemming from Neanderthal introgression and to associate with pain symptomatology in UK BioBank data. In 1000 genomes data, these variants are absent in Europeans but common in Latin Americans. Analysing high-density genotype data from 7594 Latin Americans, we characterized Neanderthal introgression in SCN9A. We find that tracts of introgression occur on a Native American genomic background, have an average length of ~123 kb and overlap the M932L, V991L, and D1908G coding positions. Furthermore, we measured experimentally six pain thresholds in 1623 healthy Colombians. We found that Neanderthal ancestry in SCN9A is significantly associated with a lower mechanical pain threshold after sensitization with mustard oil and evidence of additivity of effects across Nav1.7 variants. Our findings support the reported association of Neanderthal Nav1.7 variants with clinical pain, define a specific sensory modality affected by archaic introgression in SCN9A and are consistent with independent effects of the Neanderthal variants on Nav1.7 function.}, }
@article {pmid37808839, year = {2023}, author = {Villanea, FA and Peede, D and Kaufman, EJ and Añorve-Garibay, V and Witt, KE and Villa-Islas, V and Zeloni, R and Marnetto, D and Moorjani, P and Jay, F and Valdmanis, PN and Ávila-Arcos, MC and Huerta-Sánchez, E}, title = {The MUC19 gene in Denisovans, Neanderthals, and Modern Humans: An Evolutionary History of Recurrent Introgression and Natural Selection.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37808839}, issn = {2692-8205}, support = {R01 NS122766/NS/NINDS NIH HHS/United States ; R35 GM128946/GM/NIGMS NIH HHS/United States ; R35 GM142978/GM/NIGMS NIH HHS/United States ; T32 GM128596/GM/NIGMS NIH HHS/United States ; }, abstract = {All humans carry a small fraction of archaic ancestry across the genome, the legacy of gene flow from Neanderthals, Denisovans, and other hominids into the ancestors of modern humans. While the effects of Neanderthal ancestry on human fitness and health have been explored more thoroughly, there are fewer examples of adaptive introgression of Denisovan variants. Here, we study the gene MUC19, for which some modern humans carry a Denisovan-like haplotype. MUC19 is a mucin, a glycoprotein that forms gels with various biological functions, from lubrication to immunity. We find the diagnostic variants for the Denisovan-like MUC19 haplotype at high frequencies in admixed Latin American individuals among global population, and at highest frequency in 23 ancient Indigenous American individuals, all predating population admixture with Europeans and Africans. We find that some Neanderthals--Vindija and Chagyrskaya--carry the Denisovan-like MUC19 haplotype, and that it was likely introgressed into human populations through Neanderthal introgression rather than Denisovan introgression. Finally, we find that the Denisovan-like MUC19 haplotype carries a higher copy number of a 30 base-pair variable number tandem repeat relative to the Human-like haplotype, and that copy numbers of this repeat are exceedingly high in American populations. Our results suggest that the Denisovan-like MUC19 haplotype served as the raw genetic material for positive selection as American populations adapted to novel environments during their movement from Beringia into North and then South America.}, }
@article {pmid37794824, year = {2024}, author = {Carretero, JM and Rodríguez, L and García-González, R and Arsuaga, JL}, title = {Main morphological characteristics and sexual dimorphism of hominin adult femora from the Sima de los Huesos Middle Pleistocene site (Sierra de Atapuerca, Spain).}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {307}, number = {7}, pages = {2575-2605}, doi = {10.1002/ar.25331}, pmid = {37794824}, issn = {1932-8494}, support = {PID2021-122355NB-C31//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; //MCIN/AEI// ; //Junta de Castilla y Le&#xf3;n/ ; //Fundaci&#xf3;n Atapuerca/ ; }, mesh = {Animals ; *Femur/anatomy &amp; histology ; Female ; *Sex Characteristics ; Male ; *Fossils/anatomy &amp; histology ; Spain ; *Hominidae/anatomy &amp; histology ; Neanderthals/anatomy &amp; histology ; Biological Evolution ; Humans ; }, abstract = {The excellent fossil record from Sima de los Huesos (SH) includes three well-known complete adult femora and several partial specimens that have not yet been published in detail. This fossil record provides an opportunity to analyze the morphology of European pre-Neandertal adult femur and its variation with different evolution patterns. Currently, there are a minimum of five adult individuals (males or females). In this study, we compiled previously published basic anatomical and biometric characteristics of SH adult femora, emphasizing the most relevant features compared to other recent and fossil hominins. The SH femora exhibited a primitive morphological pattern common to all non-Homo sapiens femora, as well as most of the Neandertal traits. Therefore, the complete Upper Pleistocene Neandertal pattern was well-established in Middle Pleistocene ancestors long before the proper Neandertals appeared. Additionally, we highlight that the SH and Neandertal femora share some morphological traits and proportions with modern humans that hold sexual significance in our species, regardless of size. Keeping this in mind, we discussed the sex determination of the complete SH specimens and re-evaluated sex allocation in two of them.}, }
@article {pmid37790518, year = {2023}, author = {Yee, SW and Ferrández-Peral, L and Alentorn, P and Fontsere, C and Ceylan, M and Koleske, ML and Handin, N and Artegoitia, VM and Lara, G and Chien, HC and Zhou, X and Dainat, J and Zalevsky, A and Sali, A and Brand, CM and Capra, JA and Artursson, P and Newman, JW and Marques-Bonet, T and Giacomini, KM}, title = {Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {37790518}, issn = {2693-5015}, support = {R01 GM117163/GM/NIGMS NIH HHS/United States ; R01 GM139875/GM/NIGMS NIH HHS/United States ; }, abstract = {SLC22A10 is classified as an orphan transporter with unknown substrates and function. Here we describe the discovery of the substrate specificity and functional characteristics of SLC22A10. The human SLC22A10 tagged with green fluorescent protein was found to be absent from the plasma membrane, in contrast to the SLC22A10 orthologs found in great apes. Estradiol-17β-glucuronide accumulated in cells expressing great ape SLC22A10 orthologs (over 4-fold, p<0.001). In contrast, human SLC22A10 displayed no uptake function. Sequence alignments revealed two amino acid differences including a proline at position 220 of the human SLC22A10 and a leucine at the same position of great ape orthologs. Site-directed mutagenesis yielding the human SLC22A10-P220L produced a protein with excellent plasma membrane localization and associated uptake function. Neanderthal and Denisovan genomes show human-like sequences at proline 220 position, corroborating that SLC22A10 were rendered nonfunctional during hominin evolution after the divergence from the pan lineage (chimpanzees and bonobos). These findings demonstrate that human SLC22A10 is a unitary pseudogene and was inactivated by a missense mutation that is fixed in humans, whereas orthologs in great apes transport sex steroid conjugates.}, }
@article {pmid37747127, year = {2023}, author = {Hui, J and Balzeau, A}, title = {The diploic venous system in Homo neanderthalensis and fossil Homo sapiens: A study using high-resolution computed tomography.}, journal = {American journal of biological anthropology}, volume = {182}, number = {3}, pages = {412-427}, doi = {10.1002/ajpa.24843}, pmid = {37747127}, issn = {2692-7691}, support = {ANR-20-CE27-0009//Agence Nationale de la Recherche/ ; //China Scholarship Council/ ; }, abstract = {OBJECTIVES: The diploic venous system has been hypothesized to be related to human brain evolution, though its evolutionary trajectory and physiological functions remain largely unclear. This study examines the characteristics of the diploic venous channels (DCs) in a selection of well-preserved Homo neanderthalensis and Upper Paleolithic Homo sapiens crania, searching for the differences between the two taxa and exploring the associations between brain anatomy and DCs.<br><br>MATERIALS AND METHODS: Five H. neanderthalensis and four H. sapiens fossil specimens from Western Europe were analyzed. Based on Micro-CT scanning and 3D reconstruction, the distribution pattern and draining orifices of the DCs were inspected qualitatively. The size of the DCs was quantified by volume calculation, and the degree of complexity was quantified by fractal analyses.<br><br>RESULTS: High-resolution data show the details of the DC structures not documented in previous studies. H. neanderthalensis and H. sapiens specimens share substantial similarities in the DCs. The noticeable differences between the two samples manifest in the connecting points surrounding the frontal sinuses, parietal foramina, and asterional area.<br><br>DISCUSSION: This study provides a better understanding of the anatomy of the DCs in H. neanderthalensis and H. sapiens. The connection patterns of the DCs have potential utility in distinguishing between the two taxa and in the phylogenetic and taxonomic discussion of the Neandertal-like specimens with controversial taxonomic status.}, }
@article {pmid37738342, year = {2023}, author = {Vidal-Cordasco, M and Terlato, G and Ocio, D and Marín-Arroyo, AB}, title = {Neanderthal coexistence with Homo sapiens in Europe was affected by herbivore carrying capacity.}, journal = {Science advances}, volume = {9}, number = {38}, pages = {eadi4099}, pmid = {37738342}, issn = {2375-2548}, mesh = {Humans ; Animals ; *Neanderthals ; Herbivory ; Bayes Theorem ; Conservation of Natural Resources ; Ecosystem ; Europe ; }, abstract = {It has been proposed that climate change and the arrival of modern humans in Europe affected the disappearance of Neanderthals due to their impact on trophic resources; however, it has remained challenging to quantify the effect of these factors. By using Bayesian age models to derive the chronology of the European Middle to Upper Paleolithic transition, followed by a dynamic vegetation model that provides the Net Primary Productivity, and a macroecological model to compute herbivore abundance, we show that in continental regions where the ecosystem productivity was low or unstable, Neanderthals disappeared before or just after the arrival of Homo sapiens. In contrast, regions with high and stable productivity witnessed a prolonged coexistence between both species. The temporal overlap between Neanderthals and H. sapiens is significantly correlated with the carrying capacity of small- and medium-sized herbivores. These results suggest that herbivore abundance released the trophic pressure of the secondary consumers guild, which affected the coexistence likelihood between both human species.}, }
@article {pmid37737280, year = {2023}, author = {Fajardo, S and Kozowyk, PRB and Langejans, GHJ}, title = {Measuring ancient technological complexity and its cognitive implications using Petri nets.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {14961}, pmid = {37737280}, issn = {2045-2322}, mesh = {Humans ; Animals ; *Neanderthals ; Archaeology ; Benchmarking ; Cognition ; Receptor Protein-Tyrosine Kinases ; Technology ; }, abstract = {We implement a method from computer sciences to address a challenge in Paleolithic archaeology: how to infer cognition differences from material culture. Archaeological material culture is linked to cognition, and more complex ancient technologies are assumed to have required complex cognition. We present an application of Petri net analysis to compare Neanderthal tar production technologies and tie the results to cognitive requirements. We applied three complexity metrics, each relying on their own unique definitions of complexity, to the modeled production processes. Based on the results, we propose that Neanderthal technical cognition may have been analogous to that of contemporary modern humans. This method also enables us to distinguish the high-order cognitive functions combining traits like planning, inhibitory control, and learning that were likely required by different ancient technological processes. The Petri net approach can contribute to our understanding of technology and cognitive evolution as it can be used on different materials and technologies, across time and species.}, }
@article {pmid37713634, year = {2023}, author = {Ge, X and Lu, Y and Chen, S and Gao, Y and Ma, L and Liu, L and Liu, J and Ma, X and Kang, L and Xu, S}, title = {Genetic Origins and Adaptive Evolution of the Deng People on the Tibetan Plateau.}, journal = {Molecular biology and evolution}, volume = {40}, number = {10}, pages = {}, pmid = {37713634}, issn = {1537-1719}, mesh = {Humans ; Adaptor Proteins, Signal Transducing ; Altitude ; *Asian People/genetics ; Haplotypes ; Tibet ; }, abstract = {The Tibetan Plateau is populated by diverse ethnic groups, but most of them are underrepresented in genomics studies compared with the Tibetans (TIB). Here, to gain further insight into the genetic diversity and evolutionary history of the people living in the Tibetan Plateau, we sequenced 54 whole genomes of the Deng people with high coverage (30-60×) and analyzed the data together with that of TIB and Sherpas, as well as 968 ancient Asian genomes and available archaic and modern human data. We identified 17.74 million novel single-nucleotide variants from the newly sequenced genomes, although the Deng people showed reduced genomic diversity and a relatively small effective population size. Compared with the other Tibetan highlander groups which are highly admixed, the Deng people are dominated by a sole ancestry that could be traced to some ancient northern East Asian populations. The divergence between Deng and Tibetan people (∼4,700-7,200 years) was more recent than that between highlanders and the Han Chinese (Deng-HAN, ∼9,000-14,000 years; TIB-HAN, 7,200-10,000 years). Adaptive genetic variants (AGVs) identified in the Deng are only partially shared with those previously reported in the TIB like HLA-DQB1, whereas others like KLHL12 were not reported in TIB. In contrast, the top candidate genes harboring AGVs as previously identified in TIB, like EPAS1 and EGLN1, do not show strong positive selection signals in Deng. Interestingly, Deng also showed a different archaic introgression scenario from that observed in the TIB. Our results suggest that convergent adaptation might be prevalent on the Tibetan Plateau.}, }
@article {pmid37679497, year = {2023}, author = {Kozowyk, PRB and Fajardo, S and Langejans, GHJ}, title = {Scaling Palaeolithic tar production processes exponentially increases behavioural complexity.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {14709}, pmid = {37679497}, issn = {2045-2322}, mesh = {Humans ; Animals ; *Neanderthals ; Cognition ; Archaeology ; Commerce ; Food Handling ; Tars ; }, abstract = {Technological processes, reconstructed from the archaeological record, are used to study the evolution of behaviour and cognition of Neanderthals and early modern humans. In comparisons, technologies that are more complex infer more complex behaviour and cognition. The manufacture of birch bark tar adhesives is regarded as particularly telling and often features in debates about Neanderthal cognition. One method of tar production, the 'condensation technique', demonstrates a pathway for Neanderthals to have discovered birch bark tar. However, to improve on the relatively low yield, and to turn tar into a perennial innovation, this method likely needed to be scaled up. Yet, it is currently unknown how scaling Palaeolithic technological processes influences their complexity. We used Petri net models and the Extended Cyclomatic Metric to measure system complexity of birch tar production with a single and three concurrent condensation assemblies. Our results show that changing the number of concurrent tar production assemblies substantially increases the measured complexity. This has potential implications on the behavioural and cognitive capacities required by Neanderthals, such as an increase in cooperation or inhibition control.}, }
@article {pmid37675658, year = {2024}, author = {Mester, Z and Coqueugniot, H and Tillier, AM and Rosendahl, W and Friedrich, R and Zink, A and Maixner, F and Dutour, O and Bereczki, Z and Gasparik, M and Pap, I and Pálfi, G}, title = {First direct dating of the Late Neanderthal remains from Subalyuk Cave in Northern Hungary.}, journal = {Anthropologischer Anzeiger; Bericht uber die biologisch-anthropologische Literatur}, volume = {81}, number = {2}, pages = {169-181}, doi = {10.1127/anthranz/2023/1716}, pmid = {37675658}, issn = {0003-5548}, mesh = {Animals ; Child ; Humans ; *Neanderthals ; Hungary ; Fossils ; *Hominidae ; Europe ; Archaeology ; Radiometric Dating ; }, abstract = {The Subalyuk hominin remains were uncovered in 1932 in a cave of the same name in the Bükk Mountains, near the village of Cserépfalu in Borsod-Abaúj-Zemplén County, Northern Hungary. The remains represent two individuals, an adult and a young child who have been described in a few publications since their discovery, providing substantial anthropological data and general assessments of their Neanderthal affiliation. They were associated with Late Mousterian industry. Thus, the Bükk Mountains gain importance in the discussion concerning the contribution of East Central European sites to the debate on the peopling history of Europe during the Late Middle to Early Upper Palaeolithic transition. In this paper, we summarize the archaeological and chronological context of the two individuals, and publish the first direct dating results that place them among the Last Neanderthals of Central Europe.}, }
@article {pmid37660151, year = {2023}, author = {Glunčić, M and Vlahović, I and Rosandić, M and Paar, V}, title = {Tandem NBPF 3mer HORs (Olduvai triplets) in Neanderthal and two novel HOR tandem arrays in human chromosome 1 T2T-CHM13 assembly.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {14420}, pmid = {37660151}, issn = {2045-2322}, mesh = {Humans ; Animals ; *Neanderthals/genetics ; Chromosomes, Human ; Chromosomes, Human, Pair 1 ; *Neuroblastoma ; Family ; Pan troglodytes ; }, abstract = {It is known that the ~ 1.6 kb Neuroblastoma BreakPoint Family (NBPF) repeats are human specific and contributing to cognitive capabilities, with increasing frequency in higher order repeat 3mer HORs (Olduvai triplets). From chimpanzee to modern human there is a discontinuous jump from 0 to ~ 50 tandemly organized 3mer HORs. Here we investigate the structure of NBPF 3mer HORs in the Neanderthal genome assembly of Pääbo et al., comparing it to the results obtained for human hg38.p14 chromosome 1. Our findings reveal corresponding NBPF 3mer HOR arrays in Neanderthals with slightly different monomer structures and numbers of HOR copies compared to humans. Additionally, we compute the NBPF 3mer HOR pattern for the complete telomere-to-telomere human genome assembly (T2T-CHM13) by Miga et al., identifying two novel tandem arrays of NBPF 3mer HOR repeats with 5 and 9 NBPF 3mer HOR copies. We hypothesize that these arrays correspond to novel NBPF genes (here referred to as NBPFA1 and NBPFA2). Further improving the quality of the Neanderthal genome using T2T-CHM13 as a reference would be of great interest in determining the presence of such distant novel NBPF genes in the Neanderthal genome and enhancing our understanding of human evolution.}, }
@article {pmid37659139, year = {2023}, author = {Fiorenza, L and Habashi, W and Moggi-Cecchi, J and Benazzi, S and Sarig, R}, title = {Relationship between interproximal and occlusal wear in Australopithecus africanus and Neanderthal molars.}, journal = {Journal of human evolution}, volume = {183}, number = {}, pages = {103423}, doi = {10.1016/j.jhevol.2023.103423}, pmid = {37659139}, issn = {1095-8606}, mesh = {Humans ; Animals ; *Tooth Attrition ; *Neanderthals ; Molar ; *Tooth ; *Hominidae ; Fossils ; *Tooth Wear ; }, }
@article {pmid37609337, year = {2023}, author = {Yee, SW and Ferrández-Peral, L and Alentorn, P and Fontsere, C and Ceylan, M and Koleske, ML and Handin, N and Artegoitia, VM and Lara, G and Chien, HC and Zhou, X and Dainat, J and Zalevsky, A and Sali, A and Brand, CM and Capra, JA and Artursson, P and Newman, JW and Marques-Bonet, T and Giacomini, KM}, title = {Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37609337}, issn = {2692-8205}, support = {R01 GM117163/GM/NIGMS NIH HHS/United States ; R01 GM139875/GM/NIGMS NIH HHS/United States ; }, abstract = {SLC22A10 is classified as an orphan transporter with unknown substrates and function. Here we describe the discovery of the substrate specificity and functional characteristics of SLC22A10. The human SLC22A10 tagged with green fluorescent protein was found to be absent from the plasma membrane, in contrast to the SLC22A10 orthologs found in great apes. Estradiol-17β-glucuronide accumulated in cells expressing great ape SLC22A10 orthologs (over 4-fold, p<0.001). In contrast, human SLC22A10 displayed no uptake function. Sequence alignments revealed two amino acid differences including a proline at position 220 of the human SLC22A10 and a leucine at the same position of great ape orthologs. Site-directed mutagenesis yielding the human SLC22A10-P220L produced a protein with excellent plasma membrane localization and associated uptake function. Neanderthal and Denisovan genomes show human-like sequences at proline 220 position, corroborating that SLC22A10 were rendered nonfunctional during hominin evolution after the divergence from the pan lineage (chimpanzees and bonobos). These findings demonstrate that human SLC22A10 is a unitary pseudogene and was inactivated by a missense mutation that is fixed in humans, whereas orthologs in great apes transport sex steroid conjugates.}, }
@article {pmid37574541, year = {2023}, author = {Piccardi, M and Gentiluomo, M and Bertoncini, S and Pezzilli, R and Erőss, B and Bunduc, S and Uzunoglu, FG and Talar-Wojnarowska, R and Vanagas, T and Sperti, C and Oliverius, M and Aoki, MN and Ermini, S and Hussein, T and Boggi, U and Jamroziak, K and Maiello, E and Morelli, L and Vodickova, L and Di Franco, G and Landi, S and Szentesi, A and Lovecek, M and Puzzono, M and Tavano, F and van Laarhoven, HWM and Zerbi, A and Mohelnikova-Duchonova, B and Stocker, H and Costello, E and Capurso, G and Ginocchi, L and Lawlor, RT and Vanella, G and Bazzocchi, F and Izbicki, JR and Latiano, A and Bueno-de-Mesquita, B and Ponz de Leon Pisani, R and Schöttker, B and Soucek, P and Hegyi, P and Gazouli, M and Hackert, T and Kupcinskas, J and Poskiene, L and Tacelli, M and Roth, S and Carrara, S and Perri, F and Hlavac, V and Theodoropoulos, GE and Busch, OR and Mambrini, A and van Eijck, CHJ and Arcidiacono, P and Scarpa, A and Pasquali, C and Basso, D and Lucchesi, M and Milanetto, AC and Neoptolemos, JP and Cavestro, GM and Janciauskas, D and Chen, X and Chammas, R and Goetz, M and Brenner, H and Archibugi, L and Dannemann, M and Canzian, F and Tofanelli, S and Campa, D}, title = {Exploring the Neandertal legacy of pancreatic ductal adenocarcinoma risk in Eurasians.}, journal = {Biological research}, volume = {56}, number = {1}, pages = {46}, pmid = {37574541}, issn = {0717-6287}, support = {26881/CRUK_/Cancer Research UK/United Kingdom ; C7690/A26881/CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {Humans ; Animals ; *Neanderthals/genetics ; *Diabetes Mellitus, Type 2 ; Polymorphism, Single Nucleotide ; *Carcinoma, Pancreatic Ductal/genetics ; *Pancreatic Neoplasms/genetics ; }, abstract = {BACKGROUND: The genomes of present-day non-Africans are composed of 1-3% of Neandertal-derived DNA as a consequence of admixture events between Neandertals and anatomically modern humans about 50-60 thousand years ago. Neandertal-introgressed single nucleotide polymorphisms (aSNPs) have been associated with modern human disease-related traits, which are risk factors for pancreatic ductal adenocarcinoma (PDAC), such as obesity, type 2 diabetes, and inflammation. In this study, we aimed at investigating the role of aSNPs in PDAC in three Eurasian populations.<br><br>RESULTS: The high-coverage Vindija Neandertal genome was used to select aSNPs in non-African populations from 1000 Genomes project phase 3 data. Then, the association between aSNPs and PDAC risk was tested independently in Europeans and East Asians, using existing GWAS data on more than 200 000 individuals. We did not find any significant associations between aSNPs and PDAC in samples of European descent, whereas, in East Asians, we observed that the Chr10p12.1-rs117585753-T allele (MAF&#x2009;=&#x2009;10%) increased the risk to develop PDAC (OR&#x2009;=&#x2009;1.35, 95%CI 1.19-1.54, P&#x2009;=&#x2009;3.59&#x2009;&#xd7;&#x2009;10[-6]), with a P-value close to a threshold that takes into account multiple testing.<br><br>CONCLUSIONS: Our results show only a minimal contribution of Neandertal SNPs to PDAC risk.}, }
@article {pmid37561879, year = {2023}, author = {Ruan, J and Timmermann, A and Raia, P and Yun, KS and Zeller, E and Mondanaro, A and Di Febbraro, M and Lemmon, D and Castiglione, S and Melchionna, M}, title = {Climate shifts orchestrated hominin interbreeding events across Eurasia.}, journal = {Science (New York, N.Y.)}, volume = {381}, number = {6658}, pages = {699-704}, doi = {10.1126/science.add4459}, pmid = {37561879}, issn = {1095-9203}, mesh = {Animals ; Humans ; Fossils ; Gene Flow ; *Neanderthals/genetics ; *Climate Change ; }, abstract = {When, where, and how often hominin interbreeding happened is largely unknown. We study the potential for Neanderthal-Denisovan admixture using species distribution models that integrate extensive fossil, archaeological, and genetic data with transient coupled general circulation model simulations of global climate and biomes. Our Pleistocene hindcast of past hominins' habitat suitability reveals pronounced climate-driven zonal shifts in the main overlap region of Denisovans and Neanderthals in central Eurasia. These shifts, which influenced the timing and intensity of potential interbreeding events, can be attributed to the response of climate and vegetation to past variations in atmospheric carbon dioxide and Northern Hemisphere ice-sheet volume. Therefore, glacial-interglacial climate swings likely played an important role in favoring gene flow between archaic humans.}, }
@article {pmid37561595, year = {2023}, author = {Garralda, MD and Le Cabec, A and Maíllo Fernández, JM and Maureille, B and Gunz, P and Neira, A and Hublin, JJ and Bernaldo de Quirós, F}, title = {Mousterian human fossils from El Castillo cave (Puente Viesgo, Cantabria, Spain).}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {100}, number = {}, pages = {123-142}, doi = {10.4436/JASS.10021}, pmid = {37561595}, issn = {2037-0644}, abstract = {El Castillo cave is a well-known site because of its Paleolithic archaeology and parietal rock art. This paper is focused on the human remains found by V. Cabrera in the Mousterian Unit XX assigned to MIS 4 and early MIS 3. The fossils consist of one upper left second premolar (ULP4), one incomplete proximal hand phalanx, and one partial femoral head. The tooth and the phalanx were assigned to adults, whereas the femoral head belonged to an immature individual due to the absence of fusion traces to the metaphyseal surface. The external morphology and metrical characterization of the Castillo-1466 (ULP4) tooth crown was quantified and compared to the variability of other Neanderthal dental remains and a sample of modern human populations. We also quantified its 3D enamel thickness distribution, its roots morphology, as well as the presence of chipping, and their possible relation to masticatory or paramasticatory activities. Castillo-1466 shows crown dimensions compatible with middle-sized Neanderthal teeth, but with a remarkably thicker enamel than other Neanderthal premolars, such as Marillac 13. The femoral head and the hand phalanx fragment are compared to published values for Neanderthals, although both partial fossils lack diagnostic features precluding any clear taxonomic diagnostic. Therefore, their attribution to Neanderthals is assumed based on the dating of the layers in which they were discovered. El Castillo cave Mousterian fossils represent another contribution to the knowledge of the Middle Paleolithic populations of Northern Spain, where different sites along the Cantabrian mountains yielded several human remains assigned to MIS 4 and early MIS 3.}, }
@article {pmid37558883, year = {2023}, author = {Aquino, Y and Bisiaux, A and Li, Z and O'Neill, M and Mendoza-Revilla, J and Merkling, SH and Kerner, G and Hasan, M and Libri, V and Bondet, V and Smith, N and de Cevins, C and Ménager, M and Luca, F and Pique-Regi, R and Barba-Spaeth, G and Pietropaoli, S and Schwartz, O and Leroux-Roels, G and Lee, CK and Leung, K and Wu, JT and Peiris, M and Bruzzone, R and Abel, L and Casanova, JL and Valkenburg, SA and Duffy, D and Patin, E and Rotival, M and Quintana-Murci, L}, title = {Dissecting human population variation in single-cell responses to SARS-CoV-2.}, journal = {Nature}, volume = {621}, number = {7977}, pages = {120-128}, pmid = {37558883}, issn = {1476-4687}, mesh = {Animals ; Humans ; Cell Differentiation ; *COVID-19/genetics/immunology/virology ; Cytomegalovirus/physiology ; East Asian People/genetics ; Genetic Introgression ; *Genetics, Population ; Influenza A virus/pathogenicity/physiology ; Interferons/immunology ; Leukocytes, Mononuclear/immunology/metabolism ; Myeloid Cells/immunology ; Neanderthals/genetics/immunology ; *SARS-CoV-2/genetics/immunology/pathogenicity/physiology ; Selection, Genetic ; *Single-Cell Gene Expression Analysis ; Virus Latency ; }, abstract = {Humans display substantial interindividual clinical variability after SARS-CoV-2 infection[1-3], the genetic and immunological basis of which has begun to be deciphered[4]. However, the extent and drivers of population differences in immune responses to SARS-CoV-2 remain unclear. Here we report single-cell RNA-sequencing data for peripheral blood mononuclear cells-from 222 healthy donors of diverse ancestries-that were stimulated with SARS-CoV-2 or influenza A virus. We show that SARS-CoV-2 induces weaker, but more heterogeneous, interferon-stimulated gene activity compared with influenza A virus, and a unique pro-inflammatory signature in myeloid cells. Transcriptional responses to viruses display marked population differences, primarily driven by changes in cell abundance including increased lymphoid differentiation associated with latent cytomegalovirus infection. Expression quantitative trait loci and mediation analyses reveal a broad effect of cell composition on population disparities in immune responses, with genetic variants exerting a strong effect on specific loci. Furthermore, we show that natural selection has increased population differences in immune responses, particularly for variants associated with SARS-CoV-2 response in East Asians, and document the cellular and molecular mechanisms by which Neanderthal introgression has altered immune functions, such as the response of myeloid cells to viruses. Finally, colocalization and transcriptome-wide association analyses reveal an overlap between the genetic basis of immune responses to SARS-CoV-2 and COVID-19 severity, providing insights into the factors contributing to current disparities in COVID-19 risk.}, }
@article {pmid37543983, year = {2023}, author = {Augoyard, M and Zanolli, C and Santos, F and Oettlé, AC and L'Abbé, EN and Le Luyer, M and Cazenave, M and Colard, T and Hoffman, J and Profico, A and Bayle, P}, title = {Evaluation of age, sex, and ancestry-related variation in cortical bone and dentine volumes in modern humans, and a preliminary assessment of cortical bone-dentine covariation in later Homo.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {100}, number = {}, pages = {143-169}, doi = {10.4436/JASS.10019}, pmid = {37543983}, issn = {2037-0644}, abstract = {Cortical bone and dentine share similarities in their embryological origin, development, and genetic background. Few analyses have combined the study of cortical bone and dentine to quantify their covariation relative to endogenous and exogenous factors. However, knowing how these tissues relate in individuals is of great importance to decipher the factors acting on their evolution, and ultimately to understand the mechanisms responsible for the different patterns of tissue proportions shown in hominins. The aims of this study are to examine age-, sex-, and ancestry-related variation in cortical bone and dentine volumes, and to preliminary assess the possible covariation between these tissues in modern humans and in five composite Neandertals. The modern analytical sample includes 12 immature individuals from France and 49 adults from France and South Africa. Three-dimensional tissue proportions were assessed from microtomographic records of radii and permanent maxillary canines. Results suggest ontogenic differences and a strong sexual dimorphism in cortical bone and dentine developments. The developmental pattern of dentine also seems to vary according to individual's ancestry. We measure a stronger covariation signal between cortical bone and dentine volumes than with any other dental tissue. A more complex covariation pattern is shown when splitting the modern sample by age, sex, and ancestry, as no signal is found in some subsamples while others show a covariation between cortical bone and either crown or radicular dentine. Finally, no difference in cortical bone volume is noticed between the modern young adults and the five young adult composite Neandertals from Marine Isotopic Stages (MIS) 5 and 3. Greater dentine Cortical bone and dentine (co)variation volumes are measured in the MIS 5 chimeric Neandertals whereas a strong interpopulation variation in dentine thickness is noticed in the MIS 3 chimeric Neandertals. Further research on the cortical bonedentine covariation will increase understanding of the impact of endogenous and exogenous factors on the development of the mineralized tissues.}, }
@article {pmid37542146, year = {2023}, author = {Gicqueau, A and Schuh, A and Henrion, J and Viola, B and Partiot, C and Guillon, M and Golovanova, L and Doronichev, V and Gunz, P and Hublin, JJ and Maureille, B}, title = {Anatomically modern human in the Châtelperronian hominin collection from the Grotte du Renne (Arcy-sur-Cure, Northeast France).}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {12682}, pmid = {37542146}, issn = {2045-2322}, mesh = {Animals ; Infant, Newborn ; Humans ; *Hominidae/anatomy &amp; histology ; *Neanderthals ; France ; Europe ; Spain ; Fossils ; }, abstract = {Around 42,000 years ago, anatomically modern humans appeared in Western Europe to the detriment of indigenous Neanderthal groups. It is during this period that new techno-cultural complexes appear, such as the Châtelperronian that extends from northern Spain to the Paris Basin. The Grotte du Renne (Arcy-sur-Cure) is a key site for discussing the biological identity of its makers. This deposit has yielded several Neanderthal human remains in its Châtelperronian levels. However, the last inventory of the paleoanthropological collection attributed to this techno-complex allowed the identification of an ilium belonging to a neonate (AR-63) whose morphology required a thorough analysis to assess its taxonomic attribution. Using geometric morphometrics, we quantified its morphology and compared it to that of 2 Neanderthals and 32 recent individuals deceased during the perinatal period to explore their morphological variation. Our results indicate a morphological distinction between the ilia of Neanderthals and anatomically modern neonates. Although AR-63 is slightly outside recent variability, it clearly differs from the Neanderthals. We propose that this is due to its belonging to an early modern human lineage whose morphology differs slightly from present-day humans. We also explore different hypotheses about the presence of this anatomically modern neonate ilium among Neanderthal remains.}, }
@article {pmid37528143, year = {2023}, author = {Badino, F and Pini, R and Ravazzi, C and Chytrý, M and Bertuletti, P and Bortolini, E and Dudová, L and Peresani, M and Romandini, M and Benazzi, S}, title = {High-resolution ecosystem changes pacing the millennial climate variability at the Middle to Upper Palaeolithic transition in NE-Italy.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {12478}, pmid = {37528143}, issn = {2045-2322}, mesh = {Humans ; Animals ; *Ecosystem ; *Neanderthals ; Forests ; Trees ; Italy ; }, abstract = {Observation of high-resolution terrestrial palaeoecological series can decipher relationships between past climatic transitions, their effects on ecosystems and wildfire cyclicity. Here we present a new radiocarbon dated record from Lake Fimon (NE-Italy) covering the 60-27 ka interval. Palynological, charcoal fragments and sediment lithology analysis were carried out at centennial to sub-centennial resolutions. Identification of the best modern analogues for MIS 3 ecosystems further enabled to thoroughly reconstruct structural changes in the vegetation through time. This series also represents an "off-site" reference record for chronologically well-constrained Palaeolithic sites documenting Neanderthal and Homo sapiens occupations within the same region. Neanderthals lived in a mosaic of grasslands and woodlands, composed of a mixture of boreal and broad-leaved temperate trees analogous to those of the modern Central-Eastern Europe, the Southern Urals and central-southern Siberia. Dry and other grassland types expanded steadily from 44 to 43 ka and peaked between 42 and 39 ka, i.e., about the same time when Sapiens reached this region. This vegetation, which finds very few reliable modern analogues in the adopted Eurasian calibration set, led to the expansion of ecosystems able to sustain large herds of herbivores. During 39-27 ka, the landscape was covered by steppe, desert-steppe and open dry boreal forests similar to those of the modern Altai-Sayan region. Both Neanderthal and Sapiens lived in contexts of expanded fire-prone ecosystems modulated by the high-frequency climatic cycles of MIS 3.}, }
@article {pmid37516110, year = {2023}, author = {Maasch, JRMA and Torres, MDT and Melo, MCR and de la Fuente-Nunez, C}, title = {Molecular de-extinction of ancient antimicrobial peptides enabled by machine learning.}, journal = {Cell host &amp; microbe}, volume = {31}, number = {8}, pages = {1260-1274.e6}, doi = {10.1016/j.chom.2023.07.001}, pmid = {37516110}, issn = {1934-6069}, support = {R35 GM138201/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Humans ; Mice ; *Antimicrobial Peptides ; *Anti-Infective Agents ; Peptides/pharmacology ; Anti-Bacterial Agents/pharmacology ; Machine Learning ; Peptide Hydrolases ; Microbial Sensitivity Tests ; }, abstract = {Molecular de-extinction could offer avenues for drug discovery by reintroducing bioactive molecules that are no longer encoded by extant organisms. To prospect for antimicrobial peptides encrypted within extinct and extant human proteins, we introduce the panCleave random forest model for proteome-wide cleavage site prediction. Our model outperformed multiple protease-specific cleavage site classifiers for three modern human caspases, despite its pan-protease design. Antimicrobial activity was observed in vitro for modern and archaic protein fragments identified with panCleave. Lead peptides showed resistance to proteolysis and exhibited variable membrane permeabilization. Additionally, representative modern and archaic protein fragments showed anti-infective efficacy against A. baumannii in both a skin abscess infection model and a preclinical murine thigh infection model. These results suggest that machine-learning-based encrypted peptide prospection can identify stable, nontoxic peptide antibiotics. Moreover, we establish molecular de-extinction through paleoproteome mining as a framework for antibacterial drug discovery.}, }
@article {pmid37507506, year = {2023}, author = {Sidik, S}, title = {AI search of Neanderthal proteins resurrects 'extinct' antibiotics.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {37507506}, issn = {1476-4687}, }
@article {pmid37496118, year = {2023}, author = {Muotri, AR}, title = {Brain Model Technology and Its Implications.}, journal = {Cambridge quarterly of healthcare ethics : CQ : the international journal of healthcare ethics committees}, volume = {}, number = {}, pages = {1-5}, doi = {10.1017/S096318012300018X}, pmid = {37496118}, issn = {1469-2147}, abstract = {The complexity of the human brain creates a spectrum of sophisticated behavioral repertoires, such as language, tool use, self-awareness, symbolic thought, cultural learning, and consciousness. Understanding how the human brain achieves that has been a longstanding challenge for neuroscientists and may bring insights into the evolution of human cognition and disease states. Human pluripotent stem cells could differentiate into specialized cell types and tissues in vitro. From this pluripotent state, it is possible to generate models of the human brain, such as brain organoids. The recent observation that brain organoids can spontaneously develop complex neural network activity in a dish can help one understand how neural network oscillations evolve and vary between normal and disease states. Moreover, this finding can be leveraged to other applications outside medicine, including engineering and artificial intelligence. However, as the brain model technology becomes more complex, it raises a series of ethical and moral dilemmas. This article discusses the status of this technology, some of its current limitations, and a vision of the future.}, }
@article {pmid37452091, year = {2023}, author = {Yang, C and Zhou, Y and Song, Y and Wu, D and Zeng, Y and Nie, L and Liu, P and Zhang, S and Chen, G and Xu, J and Zhou, H and Zhou, L and Qian, X and Liu, C and Tan, S and Zhou, C and Dai, W and Xu, M and Qi, Y and Wang, X and Guo, L and Fan, G and Wang, A and Deng, Y and Zhang, Y and Jin, J and He, Y and Guo, C and Guo, G and Zhou, Q and Xu, X and Yang, H and Wang, J and Xu, S and Mao, Y and Jin, X and Ruan, J and Zhang, G}, title = {The complete and fully-phased diploid genome of a male Han Chinese.}, journal = {Cell research}, volume = {33}, number = {10}, pages = {745-761}, pmid = {37452091}, issn = {1748-7838}, mesh = {Humans ; Male ; Asian People/genetics ; *Diploidy ; *East Asian People/ethnology/genetics ; *Genome, Human/genetics ; Genomics ; *Telomere/genetics ; }, abstract = {Since the release of the complete human genome, the priority of human genomic study has now been shifting towards closing gaps in ethnic diversity. Here, we present a fully phased and well-annotated diploid human genome from a Han Chinese male individual (CN1), in which the assemblies of both haploids achieve the telomere-to-telomere (T2T) level. Comparison of this diploid genome with the CHM13 haploid T2T genome revealed significant variations in the centromere. Outside the centromere, we discovered 11,413 structural variations, including numerous novel ones. We also detected thousands of CN1 alleles that have accumulated high substitution rates and a few that have been under positive selection in the East Asian population. Further, we found that CN1 outperforms CHM13 as a reference genome in mapping and variant calling for the East Asian population owing to the distinct structural variants of the two references. Comparison of SNP calling for a large cohort of 8869 Chinese genomes using CN1 and CHM13 as reference respectively showed that the reference bias profoundly impacts rare SNP calling, with nearly 2 million rare SNPs miss-called with different reference genomes. Finally, applying the CN1 as a reference, we discovered 5.80 Mb and 4.21 Mb putative introgression sequences from Neanderthal and Denisovan, respectively, including many East Asian specific ones undetected using CHM13 as the reference. Our analyses reveal the advances of using CN1 as a reference for population genomic studies and paleo-genomic studies. This complete genome will serve as an alternative reference for future genomic studies on the East Asian population.}, }
@article {pmid37406034, year = {2023}, author = {Smith, TM and Arora, M and Bharatiya, M and Dirks, W and Austin, C}, title = {Brief Communication: Elemental Models of Primate Nursing and Weaning Revisited.}, journal = {American journal of biological anthropology}, volume = {180}, number = {1}, pages = {216-223}, pmid = {37406034}, issn = {2692-7691}, support = {R00 HD087523/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Humans ; Weaning ; Barium/analysis ; *Tooth/chemistry ; Strontium/analysis ; Papio ; }, abstract = {OBJECTIVES: Intra-tooth patterns of trace elements barium (Ba) and strontium (Sr) have been used to infer human and nonhuman primate nursing histories, including australopithecine and Neanderthal juveniles. Here we contrast the two elemental models in first molars (M1s) of four wild baboons and explore the assumptions that underlie each.<br><br>MATERIALS AND METHODS: Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) was employed to create comprehensive calcium-normalized barium and strontium (Ba/Ca, Sr/Ca) maps of M1 enamel and dentine at 35 micron resolution.<br><br>RESULTS: Postnatal Ba/Ca values were typically high, peaking ~0.5 years of age and then decreasing throughout M1 crown formation; all four individuals showed minimal Ba/Ca values between ~1.2-1.8 years, consistent with field reports of the cessation of suckling. Enamel Sr/Ca did not support patterns of previous LA-ICP-MS spot sampling as the enamel rarely showed discrete Sr/Ca secretory zonation. Increases in Sr/Ca appeared in coronal dentine beginning ~0.3 years, with varied peak value ages (~0.7-2.7 years) and no evidence of a predicted postweaning decline.<br><br>DISCUSSION: Inferences of baboon weaning ages from initial Ba/Ca minima are more congruent with behavioral observations than Sr/Ca maxima; this is consistent with studies of captive macaques of known weaning ages. Elemental variation is more apparent in the coronal dentine than the enamel of these baboons, which may relate to its more rapid mineralization and protection from the oral environment. Inferences of nursing histories from enamel Sr/Ca patterns alone should be reconsidered, and elevated values of Ba/Ca and Sr/Ca in teeth formed after weaning require further study.}, }
@article {pmid37379741, year = {2023}, author = {Henrion, J and Hublin, JJ and Maureille, B}, title = {New Neanderthal remains from the Châtelperronian-attributed layer X of the Grotte du Renne (Arcy-sur-Cure, France).}, journal = {Journal of human evolution}, volume = {181}, number = {}, pages = {103402}, doi = {10.1016/j.jhevol.2023.103402}, pmid = {37379741}, issn = {1095-8606}, mesh = {Animals ; *Neanderthals ; France ; *Hominidae ; Fossils ; }, }
@article {pmid37359819, year = {2023}, author = {Tozzi, A}, title = {Non-ultrametric phylogenetic trees shed new light on Neanderthal introgression.}, journal = {Organisms, diversity &amp; evolution}, volume = {}, number = {}, pages = {1-9}, pmid = {37359819}, issn = {1439-6092}, abstract = {Ultrametric spaces are widely used to depict evolutionary times in phylogenetic trees since they assume that every population/species is located at the tips of bifurcating branches of the same length. The discrete branching of ultrametric trees permits the measurement of distances between pairs of individuals that are proportional to their divergence time. Here the traditional ultrametric concept of bifurcating and divergent phylogenetic tree is overturned and a new type of non-ultrametric diagram is introduced. The objective of this study is the description of gene flows in branching species/populations in terms of converging trees instead of bifurcating trees. To provide an operational example, the paleoanthropological issue of the date of Neanderthal genome's introgression in non-African humans is examined. Neanderthals and ancient humans are not anymore two species that exchange chunks of DNA, rather become a single, novel cluster of extant hominins that must be considered by itself. The novel converging, non-ultrametric phylogenetic trees permit the calibration of molecular clocks with a twofold benefit. When the date of the branching of two population/species from a common ancestor is known, the novel approach allows to calculate the time of subsequent introgressions. On the contrary, when the date of the introgression between two population/species is known, the novel approach allows to detect the time of their previous branching from a common ancestor.}, }
@article {pmid37354658, year = {2023}, author = {Condemi, S and Panuel, M and Chaumoitre, K and Belcastro, MG and Pietrobelli, A and Voisin, JL}, title = {A pathological Neandertal thumb phalanx from Moula-Guercy (France).}, journal = {International journal of paleopathology}, volume = {42}, number = {}, pages = {14-17}, doi = {10.1016/j.ijpp.2023.06.002}, pmid = {37354658}, issn = {1879-9825}, mesh = {Animals ; Humans ; *Neanderthals ; Thumb/anatomy &amp; histology ; Fossils ; *Hominidae ; France ; *Osteoarthritis ; }, abstract = {OBJECTIVE: To discuss a Neandertal pathological adult first pollical proximal phalanx (I2-104) from the Baume de Moula-Guercy (Ardèche, France) and evaluate the possible causes of this pathology.<br><br>METHODS: Macroscopic analyses of external features, as well as CT imaging, were used in the analysis RESULTS: The presence of asymmetric eburnation on the distal epiphysis associated with an osteophyte on the palmar surface, as well as the absence of periosteal bone reaction visible on CT images, is consistent with osteoarthritis.<br><br>CONCLUSION: Osteoarthritis (OA) can have different origins and the cause is difficult to identify. The pathology of the Moula-Guercy I2-104 phalanx may be due to a genetic predisposition for OA known in Neandertals and associated with short limb bones. The OA could have been aggravated by the age of this individual and by an inflammatory reaction caused by repeated movements and intense vibrations provoked by high-frequency knapping or by other use of the hands SIGNIFICANCE: The I2-104 phalanx is the first Neandertal pollical phalanx known to display OA, although joints of this bone are frequently affected by this pathology in modern humans. Thus, greater insight into the presence and consequences of Neandertal behaviors is offered LIMITATION: It is impossible to give a definitive conclusion on the cause(s) of the OA in this case.<br><br>More data is needed concerning OA within Neandertals and its relationship with behavior and genetics.}, }
@article {pmid37345623, year = {2024}, author = {Rodríguez, L and García-González, R and Arsuaga, JL and Carretero, JM}, title = {Uncovering the adult morphology of the forearm bones from the Sima de los Huesos Site in Atapuerca (Spain), with comments on biomechanical features.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {307}, number = {7}, pages = {2550-2574}, doi = {10.1002/ar.25281}, pmid = {37345623}, issn = {1932-8494}, support = {//Fieldwork at the Atapuerca sites is funded by the Junta de Castilla y Le&#xf3;n and the Fundaci&#xf3;n Atapuerca/ ; PID2021-122355NB-C31//MCIN/AEI/10.13039/501100011033/FEDER, UE/ ; }, mesh = {Humans ; Spain ; *Ulna/anatomy &amp; histology/physiology ; *Fossils ; Biomechanical Phenomena/physiology ; *Radius/anatomy &amp; histology/physiology ; Forearm/anatomy &amp; histology/physiology ; Adult ; Male ; Female ; Animals ; }, abstract = {The forearm skeleton is composed of two bones: the radius and the ulna. This is closely related to manipulative movements. The ulna is part of the elbow joint, whereas the radius and ulna together with the scaphoid and lunate bones, form the wrist joints. Thus, morphofunctional analysis of the adult Sima de los Huesos (SH) forearm bones, provides clues about manipulative activities in one Pleistocene population. From 1976 to the present, over 7000 human fossils have been recovered from the SH site. The radial sample comprised 98 labeled fragments, of which 49 belonged to adult individuals, representing at least 7 individuals. The ulnar sample included 31 labeled adult fossils representing at least nine individuals. In this study, we describe the SH radii and ulnae and analyze their functional implications for manipulative and forearm movements. We confirmed that the SH radii are long and curved, with variations in robusticity and radial tuberosity orientation. The SH ulnae are characterized by an anteriorly oriented trochlear notch, a massive olecranon process, an obliquely oriented radial notch, a blunt and short supinator crest, a gracile and curved diaphysis, and a round and anteriorly oriented pronator crests. In general, they exhibit Neanderthal morphology. The SH collection provides a unique opportunity to conduct morphological analyses of these bones in the Middle Pleistocene population.}, }
@article {pmid37343032, year = {2023}, author = {Marquet, JC and Freiesleben, TH and Thomsen, KJ and Murray, AS and Calligaro, M and Macaire, JJ and Robert, E and Lorblanchet, M and Aubry, T and Bayle, G and Bréhéret, JG and Camus, H and Chareille, P and Egels, Y and Guillaud, &#xc9; and Guérin, G and Gautret, P and Liard, M and O'Farrell, M and Peyrouse, JB and Thamó-Bozsó, E and Verdin, P and Wojtczak, D and Oberlin, C and Jaubert, J}, title = {The earliest unambiguous Neanderthal engravings on cave walls: La Roche-Cotard, Loire Valley, France.}, journal = {PloS one}, volume = {18}, number = {6}, pages = {e0286568}, pmid = {37343032}, issn = {1932-6203}, mesh = {Humans ; Animals ; *Neanderthals ; Engraving and Engravings ; Caves ; France ; Europe ; Fossils ; Archaeology ; }, abstract = {Here we report on Neanderthal engravings on a cave wall at La Roche-Cotard (LRC) in central France, made more than 57±3 thousand years ago. Following human occupation, the cave was completely sealed by cold-period sediments, which prevented access until its discovery in the 19th century and first excavation in the early 20th century. The timing of the closure of the cave is based on 50 optically stimulated luminescence ages derived from sediment collected inside and from around the cave. The anthropogenic origin of the spatially-structured, non-figurative marks found within the cave is confirmed using taphonomic, traceological and experimental evidence. Cave closure occurred significantly before the regional arrival of H. sapiens, and all artefacts from within the cave are typical Mousterian lithics; in Western Europe these are uniquely attributed to H. neanderthalensis. We conclude that the LRC engravings are unambiguous examples of Neanderthal abstract design.}, }
@article {pmid37342325, year = {2023}, author = {Mocci, S and Littera, R and Chessa, L and Campagna, M and Melis, M and Ottelio, CM and Piras, IS and Lai, S and Firinu, D and Tranquilli, S and Mascia, A and Vacca, M and Schirru, D and Lecca, LI and Rassu, S and Cannas, F and Sanna, C and Carta, MG and Sedda, F and Giuressi, E and Cipri, S and Miglianti, M and Perra, A and Giglio, S}, title = {A review of the main genetic factors influencing the course of COVID-19 in Sardinia: the role of human leukocyte antigen-G.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1138559}, pmid = {37342325}, issn = {1664-3224}, mesh = {Humans ; *HLA-G Antigens/genetics ; Gene Frequency ; 3' Untranslated Regions/genetics ; *COVID-19/genetics ; SARS-CoV-2/genetics ; }, abstract = {INTRODUCTION: A large number of risk and protective factors have been identified during the SARS-CoV-2 pandemic which may influence the outcome of COVID-19. Among these, recent studies have explored the role of HLA-G molecules and their immunomodulatory effects in COVID-19, but there are very few reports exploring the genetic basis of these manifestations. The present study aims to investigate how host genetic factors, including HLA-G gene polymorphisms and sHLA-G, can affect SARS-CoV-2 infection.<br><br>MATERIALS AND METHODS: We compared the immune-genetic and phenotypic characteristics between COVID-19 patients (n = 381) with varying degrees of severity of the disease and 420 healthy controls from Sardinia (Italy).<br><br>RESULTS: HLA-G locus analysis showed that the extended haplotype HLA-G*01:01:01:01/UTR-1 was more prevalent in both COVID-19 patients and controls. In particular, this extended haplotype was more common among patients with mild symptoms than those with severe symptoms [22.7% vs 15.7%, OR = 0.634 (95% CI 0.440 - 0.913); P = 0.016]. Furthermore, the most significant HLA-G 3'UTR polymorphism (rs371194629) shows that the HLA-G 3'UTR Del/Del genotype frequency decreases gradually from 27.6% in paucisymptomatic patients to 15.9% in patients with severe symptoms (X[2&#xa0;]=&#xa0;7.095, P = 0.029), reaching the lowest frequency (7.0%) in ICU patients (X[2&#xa0;]=&#xa0;11.257, P = 0.004). However, no significant differences were observed for the soluble HLA-G levels in patients and controls. Finally, we showed that SARS-CoV-2 infection in the Sardinian population is also influenced by other genetic factors such as &#x3b2;-thalassemia trait (rs11549407C>T in the HBB gene), KIR2DS2/HLA-C C1+ group combination and the HLA-B*58:01, C*07:01, DRB1*03:01 haplotype which exert a protective effect [P = 0.005, P = 0.001 and P = 0.026 respectively]. Conversely, the Neanderthal LZTFL1 gene variant (rs35044562A>G) shows a detrimental consequence on the disease course [P = 0.001]. However, by using a logistic regression model, HLA-G 3'UTR Del/Del genotype was independent from the other significant variables [ORM = 0.4 (95% CI 0.2 - 0.7), PM = 6.5 x 10[-4]].<br><br>CONCLUSION: Our results reveal novel genetic variants which could potentially serve as biomarkers for disease prognosis and treatment, highlighting the importance of considering genetic factors in the management of COVID-19 patients.}, }
@article {pmid37337589, year = {2023}, author = {Groh, J and Coop, G}, title = {The temporal and genomic scale of selection following hybridization.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37337589}, issn = {2692-8205}, support = {R35 GM136290/GM/NIGMS NIH HHS/United States ; }, abstract = {Genomic evidence supports an important role for selection in shaping patterns of introgression along the genome, but frameworks for understanding the dynamics underlying these patterns within hybrid populations have been lacking. Here, we develop methods based on the Wavelet Transform to understand the spatial genomic scale of local ancestry variation and its association with recombination rates. We present theory and use simulations to show how wavelet-based decompositions of ancestry variance along the genome and the correlation between ancestry and recombination reflect the joint effects of recombination, genetic drift, and genome-wide selection against introgressed alleles. Due to the clock-like effect of recombination in hybrids breaking up parental haplotypes, drift and selection produce predictable patterns of local ancestry variation at varying spatial genomic scales through time. Using wavelet approaches to identify the genomic scale of variance in ancestry and its correlates, we show that these methods can detect temporally localized effects of drift and selection. We apply these methods to previously published datasets from hybrid populations of swordtail fish (Xiphophorus) and baboons (Papio), and to inferred Neanderthal introgression in modern humans. Across systems, we find that upwards of 20% of the variation in local ancestry at the broadest genomic scales can be attributed to systematic selection against introgressed alleles, consistent with strong selection acting on early-generation hybrids. We also see signals of selection at fine genomic scales and much longer time scales. However, we show that our ability to confidently infer selection at fine scales is likely limited by inherent biases in current methods for estimating local ancestry from genomic similarity. Wavelet approaches will become widely applicable as genomic data from systems with introgression become increasingly available, and can help shed light on generalities of the genomic consequences of interspecific hybridization.}, }
@article {pmid37337097, year = {2023}, author = {Baquedano, E and Arsuaga, JL and Pérez-González, A and Laplana, C and Márquez, B and Huguet, R and Gómez-Soler, S and Villaescusa, L and Galindo-Pellicena, M&#xc1; and Rodríguez, L and García-González, R and Ortega, MC and Martín-Perea, DM and Ortega, AI and Hernández-Vivanco, L and Ruiz-Liso, G and Gómez-Hernanz, J and Alonso-Martín, JI and Abrunhosa, A and Moclán, A and Casado, AI and Vegara-Riquelme, M and Álvarez-Fernández, A and Domínguez-García, &#xc1;C and Álvarez-Lao, DJ and García, N and Sevilla, P and Blain, HA and Ruiz-Zapata, B and Gil-García, MJ and Álvarez-Vena, A and Sanz, T and Quam, R and Higham, T}, title = {Author Correction: A symbolic Neanderthal accumulation of large herbivore crania.}, journal = {Nature human behaviour}, volume = {7}, number = {7}, pages = {1228}, doi = {10.1038/s41562-023-01650-5}, pmid = {37337097}, issn = {2397-3374}, }
@article {pmid37315093, year = {2023}, author = {Ågren, R and Patil, S and Zhou, X and ,  and Sahlholm, K and Pääbo, S and Zeberg, H}, title = {Major Genetic Risk Factors for Dupuytren's Disease Are Inherited From Neandertals.}, journal = {Molecular biology and evolution}, volume = {40}, number = {6}, pages = {}, pmid = {37315093}, issn = {1537-1719}, mesh = {Animals ; Humans ; Male ; Alleles ; *Dupuytren Contracture/genetics ; *Neanderthals/genetics ; Risk Factors ; }, abstract = {Dupuytren's disease is characterized by fingers becoming permanently bent in a flexed position. Whereas people of African ancestry are rarely afflicted by Dupuytren's disease, up to ∼30% of men over 60 years suffer from this condition in northern Europe. Here, we meta-analyze 3 biobanks comprising 7,871 cases and 645,880 controls and find 61 genome-wide significant variants associated with Dupuytren's disease. We show that 3 of the 61 loci harbor alleles of Neandertal origin, including the second and third most strongly associated ones (P = 6.4 × 10-132 and P = 9.2 × 10-69, respectively). For the most strongly associated Neandertal variant, we identify EPDR1 as the causal gene. Dupuytren's disease is an example of how admixture with Neandertals has shaped regional differences in disease prevalence.}, }
@article {pmid37315040, year = {2023}, author = {Baumann, M and Plisson, H and Maury, S and Renou, S and Coqueugniot, H and Vanderesse, N and Kolobova, K and Shnaider, S and Rots, V and Guérin, G and Rendu, W}, title = {On the Quina side: A Neanderthal bone industry at Chez-Pinaud site, France.}, journal = {PloS one}, volume = {18}, number = {6}, pages = {e0284081}, pmid = {37315040}, issn = {1932-6203}, mesh = {Animals ; *Neanderthals ; Acclimatization ; Artifacts ; France ; Industry ; *Reindeer ; }, abstract = {Did Neanderthal produce a bone industry? The recent discovery of a large bone tool assemblage at the Neanderthal site of Chagyrskaya (Altai, Siberia, Russia) and the increasing discoveries of isolated finds of bone tools in various Mousterian sites across Eurasia stimulate the debate. Assuming that the isolate finds may be the tip of the iceberg and that the Siberian occurrence did not result from a local adaptation of easternmost Neanderthals, we looked for evidence of a similar industry in the Western side of their spread area. We assessed the bone tool potential of the Quina bone-bed level currently under excavation at chez Pinaud site (Jonzac, Charente-Maritime, France) and found as many bone tools as flint ones: not only the well-known retouchers but also beveled tools, retouched artifacts and a smooth-ended rib. Their diversity opens a window on a range of activities not expected in a butchering site and not documented by the flint tools, all involved in the carcass processing. The re-use of 20% of the bone blanks, which are mainly from large ungulates among faunal remains largely dominated by reindeer, raises the question of blank procurement and management. From the Altai to the Atlantic shore, through a multitude of sites where only a few objects have been reported so far, evidence of a Neanderthal bone industry is emerging which provides new insights on Middle Paleolithic subsistence strategies.}, }
@article {pmid37308599, year = {2024}, author = {Curtis, D and Amos, W}, title = {The human genome harbours widespread exclusive yin yang haplotypes.}, journal = {European journal of human genetics : EJHG}, volume = {32}, number = {6}, pages = {691-696}, pmid = {37308599}, issn = {1476-5438}, mesh = {Humans ; *Haplotypes ; *Polymorphism, Single Nucleotide ; *Genome, Human ; Yin-Yang ; Animals ; Linkage Disequilibrium ; Gene Frequency ; Pan troglodytes/genetics ; }, abstract = {There have been reports of examples of exclusive yin yang haplotypes, differing at every locus, but there has been no systematic search for them. Unphased whole genome sequence data for 2504 unrelated 1000 Genomes subjects was searched for chains of SNPs having global minor allele frequency (MAF) > =0.1 made up of at least 20 SNPs in complete linkage disequilibrium with each other and with no pair being separated by more than 9 other SNPs. The global distribution of these haplotypes was investigated, along with their ancestral origins and associations with genes and phenotypes. A number of previously unrecognised repeats were noted, flagged by all or most subjects being called as heterozygotes, and these were discarded. There were 5114 exclusive yin yang haplotypes each consisting of on average 34.8 SNPs, each spanning on average 15.7 kb and cumulatively covering 80 Mb. Although for some haplotypes the MAF varied markedly between populations the average global fixation index was similar to that for SNPs elsewhere in the genome and there was no evidence of enrichment for genes or gene ontologies. For all but 92 haplotypes there were partial forms present in the chimpanzee and/or Neanderthal genome, indicating that they had been formed in a gradual process but that intermediate haplotypes were now absent from modern humans. Exclusive yin yang haplotypes cover over 2% of the human genome. The mechanisms accounting for their formation and preservation are unclear. They may serve as useful markers of the dispersal of chromosomal regions through human history.}, }
@article {pmid37269363, year = {2023}, author = {Garcia-Heras, J}, title = {The 2022 Nobel Prize in Physiology or Medicine.}, journal = {Journal of the Association of Genetic Technologists}, volume = {49}, number = {2}, pages = {56-67}, pmid = {37269363}, issn = {1523-7834}, abstract = {The Nobel Assembly at the Karolinska Institute awarded the 2022 Nobel Prize in Physiology or Medicine to Svante Pääbo (Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany). This award acknowledged his discoveries about the genomes of extinct hominins (Neandertal man and the Denisovans), the molecular genetic insights of human origin and evolutionary history, and the understanding of phylogenetic relationships between archaic hominins and modern humans. The scientific advances included detection of Neandertal and Denisovan DNA carried by modern humans due to past admixture events, which in turn stimulated active research about the functional and phenotypic significance of such archaic ancestry on non-disease and disease phenotypic features in modern populations. In addition, comparative genomic studies started to delineate the genes and genetic regulation mechanisms that distinguish modern-day humans from the archaic hominins and our immediate ancestors, the anatomically modern humans. These breakthroughs allowed a more thorough understanding of ancestral and modern human population genetics, and propelled the take-off of human paleogenomics as a new scientific discipline in its own right.}, }
@article {pmid37246494, year = {2023}, author = {Boneta Jiménez, I and Cardoso, JL and Pérez-García, A}, title = {The turtles from the middle Paleolithic site of Gruta Nova da Columbeira (Bombarral, Portugal): Update through an archaeozoological perspective.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {}, number = {}, pages = {}, doi = {10.1002/ar.25229}, pmid = {37246494}, issn = {1932-8494}, support = {PID2019-111210GB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, abstract = {Twenty-five years after the preliminary systematic study of the turtle remains (Agrionemys [=Testudo] hermanni and Emys or Mauremys) recovered from Gruta Nova da Columbeira site (Bombarral, Portugal), the results of its review from systematic and archaeozoological perspectives are presented here. Tortoise remains studies from pre-Upper Paleolithic sites worldwide have provided relevant data confirming its role as a dietary supply for hominid populations and informing about their ability to adapt to local environmental resources. The Iberian Peninsula record in general, and specifically, that from Portugal, have yielded substantial evidence to this highly debated topic. In this sense, turtle remains recovered in Gruta Nova da Columbeira site, discovered in the 1960s and the main ensemble chronologically ascribed to the MIS-5 (87.1 ± 6.3 ka BP), offer new information to this debate. Its detailed restudy, has allowed us the identification, justification, and figuration of remains attributed to two Iberian turtle taxa, Chersine hermanni and Emys orbicularis. Therefore, this update on the data concerning the turtle record from Gruta Nova da Columbeira provides new justified taxonomic evidence regarding the Iberian turtle taxa distribution during the Upper Pleistocene. The previously suggested hypothesis about the tortoise human consumption on the site is here evaluated through the development of an archaeozoological and taphonomical analysis, as well as considering the potential documentation of anthropic alterations (e.g., burning, cutmarks, percussion marks). In this sense, this hypothesis is confirmed. In addition, the presence of carnivore activity evidence indicates the engagement of other agents in the deposit formation.}, }
@article {pmid37228449, year = {2023}, author = {Schmidt, P and Koch, TJ and Blessing, MA and Karakostis, FA and Harvati, K and Dresely, V and Charrié-Duhaut, A}, title = {Production method of the Königsaue birch tar documents cumulative culture in Neanderthals.}, journal = {Archaeological and anthropological sciences}, volume = {15}, number = {6}, pages = {84}, pmid = {37228449}, issn = {1866-9557}, abstract = {UNLABELLED: Birch tar is the oldest synthetic substance made by early humans. The earliest such artefacts are associated with Neanderthals. According to traditional interpretations, their study allows understanding Neanderthal tool behaviours, skills and cultural evolution. However, recent work has found that birch tar can also be produced with simple processes, or even result from fortuitous accidents. Even though these findings suggest that birch tar per se is not a proxy for cognition, they do not shed light on the process by which Neanderthals produced it, and, therefore, cannot evaluate the implications of that behaviour. Here, we address the question of how tar was made by Neanderthals. Through a comparative chemical analysis of the two exceptional birch tar pieces from Königsaue (Germany) and a large reference birch tar collection made with Stone Age techniques, we found that Neanderthals did not use the simplest method to make tar. Rather, they distilled tar in an intentionally created underground environment that restricted oxygen flow and remained invisible during the process. This degree of complexity is unlikely to have been invented spontaneously. Our results suggest that Neanderthals invented or developed this process based on previous simpler methods and constitute one of the clearest indicators of cumulative cultural evolution in the European Middle Palaeolithic.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12520-023-01789-2.}, }
@article {pmid37220274, year = {2023}, author = {Tobler, R and Souilmi, Y and Huber, CD and Bean, N and Turney, CSM and Grey, ST and Cooper, A}, title = {The role of genetic selection and climatic factors in the dispersal of anatomically modern humans out of Africa.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {22}, pages = {e2213061120}, pmid = {37220274}, issn = {1091-6490}, mesh = {Humans ; Animals ; Africa ; *Neanderthals ; Acclimatization ; Arabia ; Selection, Genetic ; }, abstract = {The evolutionarily recent dispersal of anatomically modern humans (AMH) out of Africa (OoA) and across Eurasia provides a unique opportunity to examine the impacts of genetic selection as humans adapted to multiple new environments. Analysis of ancient Eurasian genomic datasets (~1,000 to 45,000 y old) reveals signatures of strong selection, including at least 57 hard sweeps after the initial AMH movement OoA, which have been obscured in modern populations by extensive admixture during the Holocene. The spatiotemporal patterns of these hard sweeps provide a means to reconstruct early AMH population dispersals OoA. We identify a previously unsuspected extended period of genetic adaptation lasting ~30,000 y, potentially in the Arabian Peninsula area, prior to a major Neandertal genetic introgression and subsequent rapid dispersal across Eurasia as far as Australia. Consistent functional targets of selection initiated during this period, which we term the Arabian Standstill, include loci involved in the regulation of fat storage, neural development, skin physiology, and cilia function. Similar adaptive signatures are also evident in introgressed archaic hominin loci and modern Arctic human groups, and we suggest that this signal represents selection for cold adaptation. Surprisingly, many of the candidate selected loci across these groups appear to directly interact and coordinately regulate biological processes, with a number associated with major modern diseases including the ciliopathies, metabolic syndrome, and neurodegenerative disorders. This expands the potential for ancestral human adaptation to directly impact modern diseases, providing a platform for evolutionary medicine.}, }
@article {pmid37202264, year = {2023}, author = {Klein, K and Weniger, GC and Ludwig, P and Stepanek, C and Zhang, X and Wegener, C and Shao, Y}, title = {Assessing climatic impact on transition from Neanderthal to anatomically modern human population on Iberian Peninsula: a macroscopic perspective.}, journal = {Science bulletin}, volume = {68}, number = {11}, pages = {1176-1186}, doi = {10.1016/j.scib.2023.04.025}, pmid = {37202264}, issn = {2095-9281}, mesh = {Humans ; Animals ; *Neanderthals ; Fossils ; Europe ; Europe, Eastern ; Archaeology ; Anti-Mullerian Hormone ; }, abstract = {The Iberian Peninsula is of particular interest for the research on the Neanderthal (NEA) to anatomically modern human (AMH) population transition. The AMHs arrived in Iberia last from Eastern Europe and thus any possible contacts between the two populations occurred here later than elsewhere. The transition process took place in the earlier part of the Marine Isotope Stage 3 (∼60-27 cal ka BP) as repeated and profound climate changes challenged the population stability. To investigate how climate change and population interactions influenced the transition, we combine climate data with archaeological-site data to reconstruct the Human Existence Potential, a measure of the probability of human existence, for both the NEA and AMH populations in the Greenland Interstadial 11-10 (GI11-10) and Stadial 10-9/Heinrich event 4 (GS10-9/HE4) times. It is found that during GS10-9/HE4, large parts of the peninsula became unsuitable for NEA human existence and the NEA settlement areas contracted to isolated coastal hot spots. As a consequence, the NEA networks became highly unstable, triggering the final collapse of the population. The AMHs arrived in Iberia in GI10 but were confined to patches in the northern most strip of the peninsula. They were soon facing the much colder climate of GS10-9/HE4, which prevented their further expansion or even caused a contraction of their settlement areas. Thus, due to the constellation of climate change and the dispersal of the two populations into different regions of the peninsula, it is unlikely that the NEAs and AMHs coexisted in extensive areas and the AMHs had a significant influence on the demography of the NEAs.}, }
@article {pmid37192163, year = {2023}, author = {Rong, S and Neil, CR and Welch, A and Duan, C and Maguire, S and Meremikwu, IC and Meyerson, M and Evans, BJ and Fairbrother, WG}, title = {Large-scale functional screen identifies genetic variants with splicing effects in modern and archaic humans.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {21}, pages = {e2218308120}, pmid = {37192163}, issn = {1091-6490}, support = {R01 GM127472/GM/NIGMS NIH HHS/United States ; }, mesh = {Male ; Animals ; Humans ; *Neanderthals/genetics ; Semen ; *Hominidae/genetics ; Alleles ; Gene Expression Regulation ; Genome, Human ; }, abstract = {Humans coexisted and interbred with other hominins which later became extinct. These archaic hominins are known to us only through fossil records and for two cases, genome sequences. Here, we engineer Neanderthal and Denisovan sequences into thousands of artificial genes to reconstruct the pre-mRNA processing patterns of these extinct populations. Of the 5,169 alleles tested in this massively parallel splicing reporter assay (MaPSy), we report 962 exonic splicing mutations that correspond to differences in exon recognition between extant and extinct hominins. Using MaPSy splicing variants, predicted splicing variants, and splicing quantitative trait loci, we show that splice-disrupting variants experienced greater purifying selection in anatomically modern humans than that in Neanderthals. Adaptively introgressed variants were enriched for moderate-effect splicing variants, consistent with positive selection for alternative spliced alleles following introgression. As particularly compelling examples, we characterized a unique tissue-specific alternative splicing variant at the adaptively introgressed innate immunity gene TLR1, as well as a unique Neanderthal introgressed alternative splicing variant in the gene HSPG2 that encodes perlecan. We further identified potentially pathogenic splicing variants found only in Neanderthals and Denisovans in genes related to sperm maturation and immunity. Finally, we found splicing variants that may contribute to variation among modern humans in total bilirubin, balding, hemoglobin levels, and lung capacity. Our findings provide unique insights into natural selection acting on splicing in human evolution and demonstrate how functional assays can be used to identify candidate causal variants underlying differences in gene regulation and phenotype.}, }
@article {pmid37156940, year = {2023}, author = {Li, Q and Chen, J and Faux, P and Delgado, ME and Bonfante, B and Fuentes-Guajardo, M and Mendoza-Revilla, J and Chacón-Duque, JC and Hurtado, M and Villegas, V and Granja, V and Jaramillo, C and Arias, W and Barquera, R and Everardo-Martínez, P and Sánchez-Quinto, M and Gómez-Valdés, J and Villamil-Ramírez, H and Silva de Cerqueira, CC and Hünemeier, T and Ramallo, V and Wu, S and Du, S and Giardina, A and Paria, SS and Khokan, MR and Gonzalez-José, R and Schüler-Faccini, L and Bortolini, MC and Acuña-Alonzo, V and Canizales-Quinteros, S and Gallo, C and Poletti, G and Rojas, W and Rothhammer, F and Navarro, N and Wang, S and Adhikari, K and Ruiz-Linares, A}, title = {Automatic landmarking identifies new loci associated with face morphology and implicates Neanderthal introgression in human nasal shape.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {481}, pmid = {37156940}, issn = {2399-3642}, support = {R01 DE027023/DE/NIDCR NIH HHS/United States ; U01 DE020078/DE/NIDCR NIH HHS/United States ; R01 DE016148/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; Animals ; Mice ; *Neanderthals/genetics ; Genome-Wide Association Study ; Nose ; Cell Differentiation ; }, abstract = {We report a genome-wide association study of facial features in >6000 Latin Americans based on automatic landmarking of 2D portraits and testing for association with inter-landmark distances. We detected significant associations (P-value <5 × 10[-8]) at 42 genome regions, nine of which have been previously reported. In follow-up analyses, 26 of the 33 novel regions replicate in East Asians, Europeans, or Africans, and one mouse homologous region influences craniofacial morphology in mice. The novel region in 1q32.3 shows introgression from Neanderthals and we find that the introgressed tract increases nasal height (consistent with the differentiation between Neanderthals and modern humans). Novel regions include candidate genes and genome regulatory elements previously implicated in craniofacial development, and show preferential transcription in cranial neural crest cells. The automated approach used here should simplify the collection of large study samples from across the world, facilitating a cosmopolitan characterization of the genetics of facial features.}, }
@article {pmid37155903, year = {2023}, author = {Linscott, B and Pike, AWG and Angelucci, DE and Cooper, MJ and Milton, JS and Matias, H and Zilhão, J}, title = {Reconstructing Middle and Upper Paleolithic human mobility in Portuguese Estremadura through laser ablation strontium isotope analysis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {20}, pages = {e2204501120}, pmid = {37155903}, issn = {1091-6490}, mesh = {Animals ; Humans ; Portugal ; *Hominidae ; *Tooth/chemistry ; Strontium Isotopes/analysis ; *Neanderthals ; *Laser Therapy ; Strontium/analysis ; }, abstract = {Understanding mobility and landscape use is important in reconstructing subsistence behavior, range, and group size, and it may contribute to our understanding of phenomena such as the dynamics of biological and cultural interactions between distinct populations of Upper Pleistocene humans. However, studies using traditional strontium isotope analysis are generally limited to identifying locations of childhood residence or nonlocal individuals and lack the sampling resolution to detect movement over short timescales. Here, using an optimized methodology, we present highly spatially resolved [87]Sr/[86]Sr measurements made by laser ablation multicollector inductively coupled plasma mass spectrometry along the growth axis of the enamel of two marine isotope stage 5b, Middle Paleolithic Neanderthal teeth (Gruta da Oliveira), a Tardiglacial, Late Magdalenian human tooth (Galeria da Cisterna), and associated contemporaneous fauna from the Almonda karst system, Torres Novas, Portugal. Strontium isotope mapping of the region shows extreme variation in [87]Sr/[86]Sr, with values ranging from 0.7080 to 0.7160 over a distance of c. 50 km, allowing short-distance (and arguably short-duration) movement to be detected. We find that the early Middle Paleolithic individuals roamed across a subsistence territory of approximately 600 km[2], while the Late Magdalenian individual parsimoniously fits a pattern of limited, probably seasonal movement along the right bank of the 20-km-long Almonda River valley, between mouth and spring, exploiting a smaller territory of approximately 300 km[2]. We argue that the differences in territory size are due to an increase in population density during the Late Upper Paleolithic.}, }
@article {pmid37142741, year = {2023}, author = {Brand, CM and Colbran, LL and Capra, JA}, title = {Resurrecting the alternative splicing landscape of archaic hominins using machine learning.}, journal = {Nature ecology &amp; evolution}, volume = {7}, number = {6}, pages = {939-953}, pmid = {37142741}, issn = {2397-334X}, support = {R35 GM127087/GM/NIGMS NIH HHS/United States ; T32 HG009495/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Hominidae/genetics ; *Neanderthals/genetics ; Alternative Splicing ; Genome, Human ; Population Density ; }, abstract = {Alternative splicing contributes to adaptation and divergence in many species. However, it has not been possible to directly compare splicing between modern and archaic hominins. Here, we unmask the recent evolution of this previously unobservable regulatory mechanism by applying SpliceAI, a machine-learning algorithm that identifies splice-altering variants (SAVs), to high-coverage genomes from three Neanderthals and a Denisovan. We discover 5,950 putative archaic SAVs, of which 2,186 are archaic-specific and 3,607 also occur in modern humans via introgression (244) or shared ancestry (3,520). Archaic-specific SAVs are enriched in genes that contribute to traits potentially relevant to hominin phenotypic divergence, such as the epidermis, respiration and spinal rigidity. Compared to shared SAVs, archaic-specific SAVs occur in sites under weaker selection and are more common in genes with tissue-specific expression. Further underscoring the importance of negative selection on SAVs, Neanderthal lineages with low effective population sizes are enriched for SAVs compared to Denisovan and shared SAVs. Finally, we find that nearly all introgressed SAVs in humans were shared across the three Neanderthals, suggesting that older SAVs were more tolerated in human genomes. Our results reveal the splicing landscape of archaic hominins and identify potential contributions of splicing to phenotypic differences among hominins.}, }
@article {pmid37134082, year = {2023}, author = {Slimak, L}, title = {The three waves: Rethinking the structure of the first Upper Paleolithic in Western Eurasia.}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0277444}, pmid = {37134082}, issn = {1932-6203}, mesh = {Animals ; Humans ; *Hominidae ; Europe ; Archaeology ; France ; *Neanderthals ; Fossils ; }, abstract = {The Neronian is a lithic tradition recognized in the Middle Rhône Valley of Mediterranean France now directly linked to Homo sapiens and securely dated to 54,000 years ago (ka), pushing back the arrival of modern humans in Europe by 10 ka. This incursion of modern humans into Neandertal territory and the relationships evoked between the Neronian and the Levantine Initial Upper Paleolithic (IUP) question the validity of concepts that define the first H. sapiens migrations and the very nature of the first Upper Paleolithic in western Eurasia. Direct comparative analyses between lithic technology from Grotte Mandrin and East Mediterranean archeological sequences, especially Ksar Akil, suggest that the three key phases of the earliest Levantine Upper Paleolithic have very precise technical and chronological counterparts in Western Europe, recognized from the Rhône Valley to Franco-Cantabria. These trans-Mediterranean technical connections suggest three distinct waves of H. sapiens expansion into Europe between 55-42 ka. These elements support an original thesis on the origin, structure, and evolution of the first moments of the Upper Paleolithic in Europe tracing parallel archaeological changes in the East Mediterranean region and Europe.}, }
@article {pmid37091460, year = {2023}, author = {Sinaei, R and Pezeshki, S and Sinaei, R}, title = {What Kept Back on the Mirror of COVID-19-Related Acute Transverse Myelitis? A Genetic Background!.}, journal = {Iranian journal of child neurology}, volume = {17}, number = {2}, pages = {143-147}, pmid = {37091460}, issn = {1735-4668}, abstract = {COVID-19-associated acute transverse myelitis (ATM) cases have been reported worldwide. Nevertheless, Iran, Italy, and the USA are the most affected countries, witnessing the possibility that genetic factors might be associated with this susceptibility. The genetic variants of the coronavirus-2 entry mechanisms and host innate immune response-related genes like interferons, interleukins, Toll-like receptors, human leukocyte antigens, blood groups, and some risk loci may be accountable. This study describes the compatibility of the geographical distribution between ATM and the Neanderthal core haplotype that confers risk for severe COVID-19 and some possible culprit genes.}, }
@article {pmid37070424, year = {2024}, author = {Gómez-Olivencia, A and Arsuaga, JL}, title = {The Sima de los Huesos cervical spine.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {307}, number = {7}, pages = {2451-2464}, doi = {10.1002/ar.25224}, pmid = {37070424}, issn = {1932-8494}, support = {//Fundaci&#xf3;n Atapuerca/ ; //Junta de Castilla y Le&#xf3;n/ ; PGC2018-093925-B-C33, MCI/AEI/FEDER, UE//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2021-122355NB-C31, MCIN/AEI/10.13039/5011000110, UE//Ministerio de Ciencia e Innovaci&#xf3;n/ ; RYC-2017-22558//Ram&#xf3;n y Cajal fellowship/ ; }, mesh = {*Cervical Vertebrae/anatomy &amp; histology ; Animals ; *Fossils/anatomy &amp; histology ; Humans ; *Neanderthals/anatomy &amp; histology ; *Biological Evolution ; Hominidae/anatomy &amp; histology ; Phylogeny ; }, abstract = {Information regarding the evolution of the neck in genus Homo is hampered owing to a limited fossil record. Neandertals display significant metric and/or morphological differences in all the cervical vertebrae, when compared to Homo sapiens. Thus, the important fossil record from the Middle Pleistocene site of Sima de los Huesos (SH) not only offers important information about the evolution of this anatomical region within the Neandertal lineage, but also provides important clues to understand the evolution of this region at the genus level. We present the current knowledge of the anatomy of the cervical spine of the hominins found in SH compared to that of Neandertals and modern humans, and, when possible, to Homo erectus and Homo antecessor. The current SH fossil record comprises 172 cervical specimens (after refittings) belonging to a minimum of 11 atlases, 13 axes, and 52 subaxial cervical vertebrae. The SH hominins exhibit a morphological pattern in their cervical spine more similar to that of Neandertals than that of H. sapiens, which is consistent with the phylogenetic position of these hominins. However, there are some differences between the SH hominins and Neandertals in this anatomical region, primarily in the length and robusticity, and to a lesser extent in the orientation of the spinous processes of the lowermost cervical vertebrae. We hypothesize that these differences in the lowermost subaxial cervical vertebrae could be related to the increase in the brain size and/or changes in the morphology of the skull that occurred in the Neandertal lineage.}, }
@article {pmid37053172, year = {2023}, author = {Doronicheva, EV and Golovanova, LV and Doronichev, VB and Kurbanov, RN}, title = {Archaeological evidence for two culture diverse Neanderthal populations in the North Caucasus and contacts between them.}, journal = {PloS one}, volume = {18}, number = {4}, pages = {e0284093}, pmid = {37053172}, issn = {1932-6203}, mesh = {Animals ; *Neanderthals ; Fossils ; *Hominidae ; Europe ; Europe, Eastern ; Archaeology ; }, abstract = {Neanderthals were widespread during the Middle Palaeolithic (MP) across Europe and Asia, including the Caucasus Mountains. Occupying the border between eastern Europe and West Asia, the Caucasus is important region regarding the Neanderthal occupation of Eurasia. On current radiometric estimates, the MP is represented in the Caucasus between about 260-210 ka and about 40 ka. Archaeological record indicates that several culture diverse MP hominin populations inhabited the Caucasus, but the region complex population history during this period remains poorly understood. In this paper, we identify for the first time the archaeological evidence indicating contacts between two culture diverse MP Neanderthal populations in the North Caucasus and discuss the nature of these contacts. Basing on the lithic assemblages that we excavated at Mezmaiskaya cave in the north-western Caucasus (Kuban River basin) and Saradj-Chuko grotto in the north-central Caucasus (Terek River basin), dating from MIS 5 to MIS 3, and comparative data from other MP sites in the Caucasus, we identify two large cultural regions that existed during the late MP in the North Caucasus. The distinctive toolkits and stone knapping technologies indicate that the MP assemblages from Mezmaiskaya cave and other sites in the west of North Caucasus represent a Caucasian variant of the Eastern Micoquian industry that was wide spread in central and eastern Europe, while the assemblages from Saradj-Chuko Grotto and other sites in the east of North Caucasus closely resemble the Zagros Mousterian industry that was wide spread in the Armenian Highlands, Lesser Caucasus and Zagros Mountains. The archaeological evidence implies that two culture diverse populations of Neanderthals settled the North Caucasus during the Late Pleistocene from two various source regions: from the Armenian Highlands and Lesser Caucasus along the Caspian Sea coast, and from Russian plain along the Sea of Azov coast.}, }
@article {pmid37035790, year = {2023}, author = {Chung, S and Son, JW}, title = {How Well Do We Understand Autistic Savant Artists: A Review of Various Hypotheses and Research Findings to Date.}, journal = {Soa--ch'ongsonyon chongsin uihak = Journal of child &amp; adolescent psychiatry}, volume = {34}, number = {2}, pages = {93-111}, pmid = {37035790}, issn = {1225-729X}, abstract = {The authors investigated the artistic characteristics of autistic savant artists, hypotheses on the proximate and ultimate causes of their emergence, recent psychological and other studies about them, and psychological and neuroaesthetic studies about non-savant autistic individuals. The artistic features of autistic savant artists were significantly similar to those of outsider artists. Furthermore, the authors investigated the explanatory power of the paradoxical functional facilitation theory, the superior visual perception hypothesis, the "Hmmmmm" hypothesis, and the Neanderthal theory of autism regarding the emergence of autistic savant artists. In addition, we investigated whether an increase in savant characteristics was related to a decrease in the ability for social communication. The authors suggested that in studies on the aesthetic experience of non-savant autistic individuals, their aesthetic experience ability is never lower than that of neurotypical individuals and that some non-savant autistic individuals may potentially have artistic talent. Finally, the authors reviewed the effectiveness of the "autism savant spectrum syndromic disorder" proposed by some researchers. More scientific and systematic studies on autistic savant artists from a multidisciplinary perspective are warranted.}, }
@article {pmid37016656, year = {2023}, author = {Turner, MD}, title = {Possible Causes of Hypertrophic Osteoarthropathy in the La Ferrassie 1 Neanderthal.}, journal = {Cureus}, volume = {15}, number = {3}, pages = {e35721}, pmid = {37016656}, issn = {2168-8184}, abstract = {For over a century, researchers have been perplexed by the unique osteological findings on La Ferrassie 1 (LF1), one of the most complete Neanderthal remains ever found. In 1997, Fennel and Trinkaus proposed that LF1 suffered from hypertrophic osteoarthropathy (HOA), likely secondary to chronic thoracic infection or pulmonary malignancy. This disease process can have many etiologies, and no study has fully explored the possible origin of LF1's HOA. Ultimately, it is most likely that LF1's HOA etiology arose from one of the many infectious diseases that prehistoric Neanderthals were exposed to, specifically a chronic pulmonary RNA virus.}, }
@article {pmid37010952, year = {2023}, author = {Richards, GD and Jabbour, RS and Guipert, G and Defleur, A}, title = {Neanderthal child's maxilla from Baume Moula-Guercy (Soyons, Ardèche, France).}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {306}, number = {10}, pages = {2484-2513}, doi = {10.1002/ar.25218}, pmid = {37010952}, issn = {1932-8494}, mesh = {Humans ; Child ; Animals ; *Neanderthals/anatomy &amp; histology ; Maxilla/anatomy &amp; histology ; Skull/anatomy &amp; histology ; France ; Fossils ; *Hominidae/anatomy &amp; histology ; }, abstract = {This article provides an ontogenetically-based comparative description of the Guercy 3 partial child's maxilla with Rdm[2] -RM[1] and unerupted RI[2] -RP[4] from Baume Moula-Guercy (MIS 5e) and examines its affinities to European and Middle Eastern Middle-to-Late Pleistocene (≈MIS 14-MIS 1) Homo. Description of the Guercy 3 maxilla and dentition (7.0 year ± 0.9 month) is based on observations of original fossils, casts, CT scans, literature descriptions, and virtual reconstructions. Our ontogenetic sample comprises a Preneanderthal-Neanderthal group and a Homo sapiens group. These groups are subdivided into (1) Preneanderthals (≈MIS 14-9), Early Neanderthals (MIS 7-5e), and Late Neanderthals (MIS 5d-3), and (2) Middle (MIS 5), Upper (MIS 3-2), and Late Upper Paleolithic (≈MIS 1), and recent H. sapiens. Standard techniques were employed for measurements and developmental age determinations.The Guercy 3 maxilla lacks changes found in Late Neanderthals, including the positioning of the root of the zygomatic process, infraorbital and nasal plates, premaxilla, buccal and labial alveolus, maxillary sinus, nasal cavity, and verticality of anterior tooth implantation. The morphology of the Guercy 3 maxilla more closely approximates that of Sima de los Huesos Preneanderthals, while the dentition more closely approximates the Early-Late Neanderthal condition. Maxillary remains of children and juveniles between MIS 14-MIS 5e are rare, and the available sample is fragmentary and distorted. Although fragmentary, the Guercy 3 maxilla is undistorted and provides new insights into the evolution of the midface in Neanderthals.}, }
@article {pmid37001690, year = {2023}, author = {Pomeroy, E}, title = {Review: The different adaptive trajectories in Neanderthals and Homo sapiens and their implications for contemporary human physiological variation.}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {280}, number = {}, pages = {111420}, doi = {10.1016/j.cbpa.2023.111420}, pmid = {37001690}, issn = {1531-4332}, mesh = {Humans ; Animals ; *Neanderthals/anatomy &amp; histology/physiology ; Acclimatization ; Climate ; Adaptation, Physiological ; Cold Climate ; Fossils ; }, abstract = {Neanderthals are our one of our closest evolutionary cousins, but while they evolved in Eurasia, we (anatomically modern humans, AMH) originated in Africa. This contrasting evolutionary history has led to morphological and genetic distinctions between our species. Neanderthals are characterised by a relatively stocky build, high body mass, proportionally wide bodies and shorter limbs, a bell-shaped ribcage with a wide pelvis, and a long, low cranial vault compared with AMH. Classic readings of Neanderthal morphology link many of these traits to cold climate adaptations, however these interpretations have been questioned and alternative hypotheses including behavioural factors, dietary adaptations, locomotor specialisations, evolutionary history and neutral evolutionary processes have been invoked. Compared with AMH, Neanderthals may have been adapted for strength and power rather than endurance and may have consumed a diet high in animal products. However, reviewing these hypotheses highlights a number of limitations in our understanding of contemporary human physiology and metabolism, including the relationship between climate and morphology in AMH and Neanderthals, physiological limits on protein consumption, and the relationship between gut morphology and diet. As various relevant factors are clearly linked (e.g. diet, behaviour, metabolism, morphology, activity), ultimately a more integrated approach may be needed to fully understand Neanderthal biology. Variation among contemporary AMHs may offer, with caveats, a useful model for understanding the evolution of both Neanderthal and modern human characteristics, which in turn may further deepen our understanding of variability within and between contemporary humans. Neanderthals; Anatomically modern humans; morphology; climate adaptation; power adaptations; metabolism; diet; physiology; endurance running.}, }
@article {pmid36998196, year = {2024}, author = {Quam, R and Martínez, I and Rak, Y and Hylander, B and Pantoja, A and Lorenzo, C and Conde-Valverde, M and Keeling, B and Ortega Martínez, MC and Arsuaga, JL}, title = {The Neandertal nature of the Atapuerca Sima de los Huesos mandibles.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {307}, number = {7}, pages = {2343-2393}, doi = {10.1002/ar.25190}, pmid = {36998196}, issn = {1932-8494}, support = {PID2021-122355NB-C31MCIN/AEI/10.13039/501100011033/FEDER,UE,//Ministerio de Ciencia e Innovaci&#xf3;n of the Government of Spain/ ; }, mesh = {*Mandible/anatomy &amp; histology ; Animals ; *Neanderthals/anatomy &amp; histology ; *Fossils ; *Biological Evolution ; Male ; Humans ; Hominidae/anatomy &amp; histology ; Female ; Phylogeny ; }, abstract = {The recovery of additional mandibular fossils from the Atapuerca Sima de los Huesos (SH) site provides new insights into the evolutionary significance of this sample. In particular, morphological descriptions of the new adult specimens are provided, along with standardized metric data and phylogenetically relevant morphological features for the expanded adult sample. The new and more complete specimens extend the known range of variation in the Atapuerca (SH) mandibles in some metric and morphological details. In other aspects, the addition of new specimens has made it possible to confirm previous observations based on more limited evidence. Pairwise comparisons of individual metric variables revealed the only significant difference between the Atapuerca (SH) hominins and Neandertals was a more vertical symphysis in the latter. Similarly, principal components analysis of size-adjusted variables showed a strong similarity between the Atapuerca (SH) hominins and Neandertals. Morphologically, the Atapuerca (SH) mandibles show nearly the full complement of Neandertal-derived features. Nevertheless, the Neandertals differ from the Atapuerca (SH) mandibles in showing a high frequency of the H/O mandibular foramen, a truncated, thinned and inverted gonial margin, a high placement of the mylohyoid line at the level of the M3, a more vertical symphysis and somewhat more pronounced expression of the chin structures. Size-related morphological variation in the SH hominins includes larger retromolar spaces, more posterior placement of the lateral corpus structures, and stronger markings associated with the muscles of mastication in larger specimens. However, phylogenetically relevant features in the SH sample are fairly stable and do not vary with the overall size of the mandible. Direct comparison of the enlarged mandibular sample from Atapuerca (SH) with the Mauer mandible, the type specimen of H. heidelbergensis, reveals important differences from the SH hominins, and there is no morphological counterpart of Mauer within the SH sample, suggesting the SH fossils should not be assigned to this taxon. The Atapuerca (SH) mandibles show a greater number of derived Neandertal features, particularly those related to midfacial prognathism and in the configuration of the superior ramus, than other European middle Pleistocene specimens. This suggests that more than one evolutionary lineage co-existed in the middle Pleistocene, and, broadly speaking, it appears possible to separate the European middle Pleistocene mandibular remains into two distinct groupings. One group shows a suite of derived Neandertal features and includes specimens from the sites of Atapuerca (SH), Payre, l'Aubesier and Ehringsdorf. The other group includes specimens that generally lack derived Neandertal features and includes the mandibles from the sites of Mauer, Mala Balanica, Montmaurin and (probably) Visogliano. The two published Arago mandibles differ strongly from one another, with Arago 2 probably belonging to this former group, and Neandertal affinities being more difficult to identify in Arago 13. Outside of the SH sample, derived Neandertal features in the mandible only become more common during the second half of the middle Pleistocene. Acceptance of a cladogenetic pattern of evolution during the European middle Pleistocene has the potential to reconcile the predictions of the accretion model and the two phases model for the appearance of Neandertal morphology. The precise taxonomic classification of the SH hominins must contemplate features from the dentition, cranium, mandible and postcranial skeleton, all of which are preserved at the SH site. Nevertheless, the origin of the Neandertal clade may be tied to a speciation event reflected in the appearance of a suite of derived Neandertal features in the face, dentition and mandible, all of which are present in the Atapuerca (SH) hominins. This same suite of features also provides a useful anatomical basis to include other European middle Pleistocene mandibles and crania within the Neandertal clade.}, }
@article {pmid36980999, year = {2023}, author = {Toncheva, D and Marinova, M and Chobanov, T and Serbezov, D}, title = {Pathogenic Variants Associated with Rare Monogenic Diseases Established in Ancient Neanderthal and Denisovan Genome-Wide Data.}, journal = {Genes}, volume = {14}, number = {3}, pages = {}, pmid = {36980999}, issn = {2073-4425}, mesh = {Animals ; Humans ; Infant, Newborn ; *Neanderthals/genetics ; Rare Diseases/genetics ; *Hominidae/genetics ; Genome, Human ; DNA ; }, abstract = {Ancient anatomically modern humans (AMHs) encountered other archaic human species, most notably Neanderthals and Denisovans, when they left Africa and spread across Europe and Asia ~60,000 years ago. They interbred with them, and modern human genomes retain DNA inherited from these interbreeding events. High quality (high coverage) ancient human genomes have recently been sequenced allowing for a direct estimation of individual heterozygosity, which has shown that genetic diversity in these archaic human groups was very low, indicating low population sizes. In this study, we analyze ten ancient human genome-wide data, including four sequenced with high-coverage. We screened these ancient genome-wide data for pathogenic mutations associated with monogenic diseases, and established unusual aggregation of pathogenic mutations in individual subjects, including quadruple homozygous cases of pathogenic variants in the PAH gene associated with the condition phenylketonuria in a ~120,000 years old Neanderthal. Such aggregation of pathogenic mutations is extremely rare in contemporary populations, and their existence in ancient humans could be explained by less significant clinical manifestations coupled with small community sizes, leading to higher inbreeding levels. Our results suggest that pathogenic variants associated with rare diseases might be the result of introgression from other archaic human species, and archaic admixture thus could have influenced disease risk in modern humans.}, }
@article {pmid36966596, year = {2023}, author = {Zhang, Y and Li, Z}, title = {Three-dimensional geometric morphometric study of the Xuchang 2 cranium.}, journal = {Journal of human evolution}, volume = {178}, number = {}, pages = {103347}, doi = {10.1016/j.jhevol.2023.103347}, pmid = {36966596}, issn = {1095-8606}, mesh = {Animals ; Humans ; *Neanderthals/anatomy &amp; histology ; Biological Evolution ; Fossils ; Skull/anatomy &amp; histology ; *Hominidae/anatomy &amp; histology ; }, abstract = {Results of traditional metric and nonmetric assessments suggest that the Xuchang hominin shares features with Neanderthals. To comprehensively compare the nuchal morphology of XC 2 to those of the genus Homo, we conduct a three-dimensional geometric morphometric study with 35 cranial landmarks and surface semilandmarks of XC 2, Homo erectus, Middle Pleistocene humans, Neanderthals, and early and recent modern humans. Results reveal that the centroid size of XC 2 is larger than that of early and recent modern humans and can only be compared to that of Middle Pleistocene humans and H. erectus. Early and recent modern humans share a nuchal morphology distinct from archaic hominins (Ngandong H. erectus, Middle Pleistocene humans, and Neanderthals), except for SM 3, Sangiran 17, and Asian and African H. erectus. Although Ngandong specimens differ from the other H. erectus, it is unclear whether this represents a temporal or spatial trend in the process of evolution of this species. The nuchal morphological resemblance between Middle Pleistocene humans and Neanderthals may be attributed to similar cranial architecture and cerebellar shape. The great nuchal morphological variation shared by recent modern humans may indicate a particular developmental pattern. In conclusion, the nuchal morphology of different human groups is highly variable and may be caused by different factors including brain globularization and developmental plasticity. XC 2 shares similar nuchal morphology with Middle Pleistocene humans and Neanderthals, but these results are insufficient to fully resolve the taxonomic status of XC 2.}, }
@article {pmid36964200, year = {2023}, author = {Profico, A and Buzi, C and Di Vincenzo, F and Boggioni, M and Borsato, A and Boschian, G and Marchi, D and Micheli, M and Cecchi, JM and Samadelli, M and Tafuri, MA and Arsuaga, JL and Manzi, G}, title = {Virtual excavation and analysis of the early Neanderthal cranium from Altamura (Italy).}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {316}, pmid = {36964200}, issn = {2399-3642}, mesh = {Animals ; *Neanderthals ; *Hominidae/anatomy &amp; histology ; Skull/anatomy &amp; histology ; Fossils ; Italy ; }, abstract = {Complete Neanderthal skeletons are almost unique findings. A very well-preserved specimen of this kind was discovered in 1993 in the deepest recesses of a karstic system near the town of Altamura in Southern Italy. We present here a detailed description of the cranium, after we virtually extracted it from the surrounding stalagmites and stalactites. The morphology of the Altamura cranium fits within the Neanderthal variability, though it retains features occurring in more archaic European samples. Some of these features were never observed in Homo neanderthalensis, i.e. in fossil specimens dated between 300 and 40 ka. Considering the U-Th age we previously obtained (>130 ka), the morphology of Altamura suggests that the archaic traits it retains may have been originated by geographic isolation of the early Neanderthal populations from Southern Italy.}, }
@article {pmid36950386, year = {2023}, author = {Skov, L and Coll Macià, M and Lucotte, EA and Cavassim, MIA and Castellano, D and Schierup, MH and Munch, K}, title = {Extraordinary selection on the human X chromosome associated with archaic admixture.}, journal = {Cell genomics}, volume = {3}, number = {3}, pages = {100274}, pmid = {36950386}, issn = {2666-979X}, abstract = {The X chromosome in non-African humans shows less diversity and less Neanderthal introgression than expected from neutral evolution. Analyzing 162 human male X chromosomes worldwide, we identified fourteen chromosomal regions where nearly identical haplotypes spanning several hundred kilobases are found at high frequencies in non-Africans. Genetic drift alone cannot explain the existence of these haplotypes, which must have been associated with strong positive selection in partial selective sweeps. Moreover, the swept haplotypes are entirely devoid of archaic ancestry as opposed to the non-swept haplotypes in the same genomic regions. The ancient Ust'-Ishim male dated at 45,000 before the present (BP) also carries the swept haplotypes, implying that selection on the haplotypes must have occurred between 45,000 and 55,000 years ago. Finally, we find that the chromosomal positions of sweeps overlap previously reported hotspots of selective sweeps in great ape evolution, suggesting a mechanism of selection unique to X chromosomes.}, }
@article {pmid36939312, year = {2023}, author = {Wei, X and Robles, CR and Pazokitoroudi, A and Ganna, A and Gusev, A and Durvasula, A and Gazal, S and Loh, PR and Reich, D and Sankararaman, S}, title = {The lingering effects of Neanderthal introgression on human complex traits.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {36939312}, issn = {2050-084X}, support = {R01 HG012287/HG/NHGRI NIH HHS/United States ; R35 GM125055/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R35GM125055/NH/NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Neanderthals/genetics ; Multifactorial Inheritance ; *Hominidae/genetics ; Gene Frequency ; Genetics, Population ; Genome, Human ; }, abstract = {The genetic variants introduced into the ancestors of modern humans from interbreeding with Neanderthals have been suggested to contribute an unexpected extent to complex human traits. However, testing this hypothesis has been challenging due to the idiosyncratic population genetic properties of introgressed variants. We developed rigorous methods to assess the contribution of introgressed Neanderthal variants to heritable trait variation and applied these methods to analyze 235,592 introgressed Neanderthal variants and 96 distinct phenotypes measured in about 300,000 unrelated white British individuals in the UK Biobank. Introgressed Neanderthal variants make a significant contribution to trait variation (explaining 0.12% of trait variation on average). However, the contribution of introgressed variants tends to be significantly depleted relative to modern human variants matched for allele frequency and linkage disequilibrium (about 59% depletion on average), consistent with purifying selection on introgressed variants. Different from previous studies (McArthur et al., 2021), we find no evidence for elevated heritability across the phenotypes examined. We identified 348 independent significant associations of introgressed Neanderthal variants with 64 phenotypes. Previous work (Skov et al., 2020) has suggested that a majority of such associations are likely driven by statistical association with nearby modern human variants that are the true causal variants. Applying a customized fine-mapping led us to identify 112 regions across 47 phenotypes containing 4303 unique genetic variants where introgressed variants are highly likely to have a phenotypic effect. Examination of these variants reveals their substantial impact on genes that are important for the immune system, development, and metabolism.}, }
@article {pmid36925053, year = {2023}, author = {Chen, Z and Reynolds, RH and Pardiñas, AF and Gagliano Taliun, SA and van Rheenen, W and Lin, K and Shatunov, A and Gustavsson, EK and Fogh, I and Jones, AR and Robberecht, W and Corcia, P and Chiò, A and Shaw, PJ and Morrison, KE and Veldink, JH and van den Berg, LH and Shaw, CE and Powell, JF and Silani, V and Hardy, JA and Houlden, H and Owen, MJ and Turner, MR and Ryten, M and Al-Chalabi, A}, title = {The contribution of Neanderthal introgression and natural selection to neurodegenerative diseases.}, journal = {Neurobiology of disease}, volume = {180}, number = {}, pages = {106082}, doi = {10.1016/j.nbd.2023.106082}, pmid = {36925053}, issn = {1095-953X}, support = {MR/R024804/1/MRC_/Medical Research Council/United Kingdom ; MR/L010305/1/MRC_/Medical Research Council/United Kingdom ; TURNER/OCT18/989-797/MNDA_/Motor Neurone Disease Association/United Kingdom ; NIHR202421/DH_/Department of Health/United Kingdom ; MR/L501529/1/MRC_/Medical Research Council/United Kingdom ; MR/N008324/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Humans ; *Neanderthals/genetics ; *Neurodegenerative Diseases/genetics ; *Alzheimer Disease ; *Parkinson Disease ; *Amyotrophic Lateral Sclerosis ; Selection, Genetic ; }, abstract = {Humans are thought to be more susceptible to neurodegeneration than equivalently-aged primates. It is not known whether this vulnerability is specific to anatomically-modern humans or shared with other hominids. The contribution of introgressed Neanderthal DNA to neurodegenerative disorders remains uncertain. It is also unclear how common variants associated with neurodegenerative disease risk are maintained by natural selection in the population despite their deleterious effects. In this study, we aimed to quantify the genome-wide contribution of Neanderthal introgression and positive selection to the heritability of complex neurodegenerative disorders to address these questions. We used stratified-linkage disequilibrium score regression to investigate the relationship between five SNP-based signatures of natural selection, reflecting different timepoints of evolution, and genome-wide associated variants of the three most prevalent neurodegenerative disorders: Alzheimer's disease, amyotrophic lateral sclerosis and Parkinson's disease. We found no evidence for enrichment of positively-selected SNPs in the heritability of Alzheimer's disease, amyotrophic lateral sclerosis and Parkinson's disease, suggesting that common deleterious disease variants are unlikely to be maintained by positive selection. There was no enrichment of Neanderthal introgression in the SNP-heritability of these disorders, suggesting that Neanderthal admixture is unlikely to have contributed to disease risk. These findings provide insight into the origins of neurodegenerative disorders within the evolution of Homo sapiens and addresses a long-standing debate, showing that Neanderthal admixture is unlikely to have contributed to common genetic risk of neurodegeneration in anatomically-modern humans.}, }
@article {pmid36916962, year = {2024}, author = {Carretero, JM and García-González, R and Rodríguez, L and Arsuaga, JL}, title = {Main anatomical characteristics of the hominin fossil humeri from the Sima de los Huesos Middle Pleistocene site, Sierra de Atapuerca, Burgos, Spain: An update.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {307}, number = {7}, pages = {2519-2549}, doi = {10.1002/ar.25194}, pmid = {36916962}, issn = {1932-8494}, support = {//Fundaci&#xf3;n Atapuerca/ ; PID2021-122355NB-C31//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades (Spain)/ ; }, mesh = {Animals ; *Fossils/anatomy &amp; histology ; Spain ; *Hominidae/anatomy &amp; histology ; *Biological Evolution ; Neanderthals/anatomy &amp; histology ; Phylogeny ; }, abstract = {Some of the Sima de los Huesos (SH) humeri have been previously studied and described elsewhere. Here we present an updated inventory and a review of the specimens recovered to the present day. The morphological key traits of the adult and subadult specimens are described, discussed, and illustrated. The SH humeri share with Neandertals many traits usually considered to be Neandertal specializations, thus, most of this morphological pattern is not exclusive to them. The variation found within fossil samples stresses the frequential nature of all these traits and in the specific case of the SH humeri, most of the traits considered as phylogenetically relevant are retained by their descendants, the Neandertals. Some traits are plesiomorphic for the entire genus Homo or are present in European hominins since the early Pleistocene. Finally, some other traits display high variability within the SH sample or different hominin samples and are of uncertain phylogenetic value. Altogether, this evidence is consistent with the hypothesis based on the overall cranial and postcranial morphology that the SH hominins are a sister group to the later Neandertals.}, }
@article {pmid36893252, year = {2023}, author = {Herai, RH and Semendeferi, K and Muotri, AR}, title = {Comment on "Human TKTL1 implies greater neurogenesis in frontal neocortex of modern humans than Neanderthals".}, journal = {Science (New York, N.Y.)}, volume = {379}, number = {6636}, pages = {eadf0602}, doi = {10.1126/science.adf0602}, pmid = {36893252}, issn = {1095-9203}, mesh = {Animals ; Humans ; *Neanderthals/genetics ; *Neocortex/growth &amp; development ; Neurogenesis/genetics ; *Transketolase ; }, abstract = {Pinson et al. (1) concluded that the modern human TKTL1 gene is responsible for an increased number of cortical neurons. We show that the "putative Neanderthal variant" of TKTL1 is present in modern human backgrounds. We dispute their argument that this genetic variant is responsible for brain differences in modern humans as opposed to Neanderthals.}, }
@article {pmid36871458, year = {2023}, author = {Jones, EL and Carvalho, M}, title = {Ecospaces of the Middle to Upper Paleolithic transition: The archaeofaunal record of the Iberian Peninsula.}, journal = {Journal of human evolution}, volume = {177}, number = {}, pages = {103331}, doi = {10.1016/j.jhevol.2023.103331}, pmid = {36871458}, issn = {1095-8606}, mesh = {Animals ; Humans ; *Neanderthals ; Archaeology ; Fossils ; Mammals ; }, abstract = {The rich archaeofaunal record of Iberia provides a means of exploring potential differences between Neanderthal and anatomically modern human interactions with the environment. In this article, we present an analysis of Iberian archaeofaunas dating between 60 and 30 ka to explore if, how, and why the faunal ecospaces of Neanderthals and anatomically modern humans differed. We test for impacts of chronology (as a proxy for Neanderthal and anatomically modern human exploitation) and environmental regionalization (using bioclimatic regions) on archaeofaunal composition, using a combination of cluster (unweighted pair-group method using arithmetic averages) and nonmetric multidimensional scaling. Our chronological analysis finds no significant compositional difference between Neanderthal and anatomically modern mammalian faunal assemblages; however, bioclimatic regionalization is stronger in anatomically modern human-affiliated assemblages than in Neanderthal ones, a finding that may indicate a difference in site occupation duration or foraging mobility between Neanderthals and anatomically modern humans.}, }
@article {pmid36833167, year = {2023}, author = {González-Álvarez, R and Rodríguez-Sánchez, IP and Barrera-Saldaña, HA}, title = {Gene Content and Coding Diversity of the Growth Hormone Loci of Apes.}, journal = {Genes}, volume = {14}, number = {2}, pages = {}, pmid = {36833167}, issn = {2073-4425}, mesh = {Animals ; Female ; Pregnancy ; *Hominidae/genetics ; Pan troglodytes/genetics ; Gorilla gorilla/genetics ; Hylobates/genetics ; *Neanderthals/genetics ; Base Sequence ; Phylogeny ; Placenta ; Growth Hormone ; *Human Growth Hormone/genetics ; Primates/genetics ; Pongo/genetics ; }, abstract = {The growth hormone (GH) locus has experienced a dramatic evolution in primates, becoming multigenic and diverse in anthropoids. Despite sequence information from a vast number of primate species, it has remained unclear how the multigene family was favored. We compared the structure and composition of apes' GH loci as a prerequisite to understanding their origin and possible evolutionary role. These thorough analyses of the GH loci of the chimpanzee, gorilla, and orangutan were done by resorting to previously sequenced bacterial artificial chromosomes (BACs) harboring them, as well as to their respective genome projects data available in GenBank. The GH loci of modern man, Neanderthal, gibbon, and wild boar were retrieved from GenBank. Coding regions, regulatory elements, and repetitive sequences were identified and compared among species. The GH loci of all the analyzed species are flanked by the genes CD79B (5') and ICAM-1 (3'). In man, Neanderthal, and chimpanzee, the loci were integrated by five almost indistinguishable genes; however, in the former two, they rendered three different hormones, and in the latter, four different proteins were derived. Gorilla exhibited six genes, gibbon seven, and orangutan four. The sequences of the proximal promoters, enhancers, P-elements, and a locus control region (LCR) were highly conserved. The locus evolution might have implicated duplications of the ancestral pituitary gene (GH-N) and subsequent diversification of the copies, leading to the placental single GH-V gene and the multiple CSH genes.}, }
@article {pmid36825485, year = {2024}, author = {Conde-Valverde, M and Martínez, I and Quam, R and Arsuaga, JL}, title = {The ear of the Sima de los Huesos hominins (Atapuerca, Spain).}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {307}, number = {7}, pages = {2410-2424}, doi = {10.1002/ar.25181}, pmid = {36825485}, issn = {1932-8494}, support = {MCIN/AEI/10.13039/5011000110033//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {Animals ; Spain ; *Fossils/anatomy &amp; histology ; *Biological Evolution ; *Neanderthals/anatomy &amp; histology ; *Hominidae/anatomy &amp; histology ; Humans ; Ear, Inner/anatomy &amp; histology ; Ear, Middle/anatomy &amp; histology ; }, abstract = {Previous studies on the morphology of the inner ear (semicircular canals and cochlea) in the Sima de los Huesos hominin sample have provided important results on the evolution of these structures in the Neandertal lineage. Similarly, studies of the anatomy of the external and middle ear cavities of the Sima de los Huesos hominins have also provided important data on the auditory capacities of this European Middle Pleistocene population. The present contribution provides unpublished data on three new middle ear variables from the Sima de los Huesos fossils and compares these data with values from samples of Pan troglodytes, Homo neanderthalensis and Homo sapiens. The results of this analysis are combined with those obtained in previous studies to characterize the anatomy of the outer, middle and inner ear in the Sima de los Huesos fossils, as well as to establish the order of appearance of the features that characterize Neandertal ears. As in other cranial structures, the ear region in the Sima de los Huesos show a mosaic evolutionary pattern that includes primitive traits, others shared exclusively with Neandertals, and others that are specific to the Sima de los Huesos hominins. Neandertals and Sima de los Huesos hominins share two exclusive features of the middle ear that are among the first characteristics of the Neandertal lineage: a long tympanic cavity and a large entrance and exit of the mastoid antrum. Along with these traits, the Sima de los Huesos hominins present two specialized features: large volumes of the tympanic cavity and the mastoid antrum. Finally, the middle ear of the Neandertals is characterized by the presence of small angles between the tympanic axis and the plane of the oval window.}, }
@article {pmid36823244, year = {2023}, author = {Wang, PY and Yang, Y and Shi, XQ and Chen, Y and Liu, SD and Wang, HY and Peng, T and Shi, Q and Zhang, W and Sun, C}, title = {Distilling functional variations for human UGT2B4 upstream region based on selection signals and implications for phenotypes of Neanderthal and Denisovan.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {3134}, pmid = {36823244}, issn = {2045-2322}, mesh = {Animals ; Female ; Humans ; Breast Neoplasms/genetics ; *Genetics, Population ; Genome, Human ; *Glucuronosyltransferase/genetics ; Hominidae/genetics ; Neanderthals/genetics ; Phenotype ; }, abstract = {Our previous work identified one region upstream human UGT2B4 (UDP glucuronosyltransferase family 2 member B4) which is associated with breast cancer and under balancing selection. However, the distribution, functional variation and molecular mechanism underlying breast cancer and balancing selection remain unclear. In current study, the two haplotypes with deep divergence are described by analyzing 1000 genomes project data and observed to be with high frequencies in all human populations. Through population genetics analysis and genome annotation, the potential functional region is identified and verified by reporter gene assay. Further mutagenesis indicates that the functional mutations are rs66862535 and rs68096061. Both SNPs can alter the interaction efficiency of transcription factor POU2F1 (POU class 2 homeobox 1). Through chromosome conformation capture, it is identified that the enhancer containing these two SNPs can interact with UGT2B4 promoter. Expression quantitative trait loci analysis indicates that UGT2B4 expression is dependent on the genotype of this locus. The common haplotype in human is lost in four genomes of archaic hominins, which suggests that Neanderthal and Denisovan should present relatively lower UGT2B4 expression and further higher steroid hormone level. This study provides new insight into the contribution of ancient population structure to human phenotypes.}, }
@article {pmid36821540, year = {2023}, author = {Ghasidian, E and Kafash, A and Kehl, M and Yousefi, M and Heydari-Guran, S}, title = {Modelling Neanderthals' dispersal routes from Caucasus towards east.}, journal = {PloS one}, volume = {18}, number = {2}, pages = {e0281978}, pmid = {36821540}, issn = {1932-6203}, mesh = {Humans ; Animals ; *Neanderthals ; *Hominidae ; Europe ; Archaeology ; }, abstract = {The study of the cultural materials associated with the Neanderthal physical remains from the sites in the Caucasus, Central Asia and Siberian Altai and adjacent areas documents two distinct techno-complexes of Micoquian and Mousterian. These findings potentially outline two dispersal routes for the Neanderthals out of Europe. Using data on topography and Palaeoclimate, we generated computer-based least-cost-path modelling for the Neanderthal dispersal routes from Caucasus towards the east. In this regard, two dispersal routes have been identified: A northern route from Greater Caucasus associated with Micoquian techno-complex towards Siberian Altai and a southern route from Lesser Caucasus associated with Mousterian towards Siberian Altai via the Southern Caspian Corridor. Based on archaeological, bio- and physio-geographical data, our model hypothesises that during climatic deterioration phases (e.g. MIS 4) the connection between Greater and Lesser Caucasus was limited. This issue perhaps resulted in the separate development and spread of two cultural groups of Micoquian and Mousterian with an input from two different population sources of Neanderthal influxes: eastern and southern Europe refugia for these two northern and southern dispersal routes respectively. Of these two, we focus on the southern dispersal route, for it comprises a 'rapid dispersal route' towards east. The significant location of the Southern Caspian corridor between high mountains of Alborz and the Caspian Sea, provided a special biogeographical zone and a refugium. This exceptional physio-geographic condition brings forward the Southern Caspian corridor as a potential place of admixture of different hominin species including Neanderthals and homo sapiens.}, }
@article {pmid36806751, year = {2023}, author = {Cazenave, M and Radovčić, D}, title = {The Neanderthal patellae from Krapina (Croatia): A comparative investigation of their endostructural conformation and distinctive features compared to the extant human condition.}, journal = {American journal of biological anthropology}, volume = {181}, number = {1}, pages = {118-129}, doi = {10.1002/ajpa.24709}, pmid = {36806751}, issn = {2692-7691}, mesh = {Adult ; Animals ; Humans ; *Neanderthals ; Patella/diagnostic imaging ; Croatia ; *Hominidae ; Knee Joint ; }, abstract = {OBJECTIVES: The Neanderthal patella differs from that of extant humans by being thicker anteroposteriorly and by having more symmetric medial and lateral articular facets. However, it is still unclear to what extent these differences affect knee kinesiology. We aim at assessing the endostructural conformation of Neanderthal patellae to reveal functionally related mechanical information comparatively to the extant human condition. In principle, we expect that the Neanderthal patella (i) shows a higher amount of cortical bone and (ii) a trabecular network organization distinct from the extant human condition.<br><br>MATERIALS AND METHODS: By using micro-focus X-ray tomography, we characterized the endostructure of six adult patellae from the OIS 5e Neanderthal site of Krapina, Croatia, the largest assemblage of human fossil patellae assessed so far, and compared their pattern to the configuration displayed by a sample of 22 recent humans.<br><br>RESULTS AND DISCUSSION: The first expectation is rejected, indicating that the patellar bone might have not followed the trend of generalized gracilization of the human postcranial skeleton occurred through the Upper Pleistocene. The second prediction is at least partially supported. In Krapina the trabecular network differs from the comparative sample by showing a higher medial density and by lacking a proximal reinforcement. Such conformation indicates similar load patterns exerted in Neanderthals and extant humans by the vastus lateralis, but not by the vastus medialis, with implications on the mediolateral stabilization of the knee joint. However, the patterns of structural variation of the patellar network remain to be assessed in other Neanderthal samples.}, }
@article {pmid36796364, year = {2023}, author = {Corcoran, M and Chernyshev, M and Mandolesi, M and Narang, S and Kaduk, M and Ye, K and Sundling, C and Färnert, A and Kreslavsky, T and Bernhardsson, C and Larena, M and Jakobsson, M and Karlsson Hedestam, GB}, title = {Archaic humans have contributed to large-scale variation in modern human T cell receptor genes.}, journal = {Immunity}, volume = {56}, number = {3}, pages = {635-652.e6}, doi = {10.1016/j.immuni.2023.01.026}, pmid = {36796364}, issn = {1097-4180}, mesh = {Humans ; *Receptors, Antigen, T-Cell/genetics ; *Antigens ; Genes, T-Cell Receptor ; }, abstract = {Human T cell receptors (TCRs) are critical for mediating immune responses to pathogens and tumors and regulating self-antigen recognition. Yet, variations in the genes encoding TCRs remain insufficiently defined. Detailed analysis of expressed TCR alpha, beta, gamma, and delta genes in 45 donors from four human populations-African, East Asian, South Asian, and European-revealed 175 additional TCR variable and junctional alleles. Most of these contained coding changes and were present at widely differing frequencies in the populations, a finding confirmed using DNA samples from the 1000 Genomes Project. Importantly, we identified three Neanderthal-derived, introgressed TCR regions including a highly divergent TRGV4 variant, which mediated altered butyrophilin-like molecule 3 (BTNL3) ligand reactivity and was frequent in all modern Eurasian population groups. Our results demonstrate remarkable variation in TCR genes in both individuals and populations, providing a strong incentive for including allelic variation in studies of TCR function in human biology.}, }
@article {pmid36790758, year = {2022}, author = {Oxilia, G and Bortolini, E and Marciani, G and Menghi Sartorio, JC and Vazzana, A and Bettuzzi, M and Panetta, D and Arrighi, S and Badino, F and Figus, C and Lugli, F and Romandini, M and Silvestrini, S and Sorrentino, R and Moroni, A and Donadio, C and Morigi, MP and Slon, V and Piperno, M and Talamo, S and Collina, C and Benazzi, S}, title = {Direct evidence that late Neanderthal occupation precedes a technological shift in southwestern Italy.}, journal = {American journal of biological anthropology}, volume = {179}, number = {1}, pages = {18-30}, pmid = {36790758}, issn = {2692-7691}, mesh = {Humans ; Animals ; *Neanderthals ; Italy ; Europe ; Tooth, Deciduous ; Technology ; }, abstract = {OBJECTIVES: During the middle-to-upper Paleolithic transition (50,000 and 40,000 years ago), interaction between Neanderthals and Homo sapiens varied across Europe. In southern Italy, the association between Homo sapiens fossils and non-Mousterian material culture, as well as the mode and tempo of Neanderthal demise, are still vividly debated. In this research, we focus on the study of two human teeth by using 3D geometric morphometric approaches for a reliable taxonomical attribution as well as obtaining new radiometric dates on the archeological sequence.<br><br>MATERIAL AND METHODS: This work presents two lower deciduous molars uncovered at Roccia San Sebastiano (Mondragone-Caserta, Italy), stratigraphically associated with Mousterian (RSS1) and Uluzzian (RSS2) artifacts. To obtain a probabilistic attribution of the two RSS teeth to each reference taxa group composed of Neanderthals and Homo sapiens, we performed and compared the performance of three supervised learning algorithms (flexible discriminant analysis, multiadaptive regression splines, and random forest) on both crown and cervical outlines obtained by virtual morphometric methods.<br><br>RESULTS: We show that RSS1, whose Mousterian context appears more recent than 44,800-44,230&#x2009;cal BP, can be attributed to a Neanderthal, while RSS2, found in an Uluzzian context that we dated to 42,640-42,380&#x2009;cal BP, is attributed to Homo sapiens.<br><br>DISCUSSION: This site yields the most recent direct evidence for a Neanderthal presence in southern Italy and confirms a later shift to upper Paleolithic technology in southwestern Italy compared to the earliest Uluzzian evidence at Grotta del Cavallo (Puglia, Italy).}, }
@article {pmid36776693, year = {2023}, author = {Hagymási, K}, title = {The Nobel prize in physiology and medicine - 2022.}, journal = {Structural chemistry}, volume = {34}, number = {2}, pages = {733-736}, pmid = {36776693}, issn = {1040-0400}, abstract = {The Nobel Assembly at Karolinska Institutet awarded the 2022 Nobel Prize in Physiology or Medicine to a Swedish geneticist, Svante Pääbo, for his discoveries concerning the genomes of extinct hominins and human evolution, for the sequencing of the genome of the Neanderthal, the discovery of a previously unknown hominin, Denisova, and the establishment of a new scientific discipline, paleogenomics.}, }
@article {pmid36763080, year = {2023}, author = {Jagoda, E and Marnetto, D and Senevirathne, G and Gonzalez, V and Baid, K and Montinaro, F and Richard, D and Falzarano, D and LeBlanc, EV and Colpitts, CC and Banerjee, A and Pagani, L and Capellini, TD}, title = {Regulatory dissection of the severe COVID-19 risk locus introgressed by Neanderthals.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {36763080}, issn = {2050-084X}, support = {IIR 16-003/HX/HSRD VA/United States ; }, mesh = {Humans ; Animals ; *COVID-19/genetics ; *Neanderthals/genetics ; SARS-CoV-2/genetics ; *Virus Diseases ; Genetics, Population ; }, abstract = {Individuals infected with the SARS-CoV-2 virus present with a wide variety of symptoms ranging from asymptomatic to severe and even lethal outcomes. Past research has revealed a genetic haplotype on chromosome 3 that entered the human population via introgression from Neanderthals as the strongest genetic risk factor for the severe response to COVID-19. However, the specific variants along this introgressed haplotype that contribute to this risk and the biological mechanisms that are involved remain unclear. Here, we assess the variants present on the risk haplotype for their likelihood of driving the genetic predisposition to severe COVID-19 outcomes. We do this by first exploring their impact on the regulation of genes involved in COVID-19 infection using a variety of population genetics and functional genomics tools. We then perform a locus-specific massively parallel reporter assay to individually assess the regulatory potential of each allele on the haplotype in a multipotent immune-related cell line. We ultimately reduce the set of over 600 linked genetic variants to identify four introgressed alleles that are strong functional candidates for driving the association between this locus and severe COVID-19. Using reporter assays in the presence/absence of SARS-CoV-2, we find evidence that these variants respond to viral infection. These variants likely drive the locus' impact on severity by modulating the regulation of two critical chemokine receptor genes: CCR1 and CCR5. These alleles are ideal targets for future functional investigations into the interaction between host genomics and COVID-19 outcomes.}, }
@article {pmid36724231, year = {2023}, author = {Gaudzinski-Windheuser, S and Kindler, L and MacDonald, K and Roebroeks, W}, title = {Hunting and processing of straight-tusked elephants 125.000 years ago: Implications for Neanderthal behavior.}, journal = {Science advances}, volume = {9}, number = {5}, pages = {eadd8186}, pmid = {36724231}, issn = {2375-2548}, mesh = {Animals ; Humans ; *Elephants ; Fossils ; *Hominidae ; Hunting ; Mammals ; *Neanderthals ; }, abstract = {Straight-tusked elephants (Palaeoloxodon antiquus) were the largest terrestrial mammals of the Pleistocene, present in Eurasian landscapes between 800,000 and 100,000 years ago. The occasional co-occurrence of their skeletal remains with stone tools has generated rich speculation about the nature of interactions between these elephants and Pleistocene humans: Did hominins scavenge on elephants that died a natural death or maybe even hunt some individuals? Our archaeozoological study of the largest P. antiquus assemblage known, excavated from 125,000-year-old lake deposits in Germany, shows that hunting of elephants weighing up to 13 metric tons was part of the cultural repertoire of Last Interglacial Neanderthals there, over >2000 years, many dozens of generations. The intensity and nutritional yields of these well-documented butchering activities, combined with previously reported data from this Neumark-Nord site complex, suggest that Neanderthals were less mobile and operated within social units substantially larger than commonly envisaged.}, }
@article {pmid36719913, year = {2023}, author = {Ben-Dor, M and Barkai, R}, title = {A limited protein high-fat diet may explain the low δ[66]Zn conundrum in the Neandertal from Gabasa.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {6}, pages = {e2218081120}, pmid = {36719913}, issn = {1091-6490}, mesh = {Animals ; *Neanderthals ; Diet, High-Fat/adverse effects ; Zinc ; Diet ; }, }
@article {pmid36712807, year = {2022}, author = {Williams, SA and Zeng, I and Paton, GJ and Yelverton, C and Dunham, C and Ostrofsky, KR and Shukman, S and Avilez, MV and Eyre, J and Loewen, T and Prang, TC and Meyer, MR}, title = {Inferring lumbar lordosis in Neandertals and other hominins.}, journal = {PNAS nexus}, volume = {1}, number = {1}, pages = {pgab005}, pmid = {36712807}, issn = {2752-6542}, abstract = {Lumbar lordosis is a key adaptation to bipedal locomotion in the human lineage. Dorsoventral spinal curvatures enable the body's center of mass to be positioned above the hip, knee, and ankle joints, and minimize the muscular effort required for postural control and locomotion. Previous studies have suggested that Neandertals had less lordotic (ventrally convex) lumbar columns than modern humans, which contributed to historical perceptions of postural and locomotor differences between the two groups. Quantifying lower back curvature in extinct hominins is entirely reliant upon bony correlates of overall lordosis, since the latter is significantly influenced by soft tissue structures (e.g. intervertebral discs). Here, we investigate sexual dimorphism, ancestry, and lifestyle effects on lumbar vertebral body wedging and inferior articular facet angulation, two features previously shown to be significantly correlated with overall lordosis in living individuals, in a large sample of modern humans and Neandertals. Our results demonstrate significant differences between postindustrial cadaveric remains and archaeological samples of people that lived preindustrial lifestyles. We suggest these differences are related to activity and other aspects of lifestyle rather than innate population (ancestry) differences. Neandertal bony correlates of lumbar lordosis are significantly different from all human samples except preindustrial males. Therefore, although Neandertals demonstrate more bony kyphotic wedging than most modern humans, we cast doubt on proposed locomotor and postural differences between the two lineages based on inferred lumbar lordosis (or lack thereof), and we recommend future research compare fossils to modern humans from varied populations and not just recent, postindustrial samples.}, }
@article {pmid36702939, year = {2023}, author = {Baquedano, E and Arsuaga, JL and Pérez-González, A and Laplana, C and Márquez, B and Huguet, R and Gómez-Soler, S and Villaescusa, L and Galindo-Pellicena, M&#xc1; and Rodríguez, L and García-González, R and Ortega, MC and Martín-Perea, DM and Ortega, AI and Hernández-Vivanco, L and Ruiz-Liso, G and Gómez-Hernanz, J and Alonso-Martín, JI and Abrunhosa, A and Moclán, A and Casado, AI and Vegara-Riquelme, M and Álvarez-Fernández, A and Domínguez-García, &#xc1;C and Álvarez-Lao, DJ and García, N and Sevilla, P and Blain, HA and Ruiz-Zapata, B and Gil-García, MJ and Álvarez-Vena, A and Sanz, T and Quam, R and Higham, T}, title = {A symbolic Neanderthal accumulation of large herbivore crania.}, journal = {Nature human behaviour}, volume = {7}, number = {3}, pages = {342-352}, pmid = {36702939}, issn = {2397-3374}, mesh = {Animals ; *Neanderthals ; Herbivory ; Skull ; Archaeology ; Spain ; Mammals ; }, abstract = {This work examines the possible behaviour of Neanderthal groups at the Cueva Des-Cubierta (central Spain) via the analysis of the latter's archaeological assemblage. Alongside evidence of Mousterian lithic industry, Level 3 of the cave infill was found to contain an assemblage of mammalian bone remains dominated by the crania of large ungulates, some associated with small hearths. The scarcity of post-cranial elements, teeth, mandibles and maxillae, along with evidence of anthropogenic modification of the crania (cut and percussion marks), indicates that the carcasses of the corresponding animals were initially processed outside the cave, and the crania were later brought inside. A second round of processing then took place, possibly related to the removal of the brain. The continued presence of crania throughout Level 3 indicates that this behaviour was recurrent during this level's formation. This behaviour seems to have no subsistence-related purpose but to be more symbolic in its intent.}, }
@article {pmid36691623, year = {2023}, author = {de March, CA and Matsunami, H and Abe, M and Cobb, M and Hoover, KC}, title = {Genetic and functional odorant receptor variation in the Homo lineage.}, journal = {iScience}, volume = {26}, number = {1}, pages = {105908}, pmid = {36691623}, issn = {2589-0042}, abstract = {Humans, Neanderthals, and Denisovans independently adapted to a wide range of geographic environments and their associated food odors. Using ancient DNA sequences, we explored the in vitro function of thirty odorant receptor genes in the genus Homo. Our extinct relatives had highly conserved olfactory receptor sequence, but humans did not. Variations in odorant receptor protein sequence and structure may have produced variation in odor detection and perception. Variants led to minimal changes in specificity but had more influence on functional sensitivity. The few Neanderthal variants disturbed function, whereas Denisovan variants increased sensitivity to sweet and sulfur odors. Geographic adaptations may have produced greater functional variation in our lineage, increasing our olfactory repertoire and expanding our adaptive capacity. Our survey of olfactory genes and odorant receptors suggests that our genus has a shared repertoire with possible local ecological adaptations.}, }
@article {pmid36681659, year = {2022}, author = {Zhou, Z and M A Swagemakers, S and S Lourens, M and Suratannon, N and J van der Spek, P and A S H Dalm, V and A Dik, W and IJspeert, H and van Hagen, PM}, title = {Did variants in inborn errors of immunity genes contribute to the extinction of Neanderthals?.}, journal = {Asian Pacific journal of allergy and immunology}, volume = {40}, number = {4}, pages = {422-434}, doi = {10.12932/AP-251022-1489}, pmid = {36681659}, issn = {0125-877X}, mesh = {Humans ; Animals ; *Neanderthals/genetics ; Genome ; Genome, Human ; Membrane Proteins/genetics ; }, abstract = {BACKGROUND: Neanderthals were a species of archaic humans that became extinct around 40,000 years ago. Modern humans have inherited 1-6% of Neanderthal DNA as a result of interbreeding. These inherited Neanderthal genes have paradoxical influences, while some can provide protection to viral infections, some others are associated with autoimmune/auto-inflammatory diseases.<br><br>OBJECTIVE: We aim to investigate whether genetic variants with strong detrimental effects on the function of the immune system could have potentially contributed to the extinction of the Neanderthal population.<br><br>METHODS: We used the publically available genome information from an Altai Neanderthal and filtered for potentially damaging variants present in genes associated with inborn errors of immunity (IEI) and checked whether these variants were present in the genomes of the Denisovan, Vindija and Chagyrskaya Neanderthals.<br><br>RESULTS: We identified 24 homozygous variants and 15 heterozygous variants in IEI-related genes in the Altai Neanderthal. Two homozygous variants in the UNC13D gene and one variant in the MOGS gene were present in all archaic genomes. Defects in the UNC13D gene are known to cause a severe and often fatal disease called hemophagocytic lymphohistiocystosis (HLH). One of these variants p.(N943S) has been reported in patients with HLH. Variants in MOGS are associated with glycosylation defects in the immune system affecting the susceptibility for infections.<br><br>CONCLUSIONS: Although the exact functional impact of these three variants needs further elucidation, we speculate that they could have resulted in an increased susceptibility to severe diseases and may have contributed to the extinction of Neanderthals after exposure to specific infections.}, }
@article {pmid36652426, year = {2023}, author = {Berlioz, E and Capdepon, E and Discamps, E}, title = {A long-term perspective on Neanderthal environment and subsistence: Insights from the dental microwear texture analysis of hunted ungulates at Combe-Grenal (Dordogne, France).}, journal = {PloS one}, volume = {18}, number = {1}, pages = {e0278395}, pmid = {36652426}, issn = {1932-6203}, mesh = {Animals ; Cattle ; *Neanderthals ; *Bison ; *Deer ; France ; Ecology ; Ruminants ; *Reindeer ; Fossils ; }, abstract = {Large bovids and cervids constituted major components of the European Middle Palaeolithic faunas and hence a key resource for Neanderthal populations. In paleoenvironmental reconstructions, red deer (Cervus elaphus) occurrence is classically considered as a tree-cover indicator while Bovinae (Bison priscus and Bos primigenius) and reindeer (Rangifer tarandus) occurrences are typically associated with open landscapes. However, insights into the ecology of extant ungulate populations show a more complex reality. Exploring the diet of past ungulates allows to better comprehend the hunting strategies of Palaeolithic populations and to reconstruct the modifications through time of past landscapes. By reflecting what animals have eaten during the last days or weeks of their life, dental microwear textures of herbivores link a population and its environment. Here we analyzed, via Dental Microwear Texture Analysis (DMTA), the diet of 50 Bos/Bison, 202 R. tarandus and 116 C. elaphus preyed upon by the Neanderthals that occupied Combe-Grenal rock-shelter, one of the most important Mousterian archaeo-sequences in southwestern France considering its long stratigraphy, abundance of faunal remains and the variations perceptible in Palaeolithic material culture. Grazers and mixed-feeders are the most represented dietary categories among Combe-Grenal's guild of herbivores, highlighting the availability, along the sequence, of open landscapes. The absence of clear changes in the use of plant resources by hunted ungulates through time, even though palaeoenvironmental changes were well-documented by previous studies along the sequence, is interpreted as resulting from the hunting of non-randomly selected prey by Neanderthals, preferentially in open environments. Thus, these results provide further insight into the hunting strategies of Neanderthals and modify our perception of potential links between subsistence and material culture. Combe-Grenal hunters "stayed in the open" through millennia, and were not forced to switch to hunting tactics and material technology adapted to close encounters in forested environments.}, }
@article {pmid36625544, year = {2023}, author = {Aqil, A and Speidel, L and Pavlidis, P and Gokcumen, O}, title = {Balancing selection on genomic deletion polymorphisms in humans.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {36625544}, issn = {2050-084X}, support = {220457/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Humans ; Genome-Wide Association Study ; *Hominidae/genetics ; Polymorphism, Genetic ; Genome ; Genomics ; *Neanderthals/genetics ; Selection, Genetic ; }, abstract = {A key question in biology is why genomic variation persists in a population for extended periods. Recent studies have identified examples of genomic deletions that have remained polymorphic in the human lineage for hundreds of millennia, ostensibly owing to balancing selection. Nevertheless, genome-wide investigation of ancient and possibly adaptive deletions remains an imperative exercise. Here, we demonstrate an excess of polymorphisms in present-day humans that predate the modern human-Neanderthal split (ancient polymorphisms), which cannot be explained solely by selectively neutral scenarios. We analyze the adaptive mechanisms that underlie this excess in deletion polymorphisms. Using a previously published measure of balancing selection, we show that this excess of ancient deletions is largely owing to balancing selection. Based on the absence of signatures of overdominance, we conclude that it is a rare mode of balancing selection among ancient deletions. Instead, more complex scenarios involving spatially and temporally variable selective pressures are likely more common mechanisms. Our results suggest that balancing selection resulted in ancient deletions harboring disproportionately more exonic variants with GWAS (genome-wide association studies) associations. We further found that ancient deletions are significantly enriched for traits related to metabolism and immunity. As a by-product of our analysis, we show that deletions are, on average, more deleterious than single nucleotide variants. We can now argue that not only is a vast majority of common variants shared among human populations, but a considerable portion of biologically relevant variants has been segregating among our ancestors for hundreds of thousands, if not millions, of years.}, }
@article {pmid39017102, year = {2023}, author = {Leonard, D}, title = {Quick Hits: Synchronizing chimpanzees in Zambia, a plankton-trapping ecosystem in the Maldives, Neandertal teeth from Spain, and much more in this month's Quick Hits.}, journal = {Scientific American}, volume = {328}, number = {1}, pages = {20}, doi = {10.1038/scientificamerican0123-20a}, pmid = {39017102}, issn = {0036-8733}, }
@article {pmid36576952, year = {2022}, author = {Peresani, M}, title = {Inspecting human evolution from a cave. Late Neanderthals and early sapiens at Grotta di Fumane: present state and outlook.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {100}, number = {}, pages = {71-107}, doi = {10.4436/JASS.10016}, pmid = {36576952}, issn = {2037-0644}, mesh = {Animals ; Humans ; *Neanderthals ; Fossils ; Europe ; *Hominidae ; Paleontology ; Archaeology ; }, abstract = {Of the many critical phases of human evolution, one of the most investigated is the transition from the Middle to the Upper Palaeolithic with the pivotal bio-cultural substitution of Neanderthals by Homo sapiens in Western Eurasia. The complexity of this over ten thousands years phase raises from the ensemble of evidence ascribed to the diverse adaptations expressed by Neanderthals and the first representatives of our species. In countless archaeological records Neanderthals left clear traces of a cultural variability dotted with innovations in the technology of stone and bone tools, alongside with manifestations in the range of the symbolic sphere. Together with other aspects of daily life, this evidence contributes shedding light on the cognitive aptitudes of those hominins and reassessing gaps in Pleistocene human diversities. Among archaeological contexts, the cave of Fumane in the Monti Lessini (Veneto Pre-Alps, northeastern Italy) is a key site. It is positioned along the potential trajectory of hominins moving into southern Europe from eastern and southeastern regions and includes a finely layered sedimentary sequence with cultural layers ascribed to the Mousterian, Uluzzian, Aurignacian and Gravettian. The ensemble constitutes one of the most complete, detailed and dated continental stratigraphic series from a segment of the late Pleistocene between 50 and 30 ka cal BP in a cave context of Southern Europe. Assessments based on sedimentological and palaeontological record provide indicators for framing Neanderthals in their respective ecological contexts since the late Middle Pleistocene until their demise during MIS3. On-going research is producing data ascribable to the human ecological relations and the interaction with specific natural resources, thus contributing to shed light on the complexity of Neanderthal behavior. Thanks to the high-resolution archaeological record of the earliest appearances of Homo sapiens, Fumane also provides clues to compare life, subsistence, and cultures between these Pleistocene hominins for comprehensive reasonings on our unicity.}, }
@article {pmid36564491, year = {2022}, author = {Bañuls-Cardona, S and Blasco, R and Rosell, J and Rufà, A and Vallverdú, J and Rivals, F}, title = {New quantitative method for dental wear analysis of small mammals.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {22231}, pmid = {36564491}, issn = {2045-2322}, mesh = {Animals ; Mice ; Fossils ; Mammals ; Molar ; *Neanderthals/anatomy &amp; histology ; *Tooth Wear ; }, abstract = {The application of dental wear study to murids has always been ruled out because of their omnivorous diet, which does not leave significant wear on the dentition. Nevertheless, in our work we select Apodemus sylvaticus (wood mouse) as the object of study for several reasons: its seasonal diet, its ability to resist the gastric juices of predators, the fact that it has not undergone major morphological changes since its appearance 3 million years ago, and its widespread distribution throughout much of Europe and part of Africa. The importance of this work lies in the modifications we make to the dental wear methodology for its application to murids. These enable us to obtain quantitative data on the entire tooth surface. The sample chosen was a total of 75 lower first molars from two different archaeological sites: Teixoneres cave and Xaragalls cave. The chronology of the samples chosen ranges from Marine Isotope Stages 5-3. The data obtained reveal that the part of the tooth that shows most wear is the distal part (entoconid). Furthermore, the results provide us with relevant information on the types of accumulations of remains in the caves (short vs. long term), as well as on the seasonality of Neanderthal occupations during the Upper Pleistocene (MIS5-3) of the northeastern Iberian Peninsula.}, }
@article {pmid36560850, year = {2023}, author = {Yermakovich, D and Pankratov, V and Võsa, U and Yunusbayev, B and ,  and Dannemann, M}, title = {Long-range regulatory effects of Neandertal DNA in modern humans.}, journal = {Genetics}, volume = {223}, number = {3}, pages = {}, pmid = {36560850}, issn = {1943-2631}, mesh = {Humans ; Animals ; *Neanderthals/genetics ; Gene Frequency ; Genome ; Phenotype ; DNA/genetics ; }, abstract = {The admixture between modern humans and Neandertals has resulted in ∼2% of the genomes of present-day non-Africans being composed of Neandertal DNA. Introgressed Neandertal DNA has been demonstrated to significantly affect the transcriptomic landscape in people today and via this molecular mechanism influence phenotype variation as well. However, little is known about how much of that regulatory impact is mediated through long-range regulatory effects that have been shown to explain ∼20% of expression variation. Here we identified 60 transcription factors (TFs) with their top cis-eQTL SNP in GTEx being of Neandertal ancestry and predicted long-range Neandertal DNA-induced regulatory effects by screening for the predicted target genes of those TFs. We show that the TFs form a significantly connected protein-protein interaction network. Among them are JUN and PRDM5, two brain-expressed TFs that have their predicted target genes enriched in regions devoid of Neandertal DNA. Archaic cis-eQTLs for the 60 TFs include multiple candidates for local adaptation, some of which show significant allele frequency increases over the last ∼10,000 years. A large proportion of the cis-eQTL-associated archaic SNPs have additional associations with various immune traits, schizophrenia, blood cell type composition and anthropometric measures. Finally, we demonstrate that our results are consistent with those of Neandertal DNA-associated empirical trans-eQTLs. Our results suggest that Neandertal DNA significantly influences regulatory networks, that its regulatory reach goes beyond the 40% of genomic sequence it still covers in present-day non-Africans and that via the investigated mechanism Neandertal DNA influences the phenotypic variation in people today.}, }
@article {pmid36511798, year = {2022}, author = {Stringer, C}, title = {The development of ideas about a recent African origin for Homo sapiens.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {100}, number = {}, pages = {5-18}, doi = {10.4436/JASS.10009}, pmid = {36511798}, issn = {2037-0644}, mesh = {Animals ; Humans ; Biological Evolution ; *Hominidae/genetics ; *Neanderthals/genetics ; Fossils ; France ; }, abstract = {In this contribution I will review the development of ideas about a recent African origin for our species over the last 50 years, starting from the time of my PhD in the early 1970s. I will examine the instructive and quite different interpretations placed on the 1979 discovery of a partial Neanderthal skeleton associated with a Châtelperronian industry at the rock shelter of St-Césaire in France, and then focus on the crucial years from 1987-1989, including the so-called 'Human Revolution' conference of 1987, and my 1988 Science paper with Peter Andrews: 'Genetic and Fossil Evidence for the Origin of Modern Humans'. Following the historical review, I will assess the status of five proposed models for the evolution of derived Homo sapiens: Recent African Origin (RAO); RAO and Hybridisation (RAOH); Assimilation (AM); Multiregional Evolution (MRE); and Braided Stream (BS). I conclude that a recent African origin model with hybridization (RAOH) is the best supported from the fossil and genetic evidence.}, }
@article {pmid36503519, year = {2022}, author = {Taravella Oill, AM and Buetow, KH and Wilson, MA}, title = {The role of Neanderthal introgression in liver cancer.}, journal = {BMC medical genomics}, volume = {15}, number = {1}, pages = {255}, pmid = {36503519}, issn = {1755-8794}, support = {R35 GM124827/GM/NIGMS NIH HHS/United States ; R35GM124827/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Animals ; *Neanderthals/genetics ; Haplotypes ; Alleles ; *Liver Neoplasms/genetics ; }, abstract = {BACKGROUND: Neanderthal introgressed DNA has been linked to different normal and disease traits including immunity and metabolism-two important functions that are altered in liver cancer. However, there is limited understanding of the relationship between Neanderthal introgression and liver cancer risk. The aim of this study was to investigate the relationship between Neanderthal introgression and liver cancer risk.<br><br>METHODS: Using germline and somatic DNA and tumor RNA from liver cancer patients from The Cancer Genome Atlas, along with ancestry-match germline DNA from unaffected individuals from the 1000 Genomes Resource, and allele specific expression data from normal liver tissue from The Genotype-Tissue Expression project we investigated whether Neanderthal introgression impacts cancer etiology. Using a previously generated set of Neanderthal alleles, we identified Neanderthal introgressed haplotypes. We then tested whether somatic mutations are enriched or depleted on Neanderthal introgressed haplotypes compared to modern haplotypes. We also computationally assessed whether somatic mutations have a functional effect or show evidence of regulating expression of Neanderthal haplotypes. Finally, we compared patterns of Neanderthal introgression in liver cancer patients and the general population.<br><br>RESULTS: We find Neanderthal introgressed haplotypes exhibit an excess of somatic mutations compared to modern haplotypes. Variant Effect Predictor analysis revealed that most of the somatic mutations on these Neanderthal introgressed haplotypes are not functional. We did observe expression differences of Neanderthal alleles between tumor and normal for four genes that also showed a pattern of enrichment of somatic mutations on Neanderthal haplotypes. However, gene expression was similar between liver cancer patients with modern ancestry and liver cancer patients with Neanderthal ancestry at these genes. Provocatively, when analyzing all genes, we find evidence of Neanderthal introgression regulating expression in tumor from liver cancer patients in two genes, ARK1C4 and OAS1. Finally, we find that most genes do not show a difference in the proportion of Neanderthal introgression between liver cancer patients and the general population.<br><br>CONCLUSION: Our results suggest that Neanderthal introgression provides opportunity for somatic mutations to accumulate, and that some Neanderthal introgression may impact liver cancer risk.}, }
@article {pmid36493597, year = {2023}, author = {Keeling, BA and Quam, R and Martínez, I and Arsuaga, JL and Maroto, J}, title = {Reassessment of the human mandible from Banyoles (Girona, Spain).}, journal = {Journal of human evolution}, volume = {174}, number = {}, pages = {103291}, doi = {10.1016/j.jhevol.2022.103291}, pmid = {36493597}, issn = {1095-8606}, mesh = {Animals ; Humans ; Spain ; Proteomics ; *Hominidae/anatomy &amp; histology ; Mandible/anatomy &amp; histology ; *Neanderthals/anatomy &amp; histology ; Fossils ; Biological Evolution ; }, abstract = {Since the discovery of a human mandible in 1887 near the present-day city of Banyoles, northeastern Spain, researchers have generally emphasized its archaic features, including the lack of chin structures, and suggested affinities with the Neandertals or European Middle Pleistocene (Chibanian) specimens. Uranium-series and electron spin resonance dating suggest the mandible dates to the Late Pleistocene (Tarantian), approximately ca. 45-66 ka. In this study, we reassessed the taxonomic affinities of the Banyoles mandible by comparing it to samples of Middle Pleistocene fossils from Africa and Europe, Neandertals, Early and Upper Paleolithic modern humans, and recent modern humans. We evaluated the frequencies and expressions of morphological features and performed a three-dimensional geometric morphometric analysis on a virtual reconstruction of Banyoles to capture overall mandibular shape. Our results revealed no derived Neandertal morphological features in Banyoles. While a principal component analysis based on Euclidean distances from the first two principal components clearly grouped Banyoles with both fossil and recent Homo sapiens individuals, an analysis of the Procrustes residuals demonstrated that Banyoles did not fit into any of the comparative groups. The lack of Neandertal features in Banyoles is surprising considering its Late Pleistocene age. A consideration of the Middle Pleistocene fossil record in Europe and southwest Asia suggests that Banyoles is unlikely to represent a late-surviving Middle Pleistocene population. The lack of chin structures also complicates an assignment to H. sapiens, although early fossil H. sapiens do show somewhat variable development of the chin structures. Thus, Banyoles represents a non-Neandertal Late Pleistocene European individual and highlights the continuing signal of diversity in the hominin fossil record. The present situation makes Banyoles a prime candidate for ancient DNA or proteomic analyses, which may shed additional light on its taxonomic affinities.}, }
@article {pmid36480515, year = {2022}, author = {Vespasiani, DM and Jacobs, GS and Cook, LE and Brucato, N and Leavesley, M and Kinipi, C and Ricaut, FX and Cox, MP and Gallego Romero, I}, title = {Denisovan introgression has shaped the immune system of present-day Papuans.}, journal = {PLoS genetics}, volume = {18}, number = {12}, pages = {e1010470}, pmid = {36480515}, issn = {1553-7404}, mesh = {Humans ; *Immune System ; *Hominidae/genetics ; *Neanderthals/genetics ; Papua New Guinea ; *Evolution, Molecular ; }, abstract = {Modern humans have admixed with multiple archaic hominins. Papuans, in particular, owe up to 5% of their genome to Denisovans, a sister group to Neanderthals whose remains have only been identified in Siberia and Tibet. Unfortunately, the biological and evolutionary significance of these introgression events remain poorly understood. Here we investigate the function of both Denisovan and Neanderthal alleles characterised within a set of 56 genomes from Papuan individuals. By comparing the distribution of archaic and non-archaic variants we assess the consequences of archaic admixture across a multitude of different cell types and functional elements. We observe an enrichment of archaic alleles within cis-regulatory elements and transcribed regions of the genome, with Denisovan variants strongly affecting elements active within immune-related cells. We identify 16,048 and 10,032 high-confidence Denisovan and Neanderthal variants that fall within annotated cis-regulatory elements and with the potential to alter the affinity of multiple transcription factors to their cognate DNA motifs, highlighting a likely mechanism by which introgressed DNA can impact phenotypes. Lastly, we experimentally validate these predictions by testing the regulatory potential of five Denisovan variants segregating within Papuan individuals, and find that two are associated with a significant reduction of transcriptional activity in plasmid reporter assays. Together, these data provide support for a widespread contribution of archaic DNA in shaping the present levels of modern human genetic diversity, with different archaic ancestries potentially affecting multiple phenotypic traits within non-Africans.}, }
@article {pmid36471017, year = {2023}, author = {Saraiva, LR}, title = {The Neanderthal inside us.}, journal = {Nature reviews. Genetics}, volume = {24}, number = {3}, pages = {142}, pmid = {36471017}, issn = {1471-0064}, mesh = {Animals ; *Neanderthals ; *Hominidae ; Biological Evolution ; Fossils ; }, }
@article {pmid36467077, year = {2022}, author = {Schäfer, W and Stähler, T and Pinto Espinoza, C and Danquah, W and Knop, JH and Rissiek, B and Haag, F and Koch-Nolte, F}, title = {Origin, distribution, and function of three frequent coding polymorphisms in the gene for the human P2X7 ion channel.}, journal = {Frontiers in pharmacology}, volume = {13}, number = {}, pages = {1033135}, pmid = {36467077}, issn = {1663-9812}, abstract = {P2X7, an ion channel gated by extracellular ATP, is widely expressed on the plasma membrane of immune cells and plays important roles in inflammation and apoptosis. Several single nucleotide polymorphisms have been identified in the human P2RX7 gene. In contrast to other members of the P2X family, non-synonymous polymorphisms in P2X7 are common. Three of these occur at overall frequencies of more than 25% and affect residues in the extracellular "head"-domain of P2X7 (155 Y/H), its "lower body" (270 R/H), and its "tail" in the second transmembrane domain (348 T/A). Comparison of the P2X7 orthologues of human and other great apes indicates that the ancestral allele is Y-R-T (at 155-270-348). Interestingly, each single amino acid variant displays lower ATP-sensitivity than the ancestral allele. The originally published reference sequence of human P2X7, often referred to as "wildtype," differs from the ancestral allele at all three positions, i.e. H-H-A. The 1,000 Genome Project determined the sequences of both alleles of 2,500 human individuals, including roughly 500 persons from each of the five major continental regions. This rich resource shows that the ancestral alleles Y155, R270, and T348 occur in all analyzed human populations, albeit at strikingly different frequencies in various subpopulations (e.g., 25%-59% for Y155, 59%-77% for R270, and 13%-47% for T348). BLAST analyses of ancient human genome sequences uncovered several homozygous carriers of variant P2X7 alleles, possibly reflecting a high degree of inbreeding, e.g., H-R-T for a 50.000 year old Neanderthal, H-R-A for a 24.000 year old Siberian, and Y-R-A for a 7,000 year old mesolithic European. In contrast, most present-day individuals co-express two copies of P2X7 that differ in one or more amino acids at positions 155, 270, and 348. Our results improve the understanding of how P2X7 structure affects its function and suggest the importance of considering P2X7 variants of participants when designing clinical trials targeting P2X7.}, }
@article {pmid36465121, year = {2022}, author = {Ma, X and Xu, S}, title = {Archaic introgression contributed to the pre-agriculture adaptation of vitamin B1 metabolism in East Asia.}, journal = {iScience}, volume = {25}, number = {12}, pages = {105614}, pmid = {36465121}, issn = {2589-0042}, abstract = {Thiamine (vitamin B1) is an essential micronutrient. Genes involved in thiamine metabolisms, such as SLC19A2, SLC35F3, and SLC35F4, were assumed to be underlying positive selection in East Asians, but the detailed mechanism remains unknown. Here, we analyzed genome data of 3,823 individuals representing 223 global populations and identified the adaptive haplotypes at thiamine genes. Interestingly, the putative adaptive haplotype at SLC35F4 was of Neanderthal ancestry, while that at SLC35F3 was also likely of archaic origins. Leveraging new methods and available ancient DNA data, we further demonstrated that the beneficial haplotypes reached a high frequency at least 10,000 years ago and are maintained persistently in present-day East Asians. We argue that pathogens, rather than agriculture developed ∼10,000 years ago in East Asia, were likely the initial driving force of the putative positive selection. Notably, the first American people did not carry the putative adaptive haplotype at SLC35F4.}, }
@article {pmid36455404, year = {2023}, author = {Velez, AD and Quam, R and Conde-Valverde, M and Martínez, I and Lorenzo, C and Arsuaga, JL}, title = {Geometric morphometric analysis of the bony labyrinth of the Sima de los Huesos hominins.}, journal = {Journal of human evolution}, volume = {174}, number = {}, pages = {103280}, doi = {10.1016/j.jhevol.2022.103280}, pmid = {36455404}, issn = {1095-8606}, mesh = {Animals ; Humans ; *Hominidae ; *Neanderthals ; Phylogeny ; *Ear, Inner ; Cochlea ; Fossils ; }, abstract = {The bony labyrinth contains phylogenetic information that can be used to determine interspecific differences between fossil hominins. The present study conducted a comparative 3D geometric morphometric analysis on the bony labyrinth of the Middle Pleistocene Sima de los Huesos (SH) hominins. The findings of this study corroborate previous multivariate analyses of the SH hominin bony labyrinth. The analysis of the semicircular canals revealed the SH hominin canal morphologies appear closer to those of the Neandertals than to those of Homo sapiens. This is attributable to a Neandertal-like ovoid anterior canal, and mediolaterally expanded, circular posterior canal. However, the SH hominins lack the increased torsion in the anterior canal and the inferior orientation of the lateral canal seen in Neandertals. The results of the cochlear analysis indicated that, although there is some overlap, there are notable differences between the SH hominins and the Neandertals. In particular, the SH hominin cochlea appears more constricted than in Neandertals in the first and second turns. A principal component analysis of the full bony labyrinth separated most SH hominins from the Neandertals, which largely clustered with modern humans. A covariance ratio analysis found a significant degree of modularity within the bony labyrinth of all three groups, with the SH hominins and Neandertals displaying the highest modularity. This modular signal in the bony labyrinth may be attributable to different selective pressures related to locomotion and audition. Overall, the results of this study confirm previous suggestions that the semicircular canals in the SH hominins are somewhat derived toward Neandertals, while their cochlea is largely primitive within the genus Homo.}, }
@article {pmid36455403, year = {2023}, author = {Britton, K and Jimenez, EL and Le Corre, M and Pederzani, S and Daujeard, C and Jaouen, K and Vettese, D and Tütken, T and Hublin, JJ and Moncel, MH}, title = {Multi-isotope zooarchaeological investigations at Abri du Maras: The paleoecological and paleoenvironmental context of Neanderthal subsistence strategies in the Rhône Valley during MIS 3.}, journal = {Journal of human evolution}, volume = {174}, number = {}, pages = {103292}, doi = {10.1016/j.jhevol.2022.103292}, pmid = {36455403}, issn = {1095-8606}, mesh = {Humans ; Animals ; Horses ; *Neanderthals ; *Deer ; *Reindeer ; *Bison ; *Hominidae ; Oxygen Isotopes/analysis ; Archaeology ; Fossils ; }, abstract = {The exploitation of mid- and large-sized herbivores (ungulates) was central to hominin subsistence across Late Pleistocene Europe. Reconstructing the paleoecology of prey-taxa is key to better understanding procurement strategies, decisions and behaviors, and the isotope analysis of faunal bones and teeth found at archaeological sites represent a powerful means of accessing information about past faunal behaviors. These isotope zooarchaeological approaches also have a near-unique ability to reveal environmental conditions contemporary to the human activities that produced these remains. Here, we present the results of a multi-isotope, multitissue study of ungulate remains from the Middle Paleolithic site of Abri du Maras, southern France, providing new insights into the living landscapes of the Rhône Valley during MIS 3 (level 4.2 = 55 ± 2 to 42 ± 3 ka; level 4.1 = 46 ± 3 to 40 ± 3 ka). Isotope data (carbon, nitrogen) reveal the dietary niches of different ungulate taxa, including the now-extinct giant deer (Megaloceros). Oxygen isotope data are consistent with a mild seasonal climate during level 4.2, where horse (Equus), bison (Bison), and red deer (Cervus elaphus) were exploited year-round. Strontium and sulfur isotope analyses provide new evidence for behavioral plasticity in Late Pleistocene European reindeer (Rangifer) between level 4.2 and level 4.1, indicating a change from the migratory to the sedentary ecotype. In level 4.1, the strong seasonal nature of reindeer exploitation, combined with their nonmigratory behavior, is consistent with a seasonally restricted use of the site by Neanderthals at that time or the preferential hunting of reindeer when in peak physical condition during the autumn.}, }
@article {pmid36423581, year = {2022}, author = {Mangan, RJ and Alsina, FC and Mosti, F and Sotelo-Fonseca, JE and Snellings, DA and Au, EH and Carvalho, J and Sathyan, L and Johnson, GD and Reddy, TE and Silver, DL and Lowe, CB}, title = {Adaptive sequence divergence forged new neurodevelopmental enhancers in humans.}, journal = {Cell}, volume = {185}, number = {24}, pages = {4587-4603.e23}, pmid = {36423581}, issn = {1097-4172}, support = {R01 NS083897/NS/NINDS NIH HHS/United States ; R01 NS110388/NS/NINDS NIH HHS/United States ; R35 HG011332/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Hominidae/genetics ; Regulatory Sequences, Nucleic Acid ; *Neanderthals/genetics ; Genome, Human ; Genomics ; }, abstract = {Searches for the genetic underpinnings of uniquely human traits have focused on human-specific divergence in conserved genomic regions, which reflects adaptive modifications of existing functional elements. However, the study of conserved regions excludes functional elements that descended from previously neutral regions. Here, we demonstrate that the fastest-evolved regions of the human genome, which we term "human ancestor quickly evolved regions" (HAQERs), rapidly diverged in an episodic burst of directional positive selection prior to the human-Neanderthal split, before transitioning to constraint within hominins. HAQERs are enriched for bivalent chromatin states, particularly in gastrointestinal and neurodevelopmental tissues, and genetic variants linked to neurodevelopmental disease. We developed a multiplex, single-cell in vivo enhancer assay to discover that rapid sequence divergence in HAQERs generated hominin-unique enhancers in the developing cerebral cortex. We propose that a lack of pleiotropic constraints and elevated mutation rates poised HAQERs for rapid adaptation and subsequent susceptibility to disease.}, }
@article {pmid36418334, year = {2022}, author = {Deschamps, M and Martín-Lerma, I and Linares-Matás, G and Zilhão, J}, title = {Organization of residential space, site function variability, and seasonality of activities among MIS 5 Iberian Neandertals.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {20221}, pmid = {36418334}, issn = {2045-2322}, mesh = {Animals ; *Neanderthals ; Archaeology ; Climate ; Seasons ; Anthropology, Cultural ; }, abstract = {Whether ethnoarcheological models of hunter-gatherer mobility, landscape use, and structuration of the inhabited space are relevant to the archeology of Neandertals and the Middle Paleolithic remains controversial. The thin lenses of hearth-associated stone tools and faunal remains excavated in sub-complex AS5 of Cueva Antón (Murcia, Spain) significantly advance these debates. Dated to 77.8-85.1 ka, these living floors are interstratified in river-accumulated sands and were buried shortly after abandonment by low-energy inundation events, with minimal disturbance and negligible palimpsest formation. Stone tools were made and ergonomically modified to fit tasks; their spatial distributions and use-wear reveal hearth-focused activities and a division of the inhabited space into resting and working areas. Site function varied with season of the year: units III-i/j1 and III-i/j2-3 record winter visits focused on filleting and hide processing, while woodworking predominated in unit III-b/d, which subsumes visits to the site over the course of at least one winter, one spring, and one summer. These snapshots of Neandertal behavior match expectations derived from the ethnographic and Upper Paleolithic records for the lifeways of hunter-gatherers inhabiting temperate regions with a markedly seasonal climate.}, }
@article {pmid36394417, year = {2023}, author = {Wielgus, K and Danielewski, M and Walkowiak, J}, title = {Svante Pääbo, reader of the Neanderthal genome.}, journal = {Acta physiologica (Oxford, England)}, volume = {237}, number = {1}, pages = {e13902}, pmid = {36394417}, issn = {1748-1716}, mesh = {Animals ; *Neanderthals/genetics ; Biological Evolution ; }, }
@article {pmid36345622, year = {2022}, author = {Tveito, K}, title = {From Icelandic family sagas to Neanderthal genes.}, journal = {Tidsskrift for den Norske laegeforening : tidsskrift for praktisk medicin, ny raekke}, volume = {142}, number = {16}, pages = {}, doi = {10.4045/tidsskr.22.0684}, pmid = {36345622}, issn = {0807-7096}, mesh = {Humans ; Animals ; *Neanderthals/genetics ; Iceland ; }, }
@article {pmid36344982, year = {2022}, author = {Koller, D and Wendt, FR and Pathak, GA and De Lillo, A and De Angelis, F and Cabrera-Mendoza, B and Tucci, S and Polimanti, R}, title = {Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {249}, pmid = {36344982}, issn = {1741-7007}, support = {MC_PC_17228/MRC_/Medical Research Council/United Kingdom ; R21 DC018098/DC/NIDCD NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; F32 MH122058/MH/NIMH NIH HHS/United States ; R33 DA047527/DA/NIDA NIH HHS/United States ; MC_QA137853/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; Animals ; *Neanderthals/genetics ; Multifactorial Inheritance ; Genome-Wide Association Study ; Genome, Human ; Asian People ; }, abstract = {BACKGROUND: Introgression from extinct Neanderthal and Denisovan human species has been shown to contribute to the genetic pool of modern human populations and their phenotypic spectrum. Evidence of how Neanderthal introgression shaped the genetics of human traits and diseases has been extensively studied in populations of European descent, with signatures of admixture reported for instance in genes associated with pigmentation, immunity, and metabolic traits. However, limited information is currently available about the impact of archaic introgression on other ancestry groups. Additionally, to date, no study has been conducted with respect to the impact of Denisovan introgression on the health and disease of modern populations. Here, we compare the way evolutionary pressures shaped the genetics of complex traits in East Asian and European populations, and provide evidence of the impact of Denisovan introgression on the health of East Asian and Central/South Asian populations.<br><br>RESULTS: Leveraging genome-wide association statistics from the Biobank Japan and UK Biobank, we assessed whether Denisovan and Neanderthal introgression together with other evolutionary genomic signatures were enriched for the heritability of physiological and pathological conditions in populations of East Asian and European descent. In EAS, Denisovan-introgressed loci were enriched for coronary artery disease heritability (1.69-fold enrichment, p=0.003). No enrichment for archaic introgression was observed in EUR. We also performed a phenome-wide association study of Denisovan and Neanderthal alleles in six ancestry groups available in the UK Biobank. In EAS, the Denisovan-introgressed SNP rs62391664 in the major histocompatibility complex region was associated with albumin/globulin ratio (beta=-0.17, p=3.57&#xd7;10[-7]). Neanderthal-introgressed alleles were associated with psychiatric and cognitive traits in EAS (e.g., "No Bipolar or Depression"-rs79043717 beta=-1.5, p=1.1&#xd7;10[-7]), and with blood biomarkers (e.g., alkaline phosphatase-rs11244089 beta=0.1, p=3.69&#xd7;10[-116]) and red hair color (rs60733936 beta=-0.86, p=4.49&#xd7;10[-165]) in EUR. In the other ancestry groups, Neanderthal alleles were associated with several traits, also including the use of certain medications (e.g., Central/South East Asia: indapamide - rs732632 beta=-2.38, p=5.22&#xd7;10[-7]).<br><br>CONCLUSIONS: Our study provides novel evidence regarding the impact of archaic introgression on the genetics of complex traits in worldwide populations, highlighting the specific contribution of Denisovan introgression in EAS populations.}, }
@article {pmid36336759, year = {2023}, author = {Richards, GD and Jabbour, RS and Guipert, G and Defleur, A}, title = {Endocranial anatomy of the Guercy 1 early Neanderthal from Baume Moula-Guercy (Soyons, Ardèche, France).}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {306}, number = {3}, pages = {564-593}, doi = {10.1002/ar.25118}, pmid = {36336759}, issn = {1932-8494}, mesh = {Adult ; Animals ; Humans ; *Neanderthals/anatomy &amp; histology ; *Hominidae/anatomy &amp; histology ; Skull/anatomy &amp; histology ; Brain ; France ; Fossils ; Biological Evolution ; }, abstract = {We provide the first comparative description of the endocranium of the Guercy 1 Early Neanderthal and examine its affinities to Preneanderthals, Neanderthals, and Homo sapiens. The Guercy 1 cranium derives from deposits chronostratigraphically and biostratigraphically dated to the Eemian Interglacial (MIS 5e). For comparative purposes, we compiled a sample of European and Southwest Asian subadult and adult Middle-to-Late Pleistocene hominins (≈MIS 12-MIS 1; N = 65). We sampled both a Preneanderthal-Neanderthal group and a Homo sapiens group. The Preneanderthal-Neanderthal group was further divided into three time-successive subgroups defined by associated MIS stages. Metric and morphological observations were made on original fossils and physical and virtual endocranial reconstructions. Guercy 1 and other Early Neanderthals, differ from Preneanderthals by increased development of the prefrontal cortex, precentral and postcentral gyri, inferior parietal lobule, and frontoparietal operculum. Early Neanderthal differ, in general, from Late Neanderthals by exhibiting less development in most of the latter brain structures. The late group additionally differentiates itself from the early group by a greater development of the rostral superior parietal lobule, angular gyrus, superior and middle temporal gyri, and caudal branches of the superior temporal gyrus. Endocranial morphology assessed along the Preneanderthal-Neanderthal sequence show that brain structures prominent in Preneanderthals are accentuated in Early-to-Late Neanderthals. However, both the Early and Late groups differentiate themselves by also showing regionally specific changes in brain development. This pattern of morphological change is consistent with a mosaic pattern of neural evolution in these Middle-to-Late Pleistocene hominins.}, }
@article {pmid36323899, year = {2022}, author = {Graham, F}, title = {Daily briefing: First known Neanderthal family discovered.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41586-022-03378-0}, pmid = {36323899}, issn = {1476-4687}, }
@article {pmid36322514, year = {2022}, author = {Campelo Dos Santos, AL and Owings, A and Sullasi, HSL and Gokcumen, O and DeGiorgio, M and Lindo, J}, title = {Genomic evidence for ancient human migration routes along South America's Atlantic coast.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1986}, pages = {20221078}, pmid = {36322514}, issn = {1471-2954}, support = {R35 GM128590/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; History, Ancient ; Animals ; *Human Migration ; Genomics ; Genome, Human ; *Neanderthals ; Brazil ; }, abstract = {An increasing body of archaeological and genomic evidence has hinted at a complex settlement process of the Americas by humans. This is especially true for South America, where unexpected ancestral signals have raised perplexing scenarios for the early migrations into different regions of the continent. Here, we present ancient human genomes from the archaeologically rich Northeast Brazil and compare them to ancient and present-day genomic data. We find a distinct relationship between ancient genomes from Northeast Brazil, Lagoa Santa, Uruguay and Panama, representing evidence for ancient migration routes along South America's Atlantic coast. To further add to the existing complexity, we also detect greater Denisovan than Neanderthal ancestry in ancient Uruguay and Panama individuals. Moreover, we find a strong Australasian signal in an ancient genome from Panama. This work sheds light on the deep demographic history of eastern South America and presents a starting point for future fine-scale investigations on the regional level.}, }
@article {pmid36313404, year = {2022}, author = {Mortazavi, SA and Bevelacqua, JJ and Welsh, JS and Masoumi, SJ and Bahaaddini Beigy Zarandi, BF and Ghadimi-Moghadam, A and Haghani, M and Mortazavi, SMJ}, title = {The Paradox of COVID-19 in Sub-Saharan Africa: Why it is More Unethical Not to Investigate Low Dose Radiotherapy for COVID-19.}, journal = {Journal of biomedical physics &amp; engineering}, volume = {12}, number = {5}, pages = {539-542}, pmid = {36313404}, issn = {2251-7200}, abstract = {An accumulating body of evidence shows that various ethnicities are differentially affected by SARS-COV-2 infection. Moreover, some evidence shows that due to the vaccine inequity and millions of people living with HIV, a major catastrophe could occur in African countries that possibly affects the whole world. Given the possibility that Neanderthal genes confer a slight increase in susceptibility, this difference, at least to some extent, might possibly decrease the risk of the emergence of new SARS-CoV-2 variants among black people in Africa. Recent studies show less death and fewer cases among the ethnic group classified as "Black Africans". Although Neanderthal DNA might explain some differences in morbidity and mortality of COVID-19, a multitude of confounders complicate things to where drawing definite conclusions is hard or even impossible. Using selective-pressure-free treatments (e.g. low dose radiotherapy) for COVID-19 pneumonia would be of crucial importance everywhere, but particularly in sub-Saharan Africa, where "long COVID" in millions of people with HIV paves the road for the more frequent emergence of new variants.}, }
@article {pmid36261727, year = {2022}, author = {Callaway, E}, title = {First known Neanderthal family discovered in Siberian cave.}, journal = {Nature}, volume = {610}, number = {7933}, pages = {615-616}, pmid = {36261727}, issn = {1476-4687}, mesh = {Animals ; *Caves ; *Fossils ; *Neanderthals/genetics ; History, Ancient ; }, }
@article {pmid36261548, year = {2022}, author = {Skov, L and Peyrégne, S and Popli, D and Iasi, LNM and Devièse, T and Slon, V and Zavala, EI and Hajdinjak, M and Sümer, AP and Grote, S and Bossoms Mesa, A and López Herráez, D and Nickel, B and Nagel, S and Richter, J and Essel, E and Gansauge, M and Schmidt, A and Korlević, P and Comeskey, D and Derevianko, AP and Kharevich, A and Markin, SV and Talamo, S and Douka, K and Krajcarz, MT and Roberts, RG and Higham, T and Viola, B and Krivoshapkin, AI and Kolobova, KA and Kelso, J and Meyer, M and Pääbo, S and Peter, BM}, title = {Genetic insights into the social organization of Neanderthals.}, journal = {Nature}, volume = {610}, number = {7932}, pages = {519-525}, pmid = {36261548}, issn = {1476-4687}, support = {803147/ERC_/European Research Council/International ; 715069/ERC_/European Research Council/International ; FP7/2007-2013/ERC_/European Research Council/International ; 694707/ERC_/European Research Council/International ; }, mesh = {Animals ; Female ; Humans ; Caves ; Genome/genetics ; Hybridization, Genetic ; *Neanderthals/genetics ; Siberia ; DNA, Mitochondrial/genetics ; Y Chromosome/genetics ; Male ; Family ; Homozygote ; }, abstract = {Genomic analyses of Neanderthals have previously provided insights into their population history and relationship to modern humans[1-8], but the social organization of Neanderthal communities remains poorly understood. Here we present genetic data for 13 Neanderthals from two Middle Palaeolithic sites in the Altai Mountains of southern Siberia: 11 from Chagyrskaya Cave[9,10] and 2 from Okladnikov Cave[11]-making this one of the largest genetic studies of a Neanderthal population to date. We used hybridization capture to obtain genome-wide nuclear data, as well as mitochondrial and Y-chromosome sequences. Some Chagyrskaya individuals were closely related, including a father-daughter pair and a pair of second-degree relatives, indicating that at least some of the individuals lived at the same time. Up to one-third of these individuals' genomes had long segments of homozygosity, suggesting that the Chagyrskaya Neanderthals were part of a small community. In addition, the Y-chromosome diversity is an order of magnitude lower than the mitochondrial diversity, a pattern that we found is best explained by female migration between communities. Thus, the genetic data presented here provide a detailed documentation of the social organization of an isolated Neanderthal community at the easternmost extent of their known range.}, }
@article {pmid36261544, year = {2022}, author = {Cassidy, LM}, title = {The first genomic portrait of a Neanderthal family.}, journal = {Nature}, volume = {610}, number = {7932}, pages = {454-455}, pmid = {36261544}, issn = {1476-4687}, mesh = {Animals ; *Neanderthals/genetics ; Genome/genetics ; Genomics ; }, }
@article {pmid36261474, year = {2022}, author = {Mayoral, E and Duveau, J and Santos, A and Ramírez, AR and Morales, JA and Díaz-Delgado, R and Rivera-Silva, J and Gómez-Olivencia, A and Díaz-Martínez, I}, title = {New dating of the Matalascañas footprints provides new evidence of the Middle Pleistocene (MIS 9-8) hominin paleoecology in southern Europe.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {17505}, pmid = {36261474}, issn = {2045-2322}, mesh = {Animals ; Humans ; *Hominidae ; Fossils ; *Neanderthals ; Europe ; Luminescence ; }, abstract = {Hominin footprints were recently discovered at Matalascañas (Huelva; South of Iberian Peninsula). They were dated thanks to a previous study in deposits of the Asperillo cliff to 106 ± 19 ka, Upper Pleistocene, making Neandertals the most likely track-makers. In this paper, we report new Optically Stimulated Luminescence dating that places the hominin footprints surface in the range of 295.8 ± 17 ka (MIS 9-MIS 8 transition, Middle Pleistocene). This new age implies that the possible track-makers are individuals more likely from the Neandertal evolutionary lineage. Regardless of the taxon attributed to the Matalascañas footprints, they supplement the existing partial fossil record for the European Middle Pleistocene Hominins being notably the first palaeoanthropological evidence (hominin skeleton or footprints) from the MIS 9 and MIS 8 transition discovered in the Iberian Peninsula, a moment of climatic evolution from warm to cool. Thus, the Matalascañas footprints represent a crucial record for understanding human occupations in Europe in the Pleistocene.}, }
@article {pmid36253794, year = {2022}, author = {Bergman, J and Schierup, MH}, title = {Evolutionary dynamics of pseudoautosomal region 1 in humans and great apes.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {215}, pmid = {36253794}, issn = {1474-760X}, mesh = {Animals ; Female ; *Hominidae/genetics ; Humans ; Male ; Nucleotides ; *Pseudoautosomal Regions ; Receptor, PAR-1/genetics ; Y Chromosome/genetics ; }, abstract = {BACKGROUND: The pseudoautosomal region 1 (PAR1) is a 2.7 Mb telomeric region of human sex chromosomes. PAR1 has a crucial role in ensuring proper segregation of sex chromosomes during male meiosis, exposing it to extreme recombination and mutation processes. We investigate PAR1 evolution using population genomic datasets of extant humans, eight populations of great apes, and two archaic human genome sequences.<br><br>RESULTS: We find that PAR1 is fast evolving and closer to evolutionary nucleotide equilibrium than autosomal telomeres. We detect a difference between substitution patterns and extant diversity in PAR1, mainly driven by the conflict between strong mutation and recombination-associated fixation bias at CpG sites. We detect excess C-to-G mutations in PAR1 of all great apes, specific to the mutagenic effect of male recombination. Despite recent evidence for Y chromosome introgression from humans into Neanderthals, we find that the Neanderthal PAR1 retained similarity to the Denisovan sequence. We find differences between substitution spectra of these archaics suggesting rapid evolution of PAR1 in recent hominin history. Frequency analysis of alleles segregating in females and males provided no evidence for recent sexual antagonism in this region. We study repeat content and double-strand break hotspot regions in PAR1 and find that they may play roles in ensuring the obligate X-Y recombination event during male meiosis.<br><br>CONCLUSIONS: Our study provides an unprecedented quantification of population genetic forces governing PAR1 biology across extant and extinct hominids. PAR1 evolutionary dynamics are predominantly governed by recombination processes with a strong impact on mutation patterns across all species.}, }
@article {pmid36252021, year = {2022}, author = {Jaouen, K and Villalba-Mouco, V and Smith, GM and Trost, M and Leichliter, J and Lüdecke, T and Méjean, P and Mandrou, S and Chmeleff, J and Guiserix, D and Bourgon, N and Blasco, F and Mendes Cardoso, J and Duquenoy, C and Moubtahij, Z and Salazar Garcia, DC and Richards, M and Tütken, T and Hublin, JJ and Utrilla, P and Montes, L}, title = {A Neandertal dietary conundrum: Insights provided by tooth enamel Zn isotopes from Gabasa, Spain.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {43}, pages = {e2109315119}, pmid = {36252021}, issn = {1091-6490}, mesh = {Animals ; Carbon/analysis ; Carbon Isotopes/analysis ; *Carnivora ; Collagen ; Dental Enamel/chemistry ; Diet ; *Neanderthals ; Nitrogen Isotopes/analysis ; Oxygen/analysis ; Spain ; Strontium/analysis ; *Tooth/chemistry ; *Trace Elements/analysis ; Zinc/analysis ; Zinc Isotopes/analysis ; }, abstract = {The characterization of Neandertals' diets has mostly relied on nitrogen isotope analyses of bone and tooth collagen. However, few nitrogen isotope data have been recovered from bones or teeth from Iberia due to poor collagen preservation at Paleolithic sites in the region. Zinc isotopes have been shown to be a reliable method for reconstructing trophic levels in the absence of organic matter preservation. Here, we present the results of zinc (Zn), strontium (Sr), carbon (C), and oxygen (O) isotope and trace element ratio analysis measured in dental enamel on a Pleistocene food web in Gabasa, Spain, to characterize the diet and ecology of a Middle Paleolithic Neandertal individual. Based on the extremely low δ[66]Zn value observed in the Neandertal's tooth enamel, our results support the interpretation of Neandertals as carnivores as already suggested by δ[15]N isotope values of specimens from other regions. Further work could help identify if such isotopic peculiarities (lowest δ[66]Zn and highest δ[15]N of the food web) are due to a metabolic and/or dietary specificity of the Neandertals.}, }
@article {pmid36229473, year = {2022}, author = {Djakovic, I and Key, A and Soressi, M}, title = {Optimal linear estimation models predict 1400-2900 years of overlap between Homo sapiens and Neandertals prior to their disappearance from France and northern Spain.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {15000}, pmid = {36229473}, issn = {2045-2322}, mesh = {Animals ; Bayes Theorem ; Fossils ; France ; *Hominidae ; Humans ; *Neanderthals ; Spain ; }, abstract = {Recent fossil discoveries suggest that Neandertals and Homo sapiens may have co-existed in Europe for as long as 5 to 6000 years. Yet, evidence for their contemporaneity at any regional scale remains highly elusive. In France and northern Spain, a region which features some of the latest directly-dated Neandertals in Europe, Protoaurignacian assemblages attributed to Homo sapiens appear to 'replace' Neandertal-associated Châtelperronian assemblages. Using the earliest and latest known occurrences as starting points, Bayesian modelling has provided indication that these occupations may in fact have been partly contemporaneous. The reality, however, is that we are unlikely to ever identify the 'first' or 'last' appearance of a species or cultural tradition in the archaeological and fossil record. Here, we use optimal linear estimation modelling to estimate the first appearance date of Homo sapiens and the extinction date of Neandertals in France and northern Spain by statistically inferring these 'missing' portions of the Protoaurignacian and Châtelperronian archaeological records. Additionally, we estimate the extinction date of Neandertals in this region using a dataset of directly-dated Neandertal fossil remains. Our total dataset consists of sixty-six modernly produced radiocarbon determinations which we recalibrated using the newest calibration curve (IntCal20) to produce updated age ranges. The results suggest that the onset of the Homo sapiens occupation of this region likely preceded the extinction of Neandertals and the Châtelperronian by up to 1400-2900 years. This reaffirms the Bayesian-derived duration of co-existence between these groups during the initial Upper Palaeolithic of this region using a novel independent method, and indicates that our understanding of the timing of these occupations may not be suffering from substantial gaps in the record. Whether or not this co-existence featured some form of direct interaction, however, remains to be resolved.}, }
@article {pmid36207518, year = {2022}, author = {Callaway, E}, title = {From Neanderthal genome to Nobel prize: meet geneticist Svante Pääbo.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {36207518}, issn = {1476-4687}, }
@article {pmid36198681, year = {2022}, author = {Dannemann, M and Milaneschi, Y and Yermakovich, D and Stiglbauer, V and Kariis, HM and Krebs, K and Friese, MA and Otte, C and ,  and Lehto, K and Penninx, BWJH and Kelso, J and Gold, SM}, title = {Neandertal introgression partitions the genetic landscape of neuropsychiatric disorders and associated behavioral phenotypes.}, journal = {Translational psychiatry}, volume = {12}, number = {1}, pages = {433}, pmid = {36198681}, issn = {2158-3188}, support = {MC_PC_17228/MRC_/Medical Research Council/United Kingdom ; MC_QA137853/MRC_/Medical Research Council/United Kingdom ; RC2 MH089951/MH/NIMH NIH HHS/United States ; RC2 MH089995/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; Genetic Variation ; Genome ; Haplotypes ; Humans ; *Neanderthals/genetics ; Phenotype ; }, abstract = {Despite advances in identifying the genetic basis of psychiatric and neurological disorders, fundamental questions about their evolutionary origins remain elusive. Here, introgressed variants from archaic humans such as Neandertals can serve as an intriguing research paradigm. We compared the number of associations for Neandertal variants to the number of associations of frequency-matched non-archaic variants with regard to human CNS disorders (neurological and psychiatric), nervous system drug prescriptions (as a proxy for disease), and related, non-disease phenotypes in the UK biobank (UKBB). While no enrichment for Neandertal genetic variants were observed in the UKBB for psychiatric or neurological disease categories, we found significant associations with certain behavioral phenotypes including pain, chronotype/sleep, smoking and alcohol consumption. In some instances, the enrichment signal was driven by Neandertal variants that represented the strongest association genome-wide. SNPs within a Neandertal haplotype that was associated with smoking in the UKBB could be replicated in four independent genomics datasets.Our data suggest that evolutionary processes in recent human evolution like admixture with Neandertals significantly contribute to behavioral phenotypes but not psychiatric and neurological diseases. These findings help to link genetic variants in a population to putative past beneficial effects, which likely only indirectly contribute to pathology in modern day humans.}, }
@article {pmid36181428, year = {2022}, author = {Huang, X and Kruisz, P and Kuhlwilm, M}, title = {sstar: A Python Package for Detecting Archaic Introgression from Population Genetic Data with S.}, journal = {Molecular biology and evolution}, volume = {39}, number = {11}, pages = {}, pmid = {36181428}, issn = {1537-1719}, mesh = {Humans ; Animals ; *Genome, Human ; *Neanderthals/genetics ; Genetics, Population ; }, abstract = {S* is a widely used statistic for detecting archaic admixture from population genetic data. Previous studies used freezing-archer to apply S*, which is only directly applicable to the specific case of Neanderthal and Denisovan introgression in Papuans. Here, we implemented sstar for a more general purpose. Compared with several tools, including SPrime, SkovHMM, and ArchaicSeeker2.0, for detecting introgressed fragments with simulations, our results suggest that sstar is robust to differences in demographic models, including ghost introgression and two-source introgression. We believe sstar will be a useful tool for detecting introgressed fragments in various scenarios and in non-human species.}, }
@article {pmid36175541, year = {2022}, author = {Vidal-Cordasco, M and Ocio, D and Hickler, T and Marín-Arroyo, AB}, title = {Ecosystem productivity affected the spatiotemporal disappearance of Neanderthals in Iberia.}, journal = {Nature ecology &amp; evolution}, volume = {6}, number = {11}, pages = {1644-1657}, pmid = {36175541}, issn = {2397-334X}, mesh = {Humans ; Animals ; *Neanderthals ; Ecosystem ; Bayes Theorem ; }, abstract = {What role did fluctuations play in biomass availability for secondary consumers in the disappearance of Neanderthals and the survival of modern humans? To answer this, we quantify the effects of stadial and interstadial conditions on ecosystem productivity and human spatiotemporal distribution patterns during the Middle to Upper Palaeolithic transition (50,000-30,000 calibrated years before the present) in Iberia. First, we used summed probability distribution, optimal linear estimation and Bayesian age modelling to reconstruct an updated timescale for the transition. Next, we executed a generalized dynamic vegetation model to estimate the net primary productivity. Finally, we developed a macroecological model validated with present-day observations to calculate herbivore abundance. The results indicate that, in the Eurosiberian region, the disappearance of Neanderthal groups was contemporaneous with a significant decrease in the available biomass for secondary consumers, and the arrival of the first Homo sapiens populations coincided with an increase in herbivore carrying capacity. During stadials, the Mediterranean region had the most stable conditions and the highest biomass of medium and medium-large herbivores. These outcomes support an ecological cause for the hiatus between the Mousterian and Aurignacian technocomplexes in Northern Iberia and the longer persistence of Neanderthals in southern latitudes.}, }
@article {pmid36167050, year = {2022}, author = {Reilly, PF and Tjahjadi, A and Miller, SL and Akey, JM and Tucci, S}, title = {The contribution of Neanderthal introgression to modern human traits.}, journal = {Current biology : CB}, volume = {32}, number = {18}, pages = {R970-R983}, pmid = {36167050}, issn = {1879-0445}, support = {R01 GM110068/GM/NIGMS NIH HHS/United States ; R35 GM147565/GM/NIGMS NIH HHS/United States ; }, mesh = {Africa ; Alleles ; Animals ; Biological Evolution ; Genome, Human ; Humans ; *Neanderthals/genetics ; }, abstract = {Neanderthals, our closest extinct relatives, lived in western Eurasia from 400,000 years ago until they went extinct around 40,000 years ago. DNA retrieved from ancient specimens revealed that Neanderthals mated with modern human contemporaries. As a consequence, introgressed Neanderthal DNA survives scattered across the human genome such that 1-4% of the genome of present-day people outside Africa are inherited from Neanderthal ancestors. Patterns of Neanderthal introgressed genomic sequences suggest that Neanderthal alleles had distinct fates in the modern human genetic background. Some Neanderthal alleles facilitated human adaptation to new environments such as novel climate conditions, UV exposure levels and pathogens, while others had deleterious consequences. Here, we review the body of work on Neanderthal introgression over the past decade. We describe how evolutionary forces shaped the genomic landscape of Neanderthal introgression and highlight the impact of introgressed alleles on human biology and phenotypic variation.}, }
@article {pmid36162354, year = {2022}, author = {Lockey, AL and Rodríguez, L and Martín-Francés, L and Arsuaga, JL and Bermúdez de Castro, JM and Crété, L and Martinón-Torres, M and Parfitt, S and Pope, M and Stringer, C}, title = {Comparing the Boxgrove and Atapuerca (Sima de los Huesos) human fossils: Do they represent distinct paleodemes?.}, journal = {Journal of human evolution}, volume = {172}, number = {}, pages = {103253}, doi = {10.1016/j.jhevol.2022.103253}, pmid = {36162354}, issn = {1095-8606}, mesh = {Animals ; Adult ; Humans ; Fossils ; Cross-Sectional Studies ; *Hominidae/anatomy &amp; histology ; *Neanderthals/anatomy &amp; histology ; Tibia/anatomy &amp; histology ; Spain ; }, abstract = {The early Middle Pleistocene human material from Boxgrove (West Sussex, UK) consists of a partial left tibia and two lower incisors from a separate adult individual. These remains derive from deposits assigned to the MIS 13 interglacial at about 480 ka and have been referred to as Homo cf. heidelbergensis. The much larger skeletal sample from the Sima de los Huesos (Atapuerca, Spain) is dated to the succeeding MIS 12, at about 430 ka. This fossil material has previously been assigned to Homo heidelbergensis but is now placed within the Neanderthal clade. Because of the scarcity of human remains from the Middle Pleistocene and their morphological variability, this study assessed whether the Boxgrove specimens fit within the morphological variability of the homogeneous Sima de los Huesos population. Based on morphometric analyses performed against 22 lower incisors from Sima de los Huesos and published material, the data from the Boxgrove incisors place them comfortably within the range of Sima de los Huesos. Both assemblages present robust incisors distinct from the overall small recent Homo sapiens incisors, and Boxgrove also aligns closely with Homo neanderthalensis and some other European Middle Pleistocene hominins. Following morphological and cross-sectional analyses of the Boxgrove tibia compared to seven adult Sima de los Huesos specimens and a set of comparative tibiae, Boxgrove is shown to be similar to Sima de los Huesos and Neanderthals in having thick cortices and bone walls, but in contrast resembles modern humans in having a straight anterior tibial crest and a suggestion of a lateral concavity. Based on the patterns observed, there is no justification for assigning the Boxgrove and Sima de los Huesos incisors to distinct paleodemes, but the tibial data show greater contrasts and suggest that all three of these samples are unlikely to represent the same paleodeme.}, }
@article {pmid36161899, year = {2022}, author = {Alagöz, G and Molz, B and Eising, E and Schijven, D and Francks, C and Stein, JL and Fisher, SE}, title = {Using neuroimaging genomics to investigate the evolution of human brain structure.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {40}, pages = {e2200638119}, pmid = {36161899}, issn = {1091-6490}, support = {MC_PC_17228/MRC_/Medical Research Council/United Kingdom ; MC_QA137853/MRC_/Medical Research Council/United Kingdom ; R01 DC016977/DC/NIDCD NIH HHS/United States ; }, mesh = {*Biological Evolution ; *Brain/growth &amp; development/ultrastructure ; DNA, Ancient ; *Genomics/methods ; Humans ; *Neuroimaging/methods ; *Polymorphism, Single Nucleotide ; }, abstract = {Alterations in brain size and organization represent some of the most distinctive changes in the emergence of our species. Yet, there is limited understanding of how genetic factors contributed to altered neuroanatomy during human evolution. Here, we analyze neuroimaging and genetic data from up to 30,000 people in the UK Biobank and integrate with genomic annotations for different aspects of human evolution, including those based on ancient DNA and comparative genomics. We show that previously reported signals of recent polygenic selection for cortical anatomy are not replicable in a more ancestrally homogeneous sample. We then investigate relationships between evolutionary annotations and common genetic variants shaping cortical surface area and white-matter connectivity for each hemisphere. Our analyses identify single-nucleotide polymorphism heritability enrichment in human-gained regulatory elements that are active in early brain development, affecting surface areas of several parts of the cortex, including left-hemispheric speech-associated regions. We also detect heritability depletion in genomic regions with Neanderthal ancestry for connectivity of the uncinate fasciculus; this is a white-matter tract involved in memory, language, and socioemotional processing with relevance to neuropsychiatric disorders. Finally, we show that common genetic loci associated with left-hemispheric pars triangularis surface area overlap with a human-gained enhancer and affect regulation of ZIC4, a gene implicated in neurogenesis. This work demonstrates how genomic investigations of present-day neuroanatomical variation can help shed light on the complexities of our evolutionary past.}, }
@article {pmid36151242, year = {2022}, author = {Sossa-Ríos, S and Mayor, A and Hernández, CM and Bencomo, M and Pérez, L and Galván, B and Mallol, C and Vaquero, M}, title = {Multidisciplinary evidence of an isolated Neanderthal occupation in Abric del Pastor (Alcoi, Iberian Peninsula).}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {15883}, pmid = {36151242}, issn = {2045-2322}, mesh = {Animals ; Archaeology ; Clergy ; Fossils ; Humans ; *Neanderthals ; Occupations ; *Starlings ; }, abstract = {Testing Neanderthal behavioural hypotheses requires a spatial-temporal resolution to the level of a human single occupation episode. Yet, most of the behavioural data on Neanderthals has been obtained from coarsely dated, time-averaged contexts affected by the archaeological palimpsest effect and a diversity of postdepositional processes. This implies that time-resolved Neanderthal behaviour remains largely unknown. In this study, we performed archaeostratigraphic analysis on stratigraphic units IVe, IVf, IVg, Va, Vb and Vc from Abric del Pastor (Alcoi, Iberian Peninsula). Further, we isolated the archaeological remains associated with the resulting archaeostratigraphic unit and applied raw material, technological, use-wear, archaeozoological and spatial analyses. Our results show a low-density accumulation of remains from flintknapping, flint tool-use and animal processing around a hearth. These data provide a time-resolved human dimension to previous high-resolution environmental and pyrotechnological data on the same hearth, representing the first comprehensive characterisation of a Neanderthal single occupation episode. Our integrated, multidisciplinary method also contributes to advance our understanding of archaeological record formation processes.}, }
@article {pmid36138831, year = {2022}, author = {Garralda, MD and Weiner, S and Arensburg, B and Maureille, B and Vandermeersch, B}, title = {Dental Paleobiology in a Juvenile Neanderthal (Combe-Grenal, Southwestern France).}, journal = {Biology}, volume = {11}, number = {9}, pages = {}, pmid = {36138831}, issn = {2079-7737}, support = {00//Ministerio de Educaci&#xf3;n y Ciencia, Spain/ ; }, abstract = {Combe-Grenal site (Southwest France) was excavated by F. Bordes between 1953 and 1965. He found several human remains in Mousterian levels 60, 39, 35 and especially 25, corresponding to MIS 4 (~75-70/60 ky BP) and with Quina Mousterian lithics. One of the fossils found in level 25 is Combe-Grenal IV, consisting of a fragment of the left corpus of a juvenile mandible. This fragment displays initial juvenile periodontitis, and the two preserved teeth (LLP4 and LLM1) show moderate attrition and dental calculus. The SEM tartar analysis demonstrates the presence of cocci and filamentous types of bacteria, the former being more prevalent. This result is quite different from those obtained for the two adult Neanderthals Kebara 2 and Subalyuk 1, where more filamentous bacteria appear, especially in the Subalyuk 1 sample from Central Europe. These findings agree with the available biomedical data on periodontitis and tartar development in extant individuals, despite the different environmental conditions and diets documented by numerous archeological, taphonomical and geological data available on Neanderthals and present-day populations. New metagenomic analyses are extending this information, and despite the inherent difficulties, they will open important perspectives in studying this ancient human pathology.}, }
@article {pmid36074851, year = {2022}, author = {Pinson, A and Xing, L and Namba, T and Kalebic, N and Peters, J and Oegema, CE and Traikov, S and Reppe, K and Riesenberg, S and Maricic, T and Derihaci, R and Wimberger, P and Pääbo, S and Huttner, WB}, title = {Human TKTL1 implies greater neurogenesis in frontal neocortex of modern humans than Neanderthals.}, journal = {Science (New York, N.Y.)}, volume = {377}, number = {6611}, pages = {eabl6422}, doi = {10.1126/science.abl6422}, pmid = {36074851}, issn = {1095-9203}, support = {MR/N004272/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Ependymoglial Cells/cytology ; Ferrets ; Humans ; Mice ; *Neanderthals/embryology/genetics ; *Neocortex/embryology ; *Neurogenesis/genetics/physiology ; *Transketolase/genetics/metabolism ; }, abstract = {Neanderthal brains were similar in size to those of modern humans. We sought to investigate potential differences in neurogenesis during neocortex development. Modern human transketolase-like 1 (TKTL1) differs from Neanderthal TKTL1 by a lysine-to-arginine amino acid substitution. Using overexpression in developing mouse and ferret neocortex, knockout in fetal human neocortical tissue, and genome-edited cerebral organoids, we found that the modern human variant, hTKTL1, but not the Neanderthal variant, increases the abundance of basal radial glia (bRG) but not that of intermediate progenitors (bIPs). bRG generate more neocortical neurons than bIPs. The hTKTL1 effect requires the pentose phosphate pathway and fatty acid synthesis. Inhibition of these metabolic pathways reduces bRG abundance in fetal human neocortical tissue. Our data suggest that neocortical neurogenesis in modern humans differs from that in Neanderthals.}, }
@article {pmid36044840, year = {2022}, author = {Kaczanowska, J and Ganglberger, F and Chernomor, O and Kargl, D and Galik, B and Hess, A and Moodley, Y and von Haeseler, A and Bühler, K and Haubensak, W}, title = {Molecular archaeology of human cognitive traits.}, journal = {Cell reports}, volume = {40}, number = {9}, pages = {111287}, doi = {10.1016/j.celrep.2022.111287}, pmid = {36044840}, issn = {2211-1247}, mesh = {Animals ; Archaeology ; Cognition/physiology ; Evolution, Molecular ; Genome, Human ; *Hominidae/genetics ; Humans ; Mammals ; *Neanderthals/genetics ; Phenotype ; }, abstract = {The brains and minds of our human ancestors remain inaccessible for experimental exploration. Therefore, we reconstructed human cognitive evolution by projecting nonsynonymous/synonymous rate ratios (ω values) in mammalian phylogeny onto the anatomically modern human (AMH) brain. This atlas retraces human neurogenetic selection and allows imputation of ancestral evolution in task-related functional networks (FNs). Adaptive evolution (high ω values) is associated with excitatory neurons and synaptic function. It shifted from FNs for motor control in anthropoid ancestry (60-41 mya) to attention in ancient hominoids (26-19 mya) and hominids (19-7.4 mya). Selection in FNs for language emerged with an early hominin ancestor (7.4-1.7 mya) and was later accompanied by adaptive evolution in FNs for strategic thinking during recent (0.8 mya-present) speciation of AMHs. This pattern mirrors increasingly complex cognitive demands and suggests that co-selection for language alongside strategic thinking may have separated AMHs from their archaic Denisovan and Neanderthal relatives.}, }
@article {pmid36009790, year = {2022}, author = {Churchill, SE and Keys, K and Ross, AH}, title = {Midfacial Morphology and Neandertal-Modern Human Interbreeding.}, journal = {Biology}, volume = {11}, number = {8}, pages = {}, pmid = {36009790}, issn = {2079-7737}, abstract = {Ancient DNA from, Neandertal and modern human fossils, and comparative morphological analyses of them, reveal a complex history of interbreeding between these lineages and the introgression of Neandertal genes into modern human genomes. Despite substantial increases in our knowledge of these events, the timing and geographic location of hybridization events remain unclear. Six measures of facial size and shape, from regional samples of Neandertals and early modern humans, were used in a multivariate exploratory analysis to try to identify regions in which early modern human facial morphology was more similar to that of Neandertals, which might thus represent regions of greater introgression of Neandertal genes. The results of canonical variates analysis and hierarchical cluster analysis suggest important affinities in facial morphology between both Middle and Upper Paleolithic early modern humans of the Near East with Neandertals, highlighting the importance of this region for interbreeding between the two lineages.}, }
@article {pmid35998220, year = {2022}, author = {Eising, E and Mirza-Schreiber, N and de Zeeuw, EL and Wang, CA and Truong, DT and Allegrini, AG and Shapland, CY and Zhu, G and Wigg, KG and Gerritse, ML and Molz, B and Alagöz, G and Gialluisi, A and Abbondanza, F and Rimfeld, K and van Donkelaar, M and Liao, Z and Jansen, PR and Andlauer, TFM and Bates, TC and Bernard, M and Blokland, K and Bonte, M and Børglum, AD and Bourgeron, T and Brandeis, D and Ceroni, F and Csépe, V and Dale, PS and de Jong, PF and DeFries, JC and Démonet, JF and Demontis, D and Feng, Y and Gordon, SD and Guger, SL and Hayiou-Thomas, ME and Hernández-Cabrera, JA and Hottenga, JJ and Hulme, C and Kere, J and Kerr, EN and Koomar, T and Landerl, K and Leonard, GT and Lovett, MW and Lyytinen, H and Martin, NG and Martinelli, A and Maurer, U and Michaelson, JJ and Moll, K and Monaco, AP and Morgan, AT and Nöthen, MM and Pausova, Z and Pennell, CE and Pennington, BF and Price, KM and Rajagopal, VM and Ramus, F and Richer, L and Simpson, NH and Smith, SD and Snowling, MJ and Stein, J and Strug, LJ and Talcott, JB and Tiemeier, H and van der Schroeff, MP and Verhoef, E and Watkins, KE and Wilkinson, M and Wright, MJ and Barr, CL and Boomsma, DI and Carreiras, M and Franken, MJ and Gruen, JR and Luciano, M and Müller-Myhsok, B and Newbury, DF and Olson, RK and Paracchini, S and Paus, T and Plomin, R and Reilly, S and Schulte-Körne, G and Tomblin, JB and van Bergen, E and Whitehouse, AJO and Willcutt, EG and St Pourcain, B and Francks, C and Fisher, SE}, title = {Genome-wide analyses of individual differences in quantitatively assessed reading- and language-related skills in up to 34,000 people.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {35}, pages = {e2202764119}, pmid = {35998220}, issn = {1091-6490}, support = {U24 DA041147/DA/NIDA NIH HHS/United States ; U01 DA051039/DA/NIDA NIH HHS/United States ; EP-C-15-001/EPA/EPA/United States ; U01 DA051038/DA/NIDA NIH HHS/United States ; G1000569/MRC_/Medical Research Council/United Kingdom ; U01 DA051037/DA/NIDA NIH HHS/United States ; U01 MH109514/MH/NIMH NIH HHS/United States ; U01 DA041106/DA/NIDA NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; RC2 MH089983/MH/NIMH NIH HHS/United States ; P50 HD027802/HD/NICHD NIH HHS/United States ; U01 DA041120/DA/NIDA NIH HHS/United States ; R01 DC014489/DC/NIDCD NIH HHS/United States ; 082036/B/07/Z/WT_/Wellcome Trust/United Kingdom ; MC_PC_19009/MRC_/Medical Research Council/United Kingdom ; RC2 MH089995/MH/NIMH NIH HHS/United States ; U01 DA051018/DA/NIDA NIH HHS/United States ; K99 HD094902/HD/NICHD NIH HHS/United States ; 075491/Z/04/WT_/Wellcome Trust/United Kingdom ; UL1 TR001863/TR/NCATS NIH HHS/United States ; U01 DA041093/DA/NIDA NIH HHS/United States ; R01 DC016977/DC/NIDCD NIH HHS/United States ; 217065/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; U24 DA041123/DA/NIDA NIH HHS/United States ; U01 DA041134/DA/NIDA NIH HHS/United States ; U01 DA041022/DA/NIDA NIH HHS/United States ; R01 AG046938/AG/NIA NIH HHS/United States ; RC2 MH089924/MH/NIMH NIH HHS/United States ; MC_PC_15018/MRC_/Medical Research Council/United Kingdom ; R01 MH058799/MH/NIMH NIH HHS/United States ; U01 DA041156/DA/NIDA NIH HHS/United States ; 076566/Z/05/Z/WT_/Wellcome Trust/United Kingdom ; U01 DA050987/DA/NIDA NIH HHS/United States ; U01 DA051016/DA/NIDA NIH HHS/United States ; 204821/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; U01 DA041025/DA/NIDA NIH HHS/United States ; U01 DA050989/DA/NIDA NIH HHS/United States ; R01 NS043530/NS/NINDS NIH HHS/United States ; U01 DA041089/DA/NIDA NIH HHS/United States ; MR/M021475/1/MRC_/Medical Research Council/United Kingdom ; U01 DA050988/DA/NIDA NIH HHS/United States ; U24 MH068457/MH/NIMH NIH HHS/United States ; 105621/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; U01 DA041117/DA/NIDA NIH HHS/United States ; U01 DA041028/DA/NIDA NIH HHS/United States ; U01 DA041048/DA/NIDA NIH HHS/United States ; G9815508/MRC_/Medical Research Council/United Kingdom ; P50 HD103556/HD/NICHD NIH HHS/United States ; U01 DA041148/DA/NIDA NIH HHS/United States ; MR/V012878/MRC_/Medical Research Council/United Kingdom ; MR/V012878/1/MRC_/Medical Research Council/United Kingdom ; U01 DA041174/DA/NIDA NIH HHS/United States ; 076566/WT_/Wellcome Trust/United Kingdom ; RC2 DA029475/DA/NIDA NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Child ; Child, Preschool ; Genetic Loci ; *Genome-Wide Association Study ; Humans ; *Individuality ; Language ; Polymorphism, Single Nucleotide ; *Reading ; *Speech ; Young Adult ; }, abstract = {The use of spoken and written language is a fundamental human capacity. Individual differences in reading- and language-related skills are influenced by genetic variation, with twin-based heritability estimates of 30 to 80% depending on the trait. The genetic architecture is complex, heterogeneous, and multifactorial, but investigations of contributions of single-nucleotide polymorphisms (SNPs) were thus far underpowered. We present a multicohort genome-wide association study (GWAS) of five traits assessed individually using psychometric measures (word reading, nonword reading, spelling, phoneme awareness, and nonword repetition) in samples of 13,633 to 33,959 participants aged 5 to 26 y. We identified genome-wide significant association with word reading (rs11208009, P = 1.098 × 10[-8]) at a locus that has not been associated with intelligence or educational attainment. All five reading-/language-related traits showed robust SNP heritability, accounting for 13 to 26% of trait variability. Genomic structural equation modeling revealed a shared genetic factor explaining most of the variation in word/nonword reading, spelling, and phoneme awareness, which only partially overlapped with genetic variation contributing to nonword repetition, intelligence, and educational attainment. A multivariate GWAS of word/nonword reading, spelling, and phoneme awareness maximized power for follow-up investigation. Genetic correlation analysis with neuroimaging traits identified an association with the surface area of the banks of the left superior temporal sulcus, a brain region linked to the processing of spoken and written language. Heritability was enriched for genomic elements regulating gene expression in the fetal brain and in chromosomal regions that are depleted of Neanderthal variants. Together, these results provide avenues for deciphering the biological underpinnings of uniquely human traits.}, }
@article {pmid35976853, year = {2022}, author = {Vettese, D and Borel, A and Blasco, R and Chevillard, L and Stavrova, T and Thun Hohenstein, U and Arzarello, M and Moncel, MH and Daujeard, C}, title = {New evidence of Neandertal butchery traditions through the marrow extraction in southwestern Europe (MIS 5-3).}, journal = {PloS one}, volume = {17}, number = {8}, pages = {e0271816}, pmid = {35976853}, issn = {1932-6203}, mesh = {Animals ; Archaeology ; Bone Marrow ; Bone and Bones ; Europe ; Fossils ; Humans ; *Neanderthals ; Technology ; Vegetables ; }, abstract = {Long bone breakage for bone marrow recovery is a commonly observed practice in Middle Palaeolithic contexts, regardless of the climatic conditions. While lithic technology is largely used to define cultural patterns in human groups, despite dedicating research by zooarchaeologists, for now butchering techniques rarely allowed the identification of clear traditions, notably for ancient Palaeolithic periods. In this paper, we test the hypothesis of butchery traditions among Neandertal groupsusing the bone assemblages from three sites in southwestern Europe. These sites are located in southeastern France and northern Italy and are dated to the Late Middle Palaeolithic: Abri du Maras (Marine Isotopic Stages (MIS) 4-3, Ardèche), Saint-Marcel (MIS 3, Ardèche), and Riparo Tagliente (MIS 4-3, Verona). The detection of culturally-induced patterns of bone breakage involves differentiating them from intuitively generated patterns. To tackle this issue, we used a zooarchaeological approach focusing on the percussion marks produced during the bone breakage process. Statistical analyses as the chi-square test of independence were employed to verify if percussion mark locations were randomly distributed, and if these distributions were different from the intuitive ones. For femurs and humeri, our results demonstrate that Neandertal groups occupying the Abri du Maras (levels 4.1 and 4.2) and the Saint-Marcel Cave (levels g and h) sites in France applied butchery traditions to recover yellow marrow. However, the traditions developed at each site were different. On the contrary, in Riparo Tagliente, in Italy, several groups or individuals of a same group did not share the same butchery traditions over time. Regarding the Abri du Maras and Saint Marcel Cave assemblages, our research demonstrates that Neandertal groups applied intense standardized bone breakage, far from the intuitive practice observed experimentally and related to bone density and/or skeletal morphology. These standardized patterns, which are systematic and counter-intuitive, can be interpreted as culturally induced for the Abri du Maras and Saint Marcel Cave. The diversity of Neandertal traditions should be considered by taking into account the butchery, in particular the practice of bone marrow extraction, and not only technological behaviours and types of tool kits.}, }
@article {pmid35906446, year = {2022}, author = {Andreeva, TV and Manakhov, AD and Gusev, FE and Patrikeev, AD and Golovanova, LV and Doronichev, VB and Shirobokov, IG and Rogaev, EI}, title = {Genomic analysis of a novel Neanderthal from Mezmaiskaya Cave provides insights into the genetic relationships of Middle Palaeolithic populations.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {13016}, pmid = {35906446}, issn = {2045-2322}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Female ; Fossils ; Genomics ; *Hominidae/genetics ; Humans ; *Neanderthals/genetics ; }, abstract = {The Mezmaiskaya cave is located on the North Caucasus near the border that divides Europe and Asia. Previously, fossil remains for two Neanderthals were reported from Mezmaiskaya Cave. A tooth from the third archaic hominin specimen (Mezmaiskaya 3) was retrieved from layer 3 in Mezmaiskaya Cave. We performed genome sequencing of Mezmaiskaya 3. Analysis of partial nuclear genome sequence revealed that it belongs to a Homo sapiens neanderthalensis female. Based on a high-coverage mitochondrial genome sequence, we demonstrated that the relationships of Mezmaiskaya 3 to Mezmaiskaya 1 and Stajnia S5000 individuals were closer than those to other Neanderthals. Our data demonstrate the close genetic connections between the early Middle Palaeolithic Neanderthals that were replaced by genetically distant later group in the same geographic areas. Based on mitochondrial DNA (mtDNA) data, we suggest that Mezmaiskaya 3 was the latest Neanderthal individual from the early Neanderthal's branches. We proposed a hierarchical nomenclature for the mtDNA haplogroups of Neanderthals. In addition, we retrieved ancestral mtDNA mutations in presumably functional sites fixed in the Neanderthal clades, and also provided the first data showing mtDNA heteroplasmy in Neanderthal specimen.}, }
@article {pmid35905187, year = {2022}, author = {Mora-Bermúdez, F and Kanis, P and Macak, D and Peters, J and Naumann, R and Xing, L and Sarov, M and Winkler, S and Oegema, CE and Haffner, C and Wimberger, P and Riesenberg, S and Maricic, T and Huttner, WB and Pääbo, S}, title = {Longer metaphase and fewer chromosome segregation errors in modern human than Neanderthal brain development.}, journal = {Science advances}, volume = {8}, number = {30}, pages = {eabn7702}, pmid = {35905187}, issn = {2375-2548}, mesh = {Animals ; Brain ; Chromosome Segregation/genetics ; *Hominidae ; Humans ; Kinesins ; Metaphase ; Mice ; *Neanderthals/genetics ; }, abstract = {Since the ancestors of modern humans separated from those of Neanderthals, around 100 amino acid substitutions spread to essentially all modern humans. The biological significance of these changes is largely unknown. Here, we examine all six such amino acid substitutions in three proteins known to have key roles in kinetochore function and chromosome segregation and to be highly expressed in the stem cells of the developing neocortex. When we introduce these modern human-specific substitutions in mice, three substitutions in two of these proteins, KIF18a and KNL1, cause metaphase prolongation and fewer chromosome segregation errors in apical progenitors of the developing neocortex. Conversely, the ancestral substitutions cause shorter metaphase length and more chromosome segregation errors in human brain organoids, similar to what we find in chimpanzee organoids. These results imply that the fidelity of chromosome segregation during neocortex development improved in modern humans after their divergence from Neanderthals.}, }
@article {pmid35865048, year = {2022}, author = {D Farhud, D and Azari, M and Mehrabi, A}, title = {The History of Corona Virus: From Neanderthals to the Present Time: A Brief Review.}, journal = {Iranian journal of public health}, volume = {51}, number = {3}, pages = {531-534}, pmid = {35865048}, issn = {2251-6093}, abstract = {Contrary to popular belief, 2019 was not the first time humans were infected by the Coronavirus. Coronavirus is one of the oldest viruses on the earth. This article discusses the history of this virus from Neanderthal time so far. We have collected a variety of articles related to coronaviruses and the extent of their interaction with humans from the first time probably appeared on earth, given that this virus is one of the ancient viruses. By examining and following the footsteps of coronaviruses in different works of literature, we found that the first homo that was infected with the coronavirus was Neanderthal. Moreover, we realized that in addition to risk factors such as age and background diseases, genetic evolution also plays an essential role in the protection of the body against coronavirus. On the other hand, this virus has evolved throughout history gradually, the same as humans. The presence of disease in humans, in any period of history, causes changes in human quality of life. Therefore, paying attention to the background of ancient diseases reveals principal information about the complexity of pathogens.}, }
@article {pmid35757177, year = {2022}, author = {Theofanopoulou, C and Andirkó, A and Boeckx, C and Jarvis, ED}, title = {Oxytocin and vasotocin receptor variation and the evolution of human prosociality.}, journal = {Comprehensive psychoneuroendocrinology}, volume = {11}, number = {}, pages = {100139}, pmid = {35757177}, issn = {2666-4976}, abstract = {Modern human lifestyle strongly depends on complex social traits like empathy, tolerance and cooperation. These diverse facets of social cognition have been associated with variation in the oxytocin receptor (OTR) and its sister genes, the vasotocin/vasopressin receptors (VTR1A/AVPR1A and AVPR1B/VTR1B). Here, we compared the available genomic sequences of these receptors between modern humans, archaic humans, and 12 non-human primate species, and identified sites that show heterozygous variation in modern humans and archaic humans distinct from variation in other primates, and for which we could find association studies with clinical implications. On these sites, we performed a range of analyses (variant clustering, pathogenicity prediction, regulation, linkage disequilibrium frequency), and reviewed the literature on selection data in different modern-human populations. We found five sites with modern human specific variation, where the modern human allele is the major allele in the global population (OTR: rs1042778, rs237885, rs6770632; VTR1A: rs10877969; VTR1B: rs33985287). Among them, variation in the OTR-rs6770632 site was predicted to be the most functional. Two alleles (OTR: rs59190448 and rs237888) present only in modern humans and archaic humans were putatively under positive selection in modern humans, with rs237888 predicted to be a highly functional site. Three sites showed convergent evolution between modern humans and bonobos (OTR: rs2228485 and rs237897; VTR1A: rs1042615), with OTR-rs2228485 ranking highly in terms of functionality and reported to be under balancing selection in modern humans (Schaschl, 2015) [1]. Our findings have implications for understanding hominid prosociality, as well as the similarities between modern human and bonobo social behavior.}, }
@article {pmid35737986, year = {2022}, author = {Weasel, L}, title = {How Neanderthals Became White: The Introgression of Race into Contemporary Human Evolutionary Genetics.}, journal = {The American naturalist}, volume = {200}, number = {1}, pages = {129-139}, doi = {10.1086/720130}, pmid = {35737986}, issn = {1537-5323}, mesh = {Animals ; Genome, Human ; Genomics ; Humans ; Hybridization, Genetic ; *Neanderthals/genetics ; }, abstract = {AbstractHuman evolutionary theory has a history rife with racial biases in what might be considered its distant past that can appear glaringly obvious from our current vantage point. Despite the recognition that as a social activity science is always vulnerable to such biases (and science that attempts to uncover human origin stories all the more so), commitment to the scientific method can lead us to believe that we have improved on, overcome, or otherwise escaped these tendencies in our contemporary practices, whether through scientific contrition, changing social context, or better training and composition of research teams or as a result of advances in technologies and methodologies. This article adapts the evolutionary biology concept of introgression, which refers to the hybridization and repeated bidirectional backcross exchange of information between species, as a metaphorical frame to examine science itself and to trace the ways in which historic race biases from earlier, disowned human evolution research have been retained and selected for beneath the surface of current genomic research today. It takes as its focus the sequencing of the Neanderthal genome, first announced in 2006 and refined since, and the explosion of scientific research comparing that sequence to present-day human DNA from individuals around the world to illustrate the ways in which current research questions and findings in comparative evolutionary genomics draw on and dredge up earlier biases, albeit adapted to and disguised within contemporary social relations and power differentials.}, }
@article {pmid35652784, year = {2023}, author = {Marcazzan, D and Miller, CE and Ligouis, B and Duches, R and Conard, NJ and Peresani, M}, title = {Middle and Upper Paleolithic occupations of Fumane Cave (Italy): a geoarchaeological investigation of the anthropogenic features.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {101}, number = {}, pages = {37-62}, doi = {10.4436/JASS.10002}, pmid = {35652784}, issn = {2037-0644}, abstract = {Here we present the results of a microcontextual analysis of purported combustion features recovered from Middle and Upper Paleolithic occupations at the cave site of Fumane, Italy. Our analyses, which integrate micromorphology with organic petrology, show that only a few of the features represent primary, intact hearths; some of them show evidence for various phases of anthropogenic reworking, either through trampling or sweeping and dumping. Several of the features are multi-layered and reflect a complex formation history of various activities related to combustion and site maintenance. Many appear to be the remnants of occupation horizons only partially preserved and peripherally related to combustion. Within several of the intact hearths from the Mousterian, we were able to identify variable fuel sources in different features, implying a degree of flexibility in the fuel-selection strategies of the Neanderthal occupants of Fumane. In this study we design a classification system of the anthropogenic features and also conduct a spatial analysis, through which we can infer diachronic patterns in the frequency and intensity of site occupation and the spatial distribution of activities. We note a decrease in frequency of combustion features throughout the Mousterian which continues into the Uluzzian. The features associated with the Protoaurignacian occupation, in contrast with those from the Mousterian, are multi-layered and well-defined. We argue that these trends, which correspond with other trends in artefact frequency, imply changes in the settlement dynamics of the site during the transition from the last Neanderthal occupation of the cave to the arrival of modern humans.}, }
@article {pmid35514995, year = {2022}, author = {Mocci, S and Littera, R and Tranquilli, S and Provenzano, A and Mascia, A and Cannas, F and Lai, S and Giuressi, E and Chessa, L and Angioni, G and Campagna, M and Firinu, D and Del Zompo, M and La Nasa, G and Perra, A and Giglio, S}, title = {A Protective HLA Extended Haplotype Outweighs the Major COVID-19 Risk Factor Inherited From Neanderthals in the Sardinian Population.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {891147}, pmid = {35514995}, issn = {1664-3224}, mesh = {Animals ; *COVID-19/genetics ; Haplotypes ; Humans ; *Neanderthals/genetics ; Risk Factors ; SARS-CoV-2 ; }, abstract = {Sardinia has one of the lowest incidences of hospitalization and related mortality in Europe and yet a very high frequency of the Neanderthal risk locus variant on chromosome 3 (rs35044562), considered to be a major risk factor for a severe SARS-CoV-2 disease course. We evaluated 358 SARS-CoV-2 patients and 314 healthy Sardinian controls. One hundred and twenty patients were asymptomatic, 90 were pauci-symptomatic, 108 presented a moderate disease course and 40 were severely ill. All patients were analyzed for the Neanderthal-derived genetic variants reported as being protective (rs1156361) or causative (rs35044562) for severe illness. The β°39 C>T Thalassemia variant (rs11549407), HLA haplotypes, KIR genes, KIRs and their HLA class I ligand combinations were also investigated. Our findings revealed an increased risk for severe disease in Sardinian patients carrying the rs35044562 high risk variant [OR 5.32 (95% CI 2.53 - 12.01), p = 0.000]. Conversely, the protective effect of the HLA-A*02:01, B*18:01, DRB*03:01 three-loci extended haplotype in the Sardinian population was shown to efficiently contrast the high risk of a severe and devastating outcome of the infection predicted for carriers of the Neanderthal locus [OR 15.47 (95% CI 5.8 - 41.0), p < 0.0001]. This result suggests that the balance between risk and protective immunogenetic factors plays an important role in the evolution of COVID-19. A better understanding of these mechanisms may well turn out to be the biggest advantage in the race for the development of more efficient drugs and vaccines.}, }
@article {pmid35513387, year = {2022}, author = {Rüther, PL and Husic, IM and Bangsgaard, P and Gregersen, KM and Pantmann, P and Carvalho, M and Godinho, RM and Friedl, L and Cascalheira, J and Taurozzi, AJ and Jørkov, MLS and Benedetti, MM and Haws, J and Bicho, N and Welker, F and Cappellini, E and Olsen, JV}, title = {SPIN enables high throughput species identification of archaeological bone by proteomics.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {2458}, pmid = {35513387}, issn = {2041-1723}, mesh = {Animals ; Archaeology/methods ; Chromatography, Liquid ; Mammals ; Peptides ; *Proteome ; *Proteomics/methods ; Tandem Mass Spectrometry ; }, abstract = {Species determination based on genetic evidence is an indispensable tool in archaeology, forensics, ecology, and food authentication. Most available analytical approaches involve compromises with regard to the number of detectable species, high cost due to low throughput, or a labor-intensive manual process. Here, we introduce "Species by Proteome INvestigation" (SPIN), a shotgun proteomics workflow for analyzing archaeological bone capable of querying over 150 mammalian species by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Rapid peptide chromatography and data-independent acquisition (DIA) with throughput of 200 samples per day reduce expensive MS time, whereas streamlined sample preparation and automated data interpretation save labor costs. We confirm the successful classification of known reference bones, including domestic species and great apes, beyond the taxonomic resolution of the conventional peptide mass fingerprinting (PMF)-based Zooarchaeology by Mass Spectrometry (ZooMS) method. In a blinded study of degraded Iron-Age material from Scandinavia, SPIN produces reproducible results between replicates, which are consistent with morphological analysis. Finally, we demonstrate the high throughput capabilities of the method in a high-degradation context by analyzing more than two hundred Middle and Upper Palaeolithic bones from Southern European sites with late Neanderthal occupation. While this initial study is focused on modern and archaeological mammalian bone, SPIN will be open and expandable to other biological tissues and taxa.}, }
@article {pmid35484382, year = {2022}, author = {Rodríguez, J and Willmes, C and Sommer, C and Mateos, A}, title = {Sustainable human population density in Western Europe between 560.000 and 360.000 years ago.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6907}, pmid = {35484382}, issn = {2045-2322}, mesh = {Animals ; Climate Change ; Europe ; *Hominidae ; Humans ; *Neanderthals ; Population Density ; }, abstract = {The time period between 560 and 360 ka (MIS14 to MIS11) was critical for the evolution of the Neanderthal lineage and the appearance of Levallois technology in Europe. The shifts in the distribution of the human populations, driven by cyclical climate changes, are generally accepted to have played major roles in both processes. We used a dataset of palaeoclimate maps and a species distribution model to reconstruct the changes in the area of Western Europe with suitable environmental conditions for humans during 11 time intervals of the MIS14 to MIS 11 period. Eventually, the maximum sustainable human population within the suitable area during each time interval was estimated by extrapolating the relationship observed between recent hunter-gatherer population density and net primary productivity and applying it to the past. Contrary to common assumptions, our results showed the three Mediterranean Peninsulas were not the only region suitable for humans during the glacial periods. The estimated total sustainable population of Western Europe from MIS14 to MIS11 oscillated between 13,000 and 25,000 individuals. These results offer a new theoretical scenario to develop models and hypotheses to explain cultural and biological evolution during the Middle Pleistocene in Western Europe.}, }
@article {pmid35445261, year = {2022}, author = {Vallini, L and Marciani, G and Aneli, S and Bortolini, E and Benazzi, S and Pievani, T and Pagani, L}, title = {Genetics and Material Culture Support Repeated Expansions into Paleolithic Eurasia from a Population Hub Out of Africa.}, journal = {Genome biology and evolution}, volume = {14}, number = {4}, pages = {}, pmid = {35445261}, issn = {1759-6653}, mesh = {Africa ; Animals ; Anthropology, Cultural ; Europe ; Genetics, Population ; Humans ; *Neanderthals/genetics ; Siberia ; }, abstract = {The population dynamics that followed the Out of Africa (OoA) expansion and the whereabouts of the early migrants before the differentiation that ultimately led to the formation of Oceanian, West and East Eurasian macropopulations have long been debated. Shedding light on these events may, in turn, provide clues to better understand the cultural evolution in Eurasia between 50 and 35 ka. Here, we analyze Eurasian Paleolithic DNA evidence to provide a comprehensive population model and validate it in light of available material culture. Leveraging on our integrated approach we propose the existence of a Eurasian population Hub, where Homo sapiens lived between the OoA and the broader colonization of Eurasia, which was characterized by multiple events of expansion and local extinction. A major population wave out of Hub, of which Ust'Ishim, Bacho Kiro, and Tianyuan are unadmixed representatives, is broadly associated with Initial Upper Paleolithic lithics and populated West and East Eurasia before or around 45 ka, before getting largely extinct in Europe. In this light, we suggest a parsimonious placement of Oase1 as an individual related to Bacho Kiro who experienced additional Neanderthal introgression. Another expansion, started before 38 ka, is broadly associated with Upper Paleolithic industries and repopulated Europe with sporadic admixtures with the previous wave (GoyetQ116-1) and more systematic ones, whereas moving through Siberia (Yana, Mal'ta). Before these events, we also confirm Zlatý Kůň as the most basal human lineage sequenced to date OoA, potentially representing an earlier wave of expansion out of the Hub.}, }
@article {pmid35440148, year = {2022}, author = {Brand, CM and Colbran, LL and Capra, JA}, title = {Predicting Archaic Hominin Phenotypes from Genomic Data.}, journal = {Annual review of genomics and human genetics}, volume = {23}, number = {}, pages = {591-612}, pmid = {35440148}, issn = {1545-293X}, support = {R35 GM127087/GM/NIGMS NIH HHS/United States ; T32 HG009495/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; DNA, Ancient ; Genome, Human ; Genomics ; *Hominidae/genetics ; Humans ; *Neanderthals/genetics ; Phenotype ; }, abstract = {Ancient DNA provides a powerful window into the biology of extant and extinct species, including humans' closest relatives: Denisovans and Neanderthals. Here, we review what is known about archaic hominin phenotypes from genomic data and how those inferences have been made. We contend that understanding the influence of variants on lower-level molecular phenotypes-such as gene expression and protein function-is a promising approach to using ancient DNA to learn about archaic hominin traits. Molecular phenotypes have simpler genetic architectures than organism-level complex phenotypes, and this approach enables moving beyond association studies by proposing hypotheses about the effects of archaic variants that are testable in model systems. The major challenge to understanding archaic hominin phenotypes is broadening our ability to accurately map genotypes to phenotypes, but ongoing advances ensure that there will be much more to learn about archaic hominin phenotypes from their genomes.}, }
@article {pmid35430882, year = {2022}, author = {Witt, KE and Villanea, F and Loughran, E and Zhang, X and Huerta-Sanchez, E}, title = {Apportioning archaic variants among modern populations.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {377}, number = {1852}, pages = {20200411}, pmid = {35430882}, issn = {1471-2970}, support = {K99 GM143466/GM/NIGMS NIH HHS/United States ; R35 GM128946/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Asian People/genetics ; Genetic Drift ; Genome, Human ; *Hominidae/genetics ; Humans ; *Neanderthals/genetics ; }, abstract = {The apportionment of human genetic diversity within and between populations has been measured to understand human relatedness and demographic history. Likewise, the distribution of archaic ancestry in modern populations can be leveraged to better understand the interaction between our species and its archaic relatives. Resolving the interactions between modern and archaic human populations can be difficult, as archaic variants in modern populations have been shaped by genetic drift, bottlenecks and gene flow. Here, we investigate the distribution of archaic variation in Eurasian populations. We find that archaic ancestry coverage at the individual- and population-level present distinct patterns in modern human populations: South Asians have nearly twice the number of population-unique archaic alleles compared with Europeans or East Asians, indicating that these populations experienced differing demographic and archaic admixture events. We confirm previous observations that East Asian individuals have more Neanderthal ancestry than European individuals, but surprisingly, when we compare the number of single nucleotide polymorphisms with archaic alleles found across a population, Europeans have more Neanderthal ancestry than East Asians. We compare these results to simulated models and conclude that these patterns are consistent with multiple admixture events between modern humans and Neanderthals. This article is part of the theme issue 'Celebrating 50 years since Lewontin's apportionment of human diversity'.}, }
@article {pmid35353845, year = {2022}, author = {Rios-Garaizar, J and Iriarte, E and Arnold, LJ and Sánchez-Romero, L and Marín-Arroyo, AB and San Emeterio, A and Gómez-Olivencia, A and Pérez-Garrido, C and Demuro, M and Campaña, I and Bourguignon, L and Benito-Calvo, A and Iriarte, MJ and Aranburu, A and Arranz-Otaegi, A and Garate, D and Silva-Gago, M and Lahaye, C and Ortega, I}, title = {The intrusive nature of the Châtelperronian in the Iberian Peninsula.}, journal = {PloS one}, volume = {17}, number = {3}, pages = {e0265219}, pmid = {35353845}, issn = {1932-6203}, mesh = {Animals ; Europe ; Fossils ; France ; *Neanderthals ; Paris ; Technology ; }, abstract = {Multiple factors have been proposed to explain the disappearance of Neandertals between ca. 50 and 40 kyr BP. Central to these discussions has been the identification of new techno-cultural complexes that overlap with the period of Neandertal demise in Europe. One such complex is the Châtelperronian, which extends from the Paris Basin to the Northern Iberian Peninsula between 43,760-39,220 BP. In this study we present the first open-air Châtelperronian site in the Northern Iberian Peninsula, Aranbaltza II. The technological features of its stone tool assemblage show no links with previous Middle Paleolithic technology in the region, and chronological modeling reveals a gap between the latest Middle Paleolithic and the Châtelperronian in this area. We interpret this as evidence of local Neandertal extinction and replacement by other Neandertal groups coming from southern France, illustrating how local extinction episodes could have played a role in the process of disappearance of Neandertals.}, }
@article {pmid35339947, year = {2022}, author = {Roksandic, M and Radović, P and Lindal, J and Mihailović, D}, title = {Early Neanderthals in contact: The Chibanian (Middle Pleistocene) hominin dentition from Velika Balanica Cave, Southern Serbia.}, journal = {Journal of human evolution}, volume = {166}, number = {}, pages = {103175}, doi = {10.1016/j.jhevol.2022.103175}, pmid = {35339947}, issn = {1095-8606}, mesh = {Animals ; Dentition ; Fossils ; *Hominidae/anatomy &amp; histology ; Humans ; *Neanderthals ; Serbia ; }, abstract = {Neanderthals are Eurasian fossil hominins whose distinctive morphology developed in the southwestern corner of Europe and later spread throughout the continent, reaching Southwest Asia before the Late Pleistocene and spreading into Central Asia by 59-49 ka. The timing, tempo, and route of the Neanderthal movements eastward are poorly documented. The earliest probable evidence of Neanderthals in Asia comes from Karain E Cave (Anatolia, Turkey), dated to 250-200 ka. We present four Chibanian (Middle Pleistocene) hominin specimens, representing at least two individuals, from Velika Balanica Cave (Serbia): a permanent upper third molar (BH-2), a deciduous upper fourth premolar (BH-3) refitted to a poorly preserved maxillary fragment with the permanent first molar in the alveolus (BH-4), and a permanent upper central incisor (BH-5). We provide descriptions of the teeth, as well as a comparative analysis of the well-preserved M[1] (BH-4), including assessments of cusp angles, relative occlusal polygon area, relative cusp base areas, two- and three-dimensional enamel thickness, and taurodontism. Morphology of both the occlusal surface and the enamel dentine junction of the M[1] indicates that the maxillary fragment and associated dP[4] belonged to an early Neanderthal child. The heavily worn I[1] and M[3] are consistent with the Neanderthal morphology, although they are less distinct taxonomically. These Chibanian remains with provenance from layer 3a are constrained by two thermoluminescence dates: 285 ± 34 ka and 295 ± 74 ka. They represent the earliest current evidence of Neanderthal spread into the Eastern Mediterranean Area. We discuss these findings in light of recent direct evidence for cultural connections between Southwestern Asia and Southeast Europe in the Chibanian.}, }
@article {pmid35338861, year = {2022}, author = {Pop, CM and Wilson, L and Browne, CL}, title = {Evaluating landscape knowledge and lithic resource selection at the French Middle Paleolithic site of the Bau de l'Aubesier.}, journal = {Journal of human evolution}, volume = {166}, number = {}, pages = {103152}, doi = {10.1016/j.jhevol.2022.103152}, pmid = {35338861}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; *Hominidae ; }, abstract = {We report on the application of a novel approach to exploring the degree of landscape knowledge, wayfinding abilities, and the nature of decision-making processes reflected in the utilization of stone resources in the French Middle Paleolithic. Specifically, we use data from the site of the Bau de l'Aubesier to explore the reasons why a majority of the 350 raw material sources cataloged in the surrounding region appear not to have been utilized, including several located near the site and yielding high-quality lithic materials. To this end, we focus on the spatial relationships between sources as an explanatory variable, operationalized in terms of minimum travel times. Using geographic information system software and a generalized linear model of resource selection derived from the Bau assemblages, we compute source utilization probabilities from the perspective of hominins located off-site. We do so under three optimization scenarios, factoring in the intrinsic characteristics (e.g., quality) and time required to reach each source on the way to the Bau. More generally, we find that in slightly more than 50% of cases, seemingly viable sources may have been ignored simply because the minimum cost path leading back to the Bau passes through or requires only minimal deviations to reach, higher quality options. More generally, we found that throughout the entire region, a cost/benefit analysis of competing sources favors those from source areas known to have been utilized. Virtually all the available information on lithic procurement at the Bau is consistent with a model of landscape utilization premised on detailed knowledge of a very large area, an ability to accurately estimate travel times between locations, and a pragmatic strategy of stone resource exploitation based on minimizing costs (travel and search times) and maximizing utility.}, }
@article {pmid35260774, year = {2022}, author = {Picin, A and Hajdinjak, M and Nowaczewska, W and Benazzi, S and Urbanowski, M and Marciszak, A and Fewlass, H and Bosch, MD and Socha, P and Stefaniak, K and Żarski, M and Wiśniewski, A and Hublin, JJ and Nadachowski, A and Talamo, S}, title = {Author Correction: New perspectives on Neanderthal dispersal and turnover from Stajnia Cave (Poland).}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {4060}, doi = {10.1038/s41598-022-08141-z}, pmid = {35260774}, issn = {2045-2322}, }
@article {pmid35193386, year = {2022}, author = {Cerrito, P and Nava, A and Radovčić, D and Borić, D and Cerrito, L and Basdeo, T and Ruggiero, G and Frayer, DW and Kao, AP and Bondioli, L and Mancini, L and Bromage, TG}, title = {Dental cementum virtual histology of Neanderthal teeth from Krapina (Croatia, 130-120 kyr): an informed estimate of age, sex and adult stressors.}, journal = {Journal of the Royal Society, Interface}, volume = {19}, number = {187}, pages = {20210820}, pmid = {35193386}, issn = {1742-5662}, mesh = {Adult ; Animals ; Croatia ; Dental Cementum/diagnostic imaging ; Female ; Fossils ; *Hominidae ; Humans ; *Neanderthals ; *Tooth/diagnostic imaging ; }, abstract = {The evolution of modern human reproductive scheduling is an aspect of our life history that remains vastly uncomprehended. The present work aims to address this gap by validating a non-destructive cutting-edge methodology to infer adult life-history events on modern teeth with known life history and then applying it to fossil specimens. We use phase-contrast synchrotron X-ray microtomography to visualize the dental cementum of 21 specimens: nine contemporary humans; 10 Neanderthals from Krapina (Croatia, 130-120 kyr); one Neolithic Homo sapiens from Ajmana (Serbia); and one Mesolithic H. sapiens from Vlasac (Serbia). We were able to correctly detect and time (root mean square error = 2.1 years; R[2] = 0.98) all reproductive (menarche, parturition, menopause) and other physiologically impactful events in the modern sample. Nonetheless, we could not distinguish between the causes of the events detected. For the fossil specimens, we estimated age at death and age at occurrence of biologically significant events. Finally, we performed an exploratory analysis regarding possible sexual dimorphism in dental cementum microstructure, which allowed us to correctly infer the sex of the Neolithic specimen, for which the true value was known via DNA analysis.}, }
@article {pmid35181735, year = {2022}, author = {Lee, HK and Knabl, L and Knabl, L and Wieser, M and Mur, A and Zabernigg, A and Schumacher, J and Kapferer, S and Kaiser, N and Furth, PA and Hennighausen, L}, title = {Immune transcriptome analysis of COVID-19 patients infected with SARS-CoV-2 variants carrying the E484K escape mutation identifies a distinct gene module.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {2784}, pmid = {35181735}, issn = {2045-2322}, mesh = {2',5'-Oligoadenylate Synthetase/genetics ; Adult ; Aged ; COVID-19/genetics/*immunology/virology ; Female ; *Gene Regulatory Networks ; Humans ; Longitudinal Studies ; Male ; Middle Aged ; SARS-CoV-2/*genetics ; *Transcriptome ; Young Adult ; }, abstract = {Fast-spreading variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) energize the COVID-19 pandemic. While viral infections elicit a conserved immune response, it is not known whether SARS-CoV-2 variants, which display enhanced binding to the ACE2 receptor and reduced neutralizing activity by vaccine-elicited antibodies, prompt specific genomic immune responses. To test this, we generated and investigated the transcriptomes in BCs from hospitalized patients infected with either the Alpha variant (n = 36) or with the Alpha variant that had acquired the E484K escape mutation (Alpha+E484K) (n = 13). We identified a gene module preferentially activated in patients infected with the Alpha+E484K variant and in patients infected with the Beta (n = 9) and Gamma (n = 3) variants that also carry by the E484K escape mutation. The E484K signature was enriched for genes preferentially expressed in monocytes and linked to severe viral infection. However, both cohorts had undergone similar treatments and no differences in disease severity were reported suggesting that this signature reflects a variant response and does not necessarily associate with disease outcome. Additionally, longitudinal transcriptome analyses revealed a more persistent retention of immune signatures in Alpha+E484K patients throughout the entire course of COVID-19 disease and convalescence. While the OAS1 Neanderthal mutation has been linked to a milder COVID-19 pathology, we did not identify significant immune transcriptomes differences in the 25 patients homozygous for this mutation. Our study offers insights into distinct molecular immune responses elicited by SARS-CoV-2 variants carrying the E484K escape mutation throughout the COVID-19 disease.}, }
@article {pmid35143674, year = {2022}, author = {Göllner, T and Larena, M and Kutanan, W and Lukas, H and Fieder, M and Schaschl, H}, title = {Unveiling the Genetic History of the Maniq, a Primary Hunter-Gatherer Society.}, journal = {Genome biology and evolution}, volume = {14}, number = {4}, pages = {}, pmid = {35143674}, issn = {1759-6653}, mesh = {Animals ; Asia, Southeastern ; *Asian People ; Genetics, Population ; Humans ; *Neanderthals/genetics ; Polymorphism, Single Nucleotide ; Thailand ; }, abstract = {The Maniq of southern Thailand is one of the last remaining practicing hunter-gatherer communities in the world. However, our knowledge on their genetic origins and demographic history is still largely limited. We present here the genotype data covering ∼2.3 million single nucleotide polymorphisms of 11 unrelated Maniq individuals. Our analyses reveal the Maniq to be closely related to the Semang populations of Malaysia (Malay Negritos), who altogether carry an Andamanese-related ancestry linked to the ancient Hòabìnhian hunter-gatherers of Mainland Southeast Asia (MSEA). Moreover, the Maniq possess ∼35% East Asian-related ancestry, likely brought about by recent admixture with surrounding agriculturist communities in the region. In addition, the Maniq exhibit one of the highest levels of genetic differentiation found among living human populations, indicative of their small population size and historical practice of endogamy. Similar to other hunter-gatherer populations of MSEA, we also find the Maniq to possess low levels of Neanderthal ancestry and undetectable levels of Denisovan ancestry. Altogether, we reveal the Maniq to be a Semang group that experienced intense genetic drift and exhibits signs of ancient Hòabìnhian ancestry.}, }
@article {pmid35138885, year = {2022}, author = {Slimak, L and Zanolli, C and Higham, T and Frouin, M and Schwenninger, JL and Arnold, LJ and Demuro, M and Douka, K and Mercier, N and Guérin, G and Valladas, H and Yvorra, P and Giraud, Y and Seguin-Orlando, A and Orlando, L and Lewis, JE and Muth, X and Camus, H and Vandevelde, S and Buckley, M and Mallol, C and Stringer, C and Metz, L}, title = {Modern human incursion into Neanderthal territories 54,000 years ago at Mandrin, France.}, journal = {Science advances}, volume = {8}, number = {6}, pages = {eabj9496}, pmid = {35138885}, issn = {2375-2548}, abstract = {Determining the extent of overlap between modern humans and other hominins in Eurasia, such as Neanderthals and Denisovans, is fundamental to understanding the nature of their interactions and what led to the disappearance of archaic hominins. Apart from a possible sporadic pulse recorded in Greece during the Middle Pleistocene, the first settlements of modern humans in Europe have been constrained to ~45,000 to 43,000 years ago. Here, we report hominin fossils from Grotte Mandrin in France that reveal the earliest known presence of modern humans in Europe between 56,800 and 51,700 years ago. This early modern human incursion in the Rhône Valley is associated with technologies unknown in any industry of that age outside Africa or the Levant. Mandrin documents the first alternating occupation of Neanderthals and modern humans, with a modern human fossil and associated Neronian lithic industry found stratigraphically between layers containing Neanderthal remains associated with Mousterian industries.}, }
@article {pmid35066426, year = {2022}, author = {Mihailović, D and Kuhn, SL and Bogićević, K and Dimitrijević, V and Marín-Arroyo, AB and Marković, J and Mercier, N and Mihailović, B and Morley, MW and Radović, P and Rink, WJ and Plavšić, S and Roksandic, M}, title = {Connections between the Levant and the Balkans in the late Middle Pleistocene: Archaeological findings from Velika and Mala Balanica Caves (Serbia).}, journal = {Journal of human evolution}, volume = {163}, number = {}, pages = {103138}, doi = {10.1016/j.jhevol.2021.103138}, pmid = {35066426}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; Balkan Peninsula ; Caves ; Fossils ; *Hominidae ; Humans ; *Neanderthals ; Serbia ; }, abstract = {Major changes in the technological, economic, and social behavior of Middle Pleistocene hominins occurred at the onset of the Middle Paleolithic, 400-200 ka. However, until recently it was not possible to establish when, where, and how certain forms of Middle Paleolithic behavior appeared and spread into Southeastern Europe, mainly owing to gaps in the Paleolithic record. Here we report new results of dating, material culture, and the archaeological context of finds from the Balanica Cave Complex in Sićevo (Serbia). Two methods-thermoluminescence and electron spin resonance-were used to date the sequence. The geoarchaeological context was examined through sedimentology, micromorphology, and spatial analysis. Microfaunal remains were used to constrain the dates within an ecological zone, whereas macrofauna was analyzed for taxonomy and taphonomy to examine the source of accumulation and hominin behavior. Technological and typological features of the lithic assemblage were used to characterize lithic production at the site. Materials recovered from Layer 3 in Velika Balanica and from Layer 2 in Mala Balanica, both dated to MIS 9-7, include a distinctive set of archaeological assemblages which resemble contemporaneous Yabrudian assemblages from the Levant in important ways, and which are unlike contemporary material from the surrounding regions. In Velika Balanica, the lithic assemblages are associated with a large fireplace containing evidence of human activities similar to those from Qesem Cave (Israel). Dental remains uncovered in the same layer are consistent with Neanderthals. These findings suggest that the end of the Middle Pleistocene (before 300-240 ka) saw population movement and/or cultural transmission between Southwest Asia and the Balkans, which led eventually to a transfer of technology between Middle Eastern and European hominin populations and contributed to the shaping of Neanderthal behaviors throughout the eastern and northern Mediterranean.}, }
@article {pmid34969841, year = {2022}, author = {Massilani, D and Morley, MW and Mentzer, SM and Aldeias, V and Vernot, B and Miller, C and Stahlschmidt, M and Kozlikin, MB and Shunkov, MV and Derevianko, AP and Conard, NJ and Wurz, S and Henshilwood, CS and Vasquez, J and Essel, E and Nagel, S and Richter, J and Nickel, B and Roberts, RG and Pääbo, S and Slon, V and Goldberg, P and Meyer, M}, title = {Microstratigraphic preservation of ancient faunal and hominin DNA in Pleistocene cave sediments.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {1}, pages = {}, pmid = {34969841}, issn = {1091-6490}, mesh = {Animals ; *Caves ; *DNA, Ancient ; *Fossils ; Hominidae/*genetics ; Neanderthals/*genetics ; }, abstract = {Ancient DNA recovered from Pleistocene sediments represents a rich resource for the study of past hominin and environmental diversity. However, little is known about how DNA is preserved in sediments and the extent to which it may be translocated between archaeological strata. Here, we investigate DNA preservation in 47 blocks of resin-impregnated archaeological sediment collected over the last four decades for micromorphological analyses at 13 prehistoric sites in Europe, Asia, Africa, and North America and show that such blocks can preserve DNA of hominins and other mammals. Extensive microsampling of sediment blocks from Denisova Cave in the Altai Mountains reveals that the taxonomic composition of mammalian DNA differs drastically at the millimeter-scale and that DNA is concentrated in small particles, especially in fragments of bone and feces (coprolites), suggesting that these are substantial sources of DNA in sediments. Three microsamples taken in close proximity in one of the blocks yielded Neanderthal DNA from at least two male individuals closely related to Denisova 5, a Neanderthal toe bone previously recovered from the same layer. Our work indicates that DNA can remain stably localized in sediments over time and provides a means of linking genetic information to the archaeological and ecological records on a microstratigraphic scale.}, }
@article {pmid34943532, year = {2021}, author = {Durand, S and Dufour, J and Rosas, A and Becce, F and Orr, C}, title = {Three-Dimensional Comparative Study of Human Bipartite Scaphoids and the Os Centrale of the Wrist in Neandertals and Non-Human Anthropoid Primates.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {11}, number = {12}, pages = {}, pmid = {34943532}, issn = {2075-4418}, support = {7484 and 8318//Wenner-Gren Foundation/ ; }, abstract = {In humans, bipartite scaphoid still does not differentiate clearly from traumatic non-union of the scaphoid. To aid diagnosis, we sought to analyze the main geometrical similarities among bipartite scaphoids from primate species with fused and unfused scaphoid centrales. Four human embryos, four cases of adult humans with bipartite scaphoid, twelve adult specimens of other extant anthropoid primates, and two Neandertal scaphoid specimens were included in this study. Three-dimensional polygon models of the scaphoid and os centrale were generated from CT scan, micro-CT scan, or histological sections. A 3D comparative study of the morphological and morphometrical parameters was performed using the MSC Patran software. The os centrale was smaller than the scaphoid in all specimens and its shape was elongated in the anteroposterior scaphoid direction. The position of the os centrale centroid compared to the scaphoid using direction vectors had a strong orientation along the proximodistal axis in all species. The main morphological feature of bipartite scaphoid was the continuity of the scaphoid from its proximal pole to its tubercule along the anteroposterior axis. In all specimens, if the os centrale was removed, the scaphoid still appeared normal and whole. The bipartite scaphoid in adult humans shares geometrical analogies with monkeys and orangutans, human embryos, and Neandertals. Morphological and morphometrical features identified in this study are useful to differentiate bipartite scaphoid from scaphoid pseudarthrosis. All other criteria suggested in the past lead to misdiagnosis.}, }
@article {pmid34923240, year = {2022}, author = {Hardy, K and Bocherens, H and Miller, JB and Copeland, L}, title = {Reconstructing Neanderthal diet: The case for carbohydrates.}, journal = {Journal of human evolution}, volume = {162}, number = {}, pages = {103105}, doi = {10.1016/j.jhevol.2021.103105}, pmid = {34923240}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; Carbohydrates ; Diet ; *Hominidae ; Humans ; *Neanderthals/physiology ; }, abstract = {Evidence for plants rarely survives on Paleolithic sites, while animal bones and biomolecular analyses suggest animal produce was important to hominin populations, leading to the perspective that Neanderthals had a very-high-protein diet. But although individual and short-term survival is possible on a relatively low-carbohydrate diet, populations are unlikely to have thrived and reproduced without plants and the carbohydrates they provide. Today, nutritional guidelines recommend that around half the diet should be carbohydrate, while low intake is considered to compromise physical performance and successful reproduction. This is likely to have been the same for Paleolithic populations, highlighting an anomaly in that the basic physiological recommendations do not match the extensive archaeological evidence. Neanderthals had large, energy-expensive brains and led physically active lifestyles, suggesting that for optimal health they would have required high amounts of carbohydrates. To address this anomaly, we begin by outlining the essential role of carbohydrates in the human reproduction cycle and the brain and the effects on physical performance. We then evaluate the evidence for resource availability and the archaeological evidence for Neanderthal diet and investigate three ways that the anomaly between the archaeological evidence and the hypothetical dietary requirements might be explained. First, Neanderthals may have had an as yet unidentified genetic adaptation to an alternative physiological method to spare blood glucose and glycogen reserves for essential purposes. Second, they may have existed on a less-than-optimum diet and survived rather than thrived. Third, the methods used in dietary reconstruction could mask a complex combination of dietary plant and animal proportions. We end by proposing that analyses of Paleolithic diet and subsistence strategies need to be grounded in the minimum recommendations throughout the life course and that this provides a context for interpretation of the archaeological evidence from the behavioral and environmental perspectives.}, }
@article {pmid34919805, year = {2022}, author = {Natri, HM and Hudjashov, G and Jacobs, G and Kusuma, P and Saag, L and Darusallam, CC and Metspalu, M and Sudoyo, H and Cox, MP and Gallego Romero, I and Banovich, NE}, title = {Genetic architecture of gene regulation in Indonesian populations identifies QTLs associated with global and local ancestries.}, journal = {American journal of human genetics}, volume = {109}, number = {1}, pages = {50-65}, pmid = {34919805}, issn = {1537-6605}, mesh = {Computational Biology/methods ; DNA Methylation ; Databases, Genetic ; *Gene Expression Regulation ; *Genetics, Population ; *Genome, Human ; Genome-Wide Association Study ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Humans ; Indonesia ; Male ; Models, Genetic ; Molecular Sequence Annotation ; Multifactorial Inheritance ; *Quantitative Trait Loci ; Quantitative Trait, Heritable ; Selection, Genetic ; Whole Genome Sequencing ; }, abstract = {Lack of diversity in human genomics limits our understanding of the genetic underpinnings of complex traits, hinders precision medicine, and contributes to health disparities. To map genetic effects on gene regulation in the underrepresented Indonesian population, we have integrated genotype, gene expression, and CpG methylation data from 115 participants across three island populations that capture the major sources of genomic diversity in the region. In a comparison with European datasets, we identify eQTLs shared between Indonesia and Europe as well as population-specific eQTLs that exhibit differences in allele frequencies and/or overall expression levels between populations. By combining local ancestry and archaic introgression inference with eQTLs and methylQTLs, we identify regulatory loci driven by modern Papuan ancestry as well as introgressed Denisovan and Neanderthal variation. GWAS colocalization connects QTLs detected here to hematological traits, and further comparison with European datasets reflects the poor overall transferability of GWAS statistics across diverse populations. Our findings illustrate how population-specific genetic architecture, local ancestry, and archaic introgression drive variation in gene regulation across genetically distinct and in admixed populations and highlight the need for performing association studies on non-European populations.}, }
@article {pmid34897365, year = {2022}, author = {Decaup, PH and Couture, C and Colin, M and Garot, E}, title = {Prevalence of taurodontism: meta-analysis in recent humans and evolutionary perspectives.}, journal = {Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen}, volume = {73}, number = {1}, pages = {1-11}, doi = {10.1127/homo/2021/1447}, pmid = {34897365}, issn = {1618-1301}, mesh = {Animals ; Humans ; *Neanderthals ; Prevalence ; Cross-Sectional Studies ; *Tooth Abnormalities ; *Hominidae ; }, abstract = {Taurodontism is a continuous anatomical variation of permanent and primary posterior teeth represented by an enlargement of the pulp cavity. A high prevalence of the trait is reported in Homo neanderthalensis remains. Exploring and refining epidemiology of taurodontism in actual populations could strengthen the hypothesis of a selective advantage for a high attrition diet (as heavy tooth wear in Homo sapiens evolution changed little until recently) or favour pleiotropic or genetic drift effects to explain the high frequency of the trait in Neandertal remains. Prevalence ranges between 0.1% and 48% in the literature. The aim of the present study is to assess the prevalence of taurodontism in recent populations by means of meta-analysis, that is, is the prevalence of taurodontism lower or higher in modern human living populations, where the selective advantages of high attrition diet are still expected? From 90 potentially eligible studies, 15 were included in the meta-analysis. Only cross-sectional studies were reported, and 14,771 participants were included. The meta-analyses were performed with a random model, calculating a weighted-mean prevalence of 11.8%. Gender was found to be unrelated to the prevalence of taurodontism (OR = 0.84 (95% CI 0.67-1.05), p > 0.05). Taurodontism occurs in approximately 11.8% of the living population. This result questions the status of taurodontism as a "typical trait" in Homo neanderthalensis and allows a possible common evolutionary mechanism in Homo sapiens and Homo neanderthalensis for the trait. Further studies should include more accurate and standardized methods to assess the condition.}, }
@article {pmid34866354, year = {2024}, author = {Bermúdez de Castro, JM and Martínez de Pinillos, M and Martín-Francés, L and Modesto-Mata, M and García-Campos, C and Arsuaga, JL and Martinón-Torres, M}, title = {Dental remains of the Middle Pleistocene hominins from the Sima de los Huesos site (Sierra de Atapuerca, Spain): Maxillary dentition.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {307}, number = {7}, pages = {2325-2342}, doi = {10.1002/ar.24841}, pmid = {34866354}, issn = {1932-8494}, support = {//Consejer&#xed;a de Cultura y Turismo of the Junta de Castilla y Le&#xf3;n/ ; //Fundaci&#xf3;n Atapuerca/ ; PGC2018-093925-B.C31-C33//Spanish Ministry of "Ciencia, Innovaci&#xf3;n y Universidades"/ ; //Leakey Foundation/ ; }, mesh = {Animals ; Spain ; *Maxilla/anatomy &amp; histology ; *Fossils ; *Hominidae/anatomy &amp; histology ; *Tooth/anatomy &amp; histology ; *Neanderthals/anatomy &amp; histology ; Dentition ; Humans ; Biological Evolution ; }, abstract = {The Middle Pleistocene site of the Sima de los Huesos (Sierra de Atapuerca, northern Spain) has yielded a considerable number of human fossils during the period 1984-2020. Among them, up to 253 maxillary teeth have been recovered. In this article, we present the description of the eight dental classes of the maxilla following the Arizona State University Dental Anthropology System classification. In addition, we present the mean mesiodistal and buccolingual diameters of these teeth compared to those of Neanderthals and a modern human sample. The morphology of both the anterior and posterior teeth suggests a close relationship of the Sima de los Huesos hominins with the populations of the second half of the Middle Pleistocene of Europe and the Near East, as well as with the so-called classic Neanderthals of Europe. Features with a recognizable taxonomic signal allow grouping the Sima de los Huesos hominins with different paleodemes into a Neanderthal clade. The dental evidence of the Sima de los Huesos hominins is key to suggest a complex model for the settlement of Europe during the Middle Pleistocene. During this period, different migrations of human groups probably coming from Southwest Asia, replacements, prolonged isolations, as well as hybridization and introgression processes would have contributed to the diversity of hominins in Europe.}, }
@article {pmid34855484, year = {2021}, author = {Marom, A and Rak, Y}, title = {Comment on "A Middle Pleistocene Homo from Nesher Ramla, Israel".}, journal = {Science (New York, N.Y.)}, volume = {374}, number = {6572}, pages = {eabl4336}, doi = {10.1126/science.abl4336}, pmid = {34855484}, issn = {1095-9203}, mesh = {Animals ; *Fossils ; Hominidae/classification ; Israel ; Mandible/anatomy &amp; histology ; Neanderthals/*classification ; }, abstract = {Hershkovitz et al. (Reports, 25 June 2021, p. 1424) conclude that the Nesher Ramla (NR) fossils represent a distinctive Homo paleodeme that played a role as a source population for Neanderthals. However, the highly diagnostic features of the Neanderthal mandible—clearly displayed by the NR fossils—are largely overlooked. Our analyses indicate that the NR fossils represent simply a Neanderthal.}, }
@article {pmid34855476, year = {2021}, author = {May, H and Sarig, R and Pokhojaev, A and Fornai, C and Martinón-Torres, M and Bermúdez de Castro, JM and Weber, GW and Zaidner, Y and Hershkovitz, I}, title = {Response to Comment on "A Middle Pleistocene Homo from Nesher Ramla, Israel".}, journal = {Science (New York, N.Y.)}, volume = {374}, number = {6572}, pages = {eabl5789}, doi = {10.1126/science.abl5789}, pmid = {34855476}, issn = {1095-9203}, mesh = {*Fossils ; Israel ; }, abstract = {Marom and Rak claim, on the basis of a few mandibular features, that the Nesher Ramla (NR) Homo is a Neanderthal. Their comments lack substance and contribute little to the debate surrounding the evolution of Middle Pleistocene Homo. Limitations and preconceptions in their study prevented them from achieving resolution beyond a dichotomous interpretation of the NR as either a Neanderthal or a modern human.}, }
@article {pmid34851548, year = {2024}, author = {Bermúdez de Castro, JM and Martínez de Pinillos, M and Martín-Francés, L and Modesto-Mata, M and García-Campos, C and Arsuaga, JL and Martinón-Torres, M}, title = {Dental remains of the Middle Pleistocene hominins from the Sima de los Huesos site (Sierra de Atapuerca, Spain): Mandibular dentition.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {307}, number = {7}, pages = {2394-2409}, doi = {10.1002/ar.24840}, pmid = {34851548}, issn = {1932-8494}, support = {//Consejer&#xed;a de Cultura y Turismo of the Junta de Castilla y Le&#xf3;n/ ; PGC2018-093925-B.C31-C33//Direcci&#xf3;n General de Investigaci&#xf3;n of the Spanish Ministry of "Ciencia, Innovaci&#xf3;n y Universidades/ ; //The Leakey Foundation/ ; //Atapuerca Foundation/ ; }, mesh = {Animals ; *Mandible/anatomy &amp; histology ; Spain ; *Fossils ; *Hominidae/anatomy &amp; histology ; *Tooth/anatomy &amp; histology ; *Dentition ; Neanderthals/anatomy &amp; histology ; Humans ; Biological Evolution ; }, abstract = {The Middle Pleistocene site of the Sima de los Huesos (Sierra de Atapuerca, northern Spain) has yielded a considerable number of human fossils during the period 1984-2020. Among them, up to 314 mandibular teeth have been identified. In this second paper dedicated to the dentition we present the description of the eight dental classes of the mandible following the Arizona State University Dental Anthropology System (ASUDAS) classification. In addition, we show the mean mesiodistal and buccolingual diameters obtained in these teeth compared to those of Neanderthals and a modern human sample. The morphology of both the anterior and posterior teeth suggests a close relationship of the Sima de los Huesos hominins with the populations of the second half of the Middle Pleistocene of Europe and the Near East, as well as with the so-called classic Neanderthals of Europe. The combination of dental traits in these populations is characteristic and diagnostic and suggests grouping the Sima de los Huesos hominins with the other paleodemes in a Neanderthal clade. The dental evidence of the Sima de los Huesos hominins is key to propose a complex model for the settlement of Europe during the Middle Pleistocene. In this period, different migrations of human groups probably coming from Southwest Asia, replacements, prolonged isolations, as well as hybridization and introgression processes would have contributed to the diversity of hominins in Europe.}, }
@article {pmid34839228, year = {2022}, author = {Bahain, JJ and Mercier, N and Valladas, H and Falguères, C and Masaoudi, H and Joron, JL and Froget, L and Moigne, AM and Combier, J and Moncel, MH}, title = {Reappraisal of the chronology of Orgnac 3 Lower-to-Middle Paleolithic site (Ardèche, France), a regional key sequence for the Middle Pleistocene of southern France.}, journal = {Journal of human evolution}, volume = {162}, number = {}, pages = {103092}, doi = {10.1016/j.jhevol.2021.103092}, pmid = {34839228}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; Fossils ; France ; Humans ; *Neanderthals ; Technology ; *Tooth ; }, abstract = {Previous studies have suggested that the Lower-to-Middle Paleolithic transition was associated with the earliest Neanderthals, but recent research has established that the oldest Neanderthal fossils and the first signs of their technologies and behavior appear from MIS 11 or possibly earlier. To understand these changes, re-evaluation of the evidence is necessary to determine if this transition corresponds to a progressive evolution rather than abrupt change. Orgnac 3 is a key and appropriate site to study this research context. Located in southern France, it yields a long stratigraphic sequence testifying the evolution of technical and subsistence behaviors of pre-Neanderthal human groups during a Middle Pleistocene interglacial-glacial cycle. In this article, a new chronological framework is provided for the sequence based on results of dating methods applied to various types of geological materials. Speleothems and volcanic minerals, dated in previous studies by U-series and [40]Ar/[39]Ar, respectively, show periods of calcitic crystallization and regional volcanic activity. Other materials, such as heated flints and herbivore teeth, are directly related to evidence of anthropogenic activities and are analyzed in the present work by trapped-charge dating methods such as thermoluminescence and electron spin resonance combined with uranium series (ESR/U-series). The new thermoluminescence and ESR/U-series dates confirm the attribution of the Orgnac 3 stratigraphic sequence to the MIS 10-MIS 8 period and are discussed in relation to paleoenvironmental data derived from bioarchaeological studies. The paleoanthropological levels, including the emergence of Levallois technology, are dated to ca. 275 ka (early MIS 8) and appear coeval to a wet and temperate period recorded locally, the Amargiers interstadial, defined in the regional palynological records. The implications of this reassessed chronology for the archaeological assemblages are discussed in the wider context of behavioral innovations from MIS 11 onward and their establishment in subsequent periods.}, }
@article {pmid34824388, year = {2022}, author = {Brown, S and Massilani, D and Kozlikin, MB and Shunkov, MV and Derevianko, AP and Stoessel, A and Jope-Street, B and Meyer, M and Kelso, J and Pääbo, S and Higham, T and Douka, K}, title = {The earliest Denisovans and their cultural adaptation.}, journal = {Nature ecology &amp; evolution}, volume = {6}, number = {1}, pages = {28-35}, pmid = {34824388}, issn = {2397-334X}, support = {694707/ERC_/European Research Council/International ; 715069/ERC_/European Research Council/International ; 324139/ERC_/European Research Council/International ; }, mesh = {Animals ; Archaeology ; Caves ; DNA, Mitochondrial/genetics ; *Hominidae/genetics ; *Neanderthals/genetics ; }, abstract = {Since the initial identification of the Denisovans a decade ago, only a handful of their physical remains have been discovered. Here we analysed ~3,800 non-diagnostic bone fragments using collagen peptide mass fingerprinting to locate new hominin remains from Denisova Cave (Siberia, Russia). We identified five new hominin bones, four of which contained sufficient DNA for mitochondrial analysis. Three carry mitochondrial DNA of the Denisovan type and one was found to carry mtDNA of the Neanderthal type. The former come from the same archaeological layer near the base of the cave's sequence and are the oldest securely dated evidence of Denisovans at 200 ka (thousand years ago) (205-192 ka at 68.2% or 217-187 ka at 95% probability). The stratigraphic context in which they were located contains a wealth of archaeological material in the form of lithics and faunal remains, allowing us to determine the material culture associated with these early hominins and explore their behavioural and environmental adaptations. The combination of bone collagen fingerprinting and genetic analyses has so far more-than-doubled the number of hominin bones at Denisova Cave and has expanded our understanding of Denisovan and Neanderthal interactions, as well as their archaeological signatures.}, }
@article {pmid34819448, year = {2021}, author = {Dhakal, B and Makaju, R and Dhakal R, R}, title = {The Risk of COVID-19 in People Having a Particular Set of Gene.}, journal = {Kathmandu University medical journal (KUMJ)}, volume = {19}, number = {74}, pages = {265-267}, pmid = {34819448}, issn = {1812-2078}, mesh = {*COVID-19 ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Humans ; Male ; Risk Factors ; SARS-CoV-2 ; }, abstract = {These risk factors of advancing age, male gender and co-existing health conditions like cancer, cardiovascular diseases, diabetes and obesity do not fully explain why some people have no or mild symptoms whereas others have severe symptoms. Genomewide association study (GWAS) identify a 3p21.31 gene cluster as a genetic susceptibility locus in patients with COVID-19 with respiratory failure. They also found a higher risk among persons with blood group A and protective effect for blood group O than among patients with other blood groups. The particular haplotype in a region of chromosome 3 is contributed to modern humans by neandertals. Another Neanderthal haplotype on chromosome 12 is associated with a 22% reduction in relative risk of becoming severely ill with COVID-19. The ApoE e4e4 homozygous genotype was found to increase the risk of severe COVID-19. Change in angiotensin converting enzyme (ACE) 2 gene was also found to be associated with increased risk of COVID-19, cardiovascular and pulmonary conditions.}, }
@article {pmid34814754, year = {2021}, author = {Mahoney, P and McFarlane, G and Smith, BH and Miszkiewicz, JJ and Cerrito, P and Liversidge, H and Mancini, L and Dreossi, D and Veneziano, A and Bernardini, F and Cristiani, E and Behie, A and Coppa, A and Bondioli, L and Frayer, DW and Radovčić, D and Nava, A}, title = {Growth of Neanderthal infants from Krapina (120-130 ka), Croatia.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1963}, pages = {20212079}, pmid = {34814754}, issn = {1471-2954}, mesh = {Animals ; Croatia ; Fossils ; *Hominidae ; Humans ; *Neanderthals ; *Tooth ; }, abstract = {Modern humans have a slow and extended period of childhood growth, but to what extent this ontogenetic pathway was present in Neanderthals is debated. Dental development, linked to the duration of somatic growth across modern primates, is the main source for information about growth and development in a variety of fossil primates, including humans. Studies of Neanderthal permanent teeth report a pace of development either similar to recent humans or relatively accelerated. Neanderthal milk teeth, which form and emerge before permanent teeth, provide an opportunity to determine which pattern was present at birth. Here we present a comparative study of the prenatal and early postnatal growth of five milk teeth from three Neanderthals (120 000-130 000 years ago) using virtual histology. Results reveal regions of their milk teeth formed quickly before birth and over a relatively short period of time after birth. Tooth emergence commenced towards the earliest end of the eruption schedules displayed by extant human children. Advanced dental development is consistent with expectations for Neanderthal infant feeding.}, }
@article {pmid34795445, year = {2021}, author = {Liston, A and Humblet-Baron, S and Duffy, D and Goris, A}, title = {Human immune diversity: from evolution to modernity.}, journal = {Nature immunology}, volume = {22}, number = {12}, pages = {1479-1489}, pmid = {34795445}, issn = {1529-2916}, support = {BBS/E/B/000C0427/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/B/000C0428/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Age Factors ; Diet ; *Evolution, Molecular ; Female ; Gene-Environment Interaction ; *Genetic Variation ; Host-Pathogen Interactions ; Humans ; Immune System/immunology/metabolism/*physiology ; Male ; Microbiota/immunology ; Sex Factors ; Species Specificity ; }, abstract = {The extreme diversity of the human immune system, forged and maintained throughout evolutionary history, provides a potent defense against opportunistic pathogens. At the same time, this immune variation is the substrate upon which a plethora of immune-associated diseases develop. Genetic analysis suggests that thousands of individually weak loci together drive up to half of the observed immune variation. Intense selection maintains this genetic diversity, even selecting for the introgressed Neanderthal or Denisovan alleles that have reintroduced variation lost during the out-of-Africa migration. Variations in age, sex, diet, environmental exposure, and microbiome each potentially explain the residual variation, with proof-of-concept studies demonstrating both plausible mechanisms and correlative associations. The confounding interaction of many of these variables currently makes it difficult to assign definitive contributions. Here, we review the current state of play in the field, identify the key unknowns in the causality of immune variation, and identify the multidisciplinary pathways toward an improved understanding.}, }
@article {pmid34749003, year = {2021}, author = {Sorrentino, R and Stephens, NB and Marchi, D and DeMars, LJD and Figus, C and Bortolini, E and Badino, F and Saers, JPP and Bettuzzi, M and Boschin, F and Capecchi, G and Feletti, F and Guarnieri, T and May, H and Morigi, MP and Parr, W and Ricci, S and Ronchitelli, A and Stock, JT and Carlson, KJ and Ryan, TM and Belcastro, MG and Benazzi, S}, title = {Unique foot posture in Neanderthals reflects their body mass and high mechanical stress.}, journal = {Journal of human evolution}, volume = {161}, number = {}, pages = {103093}, doi = {10.1016/j.jhevol.2021.103093}, pmid = {34749003}, issn = {1095-8606}, mesh = {Animals ; Fossils ; Humans ; *Neanderthals ; Phylogeny ; Posture ; Stress, Mechanical ; *Talus/anatomy &amp; histology ; }, abstract = {Neanderthal foot bone proportions and morphology are mostly indistinguishable from those of Homo sapiens, with the exception of several distinct Neanderthal features in the talus. The biomechanical implications of these distinct talar features remain contentious, fueling debate around the adaptive meaning of this distinctiveness. With the aim of clarifying this controversy, we test phylogenetic and behavioral factors as possible contributors, comparing tali of 10 Neanderthals and 81 H. sapiens (Upper Paleolithic and Holocene hunter-gatherers, agriculturalists, and postindustrial group) along with the Clark Howell talus (Omo, Ethiopia). Variation in external talar structures was assessed through geometric morphometric methods, while bone volume fraction and degree of anisotropy were quantified in a subsample (n = 45). Finally, covariation between point clouds of site-specific trabecular variables and surface landmark coordinates was assessed. Our results show that although Neanderthal talar external and internal morphologies were distinct from those of H. sapiens groups, shape did not significantly covary with either bone volume fraction or degree of anisotropy, suggesting limited covariation between external and internal talar structures. Neanderthal external talar morphology reflects ancestral retentions, along with various adaptations to high levels of mobility correlated to their presumably unshod hunter-gatherer lifestyle. This pairs with their high site-specific trabecular bone volume fraction and anisotropy, suggesting intense and consistently oriented locomotor loading, respectively. Relative to H.sapiens, Neanderthals exhibit differences in the talocrural joint that are potentially attributable to cultural and locomotor behavior dissimilarity, a talonavicular joint that mixes ancestral and functional traits, and a derived subtalar joint that suggests a predisposition for a pronated foot during stance phase. Overall, Neanderthal talar variation is attributable to mobility strategy and phylogenesis, while H. sapiens talar variation results from the same factors plus footwear. Our results suggest that greater Neanderthal body mass and/or higher mechanical stress uniquely led to their habitually pronated foot posture.}, }
@article {pmid34716352, year = {2021}, author = {Di Pietro, L and Barba, M and Palacios, D and Tiberio, F and Prampolini, C and Baranzini, M and Parolini, O and Arcovito, A and Lattanzi, W}, title = {Shaping modern human skull through epigenetic, transcriptional and post-transcriptional regulation of the RUNX2 master bone gene.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {21316}, pmid = {34716352}, issn = {2045-2322}, support = {Linea D1 - 2018//Universit&#xe0; Cattolica del Sacro Cuore/ ; Linea D1 - 2017//Universit&#xe0; Cattolica del Sacro Cuore/ ; }, mesh = {Animals ; *Biological Evolution ; Core Binding Factor Alpha 1 Subunit/*genetics/metabolism ; Cranial Sutures/growth &amp; development ; Craniosynostoses/genetics ; Epigenesis, Genetic ; Genome, Human ; Hominidae/anatomy &amp; histology/genetics ; Humans ; Mesenchymal Stem Cells ; MicroRNAs/genetics ; Neanderthals/anatomy &amp; histology/genetics ; Osteogenesis/genetics ; RNA, Long Noncoding/genetics ; Skull/*anatomy &amp; histology ; }, abstract = {RUNX2 encodes the master bone transcription factor driving skeletal development in vertebrates, and playing a specific role in craniofacial and skull morphogenesis. The anatomically modern human (AMH) features sequence changes in the RUNX2 locus compared with archaic hominins' species. We aimed to understand how these changes may have contributed to human skull globularization occurred in recent evolution. We compared in silico AMH and archaic hominins' genomes, and used mesenchymal stromal cells isolated from skull sutures of craniosynostosis patients for in vitro functional assays. We detected 459 and 470 nucleotide changes in noncoding regions of the AMH RUNX2 locus, compared with the Neandertal and Denisovan genomes, respectively. Three nucleotide changes in the proximal promoter were predicted to alter the binding of the zinc finger protein Znf263 and long-distance interactions with other cis-regulatory regions. By surface plasmon resonance, we selected nucleotide substitutions in the 3'UTRs able to affect miRNA binding affinity. Specifically, miR-3150a-3p and miR-6785-5p expression inversely correlated with RUNX2 expression during in vitro osteogenic differentiation. The expression of two long non-coding RNAs, AL096865.1 and RUNX2-AS1, within the same locus, was modulated during in vitro osteogenic differentiation and correlated with the expression of specific RUNX2 isoforms. Our data suggest that RUNX2 may have undergone adaptive phenotypic evolution caused by epigenetic and post-transcriptional regulatory mechanisms, which may explain the delayed suture fusion leading to the present-day globular skull shape.}, }
@article {pmid34716342, year = {2021}, author = {Yuan, K and Ni, X and Liu, C and Pan, Y and Deng, L and Zhang, R and Gao, Y and Ge, X and Liu, J and Ma, X and Lou, H and Wu, T and Xu, S}, title = {Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {6232}, pmid = {34716342}, issn = {2041-1723}, mesh = {Algorithms ; Animals ; Asia ; DNA-Binding Proteins/genetics ; Europe ; *Genetic Introgression ; Genome, Human ; Hominidae/*genetics ; Humans ; Metagenomics/*methods ; *Models, Genetic ; Neanderthals/genetics ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Siberia ; }, abstract = {We developed a method, ArchaicSeeker 2.0, to identify introgressed hominin sequences and model multiple-wave admixture. The new method enabled us to discern two waves of introgression from both Denisovan-like and Neanderthal-like hominins in present-day Eurasian populations and an ancient Siberian individual. We estimated that an early Denisovan-like introgression occurred in Eurasia around 118.8-94.0 thousand years ago (kya). In contrast, we detected only one single episode of Denisovan-like admixture in indigenous peoples eastern to the Wallace-Line. Modeling ancient admixtures suggested an early dispersal of modern humans throughout Asia before the Toba volcanic super-eruption 74 kya, predating the initial peopling of Asia as proposed by the traditional Out-of-Africa model. Survived archaic sequences are involved in various phenotypes including immune and body mass (e.g., ZNF169), cardiovascular and lung function (e.g., HHAT), UV response and carbohydrate metabolism (e.g., HYAL1/HYAL2/HYAL3), while "archaic deserts" are enriched with genes associated with skin development and keratinization.}, }
@article {pmid34710249, year = {2022}, author = {Roksandic, M and Radović, P and Wu, XJ and Bae, CJ}, title = {Resolving the "muddle in the middle": The case for Homo bodoensis sp. nov.}, journal = {Evolutionary anthropology}, volume = {31}, number = {1}, pages = {20-29}, pmid = {34710249}, issn = {1520-6505}, support = {XDB26000000//Chinese Academy of Sciences/ ; RGPIN-2019-04113//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; Biological Evolution ; China ; Europe ; Fossils ; *Hominidae ; Humans ; *Neanderthals ; }, abstract = {Recent developments in the field of palaeoanthropology necessitate the suppression of two hominin taxa and the introduction of a new species of hominins to help resolve the current nebulous state of Middle Pleistocene (Chibanian) hominin taxonomy. In particular, the poorly defined and variably understood hominin taxa Homo heidelbergensis (both sensu stricto and sensu lato) and Homo rhodesiensis need to be abandoned as they fail to reflect the full range of hominin variability in the Middle Pleistocene. Instead, we propose: (1) introduction of a new taxon, Homo bodoensis sp. nov., as an early Middle Pleistocene ancestor of the Homo sapiens lineage, with a pan-African distribution that extends into the eastern Mediterranean (Southeast Europe and the Levant); (2) that many of the fossils from Western Europe (e.g. Sima de los Huesos) currently assigned to H. heidelbergensis s.s. be reassigned to Homo neanderthalensis to reflect the early appearance of Neanderthal derived traits in the Middle Pleistocene in the region; and (3) that the Middle Pleistocene Asian fossils, particularly from China, likely represent a different lineage altogether.}, }
@article {pmid34705887, year = {2021}, author = {Zilhão, J and Angelucci, DE and Arnold, LJ and d'Errico, F and Dayet, L and Demuro, M and Deschamps, M and Fewlass, H and Gomes, L and Linscott, B and Matias, H and Pike, AWG and Steier, P and Talamo, S and Wild, EM}, title = {Revisiting the Middle and Upper Palaeolithic archaeology of Gruta do Caldeirão (Tomar, Portugal).}, journal = {PloS one}, volume = {16}, number = {10}, pages = {e0259089}, pmid = {34705887}, issn = {1932-6203}, mesh = {Animals ; Archaeology/*methods ; Fossils ; Geologic Sediments/*analysis ; Humans ; Portugal ; Radiometric Dating/*methods ; Spain ; }, abstract = {Gruta do Caldeirão features a c. 6 m-thick archaeological stratification capped by Holocene layers ABC-D and Ea, which overlie layer Eb, a deposit of Magdalenian age that underwent significant disturbance, intrusion, and component mixing caused by funerary use of the cave during the Early Neolithic. Here, we provide an updated overview of the stratigraphy and archaeological content of the underlying Pleistocene succession, whose chronology we refine using radiocarbon and single-grain optically stimulated luminescence dating. We find a high degree of stratigraphic integrity. Dating anomalies exist in association with the succession's two major discontinuities: between layer Eb and Upper Solutrean layer Fa, and between Early Upper Palaeolithic layer K and Middle Palaeolithic layer L. Mostly, the anomalies consist of older-than-expected radiocarbon ages and can be explained by bioturbation and palimpsest-forming sedimentation hiatuses. Combined with palaeoenvironmental inferences derived from magnetic susceptibility analyses, the dating shows that sedimentation rates varied in tandem with the oscillations in global climate revealed by the Greenland oxygen isotope record. A steep increase in sedimentation rate is observed through the Last Glacial Maximum, resulting in a c. 1.5 m-thick accumulation containing conspicuous remains of occupation by people of the Solutrean technocomplex, whose traditional subdivision is corroborated: the index fossils appear in the expected stratigraphic order; the diagnostics of the Protosolutrean and the Lower Solutrean predate 24,000 years ago; and the constraints on the Upper Solutrean place it after Greenland Interstadial 2.2. (23,220-23,340 years ago). Human usage of the site during the Early Upper and the Middle Palaeolithic is episodic and low-intensity: stone tools are few, and the faunal remains relate to carnivore activity. The Middle Palaeolithic is found to persist beyond 39,000 years ago, at least three millennia longer than in the Franco-Cantabrian region. This conclusion is upheld by Bayesian modelling and stands even if the radiocarbon ages for the Middle Palaeolithic levels are removed from consideration (on account of observed inversions and the method's potential for underestimation when used close to its limit of applicability). A number of localities in Spain and Portugal reveal a similar persistence pattern. The key evidence comes from high-resolution fluviatile contexts spared by the site formation issues that our study of Caldeirão brings to light-palimpsest formation, post-depositional disturbance, and erosion. These processes. are ubiquitous in the cave and rock-shelter sites of Iberia, reflecting the impact on karst archives of the variation in climate and environments that occurred through the Upper Pleistocene, and especially at two key points in time: between 37,000 and 42,000 years ago, and after the Last Glacial Maximum. Such empirical difficulties go a long way towards explaining the controversies surrounding the associated cultural transitions: from the Middle to the Upper Palaeolithic, and from the Solutrean to the Magdalenian. Alongside potential dating error caused by incomplete decontamination, proper consideration of sample association issues is required if we are ever to fully understand what happened with the human settlement of Iberia during these critical intervals, and especially so with regards to the fate of Iberia's last Neandertal populations.}, }
@article {pmid34702870, year = {2021}, author = {Mahadevan, J and Pathak, AK and Vemula, A and Nadella, RK and Viswanath, B and Jain, S and ,  and Purushottam, M and Mondal, M}, title = {Analysis of whole exome sequencing in severe mental illness hints at selection of brain development and immune related genes.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {21088}, pmid = {34702870}, issn = {2045-2322}, mesh = {Animals ; *Brain/growth &amp; development/immunology ; Female ; Humans ; Immunity, Innate/*genetics ; Male ; *Mental Disorders/genetics/immunology ; Neanderthals/genetics/immunology ; *Exome Sequencing ; }, abstract = {Evolutionary trends may underlie some aspects of the risk for common, non-communicable disorders, including psychiatric disease. We analyzed whole exome sequencing data from 80 unique individuals from India coming from families with two or more individuals with severe mental illness. We used Population Branch Statistics (PBS) to identify variants and genes under positive selection and identified 74 genes as candidates for positive selection. Of these, 20 were previously associated with Schizophrenia, Alzheimer's disease and cognitive abilities in genome wide association studies. We then checked whether any of these 74 genes were involved in common biological pathways or related to specific cellular or molecular functions. We found that immune related pathways and functions related to innate immunity such as antigen binding were over-represented. We also evaluated for the presence of Neanderthal introgressed segments in these genes and found Neanderthal introgression in a single gene out of the 74 candidate genes. However, the introgression pattern indicates the region is unlikely to be the source for selection. Our findings hint at how selection pressures in individuals from families with a history of severe mental illness may diverge from the general population. Further, it also provides insights into the genetic architecture of severe mental illness, such as schizophrenia and its link to immune factors.}, }
@article {pmid34662402, year = {2022}, author = {Jagoda, E and Xue, JR and Reilly, SK and Dannemann, M and Racimo, F and Huerta-Sanchez, E and Sankararaman, S and Kelso, J and Pagani, L and Sabeti, PC and Capellini, TD}, title = {Detection of Neanderthal Adaptively Introgressed Genetic Variants That Modulate Reporter Gene Expression in Human Immune Cells.}, journal = {Molecular biology and evolution}, volume = {39}, number = {1}, pages = {}, pmid = {34662402}, issn = {1537-1719}, support = {K99 HG010669/HG/NHGRI NIH HHS/United States ; R35 GM125055/GM/NIGMS NIH HHS/United States ; R35 GM128946/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Gene Expression ; *Genetic Variation ; *Genome, Human ; Humans ; Immunity, Innate/*genetics ; Inflammation ; *Neanderthals/genetics ; }, abstract = {Although some variation introgressed from Neanderthals has undergone selective sweeps, little is known about its functional significance. We used a Massively Parallel Reporter Assay (MPRA) to assay 5,353 high-frequency introgressed variants for their ability to modulate the gene expression within 170 bp of endogenous sequence. We identified 2,548 variants in active putative cis-regulatory elements (CREs) and 292 expression-modulating variants (emVars). These emVars are predicted to alter the binding motifs of important immune transcription factors, are enriched for associations with neutrophil and white blood cell count, and are associated with the expression of genes that function in innate immune pathways including inflammatory response and antiviral defense. We combined the MPRA data with other data sets to identify strong candidates to be driver variants of positive selection including an emVar that may contribute to protection against severe COVID-19 response. We endogenously deleted two CREs containing expression-modulation variants linked to immune function, rs11624425 and rs80317430, identifying their primary genic targets as ELMSAN1, and PAN2 and STAT2, respectively, three genes differentially expressed during influenza infection. Overall, we present the first database of experimentally identified expression-modulating Neanderthal-introgressed alleles contributing to potential immune response in modern humans.}, }
@article {pmid34615929, year = {2021}, author = {Rothschild, B and Haeusler, M}, title = {Possible vertebral brucellosis infection in a Neanderthal.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {19846}, pmid = {34615929}, issn = {2045-2322}, mesh = {Animals ; Brucellosis/*diagnosis/*microbiology ; Imaging, Three-Dimensional ; Male ; *Neanderthals ; Osteoarthritis/*diagnosis/*microbiology ; Skeleton ; Spine/diagnostic imaging/*microbiology/*pathology ; Tomography, X-Ray Computed ; }, abstract = {The La Chapelle-aux-Saints 1 skeleton of an old (>60-year-old) male Neanderthal is renowned for the advanced osteoarthritis of its spinal column and hip joint, and their implications for posture and lifestyle in these Mid- to Late Pleistocene humans. Reassessment of the pathologic lesions reveals erosions at multiple non-contiguous vertebrae and reactive bone formation extending far beyond the left hip joint, which suggests the additional diagnosis of brucellosis. This implies the earliest secure evidence of this zoonotic disease in hominin evolution. Brucellosis might have been transmitted via butchering or eating raw meat and is well compatible with the range of prey animals documented for Neanderthals. The associated infertility could have represented an important aspect of health in these late archaic humans.}, }
@article {pmid36465976, year = {2021}, author = {Smith, R and Moots, RJ and Murad, M and Wallace, GR}, title = {A Darwinian View of Behçet's Disease.}, journal = {Rheumatology and immunology research}, volume = {2}, number = {2}, pages = {91-99}, pmid = {36465976}, issn = {2719-4523}, abstract = {Behçet's disease (BD) is a multisystem inflammatory disorder of unknown etiology, characterized by oral and genital ulceration, with other complications including eye, skin, joint, and central nervous system (CNS) lesions. Diagnosis is based on clinical findings, which may differ between patients. There is a strong genetic basis for BD; however, only a few genes have been associated with the disease across the geographical spread of BD. In this article, we discuss the history and combination of genes involved in this complex disease in relation to the geographical range and present our view that the disease has developed from a Darwinian perspective, with different gene polymorphisms that affect the same biological pathway. Moreover, these mutations individually are protective mechanisms against the disease relevant to each region, which affected both archaic and modern humans.}, }
@article {pmid34570765, year = {2021}, author = {Findley, AS and Zhang, X and Boye, C and Lin, YL and Kalita, CA and Barreiro, L and Lohmueller, KE and Pique-Regi, R and Luca, F}, title = {A signature of Neanderthal introgression on molecular mechanisms of environmental responses.}, journal = {PLoS genetics}, volume = {17}, number = {9}, pages = {e1009493}, pmid = {34570765}, issn = {1553-7404}, support = {F30 GM131580/GM/NIGMS NIH HHS/United States ; R01 GM109215/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/genetics ; Alleles ; Animals ; *Environmental Exposure ; Gene Expression Regulation ; *Genome, Human ; Human Migration ; Humans ; Neanderthals/*genetics ; Polymorphism, Single Nucleotide ; Protein Binding ; Quantitative Trait Loci ; Transcription Factors/metabolism ; }, abstract = {Ancient human migrations led to the settlement of population groups in varied environmental contexts worldwide. The extent to which adaptation to local environments has shaped human genetic diversity is a longstanding question in human evolution. Recent studies have suggested that introgression of archaic alleles in the genome of modern humans may have contributed to adaptation to environmental pressures such as pathogen exposure. Functional genomic studies have demonstrated that variation in gene expression across individuals and in response to environmental perturbations is a main mechanism underlying complex trait variation. We considered gene expression response to in vitro treatments as a molecular phenotype to identify genes and regulatory variants that may have played an important role in adaptations to local environments. We investigated if Neanderthal introgression in the human genome may contribute to the transcriptional response to environmental perturbations. To this end we used eQTLs for genes differentially expressed in a panel of 52 cellular environments, resulting from 5 cell types and 26 treatments, including hormones, vitamins, drugs, and environmental contaminants. We found that SNPs with introgressed Neanderthal alleles (N-SNPs) disrupt binding of transcription factors important for environmental responses, including ionizing radiation and hypoxia, and for glucose metabolism. We identified an enrichment for N-SNPs among eQTLs for genes differentially expressed in response to 8 treatments, including glucocorticoids, caffeine, and vitamin D. Using Massively Parallel Reporter Assays (MPRA) data, we validated the regulatory function of 21 introgressed Neanderthal variants in the human genome, corresponding to 8 eQTLs regulating 15 genes that respond to environmental perturbations. These findings expand the set of environments where archaic introgression may have contributed to adaptations to local environments in modern humans and provide experimental validation for the regulatory function of introgressed variants.}, }
@article {pmid34528508, year = {2021}, author = {Yan, SM and Sherman, RM and Taylor, DJ and Nair, DR and Bortvin, AN and Schatz, MC and McCoy, RC}, title = {Local adaptation and archaic introgression shape global diversity at human structural variant loci.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34528508}, issn = {2050-084X}, support = {F31 HG012495/HG/NHGRI NIH HHS/United States ; R35 GM133747/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Animals ; Asian People ; *Evolution, Molecular ; Gene Flow ; *Genome, Human ; Genomics ; *Genotype ; Haplotypes/genetics ; Humans ; Linkage Disequilibrium ; Neanderthals/genetics ; Selection, Genetic ; }, abstract = {Large genomic insertions and deletions are a potent source of functional variation, but are challenging to resolve with short-read sequencing, limiting knowledge of the role of such structural variants (SVs) in human evolution. Here, we used a graph-based method to genotype long-read-discovered SVs in short-read data from diverse human genomes. We then applied an admixture-aware method to identify 220 SVs exhibiting extreme patterns of frequency differentiation - a signature of local adaptation. The top two variants traced to the immunoglobulin heavy chain locus, tagging a haplotype that swept to near fixation in certain southeast Asian populations, but is rare in other global populations. Further investigation revealed evidence that the haplotype traces to gene flow from Neanderthals, corroborating the role of immune-related genes as prominent targets of adaptive introgression. Our study demonstrates how recent technical advances can help resolve signatures of key evolutionary events that remained obscured within technically challenging regions of the genome.}, }
@article {pmid34493715, year = {2021}, author = {Coll Macià, M and Skov, L and Peter, BM and Schierup, MH}, title = {Different historical generation intervals in human populations inferred from Neanderthal fragment lengths and mutation signatures.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {5317}, pmid = {34493715}, issn = {2041-1723}, mesh = {Animals ; Asia ; Crosses, Genetic ; DNA, Ancient/*analysis ; Europe ; Female ; *Gene Flow ; *Genome, Human ; History, 21st Century ; History, Ancient ; Humans ; Male ; *Mutation ; Neanderthals/*genetics ; Polymorphism, Restriction Fragment Length ; }, abstract = {After the main Out-of-Africa event, humans interbred with Neanderthals leaving 1-2% of Neanderthal DNA scattered in small fragments in all non-African genomes today. Here we investigate what can be learned about human demographic processes from the size distribution of these fragments. We observe differences in fragment length across Eurasia with 12% longer fragments in East Asians than West Eurasians. Comparisons between extant populations with ancient samples show that these differences are caused by different rates of decay in length by recombination since the Neanderthal admixture. In concordance, we observe a strong correlation between the average fragment length and the mutation accumulation, similar to what is expected by changing the ages at reproduction as estimated from trio studies. Altogether, our results suggest differences in the generation interval across Eurasia, by up 10-20%, over the past 40,000 years. We use sex-specific mutation signatures to infer whether these changes were driven by shifts in either male or female age at reproduction, or both. We also find that previously reported variation in the mutational spectrum may be largely explained by changes to the generation interval. We conclude that Neanderthal fragment lengths provide unique insight into differences among human populations over recent history.}, }
@article {pmid34487600, year = {2021}, author = {Gregory, MD and Eisenberg, DP and Hamborg, M and Kippenhan, JS and Kohn, P and Kolachana, B and Dickinson, D and Berman, KF}, title = {Neanderthal-derived genetic variation in living humans relates to schizophrenia diagnosis, to psychotic symptom severity, and to dopamine synthesis.}, journal = {American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics}, volume = {186}, number = {5}, pages = {329-338}, pmid = {34487600}, issn = {1552-485X}, support = {ZIA MH002717/ImNIH/Intramural NIH HHS/United States ; U01 MH079469/MH/NIMH NIH HHS/United States ; R01 MH067257/MH/NIMH NIH HHS/United States ; R01 MH059587/MH/NIMH NIH HHS/United States ; R01 MH059586/MH/NIMH NIH HHS/United States ; R01 MH059566/MH/NIMH NIH HHS/United States ; R01 MH060879/MH/NIMH NIH HHS/United States ; R01 MH061675/MH/NIMH NIH HHS/United States ; Z99 MH999999/ImNIH/Intramural NIH HHS/United States ; R01 MH084098/MH/NIMH NIH HHS/United States ; U01 MH046276/MH/NIMH NIH HHS/United States ; R01 MH060870/MH/NIMH NIH HHS/United States ; R01 MH081800/MH/NIMH NIH HHS/United States ; ZIA MH002652/ImNIH/Intramural NIH HHS/United States ; R01 MH059571/MH/NIMH NIH HHS/United States ; R01 MH059565/MH/NIMH NIH HHS/United States ; U01 MH079470/MH/NIMH NIH HHS/United States ; ZIA MH002942/ImNIH/Intramural NIH HHS/United States ; U01 MH046289/MH/NIMH NIH HHS/United States ; RC2 MH089964/MH/NIMH NIH HHS/United States ; R01 MH059588/MH/NIMH NIH HHS/United States ; U01 MH046318/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; Dopamine ; Genetic Variation ; *Hominidae ; Humans ; *Neanderthals/genetics ; *Psychotic Disorders/diagnosis/genetics ; *Schizophrenia/diagnosis/genetics ; }, abstract = {Schizophrenia has been hypothesized to be a human-specific condition, but experimental approaches to testing this idea have been limited. Because Neanderthals, our closest evolutionary relatives, interbred with modern humans prior to their disappearance from the fossil record, leaving a residual echo that survives in our DNA today, we leveraged new discoveries about ancient hominid DNA to explore this hypothesis in living people in three converging ways. First, in four independent case-control datasets totaling 9,362 individuals, individuals with schizophrenia had less Neanderthal-derived genetic variation than controls (p = .044). Second, in 49 unmedicated inpatients with schizophrenia, having more Neanderthal admixture predicted less severe positive symptoms (p = .046). Finally, using [18] F-fluorodopa PET scanning in 172 healthy individuals, having greater Neanderthal introgression was significantly associated with lower dopamine synthesis capacity in the striatum and pons (p's < 2 × 10[-5]), which is fundamentally important in the pathophysiology and treatment of psychosis. These results may help to elucidate the evolutionary history of a devastating neuropsychiatric disease by supporting the notion of schizophrenia as a human-specific condition. Additionally, the relationship between Neanderthal admixture and dopamine function suggests a potential mechanism whereby Neanderthal admixture may have affected our gene pool to alter schizophrenia risk and/or course.}, }
@article {pmid34437543, year = {2021}, author = {Heydari-Guran, S and Benazzi, S and Talamo, S and Ghasidian, E and Hariri, N and Oxilia, G and Asiabani, S and Azizi, F and Naderi, R and Safaierad, R and Hublin, JJ and Foley, RA and Lahr, MM}, title = {The discovery of an in situ Neanderthal remain in the Bawa Yawan Rockshelter, West-Central Zagros Mountains, Kermanshah.}, journal = {PloS one}, volume = {16}, number = {8}, pages = {e0253708}, pmid = {34437543}, issn = {1932-6203}, mesh = {Animals ; Body Remains/anatomy &amp; histology ; Fossils/*anatomy &amp; histology ; History, Ancient ; Iran ; Neanderthals/*anatomy &amp; histology ; Tooth/anatomy &amp; histology ; }, abstract = {Neanderthal extinction has been a matter of debate for many years. New discoveries, better chronologies and genomic evidence have done much to clarify some of the issues. This evidence suggests that Neanderthals became extinct around 40,000-37,000 years before present (BP), after a period of coexistence with Homo sapiens of several millennia, involving biological and cultural interactions between the two groups. However, the bulk of this evidence relates to Western Eurasia, and recent work in Central Asia and Siberia has shown that there is considerable local variation. Southwestern Asia, despite having a number of significant Neanderthal remains, has not played a major part in the debate over extinction. Here we report a Neanderthal deciduous canine from the site of Bawa Yawan in the West-Central Zagros Mountains of Iran. The tooth is associated with Zagros Mousterian lithics, and its context is preliminary dated to between ~43,600 and ~41,500 years ago.}, }
@article {pmid34428206, year = {2021}, author = {Richards, MP and Mannino, MA and Jaouen, K and Dozio, A and Hublin, JJ and Peresani, M}, title = {Strontium isotope evidence for Neanderthal and modern human mobility at the upper and middle palaeolithic site of Fumane Cave (Italy).}, journal = {PloS one}, volume = {16}, number = {8}, pages = {e0254848}, pmid = {34428206}, issn = {1932-6203}, mesh = {Animals ; Archaeology ; *Caves ; Dental Enamel/chemistry ; Geography ; Hominidae ; Humans ; Italy ; Neanderthals/*physiology ; Strontium Isotopes/*analysis ; Time Factors ; Tooth/chemistry ; }, abstract = {To investigate the mobility patterns of Neanderthals and modern humans in Europe during the Middle-to-Upper Palaeolithic transition period, we applied strontium isotope analysis to Neanderthal (n = 3) and modern human (n = 2) teeth recovered from the site of Fumane Cave in the Monti Lessini region of Northern Italy. We also measured a large number of environmental samples from the region, to establish a strontium 'baseline', and also micromammals (vole teeth) from the levels associated with the hominin teeth. We found that the modern humans and Neanderthals had similar strontium isotope values, and these values match the local baseline values we obtained for the site and the surrounding region. We conclude that both groups were utilizing the local mountainous region where Fumane Cave is situated, and likely the nearby Lessini highlands and Adige plains, and therefore the strontium evidence does not show differening mobility patterns between Neanderthals and modern humans at the Fumane site.}, }
@article {pmid34403991, year = {2021}, author = {Estalrrich, A and Marín-Arroyo, AB}, title = {Evidence of habitual behavior from non-alimentary dental wear on deciduous teeth from the Middle and Upper Paleolithic Cantabrian region, Northern Spain.}, journal = {Journal of human evolution}, volume = {158}, number = {}, pages = {103047}, doi = {10.1016/j.jhevol.2021.103047}, pmid = {34403991}, issn = {1095-8606}, mesh = {Animals ; *Fossils ; History, Ancient ; Humans ; *Neanderthals ; Paleodontology ; Spain ; *Tooth Wear ; Tooth, Deciduous/*anatomy &amp; histology ; }, abstract = {The use of 'teeth as tools' (non-masticatory or cultural-related dental wear) has largely been employed as a proxy for studying of past human behavior, mainly in permanent dentition from adult individuals. Here we present the analysis of the non-masticatory dental wear modifications on the deciduous dentition assigned to eight Neanderthal and anatomically modern human subadult individuals from Mousterian to Magdalenian technocultural contexts in the Cantabrian region (Northern Spain). Although preliminary, we tentatively suggest that these eight subadults present activity-related dental wear, including cultural striations, chipped enamel, toothpick grooves, and subvertical grooves. We also found evidence of habitual dental hygienic practices in the form of toothpicking on a deciduous premolar. Orientation of the cultural striations indicates similar handedness development as in modern children. Taken together, these dental wear patterns support the participation of young individuals in group activities, making them potential contributors to group welfare. This study potentially adds new evidence to the importance of the use of the mouth in paramasticatory activities or as a third hand throughout the Pleistocene, which can be confirmed with a more specific reference sample.}, }
@article {pmid34386877, year = {2021}, author = {Paar, V and Vlahović, I and Rosandić, M and Glunčić, M}, title = {Global Repeat Map (GRM): Advantageous Method for Discovery of Largest Higher-Order Repeats (HORs) in Neuroblastoma Breakpoint Family (NBPF) Genes, in Hornerin Exon and in Chromosome 21 Centromere.}, journal = {Progress in molecular and subcellular biology}, volume = {60}, number = {}, pages = {203-234}, pmid = {34386877}, issn = {0079-6484}, mesh = {Animals ; Centromere ; *Chromosomes, Human, Pair 21 ; DNA, Satellite ; Exons ; Genome, Human/genetics ; Humans ; *Neuroblastoma/genetics ; }, abstract = {Here we present three interesting novel human Higher-Order Repeats (HORs) discovered using the HOR-searching method with GRM algorithm: (a) The novel Neuroblastoma Breakpoint Family gene (NBPF) 3mer HOR, discovered applying GRM algorithm to human chromosome 1 (Paar et al., Mol Biol Evol 28:1877-1892, 2011). NBPF 3mer HOR is based on previously known ~1.6 kb NBPF primary repeat monomers (known as DUF1220 domain) in human chromosome 1, but the NBPF HOR was not known before its discovery by using GRM. It should be stressed that the NBPF HOR presents a unique human-specific pattern, distinguishing human from nonhuman primates. (b) The novel quartic HOR (2mer⊃2mer⊃9mer) discovered using the GRM algorithm for analysis of hornerin genes in human chromosome 1 (Paar et al., Mol Biol Evol 28:1877-1892, 2011). This quartic HOR is based on 39 bp hornerin primary repeat monomer in human chromosome 1. To our knowledge, this is the first known case of quartic HOR, with four levels of hierarchy of HOR organization. (c) The novel 33mer alpha satellite HOR in human chromosome 21, discovered using the GRM algorithm (Glunčić et al., Sci Rep 9:12629, 2019). This 33mer HOR in the smallest human chromosome is the largest alpha satellite HOR copy among all 22 somatic human chromosomes. Moreover, the same 33mer HOR is present in the hg38 human genome assembly of four human chromosomes: 21, 22, 13, and 14. We point out that the DUF1220 encoding genomic structures in NBPF genes in human chromosome 1, recently studied and related to the brain evolution and pathologies and cognitive aptitude, can be considered in the framework of the general concept of HORs, already extensively studied in genomics, especially in the centromeric region.}, }
@article {pmid34352227, year = {2021}, author = {Almarri, MA and Haber, M and Lootah, RA and Hallast, P and Al Turki, S and Martin, HC and Xue, Y and Tyler-Smith, C}, title = {The genomic history of the Middle East.}, journal = {Cell}, volume = {184}, number = {18}, pages = {4612-4625.e14}, pmid = {34352227}, issn = {1097-4172}, support = {/WT_/Wellcome Trust/United Kingdom ; 098051//Wellcome/ ; }, mesh = {Animals ; Chromosomes, Human, Y/genetics ; Databases, Genetic ; Gene Pool ; Genetic Introgression ; Genetics, Population/*history ; *Genome, Human ; Geography ; History, Ancient ; Human Migration ; Humans ; Middle East ; Models, Genetic ; Neanderthals/genetics ; Phylogeny ; Population Density ; Selection, Genetic ; Sequence Analysis, DNA ; }, abstract = {The Middle East region is important to understand human evolution and migrations but is underrepresented in genomic studies. Here, we generated 137 high-coverage physically phased genome sequences from eight Middle Eastern populations using linked-read sequencing. We found no genetic traces of early expansions out-of-Africa in present-day populations but found Arabians have elevated Basal Eurasian ancestry that dilutes their Neanderthal ancestry. Population sizes within the region started diverging 15-20 kya, when Levantines expanded while Arabians maintained smaller populations that derived ancestry from local hunter-gatherers. Arabians suffered a population bottleneck around the aridification of Arabia 6 kya, while Levantines had a distinct bottleneck overlapping the 4.2 kya aridification event. We found an association between movement and admixture of populations in the region and the spread of Semitic languages. Finally, we identify variants that show evidence of selection, including polygenic selection. Our results provide detailed insights into the genomic and selective histories of the Middle East.}, }
@article {pmid34350666, year = {2021}, author = {Madison, P}, title = {Brutish Neanderthals: History of a merciless characterization.}, journal = {Evolutionary anthropology}, volume = {30}, number = {6}, pages = {366-374}, doi = {10.1002/evan.21918}, pmid = {34350666}, issn = {1520-6505}, support = {60669//John Templeton Foundation/ ; //School of Life Sciences, Arizona State University/ ; }, mesh = {Animals ; Humans ; *Neanderthals ; }, abstract = {The idea that Neanderthals were brutish and unintelligent is often traced back to Marcellin Boule, a French paleontologist who examined the specimen known as the Old Man in the first decades of the 20th century. This article examines the work of Boule's predecessors and aggregate a variety of literature to underline an argument that this idea has much earlier origins and is rooted in the first recognized specimen discovered in the Neander Valley in 1856. Reorienting our understanding of the brutish Neanderthal to account for its 19th-century origins, allows for a reexamination of the factors in 19th-century culture, science, and society which contributed to this caricature, especially the concepts of race and species' extinction. Such a reexamination dismantles the narrative of Boule's error while providing a new vantage point to think about Neanderthals in the present.}, }
@article {pmid34340120, year = {2021}, author = {Bowland, LA and Scott, JE and Kivell, TL and Patel, BA and Tocheri, MW and Orr, CM}, title = {Homo naledi pollical metacarpal shaft morphology is distinctive and intermediate between that of australopiths and other members of the genus Homo.}, journal = {Journal of human evolution}, volume = {158}, number = {}, pages = {103048}, doi = {10.1016/j.jhevol.2021.103048}, pmid = {34340120}, issn = {1095-8606}, support = {BCS-1539741//National Science Foundation/ ; BCS-1317047//National Science Foundation/ ; P40 OD012217/OD/NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Caves ; *Fossils ; Haplorhini/anatomy &amp; histology ; Hominidae/*anatomy &amp; histology ; Humans ; Metacarpal Bones/*anatomy &amp; histology ; Neanderthals/anatomy &amp; histology ; }, abstract = {Homo naledi fossils from the Rising Star cave system provide important insights into the diversity of hand morphology within the genus Homo. Notably, the pollical (thumb) metacarpal (Mc1) displays an unusual suite of characteristics including a median longitudinal crest, a narrow proximal base, and broad flaring intrinsic muscle flanges. The present study evaluates the affinities of H. naledi Mc1 morphology via 3D geometric morphometric analysis of shaft shape using a broader comparative sample (n = 337) of fossil hominins, recent humans, apes, and cercopithecoid monkeys than in prior work. Results confirm that the H. naledi Mc1 is distinctive from most other hominins in being narrow at the proximal end but surmounted by flaring muscle flanges distally. Only StW 418 (Australopithecus cf. africanus) is similar in these aspects of shape. The gracile proximal shaft is most similar to cercopithecoids, Pan, Pongo, Australopithecus afarensis, and Australopithecus sediba, suggesting that H. naledi retains the condition primitive for the genus Homo. In contrast, Neandertal Mc1s are characterized by wide proximal bases and shafts, pinched midshafts, and broad distal flanges, while those of recent humans generally have straight shafts, less robust muscle flanges, and wide proximal shafts/bases. Although uncertainties remain regarding character polarity, the morphology of the H. naledi thumb might be interpreted as a retained intermediate state in a transformation series between the overall gracility of the shaft and the robust shafts of later hominins. Such a model suggests that the addition of broad medial and lateral muscle flanges to a primitively slender shaft was the first modification in transforming the Mc1 into the overall more robust structure exhibited by other Homo taxa including Neandertals and recent Homo sapiens in whose shared lineage the bases and proximal shafts became expanded, possibly as an adaptation to the repeated recruitment of powerful intrinsic pollical muscles.}, }
@article {pmid34335974, year = {2021}, author = {Zhang, Q and Wadgaonkar, P and Xu, L and Thakur, C and Fu, Y and Bi, Z and Qiu, Y and Almutairy, B and Zhang, W and Stemmer, P and Chen, F}, title = {Environmentally-induced mdig contributes to the severity of COVID-19 through fostering expression of SARS-CoV-2 receptor NRPs and glycan metabolism.}, journal = {Theranostics}, volume = {11}, number = {16}, pages = {7970-7983}, pmid = {34335974}, issn = {1838-7640}, support = {R01 ES028263/ES/NIEHS NIH HHS/United States ; R01 ES028335/ES/NIEHS NIH HHS/United States ; R01 ES031822/ES/NIEHS NIH HHS/United States ; }, mesh = {Alveolar Epithelial Cells/metabolism ; Animals ; COVID-19/epidemiology/*metabolism/*virology ; Cathepsins/metabolism ; Cell Line ; Cells, Cultured ; Dioxygenases/biosynthesis/genetics/*metabolism ; Environmental Exposure ; Histone Demethylases/biosynthesis/genetics/*metabolism ; Histones/metabolism ; Humans ; Neuropilin-1/*metabolism ; Nuclear Proteins/biosynthesis/genetics/*metabolism ; Pandemics ; Polysaccharides/*metabolism ; Rats ; SARS-CoV-2/*metabolism/pathogenicity ; Spike Glycoprotein, Coronavirus/metabolism ; }, abstract = {The novel β-coronavirus, SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19), has infected more than 177 million people and resulted in 3.84 million death worldwide. Recent epidemiological studies suggested that some environmental factors, such as air pollution, might be the important contributors to the mortality of COVID-19. However, how environmental exposure enhances the severity of COVID-19 remains to be fully understood. In the present report, we provided evidence showing that mdig, a previously reported environmentally-induced oncogene that antagonizes repressive trimethylation of histone proteins, is an important regulator for SARS-CoV-2 receptors neuropilin-1 (NRP1) and NRP2, cathepsins, glycan metabolism and inflammation, key determinants for viral infection and cytokine storm of the patients. Depletion of mdig in bronchial epithelial cells by CRISPR-Cas-9 gene editing resulted in a decreased expression of NRP1, NRP2, cathepsins, and genes involved in protein glycosylation and inflammation, largely due to a substantial enrichment of lysine 9 and/or lysine 27 trimethylation of histone H3 (H3K9me3/H3K27me3) on these genes as determined by ChIP-seq. Meanwhile, we also validated that environmental factor arsenic is able to induce mdig, NRP1 and NRP2, and genetic disruption of mdig lowered expression of NRP1 and NRP2. Furthermore, mdig may coordinate with the Neanderthal variants linked to an elevated mortality of COVID-19. These data, thus, suggest that mdig is a key mediator for the severity of COVID-19 in response to environmental exposure and targeting mdig may be the one of the effective strategies in ameliorating the symptom and reducing the mortality of COVID-19.}, }
@article {pmid34320013, year = {2021}, author = {Condemi, S and Mazières, S and Faux, P and Costedoat, C and Ruiz-Linares, A and Bailly, P and Chiaroni, J}, title = {Blood groups of Neandertals and Denisova decrypted.}, journal = {PloS one}, volume = {16}, number = {7}, pages = {e0254175}, pmid = {34320013}, issn = {1932-6203}, mesh = {Alleles ; Animals ; Blood Group Antigens/*genetics ; Fossils ; Genetic Variation ; Genotype ; Hominidae/*genetics ; INDEL Mutation ; Neanderthals/*genetics ; Phenotype ; Polymorphism, Genetic ; }, abstract = {Blood group systems were the first phenotypic markers used in anthropology to decipher the origin of populations, their migratory movements, and their admixture. The recent emergence of new technologies based on the decoding of nucleic acids from an individual's entire genome has relegated them to their primary application, blood transfusion. Thus, despite the finer mapping of the modern human genome in relation to Neanderthal and Denisova populations, little is known about red cell blood groups in these archaic populations. Here we analyze the available high-quality sequences of three Neanderthals and one Denisovan individuals for 7 blood group systems that are used today in transfusion (ABO including H/Se, Rh (Rhesus), Kell, Duffy, Kidd, MNS, Diego). We show that Neanderthal and Denisova were polymorphic for ABO and shared blood group alleles recurrent in modern Sub-Saharan populations. Furthermore, we found ABO-related alleles currently preventing from viral gut infection and Neanderthal RHD and RHCE alleles nowadays associated with a high risk of hemolytic disease of the fetus and newborn. Such a common blood group pattern across time and space is coherent with a Neanderthal population of low genetic diversity exposed to low reproductive success and with their inevitable demise. Lastly, we connect a Neanderthal RHD allele to two present-day Aboriginal Australian and Papuan, suggesting that a segment of archaic genome was introgressed in this gene in non-Eurasian populations. While contributing to both the origin and late evolutionary history of Neanderthal and Denisova, our results further illustrate that blood group systems are a relevant piece of the puzzle helping to decipher it.}, }
@article {pmid34294692, year = {2021}, author = {McArthur, E and Rinker, DC and Capra, JA}, title = {Quantifying the contribution of Neanderthal introgression to the heritability of complex traits.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {4481}, pmid = {34294692}, issn = {2041-1723}, support = {F30 HG011200/HG/NHGRI NIH HHS/United States ; R35 GM127087/GM/NIGMS NIH HHS/United States ; T32 GM007347/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/genetics ; Alleles ; Animals ; Cognition ; Female ; *Genetic Introgression ; Genetic Variation ; Genome, Human ; Genome-Wide Association Study ; Hair/anatomy &amp; histology ; Humans ; Linkage Disequilibrium ; Male ; *Models, Genetic ; *Multifactorial Inheritance ; Neanderthals/anatomy &amp; histology/*genetics/physiology ; Phenotype ; Selection, Genetic ; }, abstract = {Eurasians have ~2% Neanderthal ancestry, but we lack a comprehensive understanding of the genome-wide influence of Neanderthal introgression on modern human diseases and traits. Here, we quantify the contribution of introgressed alleles to the heritability of more than 400 diverse traits. We show that genomic regions in which detectable Neanderthal ancestry remains are depleted of heritability for all traits considered, except those related to skin and hair. Introgressed variants themselves are also depleted for contributions to the heritability of most traits. However, introgressed variants shared across multiple Neanderthal populations are enriched for heritability and have consistent directions of effect on several traits with potential relevance to human adaptation to non-African environments, including hair and skin traits, autoimmunity, chronotype, bone density, lung capacity, and menopause age. Integrating our results, we propose a model in which selection against introgressed functional variation was the dominant trend (especially for cognitive traits); however, for a few traits, introgressed variants provided beneficial variation via uni-directional (e.g., lightening skin color) or bi-directional (e.g., modulating immune response) effects.}, }
@article {pmid34272242, year = {2021}, author = {Schaefer, NK and Shapiro, B and Green, RE}, title = {An ancestral recombination graph of human, Neanderthal, and Denisovan genomes.}, journal = {Science advances}, volume = {7}, number = {29}, pages = {}, pmid = {34272242}, issn = {2375-2548}, support = {T32 HG008345/HG/NHGRI NIH HHS/United States ; T32 HG00834/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Genome, Human ; Genomics ; *Hominidae/genetics ; Humans ; *Neanderthals/genetics ; Recombination, Genetic ; }, abstract = {Many humans carry genes from Neanderthals, a legacy of past admixture. Existing methods detect this archaic hominin ancestry within human genomes using patterns of linkage disequilibrium or direct comparison to Neanderthal genomes. Each of these methods is limited in sensitivity and scalability. We describe a new ancestral recombination graph inference algorithm that scales to large genome-wide datasets and demonstrate its accuracy on real and simulated data. We then generate a genome-wide ancestral recombination graph including human and archaic hominin genomes. From this, we generate a map within human genomes of archaic ancestry and of genomic regions not shared with archaic hominins either by admixture or incomplete lineage sorting. We find that only 1.5 to 7% of the modern human genome is uniquely human. We also find evidence of multiple bursts of adaptive changes specific to modern humans within the past 600,000 years involving genes related to brain development and function.}, }
@article {pmid34254144, year = {2021}, author = {Iasi, LNM and Ringbauer, H and Peter, BM}, title = {An Extended Admixture Pulse Model Reveals the Limitations to Human-Neandertal Introgression Dating.}, journal = {Molecular biology and evolution}, volume = {38}, number = {11}, pages = {5156-5174}, pmid = {34254144}, issn = {1537-1719}, support = {694707/ERC_/European Research Council/International ; }, mesh = {Animals ; DNA/genetics ; Gene Flow ; Genome ; Humans ; *Neanderthals/genetics ; }, abstract = {Neandertal DNA makes up 2-3% of the genomes of all non-African individuals. The patterns of Neandertal ancestry in modern humans have been used to estimate that this is the result of gene flow that occurred during the expansion of modern humans into Eurasia, but the precise dates of this event remain largely unknown. Here, we introduce an extended admixture pulse model that allows joint estimation of the timing and duration of gene flow. This model leads to simple expressions for both the admixture segment distribution and the decay curve of ancestry linkage disequilibrium, and we show that these two statistics are closely related. In simulations, we find that estimates of the mean time of admixture are largely robust to details in gene flow models, but that the duration of the gene flow can only be recovered if gene flow is very recent and the exact recombination map is known. These results imply that gene flow from Neandertals into modern humans could have happened over hundreds of generations. Ancient genomes from the time around the admixture event are thus likely required to resolve the question when, where, and for how long humans and Neandertals interacted.}, }
@article {pmid34226702, year = {2021}, author = {Leder, D and Hermann, R and Hüls, M and Russo, G and Hoelzmann, P and Nielbock, R and Böhner, U and Lehmann, J and Meier, M and Schwalb, A and Tröller-Reimer, A and Koddenberg, T and Terberger, T}, title = {A 51,000-year-old engraved bone reveals Neanderthals' capacity for symbolic behaviour.}, journal = {Nature ecology &amp; evolution}, volume = {5}, number = {9}, pages = {1273-1282}, pmid = {34226702}, issn = {2397-334X}, mesh = {Animals ; Bone and Bones ; Caves ; *Deer ; Europe ; Humans ; Infant, Newborn ; *Neanderthals ; }, abstract = {While there is substantial evidence for art and symbolic behaviour in early Homo sapiens across Africa and Eurasia, similar evidence connected to Neanderthals is sparse and often contested in scientific debates. Each new discovery is thus crucial for our understanding of Neanderthals' cognitive capacity. Here we report on the discovery of an at least 51,000-year-old engraved giant deer phalanx found at the former cave entrance of Einhornhöhle, northern Germany. The find comes from an apparent Middle Palaeolithic context that is linked to Neanderthals. The engraved bone demonstrates that conceptual imagination, as a prerequisite to compose individual lines into a coherent design, was present in Neanderthals. Therefore, Neanderthal's awareness of symbolic meaning is very likely. Our findings show that Neanderthals were capable of creating symbolic expressions before H. sapiens arrived in Central Europe.}, }
@article {pmid34226701, year = {2021}, author = {Bello, SM}, title = {Boning up on Neanderthal art.}, journal = {Nature ecology &amp; evolution}, volume = {5}, number = {9}, pages = {1201-1202}, pmid = {34226701}, issn = {2397-334X}, mesh = {Animals ; Meat/analysis ; *Neanderthals ; }, }
@article {pmid34214909, year = {2021}, author = {Bergmann, I and Hublin, JJ and Gunz, P and Freidline, SE}, title = {How did modern morphology evolve in the human mandible? The relationship between static adult allometry and mandibular variability in Homo sapiens.}, journal = {Journal of human evolution}, volume = {157}, number = {}, pages = {103026}, doi = {10.1016/j.jhevol.2021.103026}, pmid = {34214909}, issn = {1095-8606}, mesh = {Adult ; Animals ; Female ; *Fossils ; Humans ; Male ; Mandible/*anatomy &amp; histology ; Neanderthals/anatomy &amp; histology ; }, abstract = {Key to understanding human origins are early Homo sapiens fossils from Jebel Irhoud, as well as from the early Late Pleistocene sites Tabun, Border Cave, Klasies River Mouth, Skhul, and Qafzeh. While their upper facial shape falls within the recent human range of variation, their mandibles display a mosaic morphology. Here we quantify how mandibular shape covaries with mandible size and how static allometry differs between Neanderthals, early H. sapiens, and modern humans from the Upper Paleolithic/Later Stone Age and Holocene (= later H. sapiens). We use 3D (semi)landmark geometric morphometric methods to visualize allometric trends and to explore how gracilization affects the expression of diagnostic shape features. Early H. sapiens were highly variable in mandible size, exhibiting a unique allometric trajectory that explains aspects of their 'archaic' appearance. At the same time, early H. sapiens share a suite of diagnostic features with later H. sapiens that are not related to mandibular sizes, such as an incipient chin and an anteroposteriorly decreasing corpus height. The mandibular morphology, often referred to as 'modern', can partly be explained by gracilization owing to size reduction. Despite distinct static allometric shape changes in each group studied, bicondylar and bigonial breadth represent important structural constraints for the expression of shape features in most Middle to Late Pleistocene hominin mandibles.}, }
@article {pmid34163072, year = {2021}, author = {Zavala, EI and Jacobs, Z and Vernot, B and Shunkov, MV and Kozlikin, MB and Derevianko, AP and Essel, E and de Fillipo, C and Nagel, S and Richter, J and Romagné, F and Schmidt, A and Li, B and O'Gorman, K and Slon, V and Kelso, J and Pääbo, S and Roberts, RG and Meyer, M}, title = {Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave.}, journal = {Nature}, volume = {595}, number = {7867}, pages = {399-403}, pmid = {34163072}, issn = {1476-4687}, support = {/ERC_/European Research Council/International ; }, mesh = {Animals ; Archaeology ; *Caves ; DNA, Ancient/*analysis ; DNA, Mitochondrial/analysis/genetics ; Fossils ; Geologic Sediments/*chemistry ; History, Ancient ; Hominidae/*genetics ; Neanderthals/genetics ; Siberia ; }, abstract = {Denisova Cave in southern Siberia is the type locality of the Denisovans, an archaic hominin group who were related to Neanderthals[1-4]. The dozen hominin remains recovered from the deposits also include Neanderthals[5,6] and the child of a Neanderthal and a Denisovan[7], which suggests that Denisova Cave was a contact zone between these archaic hominins. However, uncertainties persist about the order in which these groups appeared at the site, the timing and environmental context of hominin occupation, and the association of particular hominin groups with archaeological assemblages[5,8-11]. Here we report the analysis of DNA from 728 sediment samples that were collected in a grid-like manner from layers dating to the Pleistocene epoch. We retrieved ancient faunal and hominin mitochondrial (mt)DNA from 685 and 175 samples, respectively. The earliest evidence for hominin mtDNA is of Denisovans, and is associated with early Middle Palaeolithic stone tools that were deposited approximately 250,000 to 170,000 years ago; Neanderthal mtDNA first appears towards the end of this period. We detect a turnover in the mtDNA of Denisovans that coincides with changes in the composition of faunal mtDNA, and evidence that Denisovans and Neanderthals occupied the site repeatedly-possibly until, or after, the onset of the Initial Upper Palaeolithic at least 45,000 years ago, when modern human mtDNA is first recorded in the sediments.}, }
@article {pmid34155119, year = {2021}, author = {Van Peer, P}, title = {The stratigraphic context of Spy Cave and the timing of Neanderthal disappearance in Northwest Europe.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {26}, pages = {}, pmid = {34155119}, issn = {1091-6490}, mesh = {Animals ; Caves ; Europe ; *Neanderthals ; Radiometric Dating ; }, }
@article {pmid34150310, year = {2021}, author = {Amos, W}, title = {Correlated and geographically predictable Neanderthal and Denisovan legacies are difficult to reconcile with a simple model based on inter-breeding.}, journal = {Royal Society open science}, volume = {8}, number = {6}, pages = {201229}, pmid = {34150310}, issn = {2054-5703}, abstract = {Although the presence of archaic hominin legacies in humans is taken for granted, little attention has been given as to how the data fit with how humans colonized the world. Here, I show that Neanderthal and Denisovan legacies are strongly correlated and that inferred legacy size, like heterozygosity, exhibits a strong correlation with distance from Africa. Simulations confirm that, once created, legacy size is extremely stable: it may reduce through admixture with lower legacy populations but cannot increase significantly through neutral drift. Consequently, populations carrying the highest legacies are likely to be those whose ancestors inter-bred most with archaics. However, the populations with the highest legacies are globally scattered and are unified, not by having origins within the known Neanderthal range, but instead by living in locations that lie furthest from Africa. Furthermore, the Simons Genome Diversity Project data reveal two distinct correlations between Neanderthal and Denisovan legacies, one that starts in North Africa and increases west to east across Eurasia and into some parts of Oceania, and a second, much steeper trend that starts in Africa, peaking with the San and Ju/'hoansi and which, if extrapolated, predicts the large inferred legacies of both archaics found in Oceania/Australia. Similar 'double' trends are observed for the introgression statistic f 4 in a second large dataset published by Qin and Stoneking (Qin &amp; Stoneking 2015 Mol. Biol. Evol. 32, 2665-2674 (doi:10.1093/molbev/msv141)). These trends appear at odds with simple models of how introgression occurred though more complicated patterns of introgression could potentially generate better fits. Moreover, substituting archaic genomes with those of great apes yields similar but biologically impossible signals of introgression, suggesting that the signals these metrics capture arise within humans and are largely independent of the test group. Interestingly, the data do appear to fit a speculative model in which the loss of diversity that occurred when humans moved further from Africa created a gradient in heterozygosity that in turn progressively reduced mutation rate such that populations furthest from Africa have diverged less from our common ancestor and hence from the archaics. In this light, the two distinct trends could be interpreted in terms of two 'out of Africa' events, an early one ending in Oceania and Australia and a later one that colonized Eurasia and the Americas.}, }
@article {pmid34148308, year = {2021}, author = {Jeworutzki, E and Tüttelmann, F and Rothenberg, I and Pusch, M and Schreiber, JA and Kliesch, S and Wünsch, B and Strutz-Seebohm, N and Seebohm, G}, title = {Can Unlikely Neanderthal Chloride Channel CLC-2 Gene Variants Provide Insights in Modern Human Infertility?.}, journal = {Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology}, volume = {55}, number = {3}, pages = {301-310}, doi = {10.33594/000000376}, pmid = {34148308}, issn = {1421-9778}, support = {CRU326//Deutsche Forschungsgemeinschaft (DFG)/Germany ; GRK2515//Deutsche Forschungsgemeinschaft (DFG)/Germany ; #IG21558//Fondazione AIRC per la Ricerca sul Cancro/Italy ; PRIN 20174TB8KW//Italian Research Ministry/Italy ; }, mesh = {Animals ; CLC-2 Chloride Channels ; *Chloride Channels/genetics/metabolism ; *Genetic Variation ; Humans ; *Infertility, Male ; Male ; *Neanderthals/genetics/metabolism ; Oocytes/metabolism ; Xenopus laevis ; }, abstract = {BACKGROUND/AIMS: Neanderthals, although well adapted to local environments, were rapidly replaced by anatomically modern humans (AMH) for unknown reasons. Genetic information on Neanderthals is limited restricting applicability of standard population genetics.<br><br>METHODS: Here, we apply a novel combination of restricted genetic analyses on preselected physiological key players (ion channels), electrophysiological analyses of gene variants of unclear significance expressed in Xenopus laevis oocytes using two electrode voltage clamp and transfer of results to AMH genetics. Using genetic screening in infertile men identified a loss of CLC-2 associated with sperm deficiency.<br><br>RESULTS: Increased genetic variation caused functionally impaired Neanderthals CLC-2 channels.<br><br>CONCLUSION: Increased genetic variation could reflect an adaptation to different local salt supplies at the cost of reduced sperm density. Interestingly and consistent with this hypothesis, lack of CLC-2 protein in a patient associates with high blood K[+] concentration and azoospermia.}, }
@article {pmid34140364, year = {2021}, author = {Gibbons, A}, title = {Genomes offer rare glimpse of Neanderthal family groups.}, journal = {Science (New York, N.Y.)}, volume = {372}, number = {6548}, pages = {1251-1252}, doi = {10.1126/science.372.6548.1251}, pmid = {34140364}, issn = {1095-9203}, mesh = {Animals ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; Family ; Female ; *Genome ; Male ; Neanderthals/*genetics ; Sociological Factors ; Y Chromosome ; }, }
@article {pmid34132815, year = {2021}, author = {Levi, G and de Lombares, C and Giuliani, C and Iannuzzi, V and Aouci, R and Garagnani, P and Franceschi, C and Grimaud-Hervé, D and Narboux-Nême, N}, title = {DLX5/6 GABAergic Expression Affects Social Vocalization: Implications for Human Evolution.}, journal = {Molecular biology and evolution}, volume = {38}, number = {11}, pages = {4748-4764}, pmid = {34132815}, issn = {1537-1719}, mesh = {Animals ; Genes, Homeobox ; Homeodomain Proteins/genetics/metabolism ; Humans ; Mice ; *Neanderthals/genetics ; Transcription Factors/genetics/metabolism ; *Transcription Factors, TFII/genetics ; Vocalization, Animal ; }, abstract = {DLX5 and DLX6 are two closely related transcription factors involved in brain development and in GABAergic differentiation. The DLX5/6 locus is regulated by FoxP2, a gene involved in language evolution and has been associated with neurodevelopmental disorders and mental retardation. Targeted inactivation of Dlx5/6 in mouse GABAergic neurons (Dlx5/6VgatCre mice) results in behavioral and metabolic phenotypes notably increasing lifespan by 33%. Here, we show that Dlx5/6VgatCre mice present a hyper-vocalization and hyper-socialization phenotype. While only 7% of control mice emitted more than 700 vocalizations/10 min, 30% and 56% of heterozygous or homozygous Dlx5/6VgatCre mice emitted more than 700 and up to 1,400 calls/10 min with a higher proportion of complex and modulated calls. Hyper-vocalizing animals were more sociable: the time spent in dynamic interactions with an unknown visitor was more than doubled compared to low-vocalizing individuals. The characters affected by Dlx5/6 in the mouse (sociability, vocalization, skull, and brain shape…) overlap those affected in the "domestication syndrome". We therefore explored the possibility that DLX5/6 played a role in human evolution and "self-domestication" comparing DLX5/6 genomic regions from Neanderthal and modern humans. We identified an introgressed Neanderthal haplotype (DLX5/6-N-Haplotype) present in 12.6% of European individuals that covers DLX5/6 coding and regulatory sequences. The DLX5/6-N-Haplotype includes the binding site for GTF2I, a gene associated with Williams-Beuren syndrome, a hyper-sociability and hyper-vocalization neurodevelopmental disorder. The DLX5/6-N-Haplotype is significantly underrepresented in semi-supercentenarians (>105 years of age), a well-established human model of healthy aging and longevity, suggesting their involvement in the coevolution of longevity, sociability, and speech.}, }
@article {pmid34117635, year = {2021}, author = {Antonio, P and Costantino, B and Silvia, C and Marina, M and Paolo, P and Alessio, V and Pasquale, R}, title = {Arothron: An R package for geometric morphometric methods and virtual anthropology applications.}, journal = {American journal of physical anthropology}, volume = {176}, number = {1}, pages = {144-151}, doi = {10.1002/ajpa.24340}, pmid = {34117635}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; Anthropometry/*methods ; Bone and Bones/*anatomy &amp; histology/diagnostic imaging ; Female ; Fossils/*anatomy &amp; histology/diagnostic imaging ; Humans ; Imaging, Three-Dimensional/*methods ; Male ; Neanderthals ; *Software ; Tooth/anatomy &amp; histology/diagnostic imaging ; }, abstract = {OBJECTIVES: The statistical analysis of fossil remains is essential to understand the evolution of the genus Homo. Unfortunately, the human fossil record is straight away scarce and plagued with severe loss of information caused by taphonomic processes. The recently developed field of Virtual Anthropology helps to ameliorate this situation by using digital techniques to restore damaged and incomplete fossils.<br><br>MATERIALS AND METHODS: We present the package Arothron, an R software suite meant to process and analyze digital models of skeletal elements. Arothron includes tools to digitally extract virtual cavities such as cranial endocasts, to statistically align disarticulated or broken bony elements, and to visualize local variations between surface meshes and landmark configurations.<br><br>RESULTS: We describe the main functionalities of Arothron and illustrate their usage through reproducible case studies. We describe a tool for segmentation of skeletal cavities by showing its application on a malleus bone, a Neanderthal tooth, and a modern human cranium, reproducing their shape and calculating their volume. We illustrate how to digitally align a disarticulated model of a modern human cranium, and how to combine piecemeal shape information on individual specimens into one. In addition, we present useful visualization tools by comparing the morphological differences between the right hemisphere of the Neanderthal and the modern human brain.<br><br>CONCLUSIONS: The Arothron R package is designed to study digital models of fossil specimens. By using Arothron, scientists can handle digital models with ease, investigate the inner morphology of 3D skeletal models, gain a full representation of the original shapes of damaged specimens, and compare shapes across specimens.}, }
@article {pmid34117310, year = {2021}, author = {Singh, PP and Srivastava, A and Sultana, GNN and Khanam, N and Pathak, A and Suravajhala, P and Singh, R and Shrivastava, P and van Driem, G and Thangaraj, K and Chaubey, G}, title = {The major genetic risk factor for severe COVID-19 does not show any association among South Asian populations.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {12346}, pmid = {34117310}, issn = {2045-2322}, mesh = {Angiotensin-Converting Enzyme 2/genetics ; Asian People/*genetics ; COVID-19/*pathology/virology ; Gene Frequency ; Genetic Loci ; Haplotypes ; Humans ; Polymorphism, Single Nucleotide ; Risk Factors ; SARS-CoV-2/isolation &amp; purification ; }, abstract = {With the growing evidence on the variable human susceptibility against COVID-19, it is evident that some genetic loci modulate the severity of the infection. Recent studies have identified several loci associated with greater severity. More recently, a study has identified a 50 kb genomic segment introgressed from Neanderthal adding a risk for COVID-19, and this genomic segment is present among 16% and 50% people of European and South Asian descent, respectively. Our studies on ACE2 identified a haplotype present among 20% and 60% of European and South Asian populations, respectively, which appears to be responsible for the low case fatality rate among South Asian populations. This result was also consistent with the real-time infection rate and case fatality rate among various states of India. We readdressed this issue using both of the contrasting datasets and compared them with the real-time infection rates and case fatality rate in India. We found that the polymorphism present in the 50 kb introgressed genomic segment (rs10490770) did not show any significant correlation with the infection and case fatality rate in India.}, }
@article {pmid34095864, year = {2021}, author = {Zhou, Y and Browning, SR}, title = {Protocol for detecting introgressed archaic variants with SPrime.}, journal = {STAR protocols}, volume = {2}, number = {2}, pages = {100550}, pmid = {34095864}, issn = {2666-1667}, support = {R01 HG010869/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; DNA, Ancient/analysis ; Genetic Introgression/*genetics ; Genomics/*methods ; Hominidae/genetics ; Humans ; Neanderthals/*genetics ; }, abstract = {The SPrime program detects the variants in current-day populations that were introgressed from an archaic source in the past. It is optimized for detecting introgression from Neanderthals and Denisovans in modern humans. We provide a protocol for detecting Neanderthal and Denisovan introgression in 1000 Genomes Project data, specifically focusing on the CHB (Han Chinese in Beijing) population. For complete details on the use and execution of this protocol, please refer to Browning et al. (2018).}, }
@article {pmid34073168, year = {2021}, author = {Folgerø, PO and Johansson, C and Stokkedal, LH}, title = {The Superior Visual Perception Hypothesis: Neuroaesthetics of Cave Art.}, journal = {Behavioral sciences (Basel, Switzerland)}, volume = {11}, number = {6}, pages = {}, pmid = {34073168}, issn = {2076-328X}, abstract = {Cave Art in the Upper Paleolithic presents a boost of creativity and visual thinking. What can explain these savant-like paintings? The normal brain function in modern man rarely supports the creation of highly detailed paintings, particularly the convincing representation of animal movement, without extensive training and access to modern technology. Differences in neuro-signaling and brain anatomy between modern and archaic Homo sapiens could also cause differences in perception. The brain of archaic Homo sapiens could perceive raw detailed information without using pre-established top-down concepts, as opposed to the common understanding of the normal modern non-savant brain driven by top-down control. Some ancient genes preserved in modern humans may be expressed in rare disorders. Researchers have compared Cave Art with art made by people with autism spectrum disorder. We propose that archaic primary consciousness, as opposed to modern secondary consciousness, included a savant-like perception with a superior richness of details compared to modern man. Modern people with high frequencies of Neanderthal genes, have notable anatomical features such as increased skull width in the occipital and parietal visual areas. We hypothesize that the anatomical differences are functional and may allow a different path to visual perception.}, }
@article {pmid34051612, year = {2021}, author = {Salazar-García, DC and Power, RC and Rudaya, N and Kolobova, K and Markin, S and Krivoshapkin, A and Henry, AG and Richards, MP and Viola, B}, title = {Dietary evidence from Central Asian Neanderthals: A combined isotope and plant microremains approach at Chagyrskaya Cave (Altai, Russia).}, journal = {Journal of human evolution}, volume = {156}, number = {}, pages = {102985}, doi = {10.1016/j.jhevol.2021.102985}, pmid = {34051612}, issn = {1095-8606}, mesh = {Animals ; *Archaeology ; *Caves ; Diet/*history ; History, Ancient ; Humans ; Isotopes/analysis ; *Neanderthals ; *Plants ; Russia ; }, abstract = {Neanderthals are known primarily from their habitation of Western Eurasia, but they also populated large expanses of Northern Asia for thousands of years. Owing to a sparse archaeological record, relatively little is known about these eastern Neanderthal populations. Unlike in their western range, there are limited zooarchaeological and paleobotanical studies that inform us about the nature of their subsistence. Here, we perform a combined analysis of carbon and nitrogen stable isotopes on bone collagen and microbotanical remains in dental calculus to reconstruct the diet of eastern Neanderthals at Chagyrskaya Cave in the Altai Mountains of Southern Siberia, Russia. Stable isotopes identify one individual as possessing a high trophic level due to the hunting of large- and medium-sized ungulates, while the analysis of dental calculus also indicates the presence of plants in the diet of this individual and others from the site. These findings indicate eastern Neanderthals may have had broadly similar subsistence patterns to those elsewhere in their range.}, }
@article {pmid34028527, year = {2021}, author = {Ahlquist, KD and Bañuelos, MM and Funk, A and Lai, J and Rong, S and Villanea, FA and Witt, KE}, title = {Our Tangled Family Tree: New Genomic Methods Offer Insight into the Legacy of Archaic Admixture.}, journal = {Genome biology and evolution}, volume = {13}, number = {7}, pages = {}, pmid = {34028527}, issn = {1759-6653}, support = {T32 GM007601/GM/NIGMS NIH HHS/United States ; R35 GM139628/GM/NIGMS NIH HHS/United States ; T32 GM128596/GM/NIGMS NIH HHS/United States ; R35 GM128946/GM/NIGMS NIH HHS/United States ; R01 GM127472/GM/NIGMS NIH HHS/United States ; R01 GM118652/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Genome, Human ; Genomics ; *Hominidae/genetics ; Humans ; *Neanderthals/genetics ; Pedigree ; }, abstract = {The archaic ancestry present in the human genome has captured the imagination of both scientists and the wider public in recent years. This excitement is the result of new studies pushing the envelope of what we can learn from the archaic genetic information that has survived for over 50,000 years in the human genome. Here, we review the most recent ten years of literature on the topic of archaic introgression, including the current state of knowledge on Neanderthal and Denisovan introgression, as well as introgression from other as-yet unidentified archaic populations. We focus this review on four topics: 1) a reimagining of human demographic history, including evidence for multiple admixture events between modern humans, Neanderthals, Denisovans, and other archaic populations; 2) state-of-the-art methods for detecting archaic ancestry in population-level genomic data; 3) how these novel methods can detect archaic introgression in modern African populations; and 4) the functional consequences of archaic gene variants, including how those variants were co-opted into novel function in modern human populations. The goal of this review is to provide a simple-to-access reference for the relevant methods and novel data, which has changed our understanding of the relationship between our species and its siblings. This body of literature reveals the large degree to which the genetic legacy of these extinct hominins has been integrated into the human populations of today.}, }
@article {pmid34010592, year = {2021}, author = {Svensson, E and Günther, T and Hoischen, A and Hervella, M and Munters, AR and Ioana, M and Ridiche, F and Edlund, H and van Deuren, RC and Soficaru, A and de-la-Rua, C and Netea, MG and Jakobsson, M}, title = {Genome of Peştera Muierii skull shows high diversity and low mutational load in pre-glacial Europe.}, journal = {Current biology : CB}, volume = {31}, number = {14}, pages = {2973-2983.e9}, doi = {10.1016/j.cub.2021.04.045}, pmid = {34010592}, issn = {1879-0445}, mesh = {Animals ; Emigration and Immigration ; Europe ; Female ; Genome, Human ; Humans ; Infant, Newborn ; *Neanderthals/genetics ; Skull ; }, abstract = {Few complete human genomes from the European Early Upper Palaeolithic (EUP) have been sequenced. Using novel sampling and DNA extraction approaches, we sequenced the genome of a woman from "Peştera Muierii," Romania who lived ∼34,000 years ago to 13.5× coverage. The genome shows similarities to modern-day Europeans, but she is not a direct ancestor. Although her cranium exhibits both modern human and Neanderthal features, the genome shows similar levels of Neanderthal admixture (∼3.1%) to most EUP humans but only half compared to the ∼40,000-year-old Peştera Oase 1. All EUP European hunter-gatherers display high genetic diversity, demonstrating that the severe loss of diversity occurred during and after the Last Glacial Maximum (LGM) rather than just during the out-of-Africa migration. The prevalence of genetic diseases is expected to increase with low diversity; however, pathogenic variant load was relatively constant from EUP to modern times, despite post-LGM hunter-gatherers having the lowest diversity ever observed among Europeans.}, }
@article {pmid33992907, year = {2021}, author = {Kerner, G and Patin, E and Quintana-Murci, L}, title = {New insights into human immunity from ancient genomics.}, journal = {Current opinion in immunology}, volume = {72}, number = {}, pages = {116-125}, pmid = {33992907}, issn = {1879-0372}, mesh = {Animals ; COVID-19/epidemiology/genetics/*immunology ; Evolution, Molecular ; Genetic Predisposition to Disease ; Genetics, Population ; Genomics ; Hominidae ; Humans ; Immunity/*genetics ; SARS-CoV-2/*physiology ; }, abstract = {Population genetic studies have clearly indicated that immunity and host defense are among the functions most frequently subject to natural selection, and increased our understanding of the biological relevance of the corresponding genes and their contribution to variable immune traits and diseases. Herein, we will focus on some recently studied forms of human adaptation to infectious agents, including hybridization with now-extinct hominins, such as Neanderthals and Denisovans, and admixture between modern human populations. These studies, which are partly enabled by the technological advances in the sequencing of DNA from ancient remains, provide new insight into the sources of immune response variation in contemporary humans, such as the recently reported link between Neanderthal heritage and susceptibility to severe COVID-19 disease. Furthermore, ancient DNA analyses, in both humans and pathogens, allow to measure the action of natural selection on immune genes across time and to reconstruct the impact of past epidemics on the evolution of human immunity.}, }
@article {pmid33974862, year = {2021}, author = {Harvati, K}, title = {Katerina Harvati.}, journal = {Current biology : CB}, volume = {31}, number = {9}, pages = {R418-R419}, doi = {10.1016/j.cub.2021.04.003}, pmid = {33974862}, issn = {1879-0445}, mesh = {Animals ; Biological Evolution ; Fossils ; History, 20th Century ; History, 21st Century ; Humans ; Interdisciplinary Communication ; Mentors ; *Neanderthals ; *Paleontology/education ; }, abstract = {Interview with paleoanthropologist Katerina Harvati, who studies Neanderthal evolution and modern human origins at the Eberhard Karls University of Tübingen.}, }
@article {pmid33972424, year = {2021}, author = {Fellows Yates, JA and Velsko, IM and Aron, F and Posth, C and Hofman, CA and Austin, RM and Parker, CE and Mann, AE and Nägele, K and Arthur, KW and Arthur, JW and Bauer, CC and Crevecoeur, I and Cupillard, C and Curtis, MC and Dalén, L and Díaz-Zorita Bonilla, M and Díez Fernández-Lomana, JC and Drucker, DG and Escribano Escrivá, E and Francken, M and Gibbon, VE and González Morales, MR and Grande Mateu, A and Harvati, K and Henry, AG and Humphrey, L and Menéndez, M and Mihailović, D and Peresani, M and Rodríguez Moroder, S and Roksandic, M and Rougier, H and Sázelová, S and Stock, JT and Straus, LG and Svoboda, J and Teßmann, B and Walker, MJ and Power, RC and Lewis, CM and Sankaranarayanan, K and Guschanski, K and Wrangham, RW and Dewhirst, FE and Salazar-García, DC and Krause, J and Herbig, A and Warinner, C}, title = {The evolution and changing ecology of the African hominid oral microbiome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {20}, pages = {}, pmid = {33972424}, issn = {1091-6490}, support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE024468/DE/NIDCR NIH HHS/United States ; R01 GM089886/GM/NIGMS NIH HHS/United States ; R37 DE016937/DE/NIDCR NIH HHS/United States ; }, mesh = {Africa ; Animals ; Bacteria/classification/genetics ; Biofilms ; *Biological Evolution ; Dental Plaque/microbiology ; Ecology/*methods ; Geography ; Gorilla gorilla/microbiology ; Hominidae/classification/*microbiology ; Humans ; Metagenome/*genetics ; Microbiota/*genetics ; Mouth/*microbiology ; Pan troglodytes/microbiology ; Phylogeny ; }, abstract = {The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine-platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease.}, }
@article {pmid33951239, year = {2021}, author = {Gopalan, S and Atkinson, EG and Buck, LT and Weaver, TD and Henn, BM}, title = {Inferring archaic introgression from hominin genetic data.}, journal = {Evolutionary anthropology}, volume = {30}, number = {3}, pages = {199-220}, pmid = {33951239}, issn = {1520-6505}, support = {R35 GM133531/GM/NIGMS NIH HHS/United States ; K12-GM102778/NH/NIH HHS/United States ; K01-MH121659/NH/NIH HHS/United States ; R35-GM133531/NH/NIH HHS/United States ; K01 MH121659/MH/NIMH NIH HHS/United States ; K12 GM102778/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anthropology, Physical ; *Biological Evolution ; DNA, Ancient/*analysis ; DNA, Mitochondrial/genetics ; Genetic Introgression/*genetics ; Hominidae/classification/genetics ; Humans ; Neanderthals/classification/*genetics ; }, abstract = {Questions surrounding the timing, extent, and evolutionary consequences of archaic admixture into human populations have a long history in evolutionary anthropology. More recently, advances in human genetics, particularly in the field of ancient DNA, have shed new light on the question of whether or not Homo sapiens interbred with other hominin groups. By the late 1990s, published genetic work had largely concluded that archaic groups made no lasting genetic contribution to modern humans; less than a decade later, this conclusion was reversed following the successful DNA sequencing of an ancient Neanderthal. This reversal of consensus is noteworthy, but the reasoning behind it is not widely understood across all academic communities. There remains a communication gap between population geneticists and paleoanthropologists. In this review, we endeavor to bridge this gap by outlining how technological advancements, new statistical methods, and notable controversies ultimately led to the current consensus.}, }
@article {pmid33942714, year = {2021}, author = {Stepanova, V and Moczulska, KE and Vacano, GN and Kurochkin, I and Ju, X and Riesenberg, S and Macak, D and Maricic, T and Dombrowski, L and Schörnig, M and Anastassiadis, K and Baker, O and Naumann, R and Khrameeva, E and Vanushkina, A and Stekolshchikova, E and Egorova, A and Tkachev, A and Mazzarino, R and Duval, N and Zubkov, D and Giavalisco, P and Wilkinson, TG and Patterson, D and Khaitovich, P and Pääbo, S}, title = {Reduced purine biosynthesis in humans after their divergence from Neandertals.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {33942714}, issn = {2050-084X}, mesh = {Animals ; Biosynthetic Pathways/*genetics ; Female ; Gene Editing ; Humans ; Macaca/metabolism ; Male ; Metabolome/*genetics ; Mice ; Mice, Transgenic ; Mutation, Missense ; Neanderthals/*metabolism ; Pan troglodytes/metabolism ; Purines/*biosynthesis/*metabolism ; }, abstract = {We analyze the metabolomes of humans, chimpanzees, and macaques in muscle, kidney and three different regions of the brain. Although several compounds in amino acid metabolism occur at either higher or lower concentrations in humans than in the other primates, metabolites downstream of adenylosuccinate lyase, which catalyzes two reactions in purine synthesis, occur at lower concentrations in humans. This enzyme carries an amino acid substitution that is present in all humans today but absent in Neandertals. By introducing the modern human substitution into the genomes of mice, as well as the ancestral, Neandertal-like substitution into the genomes of human cells, we show that this amino acid substitution contributes to much or all of the reduction of de novo synthesis of purines in humans.}, }
@article {pmid33892510, year = {2021}, author = {Villanea, FA and Huerta-Sanchez, E and Fox, K}, title = {ABO Genetic Variation in Neanderthals and Denisovans.}, journal = {Molecular biology and evolution}, volume = {38}, number = {8}, pages = {3373-3382}, pmid = {33892510}, issn = {1537-1719}, support = {R35 GM128946/GM/NIGMS NIH HHS/United States ; }, mesh = {ABO Blood-Group System/*genetics ; Animals ; Genetic Variation ; Genome, Human ; Haplotypes ; Humans ; Neanderthals/*genetics ; }, abstract = {Variation at the ABO locus was one of the earliest sources of data in the study of human population identity and history, and to this day remains widely genotyped due to its importance in blood and tissue transfusions. Here, we look at ABO blood type variants in our archaic relatives: Neanderthals and Denisovans. Our goal is to understand the genetic landscape of the ABO gene in archaic humans, and how it relates to modern human ABO variation. We found two Neanderthal variants of the O allele in the Siberian Neanderthals (O1 and O2), one of these variants is shared with an European Neanderthal, who is a heterozygote for this O1 variant and a rare cis-AB variant. The Denisovan individual is heterozygous for two variants of the O1 allele, functionally similar to variants found widely in modern humans. Perhaps more surprisingly, the O2 allele variant found in Siberian Neanderthals can be found at low frequencies in modern Europeans and Southeast Asians, and the O1 allele variant found in Siberian and European Neanderthal is also found at very low frequency in modern East Asians. Our genetic distance analyses suggest both alleles survive in modern humans due to inbreeding with Neanderthals. We find that the sequence backgrounds of the surviving Neanderthal-like O alleles in modern humans retain a higher sequence divergence than other surviving Neanderthal genome fragments, supporting a view of balancing selection operating in the Neanderthal ABO alleles by retaining highly diverse haplotypes compared with portions of the genome evolving neutrally.}, }
@article {pmid33885362, year = {2021}, author = {Weiss, CV and Harshman, L and Inoue, F and Fraser, HB and Petrov, DA and Ahituv, N and Gokhman, D}, title = {The cis-regulatory effects of modern human-specific variants.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {33885362}, issn = {2050-084X}, support = {U01 MH116438/MH/NIMH NIH HHS/United States ; 1U01MH116438/MH/NIMH NIH HHS/United States ; UM1 HG009408/HG/NHGRI NIH HHS/United States ; P01 HD084387/HD/NICHD NIH HHS/United States ; R01 MH109907/MH/NIMH NIH HHS/United States ; 1R01MH109907/MH/NIMH NIH HHS/United States ; R01 MH116438/MH/NIMH NIH HHS/United States ; R35 GM118165/GM/NIGMS NIH HHS/United States ; 1UM1HG009408/HG/NHGRI NIH HHS/United States ; F31 HG011568/HG/NHGRI NIH HHS/United States ; }, mesh = {Embryonic Stem Cells/*metabolism ; *Gene Expression Regulation ; Genome, Human ; Humans ; Osteoblasts/*metabolism ; *Polymorphism, Single Nucleotide ; Stem Cells/*metabolism ; Transcription Factors/*metabolism ; }, abstract = {The Neanderthal and Denisovan genomes enabled the discovery of sequences that differ between modern and archaic humans, the majority of which are noncoding. However, our understanding of the regulatory consequences of these differences remains limited, in part due to the decay of regulatory marks in ancient samples. Here, we used a massively parallel reporter assay in embryonic stem cells, neural progenitor cells, and bone osteoblasts to investigate the regulatory effects of the 14,042 single-nucleotide modern human-specific variants. Overall, 1791 (13%) of sequences containing these variants showed active regulatory activity, and 407 (23%) of these drove differential expression between human groups. Differentially active sequences were associated with divergent transcription factor binding motifs, and with genes enriched for vocal tract and brain anatomy and function. This work provides insight into the regulatory function of variants that emerged along the modern human lineage and the recent evolution of human gene expression.}, }
@article {pmid33860534, year = {2021}, author = {Yi, Z and Zanolli, C and Liao, W and Wang, W}, title = {A deep-learning-based workflow to assess taxonomic affinity of hominid teeth with a test on discriminating Pongo and Homo upper molars.}, journal = {American journal of physical anthropology}, volume = {175}, number = {4}, pages = {931-942}, doi = {10.1002/ajpa.24286}, pmid = {33860534}, issn = {1096-8644}, mesh = {Animals ; *Deep Learning ; Dentin ; *Hominidae ; Humans ; Pongo ; Workflow ; }, abstract = {OBJECTIVES: Convolutional neural network (CNN) is a state-of-art deep learning (DL) method with superior performance in image classification. Here, a CNN-based workflow is proposed to discriminate hominid teeth. Our hope is that this method could help confirm otherwise questionable records of Homo from Pleistocene deposits where there is a standing risk of mis-attributing molars of Pongo to Homo.<br><br>METHODS AND MATERIALS: A two-step workflow was designed. The first step is converting the enamel-dentine junction (EDJ) into EDJ card, that is, a two-dimensional image conversion of the three-dimensional EDJ surface. In this step, researchers must carefully orient the teeth according to the cervical plane. The second step is training the CNN learner with labeled EDJ cards. A sample consisting of 53 fossil Pongo and 53 Homo (modern human and Neanderthal) was adopted to generate EDJ cards, which were then separated into training set (n&#xa0;=&#x2009;84) and validation set (n&#xa0;=&#x2009;22). To assess the feasibility of this workflow, a Pongo-Homo classifier was trained from the aforementioned EDJ card set, and then the classifier was used to predict the taxonomic affinities of six samples (test set) from von Koenigswald's Chinese Apothecary collection.<br><br>RESULTS: Results show that EDJ cards in validation set are classified accurately by the CNN learner. More importantly, taxonomic predictions for six specimens in test set match well with the diagnosis results deduced from multiple lines of evidence, implying the great potential of CNN method.<br><br>DISCUSSION: This workflow paves a way for future studies using CNN to address taxonomic complexity (e.g., distinguishing Pongo and Homo teeth from the Pleistocene of Asia). Further improvements include visual interpretation and extending the applicability to moderately worn teeth.}, }
@article {pmid33859012, year = {2021}, author = {Gibbons, A}, title = {DNA from cave dirt traces Neanderthal upheaval.}, journal = {Science (New York, N.Y.)}, volume = {372}, number = {6539}, pages = {222-223}, doi = {10.1126/science.372.6539.222}, pmid = {33859012}, issn = {1095-9203}, mesh = {Animals ; Caves ; DNA ; *Hominidae/genetics ; *Neanderthals/genetics ; }, }
@article {pmid33858989, year = {2021}, author = {Vernot, B and Zavala, EI and Gómez-Olivencia, A and Jacobs, Z and Slon, V and Mafessoni, F and Romagné, F and Pearson, A and Petr, M and Sala, N and Pablos, A and Aranburu, A and de Castro, JMB and Carbonell, E and Li, B and Krajcarz, MT and Krivoshapkin, AI and Kolobova, KA and Kozlikin, MB and Shunkov, MV and Derevianko, AP and Viola, B and Grote, S and Essel, E and Herráez, DL and Nagel, S and Nickel, B and Richter, J and Schmidt, A and Peter, B and Kelso, J and Roberts, RG and Arsuaga, JL and Meyer, M}, title = {Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments.}, journal = {Science (New York, N.Y.)}, volume = {372}, number = {6542}, pages = {}, doi = {10.1126/science.abf1667}, pmid = {33858989}, issn = {1095-9203}, support = {694707/ERC_/European Research Council/International ; }, mesh = {Animals ; Caves/chemistry ; Cell Nucleus/*genetics ; DNA, Mitochondrial/analysis/*genetics/isolation &amp; purification ; Geologic Sediments/chemistry ; Neanderthals/*classification/*genetics ; Phylogeny ; Population/genetics ; Sequence Analysis, DNA ; Siberia ; Spain ; }, abstract = {Bones and teeth are important sources of Pleistocene hominin DNA, but are rarely recovered at archaeological sites. Mitochondrial DNA (mtDNA) has been retrieved from cave sediments but provides limited value for studying population relationships. We therefore developed methods for the enrichment and analysis of nuclear DNA from sediments and applied them to cave deposits in western Europe and southern Siberia dated to between 200,000 and 50,000 years ago. We detected a population replacement in northern Spain about 100,000 years ago, which was accompanied by a turnover of mtDNA. We also identified two radiation events in Neanderthal history during the early part of the Late Pleistocene. Our work lays the ground for studying the population history of ancient hominins from trace amounts of nuclear DNA in sediments.}, }
@article {pmid33854233, year = {2021}, author = {Choin, J and Mendoza-Revilla, J and Arauna, LR and Cuadros-Espinoza, S and Cassar, O and Larena, M and Ko, AM and Harmant, C and Laurent, R and Verdu, P and Laval, G and Boland, A and Olaso, R and Deleuze, JF and Valentin, F and Ko, YC and Jakobsson, M and Gessain, A and Excoffier, L and Stoneking, M and Patin, E and Quintana-Murci, L}, title = {Genomic insights into population history and biological adaptation in Oceania.}, journal = {Nature}, volume = {592}, number = {7855}, pages = {583-589}, pmid = {33854233}, issn = {1476-4687}, mesh = {Adaptation, Biological/*genetics ; Animals ; Australia ; *Biological Evolution ; Datasets as Topic ; Asia, Eastern ; Genetic Introgression ; *Genetics, Population ; Genome, Human/*genetics ; *Genomics ; History, Ancient ; Human Migration/*history ; Humans ; *Islands ; Native Hawaiian or Other Pacific Islander/*genetics ; Neanderthals/genetics ; Oceania ; Pacific Ocean ; Taiwan ; }, abstract = {The Pacific region is of major importance for addressing questions regarding human dispersals, interactions with archaic hominins and natural selection processes[1]. However, the demographic and adaptive history of Oceanian populations remains largely uncharacterized. Here we report high-coverage genomes of 317 individuals from 20 populations from the Pacific region. We find that the ancestors of Papuan-related ('Near Oceanian') groups underwent a strong bottleneck before the settlement of the region, and separated around 20,000-40,000 years ago. We infer that the East Asian ancestors of Pacific populations may have diverged from Taiwanese Indigenous peoples before the Neolithic expansion, which is thought to have started from Taiwan around 5,000 years ago[2-4]. Additionally, this dispersal was not followed by an immediate, single admixture event with Near Oceanian populations, but involved recurrent episodes of genetic interactions. Our analyses reveal marked differences in the proportion and nature of Denisovan heritage among Pacific groups, suggesting that independent interbreeding with highly structured archaic populations occurred. Furthermore, whereas introgression of Neanderthal genetic information facilitated the adaptation of modern humans related to multiple phenotypes (for example, metabolism, pigmentation and neuronal development), Denisovan introgression was primarily beneficial for immune-related functions. Finally, we report evidence of selective sweeps and polygenic adaptation associated with pathogen exposure and lipid metabolism in the Pacific region, increasing our understanding of the mechanisms of biological adaptation to island environments.}, }
@article {pmid33828320, year = {2021}, author = {Hajdinjak, M and Mafessoni, F and Skov, L and Vernot, B and Hübner, A and Fu, Q and Essel, E and Nagel, S and Nickel, B and Richter, J and Moldovan, OT and Constantin, S and Endarova, E and Zahariev, N and Spasov, R and Welker, F and Smith, GM and Sinet-Mathiot, V and Paskulin, L and Fewlass, H and Talamo, S and Rezek, Z and Sirakova, S and Sirakov, N and McPherron, SP and Tsanova, T and Hublin, JJ and Peter, BM and Meyer, M and Skoglund, P and Kelso, J and Pääbo, S}, title = {Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry.}, journal = {Nature}, volume = {592}, number = {7853}, pages = {253-257}, pmid = {33828320}, issn = {1476-4687}, support = {852558/ERC_/European Research Council/International ; FC001595/MRC_/Medical Research Council/United Kingdom ; FC001595/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 694707/ERC_/European Research Council/International ; FC001595/ARC_/Arthritis Research UK/United Kingdom ; FC001595/CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {Alleles ; Americas/ethnology ; Animals ; Archaeology ; Bulgaria/ethnology ; Caves ; DNA, Ancient/*analysis ; Asia, Eastern/ethnology ; Female ; Genome, Human/*genetics ; History, Ancient ; Humans ; Male ; Neanderthals/*genetics ; Phylogeny ; }, abstract = {Modern humans appeared in Europe by at least 45,000 years ago[1-5], but the extent of their interactions with Neanderthals, who disappeared by about 40,000 years ago[6], and their relationship to the broader expansion of modern humans outside Africa are poorly understood. Here we present genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from Bacho Kiro Cave, Bulgaria[1,2]. They are the earliest Late Pleistocene modern humans known to have been recovered in Europe so far, and were found in association with an Initial Upper Palaeolithic artefact assemblage. Unlike two previously studied individuals of similar ages from Romania[7] and Siberia[8] who did not contribute detectably to later populations, these individuals are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations. This indicates that they belonged to a modern human migration into Europe that was not previously known from the genetic record, and provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia. Moreover, we find that all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common.}, }
@article {pmid33828282, year = {2021}, author = {Callaway, E}, title = {Oldest DNA from a Homo sapiens reveals surprisingly recent Neanderthal ancestry.}, journal = {Nature}, volume = {592}, number = {7854}, pages = {339}, pmid = {33828282}, issn = {1476-4687}, mesh = {Animals ; DNA/genetics ; Fossils ; *Hominidae/genetics ; Humans ; *Neanderthals/genetics ; }, }
@article {pmid33828250, year = {2021}, author = {Lalueza-Fox, C}, title = {Neanderthal assimilation?.}, journal = {Nature ecology &amp; evolution}, volume = {5}, number = {6}, pages = {711-712}, pmid = {33828250}, issn = {2397-334X}, mesh = {Animals ; Czech Republic ; Genome ; *Hominidae/genetics ; Humans ; Infant, Newborn ; *Neanderthals/genetics ; Skull ; }, }
@article {pmid33828249, year = {2021}, author = {Prüfer, K and Posth, C and Yu, H and Stoessel, A and Spyrou, MA and Deviese, T and Mattonai, M and Ribechini, E and Higham, T and Velemínský, P and Brůžek, J and Krause, J}, title = {A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia.}, journal = {Nature ecology &amp; evolution}, volume = {5}, number = {6}, pages = {820-825}, pmid = {33828249}, issn = {2397-334X}, mesh = {Africa ; Czech Republic ; Europe ; Female ; Humans ; Infant, Newborn ; Middle East ; Siberia ; *Skull ; }, abstract = {Modern humans expanded into Eurasia more than 40,000 years ago following their dispersal out of Africa. These Eurasians carried ~2-3% Neanderthal ancestry in their genomes, originating from admixture with Neanderthals that took place sometime between 50,000 and 60,000 years ago, probably in the Middle East. In Europe, the modern human expansion preceded the disappearance of Neanderthals from the fossil record by 3,000-5,000 years. The genetic makeup of the first Europeans who colonized the continent more than 40,000 years ago remains poorly understood since few specimens have been studied. Here, we analyse a genome generated from the skull of a female individual from Zlatý kůň, Czechia. We found that she belonged to a population that appears to have contributed genetically neither to later Europeans nor to Asians. Her genome carries ~3% Neanderthal ancestry, similar to those of other Upper Palaeolithic hunter-gatherers. However, the lengths of the Neanderthal segments are longer than those observed in the currently oldest modern human genome of the ~45,000-year-old Ust'-Ishim individual from Siberia, suggesting that this individual from Zlatý kůň is one of the earliest Eurasian inhabitants following the expansion out of Africa.}, }
@article {pmid33798098, year = {2021}, author = {Devièse, T and Abrams, G and Hajdinjak, M and Pirson, S and De Groote, I and Di Modica, K and Toussaint, M and Fischer, V and Comeskey, D and Spindler, L and Meyer, M and Semal, P and Higham, T}, title = {Reevaluating the timing of Neanderthal disappearance in Northwest Europe.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {12}, pages = {}, pmid = {33798098}, issn = {1091-6490}, mesh = {Animals ; *Anthropology ; Archaeology ; Europe ; *Extinction, Biological ; Fossils ; Genomics/methods ; Humans ; *Neanderthals ; Radiometric Dating ; }, abstract = {Elucidating when Neanderthal populations disappeared from Eurasia is a key question in paleoanthropology, and Belgium is one of the key regions for studying the Middle to Upper Paleolithic transition. Previous radiocarbon dating placed the Spy Neanderthals among the latest surviving Neanderthals in Northwest Europe with reported dates as young as 23,880 ± 240 B.P. (OxA-8912). Questions were raised, however, regarding the reliability of these dates. Soil contamination and carbon-based conservation products are known to cause problems during the radiocarbon dating of bulk collagen samples. Employing a compound-specific approach that is today the most efficient in removing contamination and ancient genomic analysis, we demonstrate here that previous dates produced on Neanderthal specimens from Spy were inaccurately young by up to 10,000 y due to the presence of unremoved contamination. Our compound-specific radiocarbon dates on the Neanderthals from Spy and those from Engis and Fonds-de-Forêt demonstrate that they disappeared from Northwest Europe at 44,200 to 40,600 cal B.P. (at 95.4% probability), much earlier than previously suggested. Our data contribute significantly to refining models for Neanderthal disappearance in Europe and, more broadly, show that chronometric models regarding the appearance or disappearance of animal or hominin groups should be based only on radiocarbon dates obtained using robust pretreatment methods.}, }
@article {pmid33797824, year = {2021}, author = {Ocobock, C and Lacy, S and Niclou, A}, title = {Between a rock and a cold place: Neanderthal biocultural cold adaptations.}, journal = {Evolutionary anthropology}, volume = {30}, number = {4}, pages = {262-279}, doi = {10.1002/evan.21894}, pmid = {33797824}, issn = {1520-6505}, mesh = {Adaptation, Physiological/*physiology ; Animals ; Anthropology, Physical ; Body Temperature Regulation/physiology ; *Cold Temperature ; Energy Metabolism/physiology ; Female ; Humans ; Male ; Neanderthals/*anatomy &amp; histology/*physiology ; }, abstract = {A large body of work focuses on the unique aspects of Neanderthal anatomy, inferred physiology, and behavior to test the assumption that Neanderthals were hyper-adapted to living in cold environments. This research has expanded over the years to include previously unexplored and potentially adaptive features such as brown adipose tissue and fire-usage. Here we review the current state of knowledge of Neanderthal cold adaptations along morphological, physiological, and behavioral lines. While highlighting foundational as well as recent work, we also emphasize key areas for future research. Despite thriving in a variety of climates, it is well-accepted that Neanderthals appear to be the most cold-adapted of known fossil hominin groups; however, there are still many unknowns. There is a great deal yet to be uncovered about the nature and manifestation of Neanderthal adaptation and how the synergy of biology and culture helped buffer them against extreme and variable environments.}, }
@article {pmid33791713, year = {2021}, author = {Huffman, J and Butler-Laporte, G and Khan, A and Drivas, TG and Peloso, GM and Nakanishi, T and Verma, A and Kiryluk, K and Richards, JB and Zeberg, H}, title = {Alternative splicing of OAS1 alters the risk for severe COVID-19.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {33791713}, support = {UL1 TR001873/TR/NCATS NIH HHS/United States ; UL1 TR001878/TR/NCATS NIH HHS/United States ; }, abstract = {A locus containing OAS1/2/3 has been identified as a risk locus for severe COVID-19 among Europeans ancestry individuals, with a protective haplotype of ∼75 kilobases derived from Neanderthals. Here, we show that among several potentially causal variants at this locus, a splice variant of OAS1 occurs in people of African ancestry independently of the Neanderthal haplotype and confers protection against COVID-19 of a magnitude similar to that seen in individuals without African ancestry.}, }
@article {pmid33787889, year = {2021}, author = {Yair, S and Lee, KM and Coop, G}, title = {The timing of human adaptation from Neanderthal introgression.}, journal = {Genetics}, volume = {218}, number = {1}, pages = {}, pmid = {33787889}, issn = {1943-2631}, support = {R01 GM108779/GM/NIGMS NIH HHS/United States ; R01 GM121372/GM/NIGMS NIH HHS/United States ; R35 GM136290/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Biological/genetics/physiology ; Adaptation, Physiological/genetics ; Alleles ; Animals ; Biological Evolution ; Evolution, Molecular ; Gene Frequency/genetics ; Genetic Introgression/*genetics ; Genome, Human/genetics ; Haplotypes/genetics ; Hominidae/*genetics ; Humans ; Neanderthals/*genetics ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Selection, Genetic/genetics ; }, abstract = {Admixture has the potential to facilitate adaptation by providing alleles that are immediately adaptive in a new environment or by simply increasing the long-term reservoir of genetic diversity for future adaptation. A growing number of cases of adaptive introgression are being identified in species across the tree of life, however the timing of selection, and therefore the importance of the different evolutionary roles of admixture, is typically unknown. Here, we investigate the spatio-temporal history of selection favoring Neanderthal-introgressed alleles in modern human populations. Using both ancient and present-day samples of modern humans, we integrate the known demographic history of populations, namely population divergence and migration, with tests for selection. We model how a sweep placed along different branches of an admixture graph acts to modify the variance and covariance in neutral allele frequencies among populations at linked loci. Using a method based on this model of allele frequencies, we study previously identified cases of adaptive Neanderthal introgression. From these, we identify cases in which Neanderthal-introgressed alleles were quickly beneficial and other cases in which they persisted at low frequency for some time. For some of the alleles that persisted at low frequency, we show that selection likely independently favored them later on in geographically separated populations. Our work highlights how admixture with ancient hominins has contributed to modern human adaptation and contextualizes observed levels of Neanderthal ancestry in present-day and ancient samples.}, }
@article {pmid33774376, year = {2021}, author = {Chevalier, T and Colard, T and Colombo, A and Golovanova, L and Doronichev, V and Hublin, JJ}, title = {Early ontogeny of humeral trabecular bone in Neandertals and recent modern humans.}, journal = {Journal of human evolution}, volume = {154}, number = {}, pages = {102968}, doi = {10.1016/j.jhevol.2021.102968}, pmid = {33774376}, issn = {1095-8606}, mesh = {Adolescent ; Animals ; Cancellous Bone/*growth &amp; development ; Child ; Child, Preschool ; Female ; *Fossils ; Humans ; *Humerus/growth &amp; development ; Infant ; Male ; *Neanderthals ; Pan troglodytes ; }, abstract = {Trabecular bone ontogeny is well known in modern humans and unknown in Neandertals. Yet the bone developmental pattern is useful for interpreting fossils from evolutionary and functional perspectives. Interestingly, microstructure in early ontogeny is supposedly not influenced by high and specific mechanical loading related to the lifestyle of a human group and consequently does not directly depend on the activities of hunter-gatherers. Here, we specifically explored the early growth trajectories of the trabecular bone structure of the humerus and emphasized in particular how bone fraction (bone volume/total volume [BV/TV]) was built up in Neandertals, given the specific modern human bone loss after birth and the use of BV/TV in functional studies. Six Neandertals and 26 recent modern humans ranging from perinates to adolescents were included in this study. Six trabecular parameters were measured within a cubic region of interest extracted from the proximal metaphysis of the humerus. We found that the microstructural changes in Neandertals during early ontogeny (<1 year) fit with modern human growth trajectories for each parameter. The specific bone loss occurring immediately after birth in modern humans also occurred in Neandertals (but not in chimpanzees). However, the early childhood fossil Ferrassie 6 presented unexpectedly high BV/TV, whereas the high BV/TV in the Crouzade I adolescent was predictable. These results suggest that Neandertals and modern humans shared predetermined early growth trajectories and developmental mechanisms. We assume that the close relationship between skeletal characteristics in early ontogeny and adults in modern humans also existed in Neandertals. However, it was difficult to ensure that the high BV/TV in Neandertal early childhood, represented by only one individual, was at the origin of the high BV/TV observed in adults. Consequently, our study does not challenge the mechanical hypothesis that explains the trabecular gracilization of the humerus during the Holocene.}, }
@article {pmid33707474, year = {2021}, author = {Mayoral, E and Díaz-Martínez, I and Duveau, J and Santos, A and Ramírez, AR and Morales, JA and Morales, LA and Díaz-Delgado, R}, title = {Tracking late Pleistocene Neandertals on the Iberian coast.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4103}, pmid = {33707474}, issn = {2045-2322}, abstract = {Here, we report the recent discovery of 87 Neandertal footprints on the Southwest of the Iberian Peninsula (Doñana shoreline, Spain) located on an upper Pleistocene aeolian littoral setting (about 106 ± 19 kyr). Morphometric comparisons, high resolution digital photogrammetric 3D models and detailed sedimentary analysis have been provided to characterized the footprints and the palaeoenvironment. The footprints were impressed in the shoreline of a hypersaline swamped area related to benthic microbial mats, close to the coastline. They have a rounded heel, a longitudinal arch, relatively short toes, and adducted hallux, and represent the oldest upper Pleistocene record of Neandertal footprints in the world. Among these 87 footprints, 31 are longitudinally complete and measure from 14 to 29 cm. The calculated statures range from 104 to 188 cm, with half of the data between 130 and 150 cm. The wide range of sizes of the footprints suggests the existence of a social group integrated by individuals of different age classes but dominated, however, by non-adult individuals. The footprints, which are outside the flooded area are oriented perpendicular to the shoreline. These 87 footprints reinforce the ecological scenario of Neandertal groups established in coastal areas.}, }
@article {pmid33707343, year = {2021}, author = {García-Campos, C and Martinén-Torres, M and Modesto-Mata, M and Martín-Francés, L and Martínez de Pinillos, M and Bermúdez de Castro, JM}, title = {Indicators of sexual dimorphism in Homo antecessor permanent canines.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {99}, number = {}, pages = {1-18}, doi = {10.4436/JASS.99001}, pmid = {33707343}, issn = {2037-0644}, abstract = {One of the main concerns of paleoanthropologists is to make a correct interpretation of the variability observed in the fossil record. However, the current knowledge about sexual dimorphism in the human lineage comes mainly from the study of modern human, Neanderthal and pre-Neanderthal populations, whereas information available about the intrapopulation variability of the groups that preceded these taxa is still ambiguous. In this preliminary study, Homo antecessor dental sample was assessed with the aim of trying to evaluate the degree of variability of their permanent canines` dental tissue proportions. Microtomographic techniques were here employed in order to measure and compare the crown volumes and surface areas of their enamel caps and dentine-pulp complexes. Then, the Pearson`s Coefficient of Variation and the Euclidean Distance were assessed to evaluate of intrapopulation variability of Gran Dolina TD6.2 dental sample. The values obtained were also compared with those of the dental samples from Sima de los Huesos site (Spain), the Neanderthal site of Krapina (Croatia), as well as from a broad forensic collection of known sex. Our results showed a marked intrapopulation variability in the dental tissues measurements of the canines of the individuals H1 and H3 from this site. This variability may be interpreted as an indicator of sexual dimorphism. If this is the case, H1 may be considered as a male individual, whereas H3 would be a female. Future discoveries of new fossils in the level TD6.2 of Gran Dolina site might help to confirm or refute this hypothesis.}, }
@article {pmid33674720, year = {2021}, author = {Banks, WE and Moncel, MH and Raynal, JP and Cobos, ME and Romero-Alvarez, D and Woillez, MN and Faivre, JP and Gravina, B and d'Errico, F and Locht, JL and Santos, F}, title = {An ecological niche shift for Neanderthal populations in Western Europe 70,000 years ago.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {5346}, pmid = {33674720}, issn = {2045-2322}, abstract = {Middle Paleolithic Neanderthal populations occupied Eurasia for at least 250,000 years prior to the arrival of anatomically modern humans. While a considerable body of archaeological research has focused on Neanderthal material culture and subsistence strategies, little attention has been paid to the relationship between regionally specific cultural trajectories and their associated existing fundamental ecological niches, nor to how the latter varied across periods of climatic variability. We examine the Middle Paleolithic archaeological record of a naturally constrained region of Western Europe between 82,000 and 60,000 years ago using ecological niche modeling methods. Evaluations of ecological niche estimations, in both geographic and environmental dimensions, indicate that 70,000 years ago the range of suitable habitats exploited by these Neanderthal populations contracted and shifted. These ecological niche dynamics are the result of groups continuing to occupy habitual territories that were characterized by new environmental conditions during Marine Isotope Stage 4. The development of original cultural adaptations permitted this territorial stability.}, }
@article {pmid33649483, year = {2021}, author = {Vaesen, K and Dusseldorp, GL and Brandt, MJ}, title = {An emerging consensus in palaeoanthropology: demography was the main factor responsible for the disappearance of Neanderthals.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4925}, pmid = {33649483}, issn = {2045-2322}, abstract = {The causes of Neanderthal disappearance about 40,000 years ago remain highly contested. Over a dozen serious hypotheses are currently endorsed to explain this enigmatic event. Given the relatively large number of contending explanations and the relatively large number of participants in the debate, it is unclear how strongly each contender is supported by the research community. What does the community actually believe about the demise of Neanderthals? To address this question, we conducted a survey among practicing palaeo-anthropologists (total number of respondents = 216). It appears that received wisdom is that demography was the principal cause of the demise of Neanderthals. In contrast, there is no received wisdom about the role that environmental factors and competition with modern humans played in the extinction process; the research community is deeply divided about these issues. Finally, we tested the hypothesis that palaeo-anthropologists' stand in the debate co-varies with their socio-political views and attitudes. We found no evidence for such a correlation.}, }
@article {pmid33644865, year = {2021}, author = {Richards, GD and Guipert, G and Jabbour, RS and Defleur, AR}, title = {Neanderthal cranial remains from Baume Moula-Guercy (Soyons, Ardèche, France).}, journal = {American journal of physical anthropology}, volume = {175}, number = {1}, pages = {201-226}, doi = {10.1002/ajpa.24256}, pmid = {33644865}, issn = {1096-8644}, mesh = {Adult ; Animals ; Anthropology, Physical ; Female ; France ; Humans ; Male ; Neanderthals/*anatomy &amp; histology ; Skull/*anatomy &amp; histology ; }, abstract = {OBJECTIVES: We provide the first comparative description of the Guercy 1 cranium and isolated cranial fragments from Baume Moula-Guercy and examine their affinities to European Preneanderthals, Neanderthals, and Homo sapiens.<br><br>MATERIALS AND METHODS: The Moula-Guercy hominins derive from deposits chronostratigraphically and biostratigraphically dated to the Eemian Interglacial (MIS 5e). For comparisons we compiled a sample of European and Southwest Asian subadult-adult Middle-to-Late Pleistocene hominins (&#x2248;MIS 14-MIS 2; N = 184). This sample represents a Preneanderthal-Neanderthal group and a H. sapiens group, both of which were further divided into three time-successive subgroups defined by associated marine isotope stages (MIS). Metric and morphological observations were made on the original fossils and a virtual reconstruction of Guercy 1. Developmental age and sex and the minimum-maximum number of individuals were assessed.<br><br>RESULTS: Guercy 1 represents the remains of a late stage adolescent (&#x2248;15-16.0&#x2009;years) female. Morphological and metric data combine to associate the total morphological pattern expressed in Guercy 1 with our MIS 7-MIS 5e ("Early Neanderthal") subgroup. Some features, especially those related to the frontal, suggest linkage to a paleodeme comprising the Moula-Guercy, Artenac, La Chaise Abri Suard and, possibly, the Biache-Saint-Vaast samples.<br><br>DISCUSSION: Remains of MIS 7-MIS 5e Neanderthals are rare and fragmentary, especially those dated to the Last Interglacial. The Baume Moula-Guercy sample provides new insights into the total morphological pattern expressed in MIS 5e Neanderthals. Further, our results support earlier suggestions that MIS 7-MIS 5e European hominins represent a morphotype that is distinct from both earlier and later members of the Preneanderthal-Neanderthal group.}, }
@article {pmid33633408, year = {2021}, author = {Zhou, S and Butler-Laporte, G and Nakanishi, T and Morrison, DR and Afilalo, J and Afilalo, M and Laurent, L and Pietzner, M and Kerrison, N and Zhao, K and Brunet-Ratnasingham, E and Henry, D and Kimchi, N and Afrasiabi, Z and Rezk, N and Bouab, M and Petitjean, L and Guzman, C and Xue, X and Tselios, C and Vulesevic, B and Adeleye, O and Abdullah, T and Almamlouk, N and Chen, Y and Chassé, M and Durand, M and Paterson, C and Normark, J and Frithiof, R and Lipcsey, M and Hultström, M and Greenwood, CMT and Zeberg, H and Langenberg, C and Thysell, E and Pollak, M and Mooser, V and Forgetta, V and Kaufmann, DE and Richards, JB}, title = {A Neanderthal OAS1 isoform protects individuals of European ancestry against COVID-19 susceptibility and severity.}, journal = {Nature medicine}, volume = {27}, number = {4}, pages = {659-667}, pmid = {33633408}, issn = {1546-170X}, support = {MC_UU_00006/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {2',5'-Oligoadenylate Synthetase/genetics/*physiology ; Aged ; Aged, 80 and over ; Animals ; COVID-19/*etiology/genetics ; Case-Control Studies ; Female ; *Genetic Predisposition to Disease ; Humans ; Interleukin-10 Receptor beta Subunit/genetics ; Male ; Mendelian Randomization Analysis ; Middle Aged ; Neanderthals ; Protein Isoforms/physiology ; Quantitative Trait Loci ; *SARS-CoV-2 ; Severity of Illness Index ; White People ; }, abstract = {To identify circulating proteins influencing Coronavirus Disease 2019 (COVID-19) susceptibility and severity, we undertook a two-sample Mendelian randomization (MR) study, rapidly scanning hundreds of circulating proteins while reducing bias due to reverse causation and confounding. In up to 14,134 cases and 1.2 million controls, we found that an s.d. increase in OAS1 levels was associated with reduced COVID-19 death or ventilation (odds ratio (OR) = 0.54, P = 7 × 10[-8]), hospitalization (OR = 0.61, P = 8 × 10[-8]) and susceptibility (OR = 0.78, P = 8 × 10[-6]). Measuring OAS1 levels in 504 individuals, we found that higher plasma OAS1 levels in a non-infectious state were associated with reduced COVID-19 susceptibility and severity. Further analyses suggested that a Neanderthal isoform of OAS1 in individuals of European ancestry affords this protection. Thus, evidence from MR and a case-control study support a protective role for OAS1 in COVID-19 adverse outcomes. Available pharmacological agents that increase OAS1 levels could be prioritized for drug development.}, }
@article {pmid33620372, year = {2021}, author = {Baldoni, M and Al-Hashmi, M and Bianchi, AE and Sakal, F and Al-Naimi, F and Leisten, T and Martínez-Labarga, C and Tomei, S}, title = {Bioarchaeology-related studies in the Arabian Gulf: potentialities and shortcomings.}, journal = {Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen}, volume = {72}, number = {1}, pages = {17-32}, doi = {10.1127/homo/2021/1282}, pmid = {33620372}, issn = {1618-1301}, mesh = {Animals ; *Archaeology ; Human Migration ; Humans ; *Neanderthals/genetics ; }, abstract = {Archaeological studies provide a powerful tool to understand the prehistoric societies, especially when combined to cutting-edge morphological and molecular anthropological analyses, allowing reconstructing past population dynamics, admixture events, and socio-cultural changes. Despite the advances achieved in the last decades by archaeological studies worldwide, several regions of the World have been spared from this scientific improvement due to various reasons. The Arabian Gulf represents a unique ground to investigate, being the passageway for human migrations and one of the hypothesized areas in which Neanderthal introgression occurred. A number of archaeological sites are currently present in the Arabian Gulf and have witnessed the antiquity and the intensiveness of the human settlements in the region. Nevertheless, the archaeological and anthropological investigation in the Gulf is still in its infancy. Data collected through archaeological studies in the area have the potential to help answering adamant questions of human history from the beginning of the structuring of genetic diversity in human species to the Neolithisation process. This review aims at providing an overview of the archaeological studies in the Arabian Gulf with special focus to Qatar, highlighting potentialities and shortcomings.}, }
@article {pmid33619340, year = {2021}, author = {Zilio, L and Hammond, H and Karampaglidis, T and Sánchez-Romero, L and Blasco, R and Rivals, F and Rufà, A and Picin, A and Chacón, MG and Demuro, M and Arnold, LJ and Rosell, J}, title = {Examining Neanderthal and carnivore occupations of Teixoneres Cave (Moià, Barcelona, Spain) using archaeostratigraphic and intra-site spatial analysis.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {4339}, pmid = {33619340}, issn = {2045-2322}, abstract = {Teixoneres Cave (Moià, Barcelona, Spain) is a reference site for Middle Palaeolithic studies of the Iberian Peninsula. The cave preserves an extensive stratigraphic sequence made up of eight units, which is presented in depth in this work. The main goal of this study is to undertake an initial spatial examination of Unit III, formed during Marine Isotope Stage 3, with the aim of understanding spatial organization and past activities developed by Neanderthals and carnivores (bears, hyenas and smaller carnivores). The total sample analysed includes 38,244 archaeological items and 5888 limestone blocks. The application of GIS tools allows us to clearly distinguish three geologically-defined stratigraphic subunits. Unit III has been previously interpreted as a palimpsest resulting from alternating occupation of the cave by human groups and carnivores. The distribution study shows that faunal specimens, lithic artefacts, hearths and charcoal fragments are significantly concentrated at the entrance of the cave where, it is inferred, hominins carried out different activities, while carnivores preferred the sheltered zones in the inner areas of the cave. The results obtained reveal a spatial pattern characterized by fire use related zones, and show that the site was occupied by Neanderthals in a similar and consistent way throughout the ˃ 7000 years range covered by the analysed subunits. This spatial pattern is interpreted as resulting from repeated short-term human occupations.}, }
@article {pmid33593941, year = {2021}, author = {Zeberg, H and Pääbo, S}, title = {A genomic region associated with protection against severe COVID-19 is inherited from Neandertals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {9}, pages = {}, pmid = {33593941}, issn = {1091-6490}, mesh = {Animals ; COVID-19/*genetics/immunology ; Chromosomes, Human, Pair 12/*genetics ; *Evolution, Molecular ; *Genetic Predisposition to Disease ; Haplotypes ; Humans ; Neanderthals/*genetics ; Quantitative Trait Loci ; }, abstract = {It was recently shown that the major genetic risk factor associated with becoming severely ill with COVID-19 when infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is inherited from Neandertals. New, larger genetic association studies now allow additional genetic risk factors to be discovered. Using data from the Genetics of Mortality in Critical Care (GenOMICC) consortium, we show that a haplotype at a region on chromosome 12 associated with requiring intensive care when infected with the virus is inherited from Neandertals. This region encodes proteins that activate enzymes that are important during infections with RNA viruses. In contrast to the previously described Neandertal haplotype that increases the risk for severe COVID-19, this Neandertal haplotype is protective against severe disease. It also differs from the risk haplotype in that it has a more moderate effect and occurs at substantial frequencies in all regions of the world outside Africa. Among ancient human genomes in western Eurasia, the frequency of the protective Neandertal haplotype may have increased between 20,000 and 10,000 y ago and again during the past 1,000 y.}, }
@article {pmid33589653, year = {2021}, author = {Blinkhorn, J and Zanolli, C and Compton, T and Groucutt, HS and Scerri, EML and Crété, L and Stringer, C and Petraglia, MD and Blockley, S}, title = {Nubian Levallois technology associated with southernmost Neanderthals.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {2869}, pmid = {33589653}, issn = {2045-2322}, abstract = {Neanderthals occurred widely across north Eurasian landscapes, but between ~ 70 and 50 thousand years ago (ka) they expanded southwards into the Levant, which had previously been inhabited by Homo sapiens. Palaeoanthropological research in the first half of the twentieth century demonstrated alternate occupations of the Levant by Neanderthal and Homo sapiens populations, yet key early findings have largely been overlooked in later studies. Here, we present the results of new examinations of both the fossil and archaeological collections from Shukbah Cave, located in the Palestinian West Bank, presenting new quantitative analyses of a hominin lower first molar and associated stone tool assemblage. The hominin tooth shows clear Neanderthal affinities, making it the southernmost known fossil specimen of this population/species. The associated Middle Palaeolithic stone tool assemblage is dominated by Levallois reduction methods, including the presence of Nubian Levallois points and cores. This is the first direct association between Neanderthals and Nubian Levallois technology, demonstrating that this stone tool technology should not be considered an exclusive marker of Homo sapiens.}, }
@article {pmid33574596, year = {2021}, author = {Remmel, A}, title = {Neanderthal-like 'mini-brains' created in lab with CRISPR.}, journal = {Nature}, volume = {590}, number = {7846}, pages = {376-377}, pmid = {33574596}, issn = {1476-4687}, mesh = {Brain ; Clustered Regularly Interspaced Short Palindromic Repeats ; DNA ; Humans ; *Neanderthals/genetics ; Stem Cells ; }, }
@article {pmid33574182, year = {2021}, author = {Trujillo, CA and Rice, ES and Schaefer, NK and Chaim, IA and Wheeler, EC and Madrigal, AA and Buchanan, J and Preissl, S and Wang, A and Negraes, PD and Szeto, RA and Herai, RH and Huseynov, A and Ferraz, MSA and Borges, FS and Kihara, AH and Byrne, A and Marin, M and Vollmers, C and Brooks, AN and Lautz, JD and Semendeferi, K and Shapiro, B and Yeo, GW and Smith, SEP and Green, RE and Muotri, AR}, title = {Reintroduction of the archaic variant of NOVA1 in cortical organoids alters neurodevelopment.}, journal = {Science (New York, N.Y.)}, volume = {371}, number = {6530}, pages = {}, pmid = {33574182}, issn = {1095-9203}, support = {R01 HL137223/HL/NHLBI NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; R01 MH121487/MH/NIMH NIH HHS/United States ; U24 HG009889/HG/NHGRI NIH HHS/United States ; S10 OD026929/OD/NIH HHS/United States ; R01 HG004659/HG/NHGRI NIH HHS/United States ; R01 MH113545/MH/NIMH NIH HHS/United States ; K01 AA026911/AA/NIAAA NIH HHS/United States ; U19 MH107367/MH/NIMH NIH HHS/United States ; T32 HG008345/HG/NHGRI NIH HHS/United States ; U41 HG009889/HG/NHGRI NIH HHS/United States ; }, mesh = {Alleles ; Alternative Splicing ; Amino Acid Substitution ; Animals ; Binding Sites ; Biological Evolution ; CRISPR-Cas Systems ; Cell Proliferation ; Cerebral Cortex/cytology/*growth &amp; development/*physiology ; Gene Expression Regulation, Developmental ; Genetic Variation ; Genome ; Genome, Human ; Haplotypes ; Hominidae/genetics ; Humans ; Induced Pluripotent Stem Cells ; Neanderthals/*genetics ; Nerve Net/physiology ; Nerve Tissue Proteins/genetics/metabolism ; Neuro-Oncological Ventral Antigen ; Neurons/*physiology ; Organoids ; RNA-Binding Proteins/*genetics/*metabolism ; Synapses/physiology ; }, abstract = {The evolutionarily conserved splicing regulator neuro-oncological ventral antigen 1 (NOVA1) plays a key role in neural development and function. NOVA1 also includes a protein-coding difference between the modern human genome and Neanderthal and Denisovan genomes. To investigate the functional importance of an amino acid change in humans, we reintroduced the archaic allele into human induced pluripotent cells using genome editing and then followed their neural development through cortical organoids. This modification promoted slower development and higher surface complexity in cortical organoids with the archaic version of NOVA1 Moreover, levels of synaptic markers and synaptic protein coassociations correlated with altered electrophysiological properties in organoids expressing the archaic variant. Our results suggest that the human-specific substitution in NOVA1, which is exclusive to modern humans since divergence from Neanderthals, may have had functional consequences for our species' evolution.}, }
@article {pmid33564646, year = {2021}, author = {Mortazavi, SAR and Kaveh-Ahangar, K and Mortazavi, SMJ and Firoozi, D and Haghani, M}, title = {How Our Neanderthal Genes Affect the COVID-19 Mortality: Iran and Mongolia, Two Countries with the Same SARS-CoV-2 Mutation Cluster but Different Mortality Rates.}, journal = {Journal of biomedical physics &amp; engineering}, volume = {11}, number = {1}, pages = {109-114}, pmid = {33564646}, issn = {2251-7200}, abstract = {Neanderthal genes possibly gave modern human protection against viruses. However, a recent study revealed that that a long sequence of DNA that is inherited from our Neanderthal ancestors can be linked to severe COVID-19 infection and hospitalization. Substantial evidence now indicates that our genetic background may be involved in the transmissibility of SARS-CoV-2 and the rapid progress of COVID-19 in some infected individuals. Although both morbidity and mortality of COVID-19 strongly depends on key factors such as age and co-existing health conditions, potential classes of human genomic variants possibly affect the likelihood of SARS-CoV-2 infection and its progress. Despite Iran and Mongolia seem to share the same SARS-CoV-2 mutation cluster, the COVID-19 mortality rates in these two countries are drastically different. While the population in Iran is 25.8 times higher than that of Mongolia, the number of confirmed cases is 1170 times higher. Moreover, the death rate shows a drastic difference. Since Neanderthals interbred with modern humans in Middle East between 47,000 and 65,000 years ago before going extinct 40,000 years ago, some Iranians have much more Neanderthal DNA than other people. Although neither genetic background nor environmental factors alone can determine our risk of developing severe COVID-19, our genes clearly affect both the development and progression of infectious diseases including COVID-19. Given these considerations, we believe that these great differences, at least to some extent, can be due to the proportion of Neanderthal genes among the people of these two countries.}, }
@article {pmid33556445, year = {2021}, author = {Reinscheid, RK and Mafessoni, F and Lüttjohann, A and Jüngling, K and Pape, HC and Schulz, S}, title = {Neandertal introgression and accumulation of hypomorphic mutations in the neuropeptide S (NPS) system promote attenuated functionality.}, journal = {Peptides}, volume = {138}, number = {}, pages = {170506}, doi = {10.1016/j.peptides.2021.170506}, pmid = {33556445}, issn = {1873-5169}, mesh = {Animals ; *Biological Evolution ; Genetic Introgression/*genetics ; Hominidae/genetics ; Humans ; Mutation/genetics ; Neanderthals/genetics ; Neuropeptides/genetics ; Polymorphism, Single Nucleotide/genetics ; Receptors, G-Protein-Coupled/*genetics ; *Selection, Genetic ; }, abstract = {The neuropeptide S (NPS) system plays an important role in fear and fear memory processing but has also been associated with allergic and inflammatory diseases. Genes for NPS and its receptor NPSR1 are found in all tetrapods. Compared to non-human primates, several non-synonymous single-nucleotide polymorphisms (SNPs) occur in both human genes that collectively result in functional attenuation, suggesting adaptive mechanisms in a human context. To investigate historic and geographic origins of these hypomorphic mutations and explore genetic signs of selection, we analyzed ancient genomes and worldwide genotype frequencies of four prototypic SNPs in the NPS system. Neandertal and Denisovan genomes contain exclusively ancestral alleles for NPSR1 while all derived alleles occur in ancient genomes of anatomically modern humans, indicating that they arose in modern Homo sapiens. Worldwide genotype frequencies for three hypomorphic NPSR1 SNPs show significant regional homogeneity but follow a gradient towards increasing derived allele frequencies that supports an out-of-Africa scenario. Increased density of high-frequency polymorphisms around the three NPSR1 loci suggests weak or possibly balancing selection. A hypomorphic mutation in the NPS precursor, however, was detected at high frequency in Eurasian Neandertal genomes and shows genetic signatures indicating that it was introgressed into the human gene pool, particularly in Southern Europe, by interbreeding with Neandertals. We discuss potential evolutionary scenarios including behavior and immune-based natural selection.}, }
@article {pmid33547403, year = {2021}, author = {Rampelli, S and Turroni, S and Mallol, C and Hernandez, C and Galván, B and Sistiaga, A and Biagi, E and Astolfi, A and Brigidi, P and Benazzi, S and Lewis, CM and Warinner, C and Hofman, CA and Schnorr, SL and Candela, M}, title = {Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {169}, pmid = {33547403}, issn = {2399-3642}, support = {R01 GM089886/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Archaeology ; DNA, Ancient/isolation &amp; purification ; Ecosystem ; Feces/*microbiology ; Fossils/microbiology ; *Gastrointestinal Microbiome ; Geologic Sediments/analysis/microbiology ; History, Ancient ; Humans ; Metagenomics ; Neanderthals/*microbiology ; Sequence Analysis, DNA ; Spain ; }, abstract = {A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium and Bifidobacterium already populated the intestinal microbiome of Homo since as far back as the last common ancestor between humans and Neanderthals.}, }
@article {pmid33524842, year = {2021}, author = {Lacy, SA}, title = {Evidence of dental agenesis in late pleistocene Homo.}, journal = {International journal of paleopathology}, volume = {32}, number = {}, pages = {103-110}, doi = {10.1016/j.ijpp.2021.01.001}, pmid = {33524842}, issn = {1879-9825}, mesh = {Animals ; *Anodontia ; *Hominidae ; Humans ; Molar, Third/diagnostic imaging ; }, abstract = {OBJECTIVE: Differential diagnosis and tabulation of cases of dental agenesis in Middle and Upper Paleolithic Western Eurasian humans to synthesize this data and to test previous hypotheses about when recent human patterns of third molar agenesis were established.<br><br>MATERIALS: 139 Late Pleistocene human remains and 149 individuals from three Epi-Paleolithic/ Holocene non-agricultural comparative collections.<br><br>METHODS: All remains were visually and radiographically recorded by the author.<br><br>RESULTS: In addition to establishing that third molar agenesis was common during the Late Upper Paleolithic (22,500-10,000 years BP), this study suggests a pattern of increasing prevalence through time.<br><br>CONCLUSIONS: An increase in the prevalence of third molar agenesis in the Late Upper Paleolithic could indicate selection for dental size reduction and orthognathy, but also bio-cultural changes from more intensive food preparation techniques.<br><br>SIGNIFICANCE: Third molar agenesis, a well-known developmental defect, is often reported for recent human skeletal collections, but the prevalence of the condition for Pleistocene hominins had not been previously quantified in order to consider patterns through time. Hypotheses posited for the high prevalence of third molar agenesis, or hypodontia in general, in some recent human groups require an understanding of the prevalence of these traits in the past.<br><br>LIMITATIONS: Paleolithic skeletal remains are incomplete, so these values are under-estimations. Individuals are also separated diachronically and geographically and should not be assumed to represent a single population sample.<br><br>Hypotheses on some of the potential selective forces acting on dental size reduction and subsequent agenesis could be tested in recent humans.}, }
@article {pmid33517134, year = {2021}, author = {Compton, T and Skinner, MM and Humphrey, L and Pope, M and Bates, M and Davies, TW and Parfitt, SA and Plummer, WP and Scott, B and Shaw, A and Stringer, C}, title = {The morphology of the Late Pleistocene hominin remains from the site of La Cotte de St Brelade, Jersey (Channel Islands).}, journal = {Journal of human evolution}, volume = {152}, number = {}, pages = {102939}, doi = {10.1016/j.jhevol.2020.102939}, pmid = {33517134}, issn = {1095-8606}, mesh = {Animals ; Biological Evolution ; Channel Islands ; Female ; Fossils/*anatomy &amp; histology ; Neanderthals/*anatomy &amp; histology ; Paleodontology ; Tooth/*anatomy &amp; histology ; }, abstract = {Thirteen permanent fully erupted teeth were excavated at the Paleolithic site of La Cotte de St Brelade in Jersey in 1910 and 1911. These were all found in the same location, on a ledge behind a hearth in a Mousterian occupation level. They were originally identified as being Neanderthal. A fragment of occipital bone was found in a separate locality in a later season. Recent dating of adjacent sediments gives a probable age of <48 ka. The purpose of this article is to provide an updated description of the morphology of this material and consider its likely taxonomic assignment from comparison with Neanderthal and Homo sapiens samples. One of the original teeth has been lost, and we identify one as nonhominin. At least two adult individuals are represented. Cervix shape and the absence of common Neanderthal traits in several teeth suggest affinities with H. sapiens in both individuals, while crown and root dimensions and root morphology of all the teeth are entirely consistent with a Neanderthal attribution, pointing toward a possible shared Neanderthal and H. sapiens ancestry (the likely date of this material corresponds with the time in which both Neanderthals and H. sapiens were present in Europe). The occipital fragment is stratigraphically more recent and does not exhibit any diagnostic Neanderthal features.}, }
@article {pmid33459351, year = {2020}, author = {VanSickle, C and Cofran, Z and Hunt, D}, title = {Did Neandertals have large brains? Factors affecting endocranial volume comparisons.}, journal = {American journal of physical anthropology}, volume = {173}, number = {4}, pages = {768-775}, doi = {10.1002/ajpa.24124}, pmid = {33459351}, issn = {1096-8644}, mesh = {Adult ; Aged ; Aged, 80 and over ; Animals ; Anthropology, Physical ; Brain/*anatomy &amp; histology ; Cephalometry ; Female ; Fossils ; Humans ; Male ; Middle Aged ; Neanderthals/*anatomy &amp; histology ; Sex Characteristics ; Skull/*anatomy &amp; histology ; Young Adult ; }, abstract = {OBJECTIVES: Common wisdom in paleoanthropology is that Neandertals had bigger brains than recent humans. Here we tested the hypothesis that there is no difference in brain size between Neandertals and recent humans while accounting for methodological variation and the makeup of both the Neandertal and recent human samples.<br><br>MATERIALS AND METHODS: We examined endocranial volume (ECV) derived from virtually reconstructed endocasts of 11 Neandertals, six of which had associated femoral head diameters (FHD). Our recent human comparative dataset consisted of virtually measured ECV and associated FHD from 94 recent humans from the Robert J. Terry Anatomical Collection (63 male, 31 female). ECV of Neandertals and recent humans was compared using bootstrap resampling, repeating the analysis for two groupings of Neandertals (all and classic) and for three groupings of recent humans (all, males, and females). To examine brain size scaling, we completed an ordinary least squares regression of log (ECV) against log (FHD) for Neandertals and recent humans.<br><br>RESULTS: The results of the bootstrap resampling analyses indicated that Neandertals only had significantly larger ECV when compared with recent human females. The regression between ECV and FHD suggested that Neandertals fall within the range of variation for larger humans.<br><br>DISCUSSION: Our results demonstrate that Neandertals do not have uniquely large brains when compared with recent humans. Their brain size falls in the large end of the recent human range of variation, but does not exceed it. These results have implications for future research on Neandertal encephalization.}, }
@article {pmid33446842, year = {2021}, author = {Pederzani, S and Aldeias, V and Dibble, HL and Goldberg, P and Hublin, JJ and Madelaine, S and McPherron, SP and Sandgathe, D and Steele, TE and Turq, A and Britton, K}, title = {Reconstructing Late Pleistocene paleoclimate at the scale of human behavior: an example from the Neandertal occupation of La Ferrassie (France).}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1419}, pmid = {33446842}, issn = {2045-2322}, mesh = {Animals ; *Archaeology ; *Behavior, Animal ; *Fossils ; France ; Humans ; *Neanderthals ; }, abstract = {Exploring the role of changing climates in human evolution is currently impeded by a scarcity of climatic information at the same temporal scale as the human behaviors documented in archaeological sites. This is mainly caused by high uncertainties in the chronometric dates used to correlate long-term climatic records with archaeological deposits. One solution is to generate climatic data directly from archaeological materials representing human behavior. Here we use oxygen isotope measurements of Bos/Bison tooth enamel to reconstruct summer and winter temperatures in the Late Pleistocene when Neandertals were using the site of La Ferrassie. Our results indicate that, despite the generally cold conditions of the broader period and despite direct evidence for cold features in certain sediments at the site, Neandertals used the site predominantly when climatic conditions were mild, similar to conditions in modern day France. We suggest that due to millennial scale climate variability, the periods of human activity and their climatic characteristics may not be representative of average conditions inferred from chronological correlations with long-term climatic records. These results highlight the importance of using direct routes, such as the high-resolution archives in tooth enamel from anthropogenically accumulated faunal assemblages, to establish climatic conditions at a human scale.}, }
@article {pmid33436796, year = {2021}, author = {McGrath, K and Limmer, LS and Lockey, AL and Guatelli-Steinberg, D and Reid, DJ and Witzel, C and Bocaege, E and McFarlin, SC and El Zaatari, S}, title = {3D enamel profilometry reveals faster growth but similar stress severity in Neanderthal versus Homo sapiens teeth.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {522}, pmid = {33436796}, issn = {2045-2322}, mesh = {*Adverse Childhood Experiences ; Animals ; Child ; Dental Enamel/diagnostic imaging/*growth &amp; development/*pathology ; Hominidae/*anatomy &amp; histology ; Humans ; Imaging, Three-Dimensional/*methods ; Moire Topography/*methods ; Neanderthals/*anatomy &amp; histology ; Species Specificity ; Tooth/diagnostic imaging/*growth &amp; development/pathology ; }, abstract = {Early life stress disrupts growth and creates horizontal grooves on the tooth surface in humans and other mammals, yet there is no consensus for their quantitative analysis. Linear defects are considered to be nonspecific stress indicators, but evidence suggests that intermittent, severe stressors create deeper defects than chronic, low-level stressors. However, species-specific growth patterns also influence defect morphology, with faster-growing teeth having shallower defects at the population level. Here we describe a method to measure the depth of linear enamel defects and normal growth increments (i.e., perikymata) from high-resolution 3D topographies using confocal profilometry and apply it to a diverse sample of Homo neanderthalensis and H. sapiens anterior teeth. Debate surrounds whether Neanderthals exhibited modern human-like growth patterns in their teeth and other systems, with some researchers suggesting that they experienced more severe childhood stress. Our results suggest that Neanderthals have shallower features than H. sapiens from the Upper Paleolithic, Neolithic, and medieval eras, mirroring the faster growth rates in Neanderthal anterior teeth. However, when defect depth is scaled by perikymata depth to assess their severity, Neolithic humans have less severe defects, while Neanderthals and the other H. sapiens groups show evidence of more severe early life growth disruptions.}, }
@article {pmid33418451, year = {2021}, author = {Nowaczewska, W and Binkowski, M and Benazzi, S and Vazzana, A and Nadachowski, A and Stefaniak, K and Żarski, M and Talamo, S and Compton, T and Stringer, CB and Hajdinjak, M and Hublin, JJ}, title = {New hominin teeth from Stajnia Cave, Poland.}, journal = {Journal of human evolution}, volume = {151}, number = {}, pages = {102929}, doi = {10.1016/j.jhevol.2020.102929}, pmid = {33418451}, issn = {1095-8606}, mesh = {Animals ; Caves ; Fossils/*anatomy &amp; histology ; Hominidae/*anatomy &amp; histology ; Paleodontology ; Poland ; Tooth/*anatomy &amp; histology ; }, }
@article {pmid33417716, year = {2021}, author = {Greer, C and Bhakta, H and Ghanem, L and Refai, F and Linn, E and Avella, M}, title = {Deleterious variants in genes regulating mammalian reproduction in Neanderthals, Denisovans and extant humans.}, journal = {Human reproduction (Oxford, England)}, volume = {36}, number = {3}, pages = {734-755}, doi = {10.1093/humrep/deaa347}, pmid = {33417716}, issn = {1460-2350}, mesh = {Animals ; Europe ; Genome, Human ; *Hominidae/genetics ; Humans ; Male ; *Neanderthals/genetics ; Nuclear Proteins ; Reproduction/genetics ; Trans-Activators ; }, abstract = {STUDY QUESTION: Were Neanderthals and Denisovans (referred here also as extinct hominidae) carrying deleterious variants in genes regulating reproduction?<br><br>SUMMARY ANSWER: The majority of extinct hominidae analyzed here, presented a considerable number of deleterious variants per individual in proteins regulating different aspects of reproduction, including gonad and uterine function, and gametogenesis.<br><br>WHAT IS KNOWN ALREADY: Neanderthals, Denisovans and extant humans were interfertile and hybridized while occupying geographically overlapping areas in Europe and Asia. This is evidenced by the small archaic genome component (average &#x223c;2%) present in non-African extant humans.<br><br>STUDY DESIGN, SIZE, DURATION: The genome of eight extinct hominidae, together with five human genome databases, plus 44 mothers and 48 fathers (fertile controls), were screened to look for deleterious variants in 1734 protein-coding genes regulating reproduction.<br><br>Ancient DNA from six Neanderthals and two Denisovans dated between &#x223c;82&#xa0;000 and 43&#xa0;000 calibrated years was retrieved from the public European Nucleotide Archive. The hominins analyzed include Altai, Vindija 33.15, 33.19, 33.25 and 33.26, El Sidron 1253, Denisova 3 and 11. Their DNA was analyzed using the CLC Genomics Workbench 12, by mapping overlapping paired-end reads (Illumina, FASTQ files) to the human genome assembly GRCh37 (hg19) (Vindija 33.19, 33.25, 33.26, Denisova 3 and Denisova 11) or by analyzing BAM files (Altai, El Sidron 1253 and Vindija 33.15) (human genome reference, GRCh37 (hg19)). Non-synonymous reproductive variants were classified as deleterious or tolerated (PolyPhen-2 and SIFT analyses) and were compared to deleterious variants obtained from extant human genome databases (Genome Aggregation Database (GnomAD), 1000 Genomes, the Haplotype Map (HapMap), Single Nucleotide Polymorphism Database (dbSNPs)) across different populations. A genetic intersection between extant or extinct DNA variants and other genetic disorders was evaluated by annotating the obtained variants with the Clinical Variant (ClinVar) database.<br><br>Among the eight extinct hominidae analyzed, a total of 9650 non-synonymous variants (only coverage &#x2265;20 reads included; frameshift mutations were excluded) in 1734 reproductive protein-coding genes were found, 24% of which were classified as deleterious. The majority (73%) of the deleterious alleles present in extant humans that are shared between extant humans and extinct hominidae were found to be rare (<1%) in extant human populations. A set of 8044 variants were found uniquely in extinct hominidae. At the single-gene level, no extinct individual was found to be homozygous for deleterious variants in genes necessary for gamete recognition and fusion, and no higher chance of embryo-lethality (calculated by Mendelian Genetics) was found upon simulated mating between extant human and extinct hominidae compared to extant human-extant human. However, three of the eight extinct hominidae were found to be homozygous for 48-69 deleterious variants in 55 genes controlling ovarian and uterine functions, or oogenesis (AKAP1, BUB1B, CCDC141, CDC73, DUSP6, ESR1, ESR2, PATL2, PSMC3IP, SEMA3A, WT1 and WNT4). Moreover, we report the distribution of nine Neanderthal variants in genes associated with a human fertility phenotype found in extant human populations, one of which has been associated with polycystic ovarian syndrome and primary congenital glaucoma.<br><br>While analyzing archaic DNA, stringent filtering criteria were adopted to screen for deleterious variants in Neanderthals and Denisovans, which could result in missing a number of variants. Such restraints preserve the potential for detection of additional deleterious variants in reproductive proteins in extinct hominidae.<br><br>This study provides a comprehensive overview of putatively deleterious variants in extant human populations and extinct individuals occurring in 1734 protein-coding genes controlling reproduction and provides the fundaments for future functional studies of extinct variants in human reproduction.<br><br>This study was supported by the Department of Biological Science and by the Office of Research and Sponsored Programs at the University of Tulsa (Faculty Research Grant and Faculty Research Summer Fellowship) to M.A. and the University of Tulsa, Tulsa Undergraduate Research Challenge (TURC) program to E.L.; no conflict of interest to declare.<br><br>TRIAL REGISTRATION NUMBER: N/A.}, }
@article {pmid33412453, year = {2021}, author = {Dodat, PJ and Tacail, T and Albalat, E and Gómez-Olivencia, A and Couture-Veschambre, C and Holliday, T and Madelaine, S and Martin, JE and Rmoutilova, R and Maureille, B and Balter, V}, title = {Isotopic calcium biogeochemistry of MIS 5 fossil vertebrate bones: application to the study of the dietary reconstruction of Regourdou 1 Neandertal fossil.}, journal = {Journal of human evolution}, volume = {151}, number = {}, pages = {102925}, doi = {10.1016/j.jhevol.2020.102925}, pmid = {33412453}, issn = {1095-8606}, mesh = {Animals ; Bone and Bones/*chemistry ; Calcium Isotopes/*analysis ; *Diet ; *Fossils ; France ; *Neanderthals ; *Vertebrates ; }, abstract = {The calcium isotopic composition (δ[44/42]Ca) of bone and tooth enamel can be used for dietary reconstructions of extant and extinct mammals. In natural conditions, the δ[44/42]Ca value of bone and teeth varies according to dietary intake with a constant isotopic offset of about -0.6‰. Owing to the poor conservation of collagen, carbon (C), and nitrogen (N) isotopic compositions of the Regourdou Mousterian site (MIS 5, Dordogne, France) previously failed to provide any paleodietary information. Therefore, to reconstruct the trophic chain, we have measured calcium (Ca) isotopes from fossil bone samples of the fauna from the Regourdou site, as well as from three bone samples of the Regourdou 1 Neandertal specimen. The results show a taxon-dependent patterning of the Ca isotopic compositions: herbivores generally have higher δ[44/42]Ca values than carnivores. All the δ[44/42]Ca values of Regourdou 1 are low (<-1.6‰), placing this specimen amid carnivores. Using a bone-muscle Ca isotopic offset determined on extant animals, we further show that the δ[44/42]Ca value of the Regourdou 1 diet, and that of most carnivores, cannot be accounted for by the consumption of meat only, as plants and meat have indistinguishable δ[44/42]Ca values. Mass balance calculations indicate that the low δ[44/42]Ca values of the Neandertal's carnivorous diet are explained by the ingestion of bone marrow containing as little as 1% trabecular bone. Our results show that the Regourdou 1 Neanderthal consumed a mixture of various herbivorous prey, as well as trabecular bone, which probably occurred when marrow was ingested, by accident or intentionally.}, }
@article {pmid33360685, year = {2021}, author = {Adegboyega, MT and Stamos, PA and Hublin, JJ and Weaver, TD}, title = {Virtual reconstruction of the Kebara 2 Neanderthal pelvis.}, journal = {Journal of human evolution}, volume = {151}, number = {}, pages = {102922}, doi = {10.1016/j.jhevol.2020.102922}, pmid = {33360685}, issn = {1095-8606}, mesh = {Animals ; Fossils/*anatomy &amp; histology ; Male ; Neanderthals/*anatomy &amp; histology ; Observer Variation ; Pelvis/*anatomy &amp; histology ; Printing, Three-Dimensional ; Tomography, X-Ray Computed ; }, abstract = {The paucity of well-preserved pelvises in the hominin fossil record has hindered robust analyses of shifts in critical biological processes throughout human evolution. The Kebara 2 pelvis remains one of the best preserved hominin pelvises, providing a rare opportunity to assess Neanderthal pelvic morphology and function. Here, we present two new reconstructions of the Kebara 2 pelvis created from CT scans of the right hip bone and sacrum. For both reconstructions, we proceeded as follows. First, we virtually reconstructed the right hip bone and the sacrum by repositioning the fragments of the hip bone and sacrum. Then, we created a mirrored copy of the right hip bone to act as the left hip bone. Next, we 3D printed the three bones and physically articulated them. Finally, we used fiducial points collected from the physically articulated models to articulate the hip bones and sacrum in virtual space. Our objectives were to (1) reposition misaligned fragments, particularly the ischiopubic ramus; (2) create a 3D model of a complete pelvis; and (3) assess interobserver reconstruction variation. These new reconstructions show that, in comparison with previous measurements, Kebara 2 possessed a higher shape index (maximum anteroposterior length/maximum mediolateral width) for the pelvic inlet and perhaps the outlet and a more anteriorly positioned sacral promontory and pubic symphysis relative to the acetabula. The latter differences result in a lower ratio between the distances anterior and posterior to the anterior margins of the acetabula. Generally, the new reconstructions tend to accentuate features of the Kebara 2 pelvis--the long superior pubic ramus and anteriorly positioned pelvic inlet--that have already been discussed for Kebara 2 and other Neanderthals.}, }
@article {pmid33356949, year = {2021}, author = {Higgitt, R}, title = {Neanderthal and the fossilization of the Third World.}, journal = {Social studies of science}, volume = {51}, number = {3}, pages = {439-462}, doi = {10.1177/0306312720983460}, pmid = {33356949}, issn = {1460-3659}, mesh = {Animals ; Europe ; Humans ; *Neanderthals ; White People ; }, abstract = {Neanderthal is the quintessential scientific Other. In the late nineteenth century gentlemen-scientists, including business magnates, investment bankers and lawmakers with interest in questions of human and human societal development, framed Europe's Neanderthal and South Asia's indigenous Negritos as close evolutionary kin. Simultaneously, they explained Neanderthal's extinction as the consequence of an inherent backwardness in the face of fair-skinned, steadily-progressing newcomers to ancient Europe who behaved in ways associated with capitalism. This racialization and economization of Neanderthal helped bring meaning and actual legal reality to Negritos via the British Raj's official 'schedules of backward castes and tribes'. It also helped justify the Raj's initiation of market-oriented reforms in order to break a developmental equilibrium deemed created when fair-skinned newcomers to ancient South Asia enslaved Negritos in an enduring caste system. Neanderthal was integral to the scientism behind the British construction of caste, and contributed to India's becoming a principal 'Third World' target of Western structural adjustment policies as continuation of South Asia's 'evolution assistance'.}, }
@article {pmid33299013, year = {2020}, author = {Balzeau, A and Turq, A and Talamo, S and Daujeard, C and Guérin, G and Welker, F and Crevecoeur, I and Fewlass, H and Hublin, JJ and Lahaye, C and Maureille, B and Meyer, M and Schwab, C and Gómez-Olivencia, A}, title = {Pluridisciplinary evidence for burial for the La Ferrassie 8 Neandertal child.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {21230}, pmid = {33299013}, issn = {2045-2322}, mesh = {Animals ; Archaeology ; Bone and Bones/metabolism ; Burial/*history/*methods ; Child, Preschool ; DNA, Mitochondrial/genetics ; Fossils ; France ; Geology ; History, Ancient ; Hominidae ; Humans ; Mass Spectrometry/methods ; Neanderthals/*psychology ; Paleontology ; }, abstract = {The origin of funerary practices has important implications for the emergence of so-called modern cognitive capacities and behaviour. We provide new multidisciplinary information on the archaeological context of the La Ferrassie 8 Neandertal skeleton (grand abri of La Ferrassie, Dordogne, France), including geochronological data -[14]C and OSL-, ZooMS and ancient DNA data, geological and stratigraphic information from the surrounding context, complete taphonomic study of the skeleton and associated remains, spatial information from the 1968-1973 excavations, and new (2014) fieldwork data. Our results show that a pit was dug in a sterile sediment layer and the corpse of a two-year-old child was laid there. A hominin bone from this context, identified through Zooarchaeology by Mass Spectrometry (ZooMS) and associated with Neandertal based on its mitochondrial DNA, yielded a direct [14]C age of 41.7-40.8 ka cal BP (95%), younger than the [14]C dates of the overlying archaeopaleontological layers and the OSL age of the surrounding sediment. This age makes the bone one of the most recent directly dated Neandertals. It is consistent with the age range for the Châtelperronian in the site and in this region and represents the third association of Neandertal taxa to Initial Upper Palaeolithic lithic technocomplex in Western Europe. A detailed multidisciplinary approach, as presented here, is essential to advance understanding of Neandertal behavior, including funerary practices.}, }
@article {pmid33296644, year = {2020}, author = {Jordan, B}, title = {[A poisoned gift].}, journal = {Medecine sciences : M/S}, volume = {36}, number = {12}, pages = {1233-1236}, doi = {10.1051/medsci/2020240}, pmid = {33296644}, issn = {1958-5381}, mesh = {Adaptor Proteins, Signal Transducing/genetics/metabolism ; Angiotensin-Converting Enzyme 2/metabolism ; Animals ; COVID-19/epidemiology/*genetics/pathology/therapy ; Case-Control Studies ; Chromosomes, Human, Pair 3/*genetics ; Europe/epidemiology ; Evolution, Molecular ; *Genetic Loci ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Hominidae/genetics ; Humans ; Membrane Glycoproteins/genetics/metabolism ; Membrane Transport Proteins/genetics/metabolism ; Neanderthals/*genetics ; Pandemics ; Polymorphism, Single Nucleotide ; Protein Binding ; Receptors, CCR/genetics ; Receptors, CXCR6/genetics ; SARS-CoV-2/metabolism/*pathogenicity ; Severity of Illness Index ; }, abstract = {GWAS analysis of severe Covid patients implicates a major locus on chromosome 3. The corresponding 50 kb segment appears to originate from Neanderthal/Sapiens crossings, raising interesting evolutionary questions.}, }
@article {pmid33278486, year = {2021}, author = {Wendt, FR and Pathak, GA and Overstreet, C and Tylee, DS and Gelernter, J and Atkinson, EG and Polimanti, R}, title = {Characterizing the effect of background selection on the polygenicity of brain-related traits.}, journal = {Genomics}, volume = {113}, number = {1 Pt 1}, pages = {111-119}, pmid = {33278486}, issn = {1089-8646}, support = {F32 MH122058/MH/NIMH NIH HHS/United States ; R21 DA047527/DA/NIDA NIH HHS/United States ; R21 DC018098/DC/NIDCD NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; }, mesh = {Brain/*metabolism ; *Genetic Background ; *Genetic Heterogeneity ; Humans ; Mental Disorders/diagnosis/*genetics ; *Multifactorial Inheritance ; Phenotype ; Polymorphism, Single Nucleotide ; *Selection, Genetic ; }, abstract = {BACKGROUND: Genome-wide association studies (GWAS) have demonstrated that psychopathology phenotypes are affected by many risk alleles with small effect (polygenicity). It is unclear how ubiquitously evolutionary pressures influence the genetic architecture of these traits.<br><br>METHODS: We partitioned SNP heritability to assess the contribution of background (BGS) and positive selection, Neanderthal local ancestry, functional significance, and genotype networks in 75 brain-related traits (8411&#xa0;&#x2264;&#xa0;N&#xa0;&#x2264;&#xa0;1,131,181, mean N&#xa0;=&#xa0;205,289). We applied binary annotations by dichotomizing each measure based on top 2%, 1%, and 0.5% of all scores genome-wide. Effect size distribution features were calculated using GENESIS. We tested the relationship between effect size distribution descriptive statistics and natural selection. In a subset of traits, we explore the inclusion of diagnostic heterogeneity (e.g., number of diagnostic combinations and total symptoms) in the tested relationship.<br><br>RESULTS: SNP-heritability was enriched (false discovery rate q&#xa0;<&#xa0;0.05) for loci with elevated BGS (7 phenotypes) and in genic (34 phenotypes) and loss-of-function (LoF)-intolerant regions (67 phenotypes). These effects were strongest in GWAS of schizophrenia (1.90-fold BGS, 1.16-fold genic, and 1.92-fold LoF), educational attainment (1.86-fold BGS, 1.12-fold genic, and 1.79-fold LoF), and cognitive performance (2.29-fold BGS, 1.12-fold genic, and 1.79-fold LoF). BGS (top 2%) significantly predicted effect size variance for trait-associated loci (&#x3c3;[2] parameter) in 75 brain-related traits (&#x3b2;&#xa0;=&#xa0;4.39&#xa0;&#xd7;&#xa0;10[-5], p&#xa0;=&#xa0;1.43&#xa0;&#xd7;&#xa0;10[-5], model r[2]&#xa0;=&#xa0;0.548). Considering the number of DSM-5 diagnostic combinations per psychiatric disorder improved model fit (&#x3c3;[2]&#xa0;~&#xa0;BTop2%&#xa0;&#xd7;&#xa0;Genic &#xd7; diagnostic combinations; model r[2]&#xa0;=&#xa0;0.661).<br><br>CONCLUSIONS: Brain-related phenotypes with larger variance in risk locus effect sizes are associated with loci under BGS. We show exploratory results suggesting that diagnostic complexity may also contribute to the increased polygenicity of psychiatric disorders.}, }
@article {pmid33264306, year = {2020}, author = {Riga, A and Boggioni, M and Papini, A and Buzi, C and Profico, A and Di Vincenzo, F and Marchi, D and Moggi-Cecchi, J and Manzi, G}, title = {In situ observations on the dentition and oral cavity of the Neanderthal skeleton from Altamura (Italy).}, journal = {PloS one}, volume = {15}, number = {12}, pages = {e0241713}, pmid = {33264306}, issn = {1932-6203}, mesh = {Animals ; Caves ; *Dentition ; *Fossils ; Hominidae/*anatomy &amp; histology ; Humans ; Italy ; Mandible/anatomy &amp; histology ; Maxilla/anatomy &amp; histology ; Mouth/physiology ; Neanderthals/*anatomy &amp; histology ; Paleodontology ; Skull/anatomy &amp; histology ; Tooth/anatomy &amp; histology ; }, abstract = {The Neanderthal specimen from Lamalunga Cave, near Altamura (Apulia, Italy), was discovered during a speleological survey in 1993. The specimen is one of the most complete fossil hominins in Europe and its state of preservation is exceptional, although it is stuck in calcareous concretions and the bones are mostly covered by calcite depositions. Nevertheless, it is possible to carry out some observations on craniodental features that have not previously been described. In this work, we present an account of the oral cavity, made possible by the use of a videoscope, which allowed us to reach some hidden parts of the mandible and palate. This is the first detailed overview of the teeth and maxillary bones of the Neanderthal skeleton from Altamura. The dentition is almost complete. However, two teeth (upper right P3 and upper left M1) were lost ante mortem and four teeth (lower right I1 and P3 and lower left I1 and I2) were lost most probably post mortem. Dental wear is marked. The erupted M3s and the inversion of the compensating curve of Wilson in the M1s and M2s but not in the M3s suggest that the individual is fully adult, but not old. Although most of the teeth have their roots exposed for several millimeters, the periodontal bone appears to be in good condition overall, except in correspondence of the two ante-mortem tooth losses. X-rays of the anterior teeth show a periapical lesion, probably linked to the advanced dental wear. We also observed a weak expression of taurodontism in the posterior dentition and the presence of a retromolar space, features consistent with an attribution to the Neanderthal hypodigm; this attribution is also supported by aspects of the cranial morphology, the morphometric analysis of the scapula and preliminary mtDNA data. There is also a well-developed palatine torus, to the best of our knowledge a feature not previously described in Neanderthals.}, }
@article {pmid33247712, year = {2021}, author = {Dannemann, M}, title = {The Population-Specific Impact of Neandertal Introgression on Human Disease.}, journal = {Genome biology and evolution}, volume = {13}, number = {1}, pages = {}, pmid = {33247712}, issn = {1759-6653}, mesh = {Alleles ; Animals ; Diabetes Mellitus, Type 2/genetics ; Disease/*genetics ; Evolution, Molecular ; Female ; Fossils ; Genetic Variation ; *Genome, Human ; *Genome-Wide Association Study ; Humans ; Japan ; Male ; Neanderthals/*genetics ; Phenotype ; Polymorphism, Single Nucleotide ; White People/genetics ; }, abstract = {Since the discovery of admixture between modern humans and Neandertals, multiple studies investigated the effect of Neandertal-derived DNA on human disease and nondisease phenotypes. These studies have linked Neandertal ancestry to skin- and hair-related phenotypes, immunity, neurological, and behavioral traits. However, these inferences have so far been limited to cohorts with participants of European ancestry. Here, I analyze summary statistics from 40 disease GWAS (genome-wide association study) cohorts of ∼212,000 individuals provided by the Biobank Japan Project for phenotypic effects of Neandertal DNA. I show that Neandertal DNA is associated with autoimmune diseases, prostate cancer and type 2 diabetes. Many of these disease associations are linked to population-specific Neandertal DNA, highlighting the importance of studying a wider range of ancestries to characterize the phenotypic legacy of Neandertals in people today.}, }
@article {pmid33245148, year = {2021}, author = {Mineta, K and Goto, K and Gojobori, T and Alkuraya, FS}, title = {Indigenous Arabs have an intermediate frequency of a Neanderthal-derived COVID-19 risk haplotype compared with other world populations.}, journal = {Clinical genetics}, volume = {99}, number = {3}, pages = {484-485}, pmid = {33245148}, issn = {1399-0004}, mesh = {Alleles ; Animals ; Arabs/*genetics ; COVID-19/*genetics/virology ; *Gene Frequency ; *Genetic Predisposition to Disease ; Haplotypes/*genetics ; Heterozygote ; Homozygote ; Humans ; Neanderthals/*genetics ; Polymorphism, Single Nucleotide/genetics ; Population Groups/*genetics ; Risk Factors ; SARS-CoV-2/physiology ; Saudi Arabia ; }, }
@article {pmid33244047, year = {2020}, author = {Bardo, A and Moncel, MH and Dunmore, CJ and Kivell, TL and Pouydebat, E and Cornette, R}, title = {The implications of thumb movements for Neanderthal and modern human manipulation.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {19323}, pmid = {33244047}, issn = {2045-2322}, support = {819960/ERC_/European Research Council/International ; }, mesh = {Adult ; Animals ; Anthropology, Physical ; Biological Evolution ; Female ; Fossils/anatomy &amp; histology ; Hand Strength/physiology ; History, 21st Century ; History, Ancient ; Humans ; Imaging, Three-Dimensional ; Male ; Metacarpal Bones/anatomy &amp; histology ; Models, Biological ; Movement ; Neanderthals/*anatomy &amp; histology/*physiology ; Species Specificity ; Thumb/*anatomy &amp; histology/*physiology ; Trapezium Bone/anatomy &amp; histology ; }, abstract = {Much research has debated the technological abilities of Neanderthals relative to those of early modern humans, with a particular focus on subtle differences in thumb morphology and how this may reflect differences in manipulative behaviors in these two species. Here, we provide a novel perspective on this debate through a 3D geometric morphometric analysis of shape covariation between the trapezial and proximal first metacarpal articular surfaces of Neanderthals (Homo neanderthalensis) in comparison to early and recent humans (Homo sapiens). Results show a distinct pattern of shape covariation in Neanderthals, consistent with more extended and adducted thumb postures that may reflect habitual use of grips commonly used for hafted tools. Both Neanderthals and recent humans demonstrate high intraspecific variation in shape covariation. This intraspecific variation is likely the result of genetic and/or developmental differences, but may also reflect, in part, differing functional requirements imposed by the use of varied tool-kits. These results underscore the importance of holistic joint shape analysis for understanding the functional capabilities and evolution of the modern human thumb.}, }
@article {pmid33230523, year = {2021}, author = {Aarts, JMMJG and Alink, GM and Franssen, HJ and Roebroeks, W}, title = {Evolution of Hominin Detoxification: Neanderthal and Modern Human Ah Receptor Respond Similarly to TCDD.}, journal = {Molecular biology and evolution}, volume = {38}, number = {4}, pages = {1292-1305}, pmid = {33230523}, issn = {1537-1719}, mesh = {Animals ; Cytochrome P-450 CYP1A1/*metabolism ; Environmental Pollutants/*metabolism ; *Evolution, Molecular ; HeLa Cells ; Hep G2 Cells ; Humans ; Inactivation, Metabolic/genetics ; Neanderthals/*genetics/metabolism ; Polychlorinated Dibenzodioxins/*metabolism ; Receptors, Aryl Hydrocarbon/chemistry/*genetics/metabolism ; }, abstract = {In studies of hominin adaptations to fire use, the role of the aryl hydrocarbon receptor (AHR) in the evolution of detoxification has been highlighted, including statements that the modern human AHR confers a significantly better capacity to deal with toxic smoke components than the Neanderthal AHR. To evaluate this, we compared the AHR-controlled induction of cytochrome P4501A1 (CYP1A1) mRNA in HeLa human cervix epithelial adenocarcinoma cells transfected with an Altai-Neanderthal or a modern human reference AHR expression construct, and exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). We compared the complete AHR mRNA sequences including the untranslated regions (UTRs), maintaining the original codon usage. We observe no significant difference in CYP1A1 induction by TCDD between Neanderthal and modern human AHR, whereas a 150-1,000 times difference was previously reported in a study of the AHR coding region optimized for mammalian codon usage and expressed in rat cells. Our study exemplifies that expression in a homologous cellular background is of major importance to determine (ancient) protein activity. The Neanderthal and modern human dose-response curves almost coincide, except for a slightly higher extrapolated maximum for the Neanderthal AHR, possibly caused by a 5'-UTR G-variant known from modern humans (rs7796976). Our results are strongly at odds with a major role of the modern human AHR in the evolution of hominin detoxification of smoke components and consistent with our previous study based on 18 relevant genes in addition to AHR, which concluded that efficient detoxification alleles are more dominant in ancient hominins, chimpanzees, and gorillas than in modern humans.}, }
@article {pmid33226710, year = {2021}, author = {Weyrich, LS}, title = {The evolutionary history of the human oral microbiota and its implications for modern health.}, journal = {Periodontology 2000}, volume = {85}, number = {1}, pages = {90-100}, doi = {10.1111/prd.12353}, pmid = {33226710}, issn = {1600-0757}, mesh = {Diet ; Humans ; *Microbiota/genetics ; *Mouth Diseases ; Oral Health ; }, abstract = {Numerous biological and cultural factors influence the microbial communities (microbiota) that inhabit the human mouth, including diet, environment, hygiene, physiology, health status, genetics, and lifestyle. As oral microbiota can underpin oral and systemic diseases, tracing the evolutionary history of oral microbiota and the factors that shape its origins will unlock information to mitigate disease today. Despite this, the origins of many oral microbes remain unknown, and the key factors in the past that shaped our oral microbiota are only now emerging. High throughput DNA sequencing of oral microbiota using ancient DNA and comparative anthropological methodologies has been employed to investigate oral microbiota origins, revealing a complex, rich history. Here, I review the current literature on the factors that shaped and guided oral microbiota evolution, both in Europe and globally. In Europe, oral microbiota evolution was shaped by interactions with Neandertals, the adaptation of farming, widespread integration of industrialization, and postindustrial lifestyles that emerged after World War II. Globally, evidence for a multitude of different oral microbiota histories is emerging, likely supporting dissimilarities in modern oral health across discrete human populations. I highlight how these evolutionary changes are linked to the development of modern oral diseases and discuss the remaining factors that need to be addressed to improve this embryonic field of research. I argue that understanding the evolutionary history of our oral microbiota is necessary to identify new treatment and prevention options to improve oral and systemic health in the future.}, }
@article {pmid33218283, year = {2021}, author = {Gregory, MD and Kippenhan, JS and Kohn, P and Eisenberg, DP and Callicott, JH and Kolachana, B and Berman, KF}, title = {Neanderthal-Derived Genetic Variation is Associated with Functional Connectivity in the Brains of Living Humans.}, journal = {Brain connectivity}, volume = {11}, number = {1}, pages = {38-44}, pmid = {33218283}, issn = {2158-0022}, support = {ZIA MH002942/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Animals ; Brain ; Genetic Variation/genetics ; Humans ; Magnetic Resonance Imaging ; *Neanderthals/genetics ; }, abstract = {Aim: To determine whether Neanderthal-derived genetic variation relates to functional connectivity patterns in the brains of living modern humans. Introduction: Nearly 50,000 years ago, Neanderthals interbred with ancestors of modern humans, imparting a genetic legacy that lives on today. The vestiges of this Neanderthal-derived genetic variation have been previously shown to be enriched in genes coding for neurogenesis and myelination and to alter skull shape and brain structure in living people. Materials and Methods: Using two independent cohorts totaling 553 healthy individuals, we employed multivariate distance matrix regression (MDMR) to determine whether any brain areas exhibited whole-brain functional connectivity patterns that significantly related to the degree of Neanderthal introgression. Identified clusters were then used as regions of interest in follow-up seed-based functional connectivity analyses to determine the connectivity patterns driving the relationships. Results: The MDMR analysis revealed that the percentage of Neanderthal-originating polymorphisms was significantly associated with the functional connectivity patterns of an area of the intraparietal sulcus (IPS) that was nearly identical in both cohorts. Using these IPS clusters as regions of interest in seed-based connectivity analyses, we found, again in both cohorts, that individuals with a higher proportion of Neanderthal-derived genetic variation showed increased IPS functional connectivity with visual processing regions, but decreased IPS connectivity with regions underlying social cognition. Conclusions: These findings demonstrate that the remnants of Neanderthal admixture continue to influence human brain function today, in ways that are consistent with anthropological conceptualizations of Neanderthal phenotypes, including the possibility that Neanderthals may have depended upon visual processing capabilities at the expense of social cognition, and this may have contributed to the extinction of this species through reduced cultural maintenance and inability to cope with fluctuating resources. This and other studies capitalizing on the emerging science surrounding ancient DNA provide a window through which to view an ancient lineage long past.}, }
@article {pmid33170414, year = {2020}, author = {Madison, P}, title = {Characterized by Darkness: Reconsidering the Origins of the Brutish Neanderthal.}, journal = {Journal of the history of biology}, volume = {53}, number = {4}, pages = {493-519}, pmid = {33170414}, issn = {1573-0387}, support = {60669//John Templeton Foundation/International ; Center for Biology//School of Life Sciences, Arizona State University/International ; Society//School of Life Sciences, Arizona State University/International ; }, abstract = {The extinct human relatives known as Neanderthals (Homo neanderthalensis) have long been described as brutish and dumb. This conception is often traced to paleontologist Marcellin Boule (1861-1942), who published a detailed analysis on a Neanderthal skeleton in the early twentieth century. The conventional historical narrative claims that Boule made an error in his analysis, causing the Neanderthals to be considered brutish. This essay challenges the narrative of "Boule's error," arguing instead that the brutish Neanderthal concept originated much earlier in the history of Neanderthal research and was, in fact, an invention of the earliest analyses of the first specimen recognized as a Neanderthal in the mid-nineteenth century. I argue that temporally relocating this conception of Neanderthals allows for a better understanding of the interconnected nature of the study of fossil humans and the science of living human races during the nineteenth century. This new view of the brutish Neanderthal sheds light on the earliest phases of the science that became paleoanthropology, while examining the racial, cultural, and political attitudes about race and extinction that accompanied the science at that time. By inspecting the ways in which the Neanderthals' image was a product of a particular time and place, we gain a perspective that provides a new basis for thinking about the conceptions of hominin fossil species.}, }
@article {pmid33139541, year = {2020}, author = {Nava, A and Lugli, F and Romandini, M and Badino, F and Evans, D and Helbling, AH and Oxilia, G and Arrighi, S and Bortolini, E and Delpiano, D and Duches, R and Figus, C and Livraghi, A and Marciani, G and Silvestrini, S and Cipriani, A and Giovanardi, T and Pini, R and Tuniz, C and Bernardini, F and Dori, I and Coppa, A and Cristiani, E and Dean, C and Bondioli, L and Peresani, M and Müller, W and Benazzi, S}, title = {Early life of Neanderthals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {46}, pages = {28719-28726}, pmid = {33139541}, issn = {1091-6490}, mesh = {Animals ; Dental Enamel/chemistry/*growth &amp; development ; Humans ; Infant ; Infant, Newborn ; Neanderthals/*growth &amp; development ; *Weaning ; }, abstract = {The early onset of weaning in modern humans has been linked to the high nutritional demand of brain development that is intimately connected with infant physiology and growth rate. In Neanderthals, ontogenetic patterns in early life are still debated, with some studies suggesting an accelerated development and others indicating only subtle differences vs. modern humans. Here we report the onset of weaning and rates of enamel growth using an unprecedented sample set of three late (∼70 to 50 ka) Neanderthals and one Upper Paleolithic modern human from northeastern Italy via spatially resolved chemical/isotopic analyses and histomorphometry of deciduous teeth. Our results reveal that the modern human nursing strategy, with onset of weaning at 5 to 6 mo, was present among these Neanderthals. This evidence, combined with dental development akin to modern humans, highlights their similar metabolic constraints during early life and excludes late weaning as a factor contributing to Neanderthals' demise.}, }
@article {pmid33137550, year = {2020}, author = {Palancar, CA and Torres-Tamayo, N and García-Martínez, D and García-Tabernero, A and Rosas, A and Bastir, M}, title = {Comparative anatomy and 3D geometric morphometrics of the El Sidrón atlases (C1).}, journal = {Journal of human evolution}, volume = {149}, number = {}, pages = {102897}, doi = {10.1016/j.jhevol.2020.102897}, pmid = {33137550}, issn = {1095-8606}, mesh = {Animals ; Biological Evolution ; Cervical Atlas/*anatomy &amp; histology ; Fossils/*anatomy &amp; histology ; Neanderthals/*anatomy &amp; histology ; Spain ; }, abstract = {The first cervical vertebra (atlas, C1) is an important element of the vertebral column because it connects the cranial base with the cervical column, thus helping to maintain head posture and contributing to neck mobility. However, few atlases are preserved in the fossil record because of the fragility of this vertebra. Consequently, only eight well-preserved atlases from adult Neandertals have been recovered and described. Here, we present nine new atlas remains from the El Sidrón Neandertal site (Asturias, Spain), two of which (SD-1643 and SD-1605/1595) are sufficiently well preserved to allow for a detailed comparative and three-dimensional geometric morphometric analysis. We compared standard linear measurements of SD-1643 and SD-1605/1595 with those of other Neandertal atlases and carried out three-dimensional geometric morphometric analyses to compare size and shape of SD-1643 and SD-1605/1595 with those of 28 Pan (Pan troglodytes and Pan paniscus), a broad comparative sample of 55 anatomically modern humans from African and European populations, and other fossil hominins (Neandertals, Homo antecessor, Paranthropus boisei). The El Sidrón atlas fossils show typical features of the Neandertal atlas morphology, such as caudal projection of the anterior tubercle, gracility of both the posterior tubercle and the tuberosity for the insertion of the transverse ligament, and an anteroposteriorly elongated neural canal. Furthermore, when compared with atlases from the other taxa, Neandertals exhibit species-specific features of atlas morphology including a relatively lower lateral mass height, relatively narrower transverse foramina, and flatter and more horizontally oriented articular facets. Some of these features fit with previous suggestions of shorter overall length of the cervical spine and potential differences in craniocervical posture and mobility. Our results may support a different spinopelvic alignment in this species, as the atlas morphology suggests reduced cervical lordosis.}, }
@article {pmid33111974, year = {2021}, author = {Cofran, Z and Boone, M and Petticord, M}, title = {Virtually estimated endocranial volumes of the Krapina Neandertals.}, journal = {American journal of physical anthropology}, volume = {174}, number = {1}, pages = {117-128}, doi = {10.1002/ajpa.24165}, pmid = {33111974}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; Cephalometry/*methods ; Female ; Fossils ; Hominidae/anatomy &amp; histology ; Humans ; Imaging, Three-Dimensional ; Male ; Neanderthals/*anatomy &amp; histology ; Skull/*anatomy &amp; histology/*diagnostic imaging ; }, abstract = {OBJECTIVES: The Krapina rock shelter has yielded a large assemblage of early Neandertals. Although endocranial volume (ECV) has been estimated for four individuals from the site, several published values that appear in the literature warrant revisiting.<br><br>MATERIALS AND METHODS: We used virtual methods, including high-resolution surface models of fossils and 3D geometric morphometrics, to reconstruct endocasts and estimate ECV for five Krapina crania. We generated 10 reconstructions of each endocast to quantify missing data uncertainty. To assess the method and our ECV estimates, we applied these techniques to the Spy II Neandertal, and estimated ECV of a human reference endocast simulating the missing data of the Krapina fossils.<br><br>RESULTS: We obtained an average ECV estimate of 1,526&#x2009;cm[3] for Spy II, consistent with previous research. Estimated ECV of juveniles Krapina 1 and 2 average 1,419 and 1,286&#x2009;cm[3] , respectively. Estimates for the relatively complete adults Krapina 3 and 6 range from 1,247 to 1,310&#x2009;cm[3] and 1,135 to 1,207&#x2009;cm[3] , respectively, while the more fragmentary Krapina 5 averaged 1,397&#x2009;cm[3] . The missing data simulation suggests more fragmentary crania yield more uncertain and possibly overestimated ECVs.<br><br>CONCLUSIONS: We have provided new estimates of brain size of the Krapina Neandertals, including the first estimates for Krapina 2. Brain size at Krapina was similar to other pre-W&#xfc;rm Neandertals, within the range of but lower than the average of later Neandertals. Although the virtual approach overcomes many challenges of fossil preservation, our results are nevertheless subject to future revision.}, }
@article {pmid37588361, year = {2020}, author = {Sánchez Goñi, MF}, title = {Regional impacts of climate change and its relevance to human evolution.}, journal = {Evolutionary human sciences}, volume = {2}, number = {}, pages = {e55}, pmid = {37588361}, issn = {2513-843X}, abstract = {The traditional concept of long and gradual, glacial-interglacial climate changes during the Quaternary has been challenged since the 1980s. High temporal resolution analysis of marine, terrestrial and ice geological archives has identified rapid, millennial- to centennial-scale, and large-amplitude climatic cycles throughout the last few million years. These changes were global but have had contrasting regional impacts on the terrestrial and marine ecosystems, with in some cases strong changes in the high latitudes of both hemispheres but muted changes elsewhere. Such a regionalization has produced environmental barriers and corridors that have probably triggered niche contractions/expansions of hominin populations living in Eurasia and Africa. This article reviews the long- and short-timescale ecosystem changes that have punctuated the last few million years, paying particular attention to the environments of the last 650,000 years, which have witnessed key events in the evolution of our lineage in Africa and Eurasia. This review highlights, for the first time, a contemporaneity between the split between Denisovan and Neanderthals, at ~650-400 ka, and the strong Eurasian ice-sheet expansion down to the Black Sea. This ice expansion could form an ice barrier between Europe and Asia that may have triggered the genetic drift between these two populations.}, }
@article {pmid33106620, year = {2020}, author = {Luo, Y}, title = {Neanderthal DNA highlights complexity of COVID risk factors.}, journal = {Nature}, volume = {587}, number = {7835}, pages = {552-553}, pmid = {33106620}, issn = {1476-4687}, mesh = {Betacoronavirus ; COVID-19 ; *Coronavirus Infections/epidemiology ; DNA ; Humans ; *Neanderthals/genetics ; *Pandemics ; *Pneumonia, Viral ; Risk Factors ; SARS-CoV-2 ; }, }
@article {pmid33028520, year = {2020}, author = {García-Martínez, D and Bastir, M and Gómez-Olivencia, A and Maureille, B and Golovanova, L and Doronichev, V and Akazawa, T and Kondo, O and Ishida, H and Gascho, D and Zollikofer, CPE and de León, MP and Heuzé, Y}, title = {Early development of the Neanderthal ribcage reveals a different body shape at birth compared to modern humans.}, journal = {Science advances}, volume = {6}, number = {41}, pages = {}, pmid = {33028520}, issn = {2375-2548}, abstract = {Ontogenetic studies provide clues for understanding important paleobiological aspects of extinct species. When compared to that of modern humans, the adult Neanderthal thorax was shorter, deeper, and wider. This is related to the wide Neanderthal body and is consistent with their hypothetical large requirements for energy and oxygen. Whether these differences were already established at birth or appeared later during development is unknown. To delve into this question, we use virtual reconstruction tools and geometric morphometrics to recover the 3D morphology of the ribcages of four Neanderthal individuals from birth to around 3 years old: Mezmaiskaya 1, Le Moustier 2, Dederiyeh 1, and Roc de Marsal. Our results indicate that the comparatively deep and short ribcage of the Neanderthals was already present at birth, as were other skeletal species-specific traits. This morphology possibly represents the plesiomorphic condition shared with Homo erectus, and it is likely linked to large energetic requirements.}, }
@article {pmid32989161, year = {2020}, author = {Haws, JA and Benedetti, MM and Talamo, S and Bicho, N and Cascalheira, J and Ellis, MG and Carvalho, MM and Friedl, L and Pereira, T and Zinsious, BK}, title = {The early Aurignacian dispersal of modern humans into westernmost Eurasia.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {41}, pages = {25414-25422}, pmid = {32989161}, issn = {1091-6490}, mesh = {*Archaeology ; *Demography ; Emigration and Immigration/history ; *Fossils ; History, Ancient ; Humans ; Portugal ; Radiometric Dating ; }, abstract = {Documenting the first appearance of modern humans in a given region is key to understanding the dispersal process and the replacement or assimilation of indigenous human populations such as the Neanderthals. The Iberian Peninsula was the last refuge of Neanderthal populations as modern humans advanced across Eurasia. Here we present evidence of an early Aurignacian occupation at Lapa do Picareiro in central Portugal. Diagnostic artifacts were found in a sealed stratigraphic layer dated 41.1 to 38.1 ka cal BP, documenting a modern human presence on the western margin of Iberia ∼5,000 years earlier than previously known. The data indicate a rapid modern human dispersal across southern Europe, reaching the westernmost edge where Neanderthals were thought to persist. The results support the notion of a mosaic process of modern human dispersal and replacement of indigenous Neanderthal populations.}, }
@article {pmid32973032, year = {2020}, author = {Petr, M and Hajdinjak, M and Fu, Q and Essel, E and Rougier, H and Crevecoeur, I and Semal, P and Golovanova, LV and Doronichev, VB and Lalueza-Fox, C and de la Rasilla, M and Rosas, A and Shunkov, MV and Kozlikin, MB and Derevianko, AP and Vernot, B and Meyer, M and Kelso, J}, title = {The evolutionary history of Neanderthal and Denisovan Y chromosomes.}, journal = {Science (New York, N.Y.)}, volume = {369}, number = {6511}, pages = {1653-1656}, doi = {10.1126/science.abb6460}, pmid = {32973032}, issn = {1095-9203}, support = {694707/ERC_/European Research Council/International ; }, mesh = {Animals ; Chromosomes, Human, Y/genetics ; DNA, Ancient ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Humans ; *Life History Traits ; Male ; Neanderthals/classification/*genetics ; Phylogeny ; Y Chromosome/*genetics ; }, abstract = {Ancient DNA has provided new insights into many aspects of human history. However, we lack comprehensive studies of the Y chromosomes of Denisovans and Neanderthals because the majority of specimens that have been sequenced to sufficient coverage are female. Sequencing Y chromosomes from two Denisovans and three Neanderthals shows that the Y chromosomes of Denisovans split around 700 thousand years ago from a lineage shared by Neanderthals and modern human Y chromosomes, which diverged from each other around 370 thousand years ago. The phylogenetic relationships of archaic and modern human Y chromosomes differ from the population relationships inferred from the autosomal genomes and mirror mitochondrial DNA phylogenies, indicating replacement of both the mitochondrial and Y chromosomal gene pools in late Neanderthals. This replacement is plausible if the low effective population size of Neanderthals resulted in an increased genetic load in Neanderthals relative to modern humans.}, }
@article {pmid32963029, year = {2020}, author = {Bokelmann, L and Glocke, I and Meyer, M}, title = {Reconstructing double-stranded DNA fragments on a single-molecule level reveals patterns of degradation in ancient samples.}, journal = {Genome research}, volume = {30}, number = {10}, pages = {1449-1457}, pmid = {32963029}, issn = {1549-5469}, mesh = {Animals ; Cell-Free Nucleic Acids/blood ; Cytosine/metabolism ; DNA/blood ; DNA, Ancient/*chemistry ; Deamination ; High-Throughput Nucleotide Sequencing ; Humans ; Neanderthals/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Extensive manipulations involved in the preparation of DNA samples for sequencing have hitherto made it impossible to determine the precise structure of double-stranded DNA fragments being sequenced, such as the presence of blunt ends, single-stranded overhangs, or single-strand breaks. We here describe MatchSeq, a method that combines single-stranded DNA library preparation from diluted DNA samples with computational sequence matching, allowing the reconstruction of double-stranded DNA fragments on a single-molecule level. The application of MatchSeq to Neanderthal DNA, a particularly complex source of degraded DNA, reveals that 1- or 2-nt overhangs and blunt ends dominate the ends of ancient DNA molecules and that short gaps exist, which are predominantly caused by the loss of individual purines. We further show that deamination of cytosine to uracil occurs in both single- and double-stranded contexts close to the ends of molecules, and that single-stranded parts of DNA fragments are enriched in pyrimidines. MatchSeq provides unprecedented resolution for interrogating the structures of fragmented double-stranded DNA and can be applied to fragmented double-stranded DNA isolated from any biological source. The method relies on well-established laboratory techniques and can easily be integrated into routine data generation. This possibility is shown by the successful reconstruction of double-stranded DNA fragments from previously published single-stranded sequence data, allowing a more comprehensive characterization of the biochemical properties not only of ancient DNA but also of cell-free DNA from human blood plasma, a clinically relevant marker for the diagnosis and monitoring of disease.}, }
@article {pmid32918796, year = {2021}, author = {Breyl, M}, title = {Triangulating Neanderthal cognition: A tale of not seeing the forest for the trees.}, journal = {Wiley interdisciplinary reviews. Cognitive science}, volume = {12}, number = {2}, pages = {e1545}, doi = {10.1002/wcs.1545}, pmid = {32918796}, issn = {1939-5086}, mesh = {Animals ; *Biological Evolution ; *Cognition ; Humans ; *Language ; *Neanderthals ; }, abstract = {The inference of Neanderthal cognition, including their cultural and linguistic capabilities, has persisted as a fiercely debated research topic for decades. This lack of consensus is substantially based on inherent uncertainties in reconstructing prehistory out of indirect evidence as well as other methodological limitations. Further factors include systemic difficulties within interdisciplinary discourse, data artifacts, historic research biases, and the sheer scope of the relevant research. Given the degrees of freedom in interpretation ensuing from these complications, any attempt to find approximate answers to the yet unsettled pertinent discourse may not rest on single studies, but instead a careful and comprehensive interdisciplinary synthesis of findings. Triangulating Neanderthals' cognition by considering the plethora of data, diverse perspectives and aforementioned complexities present within the literature constitutes the currently most reliable pathway to tentative conclusions. While some uncertainties remain, such an approach paints the picture of an extensive shared humanity between anatomically modern humans and Neanderthals. This article is categorized under: Cognitive Biology > Evolutionary Roots of Cognition Linguistics > Evolution of Language.}, }
@article {pmid32901061, year = {2020}, author = {Picin, A and Hajdinjak, M and Nowaczewska, W and Benazzi, S and Urbanowski, M and Marciszak, A and Fewlass, H and Bosch, MD and Socha, P and Stefaniak, K and Żarski, M and Wiśniewski, A and Hublin, JJ and Nadachowski, A and Talamo, S}, title = {New perspectives on Neanderthal dispersal and turnover from Stajnia Cave (Poland).}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {14778}, pmid = {32901061}, issn = {2045-2322}, mesh = {Animals ; Archaeology ; *Caves ; DNA, Mitochondrial/*analysis/genetics ; *Fossils ; Humans ; Neanderthals/classification/*genetics ; Phylogeny ; Poland ; Radiometric Dating ; Sequence Analysis, DNA ; Tooth/*anatomy &amp; histology/physiology ; }, abstract = {The Micoquian is the broadest and longest enduring cultural facies of the Late Middle Palaeolithic that spread across the periglacial and boreal environments of Europe between Eastern France, Poland, and Northern Caucasus. Here, we present new data from the archaeological record of Stajnia Cave (Poland) and the paleogenetic analysis of a Neanderthal molar S5000, found in a Micoquian context. Our results demonstrate that the mtDNA genome of Stajnia S5000 dates to MIS 5a making the tooth the oldest Neanderthal specimen from Central-Eastern Europe. Furthermore, S5000 mtDNA has the fewest number of differences to mtDNA of Mezmaiskaya 1 Neanderthal from Northern Caucasus, and is more distant from almost contemporaneous Neanderthals of Scladina and Hohlenstein-Stadel. This observation and the technological affinity between Poland and the Northern Caucasus could be the result of increased mobility of Neanderthals that changed their subsistence strategy for coping with the new low biomass environments and the increased foraging radius of gregarious animals. The Prut and Dniester rivers were probably used as the main corridors of dispersal. The persistence of the Micoquian techno-complex in South-Eastern Europe infers that this axis of mobility was also used at the beginning of MIS 3 when a Neanderthal population turnover occurred in the Northern Caucasus.}, }
@article {pmid32889336, year = {2020}, author = {Romandini, M and Oxilia, G and Bortolini, E and Peyrégne, S and Delpiano, D and Nava, A and Panetta, D and Di Domenico, G and Martini, P and Arrighi, S and Badino, F and Figus, C and Lugli, F and Marciani, G and Silvestrini, S and Menghi Sartorio, JC and Terlato, G and Hublin, JJ and Meyer, M and Bondioli, L and Higham, T and Slon, V and Peresani, M and Benazzi, S}, title = {A late Neanderthal tooth from northeastern Italy.}, journal = {Journal of human evolution}, volume = {147}, number = {}, pages = {102867}, doi = {10.1016/j.jhevol.2020.102867}, pmid = {32889336}, issn = {1095-8606}, support = {694707/ERC_/European Research Council/International ; }, mesh = {Animals ; Cuspid/*anatomy &amp; histology ; Fossils/*anatomy &amp; histology ; Italy ; Maxilla ; Neanderthals/*anatomy &amp; histology ; Paleodontology ; Tooth, Deciduous/*anatomy &amp; histology ; }, abstract = {The site of Riparo Broion (Vicenza, northeastern Italy) preserves a stratigraphic sequence documenting the Middle-to-Upper Paleolithic transition, in particular the final Mousterian and the Uluzzian cultures. In 2018, a human tooth was retrieved from a late Mousterian level, representing the first human remain ever found from this rock shelter (Riparo Broion 1). Here, we provide the morphological description and taxonomic assessment of Riparo Broion 1 with the support of classic and virtual morphology, 2D and 3D analysis of the topography of enamel thickness, and DNA analysis. The tooth is an exfoliated right upper deciduous canine, and its general morphology and enamel thickness distribution support attribution to a Neanderthal child. Correspondingly, the mitochondrial DNA sequence from Riparo Broion 1 falls within the known genetic variation of Late Pleistocene Neanderthals, in accordance with newly obtained radiocarbon dates that point to approximately 48 ka cal BP as the most likely minimum age for this specimen. The present work describes novel and direct evidence of the late Neanderthal occupation in northern Italy that preceded the marked cultural and technological shift documented by the Uluzzian layers in the archaeological sequence at Riparo Broion. Here, we provide a new full morphological, morphometric, and taxonomic analysis of Riparo Broion 1, in addition to generating the wider reference sample of Neanderthal and modern human upper deciduous canines. This research contributes to increasing the sample of fossil remains from Italy, as well as the number of currently available upper deciduous canines, which are presently poorly documented in the scientific literature.}, }
@article {pmid32874601, year = {2020}, author = {Amos, W}, title = {Signals interpreted as archaic introgression appear to be driven primarily by faster evolution in Africa.}, journal = {Royal Society open science}, volume = {7}, number = {7}, pages = {191900}, pmid = {32874601}, issn = {2054-5703}, abstract = {Non-African humans appear to carry a few per cent archaic DNA due to ancient inter-breeding. This modest legacy and its likely recent timing imply that most introgressed fragments will be rare and hence will occur mainly in the heterozygous state. I tested this prediction by calculating D statistics, a measure of legacy size, for pairs of humans where one of the pair was conditioned always to be either homozygous or heterozygous. Using coalescent simulations, I confirmed that conditioning the non-African to be heterozygous increased D, while conditioning the non-African to be homozygous reduced D to zero. Repeating with real data reveals the exact opposite pattern. In African-non-African comparisons, D is near-zero if the African individual is held homozygous. Conditioning one of two Africans to be either homozygous or heterozygous invariably generates large values of D, even when both individuals are drawn from the same population. Invariably, the African with more heterozygous sites (conditioned heterozygous > unconditioned > conditioned homozygous) appears less related to the archaic. By contrast, the same analysis applied to pairs of non-Africans always yields near-zero D, showing that conditioning does not create large D without an underlying signal to expose. Large D values in humans are therefore driven almost entirely by heterozygous sites in Africans acting to increase divergence from related taxa such as Neanderthals. In comparison with heterozygous Africans, individuals that lack African heterozygous sites, whether non-African or conditioned homozygous African, always appear more similar to archaic outgroups, a signal previously interpreted as evidence for introgression. I hope these analyses will encourage others to consider increased divergence as well as increased similarity to archaics as mechanisms capable of driving asymmetrical base-sharing.}, }
@article {pmid32853200, year = {2020}, author = {Mughal, MR and Koch, H and Huang, J and Chiaromonte, F and DeGiorgio, M}, title = {Learning the properties of adaptive regions with functional data analysis.}, journal = {PLoS genetics}, volume = {16}, number = {8}, pages = {e1008896}, pmid = {32853200}, issn = {1553-7404}, support = {F31 HG010574/HG/NHGRI NIH HHS/United States ; R35 GM128590/GM/NIGMS NIH HHS/United States ; T32 GM102057/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA-Binding Proteins/genetics ; Genetic Variation ; Humans ; Membrane Transport Proteins ; *Models, Genetic ; *Mutation Rate ; Neanderthals/genetics ; Selection, Genetic ; Software ; White People/*genetics ; }, abstract = {Identifying regions of positive selection in genomic data remains a challenge in population genetics. Most current approaches rely on comparing values of summary statistics calculated in windows. We present an approach termed SURFDAWave, which translates measures of genetic diversity calculated in genomic windows to functional data. By transforming our discrete data points to be outputs of continuous functions defined over genomic space, we are able to learn the features of these functions that signify selection. This enables us to confidently identify complex modes of natural selection, including adaptive introgression. We are also able to predict important selection parameters that are responsible for shaping the inferred selection events. By applying our model to human population-genomic data, we recapitulate previously identified regions of selective sweeps, such as OCA2 in Europeans, and predict that its beneficial mutation reached a frequency of 0.02 before it swept 1,802 generations ago, a time when humans were relatively new to Europe. In addition, we identify BNC2 in Europeans as a target of adaptive introgression, and predict that it harbors a beneficial mutation that arose in an archaic human population that split from modern humans within the hypothesized modern human-Neanderthal divergence range.}, }
@article {pmid32839541, year = {2020}, author = {Telis, N and Aguilar, R and Harris, K}, title = {Selection against archaic hominin genetic variation in regulatory regions.}, journal = {Nature ecology &amp; evolution}, volume = {4}, number = {11}, pages = {1558-1566}, pmid = {32839541}, issn = {2397-334X}, support = {R35 GM133428/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; *Hominidae/genetics ; Humans ; *Neanderthals/genetics ; Regulatory Sequences, Nucleic Acid ; Selection, Genetic ; }, abstract = {Traces of Neandertal and Denisovan DNA persist in the modern human gene pool, but have been systematically purged by natural selection from genes and other functionally important regions. This implies that many archaic alleles harmed the fitness of hybrid individuals, but the nature of this harm is poorly understood. Here, we show that enhancers contain less Neandertal and Denisovan variation than expected given the background selection they experience, suggesting that selection acted to purge these regions of archaic alleles that disrupted their gene regulatory functions. We infer that selection acted mainly on young archaic variation that arose in Neandertals or Denisovans shortly before their contact with humans; enhancers are not depleted of older variants found in both archaic species. Some types of enhancer appear to have tolerated introgression better than others; compared with tissue-specific enhancers, pleiotropic enhancers show stronger depletion of archaic single-nucleotide polymorphisms. To some extent, evolutionary constraint is predictive of introgression depletion, but certain tissues' enhancers are more depleted of Neandertal and Denisovan alleles than expected given their comparative tolerance to new mutations. Foetal brain and muscle are the tissues whose enhancers show the strongest depletion of archaic alleles, but only brain enhancers show evidence of unusually stringent purifying selection. We conclude that epistatic incompatibilities between human and archaic alleles are needed to explain the degree of archaic variant depletion from foetal muscle enhancers, perhaps due to divergent selection for higher muscle mass in archaic hominins compared with humans.}, }
@article {pmid32817536, year = {2020}, author = {Bard, E and Heaton, TJ and Talamo, S and Kromer, B and Reimer, RW and Reimer, PJ}, title = {Extended dilation of the radiocarbon time scale between 40,000 and 48,000 y BP and the overlap between Neanderthals and Homo sapiens.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {35}, pages = {21005-21007}, pmid = {32817536}, issn = {1091-6490}, mesh = {Animals ; Calibration/standards ; Fossils ; Humans ; Neanderthals ; Paleontology/*methods ; Radiometric Dating/*methods ; }, abstract = {The new radiocarbon calibration curve (IntCal20) allows us to calculate the gradient of the relationship between [14]C age and calendar age over the past 55 millennia before the present (55 ka BP). The new gradient curve exhibits a prolonged and prominent maximum between 48 and 40 ka BP during which the radiocarbon clock runs almost twice as fast as it should. This radiocarbon time dilation is due to the increase in the atmospheric [14]C/[12]C ratio caused by the [14]C production rise linked to the transition into the Laschamp geomagnetic excursion centered around 41 ka BP. The major maximum in the gradient from 48 to 40 ka BP is a new feature of the IntCal20 calibration curve, with far-reaching impacts for scientific communities, such as prehistory and paleoclimatology, relying on accurate ages in this time range. To illustrate, we consider the duration of the overlap between Neanderthals and Homo sapiens in Eurasia.}, }
@article {pmid32813722, year = {2020}, author = {Delpiano, D and Uthmeier, T}, title = {Techno-functional and 3D shape analysis applied for investigating the variability of backed tools in the Late Middle Paleolithic of Central Europe.}, journal = {PloS one}, volume = {15}, number = {8}, pages = {e0236548}, pmid = {32813722}, issn = {1932-6203}, mesh = {Animals ; Archaeology/*instrumentation ; Artifacts ; Behavior Rating Scale ; Fossils/*diagnostic imaging ; Humans ; Neanderthals ; Paleontology/*instrumentation ; Technology/*instrumentation ; Tool Use Behavior/classification ; }, abstract = {In the Late Middle Paleolithic of Central Europe, two main cultural complexes have been distinguished: the Micoquian or Keilmessergruppe (KMG), and the Mousterian. Their differences mainly consist in the frequence of some retouched tools and the presence of bifacial technology. When these industries coexist, one element of discussion is the application of different concepts to manufacture tools with the same techno-functionality. This is particularly true for backed artifacts, such as Keilmesser (backed, asymmetrical bifacially-shaped knives) opposed to flake-tools equipped with a natural or knapped back. We conducted a techno-functional analysis of the backed tools from the G-Layer-Complex of Sesselfelsgrotte, one of the main Late Middle Paleolithic sequences in Central Europe, characterized by a combination of KMG and Mousterian aspects. In order to better understand the morpho-metrical data, 3D scans were used for recording technical features and performing semi-automatic geometric morphometrics. Results indicate that the techno-functional schemes of Keilmesser show a moderate variability and often overlap with the schemes of other typological groups. Within bifacial backed knives, a process of imitation of unifacial flake tools' functionaly was recognized particularly in the cutting edge manufacturing. Keilmesser proved to be the long-life, versatile version of backed flake-tools, also due to the recurrent valence as both tool and core. This is why Keilmesser represent an ideal strategic blank when a mobile and multi-functional tool is needed. Based on these data, it is assumed that the relationship between Mousterian and KMG is deeply rooted and the emergence of KMG aspects could be related to constrained situations characterizing the long cold stages of the Early Weichselian. A higher regional mobility caused by the comparably low predictability of resources characterized the subsistence tactics of Neanderthal groups especially at the borders of their overall distribution. For this reason, Keilmesser could have represented an ecological answer before possibly becoming a marker of cultural identity.}, }
@article {pmid32805525, year = {2020}, author = {Torres-Tamayo, N and Schlager, S and García-Martínez, D and Sanchis-Gimeno, JA and Nalla, S and Ogihara, N and Oishi, M and Martelli, S and Bastir, M}, title = {Three-dimensional geometric morphometrics of thorax-pelvis covariation and its potential for predicting the thorax morphology: A case study on Kebara 2 Neandertal.}, journal = {Journal of human evolution}, volume = {147}, number = {}, pages = {102854}, doi = {10.1016/j.jhevol.2020.102854}, pmid = {32805525}, issn = {1095-8606}, mesh = {Animals ; Anthropology, Physical ; Fossils/*anatomy &amp; histology ; Image Processing, Computer-Assisted ; Israel ; Male ; Neanderthals/*anatomy &amp; histology ; Pelvis/*anatomy &amp; histology ; Thorax/*anatomy &amp; histology ; Tomography, X-Ray Computed ; }, abstract = {The skeletal torso is a complex structure of outstanding importance in understanding human body shape evolution, but reconstruction usually entails an element of subjectivity as researchers apply their own anatomical expertise to the process. Among different fossil reconstruction methods, 3D geometric morphometric techniques have been increasingly used in the last decades. Two-block partial least squares analysis has shown great potential for predicting missing elements by exploiting the covariation between two structures (blocks) in a reference sample: one block can be predicted from the other one based on the strength of covariation between blocks. The first aim of this study is to test whether this predictive approach can be used for predicting thorax morphologies from pelvis morphologies within adult Homo sapiens reference samples with known covariation between the thorax and the pelvis. The second aim is to apply this method to Kebara 2 Neandertal (Israel, ∼60 ka) to predict its thorax morphology using two different pelvis reconstructions as predictors. We measured 134 true landmarks, 720 curve semilandmarks, and 160 surface semilandmarks on 60 3D virtual torso models segmented from CT scans. We conducted three two-block partial least squares analyses between the thorax (block 1) and the pelvis (block 2) based on the H. sapiens reference samples after performing generalized Procrustes superimposition on each block separately. Comparisons of these predictions in full shape space by means of Procrustes distances show that the male-only predictive model yields the most reliable predictions within modern humans. In addition, Kebara 2 thorax predictions based on this model concur with the thorax morphology proposed for Neandertals. The method presented here does not aim to replace other techniques, but to rather complement them through quantitative prediction of a virtual 'scaffold' to articulate the thoracic fossil elements, thus extending the potential of missing data estimation beyond the methods proposed in previous works.}, }
@article {pmid32760067, year = {2020}, author = {Hubisz, MJ and Williams, AL and Siepel, A}, title = {Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph.}, journal = {PLoS genetics}, volume = {16}, number = {8}, pages = {e1008895}, pmid = {32760067}, issn = {1553-7404}, support = {R35 GM127070/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Evolution, Molecular ; *Gene Flow ; Human Migration ; Humans ; *Models, Genetic ; Neanderthals/*genetics ; Population/*genetics ; *Recombination, Genetic ; }, abstract = {The sequencing of Neanderthal and Denisovan genomes has yielded many new insights about interbreeding events between extinct hominins and the ancestors of modern humans. While much attention has been paid to the relatively recent gene flow from Neanderthals and Denisovans into modern humans, other instances of introgression leave more subtle genomic evidence and have received less attention. Here, we present a major extension of the ARGweaver algorithm, called ARGweaver-D, which can infer local genetic relationships under a user-defined demographic model that includes population splits and migration events. This Bayesian algorithm probabilistically samples ancestral recombination graphs (ARGs) that specify not only tree topologies and branch lengths along the genome, but also indicate migrant lineages. The sampled ARGs can therefore be parsed to produce probabilities of introgression along the genome. We show that this method is well powered to detect the archaic migration into modern humans, even with only a few samples. We then show that the method can also detect introgressed regions stemming from older migration events, or from unsampled populations. We apply it to human, Neanderthal, and Denisovan genomes, looking for signatures of older proposed migration events, including ancient humans into Neanderthal, and unknown archaic hominins into Denisovans. We identify 3% of the Neanderthal genome that is putatively introgressed from ancient humans, and estimate that the gene flow occurred between 200-300kya. We find no convincing evidence that negative selection acted against these regions. Finally, we predict that 1% of the Denisovan genome was introgressed from an unsequenced, but highly diverged, archaic hominin ancestor. About 15% of these "super-archaic" regions-comprising at least about 4Mb-were, in turn, introgressed into modern humans and continue to exist in the genomes of people alive today.}, }
@article {pmid32750315, year = {2020}, author = {Course, MM and Gudsnuk, K and Smukowski, SN and Winston, K and Desai, N and Ross, JP and Sulovari, A and Bourassa, CV and Spiegelman, D and Couthouis, J and Yu, CE and Tsuang, DW and Jayadev, S and Kay, MA and Gitler, AD and Dupre, N and Eichler, EE and Dion, PA and Rouleau, GA and Valdmanis, PN}, title = {Evolution of a Human-Specific Tandem Repeat Associated with ALS.}, journal = {American journal of human genetics}, volume = {107}, number = {3}, pages = {445-460}, pmid = {32750315}, issn = {1537-6605}, support = {T32 GM007454/GM/NIGMS NIH HHS/United States ; U24 AG041689/AG/NIA NIH HHS/United States ; R01 DK078424/DK/NIDDK NIH HHS/United States ; P30 AG066509/AG/NIA NIH HHS/United States ; P50 AG005136/AG/NIA NIH HHS/United States ; R01 HG010169/HG/NHGRI NIH HHS/United States ; }, mesh = {Adaptor Proteins, Signal Transducing/*genetics ; Aged ; Alzheimer Disease/genetics/pathology ; Amyotrophic Lateral Sclerosis/*genetics/pathology ; DNA Repeat Expansion/genetics ; *Evolution, Molecular ; Female ; Gene Expression Regulation/genetics ; Humans ; Male ; Minisatellite Repeats/genetics ; Phenotype ; Species Specificity ; Tandem Repeat Sequences/*genetics ; }, abstract = {Tandem repeats are proposed to contribute to human-specific traits, and more than 40 tandem repeat expansions are known to cause neurological disease. Here, we characterize a human-specific 69 bp variable number tandem repeat (VNTR) in the last intron of WDR7, which exhibits striking variability in both copy number and nucleotide composition, as revealed by long-read sequencing. In addition, greater repeat copy number is significantly enriched in three independent cohorts of individuals with sporadic amyotrophic lateral sclerosis (ALS). Each unit of the repeat forms a stem-loop structure with the potential to produce microRNAs, and the repeat RNA can aggregate when expressed in cells. We leveraged its remarkable sequence variability to align the repeat in 288 samples and uncover its mechanism of expansion. We found that the repeat expands in the 3'-5' direction, in groups of repeat units divisible by two. The expansion patterns we observed were consistent with duplication events, and a replication error called template switching. We also observed that the VNTR is expanded in both Denisovan and Neanderthal genomes but is fixed at one copy or fewer in non-human primates. Evaluating the repeat in 1000 Genomes Project samples reveals that some repeat segments are solely present or absent in certain geographic populations. The large size of the repeat unit in this VNTR, along with our multiplexed sequencing strategy, provides an unprecedented opportunity to study mechanisms of repeat expansion, and a framework for evaluating the roles of VNTRs in human evolution and disease.}, }
@article {pmid32745133, year = {2020}, author = {Örd, T and Puurand, T and Örd, D and Annilo, T and Möls, M and Remm, M and Örd, T}, title = {A human-specific VNTR in the TRIB3 promoter causes gene expression variation between individuals.}, journal = {PLoS genetics}, volume = {16}, number = {8}, pages = {e1008981}, pmid = {32745133}, issn = {1553-7404}, support = {HHSN268201000029C/HL/NHLBI NIH HHS/United States ; HHSN261200800001E/CA/NCI NIH HHS/United States ; }, mesh = {Cell Cycle Proteins/*genetics ; Estonia/epidemiology ; Female ; Gene Expression Regulation/genetics ; *Genetic Heterogeneity ; *Genetics, Population ; Genotype ; Humans ; Male ; Minisatellite Repeats/*genetics ; Promoter Regions, Genetic ; Protein Serine-Threonine Kinases/*antagonists &amp; inhibitors/genetics ; RNA-Seq ; Repressor Proteins/*genetics ; Whole Genome Sequencing ; }, abstract = {Tribbles homolog 3 (TRIB3) is pseudokinase involved in intracellular regulatory processes and has been implicated in several diseases. In this article, we report that human TRIB3 promoter contains a 33-bp variable number tandem repeat (VNTR) and characterize the heterogeneity and function of this genetic element. Analysis of human populations around the world uncovered the existence of alleles ranging from 1 to 5 copies of the repeat, with 2-, 3- and 5-copy alleles being the most common but displaying considerable geographical differences in frequency. The repeated sequence overlaps a C/EBP-ATF transcriptional regulatory element and is highly conserved, but not repeated, in various mammalian species, including great apes. The repeat is however evident in Neanderthal and Denisovan genomes. Reporter plasmid experiments in human cell culture reveal that an increased copy number of the TRIB3 promoter 33-bp repeat results in increased transcriptional activity. In line with this, analysis of whole genome sequencing and RNA-Seq data from human cohorts demonstrates that the copy number of TRIB3 promoter 33-bp repeats is positively correlated with TRIB3 mRNA expression level in many tissues throughout the body. Moreover, the copy number of the TRIB3 33-bp repeat appears to be linked to known TRIB3 eQTL SNPs as well as TRIB3 SNPs reported in genetic association studies. Taken together, the results indicate that the promoter 33-bp VNTR constitutes a causal variant for TRIB3 expression variation between individuals and could underlie the results of SNP-based genetic studies.}, }
@article {pmid32735718, year = {2020}, author = {Ríos, L and Cardoso, HFV}, title = {Comment on 'Krapina atlases suggest a high prevalence of anatomical variations in the first cervical vertebra of Neanderthals'.}, journal = {Journal of anatomy}, volume = {237}, number = {6}, pages = {1185-1188}, pmid = {32735718}, issn = {1469-7580}, mesh = {*Neanderthals ; Prevalence ; Spine ; }, abstract = {A review of the observation of an anterior cleft on the atlas of a Neanderthal from Krapina.}, }
@article {pmid32721654, year = {2020}, author = {Grine, FE and Mongle, CS and Smith, SL and Black, W and du Plessis, A and Braga, J}, title = {Human manual distal phalanges from the Middle Stone Age deposits of Klasies River Main Site, Western Cape Province, South Africa.}, journal = {Journal of human evolution}, volume = {146}, number = {}, pages = {102849}, doi = {10.1016/j.jhevol.2020.102849}, pmid = {32721654}, issn = {1095-8606}, mesh = {Caves ; Finger Phalanges/*anatomy &amp; histology ; Fossils/*anatomy &amp; histology ; Humans ; South Africa ; }, abstract = {Two new distal manual phalanges from the Middle Stone Age deposits of Klasies River Main Site are described. One (SAM-AP 6387) likely derives from ray II or ray III, whereas the other (SAM-AP 6388) is from the thumb. Both derive from a late adolescent or fully adult individual. They were recovered by H. Deacon from the same stratigraphic unit (submember W or possibly submember R) of the Shell and Sand Member of Cave 1, which places them between 100 and 90 ka. Both are comparatively small elements, and the possibility that they came from the same hand cannot be discounted at this time. These bones add to the meager and all too fragmentary postcranial human fossil sample from the Late Pleistocene of South Africa. These two specimens provide some additional evidence pertaining to the morphological attributes of the distal phalanges of the Middle Stone Age inhabitants of South Africa. Together with the distal pollical phalanx from Die Kelders (SAM-AP 6402), they are relatively small in comparison with homologs from recent human samples as well as Late Pleistocene specimens from Eurasia. Given their small sizes, the distal pollical phalanges from Klasies and Die Kelders are not dissimilar to Holocene Khoesan homologs. As expected, the Klasies elements differ noticeably from Neandertal homologs, especially in the narrowness of their shafts and distal tuberosities.}, }
@article {pmid32719451, year = {2020}, author = {Rinker, DC and Simonti, CN and McArthur, E and Shaw, D and Hodges, E and Capra, JA}, title = {Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations.}, journal = {Nature ecology &amp; evolution}, volume = {4}, number = {10}, pages = {1332-1341}, pmid = {32719451}, issn = {2397-334X}, support = {K22 CA184308/CA/NCI NIH HHS/United States ; T32 GM080178/GM/NIGMS NIH HHS/United States ; T32 EY021453/EY/NEI NIH HHS/United States ; F30 HG011200/HG/NHGRI NIH HHS/United States ; R01 GM115836/GM/NIGMS NIH HHS/United States ; T32 GM007347/GM/NIGMS NIH HHS/United States ; R35 GM127087/GM/NIGMS NIH HHS/United States ; }, mesh = {Alleles ; Animals ; Haplotypes ; *Hominidae ; Humans ; *Neanderthals/genetics ; Population ; }, abstract = {Neanderthal ancestry remains across modern Eurasian genomes and introgressed sequences influence diverse phenotypes. Here, we demonstrate that introgressed sequences reintroduced thousands of ancestral alleles that were lost in Eurasian populations before introgression. Our simulations and variant effect predictions argue that these reintroduced alleles (RAs) are more likely to be tolerated by modern humans than are introgressed Neanderthal-derived alleles (NDAs) due to their distinct evolutionary histories. Consistent with this, we show enrichment for RAs and depletion for NDAs on introgressed haplotypes with expression quantitative trait loci (eQTL) and phenotype associations. Analysis of available cross-population eQTLs and massively parallel reporter assay data show that RAs commonly influence gene expression independent of linked NDAs. We further validate these independent effects for one RA in vitro. Finally, we demonstrate that NDAs are depleted for regulatory activity compared to RAs, while RAs have activity levels similar to non-introgressed variants. In summary, our study reveals that Neanderthal introgression reintroduced thousands of lost ancestral variants with gene regulatory activity and that these RAs were more tolerated than NDAs. Thus, RAs and their distinct evolutionary histories must be considered when evaluating the effects of introgression.}, }
@article {pmid32707058, year = {2020}, author = {Zeberg, H and Dannemann, M and Sahlholm, K and Tsuo, K and Maricic, T and Wiebe, V and Hevers, W and Robinson, HPC and Kelso, J and Pääbo, S}, title = {A Neanderthal Sodium Channel Increases Pain Sensitivity in Present-Day Humans.}, journal = {Current biology : CB}, volume = {30}, number = {17}, pages = {3465-3469.e4}, doi = {10.1016/j.cub.2020.06.045}, pmid = {32707058}, issn = {1879-0445}, mesh = {Adult ; Aged ; Amino Acid Substitution ; Animals ; Female ; Humans ; Male ; Middle Aged ; *Mutation ; NAV1.7 Voltage-Gated Sodium Channel/genetics/*metabolism ; Neanderthals ; Pain/genetics/metabolism/*pathology ; Xenopus laevis ; }, abstract = {The sodium channel Nav1.7 is crucial for impulse generation and conduction in peripheral pain pathways [1]. In Neanderthals, the Nav1.7 protein carried three amino acid substitutions (M932L, V991L, and D1908G) relative to modern humans. We expressed Nav1.7 proteins carrying all combinations of these substitutions and studied their electrophysiological effects. Whereas the single amino acid substitutions do not affect the function of the ion channel, the full Neanderthal variant carrying all three substitutions, as well as the combination of V991L with D1908G, shows reduced inactivation, suggesting that peripheral nerves were more sensitive to painful stimuli in Neanderthals than in modern humans. We show that, due to gene flow from Neanderthals, the three Neanderthal substitutions are found in ∼0.4% of present-day Britons, where they are associated with heightened pain sensitivity.}, }
@article {pmid32704108, year = {2020}, author = {Callaway, E}, title = {Neanderthal gene linked to increased pain sensitivity.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {32704108}, issn = {1476-4687}, }
@article {pmid32699254, year = {2020}, author = {Sánchez-Romero, L and Benito-Calvo, A and Marín-Arroyo, AB and Agudo-Pérez, L and Karampaglidis, T and Rios-Garaizar, J}, title = {Author Correction: New insights for understanding spatial patterning and formation processes of the Neanderthal occupation in the Amalda I cave (Gipuzkoa, Spain).}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {12456}, doi = {10.1038/s41598-020-68761-1}, pmid = {32699254}, issn = {2045-2322}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid32696095, year = {2020}, author = {Peeters, S and Zwart, H}, title = {Neanderthals as familiar strangers and the human spark: How the 'golden years' of Neanderthal research reopen the question of human uniqueness.}, journal = {History and philosophy of the life sciences}, volume = {42}, number = {3}, pages = {33}, pmid = {32696095}, issn = {1742-6316}, mesh = {Animals ; *Biological Evolution ; Humans ; Neanderthals/*psychology ; }, abstract = {During the past decades, our image of Homo neanderthalensis has changed dramatically. Initially, Neanderthals were seen as primitive brutes. Increasingly, however, Neanderthals are regarded as basically human. New discoveries and technologies have led to an avalanche of data, and as a result of that it becomes increasingly difficult to pinpoint what the difference between modern humans and Neanderthals really is. And yet, the persistent quest for a minimal difference which separates them from us is still noticeable in Neanderthal research. Neanderthal discourse is a vantage point from which the logic of 'us' versus 'other' is critically reconsidered. Studying contemporary academic literature and science autobiographies from an oblique perspective, focusing not on Neanderthals as objects, but on the dynamics of interaction between Neanderthal researchers and their finds, basic convictions at work in this type of research are retrieved. What is at issue is not the actual distinction between modern humans and Neanderthals (which is continuously being redefined), but rather the dualistic construction of human and nonhuman. Neanderthal understanding is affected by the desire to safeguard human uniqueness. The overall trend is to identify the human mark or spark, which defines us as favoured 'winners'. The paradoxes emerging in contemporary Neanderthal discourse are symptomatic of the fact that a dualistic style of thinking is no longer tenable.}, }
@article {pmid32681013, year = {2020}, author = {Marra, F and Rolfo, MF and Gaeta, M and Florindo, F}, title = {Anomalous Last Interglacial Tyrrhenian sea levels and Neanderthal settling at Guattari and Moscerini caves (central Italy).}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {11929}, pmid = {32681013}, issn = {2045-2322}, abstract = {We present a geological-stratigraphical study aimed to provide chronologic constraints to the sea-level markers occurring at two coastal caves of central Italy (Grotta Guattari and Grotta dei Moscerini) and to the Neanderthal frequentation of these caves, in the light of recent archaeological and geomorphological-geochronological studies suggesting similar sea levels during MIS 5.5 and MIS 5.3, and only few m below the Present during MIS 5.1 in this region. Based on the review of previous literature data, combined with new stratigraphic observations at Grotta Guattari and re-analysis of archive material including unpublished field notes from Grotta dei Moscerini, we reconstruct a plausible sea-level history accounting for the lithological and paleoenvironmental features of their sedimentary fillings. In particular, we outline the abundant occurrence of well-rounded pumice clasts within the sedimentary deposits of Moscerini Cave, attesting for the proximity to the beach where this pumice was gathered by wave action. Through the petrographic and geochemical analysis of this pumice we evidence provenance from Phlegraean Fields and Ischia Island volcanic districts, framing their chronology in the time span 118-40 ka, consistent with literature ESR-U/Th dates providing ages ranging 101 ± 5-74 ± 7 ka for the sedimentary filling of both Moscerini and Guattari caves.}, }
@article {pmid32661407, year = {2020}, author = {Columbu, A and Chiarini, V and Spötl, C and Benazzi, S and Hellstrom, J and Cheng, H and De Waele, J}, title = {Author Correction: Speleothem record attests to stable environmental conditions during Neanderthal-modern human turnover in southern Italy.}, journal = {Nature ecology &amp; evolution}, volume = {4}, number = {9}, pages = {1279}, doi = {10.1038/s41559-020-1267-6}, pmid = {32661407}, issn = {2397-334X}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid32652819, year = {2020}, author = {Pomeroy, E and Hunt, CO and Reynolds, T and Abdulmutalb, D and Asouti, E and Bennett, P and Bosch, M and Burke, A and Farr, L and Foley, R and French, C and Frumkin, A and Goldberg, P and Hill, E and Kabukcu, C and Lahr, MM and Lane, R and Marean, C and Maureille, B and Mutri, G and Miller, CE and Mustafa, KA and Nymark, A and Pettitt, P and Sala, N and Sandgathe, D and Stringer, C and Tilby, E and Barker, G}, title = {Issues of theory and method in the analysis of Paleolithic mortuary behavior: A view from Shanidar Cave.}, journal = {Evolutionary anthropology}, volume = {29}, number = {5}, pages = {263-279}, doi = {10.1002/evan.21854}, pmid = {32652819}, issn = {1520-6505}, support = {//British Academy/ ; //Calleva Foundation/ ; //Human Origins Research Fund/ ; ECF-2017-284//Leverhulme Trust/ ; RPG-2013-105//Leverhulme Trust/ ; //McDonald Institute for Archaeological Research/ ; NE/L002507/1//Natural Environment Research Council/ ; NF/2016/2/14//Natural Environment Research Council/ ; //Rust Family Foundation/ ; //Society of Antiquaries of London/ ; CONF-788//Wenner-Gren Foundation/ ; }, mesh = {Animals ; Burial/*history ; Caves ; Fossils ; Fractures, Bone/pathology ; Geologic Sediments/chemistry ; History, Ancient ; Iraq ; Neanderthals/*physiology ; *Paleontology ; }, abstract = {Mortuary behavior (activities concerning dead conspecifics) is one of many traits that were previously widely considered to have been uniquely human, but on which perspectives have changed markedly in recent years. Theoretical approaches to hominin mortuary activity and its evolution have undergone major revision, and advances in diverse archeological and paleoanthropological methods have brought new ways of identifying behaviors such as intentional burial. Despite these advances, debates concerning the nature of hominin mortuary activity, particularly among the Neanderthals, rely heavily on the rereading of old excavations as new finds are relatively rare, limiting the extent to which such debates can benefit from advances in the field. The recent discovery of in situ articulated Neanderthal remains at Shanidar Cave offers a rare opportunity to take full advantage of these methodological and theoretical developments to understand Neanderthal mortuary activity, making a review of these advances relevant and timely.}, }
@article {pmid32632262, year = {2020}, author = {Columbu, A and Chiarini, V and Spötl, C and Benazzi, S and Hellstrom, J and Cheng, H and De Waele, J}, title = {Speleothem record attests to stable environmental conditions during Neanderthal-modern human turnover in southern Italy.}, journal = {Nature ecology &amp; evolution}, volume = {4}, number = {9}, pages = {1188-1195}, pmid = {32632262}, issn = {2397-334X}, mesh = {Europe ; Humans ; Italy ; *Neanderthals ; }, abstract = {The causes of Neanderthal-modern human (MH) turnover are ambiguous. While potential biocultural interactions between the two groups are still little known, it is clear that Neanderthals in southern Europe disappeared about 42 thousand years ago (ka) after cohabitation for ~3,000 years with MH. Among a plethora of hypotheses on Neanderthal extinction, rapid climate changes during the Middle to Upper Palaeolithic transition (MUPT) are regarded as a primary factor. Here we show evidence for stable climatic and environmental conditions during the MUPT in a region (Apulia) where Neanderthals and MH coexisted. We base our findings on a rare glacial stalagmite deposited between ~106 and ~27 ka, providing the first continuous western Mediterranean speleothem palaeoclimate archive for this period. The uninterrupted growth of the stalagmite attests to the constant availability of rainfall and vegetated soils, while its δ[13]C-δ[18]O palaeoclimate proxies demonstrate that Apulia was not affected by dramatic climate oscillations during the MUPT. Our results imply that, because climate did not play a key role in the disappearance of Neanderthals in this area, Neanderthal-MH turnover must be approached from a perspective that takes into account climatic and environmental conditions favourable for both species.}, }
@article {pmid32632258, year = {2020}, author = {Bastir, M and García-Martínez, D and Torres-Tamayo, N and Palancar, CA and Beyer, B and Barash, A and Villa, C and Sanchis-Gimeno, JA and Riesco-López, A and Nalla, S and Torres-Sánchez, I and García-Río, F and Been, E and Gómez-Olivencia, A and Haeusler, M and Williams, SA and Spoor, F}, title = {Rib cage anatomy in Homo erectus suggests a recent evolutionary origin of modern human body shape.}, journal = {Nature ecology &amp; evolution}, volume = {4}, number = {9}, pages = {1178-1187}, pmid = {32632258}, issn = {2397-334X}, mesh = {Adolescent ; Adult ; Animals ; Biological Evolution ; *Hominidae ; Human Body ; Humans ; *Neanderthals ; *Rib Cage ; }, abstract = {The tall and narrow body shape of anatomically modern humans (Homo sapiens) evolved via changes in the thorax, pelvis and limbs. It is debated, however, whether these modifications first evolved together in African Homo erectus, or whether H. erectus had a more primitive body shape that was distinct from both the more ape-like Australopithecus species and H. sapiens. Here we present the first quantitative three-dimensional reconstruction of the thorax of the juvenile H. erectus skeleton, KNM-WT 15000, from Nariokotome, Kenya, along with its estimated adult rib cage, for comparison with H. sapiens and the Kebara 2 Neanderthal. Our three-dimensional reconstruction demonstrates a short, mediolaterally wide and anteroposteriorly deep thorax in KNM-WT 15000 that differs considerably from the much shallower thorax of H. sapiens, pointing to a recent evolutionary origin of fully modern human body shape. The large respiratory capacity of KNM-WT 15000 is compatible with the relatively stocky, more primitive, body shape of H. erectus.}, }
@article {pmid32612423, year = {2020}, author = {Senturk, N and Ergoren, MC}, title = {Developing an Online Portal for Determining the Genomic Signature of Archaic DNA that are Associated to Modern Human Genetic Diseases: A Meta-Analysis Study.}, journal = {The Eurasian journal of medicine}, volume = {52}, number = {2}, pages = {153-160}, pmid = {32612423}, issn = {1308-8734}, abstract = {OBJECTIVE: Mutations or introgression can cause and rise adaptive alleles of which some can be beneficial. Archaic humans lived more than 200,000 years ago in Europe and Western Asia. They were adapted to the environment and pathogens that prevailed in these locations. It can therefore be thought that modern humans obtained significant immune advantage from the archaic alleles.<br><br>MATERIALS AND METHODS: First, data were collected by meta-analysis from previously identified genetic diseases caused by alleles that were introgressed from archaics. Second, the in silico model portal (http://www.archaics2phenotype.xxx.edu.tr) was designed to trace the history of the Neanderthal allele. The portal also shows the current distribution of the genotypes of the selected alleles within different populations and correlates with the individuals phenotype.<br><br>RESULTS: Our developed model provides a better understanding for the origin of genetic diseases or traits that are associated with the Neanderthal genome.<br><br>CONCLUSION: The developed medicine model will help individuals and their populations to receive the best treatment. It also clarifies why there are differences in disease phenotypes in modern humans.}, }
@article {pmid32594872, year = {2020}, author = {Nielsen, M and Langley, MC and Shipton, C and Kapitány, R}, title = {Homo neanderthalensis and the evolutionary origins of ritual in Homo sapiens.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1805}, pages = {20190424}, pmid = {32594872}, issn = {1471-2970}, mesh = {Animals ; Archaeology ; *Ceremonial Behavior ; *Cultural Evolution ; Neanderthals/*psychology ; }, abstract = {There is a large, if disparate, body of archaeological literature discussing specific instantiations of symbolic material culture and the possibility of ritual practices in Neanderthal populations. Despite this attention, however, no single synthesis exists that draws upon cognitive, psychological and cultural evolutionary theories of ritual. Here, we review the evidence for ritual-practice among now-extinct Homo neanderthalensis, as well as the necessary cognitive pre-conditions for such behaviour, in order to explore the evolution of ritual in Homo sapiens. We suggest that the currently available archaeological evidence indicates that Neanderthals may have used 'ritualization' to increase the successful transmission of technical knowledge across generations-providing an explanation for the technological stability of the Middle Palaeolithic and attesting to a survival strategy differing from near-contemporary H. sapiens. This article is part of the theme issue 'Ritual renaissance: new insights into the most human of behaviours'.}, }
@article {pmid32593870, year = {2020}, author = {Martínez de Pinillos, M and Martín-Francés, L and de Castro, JMB and García-Campos, C and Modesto-Mata, M and Martinón-Torres, M and Vialet, A}, title = {Inner morphological and metric characterization of the molar remains from the Montmaurin-La Niche mandible: The Neanderthal signal.}, journal = {Journal of human evolution}, volume = {145}, number = {}, pages = {102739}, doi = {10.1016/j.jhevol.2019.102739}, pmid = {32593870}, issn = {1095-8606}, mesh = {*Animal Migration ; Animals ; Biological Evolution ; Dentin/*anatomy &amp; histology ; Europe ; Fossils/anatomy &amp; histology ; Mandible/*anatomy &amp; histology ; Molar/*anatomy &amp; histology ; Neanderthals/*anatomy &amp; histology ; Paleontology ; X-Ray Microtomography ; }, abstract = {Here, we present a metric and morphological study of the molar remains from the Montmaurin-La Niche mandible by means of microcomputed tomography. According to the last analysis, based on the combination of geomorphological and paleontological data, the level bearing this human mandible probably corresponds to the marine isotope stages (MIS) 7. These data place the Montmaurin-La Niche in a chronologically intermediate position between the Neanderthals and the Middle Pleistocene fossils (e.g., Sima de los Huesos, la Caune de l'Arago). A recent study has revealed that while the mandible is more closely related to the Early and Middle Pleistocene African and Eurasian populations, the morphology of the outer enamel surfaces of its molars is typical of the Neanderthal linage. The data presented here are in line with this finding because the morphology of the enamel-dentine junction of the molars is similar to that of Neanderthals, whereas the absolute and relative enamel thickness values (2D and 3D) are closer to those exhibited by some Early Pleistocene hominins. Moreover, the pulp cavity morphology and proportions are in concordance with the Neanderthal populations. Our results strengthen the hypothesis that the settlement of Europe could be the result of several migrations, at different times, originated from a common source population. Thus, the variability in the European Middle Pleistocene populations (e.g., Montmaurin, Sima de los Huesos, Arago, Mala Balanica) could indicate different migrations at different times and/or population fragmentation, without excluding the possible hybridization between residents and new settlers.}, }
@article {pmid32586278, year = {2020}, author = {Weiß, CL and Gansauge, MT and Aximu-Petri, A and Meyer, M and Burbano, HA}, title = {Mining ancient microbiomes using selective enrichment of damaged DNA molecules.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {432}, pmid = {32586278}, issn = {1471-2164}, support = {Presidential Innovation Fund//Max-Planck-Gesellschaft/ ; }, mesh = {Animals ; Bacteria/*classification/genetics ; DNA, Ancient/*analysis/chemistry ; DNA, Bacterial/genetics ; Data Mining ; Fossils/*microbiology ; Gene Library ; Metagenomics ; Microbiota ; Neanderthals/microbiology ; Plants/microbiology ; Sequence Analysis, DNA/*methods ; Uracil/*chemistry ; }, abstract = {BACKGROUND: The identification of bona fide microbial taxa in microbiomes derived from ancient and historical samples is complicated by the unavoidable mixture between DNA from ante- and post-mortem microbial colonizers. One possibility to distinguish between these sources of microbial DNA is querying for the presence of age-associated degradation patterns typical of ancient DNA (aDNA). The presence of uracils, resulting from cytosine deamination, has been detected ubiquitously in aDNA retrieved from diverse sources, and used as an authentication criterion. Here, we employ a library preparation method that separates molecules that carry uracils from those that do not for a set of samples that includes Neandertal remains, herbarium specimens and archaeological plant remains.<br><br>RESULTS: We show that sequencing DNA libraries enriched in molecules carrying uracils effectively amplifies age associated degradation patterns in microbial mixtures of ancient and historical origin. This facilitates the discovery of authentic ancient microbial taxa in cases where degradation patterns are difficult to detect due to large sequence divergence in microbial mixtures. Additionally, the relative enrichment of taxa in the uracil enriched fraction can help to identify bona fide ancient microbial taxa that could be missed using a more targeted approach.<br><br>CONCLUSIONS: Our experiments show, that in addition to its use in enriching authentic endogenous DNA of organisms of interest, the selective enrichment of damaged DNA molecules can be a valuable tool in the discovery of ancient microbial taxa.}, }
@article {pmid32580077, year = {2020}, author = {Bosman, AM and Reyes-Centeno, H and Harvati, K}, title = {A virtual assessment of the suprainiac depressions on the Eyasi I (Tanzania) and Aduma ADU-VP-1/3 (Ethiopia) Pleistocene hominin crania.}, journal = {Journal of human evolution}, volume = {145}, number = {}, pages = {102815}, doi = {10.1016/j.jhevol.2020.102815}, pmid = {32580077}, issn = {1095-8606}, mesh = {Animals ; Anthropology, Physical ; Biological Evolution ; Ethiopia ; Fossils/*anatomy &amp; histology ; Humans ; Neanderthals/*anatomy &amp; histology ; Occipital Bone/*anatomy &amp; histology ; Principal Component Analysis ; Tanzania ; Tomography, X-Ray Computed ; }, abstract = {Despite a steady increase in our understanding of the phenotypic variation of Pleistocene Homo, debate continues over phylogenetically informative features. One such trait is the suprainiac fossa, a depression on the occipital bone above inion that is commonly considered an autapomorphy of the Neanderthal lineage. Challenging this convention, depressions in the suprainiac region have also been described for two Pleistocene hominin crania from sub-Saharan Africa: Eyasi I (Tanzania) and ADU-VP-1/3 (Ethiopia). Here, we use a combined quantitative and qualitative approach, using μCT imaging, to investigate the occipital depressions on these specimens. The results show that neither the external nor the internal morphologies of these depressions bear any resemblance to the Neanderthal condition. A principal component analysis based on multiple thickness measurements along the occipital squama demonstrates that the relative thickness values for the internal structures in Eyasi I and ADU-VP-1/3 are within the range of Homo sapiens. Thus, our results support the autapomorphic status of the Neanderthal suprainiac fossa and highlight the need to use nuanced approaches and multiple lines of evidence.}, }
@article {pmid32574964, year = {2020}, author = {Mathov, Y and Batyrev, D and Meshorer, E and Carmel, L}, title = {Harnessing epigenetics to study human evolution.}, journal = {Current opinion in genetics &amp; development}, volume = {62}, number = {}, pages = {23-29}, doi = {10.1016/j.gde.2020.05.023}, pmid = {32574964}, issn = {1879-0380}, mesh = {*DNA Methylation ; *Epigenesis, Genetic ; *Evolution, Molecular ; *Genetic Variation ; *Genome, Human ; Humans ; }, abstract = {Recent advances in ancient DNA extraction and high-throughput sequencing technologies enabled the high-quality sequencing of archaic genomes, including the Neanderthal and the Denisovan. While comparisons with modern humans revealed both archaic-specific and human-specific sequence changes, in the absence of gene expression information, understanding the functional implications of such genetic variations remains a major challenge. To study gene regulation in archaic humans, epigenetic research comes to our aid. DNA methylation, which is highly correlated with transcription, can be directly measured in modern samples, as well as reconstructed in ancient samples. This puts DNA methylation as a natural basis for comparative epigenetics between modern humans, archaic humans and nonhuman primates.}, }
@article {pmid32559457, year = {2020}, author = {Dannemann, M and He, Z and Heide, C and Vernot, B and Sidow, L and Kanton, S and Weigert, A and Treutlein, B and Pääbo, S and Kelso, J and Camp, JG}, title = {Human Stem Cell Resources Are an Inroad to Neandertal DNA Functions.}, journal = {Stem cell reports}, volume = {15}, number = {1}, pages = {214-225}, pmid = {32559457}, issn = {2213-6711}, mesh = {Alleles ; Animals ; Brain/metabolism ; Cell Line ; DNA/*genetics ; Haplotypes/genetics ; Humans ; Neanderthals/*genetics ; Phenotype ; Pluripotent Stem Cells/cytology ; RNA/metabolism ; Stem Cells/cytology/*metabolism ; }, abstract = {Induced pluripotent stem cells (iPSCs) from diverse humans offer the potential to study human functional variation in controlled culture environments. A portion of this variation originates from an ancient admixture between modern humans and Neandertals, which introduced alleles that left a phenotypic legacy on individual humans today. Here, we show that a large iPSC repository harbors extensive Neandertal DNA, including alleles that contribute to human phenotypes and diseases, encode hundreds of amino acid changes, and alter gene expression in specific tissues. We provide a database of the inferred introgressed Neandertal alleles for each individual iPSC line, together with the annotation of the predicted functional variants. We also show that transcriptomic data from organoids generated from iPSCs can be used to track Neandertal-derived RNA over developmental processes. Human iPSC resources provide an opportunity to experimentally explore Neandertal DNA function and its contribution to present-day phenotypes, and potentially study Neandertal traits.}, }
@article {pmid32556248, year = {2020}, author = {Khan, N and de Manuel, M and Peyregne, S and Do, R and Prufer, K and Marques-Bonet, T and Varki, N and Gagneux, P and Varki, A}, title = {Multiple Genomic Events Altering Hominin SIGLEC Biology and Innate Immunity Predated the Common Ancestor of Humans and Archaic Hominins.}, journal = {Genome biology and evolution}, volume = {12}, number = {7}, pages = {1040-1050}, pmid = {32556248}, issn = {1759-6653}, support = {R01 GM032373/GM/NIGMS NIH HHS/United States ; U01 MH106874/MH/NIMH NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; *Evolution, Molecular ; Gene Expression ; Genome ; Hominidae/*genetics/immunology ; Humans ; Immunity, Innate/genetics ; Multigene Family ; Mutation ; Polymorphism, Genetic ; Selection, Genetic ; Sialic Acid Binding Ig-like Lectin 3/*genetics ; }, abstract = {Human-specific pseudogenization of the CMAH gene eliminated the mammalian sialic acid (Sia) Neu5Gc (generating an excess of its precursor Neu5Ac), thus changing ubiquitous cell surface "self-associated molecular patterns" that modulate innate immunity via engagement of CD33-related-Siglec receptors. The Alu-fusion-mediated loss-of-function of CMAH fixed ∼2-3 Ma, possibly contributing to the origins of the genus Homo. The mutation likely altered human self-associated molecular patterns, triggering multiple events, including emergence of human-adapted pathogens with strong preference for Neu5Ac recognition and/or presenting Neu5Ac-containing molecular mimics of human glycans, which can suppress immune responses via CD33-related-Siglec engagement. Human-specific alterations reported in some gene-encoding Sia-sensing proteins suggested a "hotspot" in hominin evolution. The availability of more hominid genomes including those of two extinct hominins now allows full reanalysis and evolutionary timing. Functional changes occur in 8/13 members of the human genomic cluster encoding CD33-related Siglecs, all predating the human common ancestor. Comparisons with great ape genomes indicate that these changes are unique to hominins. We found no evidence for strong selection after the Human-Neanderthal/Denisovan common ancestor, and these extinct hominin genomes include almost all major changes found in humans, indicating that these changes in hominin sialobiology predate the Neanderthal-human divergence ∼0.6 Ma. Multiple changes in this genomic cluster may also explain human-specific expression of CD33rSiglecs in unexpected locations such as amnion, placental trophoblast, pancreatic islets, ovarian fibroblasts, microglia, Natural Killer(NK) cells, and epithelia. Taken together, our data suggest that innate immune interactions with pathogens markedly altered hominin Siglec biology between 0.6 and 2 Ma, potentially affecting human evolution.}, }
@article {pmid32546518, year = {2020}, author = {Mafessoni, F and Grote, S and de Filippo, C and Slon, V and Kolobova, KA and Viola, B and Markin, SV and Chintalapati, M and Peyrégne, S and Skov, L and Skoglund, P and Krivoshapkin, AI and Derevianko, AP and Meyer, M and Kelso, J and Peter, B and Prüfer, K and Pääbo, S}, title = {A high-coverage Neandertal genome from Chagyrskaya Cave.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {26}, pages = {15132-15136}, pmid = {32546518}, issn = {1091-6490}, mesh = {Animals ; Biological Evolution ; Female ; Fossils ; Gene Expression Regulation ; Genetic Variation ; *Genome ; Humans ; Inbreeding ; Neanderthals/*genetics ; Population Density ; Russia ; }, abstract = {We sequenced the genome of a Neandertal from Chagyrskaya Cave in the Altai Mountains, Russia, to 27-fold genomic coverage. We show that this Neandertal was a female and that she was more related to Neandertals in western Eurasia [Prüfer et al., Science 358, 655-658 (2017); Hajdinjak et al., Nature 555, 652-656 (2018)] than to Neandertals who lived earlier in Denisova Cave [Prüfer et al., Nature 505, 43-49 (2014)], which is located about 100 km away. About 12.9% of the Chagyrskaya genome is spanned by homozygous regions that are between 2.5 and 10 centiMorgans (cM) long. This is consistent with the fact that Siberian Neandertals lived in relatively isolated populations of less than 60 individuals. In contrast, a Neandertal from Europe, a Denisovan from the Altai Mountains, and ancient modern humans seem to have lived in populations of larger sizes. The availability of three Neandertal genomes of high quality allows a view of genetic features that were unique to Neandertals and that are likely to have been at high frequency among them. We find that genes highly expressed in the striatum in the basal ganglia of the brain carry more amino-acid-changing substitutions than genes expressed elsewhere in the brain, suggesting that the striatum may have evolved unique functions in Neandertals.}, }
@article {pmid32531199, year = {2020}, author = {Almarri, MA and Bergström, A and Prado-Martinez, J and Yang, F and Fu, B and Dunham, AS and Chen, Y and Hurles, ME and Tyler-Smith, C and Xue, Y}, title = {Population Structure, Stratification, and Introgression of Human Structural Variation.}, journal = {Cell}, volume = {182}, number = {1}, pages = {189-199.e15}, pmid = {32531199}, issn = {1097-4172}, support = {FC001595/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; FC001595/CRUK_/Cancer Research UK/United Kingdom ; FC001595/WT_/Wellcome Trust/United Kingdom ; FC001595/ARC_/Arthritis Research UK/United Kingdom ; }, mesh = {Alleles ; Databases, Genetic ; Gene Dosage ; Gene Duplication ; Gene Frequency/genetics ; Genetic Variation ; *Genetics, Population ; Genome, Human ; *Genomic Structural Variation ; Humans ; }, abstract = {Structural variants contribute substantially to genetic diversity and are important evolutionarily and medically, but they are still understudied. Here we present a comprehensive analysis of structural variation in the Human Genome Diversity panel, a high-coverage dataset of 911 samples from 54 diverse worldwide populations. We identify, in total, 126,018 variants, 78% of which were not identified in previous global sequencing projects. Some reach high frequency and are private to continental groups or even individual populations, including regionally restricted runaway duplications and putatively introgressed variants from archaic hominins. By de novo assembly of 25 genomes using linked-read sequencing, we discover 1,643 breakpoint-resolved unique insertions, in aggregate accounting for 1.9 Mb of sequence absent from the GRCh38 reference. Our results illustrate the limitation of a single human reference and the need for high-quality genomes from diverse populations to fully discover and understand human genetic variation.}, }
@article {pmid32511250, year = {2020}, author = {Martín-Francés, L and Martinón-Torres, M and Martínez de Pinillos, M and García-Campos, C and Zanolli, C and Bayle, P and Modesto-Mata, M and Arsuaga, JL and Bermúdez de Castro, JM}, title = {Crown tissue proportions and enamel thickness distribution in the Middle Pleistocene hominin molars from Sima de los Huesos (SH) population (Atapuerca, Spain).}, journal = {PloS one}, volume = {15}, number = {6}, pages = {e0233281}, pmid = {32511250}, issn = {1932-6203}, mesh = {Animals ; Biological Evolution ; Dental Enamel/anatomy &amp; histology/metabolism ; Fossils/*anatomy &amp; histology ; Hominidae/*anatomy &amp; histology ; Humans ; Molar/*anatomy &amp; histology/metabolism ; Neanderthals ; Phylogeny ; Spain ; Tooth ; Tooth Crown/anatomy &amp; histology/metabolism ; }, abstract = {Dental enamel thickness, topography, growth and development vary among hominins. In Homo, the thickness of dental enamel in most Pleistocene hominins display variations from thick to hyper-thick, while Neanderthals exhibit proportionally thinner enamel. The origin of the thin trait remains unclear. In this context, the Middle Pleistocene human dental assemblage from Atapuerca-Sima de los Huesos (SH) provides a unique opportunity to trace the evolution of enamel thickness in European hominins. In this study, we aim to test the hypothesis if the SH molar sample approximates the Neanderthal condition for enamel thickness and/or distribution. This study includes 626 molars, both original and comparative data. We analysed the molar inner structural organization of the original collections (n = 124), belonging to SH(n = 72) and modern humans from Spanish origin (n = 52). We compared the SH estimates to those of extinct and extant populations of the genus Homo from African, Asian and European origin (estimates extracted from literature n = 502). The comparative sample included maxillary and mandibular molars belonging to H. erectus, East and North African Homo, European Middle Pleistocene Homo, Neanderthals, and fossil and extant H. sapiens. We used high-resolution images to investigate the endostructural configuration of SH molars (tissue proportions, enamel thickness and distribution). The SH molars exhibit on average thick absolute and relative enamel in 2D and 3D estimates, both in the complete crown and the lateral enamel. This primitive condition is shared with the majority of extinct and extant hominin sample, except for Neanderthals and some isolated specimens. On the contrary, the SH molar enamel distribution maps reveal a distribution pattern similar to the Neanderthal signal (with thicker enamel on the lingual cusps and more peripherally distributed), compared to H. antecessor and modern humans. Due to the phylogenetic position of the SH population, the thick condition in molars could represent the persistence of the plesiomorphic condition in this group. Still, more data is needed on other Early and Middle Pleistocene populations to fully understand the evolutionary meaning of this trait.}, }
@article {pmid32494067, year = {2020}, author = {Skov, L and Coll Macià, M and Sveinbjörnsson, G and Mafessoni, F and Lucotte, EA and Einarsdóttir, MS and Jonsson, H and Halldorsson, B and Gudbjartsson, DF and Helgason, A and Schierup, MH and Stefansson, K}, title = {The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes.}, journal = {Nature}, volume = {582}, number = {7810}, pages = {78-83}, pmid = {32494067}, issn = {1476-4687}, mesh = {Animals ; Female ; Genetic Association Studies ; Genetic Introgression/*genetics ; Genome, Human/*genetics ; *Genomics ; Haploidy ; Humans ; Iceland ; Male ; *Mutation ; Neanderthals/*genetics ; Phenotype ; Phylogeny ; }, abstract = {Human evolutionary history is rich with the interbreeding of divergent populations. Most humans outside of Africa trace about 2% of their genomes to admixture from Neanderthals, which occurred 50-60 thousand years ago[1]. Here we examine the effect of this event using 14.4 million putative archaic chromosome fragments that were detected in fully phased whole-genome sequences from 27,566 Icelanders, corresponding to a range of 56,388-112,709 unique archaic fragments that cover 38.0-48.2% of the callable genome. On the basis of the similarity with known archaic genomes, we assign 84.5% of fragments to an Altai or Vindija Neanderthal origin and 3.3% to Denisovan origin; 12.2% of fragments are of unknown origin. We find that Icelanders have more Denisovan-like fragments than expected through incomplete lineage sorting. This is best explained by Denisovan gene flow, either into ancestors of the introgressing Neanderthals or directly into humans. A within-individual, paired comparison of archaic fragments with syntenic non-archaic fragments revealed that, although the overall rate of mutation was similar in humans and Neanderthals during the 500 thousand years that their lineages were separate, there were differences in the relative frequencies of mutation types-perhaps due to different generation intervals for males and females. Finally, we assessed 271 phenotypes, report 5 associations driven by variants in archaic fragments and show that the majority of previously reported associations are better explained by non-archaic variants.}, }
@article {pmid32490227, year = {2020}, author = {Kolendrianou, M and Ligkovanlis, S and Maniakas, I and Tzortzi, M and Iliopoulos, G}, title = {The Palaeolithic cave of Kalamakia (Mani Peninsula), Greece: new insights on the palaeoenvironment using microvertebrates and mesowear analysis of ruminant teeth.}, journal = {Heliyon}, volume = {6}, number = {5}, pages = {e03958}, pmid = {32490227}, issn = {2405-8440}, abstract = {In the present study, results from the examination of mammalian teeth from the cave of Kalamakia with modern techniques, as well as a qualitative overview of the microvertebrate and lithic material, are presented together with a revision of previous related work done for the site, in order to assess the palaeoenvironmental conditions in the area and the role they played in the Neanderthal's repeated occupation of the cave. Geometric morphometrics analyses performed on the first lower molars of Microtus spp. individuals revealed persistent populations of the subgenus Terricola, in which the presence of Microtus thomasi and Microtus subterraneus are continuous through the stratigraphic units. Mesowear analyses performed on ruminant teeth showed no significant variation in toothwear through time, except for relatively elevated levels of dietary abrasion for the more recent samples. The study of the lithics revealed that Neanderthals visited the cave in alternating short and more permanent episodes of occupation, with the human occupants exhibiting special concern for raw material economy, while exploiting poor raw materials for the construction of their tools. The overview of the microvertebrate remains showed a growing trend towards the upper stratigraphic units, where taxa typical of temperate climate, open woodland and shrubland become more dominant. These results, along with observations derived from previous studies, suggest that temperate climate and open environment were the factors that mainly contributed to making the cave of Kalamakia attractive as a habitation site to the humans of the area.}, }
@article {pmid32457436, year = {2020}, author = {Sánchez-Romero, L and Benito-Calvo, A and Marín-Arroyo, AB and Agudo-Pérez, L and Karampaglidis, T and Rios-Garaizar, J}, title = {New insights for understanding spatial patterning and formation processes of the Neanderthal occupation in theAmalda I cave (Gipuzkoa, Spain).}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {8733}, pmid = {32457436}, issn = {2045-2322}, abstract = {The Level VII of Amalda I cave (Gipuzkoa, Spain) represents one of the latest Middle Palaeolithic occupations in the Cantabrian Region. It is characterized by the presence of Middle Palaeolithic lithic industry and animal remains, with clear evidences of anthropic and carnivore manipulation. At this site, the Neanderthal presence has been questioned in relation to the role of carnivores in the accumulation of large, medium-sized and small mammals. It has also been proposed that the Neanderthal occupation could have consisted of short-term occupations, where different activities took place in a structured space within the cave. However, all hypotheses lacked any integrative analysis of the site formation processes. With the aim of understanding these processes, a combination of spatial techniques, based on GIS and inferential statistics (density analysis, hotspots tools and palaeotopographic reconstruction), along with the taphonomic study of identifiable and non-identifiable macromammals remains, were employed. This study has revealed distinct use of the cave space by Neanderthals and carnivores. The major concentrations of lithics and medium-size mammal remains were clearly accumulated by humans at the cave entrance, while the small-size mammals were gathered by carnivores in an inner zone. The activities of the Neanderthals seem to be distinctly structured, suggesting a parallel exploitation of resources.}, }
@article {pmid32451437, year = {2020}, author = {Esteller-Cucala, P and Maceda, I and Børglum, AD and Demontis, D and Faraone, SV and Cormand, B and Lao, O}, title = {Genomic analysis of the natural history of attention-deficit/hyperactivity disorder using Neanderthal and ancient Homo sapiens samples.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {8622}, pmid = {32451437}, issn = {2045-2322}, support = {R01 MH101519/MH/NIMH NIH HHS/United States ; U01 MH109536/MH/NIMH NIH HHS/United States ; }, mesh = {Alleles ; Animals ; Attention Deficit Disorder with Hyperactivity/*genetics/history/pathology ; Bayes Theorem ; Databases, Genetic ; Deep Learning ; Evolution, Molecular ; *Genome, Human ; Genomics/*methods ; History, Ancient ; Humans ; Neanderthals/*genetics ; }, abstract = {Attention-deficit/hyperactivity disorder (ADHD) is an impairing neurodevelopmental condition highly prevalent in current populations. Several hypotheses have been proposed to explain this paradox, mainly in the context of the Paleolithic versus Neolithic cultural shift but especially within the framework of the mismatch theory. This theory elaborates on how a particular trait once favoured in an ancient environment might become maladaptive upon environmental changes. However, given the lack of genomic data available for ADHD, these theories have not been empirically tested. We took advantage of the largest GWAS meta-analysis available for this disorder consisting of over 20,000 individuals diagnosed with ADHD and 35,000 controls, to assess the evolution of ADHD-associated alleles in European populations using archaic, ancient and modern human samples. We also included Approximate Bayesian computation coupled with deep learning analyses and singleton density scores to detect human adaptation. Our analyses indicate that ADHD-associated alleles are enriched in loss of function intolerant genes, supporting the role of selective pressures in this early-onset phenotype. Furthermore, we observed that the frequency of variants associated with ADHD has steadily decreased since Paleolithic times, particularly in Paleolithic European populations compared to samples from the Neolithic Fertile Crescent. We demonstrate this trend cannot be explained by African admixture nor Neanderthal introgression, since introgressed Neanderthal alleles are enriched in ADHD risk variants. All analyses performed support the presence of long-standing selective pressures acting against ADHD-associated alleles until recent times. Overall, our results are compatible with the mismatch theory for ADHD but suggest a much older time frame for the evolution of ADHD-associated alleles compared to previous hypotheses.}, }
@article {pmid32451090, year = {2020}, author = {Hoffmann, DL and Standish, CD and García-Diez, M and Pettitt, PB and Milton, JA and Zilhão, J and Alcolea-González, JJ and Cantalejo-Duarte, P and Collado, H and de Balbín, R and Lorblanchet, M and Ramos-Muñoz, J and Weniger, GC and Pike, AWG}, title = {Response to White et al.'s reply: 'Still no archaeological evidence that Neanderthals created Iberian cave art' [J. Hum. Evol. (2020) 102640].}, journal = {Journal of human evolution}, volume = {144}, number = {}, pages = {102810}, doi = {10.1016/j.jhevol.2020.102810}, pmid = {32451090}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; Caves ; *Neanderthals ; }, }
@article {pmid32437543, year = {2020}, author = {Zeberg, H and Kelso, J and Pääbo, S}, title = {The Neandertal Progesterone Receptor.}, journal = {Molecular biology and evolution}, volume = {37}, number = {9}, pages = {2655-2660}, pmid = {32437543}, issn = {1537-1719}, mesh = {Alleles ; Alu Elements ; Animals ; Female ; Fertility/*genetics ; *Genetic Introgression ; Haplotypes ; Humans ; Neanderthals/*genetics ; Pregnancy ; Premature Birth/*genetics ; Receptors, Progesterone/*genetics ; }, abstract = {The hormone progesterone is important for preparing the uterine lining for egg implantation and for maintaining the early stages of pregnancy. The gene encoding the progesterone receptor (PGR) carries introgressed Neandertal haplotypes with two missense substitutions and a mobile Alu element. These Neandertal gene variants have reached nearly 20% frequency in non-Africans and have been associated with preterm birth. Here, we show that one of the missense substitutions appears fixed in Neandertals, while the other substitution as well as the Alu insertion were polymorphic among Neandertals. We show that two Neandertal haplotypes carrying the PGR gene entered the modern human population and that present-day carriers of the Neandertal haplotypes express higher levels of the receptor. In a cohort of present-day Britons, these carriers have more siblings, fewer miscarriages, and less bleeding during early pregnancy suggesting that the Neandertal progesterone receptor alleles promote fertility. This may explain their high frequency in modern human populations.}, }
@article {pmid32436615, year = {2020}, author = {Palancar, CA and García-Martínez, D and Radovčić, D and Llidó, S and Mata-Escolano, F and Bastir, M and Sanchis-Gimeno, JA}, title = {Krapina atlases suggest a high prevalence of anatomical variations in the first cervical vertebra of Neanderthals.}, journal = {Journal of anatomy}, volume = {237}, number = {3}, pages = {579-586}, pmid = {32436615}, issn = {1469-7580}, mesh = {Animals ; Biological Evolution ; Biological Variation, Individual ; Cervical Atlas/*anatomy &amp; histology ; Fossils ; Neanderthals/*anatomy &amp; histology ; }, abstract = {The first cervical vertebra, atlas, and its anatomical variants have been widely studied in Homo sapiens. However, in Neanderthals, the presence of anatomical variants of the atlas has been very little studied until very recently. Only the Neanderthal group from the El Sidrón site (Spain) has been analysed with regard to the anatomical variants of the atlas. A high prevalence of anatomical variants has been described in this sample, which points to low genetic diversity in this Neanderthal group. Even so, the high prevalence of anatomical variations detected in El Sidrón Neanderthal atlases needs to be confirmed by analysing more Neanderthal remains. In this context, we analysed the possible presence of anatomical variants in the three Neanderthal atlases recovered from the Krapina site (Croatia) within the Neanderthal lineage. Two of the three Krapina atlases presented anatomical variations. One atlas (Krapina 98) had an unclosed transverse foramen and the other (Krapina 99) presented a non-fused anterior atlas arch. Moreover, an extended review of the bibliography also showed these anatomical variations in other Middle and Upper Pleistocene hominins, leading us to hypothesise that anatomical variations of the atlas had a higher prevalence in extinct hominins than in modern humans.}, }
@article {pmid32433609, year = {2020}, author = {Hublin, JJ and Sirakov, N and Aldeias, V and Bailey, S and Bard, E and Delvigne, V and Endarova, E and Fagault, Y and Fewlass, H and Hajdinjak, M and Kromer, B and Krumov, I and Marreiros, J and Martisius, NL and Paskulin, L and Sinet-Mathiot, V and Meyer, M and Pääbo, S and Popov, V and Rezek, Z and Sirakova, S and Skinner, MM and Smith, GM and Spasov, R and Talamo, S and Tuna, T and Wacker, L and Welker, F and Wilcke, A and Zahariev, N and McPherron, SP and Tsanova, T}, title = {Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria.}, journal = {Nature}, volume = {581}, number = {7808}, pages = {299-302}, pmid = {32433609}, issn = {1476-4687}, support = {/ERC_/European Research Council/International ; }, mesh = {Animals ; Asia ; Bone and Bones/metabolism ; Bulgaria ; Caves ; DNA, Ancient/isolation &amp; purification ; DNA, Mitochondrial/genetics/isolation &amp; purification ; Europe ; *Fossils ; History, Ancient ; Human Migration/*history ; Humans ; Neanderthals/genetics ; Phylogeny ; Tool Use Behavior ; Tooth/anatomy &amp; histology/metabolism ; }, abstract = {The Middle to Upper Palaeolithic transition in Europe witnessed the replacement and partial absorption of local Neanderthal populations by Homo sapiens populations of African origin[1]. However, this process probably varied across regions and its details remain largely unknown. In particular, the duration of chronological overlap between the two groups is much debated, as are the implications of this overlap for the nature of the biological and cultural interactions between Neanderthals and H. sapiens. Here we report the discovery and direct dating of human remains found in association with Initial Upper Palaeolithic artefacts[2], from excavations at Bacho Kiro Cave (Bulgaria). Morphological analysis of a tooth and mitochondrial DNA from several hominin bone fragments, identified through proteomic screening, assign these finds to H. sapiens and link the expansion of Initial Upper Palaeolithic technologies with the spread of H. sapiens into the mid-latitudes of Eurasia before 45 thousand years ago[3]. The excavations yielded a wealth of bone artefacts, including pendants manufactured from cave bear teeth that are reminiscent of those later produced by the last Neanderthals of western Europe[4-6]. These finds are consistent with models based on the arrival of multiple waves of H. sapiens into Europe coming into contact with declining Neanderthal populations[7,8].}, }
@article {pmid32398823, year = {2020}, author = {Hardy, BL and Moncel, MH and Kerfant, C and Lebon, M and Bellot-Gurlet, L and Mélard, N}, title = {Author Correction: Direct evidence of Neanderthal fibre technology and its cognitive and behavioral implications.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {8167}, doi = {10.1038/s41598-020-65143-5}, pmid = {32398823}, issn = {2045-2322}, abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.}, }
@article {pmid32380300, year = {2020}, author = {Verna, C and Détroit, F and Kupczik, K and Arnaud, J and Balzeau, A and Grimaud-Hervé, D and Bertrand, S and Riou, B and Moncel, MH}, title = {The Middle Pleistocene hominin mandible from Payre (Ardèche, France).}, journal = {Journal of human evolution}, volume = {144}, number = {}, pages = {102775}, doi = {10.1016/j.jhevol.2020.102775}, pmid = {32380300}, issn = {1095-8606}, mesh = {Animals ; Biological Evolution ; Fossils ; France ; Hominidae/*anatomy &amp; histology ; Mandible/*anatomy &amp; histology ; Neanderthals/anatomy &amp; histology ; }, abstract = {Although Neandertals are the best-known fossil hominins, the tempo and evolutionary processes in their lineage are strongly debated. This is in part due to the scarcity of the fossil record, in particular before the marine isotopic stage (MIS) 5. In 2010, a partial hominin mandible was discovered at the Middle Paleolithic site of Payre (France) in a layer that is dated to the end of MIS 8/beginning of MIS 7, a time period for which very few fossils are known in Europe. The Payre 15 mandible retains the complete symphyseal region and right lateral corpus with heavily worn P4, M1, and M2 in situ. Taphonomic modifications in the form of three notches suggest that this individual was chewed by a carnivore. We provide here the first detailed description of this specimen and a comparative analysis that includes morphological features, linear mandibular dimensions, an elliptic Fourier analysis of the symphysis, and a morphometric analysis of the M1 roots (based on segmented CT scan data). Our comparative sample encompasses European Middle and Upper Pleistocene specimens attributed to Homo heidelbergensis and Homo neanderthalensis, Upper Pleistocene Homo sapiens, and Holocene Homo sapiens. The Payre 15 mandible shows a combination of primitive and Neandertal-like features, with a receding symphyseal profile without any element of the mentum osseum, a posterior location of the mental foramen and lateral prominence. Its mandibular body is tall and thick anteriorly. Payre 15 has mesotaurodont M1 roots and a three-rooted M2. By its dimensions and combination of features, Payre 15 aligns better with Middle Pleistocene European hominins than with MIS 6-3 Neandertals. Noteworthy, it falls well within the range of variation of the Sima de los Huesos sample. Our results underscore that the total pattern of Neandertal-derived morphology was not achieved at the beginning of the MIS 7 and suggest a low level of mandibular diachronic changes for the period MIS 11-7.}, }
@article {pmid32371290, year = {2020}, author = {Yeshurun, R and Malkinson, D and Crater Gershtein, KM and Zaidner, Y and Weinstein-Evron, M}, title = {Site occupation dynamics of early modern humans at Misliya Cave (Mount Carmel, Israel): Evidence from the spatial taphonomy of faunal remains.}, journal = {Journal of human evolution}, volume = {143}, number = {}, pages = {102797}, doi = {10.1016/j.jhevol.2020.102797}, pmid = {32371290}, issn = {1095-8606}, mesh = {*Archaeology ; Caves ; *Feeding Behavior ; *Food Handling ; Fossils ; Humans ; Israel ; }, abstract = {Space use in Middle Paleolithic (MP) camps has been suggested as a source of information on the intensity and repetition of occupations and, by extension, of demographics. In the Levant, clear evidence for differential intrasite use and maintenance was important in viewing the late MP Neanderthal sites as base camps inhabited for a significant duration, relative to the Early MP (EMP). We test this model with the rich faunal assemblage from the EMP (>140 ka) site of Misliya Cave, Mount Carmel, Israel. Excavations in Misliya yielded a large and diverse lithic assemblage, combustion features, and a modern human maxilla, together with a large archaeofaunal assemblage that we use as a spatial marker. We analyzed the distribution of bone items with variable taphonomic properties (anthropogenic, biogenic, and abiotic bone-surface modifications) in a hearth-related context, both by comparing grid squares and point patterns. Both analyses are largely congruent. They indicate repeated and consistent use of the site's space that includes hearth-related consumption activities and peripheral activities further away, albeit with little evidence for site maintenance. Thus, the Misliya results display a mixed signal of clear around-the-fire pattern and differential space use in the EMP that is reminiscent of the much later MP sites in the Levant, but without the more elaborate camp maintenance. More case studies and detailed proxies are needed before we can fine-tune our understanding of camp structure in the Levantine MP and its bearing to site occupation dynamics.}, }
@article {pmid32356723, year = {2020}, author = {Jordan, B}, title = {[Neandertal DNA in Africans].}, journal = {Medecine sciences : M/S}, volume = {36}, number = {4}, pages = {421-423}, doi = {10.1051/medsci/2020055}, pmid = {32356723}, issn = {1958-5381}, mesh = {Africa ; Animals ; DNA/analysis/*genetics ; Evolution, Molecular ; Genetics, Population ; Genome ; History, 21st Century ; History, Ancient ; Hominidae/classification/*genetics ; Humans ; Hybridization, Genetic ; Neanderthals/classification/*genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; }, abstract = {Sophisticated analyses of current human populations compared to a high-coverage Neandertal genome sequence indicate that, contrary to the previous consensus, African genomes carry a small but significant amount of Neandertal-specific DNA. This indicates back-migration into Africa of modern humans (carrying some Neandertal sequences) and underlines the complexity of ancient human migrations.}, }
@article {pmid32330268, year = {2020}, author = {Lodewijk, GA and Fernandes, DP and Vretzakis, I and Savage, JE and Jacobs, FMJ}, title = {Evolution of Human Brain Size-Associated NOTCH2NL Genes Proceeds toward Reduced Protein Levels.}, journal = {Molecular biology and evolution}, volume = {37}, number = {9}, pages = {2531-2548}, pmid = {32330268}, issn = {1537-1719}, mesh = {Animals ; *Biological Evolution ; Genome, Human ; Genomic Structural Variation ; Humans ; Multigene Family ; Neanderthals/*genetics ; Receptor, Notch2/*genetics/metabolism ; }, abstract = {Ever since the availability of genomes from Neanderthals, Denisovans, and ancient humans, the field of evolutionary genomics has been searching for protein-coding variants that may hold clues to how our species evolved over the last ∼600,000 years. In this study, we identify such variants in the human-specific NOTCH2NL gene family, which were recently identified as possible contributors to the evolutionary expansion of the human brain. We find evidence for the existence of unique protein-coding NOTCH2NL variants in Neanderthals and Denisovans which could affect their ability to activate Notch signaling. Furthermore, in the Neanderthal and Denisovan genomes, we find unusual NOTCH2NL configurations, not found in any of the modern human genomes analyzed. Finally, genetic analysis of archaic and modern humans reveals ongoing adaptive evolution of modern human NOTCH2NL genes, identifying three structural variants acting complementary to drive our genome to produce a lower dosage of NOTCH2NL protein. Because copy-number variations of the 1q21.1 locus, encompassing NOTCH2NL genes, are associated with severe neurological disorders, this seemingly contradicting drive toward low levels of NOTCH2NL protein indicates that the optimal dosage of NOTCH2NL may have not yet been settled in the human population.}, }
@article {pmid32273518, year = {2020}, author = {Hardy, BL and Moncel, MH and Kerfant, C and Lebon, M and Bellot-Gurlet, L and Mélard, N}, title = {Direct evidence of Neanderthal fibre technology and its cognitive and behavioral implications.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {4889}, pmid = {32273518}, issn = {2045-2322}, mesh = {Animals ; Archaeology ; Cellulose/analysis ; *Cognition ; *Fossils ; France ; History, Ancient ; Lignin/analysis ; Microscopy, Electron, Scanning ; Neanderthals/*psychology ; Soil/chemistry ; Spectroscopy, Fourier Transform Infrared ; Spectrum Analysis, Raman ; Technology/*history ; Textiles/analysis/*history ; }, abstract = {Neanderthals are often considered as less technologically advanced than modern humans. However, we typically only find faunal remains or stone tools at Paleolithic sites. Perishable materials, comprising the vast majority of material culture items, are typically missing. Individual twisted fibres on stone tools from the Abri du Maras led to the hypothesis of Neanderthal string production in the past, but conclusive evidence was lacking. Here we show direct evidence of fibre technology in the form of a 3-ply cord fragment made from inner bark fibres on a stone tool recovered in situ from the same site. Twisted fibres provide the basis for clothing, rope, bags, nets, mats, boats, etc. which, once discovered, would have become an indispensable part of daily life. Understanding and use of twisted fibres implies the use of complex multi-component technology as well as a mathematical understanding of pairs, sets, and numbers. Added to recent evidence of birch bark tar, art, and shell beads, the idea that Neanderthals were cognitively inferior to modern humans is becoming increasingly untenable.}, }
@article {pmid32247528, year = {2021}, author = {Grimaud-Hervé, D and Albessard-Ball, L and Pokhojaev, A and Balzeau, A and Sarig, R and Latimer, B and McDermott, Y and May, H and Hershkovitz, I}, title = {The endocast of the late Middle Paleolithic Manot 1 specimen, Western Galilee, Israel.}, journal = {Journal of human evolution}, volume = {160}, number = {}, pages = {102734}, doi = {10.1016/j.jhevol.2019.102734}, pmid = {32247528}, issn = {1095-8606}, mesh = {Animals ; Biological Evolution ; Fossils ; *Hominidae ; Humans ; Israel ; *Neanderthals ; Skull/anatomy &amp; histology ; }, abstract = {Studying endocasts has long allowed anthropologists to examine changes in the external topography and the overall size of the brain throughout the evolutionary history of hominins. The nearly complete calvaria of Manot 1 presents an opportunity to gain insights into the external brain morphology, vascular system, and dimensions of the brain of this late Middle Paleolithic hominin. Detailed size and shape analyses of the Manot 1 endocast indicate a modern Homo sapiens anatomy, despite the presence of some primitive features of the calvaria. Traits considered to be derived endocranial features for H. sapiens are present in Manot 1, including an elongated parietal sagittal chord with an elevated superior part of the hemisphere, a widened posterior part of the frontal lobes, a considerable development of the parietal reliefs such as the supramarginal lobules, and a slight posterior projection of the occipital lobes. These findings, together with data presented in previous studies, rule out the possibility of a direct Neanderthal ancestry for the Manot 1 hominin and instead confirm its affiliation with H. sapiens. The Manot 1 calvaria is more similar to that of later Upper Paleolithic H. sapiens than it is to the earlier Levantine populations of Skhul and Qafzeh. The late Middle Paleolithic date of Manot 1 provides an opportunity to analyze the recent developments in human cerebral morphology and organization.}, }
@article {pmid32234956, year = {2020}, author = {Taskent, O and Lin, YL and Patramanis, I and Pavlidis, P and Gokcumen, O}, title = {Analysis of Haplotypic Variation and Deletion Polymorphisms Point to Multiple Archaic Introgression Events, Including from Altai Neanderthal Lineage.}, journal = {Genetics}, volume = {215}, number = {2}, pages = {497-509}, pmid = {32234956}, issn = {1943-2631}, mesh = {Animals ; *Genetics, Population ; Genome, Human ; *Haplotypes ; Hominidae ; Humans ; Neanderthals/*genetics ; *Phenotype ; *Polymorphism, Genetic ; Russia ; *Selection, Genetic ; }, abstract = {The time, extent, and genomic effect of the introgressions from archaic humans into ancestors of extant human populations remain some of the most exciting venues of population genetics research in the past decade. Several studies have shown population-specific signatures of introgression events from Neanderthals, Denisovans, and potentially other unknown hominin populations in different human groups. Moreover, it was shown that these introgression events may have contributed to phenotypic variation in extant humans, with biomedical and evolutionary consequences. In this study, we present a comprehensive analysis of the unusually divergent haplotypes in the Eurasian genomes and show that they can be traced back to multiple introgression events. In parallel, we document hundreds of deletion polymorphisms shared with Neanderthals. A locus-specific analysis of one such shared deletion suggests the existence of a direct introgression event from the Altai Neanderthal lineage into the ancestors of extant East Asian populations. Overall, our study is in agreement with the emergent notion that various Neanderthal populations contributed to extant human genetic variation in a population-specific manner.}, }
@article {pmid32217711, year = {2020}, author = {Will, M}, title = {Neanderthal surf and turf.}, journal = {Science (New York, N.Y.)}, volume = {367}, number = {6485}, pages = {1422-1423}, doi = {10.1126/science.abb3568}, pmid = {32217711}, issn = {1095-9203}, mesh = {Animals ; Fossils ; *Hominidae ; *Neanderthals ; }, }
@article {pmid32217702, year = {2020}, author = {Zilhão, J and Angelucci, DE and Igreja, MA and Arnold, LJ and Badal, E and Callapez, P and Cardoso, JL and d'Errico, F and Daura, J and Demuro, M and Deschamps, M and Dupont, C and Gabriel, S and Hoffmann, DL and Legoinha, P and Matias, H and Monge Soares, AM and Nabais, M and Portela, P and Queffelec, A and Rodrigues, F and Souto, P}, title = {Last Interglacial Iberian Neandertals as fisher-hunter-gatherers.}, journal = {Science (New York, N.Y.)}, volume = {367}, number = {6485}, pages = {}, doi = {10.1126/science.aaz7943}, pmid = {32217702}, issn = {1095-9203}, mesh = {Animal Shells ; Animals ; Archaeology ; Atlantic Ocean ; Birds ; Caves ; *Diet ; Fishes ; Mammals ; *Neanderthals ; Nuts ; Pinus ; Portugal ; Seafood ; Turtles ; }, abstract = {Marine food-reliant subsistence systems such as those in the African Middle Stone Age (MSA) were not thought to exist in Europe until the much later Mesolithic. Whether this apparent lag reflects taphonomic biases or behavioral distinctions between archaic and modern humans remains much debated. Figueira Brava cave, in the Arrábida range (Portugal), provides an exceptionally well preserved record of Neandertal coastal resource exploitation on a comparable scale to the MSA and dated to ~86 to 106 thousand years ago. The breadth of the subsistence base-pine nuts, marine invertebrates, fish, marine birds and mammals, tortoises, waterfowl, and hoofed game-exceeds that of regional early Holocene sites. Fisher-hunter-gatherer economies are not the preserve of anatomically modern people; by the Last Interglacial, they were in place across the Old World in the appropriate settings.}, }
@article {pmid32193295, year = {2020}, author = {Bergström, A and McCarthy, SA and Hui, R and Almarri, MA and Ayub, Q and Danecek, P and Chen, Y and Felkel, S and Hallast, P and Kamm, J and Blanché, H and Deleuze, JF and Cann, H and Mallick, S and Reich, D and Sandhu, MS and Skoglund, P and Scally, A and Xue, Y and Durbin, R and Tyler-Smith, C}, title = {Insights into human genetic variation and population history from 929 diverse genomes.}, journal = {Science (New York, N.Y.)}, volume = {367}, number = {6484}, pages = {}, pmid = {32193295}, issn = {1095-9203}, support = {207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; /ERC_/European Research Council/International ; /HHMI/Howard Hughes Medical Institute/United States ; 206194/WT_/Wellcome Trust/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; FC001595/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; FC001595/MRC_/Medical Research Council/United Kingdom ; 207492/WT_/Wellcome Trust/United Kingdom ; FC001595/ARC_/Arthritis Research UK/United Kingdom ; FC001595/CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {Africa ; Americas ; Animals ; Asia ; DNA Copy Number Variations ; *Genetic Variation ; *Genetics, Population ; *Genome, Human ; Haplotypes ; Hominidae/genetics ; Humans ; INDEL Mutation ; Neanderthals/genetics ; Oceania ; Phylogeny ; Polymorphism, Single Nucleotide ; Population Density ; Racial Groups/genetics ; *Whole Genome Sequencing ; }, abstract = {Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented common genetic variation private to southern Africa, central Africa, Oceania, and the Americas, but an absence of such variants fixed between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the past 10,000 years, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations.}, }
@article {pmid32170098, year = {2020}, author = {Modesto-Mata, M and Dean, MC and Lacruz, RS and Bromage, TG and García-Campos, C and Martínez de Pinillos, M and Martín-Francés, L and Martinón-Torres, M and Carbonell, E and Arsuaga, JL and Bermúdez de Castro, JM}, title = {Short and long period growth markers of enamel formation distinguish European Pleistocene hominins.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {4665}, pmid = {32170098}, issn = {2045-2322}, mesh = {Animals ; Biological Evolution ; *Biomarkers ; Dental Enamel/*anatomy &amp; histology/growth &amp; development/metabolism ; *Fossils ; *Hominidae ; Humans ; Microscopy, Confocal ; *Osteogenesis ; Tooth/anatomy &amp; histology/growth &amp; development/metabolism ; }, abstract = {Characterizing dental development in fossil hominins is important for distinguishing between them and for establishing where and when the slow overall growth and development of modern humans appeared. Dental development of australopiths and early Homo was faster than modern humans. The Atapuerca fossils (Spain) fill a barely known gap in human evolution, spanning ~1.2 to ~0.4 million years (Ma), during which H. sapiens and Neandertal dental growth characteristics may have developed. We report here perikymata counts, perikymata distributions and periodicities of all teeth belonging to the TE9 level of Sima del Elefante, level TD6.2 of Gran Dolina (H. antecessor) and Sima de los Huesos. We found some components of dental growth in the Atapuerca fossils resembled more recent H. sapiens. Mosaic evolution of perikymata counts and distribution generate three distinct clusters: H. antecessor, Sima de los Huesos and H. sapiens.}, }
@article {pmid32163763, year = {2020}, author = {Belcastro, MG and Mariotti, V and Pietrobelli, A and Sorrentino, R and García-Tabernero, A and Estalrrich, A and Rosas, A}, title = {The study of the lower limb entheses in the Neanderthal sample from El Sidrón (Asturias, Spain): How much musculoskeletal variability did Neanderthals accumulate?.}, journal = {Journal of human evolution}, volume = {141}, number = {}, pages = {102746}, doi = {10.1016/j.jhevol.2020.102746}, pmid = {32163763}, issn = {1095-8606}, mesh = {Animals ; Female ; Lower Extremity/growth &amp; development/*physiology ; Male ; Muscle, Skeletal/*growth &amp; development ; *Musculoskeletal Development ; Neanderthals/growth &amp; development/*physiology ; Spain ; }, abstract = {Entheses have rarely been systematically studied in the field of human evolution. However, the investigation of their morphological variability (e.g., robusticity) could provide new insight into their evolutionary significance in the European Neanderthal populations. The aim of this work is to study the entheses and joint features of the lower limbs of El Sidrón Neanderthals (Spain; 49 ka), using standardized scoring methods developed on modern samples. Paleobiology, growth, and development of both juveniles and adults from El Sidrón are studied and compared with those of Krapina Neanderthals (Croatia, 130 ka) and extant humans. The morphological patterns of the gluteus maximus and vastus intermedius entheses in El Sidrón, Krapina, and modern humans differ from one another. Both Neanderthal groups show a definite enthesis design for the gluteus maximus, with little intrapopulation variability with respect to modern humans, who are characterized by a wider range of morphological variability. The gluteus maximus enthesis in the El Sidrón sample shows the osseous features of fibrous entheses, as in modern humans, whereas the Krapina sample shows the aspects of fibrocartilaginous ones. The morphology and anatomical pattern of this enthesis has already been established during growth in all three human groups. One of two and three of five adult femurs from El Sidrón and from Krapina, respectively, show the imprint of the vastus intermedius, which is absent among juveniles from those Neanderthal samples and in modern samples. The scant intrapopulation and the high interpopulation variability in the two Neanderthal samples is likely due to a long-term history of small, isolated populations with high levels of inbreeding, who also lived in different ecological conditions. The comparison of different anatomical entheseal patterns (fibrous vs. fibrocartilaginous) in the Neanderthals and modern humans provides additional elements in the discussion of their functional and genetic origin.}, }
@article {pmid32146203, year = {2020}, author = {Rosas, A and Losada Agustina, B and García-Martínez, D and Torres-Tamayo, N and García-Tabernero, A and Pastor, JF and Rasilla, M and Bastir, M}, title = {Analyses of the neandertal patellae from El Sidrón (Asturias, Spain) with implications for the evolution of body form in Homo.}, journal = {Journal of human evolution}, volume = {141}, number = {}, pages = {102738}, doi = {10.1016/j.jhevol.2019.102738}, pmid = {32146203}, issn = {1095-8606}, mesh = {Animals ; *Biological Evolution ; Fossils/*anatomy &amp; histology ; Neanderthals/*anatomy &amp; histology ; Patella/*anatomy &amp; histology ; *Somatotypes ; Spain ; }, abstract = {The evolution of the body form in Homo and its potential morphological connection to the arrangement of different skeletal systems is of major interest in human evolution. Patella morphology as part of the knee is potentially influenced by body form. Here, we describe for the first time the patellae remains recovered at El Sidrón Neandertal site and analyze them in a comparative evolutionary framework. We aim to clarify whether morphometric features frequently observed in Neandertal and modern human patellae are retained from a primitive anatomical arrangement or whether they represent derived features (apomorphies). For this purpose, we combine analyses of discrete features, classic anthropological measurements, and 3D geometric morphometrics based on generalized Procrustes analysis, mean size and shape comparisons, and principal components analysis. We found a size increment of the patella in hominin evolution, with large species showing a larger patella. Modern humans and Neandertals exhibit overall larger patellae, with maximum values observed in the latter, likely as a consequence of their broader body shape. Also, some Neandertals display a thicker patella, which has been linked to larger quadriceps muscles. However, Neandertals retain a primitive morphology in their patellar articular surfaces, with similar-sized lateral and medial articular facets, leading to a more symmetrical internal face. This feature is inherited from a primitive Homo ancestor and suggests a different configuration of the knee in Neandertals. Conversely, Homo sapiens exhibits an autoapomorphic patellar anatomy with expanded lateral articular facets. We propose that these distinct configurations of the patella within Homo may be a consequence of different body forms rather than specific functional adaptations of the knee. Thus, the slender body form of modern humans may entail a medial reorientation of the tibial tuberosity (patellar ligament), allowing lateral surface expansion. These anatomical evolutionary variations may involve subtle secondary differences in bipedalism within Homo.}, }
@article {pmid32128408, year = {2020}, author = {Rogers, AR and Harris, NS and Achenbach, AA}, title = {Neanderthal-Denisovan ancestors interbred with a distantly related hominin.}, journal = {Science advances}, volume = {6}, number = {8}, pages = {eaay5483}, pmid = {32128408}, issn = {2375-2548}, mesh = {Animals ; Confidence Intervals ; *Consanguinity ; Gene Flow ; Genetics, Population ; Hominidae/*genetics ; Models, Genetic ; Neanderthals/*genetics ; Phylogeny ; }, abstract = {Previous research has shown that modern Eurasians interbred with their Neanderthal and Denisovan predecessors. We show here that hundreds of thousands of years earlier, the ancestors of Neanderthals and Denisovans interbred with their own Eurasian predecessors-members of a "superarchaic" population that separated from other humans about 2 million years ago. The superarchaic population was large, with an effective size between 20 and 50 thousand individuals. We confirm previous findings that (i) Denisovans also interbred with superarchaics, (ii) Neanderthals and Denisovans separated early in the middle Pleistocene, (iii) their ancestors endured a bottleneck of population size, and (iv) the Neanderthal population was large at first but then declined in size. We provide qualified support for the view that (v) Neanderthals interbred with the ancestors of modern humans.}, }
@article {pmid32078934, year = {2020}, author = {Moncel, MH and Ashton, N and Arzarello, M and Fontana, F and Lamotte, A and Scott, B and Muttillo, B and Berruti, G and Nenzioni, G and Tuffreau, A and Peretto, C}, title = {Early Levallois core technology between Marine Isotope Stage 12 and 9 in Western Europe.}, journal = {Journal of human evolution}, volume = {139}, number = {}, pages = {102735}, doi = {10.1016/j.jhevol.2019.102735}, pmid = {32078934}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; *Biological Evolution ; France ; *Hominidae ; Italy ; Neanderthals ; *Technology ; United Kingdom ; }, abstract = {Early Levallois core technology is usually dated in Europe to the end of Marine Isotope Stage (MIS) 9 and particularly from the beginning of MIS 8 to MIS 6. This technology is considered as one of the markers of the transition from lower to Middle Paleolithic or from Mode 2 to Mode 3. Recent discoveries show that some lithic innovations actually appeared earlier in western Europe, from MIS 12 to MIS 9, contemporaneous with changes in subsistence strategies and the first appearance of early Neanderthal anatomical features. Among these discoveries, there is the iconic Levallois core technology. A selection of well-dated assemblages in the United Kingdom, France, and Italy dated from MIS 12 to 9, which include both cores and flakes with Levallois features, has been described and compared with the aim of characterizing this technology. The conclusion supports the interpretation that several technical features may be attributed to a Levallois technology similar to those observed in younger Middle Paleolithic sites, distinct from the main associated core technologies in each level. Some features in the sample of sites suggest a gradual transformation of existing core technologies. The small evidence of Levallois could indicate occasional local innovations from different technological backgrounds and would explain the diversity of Levallois methods that is observed from MIS 12. The technological roots of Levallois technology in the Middle Pleistocene would suggest a multiregional origin and diffusion in Europe and early evidence of regionalization of local traditions through Europe from MIS 12 to 9. The relationships of Levallois technology with new needs and behaviors are discussed, such as flake preference, functional reasons related to hunting and hafting, an increase in the use of mental templates in European populations, and changes in the structure of hominin groups adapting to climatic and environmental changes.}, }
@article {pmid32062432, year = {2020}, author = {Weissbrod, L and Weinstein-Evron, M}, title = {Climate variability in early expansions of Homo sapiens in light of the new record of micromammals in Misliya Cave, Israel.}, journal = {Journal of human evolution}, volume = {139}, number = {}, pages = {102741}, doi = {10.1016/j.jhevol.2020.102741}, pmid = {32062432}, issn = {1095-8606}, mesh = {Animals ; *Biological Evolution ; Caves ; *Climate ; Climate Change ; Fossils ; *Human Migration ; Humans ; Israel ; Mammals ; Neanderthals ; }, abstract = {In this study, we provide the first taphonomic and taxonomic descriptions of the micromammals from Misliya Cave, where recently a Homo sapiens hemimaxilla has been reported. This finding significantly extends the time frame for the out-of-Africa presence of anatomically modern humans. It also provides an opportunity to reassess variation in early modern human population responses to climate change in the Levantine sequence. Information on species ranking and diversity estimations (Shannon functions) is obtained from quantitative data across 31 Levantine assemblages and investigated in a broad comparative frame using multivariate analyses. Recent models of human-climate interactions in the late Early-Middle Paleolithic of the southern Levant have drawn heavily on on-site associations of human fossils with remains of micromammals. However, there has been little, if any, attempt to examine the long-term picture of how paleocommunities of micromammals responded qualitatively and quantitatively to climatic oscillations of the region by altering their compositional complexity. Consequently, our understanding is vastly limited in regard to the paleoecosystem functions that linked past precipitation shifts to changes in primary producers and consumers or as to the background climatic conditions that allowed for the development of highly nonanalog ancient communities in the region. Although previous studies argued for a correspondence between alternations in H. sapiens and Neanderthal occupations of the Levant and faunal shifts in key biostratigraphic indicator taxa (such as Euro-Siberian Ellobius versus Saharo-Arabian Mastomys and Arvicanthis), our data indicate the likelihood that early H. sapiens populations (Misliya and Qafzeh hominins) persisted through high amplitudes of paleoecological and climatic oscillations. It is unlikely, given these results, that climate functioned as a significant filter of early modern human persistence and genetic interactions with Neanderthals in the Levant.}, }
@article {pmid34692055, year = {2020}, author = {,  and He, Y and Lou, H and Cui, C and Deng, L and Gao, Y and Zheng, W and Guo, Y and Wang, X and Ning, Z and Li, J and Li, B and Bai, C and ,  and ,  and ,  and ,  and ,  and Liu, S and Wu, T and Xu, S and Qi, X and Su, B}, title = {De novo assembly of a Tibetan genome and identification of novel structural variants associated with high-altitude adaptation.}, journal = {National science review}, volume = {7}, number = {2}, pages = {391-402}, pmid = {34692055}, issn = {2053-714X}, abstract = {Structural variants (SVs) may play important roles in human adaptation to extreme environments such as high altitude but have been under-investigated. Here, combining long-read sequencing with multiple scaffolding techniques, we assembled a high-quality Tibetan genome (ZF1), with a contig N50 length of 24.57 mega-base pairs (Mb) and a scaffold N50 length of 58.80 Mb. The ZF1 assembly filled 80 remaining N-gaps (0.25 Mb in total length) in the reference human genome (GRCh38). Markedly, we detected 17 900 SVs, among which the ZF1-specific SVs are enriched in GTPase activity that is required for activation of the hypoxic pathway. Further population analysis uncovered a 163-bp intronic deletion in the MKL1 gene showing large divergence between highland Tibetans and lowland Han Chinese. This deletion is significantly associated with lower systolic pulmonary arterial pressure, one of the key adaptive physiological traits in Tibetans. Moreover, with the use of the high-quality de novo assembly, we observed a much higher rate of genome-wide archaic hominid (Altai Neanderthal and Denisovan) shared non-reference sequences in ZF1 (1.32%-1.53%) compared to other East Asian genomes (0.70%-0.98%), reflecting a unique genomic composition of Tibetans. One such archaic hominid shared sequence-a 662-bp intronic insertion in the SCUBE2 gene-is enriched and associated with better lung function (the FEV1/FVC ratio) in Tibetans. Collectively, we generated the first high-resolution Tibetan reference genome, and the identified SVs may serve as valuable resources for future evolutionary and medical studies.}, }
@article {pmid32004458, year = {2020}, author = {Chen, L and Wolf, AB and Fu, W and Li, L and Akey, JM}, title = {Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals.}, journal = {Cell}, volume = {180}, number = {4}, pages = {677-687.e16}, doi = {10.1016/j.cell.2020.01.012}, pmid = {32004458}, issn = {1097-4172}, support = {R01 GM110068/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Black People/*genetics ; *Evolution, Molecular ; Gene Flow ; Human Migration ; Humans ; Models, Genetic ; Neanderthals/*genetics ; Pedigree ; Polymorphism, Genetic ; }, abstract = {Admixture has played a prominent role in shaping patterns of human genomic variation, including gene flow with now-extinct hominins like Neanderthals and Denisovans. Here, we describe a novel probabilistic method called IBDmix to identify introgressed hominin sequences, which, unlike existing approaches, does not use a modern reference population. We applied IBDmix to 2,504 individuals from geographically diverse populations to identify and analyze Neanderthal sequences segregating in modern humans. Strikingly, we find that African individuals carry a stronger signal of Neanderthal ancestry than previously thought. We show that this can be explained by genuine Neanderthal ancestry due to migrations back to Africa, predominately from ancestral Europeans, and gene flow into Neanderthals from an early dispersing group of humans out of Africa. Our results refine our understanding of Neanderthal ancestry in African and non-African populations and demonstrate that remnants of Neanderthal genomes survive in every modern human population studied to date.}, }
@article {pmid32001636, year = {2020}, author = {Price, M}, title = {Africans, too, carry Neanderthal genetic legacy.}, journal = {Science (New York, N.Y.)}, volume = {367}, number = {6477}, pages = {497}, doi = {10.1126/science.367.6477.497}, pmid = {32001636}, issn = {1095-9203}, mesh = {Africa ; Animals ; Black People/*genetics ; Europe ; Fossils ; *Gene Flow ; Humans ; Neanderthals/*genetics ; }, }
@article {pmid31988114, year = {2020}, author = {Kolobova, KA and Roberts, RG and Chabai, VP and Jacobs, Z and Krajcarz, MT and Shalagina, AV and Krivoshapkin, AI and Li, B and Uthmeier, T and Markin, SV and Morley, MW and O'Gorman, K and Rudaya, NA and Talamo, S and Viola, B and Derevianko, AP}, title = {Archaeological evidence for two separate dispersals of Neanderthals into southern Siberia.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {6}, pages = {2879-2885}, pmid = {31988114}, issn = {1091-6490}, mesh = {Animals ; *Archaeology ; Caves ; Fossils/history ; History, Ancient ; Neanderthals/*genetics ; Siberia ; }, abstract = {Neanderthals were once widespread across Europe and western Asia. They also penetrated into the Altai Mountains of southern Siberia, but the geographical origin of these populations and the timing of their dispersal have remained elusive. Here we describe an archaeological assemblage from Chagyrskaya Cave, situated in the Altai foothills, where around 90,000 Middle Paleolithic artifacts and 74 Neanderthal remains have been recovered from deposits dating to between 59 and 49 thousand years ago (age range at 95.4% probability). Environmental reconstructions suggest that the Chagyrskaya hominins were adapted to the dry steppe and hunted bison. Their distinctive toolkit closely resembles Micoquian assemblages from central and eastern Europe, including the northern Caucasus, more than 3,000 kilometers to the west of Chagyrskaya Cave. At other Altai sites, evidence of earlier Neanderthal populations lacking associated Micoquian-like artifacts implies two or more Neanderthal incursions into this region. We identify eastern Europe as the most probable ancestral source region for the Chagyrskaya toolmakers, supported by DNA results linking the Neanderthal remains with populations in northern Croatia and the northern Caucasus, and providing a rare example of a long-distance, intercontinental population movement associated with a distinctive Paleolithic toolkit.}, }
@article {pmid31975170, year = {2020}, author = {Hubisz, M and Siepel, A}, title = {Inference of Ancestral Recombination Graphs Using ARGweaver.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2090}, number = {}, pages = {231-266}, pmid = {31975170}, issn = {1940-6029}, mesh = {Algorithms ; Animals ; Computational Biology/*methods ; Genetics, Population ; Markov Chains ; Models, Genetic ; Mutation ; Neanderthals/*genetics ; *Recombination, Genetic ; Selection, Genetic ; }, abstract = {This chapter describes the usage of the program ARGweaver, which estimates the ancestral recombination graph for as many as about 100 genome sequences. The ancestral recombination graph is a detailed description of the coalescence and recombination events that define the relationships among the sampled sequences. This rich description is useful for a wide variety of population genetic analyses. We describe the preparation of data and major considerations for running ARGweaver, as well as the interpretation of results. We then demonstrate an analysis using the DARC (Duffy) gene as an example, and show how ARGweaver can be used to detect signatures of natural selection and Neandertal introgression, as well as to estimate the dates of mutation events. This chapter provides sufficient detail to get a new user up and running with this complex but powerful analysis tool.}, }
@article {pmid31940356, year = {2020}, author = {Villa, P and Soriano, S and Pollarolo, L and Smriglio, C and Gaeta, M and D'Orazio, M and Conforti, J and Tozzi, C}, title = {Neandertals on the beach: Use of marine resources at Grotta dei Moscerini (Latium, Italy).}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0226690}, pmid = {31940356}, issn = {1932-6203}, mesh = {Animal Shells ; Animals ; *Aquatic Organisms ; Archaeology ; Bivalvia/anatomy &amp; histology ; Italy ; *Neanderthals ; Silicates ; *Tool Use Behavior ; }, abstract = {Excavated in 1949, Grotta dei Moscerini, dated MIS 5 to early MIS 4, is one of two Italian Neandertal sites with a large assemblage of retouched shells (n = 171) from 21 layers. The other occurrence is from the broadly contemporaneous layer L of Grotta del Cavallo in southern Italy (n = 126). Eight other Mousterian sites in Italy and one in Greece also have shell tools but in a very small number. The shell tools are made on valves of the smooth clam Callista chione. The general idea that the valves of Callista chione were collected by Neandertals on the beach after the death of the mollusk is incomplete. At Moscerini 23.9% of the specimens were gathered directly from the sea floor as live animals by skin diving Neandertals. Archaeological data from sites in Italy, France and Spain confirm that shell fishing and fresh water fishing was a common activity of Neandertals, as indicated by anatomical studies recently published by E. Trinkaus. Lithic analysis provides data to show the relation between stone tools and shell tools. Several layers contain pumices derived from volcanic eruptions in the Ischia Island or the Campi Flegrei (prior to the Campanian Ignimbrite mega-eruption). Their rounded edges indicate that they were transported by sea currents to the beach at the base of the Moscerini sequence. Their presence in the occupation layers above the beach is discussed. The most plausible hypothesis is that they were collected by Neandertals. Incontrovertible evidence that Neandertals collected pumices is provided by a cave in Liguria. Use of pumices as abraders is well documented in the Upper Paleolithic. We prove that the exploitation of submerged aquatic resources and the collection of pumices common in the Upper Paleolithic were part of Neandertal behavior well before the arrival of modern humans in Western Europe.}, }
@article {pmid31935281, year = {2020}, author = {Gouy, A and Excoffier, L}, title = {Polygenic Patterns of Adaptive Introgression in Modern Humans Are Mainly Shaped by Response to Pathogens.}, journal = {Molecular biology and evolution}, volume = {37}, number = {5}, pages = {1420-1433}, doi = {10.1093/molbev/msz306}, pmid = {31935281}, issn = {1537-1719}, mesh = {Adaptation, Biological/*genetics ; *Genetic Introgression ; Host-Pathogen Interactions/*genetics ; Humans ; Melanesia ; *Multifactorial Inheritance ; *Selection, Genetic ; }, abstract = {Anatomically modern humans carry many introgressed variants from other hominins in their genomes. Some of them affect their phenotype and can thus be negatively or positively selected. Several individual genes have been proposed to be the subject of adaptive introgression, but the possibility of polygenic adaptive introgression has not been extensively investigated yet. In this study, we analyze archaic introgression maps with refined functional enrichment methods to find signals of polygenic adaptation of introgressed variants. We first apply a method to detect sets of connected genes (subnetworks) within biological pathways that present higher-than-expected levels of archaic introgression. We then introduce and apply a new statistical test to distinguish between epistatic and independent selection in gene sets of present-day humans. We identify several known targets of adaptive introgression, and we show that they belong to larger networks of introgressed genes. After correction for genetic linkage, we find that signals of polygenic adaptation are mostly explained by independent and potentially sequential selection episodes. However, we also find some gene sets where introgressed variants present significant signals of epistatic selection. Our results confirm that archaic introgression has facilitated local adaptation, especially in immunity related and metabolic functions and highlight its involvement in a coordinated response to pathogens out of Africa.}, }
@article {pmid31889305, year = {2020}, author = {Gómez-Olivencia, A and López-Onaindia, D and Sala, N and Balzeau, A and Pantoja-Pérez, A and Arganda-Carreras, I and Arlegi, M and Rios-Garaizar, J and Gómez-Robles, A}, title = {The human remains from Axlor (Dima, Biscay, northern Iberian Peninsula).}, journal = {American journal of physical anthropology}, volume = {172}, number = {3}, pages = {475-491}, doi = {10.1002/ajpa.23989}, pmid = {31889305}, issn = {1096-8644}, mesh = {Adult ; Animals ; Anthropology, Physical ; Child ; *Fossils ; History, Ancient ; Humans ; Neanderthals ; Skull/*anatomy &amp; histology ; Spain ; Tooth/*anatomy &amp; histology ; }, abstract = {OBJECTIVES: We provide the description and comparative analysis of all the human fossil remains found at Axlor during the excavations carried out by J. M. de Barandiarán from 1967 to 1974: a cranial vault fragment and seven teeth, five of which likely belonged to the same individual, although two are currently lost. Our goal is to describe in detail all these human remains and discuss both their taxonomic attribution and their stratigraphic context.<br><br>MATERIALS AND METHODS: We describe external and internal anatomy, and use classic and geometric morphometrics. The teeth from Axlor are compared to Neandertals, Upper Paleolithic, and recent modern humans.<br><br>RESULTS: Two teeth (a left dm[2] , a left di[1]) and the parietal fragment show morphological features consistent with a Neandertal classification, and were found in an undisturbed Mousterian context. The remaining three teeth (plus the two lost ones), initially classified as Neandertals, show morphological features and a general size that are more compatible with their classification as modern humans.<br><br>DISCUSSION: A left parietal fragment (Level VIII) from a single probably adult Neandertal individual was recovered during the old excavations performed by Barandiar&#xe1;n. Additionally, two different Neandertal children lost deciduous teeth during the formations of levels V (left di[1]) and IV (right dm[2]). In addition, a modern human individual is represented by five remains (two currently lost) from a complex stratigraphic setting. Some of the morphological features of these remains suggest that they may represent one of the scarce examples of Upper Paleolithic modern human remains in the northern Iberian Peninsula, which should be confirmed by direct dating.}, }
@article {pmid31809748, year = {2019}, author = {Wall, JD and Ratan, A and Stawiski, E and , }, title = {Identification of African-Specific Admixture between Modern and Archaic Humans.}, journal = {American journal of human genetics}, volume = {105}, number = {6}, pages = {1254-1261}, pmid = {31809748}, issn = {1537-6605}, support = {P30 CA044579/CA/NCI NIH HHS/United States ; R01 GM115433/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Black People/*genetics ; *Fossils ; Gene Pool ; *Genetics, Population ; *Genome, Human ; Hominidae/*genetics ; Humans ; Neanderthals/*genetics ; }, abstract = {Recent work has demonstrated that two archaic human groups (Neanderthals and Denisovans) interbred with modern humans and contributed to the contemporary human gene pool. These findings relied on the availability of high-coverage genomes from both Neanderthals and Denisovans. Here we search for evidence of archaic admixture from a worldwide panel of 1,667 individuals using an approach that does not require the presence of an archaic human reference genome. We find no evidence for archaic admixture in the Andaman Islands, as previously claimed, or on the island of Flores, where Homo floresiensis fossils have been found. However, we do find evidence for at least one archaic admixture event in sub-Saharan Africa, with the strongest signal in Khoesan and Pygmy individuals from Southern and Central Africa. The locations of these putative archaic admixture tracts are weighted against functional regions of the genome, consistent with the long-term effects of purifying selection against introgressed genetic material.}, }
@article {pmid31797875, year = {2019}, author = {Mallol, C and Hernández, C and Mercier, N and Falguères, C and Carrancho, &#xc1; and Cabanes, D and Vidal-Matutano, P and Connolly, R and Pérez, L and Mayor, A and Ben Arous, E and Galván, B}, title = {Fire and brief human occupations in Iberia during MIS 4: Evidence from Abric del Pastor (Alcoy, Spain).}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {18281}, pmid = {31797875}, issn = {2045-2322}, mesh = {Animals ; Archaeology ; Caves ; *Fires ; *Fossils ; Humans ; *Neanderthals ; Radiometric Dating ; Spain ; }, abstract = {There is a relatively low amount of Middle Paleolithic sites in Europe dating to MIS 4. Of the few that exist, several of them lack evidence for anthropogenic fire, raising the question of how this period of global cooling may have affected the Neanderthal population. The Iberian Peninsula is a key area to explore this issue, as it has been considered as a glacial refugium during critical periods of the Neanderthal timeline and might therefore yield archaeological contexts in which we can explore possible changes in the behaviour and settlement patterns of Neanderthal groups during MIS 4. Here we report recent data from Abric del Pastor, a small rock shelter in Alcoy (Alicante, Spain) with a stratified deposit containing Middle Palaeolithic remains. We present absolute dates that frame the sequence within MIS 4 and multi-proxy geoarchaeological evidence of in situ anthropogenic fire, including microscopic evidence of in situ combustion residues and thermally altered sediment. We also present archaeostratigraphic evidence of recurrent, functionally diverse, brief human occupation of the rock shelter. Our results suggest that Neanderthals occupied the Central Mediterranean coast of the Iberian Peninsula during MIS 4, that these Neanderthals were not undergoing climatic stress and they were habitual fire users.}, }
@article {pmid31797354, year = {2020}, author = {Karban, ME}, title = {Occipital hemi-bun development and shape covariation in a longitudinal extant human growth sample.}, journal = {American journal of physical anthropology}, volume = {172}, number = {1}, pages = {123-134}, doi = {10.1002/ajpa.23981}, pmid = {31797354}, issn = {1096-8644}, mesh = {Adolescent ; Canada ; Child ; Child, Preschool ; Female ; Humans ; Male ; Occipital Bone/*anatomy &amp; histology/growth &amp; development ; United States ; Young Adult ; }, abstract = {OBJECTIVES: Although the homology of the Neanderthal occipital bun and anatomically modern human "hemi-bun" has long been debated, little is known about the developmental timing and patterning of these two patterns of prominent occipital squama convexity. In this study, occipital hemi-bun ontogeny and cranial shape covariation are assessed in a comparative extant human sample.<br><br>MATERIALS AND METHODS: Two-dimensional geometric morphometric methods were used to investigate hemi-bun development in a longitudinal sample of growth study cephalograms representing extant human subjects predominantly of European ancestry. Subjects were each measured at three distinct age points, ranging from 3.0 to 20.4&#x2009;years, and two-block partial least squares analysis was used to assess patterns of covariation between midsagittal occipital bone morphology and other aspects of craniofacial shape.<br><br>RESULTS: Occipital hemi-bun morphology, when present, was found to develop early in ontogeny, in association with anteroposterior elongation of the frontal and parietal bones. No significant pattern of covariation was found between occipital hemi-bun shape and cranial/basicranial breadth, basicranial length, basicranial angle, or midfacial prognathism.<br><br>DISCUSSION: This study suggests that the occipital hemi-bun, at least in this extant human population, should not be considered an independent trait, as its development is closely linked to shape variation in the frontal and parietal bones. Importantly, these results suggest that occipital hemi-bun morphology is not significantly influenced by basicranial morphology during development, but instead covaries with changes in midsagittal neurocranial vault shape.}, }
@article {pmid31774843, year = {2019}, author = {Vaesen, K and Scherjon, F and Hemerik, L and Verpoorte, A}, title = {Inbreeding, Allee effects and stochasticity might be sufficient to account for Neanderthal extinction.}, journal = {PloS one}, volume = {14}, number = {11}, pages = {e0225117}, pmid = {31774843}, issn = {1932-6203}, mesh = {Animals ; Biological Evolution ; Extinction, Biological ; Female ; Humans ; *Inbreeding ; Models, Biological ; Neanderthals/*physiology ; Stochastic Processes ; }, abstract = {The replacement of Neanderthals by Anatomically Modern Humans has typically been attributed to environmental pressure or a superiority of modern humans with respect to competition for resources. Here we present two independent models that suggest that no such heatedly debated factors might be needed to account for the demise of Neanderthals. Starting from the observation that Neanderthal populations already were small before the arrival of modern humans, the models implement three factors that conservation biology identifies as critical for a small population's persistence, namely inbreeding, Allee effects and stochasticity. Our results indicate that the disappearance of Neanderthals might have resided in the smallness of their population(s) alone: even if they had been identical to modern humans in their cognitive, social and cultural traits, and even in the absence of inter-specific competition, Neanderthals faced a considerable risk of extinction. Furthermore, we suggest that if modern humans contributed to the demise of Neanderthals, that contribution might have had nothing to do with resource competition, but rather with how the incoming populations geographically restructured the resident populations, in a way that reinforced Allee effects, and the effects of inbreeding and stochasticity.}, }
@article {pmid31774826, year = {2019}, author = {Krueger, KL and Willman, JC and Matthews, GJ and Hublin, JJ and Pérez-Pérez, A}, title = {Anterior tooth-use behaviors among early modern humans and Neandertals.}, journal = {PloS one}, volume = {14}, number = {11}, pages = {e0224573}, pmid = {31774826}, issn = {1932-6203}, mesh = {Animals ; Anthropology, Physical ; Behavior/*physiology ; Biomechanical Phenomena ; Ecosystem ; Fossils/*anatomy &amp; histology ; Humans ; Incisor/*anatomy &amp; histology/diagnostic imaging/physiology ; Mastication/physiology ; Neanderthals/*anatomy &amp; histology/physiology ; Surface Properties ; Tooth Wear/diagnostic imaging/*etiology ; }, abstract = {Early modern humans (EMH) are often touted as behaviorally advanced to Neandertals, with more sophisticated technologies, expanded resource exploitation, and more complex clothing production. However, recent analyses have indicated that Neandertals were more nuanced in their behavioral adaptations, with the production of the Châtelperronian technocomplex, the processing and cooking of plant foods, and differences in behavioral adaptations according to habitat. This study adds to this debate by addressing the behavioral strategies of EMH (n = 30) within the context of non-dietary anterior tooth-use behaviors to glean possible differences between them and their Neandertal (n = 45) counterparts. High-resolution casts of permanent anterior teeth were used to collect microwear textures of fossil and comparative bioarchaeological samples using a Sensofar white-light confocal profiler with a 100x objective lens. Labial surfaces were scanned, totaling a work envelope of 204 x 276 μm for each individual. The microwear textures were examined for post-mortem damage and uploaded to SSFA software packages for surface characterization. Statistical analyses were performed to examine differences in central tendencies and distributions of anisotropy and textural fill volume variables among the EMH sample itself by habitat, location, and time interval, and between the EMH and Neandertal samples by habitat and location. Descriptive statistics for the EMH sample were compared to seven bioarchaeological samples (n = 156) that utilized different tooth-use behaviors to better elucidate specific activities that may have been performed by EMH. Results show no significant differences between the means within the EMH sample by habitat, location, or time interval. Furthermore, there are no significant differences found here between EMH and Neandertals. Comparisons to the bioarchaeological samples suggest both fossil groups participated in clamping and grasping activities. These results indicate that EMH and Neandertals were similar in their non-dietary anterior tooth-use behaviors and provide additional evidence for overlapping behavioral strategies employed by these two hominins.}, }
@article {pmid31765984, year = {2020}, author = {Garralda, MD and Maureille, B and Le Cabec, A and Oxilia, G and Benazzi, S and Skinner, MM and Hublin, JJ and Vandermeersch, B}, title = {The Neanderthal teeth from Marillac (Charente, Southwestern France): Morphology, comparisons and paleobiology.}, journal = {Journal of human evolution}, volume = {138}, number = {}, pages = {102683}, doi = {10.1016/j.jhevol.2019.102683}, pmid = {31765984}, issn = {1095-8606}, support = {724046/ERC_/European Research Council/International ; }, mesh = {Animals ; Archaeology ; Fossils/*anatomy &amp; histology ; France ; Neanderthals/*anatomy &amp; histology ; Tooth/*anatomy &amp; histology ; }, abstract = {Few European sites have yielded human dental remains safely dated to the end of MIS 4/beginning of MIS 3. One of those sites is Marillac (Southwestern France), a collapsed karstic cave where archeological excavations (1967-1980) conducted by B. Vandermeersch unearthed numerous faunal and human remains, as well as a few Mousterian Quina tools. The Marillac sinkhole was occasionally used by humans to process the carcasses of different prey, but there is no evidence for a residential use of the site, nor have any hearths been found. Rare carnivore bones were also discovered, demonstrating that the sinkhole was seasonally used, not only by Neanderthals, but also by predators across several millennia. The lithostratigraphic units containing the human remains were dated to ∼60 kyr. The fossils consisted of numerous fragments of skulls and jaws, isolated teeth and several post-cranial bones, many of them with traces of perimortem manipulations. For those already published, their morphological characteristics and chronostratigraphic context allowed their attribution to Neanderthals. This paper analyzes sixteen unpublished human teeth (fourteen permanent and two deciduous) by investigating the external morphology and metrical variation with respect to other Neanderthal remains and a sample from modern populations. We also investigate their enamel thickness distribution in 2D and 3D, the enamel-dentine junction morphology (using geometric morphometrics) of one molar and two premolars, the roots and the possible expression of taurodontism, as well as pathologies and developmental defects. The anterior tooth use and paramasticatory activities are also discussed. Morphological and structural alterations were found on several teeth, and interpreted in light of human behavior (tooth-pick) and carnivores' actions (partial digestion). The data are interpreted in the context of the available information for the Eurasian Neanderthals.}, }
@article {pmid31710710, year = {2020}, author = {Rmoutilová, R and Gómez-Olivencia, A and Brůžek, J and Holliday, T and Ledevin, R and Couture-Veschambre, C and Madelaine, S and Džupa, V and Velemínská, J and Maureille, B}, title = {A case of marked bilateral asymmetry in the sacral alae of the Neandertal specimen Regourdou 1 (Périgord, France).}, journal = {American journal of physical anthropology}, volume = {171}, number = {2}, pages = {242-259}, doi = {10.1002/ajpa.23968}, pmid = {31710710}, issn = {1096-8644}, support = {ANR-10-LABX-52//French National Research Agency/International ; 1088217//Agency of Charles University/International ; //Irene Levi Sala CARE Archaeological Foundation/International ; //Leakey Foundation/International ; LEQSF(2015-18)-RD-A-22//Louisiana Board of Regents/International ; PGC2018-093925-B-C33//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/International ; CGL2015-65387-C3-2-P//Ministerio de Econom&#xed;a y Competitividad/International ; 2016-1R40240-00007349-00007350//R&#xe9;gion Nouvelle Aquitaine/International ; 1044-16//Universidad del Pa&#xed;s Vasco/Euskal Herriko Unibertsitatea/International ; IT1418-19//Eusko Jaurlaritza-Gobierno Vasco/International ; }, mesh = {Animals ; Fossils/*anatomy &amp; histology ; France ; Neanderthals/*abnormalities ; Sacrum/*abnormalities ; }, abstract = {OBJECTIVES: A marked asymmetry was previously reported in the sacral alae and S1-L5 facets orientation of the Neandertal individual Regourdou 1. Here, we provide a detailed description and quantification of the morphology and degree of asymmetry of this sacrum.<br><br>MATERIAL AND METHODS: Regourdou 1 was compared to a modern human sample composed of 24 females and 17 males, and to other Neandertal individuals. Both traditional and geometric morphometric analyses were used in order to quantify the degree of sacral asymmetry of Regourdou 1.<br><br>RESULTS: The asymmetry of both sacral alae and facets orientation substantially exceeds directional and absolute asymmetry of the healthy modern sample. Regourdou 1 shows a considerably shorter right ala, which is absolutely and relatively outside of the modern and Neandertal variations.<br><br>CONCLUSION: Regourdou 1 shows marked sacral asymmetry that probably originated in early ontogenetic development. An asymmetric sacrum reflects asymmetric load dissipation and could relate to other morphological abnormalities observed in the skeleton, especially the mild scoliosis of the spine and the asymmetry of the femoral diaphyses. Further investigation is necessary to elucidate the relationship between those morphologies as well as a potential impact on the life of the individual.}, }
@article {pmid31702050, year = {2020}, author = {Gokcumen, O}, title = {Archaic hominin introgression into modern human genomes.}, journal = {American journal of physical anthropology}, volume = {171 Suppl 70}, number = {}, pages = {60-73}, doi = {10.1002/ajpa.23951}, pmid = {31702050}, issn = {1096-8644}, support = {1714867//United States National Science Foundation/International ; }, mesh = {Animals ; DNA/genetics ; *Gene Flow ; *Genetic Introgression ; *Genome, Human ; Hominidae/*genetics ; Humans ; Neanderthals/genetics ; }, abstract = {Ancient genomes from multiple Neanderthal and the Denisovan individuals, along with DNA sequence data from diverse contemporary human populations strongly support the prevalence of gene flow among different hominins. Recent studies now provide evidence for multiple gene flow events that leave genetic signatures in extant and ancient human populations. These events include older gene flow from an unknown hominin in Africa predating out-of-Africa migrations, and in the last 50,000-100,000 years, multiple gene flow events from Neanderthals into ancestral Eurasian human populations, and at least three distinct introgression events from a lineage close to Denisovans into ancestors of extant Southeast Asian and Oceanic populations. Some of these introgression events may have happened as late as 20,000 years before present and reshaped the way in which we think about human evolution. In this review, I aim to answer anthropologically relevant questions with regard to recent research on ancient hominin introgression in the human lineage. How have genomic data from archaic hominins changed our view of human evolution? Is there any doubt about whether introgression from ancient hominins to the ancestors of present-day humans occurred? What is the current view of human evolutionary history from the genomics perspective? What is the impact of introgression on human phenotypes?}, }
@article {pmid31701003, year = {2019}, author = {Rodríguez-Hidalgo, A and Morales, JI and Cebrià, A and Courtenay, LA and Fernández-Marchena, JL and García-Argudo, G and Marín, J and Saladié, P and Soto, M and Tejero, JM and Fullola, JM}, title = {The Châtelperronian Neanderthals of Cova Foradada (Calafell, Spain) used imperial eagle phalanges for symbolic purposes.}, journal = {Science advances}, volume = {5}, number = {11}, pages = {eaax1984}, pmid = {31701003}, issn = {2375-2548}, mesh = {Animals ; *Archaeology ; Fossils ; Geography ; Humans ; *Neanderthals ; Spain ; }, abstract = {Evidence for the symbolic behavior of Neanderthals in the use of personal ornaments is relatively scarce. Among the few ornaments documented, eagle talons, which were presumably used as pendants, are the most frequently recorded. This phenomenon appears concentrated in a specific area of southern Europe during a span of 80 thousand years. Here, we present the analysis of one eagle pedal phalange recovered from the Châtelperronian layer of Foradada Cave (Spain). Our research broadens the known geographical and temporal range of this symbolic behavior, providing the first documentation of its use among the Iberian populations, as well as of its oldest use in the peninsula. The recurrent appearance of large raptor talons throughout the Middle Paleolithic time frame, including their presence among the last Neanderthal populations, raises the question of the survival of some cultural elements of the Middle Paleolithic into the transitional Middle to Upper Paleolithic assemblages and beyond.}, }
@article {pmid31675491, year = {2019}, author = {Kozowyk, PRB and Poulis, JA}, title = {A new experimental methodology for assessing adhesive properties shows that Neandertals used the most suitable material available.}, journal = {Journal of human evolution}, volume = {137}, number = {}, pages = {102664}, doi = {10.1016/j.jhevol.2019.102664}, pmid = {31675491}, issn = {1095-8606}, mesh = {Adhesives/*chemistry ; Animals ; Archaeology/instrumentation/*methods ; Fossils ; Hardness ; *Neanderthals ; Rheology ; Technology ; Thermogravimetry ; }, abstract = {The use of adhesives for hafting stone tools at least 191 ka was a major technological development. Stone tools could be more securely attached to handles, thus improving their efficiency and practicality. To produce functional adhesives required forethought and planning, as well as expertise and knowledge of the resources available in the landscape. This makes adhesives important in discussions about Neandertal and early modern human technological and mental capabilities. However, we currently know very little about how these early adhesive materials behaved under different circumstances, or why certain materials were used and others were not. Here we present the results of controlled laboratory bulk property tests (hardness, rheology and thermogravimetric analysis) on replica Paleolithic adhesives. We conclude that birch tar is more versatile, has better working properties, and is more reusable than pine resin, the most likely alternative material. Neandertals may therefore have invested more time and resources to produce birch tar because it was the best material available, both functionally and economically, throughout the majority of Europe during the Middle to Late Pleistocene. Our results further demonstrate that Neandertals had high levels of technological expertise and knowledge of the natural resources available to them in their environment.}, }
@article {pmid31651929, year = {2019}, author = {Abdelhady, AA and Elewa, AMT and El-Dawy, MH}, title = {The position of Neandertal and Homo erectus within the hominid clade based on craniodental morphology and whole mtDNA genomes.}, journal = {Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen}, volume = {70}, number = {4}, pages = {303-323}, doi = {10.1127/homo/2019/1119}, pmid = {31651929}, issn = {1618-1301}, mesh = {Animals ; Anthropology, Physical ; Biological Evolution ; DNA, Mitochondrial/genetics ; Female ; *Genome, Mitochondrial/genetics ; *Hominidae/anatomy &amp; histology/classification/genetics ; Humans ; Male ; *Neanderthals/anatomy &amp; histology/classification/genetics ; Phylogeny ; Skull/*anatomy &amp; histology ; Tooth/*anatomy &amp; histology ; }, abstract = {To evaluate the taxonomic position of the Neandertal and Homo erectus within the hominid clade, the variation among and within the hominid taxa was assessed based on the craniodental morphology and integrated with molecular analyses of the whole mtDNA genomes. Ordination and clustering of the Procrustes craniodental landmarks have showed a notable shape transformation from the earliest hominid species to the modern humans. Although levels of distinction between the analyzed taxa (Homo, Pan, Gorilla, and Pongo) are generally corresponding to probable expectations based on their taxonomic rank, few exceptions were found. Notably, the craniodental morphology of Homo erectus showed a greater dissimilarity to other Homo species, where it consistently overlapped or grouped with Pan species on all ordination plots and clustering. In addition, the direct link between European humans and Neandertals, which is well-characterized on all of the phylogenetic trees based on maximum parsimony and maximum likelihood methods, was not outlined in the morphologic-based clustering. Both morphological and molecular distances between Neandertal and modern humans were consistently greater than the distances among modern humans, however, the distances are still smaller than those between any two distinct species (so they are subspecies). The topology of the phylogenetic trees based on the whole mtDNA has shown a minor discrepancy with the results obtained from the craniodental morphologies.}, }
@article {pmid31637998, year = {2019}, author = {Delgobo, M and Mendes, DA and Kozlova, E and Rocha, EL and Rodrigues-Luiz, GF and Mascarin, L and Dias, G and Patrício, DO and Dierckx, T and Bicca, MA and Bretton, G and Tenório de Menezes, YK and Starick, MR and Rovaris, D and Del Moral, J and Mansur, DS and Van Weyenbergh, J and Báfica, A}, title = {An evolutionary recent IFN/IL-6/CEBP axis is linked to monocyte expansion and tuberculosis severity in humans.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {31637998}, issn = {2050-084X}, support = {G0D6817N//FWO/International ; Global Research Initiative Program TW008276/NH/NIH HHS/United States ; Early Career Scientist 55007412/HHMI/Howard Hughes Medical Institute/United States ; VLAIO IWT141614//Fonds Wetenschappelijk Onderzoek/International ; 23038.010048/2013-27//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/International ; PQ//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/International ; G0D6817N//Fonds Wetenschappelijk Onderzoek/International ; 23038.010048/2013-27//CAPES/International ; R01 TW008276/TW/FIC NIH HHS/United States ; }, mesh = {Antigens, CD34 ; CCAAT-Enhancer-Binding Proteins/genetics/*metabolism ; Cell Differentiation ; Cell Proliferation ; Cytokines/genetics/metabolism ; Genome-Wide Association Study ; Humans ; Hydrolases ; Interferons/genetics/*metabolism ; Interleukin-6/genetics/*metabolism ; Macrophages/microbiology ; Monocytes/*metabolism/microbiology ; Mycobacterium tuberculosis/*immunology/pathogenicity ; Myeloid Cells/physiology ; Proteomics ; Receptors, Interleukin-6 ; Severity of Illness Index ; Transcriptome ; Tuberculosis/*immunology/metabolism ; }, abstract = {Monocyte counts are increased during human tuberculosis (TB) but it has not been determined whether Mycobacterium tuberculosis (Mtb) directly regulates myeloid commitment. We demonstrated that exposure to Mtb directs primary human CD34[+] cells to differentiate into monocytes/macrophages. In vitro myeloid conversion did not require type I or type II IFN signaling. In contrast, Mtb enhanced IL-6 responses by CD34[+] cell cultures and IL-6R neutralization inhibited myeloid differentiation and decreased mycobacterial growth in vitro. Integrated systems biology analysis of transcriptomic, proteomic and genomic data of large data sets of healthy controls and TB patients established the existence of a myeloid IL-6/IL6R/CEBP gene module associated with disease severity. Furthermore, genetic and functional analysis revealed the IL6/IL6R/CEBP gene module has undergone recent evolutionary selection, including Neanderthal introgression and human pathogen adaptation, connected to systemic monocyte counts. These results suggest Mtb co-opts an evolutionary recent IFN-IL6-CEBP feed-forward loop, increasing myeloid differentiation linked to severe TB in humans.}, }
@article {pmid31636186, year = {2019}, author = {Niekus, MJLT and Kozowyk, PRB and Langejans, GHJ and Ngan-Tillard, D and van Keulen, H and van der Plicht, J and Cohen, KM and van Wingerden, W and van Os, B and Smit, BI and Amkreutz, LWSW and Johansen, L and Verbaas, A and Dusseldorp, GL}, title = {Middle Paleolithic complex technology and a Neandertal tar-backed tool from the Dutch North Sea.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {44}, pages = {22081-22087}, pmid = {31636186}, issn = {1091-6490}, mesh = {Adhesives ; Animals ; *Archaeology ; Humans ; Neanderthals ; Netherlands ; Technology ; *Tool Use Behavior ; X-Ray Microtomography ; }, abstract = {We report the discovery of a 50,000-y-old birch tar-hafted flint tool found off the present-day coastline of The Netherlands. The production of adhesives and multicomponent tools is considered complex technology and has a prominent place in discussions about the evolution of human behavior. This find provides evidence on the technological capabilities of Neandertals and illuminates the currently debated conditions under which these technologies could be maintained. [14]C-accelerator mass spectrometry dating and the geological provenance of the artifact firmly associates it with a host of Middle Paleolithic stone tools and a Neandertal fossil. The find was analyzed using pyrolysis-gas chromatography-mass spectrometry, X-ray micro-computed tomography, and optical light microscopy. The object is a piece of birch tar, encompassing one-third of a flint flake. This find is from northwestern Europe and complements a small set of well-dated and chemically identified adhesives from Middle Paleolithic/Middle Stone Age contexts. Together with data from experiments and other Middle Paleolithic adhesives, it demonstrates that Neandertals mastered complex adhesive production strategies and composite tool use at the northern edge of their range. Thus, a large population size is not a necessary condition for complex behavior and technology. The mitigation of ecological risk, as demonstrated by the challenging conditions during Marine Isotope Stage 4 and 3, provides a better explanation for the transmission and maintenance of technological complexity.}, }
@article {pmid31629539, year = {2021}, author = {Borgel, S and Latimer, B and McDermott, Y and Sarig, R and Pokhojaev, A and Abulafia, T and Goder-Goldberger, M and Barzilai, O and May, H}, title = {Early Upper Paleolithic human foot bones from Manot Cave, Israel.}, journal = {Journal of human evolution}, volume = {160}, number = {}, pages = {102668}, doi = {10.1016/j.jhevol.2019.102668}, pmid = {31629539}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; Caves ; Foot Bones ; Fossils ; Humans ; Israel ; *Neanderthals ; }, abstract = {The transition from the Middle Paleolithic to the Upper Paleolithic in the Levant represents a major event in human prehistory with regards to the dispersal of modern human populations. Unfortunately, the scarcity of human remains from this period has hampered our ability to study the anatomy of Upper Paleolithic populations. This study describes and examines pedal bones recovered from the Early Upper Paleolithic period at Manot Cave, Israel, from 2014 to 2017. The Manot Cave foot bones include a partial, left foot skeleton comprising a talus, a calcaneus, a cuboid, a first metatarsal, a second metatarsal, a fifth metatarsal, and a hallucal sesamoid. All these remains were found in the same archaeological unit of the cave and belong to a young adult. Shape and size comparisons with Neanderthals, Anatomically Modern Human and modern human foot bones indicate a modern human morphology. In some characteristics, however, the Manot Cave foot bones display a Neanderthal-like pattern. Notably, the Manot Cave foot is remarkable in its overall gracility. A healed traumatic injury in the second metatarsal (Lisfranc's fracture) is most likely due to a remote impact to the dorsum of the foot. This injury, its subsequent debility, and the individual's apparent recovery suggest that the members of the Manot Cave community had a supportive environment, one with mutual responsibilities among the members.}, }
@article {pmid31621987, year = {2019}, author = {Tryon, CA}, title = {The Middle/Later Stone Age transition and cultural dynamics of late Pleistocene East Africa.}, journal = {Evolutionary anthropology}, volume = {28}, number = {5}, pages = {267-282}, doi = {10.1002/evan.21802}, pmid = {31621987}, issn = {1520-6505}, mesh = {Africa, Eastern ; Animals ; *Archaeology ; *Biological Evolution ; *Cultural Evolution ; History, Ancient ; Humans ; Neanderthals ; Technology/history ; Tool Use Behavior ; }, abstract = {The Middle to Later Stone Age (MSA/LSA) transition is a prominent feature of the African archeological record that began in some places ~30,000-60,000 years ago, historically associated with the origin and/or dispersal of "modern" humans. Unlike the analogous Middle to Upper Paleolithic transition in Eurasia and associated Neanderthal extinction, the African MSA/LSA record remains poorly documented, with its potential role in explaining changes in the behavioral diversity and geographic range of Homo sapiens largely unexplored. I review archeological and biogeographic data from East Africa, show regionally diverse pathways to the MSA/LSA transition, and emphasize the need for analytical approaches that document potential ancestor-descendent relationships visible in the archeological record, needed to assess independent invention, population interaction, dispersal, and other potential mechanisms for behavioral change. Diversity within East Africa underscores the need for regional, rather than continental-scale narratives of the later evolutionary history of H. sapiens.}, }
@article {pmid31611012, year = {2021}, author = {Sarig, R and Fornai, C and Pokhojaev, A and May, H and Hans, M and Latimer, B and Barzilai, O and Quam, R and Weber, GW}, title = {The dental remains from the Early Upper Paleolithic of Manot Cave, Israel.}, journal = {Journal of human evolution}, volume = {160}, number = {}, pages = {102648}, doi = {10.1016/j.jhevol.2019.102648}, pmid = {31611012}, issn = {1095-8606}, support = {176319/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Animals ; Caves ; *Fossils ; Humans ; Israel ; *Neanderthals ; Tooth, Deciduous ; }, abstract = {This study presents the dental remains discovered at Manot Cave (MC), Western Galilee, Israel. The cave contains evidence for human occupation during the Early Upper Paleolithic period (46-33 ka) mainly of Early Ahmarian (∼46-42 ka) and Levantine Aurignacian (∼38-34 ka) cultural levels. Six teeth (three deciduous and three permanent) were found at the site, of which four could be thoroughly analyzed. The morphology of the teeth was qualitatively described and analyzed using traditional and geometric morphometric methods. A large comparative sample was used in order to assess the morphological affiliation of the Manot specimens with other Homo groups. The results provided equivocal signals: the upper first premolar (MC-9 P[3]) is probably modern human; the upper deciduous second molar (MC-10 dm[2]) and the upper second permanent molar (MC-8 M[2]) might be modern humans; the lower second deciduous molar (MC-7 dm2) might be Neanderthal. Owing to the small sample size and the almost total lack of distinctive characteristics, our outcome could not supply conclusive evidence to address the question of whether Manot Aurignacian population came from Europe or descended from the local Ahmarian population.}, }
@article {pmid31591491, year = {2019}, author = {Colbran, LL and Gamazon, ER and Zhou, D and Evans, P and Cox, NJ and Capra, JA}, title = {Inferred divergent gene regulation in archaic hominins reveals potential phenotypic differences.}, journal = {Nature ecology &amp; evolution}, volume = {3}, number = {11}, pages = {1598-1606}, pmid = {31591491}, issn = {2397-334X}, support = {T32 GM080178/GM/NIGMS NIH HHS/United States ; R01 GM115836/GM/NIGMS NIH HHS/United States ; R01 MH101820/MH/NIMH NIH HHS/United States ; R01 MH113362/MH/NIMH NIH HHS/United States ; R35 HG010718/HG/NHGRI NIH HHS/United States ; R01 MH090937/MH/NIMH NIH HHS/United States ; R35 GM127087/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Female ; Genome, Human ; Haplotypes ; *Hominidae ; Humans ; *Neanderthals ; Phenotype ; }, abstract = {Sequencing DNA derived from archaic bones has enabled genetic comparison of Neanderthals and anatomically modern humans (AMHs), and revealed that they interbred. However, interpreting what genetic differences imply about their phenotypic differences remains challenging. Here, we introduce an approach for identifying divergent gene regulation between archaic hominins, such as Neanderthals, and AMH sequences, and find 766 genes that are likely to have been divergently regulated (DR) by Neanderthal haplotypes that do not remain in AMHs. DR genes include many involved in phenotypes known to differ between Neanderthals and AMHs, such as the structure of the rib cage and supraorbital ridge development. They are also enriched for genes associated with spontaneous abortion, polycystic ovary syndrome, myocardial infarction and melanoma. Phenotypes associated with modern human variation in these genes' regulation in ~23,000 biobank patients further support their involvement in immune and cardiovascular phenotypes. Comparing DR genes between two Neanderthals and a Denisovan revealed divergence in the immune system and in genes associated with skeletal and dental morphology that are consistent with the archaeological record. These results establish differences in gene regulatory architecture between AMHs and archaic hominins, and provide an avenue for exploring phenotypic differences between archaic groups from genomic information alone.}, }
@article {pmid31589589, year = {2019}, author = {Eisová, S and Velemínský, P and Bruner, E}, title = {The Neanderthal endocast from Gánovce (Poprad, Slovak Republic).}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {96}, number = {}, pages = {139-149}, doi = {10.4436/JASS.97005}, pmid = {31589589}, issn = {2037-0644}, mesh = {Animals ; Brain/anatomy &amp; histology ; Hominidae/anatomy &amp; histology ; Humans ; Neanderthals/*anatomy &amp; histology/classification/physiology ; Paleontology ; Skull/*anatomy &amp; histology ; Slovakia ; }, abstract = {A Neanderthal endocast, naturally formed by travertine within the crater of a thermal spring, was found at Gánovce, near Poprad (Slovakia), in 1926, and dated to 105 ka. The endocast is partially covered by fragments of the braincase. The volume of the endocast was estimated to be 1320 cc. The endocast was first studied by the Czech paleoanthropologist Emanuel Vlček, who performed metric and morphological analyses which suggested its Neanderthal origin. Vlček published his works more than fifty years ago, but the fossil is scarcely known to the general paleoanthropological community, probably because of language barriers. Here, we review the historical and anatomical information available on the endocasts, providing additional paleoneurological assessments on its features. The endocast displays typical Neanderthal traits, and its overall appearance is similar to Guattari 1, mostly because of the pronounced frontal width and occipital bulging. The morphology of the Gánovce specimen suggests once more that the Neanderthal endocranial phenotype had already evolved at 100 ka.}, }
@article {pmid31586143, year = {2019}, author = {Sánchez-Hernández, C and Gourichon, L and Pubert, E and Rendu, W and Montes, R and Rivals, F}, title = {Combined dental wear and cementum analyses in ungulates reveal the seasonality of Neanderthal occupations in Covalejos Cave (Northern Iberia).}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {14335}, pmid = {31586143}, issn = {2045-2322}, mesh = {Animals ; *Biological Evolution ; Caves ; Dental Cementum/*chemistry/physiopathology ; Feeding Behavior/*physiology ; Fossils ; Neanderthals/*physiology ; Population Dynamics ; Seasons ; Tooth Wear/*physiopathology ; }, abstract = {We propose for the first time the use of the combination of two high-resolution techniques, dental wear (meso- and microwear) and dental cementum analyses, to gain a better understanding of Neanderthal subsistence strategies and occupational patterns. Dental wear analysis provides information not only on ungulate palaeodiet and palaeoenvironments but also on hunting time and seasons. Dental cementum analysis allows the accurate determination of the age and season at death of a prey. Our study has focused on the Cantabrian region and has applied both methods to investigate the Mousterian faunal assemblages in Covalejos Cave. Identification of the ungulate palaeodiet reveals information on the environmental conditions of the studied region. Moreover, it may facilitate observation on the evolution of both palaeodiet and palaeoenvironment throughout the site sequence. Results show a general stability in the palaeoenvironmental conditions and in the ungulate palaeodiet throughout the Mousterian sequence; this finding may be attributed to the role of the area as a climate refuge, and slight differences in levels 8, 7 and 4 suggest long- or short-term but repeated Neanderthal occupations at different seasons in the annual cycle.}, }
@article {pmid31569005, year = {2019}, author = {Conde-Valverde, M and Martínez, I and Quam, RM and Bonmatí, A and Lorenzo, C and Velez, AD and Martínez-Calvo, C and Arsuaga, JL}, title = {The cochlea of the Sima de los Huesos hominins (Sierra de Atapuerca, Spain): New insights into cochlear evolution in the genus Homo.}, journal = {Journal of human evolution}, volume = {136}, number = {}, pages = {102641}, doi = {10.1016/j.jhevol.2019.102641}, pmid = {31569005}, issn = {1095-8606}, mesh = {Animals ; *Biological Evolution ; Cochlea/*anatomy &amp; histology ; Fossils/*anatomy &amp; histology ; Hominidae/anatomy &amp; histology ; Neanderthals/*anatomy &amp; histology ; Spain ; }, abstract = {The cochlea contains taxonomic and phylogenetic information and its morphology is related with hearing abilities among fossil hominins. Data for the genus Homo is presently limited to early Homo and the early Neandertals from Krapina. The present study of the middle Pleistocene hominins from the Sima de los Huesos (SH) provides new evidence on cochlear evolution in the genus Homo. We compared the absolute length, proportional lengths of each turn, number of turns, size and shape of the cross-section of the basal turn, volume, curvature gradient, and thickness of the cochlea between extant Pan troglodytes, extant Homo sapiens, Homo neanderthalensis and the SH hominins. The SH hominins resemble P. troglodytes in the proportionally long basal turn, the small size and round shape of the cross-section of the basal turn, the small cochlear volume and the low cochlear thickness. The SH hominins resemble Neandertals and H. sapiens in their long cochlear length and in the proportionally short third turn. Homo neanderthalensis and H. sapiens share several features, not present in the SH hominins, and that likely represent homoplasies: a larger volume, larger size and oval shape of the cross-section of the basal turn and higher cochlear thickness. Later Neandertals show a derived proportionally shorter apical turn. Changes in cochlear volume in Homo cannot be fully explained by variation in body mass or cochlear length but are more directly related to changes in the cross-sectional area of the basal turn. Based on previous studies of the outer and middle ear in SH hominins, changes in the outer and middle ear preceded changes in the inner ear, and the cochlea and semicircular canals seem to have evolved independently in the Neandertal clade. Finally, the small cochlear volume in the SH hominins suggests a slightly higher upper limit of hearing compared with modern humans.}, }
@article {pmid31560950, year = {2019}, author = {Mata, X and Renaud, G and Mollereau, C}, title = {The repertoire of family A-peptide GPCRs in archaic hominins.}, journal = {Peptides}, volume = {122}, number = {}, pages = {170154}, doi = {10.1016/j.peptides.2019.170154}, pmid = {31560950}, issn = {1873-5169}, mesh = {Animals ; Diabetic Nephropathies/*genetics/pathology ; *Evolution, Molecular ; Genome, Human/genetics ; Haplotypes/genetics ; Hominidae/genetics ; Humans ; Neanderthals/genetics ; Obesity/*genetics/pathology ; Peptides/genetics ; Platelet Aggregation/genetics ; Receptors, G-Protein-Coupled/*genetics ; Risk Factors ; }, abstract = {Given the importance of G-protein coupled receptors in the regulation of many physiological functions, deciphering the relationships between genotype and phenotype in past and present hominin GPCRs is of main interest to understand the evolutionary process that contributed to the present-day variability in human traits and health. Here, we carefully examined the publicly available genomic and protein sequence databases of the archaic hominins (Neanderthal and Denisova) to draw up the catalog of coding variations in GPCRs for peptide ligands, in comparison with living humans. We then searched in the literature the functional changes, phenotypes and risk of disease possibly associated with the detected variants. Our survey suggests that Neanderthal and Denisovan hominins were likely prone to lower risk of obesity, to enhanced platelet aggregation in response to thrombin, to better response to infection, to less anxiety and aggressiveness and to favorable sociability. While some archaic variants were likely advantageous in the past, they might be responsible for maladaptive disorders today in the context of modern life and/or specific regional distribution. For example, an archaic haplotype in the neuromedin receptor 2 is susceptible to confer risk of diabetic nephropathy in type 1 diabetes in present-day Europeans. Paying attention to the pharmacological properties of some of the archaic variants described in this study may be helpful to understand the variability of therapeutic efficacy between individuals or ethnic groups.}, }
@article {pmid31558742, year = {2019}, author = {Morley, MW and Goldberg, P and Uliyanov, VA and Kozlikin, MB and Shunkov, MV and Derevianko, AP and Jacobs, Z and Roberts, RG}, title = {Hominin and animal activities in the microstratigraphic record from Denisova Cave (Altai Mountains, Russia).}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {13785}, pmid = {31558742}, issn = {2045-2322}, mesh = {Animals ; Archaeology ; *Caves ; Cold Climate ; DNA, Ancient/isolation &amp; purification ; *Fossils ; History, Ancient ; *Hominidae/genetics ; Humans ; Neanderthals/genetics ; Paleontology ; Siberia ; }, abstract = {Denisova Cave in southern Siberia uniquely contains evidence of occupation by a recently discovered group of archaic hominins, the Denisovans, starting from the middle of the Middle Pleistocene. Artefacts, ancient DNA and a range of animal and plant remains have been recovered from the sedimentary deposits, along with a few fragmentary fossils of Denisovans, Neanderthals and a first-generation Neanderthal-Denisovan offspring. The deposits also contain microscopic traces of hominin and animal activities that can provide insights into the use of the cave over the last 300,000 years. Here we report the results of a micromorphological study of intact sediment blocks collected from the Pleistocene deposits in the Main and East Chambers of Denisova Cave. The presence of charcoal attests to the use of fire by hominins, but other evidence of their activities preserved in the microstratigraphic record are few. The ubiquitous occurrence of coprolites, which we attribute primarily to hyenas, indicates that the site was visited for much of its depositional history by cave-dwelling carnivores. Microscopic traces of post-depositional diagenesis, bioturbation and incipient cryoturbation are observed in only a few regions of the deposit examined here. Micromorphology can help identify areas of sedimentary deposit that are most conducive to ancient DNA preservation and could be usefully integrated with DNA analyses of sediments at archaeological sites to illuminate features of their human and environmental history that are invisible to the naked eye.}, }
@article {pmid31539495, year = {2019}, author = {Gokhman, D and Mishol, N and de Manuel, M and de Juan, D and Shuqrun, J and Meshorer, E and Marques-Bonet, T and Rak, Y and Carmel, L}, title = {Reconstructing Denisovan Anatomy Using DNA Methylation Maps.}, journal = {Cell}, volume = {179}, number = {1}, pages = {180-192.e10}, doi = {10.1016/j.cell.2019.08.035}, pmid = {31539495}, issn = {1097-4172}, mesh = {Animals ; Base Sequence ; DNA Methylation/*genetics ; Databases, Genetic ; Extinction, Biological ; Fossils ; Genome, Human/genetics ; Humans ; Neanderthals/*anatomy &amp; histology/*genetics ; Pan troglodytes/*anatomy &amp; histology/*genetics ; *Phenotype ; Polymorphism, Single Nucleotide/genetics ; Skeleton ; Skull ; }, abstract = {Denisovans are an extinct group of humans whose morphology remains unknown. Here, we present a method for reconstructing skeletal morphology using DNA methylation patterns. Our method is based on linking unidirectional methylation changes to loss-of-function phenotypes. We tested performance by reconstructing Neanderthal and chimpanzee skeletal morphologies and obtained >85% precision in identifying divergent traits. We then applied this method to the Denisovan and offer a putative morphological profile. We suggest that Denisovans likely shared with Neanderthals traits such as an elongated face and a wide pelvis. We also identify Denisovan-derived changes, such as an increased dental arch and lateral cranial expansion. Our predictions match the only morphologically informative Denisovan bone to date, as well as the Xuchang skull, which was suggested by some to be a Denisovan. We conclude that DNA methylation can be used to reconstruct anatomical features, including some that do not survive in the fossil record.}, }
@article {pmid31538229, year = {2019}, author = {Hanke, B}, title = {[On the relationship between Neanderthal alleles and cytotoxicity].}, journal = {Der Pathologe}, volume = {40}, number = {6}, pages = {627-628}, pmid = {31538229}, issn = {1432-1963}, mesh = {*Alleles ; Animals ; Humans ; *Neanderthals/genetics ; }, }
@article {pmid31517046, year = {2019}, author = {Bennett, EA and Crevecoeur, I and Viola, B and Derevianko, AP and Shunkov, MV and Grange, T and Maureille, B and Geigl, EM}, title = {Morphology of the Denisovan phalanx closer to modern humans than to Neanderthals.}, journal = {Science advances}, volume = {5}, number = {9}, pages = {eaaw3950}, pmid = {31517046}, issn = {2375-2548}, mesh = {Animals ; Finger Phalanges/*anatomy &amp; histology ; *Genome, Human ; Humans ; Molar/*anatomy &amp; histology ; *Neanderthals/anatomy &amp; histology/genetics ; Species Specificity ; }, abstract = {A fully sequenced high-quality genome has revealed in 2010 the existence of a human population in Asia, the Denisovans, related to and contemporaneous with Neanderthals. Only five skeletal remains are known from Denisovans, mostly molars; the proximal fragment of a fifth finger phalanx used to generate the genome, however, was too incomplete to yield useful morphological information. Here, we demonstrate through ancient DNA analysis that a distal fragment of a fifth finger phalanx from the Denisova Cave is the larger, missing part of this phalanx. Our morphometric analysis shows that its dimensions and shape are within the variability of Homo sapiens and distinct from the Neanderthal fifth finger phalanges. Thus, unlike Denisovan molars, which display archaic characteristics not found in modern humans, the only morphologically informative Denisovan postcranial bone identified to date is suggested here to be plesiomorphic and shared between Denisovans and modern humans.}, }
@article {pmid31517044, year = {2019}, author = {Raveane, A and Aneli, S and Montinaro, F and Athanasiadis, G and Barlera, S and Birolo, G and Boncoraglio, G and Di Blasio, AM and Di Gaetano, C and Pagani, L and Parolo, S and Paschou, P and Piazza, A and Stamatoyannopoulos, G and Angius, A and Brucato, N and Cucca, F and Hellenthal, G and Mulas, A and Peyret-Guzzon, M and Zoledziewska, M and Baali, A and Bycroft, C and Cherkaoui, M and Chiaroni, J and Di Cristofaro, J and Dina, C and Dugoujon, JM and Galan, P and Giemza, J and Kivisild, T and Mazieres, S and Melhaoui, M and Metspalu, M and Myers, S and Pereira, L and Ricaut, FX and Brisighelli, F and Cardinali, I and Grugni, V and Lancioni, H and Pascali, VL and Torroni, A and Semino, O and Matullo, G and Achilli, A and Olivieri, A and Capelli, C}, title = {Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe.}, journal = {Science advances}, volume = {5}, number = {9}, pages = {eaaw3492}, pmid = {31517044}, issn = {2375-2548}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *DNA, Ancient ; *Databases, Genetic ; *Genetic Drift ; *Genome, Human ; Genome-Wide Association Study ; History, Ancient ; Human Genetics ; Humans ; Italy ; Neanderthals/genetics ; White People/*genetics ; }, abstract = {European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non-steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.}, }
@article {pmid31501334, year = {2019}, author = {Duveau, J and Berillon, G and Verna, C and Laisné, G and Cliquet, D}, title = {The composition of a Neandertal social group revealed by the hominin footprints at Le Rozel (Normandy, France).}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {39}, pages = {19409-19414}, pmid = {31501334}, issn = {1091-6490}, mesh = {Animals ; Archaeology ; Foot/*anatomy &amp; histology ; *Fossils ; France ; Neanderthals/*anatomy &amp; histology ; Sociological Factors ; }, abstract = {Footprints represent a unique snapshot of hominin life. They provide information on the size and composition of groups that differs from osteological and archeological remains, whose contemporaneity is difficult to establish. We report here on the discovery of 257 footprints dated to 80,000 y from the Paleolithic site at Le Rozel (Normandy, France), which represent the largest known Neandertal ichnological assemblage to date. We investigate the size and composition of a track-maker group from this large set by developing a morphometric method based on experimental footprints. Our analyses indicate that the footprints were made by a small group comprising different age classes, from early childhood to adult, with a majority of children. The Le Rozel footprints thus provide direct evidence for the size and composition of a Neandertal social group.}, }
@article {pmid33951886, year = {2019}, author = {Kislev, M and Barkai, R}, title = {Neanderthal and Woolly Mammoth Molecular Resemblance: Genetic Similarities May Underlie Cold Adaptation Suite.}, journal = {Human biology}, volume = {90}, number = {2}, pages = {115-128}, doi = {10.13110/humanbiology.90.2.03}, pmid = {33951886}, issn = {1534-6617}, abstract = {With the ongoing growth of gene-based research in recent decades, examining changes that have taken place in structures over the course of evolution has become increasingly accessible. One intriguing subject at the forefront of evolutionary research is how environmental pressures affect species evolution through epigenetic adaptation. This article presents the available molecular components of adaptation to cold environments in two extinct mammals: the woolly mammoth and the Neanderthal. These two species coexisted in similar geographic and environmental European settings during the Middle and Upper Pleistocene, and both were direct descendants of African ancestors, although both fully evolved and adapted in Europe during the Middle Pleistocene. The authors assessed the degree of resemblance between mammoth and Neanderthal genetic components by reviewing three case studies of relevant gene variants and alleles associated with cold-climate adaptation found in both genomes. Their observations present the likelihood of a molecular resemblance between the suites of cold adaptation traits in the two species.}, }
@article {pmid31472033, year = {2019}, author = {Pagano, AS and Márquez, S and Laitman, JT}, title = {Reconstructing the Neanderthal Eustachian Tube: New Insights on Disease Susceptibility, Fitness Cost, and Extinction.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {302}, number = {12}, pages = {2109-2125}, doi = {10.1002/ar.24248}, pmid = {31472033}, issn = {1932-8494}, support = {1128901//Directorate for Social, Behavioral and Economic Sciences/International ; }, mesh = {Adolescent ; Adult ; Animals ; Cartilage/*pathology ; Child ; Disease Susceptibility ; Ear, Middle/*pathology ; Eustachian Tube/*pathology ; *Extinction, Biological ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Neanderthals ; Otitis Media/*pathology ; }, abstract = {Neanderthals are among the best studied and yet most enigmatic fossil human groups with aspects of their anatomy and functional morphology remaining poorly understood. We present the first anatomical reconstruction of the Neanderthal cartilaginous Eustachian tube (CET), a vital component of the upper respiratory tract and nexus for the middle ear and postnasal airway. The Eustachian (auditory, pharyngotympanic) tube, comprised of a bony and cartilaginous (CET) portion, is integral to normal physiological functions such as middle ear aeration and pressure equilibration. Findings indicate that Neanderthal tubal morphology may have predisposed them to high rates of middle ear disease (otitis media [OM]). In living humans, mechanical CET dysfunction underlies OM in infants and young children, with sequelae including hearing loss, meningitis, and pneumonia. Despite proven linkage of CET malfunction with OM, the role of CET morphology in Neanderthal health and disease remains unstudied. We reconstructed Neanderthal CET morphology, comparing their crania to a modern human growth series. Methods included geometric morphometrics and univariate measures among Procrustes-fitted coordinates. Results showed Neanderthal adults exhibiting primitively tall and narrow nasopharynges with infant-like horizontal CET and choanal orientation. As horizontal CET orientation is associated with increased OM incidence in infants and children until around age six, its appearance in Neanderthal adults strongly indicates persistence of high OM susceptibility at this time. This could have compromised fitness and disease load relative to sympatric modern humans, affecting Neanderthals' ability to compete within their ecological niche, and potentially contributing to their rapid extinction. Anat Rec, 302:2109-2125, 2019. © 2019 American Association for Anatomy.}, }
@article {pmid31427508, year = {2019}, author = {Schmidt, P and Blessing, M and Rageot, M and Iovita, R and Pfleging, J and Nickel, KG and Righetti, L and Tennie, C}, title = {Birch tar production does not prove Neanderthal behavioral complexity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {36}, pages = {17707-17711}, pmid = {31427508}, issn = {1091-6490}, mesh = {Animals ; *Archaeology ; Behavior, Animal/*physiology ; *Betula ; Cognition/*physiology ; Neanderthals/*physiology ; }, abstract = {Birch tar production by Neanderthals-used for hafting tools-has been interpreted as one of the earliest manifestations of modern cultural behavior. This is because birch tar production per se was assumed to require a cognitively demanding setup, in which birch bark is heated in anaerobic conditions, a setup whose inherent complexity was thought to require modern levels of cognition and cultural transmission. Here we demonstrate that recognizable amounts of birch tar were likely a relatively frequent byproduct of burning birch bark (a natural tinder) under common, i.e., aerobic, conditions. We show that when birch bark burns close to a vertical to subvertical hard surface, such as an adjacent stone, birch tar is naturally deposited and can be easily scraped off the surface. The burning of birch bark near suitable surfaces provides useable quantities of birch tar in a single work session (3 h; including birch bark procurement). Chemical analysis of the resulting tar showed typical markers present in archaeological tar. Mechanical tests verify the tar's suitability for hafting and for hafted tools use. Given that similarly sized stones as in our experiment are frequently found in archaeological contexts associated with Neanderthals, the cognitively undemanding connection between burning birch bark and the production of birch tar would have been readily discoverable multiple times. Thus, the presence of birch tar alone cannot indicate the presence of modern cognition and/or cultural behaviors in Neanderthals.}, }
@article {pmid31421316, year = {2019}, author = {Zanolli, C and Biglari, F and Mashkour, M and Abdi, K and Monchot, H and Debue, K and Mazurier, A and Bayle, P and Le Luyer, M and Rougier, H and Trinkaus, E and Macchiarelli, R}, title = {A Neanderthal from the Central Western Zagros, Iran. Structural reassessment of the Wezmeh 1 maxillary premolar.}, journal = {Journal of human evolution}, volume = {135}, number = {}, pages = {102643}, doi = {10.1016/j.jhevol.2019.102643}, pmid = {31421316}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; Bicuspid/*anatomy &amp; histology ; Fossils/*anatomy &amp; histology ; Iran ; Maxilla ; Neanderthals/*anatomy &amp; histology ; }, abstract = {Wezmeh Cave, in the Kermanshah region of Central Western Zagros, Iran, produced a Late Pleistocene faunal assemblage rich in carnivorans along with a human right maxillary premolar, Wezmeh 1, an unerupted tooth from an 8 ± 2 year-old individual. Uranium-series analyses of the fauna by alpha spectrometry provided age estimates between 70 and 11 ka. Crown dimensions place the tooth specimen at the upper limits of Late Pleistocene human ranges of variation. Wezmeh 1 metameric position (most likely a P[3]) remains uncertain and only its surficial morphology has been described so far. Accordingly, we used microfocus X-ray tomography (12.5 μm isotropic voxel size) to reassess the metameric position and taxonomic attribution of this specimen. We investigated its endostructural features and quantified crown tissue proportions. Topographic maps of enamel thickness (ET) distribution were also generated, and semilandmark-based geometric morphometric analyses of the enamel-dentine junction (EDJ) were performed. We compared Wezmeh 1 with unworn/slightly-moderately worn P[3] and P[4] of European Neanderthals, Middle Paleolithic modern humans from Qafzeh, an Upper Paleolithic premolar, and Holocene humans. The results confirm that Wezmeh 1 represents a P[3]. Based on its internal conformation and especially EDJ shape, Wezmeh 1 aligns closely with Neanderthals and is distinct from the fossil and extant modern human pattern of our comparative samples. Wezmeh 1 is thus the first direct evidence of Neanderthal presence on the western margin of the Iranian Plateau.}, }
@article {pmid31412053, year = {2019}, author = {Trinkaus, E and Samsel, M and Villotte, S}, title = {External auditory exostoses among western Eurasian late Middle and Late Pleistocene humans.}, journal = {PloS one}, volume = {14}, number = {8}, pages = {e0220464}, pmid = {31412053}, issn = {1932-6203}, mesh = {Animals ; Anthropology, Physical ; *Biological Evolution ; Ear Diseases/*pathology ; Exostoses/*pathology ; Fossils ; Humans ; Neanderthals ; }, abstract = {External auditory exostoses (EAE) have been noted among the Neandertals and a few other Pleistocene humans, but until recently they have been discussed primary as minor pathological lesions with possible auditory consequences. An assessment of available western Eurasian late Middle and Late Pleistocene human temporal bones with sufficiently preserved auditory canals (n = 77) provides modest levels of EAE among late Middle Pleistocene archaic humans (≈20%) and early modern humans (Middle Paleolithic: ≈25%; Early/Mid Upper Paleolithic: 20.8%; Late Upper Paleolithic: 9.5%). The Neandertals, however, exhibit an exceptionally high level of EAE (56.5%; 47.8% if two anomalous cases are considered normal). The levels of EAE for the early modern humans are well within recent human ranges of variation, frequencies which are low for equatorial inland and high latitude samples but occasionally higher elsewhere. The Early/Mid Upper Paleolithic frequency is nonetheless high for a high latitude sample under interpleniglacial conditions. Given the strong etiological and environmental associations of EAE development with exposure to cold water and/or damp wind chill, the high frequency of EAE among the Neandertals implies frequent aquatic resource exploitation, more frequent than the archeological and stable isotopic evidence for Middle Paleolithic/Neandertal littoral and freshwater resource foraging implies. As such, the Neandertal data parallel a similar pattern evident in eastern Eurasian archaic humans. Yet, factors in addition to cold water/wind exposure may well have contributed to their high EAE frequencies.}, }
@article {pmid31358177, year = {2019}, author = {Richard, M and Falguères, C and Valladas, H and Ghaleb, B and Pons-Branchu, E and Mercier, N and Richter, D and Conard, NJ}, title = {New electron spin resonance (ESR) ages from Geißenklösterle Cave: A chronological study of the Middle and early Upper Paleolithic layers.}, journal = {Journal of human evolution}, volume = {133}, number = {}, pages = {133-145}, doi = {10.1016/j.jhevol.2019.05.014}, pmid = {31358177}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; *Caves ; Dental Enamel/*chemistry ; *Electron Spin Resonance Spectroscopy ; *Fossils ; Germany ; Humans ; *Neanderthals ; }, abstract = {Geißenklösterle Cave (Germany) is one of the most important Paleolithic sites in Europe, as it is characterized by human occupation during the Middle and early Upper Paleolithic. Aurignacian layers prior to 37-38 ka cal BP feature both musical and figurative art objects that are linked to the early arrival in Europe of Homo sapiens. Middle Paleolithic layers yielded lithic artifacts attributed to Homo neanderthalensis. Since human occupation at the site is attributed to both Neanderthals and modern humans, chronology is essential to clarify the issues of Neanderthal disappearance, modern human expansion in Europe, and the origin of the Aurignacian in Western Europe. Electron spin resonance (ESR) dating was performed on fossil tooth enamel collected from the Middle Paleolithic layers, which are beyond the radiocarbon dating range, and from the nearly sterile 'transitional' geological horizon (GH) 17 and the lower Aurignacian deposits, to cross-check ESR ages with previous radiocarbon, thermoluminescence and ESR age results. The Middle Paleolithic layers were dated between 94 ± 10 ka (GH 21) and 55 ± 6 ka (GH 18) by ESR on tooth enamel. Mean ages for GH 17, at 46 ± 3 ka, and for the lower Aurignacian layers, at 37 ± 3 ka, are in agreement with previous dating results, thus supporting the reliability of ESR chronology for the base of the sequence where dating comparisons are not possible. These results suggest that Neanderthals occupied the site from Marine Isotope Stage (MIS) 5 to the second half of MIS 3 and confirm the antiquity of early Aurignacian deposits. The presence of an almost sterile layer that separates Middle and Upper Paleolithic occupations could be related to the abandonment of the site by Neanderthals, possibly during Heinrich Stadial 5 (ca. 49-47 ka), thus before the arrival of H. sapiens in the area around 42 ka cal BP. These dates for the Middle Paleolithic of the Swabian Jura represent an important contribution to the prehistory of the region, where nearly all of the excavations were conducted decades ago and prior to the development of reliable radiometric dating beyond the range of radiocarbon.}, }
@article {pmid31341308, year = {2019}, author = {El-Showk, S}, title = {Neanderthal clues to brain evolution in humans.}, journal = {Nature}, volume = {571}, number = {7766}, pages = {S10-S11}, pmid = {31341308}, issn = {1476-4687}, mesh = {Animals ; Brain ; Fossils ; *Hominidae ; Humans ; *Neanderthals ; }, }
@article {pmid31336034, year = {2020}, author = {Bräuer, G and Pitsios, T and Säring, D and von Harling, M and Jessen, F and Kroll, A and Groden, C}, title = {Virtual Reconstruction and Comparative Analyses of the Middle Pleistocene Apidima 2 Cranium (Greece).}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {303}, number = {5}, pages = {1374-1392}, doi = {10.1002/ar.24225}, pmid = {31336034}, issn = {1932-8494}, mesh = {Animals ; Biological Evolution ; *Fossils ; Greece ; Hominidae/*anatomy &amp; histology ; Image Processing, Computer-Assisted ; Neanderthals/anatomy &amp; histology ; Skull/*anatomy &amp; histology/diagnostic imaging ; }, abstract = {The Apidima 2 fossil cranium from South Peloponnese is one of the most important hominin specimens from Southeast Europe. Nevertheless, there has been continuous controversy as to whether it represents a so-called Preneandertal/Homo heidelbergensis such as, for example, the Petralona cranium from Northern Greece or a more derived Neandertal. Recent absolute dating evidence alone cannot clarify the issue because both classifications would be possible during the respective Middle Pleistocene time span. Since only limited data were available on the cranium, there have been repeated claims for the need of a broader comparative study of the hominin. The present article presents a CT-based virtual reconstruction including corrections of postmortem fractures and deformation as well as detailed metrical and morphological analyses of the specimen. Endocranial capacity could be estimated for the first time based on virtual reconstruction. Our multivariate analyses of metric data from the face and vault revealed close affinities to early and later Neandertals, especially showing the derived facial morphometrics. In addition, comparative analyses of Apidima 2 were done for many derived Neandertal features. Here again, a significant number of Neandertal features could be found in the Apidima cranium but no conditions common in Preneandertals. In agreement with a later Middle Pleistocene age Apidima is currently the earliest evidence of a hominin in Europe with such a derived Neandertal facial morphology. The place of Apidima in the complex process of Neandertal evolution as well as its taxonomic classification are discussed as well. Anat Rec, 303:1374-1392, 2020. © 2019 American Association for Anatomy.}, }
@article {pmid31314755, year = {2019}, author = {Pitarch Martí, A and d'Errico, F and Turq, A and Lebraud, E and Discamps, E and Gravina, B}, title = {Provenance, modification and use of manganese-rich rocks at Le Moustier (Dordogne, France).}, journal = {PloS one}, volume = {14}, number = {7}, pages = {e0218568}, pmid = {31314755}, issn = {1932-6203}, mesh = {Animals ; *Archaeology ; *Fossils ; France ; History, Ancient ; Humans ; *Manganese ; *Minerals ; *Neanderthals ; Technology/*history ; }, abstract = {The use of colouring materials by Neanderthals has attracted a great deal of attention in recent years. Here we present a taphonomic, technological, chemical-mineralogical and functional analysis of fifty-four manganese rich lumps recovered during past and on-going excavations at the lower rockshelter of Le Moustier (Dordogne, France). We compare compositional data for archaeological specimens with the same information for twelve potential geological sources. Morphometric analysis shows that material from Peyrony's excavations before the First World War provides a highly biased picture of the importance of these materials for Mousterian groups. These early excavations almost exclusively recovered large modified pieces, while Mn-rich lumps from the on-going excavations predominantly consist of small pieces, only half of which bear traces of modification. We estimate that at least 168 pieces were not recovered during early work at the site. Neanderthals developed a dedicated technology for processing Mn-rich fragments, which involved a variety of tools and motions. Processing techniques were adapted to the size and density of the raw material, and evidence exists for the successive or alternating use of different techniques. Morphological, textural and chemical differences between geological and archaeological samples suggest that Neanderthals did not collect Mn-rich lumps at the outcrops we sampled. The association and variability in Mn, Ni, As, Ba content, compared to that observed at the sampled outcrops, suggests that either the Le Moustier lumps come from a unique source with a broad variation in composition, associating Mn, Ni, As, Ba, or that they were collected at different sources, characterized either by Mn-Ni-As or Mn-Ba. In the latter case, changes in raw material composition across the stratigraphy support the idea that Neanderthal populations bearing different stone tool technologies collected Mn fragments from different outcrops. Our results favour a use of these materials for multiple utilitarian and symbolic purposes.}, }
@article {pmid31308224, year = {2019}, author = {Bokelmann, L and Hajdinjak, M and Peyrégne, S and Brace, S and Essel, E and de Filippo, C and Glocke, I and Grote, S and Mafessoni, F and Nagel, S and Kelso, J and Prüfer, K and Vernot, B and Barnes, I and Pääbo, S and Meyer, M and Stringer, C}, title = {A genetic analysis of the Gibraltar Neanderthals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {31}, pages = {15610-15615}, pmid = {31308224}, issn = {1091-6490}, support = {/WT_/Wellcome Trust/United Kingdom ; 100713/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *DNA, Ancient ; Gibraltar ; History, Ancient ; Humans ; Neanderthals/*genetics ; *Oligonucleotide Array Sequence Analysis ; }, abstract = {The Forbes' Quarry and Devil's Tower partial crania from Gibraltar are among the first Neanderthal remains ever found. Here, we show that small amounts of ancient DNA are preserved in the petrous bones of the 2 individuals despite unfavorable climatic conditions. However, the endogenous Neanderthal DNA is present among an overwhelming excess of recent human DNA. Using improved DNA library construction methods that enrich for DNA fragments carrying deaminated cytosine residues, we were able to sequence 70 and 0.4 megabase pairs (Mbp) nuclear DNA of the Forbes' Quarry and Devil's Tower specimens, respectively, as well as large parts of the mitochondrial genome of the Forbes' Quarry individual. We confirm that the Forbes' Quarry individual was a female and the Devil's Tower individual a male. We also show that the Forbes' Quarry individual is genetically more similar to the ∼120,000-y-old Neanderthals from Scladina Cave in Belgium (Scladina I-4A) and Hohlenstein-Stadel Cave in Germany, as well as to a ∼60,000- to 70,000-y-old Neanderthal from Russia (Mezmaiskaya 1), than to a ∼49,000-y-old Neanderthal from El Sidrón (El Sidrón 1253) in northern Spain and other younger Neanderthals from Europe and western Asia. This suggests that the Forbes' Quarry fossil predates the latter Neanderthals. The preservation of archaic human DNA in the warm coastal climate of Gibraltar, close to the shores of Africa, raises hopes for the future recovery of archaic human DNA from regions in which climatic conditions are less than optimal for DNA preservation.}, }
@article {pmid31292546, year = {2019}, author = {Harvati, K and Röding, C and Bosman, AM and Karakostis, FA and Grün, R and Stringer, C and Karkanas, P and Thompson, NC and Koutoulidis, V and Moulopoulos, LA and Gorgoulis, VG and Kouloukoussa, M}, title = {Apidima Cave fossils provide earliest evidence of Homo sapiens in Eurasia.}, journal = {Nature}, volume = {571}, number = {7766}, pages = {500-504}, pmid = {31292546}, issn = {1476-4687}, mesh = {Animals ; Biological Evolution ; *Caves ; *Fossils ; Greece ; Humans ; Neanderthals/anatomy &amp; histology/classification ; Principal Component Analysis ; Radiometric Dating ; Skull/*anatomy &amp; histology ; Time Factors ; }, abstract = {Two fossilized human crania (Apidima 1 and Apidima 2) from Apidima Cave, southern Greece, were discovered in the late 1970s but have remained enigmatic owing to their incomplete nature, taphonomic distortion and lack of archaeological context and chronology. Here we virtually reconstruct both crania, provide detailed comparative descriptions and analyses, and date them using U-series radiometric methods. Apidima 2 dates to more than 170 thousand years ago and has a Neanderthal-like morphological pattern. By contrast, Apidima 1 dates to more than 210 thousand years ago and presents a mixture of modern human and primitive features. These results suggest that two late Middle Pleistocene human groups were present at this site-an early Homo sapiens population, followed by a Neanderthal population. Our findings support multiple dispersals of early modern humans out of Africa, and highlight the complex demographic processes that characterized Pleistocene human evolution and modern human presence in southeast Europe.}, }
@article {pmid31278514, year = {2019}, author = {Brzozowska, MM and Havula, E and Allen, RB and Cox, MP}, title = {Genetics, adaptation to environmental changes and archaic admixture in the pathogenesis of diabetes mellitus in Indigenous Australians.}, journal = {Reviews in endocrine &amp; metabolic disorders}, volume = {20}, number = {3}, pages = {321-332}, pmid = {31278514}, issn = {1573-2606}, mesh = {Australia ; Diabetes Mellitus, Type 2/*genetics/*pathology ; Genome-Wide Association Study ; Humans ; Indigenous Peoples ; Obesity/genetics/pathology ; }, abstract = {Indigenous Australians are particularly affected by type 2 diabetes mellitus (T2D) due to both their genetic susceptibility and a range of environmental and lifestyle risk factors. Recent genetic studies link predisposition to some diseases, including T2D, to alleles acquired from archaic hominins, such as Neanderthals and Denisovans, which persist in the genomes of modern humans today. Indo-Pacific human populations, including Indigenous Australians, remain extremely underrepresented in genomic research with a paucity of data examining the impact of Denisovan or Neanderthal lineages on human phenotypes in Oceania. The few genetic studies undertaken emphasize the uniqueness and antiquity of Indigenous Australian genomes, with possibly the largest proportion of Denisovan ancestry of any population in the world. In this review, we focus on the potential contributions of ancient genes/pathways to modern human phenotypes, while also highlighting the evolutionary roles of genetic adaptation to dietary and environmental changes associated with an adopted Western lifestyle. We discuss the role of genetic and epigenetic factors in the pathogenesis of T2D in understudied Indigenous Australians, including the potential impact of archaic gene lineages on this disease. Finally, we propose that greater understanding of the underlying genetic predisposition may contribute to the clinical efficacy of diabetes management in Indigenous Australians. We suggest that improved identification of T2D risk variants in Oceania is needed. Such studies promise to clarify how genetic and phenotypic differences vary between populations and, crucially, provide novel targets for personalised medical therapies in currently marginalized groups.}, }
@article {pmid31258332, year = {2019}, author = {Williams, AC and Hill, LJ}, title = {Nicotinamide as Independent Variable for Intelligence, Fertility, and Health: Origin of Human Creative Explosions?.}, journal = {International journal of tryptophan research : IJTR}, volume = {12}, number = {}, pages = {1178646919855944}, pmid = {31258332}, issn = {1178-6469}, abstract = {Meat and nicotinamide acquisition was a defining force during the 2-million-year evolution of the big brains necessary for, anatomically modern, Homo sapiens to survive. Our next move was down the food chain during the Mesolithic 'broad spectrum', then horticultural, followed by the Neolithic agricultural revolutions and progressively lower average 'doses' of nicotinamide. We speculate that a fertility crisis and population bottleneck around 40 000 years ago, at the time of the Last Glacial Maximum, was overcome by Homo (but not the Neanderthals) by concerted dietary change plus profertility genes and intense sexual selection culminating in behaviourally modern Homo sapiens. Increased reliance on the 'de novo' synthesis of nicotinamide from tryptophan conditioned the immune system to welcome symbionts, such as TB (that excrete nicotinamide), and to increase tolerance of the foetus and thereby fertility. The trade-offs during the warmer Holocene were physical and mental stunting and more infectious diseases and population booms and busts. Higher nicotinamide exposure could be responsible for recent demographic and epidemiological transitions to lower fertility and higher longevity, but with more degenerative and auto-immune disease.}, }
@article {pmid31242180, year = {2019}, author = {Ekshtain, R and Malinsky-Buller, A and Greenbaum, N and Mitki, N and Stahlschmidt, MC and Shahack-Gross, R and Nir, N and Porat, N and Bar-Yosef Mayer, DE and Yeshurun, R and Been, E and Rak, Y and Agha, N and Brailovsky, L and Krakovsky, M and Spivak, P and Ullman, M and Vered, A and Barzilai, O and Hovers, E}, title = {Persistent Neanderthal occupation of the open-air site of 'Ein Qashish, Israel.}, journal = {PloS one}, volume = {14}, number = {6}, pages = {e0215668}, pmid = {31242180}, issn = {1932-6203}, mesh = {Animals ; Fossils/*anatomy &amp; histology ; Israel ; Mollusca/anatomy &amp; histology/classification ; Neanderthals/*anatomy &amp; histology ; }, abstract = {Over the last two decades, much of the recent efforts dedicated to the Levantine Middle Paleolithic has concentrated on the role of open-air sites in the settlement system in the region. Here focus on the site of 'Ein Qashish as a cases study. Located in present-day northern Israel, the area of this site is estimated to have been >1300 m2, of which ca. 670 were excavated. The site is located at the confluence of the Qishon stream with a small tributary running off the eastern flanks of the Mt. Carmel. At the area of this confluence, water channels and alluvial deposits created a dynamic depositional environment. Four Archaeological Units were identified in a 4.5-m thick stratigraphic sequence were dated by Optically Stimulated Luminescence (OSL) to between-71 and 54 ka, and probably shorter time span-~70-~60 ka. Here we present the diverse material culture remains from the site (lithics, including refitted sequences; modified limestone pieces; molluscs; faunal remains) against their changing paleogeographic backdrop. Skeletal evidence suggests that these remains were associated with Neanderthals. The large-scale repeated accumulation of late Middle Paleolithic remains in the same place on the landscape provides a unique opportunity to address questions of occupation duration and intensity in open-air sites. We find that each occupation was of ephemeral nature, yet presents a range of activities, suggesting that the locale has been used as a generalized residential site rather than specialized task-specific ones. This role of 'Ein Qashish did not change through time, suggesting that during the late Middle Paleolithic settlement system in this part of the southern Levant were stable.}, }
@article {pmid31237235, year = {2019}, author = {Langley, SA and Miga, KH and Karpen, GH and Langley, CH}, title = {Haplotypes spanning centromeric regions reveal persistence of large blocks of archaic DNA.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {31237235}, issn = {2050-084X}, support = {R01 GM117420/GM/NIGMS NIH HHS/United States ; R01 GM119011/GM/NIGMS NIH HHS/United States ; }, mesh = {*Centromere ; *Chromosomes, Human ; DNA, Satellite/genetics ; *Genetic Variation ; *Haplotypes ; Humans ; Repetitive Sequences, Nucleic Acid ; }, abstract = {Despite critical roles in chromosome segregation and disease, the repetitive structure and vast size of centromeres and their surrounding heterochromatic regions impede studies of genomic variation. Here we report the identification of large-scale haplotypes (cenhaps) in humans that span the centromere-proximal regions of all metacentric chromosomes, including the arrays of highly repeated α-satellites on which centromeres form. Cenhaps reveal deep diversity, including entire introgressed Neanderthal centromeres and equally ancient lineages among Africans. These centromere-spanning haplotypes contain variants, including large differences in α-satellite DNA content, which may influence the fidelity and bias of chromosome transmission. The discovery of cenhaps creates new opportunities to investigate their contribution to phenotypic variation, especially in meiosis and mitosis, as well as to more incisively model the unexpectedly rich evolution of these challenging genomic regions.}, }
@article {pmid31203846, year = {2019}, author = {Fiorenza, L and Benazzi, S and Kullmer, O and Zampirolo, G and Mazurier, A and Zanolli, C and Macchiarelli, R}, title = {Dental macrowear and cortical bone distribution of the Neanderthal mandible from Regourdou (Dordogne, Southwestern France).}, journal = {Journal of human evolution}, volume = {132}, number = {}, pages = {174-188}, doi = {10.1016/j.jhevol.2019.05.005}, pmid = {31203846}, issn = {1095-8606}, mesh = {Animals ; *Diet ; France ; Mandible/*anatomy &amp; histology ; *Mastication ; Neanderthals/*anatomy &amp; histology ; Tooth/*anatomy &amp; histology ; }, abstract = {Tooth wear is an important feature for reconstructing diet, food processing and cultural habits of past human populations. In particular, occlusal wear facets can be extremely useful for detecting information about diet and non-masticatory behaviors. The aim of this study is to reconstruct the diet and cultural behavior of the Neanderthal specimen Regourdou 1 (Dordogne, Southern France) from the analysis of the macrowear pattern, using the occlusal fingerprint analysis method. In addition, we have also examined whether there is any association between the observed dental macrowear and mandibular bone distribution and root dentine thickness. The posterior dentition of Regourdou 1 is characterized by an asymmetric wear pattern, with the right side significantly more worn than the left. In contrast, the left lower P3 shows a more advanced wear than the right premolar, with unusual semicircular enamel wear facets. The results from occlusal fingerprint analysis of this unique pattern suggest tooth-tool uses for daily task activities. Moreover, the left buccal aspect of the mandibular cortical bone is thicker than its right counterpart, and the left P3 has a thicker radicular dentine layer than its antimere. These results show a certain degree of asymmetry in cortical bone topography and dentine tissue that could be associated with the observed dental macrowear pattern. The molar macrowear pattern also suggests that Regourdou 1 had a mixed diet typical of those populations living in temperate deciduous woodlands and Mediterranean habitats, including animal and plant foods. Although this study is limited to one Neanderthal individual, future analyses based on a larger sample may further assist us to better understand the existing relationship between mandibular architecture, occlusal wear and the masticatory apparatus in humans.}, }
@article {pmid31196864, year = {2019}, author = {Haber, M and Jones, AL and Connell, BA and Asan,  and Arciero, E and Yang, H and Thomas, MG and Xue, Y and Tyler-Smith, C}, title = {A Rare Deep-Rooting D0 African Y-Chromosomal Haplogroup and Its Implications for the Expansion of Modern Humans Out of Africa.}, journal = {Genetics}, volume = {212}, number = {4}, pages = {1421-1428}, pmid = {31196864}, issn = {1943-2631}, support = {//Wellcome Trust/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Chromosomes, Human, Y/*genetics ; *Evolution, Molecular ; *Haplotypes ; *Human Migration ; Humans ; Male ; Nigeria ; Phylogeny ; Polymorphism, Genetic ; }, abstract = {Present-day humans outside Africa descend mainly from a single expansion out ∼50,000-70,000 years ago, but many details of this expansion remain unclear, including the history of the male-specific Y chromosome at this time. Here, we reinvestigate a rare deep-rooting African Y-chromosomal lineage by sequencing the whole genomes of three Nigerian men described in 2003 as carrying haplogroup DE* Y chromosomes, and analyzing them in the context of a calibrated worldwide Y-chromosomal phylogeny. We confirm that these three chromosomes do represent a deep-rooting DE lineage, branching close to the DE bifurcation, but place them on the D branch as an outgroup to all other known D chromosomes, and designate the new lineage D0. We consider three models for the expansion of Y lineages out of Africa ∼50,000-100,000 years ago, incorporating migration back to Africa where necessary to explain present-day Y-lineage distributions. Considering both the Y-chromosomal phylogenetic structure incorporating the D0 lineage, and published evidence for modern humans outside Africa, the most favored model involves an origin of the DE lineage within Africa with D0 and E remaining there, and migration out of the three lineages (C, D, and FT) that now form the vast majority of non-African Y chromosomes. The exit took place 50,300-81,000 years ago (latest date for FT lineage expansion outside Africa - earliest date for the D/D0 lineage split inside Africa), and most likely 50,300-59,400 years ago (considering Neanderthal admixture). This work resolves a long-running debate about Y-chromosomal out-of-Africa/back-to-Africa migrations, and provides insights into the out-of-Africa expansion more generally.}, }
@article {pmid31185865, year = {2019}, author = {Shultz, DR and Montrey, M and Shultz, TR}, title = {Comparing fitness and drift explanations of Neanderthal replacement.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1904}, pages = {20190907}, pmid = {31185865}, issn = {1471-2954}, mesh = {Animals ; *Genetic Drift ; Humans ; *Models, Theoretical ; Neanderthals/*physiology ; Population Density ; Population Dynamics ; Stochastic Processes ; }, abstract = {There is a general consensus among archaeologists that replacement of Neanderthals by anatomically modern humans in Europe occurred around 40-35 ka. However, the causal mechanism for this replacement continues to be debated. Proposed models have featured either fitness advantages in favour of anatomically modern humans or invoked neutral drift under various preconditions. Searching for specific fitness advantages in the archaeological record has proven difficult, as these may be obscured, absent or subject to interpretation. To bridge this gap, we rigorously compare the system-level properties of fitness- and drift-based explanations of Neanderthal replacement. Our stochastic simulations and analytical predictions show that, although both fitness and drift can produce replacement, they present important differences in (i) required initial conditions, (ii) reliability, (iii) time to replacement, and (iv) path to replacement (population histories). These results present useful opportunities for comparison with archaeological and genetic data. We find greater agreement between the available empirical evidence and the system-level properties of replacement by differential fitness, rather than by neutral drift.}, }
@article {pmid31182208, year = {2019}, author = {Demuro, M and Arnold, LJ and Aranburu, A and Sala, N and Arsuaga, JL}, title = {New bracketing luminescence ages constrain the Sima de los Huesos hominin fossils (Atapuerca, Spain) to MIS 12.}, journal = {Journal of human evolution}, volume = {131}, number = {}, pages = {76-95}, doi = {10.1016/j.jhevol.2018.12.003}, pmid = {31182208}, issn = {1095-8606}, mesh = {Animals ; *Archaeology ; *Fossils ; *Hominidae ; Luminescence ; Paleontology ; Spain ; }, abstract = {Recent chronological studies of the Sima de los Huesos (SH) hominin fossil site, Atapuerca, Spain, have established a close minimum age of at least 430 ka for sedimentary material immediately overlying the human remains. However, a firm maximum age limit still needs to be established for the SH fossils in order to better constrain the timing for the onset of Neandertal speciation. In the present study, we address this important chronological gap at SH by providing direct ages for the sediment deposits that host, and immediately underlie, the hominin fossils. Depositional ages were obtained using single-grain thermally-transferred optically stimulated luminescence (TT-OSL), a technique that has yielded reliable 'extended-range' luminescence chronologies at several independently dated Atapuerca sites. Four single-grain TT-OSL depositional ages of 453 ± 56 ka, 437 ± 38 ka, 457 ± 41 ka and 460 ± 39 ka were obtained for the red clay lithostratigraphic units (LU-5 and LU-6) found underlying and encasing the SH hominin bones. A Bayesian age-depth model was constructed using previously published chronologies, as well as the new single-grain TT-OSL ages for LU-5 and LU-6, in order to derive combined age estimates for individual lithostratigraphic units preserved at SH. The combined modeled ranges reveal that the hominin-bearing layer (LU-6) was deposited between 455 ± 17 ka and 440 ± 15 ka (mean lower and upper boundary 68.2% probability range ± 1σ uncertainty, respectively), with a mean age of 448 ± 15 ka. These new bracketing ages suggest that the hominin fossils at SH were most likely deposited within Marine Isotope Stage (MIS) 12, enabling more precise temporal constraint on the early evolution of the Neandertal lineage. The SH fossils represent the oldest reliably dated hominin remains displaying Neandertal features across Eurasia. These Neandertal features are first observed in the facial skeleton, including the mandible and teeth, as well as the temporomandibular joint, and appear consistently across the SH collection. Our chronological findings suggest that the appearance of these Neandertal traits may have been associated with the climatic demise of MIS 12 and the ecological changes that occurred in Iberia during this period. Other Middle Pleistocene hominin fossils from Europe dated to MIS 12-11, or later, show different morphological trends, with some lacking Neandertal specializations. The latest SH dating results enable improved temporal correlations with these contrasting hominin records from Europe, and suggest a complex picture for hominin evolution during the Middle Pleistocene.}, }
@article {pmid31182199, year = {2019}, author = {Radović, P and Lindal, J and Mihailović, D and Roksandic, M}, title = {The first Neanderthal specimen from Serbia: Maxillary first molar from the Late Pleistocene of Pešturina Cave.}, journal = {Journal of human evolution}, volume = {131}, number = {}, pages = {139-151}, doi = {10.1016/j.jhevol.2019.03.018}, pmid = {31182199}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; Fossils/*anatomy &amp; histology ; Maxilla ; Molar/*anatomy &amp; histology ; Neanderthals/*anatomy &amp; histology ; Paleodontology ; Serbia ; }, abstract = {Neanderthals were the only human group in Europe throughout the Late Pleistocene until the arrival of modern humans, and while their presence has been confirmed in the surrounding regions, no Neanderthal fossils are known to date from the Central Balkans. Systematic excavations of Pešturina Cave (Serbia) resulted in the discovery of a permanent right M[1] (Pes-3). The specimen was recovered from stratigraphic Layer 4b with an estimated age of 102.4 ± 3.2 ka, associated with Mousterian artifacts. The exceptional state of preservation and minimal wear of the molar enabled a detailed description and comparative analysis of the inner and outer dental structure, including non-metric dental traits and morphometric features of the crown, roots, and dental tissues. The results of this study strongly support the identification of Pes-3 as Neanderthal. Non-metric traits of the occlusal surface of the crown, enamel-dentine junction, and roots are consistent with Neanderthal morphology. The crown shows morphometric features typical for Neanderthal M[1], such as a buccolingually skewed crown shape, internally compressed cusps, and a relatively large hypocone. The specimen also shows Neanderthal-like dental tissue proportions, characterized by relatively thin enamel and large coronal dentine and coronal pulp volumes. The discovery of the Pes-3 molar therefore confirms the presence of Neanderthals in the territory of Serbia and the Central Balkans at the end of Marine Isotope Stage (MIS) 5c.}, }
@article {pmid31164119, year = {2019}, author = {Shebanits, K and Günther, T and Johansson, ACV and Maqbool, K and Feuk, L and Jakobsson, M and Larhammar, D}, title = {Copy number determination of the gene for the human pancreatic polypeptide receptor NPY4R using read depth analysis and droplet digital PCR.}, journal = {BMC biotechnology}, volume = {19}, number = {1}, pages = {31}, pmid = {31164119}, issn = {1472-6750}, mesh = {DNA Copy Number Variations/*genetics ; *Gene Dosage ; Genome, Human/genetics ; Genomics/methods ; Humans ; Polymerase Chain Reaction/*methods ; Receptors, Neuropeptide Y/*genetics ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: Copy number variation (CNV) plays an important role in human genetic diversity and has been associated with multiple complex disorders. Here we investigate a CNV on chromosome 10q11.22 that spans NPY4R, the gene for the appetite-regulating pancreatic polypeptide receptor Y4. This genomic region has been challenging to map due to multiple repeated elements and its precise organization has not yet been resolved. Previous studies using microarrays were interpreted to show that the most common copy number was 2 per genome.<br><br>RESULTS: We have investigated 18 individuals from the 1000 Genomes project using the well-established method of read depth analysis and the new droplet digital PCR (ddPCR) method. We find that the most common copy number for NPY4R is 4. The estimated number of copies ranged from three to seven based on read depth analyses with Control-FREEC and CNVnator, and from four to seven based on ddPCR. We suggest that the difference between our results and those published previously can be explained by methodological differences such as reference gene choice, data normalization and method reliability. Three high-quality archaic human genomes (two Neanderthal and one Denisova) display four copies of the NPY4R gene indicating that a duplication occurred prior to the human-Neanderthal/Denisova split.<br><br>CONCLUSIONS: We conclude that ddPCR is a sensitive and reliable method for CNV determination, that it can be used for read depth calibration in CNV studies based on already available whole-genome sequencing data, and that further investigation of NPY4R copy number variation and its consequences are necessary due to the role of Y4 receptor in food intake regulation.}, }
@article {pmid31163991, year = {2019}, author = {Santander, C and Montinaro, F and Capelli, C}, title = {Searching for archaic contribution in Africa.}, journal = {Annals of human biology}, volume = {46}, number = {2}, pages = {129-139}, doi = {10.1080/03014460.2019.1624823}, pmid = {31163991}, issn = {1464-5033}, mesh = {Africa ; Animals ; Black People/*genetics ; DNA, Ancient/*analysis ; Genome, Human ; Hominidae/*genetics ; Humans ; *Hybridization, Genetic ; }, abstract = {Context: Africa's role in the narrative of human evolution is indisputably emphasised in the emergence of Homo sapiens. However, once humans dispersed beyond Africa, the history of those who stayed remains vastly under-studied, lacking the proper attention the birthplace of both modern and archaic humans deserves. The sequencing of Neanderthal and Denisovan genomes has elucidated evidence of admixture between archaic and modern humans outside of Africa, but has not aided efforts in answering whether archaic admixture happened within Africa. Objectives: This article reviews the state of research for archaic introgression in African populations and discusses recent insights into this topic. Methods: Gathering published sources and recently released preprints, this review reports on the different methods developed for detecting archaic introgression. Particularly it discusses how relevant these are when implemented on African populations and what findings these studies have shown so far. Results: Methods for detecting archaic introgression have been predominantly developed and implemented on non-African populations. Recent preprints present new methods considering African populations. While a number of studies using these methods suggest archaic introgression in Africa, without an African archaic genome to validate these results, such findings remain as putative archaic introgression. Conclusion: In light of the caveats with implementing current archaic introgression detection methods in Africa, we recommend future studies to concentrate on unravelling the complicated demographic history of Africa through means of ancient DNA where possible and through more focused efforts to sequence modern DNA from more representative populations across the African continent.}, }
@article {pmid31155285, year = {2019}, author = {Silvert, M and Quintana-Murci, L and Rotival, M}, title = {Impact and Evolutionary Determinants of Neanderthal Introgression on Transcriptional and Post-Transcriptional Regulation.}, journal = {American journal of human genetics}, volume = {104}, number = {6}, pages = {1241-1250}, pmid = {31155285}, issn = {1537-6605}, mesh = {Adaptation, Physiological ; Adipogenesis ; Adipose Tissue/metabolism/pathology ; Animals ; *Evolution, Molecular ; *Gene Expression Regulation, Developmental ; Genome, Human ; Genomics ; Humans ; MicroRNAs/genetics ; Neanderthals/*genetics ; *Polymorphism, Single Nucleotide ; *RNA Processing, Post-Transcriptional ; Recombination, Genetic ; *Selection, Genetic ; T-Lymphocytes/metabolism/pathology ; *Transcription, Genetic ; }, abstract = {Archaic admixture is increasingly recognized as an important source of diversity in modern humans, and Neanderthal haplotypes cover 1%-3% of the genome of present-day Eurasians. Recent work has shown that archaic introgression has contributed to human phenotypic diversity, mostly through the regulation of gene expression. Yet the mechanisms through which archaic variants alter gene expression and the forces driving the introgression landscape at regulatory regions remain elusive. Here, we explored the impact of archaic introgression on transcriptional and post-transcriptional regulation. We focused on promoters and enhancers across 127 different tissues as well as on microRNA (miRNA)-mediated regulation. Although miRNAs themselves harbor few archaic variants, we found that some of these variants may have a strong impact on miRNA-mediated gene regulation. Enhancers were by far the regulatory elements most affected by archaic introgression: up to one-third of the tissues we tested presented significant enrichments. Specifically, we found strong enrichments of archaic variants in adipose-related tissues and primary T cells, even after accounting for various genomic and evolutionary confounders such as recombination rate and background selection. Interestingly, we identified signatures of adaptive introgression at enhancers of some key regulators of adipogenesis, raising the interesting hypothesis of a possible adaptation of early Eurasians to colder climates. Collectively, this study sheds new light on the mechanisms through which archaic admixture has impacted gene regulation in Eurasians and, more generally, increases our understanding of the contribution of Neanderthals to the regulation of acquired immunity and adipose homeostasis in modern humans.}, }
@article {pmid31141515, year = {2019}, author = {Degioanni, A and Bonenfant, C and Cabut, S and Condemi, S}, title = {Living on the edge: Was demographic weakness the cause of Neanderthal demise?.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0216742}, pmid = {31141515}, issn = {1932-6203}, mesh = {Animals ; Computer Simulation ; Demography/statistics &amp; numerical data ; Europe ; *Extinction, Biological ; Female ; Fossils ; History, Ancient ; Humans ; Male ; Models, Biological ; *Neanderthals/classification/genetics ; Population Dynamics/history ; Stochastic Processes ; }, abstract = {The causes of disappearance of the Neanderthals, the only human population living in Europe before the arrival of Homo sapiens, have been debated for decades by the scientific community. Different hypotheses have been advanced to explain this demise, such as cognitive, adaptive and cultural inferiority of Neanderthals. Here, we investigate the disappearance of Neanderthals by examining the extent of demographic changes needed over a period of 10,000 years (yrs) to lead to their extinction. In regard to such fossil populations, we inferred demographic parameters from present day and past hunter-gatherer populations, and from bio-anthropological rules. We used demographic modeling and simulations to identify the set of plausible demographic parameters of the Neanderthal population compatible with the observed dynamics, and to explore the circumstances under which they might have led to the disappearance of Neanderthals. A slight (<4%) but continuous decrease in the fertility rate of younger Neanderthal women could have had a significant impact on these dynamics, and could have precipitated their demise. Our results open the way to non-catastrophic events as plausible explanations for Neanderthal extinction.}, }
@article {pmid31136573, year = {2019}, author = {Durvasula, A and Sankararaman, S}, title = {A statistical model for reference-free inference of archaic local ancestry.}, journal = {PLoS genetics}, volume = {15}, number = {5}, pages = {e1008175}, pmid = {31136573}, issn = {1553-7404}, support = {R00 GM111744/GM/NIGMS NIH HHS/United States ; R35 GM125055/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Genetics, Population/*methods ; Genome, Human/genetics ; Genomics/*methods ; Hominidae/*genetics ; Humans ; Models, Statistical ; Neanderthals/genetics ; }, abstract = {Statistical analyses of genomic data from diverse human populations have demonstrated that archaic hominins, such as Neanderthals and Denisovans, interbred or admixed with the ancestors of present-day humans. Central to these analyses are methods for inferring archaic ancestry along the genomes of present-day individuals (archaic local ancestry). Methods for archaic local ancestry inference rely on the availability of reference genomes from the ancestral archaic populations for accurate inference. However, several instances of archaic admixture lack reference archaic genomes, making it difficult to characterize these events. We present a statistical method that combines diverse population genetic summary statistics to infer archaic local ancestry without access to an archaic reference genome. We validate the accuracy and robustness of our method in simulations. When applied to genomes of European individuals, our method recovers segments that are substantially enriched for Neanderthal ancestry, even though our method did not have access to any Neanderthal reference genomes.}, }
@article {pmid31114607, year = {2019}, author = {Liu, C and Everall, I and Pantelis, C and Bousman, C}, title = {Interrogating the Evolutionary Paradox of Schizophrenia: A Novel Framework and Evidence Supporting Recent Negative Selection of Schizophrenia Risk Alleles.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {389}, pmid = {31114607}, issn = {1664-8021}, abstract = {Schizophrenia is a psychiatric disorder with a worldwide prevalence of ∼1%. The high heritability and reduced fertility among schizophrenia patients have raised an evolutionary paradox: why has negative selection not eliminated schizophrenia associated alleles during evolution? To address this question, we examined evolutionary markers, known as modern-human-specific (MD) sites and archaic-human-specific sites, using existing genome-wide association study (GWAS) data from 34,241 individuals with schizophrenia and 45,604 healthy controls included in the Psychiatric Genomics Consortium (PGC). By testing the distribution of schizophrenia single nucleotide polymorphisms (SNPs) with risk and protective effects in the human-specific sites, we observed a negative selection of risk alleles for schizophrenia in modern humans relative to archaic humans (e.g., Neanderthal and Denisovans). Such findings indicate that risk alleles of schizophrenia have been gradually removed from the modern human genome due to negative selection pressure. This novel evidence contributes to our understanding of the genetic origins of schizophrenia.}, }
@article {pmid31113254, year = {2019}, author = {Ham, E and Underdown, SJ and Houldcroft, CJ}, title = {The relative roles of maternal survival and inter-personal violence as selection pressures on the persistence of Neanderthal hypercoagulability alleles in modern Europeans.}, journal = {Annals of human biology}, volume = {46}, number = {2}, pages = {99-108}, doi = {10.1080/03014460.2019.1622038}, pmid = {31113254}, issn = {1464-5033}, mesh = {Alleles ; Animals ; Europe ; Gene Frequency ; Humans ; Longevity/*genetics ; Mothers/*statistics &amp; numerical data ; Neanderthals/genetics ; P-Selectin/*genetics/metabolism ; Physical Abuse/*statistics &amp; numerical data ; Polymorphism, Single Nucleotide/*genetics ; *Selection, Genetic ; Tanzania ; Thrombophilia/genetics ; White People ; }, abstract = {Background: Simonti et al. reported variation in the frequency of Neanderthal alleles found in modern humans and argued that they may have provided an evolutionary advantage. One such allele is SNP rs3917862, associated with hypercoagulability. rs3917862 can be deleterious, but can also help prevent blood loss. Aim: To investigate two possible selective pressure hypotheses for rs3917862 surviving to higher frequencies: deaths from interpersonal violent trauma and childbirth. Subjects and methods: Mortality data from modern hunter-gatherers models the living conditions and causes of death of humans and Neanderthals at the point of admixture. Results: National census data indicates a positive correlation between the presence of rs3917862 and decreased maternal mortality ratios. When the maternal mortality ratio is modelled using GDP, births attended by skilled assistants and the presence of rs3917862, women are 0.1% more likely to die in childbirth in populations lacking rs3917862. Deaths due to violence show no correlation with rs3917862. Conclusion: These findings challenge the idea that Neanderthal admixture has negatively impacted the overall health of modern humans. Maternal survival may have acted as a selective pressure for the persistence of hypercoagulability alleles in modern Europeans. Understanding the role of hypercoagulability in childbirth, and the role of rs3917862, could help to reduce maternal mortality ratios.}, }
@article {pmid31106274, year = {2019}, author = {Gómez-Robles, A}, title = {Dental evolutionary rates and its implications for the Neanderthal-modern human divergence.}, journal = {Science advances}, volume = {5}, number = {5}, pages = {eaaw1268}, pmid = {31106274}, issn = {2375-2548}, mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; Computer Simulation ; DNA/analysis ; *Fossils ; Hominidae/genetics ; Humans ; Neanderthals ; Phylogeny ; Principal Component Analysis ; Spain ; Tooth/*physiology ; }, abstract = {The origin of Neanderthal and modern human lineages is a matter of intense debate. DNA analyses have generally indicated that both lineages diverged during the middle period of the Middle Pleistocene, an inferred time that has strongly influenced interpretations of the hominin fossil record. This divergence time, however, is not compatible with the anatomical and genetic Neanderthal affinities observed in Middle Pleistocene hominins from Sima de los Huesos (Spain), which are dated to 430 thousand years (ka) ago. Drawing on quantitative analyses of dental evolutionary rates and Bayesian analyses of hominin phylogenetic relationships, I show that any divergence time between Neanderthals and modern humans younger than 800 ka ago would have entailed unexpectedly rapid dental evolution in early Neanderthals from Sima de los Huesos. These results support a pre-800 ka last common ancestor for Neanderthals and modern humans unless hitherto unexplained mechanisms sped up dental evolution in early Neanderthals.}, }
@article {pmid31095578, year = {2019}, author = {Morales, JI and Cebrià, A and Burguet-Coca, A and Fernández-Marchena, JL and García-Argudo, G and Rodríguez-Hidalgo, A and Soto, M and Talamo, S and Tejero, JM and Vallverdú, J and Fullola, JM}, title = {The Middle-to-Upper Paleolithic transition occupations from Cova Foradada (Calafell, NE Iberia).}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0215832}, pmid = {31095578}, issn = {1932-6203}, mesh = {Animals ; *Archaeology ; Carnivory ; Caves ; Fossils ; *Neanderthals ; }, abstract = {The Middle-to-Upper Paleolithic transition in Europe covers the last millennia of Neanderthal life together with the appearance and expansion of Modern Human populations. Culturally, it is defined by the Late Middle Paleolithic succession, and by Early Upper Paleolithic complexes like the Châtelperronian (southwestern Europe), the Protoaurignacian, and the Early Aurignacian. Up to now, the southern boundary for the transition has been established as being situated between France and Iberia, in the Cantabrian façade and Pyrenees. According to this, the central and southern territories of Iberia are claimed to have been the refuge of the last Neanderthals for some additional millennia after they were replaced by anatomically Modern Humans on the rest of the continent. In this paper, we present the Middle-to-Upper Paleolithic transition sequence from Cova Foradada (Tarragona), a cave on the Catalan Mediterranean coastline. Archaeological research has documented a stratigraphic sequence containing a succession of very short-term occupations pertaining to the Châtelperronian, Early Aurignacian, and Gravettian. Cova Foradada therefore represents the southernmost Châtelperronian-Early Aurignacian sequence ever documented in Europe, significantly enlarging the territorial distribution of both cultures and providing an important geographical and chronological reference for understanding Neanderthal disappearance and the complete expansion of anatomically Modern Humans.}, }
@article {pmid31048924, year = {2019}, author = {Rhodes, SE and Starkovich, BM and Conard, NJ}, title = {Did climate determine Late Pleistocene settlement dynamics in the Ach Valley, SW Germany?.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0215172}, pmid = {31048924}, issn = {1932-6203}, mesh = {Animals ; *Archaeology ; Caves ; *Climate ; Ecosystem ; *Fossils ; Germany ; Humans ; Neanderthals/anatomy &amp; histology/metabolism ; Skull/anatomy &amp; histology/pathology ; Tooth/anatomy &amp; histology/pathology ; }, abstract = {The loss of Neanderthal groups across Western and Central Europe during Oxygen Isotope Stage (OIS) 3 has held the attention of archaeologists for decades. The role that climatic change, genetic interbreeding, and interspecies competition played in the extinction of Neanderthal groups is still debated. Hohle Fels is one of several important Middle and Upper Paleolithic sites from the Ach Valley in southwestern Germany which documents the presence of Neanderthals and modern humans in the region. Chronological and stratigraphic records indicate that these two groups occupied the site with little to no overlap or interaction. This provides the opportunity to examine the behavioural variability of Swabian Neanderthal populations without the complication of cross-cultural influence. In this study we contribute a terrestrial paleoenvironmental record derived from the small mammal material from Hohle Fels Cave to the ever-growing archaeological record of this period. By reconstructing the climate and landscape of the Ach Valley during this time we can identify the effect that the OIS 3 environment had on the presence of Neanderthals in the region. Based on indicator taxa and the habitat weighing method, the small mammal record, which includes rodents, insectivores, and bats, from Hohle Fels shows that the earliest Neanderthal occupation took place on a landscape characterized by substantial woodland and forest, rivers and ponds, as well as moist meadows and grasslands. A gradual increase in cold tundra and arctic environments is clear towards the end of the Middle Paleolithic, extending to the end of the early Aurignacian which may correlate with the onset of the Heinrich 4 event (~42,000 kya). Our taphonomic analysis indicates the material was accumulated primarily by opportunistic predators such as the great grey owl, snowy owl, and European eagle owl, and therefore reflects the diversity of landscapes present around the site in the past. Importantly, at the time Neanderthals abandoned the Ach Valley we find no indication for dramatic climatic deterioration. Rather, we find evidence of a gradual cooling of the Swabian landscape which may have pushed Neanderthal groups out of the Ach Valley prior to the arrival of modern human Aurignacian groups.}, }
@article {pmid31034533, year = {2019}, author = {Letsinger, AC and Granados, JZ and Little, SE and Lightfoot, JT}, title = {Alleles associated with physical activity levels are estimated to be older than anatomically modern humans.}, journal = {PloS one}, volume = {14}, number = {4}, pages = {e0216155}, pmid = {31034533}, issn = {1932-6203}, mesh = {*Alleles ; Animals ; Asian People/genetics ; Black People/genetics ; Exercise/*physiology ; Gene Frequency ; Genetics, Population ; Humans ; Mutation/genetics ; Neanderthals/genetics ; Pan troglodytes/genetics ; Polymorphism, Single Nucleotide/genetics ; Time Factors ; White People/genetics ; Black or African American ; }, abstract = {The purpose of this study was to determine the estimated mutation age and conservation of single-nucleotide polymorphisms (SNPs) associated with physical activity (PA) in humans. All human SNPs found to be significantly associated with PA levels in the literature were cross-referenced with the National Heart, Lung, and Blood Institute's Grand Opportunity Exome Sequencing Project to find estimated African-American (AA) and European-American (EA) mutation age. As a secondary measure of mutation age, SNPs were searched for in Hawk's mutation age prediction database which utilizes linkage equilibrium. To determine conservation among hominids, all SNPs were searched in the University of California, Santa Cruz Genome Browser, which contains Neanderthal and chimpanzee reference genomes. Six of the 104 SNPs associated with PA regulation were exon-located missense variants found in IFNAR2, PPARGC1A, PML, CTBP2, IL5RA, and APOE genes. The remaining 98 SNPs were located in non-protein coding regions. Average AA and EA estimated mutation age of the exon-located SNPs were 478.4 ± 327.5 kya and 542.1 ± 369.4 kya, respectively. There were four selective sweeps (suggestive of strong positive selection) of SNPs in humans when compared to Neanderthal or chimpanzee genomes. Exon-located PA candidate SNPs are older than the hypothesized emergence of anatomically modern humans. However, 95% of PA associated SNPs are found in intron and intergenic location. Across all SNPs, there seems to be a high level of conservation of alleles between humans, Neanderthals, and chimpanzees. However, the presence of four selective sweeps suggests there were selection pressures or drift unique to Homo sapiens that influenced the development of mutations associated with PA regulation.}, }
@article {pmid31025315, year = {2019}, author = {Bosman, AM and Harvati, K}, title = {A virtual assessment of the proposed suprainiac fossa on the early modern European calvaria from Cioclovina, Romania.}, journal = {American journal of physical anthropology}, volume = {169}, number = {3}, pages = {567-574}, doi = {10.1002/ajpa.23844}, pmid = {31025315}, issn = {1096-8644}, support = {//German Research Foundation/International ; }, mesh = {Animals ; Anthropology, Physical ; Fossils ; History, Ancient ; Humans ; Neanderthals/*anatomy &amp; histology ; Occipital Bone/*anatomy &amp; histology/diagnostic imaging ; Romania ; Tomography, X-Ray Computed ; }, abstract = {OBJECTIVES: The calvaria from Cioclovina (Romania) has been argued to possess some traits commonly ascribed to individuals belonging to the Neanderthal lineage, including a suprainiac fossa. However, its supranuchal morphology has only been evaluated with a qualitative analysis of the ectocranial surface. We evaluate whether the morphology of the supranuchal area of this specimen is homologous to the Neanderthal condition.<br><br>MATERIALS AND METHODS: We described in detail the external morphology, and, using computed tomography, investigated the internal morphology of the Cioclovina supranuchal area. We took measurements of the internal structures and calculated their relative contributions to total cranial vault thickness, which were compared to published data and evaluated with a principal component analysis (PCA).<br><br>RESULTS: The Cioclovina supranuchal region is characterized by superficial resorption present on the outer layer of the external table. Neither the diploic layer nor the external table decrease in relative thickness in the area above inion. In the PCA, Cioclovina falls within the convex hulls of recent modern Homo sapiens.<br><br>DISCUSSION: Our results show that the morphology of the Cioclovina supranuchal region does not correspond to the external and internal morphology of the typical Neanderthal suprainiac fossa. It cannot be characterized as a depression but rather as an area presenting superficial bone turnover. Together with earlier results, there is little phenotypic evidence that Cioclovina has high levels of Neanderthal ancestry. Our study demonstrates the usefulness of this quantitative method in assessing proposed Neanderthal-like suprainiac depressions in Upper Paleolithic and other fossil specimens.}, }
@article {pmid31017917, year = {2019}, author = {Leierer, L and Jambrina-Enríquez, M and Herrera-Herrera, AV and Connolly, R and Hernández, CM and Galván, B and Mallol, C}, title = {Insights into the timing, intensity and natural setting of Neanderthal occupation from the geoarchaeological study of combustion structures: A micromorphological and biomarker investigation of El Salt, unit Xb, Alcoy, Spain.}, journal = {PloS one}, volume = {14}, number = {4}, pages = {e0214955}, pmid = {31017917}, issn = {1932-6203}, mesh = {Animals ; *Archaeology ; *Fossils ; Humans ; *Neanderthals ; Spain ; }, abstract = {Middle Paleolithic lithic and faunal assemblages throughout Eurasia reflect short-term Neanderthal occupations, which suggest high group mobility. However, the timing of these short-term occupations, a key factor to assess group mobility and territorial range, remains unresolved. Anthropogenic combustion structures are prominent in the Middle Paleolithic record and conceal information on the timing and intensity and natural setting of their associated human occupations. This paper examines a concentration of eleven combustion structures from unit Xb of El Salt, a Middle Paleolithic site in Spain through a geoarchaeological approach, in search of temporal, human impact and paleoenvironmental indicators to assess the timing, intensity and natural setting of the associated human occupations. The study was conducted using micromorphology, lipid biomarker analysis and compound specific isotope analysis. Results show in situ hearths built on different diachronic topsoils rich in herbivore excrements and angiosperm plant residues with rare anthropogenic remains. These data are suggestive of low impact, short-term human occupations separated by relatively long periods of time, with possible indicators of seasonality. Results also show an absence of conifer biomarkers in the mentioned topsoils and presence of conifer charcoal among the fuel residues (ash), indicating that fire wood was brought to the site from elsewhere. A microscopic and molecular approach in the study of combustion structures allows us to narrow down the timescale of archaeological analysis and contributes valuable information towards an understanding of Neanderthal group mobility and settlement patterns.}, }
@article {pmid30981557, year = {2019}, author = {Jacobs, GS and Hudjashov, G and Saag, L and Kusuma, P and Darusallam, CC and Lawson, DJ and Mondal, M and Pagani, L and Ricaut, FX and Stoneking, M and Metspalu, M and Sudoyo, H and Lansing, JS and Cox, MP}, title = {Multiple Deeply Divergent Denisovan Ancestries in Papuans.}, journal = {Cell}, volume = {177}, number = {4}, pages = {1010-1021.e32}, doi = {10.1016/j.cell.2019.02.035}, pmid = {30981557}, issn = {1097-4172}, mesh = {Animals ; Asian People/genetics ; Biological Evolution ; Gene Flow ; Genetic Introgression/*genetics ; Genetic Variation/genetics ; Genome, Human/genetics ; Haplotypes/*genetics ; Hominidae/*genetics ; Humans ; Indonesia ; Neanderthals/genetics ; Oceania ; }, abstract = {Genome sequences are known for two archaic hominins-Neanderthals and Denisovans-which interbred with anatomically modern humans as they dispersed out of Africa. We identified high-confidence archaic haplotypes in 161 new genomes spanning 14 island groups in Island Southeast Asia and New Guinea and found large stretches of DNA that are inconsistent with a single introgressing Denisovan origin. Instead, modern Papuans carry hundreds of gene variants from two deeply divergent Denisovan lineages that separated over 350 thousand years ago. Spatial and temporal structure among these lineages suggest that introgression from one of these Denisovan groups predominantly took place east of the Wallace line and continued until near the end of the Pleistocene. A third Denisovan lineage occurs in modern East Asians. This regional mosaic suggests considerable complexity in archaic contact, with modern humans interbreeding with multiple Denisovan groups that were geographically isolated from each other over deep evolutionary time.}, }
@article {pmid30975994, year = {2019}, author = {Rotival, M and Quach, H and Quintana-Murci, L}, title = {Defining the genetic and evolutionary architecture of alternative splicing in response to infection.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {1671}, pmid = {30975994}, issn = {2041-1723}, mesh = {Alternative Splicing/*immunology ; Animals ; Biological Evolution ; Black People/genetics ; Genetic Variation/immunology ; Healthy Volunteers ; Humans ; Immunity/*genetics ; Infections/*immunology ; Male ; Neanderthals/genetics ; Polymorphism, Single Nucleotide ; Protein Isoforms/genetics/immunology ; Quantitative Trait Loci/immunology ; Selection, Genetic/*immunology ; Sequence Analysis, RNA ; Transcriptome/*immunology ; White People/genetics ; Exome Sequencing ; }, abstract = {Host and environmental factors contribute to variation in human immune responses, yet the genetic and evolutionary drivers of alternative splicing in response to infection remain largely uncharacterised. Leveraging 970 RNA-sequencing profiles of resting and stimulated monocytes from 200 individuals of African- and European-descent, we show that immune activation elicits a marked remodelling of the isoform repertoire, while increasing the levels of erroneous splicing. We identify 1,464 loci associated with variation in isoform usage (sQTLs), 9% of them being stimulation-specific, which are enriched in disease-related loci. Furthermore, we detect a longstanding increased plasticity of immune gene splicing, and show that positive selection and Neanderthal introgression have both contributed to diversify the splicing landscape of human populations. Together, these findings suggest that differential isoform usage has been an important substrate of innovation in the long-term evolution of immune responses and a more recent vehicle of population local adaptation.}, }
@article {pmid30943255, year = {2019}, author = {Moncel, MH and Fernandes, P and Willmes, M and James, H and Grün, R}, title = {Rocks, teeth, and tools: New insights into early Neanderthal mobility strategies in South-Eastern France from lithic reconstructions and strontium isotope analysis.}, journal = {PloS one}, volume = {14}, number = {4}, pages = {e0214925}, pmid = {30943255}, issn = {1932-6203}, mesh = {Animals ; *Archaeology ; *Climate ; *Fossils ; France ; *Neanderthals/anatomy &amp; histology/metabolism ; Strontium Isotopes/*analysis ; *Tooth/anatomy &amp; histology/chemistry/metabolism ; }, abstract = {Neanderthals had complex land use patterns, adapting to diversified landscapes and climates. Over the past decade, considerable progress has been made in reconstructing the chronology, land use and subsistence patterns, and occupation types of sites in the Rhône Valley, southeast France. In this study, Neanderthal mobility at the site of Payre is investigated by combining information from lithic procurement analysis ("chaîne evolutive" and "chaîne opératoire" concepts) and strontium isotope analysis of teeth (childhood foraging area), from two units (F and G). Both units date to the transition from Marine Isotope Stage (MIS) 8 to MIS 7, and show similar environmental conditions, but represent contrasting occupation durations. Level Gb (unit G) represents a long-term year-round use, in contrast to short-term seasonal use of the cave in level Fb (unit F). For both levels, lithic material and food were generally collected from a local to semi-local region. However, in level Gb, lithic materials were mainly collected from colluviums and food collected in the valley, whereas in level Fb, lithic procurement focused primarily on alluvial deposits and food was collected from higher elevation plateaus. These procurement or exchange patterns might be related to flint availability, knapping advantages of alluvial flint or occupation duration. The site of Payre is located in a flint rich circulation corridor and the movement of groups or exchanges between groups were organized along a north-south axis on the plateaus or towards the east following the river. The ridges were widely used as they are rich in flint, whereas the Rhône Valley is not an important source of lithic raw materials. Compared to other western European Middle Palaeolithic sites, these results indicate that procurement strategies have a moderate link with occupation types and duration, and with lithic technology. The Sr isotope ratios broadly match the proposed foraging areas, with the Rhône Valley being predominantly used in unit G and the ridges and limestone plateaus in unit F. While lithic reconstructions and childhood foraging are not directly related this suggests that the three analysed Neanderthals spend their childhood in the same general area and supports the idea of mobile Neanderthals in the Rhône Valley and neighbouring higher elevation plateaus. The combination of reconstructing lithic raw material sources, provisioning strategies, and strontium isotope analyses provides new details on how Neanderthals at Payre practised land use and mobility in the Early Middle Palaeolithic.}, }
@article {pmid30942856, year = {2019}, author = {Harris, DN and Ruczinski, I and Yanek, LR and Becker, LC and Becker, DM and Guio, H and Cui, T and Chilton, FH and Mathias, RA and O'Connor, TD}, title = {Evolution of Hominin Polyunsaturated Fatty Acid Metabolism: From Africa to the New World.}, journal = {Genome biology and evolution}, volume = {11}, number = {5}, pages = {1417-1430}, pmid = {30942856}, issn = {1759-6653}, support = {R01 AT008621/AT/NCCIH NIH HHS/United States ; R01 HL087698/HL/NHLBI NIH HHS/United States ; R01 HL112064/HL/NHLBI NIH HHS/United States ; U01 HL072518/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; *Evolution, Molecular ; Fatty Acid Desaturases/*genetics/metabolism ; Fatty Acids, Unsaturated/*metabolism ; Hominidae/*genetics/metabolism ; Humans ; Indians, North American/genetics ; Selection, Genetic ; Siberia ; }, abstract = {The metabolic conversion of dietary omega-3 and omega-6 18 carbon (18C) to long chain (>20 carbon) polyunsaturated fatty acids (LC-PUFAs) is vital for human life. The rate-limiting steps of this process are catalyzed by fatty acid desaturase (FADS) 1 and 2. Therefore, understanding the evolutionary history of the FADS genes is essential to our understanding of hominin evolution. The FADS genes have two haplogroups, ancestral and derived, with the derived haplogroup being associated with more efficient LC-PUFA biosynthesis than the ancestral haplogroup. In addition, there is a complex global distribution of these haplogroups that is suggestive of Neanderthal introgression. We confirm that Native American ancestry is nearly fixed for the ancestral haplogroup, and replicate a positive selection signal in Native Americans. This positive selection potentially continued after the founding of the Americas, although simulations suggest that the timing is dependent on the allele frequency of the ancestral Beringian population. We also find that the Neanderthal FADS haplotype is more closely related to the derived haplogroup and the Denisovan clusters closer to the ancestral haplogroup. Furthermore, the derived haplogroup has a time to the most recent common ancestor of 688,474 years before present. These results support an ancient polymorphism, as opposed to Neanderthal introgression, forming in the FADS region during the Pleistocene with possibly differential selection pressures on both haplogroups. The near fixation of the ancestral haplogroup in Native American ancestry calls for future studies to explore the potential health risk of associated low LC-PUFA levels in these populations.}, }
@article {pmid30904042, year = {2019}, author = {Poza-Rey, EM and Gómez-Robles, A and Arsuaga, JL}, title = {Brain size and organization in the Middle Pleistocene hominins from Sima de los Huesos. Inferences from endocranial variation.}, journal = {Journal of human evolution}, volume = {129}, number = {}, pages = {67-90}, doi = {10.1016/j.jhevol.2019.01.006}, pmid = {30904042}, issn = {1095-8606}, mesh = {Animals ; Biological Evolution ; Brain/*anatomy &amp; histology ; Neanderthals/*anatomy &amp; histology ; Organ Size ; Skull/*anatomy &amp; histology ; }, abstract = {The Sima de los Huesos (SH) endocranial sample includes 16 complete or partial endocasts corresponding to European Middle Pleistocene hominins. Different anatomical and molecular studies have demonstrated that these hominins are phylogenetically related to Neanderthals, thus making them the earliest unquestionable representatives of the Neanderthal lineage. The description of endocranial variation in this population is fundamental to shedding light on the evolution of the Neanderthal brain. In this contribution, we analyze and describe endocranial variation in this sample, including aspects related to brain size (endocranial volume and encephalization) and brain organization (through qualitative descriptions and quantitative analyses). Our results indicate that the SH hominins show a transitional state between a primitive hominin endocranial configuration (which is found in Homo erectus and non-SH Middle Pleistocene Homo) and the derived configurations found in Neanderthals and modern humans, without a clear anticipation of classic Neanderthal endocranial traits. In comparison with other cranial and postcranial traits that show a fully Neanderthal or clear pre-Neanderthal condition in the SH collection, endocranial variation in these hominins is surprisingly primitive and shows no Neanderthal affinity. These results and the comparison with other cranial traits confirm that Neanderthals evolved in a mosaic fashion. Traits related to mastication (dental, facial and mandibular anatomy) led the Neanderthalization process, whereas neurocranial anatomy must have acquired a fully Neanderthal condition considerably later.}, }
@article {pmid30889271, year = {2019}, author = {Vyas, DN and Mulligan, CJ}, title = {Analyses of Neanderthal introgression suggest that Levantine and southern Arabian populations have a shared population history.}, journal = {American journal of physical anthropology}, volume = {169}, number = {2}, pages = {227-239}, doi = {10.1002/ajpa.23818}, pmid = {30889271}, issn = {1096-8644}, support = {BCS-1258965//National Science Foundation/International ; }, mesh = {Animals ; Arabia ; Gene Flow/genetics ; Gene Frequency/genetics ; *Genetics, Population ; History, Ancient ; Human Migration/*history ; Humans ; Middle East ; Neanderthals/*genetics ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {OBJECTIVES: Modern humans are thought to have interbred with Neanderthals in the Near East soon after modern humans dispersed out of Africa. This introgression event likely took place in either the Levant or southern Arabia depending on the dispersal route out of Africa that was followed. In this study, we compare Neanderthal introgression in contemporary Levantine and southern Arabian populations to investigate Neanderthal introgression and to study Near Eastern population history.<br><br>MATERIALS AND METHODS: We analyzed genotyping data on >400,000 autosomal SNPs from seven Levantine and five southern Arabian populations and compared these data to those from populations from around the world including Neanderthal and Denisovan genomes. We used f4 and D statistics to estimate and compare levels of Neanderthal introgression between Levantine, southern Arabian, and comparative global populations. We also identified 1,581 putative Neanderthal-introgressed SNPs within our dataset and analyzed their allele frequencies as a means to compare introgression patterns in Levantine and southern Arabian genomes.<br><br>RESULTS: We find that Levantine and southern Arabian populations have similar levels of Neanderthal introgression to each other but lower levels than other non-Africans. Furthermore, we find that introgressed SNPs have very similar allele frequencies in the Levant and southern Arabia, which indicates that Neanderthal introgression is similarly distributed in Levantine and southern Arabian genomes.<br><br>DISCUSSION: We infer that the ancestors of contemporary Levantine and southern Arabian populations received Neanderthal introgression prior to separating from each other and that there has been extensive gene flow between these populations.}, }
@article {pmid30872714, year = {2019}, author = {Wißing, C and Rougier, H and Baumann, C and Comeyne, A and Crevecoeur, I and Drucker, DG and Gaudzinski-Windheuser, S and Germonpré, M and Gómez-Olivencia, A and Krause, J and Matthies, T and Naito, YI and Posth, C and Semal, P and Street, M and Bocherens, H}, title = {Stable isotopes reveal patterns of diet and mobility in the last Neandertals and first modern humans in Europe.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {4433}, pmid = {30872714}, issn = {2045-2322}, mesh = {Animals ; Anthropology, Physical ; *Biological Evolution ; Carbon Radioisotopes/*analysis ; Diet/statistics &amp; numerical data/*trends ; Dietary Proteins/analysis ; *Ecosystem ; Emigration and Immigration/*statistics &amp; numerical data ; Fossils ; Hominidae ; Humans ; Neanderthals ; Nitrogen Radioisotopes/*analysis ; Sulfur Radioisotopes/*analysis ; }, abstract = {Correlating cultural, technological and ecological aspects of both Upper Pleistocene modern humans (UPMHs) and Neandertals provides a useful approach for achieving robust predictions about what makes us human. Here we present ecological information for a period of special relevance in human evolution, the time of replacement of Neandertals by modern humans during the Late Pleistocene in Europe. Using the stable isotopic approach, we shed light on aspects of diet and mobility of the late Neandertals and UPMHs from the cave sites of the Troisième caverne of Goyet and Spy in Belgium. We demonstrate that their diet was essentially similar, relying on the same terrestrial herbivores, whereas mobility strategies indicate considerable differences between Neandertal groups, as well as in comparison to UPMHs. Our results indicate that UPMHs exploited their environment to a greater extent than Neandertals and support the hypothesis that UPMHs had a substantial impact not only on the population dynamics of large mammals but also on the whole structure of the ecosystem since their initial arrival in Europe.}, }
@article {pmid30861048, year = {2019}, author = {Nowaczewska, W and Binkowski, M and Kubicka, AM and Piontek, J and Balzeau, A}, title = {Neandertal-like traits visible in the internal structure of non-supranuchal fossae of some recent Homo sapiens: The problem of their identification in hominins and phylogenetic implications.}, journal = {PloS one}, volume = {14}, number = {3}, pages = {e0213687}, pmid = {30861048}, issn = {1932-6203}, mesh = {Adult ; Animals ; *Anthropology, Physical ; Australia ; Biological Evolution ; Child ; Child, Preschool ; Fossils ; Hominidae/*anatomy &amp; histology ; Humans ; Image Processing, Computer-Assisted ; Imaging, Three-Dimensional ; Neanderthals/*anatomy &amp; histology ; Occipital Bone/*anatomy &amp; histology ; Phenotype ; Phylogeny ; }, abstract = {Although recently the internal structure of the non-supranuchal fossa of Homo sapiens has been described and compared to that observed in the Neandertal suprainiac fossa, until now it has not been examined in any modern human children. In this study, the internal structure of this fossa in the occipital bones of three children (two aged 3‒4 years and one aged 5 years ± 16 months) and one adult individual representing recent Homo sapiens from Australia was analysed and compared to that of the Neandertal suprainiac fossa. In order to analyse the internal composition of the fossae of the examined specimens, initially, high-resolution micro-CT datasets were obtained for their occipital bones; next, 3D topographic maps of the variation in thickness of structural layers of the occipital bones were made and 2D virtual sections in the median region of these fossae were prepared. In the fossa of one immature individual, the thinning of the diploic layer characteristic of a Neandertal suprainiac fossa was firmly diagnosed. The other Neandertal-like trait, concerning the lack of substantial thinning of the external table of the bone in the region of the fossa, was established in two individuals (one child and one adult) due to the observation of an irregular pattern of the thickness of this table in the other specimens, suggesting the presence of an inflammatory process. Our study presents, for the first time, Neandertal-like traits (but not the whole set of features that justifies the autapomorphic status of the Neandertal supraniac fossa) in the internal structure of non-supranuchal fossae of some recent Homo sapiens. We discuss the phylogenetic implications of the results of our analysis and stress the reasons that use of the 3D topographic mapping method is important for the correct diagnosis of Neandertal traits of the internal structure of occipital fossae.}, }
@article {pmid30836076, year = {2019}, author = {Gunz, P and Tilot, AK and Wittfeld, K and Teumer, A and Shapland, CY and van Erp, TGM and Dannemann, M and Vernot, B and Neubauer, S and Guadalupe, T and Fernández, G and Brunner, HG and Enard, W and Fallon, J and Hosten, N and Völker, U and Profico, A and Di Vincenzo, F and Manzi, G and Kelso, J and St Pourcain, B and Hublin, JJ and Franke, B and Pääbo, S and Macciardi, F and Grabe, HJ and Fisher, SE}, title = {Neandertal Introgression Sheds Light on Modern Human Endocranial Globularity.}, journal = {Current biology : CB}, volume = {29}, number = {5}, pages = {895}, doi = {10.1016/j.cub.2019.02.008}, pmid = {30836076}, issn = {1879-0445}, support = {U24 RR021992/RR/NCRR NIH HHS/United States ; U24 RR025736/RR/NCRR NIH HHS/United States ; U54 EB020403/EB/NIBIB NIH HHS/United States ; }, }
@article {pmid30825980, year = {2019}, author = {Pablos, A and Gómez-Olivencia, A and Maureille, B and Holliday, TW and Madelaine, S and Trinkaus, E and Couture-Veschambre, C}, title = {Neandertal foot remains from Regourdou 1 (Montignac-sur-Vézère, Dordogne, France).}, journal = {Journal of human evolution}, volume = {128}, number = {}, pages = {17-44}, doi = {10.1016/j.jhevol.2018.11.003}, pmid = {30825980}, issn = {1095-8606}, mesh = {Animals ; Anthropology, Physical ; Foot/*anatomy &amp; histology ; Fossils/*anatomy &amp; histology ; France ; Male ; Neanderthals/*anatomy &amp; histology ; }, abstract = {Regourdou is a well-known Middle Paleolithic site which has yielded the fossil remains of a minimum of two Neandertal individuals. The first individual (Regourdou 1) is represented by a partial skeleton while the second one is represented by a calcaneus. The foot remains of Regourdou 1 have been used in a number of comparative studies, but to date a full description and comparison of all the foot remains from the Regourdou 1 Neandertal, coming from the old excavations and from the recent reanalysis of the faunal remains, does not exist. Here, we describe and comparatively assess the Regourdou 1 tarsals, metatarsals and phalanges. They display traits observed in other Neandertal feet, which are different from some traits of the Sima de los Huesos (Atapuerca) hominins and of Middle Paleolithic, Upper Paleolithic and recent modern humans. These Neandertal features are: a rectangular talar trochlea with a large lateral malleolar facet, a broad talar head, a broad calcaneus with a projecting sustentaculum tali, a wide and wedged navicular with a projecting medial tubercle, large and wide bases of the lateral metatarsals, and mediolaterally expanded and robust phalanges that also show hallux valgus in a strongly built hallux.}, }
@article {pmid30804177, year = {2019}, author = {Haeusler, M and Trinkaus, E and Fornai, C and Müller, J and Bonneau, N and Boeni, T and Frater, N}, title = {Morphology, pathology, and the vertebral posture of the La Chapelle-aux-Saints Neandertal.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {11}, pages = {4923-4927}, pmid = {30804177}, issn = {1091-6490}, mesh = {Aged ; Animals ; Humans ; Male ; Neanderthals/*anatomy &amp; histology/*physiology ; Osteoarthritis/pathology/physiopathology ; Pelvis/anatomy &amp; histology ; *Posture ; Spinal Curvatures/physiopathology ; Spine/*pathology/physiopathology ; }, abstract = {Although the early postural reconstructions of the Neandertals as incompletely erect were rejected half a century ago, recent studies of Neandertal vertebral remains have inferred a hypolordotic, flat lower back and spinal imbalance for them, including the La Chapelle-aux-Saints 1 skeleton. These studies form part of a persistent trend to view the Neandertals as less "human" than ourselves despite growing evidence for little if any differences in basic functional anatomy and behavioral capabilities. We have therefore reassessed the spinal posture of La Chapelle-aux-Saints 1 using a new pelvic reconstruction to infer lumbar lordosis, interarticulation of lower lumbar (L4-S1) and cervical (C4-T2) vertebrae, and consideration of his widespread age-related osteoarthritis. La Chapelle-aux-Saints 1 exhibits a pelvic incidence (and hence lumbar lordosis) similar to modern humans, articulation of lumbar and cervical vertebrae indicating pronounced lordosis, and Baastrup disease as a product of his advanced age, osteoarthritis, and lordosis. Our findings challenge the view of generally small spinal curvatures in Neandertals. Setting aside the developmentally abnormal Kebara 2 vertebral column, La Chapelle-aux-Saints 1 is joined by other Neandertals with sufficient vertebral remains in providing them with a fully upright (and human) axial posture.}, }
@article {pmid30782806, year = {2019}, author = {Jaouen, K and Richards, MP and Le Cabec, A and Welker, F and Rendu, W and Hublin, JJ and Soressi, M and Talamo, S}, title = {Exceptionally high δ[15]N values in collagen single amino acids confirm Neandertals as high-trophic level carnivores.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {11}, pages = {4928-4933}, pmid = {30782806}, issn = {1091-6490}, mesh = {Amino Acids/*analysis ; Animals ; Carbon Isotopes/analysis ; Carnivora/*physiology ; Collagen/*chemistry ; *Food Chain ; Neanderthals/*physiology ; Nitrogen Isotopes/*analysis ; }, abstract = {Isotope and archeological analyses of Paleolithic food webs have suggested that Neandertal subsistence relied mainly on the consumption of large herbivores. This conclusion was primarily based on elevated nitrogen isotope ratios in Neandertal bone collagen and has been significantly debated. This discussion relies on the observation that similar high nitrogen isotopes values could also be the result of the consumption of mammoths, young animals, putrid meat, cooked food, freshwater fish, carnivores, or mushrooms. Recently, compound-specific C and N isotope analyses of bone collagen amino acids have been demonstrated to add significantly more information about trophic levels and aquatic food consumption. We undertook single amino acid C and N isotope analysis on two Neandertals, which were characterized by exceptionally high N isotope ratios in their bulk bone or tooth collagen. We report here both C and N isotope ratios on single amino acids of collagen samples for these two Neandertals and associated fauna. The samples come from two sites dating to the Middle to Upper Paleolithic transition period (Les Cottés and Grotte du Renne, France). Our results reinforce the interpretation of Neandertal dietary adaptations as successful top-level carnivores, even after the arrival of modern humans in Europe. They also demonstrate that high δ[15]N values of bone collagen can solely be explained by mammal meat consumption, as supported by archeological and zooarcheological evidence, without necessarily invoking explanations including the processing of food (cooking, fermenting), the consumption of mammoths or young mammals, or additional (freshwater fish, mushrooms) dietary protein sources.}, }
@article {pmid30777361, year = {2019}, author = {Martinón-Torres, M and Bermúdez de Castro, JM and Martínez de Pinillos, M and Modesto-Mata, M and Xing, S and Martín-Francés, L and García-Campos, C and Wu, X and Liu, W}, title = {New permanent teeth from Gran Dolina-TD6 (Sierra de Atapuerca). The bearing of Homo antecessor on the evolutionary scenario of Early and Middle Pleistocene Europe.}, journal = {Journal of human evolution}, volume = {127}, number = {}, pages = {93-117}, doi = {10.1016/j.jhevol.2018.12.001}, pmid = {30777361}, issn = {1095-8606}, mesh = {Animals ; Anthropology, Physical ; *Biological Evolution ; Fossils/*anatomy &amp; histology ; Hominidae/*anatomy &amp; histology/classification ; Spain ; Tooth/*anatomy &amp; histology ; }, abstract = {Here we analyze the unpublished hominin dental remains recovered from the late Early Pleistocene Gran Dolina-TD6.2 level of the Sierra de Atapuerca (northern Spain), as well as provide a reassessment of the whole TD6.2 hominin dental sample. Comparative descriptions of the outer enamel surface (OES) and the enamel-dentine junction (EDJ) are provided. Overall, the data presented here support the taxonomic validity of Homo antecessor, since this species presents a unique mosaic of traits. Homo antecessor displays several primitive features for the genus Homo as well as some traits exclusively shared with Early and Middle Pleistocene Eurasian hominins. Some of these Eurasian traits were retained by the Middle Pleistocene hominins of Europe, and subsequently became the typical condition of the Neanderthal lineage. Although other skeletal parts present resemblances with Homo sapiens, TD6.2 teeth do not show any synapomorphy with modern humans. In addition, TD6.2 teeth can be well differentiated from those of Asian Homo erectus. The dental evidence is compatible with previous hypothesis about H. antecessor belonging to the basal population from which H. sapiens, Homo neanderthalensis, and Denisovans emerged. Future findings and additional research may help to elucidate the precise phylogenetic link among them.}, }
@article {pmid30777356, year = {2019}, author = {Dinnis, R and Bessudnov, A and Reynolds, N and Devièse, T and Pate, A and Sablin, M and Sinitsyn, A and Higham, T}, title = {New data for the Early Upper Paleolithic of Kostenki (Russia).}, journal = {Journal of human evolution}, volume = {127}, number = {}, pages = {21-40}, doi = {10.1016/j.jhevol.2018.11.012}, pmid = {30777356}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; Humans ; Neanderthals ; *Radiometric Dating ; Russia ; *Technology ; }, abstract = {Several questions remain regarding the timing and nature of the Neanderthal-anatomically modern human (AMH) transition in Europe. The situation in Eastern Europe is generally less clear due to the relatively few sites and a dearth of reliable radiocarbon dates. Claims have been made for both notably early AMH and notably late Neanderthal presence, as well as for early AMH (Aurignacian) dispersal into the region from Central/Western Europe. The Kostenki-Borshchevo complex (European Russia) of Early Upper Paleolithic (EUP) sites offers high-quality data to address these questions. Here we revise the chronology and cultural status of the key sites of Kostenki 17 and Kostenki 14. The Kostenki 17/II lithic assemblage shares important features with Proto-Aurignacian material, strengthening an association with AMHs. New radiocarbon dates for Kostenki 17/II of ∼41-40 ka cal BP agree with new dates for the recently excavated Kostenki 14/IVw, which shows some similarities to Kostenki 17/II. Dates of ≥41 ka cal BP from other Kostenki sites cannot be linked to diagnostic archaeological material, and therefore cannot be argued to date AMH occupation. Kostenki 14's Layer in Volcanic Ash assemblage, on the other hand, compares to Early Aurignacian material. New radiocarbon dates targeting diagnostic lithics date to 39-37 ka cal BP. Overall, Kostenki's early EUP is in good agreement with the archaeological record further west. Our results are therefore consistent with models predicting interregional penecontemporaneity of diagnostic EUP assemblages. Most importantly, our work highlights ongoing challenges for reliably radiocarbon dating the period. Dates for Kostenki 14 agreed with the samples' chronostratigraphic positions, but standard pre-treatment methods consistently produced incorrect ages for Kostenki 17/II. Extraction of hydroxyproline from bone collagen using preparative high-performance liquid chromatography, however, yielded results consistent with the samples' chronostratigraphic position and with the layer's archaeological contents. This suggests that for some sites compound-specific techniques are required to build reliable radiocarbon chronologies.}, }
@article {pmid30773169, year = {2019}, author = {Buttura, RV and Ramalho, J and Lima, THA and Donadi, EA and Veiga-Castelli, LC and Mendes-Junior, CT and Castelli, EC}, title = {HLA-F displays highly divergent and frequent haplotype lineages associated with different mRNA expression levels.}, journal = {Human immunology}, volume = {80}, number = {2}, pages = {112-119}, doi = {10.1016/j.humimm.2018.10.016}, pmid = {30773169}, issn = {1879-1166}, mesh = {Animals ; Brazil ; Gene Expression Regulation ; Gene Frequency ; Genetics, Population ; Haplotypes ; High-Throughput Nucleotide Sequencing ; Histocompatibility Antigens Class I/*genetics ; Humans ; Linkage Disequilibrium ; Neanderthals/genetics ; Polymorphism, Genetic ; Promoter Regions, Genetic/*genetics ; RNA, Messenger/*genetics ; }, abstract = {HLA-F is one of the most conserved loci among the HLA gene family. The exact function of HLA-F is still under investigation. HLA-F might present tolerogenic features, participate in the stabilization of HLA molecules in open conformation, and also participate in the recycling of HLA molecules. Here we evaluate the variability and haplotype structure of the HLA-F distal promoter segment (from -1893 to -943) and how this segment is correlated with the coding region. Variability at the promoter segment was surveyed in 196 Brazilian samples using second-generation sequencing. The HLA-F promoter region presents two major haplotype lineages. Most of the variable sites are in perfect linkage and associated with a single promoter haplotype, here named F[∗]distal-C. This haplotype is associated with F[∗]01:01:02 alleles, while alleles from the F[∗]01:01:01 or F[∗]01:03 groups present closely related promoter sequences. F[∗]distal-C is quite frequent in Brazil and in worldwide populations, with frequencies ranging from 8.41% at the Iberian Population in Spain to 34.34% in Vietnam. F[∗]distal-C is also present in Neanderthal and Denisovan samples. In silico analyses demonstrated that F[∗]distal-C presents a different transcription factor binding profile compared with other HLA-F promoters. Moreover, individuals carrying this haplotype present higher HLA-F mRNA expression levels. Functional studies are required to define the exact mechanism underlying this higher HLA-F mRNA expression level associated with F[∗]distal-C and F[∗]01:01:02 alleles.}, }
@article {pmid30772945, year = {2019}, author = {James, WPT and Johnson, RJ and Speakman, JR and Wallace, DC and Frühbeck, G and Iversen, PO and Stover, PJ}, title = {Nutrition and its role in human evolution.}, journal = {Journal of internal medicine}, volume = {285}, number = {5}, pages = {533-549}, doi = {10.1111/joim.12878}, pmid = {30772945}, issn = {1365-2796}, mesh = {Animals ; *Biological Evolution ; DNA, Mitochondrial/genetics ; Emigration and Immigration ; Hominidae/genetics/*physiology ; Humans ; Mutation ; *Nutritional Physiological Phenomena ; }, abstract = {Our understanding of human evolution has improved rapidly over recent decades, facilitated by large-scale cataloguing of genomic variability amongst both modern and archaic humans. It seems clear that the evolution of the ancestors of chimpanzees and hominins separated 7-9 million years ago with some migration out of Africa by the earlier hominins; Homo sapiens slowly emerged as climate change resulted in drier, less forested African conditions. The African populations expanded and evolved in many different conditions with slow mutation and selection rates in the human genome, but with much more rapid mutation occurring in mitochondrial DNA. We now have evidence stretching back 300 000 years of humans in their current form, but there are clearly four very different large African language groups that correlate with population DNA differences. Then, about 50 000-100 000 years ago a small subset of modern humans also migrated out of Africa resulting in a persistent signature of more limited genetic diversity amongst non-African populations. Hybridization with archaic hominins occurred around this time such that all non-African modern humans possess some Neanderthal ancestry and Melanesian populations additionally possess some Denisovan ancestry. Human populations both within and outside Africa also adapted to diverse aspects of their local environment including altitude, climate, UV exposure, diet and pathogens, in some cases leaving clear signatures of patterns of genetic variation. Notable examples include haemoglobin changes conferring resistance to malaria, other immune changes and the skin adaptations favouring the synthesis of vitamin D. As humans migrated across Eurasia, further major mitochondrial changes occurred with some interbreeding with ancient hominins and the development of alcohol intolerance. More recently, an ability to retain lactase persistence into adulthood has evolved rapidly under the environmental stimulus of pastoralism with the ability to husband lactating ruminants. Increased amylase copy numbers seem to relate to the availability of starchy foods, whereas the capacity to desaturase and elongate monounsaturated fatty acids in different societies seems to be influenced by whether there is a lack of supply of readily available dietary sources of long-chain polyunsaturated fatty acids. The process of human evolution includes genetic drift and adaptation to local environments, in part through changes in mitochondrial and nuclear DNA. These genetic changes may underlie susceptibilities to some modern human pathologies including folate-responsive neural tube defects, diabetes, other age-related pathologies and mental health disorders.}, }
@article {pmid30771245, year = {2019}, author = {Becam, G and Verna, C and Gómez-Robles, A and Gómez-Olivencia, A and Albessard, L and Arnaud, J and Frelat, MA and Madelaine, S and Schwab, C and Souday, C and Turq, A and Balzeau, A}, title = {Isolated teeth from La Ferrassie: Reassessment of the old collections, new remains, and their implications.}, journal = {American journal of physical anthropology}, volume = {169}, number = {1}, pages = {132-142}, doi = {10.1002/ajpa.23798}, pmid = {30771245}, issn = {1096-8644}, support = {IT1044-16//Gobierno Vasco/Eusko Jaurlaritza/International ; IT834-13//Gobierno Vasco/Eusko Jaurlaritza/International ; CGL2015-65387-C3-2-P-MINECO/FEDER-//Ministerio de Ciencia y Tecnolog&#xed;a/International ; CGL2012-38434-C03-01//Ministerio de Ciencia y Tecnolog&#xed;a/International ; //UMR 7194 CNRS-HNHP/UPVD/International ; }, mesh = {Animals ; Anthropology, Physical ; Caves ; Dental Enamel/anatomy &amp; histology/diagnostic imaging ; Dentin/anatomy &amp; histology/diagnostic imaging ; France ; Humans ; Neanderthals/*anatomy &amp; histology ; Odontometry ; Tooth/*anatomy &amp; histology/diagnostic imaging ; X-Ray Microtomography ; }, abstract = {OBJECTIVES: We provide the description and comparative analysis of six new teeth from the site of La Ferrassie. Our goal is to discuss their taxonomic attribution, and to provide an updated inventory of Neandertal and modern human remains from La Ferrassie in their associated archeological context.<br><br>MATERIALS AND METHODS: We use external and internal anatomy, classic morphometrics, and geometric morphometrics. The teeth from La Ferrassie are compared to several samples of contemporary Neandertals and upper Paleolithic modern humans and to recent modern humans.<br><br>RESULTS: Three specimens are classified as Neandertals, two as modern humans, and one remains unclassified.<br><br>DISCUSSION: Based on the previously known fossil samples and the new teeth reported here, there are currently a minimum of four adult and five immature Neandertal individuals coming from the "Grand Abri" and a minimum of two modern human adult individuals: one from "Grand Abri" and one from "Grotte." It is noteworthy that the spatial distribution of the recovered Neandertal remains is not restricted to the area where the LF1-LF 8 were found but now covers the full extension of the excavated area. Moreover, while both Neandertal and modern human occupations have yielded isolated human remains, the partial-to-complete skeletons only belong to Neandertals. These considerations open new perspectives for the understanding of the occupation and use of the La Ferrassie site.}, }
@article {pmid30737446, year = {2019}, author = {Ríos, L and Kivell, TL and Lalueza-Fox, C and Estalrrich, A and García-Tabernero, A and Huguet, R and Quintino, Y and de la Rasilla, M and Rosas, A}, title = {Skeletal Anomalies in The Neandertal Family of El Sidrón (Spain) Support A Role of Inbreeding in Neandertal Extinction.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {1697}, pmid = {30737446}, issn = {2045-2322}, support = {336301/ERC_/European Research Council/International ; }, mesh = {Animals ; Biological Evolution ; Bone and Bones/*abnormalities/diagnostic imaging ; Congenital Abnormalities/*diagnostic imaging/pathology ; Fossils/anatomy &amp; histology/diagnostic imaging ; Inbreeding ; Microscopy, Electron, Scanning ; Neanderthals/anatomy &amp; histology/*physiology ; Spain ; X-Ray Microtomography ; }, abstract = {Neandertals disappeared from the fossil record around 40,000 bp, after a demographic history of small and isolated groups with high but variable levels of inbreeding, and episodes of interbreeding with other Paleolithic hominins. It is reasonable to expect that high levels of endogamy could be expressed in the skeleton of at least some Neandertal groups. Genetic studies indicate that the 13 individuals from the site of El Sidrón, Spain, dated around 49,000 bp, constituted a closely related kin group, making these Neandertals an appropriate case study for the observation of skeletal signs of inbreeding. We present the complete study of the 1674 identified skeletal specimens from El Sidrón. Altogether, 17 congenital anomalies were observed (narrowing of the internal nasal fossa, retained deciduous canine, clefts of the first cervical vertebra, unilateral hypoplasia of the second cervical vertebra, clefting of the twelfth thoracic vertebra, diminutive thoracic or lumbar rib, os centrale carpi and bipartite scaphoid, tripartite patella, left foot anomaly and cuboid-navicular coalition), with at least four individuals presenting congenital conditions (clefts of the first cervical vertebra). At 49,000 years ago, the Neandertals from El Sidrón, with genetic and skeletal evidence of inbreeding, could be representative of the beginning of the demographic collapse of this hominin phenotype.}, }
@article {pmid30721683, year = {2019}, author = {Sherwood, CC and Bradley, BJ}, title = {Brain Evolution: Mapping the Inner Neandertal.}, journal = {Current biology : CB}, volume = {29}, number = {3}, pages = {R95-R97}, doi = {10.1016/j.cub.2018.12.024}, pmid = {30721683}, issn = {1879-0445}, mesh = {Africa ; Animals ; Brain ; Genome ; *Hominidae ; Humans ; Neanderthals/*genetics ; }, abstract = {Human populations that migrated out of Africa interbred with Neandertals. A new study assesses the effects of Neandertal gene variants on brain shape in modern humans, providing insights into the genomic basis of the uniquely globular human brain.}, }
@article {pmid30700871, year = {2019}, author = {Douka, K and Slon, V and Jacobs, Z and Ramsey, CB and Shunkov, MV and Derevianko, AP and Mafessoni, F and Kozlikin, MB and Li, B and Grün, R and Comeskey, D and Devièse, T and Brown, S and Viola, B and Kinsley, L and Buckley, M and Meyer, M and Roberts, RG and Pääbo, S and Kelso, J and Higham, T}, title = {Age estimates for hominin fossils and the onset of the Upper Palaeolithic at Denisova Cave.}, journal = {Nature}, volume = {565}, number = {7741}, pages = {640-644}, doi = {10.1038/s41586-018-0870-z}, pmid = {30700871}, issn = {1476-4687}, mesh = {Animals ; Bayes Theorem ; *Caves ; DNA, Mitochondrial/genetics ; Deer ; Femur/chemistry ; *Fossils ; Geologic Sediments/chemistry ; History, Ancient ; *Hominidae/genetics ; Humans ; Neanderthals/genetics ; Oxygen Isotopes ; *Radiometric Dating ; Siberia ; Time Factors ; Tooth/chemistry ; }, abstract = {Denisova Cave in the Siberian Altai (Russia) is a key site for understanding the complex relationships between hominin groups that inhabited Eurasia in the Middle and Late Pleistocene epoch. DNA sequenced from human remains found at this site has revealed the presence of a hitherto unknown hominin group, the Denisovans[1,2], and high-coverage genomes from both Neanderthal and Denisovan fossils provide evidence for admixture between these two populations[3]. Determining the age of these fossils is important if we are to understand the nature of hominin interaction, and aspects of their cultural and subsistence adaptations. Here we present 50 radiocarbon determinations from the late Middle and Upper Palaeolithic layers of the site. We also report three direct dates for hominin fragments and obtain a mitochondrial DNA sequence for one of them. We apply a Bayesian age modelling approach that combines chronometric (radiocarbon, uranium series and optical ages), stratigraphic and genetic data to calculate probabilistically the age of the human fossils at the site. Our modelled estimate for the age of the oldest Denisovan fossil suggests that this group was present at the site as early as 195,000 years ago (at 95.4% probability). All Neanderthal fossils-as well as Denisova 11, the daughter of a Neanderthal and a Denisovan[4]-date to between 80,000 and 140,000 years ago. The youngest Denisovan dates to 52,000-76,000 years ago. Direct radiocarbon dating of Upper Palaeolithic tooth pendants and bone points yielded the earliest evidence for the production of these artefacts in northern Eurasia, between 43,000 and 49,000 calibrated years before present (taken as AD 1950). On the basis of current archaeological evidence, it may be assumed that these artefacts are associated with the Denisovan population. It is not currently possible to determine whether anatomically modern humans were involved in their production, as modern-human fossil and genetic evidence of such antiquity has not yet been identified in the Altai region.}, }
@article {pmid30651539, year = {2019}, author = {Mondal, M and Bertranpetit, J and Lao, O}, title = {Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {246}, pmid = {30651539}, issn = {2041-1723}, abstract = {Since anatomically modern humans dispersed Out of Africa, the evolutionary history of Eurasian populations has been marked by introgressions from presently extinct hominins. Some of these introgressions have been identified using sequenced ancient genomes (Neanderthal and Denisova). Other introgressions have been proposed for still unidentified groups using the genetic diversity present in current human populations. We built a demographic model based on deep learning in an Approximate Bayesian Computation framework to infer the evolutionary history of Eurasian populations including past introgression events in Out of Africa populations fitting the current genetic evidence. In addition to the reported Neanderthal and Denisovan introgressions, our results support a third introgression in all Asian and Oceanian populations from an archaic population. This population is either related to the Neanderthal-Denisova clade or diverged early from the Denisova lineage. We propose the use of deep learning methods for clarifying situations with high complexity in evolutionary genomics.}, }
@article {pmid30647110, year = {2019}, author = {Petr, M and Pääbo, S and Kelso, J and Vernot, B}, title = {Limits of long-term selection against Neandertal introgression.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {5}, pages = {1639-1644}, pmid = {30647110}, issn = {1091-6490}, mesh = {Alleles ; Animals ; Conserved Sequence/genetics ; DNA/genetics ; Europe ; Evolution, Molecular ; Gene Flow/genetics ; Humans ; Neanderthals/*genetics ; RNA, Untranslated/genetics ; Selection, Genetic/*genetics ; White People/genetics ; }, abstract = {Several studies have suggested that introgressed Neandertal DNA was subjected to negative selection in modern humans. A striking observation in support of this is an apparent monotonic decline in Neandertal ancestry observed in modern humans in Europe over the past 45,000 years. Here, we show that this decline is an artifact likely caused by gene flow between modern human populations, which is not taken into account by statistics previously used to estimate Neandertal ancestry. When we apply a statistic that avoids assumptions about modern human demography by taking advantage of two high-coverage Neandertal genomes, we find no evidence for a change in Neandertal ancestry in Europe over the past 45,000 years. We use whole-genome simulations of selection and introgression to investigate a wide range of model parameters and find that negative selection is not expected to cause a significant long-term decline in genome-wide Neandertal ancestry. Nevertheless, these models recapitulate previously observed signals of selection against Neandertal alleles, in particular the depletion of Neandertal ancestry in conserved genomic regions. Surprisingly, we find that this depletion is strongest in regulatory and conserved noncoding regions and in the most conserved portion of protein-coding sequences.}, }
@article {pmid30589914, year = {2018}, author = {Velliky, EC and Porr, M and Conard, NJ}, title = {Ochre and pigment use at Hohle Fels cave: Results of the first systematic review of ochre and ochre-related artefacts from the Upper Palaeolithic in Germany.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0209874}, pmid = {30589914}, issn = {1932-6203}, mesh = {*Caves ; *Coloring Agents/chemistry/history ; *Culture ; Germany ; History, Ancient ; Humans ; Paintings/*history ; }, abstract = {Though many European Upper Palaeolithic sites document early examples of symbolic material expressions (e.g., cave art, personal ornaments, figurines), there exist few reports on the use of earth pigments outside of cave art-and occasionally Neanderthal-contexts. Here, we present the first in-depth study of the diachronic changes in ochre use throughout an entire Upper Palaeolithic sequence at Hohle Fels cave, Germany, spanning from ca. 44,000-14,500 cal. yr. BP. A reassessment of the assemblage has yielded 869 individual ochre artefacts, of which 27 show traces of anthropogenic modification. The ochre artefacts are from all Upper Palaeolithic layers, stemming from the earliest Aurignacian horizons to the Holocene. This wide temporal spread demonstrates the long-term presence and continuity of ochre use in a part of Europe where it has not been systematically reported before. The anthropogenic modifications present on the ochre artefacts from the Gravettian and Magdalenian are consistent with pigment powder production, whereas the only modified piece from the Aurignacian displays a possible engraved motif. The non-modified artefacts show that more hematite-rich specular ochres as well as fine-grained deep red iron oxide clays were preferred during the Gravettian and Magdalenian, while the Aurignacian layers contain a broader array of colours and textures. Furthermore, numerous other artefacts such as faunal elements, personal ornaments, shells, and an ochre grindstone further strengthen the conclusion that ochre behaviours were well established during the onset of the Aurignacian and subsequently flourished throughout the Upper Palaeolithic at Hohle Fels cave.}, }
@article {pmid30573755, year = {2018}, author = {Van Laer, B and Kapp, U and Soler-Lopez, M and Moczulska, K and Pääbo, S and Leonard, G and Mueller-Dieckmann, C}, title = {Molecular comparison of Neanderthal and Modern Human adenylosuccinate lyase.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {18008}, pmid = {30573755}, issn = {2045-2322}, mesh = {Adenylosuccinate Lyase/*chemistry/*genetics ; Amino Acid Sequence ; Animals ; Catalysis ; Catalytic Domain ; Crystallization ; Enzyme Stability ; *Evolution, Molecular ; Humans ; Models, Molecular ; Mutation, Missense ; Neanderthals/*genetics ; Protein Conformation ; Social Change ; Temperature ; }, abstract = {The availability of genomic data from extinct homini such as Neanderthals has caused a revolution in palaeontology allowing the identification of modern human-specific protein substitutions. Currently, little is known as to how these substitutions alter the proteins on a molecular level. Here, we investigate adenylosuccinate lyase, a conserved enzyme involved in purine metabolism for which several substitutions in the modern human protein (hADSL) have been described to affect intelligence and behaviour. During evolution, modern humans acquired a specific substitution (Ala429Val) in ADSL distinguishing it from the ancestral variant present in Neanderthals (nADSL). We show here that despite this conservative substitution being solvent exposed and located distant from the active site, there is a difference in thermal stability, but not enzymology or ligand binding between nADSL and hADSL. Substitutions near residue 429 which do not profoundly affect enzymology were previously reported to cause neurological symptoms in humans. This study also reveals that ADSL undergoes conformational changes during catalysis which, together with the crystal structure of a hitherto undetermined product bound conformation, explains the molecular origin of disease for several modern human ADSL mutants.}, }
@article {pmid30566634, year = {2019}, author = {Reher, D and Key, FM and Andrés, AM and Kelso, J}, title = {Immune Gene Diversity in Archaic and Present-day Humans.}, journal = {Genome biology and evolution}, volume = {11}, number = {1}, pages = {232-241}, pmid = {30566634}, issn = {1759-6653}, mesh = {Animals ; Genetic Variation ; Humans ; Immunity, Innate/*genetics ; *Major Histocompatibility Complex ; Neanderthals/*genetics/immunology ; }, abstract = {Genome-wide analyses of two Neandertals and a Denisovan have shown that these archaic humans had lower genetic heterozygosity than present-day people. A similar reduction in genetic diversity of protein-coding genes (gene diversity) was found in exome sequences of three Neandertals. Reduced gene diversity, particularly in genes involved in immunity, may have important functional consequences. In fact, it has been suggested that reduced diversity in immune genes may have contributed to Neandertal extinction. We therefore explored gene diversity in different human groups, and at different time points on the Neandertal lineage, with a particular focus on the diversity of genes involved in innate immunity and genes of the Major Histocompatibility Complex (MHC).We find that the two Neandertals and a Denisovan have similar gene diversity, all significantly lower than any present-day human. This is true across gene categories, with no gene set showing an excess decrease in diversity compared with the genome-wide average. Innate immune-related genes show a similar reduction in diversity to other genes, both in present-day and archaic humans. There is also no observable decrease in gene diversity over time in Neandertals, suggesting that there may have been no ongoing reduction in gene diversity in later Neandertals, although this needs confirmation with a larger sample size. In both archaic and present-day humans, genes with the highest levels of diversity are enriched for MHC-related functions. In fact, in archaic humans the MHC genes show evidence of having retained more diversity than genes involved only in the innate immune system.}, }
@article {pmid30566479, year = {2018}, author = {Mohammed Ismail, W and Pagel, KA and Pejaver, V and Zhang, SV and Casasa, S and Mort, M and Cooper, DN and Hahn, MW and Radivojac, P}, title = {The sequencing and interpretation of the genome obtained from a Serbian individual.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0208901}, pmid = {30566479}, issn = {1932-6203}, mesh = {Animals ; Ethnicity/*genetics ; Female ; *Genetic Predisposition to Disease ; *Genetic Variation ; *Genome, Human ; Genome-Wide Association Study ; Humans ; Male ; Neanderthals/genetics ; Serbia/ethnology ; }, abstract = {Recent genetic studies and whole-genome sequencing projects have greatly improved our understanding of human variation and clinically actionable genetic information. Smaller ethnic populations, however, remain underrepresented in both individual and large-scale sequencing efforts and hence present an opportunity to discover new variants of biomedical and demographic significance. This report describes the sequencing and analysis of a genome obtained from an individual of Serbian origin, introducing tens of thousands of previously unknown variants to the currently available pool. Ancestry analysis places this individual in close proximity to Central and Eastern European populations; i.e., closest to Croatian, Bulgarian and Hungarian individuals and, in terms of other Europeans, furthest from Ashkenazi Jewish, Spanish, Sicilian and Baltic individuals. Our analysis confirmed gene flow between Neanderthal and ancestral pan-European populations, with similar contributions to the Serbian genome as those observed in other European groups. Finally, to assess the burden of potentially disease-causing/clinically relevant variation in the sequenced genome, we utilized manually curated genotype-phenotype association databases and variant-effect predictors. We identified several variants that have previously been associated with severe early-onset disease that is not evident in the proband, as well as putatively impactful variants that could yet prove to be clinically relevant to the proband over the next decades. The presence of numerous private and low-frequency variants, along with the observed and predicted disease-causing mutations in this genome, exemplify some of the global challenges of genome interpretation, especially in the context of under-studied ethnic groups.}, }
@article {pmid30566085, year = {2018}, author = {Murphy, E and Benítez-Burraco, A}, title = {Paleo-oscillomics: inferring aspects of Neanderthal language abilities from gene regulation of neural oscillations.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {96}, number = {}, pages = {111-124}, doi = {10.4436/JASS.96010}, pmid = {30566085}, issn = {2037-0644}, mesh = {Animals ; Anthropology, Physical ; Computational Biology ; *Cultural Evolution ; DNA Methylation/genetics ; Genetic Techniques ; *Language ; *Neanderthals/genetics/physiology ; Nervous System Physiological Phenomena/genetics ; Speech/*physiology ; }, abstract = {Language seemingly evolved from changes in brain anatomy and wiring. We argue that language evolution can be better understood if particular changes in phasal and cross-frequency coupling properties of neural oscillations, resulting in core features of language, are considered. Because we cannot track the oscillatory activity of the brain from extinct hominins, we used our current understanding of the language oscillogenome (that is, the set of genes responsible for basic aspects of the oscillatory activity relevant for language) to infer some properties of the Neanderthal oscillome. We have found that several candidates for the language oscillogenome show differences in their methylation patterns between Neanderthals and humans. We argue that differences in their expression levels could be informative of differences in cognitive functions important for language.}, }
@article {pmid30564397, year = {2018}, author = {Savriama, Y and Valtonen, M and Kammonen, JI and Rastas, P and Smolander, OP and Lyyski, A and Häkkinen, TJ and Corfe, IJ and Gerber, S and Salazar-Ciudad, I and Paulin, L and Holm, L and Löytynoja, A and Auvinen, P and Jernvall, J}, title = {Bracketing phenogenotypic limits of mammalian hybridization.}, journal = {Royal Society open science}, volume = {5}, number = {11}, pages = {180903}, pmid = {30564397}, issn = {2054-5703}, abstract = {An increasing number of mammalian species have been shown to have a history of hybridization and introgression based on genetic analyses. Only relatively few fossils, however, preserve genetic material, and morphology must be used to identify the species and determine whether morphologically intermediate fossils could represent hybrids. Because dental and cranial fossils are typically the key body parts studied in mammalian palaeontology, here we bracket the potential for phenotypically extreme hybridizations by examining uniquely preserved cranio-dental material of a captive hybrid between grey and ringed seals. We analysed how distinct these species are genetically and morphologically, how easy it is to identify the hybrids using morphology and whether comparable hybridizations happen in the wild. We show that the genetic distance between these species is more than twice the modern human-Neanderthal distance, but still within that of morphologically similar species pairs known to hybridize. By contrast, morphological and developmental analyses show grey and ringed seals to be highly disparate, and that the hybrid is a predictable intermediate. Genetic analyses of the parent populations reveal introgression in the wild, suggesting that grey-ringed seal hybridization is not limited to captivity. Taken together, we postulate that there is considerable potential for mammalian hybridization between phenotypically disparate taxa.}, }
@article {pmid30564067, year = {2018}, author = {Benítez-Burraco, A}, title = {Differences in the Neanderthal BRCA2 gene might be related to their distinctive cognitive profile.}, journal = {Hereditas}, volume = {155}, number = {}, pages = {38}, pmid = {30564067}, issn = {1601-5223}, mesh = {Animals ; Brain/growth &amp; development ; *Cognition ; *Genes, BRCA2 ; Neanderthals/*genetics ; }, abstract = {The unique divergence of the BRCA2 gene in Neanderthals compared to modern humans has been hypothesized to account for a differential susceptibility to cancer. However, the role of the gene in brain development and its connection with autism suggest that these differences might be (also) related to the more encapsulated nature of the Neanderthal cognition and their (inferred) autistic-like features.}, }
@article {pmid30554901, year = {2019}, author = {Gunz, P and Tilot, AK and Wittfeld, K and Teumer, A and Shapland, CY and van Erp, TGM and Dannemann, M and Vernot, B and Neubauer, S and Guadalupe, T and Fernández, G and Brunner, HG and Enard, W and Fallon, J and Hosten, N and Völker, U and Profico, A and Di Vincenzo, F and Manzi, G and Kelso, J and St Pourcain, B and Hublin, JJ and Franke, B and Pääbo, S and Macciardi, F and Grabe, HJ and Fisher, SE}, title = {Neandertal Introgression Sheds Light on Modern Human Endocranial Globularity.}, journal = {Current biology : CB}, volume = {29}, number = {1}, pages = {120-127.e5}, pmid = {30554901}, issn = {1879-0445}, support = {U24 RR021992/RR/NCRR NIH HHS/United States ; U24 RR025736/RR/NCRR NIH HHS/United States ; U54 EB020403/EB/NIBIB NIH HHS/United States ; UL1 TR001414/TR/NCATS NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Animals ; *Biological Evolution ; Female ; Fossils ; Humans ; *Hybridization, Genetic ; Male ; Middle Aged ; Neanderthals/*anatomy &amp; histology ; Netherlands ; Phenotype ; Skull/*anatomy &amp; histology ; Young Adult ; }, abstract = {One of the features that distinguishes modern humans from our extinct relatives and ancestors is a globular shape of the braincase [1-4]. As the endocranium closely mirrors the outer shape of the brain, these differences might reflect altered neural architecture [4, 5]. However, in the absence of fossil brain tissue, the underlying neuroanatomical changes as well as their genetic bases remain elusive. To better understand the biological foundations of modern human endocranial shape, we turn to our closest extinct relatives: the Neandertals. Interbreeding between modern humans and Neandertals has resulted in introgressed fragments of Neandertal DNA in the genomes of present-day non-Africans [6, 7]. Based on shape analyses of fossil skull endocasts, we derive a measure of endocranial globularity from structural MRI scans of thousands of modern humans and study the effects of introgressed fragments of Neandertal DNA on this phenotype. We find that Neandertal alleles on chromosomes 1 and 18 are associated with reduced endocranial globularity. These alleles influence expression of two nearby genes, UBR4 and PHLPP1, which are involved in neurogenesis and myelination, respectively. Our findings show how integration of fossil skull data with archaic genomics and neuroimaging can suggest developmental mechanisms that may contribute to the unique modern human endocranial shape.}, }
@article {pmid30478305, year = {2019}, author = {Villanea, FA and Schraiber, JG}, title = {Multiple episodes of interbreeding between Neanderthal and modern humans.}, journal = {Nature ecology &amp; evolution}, volume = {3}, number = {1}, pages = {39-44}, pmid = {30478305}, issn = {2397-334X}, support = {R35 GM124745/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Gene Flow ; Genome, Human ; Humans ; *Hybridization, Genetic ; Models, Theoretical ; Neanderthals/*genetics ; }, abstract = {Neanderthals and anatomically modern humans overlapped geographically for a period of over 30,000 years following human migration out of Africa. During this period, Neanderthals and humans interbred, as evidenced by Neanderthal portions of the genome carried by non-African individuals today. A key observation is that the proportion of Neanderthal ancestry is ~12-20% higher in East Asian individuals relative to European individuals. Here, we explore various demographic models that could explain this observation. These include distinguishing between a single admixture event and multiple Neanderthal contributions to either population, and the hypothesis that reduced Neanderthal ancestry in modern Europeans resulted from more recent admixture with a ghost population that lacked a Neanderthal ancestry component (the 'dilution' hypothesis). To summarize the asymmetric pattern of Neanderthal allele frequencies, we compiled the joint fragment frequency spectrum of European and East Asian Neanderthal fragments and compared it with both analytical theory and data simulated under various models of admixture. Using maximum-likelihood and machine learning, we found that a simple model of a single admixture did not fit the empirical data, and instead favour a model of multiple episodes of gene flow into both European and East Asian populations. These findings indicate a longer-term, more complex interaction between humans and Neanderthals than was previously appreciated.}, }
@article {pmid30462354, year = {2019}, author = {Becam, G and Chevalier, T}, title = {Neandertal features of the deciduous and permanent teeth from Portel-Ouest Cave (Ariège, France).}, journal = {American journal of physical anthropology}, volume = {168}, number = {1}, pages = {45-69}, doi = {10.1002/ajpa.23719}, pmid = {30462354}, issn = {1096-8644}, support = {//Association des Membres des Palmes Acad&#xe9;miques des Pyr&#xe9;n&#xe9;es-Orientales/International ; //Mus&#xe9;um national d'Histoire naturelle de Paris/International ; //UMR 7194, laboratoire Histoire Naturelle de l'Homme Pr&#xe9;historique/International ; }, mesh = {Adolescent ; Adult ; Animals ; Anthropology, Physical ; *Caves ; Child ; Dental Enamel/anatomy &amp; histology/pathology ; Dental Enamel Hypoplasia/pathology ; Fossils ; France ; History, Ancient ; Humans ; Neanderthals/*anatomy &amp; histology ; *Tooth/anatomy &amp; histology/pathology ; Tooth, Deciduous/anatomy &amp; histology/pathology ; }, abstract = {OBJECTIVES: We describe 14 unpublished and nine published teeth from the Mousterian level of Portel-Ouest (Ariège, France), dated to 44 ka. In a comparative context, we explore the taxonomical affinities of those teeth with Neandertals and modern humans which are both known to exist at that time. We further make some paleobiological inferences about this human group.<br><br>METHODS: The comparative analysis of Neandertals and modern humans is based on nonmetric traits at the outer enamel surface and the enamel-dentine junction, crown diameters and three-dimensional (3D) enamel thickness measurements of lower permanent teeth. The crown and roots are explored in detail based on the &#x3bc;CT-scan data to identify the multiple criteria involved in the paleobiological approach.<br><br>RESULTS: Nonmetric traits and 3D enamel thickness tend to be more similar to Neandertals than modern humans, notably for C1 , P4 , and M2 (included in all analyses) as well as volume of the pulp cavity in roots of the anterior permanent teeth. The Portel-Ouest sample corresponds to a minimum of seven juveniles, one or two adolescents and one adult, which exhibit recurrent linear enamel hypoplasia (up to five events for one individual), the torsiversion of one anterior tooth and irregular oblique wear in some anterior deciduous teeth.<br><br>DISCUSSION: This morphological study confirms that the remains from Portel-Ouest are Neandertals, associated with a Mousterian complex. Furthermore, we found the expected pattern of mortality and stress for a Neandertal group, that is, various age categories and developmental defects (nonexclusive to Neandertals), while adults are underrepresented and juveniles are overrepresented. Further excavations would contribute finding new remains and maybe complete this demographic profile.}, }
@article {pmid30429606, year = {2018}, author = {Beier, J and Anthes, N and Wahl, J and Harvati, K}, title = {Similar cranial trauma prevalence among Neanderthals and Upper Palaeolithic modern humans.}, journal = {Nature}, volume = {563}, number = {7733}, pages = {686-690}, doi = {10.1038/s41586-018-0696-8}, pmid = {30429606}, issn = {1476-4687}, mesh = {Adult ; Age Determination by Skeleton ; Animals ; Brain Injuries, Traumatic/epidemiology/*history/pathology ; Child ; Female ; *Fossils ; History, Ancient ; Humans ; Incidence ; Life Style/history ; Male ; *Neanderthals ; Prevalence ; Sex Determination by Skeleton ; Skull/*pathology ; Uncertainty ; Violence/history ; Young Adult ; }, abstract = {Neanderthals are commonly depicted as leading dangerous lives and permanently struggling for survival. This view largely relies on the high incidences of trauma that have been reported[1,2] and have variously been attributed to violent social behaviour[3,4], highly mobile hunter-gatherer lifestyles[2] or attacks by carnivores[5]. The described Neanderthal pattern of predominantly cranial injuries is further thought to reflect violent encounters with large prey mammals, resulting from the use of close-range hunting weapons[1]. These interpretations directly shape our understanding of Neanderthal lifestyles, health and hunting abilities, yet mainly rest on descriptive, case-based evidence. Quantitative, population-level studies of traumatic injuries are rare. Here we reassess the hypothesis of higher cranial trauma prevalence among Neanderthals using a population-level approach-accounting for preservation bias and other contextual data-and an exhaustive fossil database. We show that Neanderthals and early Upper Palaeolithic anatomically modern humans exhibit similar overall incidences of cranial trauma, which are higher for males in both taxa, consistent with patterns shown by later populations of modern humans. Beyond these similarities, we observed species-specific, age-related variation in trauma prevalence, suggesting that there were differences in the timing of injuries during life or that there was a differential mortality risk of trauma survivors in the two groups. Finally, our results highlight the importance of preservation bias in studies of trauma prevalence.}, }
@article {pmid30410429, year = {2018}, author = {Michalak, P and Kang, L}, title = {Unique divergence of the breast cancer 2 (BRCA2) gene in Neanderthals.}, journal = {Hereditas}, volume = {155}, number = {}, pages = {34}, pmid = {30410429}, issn = {1601-5223}, mesh = {Alleles ; Animals ; BRCA2 Protein/*genetics ; *Evolution, Molecular ; Humans ; Neanderthals/*genetics ; Polymorphism, Single Nucleotide ; }, abstract = {Unique divergence of the BRCA2, a tumor suppressor gene, in Neanderthals relative to other primates, including modern humans, is highlighted. This divergence with potentially pathogenic consequences raises a question about cancer susceptibility in the archaic species that was replaced by modern humans about 40,000 years ago.}, }
@article {pmid30402544, year = {2018}, author = {Smith, TM and Austin, C and Green, DR and Joannes-Boyau, R and Bailey, S and Dumitriu, D and Fallon, S and Grün, R and James, HF and Moncel, MH and Williams, IS and Wood, R and Arora, M}, title = {Wintertime stress, nursing, and lead exposure in Neanderthal children.}, journal = {Science advances}, volume = {4}, number = {10}, pages = {eaau9483}, pmid = {30402544}, issn = {2375-2548}, support = {DP2 ES025453/ES/NIEHS NIH HHS/United States ; K99 HD087523/HD/NICHD NIH HHS/United States ; R01 ES026033/ES/NIEHS NIH HHS/United States ; T90 DE026110/DE/NIDCR NIH HHS/United States ; }, mesh = {Animals ; Animals, Newborn ; Environmental Exposure/*adverse effects ; *Fossils ; Lead/*toxicity ; Neanderthals/*anatomy &amp; histology/*physiology ; Radiometric Dating ; Seasons ; Tooth/drug effects/*growth &amp; development/pathology ; }, abstract = {Scholars endeavor to understand the relationship between human evolution and climate change. This is particularly germane for Neanderthals, who survived extreme Eurasian environmental variation and glaciations, mysteriously going extinct during a cool interglacial stage. Here, we integrate weekly records of climate, tooth growth, and metal exposure in two Neanderthals and one modern human from southeastern France. The Neanderthals inhabited cooler and more seasonal periods than the modern human, evincing childhood developmental stress during wintertime. In one instance, this stress may have included skeletal mobilization of elemental stores and weight loss; this individual was born in the spring and appears to have weaned 2.5 years later. Both Neanderthals were exposed to lead at least twice during the deep winter and/or early spring. This multidisciplinary approach elucidates direct relationships between ancient environments and hominin paleobiology.}, }
@article {pmid30386687, year = {2018}, author = {Akhtari, FS and Havener, TM and Fukudo, M and Jack, JR and McLeod, HL and Wiltshire, T and Motsinger-Reif, AA}, title = {The influence of Neanderthal alleles on cytotoxic response.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5691}, pmid = {30386687}, issn = {2167-8359}, support = {R01 CA161608/CA/NCI NIH HHS/United States ; }, abstract = {Various studies have shown that people of Eurasian origin contain traces of DNA inherited from interbreeding with Neanderthals. Recent studies have demonstrated that these Neanderthal variants influence a range of clinically important traits and diseases. Thus, understanding the genetic factors responsible for the variability in individual response to drug or chemical exposure is a key goal of pharmacogenomics and toxicogenomics, as dose responses are clinically and epidemiologically important traits. It is well established that ethnic and racial differences are important in dose response traits, but to our knowledge the influence of Neanderthal ancestry on response to xenobiotics is unknown. Towards this aim, we examined if Neanderthal ancestry plays a role in cytotoxic response to anti-cancer drugs and toxic environmental chemicals. We identified common Neanderthal variants in lymphoblastoid cell lines (LCLs) derived from the globally diverse 1000 Genomes Project and Caucasian cell lines from the Children's Hospital of Oakland Research Institute. We analyzed the effects of these Neanderthal alleles on cytotoxic response to 29 anti-cancer drugs and 179 environmental chemicals at varying concentrations using genome-wide data. We identified and replicated single nucleotide polymorphisms (SNPs) from these association results, including a SNP in the SNORD-113 cluster. Our results also show that the Neanderthal alleles cumulatively lead to increased sensitivity to both the anti-cancer drugs and the environmental chemicals. Our results demonstrate the influence of Neanderthal ancestry-informative markers on cytotoxic response. These results could be important in identifying biomarkers for personalized medicine or in dissecting the underlying etiology of dose response traits.}, }
@article {pmid30377294, year = {2018}, author = {Gómez-Olivencia, A and Barash, A and García-Martínez, D and Arlegi, M and Kramer, P and Bastir, M and Been, E}, title = {3D virtual reconstruction of the Kebara 2 Neandertal thorax.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {4387}, pmid = {30377294}, issn = {2041-1723}, mesh = {Animals ; *Fossils ; Humans ; *Imaging, Three-Dimensional ; Male ; Middle Aged ; Neanderthals/*anatomy &amp; histology ; Organ Size ; Principal Component Analysis ; Thorax/*anatomy &amp; histology ; }, abstract = {The size and shape of the Neandertal thorax has been debated since the first discovery of Neandertal ribs more than 150 years ago, with workers proposing different interpretations ranging from a Neandertal thoracic morphology that is indistinguishable from modern humans, to one that was significantly different from them. Here, we provide a virtual 3D reconstruction of the thorax of the adult male Kebara 2 Neandertal. Our analyses reveal that the Kebara 2 thorax is significantly different but not larger from that of modern humans, wider in its lower segment, which parallels his wide bi-iliac breadth, and with a more invaginated vertebral column. Kinematic analyses show that rib cages that are wider in their lower segment produce greater overall size increments (respiratory capacity) during inspiration. We hypothesize that Neandertals may have had a subtle, but somewhat different breathing mechanism compared to modern humans.}, }
@article {pmid30359256, year = {2018}, author = {de Filippo, C and Meyer, M and Prüfer, K}, title = {Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences.}, journal = {BMC biology}, volume = {16}, number = {1}, pages = {121}, pmid = {30359256}, issn = {1741-7007}, mesh = {Animals ; *Base Sequence ; DNA, Ancient/*analysis ; Fossils ; Neanderthals/*genetics ; Sequence Alignment/*methods ; Spain ; }, abstract = {BACKGROUND: The study of ancient DNA is hampered by degradation, resulting in short DNA fragments. Advances in laboratory methods have made it possible to retrieve short DNA fragments, thereby improving access to DNA preserved in highly degraded, ancient material. However, such material contains large amounts of microbial contamination in addition to DNA fragments from the ancient organism. The resulting mixture of sequences constitutes a challenge for computational analysis, since microbial sequences are hard to distinguish from the ancient sequences of interest, especially when they are short.<br><br>RESULTS: Here, we develop a method to quantify spurious alignments based on the presence or absence of rare variants. We find that spurious alignments are enriched for mismatches and insertion/deletion differences and lack substitution patterns typical of ancient DNA. The impact of spurious alignments can be reduced by filtering on these features and by imposing a sample-specific minimum length cutoff. We apply this approach to sequences from four ~&#x2009;430,000-year-old Sima de los Huesos hominin remains, which contain particularly short DNA fragments, and increase the amount of usable sequence data by 17-150%. This allows us to place a third specimen from the site on the Neandertal lineage.<br><br>CONCLUSIONS: Our method maximizes the sequence data amenable to genetic analysis from highly degraded ancient material and avoids pitfalls that are associated with the analysis of ultra-short DNA sequences.}, }
@article {pmid30351468, year = {2019}, author = {Pablos, A and Gómez-Olivencia, A and Arsuaga, JL}, title = {A Neandertal foot phalanx from the Galería de las Estatuas site (Sierra de Atapuerca, Spain).}, journal = {American journal of physical anthropology}, volume = {168}, number = {1}, pages = {222-228}, doi = {10.1002/ajpa.23729}, pmid = {30351468}, issn = {1096-8644}, support = {//Fundaci&#xf3;n Atapuerca/International ; //Junta de Castilla y Le&#xf3;n/International ; CGL2015-65387-C3-2-P MINECO/FEDER//Ministerio de Econom&#xed;a y Competitividad/International ; }, mesh = {Animals ; Anthropology, Physical ; Anthropometry ; Fossils ; Neanderthals/*anatomy &amp; histology ; Spain ; Toe Phalanges/*anatomy &amp; histology ; }, abstract = {OBJECTIVES: The Galería de las Estatuas site (GE), a new Mousterian site at the Sierra de Atapuerca site complex (Spain), has revealed a Late Pleistocene detrital sequence with at least five lithostratigraphic units. These units have yielded evidence of Mousterian occupations with sporadic carnivore activity, and have provided datings of 80-112 ka BP using single-grain optically stimulated luminescence. This places the sequence at the end of MIS5 and beginning of the MIS4. We described here a complete adult human distal foot phalanx (GE-1573) recovered during the 2017 field season in the interface between lithostratigraphic units 3 and 4 (107-112 ka BP) in the GE-I test pit.<br><br>MATERIALS AND METHOD: This phalanx (GE-1573) probably corresponds to the fifth toe from the right side due to the medial deviation of the distal tuberosity. We compared the metric variables of this phalanx to several fossil and recent Homo samples.<br><br>RESULTS: Neandertals display foot phalanges that are broader and more robust than those of recent humans. Despite the scarcity of well-identified distal phalanges in the Homo fossil record, the GE-1573 phalanx is broad, long and robust when compared with recent and Upper Paleolithic modern humans.<br><br>DISCUSSION: These traits, which align the GE-1573 foot phalanx with the Neandertal morphology, are consistent with the stratigraphic context, likely corresponding to one of the oldest Late Neandertals found inland on the Iberian Peninsula. Additionally, it provides the first evidence of a Neandertal human fossil in a stratigraphic context in the Sierra de Atapuerca.}, }
@article {pmid30332432, year = {2018}, author = {Cortés-Sánchez, M and Riquelme-Cantal, JA and Simón-Vallejo, MD and Parrilla Giráldez, R and Odriozola, CP and Calle Román, L and Carrión, JS and Monge Gómez, G and Rodríguez Vidal, J and Moyano Campos, JJ and Rico Delgado, F and Nieto Julián, JE and Antón García, D and Martínez-Aguirre, MA and Jiménez Barredo, F and Cantero-Chinchilla, FN}, title = {Pre-Solutrean rock art in southernmost Europe: Evidence from Las Ventanas Cave (Andalusia, Spain).}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0204651}, pmid = {30332432}, issn = {1932-6203}, mesh = {Animals ; Archaeology ; Art/*history ; Caves ; Coloring Agents/chemistry/history ; Engraving and Engravings/history ; History, Ancient ; Humans ; Neanderthals ; Radiometric Dating ; Spain ; }, abstract = {The south of Iberia conserves an important group of Palaeolithic rock art sites. The graphisms have been mostly attributed to the Solutrean and Magdalenian periods, while the possibility that older remains exist has provoked extensive debate. This circumstance has been linked to both the cited periods, until recently, due to the transition from the Middle to Upper Palaeolithic in the extreme southwest of Europe as well as the non-existence of some of the early periods of Palaeolithic art documented in northern Iberia. This study presents the results of interdisciplinary research conducted in Las Ventanas Cave. These results enabled us to identify a new Palaeolithic rock art site. The technical, stylistic and temporal traits point to certain similarities with the range of exterior deep engravings in Cantabrian Palaeolithic rock art. Ventanas appears to corroborate the age attributed to those kinds of graphic expression and points to the early arrival of the Upper Palaeolithic in the south of Iberia. Importantly, the results provide information on the pre-Solutrean date attributed to trilinear hind figures. These findings challenge the supposed Neanderthal survival idea at one of the main late Middle Palaeolithic southern Iberian sites (Carigüela) and, due to the parallels between them and an engraving attributed to this period in Gibraltar, it raises the possibility of interaction between modern humans and Neanderthals in the extreme southwest of Europe.}, }
@article {pmid30327578, year = {2018}, author = {Williams, AC and Hill, LJ}, title = {Nicotinamide's Ups and Downs: Consequences for Fertility, Development, Longevity and Diseases of Poverty and Affluence.}, journal = {International journal of tryptophan research : IJTR}, volume = {11}, number = {}, pages = {1178646918802289}, pmid = {30327578}, issn = {1178-6469}, abstract = {To further explore the role of dietary nicotinamide in both brain development and diseases, particularly those of ageing. Articles cover neurodegenerative disease and cancer. Also discussed are the effects of nicotinamide, contained in meat and supplements and derived from symbionts, on the major transitions of disease and fertility from ancient times up to the present day. A key role for the tryptophan - NAD 'de novo' and immune tolerance pathway are discussed at length in the context of fertility and longevity and the transitions from immune paresis to Treg-mediated immune tolerance and then finally to intolerance and their associated diseases. Abstract: Nicotinamide in human evolution increased cognitive power in a positive feedback loop originally involving hunting. As the precursor to metabolic master molecule NAD it is, as vitamin B3, vital for health. Paradoxically, a lower dose on a diverse plant then cereal-based diet fuelled population booms from the Mesolithic onwards, by upping immune tolerance of the foetus. Increased tolerance of risky symbionts, whether in the gut or TB, that excrete nicotinamide co-evolved as buffers for when diet was inadequate. High biological fertility, despite disease trade-offs, avoided the extinction of Homo sapiens and heralded the dawn of a conscious, creative, and pro-fertility culture. Nicotinamide equity now would stabilise populations and prevent NAD-based diseases of poverty and affluence.}, }
@article {pmid30310091, year = {2018}, author = {Gravina, B and Bachellerie, F and Caux, S and Discamps, E and Faivre, JP and Galland, A and Michel, A and Teyssandier, N and Bordes, JG}, title = {No Reliable Evidence for a Neanderthal-Châtelperronian Association at La Roche-à-Pierrot, Saint-Césaire.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {15134}, pmid = {30310091}, issn = {2045-2322}, mesh = {Animals ; *Archaeology ; Europe ; Fossils ; *Hominidae/anatomy &amp; histology ; *Neanderthals/anatomy &amp; histology ; }, abstract = {The demise of Neanderthals and their interaction with dispersing anatomically modern human populations remain some of the most contentious issues in palaeoanthropology. The Châtelperronian, now generally recognized as the first genuine Upper Palaeolithic industry in Western Europe and commonly attributed to the Neanderthals, plays a pivotal role in these debates. The Neanderthal authorship of this techno-complex is based on reported associations of Neanderthal skeletal material with Châtelperronian assemblages at only two sites, La Roche-à-Pierrot (Saint-Césaire) and the Grotte du Renne (Arcy-sur-Cure). The reliability of such an association has, however, been the subject of heated controversy. Here we present a detailed taphonomic, spatial and typo-technological reassessment of the level (EJOP sup) containing the Neanderthal skeletal material at Saint-Césaire. Our assessment of a new larger sample of lithic artifacts, combined with a systematic refitting program and spatial projections of diagnostic artifacts, produced no reliable evidence for a Neanderthal-Châtelperronian association at the site. These results significantly impact current models concerning the Middle-to-Upper Palaeolithic transition in Western Europe and force a critical reappraisal of who exactly were the makers of the Châtelperronian.}, }
@article {pmid30309914, year = {2018}, author = {Hoffmann, DL and Standish, CD and García-Diez, M and Pettitt, PB and Milton, JA and Zilhão, J and Alcolea-González, JJ and Cantalejo-Duarte, P and Collado, H and de Balbín, R and Lorblanchet, M and Ramos-Muñoz, J and Weniger, GC and Pike, AWG}, title = {Response to Comment on "U-Th dating of carbonate crusts reveals Neandertal origin of Iberian cave art".}, journal = {Science (New York, N.Y.)}, volume = {362}, number = {6411}, pages = {}, doi = {10.1126/science.aau1736}, pmid = {30309914}, issn = {1095-9203}, mesh = {Carbonates ; *Caves ; *Neanderthals ; Reproducibility of Results ; Spain ; }, abstract = {Slimak et al challenge the reliability of our oldest (>65,000 years) U-Th dates on carbonates associated with cave paintings in Spain. They cite a supposed lack of parietal art for the 25,000 years following this date, along with potential methodological issues relating to open-system behavior and corrections to detrital or source water [230]Th. We show that their criticisms are unfounded.}, }
@article {pmid30301990, year = {2018}, author = {}, title = {Neanderthal liaisons bestowed virus-fighting genes on humans.}, journal = {Nature}, volume = {562}, number = {7726}, pages = {166}, doi = {10.1038/d41586-018-06940-x}, pmid = {30301990}, issn = {1476-4687}, }
@article {pmid30293985, year = {2018}, author = {Rodríguez, W and Mazet, O and Grusea, S and Arredondo, A and Corujo, JM and Boitard, S and Chikhi, L}, title = {The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure.}, journal = {Heredity}, volume = {121}, number = {6}, pages = {663-678}, pmid = {30293985}, issn = {1365-2540}, mesh = {*Demography ; Humans ; Models, Theoretical ; *Population Density ; }, abstract = {In the last years, a wide range of methods allowing to reconstruct past population size changes from genome-wide data have been developed. At the same time, there has been an increasing recognition that population structure can generate genetic data similar to those produced under models of population size change. Recently, Mazet et al. (Heredity 116:362-371, 2016) showed that, for any model of population structure, it is always possible to find a panmictic model with a particular function of population size changes, having exactly the same distribution of T2 (the coalescence time for a sample of size two) as that of the structured model. They called this function IICR (Inverse Instantaneous Coalescence Rate) and showed that it does not necessarily correspond to population size changes under non-panmictic models. Besides, most of the methods used to analyse data under models of population structure tend to arbitrarily fix that structure and to minimise or neglect population size changes. Here, we extend the seminal work of Herbots (PhD thesis, University of London, 1994) on the structured coalescent and propose a new framework, the Non-Stationary Structured Coalescent (NSSC) that incorporates demographic events (changes in gene flow and/or deme sizes) to models of nearly any complexity. We show how to compute the IICR under a wide family of stationary and non-stationary models. As an example we address the question of human and Neanderthal evolution and discuss how the NSSC framework allows to interpret genomic data under this new perspective.}, }
@article {pmid30290142, year = {2018}, author = {Enard, D and Petrov, DA}, title = {Evidence that RNA Viruses Drove Adaptive Introgression between Neanderthals and Modern Humans.}, journal = {Cell}, volume = {175}, number = {2}, pages = {360-371.e13}, pmid = {30290142}, issn = {1097-4172}, support = {R01 GM100366/GM/NIGMS NIH HHS/United States ; R35 GM118165/GM/NIGMS NIH HHS/United States ; }, mesh = {Alleles ; Animals ; Biological Evolution ; Genome, Human/genetics ; Haplotypes ; Hominidae/genetics ; Humans ; Hybridization, Genetic/*genetics ; Neanderthals/*genetics ; Phylogeny ; RNA Viruses/*genetics/pathogenicity ; Selection, Genetic/genetics ; }, abstract = {Neanderthals and modern humans interbred at least twice in the past 100,000 years. While there is evidence that most introgressed DNA segments from Neanderthals to modern humans were removed by purifying selection, less is known about the adaptive nature of introgressed sequences that were retained. We hypothesized that interbreeding between Neanderthals and modern humans led to (1) the exposure of each species to novel viruses and (2) the exchange of adaptive alleles that provided resistance against these viruses. Here, we find that long, frequent-and more likely adaptive-segments of Neanderthal ancestry in modern humans are enriched for proteins that interact with viruses (VIPs). We found that VIPs that interact specifically with RNA viruses were more likely to belong to introgressed segments in modern Europeans. Our results show that retained segments of Neanderthal ancestry can be used to detect ancient epidemics.}, }
@article {pmid30290135, year = {2018}, author = {Huerta-Sánchez, E and Casey, FP}, title = {Simultaneous Viral Exposure and Protection from Neanderthal Introgression.}, journal = {Cell}, volume = {175}, number = {2}, pages = {306-307}, doi = {10.1016/j.cell.2018.09.019}, pmid = {30290135}, issn = {1097-4172}, support = {R35 GM128946/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Genome ; Hominidae/*genetics ; Humans ; Neanderthals/*genetics ; *RNA Viruses ; }, abstract = {In this issue, Enard and Petrov present intriguing results on the possibility of genetic traces left behind in our genomes from adaptation to past viral epidemics that may have been initiated by interaction with Neanderthal archaic hominins. The work highlights how powerful infectious agents can act as a selective force to shape our genetic makeup.}, }
@article {pmid30287834, year = {2018}, author = {Jones, JR and Richards, MP and Straus, LG and Reade, H and Altuna, J and Mariezkurrena, K and Marín-Arroyo, AB}, title = {Changing environments during the Middle-Upper Palaeolithic transition in the eastern Cantabrian Region (Spain): direct evidence from stable isotope studies on ungulate bones.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14842}, pmid = {30287834}, issn = {2045-2322}, support = {H2020-MSCA-IF-2014-656122)//European Commission (EC)/International ; }, mesh = {Animals ; *Archaeology ; *Bone and Bones ; Deer ; *Environment ; *Fossils ; Geography ; Geologic Sediments ; Horses ; *Isotopes ; *Mammals ; Spain ; }, abstract = {Environmental change has been proposed as a factor that contributed to the extinction of the Neanderthals in Europe during MIS3. Currently, the different local environmental conditions experienced at the time when Anatomically Modern Humans (AMH) met Neanderthals are not well known. In the Western Pyrenees, particularly, in the eastern end of the Cantabrian coast of the Iberian Peninsula, extensive evidence of Neanderthal and subsequent AMH activity exists, making it an ideal area in which to explore the palaeoenvironments experienced and resources exploited by both human species during the Middle to Upper Palaeolithic transition. Red deer and horse were analysed using bone collagen stable isotope analysis to reconstruct environmental conditions across the transition. A shift in the ecological niche of horses after the Mousterian demonstrates a change in environment, towards more open vegetation, linked to wider climatic change. In the Mousterian, Aurignacian and Gravettian, high inter-individual nitrogen ranges were observed in both herbivores. This could indicate that these individuals were procured from areas isotopically different in nitrogen. Differences in sulphur values between sites suggest some variability in the hunting locations exploited, reflecting the human use of different parts of the landscape. An alternative and complementary explanation proposed is that there were climatic fluctuations within the time of formation of these archaeological levels, as observed in pollen, marine and ice cores.}, }
@article {pmid30281595, year = {2018}, author = {Zanolli, C and Martinón-Torres, M and Bernardini, F and Boschian, G and Coppa, A and Dreossi, D and Mancini, L and Martínez de Pinillos, M and Martín-Francés, L and Bermúdez de Castro, JM and Tozzi, C and Tuniz, C and Macchiarelli, R}, title = {The Middle Pleistocene (MIS 12) human dental remains from Fontana Ranuccio (Latium) and Visogliano (Friuli-Venezia Giulia), Italy. A comparative high resolution endostructural assessment.}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0189773}, pmid = {30281595}, issn = {1932-6203}, mesh = {Animals ; Biological Evolution ; Dental Enamel/anatomy &amp; histology ; Dental Pulp Cavity/anatomy &amp; histology ; Dentin/anatomy &amp; histology ; Fossils/*anatomy &amp; histology/history ; History, Ancient ; Humans ; Italy ; Neanderthals ; Tooth/*anatomy &amp; histology ; Tooth Crown/anatomy &amp; histology ; Tooth Root/anatomy &amp; histology ; X-Ray Microtomography ; }, abstract = {The penecontemporaneous Middle Pleistocene sites of Fontana Ranuccio (Latium) and Visogliano (Friuli-Venezia Giulia), set c. 450 km apart in central and northeastern Italy, respectively, have yielded some among the oldest human fossil remains testifying to a peopling phase of the Italian Peninsula broadly during the glacial MIS 12, a stage associated with one among the harshest climatic conditions in the Northern hemisphere during the entire Quaternary period. Together with the large samples from Atapuerca Sima de los Huesos, Spain, and Caune de l'Arago at Tautavel, France, the remains from Fontana Ranuccio and Visogliano are among the few mid-Middle Pleistocene dental assemblages from Western Europe available for investigating the presence of an early Neanderthal signature in their inner structure. We applied two- three-dimensional techniques of virtual imaging and geometric morphometrics to the high-resolution X-ray microtomography record of the dental remains from these two Italian sites and compared the results to the evidence from a selected number of Pleistocene and extant human specimens/samples from Europe and North Africa. Depending on their preservation quality and on the degree of occlusal wear, we comparatively assessed: (i) the crown enamel and radicular dentine thickness topographic variation of a uniquely represented lower incisor; (ii) the lateral crown tissue proportions of premolars and molars; (iii) the enamel-dentine junction, and (iv) the pulp cavity morphology of all available specimens. Our analyses reveal in both samples a Neanderthal-like inner structural signal, for some aspects also resembling the condition shown by the contemporary assemblage from Atapuerca SH, and clearly distinct from the recent human figures. This study provides additional evidence indicating that an overall Neanderthal morphological dental template was preconfigured in Western Europe at least 430 to 450 ka ago.}, }
@article {pmid30281589, year = {2018}, author = {Martín-Francés, L and Martinón-Torres, M and Martínez de Pinillos, M and García-Campos, C and Modesto-Mata, M and Zanolli, C and Rodríguez, L and Bermúdez de Castro, JM}, title = {Tooth crown tissue proportions and enamel thickness in Early Pleistocene Homo antecessor molars (Atapuerca, Spain).}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0203334}, pmid = {30281589}, issn = {1932-6203}, mesh = {Animals ; *Biological Evolution ; Crowns ; Dental Enamel/anatomy &amp; histology/chemistry ; Fossils/*anatomy &amp; histology ; Humans ; Molar/*anatomy &amp; histology ; Neanderthals ; Paleodontology ; Phylogeny ; Spain ; Tooth Crown/*anatomy &amp; histology ; }, abstract = {Tooth crown tissue proportions and enamel thickness distribution are considered reliable characters for inferring taxonomic identity, phylogenetic relationships, dietary and behavioural adaptations in fossil and extant hominids. While most Pleistocene hominins display variations from thick to hyper-thick enamel, Neanderthals exhibit relatively thinner. However, the chronological and geographical origin for the appearance of this typical Neanderthal condition is still unknown. The European late Early Pleistocene species Homo antecessor (Gran Dolina-TD6 site, Sierra de Atapuerca) represents an opportunity to investigate the appearance of the thin condition in the fossil record. In this study, we aim to test the hypothesis if H. antecessor molars approximates the Neanderthal condition for tissue proportions and enamel thickness. To do so, for the first time we characterised the molar inner structural organization in this Early Pleistocene hominin taxon (n = 17) and compared it to extinct and extant populations of the genus Homo from African, Asian and European origin (n = 355). The comparative sample includes maxillary and mandibular molars belonging to H. erectus, East and North African Homo, European Middle Pleistocene Homo, Neanderthals, and fossil and extant H. sapiens. We used high-resolution images to investigate the endostructural configuration of TD6 molars (tissue proportions, enamel thickness and distribution). TD6 permanent molars tend to exhibit on average thick absolute and relative enamel in 2D and 3D estimates, both in the complete crown and the lateral enamel. This condition is shared with the majority of extinct and extant hominin sample, except for Neanderthals and some isolated specimens. However, while the total crown percentage of dentine in TD6 globally resembles the low modern values, the lateral crown percentage of dentine tends to be much higher, closer to the Neanderthal signal. Similarly, the H. antecessor molar enamel distribution maps reveal a relative distribution pattern that is more similar to the Neanderthal condition (with the thickest enamel more spread at the periphery of the occlusal basin) rather than that of other fossil specimens and modern humans (with thicker cuspal enamel). Future studies on European Middle Pleistocene populations will provide more insights into the evolutionary trajectory of the typical Neanderthal dental structural organization.}, }
@article {pmid30278065, year = {2018}, author = {Hoover, KC}, title = {Intragenus (Homo) variation in a chemokine receptor gene (CCR5).}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0204989}, pmid = {30278065}, issn = {1932-6203}, mesh = {Animals ; Gene Expression Regulation ; *Genetic Variation ; Hominidae/*genetics ; Humans ; Receptors, CCR5/*genetics ; Species Specificity ; }, abstract = {Humans have a comparatively higher rate of more polymorphisms in regulatory regions of the primate CCR5 gene, an immune system gene with both general and specific functions. This has been interpreted as allowing flexibility and diversity of gene expression in response to varying disease loads. A broad expression repertoire is useful to humans-the only globally distributed primate-due to our unique adaptive pattern that increased pathogen exposure and disease loads (e.g., sedentism, subsistence practices). The main objective of the study was to determine if the previously observed human pattern of increased variation extended to other members of our genus, Homo. The data for this study are mined from the published genomes of extinct hominins (four Neandertals and two Denisovans), an ancient human (Ust'-Ishim), and modern humans (1000 Genomes). An average of 15 polymorphisms per individual were found in human populations (with a total of 262 polymorphisms). There were 94 polymorphisms identified across extinct Homo (an average of 13 per individual) with 41 previously observed in modern humans and 53 novel polymorphisms (32 in Denisova and 21 in Neandertal). Neither the frequency nor distribution of polymorphisms across gene regions exhibit significant differences within the genus Homo. Thus, humans are not unique with regards to the increased frequency of regulatory polymorphisms and the evolution of variation patterns across CCR5 gene appears to have originated within the genus. A broader evolutionary perspective on regulatory flexibility may be that it provided an advantage during the transition to confrontational foraging (and later hunting) that altered human-environment interaction as well as during migration to Eurasia and encounters with novel pathogens.}, }
@article {pmid30271997, year = {2018}, author = {García-Martínez, D and Torres-Tamayo, N and Torres-Sánchez, I and García-Río, F and Rosas, A and Bastir, M}, title = {Ribcage measurements indicate greater lung capacity in Neanderthals and Lower Pleistocene hominins compared to modern humans.}, journal = {Communications biology}, volume = {1}, number = {}, pages = {117}, pmid = {30271997}, issn = {2399-3642}, abstract = {Our most recent fossil relatives, the Neanderthals, had a large brain and a very heavy body compared to modern humans. This type of body requires high levels of energetic intake. While food (meat and fat consumption) is a source of energy, oxygen via respiration is also necessary for metabolism. We would therefore expect Neanderthals to have large respiratory capacities. Here we estimate the pulmonary capacities of Neanderthals, based on costal measurements and physiological data from a modern human comparative sample. The Kebara 2 male had a lung volume of about 9.04 l; Tabun C1, a female individual, a lung volume of 5.85 l; and a Neanderthal from the El Sidrón site, a lung volume of 9.03 l. These volumes are approximately 20% greater than the corresponding volumes of modern humans of the same body size and sex. These results show that the Neanderthal body was highly sensitive to energy supply.}, }
@article {pmid30263956, year = {2018}, author = {Karakostis, FA and Hotz, G and Tourloukis, V and Harvati, K}, title = {Evidence for precision grasping in Neandertal daily activities.}, journal = {Science advances}, volume = {4}, number = {9}, pages = {eaat2369}, pmid = {30263956}, issn = {2375-2548}, mesh = {Adolescent ; Adult ; Animals ; *Biological Evolution ; Cross-Sectional Studies ; Female ; *Fossils ; Hand Strength/*physiology ; Humans ; Male ; Middle Aged ; Neanderthals/*physiology ; Young Adult ; }, abstract = {Neandertal manual activities, as previously reconstructed from their robust hand skeletons, are thought to involve systematic power grasping rather than precise hand movements. However, this interpretation is at odds with increasing archeological evidence for sophisticated cultural behavior. We reevaluate the manipulative behaviors of Neandertals and early modern humans using a historical reference sample with extensive genealogical and lifelong occupational documentation, in combination with a new and precise three-dimensional multivariate analysis of hand muscle attachments. Results show that Neandertal muscle marking patterns overlap exclusively with documented lifelong precision workers, reflecting systematic precision grasping consistent with the use of their associated cultural remains. Our findings challenge the established interpretation of Neandertal behavior and establish a solid link between biological and cultural remains in the fossil record.}, }
@article {pmid30237321, year = {2018}, author = {Slimak, L and Fietzke, J and Geneste, JM and Ontañón, R}, title = {Comment on "U-Th dating of carbonate crusts reveals Neandertal origin of Iberian cave art".}, journal = {Science (New York, N.Y.)}, volume = {361}, number = {6408}, pages = {}, doi = {10.1126/science.aau1371}, pmid = {30237321}, issn = {1095-9203}, mesh = {Archaeology ; Carbonates ; *Caves ; Fossils ; *Neanderthals ; }, abstract = {Hoffmann et al (Reports, 23 February 2018, p. 912) report the discovery of parietal art older than 64,800 years and attributed to Neanderthals, at least 25 millennia before the oldest parietal art ever found. Instead, critical evaluation of their geochronological data seems to provide stronger support for an age of 47,000 years, which is much more consistent with the archaeological background in hand.}, }
@article {pmid30230470, year = {2018}, author = {Charlier, P and Coppens, Y and Héry-Arnaud, G and Hassin, J}, title = {[A biological anthropology of the disappearance of the Neandertal Man: recent data].}, journal = {Medecine sciences : M/S}, volume = {34}, number = {8-9}, pages = {745-748}, doi = {10.1051/medsci/20183408024}, pmid = {30230470}, issn = {1958-5381}, mesh = {Animals ; Anthropology/*methods ; Anthropology, Physical ; Biological Evolution ; *Extinction, Biological ; Female ; Fossils ; Humans ; Male ; *Neanderthals ; }, abstract = {What could have been the causes of the disappearance of Neanderthals? We will try here to make a synthesis between one of the fundamental questions of biological anthropology relating to human evolution (hypotheses on the causes of the extinction of Neanderthals) and evolutionary bio-medical concepts, some of which have recently been reformulated thanks to the progress of paleogenomics (ancestral inheritance of the current human immune system, paleo-microbiology, host-pathogen relationship…).}, }
@article {pmid30226838, year = {2018}, author = {Skov, L and Hui, R and Shchur, V and Hobolth, A and Scally, A and Schierup, MH and Durbin, R}, title = {Detecting archaic introgression using an unadmixed outgroup.}, journal = {PLoS genetics}, volume = {14}, number = {9}, pages = {e1007641}, pmid = {30226838}, issn = {1553-7404}, support = {207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; WT207492/WT_/Wellcome Trust/United Kingdom ; WT206194/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Asian People/genetics ; Black People/genetics ; Fossils ; Genome, Human/*genetics ; Hominidae/*genetics ; Humans ; Hybridization, Genetic/*genetics ; Native Hawaiian or Other Pacific Islander/genetics ; Neanderthals/*genetics ; Phylogeny ; White People/genetics ; }, abstract = {Human populations outside of Africa have experienced at least two bouts of introgression from archaic humans, from Neanderthals and Denisovans. In Papuans there is prior evidence of both these introgressions. Here we present a new approach to detect segments of individual genomes of archaic origin without using an archaic reference genome. The approach is based on a hidden Markov model that identifies genomic regions with a high density of single nucleotide variants (SNVs) not seen in unadmixed populations. We show using simulations that this provides a powerful approach to identifying segments of archaic introgression with a low rate of false detection, given data from a suitable outgroup population is available, without the archaic introgression but containing a majority of the variation that arose since initial separation from the archaic lineage. Furthermore our approach is able to infer admixture proportions and the times both of admixture and of initial divergence between the human and archaic populations. We apply the model to detect archaic introgression in 89 Papuans and show how the identified segments can be assigned to likely Neanderthal or Denisovan origin. We report more Denisovan admixture than previous studies and find a shift in size distribution of fragments of Neanderthal and Denisovan origin that is compatible with a difference in admixture time. Furthermore, we identify small amounts of Denisova ancestry in South East Asians and South Asians.}, }
@article {pmid30209350, year = {2018}, author = {Clyde, D}, title = {The girl with Neanderthal and Denisovan parents.}, journal = {Nature reviews. Genetics}, volume = {19}, number = {11}, pages = {668-669}, doi = {10.1038/s41576-018-0054-6}, pmid = {30209350}, issn = {1471-0064}, mesh = {Female ; Male ; Fathers ; Genome ; Mothers ; *Neanderthals/genetics ; Parents ; Animals ; }, }
@article {pmid30201119, year = {2018}, author = {Conde-Valverde, M and Quam, R and Martínez, I and Arsuaga, JL and Daura, J and Sanz, M and Zilhão, J}, title = {The bony labyrinth in the Aroeira 3 Middle Pleistocene cranium.}, journal = {Journal of human evolution}, volume = {124}, number = {}, pages = {105-116}, doi = {10.1016/j.jhevol.2018.08.003}, pmid = {30201119}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; Biological Evolution ; Ear, Inner/*anatomy &amp; histology ; Fossils/*anatomy &amp; histology ; Hominidae/*anatomy &amp; histology ; Neanderthals/anatomy &amp; histology ; Portugal ; }, abstract = {The discovery of a partial cranium at the site of Aroeira (Portugal) dating to 389-436 ka augments the current sample of Middle Pleistocene European crania and makes this specimen penecontemporaneous with the fossils from the geographically close Atapuerca Sima de los Huesos (SH) and Arago sites. A recent study of the cranium documented a unique combination of primitive and derived features. The Aroeira 3 cranium preserves the right temporal bone, including the petrosal portion. Virtual reconstruction of the bony labyrinth from μCT scans provides an opportunity to examine its morphology. A series of standard linear and angular measures of the semicircular canals and cochlea in Aroeira 3 were compared with other fossil hominins and recent humans. Our analysis has revealed the absence of derived Neandertal features in Aroeira 3. In particular, the specimen lacks both the derived canal proportions and the low position of the posterior canal, two of the most diagnostic features of the Neandertal bony labyrinth, and Aroeira 3 is more primitive in these features than the Atapuerca (SH) sample. One potentially derived feature (low shape index of the cochlear basal turn) is shared between Aroeira 3 and the Atapuerca (SH) hominins, but is absent in Neandertals. The results of our study provide new insights into Middle Pleistocene population dynamics close to the origin of the Neandertal clade. In particular, the contrasting inner ear morphology between Aroeira 3 and the Atapuerca (SH) hominins suggests a degree of demographic isolation, despite the close geographic proximity and similar age of these two sites.}, }
@article {pmid30177445, year = {2018}, author = {Goldfield, AE and Booton, R and Marston, JM}, title = {Modeling the role of fire and cooking in the competitive exclusion of Neanderthals.}, journal = {Journal of human evolution}, volume = {124}, number = {}, pages = {91-104}, doi = {10.1016/j.jhevol.2018.07.006}, pmid = {30177445}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; *Cooking ; *Extinction, Biological ; *Fires ; Humans ; Models, Biological ; *Neanderthals ; }, abstract = {The Neanderthal body was more robust and energetically costly than the bodies of anatomically modern humans (AMH). Different metabolic budgets between competing populations of Neanderthals and AMH may have been a factor in the varied ranges of behavior and timelines for Neanderthal extinction that we see in the Paleolithic archaeological record. This paper uses an adaptation of the Lotka-Volterra model to determine whether metabolic differences alone could have accounted for Neanderthal extinction. In addition, we use a modeling approach to investigate Neanderthal fire use, evidence for which is much debated and is variable throughout different climatic phases of the Middle Paleolithic. The increased caloric yield from a cooked versus a raw diet may have played an important role in population competition between Neanderthals and AMH. We arrive at two key conclusions. First, given differences in metabolic budget between Neanderthals and AMH and their dependence on similar or overlapping food resources, Neanderthal extinction is likely inevitable over the long term. Second, the rate of Neanderthal extinction increases as the frequency of AMH fire use increases. Results highlight the importance of understanding the variable behaviors at play on a regional scale in order to understand global Neanderthal extinction. We also emphasize the importance of understanding the role of fire use in the Middle to Upper Paleolithic transition.}, }
@article {pmid30173883, year = {2018}, author = {Aubert, M and Brumm, A and Huntley, J}, title = {Early dates for 'Neanderthal cave art' may be wrong.}, journal = {Journal of human evolution}, volume = {125}, number = {}, pages = {215-217}, doi = {10.1016/j.jhevol.2018.08.004}, pmid = {30173883}, issn = {1095-8606}, mesh = {Animals ; *Archaeology ; Caves ; *Neanderthals/psychology ; *Paintings ; *Radiometric Dating/statistics &amp; numerical data ; }, }
@article {pmid30153108, year = {2018}, author = {Delpiano, D and Heasley, K and Peresani, M}, title = {Assessing Neanderthal land use and lithic raw material management in Discoid technology.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {96}, number = {}, pages = {89-110}, doi = {10.4436/JASS.96006}, pmid = {30153108}, issn = {2037-0644}, mesh = {Animals ; Archaeology ; Italy ; Neanderthals/*physiology ; *Technology ; Territoriality ; *Tool Use Behavior ; }, abstract = {Neanderthal groups developed different models of mobility and exploitation of resources across their territory: these differences can be linked to various knapping methods and are probably related to adaptative strategies and responses at many ecological and cultural levels. Neanderthals associated with Discoid knapping are known to depend on an opportunistic exploitation of lithic raw materials for daily food procurement and be more mobile than others using different technologies. However, we have no defined data for most of the geographical contexts where this technocomplex was found. This study analyzes the southern Alpine site of Grotta di Fumane, where the final Mousterian is characterized by the succession of well defined cultural entities. Unit A9 presents with entirely Discoid technology and is embedded between fully Levallois levels. The level was recently extensively investigated for almost 68m[2] on 9,000 lithic pieces. To study the lithic assemblage of Unit A9 we applied a techno-economical analysis designed to infer the spatial fragmentation of the reduction sequences, and results were corroborated through the characterization of cortex and raw materials based on geological surveys and experimental comparisons. Results show that raw materials collected within a radius of 5km, by far the most frequently used, exhibit complete and ordinary reduction sequences, which were further attested by multiple refittings. Beyond this area, semi-local raw materials (5-10 km) are introduced to perform specific tasks, and are reduced according to their different physical qualities. These data, combined with the presence of lithotypes and fossils collected from longer distances (ten to hundreds of kilometers), and to the recycling of old patinated artifacts, indicate a complex and diversified behavior encompassing both: a) opportunistic and daily residential exploitation within a local territory; b) logistical planning of the economical organization in the semi-local to exotic territory according to quality and distance of available raw materials sources.}, }
@article {pmid30135579, year = {2018}, author = {Slon, V and Mafessoni, F and Vernot, B and de Filippo, C and Grote, S and Viola, B and Hajdinjak, M and Peyrégne, S and Nagel, S and Brown, S and Douka, K and Higham, T and Kozlikin, MB and Shunkov, MV and Derevianko, AP and Kelso, J and Meyer, M and Prüfer, K and Pääbo, S}, title = {The genome of the offspring of a Neanderthal mother and a Denisovan father.}, journal = {Nature}, volume = {561}, number = {7721}, pages = {113-116}, pmid = {30135579}, issn = {1476-4687}, support = {324139/ERC_/European Research Council/International ; 694707/ERC_/European Research Council/International ; 715069/ERC_/European Research Council/International ; }, mesh = {Alleles ; Animals ; Fathers ; Female ; Gene Flow/genetics ; Genome ; Genomics ; History, Ancient ; Hominidae/*genetics ; Humans ; Hybridization, Genetic/*genetics ; Male ; Mothers ; Neanderthals/*genetics ; Time Factors ; }, abstract = {Neanderthals and Denisovans are extinct groups of hominins that separated from each other more than 390,000 years ago[1,2]. Here we present the genome of 'Denisova 11', a bone fragment from Denisova Cave (Russia)[3] and show that it comes from an individual who had a Neanderthal mother and a Denisovan father. The father, whose genome bears traces of Neanderthal ancestry, came from a population related to a later Denisovan found in the cave[4-6]. The mother came from a population more closely related to Neanderthals who lived later in Europe[2,7] than to an earlier Neanderthal found in Denisova Cave[8], suggesting that migrations of Neanderthals between eastern and western Eurasia occurred sometime after 120,000 years ago. The finding of a first-generation Neanderthal-Denisovan offspring among the small number of archaic specimens sequenced to date suggests that mixing between Late Pleistocene hominin groups was common when they met.}, }
@article {pmid30135563, year = {2018}, author = {Srinivasan, S and Bettella, F and Frei, O and Hill, WD and Wang, Y and Witoelar, A and Schork, AJ and Thompson, WK and Davies, G and Desikan, RS and Deary, IJ and Melle, I and Ueland, T and Dale, AM and Djurovic, S and Smeland, OB and Andreassen, OA}, title = {Enrichment of genetic markers of recent human evolution in educational and cognitive traits.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {12585}, pmid = {30135563}, issn = {2045-2322}, support = {223273//Norges Forskningsr&#x00E5;d (Research Council of Norway)/International ; 2016-064//Ministry of Health and Care Services | Helse S&#x00F8;r-&#x00D8;st RHF (Southern and Eastern Norway Regional Health Authority)/International ; Disconnected mind grant//Age UK/International ; 225989//Norges Forskningsr&#x00E5;d (Research Council of Norway)/International ; MR/K026992/1/MRC_/Medical Research Council/United Kingdom ; MR/K026992/1//Biotechnology and Biological Sciences Research Council (BBSRC)/International ; 248778//Norges Forskningsr&#x00E5;d (Research Council of Norway)/International ; }, mesh = {*Biological Evolution ; Brain/metabolism ; Cognition/physiology ; Educational Status ; Female ; Genetic Markers/genetics ; Genome/genetics ; Genome-Wide Association Study ; Humans ; Intelligence/*genetics ; Male ; Multifactorial Inheritance/genetics ; Phenotype ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {Higher cognitive functions are regarded as one of the main distinctive traits of humans. Evidence for the cognitive evolution of human beings is mainly based on fossil records of an expanding cranium and an increasing complexity of material culture artefacts. However, the molecular genetic factors involved in the evolution are still relatively unexplored. Here, we investigated whether genomic regions that underwent positive selection in humans after divergence from Neanderthals are enriched for genetic association with phenotypes related to cognitive functions. We used genome wide association data from a study of college completion (N = 111,114), one of educational attainment (N = 293,623) and two different studies of general cognitive ability (N = 269,867 and 53,949). We found nominally significant polygenic enrichment of associations with college completion (p = 0.025), educational attainment (p = 0.043) and general cognitive ability (p = 0.015 and 0.025, respectively), suggesting that variants influencing these phenotypes are more prevalent in evolutionarily salient regions. The enrichment remained significant after controlling for other known genetic enrichment factors, and for affiliation to genes highly expressed in the brain. These findings support the notion that phenotypes related to higher order cognitive skills typical of humans have a recent genetic component that originated after the separation of the human and Neanderthal lineages.}, }
@article {pmid30135540, year = {2018}, author = {Warren, M}, title = {Mum's a Neanderthal, Dad's a Denisovan: First discovery of an ancient-human hybrid.}, journal = {Nature}, volume = {560}, number = {7719}, pages = {417-418}, doi = {10.1038/d41586-018-06004-0}, pmid = {30135540}, issn = {1476-4687}, }
@article {pmid30026576, year = {2018}, author = {Sorensen, AC and Claud, E and Soressi, M}, title = {Neandertal fire-making technology inferred from microwear analysis.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10065}, pmid = {30026576}, issn = {2045-2322}, support = {PGW-13-42//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/International ; }, mesh = {Animals ; Archaeology ; *Artifacts ; *Fires ; Fossils ; France ; Friction ; History, Ancient ; Humans ; Iron ; Manganese Compounds ; Microscopy ; Minerals ; *Neanderthals ; Oxides ; Sulfides ; Technology/*history ; *Tool Use Behavior ; }, abstract = {Fire use appears to have been relatively common among Neandertals in the Middle Palaeolithic. However, the means by which Neandertals procured their fire-either through the collection of natural fire, or by producing it themselves using tools-is still a matter of debate. We present here the first direct artefactual evidence for regular, systematic fire production by Neandertals. From archaeological layers attributed to late Mousterian industries at multiple sites throughout France, primarily to the Mousterian of Acheulean Tradition (MTA) technoculture (ca. 50,000 years BP), we identify using microwear analysis dozens of late Middle Palaeolithic bifacial tools that exhibit macroscopic and microscopic traces suggesting repeated percussion and/or forceful abrasion with a hard mineral material. Both the locations and nature of the polish and associated striations are comparable to those obtained experimentally by obliquely percussing fragments of pyrite (FeS2) against the flat/convex sides of a biface to make fire. The striations within these discrete use zones are always oriented roughly parallel to the longitudinal axis of the tool, allowing us to rule out taphonomic origins for these traces. We therefore suggest that the occasional use of bifaces as 'strike-a-lights' was a technocultural feature shared among the late Neandertals in France.}, }
@article {pmid30022013, year = {2018}, author = {Dolgova, O and Lao, O}, title = {Evolutionary and Medical Consequences of Archaic Introgression into Modern Human Genomes.}, journal = {Genes}, volume = {9}, number = {7}, pages = {}, pmid = {30022013}, issn = {2073-4425}, abstract = {The demographic history of anatomically modern humans (AMH) involves multiple migration events, population extinctions and genetic adaptations. As genome-wide data from complete genome sequencing becomes increasingly abundant and available even from extinct hominins, new insights of the evolutionary history of our species are discovered. It is currently known that