@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}, 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 {pmid31203843, year = {2019}, author = {Galletta, L and Stephens, NB and Bardo, A and Kivell, TL and Marchi, D}, title = {Three-dimensional geometric morphometric analysis of the first metacarpal distal articular surface in humans, great apes and fossil hominins.}, journal = {Journal of human evolution}, volume = {132}, number = {}, pages = {119-136}, doi = {10.1016/j.jhevol.2019.04.008}, pmid = {31203843}, issn = {1095-8606}, abstract = {Understanding the manual abilities of fossil hominins has been a focus of palaeoanthropological research for decades. Of interest are the morphological characteristics of the thumb due to its fundamental role in manipulation, particularly that of the trapeziometacarpal joint. Considerably less attention has been given to the thumb metacarpophalangeal (MCP) joint, which plays a role in stabilizing the thumb during forceful grasps and precision pinching. In this study we use a three-dimensional geometric morphometric approach to quantify the shape of the first metacarpal head in extant hominids (Homo, Pan, Gorilla and Pongo) and six fossil hominin species (Homo neanderthalensis Tabun C1 and La Chappelle-aux-Saints, Homo naledi U.W. 101-1282, Australopithecus sediba MH2, Paranthropus robustus/early Homo SK84, Australopithecus africanus StW 418, Australopithecus afarensis A.L. 333w-39), with the aims of identifying shapes that may be correlated with human-like forceful opposition and determining if similar morphologies are present in fossil hominins. Results show that humans differ from extant great apes by having a distally flatter articular surface, larger epicondyle surface area, and a larger radial palmar condyle. We suggest that this suite of features is correlated with a lower range of motion at the MCP joint, which would enhance the thumbs ability to resist the elevated loads associated with the forceful precision grips typical of humans. Great ape genera are each differentiated by distinctive morphological features, each of which is consistently correlated with the predicted biomechanical demands of their particular locomotor and/or manipulatory habits. Neanderthals and U.W. 101-1282 fall within the modern human range of variation, StW 418, SK 84 and U.W. 88-119 fall in between humans and great apes, and A.L. 333w-39 falls within Pan variation. These results agree with those of traditional linear analyses while providing a more comprehensive quantitative basis from which to interpret the hand functional morphology of extinct hominins.}, } @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 = {}, number = {}, pages = {}, doi = {10.1534/genetics.119.302368}, pmid = {31196864}, issn = {1943-2631}, 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 re-investigate 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 {pmid31186485, year = {2019}, author = {Kuhlwilm, M and Boeckx, C}, title = {A catalog of single nucleotide changes distinguishing modern humans from archaic hominins.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {8463}, doi = {10.1038/s41598-019-44877-x}, pmid = {31186485}, issn = {2045-2322}, support = {KU 3467/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; LCF/BQ/PR19/11700002//"la Caixa" Foundation (Caixa Foundation)/ ; PIRG-GA-2009-256413//EC | EC Seventh Framework Programm | FP7 People: Marie-Curie Actions (FP7-PEOPLE - Specific Programme "People" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; JP17H06379//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 2017-SGR-341//Departament d'Innovació, Universitats i Empresa, Generalitat de Catalunya (Department of Innovation, Education and Enterprise, Government of Catalonia)/ ; FFI2016-78034-C2-1-P//Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness)/ ; }, abstract = {Throughout the past decade, studying ancient genomes has provided unique insights into human prehistory, and differences between modern humans and other branches like Neanderthals can enrich our understanding of the molecular basis of unique modern human traits. Modern human variation and the interactions between different hominin lineages are now well studied, making it reasonable to go beyond fixed genetic changes and explore changes that are observed at high frequency in present-day humans. Here, we identify 571 genes with non-synonymous changes at high frequency. We suggest that molecular mechanisms in cell division and networks affecting cellular features of neurons were prominently modified by these changes. Complex phenotypes in brain growth trajectory and cognitive traits are likely influenced by these networks and other non-coding changes presented here. We propose that at least some of these changes contributed to uniquely human traits, and should be prioritized for experimental validation.}, } @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}, doi = {10.1098/rspb.2019.0907}, pmid = {31185865}, issn = {1471-2954}, 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}, 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}, 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 M1 (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 M1, 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 {pmid30563976, year = {2018}, author = {Gibney, E and Callaway, E and Cyranoski, D and Gaind, N and Tollefson, J and Courtland, R and Law, YH and Maher, B and Else, H and Castelvecchi, D}, title = {Nature's 10: Ten people who mattered in science in 2018.}, journal = {Nature}, volume = {564}, number = {7736}, pages = {325-335}, doi = {10.1038/d41586-018-07683-5}, pmid = {30563976}, issn = {1476-4687}, mesh = {Animals ; Astronomy/*trends ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Electric Conductivity ; Environmental Pollution/*prevention & control ; Female ; *Forensic Genetics ; *Gene Editing ; Global Warming/*statistics & numerical data ; Graphite/*chemistry ; Humans ; Hybridization, Genetic ; Male ; *Minor Planets ; *Minority Groups ; Neanderthals/*genetics ; *Open Access Publishing ; Paleontology ; Pedigree ; Plastics ; Twins/*genetics ; }, } @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}, doi = {10.1186/s12896-019-0523-9}, pmid = {31164119}, issn = {1472-6750}, support = {K2013-55X-22189-01-2//Vetenskapsrådet/ ; FO2016-0217//Hjärnfonden/ ; }, 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.

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.

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 = {}, number = {}, pages = {1-39}, doi = {10.1080/03014460.2019.1624823}, pmid = {31163991}, issn = {1464-5033}, abstract = {Context: Africa's role in the narrative of human evolution is indisputably emphasised in the emergence Homo sapiens. However, once humans disperse beyond Africa, the history of those who stayed remains vastly understudied lacking the proper attention it deserves as the birthplace of both modern and archaic humans. 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: We review here the state of research for archaic introgression in African populations and discuss 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 we discuss 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 = {}, number = {}, pages = {}, doi = {10.1016/j.ajhg.2019.04.016}, pmid = {31155285}, issn = {1537-6605}, 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}, doi = {10.1371/journal.pone.0216742}, pmid = {31141515}, issn = {1932-6203}, 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}, doi = {10.1371/journal.pgen.1008175}, pmid = {31136573}, issn = {1553-7404}, 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}, doi = {10.3389/fgene.2019.00389}, 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 = {}, number = {}, pages = {1-28}, doi = {10.1080/03014460.2019.1622038}, pmid = {31113254}, issn = {1464-5033}, abstract = {BACKGROUND: Simoni et al (2016) 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 presence of rs3917862 and decreased maternal mortality ratios. When 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 {pmid29632350, year = {2018}, author = {Pearce, DG and Bonneau, A}, title = {Trouble on the dating scene.}, journal = {Nature ecology & evolution}, volume = {2}, number = {6}, pages = {925-926}, doi = {10.1038/s41559-018-0540-4}, pmid = {29632350}, issn = {2397-334X}, mesh = {Animals ; *Archaeology ; *Art ; *Caves ; Neanderthals/*psychology ; Spain ; }, } @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}, doi = {10.1126/sciadv.aaw1268}, pmid = {31106274}, issn = {2375-2548}, 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}, doi = {10.1371/journal.pone.0215832}, pmid = {31095578}, issn = {1932-6203}, 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 {pmid30672457, year = {2019}, author = {Henry, JP}, title = {[Genetics and origin of Homo sapiens].}, journal = {Medecine sciences : M/S}, volume = {35}, number = {1}, pages = {39-45}, doi = {10.1051/medsci/2018311}, pmid = {30672457}, issn = {1958-5381}, mesh = {Africa ; Animals ; Asia ; Biological Evolution ; DNA/analysis/chemistry ; Europe ; *Evolution, Molecular ; *Genome, Human ; Hominidae/*genetics ; Human Genome Project ; Humans ; Neanderthals/genetics ; Phylogeny ; Polymorphism, Single Nucleotide ; Selection, Genetic ; Sequence Homology ; }, abstract = {Usually, paleoanthropology studies remains and artefacts. However, more recently, genetics offer new avenues. Information on humanisation mechanisms has been obtained from comparison with primate or archaic Homo DNA sequences. Likewise, the 1 000 Genomes Project has characterized the geographic spectrum of human genetic variation offering a basis for a genomic study of Homo sapiens phylogeny. From these studies, a model, Out of Africa, was derived. His origin is Africa, where he lived 200 000 years ago. A small fraction of the population left Africa between 50 and 100 000 years ago that have populated the rest of the world, to Europe, coastal Asia to Australia and mainland Asia to Behring Land Bridge and America. The model is supported by the decrease of genetic diversity with the distance to Eastern Africa (serial founder effect). In Europe and Asia, Homo sapiens met archaic Homo neanderthalis and H denisova. The presence of 1-3% neanderthalis sequences in modern Homo ADN indicates admixtures between these groups. Some archaic sequences are on positive selection pressure, thus suggesting that the extinct hominins might have facilitated the adaptation of H sapiens to new environments.}, } @article {pmid31068377, year = {2019}, author = {Vangenot, C and Gagneux, P and de Groot, NG and Baumeyer, A and Mouterde, M and Crouau-Roy, B and Darlu, P and Sanchez-Mazas, A and Sabbagh, A and Poloni, ES}, title = {Humans and Chimpanzees Display Opposite Patterns of Diversity in arylamineN-acetyltranferase Genes.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1534/g3.119.400223}, pmid = {31068377}, issn = {2160-1836}, abstract = {Among the many genes involved in the metabolism of therapeutic drugs, human arylamine N-acetyltransferases (NATs) genes have been extensively studied, due to their medical importance both in pharmacogenetics and disease epidemiology. One member of this small gene family, NAT2, is established as the locus of the classic human acetylation polymorphism in drug metabolism. Current hypotheses hold that selective processes favoring haplotypes conferring lower NAT2 activity have been operating in modern humans' recent history as an adaptation to local chemical and dietary environments. To shed new light on such hypotheses, we investigated the genetic diversity of the three members of the NAT gene family in seven hominid species, including modern humans, Neanderthals and Denisovans. Little polymorphism sharing was found among hominids, yet all species displayed high NAT diversity, but distributed in an opposite fashion in chimpanzees and bonobos (Pan genus) compared to modern humans, with higher diversity in Pan species at NAT1 and lower at NAT2, while the reverse is observed in humans. This pattern was also reflected in the results returned by selective neutrality tests, which suggest, in agreement with the predicted functional impact of mutations detected in non-human primates, stronger directional selection, presumably purifying selection, at NAT1 in modern humans, and at NAT2 in chimpanzees. Overall, the results point to the evolution of divergent functions of these highly homologous genes in the different primate species, possibly related to their specific chemical/dietary environment (exposome) and we hypothesize that this is likely linked to the emergence of controlled fire use in the human lineage.}, } @article {pmid30540784, year = {2018}, author = {Caricola, I and Zupancich, A and Moscone, D and Mutri, G and Falcucci, A and Duches, R and Peresani, M and Cristiani, E}, title = {An integrated method for understanding the function of macro-lithic tools. Use wear, 3D and spatial analyses of an Early Upper Palaeolithic assemblage from North Eastern Italy.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0207773}, doi = {10.1371/journal.pone.0207773}, pmid = {30540784}, issn = {1932-6203}, mesh = {Animals ; Archaeology/*methods ; Caves ; Fossils/*diagnostic imaging ; Humans ; Italy ; Neanderthals ; Spatial Analysis ; Technology ; }, abstract = {The article presents an original analysis which combines use-wear, 3D modelling and spatial analyses to experimental archaeology in order to investigate Early Upper Palaeolithic flint-knapping gestures and techniques involving the use of macro-lithic tools. In particular, the methodological framework proposed in this paper was applied to the study of Protoaurignacian and Aurignacian macro-tools from Fumane Cave (Verona, Italy). Combining spatial analysis and use wear investigation, both at low and high magnifications, permitted the identification and detailed description of the use-related traces affecting both the hammerstones and retouchers which, at Fumane Cave, were used at different stages during flint tool production. Several experimental activities were performed including core reduction, maintenance, and blank production together with different types of edge retouching. From a methodological perspective, the protocol of analysis permitted to codify specific traces and to produce quantitative data related to their geometry and distribution over the tool's surface, according to the activities and gestures performed. The results obtained allowed a careful investigation of the function and the gestures associated to the use of the macro-lithic tools coming from the Protoaurignacian and Aurignacian levels of Fumane Cave while providing a methodological tool for interpreting different archaeological samples.}, } @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}, doi = {10.1371/journal.pone.0215172}, pmid = {31048924}, issn = {1932-6203}, 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}, doi = {10.1371/journal.pone.0216155}, pmid = {31034533}, issn = {1932-6203}, 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 = {}, number = {}, pages = {}, doi = {10.1002/ajpa.23844}, pmid = {31025315}, issn = {1096-8644}, support = {//German Research Foundation/ ; }, 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.

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).

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.

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}, doi = {10.1371/journal.pone.0214955}, pmid = {31017917}, issn = {1932-6203}, 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 {pmid31014244, year = {2019}, author = {Pfeifer, B and Kapan, DD}, title = {Estimates of introgression as a function of pairwise distances.}, journal = {BMC bioinformatics}, volume = {20}, number = {1}, pages = {207}, doi = {10.1186/s12859-019-2747-z}, pmid = {31014244}, issn = {1471-2105}, support = {1427772//Division of Biological Infrastructure/ ; }, abstract = {BACKGROUND: Research over the last 10 years highlights the increasing importance of hybridization between species as a major force structuring the evolution of genomes and potentially providing raw material for adaptation by natural and/or sexual selection. Fueled by research in a few model systems where phenotypic hybrids are easily identified, research into hybridization and introgression (the flow of genes between species) has exploded with the advent of whole-genome sequencing and emerging methods to detect the signature of hybridization at the whole-genome or chromosome level. Amongst these are a general class of methods that utilize patterns of single-nucleotide polymorphisms (SNPs) across a tree as markers of hybridization. These methods have been applied to a variety of genomic systems ranging from butterflies to Neanderthals to detect introgression, however, when employed at a fine genomic scale these methods do not perform well to quantify introgression in small sample windows.

RESULTS: We introduce a novel method to detect introgression by combining two widely used statistics: pairwise nucleotide diversity dxy and Patterson's D. The resulting statistic, the distance fraction (df), accounts for genetic distance across possible topologies and is designed to simultaneously detect and quantify introgression. We also relate our new method to the recently published fd and incorporate these statistics into the powerful genomics R-package PopGenome, freely available on GitHub (pievos101/PopGenome) and the Comprehensive R Archive Network (CRAN). The supplemental material contains a wide range of simulation studies and a detailed manual how to perform the statistics within the PopGenome framework.

CONCLUSION: We present a new distance based statistic df that avoids the pitfalls of Patterson's D when applied to small genomic regions and accurately quantifies the fraction of introgression (f) for a wide range of simulation scenarios.}, } @article {pmid30478304, year = {2019}, author = {Mafessoni, F}, title = {Encounters with archaic hominins.}, journal = {Nature ecology & evolution}, volume = {3}, number = {1}, pages = {14-15}, doi = {10.1038/s41559-018-0729-6}, pmid = {30478304}, issn = {2397-334X}, mesh = {Animals ; Fossils ; *Hominidae ; Humans ; *Neanderthals ; }, } @article {pmid29942017, year = {2018}, author = {Milks, A}, title = {Making an impact.}, journal = {Nature ecology & evolution}, volume = {2}, number = {7}, pages = {1057-1058}, doi = {10.1038/s41559-018-0600-9}, pmid = {29942017}, issn = {2397-334X}, mesh = {Decision Making ; *Neanderthals ; }, } @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 = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2019.02.035}, pmid = {30981557}, issn = {1097-4172}, 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}, doi = {10.1038/s41467-019-09689-7}, pmid = {30975994}, issn = {2041-1723}, 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}, doi = {10.1371/journal.pone.0214925}, pmid = {30943255}, issn = {1932-6203}, 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 = {}, number = {}, pages = {}, doi = {10.1093/gbe/evz071}, pmid = {30942856}, issn = {1759-6653}, 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}, 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 {pmid30893326, year = {2019}, author = {Di Maida, G and Mannino, MA and Krause-Kyora, B and Jensen, TZT and Talamo, S}, title = {Radiocarbon dating and isotope analysis on the purported Aurignacian skeletal remains from Fontana Nuova (Ragusa, Italy).}, journal = {PloS one}, volume = {14}, number = {3}, pages = {e0213173}, doi = {10.1371/journal.pone.0213173}, pmid = {30893326}, issn = {1932-6203}, abstract = {Proving voyaging at sea by Palaeolithic humans is a difficult archaeological task, even for short distances. In the Mediterranean, a commonly accepted sea crossing is that from the Italian Peninsula to Sicily by anatomically modern humans, purportedly of the Aurignacian culture. This claim, however, was only supported by the typological attribution to the Aurignacian of the lithic industries from the insular site of Fontana Nuova. AMS radiocarbon dating undertaken as part of our research shows that the faunal remains, previously considered Aurignacian, actually date to the Holocene. Absolute dating on dentinal collagen also attributes the human teeth from the site to the early Holocene, although we were unable to obtain ancient DNA to evaluate their ancestry. Ten radiocarbon dates on human and other taxa are comprised between 9910-9700 cal. BP and 8600-8480 cal. BP, indicating that Fontana Nuova was occupied by Mesolithic and not Aurignacian hunter-gatherers. Only a new study of the lithic assemblage could establish if the material from Fontana Nuova is a mixed collection that includes both late Upper Palaeolithic (Epigravettian) and Mesolithic artefacts, as can be suggested by taking into account both the results of our study and of the most recent reinterpretation of the lithics. Nevertheless, this research suggests that the notion that Aurignacian groups were present in Sicily should now be revised. Another outcome of our study is that we found that three specimens, attributed on grounds both of morphological and ZooMS identifications to Cervus elaphus, had δ13C values significantly higher than any available for such species in Europe.}, } @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 = {}, number = {}, pages = {}, doi = {10.1002/ajpa.23818}, pmid = {30889271}, issn = {1096-8644}, support = {BCS-1258965//National Science Foundation/ ; }, 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.

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.

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.

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}, doi = {10.1038/s41598-019-41033-3}, pmid = {30872714}, issn = {2045-2322}, 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}, doi = {10.1371/journal.pone.0213687}, pmid = {30861048}, issn = {1932-6203}, 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 {pmid30854435, year = {2019}, author = {Morin, E and Meier, J and El Guennouni, K and Moigne, AM and Lebreton, L and Rusch, L and Valensi, P and Conolly, J and Cochard, D}, title = {New evidence of broader diets for archaic Homo populations in the northwestern Mediterranean.}, journal = {Science advances}, volume = {5}, number = {3}, pages = {eaav9106}, doi = {10.1126/sciadv.aav9106}, pmid = {30854435}, issn = {2375-2548}, abstract = {Investigating diet breadth is critical for understanding how archaic Homo populations, including Neanderthals, competed for seasonally scarce resources. The current consensus in Western Europe is that ungulates formed the bulk of the human diet during the Lower and Middle Paleolithic, while small fast prey taxa were virtually ignored. Here, we present a multisite taphonomic study of leporid assemblages from Southern France that supports frequent exploitation of small fast game during marine isotope stages 11 to 3. Along with recent evidence from Iberia, our results indicate that the consumption of small fast game was more common prior to the Upper Paleolithic than previously thought and that archaic hominins from the northwestern Mediterranean had broader diets than those from adjacent regions. Although likely of secondary importance relative to ungulates, the frequent exploitation of leporids documented here implies that human diet breadths were substantially more variable within Europe than assumed by current evolutionary models.}, } @article {pmid30854422, year = {2019}, author = {Rogers, J and Raveendran, M and Harris, RA and Mailund, T and Leppälä, K and Athanasiadis, G and Schierup, MH and Cheng, J and Munch, K and Walker, JA and Konkel, MK and Jordan, V and Steely, CJ and Beckstrom, TO and Bergey, C and Burrell, A and Schrempf, D and Noll, A and Kothe, M and Kopp, GH and Liu, Y and Murali, S and Billis, K and Martin, FJ and Muffato, M and Cox, L and Else, J and Disotell, T and Muzny, DM and Phillips-Conroy, J and Aken, B and Eichler, EE and Marques-Bonet, T and Kosiol, C and Batzer, MA and Hahn, MW and Tung, J and Zinner, D and Roos, C and Jolly, CJ and Gibbs, RA and Worley, KC and , }, title = {The comparative genomics and complex population history of Papio baboons.}, journal = {Science advances}, volume = {5}, number = {1}, pages = {eaau6947}, doi = {10.1126/sciadv.aau6947}, pmid = {30854422}, issn = {2375-2548}, abstract = {Recent studies suggest that closely related species can accumulate substantial genetic and phenotypic differences despite ongoing gene flow, thus challenging traditional ideas regarding the genetics of speciation. Baboons (genus Papio) are Old World monkeys consisting of six readily distinguishable species. Baboon species hybridize in the wild, and prior data imply a complex history of differentiation and introgression. We produced a reference genome assembly for the olive baboon (Papio anubis) and whole-genome sequence data for all six extant species. We document multiple episodes of admixture and introgression during the radiation of Papio baboons, thus demonstrating their value as a model of complex evolutionary divergence, hybridization, and reticulation. These results help inform our understanding of similar cases, including modern humans, Neanderthals, Denisovans, and other ancient hominins.}, } @article {pmid28567860, year = {2017}, author = {Hardy, K and Buckley, S}, title = {Earliest evidence of bitumen from Homo sp. teeth is from El Sidrón.}, journal = {American journal of physical anthropology}, volume = {164}, number = {1}, pages = {212-213}, doi = {10.1002/ajpa.23255}, pmid = {28567860}, issn = {1096-8644}, mesh = {Animals ; Dentistry ; *Hominidae ; Hydrocarbons ; *Neanderthals ; Tooth ; }, } @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}, } @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}, 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 = {}, number = {}, pages = {}, doi = {10.1073/pnas.1820745116}, pmid = {30804177}, issn = {1091-6490}, 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 δ15N 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 = {}, number = {}, pages = {}, doi = {10.1073/pnas.1814087116}, pmid = {30782806}, issn = {1091-6490}, 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 δ15N 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}, 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}, 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 {pmid30777355, year = {2019}, author = {Ekshtain, R and Tryon, CA}, title = {Lithic raw material acquisition and use by early Homo sapiens at Skhul, Israel.}, journal = {Journal of human evolution}, volume = {127}, number = {}, pages = {149-170}, doi = {10.1016/j.jhevol.2018.10.005}, pmid = {30777355}, issn = {1095-8606}, abstract = {The site of Skhul in Israel has featured prominently in discussions about the early presence of Homo sapiens outside of Africa since its excavation in the 1930s. Until now, attention has been primarily focused on the site's fossil hominins and evidence for symbolic behavior in the form of burials and rare artifacts such as pierced shells and pigment objects. We present here the results of renewed analysis of the lithic artifacts from Skhul drawn from archival collections in the United States, United Kingdom, and Israel. Although lithic artifacts form the majority of the archaeological record from the site, they have rarely been the subject of comprehensive study. Our analyses of raw material selection, use and transport combined with technological analyses of artifact production methods (1) indicate selective transport to the site of large flakes, retouched pieces, and particularly Levallois points from non-local sources, and (2) demonstrate substantial variability in raw material procurement that fails to indicate clear differences in landscape use between H. sapiens and Neanderthals.}, } @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}, 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 Iverson, PO and Stover, PJ}, title = {Nutrition and its role in human evolution.}, journal = {Journal of internal medicine}, volume = {}, number = {}, pages = {}, doi = {10.1111/joim.12878}, pmid = {30772945}, issn = {1365-2796}, 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 = {}, number = {}, pages = {}, doi = {10.1002/ajpa.23798}, pmid = {30771245}, issn = {1096-8644}, support = {Research Group//Gobierno Vasco/Eusko Jaurlaritza/ ; IT1044-16//Gobierno Vasco/Eusko Jaurlaritza/ ; IT834-13//Gobierno Vasco/Eusko Jaurlaritza/ ; CGL2015-65387-C3-2-P-MINECO/FEDER-//Ministerio de Ciencia y Tecnología/ ; CGL2012-38434-C03-01//Ministerio de Ciencia y Tecnología/ ; //UMR 7194 CNRS-HNHP/UPVD/ ; }, 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.

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.

RESULTS: Three specimens are classified as Neandertals, two as modern humans, and one remains unclassified.

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}, doi = {10.1038/s41598-019-38571-1}, pmid = {30737446}, issn = {2045-2322}, support = {336301//European Research Council/International ; CGL2016-75109-P//Ministerio de Ciencia y Tecnolog&#x00ED;a (Ministry of Science and Technology)/ ; }, 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}, 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 {pmid30702428, year = {2019}, author = {Miller, IF and Barton, RA and Nunn, CL}, title = {Quantitative uniqueness of human brain evolution revealed through phylogenetic comparative analysis.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, doi = {10.7554/eLife.41250}, pmid = {30702428}, issn = {2050-084X}, support = {BCS-1355902//National Science Foundation/ ; }, abstract = {While the human brain is clearly large relative to body size, less is known about the timing of brain and brain component expansion within primates and the relative magnitude of volumetric increases. Using Bayesian phylogenetic comparative methods and data for both extant and fossil species, we identified that a distinct shift in brain-body scaling occurred as hominins diverged from other primates, and again as humans and Neanderthals diverged from other hominins. Within hominins, we detected a pattern of directional and accelerating evolution towards larger brains, consistent with a positive feedback process in the evolution of the human brain. Contrary to widespread assumptions, we found that the human neocortex is not exceptionally large relative to other brain structures. Instead, our analyses revealed a single increase in relative neocortex volume at the origin of haplorrhines, and an increase in relative cerebellar volume in apes.}, } @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}, 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 Denisovans1,2, and high-coverage genomes from both Neanderthal and Denisovan fossils provide evidence for admixture between these two populations3. 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 Denisovan4-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 {pmid30700870, year = {2019}, author = {Jacobs, Z and Li, B and Shunkov, MV and Kozlikin, MB and Bolikhovskaya, NS and Agadjanian, AK and Uliyanov, VA and Vasiliev, SK and O'Gorman, K and Derevianko, AP and Roberts, RG}, title = {Timing of archaic hominin occupation of Denisova Cave in southern Siberia.}, journal = {Nature}, volume = {565}, number = {7741}, pages = {594-599}, doi = {10.1038/s41586-018-0843-2}, pmid = {30700870}, issn = {1476-4687}, abstract = {The Altai region of Siberia was inhabited for parts of the Pleistocene by at least two groups of archaic hominins-Denisovans and Neanderthals. Denisova Cave, uniquely, contains stratified deposits that preserve skeletal and genetic evidence of both hominins, artefacts made from stone and other materials, and a range of animal and plant remains. The previous site chronology is based largely on radiocarbon ages for fragments of bone and charcoal that are up to 50,000 years old; older ages of equivocal reliability have been estimated from thermoluminescence and palaeomagnetic analyses of sediments, and genetic analyses of hominin DNA. Here we describe the stratigraphic sequences in Denisova Cave, establish a chronology for the Pleistocene deposits and associated remains from optical dating of the cave sediments, and reconstruct the environmental context of hominin occupation of the site from around 300,000 to 20,000 years ago.}, } @article {pmid30693948, year = {2019}, author = {Pan, L and Zanolli, C}, title = {Comparative observations on the premolar root and pulp canal configurations of Middle Pleistocene Homo in China.}, journal = {American journal of physical anthropology}, volume = {168}, number = {3}, pages = {637-646}, doi = {10.1002/ajpa.23777}, pmid = {30693948}, issn = {1096-8644}, support = {XDB26000000//Strategic Priority Research Program of Chinese Academy of Sciences/ ; 41702026//National Natural Science Foundation of China/ ; 41872030//National Natural Science Foundation of China/ ; 173119//State Key Laboratory of Palaeobiology and Stratigraphy/ ; }, abstract = {OBJECTIVES: The aim of this study is to explore the root and root canal morphology of Homo fossil occupying China during the Middle Pleistocene period. Human occupation and evolutionary dynamics in East Asia during the Middle Pleistocene period is one of the most intriguing issues in paleoanthropology, with the coexistence of multiple lineages and regional morphs suggesting a complex population interaction scenario. Although premolar root and canal morphology has certain phylogenetic, taxonomic, and functional implications, its morphological diversity, possible evolutionary trend and characteristics regarding Middle Pleistocene hominins inhabiting East Asia are still insufficiently understood; where these populations fits within the Homo lineage (with respect to root and pulp canal structure) needs to be explored.

MATERIALS AND METHODS: Using microtomography, we directly observed and assessed the nonmetric variability of root and canal forms in maxillary and mandibular premolars of Chinese Middle Pleistocene Homo (N = 19), and compared our observed variations with Eurasian Early Pleistocene specimens from the Asia continent (N = 1) and Java (N = 2), as well as with Neanderthals (N = 28) and recent modern humans (N = 67).

RESULTS: A total number of nine types of root-canal forms were recorded. As a whole, the Chinese Middle Pleistocene record shows an evolutionary trend toward a modern human-like condition (a reduction of root/canal number and a simplification of root surface structure). We documented primitive signals like high percentage of Tomes' root in lower premolars. A considerable occurrence of incompletely separated root branches and bifid root and canal apices, representing evolutionary transformation from multi-root to single-root condition was also noticed. The results were compared with previous publications on Early and Middle Pleistocene Homo in East Africa, North Africa, and Eurasia.

CONCLUSION: This work provides new original data, incorporates the latest human fossil discoveries and suggests that analyzing the variation of premolar root structural organization, notably integrating together root/canal form and number, could possibly contribute to taxonomic and phylogenetic assessments. The mid-Middle Pleistocene populations, or "classic" Homo erectus, in our study show closer affinity to Early and Middle Pleistocene hominins in Eurasia, than to East African early Homo, which supports the suggestion that at least some of the Early Pleistocene hominin groups in Eurasia contribute to the later population; on the other hand, it is still difficult to clearly trace the evolutionary fate of those late Middle Pleistocene populations (roughly assigned as archaic Homo sapiens through a craniodental perspective). More comparable materials from the Early to Middle Pleistocene period as well as precise chronological framework is needed to further explore the evolutionary trends of archaic hominins in the Asian continent before the arrival of modern humans.}, } @article {pmid30683877, year = {2019}, author = {Milks, A and Parker, D and Pope, M}, title = {External ballistics of Pleistocene hand-thrown spears: experimental performance data and implications for human evolution.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {820}, doi = {10.1038/s41598-018-37904-w}, pmid = {30683877}, issn = {2045-2322}, support = {817687//RCUK | Arts and Humanities Research Council (AHRC)/ ; }, abstract = {The appearance of weaponry - technology designed to kill - is a critical but poorly established threshold in human evolution. It is an important behavioural marker representing evolutionary changes in ecology, cognition, language and social behaviours. While the earliest weapons are often considered to be hand-held and consequently short-ranged, the subsequent appearance of distance weapons is a crucial development. Projectiles are seen as an improvement over contact weapons, and are considered by some to have originated only with our own species in the Middle Stone Age and Upper Palaeolithic. Despite the importance of distance weapons in the emergence of full behavioral modernity, systematic experimentation using trained throwers to evaluate the ballistics of thrown spears during flight and at impact is lacking. This paper addresses this by presenting results from a trial of trained javelin athletes, providing new estimates for key performance parameters. Overlaps in distances and impact energies between hand-thrown spears and spearthrowers are evidenced, and skill emerges as a significant factor in successful use. The results show that distance hunting was likely within the repertoire of hunting strategies of Neanderthals, and the resulting behavioural flexibility closely mirrors that of our own species.}, } @article {pmid30664696, year = {2019}, author = {Cortés-Sánchez, M and Jiménez-Espejo, FJ and Simón-Vallejo, MD and Stringer, C and Lozano Francisco, MC and García-Alix, A and Vera Peláez, JL and Odriozola, CP and Riquelme-Cantal, JA and Parrilla Giráldez, R and Maestro González, A and Ohkouchi, N and Morales-Muñiz, A}, title = {An early Aurignacian arrival in southwestern Europe.}, journal = {Nature ecology & evolution}, volume = {3}, number = {2}, pages = {207-212}, doi = {10.1038/s41559-018-0753-6}, pmid = {30664696}, issn = {2397-334X}, abstract = {Westernmost Europe constitutes a key location in determining the timing of the replacement of Neanderthals by anatomically modern humans (AMHs). In this study, the replacement of late Mousterian industries by Aurignacian ones at the site of Bajondillo Cave (Málaga, southern Spain) is reported. On the basis of Bayesian analyses, a total of 26 radiocarbon dates, including 17 new ones, show that replacement at Bajondillo took place in the millennia centring on ~45-43 calibrated thousand years before the present (cal ka BP)-well before the onset of Heinrich event 4 (~40.2-38.3 cal ka BP). These dates indicate that the arrival of AMHs at the southernmost tip of Iberia was essentially synchronous with that recorded in other regions of Europe, and significantly increases the areal expansion reached by early AMHs at that time. In agreement with human dispersal scenarios on other continents, such rapid expansion points to coastal corridors as favoured routes for early AMH. The new radiocarbon dates align Iberian chronologies with AMH dispersal patterns in Eurasia.}, } @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}, doi = {10.1038/s41467-018-08089-7}, 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}, doi = {10.1073/pnas.1814338116}, pmid = {30647110}, issn = {1091-6490}, 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 {pmid30590594, year = {2018}, author = {Taylor, ME and Snelling, T and Smith, DF and Drickamer, K}, title = {Absence of a human ortholog of rodent Kupffer cell galactose-binding receptor encoded by the CLEC4f gene.}, journal = {Glycobiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/glycob/cwy113}, pmid = {30590594}, issn = {1460-2423}, abstract = {The murine CLEC4f gene encodes the Kupffer cell receptor, a galactose-binding receptor containing a C-type carbohydrate-recognition domain. Orthologs have been identified in nearly 100 species. The receptors from rat and mouse have previously been characterized and data presented here show that functional CLEC4f protein is expressed in domestic cattle (Bos taurus). However, the human CLEC4f gene does not encode a functional receptor because a mutation in the splice acceptor site of the final exon prevents appropriate splicing and a missense mutation disrupts the sugar-binding site. Transcriptomic and PCR analysis of transcripts confirms the absence of a spliced transcript containing the final exon and only background levels of transcripts are detected in human tissues. These mutations are also present in the CLEC4f gene in Neanderthals. In contrast to humans, closely related species, including chimpanzees, do have CLEC4f genes that encode full-length receptors. Affinity chromatography and glycan array results demonstrate that the chimpanzee, bovine and murine proteins all bind to galactose, but they show preferences for different subsets of galactose-containing glycans. In non-human primates the receptor is expressed in spleen rather than in liver. The results indicate that the CLEC4f protein probably has distinct functions in different species. Absence of the receptor precludes using it for targeting of glycoconjugates to cells in human liver. The fact that CLEC4f protein is expressed in spleen in non-human primates and the close evolutionary relationship of the CLEC4f protein to langerin (CD207) suggest that it may function in the immune system, possibly as a pathogen receptor.}, } @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}, doi = {10.1371/journal.pone.0209874}, pmid = {30589914}, issn = {1932-6203}, 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 {pmid30583844, year = {2019}, author = {Lague, MR and Chirchir, H and Green, DJ and Mbua, E and Harris, JWK and Braun, DR and Griffin, NL and Richmond, BG}, title = {Cross-sectional properties of the humeral diaphysis of Paranthropus boisei: Implications for upper limb function.}, journal = {Journal of human evolution}, volume = {126}, number = {}, pages = {51-70}, doi = {10.1016/j.jhevol.2018.05.002}, pmid = {30583844}, issn = {1095-8606}, abstract = {A ∼1.52 Ma adult upper limb skeleton of Paranthropus boisei (KNM-ER 47000) recovered from the Koobi Fora Formation, Kenya (FwJj14E, Area 1A) includes most of the distal half of a right humerus (designated KNM-ER 47000B). Natural transverse fractures through the diaphysis of KNM-ER 470000B provide unobstructed views of cortical bone at two sections typically used for analyzing cross-sectional properties of hominids (i.e., 35% and 50% of humerus length from the distal end). Here we assess cross-sectional properties of KNM-ER 47000B and two other P. boisei humeri (OH 80-10, KNM-ER 739). Cross-sectional properties for P. boisei associated with bending/torsional strength (section moduli) and relative cortical thickness (%CA; percent cortical area) are compared to those reported for nonhuman hominids, AL 288-1 (Australopithecus afarensis), and multiple species of fossil and modern Homo. Polar section moduli (Zp) are assessed relative to a mechanically relevant measure of body size (i.e., the product of mass [M] and humerus length [HL]). At both diaphyseal sections, P. boisei exhibits %CA that is high among extant hominids (both human and nonhuman) and similar to that observed among specimens of Pleistocene Homo. High values for Zp relative to size (M × HL) indicate that P. boisei had humeral bending strength greater than that of modern humans and Neanderthals and similar to that of great apes, A. afarensis, and Homo habilis. Such high humeral strength is consistent with other skeletal features of P. boisei (reviewed here) that suggest routine use of powerful upper limbs for arboreal climbing.}, } @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}, doi = {10.1038/s41598-018-36195-5}, pmid = {30573755}, issn = {2045-2322}, 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}, doi = {10.1093/gbe/evy271}, pmid = {30566634}, issn = {1759-6653}, 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}, doi = {10.1371/journal.pone.0208901}, pmid = {30566479}, issn = {1932-6203}, 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}, doi = {10.1098/rsos.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}, doi = {10.1186/s41065-018-0076-2}, pmid = {30564067}, issn = {1601-5223}, mesh = {Animals ; Brain/growth & 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}, doi = {10.1016/j.cub.2018.10.065}, 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 ; }, 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 {pmid30545868, year = {2018}, author = {Gibbons, A}, title = {Why modern humans have round heads.}, journal = {Science (New York, N.Y.)}, volume = {362}, number = {6420}, pages = {1229}, doi = {10.1126/science.362.6420.1229-a}, pmid = {30545868}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; Brain/*anatomy & histology ; *DNA, Ancient ; Head/*anatomy & histology ; Humans ; Neanderthals/*genetics ; }, } @article {pmid30545758, year = {2018}, author = {Banerjee, N and Polushina, T and Bettella, F and Steen, VM and Andreassen, OA and Le Hellard, S}, title = {Analysis of differentially methylated regions in great apes and extinct hominids provides support for the evolutionary hypothesis of schizophrenia.}, journal = {Schizophrenia research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.schres.2018.11.025}, pmid = {30545758}, issn = {1573-2509}, abstract = {INTRODUCTION: The persistence of schizophrenia in human populations separated by geography and time led to the evolutionary hypothesis that proposes schizophrenia as a by-product of the higher cognitive abilities of modern humans. To explore this hypothesis, we used here an evolutionary epigenetics approach building on differentially methylated regions (DMRs) of the genome.

METHODS: We implemented a polygenic enrichment testing pipeline using the summary statistics of genome-wide association studies (GWAS) of schizophrenia and 12 other phenotypes. We investigated the enrichment of association of these traits across genomic regions with variable methylation between modern humans and great apes (orangutans, chimpanzees and gorillas; great ape DMRs) and between modern humans and recently extinct hominids (Neanderthals and Denisovans; hominid DMRs).

RESULTS: Regions that are hypo-methylated in humans compared to great apes show enrichment of association with schizophrenia only if the major histocompatibility complex (MHC) region is included. With the MHC region removed from the analysis, only a modest enrichment for SNPs of low effect persists. The INRICH pipeline confirms this finding after rigorous permutation and bootstrapping procedures.

CONCLUSION: The analyses of regions with differential methylation changes in humans and great apes do not provide compelling evidence of enrichment of association with schizophrenia, in contrast to our previous findings on more recent methylation differences between modern humans, Neanderthals and Denisovans. Our results further support the evolutionary hypothesis of schizophrenia and indicate that the origin of some of the genetic susceptibility factors of schizophrenia may lie in recent human evolution.}, } @article {pmid30520032, year = {2018}, author = {Bruner, E}, title = {Human paleoneurology: Shaping cortical evolution in fossil hominids.}, journal = {The Journal of comparative neurology}, volume = {}, number = {}, pages = {}, doi = {10.1002/cne.24591}, pmid = {30520032}, issn = {1096-9861}, support = {CGL2015-65387-C3-3-P//Ministerio de Economía y Competitividad/ ; }, abstract = {Evolutionary neuroanatomy must integrate two different sources of information, namely from fossil and from living species. Fossils supply information concerning the process of evolution, whereas living species supply information on the product of evolution. Unfortunately, the fossil record is partial and fragmented, and often cannot support validations for specific evolutionary hypotheses. Living species can provide more comprehensive indications, but they do not represent ancestral groups or primitive forms. Macaques or chimpanzees are frequently used as proxy for human ancestral conditions, despite the fact they are divergent and specialized lineages, with their own biological features. Similarly, in paleoanthropology independent lineages (such as Neanderthals) should not be confused with ancestral modern human stages. In this comparative framework, paleoneurology deals with the analysis of the endocranial cavity in extinct species, in order to make inferences on brain evolution. A main target of this field is to distinguish the endocranial variations due to brain changes, from those due to cranial constraints. Digital anatomy and computed morphometrics have provided major advances in this field. However, brains and endocasts can be hard to analyze with geometrical models, because of uncertainties due to the localization of cortical landmarks and boundaries. The study of the evolution of the parietal cortex supplies an interesting case-study in which paleontological and neontological data can integrate and test evolutionary hypotheses based on multiple sources of evidence. The relationships with visuospatial functions and brain-body-tool integration stress further that the analysis of the cognitive system should go beyond the neural boundaries of the brain.}, } @article {pmid30478367, year = {2018}, author = {Mirazón Lahr, M}, title = {The not-so-dangerous lives of Neanderthals.}, journal = {Nature}, volume = {563}, number = {7733}, pages = {634-636}, doi = {10.1038/d41586-018-07343-8}, pmid = {30478367}, issn = {1476-4687}, mesh = {Animals ; Anthropology ; *Hominidae ; Humans ; *Neanderthals ; Prevalence ; }, } @article {pmid30478305, year = {2019}, author = {Villanea, FA and Schraiber, JG}, title = {Multiple episodes of interbreeding between Neanderthal and modern humans.}, journal = {Nature ecology & evolution}, volume = {3}, number = {1}, pages = {39-44}, doi = {10.1038/s41559-018-0735-8}, pmid = {30478305}, issn = {2397-334X}, support = {R35 GM124745/GM/NIGMS NIH HHS/United States ; }, 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 Académiques des Pyrénées-Orientales/ ; //Muséum national d'Histoire naturelle de Paris/ ; //UMR 7194, laboratoire Histoire Naturelle de l'Homme Préhistorique/ ; }, 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.

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 μCT-scan data to identify the multiple criteria involved in the paleobiological approach.

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.

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}, 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 reported1,2 and have variously been attributed to violent social behaviour3,4, highly mobile hunter-gatherer lifestyles2 or attacks by carnivores5. 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 weapons1. 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 = {T90 DE026110/DE/NIDCR NIH HHS/United States ; }, 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 {pmid30387382, year = {2018}, author = {Kamnikar, KR and Herrmann, NP and Plemons, AM}, title = {New Approaches to Juvenile Age Estimation in Forensics: Application of Transition Analysis via the Shackelford et al. Method to a Diverse Modern Subadult Sample.}, journal = {Human biology}, volume = {90}, number = {1}, pages = {11-30}, pmid = {30387382}, issn = {1534-6617}, mesh = {Adolescent ; Age Determination by Teeth/*methods ; Animals ; Body Remains/pathology ; Child ; Child, Preschool ; Female ; Forensic Sciences/*methods ; Fossils ; Hominidae ; Humans ; Infant ; Infant, Newborn ; Male ; Neanderthals/anatomy & histology ; Records ; Tooth/*anatomy & histology/growth & development ; }, abstract = {Dental development is one of the most widely utilized and accurate methods available for estimating age in subadult skeletal remains. The timing of tooth growth and development is regulated by genetics and less affected by external factors, allowing reliable estimates of chronological age. Traditional methodology focuses on comparing tooth developmental scores to corresponding age charts. Using the Moorrees, Fanning, and Hunt (MFH) developmental scores, Shackelford and colleagues embed the dental development method in a statistical framework based on transition analysis. They generated numerical parameters underlining each "stage" and age-at-death distribution and applied them to fossil hominins and Neanderthals with limited application to modern humans. We use this same method on a subadult test sample (n = 201), representing modern individuals that may become part of the forensic record. We assess the probability coverage of the Shackelford et al. method derived from MFH standards as it applies to all available dentition. Results indicate promise: the age range at 90% and 95% confidence levels includes the chronological age of almost every individual tested. The maximum likelihood age estimates underestimate age by 0.5-2.5 years for individuals 0-15 years of age and by >2.5 years for individuals 16-18 years of age, as previously shown. In an attempt to refine the method, we adjusted the numerical parameters underlying the stages for developing teeth based on a combined modern reference sample (n = 1,964) and tested these revised parameters using the same test sample. The estimated ages from the modified method differ from the original Shackelford et al. methodology by underestimating age to a lesser degree. The modified method does include mean age-at-attainment values for earlier stages of several teeth, allowing for the calculation of narrower confidence intervals. While this study highlights areas of future research in refining dental developmental aging by transition analysis, it also demonstrates that the Shackelford et al. method is applicable and accurate when aging modern subadults in forensic work.}, } @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 {pmid30383862, year = {2018}, author = {Chen, Z and DeSalle, R and Schiffman, M and Herrero, R and Wood, CE and Ruiz, JC and Clifford, GM and Chan, PKS and Burk, RD}, title = {Niche adaptation and viral transmission of human papillomaviruses from archaic hominins to modern humans.}, journal = {PLoS pathogens}, volume = {14}, number = {11}, pages = {e1007352}, pmid = {30383862}, issn = {1553-7374}, support = {P30 AI124414/AI/NIAID NIH HHS/United States ; P30 CA013330/CA/NCI NIH HHS/United States ; }, abstract = {Recent discoveries on the origins of modern humans from multiple archaic hominin populations and the diversity of human papillomaviruses (HPVs) suggest a complex scenario of virus-host evolution. To evaluate the origin of HPV pathogenesis, we estimated the phylogeny, timing, and dispersal of HPV16 variants using a Bayesian Markov Chain Monte Carlo framework. To increase precision, we identified and characterized non-human primate papillomaviruses from New and Old World monkeys to set molecular clock models. We demonstrate specific host niche adaptation of primate papillomaviruses with subsequent coevolution with their primate hosts for at least 40 million years. Analyses of 212 HPV16 complete genomes and 3582 partial sequences estimated ancient divergence of HPV16 variants (between A and BCD lineages) from their most recent common ancestors around half a million years ago, roughly coinciding with the timing of the split between archaic Neanderthals and modern Homo sapiens, and nearly three times longer than divergence times of modern Homo sapiens. HPV16 A lineage variants were significantly underrepresented in present African populations, whereas the A sublineages were highly prevalent in European (A1-3) and Asian (A4) populations, indicative of viral sexual transmission from Neanderthals to modern non-African humans through multiple interbreeding events in the past 80 thousand years. Remarkably, the human leukocyte antigen B*07:02 and C*07:02 alleles associated with increased risk in cervix cancer represent introgressed regions from Neanderthals in present-day Eurasians. The archaic hominin-host-switch model was also supported by other HPV variants. Niche adaptation and virus-host codivergence appear to influence the pathogenesis of papillomaviruses.}, } @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 & histology ; Organ Size ; Principal Component Analysis ; Thorax/*anatomy & 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}, 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.

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 ~ 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.

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 = {//Fundación Atapuerca/ ; //Junta de Castilla y León/ ; CGL2015-65387-C3-2-P MINECO/FEDER//Ministerio de Economía y Competitividad/ ; }, 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.

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.

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.

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 {pmid30351445, year = {2019}, author = {Stelzer, S and Neubauer, S and Hublin, JJ and Spoor, F and Gunz, P}, title = {Morphological trends in arcade shape and size in Middle Pleistocene Homo.}, journal = {American journal of physical anthropology}, volume = {168}, number = {1}, pages = {70-91}, doi = {10.1002/ajpa.23721}, pmid = {30351445}, issn = {1096-8644}, support = {//Max Planck Society/ ; }, abstract = {OBJECTIVES: Middle Pleistocene fossil hominins, often summarized as Homo heidelbergensis sensu lato, are difficult to interpret due to a fragmentary fossil record and ambiguous combinations of primitive and derived characters. Here, we focus on one aspect of facial shape and analyze shape variation of the dental arcades of these fossils together with other Homo individuals.

MATERIALS AND METHODS: Three-dimensional landmark data were collected on computed tomographic scans and surface scans of Middle Pleistocene fossil hominins (n = 8), Homo erectus s.l. (n = 4), Homo antecessor (n = 1), Homo neanderthalensis (n = 13), recent (n = 52) and fossil (n = 19) Homo sapiens. To increase sample size, we used multiple multivariate regression to reconstruct complementary arches for isolated mandibles, and explored size and shape differences among maxillary arcades.

RESULTS: The shape of the dental arcade in H. erectus s.l. and H. antecessor differs markedly from both Neanderthals and H. sapiens. The latter two show subtle but consistent differences in arcade length and width. Shape variation among Middle Pleistocene fossil hominins does not exceed the amount of variation of other species, but includes individuals with more primitive and more derived morphology, all more similar to Neanderthals and H. sapiens than to H. erectus s.l.

DISCUSSION: Although our results cannot reject the hypothesis that the Middle Pleistocene fossil hominins belong to a single species, their shape variation comprises a more primitive morph that represents a likely candidate for the shape of the last common ancestor of Neanderthals and H. sapiens, and a more derived morph resembling Neanderthals. The arcade shape difference between Neanderthals and H. sapiens might be related to different ways to withstand mechanical stress.}, } @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}, 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 {pmid30326183, year = {2018}, author = {Hardy, K and Buckley, S and Copeland, L}, title = {Pleistocene dental calculus: Recovering information on Paleolithic food items, medicines, paleoenvironment and microbes.}, journal = {Evolutionary anthropology}, volume = {27}, number = {5}, pages = {234-246}, doi = {10.1002/evan.21718}, pmid = {30326183}, issn = {1520-6505}, mesh = {Animals ; Cooking ; Dental Calculus/*chemistry/history/*microbiology ; Diet/*history ; Environment ; Fossils ; History, Ancient ; Hominidae ; Neanderthals ; Starch/chemistry ; Vegetables/chemistry ; }, abstract = {Dental calculus is now widely used to recover information on items ingested in the past. It is particularly valuable in the earlier Paleolithic, where recovered data may represent the only evidence for plant use. Several recovery methods are used and each one produces different results. Biomolecular markers and genetic material recovered from dental calculus is providing new data on identifiable dietary and medicinal items and human microbial communities. The recovery of microfossils, in particular, starch granules, has triggered a new awareness of the role of plants in the diet throughout the Paleolithic. However, the minute amount of material recovered has little relationship with food eaten during a person's life, while salivary amylase breaks down cooked starch. Therefore, broader dietary interpretations and detection of cooked food are problematic. The study of ancient dental calculus holds great potential to recover information about past lives, within realistic parameters.}, } @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}, 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 230Th. We show that their criticisms are unfounded.}, } @article {pmid30308076, year = {2018}, author = {Bamford, CGG and Aranday-Cortes, E and Filipe, IC and Sukumar, S and Mair, D and Filipe, ADS and Mendoza, JL and Garcia, KC and Fan, S and Tishkoff, SA and McLauchlan, J}, title = {A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages.}, journal = {PLoS pathogens}, volume = {14}, number = {10}, pages = {e1007307}, pmid = {30308076}, issn = {1553-7374}, support = {MC_UU_12014/1//Medical Research Council/United Kingdom ; }, mesh = {Animals ; Antiviral Agents/*therapeutic use ; Biological Evolution ; Cardiovirus Infections/*drug therapy/genetics/virology ; Cells, Cultured ; Encephalomyocarditis virus/drug effects/isolation & purification ; Gene Expression Regulation ; Hepacivirus/drug effects/isolation & purification ; Hepatitis C/*drug therapy/genetics/virology ; Humans ; Interleukins/*genetics ; Pan troglodytes ; *Polymorphism, Single Nucleotide ; Species Specificity ; Zika Virus/drug effects/isolation & purification ; Zika Virus Infection/*drug therapy/genetics/virology ; }, abstract = {As antimicrobial signalling molecules, type III or lambda interferons (IFNλs) are critical for defence against infection by diverse pathogens, including bacteria, fungi and viruses. Counter-intuitively, expression of one member of the family, IFNλ4, is associated with decreased clearance of hepatitis C virus (HCV) in the human population; by contrast, a natural frameshift mutation that abrogates IFNλ4 production improves HCV clearance. To further understand how genetic variation between and within species affects IFNλ4 function, we screened a panel of all known extant coding variants of human IFNλ4 for their antiviral potential and identify three that substantially affect activity: P70S, L79F and K154E. The most notable variant was K154E, which was found in African Congo rainforest 'Pygmy' hunter-gatherers. K154E greatly enhanced in vitro activity in a range of antiviral (HCV, Zika virus, influenza virus and encephalomyocarditis virus) and gene expression assays. Remarkably, E154 is the ancestral residue in mammalian IFNλ4s and is extremely well conserved, yet K154 has been fixed throughout evolution of the hominid genus Homo, including Neanderthals. Compared to chimpanzee IFNλ4, the human orthologue had reduced activity due to amino acid K154. Comparison of published gene expression data from humans and chimpanzees showed that this difference in activity between K154 and E154 in IFNλ4 correlates with differences in antiviral gene expression in vivo during HCV infection. Mechanistically, our data show that the human-specific K154 negatively affects IFNλ4 activity through a novel means by reducing its secretion and potency. We thus demonstrate that attenuated activity of IFNλ4 is conserved among humans and postulate that differences in IFNλ4 activity between species contribute to distinct host-specific responses to-and outcomes of-infection, such as HCV infection. The driver of reduced IFNλ4 antiviral activity in humans remains unknown but likely arose between 6 million and 360,000 years ago in Africa.}, } @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}, 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 ; }, 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}, 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)/ ; }, 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}, 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 & histology/chemistry ; Fossils/*anatomy & histology ; Humans ; Molar/*anatomy & histology ; Neanderthals ; Paleodontology ; Phylogeny ; Spain ; Tooth Crown/*anatomy & 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}, 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}, 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 = {WT206194//Wellcome Trust/United Kingdom ; WT207492//Wellcome Trust/United Kingdom ; }, mesh = {African Continental Ancestry Group/genetics ; Animals ; Asian Continental Ancestry Group/genetics ; European Continental Ancestry Group/genetics ; Fossils ; Genome, Human/*genetics ; Hominidae/*genetics ; Humans ; Hybridization, Genetic/*genetics ; Neanderthals/*genetics ; Oceanic Ancestry Group/genetics ; Phylogeny ; }, 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 {pmid30215675, year = {2018}, author = {Kawash, JK and Smith, SD and Karaiskos, S and Grigoriev, A}, title = {ARIADNA: machine learning method for ancient DNA variant discovery.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {25}, number = {6}, pages = {619-627}, pmid = {30215675}, issn = {1756-1663}, mesh = {Animals ; DNA, Ancient/*chemistry ; *Genetic Variation ; Genome ; *Machine Learning ; Mammoths/genetics ; Mutation ; Neanderthals/genetics ; }, abstract = {Ancient DNA (aDNA) studies often rely on standard methods of mutation calling, optimized for high-quality contemporary DNA but not for excessive contamination, time- or environment-related damage of aDNA. In the absence of validated datasets and despite showing extreme sensitivity to aDNA quality, these methods have been used in many published studies, sometimes with additions of arbitrary filters or modifications, designed to overcome aDNA degradation and contamination problems. The general lack of best practices for aDNA mutation calling may lead to inaccurate results. To address these problems, we present ARIADNA (ARtificial Intelligence for Ancient DNA), a novel approach based on machine learning techniques, using specific aDNA characteristics as features to yield improved mutation calls. In our comparisons of variant callers across several ancient genomes, ARIADNA consistently detected higher-quality genome variants with fast runtimes, while reducing the false positive rate compared with other approaches.}, } @article {pmid30209385, year = {2018}, author = {}, title = {The earliest known drawing in history sends a message through 73,000 years.}, journal = {Nature}, volume = {561}, number = {7722}, pages = {149}, doi = {10.1038/d41586-018-06657-x}, pmid = {30209385}, issn = {1476-4687}, mesh = {*Archaeology ; Carbonates ; Caves ; *Neanderthals ; }, } @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}, } @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}, 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}, 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}, } @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 68m² 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 {pmid30150388, year = {2018}, author = {Staubwasser, M and Drăgușin, V and Onac, BP and Assonov, S and Ersek, V and Hoffmann, DL and Veres, D}, title = {Impact of climate change on the transition of Neanderthals to modern humans in Europe.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {37}, pages = {9116-9121}, pmid = {30150388}, issn = {1091-6490}, mesh = {Animals ; *Archaeology ; *Climate Change ; Europe ; *Extinction, Biological ; History, Ancient ; Humans ; *Neanderthals ; }, abstract = {Two speleothem stable isotope records from East-Central Europe demonstrate that Greenland Stadial 12 (GS12) and GS10-at 44.3-43.3 and 40.8-40.2 ka-were prominent intervals of cold and arid conditions. GS12, GS11, and GS10 are coeval with a regional pattern of culturally (near-)sterile layers within Europe's diachronous archeologic transition from Neanderthals to modern human Aurignacian. Sterile layers coeval with GS12 precede the Aurignacian throughout the middle and upper Danube region. In some records from the northern Iberian Peninsula, such layers are coeval with GS11 and separate the Châtelperronian from the Aurignacian. Sterile layers preceding the Aurignacian in the remaining Châtelperronian domain are coeval with GS10 and the previously reported 40.0- to 40.8-ka cal BP [calendar years before present (1950)] time range of Neanderthals' disappearance from most of Europe. This suggests that ecologic stress during stadial expansion of steppe landscape caused a diachronous pattern of depopulation of Neanderthals, which facilitated repopulation by modern humans who appear to have been better adapted to this environment. Consecutive depopulation-repopulation cycles during severe stadials of the middle pleniglacial may principally explain the repeated replacement of Europe's population and its genetic composition.}, } @article {pmid30147753, year = {2018}, author = {Guichard, E and Peona, V and Malagoli Tagliazucchi, G and Abitante, L and Jagoda, E and Musella, M and Ricci, M and Rubio-Roldán, A and Sarno, S and Luiselli, D and Pettener, D and Taccioli, C and Pagani, L and Garcia-Perez, JL and Boattini, A}, title = {Impact of non-LTR retrotransposons in the differentiation and evolution of anatomically modern humans.}, journal = {Mobile DNA}, volume = {9}, number = {}, pages = {28}, pmid = {30147753}, issn = {1759-8753}, support = {//Wellcome Trust/United Kingdom ; 295733//European Research Council/International ; }, abstract = {Background: Transposable elements are biologically important components of eukaryote genomes. In particular, non-LTR retrotransposons (N-LTRrs) played a key role in shaping the human genome throughout evolution. In this study, we compared retrotransposon insertions differentially present in the genomes of Anatomically Modern Humans, Neanderthals, Denisovans and Chimpanzees, in order to assess the possible impact of retrotransposition in the differentiation of the human lineage.

Results: We first identified species-specific N-LTRrs and established their distribution in present day human populations. These analyses shortlisted a group of N-LTRr insertions that were found exclusively in Anatomically Modern Humans. These insertions are associated with an increase in the number of transcriptional/splicing variants of those genes they inserted in. The analysis of the functionality of genes containing human-specific N-LTRr insertions reflects changes that occurred during human evolution. In particular, the expression of genes containing the most recent N-LTRr insertions is enriched in the brain, especially in undifferentiated neurons, and these genes associate in networks related to neuron maturation and migration. Additionally, we identified candidate N-LTRr insertions that have likely produced new functional variants exclusive to modern humans, whose genomic loci show traces of positive selection.

Conclusions: Our results strongly suggest that N-LTRr impacted our differentiation as a species, most likely inducing an increase in neural complexity, and have been a constant source of genomic variability all throughout the evolution of the human lineage.}, } @article {pmid30139851, year = {2018}, author = {Vogel, G}, title = {Ancient DNA reveals tryst between extinct human species.}, journal = {Science (New York, N.Y.)}, volume = {361}, number = {6404}, pages = {737}, doi = {10.1126/science.361.6404.737}, pmid = {30139851}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; Bone and Bones ; *DNA, Ancient ; *Extinction, Biological ; Fathers/history ; Female ; History, Ancient ; Humans ; Mothers/history ; Neanderthals/*genetics ; Women/*history ; }, } @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//European Research Council/International ; 694707//European Research Council/International ; 715069//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 ago1,2. 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 cave4-6. The mother came from a population more closely related to Neanderthals who lived later in Europe2,7 than to an earlier Neanderthal found in Denisova Cave8, 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 = {Disconnected mind grant//Age UK/ ; MR/K026992/1//Biotechnology and Biological Sciences Research Council (BBSRC)/ ; MR/K026992/1//Medical Research Council/United Kingdom ; 225989//Norges Forskningsr&#x00E5;d (Research Council of Norway)/ ; 248778//Norges Forskningsr&#x00E5;d (Research Council of Norway)/ ; 223273//Norges Forskningsr&#x00E5;d (Research Council of Norway)/ ; 2016-064//Ministry of Health and Care Services | Helse S&#x00F8;r-&#x00D8;st RHF (Southern and Eastern Norway Regional Health Authority)/ ; }, 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 {pmid30097198, year = {2018}, author = {Bruner, E and Fedato, A and Silva-Gago, M and Alonso-Alcalde, R and Terradillos-Bernal, M and Fernández-Durantes, MÁ and Martín-Guerra, E}, title = {Cognitive archeology, body cognition, and hand-tool interaction.}, journal = {Progress in brain research}, volume = {238}, number = {}, pages = {325-345}, doi = {10.1016/bs.pbr.2018.06.013}, pmid = {30097198}, issn = {1875-7855}, mesh = {Animals ; Archaeology ; *Biological Evolution ; Brain/*physiology ; Cognition/*physiology ; Functional Laterality/*physiology ; Humans ; Neanderthals ; Paleontology ; Tool Use Behavior/*physiology ; }, abstract = {Body cognition and lateralization can be investigated in fossils by integrating anatomical and functional aspects. Paleoneurology cannot provide strong evidence in this sense, because hemispheric asymmetries are shared in all extinct human species, and motor cortical areas are difficult to delineate in endocranial casts. However, paleoneurological analyses also suggest that modern humans and Neanderthals underwent an expansion of parietal regions crucial for visuospatial integration and eye-hand-tool management. Because of our technological specialization, haptic cognition can be particularly targeted by evolutionary processes. Hand-tool relationships can be investigated through physical and physiological correlates. In terms of metrics, size is the main factor of hand morphological variation among adult humans, followed by the ratio between thumb length and palmar size. In modern humans, emotional changes during hand-tool contact can be measured by electrodermal activity. During tool manipulation, electrodermal response, which is a physiological correlate of emotional engagement, shows differences between males and females, and it is different for distinct Paleolithic technologies. Emotional engagement, hand management, and haptic cognition are part of a specialized prosthetic technological capacity of modern humans and can provide indirect evidence of cognitive discontinuities in the archeological record.}, } @article {pmid30072539, year = {2018}, author = {Tucci, S and Vohr, SH and McCoy, RC and Vernot, B and Robinson, MR and Barbieri, C and Nelson, BJ and Fu, W and Purnomo, GA and Sudoyo, H and Eichler, EE and Barbujani, G and Visscher, PM and Akey, JM and Green, RE}, title = {Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia.}, journal = {Science (New York, N.Y.)}, volume = {361}, number = {6401}, pages = {511-516}, doi = {10.1126/science.aar8486}, pmid = {30072539}, issn = {1095-9203}, support = {R01 GM110068/GM/NIGMS NIH HHS/United States ; //European Research Council/International ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Adaptation, Biological/*genetics ; Animals ; *Biological Evolution ; Body Height/*genetics ; Dwarfism/*genetics ; Gene Flow ; Genome, Human ; Humans ; Indonesia ; *Islands ; Neanderthals/genetics ; Population/*genetics ; *Selection, Genetic ; }, abstract = {Flores Island, Indonesia, was inhabited by the small-bodied hominin species Homo floresiensis, which has an unknown evolutionary relationship to modern humans. This island is also home to an extant human pygmy population. Here we describe genome-scale single-nucleotide polymorphism data and whole-genome sequences from a contemporary human pygmy population living on Flores near the cave where H. floresiensis was found. The genomes of Flores pygmies reveal a complex history of admixture with Denisovans and Neanderthals but no evidence for gene flow with other archaic hominins. Modern individuals bear the signatures of recent positive selection encompassing the FADS (fatty acid desaturase) gene cluster, likely related to diet, and polygenic selection acting on standing variation that contributed to their short-stature phenotype. Thus, multiple independent instances of hominin insular dwarfism occurred on Flores.}, } @article {pmid30029803, year = {2019}, author = {Charlier, P and Gaultier, F and Héry-Arnaud, G}, title = {Interbreeding between Neanderthals and modern humans: Remarks and methodological dangers of a dental calculus microbiome analysis.}, journal = {Journal of human evolution}, volume = {126}, number = {}, pages = {124-126}, doi = {10.1016/j.jhevol.2018.06.007}, pmid = {30029803}, issn = {1095-8606}, } @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)/ ; }, 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 AMH interbred with archaic hominins once they left the African continent. Current non-African human genomes carry fragments of archaic origin. This review focuses on the fitness consequences of archaic interbreeding in current human populations. We discuss new insights and challenges that researchers face when interpreting the potential impact of introgression on fitness and testing hypotheses about the role of selection within the context of health and disease.}, } @article {pmid30002396, year = {2018}, author = {Gómez-Olivencia, A and Sala, N and Núñez-Lahuerta, C and Sanchis, A and Arlegi, M and Rios-Garaizar, J}, title = {First data of Neandertal bird and carnivore exploitation in the Cantabrian Region (Axlor; Barandiaran excavations; Dima, Biscay, Northern Iberian Peninsula).}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10551}, pmid = {30002396}, issn = {2045-2322}, abstract = {Neandertals were top predators who basically relied on middle- to large-sized ungulates for dietary purposes, but there is growing evidence that supports their consumption of plants, leporids, tortoises, marine resources, carnivores and birds. The Iberian Peninsula has provided the most abundant record of bird exploitation for meat in Europe, starting in the Middle Pleistocene. However, the bird and carnivore exploitation record was hitherto limited to the Mediterranean area of the Iberian Peninsula. Here we present the first evidence of bird and carnivore exploitation by Neandertals in the Cantabrian region. We have found cut-marks in two golden eagles, one raven, one wolf and one lynx remain from the Mousterian levels of Axlor. The obtaining of meat was likely the primary purpose of the cut-marks on the golden eagle and lynx remains. Corvids, raptors, felids and canids in Axlor could have likely acted as commensals of the Neandertals, scavenging upon the carcasses left behind by these hunter-gatherers. This could have brought them closer to Neandertal groups who could have preyed upon them. These new results provide additional information on their dietary scope and indicate a more complex interaction between Neandertals and their environment.}, } @article {pmid29983156, year = {2018}, author = {García-Martínez, D and Radovčić, D and Radovčić, J and Cofran, Z and Rosas, A and Bastir, M}, title = {Over 100 years of Krapina: New insights into the Neanderthal thorax from the study of rib cross-sectional morphology.}, journal = {Journal of human evolution}, volume = {122}, number = {}, pages = {124-132}, doi = {10.1016/j.jhevol.2018.05.009}, pmid = {29983156}, issn = {1095-8606}, abstract = {The Krapina costal sample was studied by Gorjanović-Kramberger in the early twentieth century. He pointed out unique features in the sample such as the rounder rib cross-section, which was recently confirmed in other Neanderthal specimens. Round rib cross-sections are characteristic of Homo ergaster, suggesting this may be plesiomorphic for Pleistocene Homo, but it is unknown whether Homo antecessor also had this rib shape. Furthermore, the influence of allometry on the cross-sectional shape of ribs is still unknown. The large costal sample from Krapina allows us to address these issues. We quantified cross-section morphology at the midshaft throughout a closed curve of one landmark and nine sliding semilandmarks in the Krapina costal remains (n = 7), as well as in other Neanderthals (n = 50), H. antecessor (n = 3) and modern humans, both fossil (n = 12) and recent (n = 160). We used principal components analysis and mean comparisons to explore interspecific differences, regression analysis to investigate allometry, and partial least squares analysis to examine covariation of cross-section shape and overall rib morphology. Neanderthal cross-sections tended to be larger than those of recent humans except for the Krapina and Tabun remains. Regarding shape, inter-group differences were found only in the diaphragmatic thorax, where Neanderthal and H. antecessor ribs were statistically significantly rounder than those of modern humans. Allometry accounted for covariation of size on shape, but the Neandertal and modern human trajectories had different slopes. While our results based on the Krapina costal sample are similar to previous findings, we also make several new insights: 1) the cross-section morphology observed in Neanderthals was probably present in H. antecessor, albeit less marked; 2) the distinct roundness of Neanderthal cross-sections is not related to size; 3) rounder cross-sections are correlated with ribs presenting less curvature in cranial view and a low degree of torsion in recent humans. These results are important for the interpretation of fragmentary Neanderthal costal remains, and the fact that the differences are marked only in the diaphragmatic thorax could have implications for breathing kinematics.}, } @article {pmid29942018, year = {2018}, author = {Hoffmann, DL and Standish, CD and Pike, AWG and García-Diez, M and Pettitt, PB and Angelucci, DE and Villaverde, V and Zapata, J and Milton, JA and Alcolea-González, J and Cantalejo-Duarte, P and Collado, H and de Balbín, R and Lorblanchet, M and Ramos-Muñoz, J and Weniger, GC and Zilhão, J}, title = {Dates for Neanderthal art and symbolic behaviour are reliable.}, journal = {Nature ecology & evolution}, volume = {2}, number = {7}, pages = {1044-1045}, doi = {10.1038/s41559-018-0598-z}, pmid = {29942018}, issn = {2397-334X}, } @article {pmid29942012, year = {2018}, author = {Gaudzinski-Windheuser, S and Noack, ES and Pop, E and Herbst, C and Pfleging, J and Buchli, J and Jacob, A and Enzmann, F and Kindler, L and Iovita, R and Street, M and Roebroeks, W}, title = {Evidence for close-range hunting by last interglacial Neanderthals.}, journal = {Nature ecology & evolution}, volume = {2}, number = {7}, pages = {1087-1092}, doi = {10.1038/s41559-018-0596-1}, pmid = {29942012}, issn = {2397-334X}, abstract = {Animal resources have been part of hominin diets since around 2.5 million years ago, with sharp-edged stone tools facilitating access to carcasses. How exactly hominins acquired animal prey and how hunting strategies varied through time and space is far from clear. The oldest possible hunting weapons known from the archaeological record are 300,000 to 400,000-year-old sharpened wooden staves. These may have been used as throwing and/or close-range thrusting spears, but actual data on how such objects were used are lacking, as unambiguous lesions caused by such weapon-like objects are unknown for most of human prehistory. Here, we report perforations observed on two fallow deer skeletons from Neumark-Nord, Germany, retrieved during excavations of 120,000-year-old lake shore deposits with abundant traces of Neanderthal presence. Detailed studies of the perforations, including micro-computed tomography imaging and ballistic experiments, demonstrate that they resulted from the close-range use of thrusting spears. Such confrontational ways of hunting require close cooperation between participants, and over time may have shaped important aspects of hominin biology and behaviour.}, } @article {pmid29937092, year = {2018}, author = {Li, J and Hong, X and Mesiano, S and Muglia, LJ and Wang, X and Snyder, M and Stevenson, DK and Shaw, GM}, title = {Natural Selection Has Differentiated the Progesterone Receptor among Human Populations.}, journal = {American journal of human genetics}, volume = {103}, number = {1}, pages = {45-57}, pmid = {29937092}, issn = {1537-6605}, support = {RC2 HL101748/HL/NHLBI NIH HHS/United States ; }, abstract = {The progesterone receptor (PGR) plays a central role in maintaining pregnancy and is significantly associated with medical conditions such as preterm birth that affects 12.6% of all the births in U.S. PGR has been evolving rapidly since the common ancestor of human and chimpanzee, and we herein investigated evolutionary dynamics of PGR during recent human migration and population differentiation. Our study revealed substantial population differentiation at the PGR locus driven by natural selection, where very recent positive selection in East Asians has substantially decreased its genetic diversity by nearly fixing evolutionarily novel alleles. On the contrary, in European populations, the PGR locus has been promoted to a highly polymorphic state likely due to balancing selection. Integrating transcriptome data across multiple tissue types together with large-scale genome-wide association data for preterm birth, our study demonstrated the consequence of the selection event in East Asians on remodeling PGR expression specifically in the ovary and determined a significant association of early spontaneous preterm birth with the evolutionarily selected variants. To reconstruct its evolutionary trajectory on the human lineage, we observed substantial differentiation between modern and archaic humans at the PGR locus, including fixation of a deleterious missense allele in the Neanderthal genome that was later introgressed in modern human populations. Taken together, our study revealed substantial evolutionary innovation in PGR even during very recent human evolution, and its different forms among human populations likely result in differential susceptibility to progesterone-associated disease conditions including preterm birth.}, } @article {pmid29931305, year = {2018}, author = {Prüfer, K}, title = {snpAD: an ancient DNA genotype caller.}, journal = {Bioinformatics (Oxford, England)}, volume = {34}, number = {24}, pages = {4165-4171}, pmid = {29931305}, issn = {1367-4811}, abstract = {Motivation: The study of ancient genomes can elucidate the evolutionary past. However, analyses are complicated by base-modifications in ancient DNA molecules that result in errors in DNA sequences. These errors are particularly common near the ends of sequences and pose a challenge for genotype calling.

Results: I describe an iterative method that estimates genotype frequencies and errors along sequences to allow for accurate genotype calling from ancient sequences. The implementation of this method, called snpAD, performs well on high-coverage ancient data, as shown by simulations and by subsampling the data of a high-coverage Neandertal genome. Although estimates for low-coverage genomes are less accurate, I am able to derive approximate estimates of heterozygosity from several low-coverage Neandertals. These estimates show that low heterozygosity, compared to modern humans, was common among Neandertals.

The C++ code of snpAD is freely available at http://bioinf.eva.mpg.de/snpAD/.

Supplementary information: Supplementary data are available at Bioinformatics online.}, } @article {pmid29930123, year = {2018}, author = {Galway-Witham, J and Stringer, C}, title = {How did Homo sapiens evolve?.}, journal = {Science (New York, N.Y.)}, volume = {360}, number = {6395}, pages = {1296-1298}, doi = {10.1126/science.aat6659}, pmid = {29930123}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; Body Size/genetics ; Fossils ; Genetic Research ; Humans ; *Models, Biological ; Neanderthals/genetics ; Phylogeny ; }, } @article {pmid29930117, year = {2018}, author = {Cohen, J}, title = {Neanderthal brain organoids come to life.}, journal = {Science (New York, N.Y.)}, volume = {360}, number = {6395}, pages = {1284}, doi = {10.1126/science.360.6395.1284}, pmid = {29930117}, issn = {1095-9203}, } @article {pmid29921229, year = {2018}, author = {Cabrera, VM and Marrero, P and Abu-Amero, KK and Larruga, JM}, title = {Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {98}, pmid = {29921229}, issn = {1471-2148}, support = {CGL2010-16195//Spanish Ministerio de Ciencia e Innovación/International ; }, mesh = {Africa ; Asia ; Base Sequence ; Chromosomes, Human, Y/genetics ; Cluster Analysis ; DNA, Mitochondrial/*genetics ; Female ; Genetics, Population ; Haplotypes/*genetics ; Heterozygote ; Humans ; Male ; *Phylogeny ; Phylogeography ; Time Factors ; }, abstract = {BACKGROUND: The main unequivocal conclusion after three decades of phylogeographic mtDNA studies is the African origin of all extant modern humans. In addition, a southern coastal route has been argued for to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, the out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion and, consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basal L3 lineages around 70 kya.

RESULTS: The coalescence ages of all Eurasian (M,N) and African (L3) lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. An Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. This correlation rather seems to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers.

CONCLUSIONS: These results are congruent with a model proposing an out-of-Africa migration into Asia, following a northern route, of early anatomically modern humans carrying pre-L3 mtDNA lineages around 125 kya, subsequent diversification of pre-L3 into the basal lineages of L3, a return to Africa of Eurasian fully modern humans around 70 kya carrying the basal L3 lineages and the subsequent diversification of Eurasian-remaining L3 lineages into the M and N lineages in the outside-of-Africa context, and a second Eurasian global expansion by 60 kya, most probably, out of southeast Asia. Climatic conditions and the presence of Neanderthals and other hominins might have played significant roles in these human movements. Moreover, recent studies based on ancient DNA and whole-genome sequencing are also compatible with this hypothesis.}, } @article {pmid29914355, year = {2018}, author = {Cserhati, MF and Mooter, ME and Peterson, L and Wicks, B and Xiao, P and Pauley, M and Guda, C}, title = {Motifome comparison between modern human, Neanderthal and Denisovan.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {472}, pmid = {29914355}, issn = {1471-2164}, support = {P20 GM103427/GM/NIGMS NIH HHS/United States ; P30 CA036727/CA/NCI NIH HHS/United States ; 2P20GM103427//Nebraska INBRE/ ; 5P30CA036727//CCSG award/ ; }, mesh = {Animals ; Endogenous Retroviruses/genetics ; *Fossils ; *Genome ; Humans ; Neanderthals/*genetics ; Nucleotide Motifs/*genetics ; Phenotype ; Promoter Regions, Genetic ; Trans-Activators ; }, abstract = {BACKGROUND: The availability of the genomes of two archaic humans, Neanderthal and Denisovan, and that of modern humans provides researchers an opportunity to investigate genetic differences between these three subspecies on a genome-wide scale. Here we describe an algorithm that predicts statistically significant motifs based on the difference between a given motif's actual and expected distributions. The algorithm was previously applied to plants but was modified for this work.

RESULTS: The result of applying the algorithm to the human, Neanderthal, and Denisovan genomes is a catalog of potential regulatory motifs in these three human subspecies. We examined the distributions of these motifs in genetic elements including human retroviruses, human accelerated regions, and human accelerated conserved noncoding sequences regions. Differences in these distributions could be the origin of differences in phenotype between the three subspecies. Twenty significant motifs common to all three genomes were found; thirty-three were found in endogenous retroviruses in Neanderthal and Denisovan. Ten of these motifs mapped to the 22 bp core of MiR-1304. The core of this genetic element regulates the ENAM and AMTN genes, which take part in odontogenesis and whose 3' UTRs contained significant motifs. The introns of 20 genes were found to contain a large number of significant motifs, which were also overrepresented in 49 human accelerated regions. These genes include NAV2, SorCS2, TRAPPC9, GRID1, PRDM16, CAMTA1, and ASIC which are all involved in neuroregulation. Further analysis of these genes using the GO database indicates that many are associated with neurodevelopment. Also, varying numbers of significant motifs were found to occur in regions of the Neanderthal and Denisovan genomes that are missing from the human genome, suggesting further functional differences between modern and archaic humans.

CONCLUSION: Although Neanderthal and Denisovan are now extinct, detailed examination of elements from their genomes can shed light on possible phenotypic and cognitive differences between these two archaic human subspecies and modern humans. Genetic similarities and differences between these three subspecies and other fossil hominids would also be of interest.}, } @article {pmid29899442, year = {2018}, author = {Hublin, JJ and Ben-Ncer, A and Bailey, SE and Freidline, SE and Neubauer, S and Skinner, MM and Bergmann, I and Le Cabec, A and Benazzi, S and Harvati, K and Gunz, P}, title = {Author Correction: New fossils from Jebel Irhoud, Morocco and the pan-African origin of Homo sapiens.}, journal = {Nature}, volume = {558}, number = {7711}, pages = {E6}, doi = {10.1038/s41586-018-0166-3}, pmid = {29899442}, issn = {1476-4687}, abstract = {In the originally published version of this Letter, the x axis in Fig. 3a should have been: 'PC1: 26%' rather than 'PC1: 46%', and the y axis should have been: 'PC2: 16%' rather than 'PC2: 29%'. We also noticed an error in the numbering of the fossils from Qafzeh: Qafzeh 27 should be removed, and Qafzeh 26 is actually Qafzeh 25, following Tillier (2014)1 and Schuh et al. (2017)2 and personal communication with B. Vandermeersch and M. D. Garralda. The correct enumeration of Qafzeh samples in the 'Mandibular metric data' section of the Methods is therefore: 'Qafzeh (9, 25)' rather than 'Qafzeh (9, 26, 27)'. Owing to the removal of Qafzeh 27, the convex hull of early modern humans changes slightly in Extended Data Fig. 1c. The sample sizes in Extended Data Fig. 1c should have read: Middle Pleistocene archaic Homo n = 19 (instead of 11), Neanderthals n = 40 (instead of 41), early modern humans n = 12 (instead of 7), and recent modern humans n = 46 (instead of 48). In Extended Data Table 2, the mean and standard deviation of corpus height and breadth at mental foramen for early modern humans should have been: x̅ = 33.15, σ = 3.26 for height (rather than x̅ = 34.23, σ = 4.57); and x̅ = 16.25, σ = 1.28 for breadth (rather than x̅ = 16.04, σ = 1.75). Accordingly, n = 12 (rather than n = 13) for both breadth and height. These errors have been corrected in the Letter online (the original Extended Data Fig. 1 is shown in Supplementary Information to this Amendment). These changes do not alter any inferences drawn from the data.}, } @article {pmid29894925, year = {2018}, author = {Dannemann, M and Racimo, F}, title = {Something old, something borrowed: admixture and adaptation in human evolution.}, journal = {Current opinion in genetics & development}, volume = {53}, number = {}, pages = {1-8}, doi = {10.1016/j.gde.2018.05.009}, pmid = {29894925}, issn = {1879-0380}, abstract = {The sequencing of ancient DNA from archaic humans-Neanderthals and Denisovans-has revealed that modern and archaic humans interbred at least twice during the Pleistocene. The field of human paleogenomics has now turned its attention towards understanding the nature of this genetic legacy in the gene pool of present-day humans. What exactly did modern humans obtain from interbreeding with Neanderthals and Denisovans? Was the introgressed genetic material beneficial, neutral or maladaptive? Can differences in phenotypes among present-day human populations be explained by archaic human introgression? These questions are of prime importance for our understanding of recent human evolution, but will require careful computational modeling and extensive functional assays before they can be answered in full. Here, we review the recent literature characterizing introgressed DNA and the likely biological consequences for their modern human carriers. We focus particularly on archaic human haplotypes that were beneficial to modern humans as they expanded across the globe, and on ways to understand how populations harboring these haplotypes evolved over time.}, } @article {pmid29754744, year = {2018}, author = {García-Martínez, D and Campo Martín, M and González Martín, A and Cambra-Moo, Ó and Barash, A and Bastir, M}, title = {Reevaluation of 'endocostal ossifications' on the Kebara 2 Neanderthal ribs.}, journal = {Journal of human evolution}, volume = {122}, number = {}, pages = {33-37}, doi = {10.1016/j.jhevol.2018.04.011}, pmid = {29754744}, issn = {1095-8606}, } @article {pmid29747567, year = {2018}, author = {Banerjee, N and Polushina, T and Bettella, F and Giddaluru, S and Steen, VM and Andreassen, OA and Le Hellard, S}, title = {Recently evolved human-specific methylated regions are enriched in schizophrenia signals.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {63}, pmid = {29747567}, issn = {1471-2148}, support = {#2 T23273//Norges Forskningsråd/International ; SKGJ-MED-008//KG Jebsen Foundation/International ; }, mesh = {Adult ; Bipolar Disorder/genetics ; Body Height/genetics ; Body Mass Index ; DNA Methylation/*genetics ; *Evolution, Molecular ; Female ; Genetic Markers ; Genome-Wide Association Study ; Genotype ; Humans ; Major Histocompatibility Complex/genetics ; Male ; Molecular Sequence Annotation ; Multifactorial Inheritance ; Phenotype ; Polymorphism, Single Nucleotide/genetics ; Schizophrenia/*genetics ; }, abstract = {BACKGROUND: One explanation for the persistence of schizophrenia despite the reduced fertility of patients is that it is a by-product of recent human evolution. This hypothesis is supported by evidence suggesting that recently-evolved genomic regions in humans are involved in the genetic risk for schizophrenia. Using summary statistics from genome-wide association studies (GWAS) of schizophrenia and 11 other phenotypes, we tested for enrichment of association with GWAS traits in regions that have undergone methylation changes in the human lineage compared to Neanderthals and Denisovans, i.e. human-specific differentially methylated regions (DMRs). We used analytical tools that evaluate polygenic enrichment of a subset of genomic variants against all variants.

RESULTS: Schizophrenia was the only trait in which DMR SNPs showed clear enrichment of association that passed the genome-wide significance threshold. The enrichment was not observed for Neanderthal or Denisovan DMRs. The enrichment seen in human DMRs is comparable to that for genomic regions tagged by Neanderthal Selective Sweep markers, and stronger than that for Human Accelerated Regions. The enrichment survives multiple testing performed through permutation (n = 10,000) and bootstrapping (n = 5000) in INRICH (p < 0.01). Some enrichment of association with height was observed at the gene level.

CONCLUSIONS: Regions where DNA methylation modifications have changed during recent human evolution show enrichment of association with schizophrenia and possibly with height. Our study further supports the hypothesis that genetic variants conferring risk of schizophrenia co-occur in genomic regions that have changed as the human species evolved. Since methylation is an epigenetic mark, potentially mediated by environmental changes, our results also suggest that interaction with the environment might have contributed to that association.}, } @article {pmid29742147, year = {2018}, author = {Villa, P and Pollarolo, L and Conforti, J and Marra, F and Biagioni, C and Degano, I and Lucejko, JJ and Tozzi, C and Pennacchioni, M and Zanchetta, G and Nicosia, C and Martini, M and Sibilia, E and Panzeri, L}, title = {From Neandertals to modern humans: New data on the Uluzzian.}, journal = {PloS one}, volume = {13}, number = {5}, pages = {e0196786}, pmid = {29742147}, issn = {1932-6203}, mesh = {Animals ; Cooking/history/instrumentation ; History, Ancient ; Humans ; Italy ; Minerals/analysis ; *Neanderthals ; Weapons/history ; }, abstract = {Having thrived in Eurasia for 350,000 years Neandertals disappeared from the record around 40,000-37,000 years ago, after modern humans entered Europe. It was a complex process of population interactions that included cultural exchanges and admixture between Neandertals and dispersing groups of modern humans. In Europe Neandertals are always associated with the Mousterian while the Aurignacian is associated with modern humans only. The onset of the Aurignacian is preceded by "transitional" industries which show some similarities with the Mousterian but also contain modern tool forms. Information on these industries is often incomplete or disputed and this is true of the Uluzzian. We present the results of taphonomic, typological and technological analyses of two Uluzzian sites, Grotta La Fabbrica (Tuscany) and the newly discovered site of Colle Rotondo (Latium). Comparisons with Castelcivita and Grotta del Cavallo show that the Uluzzian is a coherent cultural unit lasting about five millennia, replaced by the Protoaurignacian before the eruption of the Campanian Ignimbrite. The lack of skeletal remains at our two sites and the controversy surrounding the stratigraphic position of modern human teeth at Cavallo makes it difficult to reach agreement about authorship of the Uluzzian, for which alternative hypotheses have been proposed. Pending the discovery of DNA or further human remains, these hypotheses can only be evaluated by archaeological arguments, i.e. evidence of continuities and discontinuities between the Uluzzian and the preceding and succeeding culture units in Italy. However, in the context of "transitional" industries with disputed dates for the arrival of modern humans in Europe, and considering the case of the Châtelperronian, an Upper Paleolithic industry made by Neandertals, typo-technology used as an indicator of hominin authorship has limited predictive value. We corroborate previous suggestions that the Middle-to-Upper Paleolithic transition occurred as steps of rapid changes and geographically uneven rates of spread.}, } @article {pmid29739306, year = {2018}, author = {Akkuratov, EE and Gelfand, MS and Khrameeva, EE}, title = {Neanderthal and Denisovan ancestry in Papuans: A functional study.}, journal = {Journal of bioinformatics and computational biology}, volume = {16}, number = {2}, pages = {1840011}, doi = {10.1142/S0219720018400115}, pmid = {29739306}, issn = {1757-6334}, abstract = {Sequencing of complete nuclear genomes of Neanderthal and Denisovan stimulated studies about their relationship with modern humans demonstrating, in particular, that DNA alleles from both Neanderthal and Denisovan genomes are present in genomes of modern humans. The Papuan genome is a unique object because it contains both Neanderthal and Denisovan alleles. Here, we have shown that the Papuan genomes contain different gene functional groups inherited from each of the ancient people. The Papuan genomes demonstrate a relative prevalence of Neanderthal alleles in genes responsible for the regulation of transcription and neurogenesis. The enrichment of specific functional groups with Denisovan alleles is less pronounced; these groups are responsible for bone and tissue remodeling. This analysis shows that introgression of alleles from Neanderthals and Denisovans to Papuans occurred independently and retention of these alleles may carry specific adaptive advantages.}, } @article {pmid29728579, year = {2018}, author = {Wolf, D and Kolb, T and Alcaraz-Castaño, M and Heinrich, S and Baumgart, P and Calvo, R and Sánchez, J and Ryborz, K and Schäfer, I and Bliedtner, M and Zech, R and Zöller, L and Faust, D}, title = {Climate deteriorations and Neanderthal demise in interior Iberia.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {7048}, pmid = {29728579}, issn = {2045-2322}, abstract = {Time and circumstances for the disappearance of Neanderthals and its relationship with the advent of Modern Humans are not yet sufficiently resolved, especially in case of the Iberian Peninsula. Reconstructing palaeoenvironmental conditions during the last glacial period is crucial to clarifying whether climate deteriorations or competition and contacts with Modern Humans played the pivotal role in driving Neanderthals to extinction. A high-resolution loess record from the Upper Tagus Basin in central Spain demonstrates that the Neanderthal abandonment of inner Iberian territories 42 kyr ago coincided with the evolvement of hostile environmental conditions, while archaeological evidence testifies that this desertion took place regardless of modern humans' activities. According to stratigraphic findings and stable isotope analyses, this period corresponded to the driest environmental conditions of the last glacial apart from an even drier period linked to Heinrich Stadial 3. Our results show that during Marine Isotope Stages (MIS) 4 and 2 climate deteriorations in interior Iberia temporally coincided with northern hemisphere cold periods (Heinrich stadials). Solely during the middle MIS 3, in a period surrounding 42 kyr ago, this relation seems not straightforward, which may demonstrate the complexity of terrestrial climate conditions during glacial periods.}, } @article {pmid29718916, year = {2018}, author = {Majkić, A and d'Errico, F and Stepanchuk, V}, title = {Assessing the significance of Palaeolithic engraved cortexes. A case study from the Mousterian site of Kiik-Koba, Crimea.}, journal = {PloS one}, volume = {13}, number = {5}, pages = {e0195049}, pmid = {29718916}, issn = {1932-6203}, mesh = {*Engraving and Engravings ; Europe, Eastern ; *Paleontology ; }, abstract = {Twenty-Seven Lower and Middle Paleolithic sites from Europe and the Middle East are reported in the literature to have yielded incised stones. At eleven of these sites incisions are present on flint cortexes. Even when it is possible to demonstrate that the engravings are ancient and human made, it is often difficult to distinguish incisions resulting from functional activities such as butchery or use as a cutting board, from those produced deliberately, and even more difficult to identify the scope of the latter. In this paper we present results of the analysis of an engraved cortical flint flake found at Kiik-Koba, a key Mousterian site from Crimea, and create an interpretative framework to guide the interpretation of incised cortexes. The frame of inference that we propose allows for a reasoned evaluation of the actions playing a role in the marking process and aims at narrowing down the interpretation of the evidence. The object comes from layer IV, the same layer in which a Neanderthal child burial was unearthed, which contains a para-Micoquian industry of Kiik-Koba type dated to between c.35 and 37 cal kyr BP. The microscopic analysis and 3D reconstruction of the grooves on the cortex of this small flint flake, demonstrate that the incisions represent a deliberate engraving made by a skilled craftsman, probably with two different points. The lines are nearly perfectly framed into the cortex, testifying of well controlled motions. This is especially the case considering the small size of the object, which makes this a difficult task. The production of the engraving required excellent neuromotor and volitional control, which implies focused attention. Evaluation of the Kiik-Koba evidence in the light of the proposed interpretative framework supports the view that the engraving was made with a representational intent.}, } @article {pmid29709293, year = {2018}, author = {Terhune, CE and Ritzman, TB and Robinson, CA}, title = {Mandibular ramus shape variation and ontogeny in Homo sapiens and Homo neanderthalensis.}, journal = {Journal of human evolution}, volume = {121}, number = {}, pages = {55-71}, doi = {10.1016/j.jhevol.2018.03.009}, pmid = {29709293}, issn = {1095-8606}, abstract = {As the interface between the mandible and cranium, the mandibular ramus is functionally significant and its morphology has been suggested to be informative for taxonomic and phylogenetic analyses. In primates, and particularly in great apes and humans, ramus morphology is highly variable, especially in the shape of the coronoid process and the relationship of the ramus to the alveolar margin. Here we compare ramus shape variation through ontogeny in Homo neanderthalensis to that of modern and fossil Homo sapiens using geometric morphometric analyses of two-dimensional semilandmarks and univariate measurements of ramus angulation and relative coronoid and condyle height. Results suggest that ramus, especially coronoid, morphology varies within and among subadult and adult modern human populations, with the Alaskan Inuit being particularly distinct. We also identify significant differences in overall anterosuperior ramus and coronoid shapes between H. sapiens and H. neanderthalensis, both in adults and throughout ontogeny. These shape differences are subtle, however, and we therefore suggest caution when using ramus morphology to diagnose group membership for individual specimens of these taxa. Furthermore, we argue that these morphologies are unlikely to be representative of differences in masticatory biomechanics and/or paramasticatory behaviors between Neanderthals and modern humans, as has been suggested by previous authors. Assessments of ontogenetic patterns of shape change reveal that the typical Neanderthal ramus morphology is established early in ontogeny, and there is little evidence for divergent postnatal ontogenetic allometric trajectories between Neanderthals and modern humans as a whole. This analysis informs our understanding of intraspecific patterns of mandibular shape variation and ontogeny in H. sapiens and can shed further light on overall developmental and life history differences between H. sapiens and H. neanderthalensis.}, } @article {pmid29700382, year = {2018}, author = {Kochiyama, T and Ogihara, N and Tanabe, HC and Kondo, O and Amano, H and Hasegawa, K and Suzuki, H and Ponce de León, MS and Zollikofer, CPE and Bastir, M and Stringer, C and Sadato, N and Akazawa, T}, title = {Reconstructing the Neanderthal brain using computational anatomy.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {6296}, pmid = {29700382}, issn = {2045-2322}, support = {R24 NS092988/NS/NINDS NIH HHS/United States ; U54 MH091657/MH/NIMH NIH HHS/United States ; }, abstract = {The present study attempted to reconstruct 3D brain shape of Neanderthals and early Homo sapiens based on computational neuroanatomy. We found that early Homo sapiens had relatively larger cerebellar hemispheres but a smaller occipital region in the cerebrum than Neanderthals long before the time that Neanderthals disappeared. Further, using behavioural and structural imaging data of living humans, the abilities such as cognitive flexibility, attention, the language processing, episodic and working memory capacity were positively correlated with size-adjusted cerebellar volume. As the cerebellar hemispheres are structured as a large array of uniform neural modules, a larger cerebellum may possess a larger capacity for cognitive information processing. Such a neuroanatomical difference in the cerebellum may have caused important differences in cognitive and social abilities between the two species and might have contributed to the replacement of Neanderthals by early Homo sapiens.}, } @article {pmid29700241, year = {2018}, author = {Lawler, A}, title = {Searching for a Stone Age Odysseus.}, journal = {Science (New York, N.Y.)}, volume = {360}, number = {6387}, pages = {362-363}, doi = {10.1126/science.360.6387.362}, pmid = {29700241}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; Greece ; History, Ancient ; Human Migration/*history ; Humans ; Mediterranean Islands ; *Neanderthals ; Oceans and Seas ; Technology/*history ; }, } @article {pmid29685752, year = {2018}, author = {Power, RC and Salazar-García, DC and Rubini, M and Darlas, A and Harvati, K and Walker, M and Hublin, JJ and Henry, AG}, title = {Dental calculus indicates widespread plant use within the stable Neanderthal dietary niche.}, journal = {Journal of human evolution}, volume = {119}, number = {}, pages = {27-41}, doi = {10.1016/j.jhevol.2018.02.009}, pmid = {29685752}, issn = {1095-8606}, abstract = {The ecology of Neanderthals is a pressing question in the study of hominin evolution. Diet appears to have played a prominent role in their adaptation to Eurasia. Based on isotope and zooarchaeological studies, Neanderthal diet has been reconstructed as heavily meat-based and generally similar across different environments. This image persists, despite recent studies suggesting more plant use and more variation. However, we have only a fragmentary picture of their dietary ecology, and how it may have varied among habitats, because we lack broad and environmentally representative information about their use of plants and other foods. To address the problem, we examined the plant microremains in Neanderthal dental calculus from five archaeological sites representing a variety of environments from the northern Balkans, and the western, central and eastern Mediterranean. The recovered microremains revealed the consumption of a variety of non-animal foods, including starchy plants. Using a modeling approach, we explored the relationships among microremains and environment, while controlling for chronology. In the process, we compared the effectiveness of various diversity metrics and their shortcomings for studying microbotanical remains, which are often morphologically redundant for identification. We developed Minimum Botanical Units as a new way of estimating how many plant types or parts are present in a microbotanical sample. In contrast to some previous work, we found no evidence that plant use is confined to the southern-most areas of Neanderthal distribution. Although interpreting the ecogeographic variation is limited by the incomplete preservation of dietary microremains, it is clear that plant exploitation was a widespread and deeply rooted Neanderthal subsistence strategy, even if they were predominately game hunters. Given the limited dietary variation across Neanderthal range in time and space in both plant and animal food exploitation, we argue that vegetal consumption was a feature of a generally static dietary niche.}, } @article {pmid29681055, year = {2018}, author = {Profico, A and Schlager, S and Valoriani, V and Buzi, C and Melchionna, M and Veneziano, A and Raia, P and Moggi-Cecchi, J and Manzi, G}, title = {Reproducing the internal and external anatomy of fossil bones: Two new automatic digital tools.}, journal = {American journal of physical anthropology}, volume = {166}, number = {4}, pages = {979-986}, doi = {10.1002/ajpa.23493}, pmid = {29681055}, issn = {1096-8644}, mesh = {Anthropology, Physical/*methods ; Bone and Bones/*anatomy & histology/*diagnostic imaging ; *Fossils ; Humans ; Image Processing, Computer-Assisted/*methods ; Imaging, Three-Dimensional ; Lasers ; }, abstract = {OBJECTIVES: We present two new automatic tools, developed under the R environment, to reproduce the internal and external structures of bony elements. The first method, Computer-Aided Laser Scanner Emulator (CA-LSE), provides the reconstruction of the external portions of a 3D mesh by simulating the action of a laser scanner. The second method, Automatic Segmentation Tool for 3D objects (AST-3D), performs the digital reconstruction of anatomical cavities.

MATERIALS AND METHODS: We present the application of CA-LSE and AST-3D methods to different anatomical remains, highly variable in terms of shape, size and structure: a modern human skull, a malleus bone, and a Neanderthal deciduous tooth. Both methods are developed in the R environment and embedded in the packages "Arothron" and "Morpho," where both the codes and the data are fully available.

RESULTS: The application of CA-LSE and AST-3D allows the isolation and manipulation of the internal and external components of the 3D virtual representation of complex bony elements. In particular, we present the output of the four case studies: a complete modern human endocast and the right maxillary sinus, the dental pulp of the Neanderthal tooth and the inner network of blood vessels of the malleus.

DISCUSSION: Both methods demonstrated to be much faster, cheaper, and more accurate than other conventional approaches. The tools we presented are available as add-ons in existing software within the R platform. Because of ease of application, and unrestrained availability of the methods proposed, these tools can be widely used by paleoanthropologists, paleontologists and anatomists.}, } @article {pmid29668700, year = {2018}, author = {Marín-Arroyo, AB and Rios-Garaizar, J and Straus, LG and Jones, JR and de la Rasilla, M and González Morales, MR and Richards, M and Altuna, J and Mariezkurrena, K and Ocio, D}, title = {Chronological reassessment of the Middle to Upper Paleolithic transition and Early Upper Paleolithic cultures in Cantabrian Spain.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0194708}, pmid = {29668700}, issn = {1932-6203}, abstract = {Methodological advances in dating the Middle to Upper Paleolithic transition provide a better understanding of the replacement of local Neanderthal populations by Anatomically Modern Humans. Today we know that this replacement was not a single, pan-European event, but rather it took place at different times in different regions. Thus, local conditions could have played a role. Iberia represents a significant macro-region to study this process. Northern Atlantic Spain contains evidence of both Mousterian and Early Upper Paleolithic occupations, although most of them are not properly dated, thus hindering the chances of an adequate interpretation. Here we present 46 new radiocarbon dates conducted using ultrafiltration pre-treatment method of anthropogenically manipulated bones from 13 sites in the Cantabrian region containing Mousterian, Aurignacian and Gravettian levels, of which 30 are considered relevant. These dates, alongside previously reported ones, were integrated into a Bayesian age model to reconstruct an absolute timescale for the transitional period. According to it, the Mousterian disappeared in the region by 47.9-45.1ka cal BP, while the Châtelperronian lasted between 42.6k and 41.5ka cal BP. The Mousterian and Châtelperronian did not overlap, indicating that the latter might be either intrusive or an offshoot of the Mousterian. The new chronology also suggests that the Aurignacian appears between 43.3-40.5ka cal BP overlapping with the Châtelperronian, and ended around 34.6-33.1ka cal BP, after the Gravettian had already been established in the region. This evidence indicates that Neanderthals and AMH co-existed <1,000 years, with the caveat that no diagnostic human remains have been found with the latest Mousterian, Châtelperronian or earliest Aurignacian in Cantabrian Spain.}, } @article {pmid29664998, year = {2018}, author = {Bible, RC and Peterson, AT}, title = {Compatible ecological niche signals between biological and archaeological datasets for late-surviving Neandertals.}, journal = {American journal of physical anthropology}, volume = {166}, number = {4}, pages = {968-974}, doi = {10.1002/ajpa.23482}, pmid = {29664998}, issn = {1096-8644}, mesh = {Animals ; *Anthropology, Physical ; Databases, Factual ; *Ecosystem ; Europe ; Fossils ; Humans ; Neanderthals/*physiology ; Research ; }, abstract = {OBJECTIVES: To assess ecological niche similarity for biological and archaeological samples representing late-surviving Neandertals in Europe to evaluate the validity of combining these two types of data in ecological niche modeling analyses.

MATERIALS AND METHODS: Tests of niche conservatism were used to assess niche similarity and niche identity of samples of morphologically diagnostic Neandertal remains and Middle Paleolithic (MP) archaeological sites dating to the time period leading up to Neandertal extinction. Paleoenvironmental reconstructions for the Pre-H4 (43.3-40.2 ky cal BP) were used as environmental space analyses.

RESULTS: Null hypotheses of niche similarity and identity of the two types of samples could not be rejected.

CONCLUSIONS: As primary and secondary evidence of Neandertal occurrence during the Pre-H4 show high levels of niche similarity and identity, combining the two types of occurrence data to create larger samples for niche analyses is justified without the concern that different environmental signals could complicate future research.}, } @article {pmid29658973, year = {2018}, author = {Viscardi, LH and Paixão-Côrtes, VR and Comas, D and Salzano, FM and Rovaris, D and Bau, CD and Amorim, CEG and Bortolini, MC}, title = {Searching for ancient balanced polymorphisms shared between Neanderthals and Modern Humans.}, journal = {Genetics and molecular biology}, volume = {41}, number = {1}, pages = {67-81}, pmid = {29658973}, issn = {1415-4757}, abstract = {Hominin evolution is characterized by adaptive solutions often rooted in behavioral and cognitive changes. If balancing selection had an important and long-lasting impact on the evolution of these traits, it can be hypothesized that genes associated with them should carry an excess of shared polymorphisms (trans- SNPs) across recent Homo species. In this study, we investigate the role of balancing selection in human evolution using available exomes from modern (Homo sapiens) and archaic humans (H. neanderthalensis and Denisovan) for an excess of trans-SNP in two gene sets: one associated with the immune system (IMMS) and another one with behavioral system (BEHS). We identified a significant excess of trans-SNPs in IMMS (N=547), of which six of these located within genes previously associated with schizophrenia. No excess of trans-SNPs was found in BEHS, but five genes in this system harbor potential signals for balancing selection and are associated with psychiatric or neurodevelopmental disorders. Our approach evidenced recent Homo trans-SNPs that have been previously implicated in psychiatric diseases such as schizophrenia, suggesting that a genetic repertoire common to the immune and behavioral systems could have been maintained by balancing selection starting before the split between archaic and modern humans.}, } @article {pmid29624658, year = {2018}, author = {García-Tabernero, A and Peña-Melián, A and Rosas, A}, title = {Primary visual cortex in neandertals as revealed from the occipital remains from the El Sidrón site, with emphasis on the new SD-2300 specimen.}, journal = {Journal of anatomy}, volume = {233}, number = {1}, pages = {33-45}, doi = {10.1111/joa.12812}, pmid = {29624658}, issn = {1469-7580}, abstract = {The comparative analysis of the endocranial surface of the El Sidrón new occipital fragment SD-2300 shows meaningful differences in the configuration of the occipital pole region between neandertals and anatomically modern humans (AMH). The particular asymmetries found in neandertals in the venous sinus drainage and the petalial patterns are recognizable in this new specimen as well. In addition, the supra- and infracalcarine fossae of the occipital pole region appear to deviate obliquely from the mid-line when compared with sapiens. Due to the excellent preservation conditions of SD-2300, the main sulci and gyri of the occipital pole area have been identified, this degree of detail being uncommon in a fossil specimen; in general, the gyrification pattern is similar to AMH, but with some notable differences. Particularly interesting is the description of the lunate and the calcarine sulci. The lunate sulcus is located close to the occipital pole, in a similar posterior position to in other Homo species. Regarding the calcarine sulcus, there are significant differences in the primary visual cortex, with the V1 area, or Brodmann area 17, being larger in Homo neanderthalensis than in Homo sapiens. This may lead to greater visual acuity in neandertals than in sapiens.}, } @article {pmid29618551, year = {2018}, author = {Wroe, S and Parr, WCH and Ledogar, JA and Bourke, J and Evans, SP and Fiorenza, L and Benazzi, S and Hublin, JJ and Stringer, C and Kullmer, O and Curry, M and Rae, TC and Yokley, TR}, title = {Computer simulations show that Neanderthal facial morphology represents adaptation to cold and high energy demands, but not heavy biting.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1876}, pages = {}, pmid = {29618551}, issn = {1471-2954}, abstract = {Three adaptive hypotheses have been forwarded to explain the distinctive Neanderthal face: (i) an improved ability to accommodate high anterior bite forces, (ii) more effective conditioning of cold and/or dry air and, (iii) adaptation to facilitate greater ventilatory demands. We test these hypotheses using three-dimensional models of Neanderthals, modern humans, and a close outgroup (Homo heidelbergensis), applying finite-element analysis (FEA) and computational fluid dynamics (CFD). This is the most comprehensive application of either approach applied to date and the first to include both. FEA reveals few differences between H. heidelbergensis, modern humans, and Neanderthals in their capacities to sustain high anterior tooth loadings. CFD shows that the nasal cavities of Neanderthals and especially modern humans condition air more efficiently than does that of H. heidelbergensis, suggesting that both evolved to better withstand cold and/or dry climates than less derived Homo We further find that Neanderthals could move considerably more air through the nasal pathway than could H. heidelbergensis or modern humans, consistent with the propositions that, relative to our outgroup Homo, Neanderthal facial morphology evolved to reflect improved capacities to better condition cold, dry air, and, to move greater air volumes in response to higher energetic requirements.}, } @article {pmid29610322, year = {2018}, author = {Egeland, CP and Domínguez-Rodrigo, M and Pickering, TR and Menter, CG and Heaton, JL}, title = {Hominin skeletal part abundances and claims of deliberate disposal of corpses in the Middle Pleistocene.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {18}, pages = {4601-4606}, pmid = {29610322}, issn = {1091-6490}, mesh = {Animals ; Anthropology, Cultural/*methods ; Archaeology ; Bone and Bones ; Burial/ethics/*history ; Cadaver ; Ceremonial Behavior ; Fossils/history ; History, Ancient ; Hominidae/*psychology ; Humans ; Machine Learning ; Neanderthals ; South Africa ; Spain ; }, abstract = {Humans are set apart from other organisms by the realization of their own mortality. Thus, determining the prehistoric emergence of this capacity is of significant interest to understanding the uniqueness of the human animal. Tracing that capacity chronologically is possible through archaeological investigations that focus on physical markers that reflect "mortality salience." Among these markers is the deliberate and culturally mediated disposal of corpses. Some Neandertal bone assemblages are among the earliest reasonable claims for the deliberate disposal of hominins, but even these are vigorously debated. More dramatic assertions center on the Middle Pleistocene sites of Sima de los Huesos (SH, Spain) and the Dinaledi Chamber (DC, South Africa), where the remains of multiple hominin individuals were found in deep caves, and under reported taphonomic circumstances that seem to discount the possibility that nonhominin actors and processes contributed to their formation. These claims, with significant implications for charting the evolution of the "human condition," deserve scrutiny. We test these assertions through machine-learning analyses of hominin skeletal part representation in the SH and DC assemblages. Our results indicate that nonanthropogenic agents and abiotic processes cannot yet be ruled out as significant contributors to the ultimate condition of both collections. This finding does not falsify hypotheses of deliberate disposal for the SH and DC corpses, but does indicate that the data also support partially or completely nonanthropogenic formational histories.}, } @article {pmid29608725, year = {2018}, author = {Zehra, R and Abbasi, AA}, title = {Homo sapiens-Specific Binding Site Variants within Brain Exclusive Enhancers Are Subject to Accelerated Divergence across Human Population.}, journal = {Genome biology and evolution}, volume = {10}, number = {3}, pages = {956-966}, pmid = {29608725}, issn = {1759-6653}, mesh = {Animals ; Binding Sites/genetics ; Brain/metabolism ; Enhancer Elements, Genetic/*genetics ; *Evolution, Molecular ; Humans ; Primates/*genetics ; Species Specificity ; Transcription Factors/genetics ; }, abstract = {Empirical assessments of human accelerated noncoding DNA frgaments have delineated presence of many cis-regulatory elements. Enhancers make up an important category of such accelerated cis-regulatory elements that efficiently control the spatiotemporal expression of many developmental genes. Establishing plausible reasons for accelerated enhancer sequence divergence in Homo sapiens has been termed significant in various previously published studies. This acceleration by including closely related primates and archaic human data has the potential to open up evolutionary avenues for deducing present-day brain structure. This study relied on empirically confirmed brain exclusive enhancers to avoid any misjudgments about their regulatory status and categorized among them a subset of enhancers with an exceptionally accelerated rate of lineage specific divergence in humans. In this assorted set, 13 distinct transcription factor binding sites were located that possessed unique existence in humans. Three of 13 such sites belonging to transcription factors SOX2, RUNX1/3, and FOS/JUND possessed single nucleotide variants that made them unique to H. sapiens upon comparisons with Neandertal and Denisovan orthologous sequences. These variants modifying the binding sites in modern human lineage were further substantiated as single nucleotide polymorphisms via exploiting 1000 Genomes Project Phase3 data. Long range haplotype based tests laid out evidence of positive selection to be governing in African population on two of the modern human motif modifying alleles with strongest results for SOX2 binding site. In sum, our study acknowledges acceleration in noncoding regulatory landscape of the genome and highlights functional parts within it to have undergone accelerated divergence in present-day human population.}, } @article {pmid29603507, year = {2018}, author = {Steinrücken, M and Spence, JP and Kamm, JA and Wieczorek, E and Song, YS}, title = {Model-based detection and analysis of introgressed Neanderthal ancestry in modern humans.}, journal = {Molecular ecology}, volume = {27}, number = {19}, pages = {3873-3888}, pmid = {29603507}, issn = {1365-294X}, support = {//David and Lucile Packard Foundation, Packard Fellowship for Science and Engineering/ ; R01-GM094402//National Institute of General Medical Sciences/ ; R01 GM094402/GM/NIGMS NIH HHS/United States ; }, abstract = {Genetic evidence has revealed that the ancestors of modern human populations outside Africa and their hominin sister groups, notably Neanderthals, exchanged genetic material in the past. The distribution of these introgressed sequence tracts along modern-day human genomes provides insight into the selective forces acting on them and the role of introgression in the evolutionary history of hominins. Studying introgression patterns on the X-chromosome is of particular interest, as sex chromosomes are thought to play a special role in speciation. Recent studies have developed methods to localize introgressed ancestries, reporting long regions that are depleted of Neanderthal introgression and enriched in genes, suggesting negative selection against the Neanderthal variants. On the other hand, enriched Neanderthal ancestry in hair- and skin-related genes suggests that some introgressed variants facilitated adaptation to new environments. Here, we present a model-based introgression detection method called dical-admix. We demonstrate its efficiency and accuracy through extensive simulations and apply it to detect tracts of Neanderthal introgression in modern human individuals from the 1000 Genomes Project. Our findings are largely concordant with previous studies, consistent with weak selection against Neanderthal ancestry. We find evidence that selection against Neanderthal ancestry was due to higher genetic load in Neanderthals resulting from small effective population size, rather than widespread Dobzhansky-Müller incompatibilities (DMIs) that could contribute to reproductive isolation. Moreover, we confirm the previously reported low level of introgression on the X-chromosome, but find little evidence that DMIs contributed to this pattern.}, } @article {pmid29590205, year = {2018}, author = {Rios-Garaizar, J and López-Bultó, O and Iriarte, E and Pérez-Garrido, C and Piqué, R and Aranburu, A and Iriarte-Chiapusso, MJ and Ortega-Cordellat, I and Bourguignon, L and Garate, D and Libano, I}, title = {A Middle Palaeolithic wooden digging stick from Aranbaltza III, Spain.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0195044}, pmid = {29590205}, issn = {1932-6203}, mesh = {Animals ; *Archaeology ; *Fossils ; Humans ; *Neanderthals ; *Paleontology ; Spain ; Technology/*instrumentation ; *Wood ; }, abstract = {Aranbaltza is an archaeological complex formed by at least three open-air sites. Between 2014 and 2015 a test excavation carried out in Aranbaltza III revealed the presence of a sand and clay sedimentary sequence formed in floodplain environments, within which six sedimentary units have been identified. This sequence was formed between 137-50 ka, and includes several archaeological horizons, attesting to the long-term presence of Neanderthal communities in this area. One of these horizons, corresponding with Unit 4, yielded two wooden tools. One of these tools is a beveled pointed tool that was shaped through a complex operational sequence involving branch shaping, bark peeling, twig removal, shaping, polishing, thermal exposition and chopping. A use-wear analysis of the tool shows it to have traces related with digging soil so it has been interpreted as representing a digging stick. This is the first time such a tool has been identified in a European Late Middle Palaeolithic context; it also represents one of the first well-preserved Middle Palaeolithic wooden tool found in southern Europe. This artefact represents one of the few examples available of wooden tool preservation for the European Palaeolithic, allowing us to further explore the role wooden technologies played in Neanderthal communities.}, } @article {pmid29590013, year = {2018}, author = {Rosas, A and Ríos, L and Estalrrich, A and Liversidge, H and García-Tabernero, A and Huguet, R and Cardoso, H and Bastir, M and Lalueza-Fox, C and de la Rasilla, M and Dean, C}, title = {Response to Comment on "The growth pattern of Neandertals, reconstructed from a juvenile skeleton from El Sidrón (Spain)".}, journal = {Science (New York, N.Y.)}, volume = {359}, number = {6380}, pages = {}, doi = {10.1126/science.aar3820}, pmid = {29590013}, issn = {1095-9203}, mesh = {Brain ; *Fossils ; Hominidae ; Humans ; Male ; *Neanderthals ; Skeleton ; Spain ; }, abstract = {The comment by DeSilva challenges our suggestion that brain growth of the El Sidrón J1 Neandertal was still incomplete at 7.7 years of age. Evidence suggests that endocranial volume is likely to represent less than 90% adult size at El Sidrón as well as Neandertal male plus Krapina samples, in line with further evidence from endocranial surface histology and dural sinus groove size.}, } @article {pmid29590012, year = {2018}, author = {DeSilva, JM}, title = {Comment on "The growth pattern of Neandertals, reconstructed from a juvenile skeleton from El Sidrón (Spain)".}, journal = {Science (New York, N.Y.)}, volume = {359}, number = {6380}, pages = {}, doi = {10.1126/science.aar3611}, pmid = {29590012}, issn = {1095-9203}, mesh = {*Biological Evolution ; Fossils ; Hominidae ; Humans ; *Neanderthals ; Skeleton ; Spain ; }, abstract = {Rosas et al (Reports, 22 September 2017, p. 1282) calculate El Sidrón J1 to have reached only 87.5% of its adult brain size. This finding is based on an overestimation of Neandertal brain size. Pairwise comparisons with a larger sample of Neandertal fossils reveal that it is unlikely that the brain of El Sidrón would have grown appreciably larger.}, } @article {pmid29570998, year = {2018}, author = {Vernot, B and Pääbo, S}, title = {The Predecessors Within . . .}, journal = {Cell}, volume = {173}, number = {1}, pages = {6-7}, doi = {10.1016/j.cell.2018.03.023}, pmid = {29570998}, issn = {1097-4172}, mesh = {Asia ; *Family ; Humans ; }, abstract = {By examining the genomes of present-day people from Asia, researchers show that modern humans met and interbred with Denisovans, distant relatives to Neanderthals, on at least two occasions. As a result, people today carry DNA from two different Denisovan populations.}, } @article {pmid29562232, year = {2018}, author = {Hajdinjak, M and Fu, Q and Hübner, A and Petr, M and Mafessoni, F and Grote, S and Skoglund, P and Narasimham, V and Rougier, H and Crevecoeur, I and Semal, P and Soressi, M and Talamo, S and Hublin, JJ and Gušić, I and Kućan, Ž and Rudan, P and Golovanova, LV and Doronichev, VB and Posth, C and Krause, J and Korlević, P and Nagel, S and Nickel, B and Slatkin, M and Patterson, N and Reich, D and Prüfer, K and Meyer, M and Pääbo, S and Kelso, J}, title = {Reconstructing the genetic history of late Neanderthals.}, journal = {Nature}, volume = {555}, number = {7698}, pages = {652-656}, pmid = {29562232}, issn = {1476-4687}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Africa/ethnology ; Animals ; Bone and Bones ; DNA, Ancient/analysis ; Europe/ethnology ; Female ; Gene Flow ; Genetics, Population ; Genome/*genetics ; Genomics ; Humans ; Hypochlorous Acid ; Male ; Neanderthals/*classification/*genetics ; *Phylogeny ; Siberia/ethnology ; Tooth ; }, abstract = {Although it has previously been shown that Neanderthals contributed DNA to modern humans, not much is known about the genetic diversity of Neanderthals or the relationship between late Neanderthal populations at the time at which their last interactions with early modern humans occurred and before they eventually disappeared. Our ability to retrieve DNA from a larger number of Neanderthal individuals has been limited by poor preservation of endogenous DNA and contamination of Neanderthal skeletal remains by large amounts of microbial and present-day human DNA. Here we use hypochlorite treatment of as little as 9 mg of bone or tooth powder to generate between 1- and 2.7-fold genomic coverage of five Neanderthals who lived around 39,000 to 47,000 years ago (that is, late Neanderthals), thereby doubling the number of Neanderthals for which genome sequences are available. Genetic similarity among late Neanderthals is well predicted by their geographical location, and comparison to the genome of an older Neanderthal from the Caucasus indicates that a population turnover is likely to have occurred, either in the Caucasus or throughout Europe, towards the end of Neanderthal history. We find that the bulk of Neanderthal gene flow into early modern humans originated from one or more source populations that diverged from the Neanderthals that were studied here at least 70,000 years ago, but after they split from a previously sequenced Neanderthal from Siberia around 150,000 years ago. Although four of the Neanderthals studied here post-date the putative arrival of early modern humans into Europe, we do not detect any recent gene flow from early modern humans in their ancestry.}, } @article {pmid29554122, year = {2018}, author = {Schlager, S and Profico, A and Di Vincenzo, F and Manzi, G}, title = {Retrodeformation of fossil specimens based on 3D bilateral semi-landmarks: Implementation in the R package "Morpho".}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0194073}, pmid = {29554122}, issn = {1932-6203}, mesh = {Animals ; Body Weights and Measures/methods ; Fossils/*anatomy & histology ; Gorilla gorilla/anatomy & histology ; Neanderthals/anatomy & histology ; Paleontology/*methods ; Skull/chemistry ; }, abstract = {Many fossil specimens exhibit deformations caused by taphonomic processes. Due to these deformations, even important specimens have to be excluded from morphometric analyses, impoverishing an already poor paleontological record. Techniques to retrodeform and virtually restore damaged (i.e. deformed) specimens are available, but these methods genenerally imply the use of a sparse set of bilateral landmarks, ignoring the fact that the distribution and amount of control points directly affects the result of the retrodeformation. We propose a method developed in the R environment and available in the R-package "Morpho" that, in addition to the landmark configurations, also allows using a set of semi-landmarks homogeneously distributed along curves and on surfaces. We evaluated the outcome of the retrodeformation, regarding the number of semi-landmarks used and its robustness against asymmetric noise, based on simulations using a virtually deformed gorilla cranium. Finally, we applied the method to a well-known Neanderthal cranium that exhibits signs of taphonomically induced asymmetry.}, } @article {pmid29551270, year = {2018}, author = {Browning, SR and Browning, BL and Zhou, Y and Tucci, S and Akey, JM}, title = {Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture.}, journal = {Cell}, volume = {173}, number = {1}, pages = {53-61.e9}, pmid = {29551270}, issn = {1097-4172}, support = {R01 GM110068/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Asian Continental Ancestry Group/genetics ; *Genome, Human ; Humans ; Neanderthals/genetics ; Selection, Genetic ; Whole Exome Sequencing ; }, abstract = {Anatomically modern humans interbred with Neanderthals and with a related archaic population known as Denisovans. Genomes of several Neanderthals and one Denisovan have been sequenced, and these reference genomes have been used to detect introgressed genetic material in present-day human genomes. Segments of introgression also can be detected without use of reference genomes, and doing so can be advantageous for finding introgressed segments that are less closely related to the sequenced archaic genomes. We apply a new reference-free method for detecting archaic introgression to 5,639 whole-genome sequences from Eurasia and Oceania. We find Denisovan ancestry in populations from East and South Asia and Papuans. Denisovan ancestry comprises two components with differing similarity to the sequenced Altai Denisovan individual. This indicates that at least two distinct instances of Denisovan admixture into modern humans occurred, involving Denisovan populations that had different levels of relatedness to the sequenced Altai Denisovan. VIDEO ABSTRACT.}, } @article {pmid29544621, year = {2018}, author = {Gómez-Olivencia, A and Quam, R and Sala, N and Bardey, M and Ohman, JC and Balzeau, A}, title = {La Ferrassie 1: New perspectives on a "classic" Neandertal.}, journal = {Journal of human evolution}, volume = {117}, number = {}, pages = {13-32}, doi = {10.1016/j.jhevol.2017.12.004}, pmid = {29544621}, issn = {1095-8606}, abstract = {The La Ferrassie 1 (LF1) skeleton, discovered over a century ago, is one of the most important Neandertal individuals both for its completeness and due to the role it has played historically in the interpretation of Neandertal anatomy and lifeways. Here we present new skeletal remains from this individual, which include a complete right middle ear ossicular chain (malleus, incus, and stapes), three vertebral fragments, and two costal remains. Additionally, the study of the skeleton has allowed us to identify new pathological lesions, including a congenital variant in the atlas, a greenstick fracture of the left clavicle, and a lesion in a mid-thoracic rib of unknown etiology. In addition, we have quantified the amount of vertebral pathology, which is greater than previously appreciated. We have complemented the paleopathological analysis with a taphonomic analysis to identify any potential perimortem fractures. The taphonomic analysis indicates that no surface alteration is present in the LF1 skeleton and that the breakage pattern is that of bone that has lost collagen, which would be consistent with the intentional burial of this individual proposed by previous researchers. In this study, we used CT and microCT scans in order to discover new skeletal elements to better characterize the pathological lesions and to quantify the fracture orientation of those bones in which the current plaster reconstruction did not allow its direct visualization, which underlines the broad potential of imaging technologies in paleoanthropological research. A century after its discovery, LF1 is still providing new insights into Neandertal anatomy and behavior.}, } @article {pmid29544620, year = {2018}, author = {Rodríguez, L and Carretero, JM and García-González, R and Arsuaga, JL}, title = {Cross-sectional properties of the lower limb long bones in the Middle Pleistocene Sima de los Huesos sample (Sierra de Atapuerca, Spain).}, journal = {Journal of human evolution}, volume = {117}, number = {}, pages = {1-12}, doi = {10.1016/j.jhevol.2017.11.007}, pmid = {29544620}, issn = {1095-8606}, abstract = {The recovery to date of three complete and five partial femora, seven complete tibiae, and four complete fibulae from the Atapuerca Sima de los Huesos site provides an opportunity to analyze the biomechanical cross-sectional properties in this Middle Pleistocene population and to compare them with those of other fossil hominins and recent modern humans. We have performed direct comparisons of the cross-sectional geometric parameters and reduced major axis (RMA) regression lines among different samples. We have determined that Atapuerca Sima de los Huesos (SH) fossils have significantly thicker cortices than those of recent modern humans for the three leg bones at all diaphyseal levels, except that of the femur at 35% of biomechanical length. The SH bones are similar to those of Neandertals and Middle Pleistocene humans and different from Homo sapiens in their diaphyseal cross-sectional shape and strength parameters. When standardized by estimated body size, both the SH and Neandertal leg bones have in general greater strength than those of H. sapiens from the early modern (EMH), Upper Paleolithic (UP), and recent populations (RH). The Sima de los Huesos human leg bones have, in general terms, an ancestral pattern similar to that of Pleistocene humans and differing from H. sapiens.}, } @article {pmid29531093, year = {2018}, author = {}, title = {Correction for Hoffecker, The complexity of Neanderthal technology.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {13}, pages = {E3066}, doi = {10.1073/pnas.1803330115}, pmid = {29531093}, issn = {1091-6490}, } @article {pmid29507889, year = {2018}, author = {Hoffmann, DL and Angelucci, DE and Villaverde, V and Zapata, J and Zilhão, J}, title = {Symbolic use of marine shells and mineral pigments by Iberian Neandertals 115,000 years ago.}, journal = {Science advances}, volume = {4}, number = {2}, pages = {eaar5255}, pmid = {29507889}, issn = {2375-2548}, abstract = {Cueva de los Aviones (southeast Spain) is a site of the Neandertal-associated Middle Paleolithic of Europe. It has yielded ochred and perforated marine shells, red and yellow colorants, and shell containers that feature residues of complex pigmentatious mixtures. Similar finds from the Middle Stone Age of South Africa have been widely accepted as archaeological proxies for symbolic behavior. U-series dating of the flowstone capping the Cueva de los Aviones deposit shows that the symbolic finds made therein are 115,000 to 120,000 years old and predate the earliest known comparable evidence associated with modern humans by 20,000 to 40,000 years. Given our findings, it is possible that the roots of symbolic material culture may be found among the common ancestor of Neandertals and modern humans, more than half-a-million years ago.}, } @article {pmid29496322, year = {2018}, author = {Gómez-Olivencia, A and Holliday, T and Madelaine, S and Couture-Veschambre, C and Maureille, B}, title = {The costal skeleton of the Regourdou 1 Neandertal.}, journal = {Journal of human evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jhevol.2017.12.005}, pmid = {29496322}, issn = {1095-8606}, abstract = {The morphology and size of the Neandertal thorax is a subject of growing interest due to its link to general aspects of body size and shape, including physiological aspects related to bioenergetics and activity budgets. However, the number of well-preserved adult Neandertal costal remains is still low. The recent finding of new additional costal remains from the Regourdou 1 (R1) skeleton has rendered this skeleton as one of the most complete Neandertal costal skeletons with a minimum of 18 ribs represented, five of which are complete or virtually complete. Here we describe for the first time all the rib remains from R1 and compare them to a large modern Euroamerican male sample as well as to other published Neandertal individuals. The costal skeleton of this individual shows significant metric and morphological differences from our modern human male comparative sample. The perceived differences include: dorsoventrally large 1st and 2nd ribs, 3rd ribs with a very closed dorsal curvature and large maximum diameters at the posterior angle, a large tubercle-iliocostal line distance in the 4th rib, thick shafts at the dorsal end of its 6th ribs, thick mid-shafts of the 8th ribs, large articular tubercles at the 9th ribs, and thick shafts of the 11th and 12th ribs. Here we also describe a new mesosternal fragment: the left lateral half of sternebral segments 4 and 5. This portion reveals that the mesosternum of R1 had a sternal foramen in its inferiormost preserved sternal segment and supports previous estimation of the total length of this mesosternum. The new costal remains from R1 support the view that Neandertals, when compared with modern humans, show a significantly different thorax, consistent with differences found in other anatomical regions such as the vertebral column and pelvis.}, } @article {pmid29477182, year = {2018}, author = {Warren, KA and Ritzman, TB and Humphreys, RA and Percival, CJ and Hallgrímsson, B and Ackermann, RR}, title = {Craniomandibular form and body size variation of first generation mouse hybrids: A model for hominin hybridization.}, journal = {Journal of human evolution}, volume = {116}, number = {}, pages = {57-74}, doi = {10.1016/j.jhevol.2017.12.002}, pmid = {29477182}, issn = {1095-8606}, abstract = {Hybridization occurs in a number of mammalian lineages, including among primate taxa. Analyses of ancient genomes have shown that hybridization between our lineage and other archaic hominins in Eurasia occurred numerous times in the past. However, we still have limited empirical data on what a hybrid skeleton looks like, or how to spot patterns of hybridization among fossils for which there are no genetic data. Here we use experimental mouse models to supplement previous studies of primates. We characterize size and shape variation in the cranium and mandible of three wild-derived inbred mouse strains and their first generation (F1) hybrids. The three parent taxa in our analysis represent lineages that diverged over approximately the same period as the human/Neanderthal/Denisovan lineages and their hybrids are variably successful in the wild. Comparisons of body size, as quantified by long bone measurements, are also presented to determine whether the identified phenotypic effects of hybridization are localized to the cranium or represent overall body size changes. The results indicate that hybrid cranial and mandibular sizes, as well as limb length, exceed that of the parent taxa in all cases. All three F1 hybrid crosses display similar patterns of size and form variation. These results are generally consistent with earlier studies on primates and other mammals, suggesting that the effects of hybridization may be similar across very different scenarios of hybridization, including different levels of hybrid fitness. This paper serves to supplement previous studies aimed at identifying F1 hybrids in the fossil record and to introduce further research that will explore hybrid morphologies using mice as a proxy for better understanding hybridization in the hominin fossil record.}, } @article {pmid29472483, 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 = {U-Th dating of carbonate crusts reveals Neandertal origin of Iberian cave art.}, journal = {Science (New York, N.Y.)}, volume = {359}, number = {6378}, pages = {912-915}, doi = {10.1126/science.aap7778}, pmid = {29472483}, issn = {1095-9203}, mesh = {Animals ; Anthropology, Cultural ; Carbonates/chemistry ; Caves ; History, Ancient ; Humans ; *Neanderthals ; Paintings/*history ; Spain ; Thorium/analysis ; Uranium/analysis ; }, abstract = {The extent and nature of symbolic behavior among Neandertals are obscure. Although evidence for Neandertal body ornamentation has been proposed, all cave painting has been attributed to modern humans. Here we present dating results for three sites in Spain that show that cave art emerged in Iberia substantially earlier than previously thought. Uranium-thorium (U-Th) dates on carbonate crusts overlying paintings provide minimum ages for a red linear motif in La Pasiega (Cantabria), a hand stencil in Maltravieso (Extremadura), and red-painted speleothems in Ardales (Andalucía). Collectively, these results show that cave art in Iberia is older than 64.8 thousand years (ka). This cave art is the earliest dated so far and predates, by at least 20 ka, the arrival of modern humans in Europe, which implies Neandertal authorship.}, } @article {pmid29472458, year = {2018}, author = {Appenzeller, T}, title = {Europe's first artists were Neandertals.}, journal = {Science (New York, N.Y.)}, volume = {359}, number = {6378}, pages = {852-853}, doi = {10.1126/science.359.6378.852}, pmid = {29472458}, issn = {1095-9203}, mesh = {Animals ; Caves ; History, Ancient ; Humans ; *Neanderthals ; Paintings/*history ; Spain ; }, } @article {pmid29447762, year = {2018}, author = {Li, F and Kuhn, SL and Chen, F and Wang, Y and Southon, J and Peng, F and Shan, M and Wang, C and Ge, J and Wang, X and Yun, T and Gao, X}, title = {The easternmost Middle Paleolithic (Mousterian) from Jinsitai Cave, North China.}, journal = {Journal of human evolution}, volume = {114}, number = {}, pages = {76-84}, doi = {10.1016/j.jhevol.2017.10.004}, pmid = {29447762}, issn = {1095-8606}, abstract = {The dispersal of Neanderthals and their genetic and cultural interactions with anatomically modern humans and other hominin populations in Eurasia are critical issues in human evolution research. Neither Neanderthal fossils nor typical Mousterian assemblages have been reported in East Asia to date. Here we report on artifact assemblages comparable to western Eurasian Middle Paleolithic (Mousterian) at Jinsitai, a cave site in North China. The lithic industry at Jinsitai appeared at least 47-42 ka and persisted until around 40-37 ka. These findings expand the geographic range of the Mousterian-like industries at least 2000 km further to the east than what has been previously recognized. This discovery supplies a missing part of the picture of Middle Paleolithic distribution in Eurasia and also demonstrates the makers' capacity to adapt to diverse geographic regions and habitats of Eurasia.}, } @article {pmid29447761, year = {2018}, author = {Kivell, TL and Rosas, A and Estalrrich, A and Huguet, R and García-Tabernero, A and Ríos, L and de la Rasilla, M}, title = {New Neandertal wrist bones from El Sidrón, Spain (1994-2009).}, journal = {Journal of human evolution}, volume = {114}, number = {}, pages = {45-75}, doi = {10.1016/j.jhevol.2017.09.007}, pmid = {29447761}, issn = {1095-8606}, abstract = {Twenty-nine carpal bones of Homo neanderthalensis have been recovered from the site of El Sidrón (Asturias, Spain) during excavations between 1994 and 2009, alongside ∼2500 other Neandertal skeletal elements dated to ∼49,000 years ago. All bones of the wrist are represented, including adult scaphoids (n = 6), lunates (n = 2), triquetra (n = 4), pisiforms (n = 2), trapezia (n = 2), trapezoids (n = 5), capitates (n = 5), and hamates (n = 2), as well as one fragmentary and possibly juvenile scaphoid. Several of these carpals appear to belong to the complete right wrist of a single individual. Here we provide qualitative and quantitative morphological descriptions of these carpals, within a comparative context of other European and Near Eastern Neandertals, early and recent Homo sapiens, and other fossil hominins, including Homo antecessor, Homo naledi, and australopiths. Overall, the El Sidrón carpals show characteristics that typically distinguish Neandertals from H. sapiens, such as a relatively flat first metacarpal facet on the trapezium and a more laterally oriented second metacarpal facet on the capitate. However, there are some distinctive features of the El Sidrón carpals compared with most other Neandertals. For example, the tubercle of the trapezium is small with limited projection, while the scaphoid tubercle and hamate hamulus are among the largest seen in other Neandertals. Furthermore, three of the six adult scaphoids show a distinctive os-centrale portion, while another is a bipartite scaphoid with a truncated tubercle. The high frequency of rare carpal morphologies supports other evidence of a close genetic relationship among the Neandertals found at El Sidrón.}, } @article {pmid29446556, year = {2018}, author = {O'Driscoll, CA and Thompson, JC}, title = {The origins and early elaboration of projectile technology.}, journal = {Evolutionary anthropology}, volume = {27}, number = {1}, pages = {30-45}, doi = {10.1002/evan.21560}, pmid = {29446556}, issn = {1520-6505}, mesh = {Animals ; Bone and Bones/pathology ; History, Ancient ; Humans ; Neanderthals/*physiology ; Predatory Behavior/*physiology ; Technology/*history ; Tool Use Behavior/*physiology ; }, abstract = {The ability of Homo sapiens to kill prey at a distance is arguably one of the catalysts for our current ecological dominance. Many researchers have suggested its origins lie in the African Middle Stone Age or the European Middle Palaeolithic (∼300-30 thousand years ago), but the perishable components of armatures rarely preserve. Most research on this subject therefore emphasises analysis of armature tip size, shape, and diagnostic impacts or residues. Other lines of evidence have included human skeletal anatomy or analyses of the species composition of faunal assemblages. Projectile Impact Marks (PIMs) on archaeofaunal remains offer an ideal complement to this work, but their potential has been restricted mainly to the later Eurasian zooarchaeological record. A review of current evidence and approaches shows that systematic PIM research could add much to our understanding of early projectile technology, especially in Africa.}, } @article {pmid29446440, year = {2018}, author = {Marom, A and Rak, Y}, title = {Mechanical implications of the mandibular coronoid process morphology in Neandertals.}, journal = {American journal of physical anthropology}, volume = {166}, number = {2}, pages = {401-407}, doi = {10.1002/ajpa.23440}, pmid = {29446440}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; Anthropometry ; Finite Element Analysis ; Mandible/*anatomy & histology/*physiology ; Mastication/physiology ; Neanderthals/*anatomy & histology/*physiology ; Temporal Muscle/physiology ; }, abstract = {OBJECTIVES: Among the diagnostic features of the Neandertal mandible are the broad base of the coronoid process and its straight posterior margin. The adaptive value of these (and other) anatomical features has been linked to the Neandertal's need to cope with a large gape. The present study aims to test this hypothesis with regard to the morphology of the coronoid process.

MATERIALS AND METHODS: This admittedly simple, intuitive hypothesis was tested here via a comparative finite-element study of the primitive versus modified state of the coronoid process, using two-dimensional models of the mandible.

RESULTS: Our simulations demonstrate that a large gape has an unfavorable effect on the primitive state of the coronoid process: the diagonal, almost horizontal, component of the temporalis muscle resultant (relative to the long axis of the coronoid process) bends the process in the sagittal plane. Furthermore, we show that the modification of the coronoid process morphology alone reduces the process' bending in a wide gape increasing the compression to tension ratio.

DISCUSSION: These results provide indirect evidence in support of the hypothesis that the modification of the coronoid process in Neandertals is necessary for enabling their mandible to cope with a large gape.}, } @article {pmid29440434, year = {2018}, author = {Hoffecker, JF}, title = {The complexity of Neanderthal technology.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {9}, pages = {1959-1961}, pmid = {29440434}, issn = {1091-6490}, } @article {pmid29432163, year = {2018}, author = {Aranguren, B and Revedin, A and Amico, N and Cavulli, F and Giachi, G and Grimaldi, S and Macchioni, N and Santaniello, F}, title = {Wooden tools and fire technology in the early Neanderthal site of Poggetti Vecchi (Italy).}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {9}, pages = {2054-2059}, pmid = {29432163}, issn = {1091-6490}, abstract = {Excavations for the construction of thermal pools at Poggetti Vecchi (Grosseto, Tuscany, central Italy) exposed a series of wooden tools in an open-air stratified site referable to late Middle Pleistocene. The wooden artifacts were uncovered, together with stone tools and fossil bones, largely belonging to the straight-tusked elephant Paleoloxodon antiquus The site is radiometrically dated to around 171,000 y B.P., and hence correlated with the early marine isotope stage 6 [Benvenuti M, et al. (2017) Quat Res 88:327-344]. The sticks, all fragmentary, are made from boxwood (Buxus sempervirens) and were over 1 m long, rounded at one end and pointed at the other. They have been partially charred, possibly to lessen the labor of scraping boxwood, using a technique so far not documented at the time. The wooden artifacts have the size and features of multipurpose tools known as "digging sticks," which are quite commonly used by foragers. This discovery from Poggetti Vecchi provides evidence of the processing and use of wood by early Neanderthals, showing their ability to use fire in tool making from very tough wood.}, } @article {pmid29417989, year = {2018}, author = {Hanegraef, H and Martinón-Torres, M and Martínez de Pinillos, M and Martín-Francés, L and Vialet, A and Arsuaga, JL and Bermúdez de Castro, JM}, title = {Dentine morphology of Atapuerca-Sima de los Huesos lower molars: Evolutionary implications through three-dimensional geometric morphometric analysis.}, journal = {American journal of physical anthropology}, volume = {166}, number = {2}, pages = {276-295}, doi = {10.1002/ajpa.23428}, pmid = {29417989}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; *Biological Evolution ; Dentin/*anatomy & histology/diagnostic imaging ; Humans ; Imaging, Three-Dimensional ; Molar/anatomy & histology/diagnostic imaging ; Neanderthals/*anatomy & histology ; Odontometry/methods ; Principal Component Analysis ; Spain ; X-Ray Microtomography ; }, abstract = {OBJECTIVES: This study aims to explore the affinities of the Sima de los Huesos (SH) population in relation to Homo neanderthalensis, Arago, and early and contemporary Homo sapiens. By characterizing SH intra-population variation, we test current models to explain the Neanderthal origins.

MATERIALS AND METHODS: Three-dimensional reconstructions of dentine surfaces of lower first and second molars were produced by micro-computed tomography. Landmarks and sliding semilandmarks were subjected to generalized Procrustes analysis and principal components analysis.

RESULTS: SH is often similar in shape to Neanderthals, and both groups are generally discernible from Homo sapiens. For example, the crown height of SH and Neanderthals is lower than for modern humans. Differences in the presence of a mid-trigonid crest are also observed, with contemporary Homo sapiens usually lacking this feature. Although SH and Neanderthals show strong affinities, they can be discriminated based on certain traits. SH individuals are characterized by a lower intra-population variability, and show a derived dental reduction in lower second molars compared to Neanderthals. SH also differs in morphological features from specimens that are often classified as Homo heidelbergensis, such as a lower crown height and less pronounced mid-trigonid crest in the Arago fossils.

DISCUSSION: Our results are compatible with the idea that multiple evolutionary lineages or populations coexisted in Europe during the Middle Pleistocene, with the SH paradigm phylogenetically closer to Homo neanderthalensis. Further research could support the possibility of SH as a separate taxon. Alternatively, SH could be a subspecies of Neanderthals, with the variability of this clade being remarkably higher than previously thought.}, } @article {pmid29409727, year = {2018}, author = {Naskar, T and Faruq, M and Banerjee, P and Khan, M and Midha, R and Kumari, R and Devasenapathy, S and Prajapati, B and Sengupta, S and Jain, D and Mukerji, M and Singh, NC and Sinha, S}, title = {Ancestral Variations of the PCDHG Gene Cluster Predispose to Dyslexia in a Multiplex Family.}, journal = {EBioMedicine}, volume = {28}, number = {}, pages = {168-179}, pmid = {29409727}, issn = {2352-3964}, mesh = {Alleles ; Amino Acid Sequence ; Basal Ganglia/metabolism ; Base Sequence ; Cadherins/chemistry/*genetics ; Chromosome Segregation/genetics ; Dyslexia/*genetics ; Family ; Genes, Dominant ; *Genetic Predisposition to Disease ; *Genetic Variation ; Humans ; Inheritance Patterns/genetics ; Models, Molecular ; *Multigene Family ; Polymorphism, Single Nucleotide/genetics ; Protein Isoforms/chemistry/genetics ; Species Specificity ; Structural Homology, Protein ; }, abstract = {Dyslexia is a heritable neurodevelopmental disorder characterized by difficulties in reading and writing. In this study, we describe the identification of a set of 17 polymorphisms located across 1.9Mb region on chromosome 5q31.3, encompassing genes of the PCDHG cluster, TAF7, PCDH1 and ARHGAP26, dominantly inherited with dyslexia in a multi-incident family. Strikingly, the non-risk form of seven variations of the PCDHG cluster, are preponderant in the human lineage, while risk alleles are ancestral and conserved across Neanderthals to non-human primates. Four of these seven ancestral variations (c.460A>C [p.Ile154Leu], c.541G>A [p.Ala181Thr], c.2036G>C [p.Arg679Pro] and c.2059A>G [p.Lys687Glu]) result in amino acid alterations. p.Ile154Leu and p.Ala181Thr are present at EC2: EC3 interacting interface of γA3-PCDH and γA4-PCDH respectively might affect trans-homophilic interaction and hence neuronal connectivity. p.Arg679Pro and p.Lys687Glu are present within the linker region connecting trans-membrane to extracellular domain. Sequence analysis indicated the importance of p.Ile154, p.Arg679 and p.Lys687 in maintaining class specificity. Thus the observed association of PCDHG genes encoding neural adhesion proteins reinforces the hypothesis of aberrant neuronal connectivity in the pathophysiology of dyslexia. Additionally, the striking conservation of the identified variants indicates a role of PCDHG in the evolution of highly specialized cognitive skills critical to reading.}, } @article {pmid29388957, year = {2018}, author = {Callaway, E}, title = {Israeli fossils are the oldest modern humans ever found outside of Africa.}, journal = {Nature}, volume = {554}, number = {7690}, pages = {15-16}, doi = {10.1038/d41586-018-01261-5}, pmid = {29388957}, issn = {1476-4687}, mesh = {Africa/ethnology ; Animals ; Caves ; China ; *Fossils ; History, Ancient ; Human Migration/*history ; Humans ; Israel ; Jaw/anatomy & histology ; Morocco ; Neanderthals/anatomy & histology ; Phylogeography ; Time Factors ; Tooth/anatomy & histology ; }, } @article {pmid29383489, year = {2018}, author = {Yew, CW and Lu, D and Deng, L and Wong, LP and Ong, RT and Lu, Y and Wang, X and Yunus, Y and Aghakhanian, F and Mokhtar, SS and Hoque, MZ and Voo, CL and Abdul Rahman, T and Bhak, J and Phipps, ME and Xu, S and Teo, YY and Kumar, SV and Hoh, BP}, title = {Genomic structure of the native inhabitants of Peninsular Malaysia and North Borneo suggests complex human population history in Southeast Asia.}, journal = {Human genetics}, volume = {137}, number = {2}, pages = {161-173}, pmid = {29383489}, issn = {1432-1203}, support = {100-RM/BIOTEK 16/6/2 B (1/2011)//Kementerian Sains, Teknologi dan Inovasi (MY)/ ; [100-RMI/GOV 16/6/2 (19/2011]//Kementerian Sains, Teknologi dan Inovasi (MY)/ ; 100-RM/BIOTEK 16/6/2 B (1/2011)//Kementerian Sains, Teknologi dan Inovasi (MY)/ ; 100-RM/BIOTEK 16/6/2 B (1/2011)//Kementerian Sains, Teknologi dan Inovasi (MY)/ ; FRGS/1/2015/ST03/UCSI/01/1//Ministry of Higher Education, Malaysia (MY)/ ; NRF-RF-2010-05//National Foundation for Cancer Research (US)/ ; NRF-RF-2010-05//National Foundation for Cancer Research (US)/ ; NRF-RF-2010-05//National Research Foundation Singapore (SG)/ ; 91331204//National Natural Science Foundation of China (CN)/ ; 31525014//National Natural Science Foundation of China (CN)/ ; 91731303//National Natural Science Foundation of China (CN)/ ; 31771388//National Natural Science Foundation of China (CN)/ ; 31501011//National Natural Science Foundation of China (CN)/ ; 31711530221//National Institutes of Natural Sciences (JP)/ ; 10040231//Industry Strategic Development Program/ ; (1.150014.01)//Ulsan National Institute of Science and Technology (KR)/ ; }, abstract = {Southeast Asia (SEA) is enriched with a complex history of peopling. Malaysia, which is located at the crossroads of SEA, has been recognized as one of the hubs for early human migration. To unravel the genomic complexity of the native inhabitants of Malaysia, we sequenced 12 samples from 3 indigenous populations from Peninsular Malaysia and 4 native populations from North Borneo to a high coverage of 28-37×. We showed that the Negritos from Peninsular Malaysia shared a common ancestor with the East Asians, but exhibited some level of gene flow from South Asia, while the North Borneo populations exhibited closer genetic affinity towards East Asians than the Malays. The analysis of time of divergence suggested that ancestors of Negrito were the earliest settlers in the Malay Peninsula, whom first separated from the Papuans ~ 50-33 thousand years ago (kya), followed by East Asian (~ 40-15 kya), while the divergence time frame between North Borneo and East Asia populations predates the Austronesian expansion period implies a possible pre-Neolithic colonization. Substantial Neanderthal ancestry was confirmed in our genomes, as was observed in other East Asians. However, no significant difference was observed, in terms of the proportion of Denisovan gene flow into these native inhabitants from Malaysia. Judging from the similar amount of introgression in the Southeast Asians and East Asians, our findings suggest that the Denisovan gene flow may have occurred before the divergence of these populations and that the shared similarities are likely an ancestral component.}, } @article {pmid29372121, year = {2018}, author = {Xing, S and Carlson, KJ and Wei, P and He, J and Liu, W}, title = {Morphology and structure of Homo erectus humeri from Zhoukoudian, Locality 1.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e4279}, pmid = {29372121}, issn = {2167-8359}, abstract = {Background: Regional diversity in the morphology of the H. erectus postcranium is not broadly documented, in part, because of the paucity of Asian sites preserving postcranial fossils. Yet, such an understanding of the initial hominin taxon to spread throughout multiple regions of the world is fundamental to documenting the adaptive responses to selective forces operating during this period of human evolution.

Methods: The current study reports the first humeral rigidity and strength properties of East Asian H. erectus and places its diaphyseal robusticity into broader regional and temporal contexts. We estimate true cross-sectional properties of Zhoukoudian Humerus II and quantify new diaphyseal properties of Humerus III using high resolution computed tomography. Comparative data for African H. erectus and Eurasian Late Pleistocene H. sapiens were assembled, and new data were generated from two modern Chinese populations.

Results: Differences between East Asian and African H. erectus were inconsistently expressed in humeral cortical thickness. In contrast, East Asian H. erectus appears to exhibit greater humeral robusticity compared to African H. erectus when standardizing diaphyseal properties by the product of estimated body mass and humeral length. East Asian H. erectus humeri typically differed less in standardized properties from those of side-matched Late Pleistocene hominins (e.g., Neanderthals and more recent Upper Paleolithic modern humans) than did African H. erectus, and often fell in the lower range of Late Pleistocene humeral rigidity or strength properties.

Discussion: Quantitative comparisons indicate that regional variability in humeral midshaft robusticity may characterize H. erectus to a greater extent than presently recognized. This may suggest a temporal difference within H. erectus, or possibly different ecogeographical trends and/or upper limb loading patterns across the taxon. Both discovery and analysis of more adult H. erectus humeri are critical to further evaluating and potentially distinguishing between these possibilities.}, } @article {pmid29355893, year = {2018}, author = {Relethford, JH and Smith, FH}, title = {Cranial measures and ancient DNA both show greater similarity of Neandertals to recent modern Eurasians than to recent modern sub-Saharan Africans.}, journal = {American journal of physical anthropology}, volume = {166}, number = {1}, pages = {170-178}, doi = {10.1002/ajpa.23413}, pmid = {29355893}, issn = {1096-8644}, mesh = {*African Continental Ancestry Group/genetics/statistics & numerical data ; Animals ; Anthropology, Physical ; Cephalometry ; DNA, Ancient/*analysis ; *European Continental Ancestry Group/genetics/statistics & numerical data ; Female ; Humans ; Male ; *Neanderthals/anatomy & histology/genetics ; Skull/*anatomy & histology ; }, abstract = {OBJECTIVES: Ancient DNA analysis has shown that present-day humans of Eurasian ancestry are more similar to Neandertals than are present-day humans of sub-Saharan African ancestry, reflecting interbreeding after modern humans first left Africa. We use craniometric data to test the hypothesis that the crania of recent modern humans show the same pattern.

MATERIALS AND METHODS: We computed Mahalanobis squared distances between a published Neandertal centroid based on 37 craniometric traits and each of 2,413 recent modern humans from the Howells global data set (N = 373 sub-Saharan Africans, N = 2,040 individuals of Eurasian descent).

RESULTS: The average distance to the Neandertal centroid is significantly lower for Eurasian crania than for sub-Saharan African crania as expected from the findings of ancient DNA (p < 0.001). This result holds when examining distances for separate geographic regions of humans of Eurasian descent (Europeans, Asians, Australasians, Native Americans, and Pacific Islanders). Most of these results are also seen when examining distances partitioning size and shape variation.

DISCUSSION: Our results show that the genetic difference in Neandertal ancestry seen in the DNA of present-day sub-Saharan Africans and Eurasians is also found in patterns of recent modern human craniometric variation.}, } @article {pmid29351319, year = {2018}, author = {Cataldo, DM and Migliano, AB and Vinicius, L}, title = {Speech, stone tool-making and the evolution of language.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0191071}, pmid = {29351319}, issn = {1932-6203}, mesh = {Animals ; *Anthropology ; Humans ; *Language ; Neanderthals ; *Speech ; *Tool Use Behavior ; }, abstract = {The 'technological hypothesis' proposes that gestural language evolved in early hominins to enable the cultural transmission of stone tool-making skills, with speech appearing later in response to the complex lithic industries of more recent hominins. However, no flintknapping study has assessed the efficiency of speech alone (unassisted by gesture) as a tool-making transmission aid. Here we show that subjects instructed by speech alone underperform in stone tool-making experiments in comparison to subjects instructed through either gesture alone or 'full language' (gesture plus speech), and also report lower satisfaction with their received instruction. The results provide evidence that gesture was likely to be selected over speech as a teaching aid in the earliest hominin tool-makers; that speech could not have replaced gesturing as a tool-making teaching aid in later hominins, possibly explaining the functional retention of gesturing in the full language of modern humans; and that speech may have evolved for reasons unrelated to tool-making. We conclude that speech is unlikely to have evolved as tool-making teaching aid superior to gesture, as claimed by the technological hypothesis, and therefore alternative views should be considered. For example, gestural language may have evolved to enable tool-making in earlier hominins, while speech may have later emerged as a response to increased trade and more complex inter- and intra-group interactions in Middle Pleistocene ancestors of Neanderthals and Homo sapiens; or gesture and speech may have evolved in parallel rather than in sequence.}, } @article {pmid29292345, year = {2017}, author = {d'Errico, F and Doyon, L and Colagé, I and Queffelec, A and Le Vraux, E and Giacobini, G and Vandermeersch, B and Maureille, B}, title = {From number sense to number symbols. An archaeological perspective.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {373}, number = {1740}, pages = {}, pmid = {29292345}, issn = {1471-2970}, support = {249587//European Research Council/International ; }, mesh = {Animals ; Archaeology ; Bone and Bones ; *Cognition ; *Cultural Evolution ; Hominidae/psychology ; Humans ; Models, Psychological ; Neanderthals/*psychology ; }, abstract = {How and when did hominins move from the numerical cognition that we share with the rest of the animal world to number symbols? Objects with sequential markings have been used to store and retrieve numerical information since the beginning of the European Upper Palaeolithic (42 ka). An increase in the number of markings and complexity of coding is observed towards the end of this period. The application of new analytical techniques to a 44-42 ka old notched baboon fibula from Border Cave, South Africa, shows that notches were added to this bone at different times, suggesting that devices to store numerical information were in use before the Upper Palaeolithic. Analysis of a set of incisions on a 72-60 ka old hyena femur from the Les Pradelles Mousterian site, France, indicates, by comparison with markings produced by modern subjects under similar constraints, that the incisions on the Les Pradelles bone may have been produced to record, in a single session, homologous units of numerical information. This finding supports the view that numerical notations were in use among archaic hominins. Based on these findings, a testable five-stage scenario is proposed to establish how prehistoric cultures have moved from number sense to the use of number symbols.This article is part of a discussion meeting issue 'The origins of numerical abilities'.}, } @article {pmid29285967, year = {2017}, author = {Berens, AJ and Cooper, TL and Lachance, J}, title = {The Genomic Health of Ancient Hominins.}, journal = {Human biology}, volume = {89}, number = {1}, pages = {7-19}, pmid = {29285967}, issn = {1534-6617}, mesh = {Animals ; DNA Primers ; DNA, Mitochondrial/classification/genetics ; Evolution, Molecular ; Gene Library ; Genetic Association Studies ; Genetic Predisposition to Disease/classification/*genetics/history ; Genetic Variation/*genetics ; Genomics ; Geography/classification/history ; History, Ancient ; Hominidae/*genetics ; Humans ; Neanderthals/genetics ; Phylogeny ; }, abstract = {The genomes of ancient humans, Neandertals, and Denisovans contain many alleles that influence disease risks. Using genotypes at 3,180 disease-associated loci, we estimated the disease burden of 147 ancient genomes. After correcting for missing data, genetic risk scores (GRS) were generated for nine disease categories and the set of all combined diseases. We used these genetic risk scores to examine the effects of different types of subsistence, geography, and sample age on the number of risk alleles in each ancient genome. On a broad scale, hereditary disease risks are similar for ancient hominins and modern-day humans, and the GRS percentiles of ancient individuals span the full range of what is observed in present-day individuals. In addition, there is evidence that ancient pastoralists may have had healthier genomes than hunter-gatherers and agriculturalists. We also observed a temporal trend whereby genomes from the recent past are more likely to be healthier than genomes from the deep past. This calls into question the idea that modern lifestyles have caused genetic load to increase over time. Focusing on individual genomes, we found that the overall genomic health of the Altai Neandertal is worse than 97% of present-day humans and that Ötzi, the Tyrolean Iceman, had a genetic predisposition for gastrointestinal and cardiovascular diseases. As demonstrated by this work, ancient genomes afford us new opportunities to diagnose past human health, which has previously been limited by the quality and completeness of remains.}, } @article {pmid29284020, year = {2017}, author = {Frost, P and Kleisner, K and Flegr, J}, title = {Health status by gender, hair color, and eye color: Red-haired women are the most divergent.}, journal = {PloS one}, volume = {12}, number = {12}, pages = {e0190238}, pmid = {29284020}, issn = {1932-6203}, mesh = {Czech Republic ; *Eye Color ; Female ; *Hair Color ; *Health Status ; Humans ; Male ; *Sex Factors ; Slovakia ; }, abstract = {Red hair is associated in women with pain sensitivity. This medical condition, and perhaps others, seems facilitated by the combination of being red-haired and female. We tested this hypothesis by questioning a large sample of Czech and Slovak respondents about the natural redness and darkness of their hair, their natural eye color, their physical and mental health (24 categories), and other personal attributes (height, weight, number of children, lifelong number of sexual partners, frequency of smoking). Red-haired women did worse than other women in ten health categories and better in only three, being particularly prone to colorectal, cervical, uterine, and ovarian cancer. Red-haired men showed a balanced pattern, doing better than other men in three health categories and worse in three. Number of children was the only category where both male and female redheads did better than other respondents. We also confirmed earlier findings that red hair is naturally more frequent in women than in men. Of the 'new' hair and eye colors, red hair diverges the most from the ancestral state of black hair and brown eyes, being the most sexually dimorphic variant not only in population frequency but also in health status. This divergent health status may have one or more causes: direct effects of red hair pigments (pheomelanins) or their by-products; effects of other genes that show linkage with genes involved in pheomelanin production; excessive prenatal exposure to estrogen (which facilitates expression of red hair during fetal development and which, at high levels, may cause health problems later in life); evolutionary recentness of red hair and corresponding lack of time to correct negative side effects; or genetic incompatibilities associated with the allele Val92Met, which seems to be of Neanderthal origin and is one of the alleles that can cause red hair.}, } @article {pmid29265662, year = {2017}, author = {Lozano, M and Estalrrich, A and Bondioli, L and Fiore, I and Bermúdez de Castro, JM and Arsuaga, JL and Carbonell, E and Rosas, A and Frayer, DW}, title = {Right-handed fossil humans.}, journal = {Evolutionary anthropology}, volume = {26}, number = {6}, pages = {313-324}, doi = {10.1002/evan.21554}, pmid = {29265662}, issn = {1520-6505}, mesh = {Adolescent ; Adult ; Animals ; Anthropology, Physical ; Child ; Female ; *Fossils ; Functional Laterality/*physiology ; Hominidae/physiology ; Humans ; Male ; Neanderthals/*physiology ; Technology ; Tool Use Behavior ; Tooth/*pathology ; Young Adult ; }, abstract = {Fossil hominids often processed material held between their upper and lower teeth. Pulling with one hand and cutting with the other, they occasionally left impact cut marks on the lip (labial) surface of their incisors and canines. From these actions, it possible to determine the dominant hand used. The frequency of these oblique striations in an array of fossil hominins documents the typically modern pattern of 9 right- to 1 left-hander. This ratio among living Homo sapiens differs from that among chimpanzees and bonobos and more distant primate relatives. Together, all studies of living people affirm that dominant right-handedness is a uniquely modern human trait. The same pattern extends deep into our past. Thus far, the majority of inferred right-handed fossils come from Europe, but a single maxilla from a Homo habilis, OH-65, shows a predominance of right oblique scratches, thus extending right-handedness into the early Pleistocene of Africa. Other studies show right-handedness in more recent African, Chinese, and Levantine fossils, but the sample compiled for non-European fossil specimens remains small. Fossil specimens from Sima del los Huesos and a variety of European Neandertal sites are predominately right-handed. We argue the 9:1 handedness ratio in Neandertals and the earlier inhabitants of Europe constitutes evidence for a modern pattern of handedness well before the appearance of modern Homo sapiens.}, } @article {pmid29234166, year = {2018}, author = {Chikhi, L and Rodríguez, W and Grusea, S and Santos, P and Boitard, S and Mazet, O}, title = {The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: insights into demographic inference and model choice.}, journal = {Heredity}, volume = {120}, number = {1}, pages = {13-24}, pmid = {29234166}, issn = {1365-2540}, mesh = {*Algorithms ; Animals ; Gene Flow ; *Genetic Variation ; Genetics, Population ; Genome/*genetics ; Haploidy ; Humans ; *Models, Genetic ; Population Density ; Population Dynamics ; Time Factors ; }, abstract = {Several inferential methods using genomic data have been proposed to quantify and date population size changes in the history of species. At the same time an increasing number of studies have shown that population structure can generate spurious signals of population size change. Recently, Mazet et al. (2016) introduced, for a sample size of two, a time-dependent parameter, which they called the IICR (inverse instantaneous coalescence rate). The IICR is equivalent to a population size in panmictic models, but not necessarily in structured models. It is characterised by a temporal trajectory that suggests population size changes, as a function of the sampling scheme, even when the total population size was constant. Here, we extend the work of Mazet et al. (2016) by (i) showing how the IICR can be computed for any demographic model of interest, under the coalescent, (ii) applying this approach to models of population structure (1D and 2D stepping stone, split models, two- and three-island asymmetric gene flow, continent-island models), (iii) stressing the importance of the sampling strategy in generating different histories, (iv) arguing that IICR plots can be seen as summaries of genomic information that can thus be used for model choice or model exclusion (v) applying this approach to the question of admixture between humans and Neanderthals. Altogether these results are potentially important given that the widely used PSMC (pairwise sequentially Markovian coalescent) method of Li and Durbin (2011) estimates the IICR of the sample, not necessarily the history of the populations.}, } @article {pmid29216284, year = {2017}, author = {Falcucci, A and Conard, NJ and Peresani, M}, title = {A critical assessment of the Protoaurignacian lithic technology at Fumane Cave and its implications for the definition of the earliest Aurignacian.}, journal = {PloS one}, volume = {12}, number = {12}, pages = {e0189241}, pmid = {29216284}, issn = {1932-6203}, mesh = {Animals ; France ; *Geology ; History, Ancient ; Italy ; Neanderthals ; }, abstract = {In the scenario of the spread of the anatomically modern humans (AMHs) into Europe, the techno-complex known as Protoaurignacian is defined by the production of blades and bladelets within a single and continuous stone knapping sequence from the same core as the result of its progressive reduction. However, the growing re-evaluation of some assemblages is revealing that bladelets are frequently obtained from independent reduction sequences, hence discouraging the direct application of the model developed in southwestern France. High-resolution regional signatures are thus needed to reconstruct a more accurate portrait of the AMH colonization dynamic. Northeastern Italy, with the key site of Fumane Cave, is one among the regions of Mediterranean Europe worthy of consideration for reconstructing this colonization process and its cultural dynamics. Within the framework of a critical discussion of the technological definition of the Protoaurignacian and its relationship with contemporaneous industries on a regional and supra-regional scale, we present the results of a detailed analysis of the lithic technology from units A2-A1 based on reduction sequence and attribute analyses. Results show that bladelets are the first goal of production and they do not originate from reduced blade cores but from a broad range of independent and simultaneous core reduction strategies. One implication is that the most commonly used technological trait that is said to define the Protoaurignacian has been over-emphasized and that the Protoaurignacian is technologically consistent across its geographical extent. Additional data based on carinated core technology imply that this techno-complex shares a common technological background with the Early Aurignacian and that no features are restricted to one of the two facies. Furthermore, the major difference between the Protoaurignacian and Early Aurignacian appears to be more typological in nature, with retouched bladelets being less common in the Early Aurignacian.}, } @article {pmid29188235, year = {2017}, author = {Zilhão, J and Anesin, D and Aubry, T and Badal, E and Cabanes, D and Kehl, M and Klasen, N and Lucena, A and Martín-Lerma, I and Martínez, S and Matias, H and Susini, D and Steier, P and Wild, EM and Angelucci, DE and Villaverde, V and Zapata, J}, title = {Precise dating of the Middle-to-Upper Paleolithic transition in Murcia (Spain) supports late Neandertal persistence in Iberia.}, journal = {Heliyon}, volume = {3}, number = {11}, pages = {e00435}, pmid = {29188235}, issn = {2405-8440}, abstract = {The late persistence in Southern Iberia of a Neandertal-associated Middle Paleolithic is supported by the archeological stratigraphy and the radiocarbon and luminescence dating of three newly excavated localities in the Mula basin of Murcia (Spain). At Cueva Antón, Mousterian layer I-k can be no more than 37,100 years-old. At La Boja, the basal Aurignacian can be no less than 36,500 years-old. The regional Middle-to-Upper Paleolithic transition process is thereby bounded to the first half of the 37th millennium Before Present, in agreement with evidence from Andalusia, Gibraltar and Portugal. This chronology represents a lag of minimally 3000 years with the rest of Europe, where that transition and the associated process of Neandertal/modern human admixture took place between 40,000 and 42,000 years ago. The lag implies the presence of an effective barrier to migration and diffusion across the Ebro river depression, which, based on available paleoenvironmental indicators, would at that time have represented a major biogeographical divide. In addition, (a) the Phlegraean Fields caldera explosion, which occurred 39,850 years ago, would have stalled the Neandertal/modern human admixture front because of the population sink it generated in Central and Eastern Europe, and (b) the long period of ameliorated climate that came soon after (Greenland Interstadial 8, during which forests underwent a marked expansion in Iberian regions south of 40°N) would have enhanced the "Ebro Frontier" effect. These findings have two broader paleoanthropological implications: firstly, that, below the Ebro, the archeological record made prior to 37,000 years ago must be attributed, in all its aspects and components, to the Neandertals (or their ancestors); secondly, that modern human emergence is best seen as an uneven, punctuated process during which long-lasting barriers to gene flow and cultural diffusion could have existed across rather short distances, with attendant consequences for ancient genetics and models of human population history.}, } @article {pmid29169679, year = {2018}, author = {Young, M and Johannesdottir, F and Poole, K and Shaw, C and Stock, JT}, title = {Assessing the accuracy of body mass estimation equations from pelvic and femoral variables among modern British women of known mass.}, journal = {Journal of human evolution}, volume = {115}, number = {}, pages = {130-139}, doi = {10.1016/j.jhevol.2017.10.011}, pmid = {29169679}, issn = {1095-8606}, abstract = {Femoral head diameter is commonly used to estimate body mass from the skeleton. The three most frequently employed methods, designed by Ruff, Grine, and McHenry, were developed using different populations to address different research questions. They were not specifically designed for application to female remains, and their accuracy for this purpose has rarely been assessed or compared in living populations. This study analyzes the accuracy of these methods using a sample of modern British women through the use of pelvic CT scans (n = 97) and corresponding information about the individuals' known height and weight. Results showed that all methods provided reasonably accurate body mass estimates (average percent prediction errors under 20%) for the normal weight and overweight subsamples, but were inaccurate for the obese and underweight subsamples (average percent prediction errors over 20%). When women of all body mass categories were combined, the methods provided reasonable estimates (average percent prediction errors between 16 and 18%). The results demonstrate that different methods provide more accurate results within specific body mass index (BMI) ranges. The McHenry Equation provided the most accurate estimation for women of small body size, while the original Ruff Equation is most likely to be accurate if the individual was obese or severely obese. The refined Ruff Equation was the most accurate predictor of body mass on average for the entire sample, indicating that it should be utilized when there is no knowledge of the individual's body size or if the individual is assumed to be of a normal body size. The study also revealed a correlation between pubis length and body mass, and an equation for body mass estimation using pubis length was accurate in a dummy sample, suggesting that pubis length can also be used to acquire reliable body mass estimates. This has implications for how we interpret body mass in fossil hominins and has particular relevance to the interpretation of the long pubic ramus that is characteristic of Neandertals.}, } @article {pmid29166384, year = {2017}, author = {Marín, J and Saladié, P and Rodríguez-Hidalgo, A and Carbonell, E}, title = {Neanderthal hunting strategies inferred from mortality profiles within the Abric Romaní sequence.}, journal = {PloS one}, volume = {12}, number = {11}, pages = {e0186970}, pmid = {29166384}, issn = {1932-6203}, mesh = {Aging ; Animals ; Mammals/*physiology ; Mandible/anatomy & histology ; *Mortality ; Neanderthals/*physiology ; *Paleontology ; Predatory Behavior/*physiology ; Reference Standards ; Spain ; Tooth/anatomy & histology ; Tooth Crown/anatomy & histology ; }, abstract = {Ungulate mortality profiles are commonly used to study Neanderthal subsistence strategies. To assess the hunting strategies used by Neanderthals, we studied the ages at death of the cervids and equids found in levels E, H, I, Ja, Jb, K, L and M of the Abric Romaní sequence. These levels date between 43.2 ± 1.1 ka BP (14C AMS) and 54.5 ± 1.7 ka BP (U-series). The degree of eruption and development of the teeth and their wear stages were used to determine the ages of these animals at death, and mortality profiles were constructed using these data. The equids display prime dominated profiles in all of the analyzed levels, whereas the cervids display variable profiles. These results suggest that the Neanderthals of Abric Romaní employed both selective and non-selective hunting strategies. The selective strategy focused on the hunting of prime adults and generated prime dominated profiles. On the other hand, non-selective strategies, involved the consumption of animals of variable ages, resulting in catastrophic profiles. It is likely that in the selective hunting events were conducted using selective ambushes in which it was possible to select specific prey animals. On the other hand, encounter hunting or non-selective ambush hunting may have also been used at times, based on the abundances of prey animals and encounter rates. Specific hunting strategies would have been developed accordance with the taxa and the age of the individual to be hunted. The hunting groups most likely employed cooperative hunting techniques, especially in the capture of large animals. Thus, it is not possible to uniquely associate a single mortality profile with the predation tactics of Neanderthals at Abric Romaní.}, } @article {pmid29165618, year = {2018}, author = {Novakowski, KE and Yap, NVL and Yin, C and Sakamoto, K and Heit, B and Golding, GB and Bowdish, DME}, title = {Human-Specific Mutations and Positively Selected Sites in MARCO Confer Functional Changes.}, journal = {Molecular biology and evolution}, volume = {35}, number = {2}, pages = {440-450}, pmid = {29165618}, issn = {1537-1719}, support = {R15 AI094436/AI/NIAID NIH HHS/United States ; MOP-123419//CIHR/Canada ; }, mesh = {Animals ; HEK293 Cells ; Humans ; Mutation ; Phagocytosis/*genetics ; Receptors, Immunologic/*genetics/metabolism ; *Selection, Genetic ; }, abstract = {Macrophage Receptor with COllagenous structure (MARCO) is a class A scavenger receptor that binds, phagocytoses, and modifies inflammatory responses to bacterial pathogens. Multiple candidate gene approach studies have shown that polymorphisms in MARCO are associated with susceptibility or resistance to Mycobacterium tuberculosis infection, but how these variants alter function is not known. To complement candidate gene approach studies, we previously used phylogenetic analyses to identify a residue, glutamine 452 (Q452), within the ligand-binding Scavenger Receptor Cysteine Rich domain as undergoing positive selection in humans. Herein, we show that Q452 is found in Denisovans, Neanderthals, and extant humans, but all other nonprimate, terrestrial, and aquatic mammals possess an aspartic acid (D452) residue. Further analysis of hominoid sequences of MARCO identified an additional human-specific mutation, phenylalanine 282 (F282), within the collagenous domain. We show that residue 282 is polymorphic in humans, but only 17% of individuals (rs6761637) possess the ancestral serine residue at position 282. We show that rs6761637 is in linkage disequilibrium with MARCO polymorphisms that have been previously linked to susceptibility to pulmonary tuberculosis. To assess the functional importance of sites Q452 and F282 in humans, we cloned the ancestral residues and loss-of-function mutations and investigated the role of these residues in binding and internalizing polystyrene microspheres and Escherichia coli. Herein, we show that the residues at sites 452 and 282 enhance receptor function.}, } @article {pmid29138326, year = {2017}, author = {Mafessoni, F and Prüfer, K}, title = {Better support for a small effective population size of Neandertals and a long shared history of Neandertals and Denisovans.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {48}, pages = {E10256-E10257}, pmid = {29138326}, issn = {1091-6490}, mesh = {Animals ; Biological Evolution ; Fossils ; Hominidae ; *Neanderthals ; *Population Density ; }, } @article {pmid29089499, year = {2017}, author = {Kolodny, O and Feldman, MW}, title = {A parsimonious neutral model suggests Neanderthal replacement was determined by migration and random species drift.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {1040}, pmid = {29089499}, issn = {2041-1723}, mesh = {Africa ; Animal Migration ; Animals ; Computer Simulation ; Europe ; Humans ; Neanderthals/*physiology ; Transients and Migrants ; }, abstract = {Most hypotheses in the heated debate about the Neanderthals' replacement by modern humans highlight the role of environmental pressures or attribute the Neanderthals' demise to competition with modern humans, who occupied the same ecological niche. The latter assume that modern humans benefited from some selective advantage over Neanderthals, which led to the their extinction. Here we show that a scenario of migration and selectively neutral species drift predicts the Neanderthals' replacement. Our model offers a parsimonious alternative to those that invoke external factors or selective advantage, and represents a null hypothesis for assessing such alternatives. For a wide range of parameters, this hypothesis cannot be rejected. Moreover, we suggest that although selection and environmental factors may or may not have played a role in the inter-species dynamics of Neanderthals and modern humans, the eventual replacement of the Neanderthals was determined by the repeated migration of modern humans from Africa into Eurasia.}, } @article {pmid29087302, year = {2017}, author = {de Azevedo, S and González, MF and Cintas, C and Ramallo, V and Quinto-Sánchez, M and Márquez, F and Hünemeier, T and Paschetta, C and Ruderman, A and Navarro, P and Pazos, BA and Silva de Cerqueira, CC and Velan, O and Ramírez-Rozzi, F and Calvo, N and Castro, HG and Paz, RR and González-José, R}, title = {Nasal airflow simulations suggest convergent adaptation in Neanderthals and modern humans.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {47}, pages = {12442-12447}, pmid = {29087302}, issn = {1091-6490}, mesh = {Acclimatization/*physiology ; Animals ; Anthropology ; Cold Climate ; *Computer Simulation ; Fossils ; Neanderthals/anatomy & histology/*physiology ; Nose/anatomy & histology/*physiology ; Respiration ; Species Specificity ; }, abstract = {Both modern humans (MHs) and Neanderthals successfully settled across western Eurasian cold-climate landscapes. Among the many adaptations considered as essential to survival in such landscapes, changes in the nasal morphology and/or function aimed to humidify and warm the air before it reaches the lungs are of key importance. Unfortunately, the lack of soft-tissue evidence in the fossil record turns difficult any comparative study of respiratory performance. Here, we reconstruct the internal nasal cavity of a Neanderthal plus two representatives of climatically divergent MH populations (southwestern Europeans and northeastern Asians). The reconstruction includes mucosa distribution enabling a realistic simulation of the breathing cycle in different climatic conditions via computational fluid dynamics. Striking across-specimens differences in fluid residence times affecting humidification and warming performance at the anterior tract were found under cold/dry climate simulations. Specifically, the Asian model achieves a rapid air conditioning, followed by the Neanderthals, whereas the European model attains a proper conditioning only around the medium-posterior tract. In addition, quantitative-genetic evolutionary analyses of nasal morphology provided signals of stabilizing selection for MH populations, with the removal of Arctic populations turning covariation patterns compatible with evolution by genetic drift. Both results indicate that, departing from important craniofacial differences existing among Neanderthals and MHs, an advantageous species-specific respiratory performance in cold climates may have occurred in both species. Fluid dynamics and evolutionary biology independently provided evidence of nasal evolution, suggesting that adaptive explanations regarding complex functional phenotypes require interdisciplinary approaches aimed to quantify both performance and evolutionary signals on covariation patterns.}, } @article {pmid29074745, year = {2017}, author = {Gibbons, A}, title = {Neandertals gave 'lost' African DNA back to moderns.}, journal = {Science (New York, N.Y.)}, volume = {358}, number = {6362}, pages = {431}, doi = {10.1126/science.358.6362.431}, pmid = {29074745}, issn = {1095-9203}, mesh = {African Continental Ancestry Group/genetics ; Alleles ; Animals ; Asian Continental Ancestry Group/*genetics ; *DNA, Ancient ; European Continental Ancestry Group/*genetics ; Humans ; Neanderthals/*genetics ; Smoking/*genetics ; Waist Circumference/*genetics ; }, } @article {pmid29054166, year = {2017}, author = {Buti, L and Le Cabec, A and Panetta, D and Tripodi, M and Salvadori, PA and Hublin, JJ and Feeney, RNM and Benazzi, S}, title = {3D enamel thickness in Neandertal and modern human permanent canines.}, journal = {Journal of human evolution}, volume = {113}, number = {}, pages = {162-172}, pmid = {29054166}, issn = {1095-8606}, mesh = {Animals ; Dental Enamel/*anatomy & histology ; Fossils/*anatomy & histology ; Humans ; Imaging, Three-Dimensional ; Molar/*anatomy & histology ; Neanderthals/*anatomy & histology ; *Paleodontology ; Tooth/*anatomy & histology ; X-Ray Microtomography/*methods ; }, abstract = {Enamel thickness figures prominently in studies of human evolution, particularly for taxonomy, phylogeny, and paleodietary reconstruction. Attention has focused on molar teeth, through the use of advanced imaging technologies and novel protocols. Despite the important results achieved thus far, further work is needed to investigate all tooth classes. We apply a recent approach developed for anterior teeth to investigate the 3D enamel thickness of Neandertal and modern human (MH) canines. In terms of crown size, the values obtained for both upper and lower unworn/slightly worn canines are significantly greater in Neandertals than in Upper Paleolithic and recent MH. The 3D relative enamel thickness (RET) is significantly lower in Neandertals than in MH. Moreover, differences in 3D RET values between the two groups appear to decrease in worn canines beginning from wear stage 3, suggesting that both the pattern and the stage of wear may have important effects on the 3D RET value. Nevertheless, the 3D average enamel thickness (AET) does not differ between the two groups. In both groups, 3D AET and 3D RET indices are greater in upper canines than in lower canines, and overall the enamel is thicker on the occlusal half of the labial aspect of the crown, particularly in MH. By contrast, the few early modern humans investigated show the highest volumes of enamel while for all other components of 3D enamel, thickness this group holds an intermediate position between Neandertals and recent MH. Overall, our study supports the general findings that Neandertals have relatively thinner enamel than MH (as also observed in molars), indicating that unworn/slightly worn canines can be successfully used to discriminate between the two groups. Further studies, however, are needed to understand whether these differences are functionally related or are the result of pleiotropic or genetic drift effects.}, } @article {pmid29053746, year = {2017}, author = {Trinkaus, E and Villotte, S}, title = {External auditory exostoses and hearing loss in the Shanidar 1 Neandertal.}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0186684}, pmid = {29053746}, issn = {1932-6203}, mesh = {Animals ; *Ear, External ; *Exostoses ; *Fossils ; *Hearing Loss, Conductive ; *Hominidae ; *Neanderthals ; }, abstract = {The Late Pleistocene Shanidar 1 older adult male Neandertal is known for the crushing fracture of his left orbit with a probable reduction in vision, the loss of his right forearm and hand, and evidence of an abnormal gait, as well as probable diffuse idiopathic skeletal hyperostosis. He also exhibits advanced external auditory exostoses in his left auditory meatus and larger ones with complete bridging across the porus in the right meatus (both Grade 3). These growths indicate at least unilateral conductive hearing (CHL) loss, a serious sensory deprivation for a Pleistocene hunter-gatherer. This condition joins the meatal atresia of the Middle Pleistocene Atapuerca-SH Cr.4 in providing evidence of survival with conductive hearing loss (and hence serious sensory deprivation) among these Pleistocene humans. The presence of CHL in these fossils thereby reinforces the paleobiological and archeological evidence for supporting social matrices among these Pleistocene foraging peoples.}, } @article {pmid29053710, year = {2017}, author = {Soriano, S and Villa, P}, title = {Early Levallois and the beginning of the Middle Paleolithic in central Italy.}, journal = {PloS one}, volume = {12}, number = {10}, pages = {e0186082}, pmid = {29053710}, issn = {1932-6203}, mesh = {Animals ; *Archaeology ; Italy ; Neanderthals ; }, abstract = {In the second half of the 19th century Pleistocene faunas were discovered in two sites, Sedia del Diavolo and Monte delle Gioie, contained in deposits of the Aniene River in the area of Rome (Latium, Italy). Fieldwork by A.C. Blanc in the late 1930's proved the association of fauna and lithic industry within fluvial deposits interbedded with volcanoclastic layers. A human femoral diaphysis and a metatarsal were later identified in the faunal assemblage from Sedia del Diavolo and evaluated as Neandertal. The lithic assemblages from these two sites were the basis of the definition of the Protopontinian by M. Taschini, which she viewed as a late Middle Pleistocene industry very similar to the later, Upper Pleistocene Pontinian industries, thought to be characteristic of the Latium Mousterian. The chronostratigraphic framework of the Aniene river deposits has been recently updated and the lithic assemblages from these two sites are now confidently dated between 295 and 290 ka, close to the transition from MIS 9 to MIS 8. They fit chronologically between the industries of layers m and d from Torre in Pietra, a site 26 km northwest of Rome. The presence of the Levallois debitage is indisputable yet it occurs within an original technical context, different from what is known in other early occurrences of the Levallois. The date confirms the proposed chronology for the early Levallois in Europe. More importantly these two assemblages demonstrate that this technology can emerge in more diversified contexts than usually described. This suggests that its dispersal in Europe may have been rapid.}, } @article {pmid29040546, year = {2017}, author = {Taskent, RO and Alioglu, ND and Fer, E and Melike Donertas, H and Somel, M and Gokcumen, O}, title = {Variation and Functional Impact of Neanderthal Ancestry in Western Asia.}, journal = {Genome biology and evolution}, volume = {9}, number = {12}, pages = {3516-3524}, pmid = {29040546}, issn = {1759-6653}, mesh = {African Continental Ancestry Group/genetics ; Animals ; Asia, Western/epidemiology ; Asian Continental Ancestry Group/genetics ; Celiac Disease/epidemiology/genetics ; European Continental Ancestry Group/genetics ; *Gene Expression Regulation ; *Genetic Variation ; *Genome, Human ; Haplotypes ; Humans ; Neanderthals/*genetics ; *Phylogeny ; Receptors, CCR/genetics ; }, abstract = {Neanderthals contributed genetic material to modern humans via multiple admixture events. Initial admixture events presumably occurred in Western Asia shortly after humans migrated out of Africa. Despite being a focal point of admixture, earlier studies indicate lower Neanderthal introgression rates in some Western Asian populations as compared with other Eurasian populations. To better understand the genome-wide and phenotypic impact of Neanderthal introgression in the region, we sequenced whole genomes of nine present-day Europeans, Africans, and the Western Asian Druze at high depth, and analyzed available whole genome data from various other populations, including 16 genomes from present-day Turkey. Our results confirmed previous observations that contemporary Western Asian populations, on an average, have lower levels of Neanderthal-introgressed DNA relative to other Eurasian populations. Modern Western Asians also show comparatively high variability in Neanderthal ancestry, which may be attributed to the complex demographic history of the region. We further replicated the previously described depletion of putatively functional sequences among Neanderthal-introgressed haplotypes. Still, we find dozens of common Neanderthal-introgressed haplotypes in the Turkish sample associated with human phenotypes, including anthropometric and metabolic traits, as well as the immune response. One of these haplotypes is unusually long and harbors variants that affect the expression of members of the CCR gene family and are associated with celiac disease. Overall, our results paint a complex first picture of the genomic impact of Neanderthal introgression in the Western Asian populations.}, } @article {pmid29032037, year = {2018}, author = {Wakano, JY and Gilpin, W and Kadowaki, S and Feldman, MW and Aoki, K}, title = {Ecocultural range-expansion scenarios for the replacement or assimilation of Neanderthals by modern humans.}, journal = {Theoretical population biology}, volume = {119}, number = {}, pages = {3-14}, doi = {10.1016/j.tpb.2017.09.004}, pmid = {29032037}, issn = {1096-0325}, mesh = {Animals ; *Archaeology ; Culture ; Ecology ; Humans ; *Neanderthals ; Population Density ; }, abstract = {Recent archaeological records no longer support a simple dichotomous characterization of the cultures/behaviors of Neanderthals and modern humans, but indicate much cultural/behavioral variability over time and space. Thus, in modeling the replacement or assimilation of Neanderthals by modern humans, it is of interest to consider cultural dynamics and their relation to demographic change. The ecocultural framework for the competition between hominid species allows their carrying capacities to depend on some measure of the levels of culture they possess. In the present study both population densities and the densities of skilled individuals in Neanderthals and modern humans are spatially distributed and subject to change by spatial diffusion, ecological competition, and cultural transmission within each species. We analyze the resulting range expansions in terms of the demographic, ecological and cultural parameters that determine how the carrying capacities relate to the local densities of skilled individuals in each species. Of special interest is the case of cognitive and intrinsic-demographic equivalence of the two species. The range expansion dynamics may consist of multiple wave fronts of different speeds, each of which originates from a traveling wave solution. Properties of these traveling wave solutions are mathematically derived. Depending on the parameters, these traveling waves can result in replacement of Neanderthals by modern humans, or assimilation of the former by the latter. In both the replacement and assimilation scenarios, the first wave of intrusive modern humans is characterized by a low population density and a low density of skilled individuals, with implications for archaeological visibility. The first invasion is due to weak interspecific competition. A second wave of invasion may be induced by cultural differences between moderns and Neanderthals. Spatially and temporally extended coexistence of the two species, which would have facilitated the transfer of genes from Neanderthal into modern humans and vice versa, is observed in the traveling waves, except when niche overlap between the two species is extremely high. Archaeological findings on the spatial and temporal distributions of the Initial Upper Palaeolithic and the Early Upper Palaeolithic and of the coexistence of Neanderthals and modern humans are discussed.}, } @article {pmid29029809, year = {2018}, author = {Naito, YI and Chikaraishi, Y and Drucker, DG and Ohkouchi, N and Semal, P and Wißing, C and Bocherens, H}, title = {Reply to "Comment on "Ecological niche of Neanderthals from Spy Cave revealed by nitrogen isotopes of individual amino acids in collagen." [J. Hum. Evol. 93 (2016) 82-90]" [J. Hum. Evol. 117 (2018) 53-55].}, journal = {Journal of human evolution}, volume = {117}, number = {}, pages = {56-60}, doi = {10.1016/j.jhevol.2017.09.008}, pmid = {29029809}, issn = {1095-8606}, } @article {pmid29023640, year = {2018}, author = {Chapman, T and Sholukha, V and Semal, P and Louryan, S and Van Sint Jan, S}, title = {Further consideration of the curvature of the Neandertal Femur.}, journal = {American journal of physical anthropology}, volume = {165}, number = {1}, pages = {94-107}, doi = {10.1002/ajpa.23334}, pmid = {29023640}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; Female ; Femur/*anatomy & histology/diagnostic imaging ; Fossils ; Humans ; Imaging, Three-Dimensional ; Male ; Neanderthals/*anatomy & histology ; Principal Component Analysis ; Tomography, X-Ray Computed ; }, abstract = {OBJECTIVES: Neandertal femora are particularly known for having a marked sagittal femoral curvature. This study examined femoral curvature in Neandertals in comparison to a modern human population from Belgium by the use of three-dimensional (3D) quadric surfaces modeled from the bone surface. 3D models provide detailed information and enabled femoral curvature to be analyzed in conjunction with other morphological parameters.

MATERIALS AND METHODS: 3D models were created from CT scans of 75 modern human femora and 7 Neandertal femora. Quadric surfaces (QS) were created from the triangulated surface vertices in all areas of interest (neck, head, diaphyseal shaft, condyles) extracted from previously placed anatomical landmarks. The diaphyseal shaft was divided into five QS shapes and curvature was measured by degrees of difference between QS shapes. Each bone was placed in a local coordinate system enabling each bone to be analyzed in the same way.

RESULTS: The use of 3D quadric surface fitting allowed the distribution of curvature with similarly curved femora to be analyzed and the different patterns of curvature between the two groups to be determined. The Neandertals were shown to have a higher degree of femoral curvature and a more distal point of femoral curvature than the modern human population from Belgium.

CONCLUSIONS: Morphological aspects of the Neandertal femur are different from this modern human population although mainly seem unrelated to femoral curvature. The relative lack of correlations with other femoral bony morphological factors suggests femoral curvature variations may be related to other aspects.}, } @article {pmid28985494, year = {2017}, author = {Dannemann, M and Kelso, J}, title = {The Contribution of Neanderthals to Phenotypic Variation in Modern Humans.}, journal = {American journal of human genetics}, volume = {101}, number = {4}, pages = {578-589}, pmid = {28985494}, issn = {1537-6605}, mesh = {Animals ; *Biological Evolution ; Cohort Studies ; European Continental Ancestry Group/*genetics ; Gene Frequency ; Genome, Human ; Hair Color ; Haplotypes ; Humans ; Linkage Disequilibrium ; Neanderthals/*genetics ; *Phenotype ; Phylogeny ; *Polymorphism, Single Nucleotide ; Skin Pigmentation ; }, abstract = {Assessing the genetic contribution of Neanderthals to non-disease phenotypes in modern humans has been difficult because of the absence of large cohorts for which common phenotype information is available. Using baseline phenotypes collected for 112,000 individuals by the UK Biobank, we can now elaborate on previous findings that identified associations between signatures of positive selection on Neanderthal DNA and various modern human traits but not any specific phenotypic consequences. Here, we show that Neanderthal DNA affects skin tone and hair color, height, sleeping patterns, mood, and smoking status in present-day Europeans. Interestingly, multiple Neanderthal alleles at different loci contribute to skin and hair color in present-day Europeans, and these Neanderthal alleles contribute to both lighter and darker skin tones and hair color, suggesting that Neanderthals themselves were most likely variable in these traits.}, } @article {pmid28983028, year = {2017}, author = {Gibbons, A}, title = {Neandertal genome reveals greater legacy in the living.}, journal = {Science (New York, N.Y.)}, volume = {358}, number = {6359}, pages = {21}, doi = {10.1126/science.358.6359.21}, pmid = {28983028}, issn = {1095-9203}, mesh = {Animals ; DNA, Ancient ; Disease/*genetics ; Extinction, Biological ; Genome ; Neanderthals/*genetics ; Sequence Analysis, DNA ; }, } @article {pmid28982794, year = {2017}, author = {Prüfer, K and de Filippo, C and Grote, S and Mafessoni, F and Korlević, P and Hajdinjak, M and Vernot, B and Skov, L and Hsieh, P and Peyrégne, S and Reher, D and Hopfe, C and Nagel, S and Maricic, T and Fu, Q and Theunert, C and Rogers, R and Skoglund, P and Chintalapati, M and Dannemann, M and Nelson, BJ and Key, FM and Rudan, P and Kućan, Ž and Gušić, I and Golovanova, LV and Doronichev, VB and Patterson, N and Reich, D and Eichler, EE and Slatkin, M and Schierup, MH and Andrés, AM and Kelso, J and Meyer, M and Pääbo, S}, title = {A high-coverage Neandertal genome from Vindija Cave in Croatia.}, journal = {Science (New York, N.Y.)}, volume = {358}, number = {6363}, pages = {655-658}, pmid = {28982794}, issn = {1095-9203}, support = {//Howard Hughes Medical Institute/United States ; R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG002385/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Alleles ; Animals ; *Biological Evolution ; Caves ; Croatia ; DNA, Ancient ; Genome ; Humans ; Neanderthals/*genetics ; }, abstract = {To date, the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We sequenced the genome of a female Neandertal from ~50,000 years ago from Vindija Cave, Croatia, to ~30-fold genomic coverage. She carried 1.6 differences per 10,000 base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size. Our analyses indicate that she was more closely related to the Neandertals that mixed with the ancestors of present-day humans living outside of sub-Saharan Africa than the previously sequenced Neandertal from Siberia, allowing 10 to 20% more Neandertal DNA to be identified in present-day humans, including variants involved in low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases.}, } @article {pmid28973864, year = {2017}, author = {Hublin, JJ}, title = {The last Neanderthal.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {40}, pages = {10520-10522}, pmid = {28973864}, issn = {1091-6490}, mesh = {*Fossils ; Hominidae ; Humans ; *Neanderthals ; Phylogeny ; }, } @article {pmid28950836, year = {2017}, author = {Xu, D and Jaber, Y and Pavlidis, P and Gokcumen, O}, title = {VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences.}, journal = {BMC bioinformatics}, volume = {18}, number = {1}, pages = {426}, pmid = {28950836}, issn = {1471-2105}, mesh = {Algorithms ; Animals ; Base Sequence ; *Genetic Loci ; *Genome, Human ; Humans ; INDEL Mutation/genetics ; *Phylogeny ; Primates ; Sequence Alignment/*methods ; Sequence Analysis, DNA ; *Software ; User-Computer Interface ; }, abstract = {BACKGROUND: Constructing alignments and phylogenies for a given locus from large genome sequencing studies with relevant outgroups allow novel evolutionary and anthropological insights. However, no user-friendly tool has been developed to integrate thousands of recently available and anthropologically relevant genome sequences to construct complete sequence alignments and phylogenies.

RESULTS: Here, we provide VCFtoTree, a user friendly tool with a graphical user interface that directly accesses online databases to download, parse and analyze genome variation data for regions of interest. Our pipeline combines popular sequence datasets and tree building algorithms with custom data parsing to generate accurate alignments and phylogenies using all the individuals from the 1000 Genomes Project, Neanderthal and Denisovan genomes, as well as reference genomes of Chimpanzee and Rhesus Macaque. It can also be applied to other phased human genomes, as well as genomes from other species. The output of our pipeline includes an alignment in FASTA format and a tree file in newick format.

CONCLUSION: VCFtoTree fulfills the increasing demand for constructing alignments and phylogenies for a given loci from thousands of available genomes. Our software provides a user friendly interface for a wider audience without prerequisite knowledge in programming. VCFtoTree can be accessed from https://github.com/duoduoo/VCFtoTree_3.0.0 .}, } @article {pmid28935804, year = {2017}, author = {Rosas, A and Ríos, L and Estalrrich, A and Liversidge, H and García-Tabernero, A and Huguet, R and Cardoso, H and Bastir, M and Lalueza-Fox, C and de la Rasilla, M and Dean, C}, title = {The growth pattern of Neandertals, reconstructed from a juvenile skeleton from El Sidrón (Spain).}, journal = {Science (New York, N.Y.)}, volume = {357}, number = {6357}, pages = {1282-1287}, doi = {10.1126/science.aan6463}, pmid = {28935804}, issn = {1095-9203}, mesh = {Age Factors ; Animals ; *Biological Evolution ; Body Size ; Brain/growth & development ; *Extinction, Biological ; Neanderthals/*growth & development ; Skull/*growth & development ; Spain ; Thoracic Vertebrae/*growth & development ; Tooth/growth & development ; }, abstract = {Ontogenetic studies help us understand the processes of evolutionary change. Previous studies on Neandertals have focused mainly on dental development and inferred an accelerated pace of general growth. We report on a juvenile partial skeleton (El Sidrón J1) preserving cranio-dental and postcranial remains. We used dental histology to estimate the age at death to be 7.7 years. Maturation of most elements fell within the expected range of modern humans at this age. The exceptions were the atlas and mid-thoracic vertebrae, which remained at the 5- to 6-year stage of development. Furthermore, endocranial features suggest that brain growth was not yet completed. The vertebral maturation pattern and extended brain growth most likely reflect Neandertal physiology and ontogenetic energy constraints rather than any fundamental difference in the overall pace of growth in this extinct human.}, } @article {pmid28934125, year = {2017}, author = {Eduardoff, M and Xavier, C and Strobl, C and Casas-Vargas, A and Parson, W}, title = {Optimized mtDNA Control Region Primer Extension Capture Analysis for Forensically Relevant Samples and Highly Compromised mtDNA of Different Age and Origin.}, journal = {Genes}, volume = {8}, number = {10}, pages = {}, pmid = {28934125}, issn = {2073-4425}, abstract = {The analysis of mitochondrial DNA (mtDNA) has proven useful in forensic genetics and ancient DNA (aDNA) studies, where specimens are often highly compromised and DNA quality and quantity are low. In forensic genetics, the mtDNA control region (CR) is commonly sequenced using established Sanger-type Sequencing (STS) protocols involving fragment sizes down to approximately 150 base pairs (bp). Recent developments include Massively Parallel Sequencing (MPS) of (multiplex) PCR-generated libraries using the same amplicon sizes. Molecular genetic studies on archaeological remains that harbor more degraded aDNA have pioneered alternative approaches to target mtDNA, such as capture hybridization and primer extension capture (PEC) methods followed by MPS. These assays target smaller mtDNA fragment sizes (down to 50 bp or less), and have proven to be substantially more successful in obtaining useful mtDNA sequences from these samples compared to electrophoretic methods. Here, we present the modification and optimization of a PEC method, earlier developed for sequencing the Neanderthal mitochondrial genome, with forensic applications in mind. Our approach was designed for a more sensitive enrichment of the mtDNA CR in a single tube assay and short laboratory turnaround times, thus complying with forensic practices. We characterized the method using sheared, high quantity mtDNA (six samples), and tested challenging forensic samples (n = 2) as well as compromised solid tissue samples (n = 15) up to 8 kyrs of age. The PEC MPS method produced reliable and plausible mtDNA haplotypes that were useful in the forensic context. It yielded plausible data in samples that did not provide results with STS and other MPS techniques. We addressed the issue of contamination by including four generations of negative controls, and discuss the results in the forensic context. We finally offer perspectives for future research to enable the validation and accreditation of the PEC MPS method for final implementation in forensic genetic laboratories.}, } @article {pmid28902892, year = {2017}, author = {Zanolli, C and Hourset, M and Esclassan, R and Mollereau, C}, title = {Neanderthal and Denisova tooth protein variants in present-day humans.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0183802}, pmid = {28902892}, issn = {1932-6203}, mesh = {Animals ; Dental Enamel/anatomy & histology/metabolism ; Dental Enamel Proteins/*genetics/metabolism ; Fossils ; Gene Frequency ; Genome, Human ; Geography ; *Hominidae/genetics/metabolism ; Humans ; *Neanderthals/genetics/metabolism ; Organ Size ; Phylogeny ; *Polymorphism, Genetic ; Selection, Genetic ; Sequence Homology, Amino Acid ; Tooth/anatomy & histology/chemistry/*metabolism ; }, abstract = {Environment parameters, diet and genetic factors interact to shape tooth morphostructure. In the human lineage, archaic and modern hominins show differences in dental traits, including enamel thickness, but variability also exists among living populations. Several polymorphisms, in particular in the non-collagenous extracellular matrix proteins of the tooth hard tissues, like enamelin, are involved in dental structure variation and defects and may be associated with dental disorders or susceptibility to caries. To gain insights into the relationships between tooth protein polymorphisms and dental structural morphology and defects, we searched for non-synonymous polymorphisms in tooth proteins from Neanderthal and Denisova hominins. The objective was to identify archaic-specific missense variants that may explain the dental morphostructural variability between extinct and modern humans, and to explore their putative impact on present-day dental phenotypes. Thirteen non-collagenous extracellular matrix proteins specific to hard dental tissues have been selected, searched in the publicly available sequence databases of Neanderthal and Denisova individuals and compared with modern human genome data. A total of 16 non-synonymous polymorphisms were identified in 6 proteins (ameloblastin, amelotin, cementum protein 1, dentin matrix acidic phosphoprotein 1, enamelin and matrix Gla protein). Most of them are encoded by dentin and enamel genes located on chromosome 4, previously reported to show signs of archaic introgression within Africa. Among the variants shared with modern humans, two are ancestral (common with apes) and one is the derived enamelin major variant, T648I (rs7671281), associated with a thinner enamel and specific to the Homo lineage. All the others are specific to Neanderthals and Denisova, and are found at a very low frequency in modern Africans or East and South Asians, suggesting that they may be related to particular dental traits or disease susceptibility in these populations. This modern regional distribution of archaic dental polymorphisms may reflect persistence of archaic variants in some populations and may contribute in part to the geographic dental variations described in modern humans.}, } @article {pmid28890534, year = {2017}, author = {Marciniak, S and Perry, GH}, title = {Harnessing ancient genomes to study the history of human adaptation.}, journal = {Nature reviews. Genetics}, volume = {18}, number = {11}, pages = {659-674}, pmid = {28890534}, issn = {1471-0064}, mesh = {*Adaptation, Physiological ; Animals ; *Biological Evolution ; *Genome, Human ; Humans/*genetics ; Neanderthals/*genetics ; }, abstract = {The past several years have witnessed an explosion of successful ancient human genome-sequencing projects, with genomic-scale ancient DNA data sets now available for more than 1,100 ancient human and archaic hominin (for example, Neandertal) individuals. Recent 'evolution in action' analyses have started using these data sets to identify and track the spatiotemporal trajectories of genetic variants associated with human adaptations to novel and changing environments, agricultural lifestyles, and introduced or co-evolving pathogens. Together with evidence of adaptive introgression of genetic variants from archaic hominins to humans and emerging ancient genome data sets for domesticated animals and plants, these studies provide novel insights into human evolution and the evolutionary consequences of human behaviour that go well beyond those that can be obtained from modern genomic data or the fossil and archaeological records alone.}, } @article {pmid28874524, year = {2017}, author = {Devièse, T and Karavanić, I and Comeskey, D and Kubiak, C and Korlević, P and Hajdinjak, M and Radović, S and Procopio, N and Buckley, M and Pääbo, S and Higham, T}, title = {Direct dating of Neanderthal remains from the site of Vindija Cave and implications for the Middle to Upper Paleolithic transition.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {40}, pages = {10606-10611}, pmid = {28874524}, issn = {1091-6490}, mesh = {Animals ; *Caves ; Croatia ; Female ; Fossils ; Male ; *Neanderthals ; Radiometric Dating/*methods ; }, abstract = {Previous dating of the Vi-207 and Vi-208 Neanderthal remains from Vindija Cave (Croatia) led to the suggestion that Neanderthals survived there as recently as 28,000-29,000 B.P. Subsequent dating yielded older dates, interpreted as ages of at least ∼32,500 B.P. We have redated these same specimens using an approach based on the extraction of the amino acid hydroxyproline, using preparative high-performance liquid chromatography (Prep-HPLC). This method is more efficient in eliminating modern contamination in the bone collagen. The revised dates are older than 40,000 B.P., suggesting the Vindija Neanderthals did not live more recently than others across Europe, and probably predate the arrival of anatomically modern humans in Eastern Europe. We applied zooarchaeology by mass spectrometry (ZooMS) to find additional hominin remains. We identified one bone that is Neanderthal, based on its mitochondrial DNA, and dated it directly to 46,200 ± 1,500 B.P. We also attempted to date six early Upper Paleolithic bone points from stratigraphic units G1, Fd/d+G1 and Fd/d, Fd. One bone artifact gave a date of 29,500 ± 400 B.P., while the remainder yielded no collagen. We additionally dated animal bone samples from units G1 and G1-G3 These dates suggest a co-occurrence of early Upper Paleolithic osseous artifacts, particularly split-based points, alongside the remains of Neanderthals is a result of postdepositional mixing, rather than an association between the two groups, although more work is required to show this definitively.}, } @article {pmid28874276, year = {2017}, author = {García-Martínez, D and Bastir, M and Huguet, R and Estalrrich, A and García-Tabernero, A and Ríos, L and Cunha, E and Rasilla, M and Rosas, A}, title = {The costal remains of the El Sidrón Neanderthal site (Asturias, northern Spain) and their importance for understanding Neanderthal thorax morphology.}, journal = {Journal of human evolution}, volume = {111}, number = {}, pages = {85-101}, doi = {10.1016/j.jhevol.2017.06.003}, pmid = {28874276}, issn = {1095-8606}, mesh = {Animals ; Fossils/*anatomy & histology ; Humans ; Neanderthals/*anatomy & histology ; Ribs/anatomy & histology ; Spain ; Thorax/*anatomy & histology ; }, abstract = {The study of the Neanderthal thorax has attracted the attention of the scientific community for more than a century. It is agreed that Neanderthals have a more capacious thorax than modern humans, but whether this was caused by a medio-lateral or an antero-posterior expansion of the thorax is still debated, and is key to understanding breathing biomechanics and body shape in Neanderthals. The fragile nature of ribs, the metameric structure of the thorax and difficulties in quantifying thorax morphology all contribute to uncertainty regarding precise aspects of Neanderthal thoracic shape. The El Sidrón site has yielded costal remains from the upper to the lower thorax, as well as several proximal rib ends (frequently missing in the Neanderthal record), which help to shed light on Neanderthal thorax shape. We compared the El Sidrón costal elements with ribs from recent modern humans as well as with fossil modern humans and other Neanderthals through traditional morphometric methods and 3D geometric morphometrics, combined with missing data estimation and virtual reconstruction (at the 1st, 5th and 11th costal levels). Our results show that Neanderthals have larger rib heads and articular tubercles than their modern human counterparts. Neanderthal 1st ribs are smaller than in modern humans, whereas 5th and 11th ribs are considerably larger. When we articulated mean ribs (size and shape) with their corresponding vertebral elements, we observed that compared to modern humans the Neanderthal thorax is medio-laterally expanded at every level, especially at T5 and T11. Therefore, in the light of evidence from the El Sidrón costal remains, we hypothesize that the volumetric expansion of the Neanderthal thorax proposed by previous authors would mainly be produced by a medio-lateral expansion of the thorax.}, } @article {pmid28874274, year = {2017}, author = {Tillier, AM and Sirakov, N and Guadelli, A and Fernandez, P and Sirakova, S and Dimitrova, I and Ferrier, C and Guérin, G and Heidari, M and Krumov, I and Leblanc, JC and Miteva, V and Popov, V and Taneva, S and Guadelli, JL}, title = {Evidence of Neanderthals in the Balkans: The infant radius from Kozarnika Cave (Bulgaria).}, journal = {Journal of human evolution}, volume = {111}, number = {}, pages = {54-62}, doi = {10.1016/j.jhevol.2017.06.002}, pmid = {28874274}, issn = {1095-8606}, mesh = {Animals ; Balkan Peninsula ; Bulgaria ; Caves ; Fossils/*anatomy & histology ; Humans ; Infant ; *Neanderthals ; Radius/*anatomy & histology ; }, abstract = {Excavations conducted by a Bulgarian-French team at Kozarnika Cave (Balkans, Bulgaria) during several seasons yielded a long Paleolithic archaeological sequence and led to the discovery of important faunal, lithic, and human samples. This paper aims to describe the unpublished radius shaft of an infant who died approximately before the sixth month postnatal that was recovered from layer 10b, which contained East Balkan Levallois Mousterian with bifacial leaf points. The layer was dated between 130 and 200 ka (large mammals biochronology) and between 128 ± 13 ka and 183 ± 14 ka (OSL), i.e. OIS6. Here we show that, given the scarcity of Middle Pleistocene infant remains in general, and Middle Paleolithic human remains from this part of Eastern Europe in particular, the study of the Kozarnika specimen is of special interest. We discuss its place in the Middle Pleistocene European hominine record and substantiate the hypothesis of early Neanderthal presence in the eastern Balkans.}, } @article {pmid28874271, year = {2017}, author = {Bargalló, A and Mosquera, M and Lozano, S}, title = {In pursuit of our ancestors' hand laterality.}, journal = {Journal of human evolution}, volume = {111}, number = {}, pages = {18-32}, doi = {10.1016/j.jhevol.2017.06.001}, pmid = {28874271}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; Fossils ; Functional Laterality/*physiology ; Hand ; Humans ; Neanderthals ; Spain ; }, abstract = {The aim of this paper is to apply a previously published method (Bargalló and Mosquera, 2014) to the archaeological record, allowing us to identify the hand laterality of our ancestors and determine when and how this feature, which is exhibited most strongly in humans, appeared in our evolutionary history. The method focuses on identifying handedness by looking at the technical features of the flakes produced by a single knapper, and discovering how many flakes are required to ascertain their hand preference. This method can potentially be applied to the majority of archaeological sites, since flakes are the most abundant stone tools, and stone tools are the most widespread and widely-preserved remains from prehistory. For our study, we selected two Spanish sites: Gran Dolina-TD10.1 (Atapuerca) and Abric Romaní (Barcelona), which were occupied by pre-Neanderthal and Neanderthal populations, respectively. Our analyses indicate that a minimum number of eight flakes produced by the same knapper is required to ascertain their hand preference. Even though this figure is relatively low, it is quite difficult to obtain from many archaeological sites. In addition, there is no single technical feature that provides information about handedness, instead there is a combination of eight technical features, localised on the striking platforms and ventral surfaces. The raw material is not relevant where good quality rocks are used, in this case quartzite and flint, since most of them retain the technical features required for the analysis. Expertise is not an issue either, since the technical features analysed here only correlate with handedness (Bargalló and Mosquera, 2014). Our results allow us to tentatively identify one right-handed knapper among the pre-Neanderthals of level TD10.1 at Gran Dolina (Atapuerca), while four of the five Neanderthals analysed from Abric Romaní were right-handed. The hand preference of the fifth knapper from that location (AR5) remains unclear.}, } @article {pmid28874265, year = {2017}, author = {Pomeroy, E and Mirazón Lahr, M and Crivellaro, F and Farr, L and Reynolds, T and Hunt, CO and Barker, G}, title = {Newly discovered Neanderthal remains from Shanidar Cave, Iraqi Kurdistan, and their attribution to Shanidar 5.}, journal = {Journal of human evolution}, volume = {111}, number = {}, pages = {102-118}, doi = {10.1016/j.jhevol.2017.07.001}, pmid = {28874265}, issn = {1095-8606}, mesh = {Animals ; *Caves ; *Fibula ; *Fossils ; Hominidae ; Humans ; Iraq ; Male ; *Neanderthals ; *Pelvic Bones ; }, abstract = {The Neanderthal remains from Shanidar Cave, excavated between 1951 and 1960, have played a central role in debates concerning diverse aspects of Neanderthal morphology and behavior. In 2015 and 2016, renewed excavations at the site uncovered hominin remains from the immediate area where the partial skeleton of Shanidar 5 was found in 1960. Shanidar 5 was a robust adult male estimated to have been aged over 40 years at the time of death. Comparisons of photographs from the previous and recent excavations indicate that the old and new remains were directly adjacent to one another, while the disturbed arrangement and partial crushing of the new fossils is consistent with descriptions and photographs of the older discoveries. The newly discovered bones include fragments of several vertebrae, a left hamate, part of the proximal left femur, a heavily crushed partial pelvis, and the distal half of the right tibia and fibula and associated talus and navicular. All these elements were previously missing from Shanidar 5, and morphological and metric data are consistent with the new elements belonging to this individual. A newly discovered partial left pubic symphysis indicates an age at death of 40-50 years, also consistent with the age of Shanidar 5 estimated previously. Thus, the combined evidence strongly suggests that the new finds can be attributed to Shanidar 5. Ongoing analyses of associated samples, including for sediment morphology, palynology, and dating, will therefore offer new evidence as to how this individual was deposited in the cave and permit new analyses of the skeleton itself and broader discussion of Neanderthal morphology and variation.}, } @article {pmid28860591, year = {2017}, author = {Kozowyk, PRB and Soressi, M and Pomstra, D and Langejans, GHJ}, title = {Experimental methods for the Palaeolithic dry distillation of birch bark: implications for the origin and development of Neandertal adhesive technology.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8033}, pmid = {28860591}, issn = {2045-2322}, abstract = {The destructive distillation of birch bark to produce tar has recently featured in debates about the technological and cognitive abilities of Neandertals and modern humans. The abilities to precisely control fire temperatures and to manipulate adhesive properties are believed to require advanced mental traits. However, the significance given to adhesive technology in these debates has quickly outgrown our understanding of birch bark tar and its manufacture using aceramic techniques. In this paper, we detail three experimental methods of Palaeolithic tar production ranging from simple to complex. We recorded the fuel, time, materials, temperatures, and tar yield for each method and compared them with the tar known from the Palaeolithic. Our results indicate that it is possible to obtain useful amounts of tar by combining materials and technology already in use by Neandertals. A ceramic container is not required, and temperature control need not be as precise as previously thought. However, Neandertals must have been able to recognize certain material properties, such as adhesive tack and viscosity. In this way, they could develop the technology from producing small traces of tar on partially burned bark to techniques capable of manufacturing quantities of tar equal to those found in the Middle Palaeolithic archaeological record.}, } @article {pmid28860198, year = {2017}, author = {Hawks, J}, title = {Neanderthals and Denisovans as biological invaders.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {37}, pages = {9761-9763}, pmid = {28860198}, issn = {1091-6490}, mesh = {Animals ; Biological Evolution ; Fossils ; *Hominidae ; Humans ; *Neanderthals ; }, } @article {pmid28859637, year = {2017}, author = {Harris, K and Nielsen, R}, title = {Q&A: Where did the Neanderthals go?.}, journal = {BMC biology}, volume = {15}, number = {1}, pages = {73}, pmid = {28859637}, issn = {1741-7007}, support = {F32 GM116381/GM/NIGMS NIH HHS/United States ; R01 GM116044/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Evolution, Molecular ; Fossils ; *Genome, Human ; Genomics ; Humans ; *Hybridization, Genetic ; Neanderthals/*genetics ; }, abstract = {Genomic evidence has demonstrated that humans and Neanderthals interbred. Today, the genomes of most individuals outside Africa contain 2-3% Neanderthal DNA. However, it is still hotly debated why the Neanderthals went extinct and if humans contributed to the Neanderthal extinction. In this Q&A we explore what genomic data might have to say about this issue.}, } @article {pmid28855259, year = {2017}, author = {Gardner, EJ and Lam, VK and Harris, DN and Chuang, NT and Scott, EC and Pittard, WS and Mills, RE and , and Devine, SE}, title = {The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology.}, journal = {Genome research}, volume = {27}, number = {11}, pages = {1916-1929}, pmid = {28855259}, issn = {1549-5469}, support = {R01 HG002898/HG/NHGRI NIH HHS/United States ; R01 HG006849/HG/NHGRI NIH HHS/United States ; R01 GM059290/GM/NIGMS NIH HHS/United States ; R01 CA166661/CA/NCI NIH HHS/United States ; F31 HG009223/HG/NHGRI NIH HHS/United States ; T32 DK067872/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Computational Biology/*methods ; *DNA Transposable Elements ; Databases, Genetic ; Evolution, Molecular ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Neanderthals/*genetics ; Pan troglodytes/*genetics ; Polymorphism, Single Nucleotide ; Software ; Whole Genome Sequencing/methods ; }, abstract = {Mobile element insertions (MEIs) represent ∼25% of all structural variants in human genomes. Moreover, when they disrupt genes, MEIs can influence human traits and diseases. Therefore, MEIs should be fully discovered along with other forms of genetic variation in whole genome sequencing (WGS) projects involving population genetics, human diseases, and clinical genomics. Here, we describe the Mobile Element Locator Tool (MELT), which was developed as part of the 1000 Genomes Project to perform MEI discovery on a population scale. Using both Illumina WGS data and simulations, we demonstrate that MELT outperforms existing MEI discovery tools in terms of speed, scalability, specificity, and sensitivity, while also detecting a broader spectrum of MEI-associated features. Several run modes were developed to perform MEI discovery on local and cloud systems. In addition to using MELT to discover MEIs in modern humans as part of the 1000 Genomes Project, we also used it to discover MEIs in chimpanzees and ancient (Neanderthal and Denisovan) hominids. We detected diverse patterns of MEI stratification across these populations that likely were caused by (1) diverse rates of MEI production from source elements, (2) diverse patterns of MEI inheritance, and (3) the introgression of ancient MEIs into modern human genomes. Overall, our study provides the most comprehensive map of MEIs to date spanning chimpanzees, ancient hominids, and modern humans and reveals new aspects of MEI biology in these lineages. We also demonstrate that MELT is a robust platform for MEI discovery and analysis in a variety of experimental settings.}, } @article {pmid28854627, year = {2017}, author = {Sharbrough, J and Havird, JC and Noe, GR and Warren, JM and Sloan, DB}, title = {The Mitonuclear Dimension of Neanderthal and Denisovan Ancestry in Modern Human Genomes.}, journal = {Genome biology and evolution}, volume = {9}, number = {6}, pages = {1567-1581}, pmid = {28854627}, issn = {1759-6653}, mesh = {Alleles ; Animals ; Cell Nucleus/chemistry/*genetics ; DNA, Mitochondrial/chemistry/*genetics ; *Evolution, Molecular ; Gene Flow ; *Genome, Human ; Hominidae/classification/*genetics ; Humans ; Neanderthals/classification/*genetics ; Nucleic Acid Conformation ; Polymorphism, Genetic ; Reproductive Isolation ; }, abstract = {Some human populations interbred with Neanderthals and Denisovans, resulting in substantial contributions to modern-human genomes. Therefore, it is now possible to use genomic data to investigate mechanisms that shaped historical gene flow between humans and our closest hominin relatives. More generally, in eukaryotes, mitonuclear interactions have been argued to play a disproportionate role in generating reproductive isolation. There is no evidence of mtDNA introgression into modern human populations, which means that all introgressed nuclear alleles from archaic hominins must function on a modern-human mitochondrial background. Therefore, mitonuclear interactions are also potentially relevant to hominin evolution. We performed a detailed accounting of mtDNA divergence among hominin lineages and used population-genomic data to test the hypothesis that mitonuclear incompatibilities have preferentially restricted the introgression of nuclear genes with mitochondrial functions. We found a small but significant underrepresentation of introgressed Neanderthal alleles at such nuclear loci. Structural analyses of mitochondrial enzyme complexes revealed that these effects are unlikely to be mediated by physically interacting sites in mitochondrial and nuclear gene products. We did not detect any underrepresentation of introgressed Denisovan alleles at mitochondrial-targeted loci, but this may reflect reduced power because locus-specific estimates of Denisovan introgression are more conservative. Overall, we conclude that genes involved in mitochondrial function may have been subject to distinct selection pressures during the history of introgression from archaic hominins but that mitonuclear incompatibilities have had, at most, a small role in shaping genome-wide introgression patterns, perhaps because of limited functional divergence in mtDNA and interacting nuclear genes.}, } @article {pmid28836000, year = {2017}, author = {Zhou, B and Wen, S and Wang, L and Jin, L and Li, H and Zhang, H}, title = {AntCaller: an accurate variant caller incorporating ancient DNA damage.}, journal = {Molecular genetics and genomics : MGG}, volume = {292}, number = {6}, pages = {1419-1430}, pmid = {28836000}, issn = {1617-4623}, mesh = {Animals ; *DNA Damage ; *DNA, Ancient ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Neanderthals ; Ploidies ; Postmortem Changes ; }, abstract = {Ancient DNA obtained from ancient samples, such as sediments, bones, and teeth, is an important genetic resource that can be used to reconstruct an evolutional history of humans, animals, and plants. The application of high-throughput sequencing enables the research of ancient DNA to be conducted in a whole genome scale. However, post-mortem DNA damage mainly caused by deamination of cytosine to uracil (or methylated cytosine to thymine) may confound the variant calling and downstream analysis. In this article, we develop a Python program to implement a new variant caller, "AntCaller", which extracts the information on nucleotide substitutions from sequencing data and calculates the probability of each genotype based on a Bayesian rule. Through both simulation studies and real data analyses, it was shown that our method reduced the false discovery rate caused by nucleotide misincorporations and outperformed two mainstream variant callers (i.e., GATK and SAMtools) in terms of calling accuracy. In a real application with serious DNA damage, AntCaller still outperformed GATK and SAMtools combined with quality score recalling.}, } @article {pmid28815959, year = {2017}, author = {Bermúdez de Castro, JM and Martinón-Torres, M and Arsuaga, JL and Carbonell, E}, title = {Twentieth anniversary of Homo antecessor (1997-2017): a review.}, journal = {Evolutionary anthropology}, volume = {26}, number = {4}, pages = {157-171}, doi = {10.1002/evan.21540}, pmid = {28815959}, issn = {1520-6505}, mesh = {Animals ; Anthropology, Physical ; *Biological Evolution ; *Fossils ; Hominidae/*anatomy & histology ; Humans ; Neanderthals ; Spain ; }, abstract = {It has been twenty years since diagnosis and publication of the species Homo antecessor.1 Since then, new human fossils recovered from the TD6 level of the Gran Dolina site (Sierra de Atapuerca, northern Spain) have helped to refine its taxonomic and phylogenetic position. In this paper, we present a synthesis of the most characteristic features of this species, as well as our interpretation derived from the latest investigations. We focus on the phylogenetic interpretation of Homo antecessor, taking into account the most recent paleogenetic analyses and a reassessment of the European Middle Pleistocene hominin record. We try to show that, twenty years after its publication, H. antecessor provides a good opportunity to address the morphology of the last common ancestor of Neandertals and modern humans.}, } @article {pmid28794033, year = {2017}, author = {Chen, Z and Ho, WCS and Boon, SS and Law, PTY and Chan, MCW and DeSalle, R and Burk, RD and Chan, PKS}, title = {Ancient Evolution and Dispersion of Human Papillomavirus 58 Variants.}, journal = {Journal of virology}, volume = {91}, number = {21}, pages = {}, pmid = {28794033}, issn = {1098-5514}, support = {U01 CA078527/CA/NCI NIH HHS/United States ; }, mesh = {Capsid Proteins/genetics ; *Evolution, Molecular ; *Genetic Variation ; Genome, Viral ; Humans ; Papillomaviridae/*classification/*genetics ; Papillomavirus Infections/*virology ; Phylogeny ; Selection, Genetic ; }, abstract = {Human papillomavirus 58 (HPV58) is found in 10 to 18% of cervical cancers in East Asia but is rather uncommon elsewhere. The distribution and oncogenic potential of HPV58 variants appear to be heterogeneous, since the E7 T20I/G63S variant is more prevalent in East Asia and confers a 7- to 9-fold-higher risk of cervical precancer and cancer. However, the underlying genomic mechanisms that explain the geographic and carcinogenic diversity of HPV58 variants are still poorly understood. In this study, we used a combination of phylogenetic analyses and bioinformatics to investigate the deep evolutionary history of HPV58 complete genome variants. The initial splitting of HPV58 variants was estimated to occur 478,600 years ago (95% highest posterior density [HPD], 391,000 to 569,600 years ago). This divergence time is well within the era of speciation between Homo sapiens and Neanderthals/Denisovans and around three times longer than the modern Homo sapiens divergence times. The expansion of present-day variants in Eurasia could be the consequence of viral transmission from Neanderthals/Denisovans to non-African modern human populations through gene flow. A whole-genome sequence signature analysis identified 3 amino acid changes, 16 synonymous nucleotide changes, and a 12-bp insertion strongly associated with the E7 T20I/G63S variant that represents the A3 sublineage and carries higher carcinogenetic potential. Compared with the capsid proteins, the oncogenes E7 and E6 had increased substitution rates indicative of higher selection pressure. These data provide a comprehensive evolutionary history and genomic basis of HPV58 variants to assist further investigation of carcinogenic association and the development of diagnostic and therapeutic strategies.IMPORTANCE Papillomaviruses (PVs) are an ancient and heterogeneous group of double-stranded DNA viruses that preferentially infect the cutaneous and mucocutaneous epithelia of vertebrates. Persistent infection by specific oncogenic human papillomaviruses (HPVs), including HPV58, has been established as the primary cause of cervical cancer. In this work, we reveal the complex evolutionary history of HPV58 variants that explains the heterogeneity of oncogenic potential and geographic distribution. Our data suggest that HPV58 variants may have coevolved with archaic hominins and dispersed across the planet through host interbreeding and gene flow. Certain genes and codons of HPV58 variants representing higher carcinogenic potential and/or that are under positive selection may have important implications for viral host specificity, pathogenesis, and disease prevention.}, } @article {pmid28784789, year = {2017}, author = {Rogers, AR and Bohlender, RJ and Huff, CD}, title = {Early history of Neanderthals and Denisovans.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {37}, pages = {9859-9863}, pmid = {28784789}, issn = {1091-6490}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; R25 CA057730/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; *Evolution, Molecular ; Fossils ; Gene Flow/*genetics ; Genome, Human/genetics ; Hominidae/*classification/*genetics ; Humans ; Neanderthals/classification/*genetics ; *Pedigree ; Phylogeny ; }, abstract = {Extensive DNA sequence data have made it possible to reconstruct human evolutionary history in unprecedented detail. We introduce a method to study the past several hundred thousand years. Our results show that (i) the Neanderthal-Denisovan lineage declined to a small size just after separating from the modern lineage, (ii) Neanderthals and Denisovans separated soon thereafter, and (iii) the subsequent Neanderthal population was large and deeply subdivided. They also (iv) support previous estimates of gene flow from Neanderthals into modern Eurasians. These results suggest an archaic human diaspora early in the Middle Pleistocene.}, } @article {pmid28778459, year = {2017}, author = {Pelletier, M and Royer, A and Holliday, TW and Discamps, E and Madelaine, S and Maureille, B}, title = {Rabbits in the grave! Consequences of bioturbation on the Neandertal "burial" at Regourdou (Montignac-sur-Vézère, Dordogne).}, journal = {Journal of human evolution}, volume = {110}, number = {}, pages = {1-17}, doi = {10.1016/j.jhevol.2017.04.001}, pmid = {28778459}, issn = {1095-8606}, mesh = {Animals ; *Burial ; Europe ; *Fossils ; *Neanderthals ; Rabbits ; Radiometric Dating ; Reproducibility of Results ; Time Factors ; }, abstract = {The understanding of Neanderthal societies, both with regard to their funerary behaviors and their subsistence activities, is hotly debated. Old excavations and a lack of taphonomic context are often factors that limit our ability to address these questions. To better appreciate the exact nature of what is potentially the oldest burial in Western Europe, Regourdou (Montignac-sur-Vézère, Dordogne), and to better understand the taphonomy of this site excavated more than 50 years ago, we report in this contribution a study of the most abundant animals throughout its stratigraphy: the European rabbit (Oryctolagus cuniculus). In addition to questions surrounding the potential bioturbation of the site's stratigraphy, analysis of the Regourdou rabbits could provide new information on Neandertal subsistence behavior. The mortality profile, skeletal-part representation, breakage patterns, surface modification, and comparison with modern reference collections supports the hypothesis that the Regourdou rabbit remains were primarily accumulated due to natural (attritional) mortality. Radiocarbon dates performed directly on the rabbit remains give ages ranging within the second half of Marine Isotope Stage 3, notably younger than the regional Mousterian period. We posit that rabbits dug their burrows within Regourdou's sedimentological filling, likely inhabiting the site after it was filled. The impact of rabbit activity now brings into question both the reliability of the archaeostratigraphy of the site and the paleoenvironmental reconstructions previously proposed for it, and suggests rabbits may have played a role in the distribution of the Neandertal skeletal remains.}, } @article {pmid28778150, year = {2017}, author = {Chintalapati, M and Dannemann, M and Prüfer, K}, title = {Using the Neandertal genome to study the evolution of small insertions and deletions in modern humans.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {179}, pmid = {28778150}, issn = {1471-2148}, mesh = {Animals ; *Evolution, Molecular ; Gene Frequency/genetics ; Gene Ontology ; *Genome ; Genome-Wide Association Study ; Humans ; INDEL Mutation/*genetics ; Neanderthals/*genetics ; Phenotype ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Primates/genetics ; }, abstract = {BACKGROUND: Small insertions and deletions occur in humans at a lower rate compared to nucleotide changes, but evolve under more constraint than nucleotide changes. While the evolution of insertions and deletions have been investigated using ape outgroups, the now available genome of a Neandertal can shed light on the evolution of indels in more recent times.

RESULTS: We used the Neandertal genome together with several primate outgroup genomes to differentiate between human insertion/deletion changes that likely occurred before the split from Neandertals and those that likely arose later. Changes that pre-date the split from Neandertals show a smaller proportion of deletions than those that occurred later. The presence of a Neandertal-shared allele in Europeans or Asians but the absence in Africans was used to detect putatively introgressed indels in Europeans and Asians. A larger proportion of these variants reside in intergenic regions compared to other modern human variants, and some variants are linked to SNPs that have been associated with traits in modern humans.

CONCLUSIONS: Our results are in agreement with earlier results that suggested that deletions evolve under more constraint than insertions. When considering Neandertal introgressed variants, we find some evidence that negative selection affected these variants more than other variants segregating in modern humans. Among introgressed variants we also identify indels that may influence the phenotype of their carriers. In particular an introgressed deletion associated with a decrease in the time to menarche may constitute an example of a former Neandertal-specific trait contributing to modern human phenotypic diversity.}, } @article {pmid28766699, year = {2017}, author = {Bookstein, FL}, title = {A method of factor analysis for shape coordinates.}, journal = {American journal of physical anthropology}, volume = {164}, number = {2}, pages = {221-245}, doi = {10.1002/ajpa.23277}, pmid = {28766699}, issn = {1096-8644}, mesh = {Adolescent ; Adult ; Animals ; Anthropology, Physical ; Anthropometry/*methods ; Factor Analysis, Statistical ; Hominidae/anatomy & histology ; Humans ; Infant ; Neanderthals/anatomy & histology ; Principal Component Analysis ; Skull/anatomy & histology ; }, abstract = {Currently the most common reporting style for a geometric morphometric (GMM) analysis of anthropological data begins with the principal components of the shape coordinates to which the original landmark data have been converted. But this focus often frustrates the organismal biologist, mainly because principal component analysis (PCA) is not aimed at scientific interpretability of the loading patterns actually uncovered. The difficulty of making biological sense of a PCA is heightened by aspects of the shape coordinate setting that further diverge from our intuitive expectations of how morphometric measurements ought to combine. More than 50 years ago one of our sister disciplines, psychometrics, managed to build an algorithmic route from principal component analysis to scientific understanding via the toolkit generally known as factor analysis. This article introduces a modification of one standard factor-analysis approach, Henry Kaiser's varimax rotation of 1958, that accommodates two of the major differences between the GMM context and the psychometric context for these approaches: the coexistence of "general" and "special" factors of form as adumbrated by Sewall Wright, and the typical loglinearity of partial warp variance as a function of bending energy. I briefly explain the history of principal components in biometrics and the contrast with factor analysis, introduce the modified varimax algorithm I am recommending, and work three examples that are reanalyses of previously published cranial data sets. A closing discussion emphasizes the desirability of superseding PCA by algorithms aimed at anthropological understanding rather than classification or ordination.}, } @article {pmid28754955, year = {2017}, author = {Drucker, DG and Naito, YI and Péan, S and Prat, S and Crépin, L and Chikaraishi, Y and Ohkouchi, N and Puaud, S and Lázničková-Galetová, M and Patou-Mathis, M and Yanevich, A and Bocherens, H}, title = {Isotopic analyses suggest mammoth and plant in the diet of the oldest anatomically modern humans from far southeast Europe.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6833}, pmid = {28754955}, issn = {2045-2322}, mesh = {Animals ; *Carnivory ; Collagen/chemistry ; *Diet ; Europe ; *Fossils ; *Herbivory ; Humans ; Neanderthals/physiology ; Nitrogen Isotopes/analysis ; }, abstract = {Relatively high 15N abundances in bone collagen of early anatomically modern humans in Europe have often been interpreted as a specific consumption of freshwater resources, even if mammoth is an alternative high 15N prey. At Buran-Kaya III, access to associated fauna in a secured archaeological context and application of recently developed isotopic analyses of individuals amino acids offer the opportunity to further examine this hypothesis. The site of Buran-Kaya III is located in south Crimea and has provided a rich archaeological sequence including two Upper Palaeolithic layers, from which human fossils were retrieved and directly dated as from 37.8 to 33.1 ka cal BP. Results from bulk collagen of three human remains suggests the consumption of a high 15N prey besides the contribution of saiga, red deer, horse and hare, whose butchered remains were present at the site. In contrast to bulk collagen, phenylalanine and glutamic acid 15N abundances reflect not only animal but also plant protein contributions to omnivorous diet, and allow disentangling aquatic from terrestrial resource consumption. The inferred human trophic position values point to terrestrial-based diet, meaning a significant contribution of mammoth meat, in addition to a clear intake of plant protein.}, } @article {pmid28744243, year = {2017}, author = {Facco, E and Zanette, G}, title = {The Odyssey of Dental Anxiety: From Prehistory to the Present. A Narrative Review.}, journal = {Frontiers in psychology}, volume = {8}, number = {}, pages = {1155}, pmid = {28744243}, issn = {1664-1078}, abstract = {Dental anxiety (DA) can be considered as a universal phenomenon with a high prevalence worldwide; DA and pain are also the main causes for medical emergencies in the dental office, so their prevention is an essential part of patient safety and overall quality of care. Being DA and its consequences closely related to the fight-or-flight reaction, it seems reasonable to argue that the odyssey of DA began way back in the distant past, and has since probably evolved in parallel with the development of fight-or-flight reactions, implicit memory and knowledge, and ultimately consciousness. Basic emotions are related to survival functions in an inseparable psychosomatic unity that enable an immediate response to critical situations rather than generating knowledge, which is why many anxious patients are unaware of the cause of their anxiety. Archeological findings suggest that humans have been surprisingly skillful and knowledgeable since prehistory. Neanderthals used medicinal plants; and relics of dental tools bear witness to a kind of Neolithic proto-dentistry. In the two millennia BC, Egyptian and Greek physicians used both plants (such as papaver somniferum) and incubation (a forerunner of modern hypnosis, e.g., in the sleep temples dedicated to Asclepius) in the attempt to provide some form of therapy and painless surgery, whereas modern scientific medicine strongly understated the role of subjectivity and mind-body approaches until recently. DA has a wide range of causes and its management is far from being a matter of identifying the ideal sedative drug. A patient's proper management must include assessing his/her dental anxiety, ensuring good communications, and providing information (iatrosedation), effective local anesthesia, hypnosis, and/or a wise use of sedative drugs where necessary. Any weak link in this chain can cause avoidable suffering, mistrust, and emergencies, as well as having lifelong psychological consequences. Iatrosedation and hypnosis are no less relevant than drugs and should be considered as primary tools for the management of DA. Unlike pharmacological sedation, they allow to help patients cope with the dental procedure and also overcome their anxiety: achieving the latter may enable them to face future dental care autonomously, whereas pharmacological sedation can only afford a transient respite.}, } @article {pmid28740249, year = {2017}, author = {Gregory, MD and Kippenhan, JS and Eisenberg, DP and Kohn, PD and Dickinson, D and Mattay, VS and Chen, Q and Weinberger, DR and Saad, ZS and Berman, KF}, title = {Neanderthal-Derived Genetic Variation Shapes Modern Human Cranium and Brain.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6308}, pmid = {28740249}, issn = {2045-2322}, support = {ZIA MH002942/MH/NIMH NIH HHS/United States ; }, mesh = {Adult ; Animals ; Brain/*anatomy & histology ; European Continental Ancestry Group/*genetics ; Evolution, Molecular ; Female ; Fossils ; Gene Flow ; Healthy Volunteers ; Humans ; Magnetic Resonance Imaging ; Male ; Middle Aged ; Neanderthals/anatomy & histology/*genetics ; *Polymorphism, Single Nucleotide ; Skull/*anatomy & histology ; Young Adult ; }, abstract = {Before their disappearance from the fossil record approximately 40,000 years ago, Neanderthals, the ancient hominin lineage most closely related to modern humans, interbred with ancestors of present-day humans. The legacy of this gene flow persists through Neanderthal-derived variants that survive in modern human DNA; however, the neural implications of this inheritance are uncertain. Here, using MRI in a large cohort of healthy individuals of European-descent, we show that the amount of Neanderthal-originating polymorphism carried in living humans is related to cranial and brain morphology. First, as a validation of our approach, we demonstrate that a greater load of Neanderthal-derived genetic variants (higher "NeanderScore") is associated with skull shapes resembling those of known Neanderthal cranial remains, particularly in occipital and parietal bones. Next, we demonstrate convergent NeanderScore-related findings in the brain (measured by gray- and white-matter volume, sulcal depth, and gyrification index) that localize to the visual cortex and intraparietal sulcus. This work provides insights into ancestral human neurobiology and suggests that Neanderthal-derived genetic variation is neurologically functional in the contemporary population.}, } @article {pmid28738867, year = {2017}, author = {Pagel, M}, title = {Q&A: What is human language, when did it evolve and why should we care?.}, journal = {BMC biology}, volume = {15}, number = {1}, pages = {64}, pmid = {28738867}, issn = {1741-7007}, mesh = {Animals ; *Biological Evolution ; Humans ; *Language ; }, abstract = {Human language is unique among all forms of animal communication. It is unlikely that any other species, including our close genetic cousins the Neanderthals, ever had language, and so-called sign 'language' in Great Apes is nothing like human language. Language evolution shares many features with biological evolution, and this has made it useful for tracing recent human history and for studying how culture evolves among groups of people with related languages. A case can be made that language has played a more important role in our species' recent (circa last 200,000 years) evolution than have our genes.}, } @article {pmid28733602, year = {2017}, author = {Mozzi, A and Forni, D and Cagliani, R and Pozzoli, U and Clerici, M and Sironi, M}, title = {Distinct selective forces and Neanderthal introgression shaped genetic diversity at genes involved in neurodevelopmental disorders.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6116}, pmid = {28733602}, issn = {2045-2322}, mesh = {Alleles ; Animals ; *Evolution, Molecular ; Genetic Predisposition to Disease ; *Genetic Variation ; Hominidae ; Humans ; Mammals ; Neanderthals/*genetics ; Neurodevelopmental Disorders/*genetics ; Polymorphism, Single Nucleotide ; *Selection, Genetic ; }, abstract = {In addition to high intelligence, humans evolved specialized social-cognitive skills, which are specifically affected in children with autism spectrum disorder (ASD). Genes affected in ASD represent suitable candidates to study the evolution of human social cognition. We performed an evolutionary analysis on 68 genes associated to neurodevelopmental disorders; our data indicate that genetic diversity was shaped by distinct selective forces, including natural selection and introgression from archaic hominins. We discuss the possibility that segregation distortion during spermatogenesis accounts for a subset of ASD mutations. Finally, we detected modern-human-specific alleles in DYRK1A and TCF4. These variants are located within regions that display chromatin features typical of transcriptional enhancers in several brain areas, strongly suggesting a regulatory role. These SNPs thus represent candidates for association with neurodevelopmental disorders, and await experimental validation in future studies.}, } @article {pmid28726833, year = {2017}, author = {Clarkson, C and Jacobs, Z and Marwick, B and Fullagar, R and Wallis, L and Smith, M and Roberts, RG and Hayes, E and Lowe, K and Carah, X and Florin, SA and McNeil, J and Cox, D and Arnold, LJ and Hua, Q and Huntley, J and Brand, HEA and Manne, T and Fairbairn, A and Shulmeister, J and Lyle, L and Salinas, M and Page, M and Connell, K and Park, G and Norman, K and Murphy, T and Pardoe, C}, title = {Human occupation of northern Australia by 65,000 years ago.}, journal = {Nature}, volume = {547}, number = {7663}, pages = {306-310}, pmid = {28726833}, issn = {1476-4687}, mesh = {Africa/ethnology ; Animals ; Australia ; Diet/history ; Fossils ; Geologic Sediments/analysis ; History, Ancient ; Human Migration/*history ; Humans ; Neanderthals ; }, abstract = {The time of arrival of people in Australia is an unresolved question. It is relevant to debates about when modern humans first dispersed out of Africa and when their descendants incorporated genetic material from Neanderthals, Denisovans and possibly other hominins. Humans have also been implicated in the extinction of Australia's megafauna. Here we report the results of new excavations conducted at Madjedbebe, a rock shelter in northern Australia. Artefacts in primary depositional context are concentrated in three dense bands, with the stratigraphic integrity of the deposit demonstrated by artefact refits and by optical dating and other analyses of the sediments. Human occupation began around 65,000 years ago, with a distinctive stone tool assemblage including grinding stones, ground ochres, reflective additives and ground-edge hatchet heads. This evidence sets a new minimum age for the arrival of humans in Australia, the dispersal of modern humans out of Africa, and the subsequent interactions of modern humans with Neanderthals and Denisovans.}, } @article {pmid28723924, year = {2017}, author = {Alcaraz-Castaño, M and Alcolea-González, J and Kehl, M and Albert, RM and Baena-Preysler, J and de Balbín-Behrmann, R and Cuartero, F and Cuenca-Bescós, G and Jiménez-Barredo, F and López-Sáez, JA and Piqué, R and Rodríguez-Antón, D and Yravedra, J and Weniger, GC}, title = {A context for the last Neandertals of interior Iberia: Los Casares cave revisited.}, journal = {PloS one}, volume = {12}, number = {7}, pages = {e0180823}, pmid = {28723924}, issn = {1932-6203}, mesh = {Animals ; *Archaeology ; Caves ; Climate ; *Fossils ; *Neanderthals ; Radiometric Dating ; Spain ; Technology ; }, abstract = {INTRODUCTION AND OBJECTIVES: Although the Iberian Peninsula is a key area for understanding the Middle to Upper Paleolithic transition and the demise of the Neandertals, valuable evidence for these debates remains scarce and problematic in its interior regions. Sparse data supporting a late Neandertal persistence in the Iberian interior have been recently refuted and hence new evidence is needed to build new models on the timing and causes of Neandertal disappearance in inland Iberia and the whole peninsula. In this study we provide new evidence from Los Casares, a cave located in the highlands of the Spanish Meseta, where a Neandertal-associated Middle Paleolithic site was discovered and first excavated in the 1960's. Our main objective is twofold: (1) provide an updated geoarcheological, paleoenvironmental and chronological framework for this site, and (2) discuss obtained results in the context of the time and nature of the last Neandertal presence in Iberia.

METHODS: We conducted new fieldwork in an interior chamber of Los Casares cave named 'Seno A'. Our methods included micromorphology, sedimentology, radiocarbon dating, Uranium/Thorium dating, palinology, microfaunal analysis, anthracology, phytolith analysis, archeozoology and lithic technology. Here we present results on site formation processes, paleoenvironment and the chronological setting of the Neandertal occupation at Los Casares cave-Seno A.

RESULTS AND DISCUSSION: The sediment sequence reveals a mostly in situ archeological deposit containing evidence of both Neandertal activity and carnivore action in level c, dated to 44,899-42,175 calendar years ago. This occupation occurred during a warm and humid interval of Marine Isotopic Stage 3, probably correlating with Greenland Interstadial 11, representing one of the latest occurrences of Neandertals in the Iberian interior. However, overlying layer b records a deterioration of local environments, thus providing a plausible explanation for the abandonment of the site, and perhaps for the total disappearance of Neandertals of the highlands of inland Iberia during subsequent Greenland Stadials 11 or 10, or even Heinrich Stadial 4. Since layer b provided very few signs of human activity and no reliable chronometric results, and given the scarce chronostratigrapic evidence recorded so far for this period in interior Iberia, this can only be taken as a working hypothesis to be tested with future research. Meanwhile, 42,000 calendar years ago remains the most plausible date for the abandonment of interior Iberia by Neandertals, possibly due to climate deterioration. Currently, a later survival of this human species in Iberia is limited to the southern coasts.}, } @article {pmid28720580, year = {2017}, author = {Peyrégne, S and Boyle, MJ and Dannemann, M and Prüfer, K}, title = {Detecting ancient positive selection in humans using extended lineage sorting.}, journal = {Genome research}, volume = {27}, number = {9}, pages = {1563-1572}, pmid = {28720580}, issn = {1549-5469}, mesh = {Animals ; *Evolution, Molecular ; *Genetics, Population ; Genome, Human/genetics ; Hominidae/*genetics ; Humans ; Neanderthals/genetics ; Selection, Genetic/*genetics ; }, abstract = {Natural selection that affected modern humans early in their evolution has likely shaped some of the traits that set present-day humans apart from their closest extinct and living relatives. The ability to detect ancient natural selection in the human genome could provide insights into the molecular basis for these human-specific traits. Here, we introduce a method for detecting ancient selective sweeps by scanning for extended genomic regions where our closest extinct relatives, Neandertals and Denisovans, fall outside of the present-day human variation. Regions that are unusually long indicate the presence of lineages that reached fixation in the human population faster than expected under neutral evolution. Using simulations, we show that the method is able to detect ancient events of positive selection and that it can differentiate those from background selection. Applying our method to the 1000 Genomes data set, we find evidence for ancient selective sweeps favoring regulatory changes and present a list of genomic regions that are predicted to underlie positively selected human specific traits.}, } @article {pmid28714535, year = {2017}, author = {Rosas, A and Ferrando, A and Bastir, M and García-Tabernero, A and Estalrrich, A and Huguet, R and García-Martínez, D and Pastor, JF and de la Rasilla, M}, title = {Neandertal talus bones from El Sidrón site (Asturias, Spain): A 3D geometric morphometrics analysis.}, journal = {American journal of physical anthropology}, volume = {164}, number = {2}, pages = {394-415}, doi = {10.1002/ajpa.23280}, pmid = {28714535}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; Anthropometry/*methods ; Body Size ; Female ; Fossils ; Humans ; Imaging, Three-Dimensional/*methods ; Male ; Neanderthals/*anatomy & histology ; Principal Component Analysis ; Spain ; Talus/*anatomy & histology ; }, abstract = {OBJECTIVES: The El Sidrón tali sample is assessed in an evolutionary framework. We aim to explore the relationship between Neandertal talus morphology and body size/shape. We test the hypothesis 1: talar Neandertal traits are influenced by body size, and the hypothesis 2: shape variables independent of body size correspond to inherited primitive features.

MATERIALS AND METHODS: We quantify 35 landmarks through 3D geometric morphometrics techniques to describe H. neanderthalensis-H. sapiens shape variation, by Mean Shape Comparisons, Principal Component, Phenetic Clusters, Minimum spanning tree analyses and partial least square and regression of talus shape on body variables. Shape variation correlated to body size is compared to Neandertals-Modern Humans (MH) evolutionary shape variation. The Neandertal sample is compared to early hominins.

RESULTS: Neandertal talus presents trochlear hypertrophy, a larger equality of trochlear rims, a shorter neck, a more expanded head, curvature and an anterior location of the medial malleolar facet, an expanded and projected lateral malleolar facet and laterally expanded posterior calcaneal facet compared to MH.

DISCUSSION: The Neandertal talocrural joint morphology is influenced by body size. The other Neandertal talus traits do not co-vary with it or not follow the same co-variation pattern as MH. Besides, the trochlear hypertrophy, the trochlear rims equality and the short neck could be inherited primitive features; the medial malleolar facet morphology could be an inherited primitive feature or a secondarily primitive trait; and the calcaneal posterior facet would be an autapomorphic feature of the Neandertal lineage.}, } @article {pmid28689038, year = {2017}, author = {Árnason, Ú}, title = {A phylogenetic view of the Out of Asia/Eurasia and Out of Africa hypotheses in the light of recent molecular and palaeontological finds.}, journal = {Gene}, volume = {627}, number = {}, pages = {473-476}, doi = {10.1016/j.gene.2017.07.006}, pmid = {28689038}, issn = {1879-0038}, mesh = {Continental Population Groups/*genetics ; *Evolution, Molecular ; Genome, Human ; *Human Migration ; Humans ; Pedigree ; *Phylogeny ; }, abstract = {The substantiality of the Out of Africa hypothesis was addressed in the light of recent genomic analysis of extant humans (Homo sapiens sapiens, Hss) and progress in Neanderthal palaeontology. The examination lent no support to the commonly assumed Out of Africa scenario but favoured instead a Eurasian divergence between Neanderthals and Hss (the Askur/Embla hypothesis) and an Out of Asia/Eurasia hypothesis according to which all other parts of the world were colonized by Hss migrations from Asia. The examination suggested furthermore that the ancestors of extant KhoeSan and Mbuti composed the first Hss dispersal(s) into Africa and that the ancestors of Yoruba made up a later wave into the same continent. The conclusions constitute a change in paradigm for the study of human evolution.}, } @article {pmid28688460, year = {2017}, author = {Becerra-Valdivia, L and Douka, K and Comeskey, D and Bazgir, B and Conard, NJ and Marean, CW and Ollé, A and Otte, M and Tumung, L and Zeidi, M and Higham, TFG}, title = {Chronometric investigations of the Middle to Upper Paleolithic transition in the Zagros Mountains using AMS radiocarbon dating and Bayesian age modelling.}, journal = {Journal of human evolution}, volume = {109}, number = {}, pages = {57-69}, doi = {10.1016/j.jhevol.2017.05.011}, pmid = {28688460}, issn = {1095-8606}, mesh = {Africa ; Animals ; Bayes Theorem ; Biological Evolution ; Fossils ; *Hominidae ; Humans ; Iran ; Mass Spectrometry/methods ; Neanderthals ; *Paleontology ; Radiometric Dating ; }, abstract = {The Middle to Upper Paleolithic transition is often linked with a bio-cultural shift involving the dispersal of modern humans outside of Africa, the concomitant replacement of Neanderthals across Eurasia, and the emergence of new technological traditions. The Zagros Mountains region assumes importance in discussions concerning this period as its geographic location is central to all pertinent hominin migration areas, pointing to both east and west. As such, establishing a reliable chronology in the Zagros Mountains is crucial to our understanding of these biological and cultural developments. Political circumstance, coupled with the poor preservation of organic material, has meant that a clear chronological definition of the Middle to Upper Paleolithic transition for the Zagros Mountains region has not yet been achieved. To improve this situation, we have obtained new archaeological samples for AMS radiocarbon dating from three sites: Kobeh Cave, Kaldar Cave, and Ghār-e Boof (Iran). In addition, we have statistically modelled previously published radiocarbon determinations for Yafteh Cave (Iran) and Shanidar Cave (Iraqi Kurdistan), to improve their chronological resolution and enable us to compare the results with the new dataset. Bayesian modelling results suggest that the onset of the Upper Paleolithic in the Zagros Mountains dates to 45,000-40,250 cal BP (68.2% probability). Further chronometric data are required to improve the precision of this age range.}, } @article {pmid28688457, year = {2017}, author = {Bartsiokas, A and Arsuaga, JL and Aubert, M and Grün, R}, title = {U-series dating and classification of the Apidima 2 hominin from Mani Peninsula, Southern Greece.}, journal = {Journal of human evolution}, volume = {109}, number = {}, pages = {22-29}, doi = {10.1016/j.jhevol.2017.04.008}, pmid = {28688457}, issn = {1095-8606}, mesh = {Animals ; Facial Bones/anatomy & histology ; Fossils/*anatomy & histology ; Greece ; Hominidae/*anatomy & histology ; Humans ; Neanderthals/anatomy & histology ; Skull/*anatomy & histology ; }, abstract = {Laser ablation U-series dating results on a human cranial bone fragment from Apidima, on the western cost of the Mani Peninsula, Southern Greece, indicate a minimum age of 160,000 years. The dated cranial fragment belongs to Apidima 2, which preserves the facial skeleton and a large part of the braincase, lacking the occipital bone. The morphology of the preserved regions of the cranium, and especially that of the facial skeleton, indicates that the fossil belongs to the Neanderthal clade. The dating of the fossil at a minimum age of 160,000 years shows that most of the Neanderthal traits were already present in the MIS 6 and perhaps earlier. This makes Apidima 2 the earliest known fossil with a clear Neanderthal facial morphology. Together with the nearby younger Neanderthal specimens from Lakonis and Kalamakia, the Apidima crania are of crucial importance for the evolution of Neanderthals in the area during the Middle to Late Pleistocene. It can be expected that systematic direct dating of the other human fossils from this area will elucidate our understanding of Neanderthal evolution and demise.}, } @article {pmid28684477, year = {2017}, author = {Gibbons, A}, title = {Neandertals mated early with modern humans.}, journal = {Science (New York, N.Y.)}, volume = {357}, number = {6346}, pages = {14}, doi = {10.1126/science.357.6346.14}, pmid = {28684477}, issn = {1095-9203}, mesh = {Animals ; Anthropology ; *Biological Evolution ; DNA, Ancient ; DNA, Mitochondrial/*genetics ; Female ; Fossils ; Germany ; Humans ; Male ; Neanderthals/*genetics ; *Sexual Behavior, Animal ; }, } @article {pmid28675384, year = {2017}, author = {Posth, C and Wißing, C and Kitagawa, K and Pagani, L and van Holstein, L and Racimo, F and Wehrberger, K and Conard, NJ and Kind, CJ and Bocherens, H and Krause, J}, title = {Deeply divergent archaic mitochondrial genome provides lower time boundary for African gene flow into Neanderthals.}, journal = {Nature communications}, volume = {8}, number = {}, pages = {16046}, pmid = {28675384}, issn = {2041-1723}, mesh = {African Continental Ancestry Group/*genetics ; Animals ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Femur ; *Gene Flow ; Genome, Human/genetics ; *Genome, Mitochondrial ; Germany ; Hominidae/*genetics ; Humans ; Neanderthals/*genetics ; Time Factors ; }, abstract = {Ancient DNA is revealing new insights into the genetic relationship between Pleistocene hominins and modern humans. Nuclear DNA indicated Neanderthals as a sister group of Denisovans after diverging from modern humans. However, the closer affinity of the Neanderthal mitochondrial DNA (mtDNA) to modern humans than Denisovans has recently been suggested as the result of gene flow from an African source into Neanderthals before 100,000 years ago. Here we report the complete mtDNA of an archaic femur from the Hohlenstein-Stadel (HST) cave in southwestern Germany. HST carries the deepest divergent mtDNA lineage that splits from other Neanderthals ∼270,000 years ago, providing a lower boundary for the time of the putative mtDNA introgression event. We demonstrate that a complete Neanderthal mtDNA replacement is feasible over this time interval even with minimal hominin introgression. The highly divergent HST branch is indicative of greater mtDNA diversity during the Middle Pleistocene than in later periods.}, } @article {pmid28622932, year = {2017}, author = {Sullivan, AP and de Manuel, M and Marques-Bonet, T and Perry, GH}, title = {An evolutionary medicine perspective on Neandertal extinction.}, journal = {Journal of human evolution}, volume = {108}, number = {}, pages = {62-71}, doi = {10.1016/j.jhevol.2017.03.004}, pmid = {28622932}, issn = {1095-8606}, mesh = {Animals ; Biological Evolution ; *Extinction, Biological ; *Genetic Variation ; Genome, Human ; Hominidae ; Humans ; Infection/transmission ; Neanderthals/*genetics ; Polymorphism, Genetic ; *Sympatry ; Time Factors ; }, abstract = {The Eurasian sympatry of Neandertals and anatomically modern humans - beginning at least 45,000 years ago and possibly lasting for more than 5000 years - has sparked immense anthropological interest into the factors that potentially contributed to Neandertal extinction. Among many different hypotheses, the "differential pathogen resistance" extinction model posits that Neandertals were disproportionately affected by exposure to novel infectious diseases that were transmitted during the period of spatiotemporal sympatry with modern humans. Comparisons of new archaic hominin paleogenome sequences with modern human genomes have confirmed a history of genetic admixture - and thus direct contact - between humans and Neandertals. Analyses of these data have also shown that Neandertal nuclear genome genetic diversity was likely considerably lower than that of the Eurasian anatomically modern humans with whom they came into contact, perhaps leaving Neandertal innate immune systems relatively more susceptible to novel pathogens. In this study, we compared levels of genetic diversity in genes for which genetic variation is hypothesized to benefit pathogen defense among Neandertals and African, European, and Asian modern humans, using available exome sequencing data (three individuals, or six chromosomes, per population). We observed that Neandertals had only 31-39% as many nonsynonymous (amino acid changing) polymorphisms across 73 innate immune system genes compared to modern human populations. We also found that Neandertal genetic diversity was relatively low in an unbiased set of balancing selection candidate genes for primates, those genes with the highest 1% genetic diversity genome-wide in non-human hominoids (apes). In contrast, Neandertals had similar or higher levels of genetic diversity than humans in 12 major histocompatibility complex (MHC) genes. Thus, while Neandertals may have been relatively more susceptible to some novel pathogens and differential pathogen resistance could be considered as one potential contributing factor in their extinction, the expectations of this model are not universally met.}, } @article {pmid28622931, year = {2017}, author = {Bastir, M and García Martínez, D and Rios, L and Higuero, A and Barash, A and Martelli, S and García Tabernero, A and Estalrrich, A and Huguet, R and de la Rasilla, M and Rosas, A}, title = {Three-dimensional morphometrics of thoracic vertebrae in Neandertals and the fossil evidence from El Sidrón (Asturias, Northern Spain).}, journal = {Journal of human evolution}, volume = {108}, number = {}, pages = {47-61}, doi = {10.1016/j.jhevol.2017.03.008}, pmid = {28622931}, issn = {1095-8606}, mesh = {Animals ; Fossils/*anatomy & histology ; Humans ; Neanderthals/*anatomy & histology ; Organ Size ; Ribs/anatomy & histology ; Spain ; Thoracic Vertebrae/*anatomy & histology ; Thorax/anatomy & histology ; }, abstract = {Well preserved thoracic vertebrae of Neandertals are rare. However, such fossils are important as their three-dimensional (3D) spatial configuration can contribute to the understanding of the size and shape of the thoracic spine and the entire thorax. This is because the vertebral body and transverse processes provide the articulation and attachment sites for the ribs. Dorsal orientation of the transverse processes relative to the vertebral body also rotates the attached ribs in a way that could affect thorax width. Previous research indicates possible evidence for greater dorsal orientation of the transverse processes and small vertebral body heights in Neandertals, but their 3D vertebral structure has not yet been addressed. Here we present 15 new vertebral remains from the El Sidrón Neandertals (Asturias, Northern Spain) and used 3D geometric morphometrics to address the above issues by comparing two particularly well preserved El Sidrón remains (SD-1619, SD-1641) with thoracic vertebrae from other Neandertals and a sample of anatomically modern humans. Centroid sizes of El Sidrón vertebrae are within the human range. Neandertals have larger T1 and probably also T2. The El Sidrón vertebrae are similar in 3D shape to those of other Neandertals, which differ from Homo sapiens particularly in central-lower regions (T6-T10) of the thoracic spine. Differences include more dorsally and cranially oriented transverse processes, less caudally oriented spinous processes, and vertebral bodies that are anteroposteriorly and craniocaudally short. The results fit with current reconstructions of Neandertal thorax morphology.}, } @article {pmid28622926, year = {2017}, author = {Nejman, L and Wood, R and Wright, D and Lisá, L and Nerudová, Z and Neruda, P and Přichystal, A and Svoboda, J}, title = {Hominid visitation of the Moravian Karst during the Middle-Upper Paleolithic transition: New results from Pod Hradem Cave (Czech Republic).}, journal = {Journal of human evolution}, volume = {108}, number = {}, pages = {131-146}, doi = {10.1016/j.jhevol.2017.03.015}, pmid = {28622926}, issn = {1095-8606}, mesh = {Animals ; Archaeology/*methods ; *Caves ; Czech Republic ; *Hominidae ; Humans ; Radiometric Dating ; }, abstract = {In 1956-1958, excavations of Pod Hradem Cave in Moravia (eastern Czech Republic) revealed evidence for human activity during the Middle-Upper Paleolithic transition. This spanned 25,050-44,800 cal BP and contained artefacts attributed to the Aurignacian and Szeletian cultures, including those made from porcelanite (rarely used at Moravian Paleolithic sites). Coarse grained excavation techniques and major inversions in radiocarbon dates meant that site chronology could not be established adequately. This paper documents re-excavation of Pod Hradem in 2011-2012. A comprehensive AMS dating program using ultrafiltration and ABOx-SC pre-treatments provides new insights into human occupation at Pod Hradem Cave. Fine-grained excavation reveals sedimentary units spanning approximately 20,000 years of the Early Upper Paleolithic and late Middle Paleolithic periods, thus making it the first archaeological cave site in the Czech Republic with such a sedimentary and archaeological record. Recent excavation confirms infrequent human visitation, including during the Early Aurignacian by people who brought with them portable art objects that have no parallel in the Czech Republic. Raw material diversity of lithics suggests long-distance imports and ephemeral visits by highly mobile populations throughout the EUP period.}, } @article {pmid28605019, year = {2017}, author = {Toussaint, M and Verna, C and Le Cabec, A and Gómez-Robles, A and Draily, C and Richards, MP and Pirson, S}, title = {The Late Neandertal permanent lower left third premolar from Walou Cave (Trooz, Belgium) and its context.}, journal = {American journal of physical anthropology}, volume = {164}, number = {1}, pages = {193-202}, doi = {10.1002/ajpa.23252}, pmid = {28605019}, issn = {1096-8644}, mesh = {Animals ; Belgium ; Bicuspid/*anatomy & histology/*pathology ; Diet ; History, Ancient ; Neanderthals/*anatomy & histology ; Paleodontology ; }, abstract = {OBJECTIVES: We describe a hominin permanent lower left third premolar unearthed in 1997 at Walou Cave (Belgium), found in direct association with a Mousterian lithic industry, in a layer directly dated to 40-38,000 years BP.

MATERIALS AND METHODS: The taxonomical attribution of the tooth is addressed through comparative morphometric analyses, and stable isotope analyses aimed at determining the diet of the individual.

RESULTS: The Walou P3 plots within the Neandertal range of variation and is significantly different from recent modern humans in all morphometric assessments. The isotope data showed that like other Neandertals, the Walou individual acquired its dietary proteins primarily from terrestrial food sources.

DISCUSSION: We discuss the implications of the existence of a clearly Neandertal premolar dating to the period of the Middle to Upper Paleolithic transition in the Meuse river basin.}, } @article {pmid28602430, year = {2018}, author = {O'Connell, TC and Collins, MJ}, title = {Comment on "Ecological niche of Neanderthals from Spy Cave revealed by nitrogen isotopes of individual amino acids in collagen" [J. Hum. Evol. 93 (2016) 82-90].}, journal = {Journal of human evolution}, volume = {117}, number = {}, pages = {53-55}, doi = {10.1016/j.jhevol.2017.05.006}, pmid = {28602430}, issn = {1095-8606}, } @article {pmid28592838, year = {2017}, author = {Been, E and Hovers, E and Ekshtain, R and Malinski-Buller, A and Agha, N and Barash, A and Mayer, DEB and Benazzi, S and Hublin, JJ and Levin, L and Greenbaum, N and Mitki, N and Oxilia, G and Porat, N and Roskin, J and Soudack, M and Yeshurun, R and Shahack-Gross, R and Nir, N and Stahlschmidt, MC and Rak, Y and Barzilai, O}, title = {The first Neanderthal remains from an open-air Middle Palaeolithic site in the Levant.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2958}, pmid = {28592838}, issn = {2045-2322}, mesh = {Animals ; *Archaeology ; Bone and Bones/anatomy & histology ; *Fossils ; *Hominidae ; Humans ; Israel ; *Neanderthals ; }, abstract = {The late Middle Palaeolithic (MP) settlement patterns in the Levant included the repeated use of caves and open landscape sites. The fossil record shows that two types of hominins occupied the region during this period-Neandertals and Homo sapiens. Until recently, diagnostic fossil remains were found only at cave sites. Because the two populations in this region left similar material cultural remains, it was impossible to attribute any open-air site to either species. In this study, we present newly discovered fossil remains from intact archaeological layers of the open-air site 'Ein Qashish, in northern Israel. The hominin remains represent three individuals: EQH1, a nondiagnostic skull fragment; EQH2, an upper right third molar (RM3); and EQH3, lower limb bones of a young Neandertal male. EQH2 and EQH3 constitute the first diagnostic anatomical remains of Neandertals at an open-air site in the Levant. The optically stimulated luminescence ages suggest that Neandertals repeatedly visited 'Ein Qashish between 70 and 60 ka. The discovery of Neandertals at open-air sites during the late MP reinforces the view that Neandertals were a resilient population in the Levant shortly before Upper Palaeolithic Homo sapiens populated the region.}, } @article {pmid28591159, year = {2017}, author = {Carmignani, L and Moncel, MH and Fernandes, P and Wilson, L}, title = {Technological variability during the Early Middle Palaeolithic in Western Europe. Reduction systems and predetermined products at the Bau de l'Aubesier and Payre (South-East France).}, journal = {PloS one}, volume = {12}, number = {6}, pages = {e0178550}, pmid = {28591159}, issn = {1932-6203}, mesh = {Animals ; Europe ; France ; Geography ; *Geologic Sediments ; Models, Theoretical ; Neanderthals/*physiology ; *Technology ; Time Factors ; *Tool Use Behavior ; }, abstract = {The study of the lithic assemblages of two French sites, the Bau de l'Aubesier and Payre, contributes new knowledge of the earliest Neanderthal techno-cultural variability. In this paper we present the results of a detailed technological analysis of Early Middle Palaeolithic lithic assemblages of MIS 8 and 7 age from the two sites, which are located on opposite sides of the Rhône Valley in the south-east of France. The MIS 9-7 period is considered in Europe to be a time of new behaviours, especially concerning lithic strategies. The shift from the Lower Palaeolithic to the Early Middle Palaeolithic is "classically" defined by an increase in the number of core technologies, including standardized ones, which are stabilized in the full Middle Palaeolithic (MIS 5-3), associated with the decline of the "Acheulean" biface. Applying a common technological approach to the analysis of the two assemblages highlights their technological variability with respect to reduction systems and end products. Differences between Payre and the Bau de l'Aubesier concerning raw material procurement and faunal exploitation only partially explain this multifaceted technological variability, which in our opinion also reflects the existence of distinct technological strategies within the same restricted geographic area, which are related to distinct traditions, site uses, and/or as yet unknown parameters.}, } @article {pmid28542642, year = {2017}, author = {Bicho, N and Cascalheira, J and Gonçalves, C}, title = {Early Upper Paleolithic colonization across Europe: Time and mode of the Gravettian diffusion.}, journal = {PloS one}, volume = {12}, number = {5}, pages = {e0178506}, pmid = {28542642}, issn = {1932-6203}, mesh = {Animals ; Europe ; History, Ancient ; Hominidae ; Humans ; Linear Models ; Models, Theoretical ; Neanderthals ; Population Dynamics/*history ; Radiometric Dating ; }, abstract = {This study presents new models on the origin, speed and mode of the wave-of-advance leading to the definitive occupation of Europe's outskirts by Anatomically Modern Humans, during the Gravettian, between c. 37 and 30 ka ago. These models provide the estimation for possible demic dispersal routes for AMH at a stable spread rate of c. 0.7 km/year, with the likely origin in Central Europe at the site of Geissenklosterle in Germany and reaching all areas of the European landscape. The results imply that: 1. The arrival of the Gravettian populations into the far eastern European plains and to southern Iberia found regions with very low human occupation or even devoid of hominins; 2. Human demography was likely lower than previous estimates for the Upper Paleolithic; 3. The likely early AMH paths across Europe followed the European central plains and the Mediterranean coast to reach to the ends of the Italian and Iberian peninsulas.}, } @article {pmid28526291, year = {2017}, author = {Douka, K and Slon, V and Stringer, C and Potts, R and Hübner, A and Meyer, M and Spoor, F and Pääbo, S and Higham, T}, title = {Direct radiocarbon dating and DNA analysis of the Darra-i-Kur (Afghanistan) human temporal bone.}, journal = {Journal of human evolution}, volume = {107}, number = {}, pages = {86-93}, doi = {10.1016/j.jhevol.2017.03.003}, pmid = {28526291}, issn = {1095-8606}, mesh = {Afghanistan ; *Fossils ; Humans ; Male ; Radiometric Dating/*methods ; *Temporal Bone ; }, abstract = {The temporal bone discovered in the 1960s from the Darra-i-Kur cave in Afghanistan is often cited as one of the very few Pleistocene human fossils from Central Asia. Here we report the first direct radiocarbon date for the specimen and the genetic analyses of DNA extracted and sequenced from two areas of the bone. The new radiocarbon determination places the find to ∼4500 cal BP (∼2500 BCE) contradicting an assumed Palaeolithic age of ∼30,000 years, as originally suggested. The DNA retrieved from the specimen originates from a male individual who carried mitochondrial DNA of the modern human type. The petrous part yielded more endogenous ancient DNA molecules than the squamous part of the same bone. Molecular dating of the Darra-i-Kur mitochondrial DNA sequence corroborates the radiocarbon date and suggests that the specimen is younger than previously thought. Taken together, the results consolidate the fact that the human bone is not associated with the Pleistocene-age deposits of Darra-i-Kur; instead it is intrusive, possibly re-deposited from upper levels dating to much later periods (Neolithic). Despite its Holocene age, the Darra-i-Kur specimen is, so far, the first and only ancient human from Afghanistan whose DNA has been sequenced.}, } @article {pmid28464262, year = {2017}, author = {Reales, G and Rovaris, DL and Jacovas, VC and Hünemeier, T and Sandoval, JR and Salazar-Granara, A and Demarchi, DA and Tarazona-Santos, E and Felkl, AB and Serafini, MA and Salzano, FM and Bisso-Machado, R and Comas, D and Paixão-Côrtes, VR and Bortolini, MC}, title = {A tale of agriculturalists and hunter-gatherers: Exploring the thrifty genotype hypothesis in native South Americans.}, journal = {American journal of physical anthropology}, volume = {163}, number = {3}, pages = {591-601}, doi = {10.1002/ajpa.23233}, pmid = {28464262}, issn = {1096-8644}, mesh = {Agriculture/*history ; Anthropology, Physical ; Apolipoproteins E/genetics ; CD36 Antigens/genetics ; Genotype ; History, Ancient ; Humans ; Indians, South American/*genetics/*history ; Polymorphism, Single Nucleotide/*genetics ; RNA-Binding Proteins/genetics ; }, abstract = {OBJECTIVES: To determine genetic differences between agriculturalist and hunter-gatherer southern Native American populations for selected metabolism-related markers and to test whether Neel's thrifty genotype hypothesis (TGH) could explain the genetic patterns observed in these populations.

MATERIALS AND METHODS: 375 Native South American individuals from 17 populations were genotyped using six markers (APOE rs429358 and rs7412; APOA2 rs5082; CD36 rs3211883; TCF7L2 rs11196205; and IGF2BP2 rs11705701). Additionally, APOE genotypes from 39 individuals were obtained from the literature. AMOVA, main effects, and gene-gene interaction tests were performed.

RESULTS: We observed differences in allele distribution patterns between agriculturalists and hunter-gatherers for some markers. For instance, between-groups component of genetic variance (FCT) for APOE rs429358 showed strong differences in allelic distributions between hunter-gatherers and agriculturalists (p = 0.00196). Gene-gene interaction analysis indicated that the APOE E4/CD36 TT and APOE E4/IGF2BP2 A carrier combinations occur at a higher frequency in hunter-gatherers, but this combination is not replicated in archaic (Neanderthal and Denisovan) and ancient (Anzick, Saqqaq, Ust-Ishim, Mal'ta) hunter-gatherer individuals.

DISCUSSION: A complex scenario explains the observed frequencies of the tested markers in hunter-gatherers. Different factors, such as pleotropic alleles, rainforest selective pressures, and population dynamics, may be collectively shaping the observed genetic patterns. We conclude that although TGH seems a plausible hypothesis to explain part of the data, other factors may be important in our tested populations.}, } @article {pmid28450591, year = {2017}, author = {Wade, L}, title = {DNA from cave soil reveals ancient human occupants.}, journal = {Science (New York, N.Y.)}, volume = {356}, number = {6336}, pages = {363}, doi = {10.1126/science.356.6336.363}, pmid = {28450591}, issn = {1095-9203}, mesh = {Animals ; *Caves ; DNA, Ancient/*isolation & purification ; Geologic Sediments/chemistry ; Humans ; Neanderthals/*genetics ; Paleontology/*methods ; Sequence Analysis, DNA ; Soil/chemistry ; }, } @article {pmid28450384, year = {2017}, author = {Slon, V and Hopfe, C and Weiß, CL and Mafessoni, F and de la Rasilla, M and Lalueza-Fox, C and Rosas, A and Soressi, M and Knul, MV and Miller, R and Stewart, JR and Derevianko, AP and Jacobs, Z and Li, B and Roberts, RG and Shunkov, MV and de Lumley, H and Perrenoud, C and Gušić, I and Kućan, Ž and Rudan, P and Aximu-Petri, A and Essel, E and Nagel, S and Nickel, B and Schmidt, A and Prüfer, K and Kelso, J and Burbano, HA and Pääbo, S and Meyer, M}, title = {Neandertal and Denisovan DNA from Pleistocene sediments.}, journal = {Science (New York, N.Y.)}, volume = {356}, number = {6338}, pages = {605-608}, doi = {10.1126/science.aam9695}, pmid = {28450384}, issn = {1095-9203}, mesh = {Animals ; Caves ; DNA, Ancient/analysis/*isolation & purification ; DNA, Mitochondrial/analysis/*isolation & purification ; Europe ; Fossils ; Geologic Sediments/chemistry ; Hominidae/*classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {Although a rich record of Pleistocene human-associated archaeological assemblages exists, the scarcity of hominin fossils often impedes the understanding of which hominins occupied a site. Using targeted enrichment of mitochondrial DNA, we show that cave sediments represent a rich source of ancient mammalian DNA that often includes traces of hominin DNA, even at sites and in layers where no hominin remains have been discovered. By automation-assisted screening of numerous sediment samples, we detected Neandertal DNA in eight archaeological layers from four caves in Eurasia. In Denisova Cave, we retrieved Denisovan DNA in a Middle Pleistocene layer near the bottom of the stratigraphy. Our work opens the possibility of detecting the presence of hominin groups at sites and in areas where no skeletal remains are found.}, } @article {pmid28447043, year = {2017}, author = {Dehbashi, M and Kamali, E and Vallian, S}, title = {Comparative genomics of human stem cell factor (SCF).}, journal = {Molecular biology research communications}, volume = {6}, number = {1}, pages = {1-11}, pmid = {28447043}, issn = {2322-181X}, abstract = {Stem cell factor (SCF) is a critical protein with key roles in the cell such as hematopoiesis, gametogenesis and melanogenesis. In the present study a comparative analysis on nucleotide sequences of SCF was performed in Humanoids using bioinformatics tools including NCBI-BLAST, MEGA6, and JBrowse. Our analysis of nucleotide sequences to find closely evolved organisms with high similarity by NCBI-BLAST tools and MEGA6 showed that human and Chimpanzee (Pan troglodytes) were placed into the same cluster. By using JBrowse, we found that SCF in Neanderthal had a single copy number similar to modern human and partly conserved nucleotide sequences. Together, the results approved the gene flow and genetics similarity of SCF among human and P. troglodytes. This may suggest that during evolution, SCF gene transferred partly intact either on the basis of sequence or function from the same ancestors to P. troglodytes, the ancient human like Neanderthal, and then to the modern human.}, } @article {pmid28444387, year = {2017}, author = {Jégou, B and Sankararaman, S and Rolland, AD and Reich, D and Chalmel, F}, title = {Meiotic Genes Are Enriched in Regions of Reduced Archaic Ancestry.}, journal = {Molecular biology and evolution}, volume = {34}, number = {8}, pages = {1974-1980}, pmid = {28444387}, issn = {1537-1719}, support = {R00 GM111744/GM/NIGMS NIH HHS/United States ; R01 GM100233/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Alleles ; Animals ; Databases, Genetic ; Evolution, Molecular ; Gene Expression Regulation, Developmental/genetics ; Genome, Human/genetics ; Genomics ; Hominidae/*genetics ; Humans ; Male ; Meiosis/*genetics ; Neanderthals/*genetics ; Selection, Genetic ; Testis ; }, abstract = {About 1-6% of the genetic ancestry of modern humans today originates from admixture with archaic humans. It has recently been shown that autosomal genomic regions with a reduced proportion of Neanderthal and Denisovan ancestries (NA and DA) are significantly enriched in genes that are more expressed in testis than in other tissues. To determine whether a cellular segregation pattern would exist, we combined maps of archaic introgression with a cross-analysis of three transcriptomic datasets deciphering the transcriptional landscape of human gonadal cell types. We reveal that the regions deficient in both NA and DA contain a significant enrichment of genes transcribed in meiotic germ cells. The interbreeding of anatomically modern humans with archaic humans may have introduced archaic-derived alleles that contributed to genetic incompatibilities affecting meiosis that were subsequently purged by natural selection.}, } @article {pmid28434542, year = {2017}, author = {Gómez-Olivencia, A and Arlegi, M and Barash, A and Stock, JT and Been, E}, title = {The Neandertal vertebral column 2: The lumbar spine.}, journal = {Journal of human evolution}, volume = {106}, number = {}, pages = {84-101}, doi = {10.1016/j.jhevol.2017.01.006}, pmid = {28434542}, issn = {1095-8606}, mesh = {Animals ; Hominidae ; Humans ; Lordosis/pathology ; Lumbar Vertebrae/*anatomy & histology ; Neanderthals/*anatomy & histology ; Posture ; Spine/anatomy & histology ; }, abstract = {Here we provide the most extensive metric and morphological analysis performed to date on the Neandertal lumbar spine. Neandertal lumbar vertebrae show differences from modern humans in both the vertebral body and in the neural arch, although not all Neandertal lumbar vertebrae differ from modern humans in the same way. Differences in the vertebral foramen are restricted to the lowermost lumbar vertebrae (L4 and L5), differences in the orientation of the upper articular facets appear in the uppermost lumbar vertebrae (probably in L1 and L2-L3), and differences in the horizontal angle of the transverse process appear in L2-L4. Neandertals, when compared to modern humans, show a smaller degree of lumbar lordosis. Based on a still limited fossil sample, early hominins (australopiths and Homo erectus) had a lumbar lordosis that was similar to but below the mean of modern humans. Here, we hypothesize that from this ancestral degree of lumbar lordosis, the Neandertal lineage decreased their lumbar lordosis and Homo sapiens slightly increased theirs. From a postural point of view, the lower degree of lordosis is related to a more vertical position of the sacrum, which is also positioned more ventrally with respect to the dorsal end of the pelvis. This results in a spino-pelvic alignment that, though different from modern humans, maintained an economic postural equilibrium. Some features, such as a lower degree of lumbar lordosis, were already present in the middle Pleistocene populations ancestral to Neandertals. However, these middle Pleistocene populations do not show the full suite of Neandertal lumbar morphologies, which probably means that the characteristic features of the Neandertal lumbar spine did not arise all at once.}, } @article {pmid28434540, year = {2017}, author = {Ao, H and Liu, CR and Roberts, AP and Zhang, P and Xu, X}, title = {An updated age for the Xujiayao hominin from the Nihewan Basin, North China: Implications for Middle Pleistocene human evolution in East Asia.}, journal = {Journal of human evolution}, volume = {106}, number = {}, pages = {54-65}, doi = {10.1016/j.jhevol.2017.01.014}, pmid = {28434540}, issn = {1095-8606}, mesh = {Animals ; China ; *Electron Spin Resonance Spectroscopy ; *Fossils ; *Hominidae ; Humans ; Molar ; Neanderthals ; Time Factors ; }, abstract = {The Xujiayao site in the Nihewan Basin (North China) is one of the most important Paleolithic sites in East Asia. Twenty Homo fossils, which were previously assigned to an archaic Homo sapiens group, have been excavated along with more than 30,000 lithic artifacts and ∼5000 mammalian fossil specimens. Dating of the Xujiayao hominin has been pursued since its excavation in the 1970s, but its age has remained controversial because of limitations of the dating techniques that have been applied to available materials. Here, we report new ages for the Xujiayao hominin based on combined electron spin resonance (ESR) dating of quartz in the sediments and high-resolution magnetostratigraphy of the fluvio-lacustrine sequence. The magnetostratigraphy suggests that the upper Matuyama and Brunhes polarity chrons are recorded at Xujiayao. The ESR dating results indicate a pooled average age of 260-370 ka for the Homo-bearing layer, which is consistent with its position within the middle Brunhes normal polarity chron indicated by magnetostratigraphy. This age estimate makes the Xujiayao hominin among the oldest mid-Pleistocene hominins with derived Neanderthal traits in East Asia. This age is consistent with the time when early Denisovans, a sister group of Neanderthals, appeared and colonized eastern Eurasia. Our updated age and the Neanderthal-like traits of the Xujiayao Homo fossils, particularly the Denisovan-like molar teeth, make it possible that the Xujiayao hominin could represent an early Denisovan.}, } @article {pmid28434539, year = {2017}, author = {Pérez-Criado, L and Rosas, A}, title = {Evolutionary anatomy of the Neandertal ulna and radius in the light of the new El Sidrón sample.}, journal = {Journal of human evolution}, volume = {106}, number = {}, pages = {38-53}, doi = {10.1016/j.jhevol.2017.01.016}, pmid = {28434539}, issn = {1095-8606}, mesh = {Adolescent ; Adult ; Animals ; *Biological Evolution ; Fossils ; Hominidae/anatomy & histology ; Humans ; Neanderthals/*anatomy & histology ; Phylogeny ; Radius/*anatomy & histology ; Spain ; Ulna/*anatomy & histology ; }, abstract = {This paper aims to improve our understanding of the phylogenetic trait polarity related to hominin forearm evolution, in particular those traits traditionally defined as "Neandertal features." To this aim, twelve adult and adolescent fragmented forelimb elements (including ulnae and radii) of Homo neanderthalensis recovered from the site of El Sidrón (Asturias, Spain) were examined comparatively using three-dimensional geometric and traditional morphometrics. Mean centroid size and shape comparisons, principal components analysis, and phylogenetic signal analysis were undertaken. Our investigations revealed that the proximal region of the ulna discriminated best between Neandertals and modern humans, with fewer taxonomically-informative features in the distal ulna and radius. Compared to modern humans, the divergent features in the Neandertal ulna are an increase in olecranon breadth (a derived trait), lower coronoid length (primitive), and anterior orientation of the trochlear notch (primitive). In the Neandertal radius, we observe a larger neck length (primitive), medial orientation of the radial tubercle (secondarily primitive), and a curved diaphysis (secondarily primitive). Anatomically, we identified three units of evolutionary change: 1) the olecranon and its fossa, 2) the coronoid-radius neck complex, and 3) the tubercle and radial diaphysis. Based on our data, forearm evolution followed a mosaic pattern in which some features were inherited from a pre-Homo ancestor, others originated in some post-ergaster and pre-antecessor populations, and other characters emerged in the specific Homo sapiens and H. neanderthalensis lineages, sometimes appearing as secondarily primitive. Future investigations might consider the diverse phylogenetic origin of apomorphies while at the same time seeking to elucidate their functional meaning.}, } @article {pmid28432824, year = {2017}, author = {Šešelj, M}, title = {An analysis of dental development in Pleistocene Homo using skeletal growth and chronological age.}, journal = {American journal of physical anthropology}, volume = {163}, number = {3}, pages = {531-541}, doi = {10.1002/ajpa.23228}, pmid = {28432824}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; *Femur/anatomy & histology/growth & development ; *Hominidae/anatomy & histology/growth & development ; *Neanderthals/anatomy & histology/growth & development ; Odontogenesis/*physiology ; *Tooth/anatomy & histology/growth & development ; }, abstract = {OBJECTIVES: This study takes a new approach to interpreting dental development in Pleistocene Homo in comparison with recent modern humans. As rates of dental development and skeletal growth are correlated given age in modern humans, using age and skeletal growth in tandem yields more accurate dental development estimates. Here, I apply these models to fossil Homo to obtain more individualized predictions and interpretations of their dental development relative to recent modern humans.

MATERIALS AND METHODS: Proportional odds logistic regression models based on three recent modern human samples (N = 181) were used to predict permanent mandibular tooth development scores in five Pleistocene subadults: Homo erectus/ergaster, Neanderthals, and anatomically modern humans (AMHs). Explanatory variables include a skeletal growth indicator (i.e., diaphyseal femoral length), and chronological age.

RESULTS: AMHs Lagar Velho 1 and Qafzeh 10 share delayed incisor development, but exhibit considerable idiosyncratic variation within and across tooth types, relative to each other and to the reference samples. Neanderthals Dederiyeh 1 and Le Moustier 1 exhibit delayed incisor coupled with advanced molar development, but differences are reduced when femoral diaphysis length is considered. Dental development in KNM-WT 15,000 Homo erectus/ergaster, while advanced for his age, almost exactly matches the predictions once femoral length is included in the models.

DISCUSSION: This study provides a new interpretation of dental development in KNM-WT 15000 as primarily reflecting his faster rates of skeletal growth. While the two AMH specimens exhibit considerable individual variation, the Neanderthals exhibit delayed incisor development early and advanced molar development later in ontogeny.}, } @article {pmid28406567, year = {2017}, author = {Been, E and Gómez-Olivencia, A and Shefi, S and Soudack, M and Bastir, M and Barash, A}, title = {Evolution of Spinopelvic Alignment in Hominins.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {300}, number = {5}, pages = {900-911}, doi = {10.1002/ar.23559}, pmid = {28406567}, issn = {1932-8494}, mesh = {Animals ; *Biological Evolution ; Female ; Fossils ; Hominidae/*anatomy & histology ; Humans ; Male ; Neanderthals/*anatomy & histology ; Pelvis/*anatomy & histology ; Posture/physiology ; Spine/*anatomy & histology ; }, abstract = {Spinopelvic alignment refers to the interaction between pelvic orientation, spinal curvatures, and the line of gravity. In a healthy modern human, this alignment is characterized by reciprocal curves/orientation of the sacrum, lumbar lordosis, thoracic kyphosis, and cervical lordosis. In an economic sagittal posture, these curvatures keep the line of gravity close to the center of the acetabulum. The purpose of this study is to explore the spinopelvic alignment in extinct hominins. We examined spinopelvic alignment of a single representative from each of the following hominin groups: Australopithecus, Homo erectus (H. erectus), H. neanderthalensis, and early H. sapiens. Pelvic incidence, lumbar lordosis, thoracic kyphosis, and cervical lordosis for each representative was estimated and compared with that of modern humans. Three basic spinopelvic alignments were found: (1) the sinusoidal alignment with moderate to high spinal curvatures and pelvic incidence found in H. erectus and H. sapiens; (2) the straight alignment with small spinal curvatures and small pelvic incidence found in Neandertal lineage hominins; (3) the compound alignment found in Australopithecus, with moderate pelvic incidence and lumbar lordosis, and nearly straight cervical spine. Our results indicate that balanced upright posture can be achieved in different alignments. Each hominin group solved the requirements of erect posture in a slightly different way. Moreover, we propose the term "cranio-spino-pelvic balance" to substitute "spino-pelvic balance." From an evolutionary perspective, not only changes in the pelvis have conditioned the evolution of the spinal curvatures but also changes in the equilibrium of the head likely also affected this balance. Anat Rec, 300:900-911, 2017. © 2017 Wiley Periodicals, Inc.}, } @article {pmid28398903, year = {2017}, author = {Patiño, F and Luque, M and Terradillos-Bernal, M and Martín-Loeches, M}, title = {Biomechanics of microliths manufacture: a preliminary approach to Neanderthal's motor constrains in the frame of embodied cognition.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {95}, number = {}, pages = {203-217}, doi = {10.4436/JASS.95005}, pmid = {28398903}, issn = {2037-0644}, mesh = {Adult ; Animals ; Anthropology, Physical ; Biological Evolution ; Biomechanical Phenomena/*physiology ; Cognition/*physiology ; Humans ; Male ; Middle Aged ; Models, Biological ; Neanderthals ; Tool Use Behavior/*physiology ; }, abstract = {The systems of perception and action of the brain appear as important constraining factors in human evolution under current models of embodied cognition. In this view, the emergence of certain items in the archeological record is not necessarily subsequent to the emergence of a 'symbolic' mind, but instead to the appearance of the sensory-motor systems enabling that behavior. One of the products normally absent in pre- Homo sapiens species is the standardized microlith, whose production seems very demanding for the hand due to their small size and need for fine craft. In the present study, we provide preliminary empirical evidence that the biomechanical requirements of microliths manufacture made this industry difficult to achieve by Neanderthals. The biomechanical parameters of the human hand in the manufacture of microliths are here explored in two individuals with different degrees of expertise. The figures obtained in this manner are subsequently contrasted and extrapolated to Neanderthal's hand anthropometric data, as obtained from the available literature. Results indicate that Neanderthals would exhibit lower efficiency than modern humans as a consequence of their smaller hands and shorter arms, resulting in a smaller area to distribute forces and an increased mechanical stress in the microlith manufacturing processes. This might be a plausibly contributing factor for precluding microlith production in Neanderthals on noticeable scales, in consonance with the archeological record.}, } @article {pmid28376731, year = {2017}, author = {Schaefer, NK and Shapiro, B and Green, RE}, title = {AD-LIBS: inferring ancestry across hybrid genomes using low-coverage sequence data.}, journal = {BMC bioinformatics}, volume = {18}, number = {1}, pages = {203}, pmid = {28376731}, issn = {1471-2105}, support = {T32 HG008345/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Genetic Speciation ; *Genome ; Humans ; *Hybridization, Genetic ; Markov Chains ; Polymorphism, Single Nucleotide ; *Software ; Ursidae/*genetics ; }, abstract = {BACKGROUND: Inferring the ancestry of each region of admixed individuals' genomes is useful in studies ranging from disease gene mapping to speciation genetics. Current methods require high-coverage genotype data and phased reference panels, and are therefore inappropriate for many data sets. We present a software application, AD-LIBS, that uses a hidden Markov model to infer ancestry across hybrid genomes without requiring variant calling or phasing. This approach is useful for non-model organisms and in cases of low-coverage data, such as ancient DNA.

RESULTS: We demonstrate the utility of AD-LIBS with synthetic data. We then use AD-LIBS to infer ancestry in two published data sets: European human genomes with Neanderthal ancestry and brown bear genomes with polar bear ancestry. AD-LIBS correctly infers 87-91% of ancestry in simulations and produces ancestry maps that agree with published results and global ancestry estimates in humans. In brown bears, we find more polar bear ancestry than has been published previously, using both AD-LIBS and an existing software application for local ancestry inference, HAPMIX. We validate AD-LIBS polar bear ancestry maps by recovering a geographic signal within bears that mirrors what is seen in SNP data. Finally, we demonstrate that AD-LIBS is more effective than HAPMIX at inferring ancestry when preexisting phased reference data are unavailable and genomes are sequenced to low coverage.

CONCLUSIONS: AD-LIBS is an effective tool for ancestry inference that can be used even when few individuals are available for comparison or when genomes are sequenced to low coverage. AD-LIBS is therefore likely to be useful in studies of non-model or ancient organisms that lack large amounts of genomic DNA. AD-LIBS can therefore expand the range of studies in which admixture mapping is a viable tool.}, } @article {pmid28366202, year = {2017}, author = {Rodríguez-Hidalgo, A and Saladié, P and Ollé, A and Arsuaga, JL and Bermúdez de Castro, JM and Carbonell, E}, title = {Human predatory behavior and the social implications of communal hunting based on evidence from the TD10.2 bison bone bed at Gran Dolina (Atapuerca, Spain).}, journal = {Journal of human evolution}, volume = {105}, number = {}, pages = {89-122}, doi = {10.1016/j.jhevol.2017.01.007}, pmid = {28366202}, issn = {1095-8606}, mesh = {Animals ; Bison ; *Bone and Bones ; *Cooperative Behavior ; Hominidae/*physiology ; *Predatory Behavior ; Spain ; }, abstract = {Zooarcheological research is an important tool in reconstructing subsistence, as well as for inferring relevant aspects regarding social behavior in the past. The organization of hunting parties, forms of predation (number and rate of animals slaughtered), and the technology used (tactics and tools) must be taken into account in the identification and classification of hunting methods in prehistory. The archeological recognition of communal hunting reflects an interest in evolutionary terms and their inherent implications for anticipatory capacities, social complexity, and the development of cognitive tools, such as articulated language. Late and Middle Paleolithic faunal assemblages in Europe have produced convincing evidence of communal hunting of large ungulates allowing for the formation of hypotheses concerning the skills of Neanderthals anatomically modern humans as social predators. However, the emergence of this cooperative behavior is not currently understood. Here, faunal analysis, based on traditional/long-established zooarcheological methods, of nearly 25,000 faunal remains from the "bison bone bed" layer of the TD10.2 sub-unit at Gran Dolina, Atapuerca (Spain) is presented. In addition, other datasets related to the archeo-stratigraphy, paleo-landscape, paleo-environmental proxies, lithic assemblage, and ethno-archeological information of communal hunting have been considered in order to adopt a holistic approach to an investigation of the subsistence strategies developed during deposition of the archeological remains. The results indicate a monospecific assemblage heavily dominated by axial bison elements. The abundance of anthropogenic modifications and the anatomical profile are in concordance with early primary access to carcasses and the development of systematic butchering focused on the exploitation of meat and fat for transportation of high-yield elements to somewhere out of the cave. Together with a catastrophic and seasonal mortality pattern, the results indicate the procurement of bison by communal hunting as early as circa 400 kyr. This suggests that the cognitive, social, and technological capabilities required for successful communal hunting were at least fully developed among the pre-Neanderthal paleodeme of Atapuerca during the Lower Paleolithic. Similarly, the early existence of mass communal hunting as a predation technique informs our understanding of the early emergence of predatory skills similar to those exhibited by modern communal hunters.}, } @article {pmid28366197, year = {2017}, author = {Krueger, KL and Ungar, PS and Guatelli-Steinberg, D and Hublin, JJ and Pérez-Pérez, A and Trinkaus, E and Willman, JC}, title = {Anterior dental microwear textures show habitat-driven variability in Neandertal behavior.}, journal = {Journal of human evolution}, volume = {105}, number = {}, pages = {13-23}, doi = {10.1016/j.jhevol.2017.01.004}, pmid = {28366197}, issn = {1095-8606}, mesh = {Animals ; *Diet ; *Ecosystem ; Europe ; Fossils/*anatomy & histology ; Geography ; Middle East ; *Neanderthals/anatomy & histology ; Tooth Wear/*pathology ; }, abstract = {The causes of Neandertal anterior tooth wear patterns, including labial rounding, labial scratches, and differential anterior-posterior wear, have been debated for decades. The most common explanation is the "stuff-and-cut" hypothesis, which describes Neandertals clamping down on a piece of meat and slicing a portion close to their lips. "Stuff-and-cut" has been accepted as a general aspect of Neandertal behavior without fully assessing its variability. This study analyzes anterior dental microwear textures across habitats, locations, and time intervals to discern possible variation in Neandertal anterior tooth-use behavior. Forty-five Neandertals from 24 sites were analyzed, represented by high-resolution replicas of permanent anterior teeth. The labial surface was scanned for antemortem microwear using a white-light confocal profiler. The resultant 3D-point clouds, representing 204 × 276 μm for each specimen, were uploaded into SSFA software packages for texture characterization. Statistical analyses, including MANOVAs, ANOVAs, and pairwise comparisons, were completed on ranked microwear data. Neandertal descriptive statistics were also compared to 10 bioarchaeological samples of known or inferred dietary and behavioral regimes. The Neandertal sample varied significantly by habitat, suggesting this factor was a principal driving force for differences in Neandertal anterior tooth-use behaviors. The Neandertals from open habitats showed significantly lower anisotropy and higher textural fill volume than those inhabiting more closed, forested environments. The texture signature from the open-habitat Neandertals was most similar to that of the Ipiutak and Nunavut, who used their anterior teeth for intense clamping and grasping behaviors related to hide preparation. Those in more closed habitats were most similar to the Arikara, who did not participate in non-dietary behaviors. These Neandertal individuals had a broad range of texture values consistent with non-dietary and dietary behaviors, suggesting they varied more in anterior tooth-use behaviors and exploited a wider variety of plant and animal resources than did those from open habitats.}, } @article {pmid28366169, year = {2017}, author = {Dannemann, M and Prüfer, K and Kelso, J}, title = {Functional implications of Neandertal introgression in modern humans.}, journal = {Genome biology}, volume = {18}, number = {1}, pages = {61}, pmid = {28366169}, issn = {1474-760X}, mesh = {Alleles ; Amino Acid Sequence ; Animals ; *Evolution, Molecular ; Gene Expression ; Gene Frequency ; Genetic Variation ; Genome-Wide Association Study ; Humans ; Multigene Family ; Neanderthals/*genetics ; Phenotype ; }, abstract = {BACKGROUND: Admixture between early modern humans and Neandertals approximately 50,000-60,000 years ago has resulted in 1.5-4% Neandertal ancestry in the genomes of present-day non-Africans. Evidence is accumulating that some of these archaic alleles are advantageous for modern humans, while others are deleterious; however, the major mechanism by which these archaic alleles act has not been fully explored.

RESULTS: Here we assess the contributions of introgressed non-synonymous and regulatory variants to modern human protein and gene expression variation. We show that gene expression changes are more often associated with Neandertal ancestry than expected, and that the introgressed non-synonymous variants tend to have less predicted functional effect on modern human proteins than mutations that arose on the human lineage. Conversely, introgressed alleles contribute proportionally more to expression variation than non-introgressed alleles.

CONCLUSIONS: Our results suggest that the major influence of Neandertal introgressed alleles is through their effects on gene regulation.}, } @article {pmid28355292, year = {2017}, author = {Majkić, A and Evans, S and Stepanchuk, V and Tsvelykh, A and d'Errico, F}, title = {A decorated raven bone from the Zaskalnaya VI (Kolosovskaya) Neanderthal site, Crimea.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0173435}, pmid = {28355292}, issn = {1932-6203}, mesh = {Animals ; Archaeology/methods ; Bone and Bones/*anatomy & histology ; Crows/anatomy & histology ; *Fossils ; History, Ancient ; Humans ; Microscopy ; Multivariate Analysis ; Neanderthals/*psychology ; Paleontology/methods ; Russia ; }, abstract = {We analyze a radius bone fragment of a raven (Corvus corax) from Zaskalnaya VI rock shelter, Crimea. The object bears seven notches and comes from an archaeological level attributed to a Micoquian industry dated to between 38 and 43 cal kyr BP. Our study aims to examine the degree of regularity and intentionality of this set of notches through their technological and morphometric analysis, complemented by comparative experimental work. Microscopic analysis of the notches indicate that they were produced by the to-and-fro movement of a lithic cutting edge and that two notches were added to fill in the gap left between previously cut notches, probably to increase the visual consistency of the pattern. Multivariate analysis of morphometric data recorded on the archaeological notches and sets of notches cut by nine modern experimenters on radii of domestic turkeys shows that the variations recorded on the Zaskalnaya set are comparable to experimental sets made with the aim of producing similar, parallel, equidistant notches. Identification of the Weber Fraction, the constant that accounts for error in human perception, for equidistant notches cut on bone rods and its application to the Zaskalnaya set of notches and thirty-six sets of notches incised on seventeen Upper Palaeolithic bone objects from seven sites indicate that the Zaskalnaya set falls within the range of variation of regularly spaced experimental and Upper Palaeolithic sets of notches. This suggests that even if the production of the notches may have had a utilitarian reason the notches were made with the goal of producing a visually consistent pattern. This object represents the first instance of a bird bone from a Neanderthal site bearing modifications that cannot be explained as the result of butchery activities and for which a symbolic argument can be built on direct rather than circumstantial evidence.}, } @article {pmid28351985, year = {2017}, author = {Quach, H and Quintana-Murci, L}, title = {Living in an adaptive world: Genomic dissection of the genus Homo and its immune response.}, journal = {The Journal of experimental medicine}, volume = {214}, number = {4}, pages = {877-894}, pmid = {28351985}, issn = {1540-9538}, mesh = {*Adaptation, Biological ; Genetic Variation ; *Genome, Human ; Humans ; *Immunity ; Mutation ; Quantitative Trait Loci ; Selection, Genetic ; }, abstract = {More than a decade after the sequencing of the human genome, a deluge of genome-wide population data are generating a portrait of human genetic diversity at an unprecedented level of resolution. Genomic studies have provided new insight into the demographic and adaptive history of our species, Homo sapiens, including its interbreeding with other hominins, such as Neanderthals, and the ways in which natural selection, in its various guises, has shaped genome diversity. These studies, combined with functional genomic approaches, such as the mapping of expression quantitative trait loci, have helped to identify genes, functions, and mechanisms of prime importance for host survival and involved in phenotypic variation and differences in disease risk. This review summarizes new findings in this rapidly developing field, focusing on the human immune response. We discuss the importance of defining the genetic and evolutionary determinants driving immune response variation, and highlight the added value of population genomic approaches in settings relevant to immunity and infection.}, } @article {pmid28348941, year = {2017}, author = {Rijkers, G}, title = {Cutting the Stone: Health Defined in the Era of Value-based Care.}, journal = {Cureus}, volume = {9}, number = {2}, pages = {e1023}, pmid = {28348941}, issn = {2168-8184}, abstract = {The immune system contributes to the maintenance of health by preventing and limiting the clinical consequences of infections by pathogenic microorganisms. During the evolution of Homo sapiens, those with the fittest immune system survived. The immune system of Homo sapiens was further improved and adapted by admixture with Neanderthal genes. Nowadays, the human immune system provides adequate protection against the majority of infections. For some 20 infectious diseases, the immune system needs to be improved by vaccination. Vaccination is the number one value-based healthcare intervention and has resulted in global eradication of smallpox. Eradication of poliomyelitis and measles is within reach. A continuous effort will be required for recently emerged pathogens, such as Ebola and HIV, as well as the most difficult - malaria and tuberculosis.}, } @article {pmid28317553, year = {2017}, author = {Estalrrich, A and El Zaatari, S and Rosas, A}, title = {Dietary reconstruction of the El Sidrón Neandertal familial group (Spain) in the context of other Neandertal and modern hunter-gatherer groups. A molar microwear texture analysis.}, journal = {Journal of human evolution}, volume = {104}, number = {}, pages = {13-22}, doi = {10.1016/j.jhevol.2016.12.003}, pmid = {28317553}, issn = {1095-8606}, mesh = {Age Factors ; Animals ; Biological Evolution ; *Diet ; Female ; Fossils/*anatomy & histology ; Male ; Molar/*anatomy & histology/pathology ; *Neanderthals/anatomy & histology ; Spain ; Tooth Wear/*pathology ; }, abstract = {Here, we present the analysis of occlusal molar microwear textures of eight individuals from the El Sidrón Neandertal group (Spain). The aims of the study were: 1) to document potential age-, sex-, and maternal lineage-related differences in diet within a Neandertal familial group, and 2) to place the diet of El Sidrón individuals in the context of those of other Neandertal groups. This study also offers an interpretation of the diet of the El Sidrón Neandertals by comparing their microwear signatures to those of recent hunter-gatherer populations with diverse but known diets. The intra-group examination of the microwear signatures are consistent with the females of the El Sidrón group having had more abrasive diets or having used their teeth in more para-masticatory activities than did the males. Aside from the potential sex-related differences in diet, no additional intra-group dietary separation, such as by age group or maternal lineage, was observed. In comparison to other Neandertals, El Sidrón individuals, as a group, have microwear signatures most similar to those of other Neandertals from wooded habitats and different from those that lived in more open habitats. This result is expected based on the available paleoenvironmental reconstructions from El Sidrón Cave. The diet of the El Sidrón Neandertals, just like their Neandertal counterparts from similar wooded habitats, is interpreted as having been mixed, consisting of both meat and vegetable foods.}, } @article {pmid28289213, year = {2017}, author = {Daura, J and Sanz, M and Arsuaga, JL and Hoffmann, DL and Quam, RM and Ortega, MC and Santos, E and Gómez, S and Rubio, A and Villaescusa, L and Souto, P and Mauricio, J and Rodrigues, F and Ferreira, A and Godinho, P and Trinkaus, E and Zilhão, J}, title = {New Middle Pleistocene hominin cranium from Gruta da Aroeira (Portugal).}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {13}, pages = {3397-3402}, pmid = {28289213}, issn = {1091-6490}, mesh = {Animals ; Biological Evolution ; Fossils/anatomy & histology ; Hominidae/*anatomy & histology/genetics ; Humans ; Paleontology ; Portugal ; Skull/*anatomy & histology ; }, abstract = {The Middle Pleistocene is a crucial time period for studying human evolution in Europe, because it marks the appearance of both fossil hominins ancestral to the later Neandertals and the Acheulean technology. Nevertheless, European sites containing well-dated human remains associated with an Acheulean toolkit remain scarce. The earliest European hominin crania associated with Acheulean handaxes are at the sites of Arago, Atapuerca Sima de los Huesos (SH), and Swanscombe, dating to 400-500 ka (Marine Isotope Stage 11-12). The Atapuerca (SH) fossils and the Swanscombe cranium belong to the Neandertal clade, whereas the Arago hominins have been attributed to an incipient stage of Neandertal evolution, to Homo heidelbergensis, or to a subspecies of Homo erectus A recently discovered cranium (Aroeira 3) from the Gruta da Aroeira (Almonda karst system, Portugal) dating to 390-436 ka provides important evidence on the earliest European Acheulean-bearing hominins. This cranium is represented by most of the right half of a calvarium (with the exception of the missing occipital bone) and a fragmentary right maxilla preserving part of the nasal floor and two fragmentary molars. The combination of traits in the Aroeira 3 cranium augments the previously documented diversity in the European Middle Pleistocene fossil record.}, } @article {pmid28284042, year = {2017}, author = {Chapman, T and Beyer, B and Sholukha, V and Semal, P and Feipel, V and Louryan, S and Van Sint Jan, S}, title = {How different are the Kebara 2 ribs to modern humans?.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {95}, number = {}, pages = {183-201}, doi = {10.4436/JASS.95004}, pmid = {28284042}, issn = {2037-0644}, mesh = {Animals ; Anthropology, Physical ; Caves ; Female ; Humans ; Israel ; Male ; Neanderthals/*anatomy & histology ; Principal Component Analysis ; Ribs/*anatomy & histology ; }, abstract = {This study analyses rib geometric parameters of individual ribs of 14 modern human subjects (7 males and 7 females) in comparison to the reconstructed ribs of the Kebara 2 skeleton which was taken from the reconstruction of a Neandertal thorax by Sawyer & Maley (2005). Three-dimensional (3D) models were segmented from CT scans and each rib vertex cloud was placed into a local coordinate system defined from the rib principal axes. Rib clouds were then analysed using best fitting ellipses of the external contours of the cross-section areas. The centroid of each ellipse was then used to measure the centroidal pathway between each slice (rib midline). Curvature of the ribs was measured from the mid-line of the ribs as the sum of angles between successive centroids in adjacent cross sections. Distinct common patterns were noted in all rib geometric parameters for modern humans. The Kebara 2 reconstructed ribs also followed the same patterns. This study demonstrated that there are differences between the sexes in rib geometrical parameters, with females showing smaller rib width, chord length and arc length, but greater curvature (rib torsion, rib axial curvature, rib anterior-posterior bending) than males. The Kebara 2 reconstructed ribs were within the modern human range for the majority of geometrical parameters.}, } @article {pmid28277523, year = {2017}, author = {Callaway, E}, title = {Neanderthal tooth plaque hints at meals - and kisses.}, journal = {Nature}, volume = {543}, number = {7644}, pages = {163}, doi = {10.1038/543163a}, pmid = {28277523}, issn = {1476-4687}, mesh = {Animals ; Fossils ; *Hominidae ; Humans ; *Neanderthals ; Tooth ; }, } @article {pmid28273061, year = {2017}, author = {Weyrich, LS and Duchene, S and Soubrier, J and Arriola, L and Llamas, B and Breen, J and Morris, AG and Alt, KW and Caramelli, D and Dresely, V and Farrell, M and Farrer, AG and Francken, M and Gully, N and Haak, W and Hardy, K and Harvati, K and Held, P and Holmes, EC and Kaidonis, J and Lalueza-Fox, C and de la Rasilla, M and Rosas, A and Semal, P and Soltysiak, A and Townsend, G and Usai, D and Wahl, J and Huson, DH and Dobney, K and Cooper, A}, title = {Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus.}, journal = {Nature}, volume = {544}, number = {7650}, pages = {357-361}, doi = {10.1038/nature21674}, pmid = {28273061}, issn = {1476-4687}, mesh = {Animals ; Belgium ; Carnivory ; Caves ; DNA, Ancient/*analysis ; Dental Calculus/*chemistry ; Diet/*history ; Enterocytozoon/genetics/isolation & purification ; *Food Preferences ; Genome, Bacterial/genetics ; Health/*history ; History, Ancient ; Humans ; Intestines/microbiology ; Meat/history ; Methanobrevibacter/genetics/isolation & purification ; Mouth/microbiology ; Neanderthals/*microbiology/*psychology ; Pan troglodytes/microbiology ; Penicillium/chemistry ; Perissodactyla ; Sheep ; Spain ; Stomach/microbiology ; Symbiosis ; Time Factors ; Vegetarians/history ; }, abstract = {Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In contrast, no meat was detected in the diet of Neanderthals from El Sidrón cave, Spain, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota) and suggested that meat consumption contributed to substantial variation within Neanderthal microbiota. Evidence for self-medication was detected in an El Sidrón Neanderthal with a dental abscess and a chronic gastrointestinal pathogen (Enterocytozoon bieneusi). Metagenomic data from this individual also contained a nearly complete genome of the archaeal commensal Methanobrevibacter oralis (10.2× depth of coverage)-the oldest draft microbial genome generated to date, at around 48,000 years old. DNA preserved within dental calculus represents a notable source of information about the behaviour and health of ancient hominin specimens, as well as a unique system that is useful for the study of long-term microbial evolution.}, } @article {pmid28254945, year = {2017}, author = {Li, ZY and Wu, XJ and Zhou, LP and Liu, W and Gao, X and Nian, XM and Trinkaus, E}, title = {Late Pleistocene archaic human crania from Xuchang, China.}, journal = {Science (New York, N.Y.)}, volume = {355}, number = {6328}, pages = {969-972}, doi = {10.1126/science.aal2482}, pmid = {28254945}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; China ; Fossils/*anatomy & histology ; Humans ; Neanderthals/anatomy & histology ; Occipital Bone/anatomy & histology ; Semicircular Canals/anatomy & histology ; Skull/*anatomy & histology ; }, abstract = {Two early Late Pleistocene (~105,000- to 125,000-year-old) crania from Lingjing, Xuchang, China, exhibit a morphological mosaic with differences from and similarities to their western contemporaries. They share pan-Old World trends in encephalization and in supraorbital, neurocranial vault, and nuchal gracilization. They reflect eastern Eurasian ancestry in having low, sagittally flat, and inferiorly broad neurocrania. They share occipital (suprainiac and nuchal torus) and temporal labyrinthine (semicircular canal) morphology with the Neandertals. This morphological combination reflects Pleistocene human evolutionary patterns in general biology, as well as both regional continuity and interregional population dynamics.}, } @article {pmid28254895, year = {2017}, author = {Gibbons, A}, title = {Close relative of Neandertals unearthed in China.}, journal = {Science (New York, N.Y.)}, volume = {355}, number = {6328}, pages = {899}, doi = {10.1126/science.355.6328.899}, pmid = {28254895}, issn = {1095-9203}, mesh = {Animals ; China ; Fossils ; *Hominidae ; Humans ; *Neanderthals ; }, } @article {pmid28252042, year = {2017}, author = {Bazgir, B and Ollé, A and Tumung, L and Becerra-Valdivia, L and Douka, K and Higham, T and van der Made, J and Picin, A and Saladié, P and López-García, JM and Blain, HA and Allué, E and Fernández-García, M and Rey-Rodríguez, I and Arceredillo, D and Bahrololoumi, F and Azimi, M and Otte, M and Carbonell, E}, title = {Understanding the emergence of modern humans and the disappearance of Neanderthals: Insights from Kaldar Cave (Khorramabad Valley, Western Iran).}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {43460}, pmid = {28252042}, issn = {2045-2322}, mesh = {Amphibians/physiology ; Animals ; Archaeology/*methods ; Artiodactyla/physiology ; Birds/physiology ; Carbon Radioisotopes ; Carnivory/physiology ; Caves ; *Fossils ; Geologic Sediments/analysis ; Humans ; Iran ; Neanderthals/anatomy & histology/*physiology/psychology ; Perissodactyla/physiology ; Radiometric Dating/*methods ; Reptiles/physiology ; Rodentia/physiology ; }, abstract = {Kaldar Cave is a key archaeological site that provides evidence of the Middle to Upper Palaeolithic transition in Iran. Excavations at the site in 2014-2015 led to the discovery of cultural remains generally associated with anatomically modern humans (AMHs) and evidence of a probable Neanderthal-made industry in the basal layers. Attempts have been made to establish a chronology for the site. These include four thermoluminescence (TL) dates for Layer 4, ranging from 23,100 ± 3300 to 29,400 ± 2300 BP, and three AMS radiocarbon dates from charcoal samples belonging to the lower part of the same layer, yielding ages of 38,650-36,750 cal BP, 44,200-42,350 cal BP, and 54,400-46,050 cal BP (all at the 95.4% confidence level). Kaldar Cave is the first well-stratified Late Palaeolithic locality to be excavated in the Zagros which is one of the earliest sites with cultural materials attributed to early AMHs in western Asia. It also offers an opportunity to study the technological differences between the Mousterian and the first Upper Palaeolithic lithic technologies as well as the human behaviour in the region. In this study, we present a detailed description of the newly excavated stratigraphy, quantified results from the lithic assemblages, preliminary faunal remains analyses, geochronologic data, taphonomic aspects, and an interpretation of the regional paleoenvironment.}, } @article {pmid28238406, year = {2017}, author = {Nakahashi, W}, title = {The effect of trauma on Neanderthal culture: A mathematical analysis.}, journal = {Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen}, volume = {68}, number = {2}, pages = {83-100}, doi = {10.1016/j.jchb.2017.02.001}, pmid = {28238406}, issn = {1618-1301}, mesh = {Animals ; Behavior, Animal ; Cultural Characteristics ; Cultural Evolution ; Fossils ; Humans ; Mathematical Concepts ; *Models, Biological ; *Models, Psychological ; Neanderthals/*injuries/*psychology ; Reproducibility of Results ; }, abstract = {Traumatic lesions are often observed in ancient skeletal remains. Since ancient medical technology was immature, severely traumatized individuals may have frequently lost the physical ability for cultural skills that demand complex body movements. I develop a mathematical model to analyze the effect of trauma on cultural transmission and apply it to Neanderthal culture using Neanderthal fossil data. I estimate from the data that the proportion of adult individuals who suffered traumatic injuries before death was approximately 0.79-0.94, in which 0.37-0.52 were injured severely and 0.13-0.19 were injured before adulthood. Assuming that every severely traumatized individual and a quarter to a half of the other traumatized individuals lost the capacity for a cultural skill that demands complex control of the traumatized body part, I estimate that if an upper limb is associated with a cultural skill, each individual had to communicate closely with at least 1.5-2.6 individuals during adulthood to maintain the skill in Neanderthal society, and if a whole body is associated, at least 3.1-11.5 individuals were necessary. If cultural transmissions between experts and novices were inaccurate, or if low frequency skills easily disappeared from the population due to random drift, more communicable individuals were necessary. Since the community size of Neanderthals was very small, their high risk of injury may have inhibited the spread of technically difficult cultural skills in their society. It may be important to take this inhibition into consideration when we study Neanderthal culture and the replacement of Neanderthals by modern humans.}, } @article {pmid28235201, year = {2017}, author = {McCoy, RC and Wakefield, J and Akey, JM}, title = {Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression.}, journal = {Cell}, volume = {168}, number = {5}, pages = {916-927.e12}, pmid = {28235201}, issn = {1097-4172}, support = {R01 GM076036/GM/NIGMS NIH HHS/United States ; R01 DA006227/DA/NIDA NIH HHS/United States ; R01 MH101782/MH/NIMH NIH HHS/United States ; R01 MH101810/MH/NIMH NIH HHS/United States ; R01 MH101819/MH/NIMH NIH HHS/United States ; R01 GM110068/GM/NIGMS NIH HHS/United States ; R01 DA033684/DA/NIDA NIH HHS/United States ; R01 MH090936/MH/NIMH NIH HHS/United States ; T32 HG000035/HG/NHGRI NIH HHS/United States ; R01 MH090951/MH/NIMH NIH HHS/United States ; R01 MH101820/MH/NIMH NIH HHS/United States ; R01 MH101825/MH/NIMH NIH HHS/United States ; R01 MH090948/MH/NIMH NIH HHS/United States ; R01 MH090941/MH/NIMH NIH HHS/United States ; R01 MH101822/MH/NIMH NIH HHS/United States ; HHSN261200800001C/RC/CCR NIH HHS/United States ; R01 MH090937/MH/NIMH NIH HHS/United States ; HHSN268201000029C/HL/NHLBI NIH HHS/United States ; HHSN261200800001E/CA/NCI NIH HHS/United States ; R01 MH101814/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; Brain/metabolism ; *Evolution, Molecular ; *Gene Expression ; Gene Expression Regulation ; Humans ; Male ; Neanderthals/*genetics ; Organ Specificity ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Testis/metabolism ; }, abstract = {Regulatory variation influencing gene expression is a key contributor to phenotypic diversity, both within and between species. Unfortunately, RNA degrades too rapidly to be recovered from fossil remains, limiting functional genomic insights about our extinct hominin relatives. Many Neanderthal sequences survive in modern humans due to ancient hybridization, providing an opportunity to assess their contributions to transcriptional variation and to test hypotheses about regulatory evolution. We developed a flexible Bayesian statistical approach to quantify allele-specific expression (ASE) in complex RNA-seq datasets. We identified widespread expression differences between Neanderthal and modern human alleles, indicating pervasive cis-regulatory impacts of introgression. Brain regions and testes exhibited significant downregulation of Neanderthal alleles relative to other tissues, consistent with natural selection influencing the tissue-specific regulatory landscape. Our study demonstrates that Neanderthal-inherited sequences are not silent remnants of ancient interbreeding but have measurable impacts on gene expression that contribute to variation in modern human phenotypes.}, } @article {pmid28195302, year = {2017}, author = {Castillo, ER and Hsu, C and Mair, RW and Lieberman, DE}, title = {Testing biomechanical models of human lumbar lordosis variability.}, journal = {American journal of physical anthropology}, volume = {163}, number = {1}, pages = {110-121}, doi = {10.1002/ajpa.23189}, pmid = {28195302}, issn = {1096-8644}, mesh = {Adolescent ; Adult ; Anthropology, Physical ; Biomechanical Phenomena/*physiology ; Female ; Humans ; Lordosis/*diagnostic imaging ; Lumbar Vertebrae/diagnostic imaging ; Lumbosacral Region/*diagnostic imaging ; Magnetic Resonance Imaging ; Male ; Models, Biological ; Young Adult ; }, abstract = {OBJECTIVES: Lumbar lordosis (LL) is a key adaptation for bipedalism, but factors underlying curvature variations remain unclear. This study tests three biomechanical models to explain LL variability.

MATERIALS AND METHODS: Thirty adults (15 male, 15 female) were scanned using magnetic resonance imaging (MRI), a standing posture analysis was conducted, and lumbar range of motion (ROM) was assessed. Three measures of LL were compared. The trunk's center of mass was estimated from external markers to calculate hip moments (Mhip) and lumbar flexion moments. Cross-sectional areas of lumbar vertebral bodies and trunk muscles were measured from scans. Regression models tested associations between LL and the Mhip moment arm, a beam bending model, and an interaction between relative trunk strength (RTS) and ROM.

RESULTS: Hip moments were not associated with LL. Beam bending was moderately predictive of standing but not supine LL (R2 = 0.25). Stronger backs and increased ROM were associated with greater LL, especially when standing (R2 = 0.65). The strength-flexibility model demonstrates the differential influence of RTS depending on ROM: individuals with high ROM exhibited the most LL variation with RTS, while those with low ROM showed reduced LL regardless of RTS.

DISCUSSION: Hip moments appear constrained suggesting the possibility of selection, and the beam model explains some LL variability due to variations in trunk geometry. The strength-flexibility interaction best predicted LL, suggesting a tradeoff in which ROM limits the effects of back strength on LL. The strength-flexibility model may have clinical relevance for spinal alignment and pathology. This model may also suggest that straight-backed Neanderthals had reduced lumbar mobility.}, } @article {pmid28185859, year = {2017}, author = {Zervou, MI and Dorschner, JM and Ghodke-Puranik, Y and Boumpas, DT and Niewold, TB and Goulielmos, GN}, title = {Association of IRF5 polymorphisms with increased risk for systemic lupus erythematosus in population of Crete, a southern-eastern European Greek island.}, journal = {Gene}, volume = {610}, number = {}, pages = {9-14}, doi = {10.1016/j.gene.2017.02.003}, pmid = {28185859}, issn = {1879-0038}, mesh = {Adult ; Animals ; Case-Control Studies ; Female ; *Genetic Predisposition to Disease ; Greece ; Haplotypes ; Humans ; Interferon Regulatory Factors/*genetics ; Interferon Type I/blood/immunology ; Lupus Erythematosus, Systemic/*genetics/immunology ; Male ; Middle Aged ; Neanderthals/genetics ; }, abstract = {Interferon regulatory factor 5 (IRF5) regulates type I interferon (IFN)-responsive genes, and has been one of the most consistently associated genes with systemic lupus erythematosus (SLE). We sought to investigate whether IRF5 haplotypes are associated with risk for SLE in the genetically homogeneous Greek population of the island of Crete, as well as whether these haplotypes are associated with increased type I IFN. 322 SLE patients and 247 healthy controls from Crete were genotyped for rs2004640, rs3807306, rs10488631 and rs2280714 SNPs of IRF5 gene by using Taqman primer-probe sets. Type I IFN levels were measured using a functional reporter cell assay. All IRF5 SNPs examined were found to be associated with SLE in univariate case-control analysis. The 4 SNPs formed 5 major haplotypes and the Neanderthal-derived TACA risk haplotype was present in Crete and enriched in the SLE cases (OR=2.01, P=0.0003). Serum IFN levels were measured in a subset of the SLE patients, and carriage of the TACA haplotype was associated with higher circulating type I IFN levels (P=0.037). This study demonstrates the association of IRF5 with an increased susceptibility for SLE in the population of Crete and emphasizes the association of the Neanderthal-derived IRF5 haplotype with SLE susceptibility. Patients carrying allele the Neanderthal allele C had greater type I IFN, supporting a functional consequence of this polymorphism.}, } @article {pmid28170092, year = {2017}, author = {Duval, M and Martín-Francés, L}, title = {Quantifying the impact of µCT-scanning of human fossil teeth on ESR age results.}, journal = {American journal of physical anthropology}, volume = {163}, number = {1}, pages = {205-212}, doi = {10.1002/ajpa.23180}, pmid = {28170092}, issn = {1096-8644}, mesh = {Animals ; Dental Enamel/diagnostic imaging/*radiation effects ; Electron Spin Resonance Spectroscopy ; Fossils/*diagnostic imaging ; Hominidae ; Humans ; Neanderthals ; *Paleontology/methods/standards ; Tooth/diagnostic imaging/*radiation effects ; X-Ray Microtomography ; }, abstract = {Fossil human teeth are nowadays systematically CT-scanned by palaeoanthropologists prior to any further analysis. It has been recently demonstrated that this noninvasive technique has, in most cases, virtually no influence on ancient DNA preservation. However, it may have nevertheless an impact on other techniques, like Electron Spin Resonance (ESR) dating, by artificially ageing the apparent age of the sample. To evaluate this impact, we µCT-scanned several modern enamel fragments following the standard analytical procedures employed by the Dental Anthropology Group at CENIEH, Spain, and then performed ESR dose reconstruction for each of them. The results of our experiment demonstrate that the systematic high-resolution µCT-scanning of fossil hominin remains introduces a nonnegligible X-ray dose into the tooth enamel, equivalent to 15-30 Gy depending on the parameters used. This dose may be multiplied by a factor of ∼8 if no metallic filter is used. However, this dose estimate cannot be universally extrapolated to any µCT-scan experiment but has instead to be specifically assessed for each device and set of parameters employed. The impact on the ESR age results is directly dependent on the magnitude of the geological dose measured in fossil enamel but could potentially lead to an age overestimation up to 40% in case of Late Pleistocene samples, if not taken into consideration.}, } @article {pmid28166906, year = {2017}, author = {Martin, RMG and Hublin, JJ and Gunz, P and Skinner, MM}, title = {The morphology of the enamel-dentine junction in Neanderthal molars: Gross morphology, non-metric traits, and temporal trends.}, journal = {Journal of human evolution}, volume = {103}, number = {}, pages = {20-44}, doi = {10.1016/j.jhevol.2016.12.004}, pmid = {28166906}, issn = {1095-8606}, mesh = {Animals ; Dental Enamel/*anatomy & histology ; Dentin/*anatomy & histology ; Fossils ; Humans ; Image Processing, Computer-Assisted ; Mandible/*anatomy & histology ; Maxilla/*anatomy & histology ; Molar/*anatomy & histology ; Neanderthals/*anatomy & histology ; }, abstract = {This study explores the morphological differences between the enamel-dentine junction (EDJ) of maxillary and mandibular molars of Neanderthals (n = 150) and recent modern humans (n = 106), and between an earlier Neanderthal sample (consisting of Pre-Eemian and Eemian Neanderthals dating to before 115 ka) and a later Neanderthal sample (consisting of Post-Eemian Neanderthals dating to after 115 ka). The EDJ was visualised by segmenting microtomographic scans of each molar. A geometric morphometric methodology compared the positioning of the dentine horns, the shape of the marginal ridge between the dentine horns, and the shape of the cervix. We also examined the manifestation of non-metric traits at the EDJ including the crista obliqua, cusp 5, and post-paracone tubercle. Furthermore, we report on additional morphological features including centrally placed dentine horn tips and twinned dentine horns. Our results indicate that EDJ morphology can discriminate with a high degree of reliability between Neanderthals and recent modern humans at every molar position, and discriminate between the earlier and the later Neanderthal samples at every molar position, except for the M3 in shape space. The cervix in isolation can also discriminate between Neanderthals and recent modern humans, except at the M3 in form space, and is effective at discriminating between the earlier and the later Neanderthal samples, except at the M2/M2 in form space. In addition to demonstrating the taxonomic valence of the EDJ, our analysis reveals unique manifestations of dental traits in Neanderthals and expanded levels of trait variation that have implications for trait definitions and scoring.}, } @article {pmid28160308, year = {2017}, author = {Warschau, M and Hoffmann, M and Dziallas, P and Hansmann, F and Baumgärtner, W and Mischke, R and Cichowski, S and Fehr, M}, title = {Invasive histiocytic sarcoma of the lumbar spine in a ferret (Mustela putorius furo).}, journal = {The Journal of small animal practice}, volume = {58}, number = {2}, pages = {115-118}, doi = {10.1111/jsap.12632}, pmid = {28160308}, issn = {1748-5827}, mesh = {Animals ; Dysuria/veterinary ; Female ; *Ferrets ; Histiocytic Sarcoma/diagnostic imaging/pathology/*veterinary ; *Lumbar Vertebrae ; Magnetic Resonance Imaging/veterinary ; Paraplegia/veterinary ; Spinal Cord Compression/diagnostic imaging/pathology/veterinary ; Spinal Neoplasms/diagnostic imaging/pathology/*veterinary ; }, abstract = {This report describes the history, clinical examination and histopathology of a histiocytic sarcoma in a domestic ferret. Clinical signs were acute paraplegia and dysuria. Physical examination revealed a firm, smooth, touch-sensitive mass in and around the lumbar vertebral column. Neurologic examination was consistent with a lesion between spinal cord segments T3 and L3. Magnetic resonance images revealed bone lesions of L2 and L3 combined with compression of the spinal cord due to a homogenous, isointense mass that was diagnosed as a malignant round cell tumour and the ferret was euthanased. Histopathology confirmed the diagnosis of an infiltrative histiocytic sarcoma.}, } @article {pmid28158547, year = {2016}, author = {Povysil, G and Hochreiter, S}, title = {IBD Sharing between Africans, Neandertals, and Denisovans.}, journal = {Genome biology and evolution}, volume = {8}, number = {12}, pages = {3406-3416}, pmid = {28158547}, issn = {1759-6653}, mesh = {Africa ; African Continental Ancestry Group/genetics ; Animals ; Asian Continental Ancestry Group/genetics ; Breeding ; DNA/genetics ; European Continental Ancestry Group/genetics ; *Evolution, Molecular ; *Gene Flow ; Genome ; Hominidae/*genetics ; Humans ; Neanderthals/genetics ; }, abstract = {Interbreeding between ancestors of humans and other hominins outside of Africa has been studied intensively, while their common history within Africa still lacks proper attention. However, shedding light on human evolution in this time period about which little is known, is essential for understanding subsequent events outside of Africa. We investigate the genetic relationships of humans, Neandertals, and Denisovans by identifying very short DNA segments in the 1000 Genomes Phase 3 data that these hominins share identical by descent (IBD). By focusing on low frequency and rare variants, we identify very short IBD segments with high confidence. These segments reveal events from a very distant past because shorter IBD segments are presumably older than longer ones. We extracted two types of very old IBD segments that are not only shared among humans, but also with Neandertals and/or Denisovans. The first type contains longer segments that are found primarily in Asians and Europeans where more segments are found in South Asians than in East Asians for both Neandertal and Denisovan. These longer segments indicate complex admixture events outside of Africa. The second type consists of shorter segments that are shared mainly by Africans and therefore may indicate events involving ancestors of humans and other ancient hominins within Africa. Our results from the autosomes are further supported by an analysis of chromosome X, on which segments that are shared by Africans and match the Neandertal and/or Denisovan genome were even more prominent. Our results indicate that interbreeding with other hominins was a common feature of human evolution starting already long before ancestors of modern humans left Africa.}, } @article {pmid28154067, year = {2017}, author = {Sugden, AM}, title = {Interglacial Neanderthal habitats.}, journal = {Science (New York, N.Y.)}, volume = {355}, number = {6324}, pages = {491}, doi = {10.1126/science.355.6324.491-a}, pmid = {28154067}, issn = {1095-9203}, mesh = {Animals ; Ecosystem ; Fossils ; *Hominidae ; Humans ; *Neanderthals ; }, } @article {pmid28125602, year = {2017}, author = {Marra, F and Ceruleo, P and Pandolfi, L and Petronio, C and Rolfo, MF and Salari, L}, title = {The Aggradational Successions of the Aniene River Valley in Rome: Age Constraints to Early Neanderthal Presence in Europe.}, journal = {PloS one}, volume = {12}, number = {1}, pages = {e0170434}, pmid = {28125602}, issn = {1932-6203}, mesh = {Animals ; Archaeology ; Europe ; *Fossils ; Humans ; *Neanderthals ; Paleontology ; *Rivers ; Rome ; }, abstract = {We revise the chronostratigraphy of several sedimentary successions cropping out along a 5 km-long tract of the Aniene River Valley in Rome (Italy), which yielded six hominin remains previously attributed to proto- or archaic Neanderthal individuals, as well as a large number of lithic artefacts showing intermediate characteristics somewhere between the local Acheulean and Mousterian cultures. Through a method of correlation of aggradational successions with post-glacial sea-level rises, relying on a large set of published 40Ar/39Ar ages of interbedded volcanic deposits, we demonstrate that deposition of the sediments hosting the human remains spans the interval 295-220 ka. This is consistent with other well constrained ages for lithic industries recovered in England, displaying transitional features from Lower to Middle Paleolithic, suggesting the appearance of Mode 3 during the MIS 9-MIS 8 transition. Moreover, the six human bone fragments recovered in the Aniene Valley should be regarded as the most precisely dated and oldest hominin remains ascribable to Neanderthal-type individuals in Europe, discovered to date. The chronostratigraphic study presented here constitutes the groundwork for addressing re-analysis of these remains and of their associated lithic industries, in the light of their well-constrained chronological picture.}, } @article {pmid28119736, year = {2016}, author = {Goodwin, ZA and de Guzman Strong, C}, title = {Recent Positive Selection in Genes of the Mammalian Epidermal Differentiation Complex Locus.}, journal = {Frontiers in genetics}, volume = {7}, number = {}, pages = {227}, pmid = {28119736}, issn = {1664-8021}, support = {R01 AR065523/AR/NIAMS NIH HHS/United States ; T32 HG000045/HG/NHGRI NIH HHS/United States ; }, abstract = {The epidermal differentiation complex (EDC) is the most rapidly evolving locus in the human genome compared to that of the chimpanzee. Yet the EDC genes that are undergoing positive selection across mammals and in humans are not known. We sought to identify the positively selected genetic variants and determine the evolutionary events of the EDC using mammalian-wide and clade-specific branch- and branch-site likelihood ratio tests and a genetic algorithm (GA) branch test. Significant non-synonymous substitutions were found in filaggrin, SPRR4, LELP1, and S100A2 genes across 14 mammals. By contrast, we identified recent positive selection in SPRR4 in primates. Additionally, the GA branch test discovered lineage-specific evolution for distinct EDC genes occurring in each of the nodes in the 14-mammal phylogenetic tree. Multiple instances of positive selection for FLG, TCHHL1, SPRR4, LELP1, and S100A2 were noted among the primate branch nodes. Branch-site likelihood ratio tests further revealed positive selection in specific sites in SPRR4, LELP1, filaggrin, and repetin across 14 mammals. However, in addition to continuous evolution of SPRR4, site-specific positive selection was also found in S100A11, KPRP, SPRR1A, S100A7L2, and S100A3 in primates and filaggrin, filaggrin2, and S100A8 in great apes. Very recent human positive selection was identified in the filaggrin2 L41 site that was present in Neanderthal. Together, our results identifying recent positive selection in distinct EDC genes reveal an underappreciated evolution of epidermal skin barrier function in primates and humans.}, } @article {pmid28102248, year = {2017}, author = {Nielsen, R and Akey, JM and Jakobsson, M and Pritchard, JK and Tishkoff, S and Willerslev, E}, title = {Tracing the peopling of the world through genomics.}, journal = {Nature}, volume = {541}, number = {7637}, pages = {302-310}, pmid = {28102248}, issn = {1476-4687}, support = {R01 DK104339/DK/NIDDK NIH HHS/United States ; R01 GM110068/GM/NIGMS NIH HHS/United States ; R01 GM113657/GM/NIGMS NIH HHS/United States ; R01 GM116044/GM/NIGMS NIH HHS/United States ; }, mesh = {Acclimatization/genetics ; Africa/ethnology ; Animals ; *Evolution, Molecular ; Genome, Human/*genetics ; *Genomics ; Geography ; History, Ancient ; Human Migration/*history ; Humans ; Neanderthals/genetics ; Selection, Genetic ; }, abstract = {Advances in the sequencing and the analysis of the genomes of both modern and ancient peoples have facilitated a number of breakthroughs in our understanding of human evolutionary history. These include the discovery of interbreeding between anatomically modern humans and extinct hominins; the development of an increasingly detailed description of the complex dispersal of modern humans out of Africa and their population expansion worldwide; and the characterization of many of the genetic adaptions of humans to local environmental conditions. Our interpretation of the evolutionary history and adaptation of humans is being transformed by analyses of these new genomic data.}, } @article {pmid28102010, year = {2017}, author = {Belcastro, MG and Mariotti, V}, title = {A muscular imprint on the anterolateral surface of the proximal femurs of the Krapina Neandertal collection.}, journal = {American journal of physical anthropology}, volume = {162}, number = {3}, pages = {583-588}, doi = {10.1002/ajpa.23140}, pmid = {28102010}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; Female ; Femur/*anatomy & histology ; *Fossils ; Male ; Muscle, Skeletal/*physiology ; Neanderthals/*anatomy & histology/*physiology ; }, abstract = {OBJECTIVES: The purpose of this study is to report and interpret a feature on the anterolateral surface of the proximal femurs of the Krapina hominid collection that we briefly described in 2006 (Periodicum Biologorum, 108, 319-329).

MATERIALS AND METHODS: We recorded the presence or absence of the feature in all the proximal femurs of the Krapina collection (six specimens recordable) and in 622 modern human adult femurs.

RESULTS: The feature consists in a series of crests delimitating three raised or depressed areas. This feature has been found in three out of four adult Neandertal femurs observable. The two observable subadult Neandertal femurs do not show this character. None of the modern femurs displayed the feature.

CONCLUSION: We interpret this feature as a muscular imprint, probably representing the m. vastus intermedius origin and discuss a possible interpretation. We did not find any other references for such imprint in the existing literature regarding the Neandertal femurs.}, } @article {pmid28044971, year = {2016}, author = {Deschamps, M and Quintana-Murci, L}, title = {[Innate immunity and human diseases: from archaic introgression to natural selection].}, journal = {Medecine sciences : M/S}, volume = {32}, number = {12}, pages = {1079-1086}, doi = {10.1051/medsci/20163212011}, pmid = {28044971}, issn = {1958-5381}, mesh = {Animals ; *Biological Evolution ; Disease/*etiology ; Genetic Variation ; Genetics, Population ; Hominidae/genetics/immunology ; Humans ; Immunity, Innate/*physiology ; Neanderthals/genetics/immunology ; Selection, Genetic/*immunology ; }, abstract = {Throughout evolution, humans have had to face strong variation in environmental conditions, with pathogens being among the strongest threats that our species has encountered. The use of population genetic approaches provides novel insights into how natural selection imposed by pathogen pressures, in its different forms and intensities, has shaped the patterns of diversity of the human genome at the population level. These studies help to distinguish genes playing essential, non-redundant functions in host defence from genes variation in which has conferred selective advantages to specific human populations and/or has been acquired through admixture with archaic hominins, such as Neandertals. However, with the improvements in hygiene and the advent of antibiotics and vaccination, pressures imposed by pathogens have recently been relaxed. Accumulating evidence suggests that alleles having conferred an advantage against infection in the past may nowadays be associated with increased risk to develop immune-related disorders, such as autoimmunity and inflammation.}, } @article {pmid28035661, year = {2017}, author = {Estalrrich, A and Alarcón, JA and Rosas, A}, title = {Evidence of toothpick groove formation in Neandertal anterior and posterior teeth.}, journal = {American journal of physical anthropology}, volume = {162}, number = {4}, pages = {747-756}, doi = {10.1002/ajpa.23166}, pmid = {28035661}, issn = {1096-8644}, mesh = {Animals ; *Feeding Behavior ; France ; History, Ancient ; *Neanderthals ; Oral Hygiene/*history ; Spain ; Tool Use Behavior ; Tooth/*pathology ; }, abstract = {OBJECTIVES: During the microscopic examination of the Neandertal dentitions from El Sidrón (Spain) and Hortus (France), we found unusual fine parallel microstriations on the mesial and distal sides of all tooth types, near the cervix. As its appearance was similar to toothpick grooves described in other Homo species, it could correspond to early stages on its formation. To test this hypothesis we developed an experimental replication of a groove using grass stalks.

MATERIALS AND METHODS: Comparisons between 204 isolated Neandertal teeth and the two experimental dental specimens corroborate that the marks correspond to initial stages of toothpick groove formation, and we propose a five-grade recording scale that summarized the groove formation process.

RESULTS: Using this new recording procedure, we found that Hortus individuals have higher incidence of this trait (eight individuals out of nine) than the El Sidrón individuals (nine out of 11). Toothpick grooves from El Sidrón show the earliest stages of development, whereas the grooves found on Hortus Neandertals were well-developed. Toothpick grooves were also found in 21 incisors and canines.

CONCLUSIONS: These differences could be due to the more advanced occlusal dental wear in Hortus individuals, maybe age-related and with a more meat-based diet maybe favoring the inclusion of food debris and thus probing as the cleaning methodology. Our results allow the identification and characterization of incipient toothpick grooves on the human fossil record and contribute to increase our knowledge on Neandertals behavioral and oral care habits.}, } @article {pmid28025273, year = {2017}, author = {Pimenoff, VN and de Oliveira, CM and Bravo, IG}, title = {Transmission between Archaic and Modern Human Ancestors during the Evolution of the Oncogenic Human Papillomavirus 16.}, journal = {Molecular biology and evolution}, volume = {34}, number = {1}, pages = {4-19}, pmid = {28025273}, issn = {1537-1719}, mesh = {Alleles ; Animals ; Biological Evolution ; Databases, Nucleic Acid ; Genetic Variation ; Hominidae/*genetics ; Human papillomavirus 16/*genetics ; Humans ; Male ; Neanderthals/genetics ; Oncogenes ; Papillomavirus Infections/*transmission/*virology ; Phylogeny ; Phylogeography ; }, abstract = {Every human suffers through life a number of papillomaviruses (PVs) infections, most of them asymptomatic. A notable exception are persistent infections by Human papillomavirus 16 (HPV16), the most oncogenic infectious agent for humans and responsible for most infection-driven anogenital cancers. Oncogenic potential is not homogeneous among HPV16 lineages, and genetic variation within HPV16 exhibits some geographic structure. However, an in-depth analysis of the HPV16 evolutionary history was still wanting. We have analyzed extant HPV16 diversity and compared the evolutionary and phylogeographical patterns of humans and of HPV16. We show that codivergence with modern humans explains at most 30% of the present viral geographical distribution. The most explanatory scenario suggests that ancestral HPV16 already infected ancestral human populations and that viral lineages co-diverged with the hosts in parallel with the split between archaic Neanderthal-Denisovans and ancestral modern human populations, generating the ancestral HPV16A and HPV16BCD viral lineages, respectively. We propose that after out-of-Africa migration of modern human ancestors, sexual transmission between human populations introduced HPV16A into modern human ancestor populations. We hypothesize that differential coevolution of HPV16 lineages with different but closely related ancestral human populations and subsequent host-switch events in parallel with introgression of archaic alleles into the genomes of modern human ancestors may be largely responsible for the present-day differential prevalence and association with cancers for HPV16 variants.}, } @article {pmid28007980, year = {2017}, author = {Racimo, F and Gokhman, D and Fumagalli, M and Ko, A and Hansen, T and Moltke, I and Albrechtsen, A and Carmel, L and Huerta-Sánchez, E and Nielsen, R}, title = {Archaic Adaptive Introgression in TBX15/WARS2.}, journal = {Molecular biology and evolution}, volume = {34}, number = {3}, pages = {509-524}, pmid = {28007980}, issn = {1537-1719}, support = {R01 HG003229/HG/NHGRI NIH HHS/United States ; }, mesh = {Adaptation, Biological/*genetics ; Adipose Tissue/physiology ; Alleles ; Animals ; DNA Methylation ; DNA, Ancient ; Greenland ; Haplotypes ; Humans ; Inuits/*genetics ; Models, Genetic ; Neanderthals ; Polymorphism, Single Nucleotide ; Selection, Genetic ; Sequence Analysis, DNA/methods ; T-Box Domain Proteins/*genetics ; }, abstract = {A recent study conducted the first genome-wide scan for selection in Inuit from Greenland using single nucleotide polymorphism chip data. Here, we report that selection in the region with the second most extreme signal of positive selection in Greenlandic Inuit favored a deeply divergent haplotype that is closely related to the sequence in the Denisovan genome, and was likely introgressed from an archaic population. The region contains two genes, WARS2 and TBX15, and has previously been associated with adipose tissue differentiation and body-fat distribution in humans. We show that the adaptively introgressed allele has been under selection in a much larger geographic region than just Greenland. Furthermore, it is associated with changes in expression of WARS2 and TBX15 in multiple tissues including the adrenal gland and subcutaneous adipose tissue, and with regional DNA methylation changes in TBX15.}, } @article {pmid28000406, year = {2017}, author = {Weber, GW and Krenn, VA}, title = {Zygomatic Root Position in Recent and Fossil Hominids.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {300}, number = {1}, pages = {160-170}, doi = {10.1002/ar.23490}, pmid = {28000406}, issn = {1932-8494}, mesh = {Animals ; Biomechanical Phenomena/physiology ; *Fossils ; Hominidae/*anatomy & histology/physiology ; Mastication/physiology ; Maxilla/*anatomy & histology/physiology ; Zygoma/*anatomy & histology/physiology ; }, abstract = {The relative position of the zygomatic root to the dentition plays a crucial role in determining the overall strength of the face in response to bite forces. The powerful superficial head of the masseter arises there and the zygomaticoalveolar crest (ZAC) is discussed as a buttressing feature of the face. For instance, a more forwardly or backwardly positioned zygomatic root or a lower or higher vertical distance to the dentition could be indicative for evolutionary adaptations to particular loading regimes which are associated with diet. We therefore examined the morphology of the maxilla using state-of-the-art 3D Geometric Morphometric methods. The data set was reduced to a minimum of relevant measurements and includes five landmarks (pr, ol, zm, lingual and buccal midpoint of second molar alveoli) and three curves with semilandmarks along the lingual and buccal alveolar rim and the ZAC. Results show a stunning overlap in shape variation. We find no clear pattern of shape that would allow separating different hominid groups with confidence, except two extreme forms-Paranthropines and Neanderthals. We also find no clear trend over time. Australopithecines, Habilines, Erectines, and Middle Pleistocene Homo can be very similar to modern humans. Even great apes are within or not far from the central shape distribution of Homo, but they separate clearly from gracile and robust Australopithecines. We discuss the shape factors underlying our data. The geometry studied allows simple measurements and analyses and is thus potentially interesting for classification purposes of extreme forms. Anat Rec, 300:160-170, 2017. © 2016 Wiley Periodicals, Inc.}, } @article {pmid28000401, year = {2017}, author = {Rak, Y and Marom, A}, title = {Opposing Extremes of Zygomatic Bone Morphology: Australopithecus Boisei versus Homo Neanderthalensis.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {300}, number = {1}, pages = {152-159}, doi = {10.1002/ar.23491}, pmid = {28000401}, issn = {1932-8494}, mesh = {Animals ; *Biological Evolution ; Biomechanical Phenomena ; *Fossils ; Hominidae/*anatomy & histology/physiology ; Mastication ; Neanderthals/anatomy & histology/physiology ; Zygoma/*anatomy & histology/physiology ; }, abstract = {The lateral margin of the zygomatic bone of Australopithecus boisei flares both anteriorly and laterally. As a result, the bone loses the suspensory bracing of the facial frame and is transformed into a visor-like structure that supports itself and gains its rigidity from its shape. The coronally oriented bony plates and the outline of the facial mask help the A. boisei face resist the effect of the visor-like structure, which tends to pull the bone plates of the face away from the midline. On the other hand, the nearly sagittal orientation of the zygomatic bone in Homo neanderthalensis helps the face resist torque and bending forces, which themselves stem from the positioning of the bite point on the anterior teeth. Although the zygomatic bones of these two taxa are highly specialized, they differ fundamentally from each other. Anat Rec, 300:152-159, 2017. © 2016 Wiley Periodicals, Inc.}, } @article {pmid27936135, year = {2016}, author = {Muller, A and Clarkson, C}, title = {Identifying Major Transitions in the Evolution of Lithic Cutting Edge Production Rates.}, journal = {PloS one}, volume = {11}, number = {12}, pages = {e0167244}, pmid = {27936135}, issn = {1932-6203}, mesh = {Animals ; Archaeology/*methods ; *Biological Evolution ; *Fossils ; Hominidae ; Humans ; Manufactured Materials ; Neanderthals ; Paleontology ; Technology/*methods ; Time Factors ; }, abstract = {The notion that the evolution of core reduction strategies involved increasing efficiency in cutting edge production is prevalent in narratives of hominin technological evolution. Yet a number of studies comparing two different knapping technologies have found no significant differences in edge production. Using digital analysis methods we present an investigation of raw material efficiency in eight core technologies broadly representative of the long-term evolution of lithic technology. These are bipolar, multiplatform, discoidal, biface, Levallois, prismatic blade, punch blade and pressure blade production. Raw material efficiency is assessed by the ratio of cutting edge length to original core mass. We also examine which flake attributes contribute to maximising raw material efficiency, as well as compare the difference between expert and intermediate knappers in terms of cutting edge produced per gram of core. We identify a gradual increase in raw material efficiency over the broad sweep of lithic technological evolution. The results indicate that the most significant transition in efficiency likely took place with the introduction of small foliate biface, Levallois and prismatic blade knapping, all introduced in the Middle Stone Age / Middle Palaeolithic among early Homo sapiens and Neanderthals. This suggests that no difference in raw material efficiency existed between these species. With prismatic blade technology securely dated to the Middle Palaeolithic, by including the more recent punch and pressure blade technology our results dispel the notion that the transition to the Upper Palaeolithic was accompanied by an increase in efficiency. However, further increases in cutting edge efficiency are evident, with pressure blades possessing the highest efficiency in this study, indicating that late/epi-Palaeolithic and Neolithic blade technologies further increased efficiency.}, } @article {pmid27919236, year = {2016}, author = {Pajic, P and Lin, YL and Xu, D and Gokcumen, O}, title = {The psoriasis-associated deletion of late cornified envelope genes LCE3B and LCE3C has been maintained under balancing selection since Human Denisovan divergence.}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {265}, pmid = {27919236}, issn = {1471-2148}, mesh = {Alleles ; Cornified Envelope Proline-Rich Proteins/*genetics ; *Evolution, Molecular ; *Gene Deletion ; Gene Frequency ; Genetic Predisposition to Disease ; Humans ; Polymorphism, Single Nucleotide ; Psoriasis/*genetics ; Sequence Deletion ; }, abstract = {BACKGROUND: A common, 32kb deletion of LCE3B and LCE3C genes is strongly associated with psoriasis. We recently found that this deletion is ancient, predating Human-Denisovan divergence. However, it was not clear why negative selection has not removed this deletion from the population.

RESULTS: Here, we show that the haplotype block that harbors the deletion (i) retains high allele frequency among extant and ancient human populations; (ii) harbors unusually high nucleotide variation (π, P < 4.1 × 10-3); (iii) contains an excess of intermediate frequency variants (Tajima's D, P < 3.9 × 10-3); and (iv) has an unusually long time to coalescence to the most recent common ancestor (TSel, 0.1 quantile).

CONCLUSIONS: Our results are most parsimonious with the scenario where the LCE3BC deletion has evolved under balancing selection in humans. More broadly, this is consistent with the hypothesis that a balance between autoimmunity and natural vaccination through increased exposure to pathogens maintains this deletion in humans.}, } @article {pmid27916748, year = {2017}, author = {Noe, F and Polster, J and Geithe, C and Kotthoff, M and Schieberle, P and Krautwurst, D}, title = {OR2M3: A Highly Specific and Narrowly Tuned Human Odorant Receptor for the Sensitive Detection of Onion Key Food Odorant 3-Mercapto-2-methylpentan-1-ol.}, journal = {Chemical senses}, volume = {42}, number = {3}, pages = {195-210}, doi = {10.1093/chemse/bjw118}, pmid = {27916748}, issn = {1464-3553}, mesh = {Cells, Cultured ; Humans ; Molecular Structure ; Odorants/*analysis ; Onions/*chemistry ; Pentanols/*analysis/chemistry ; Receptors, Odorant/*metabolism ; *Smell ; Sulfhydryl Compounds/*analysis/chemistry ; }, abstract = {The detection of key food odorants appears to be an important capability of odorant receptors. Here, thiols occupy an outstanding position among the 230 known key food odorants because of their very low odor thresholds. Members of the homologous series of 3-mercapto-2-methylalkan-1-ols have been described as onion key food odorants or food constituents and are detected at logarithmically different thresholds. 3-Mercapto-2-methylpentan-1-ol being the only key food odorant within this series also has the lowest odor threshold. Most odorants typically activate combinations of odorant receptors, which may be narrowly or broadly tuned. Consequently, a specific receptor activation pattern will define an odor quality. In contrast, here we show that just 1 of the 391 human odorant receptors, OR2M3, responded exclusively to 3-mercapto-2-methylpentan-1-ol of the 190 key food odorants tested, with a half maximal effective concentration at submicromolar concentration. Moreover, neither the Denisovan OR2M3 nor the closest OR2M3 homologs from five species did respond to this compound. This outstanding specificity of extremely narrowly tuned human OR2M3 can explain both odor qualities and odor threshold trend within a homologous series of 3-mercapto-2-methylalkan-1-ols and suggests a modern human-specific, food-related function of OR2M3 in detecting a single onion key food odorant.}, } @article {pmid27899133, year = {2016}, author = {Sams, AJ and Dumaine, A and Nédélec, Y and Yotova, V and Alfieri, C and Tanner, JE and Messer, PW and Barreiro, LB}, title = {Adaptively introgressed Neandertal haplotype at the OAS locus functionally impacts innate immune responses in humans.}, journal = {Genome biology}, volume = {17}, number = {1}, pages = {246}, pmid = {27899133}, issn = {1474-760X}, support = {301538//CIHR/Canada ; 232519//CIHR/Canada ; }, mesh = {2',5'-Oligoadenylate Synthetase/*genetics ; Animals ; Evolution, Molecular ; Gene Expression Regulation, Enzymologic ; Genome, Human ; Haplotypes/genetics ; Humans ; Immunity, Innate/*genetics ; Infection/*genetics/immunology/pathology ; Neanderthals/genetics/immunology ; Polymorphism, Single Nucleotide ; Protein Isoforms/genetics/immunology ; Selection, Genetic/genetics/immunology ; }, abstract = {BACKGROUND: The 2'-5' oligoadenylate synthetase (OAS) locus encodes for three OAS enzymes (OAS1-3) involved in innate immune response. This region harbors high amounts of Neandertal ancestry in non-African populations; yet, strong evidence of positive selection in the OAS region is still lacking.

RESULTS: Here we used a broad array of selection tests in concert with neutral coalescent simulations to demonstrate a signal of adaptive introgression at the OAS locus. Furthermore, we characterized the functional consequences of the Neandertal haplotype in the transcriptional regulation of OAS genes at baseline and infected conditions. We found that cells from people with the Neandertal-like haplotype express lower levels of OAS3 upon infection, as well as distinct isoforms of OAS1 and OAS2.

CONCLUSIONS: We present evidence that a Neandertal haplotype at the OAS locus was subjected to positive selection in the human population. This haplotype is significantly associated with functional consequences at the level of transcriptional regulation of innate immune responses. Notably, we suggest that the Neandertal-introgressed haplotype likely reintroduced an ancestral splice variant of OAS1 encoding a more active protein, suggesting that adaptive introgression occurred as a means to resurrect adaptive variation that had been lost outside Africa.}, } @article {pmid27889059, year = {2016}, author = {Haber, M and Mezzavilla, M and Bergström, A and Prado-Martinez, J and Hallast, P and Saif-Ali, R and Al-Habori, M and Dedoussis, G and Zeggini, E and Blue-Smith, J and Wells, RS and Xue, Y and Zalloua, PA and Tyler-Smith, C}, title = {Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations.}, journal = {American journal of human genetics}, volume = {99}, number = {6}, pages = {1316-1324}, pmid = {27889059}, issn = {1537-6605}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Asia/ethnology ; Chad ; Ethiopia ; Europe/ethnology ; Gene Flow/genetics ; Genetic Variation/*genetics ; Genetics, Population ; Genome, Human/genetics ; Heterozygote ; History, Ancient ; Human Migration/*history ; Humans ; Linkage Disequilibrium ; Middle East ; Neanderthals/genetics ; Polymorphism, Single Nucleotide/genetics ; Population Density ; }, abstract = {Understanding human genetic diversity in Africa is important for interpreting the evolution of all humans, yet vast regions in Africa, such as Chad, remain genetically poorly investigated. Here, we use genotype data from 480 samples from Chad, the Near East, and southern Europe, as well as whole-genome sequencing from 19 of them, to show that many populations today derive their genomes from ancient African-Eurasian admixtures. We found evidence of early Eurasian backflow to Africa in people speaking the unclassified isolate Laal language in southern Chad and estimate from linkage-disequilibrium decay that this occurred 4,750-7,200 years ago. It brought to Africa a Y chromosome lineage (R1b-V88) whose closest relatives are widespread in present-day Eurasia; we estimate from sequence data that the Chad R1b-V88 Y chromosomes coalesced 5,700-7,300 years ago. This migration could thus have originated among Near Eastern farmers during the African Humid Period. We also found that the previously documented Eurasian backflow into Africa, which occurred ∼3,000 years ago and was thought to be mostly limited to East Africa, had a more westward impact affecting populations in northern Chad, such as the Toubou, who have 20%-30% Eurasian ancestry today. We observed a decline in heterozygosity in admixed Africans and found that the Eurasian admixture can bias inferences on their coalescent history and confound genetic signals from adaptation and archaic introgression.}, } @article {pmid27877146, year = {2016}, author = {Progovac, L}, title = {A Gradualist Scenario for Language Evolution: Precise Linguistic Reconstruction of Early Human (and Neandertal) Grammars.}, journal = {Frontiers in psychology}, volume = {7}, number = {}, pages = {1714}, pmid = {27877146}, issn = {1664-1078}, abstract = {In making an argument for the antiquity of language, based on comparative evidence, Dediu and Levinson (2013) express hope that some combinations of structural features will prove so conservative that they will allow deep linguistic reconstruction. I propose that the earliest stages of syntax/grammar as reconstructed in Progovac (2015a), based on a theoretical and data-driven linguistic analysis, provide just such a conservative platform, which would have been commanded also by Neandertals and the common ancestor. I provide a fragment of this proto-grammar, which includes flat verb-noun compounds used for naming and insult (e.g., rattle-snake, cry-baby, scatter-brain), and paratactic (loose) combinations of such flat structures (e.g., Come one, come all; You seek, you find). This flat, binary, paratactic platform is found in all languages, and can be shown to serve as foundation for any further structure building. However, given the degree and nature of variation across languages in elaborating syntax beyond this proto-stage, I propose that hierarchical syntax did not emerge once and uniformly in all its complexity, but rather multiple times, either within Africa, or after dispersion from Africa. If so, then, under the uniregional hypothesis, our common ancestor with Neandertals, H. heidelbergensis, could not have commanded hierarchical syntax, but "only" the proto-grammar. Linguistic reconstructions of this kind are necessary for formulating precise and testable hypotheses regarding language evolution. In addition to the hominin timeline, this reconstruction can also engage, and negotiate between, the fields of neuroscience and genetics, as I illustrate with one specific scenario involving FOXP2 gene.}, } @article {pmid27853181, year = {2016}, author = {Inchley, CE and Larbey, CD and Shwan, NA and Pagani, L and Saag, L and Antão, T and Jacobs, G and Hudjashov, G and Metspalu, E and Mitt, M and Eichstaedt, CA and Malyarchuk, B and Derenko, M and Wee, J and Abdullah, S and Ricaut, FX and Mormina, M and Mägi, R and Villems, R and Metspalu, M and Jones, MK and Armour, JA and Kivisild, T}, title = {Selective sweep on human amylase genes postdates the split with Neanderthals.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {37198}, pmid = {27853181}, issn = {2045-2322}, support = {261213//European Research Council/International ; }, mesh = {Amylases/*genetics ; Animals ; *Evolution, Molecular ; Female ; *Gene Dosage ; *Genetic Variation ; *Genome, Human ; Humans ; Male ; Neanderthals ; }, abstract = {Humans have more copies of amylase genes than other primates. It is still poorly understood, however, when the copy number expansion occurred and whether its spread was enhanced by selection. Here we assess amylase copy numbers in a global sample of 480 high coverage genomes and find that regions flanking the amylase locus show notable depression of genetic diversity both in African and non-African populations. Analysis of genetic variation in these regions supports the model of an early selective sweep in the human lineage after the split of humans from Neanderthals which led to the fixation of multiple copies of AMY1 in place of a single copy. We find evidence of multiple secondary losses of copy number with the highest frequency (52%) of a deletion of AMY2A and associated low copy number of AMY1 in Northeast Siberian populations whose diet has been low in starch content.}, } @article {pmid27843675, year = {2016}, author = {Shipley, GP and Kindscher, K}, title = {Evidence for the Paleoethnobotany of the Neanderthal: A Review of the Literature.}, journal = {Scientifica}, volume = {2016}, number = {}, pages = {8927654}, pmid = {27843675}, issn = {2090-908X}, abstract = {Our perception of our closest human relatives, the Neanderthals, has evolved in the last few decades from brutish ape-men to intelligent archaic human peoples. Our understanding and appreciation of their cultural sophistication has only recently extended to their diet. Only within the last few years, with new techniques and a shift in focus, have we begun to truly investigate and understand the role of plants in their diet and culture. The more we learn about Neanderthals, the more we realize that biological and cultural distinctions between them and us were relatively small. Given that we coexisted and likely interacted with them for thousands of years, the more we learn about them, the better we may understand our own past. In that light, we review the current evidence, derived from such sources as plant remains (e.g., starch, pollen, phytoliths, and seeds) in soil and dental calculus, dental and tool wear, coprolites, and genetics, for Neanderthal's nutritional, medicinal, and ritual use of plants, which includes 61 different taxa from 26 different plant families found at 17 different archaeological sites. Further, we updated and standardized botanical nomenclature from many sources published over many decades to provide a more stable foundation for future work.}, } @article {pmid27839976, year = {2016}, author = {Gittelman, RM and Schraiber, JG and Vernot, B and Mikacenic, C and Wurfel, MM and Akey, JM}, title = {Archaic Hominin Admixture Facilitated Adaptation to Out-of-Africa Environments.}, journal = {Current biology : CB}, volume = {26}, number = {24}, pages = {3375-3382}, doi = {10.1016/j.cub.2016.10.041}, pmid = {27839976}, issn = {1879-0445}, support = {R01 GM110068/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Animals ; *Biological Evolution ; DNA/*genetics ; Demography ; Gene Expression Regulation ; Genetic Variation ; *Genome, Human/genetics ; Haplotypes ; Humans ; Neanderthals ; Pigmentation ; }, abstract = {As modern humans dispersed from Africa throughout the world, they encountered and interbred with archaic hominins, including Neanderthals and Denisovans [1, 2]. Although genome-scale maps of introgressed sequences have been constructed [3-6], considerable gaps in knowledge remain about the functional, phenotypic, and evolutionary significance of archaic hominin DNA that persists in present-day individuals. Here, we describe a comprehensive set of analyses that identified 126 high-frequency archaic haplotypes as putative targets of adaptive introgression in geographically diverse populations. These loci are enriched for immune-related genes (such as OAS1/2/3, TLR1/6/10, and TNFAIP3) and also encompass genes (including OCA2 and BNC2) that influence skin pigmentation phenotypes. Furthermore, we leveraged existing and novel large-scale gene expression datasets to show many positively selected archaic haplotypes act as expression quantitative trait loci (eQTLs), suggesting that modulation of transcript abundance was a common mechanism facilitating adaptive introgression. Our results demonstrate that hybridization between modern and archaic hominins provided an important reservoir of advantageous alleles that enabled adaptation to out-of-Africa environments.}, } @article {pmid27824859, year = {2016}, author = {Juric, I and Aeschbacher, S and Coop, G}, title = {The Strength of Selection against Neanderthal Introgression.}, journal = {PLoS genetics}, volume = {12}, number = {11}, pages = {e1006340}, pmid = {27824859}, issn = {1553-7404}, support = {R01 GM108779/GM/NIGMS NIH HHS/United States ; }, mesh = {Alleles ; Animals ; Asian Continental Ancestry Group/genetics ; European Continental Ancestry Group ; Gene Frequency ; *Genetics, Population ; *Genome, Human ; Haplotypes ; Humans ; Hybridization, Genetic ; Neanderthals/*genetics ; Phylogeny ; Polymorphism, Single Nucleotide ; Selection, Genetic/*genetics ; }, abstract = {Hybridization between humans and Neanderthals has resulted in a low level of Neanderthal ancestry scattered across the genomes of many modern-day humans. After hybridization, on average, selection appears to have removed Neanderthal alleles from the human population. Quantifying the strength and causes of this selection against Neanderthal ancestry is key to understanding our relationship to Neanderthals and, more broadly, how populations remain distinct after secondary contact. Here, we develop a novel method for estimating the genome-wide average strength of selection and the density of selected sites using estimates of Neanderthal allele frequency along the genomes of modern-day humans. We confirm that East Asians had somewhat higher initial levels of Neanderthal ancestry than Europeans even after accounting for selection. We find that the bulk of purifying selection against Neanderthal ancestry is best understood as acting on many weakly deleterious alleles. We propose that the majority of these alleles were effectively neutral-and segregating at high frequency-in Neanderthals, but became selected against after entering human populations of much larger effective size. While individually of small effect, these alleles potentially imposed a heavy genetic load on the early-generation human-Neanderthal hybrids. This work suggests that differences in effective population size may play a far more important role in shaping levels of introgression than previously thought.}, } @article {pmid27808237, year = {2016}, author = {Hoffmann, DL and Rogerson, M and Spötl, C and Luetscher, M and Vance, D and Osborne, AH and Fello, NM and Moseley, GE}, title = {Timing and causes of North African wet phases during the last glacial period and implications for modern human migration.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {36367}, pmid = {27808237}, issn = {2045-2322}, mesh = {Africa, Northern ; Climate ; *Emigration and Immigration ; Geologic Sediments/*analysis ; History, Ancient ; Humans ; }, abstract = {We present the first speleothem-derived central North Africa rainfall record for the last glacial period. The record reveals three main wet periods at 65-61 ka, 52.5-50.5 ka and 37.5-33 ka that lead obliquity maxima and precession minima. We find additional minor wet episodes that are synchronous with Greenland interstadials. Our results demonstrate that sub-tropical hydrology is forced by both orbital cyclicity and North Atlantic moisture sources. The record shows that after the end of a Saharan wet phase around 70 ka ago, North Africa continued to intermittently receive substantially more rainfall than today, resulting in favourable environmental conditions for modern human expansion. The encounter and subsequent mixture of Neanderthals and modern humans - which, on genetic evidence, is considered to have occurred between 60 and 50 ka - occurred synchronously with the wet phase between 52.5 and 50.5 ka. Based on genetic evidence the dispersal of modern humans into Eurasia started less than 55 ka ago. This may have been initiated by dry conditions that prevailed in North Africa after 50.5 ka. The timing of a migration reversal of modern humans from Eurasia into North Africa is suggested to be coincident with the wet period between 37.5 and 33 ka.}, } @article {pmid27805907, year = {2017}, author = {Bock, KW}, title = {Human and rodent aryl hydrocarbon receptor (AHR): from mediator of dioxin toxicity to physiologic AHR functions and therapeutic options.}, journal = {Biological chemistry}, volume = {398}, number = {4}, pages = {455-464}, doi = {10.1515/hsz-2016-0303}, pmid = {27805907}, issn = {1437-4315}, mesh = {Animals ; *Dioxins/toxicity ; Genetic Variation ; Homeostasis/drug effects/physiology ; Humans ; Ligands ; Receptors, Aryl Hydrocarbon/genetics/*metabolism ; Rodentia ; Signal Transduction ; Stem Cells/physiology ; }, abstract = {Metabolism of aryl hydrocarbons and toxicity of dioxins led to the discovery of the aryl hydrocarbon receptor (AHR). Tremendous advances have been made on multiplicity of AHR signaling and identification of endogenous ligands including the tryptophan metabolites FICZ and kynurenine. However, human AHR functions are still poorly understood due to marked species differences as well as cell-type- and cell context-dependent AHR functions. Observations in dioxin-poisoned individuals may provide hints to physiologic AHR functions in humans. Based on these observations three human AHR functions are discussed: (1) Chemical defence and homeostasis of endobiotics. The AHR variant Val381 in modern humans leads to reduced AHR affinity to aryl hydrocarbons in comparison with Neanderthals and primates expressing the Ala381 variant while affinity to indoles remains unimpaired. (2) Homeostasis of stem/progenitor cells. Dioxins dysregulate homeostasis in sebocyte stem cells. (3) Modulation of immunity. In addition to microbial defence, AHR may be involved in a 'disease tolerance defence pathway'. Further characterization of physiologic AHR functions may lead to therapeutic options.}, } @article {pmid27783325, year = {2017}, author = {Fogarty, L and Wakano, JY and Feldman, MW and Aoki, K}, title = {The Driving Forces of Cultural Complexity : Neanderthals, Modern Humans, and the Question of Population Size.}, journal = {Human nature (Hawthorne, N.Y.)}, volume = {28}, number = {1}, pages = {39-52}, pmid = {27783325}, issn = {1936-4776}, mesh = {Animals ; *Cognition ; *Cultural Evolution ; Humans ; *Models, Theoretical ; *Neanderthals ; Population Density ; *Social Behavior ; }, abstract = {The forces driving cultural accumulation in human populations, both modern and ancient, are hotly debated. Did genetic, demographic, or cognitive features of behaviorally modern humans (as opposed to, say, early modern humans or Neanderthals) allow culture to accumulate to its current, unprecedented levels of complexity? Theoretical explanations for patterns of accumulation often invoke demographic factors such as population size or density, whereas statistical analyses of variation in cultural complexity often point to the importance of environmental factors such as food stability, in determining cultural complexity. Here we use both an analytical model and an agent-based simulation model to show that a full understanding of the emergence of behavioral modernity, and the cultural evolution that has followed, depends on understanding and untangling the complex relationships among culture, genetically determined cognitive ability, and demographic history. For example, we show that a small but growing population could have a different number of cultural traits from a shrinking population with the same absolute number of individuals in some circumstances.}, } @article {pmid27365292, year = {2016}, author = {Fabbri, PF and Panetta, D and Sarti, L and Martini, F and Salvadori, PA and Caramella, D and Fedi, M and Benazzi, S}, title = {Middle paleolithic human deciduous incisor from Grotta del Cavallo, Italy.}, journal = {American journal of physical anthropology}, volume = {161}, number = {3}, pages = {506-512}, doi = {10.1002/ajpa.23044}, pmid = {27365292}, issn = {1096-8644}, mesh = {Animals ; Humans ; Incisor/*anatomy & histology ; Italy ; Neanderthals/*anatomy & histology ; Odontometry ; Paleodontology ; Tooth, Deciduous/*anatomy & histology ; }, abstract = {OBJECTIVES: In this contribution, we present a morphological description and comparative morphometric analysis of Cavallo D, a human tooth unearthed from the Mousterian FIII sublayer of Grotta del Cavallo (Apulia, Italy).

MATERIALS AND METHODS: We used microCT data to provide a detailed morphological description and morphometric analysis of the Cavallo D human tooth based on traditional diameter measurements and 3D enamel thickness. Moreover, new AMS radiocarbon dating of charcoals from layers FII was carried out.

RESULTS: Morphological features observed in Cavallo D align the tooth to Neandertals. Similarly, the large size of the tooth (e.g., BL diameter) and the relatively thinner enamel thickness are typical Neandertal traits. 14 C datings of layer FII attribute the tooth to a time range of 45,600-42,900 cal BP (at 68% level of probability).

DISCUSSION: Up to now, the Rdi1 Cavallo D represents the most recent Neandertal human remain in southern Italy related to a radiocarbon dated stratigraphy. Moreover, since deciduous teeth have been less investigated than the permanent ones, this contribution brings new data to increase our knowledge on the variability of the Neandertal deciduous dentition.}, } @article {pmid27768889, year = {2016}, author = {Nédélec, Y and Sanz, J and Baharian, G and Szpiech, ZA and Pacis, A and Dumaine, A and Grenier, JC and Freiman, A and Sams, AJ and Hebert, S and Pagé Sabourin, A and Luca, F and Blekhman, R and Hernandez, RD and Pique-Regi, R and Tung, J and Yotova, V and Barreiro, LB}, title = {Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens.}, journal = {Cell}, volume = {167}, number = {3}, pages = {657-669.e21}, doi = {10.1016/j.cell.2016.09.025}, pmid = {27768889}, issn = {1097-4172}, support = {301538//CIHR/Canada ; 232519//CIHR/Canada ; }, abstract = {Individuals from different populations vary considerably in their susceptibility to immune-related diseases. To understand how genetic variation and natural selection contribute to these differences, we tested for the effects of African versus European ancestry on the transcriptional response of primary macrophages to live bacterial pathogens. A total of 9.3% of macrophage-expressed genes show ancestry-associated differences in the gene regulatory response to infection, and African ancestry specifically predicts a stronger inflammatory response and reduced intracellular bacterial growth. A large proportion of these differences are under genetic control: for 804 genes, more than 75% of ancestry effects on the immune response can be explained by a single cis- or trans-acting expression quantitative trait locus (eQTL). Finally, we show that genetic effects on the immune response are strongly enriched for recent, population-specific signatures of adaptation. Together, our results demonstrate how historical selective events continue to shape human phenotypic diversity today, including for traits that are key to controlling infection.}, } @article {pmid27768888, year = {2016}, author = {Quach, H and Rotival, M and Pothlichet, J and Loh, YE and Dannemann, M and Zidane, N and Laval, G and Patin, E and Harmant, C and Lopez, M and Deschamps, M and Naffakh, N and Duffy, D and Coen, A and Leroux-Roels, G and Clément, F and Boland, A and Deleuze, JF and Kelso, J and Albert, ML and Quintana-Murci, L}, title = {Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations.}, journal = {Cell}, volume = {167}, number = {3}, pages = {643-656.e17}, pmid = {27768888}, issn = {1097-4172}, support = {//European Research Council/International ; }, mesh = {Adaptation, Physiological/*genetics/*immunology ; *Adaptive Immunity/genetics ; African Continental Ancestry Group/genetics ; Alleles ; Animals ; Bacterial Infections/genetics/immunology ; Base Sequence ; Biological Evolution ; European Continental Ancestry Group/genetics ; Gene Expression Regulation ; Genetic Variation ; Humans ; Immune System ; Neanderthals/*genetics/*immunology ; Quantitative Trait Loci ; RNA/genetics ; Selection, Genetic ; Sequence Analysis, RNA ; Toll-Like Receptors/genetics ; Transcription, Genetic ; Virus Diseases/genetics/immunology ; }, abstract = {Humans differ in the outcome that follows exposure to life-threatening pathogens, yet the extent of population differences in immune responses and their genetic and evolutionary determinants remain undefined. Here, we characterized, using RNA sequencing, the transcriptional response of primary monocytes from Africans and Europeans to bacterial and viral stimuli-ligands activating Toll-like receptor pathways (TLR1/2, TLR4, and TLR7/8) and influenza virus-and mapped expression quantitative trait loci (eQTLs). We identify numerous cis-eQTLs that contribute to the marked differences in immune responses detected within and between populations and a strong trans-eQTL hotspot at TLR1 that decreases expression of pro-inflammatory genes in Europeans only. We find that immune-responsive regulatory variants are enriched in population-specific signals of natural selection and show that admixture with Neandertals introduced regulatory variants into European genomes, affecting preferentially responses to viral challenges. Together, our study uncovers evolutionarily important determinants of differences in host immune responsiveness between human populations.}, } @article {pmid27765150, year = {2016}, author = {Frayer, DW and Clarke, RJ and Fiore, I and Blumenschine, RJ and Pérez-Pérez, A and Martinez, LM and Estebaranz, F and Holloway, R and Bondioli, L}, title = {OH-65: The earliest evidence for right-handedness in the fossil record.}, journal = {Journal of human evolution}, volume = {100}, number = {}, pages = {65-72}, doi = {10.1016/j.jhevol.2016.07.002}, pmid = {27765150}, issn = {1095-8606}, mesh = {Animals ; Brain/*physiology ; Fossils/*anatomy & histology ; Functional Laterality ; Language ; Neanderthals/anatomy & histology/classification/*physiology ; Tool Use Behavior ; Tooth/*anatomy & histology/ultrastructure ; }, abstract = {Labial striations on the anterior teeth have been documented in numerous European pre-Neandertal and Neandertal fossils and serve as evidence for handedness. OH-65, dated at 1.8 mya, shows a concentration of oblique striations on, especially, the left I1 and right I1, I2 and C1, which signal that it was right-handed. From these patterns we contend that OH-65 was habitually using the right hand, over the left, in manipulating objects during some kind of oral processing. In living humans right-handedness is generally correlated with brain lateralization, although the strength of the association is questioned by some. We propose that as more specimens are found, right-handedness, as seen in living Homo, will most probably be typical of these early hominins.}, } @article {pmid27756828, year = {2017}, author = {Racimo, F and Marnetto, D and Huerta-Sánchez, E}, title = {Signatures of Archaic Adaptive Introgression in Present-Day Human Populations.}, journal = {Molecular biology and evolution}, volume = {34}, number = {2}, pages = {296-317}, pmid = {27756828}, issn = {1537-1719}, support = {R01 HG003229/HG/NHGRI NIH HHS/United States ; }, mesh = {Adaptation, Biological/*genetics ; Alleles ; Animals ; Biological Evolution ; Computer Simulation ; DNA, Ancient/*analysis ; Databases, Nucleic Acid ; Evolution, Molecular ; Gene Frequency ; Genetics, Population ; Haplotypes ; Humans ; Neanderthals ; Phylogeny ; Selection, Genetic ; Sequence Analysis, DNA/*methods ; }, abstract = {Comparisons of DNA from archaic and modern humans show that these groups interbred, and in some cases received an evolutionary advantage from doing so. This process-adaptive introgression-may lead to a faster rate of adaptation than is predicted from models with mutation and selection alone. Within the last couple of years, a series of studies have identified regions of the genome that are likely examples of adaptive introgression. In many cases, once a region was ascertained as being introgressed, commonly used statistics based on both haplotype as well as allele frequency information were employed to test for positive selection. Introgression by itself, however, changes both the haplotype structure and the distribution of allele frequencies, thus confounding traditional tests for detecting positive selection. Therefore, patterns generated by introgression alone may lead to false inferences of positive selection. Here we explore models involving both introgression and positive selection to investigate the behavior of various statistics under adaptive introgression. In particular, we find that the number and allelic frequencies of sites that are uniquely shared between archaic humans and specific present-day populations are particularly useful for detecting adaptive introgression. We then examine the 1000 Genomes dataset to characterize the landscape of uniquely shared archaic alleles in human populations. Finally, we identify regions that were likely subject to adaptive introgression and discuss some of the most promising candidate genes located in these regions.}, } @article {pmid27744216, year = {2016}, author = {Simons, YB and Sella, G}, title = {The impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives.}, journal = {Current opinion in genetics & development}, volume = {41}, number = {}, pages = {150-158}, pmid = {27744216}, issn = {1879-0380}, support = {R01 GM115889/GM/NIGMS NIH HHS/United States ; }, mesh = {Africa ; Animals ; *Evolution, Molecular ; Genetic Variation ; *Genetics, Population ; Gorilla gorilla/genetics ; Humans ; Neanderthals/genetics ; Sequence Deletion/*genetics ; }, abstract = {Over the past decade, there has been both great interest and confusion about whether recent demographic events-notably the Out-of-Africa-bottleneck and recent population growth-have led to differences in mutation load among human populations. The confusion can be traced to the use of different summary statistics to measure load, which lead to apparently conflicting results. We argue, however, that when statistics more directly related to load are used, the results of different studies and data sets consistently reveal little or no difference in the load of non-synonymous mutations among human populations. Theory helps to understand why no such differences are seen, as well as to predict in what settings they are to be expected. In particular, as predicted by modeling, there is evidence for changes in the load of recessive loss of function mutations in founder and inbred human populations. Also as predicted, eastern subspecies of gorilla, Neanderthals and Denisovans, who are thought to have undergone reductions in population sizes that exceed the human Out-of-Africa bottleneck in duration and severity, show evidence for increased load of non-synonymous mutations (relative to western subspecies of gorillas and modern humans, respectively). A coherent picture is thus starting to emerge about the effects of demographic history on the mutation load in populations of humans and close evolutionary relatives.}, } @article {pmid27719693, year = {2016}, author = {Madison, P}, title = {The most brutal of human skulls: measuring and knowing the first Neanderthal.}, journal = {British journal for the history of science}, volume = {49}, number = {3}, pages = {411-432}, doi = {10.1017/S0007087416000650}, pmid = {27719693}, issn = {1474-001X}, mesh = {Animals ; Anthropology, Physical/*history/methods ; Fossils/*anatomy & histology ; History, 19th Century ; Neanderthals/*anatomy & histology/psychology ; Skull/*anatomy & histology ; }, abstract = {A fossilized skeleton discovered in 1856 presented naturalists with a unique challenge. The strange, human-looking bones of the first recognized Neanderthal confronted naturalists with a new type of object for which they had no readily available interpretive framework. This paper explores the techniques and approaches used to understand these bones in the years immediately following the discovery, in particular 1856-1864. Historians have previously suggested that interpretations and debates about Neanderthals hinged primarily on social, political and cultural ideologies. In this paper, I will argue that much of the scientific controversy surrounding the first recognized Neanderthal centred on questions of methodology and practice, and will demonstrate this through an exploration of the tools and approaches naturalists utilized in their examinations of the fossils. This will contribute to a growing historical recognition of the complex exchange between disciplines including geology, archaeology and comparative anatomy in the early study of fossil hominins, and provide a future framework for histories of Neanderthal debates in the twentieth century.}, } @article {pmid27708712, year = {2016}, author = {Stankiewicz, P}, title = {One pedigree we all may have come from - did Adam and Eve have the chromosome 2 fusion?.}, journal = {Molecular cytogenetics}, volume = {9}, number = {}, pages = {72}, pmid = {27708712}, issn = {1755-8166}, abstract = {BACKGROUND: In contrast to Great Apes, who have 48 chromosomes, modern humans and likely Neandertals and Denisovans have and had, respectively, 46 chromosomes. The reduction in chromosome number was caused by the head-to-head fusion of two ancestral chromosomes to form human chromosome 2 (HSA2) and may have contributed to the reproductive barrier with Great Apes.

RESULTS: Next generation sequencing and molecular clock analyses estimated that this fusion arose prior to our last common ancestor with Neandertal and Denisovan hominins ~ 0.74 - 4.5 million years ago.

HYPOTHESES: I propose that, unlike recurrent Robertsonian translocations in humans, the HSA2 fusion was a single nonrecurrent event that spread through a small polygamous clan population bottleneck. Its heterozygous to homozygous conversion, fixation, and accumulation in the succeeding populations was likely facilitated by an evolutionary advantage through the genomic loss rather than deregulation of expression of the gene(s) flanking the HSA2 fusion site at 2q13.

CONCLUSIONS: The origin of HSA2 might have been a critical evolutionary event influencing higher cognitive functions in various early subspecies of hominins. Next generation sequencing of Homo heidelbergensis and Homo erectus genomes and complete reconstruction of DNA sequence of the orthologous subtelomeric chromosomes in Great Apes should enable more precise timing of HSA2 formation and better understanding of its evolutionary consequences.}, } @article {pmid27708016, year = {2016}, author = {Wade, L}, title = {Neandertals made jewelry, proteins confirm.}, journal = {Science (New York, N.Y.)}, volume = {353}, number = {6306}, pages = {1350}, doi = {10.1126/science.353.6306.1350}, pmid = {27708016}, issn = {1095-9203}, mesh = {Animals ; Asparagine/*analysis/genetics ; Aspartic Acid/analysis/genetics ; Bone and Bones/*chemistry ; Collagen/*chemistry/genetics ; *Creativity ; Fossils ; France ; Humans ; *Jewelry ; Neanderthals/genetics/*psychology ; Radiometric Dating ; }, } @article {pmid27704536, year = {2017}, author = {Arnaud, J and Benazzi, S and Romandini, M and Livraghi, A and Panetta, D and Salvadori, PA and Volpe, L and Peresani, M}, title = {A Neanderthal deciduous human molar with incipient carious infection from the Middle Palaeolithic De Nadale cave, Italy.}, journal = {American journal of physical anthropology}, volume = {162}, number = {2}, pages = {370-376}, doi = {10.1002/ajpa.23111}, pmid = {27704536}, issn = {1096-8644}, mesh = {Animals ; Archaeology ; Caves ; Dental Caries/*pathology ; Fossils ; Italy ; Molar/*pathology ; *Neanderthals ; Paleodontology ; Tooth, Deciduous/*pathology ; }, abstract = {OBJECTIVES: The aim of the study is the assessment of Nadale 1, a Neanderthal deciduous tooth recently discovered in Northeastern Italy in the De Nadale cave (Middle Palaeolithic). Together with the clear archaeological context of the site, this study brings new insight on Neanderthal behavior and dental morphological variability.

MATERIALS AND METHODS: We used microCT data to provide a morphological description and morphometric analysis (diameter measurements and dental tissue volumes) of the Nadale 1 human tooth. Microwear analysis, taphonomical investigation and caries identification were performed using a stereomicroscope and Scanning Electron Microscope.

RESULTS: In terms of morphology (i.e., incipient tuberculum molare, marked mesial marginal ridge and well-developed mid-trigonid crest connecting the protoconid and the metaconid, deep anterior fovea) and size, Nadale 1 presents features frequently observed in Neanderthal lower first deciduous molars. Microscope investigations reveal the presence of a small pit which could be correlated to an incipient caries.

CONCLUSION: Nadale 1 expands the Italian Middle Palaeolithic fossil record and provides further information on Neanderthal dm1s in terms of dimensional and morphological variability. Furthermore, the presence of an incipient caries brings further data on Neanderthal diet.}, } @article {pmid27695917, year = {2017}, author = {Yasukochi, Y and Ohashi, J}, title = {Elucidating the origin of HLA-B*73 allelic lineage: Did modern humans benefit by archaic introgression?.}, journal = {Immunogenetics}, volume = {69}, number = {1}, pages = {63-67}, pmid = {27695917}, issn = {1432-1211}, mesh = {African Continental Ancestry Group/genetics ; Alleles ; Animals ; Asian Continental Ancestry Group/genetics ; Europe ; *Evolution, Molecular ; *Genome, Human ; HLA-B Antigens/*genetics ; Haplotypes/*genetics ; Hominidae/classification/*genetics ; Humans ; Neanderthals/genetics ; Pan troglodytes/genetics ; Phylogeny ; }, abstract = {A previous study reported that some of the human leukocyte antigen (HLA) alleles and haplotypes in present-day humans were acquired by admixture with archaic humans; specifically, an exceptionally diverged HLA-B*73 allele was proposed to be transmitted from Denisovans, although the DNA sequence of HLA-B*73 has not been detected in the Denisovan genome. Here, we argue against the hypothesis that HLA-B*73 introgressed from Denisovans into early modern humans. A phylogenetic analysis revealed that HLA-B*73:01 formed a monophyletic group with a chimpanzee MHC-B allele, strongly suggesting that the HLA-B*73 allelic lineage has been maintained in humans as well as in chimpanzees since the divergence of humans and chimpanzees. The global distribution of HLA-B*73 allele showed that the population frequency of HLA-B*73 in west Asia (0.24 %)-a possible site of admixture with Denisovans-is lower than that in Europe (0.72 %) and in south Asia (0.69 %). Furthermore, HLA-B*73 is not observed in Melanesia even though the Melanesian genome contains the highest proportion of Denisovan ancestry in present-day human populations. Single nucleotide polymorphisms in HLA-A*11-HLA-C*12:02 or HLA-A*11-C*15 haplotypes, one of which was assumed to be transmitted together with HLA-B*73 from Denisovans by the study of Abi-Rached and colleagues, were not differentiated from those in other HLA-A-C haplotypes in modern humans. These results do not support the introgression hypothesis. Thus, we conclude that it is highly likely that HLA-B*73 allelic lineage has been maintained in the direct ancestors of modern humans.}, } @article {pmid27671643, year = {2016}, author = {Stoessel, A and David, R and Gunz, P and Schmidt, T and Spoor, F and Hublin, JJ}, title = {Morphology and function of Neandertal and modern human ear ossicles.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {41}, pages = {11489-11494}, pmid = {27671643}, issn = {1091-6490}, mesh = {Animals ; Biological Evolution ; Ear Ossicles/*anatomy & histology/*pathology ; Ear, Middle/anatomy & histology ; Humans ; Image Processing, Computer-Assisted ; Neanderthals/*anatomy & histology ; Principal Component Analysis ; }, abstract = {The diminutive middle ear ossicles (malleus, incus, stapes) housed in the tympanic cavity of the temporal bone play an important role in audition. The few known ossicles of Neandertals are distinctly different from those of anatomically modern humans (AMHs), despite the close relationship between both human species. Although not mutually exclusive, these differences may affect hearing capacity or could reflect covariation with the surrounding temporal bone. Until now, detailed comparisons were hampered by the small sample of Neandertal ossicles and the unavailability of methods combining analyses of ossicles with surrounding structures. Here, we present an analysis of the largest sample of Neandertal ossicles to date, including many previously unknown specimens, covering a wide geographic and temporal range. Microcomputed tomography scans and 3D geometric morphometrics were used to quantify shape and functional properties of the ossicles and the tympanic cavity and make comparisons with recent and extinct AMHs as well as African apes. We find striking morphological differences between ossicles of AMHs and Neandertals. Ossicles of both Neandertals and AMHs appear derived compared with the inferred ancestral morphology, albeit in different ways. Brain size increase evolved separately in AMHs and Neandertals, leading to differences in the tympanic cavity and, consequently, the shape and spatial configuration of the ossicles. Despite these different evolutionary trajectories, functional properties of the middle ear of AMHs and Neandertals are largely similar. The relevance of these functionally equivalent solutions is likely to conserve a similar auditory sensitivity level inherited from their last common ancestor.}, } @article {pmid27662059, year = {2016}, author = {Wall, JD and Yoshihara Caldeira Brandt, D}, title = {Archaic admixture in human history.}, journal = {Current opinion in genetics & development}, volume = {41}, number = {}, pages = {93-97}, doi = {10.1016/j.gde.2016.07.002}, pmid = {27662059}, issn = {1879-0380}, mesh = {Africa ; Animals ; DNA, Ancient/*analysis ; Genetics, Population/*history ; History, Ancient ; Hominidae/*genetics ; Humans ; Neanderthals/*genetics ; }, abstract = {Modern humans evolved in Southern or Eastern Africa, and spread from there across the rest of the world. As they expanded across Africa and Eurasia, they encountered other hominin groups. The extent to which modern and 'archaic' human groups interbred is an area of active research, and while we know that modern humans interbred with Neanderthals and Denisovans, there is not yet agreement on how many admixture events there were or on how much Neanderthal or Denisovan DNA can be found in contemporary genomes. Here we review what is known about archaic admixture in human history, with a focus on what has been discovered in the past 2 years.}, } @article {pmid27655273, year = {2016}, author = {Aarts, JM and Alink, GM and Scherjon, F and MacDonald, K and Smith, AC and Nijveen, H and Roebroeks, W}, title = {Fire Usage and Ancient Hominin Detoxification Genes: Protective Ancestral Variants Dominate While Additional Derived Risk Variants Appear in Modern Humans.}, journal = {PloS one}, volume = {11}, number = {9}, pages = {e0161102}, pmid = {27655273}, issn = {1932-6203}, abstract = {Studies of the defence capacity of ancient hominins against toxic substances may contribute importantly to the reconstruction of their niche, including their diets and use of fire. Fire usage implies frequent exposure to hazardous compounds from smoke and heated food, known to affect general health and fertility, probably resulting in genetic selection for improved detoxification. To investigate whether such genetic selection occurred, we investigated the alleles in Neanderthals, Denisovans and modern humans at gene polymorphisms well-known to be relevant from modern human epidemiological studies of habitual tobacco smoke exposure and mechanistic evidence. We compared these with the alleles in chimpanzees and gorillas. Neanderthal and Denisovan hominins predominantly possess gene variants conferring increased resistance to these toxic compounds. Surprisingly, we observed the same in chimpanzees and gorillas, implying that less efficient variants are derived and mainly evolved in modern humans. Less efficient variants are observable from the first early Upper Palaeolithic hunter-gatherers onwards. While not clarifying the deep history of fire use, our results highlight the long-term stability of the genes under consideration despite major changes in the hominin dietary niche. Specifically for detoxification gene variants characterised as deleterious by epidemiological studies, our results confirm the predominantly recent appearance reported for deleterious human gene variants, suggesting substantial impact of recent human population history, including pre-Holocene expansions.}, } @article {pmid27654912, year = {2016}, author = {Mallick, S and Li, H and Lipson, M and Mathieson, I and Gymrek, M and Racimo, F and Zhao, M and Chennagiri, N and Nordenfelt, S and Tandon, A and Skoglund, P and Lazaridis, I and Sankararaman, S and Fu, Q and Rohland, N and Renaud, G and Erlich, Y and Willems, T and Gallo, C and Spence, JP and Song, YS and Poletti, G and Balloux, F and van Driem, G and de Knijff, P and Romero, IG and Jha, AR and Behar, DM and Bravi, CM and Capelli, C and Hervig, T and Moreno-Estrada, A and Posukh, OL and Balanovska, E and Balanovsky, O and Karachanak-Yankova, S and Sahakyan, H and Toncheva, D and Yepiskoposyan, L and Tyler-Smith, C and Xue, Y and Abdullah, MS and Ruiz-Linares, A and Beall, CM and Di Rienzo, A and Jeong, C and Starikovskaya, EB and Metspalu, E and Parik, J and Villems, R and Henn, BM and Hodoglugil, U and Mahley, R and Sajantila, A and Stamatoyannopoulos, G and Wee, JT and Khusainova, R and Khusnutdinova, E and Litvinov, S and Ayodo, G and Comas, D and Hammer, MF and Kivisild, T and Klitz, W and Winkler, CA and Labuda, D and Bamshad, M and Jorde, LB and Tishkoff, SA and Watkins, WS and Metspalu, M and Dryomov, S and Sukernik, R and Singh, L and Thangaraj, K and Pääbo, S and Kelso, J and Patterson, N and Reich, D}, title = {The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.}, journal = {Nature}, volume = {538}, number = {7624}, pages = {201-206}, pmid = {27654912}, issn = {1476-4687}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG006399/HG/NHGRI NIH HHS/United States ; R01 GM059290/GM/NIGMS NIH HHS/United States ; R00 GM111744/GM/NIGMS NIH HHS/United States ; R01 GM094402/GM/NIGMS NIH HHS/United States ; UL1 TR001067/TR/NCATS NIH HHS/United States ; }, mesh = {African Continental Ancestry Group/genetics ; Animals ; Australia ; Continental Population Groups/*genetics ; Datasets as Topic ; Genetic Variation/*genetics ; Genetics, Population ; Genome, Human/*genetics ; *Genomics ; History, Ancient ; Human Migration/history ; Humans ; *Mutation Rate ; Neanderthals/genetics ; New Guinea ; Oceanic Ancestry Group/genetics ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Time Factors ; }, abstract = {Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.}, } @article {pmid27654910, year = {2016}, author = {Pagani, L and Lawson, DJ and Jagoda, E and Mörseburg, A and Eriksson, A and Mitt, M and Clemente, F and Hudjashov, G and DeGiorgio, M and Saag, L and Wall, JD and Cardona, A and Mägi, R and Wilson Sayres, MA and Kaewert, S and Inchley, C and Scheib, CL and Järve, M and Karmin, M and Jacobs, GS and Antao, T and Iliescu, FM and Kushniarevich, A and Ayub, Q and Tyler-Smith, C and Xue, Y and Yunusbayev, B and Tambets, K and Mallick, CB and Saag, L and Pocheshkhova, E and Andriadze, G and Muller, C and Westaway, MC and Lambert, DM and Zoraqi, G and Turdikulova, S and Dalimova, D and Sabitov, Z and Sultana, GNN and Lachance, J and Tishkoff, S and Momynaliev, K and Isakova, J and Damba, LD and Gubina, M and Nymadawa, P and Evseeva, I and Atramentova, L and Utevska, O and Ricaut, FX and Brucato, N and Sudoyo, H and Letellier, T and Cox, MP and Barashkov, NA and Skaro, V and Mulahasanovic, L and Primorac, D and Sahakyan, H and Mormina, M and Eichstaedt, CA and Lichman, DV and Abdullah, S and Chaubey, G and Wee, JTS and Mihailov, E and Karunas, A and Litvinov, S and Khusainova, R and Ekomasova, N and Akhmetova, V and Khidiyatova, I and Marjanović, D and Yepiskoposyan, L and Behar, DM and Balanovska, E and Metspalu, A and Derenko, M and Malyarchuk, B and Voevoda, M and Fedorova, SA and Osipova, LP and Lahr, MM and Gerbault, P and Leavesley, M and Migliano, AB and Petraglia, M and Balanovsky, O and Khusnutdinova, EK and Metspalu, E and Thomas, MG and Manica, A and Nielsen, R and Villems, R and Willerslev, E and Kivisild, T and Metspalu, M}, title = {Genomic analyses inform on migration events during the peopling of Eurasia.}, journal = {Nature}, volume = {538}, number = {7624}, pages = {238-242}, pmid = {27654910}, issn = {1476-4687}, support = {261213//European Research Council/International ; BB/H005854/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; 647787//European Research Council/International ; R01 GM113657/GM/NIGMS NIH HHS/United States ; DP1 ES022577/ES/NIEHS NIH HHS/United States ; }, mesh = {Africa/ethnology ; Animals ; Asia ; Continental Population Groups/*genetics ; Datasets as Topic ; Estonia ; Europe ; Fossils ; Gene Flow ; Genetics, Population ; Genome, Human/*genetics ; *Genomics ; Heterozygote ; History, Ancient ; Human Migration/*history ; Humans ; Neanderthals/genetics ; New Guinea ; Oceanic Ancestry Group/genetics ; Population Dynamics ; }, abstract = {High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.}, } @article {pmid27652578, year = {2017}, author = {Condemi, S and Monge, J and Quertelet, S and Frayer, DW and Combier, J}, title = {Vergisson 4: a left-handed Neandertal.}, journal = {American journal of physical anthropology}, volume = {162}, number = {1}, pages = {186-190}, doi = {10.1002/ajpa.23101}, pmid = {27652578}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; Fossils ; France ; Functional Laterality/*physiology ; Incisor/*pathology ; Neanderthals/*anatomy & histology ; }, abstract = {OBJECTIVES: Handedness is an important marker for lateralization of humans in the modern and fossil record. For the most part, Neandertals and their ancestors are strongly right-handed. We describe a single tooth from a Neandertal level at Vergisson 4 (Vg 4-83). This left upper central incisor shows all the features typical of Neandertal incisors. It also exhibits a predominance of left-handed striations.

METHODS: Striations on the incisor's labial surface were mapped at 20x magnification using Photoshop. Angulations of the striations were determined from their deviation from the maximum mesio-distal line and were analyzed using NIH's freeware, Image J.

RESULTS: Of the 60 labial surface striations, Vg 4-83 shows a strong predominance of left-handed striations (46; 76.7%), which are statistically significantly different (p < .001 with a two-tailed chi2 test) from the small number (3) of right-handed striations.

DISCUSSION: The identification of another left-handed Neandertal adds to our understanding about handedness variation in this fossil hominin. Given the high frequency of right-handed Neandertals, the 90: 10 modern ratio is still preserved in this group.}, } @article {pmid27638212, year = {2016}, author = {Welker, F and Hajdinjak, M and Talamo, S and Jaouen, K and Dannemann, M and David, F and Julien, M and Meyer, M and Kelso, J and Barnes, I and Brace, S and Kamminga, P and Fischer, R and Kessler, BM and Stewart, JR and Pääbo, S and Collins, MJ and Hublin, JJ}, title = {Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {40}, pages = {11162-11167}, pmid = {27638212}, issn = {1091-6490}, mesh = {Alleles ; Animals ; Archaeology ; Bayes Theorem ; Bone and Bones/anatomy & histology ; Carbon Isotopes ; Chromatography, Liquid ; Collagen Type X ; DNA, Mitochondrial/genetics ; France ; Hominidae/*metabolism ; Humans ; *Paleontology ; Polymorphism, Single Nucleotide/genetics ; Proteomics/*methods ; Radiometric Dating ; Tandem Mass Spectrometry ; }, abstract = {In Western Europe, the Middle to Upper Paleolithic transition is associated with the disappearance of Neandertals and the spread of anatomically modern humans (AMHs). Current chronological, behavioral, and biological models of this transitional period hinge on the Châtelperronian technocomplex. At the site of the Grotte du Renne, Arcy-sur-Cure, morphological Neandertal specimens are not directly dated but are contextually associated with the Châtelperronian, which contains bone points and beads. The association between Neandertals and this "transitional" assemblage has been controversial because of the lack either of a direct hominin radiocarbon date or of molecular confirmation of the Neandertal affiliation. Here we provide further evidence for a Neandertal-Châtelperronian association at the Grotte du Renne through biomolecular and chronological analysis. We identified 28 additional hominin specimens through zooarchaeology by mass spectrometry (ZooMS) screening of morphologically uninformative bone specimens from Châtelperronian layers at the Grotte du Renne. Next, we obtain an ancient hominin bone proteome through liquid chromatography-MS/MS analysis and error-tolerant amino acid sequence analysis. Analysis of this palaeoproteome allows us to provide phylogenetic and physiological information on these ancient hominin specimens. We distinguish Late Pleistocene clades within the genus Homo based on ancient protein evidence through the identification of an archaic-derived amino acid sequence for the collagen type X, alpha-1 (COL10α1) protein. We support this by obtaining ancient mtDNA sequences, which indicate a Neandertal ancestry for these specimens. Direct accelerator mass spectometry radiocarbon dating and Bayesian modeling confirm that the hominin specimens date to the Châtelperronian at the Grotte du Renne.}, } @article {pmid27606907, year = {2016}, author = {Slatkin, M}, title = {Statistical methods for analyzing ancient DNA from hominins.}, journal = {Current opinion in genetics & development}, volume = {41}, number = {}, pages = {72-76}, pmid = {27606907}, issn = {1879-0380}, support = {R01 GM040282/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*genetics ; Fossils ; Genetics, Population/*statistics & numerical data ; Genome/genetics ; Hominidae/*genetics ; Humans ; Neanderthals/genetics ; }, abstract = {In the past few years, the number of autosomal DNA sequences from human fossils has grown explosively and numerous partial or complete sequences are available from our closest relatives, Neanderthal and Denisovans. I review commonly used statistical methods applied to these sequences. These methods fall into three broad classes: methods for estimating levels of contamination, descriptive methods, and methods based on population genetic models. The latter two classes are largely methods developed for the analysis of present-day genomic data. When they are applied to ancient DNA (aDNA), they usually ignore the time dimension. A few methods, particularly those concerned with inferring something about selection or ancestor-descendant relationships, take explicit account of the ages of aDNA samples.}, } @article {pmid27569548, year = {2016}, author = {Lu, D and Lou, H and Yuan, K and Wang, X and Wang, Y and Zhang, C and Lu, Y and Yang, X and Deng, L and Zhou, Y and Feng, Q and Hu, Y and Ding, Q and Yang, Y and Li, S and Jin, L and Guan, Y and Su, B and Kang, L and Xu, S}, title = {Ancestral Origins and Genetic History of Tibetan Highlanders.}, journal = {American journal of human genetics}, volume = {99}, number = {3}, pages = {580-594}, pmid = {27569548}, issn = {1537-6605}, support = {K99 AA021802/AA/NIAAA NIH HHS/United States ; R00 AA021802/AA/NIAAA NIH HHS/United States ; }, mesh = {Altitude ; Animals ; Asian Continental Ancestry Group/*genetics ; China/ethnology ; Ethnic Groups/genetics ; Gene Flow/*genetics ; Gene Pool ; Genetics, Population ; Genome, Human/*genetics ; Haplotypes/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Models, Genetic ; Neanderthals/genetics ; Oceania/ethnology ; *Phylogeny ; Selection, Genetic ; Tibet ; }, abstract = {The origin of Tibetans remains one of the most contentious puzzles in history, anthropology, and genetics. Analyses of deeply sequenced (30×-60×) genomes of 38 Tibetan highlanders and 39 Han Chinese lowlanders, together with available data on archaic and modern humans, allow us to comprehensively characterize the ancestral makeup of Tibetans and uncover their origins. Non-modern human sequences compose ∼6% of the Tibetan gene pool and form unique haplotypes in some genomic regions, where Denisovan-like, Neanderthal-like, ancient-Siberian-like, and unknown ancestries are entangled and elevated. The shared ancestry of Tibetan-enriched sequences dates back to ∼62,000-38,000 years ago, predating the Last Glacial Maximum (LGM) and representing early colonization of the plateau. Nonetheless, most of the Tibetan gene pool is of modern human origin and diverged from that of Han Chinese ∼15,000 to ∼9,000 years ago, which can be largely attributed to post-LGM arrivals. Analysis of ∼200 contemporary populations showed that Tibetans share ancestry with populations from East Asia (∼82%), Central Asia and Siberia (∼11%), South Asia (∼6%), and western Eurasia and Oceania (∼1%). Our results support that Tibetans arose from a mixture of multiple ancestral gene pools but that their origins are much more complicated and ancient than previously suspected. We provide compelling evidence of the co-existence of Paleolithic and Neolithic ancestries in the Tibetan gene pool, indicating a genetic continuity between pre-historical highland-foragers and present-day Tibetans. In particular, highly differentiated sequences harbored in highlanders' genomes were most likely inherited from pre-LGM settlers of multiple ancestral origins (SUNDer) and maintained in high frequency by natural selection.}, } @article {pmid27558013, year = {2016}, author = {Ashouri, E and Norman, PJ and Guethlein, LA and Han, AS and Nemat-Gorgani, N and Norberg, SJ and Ghaderi, A and Parham, P}, title = {HLA class I variation in Iranian Lur and Kurd populations: high haplotype and allotype diversity with an abundance of KIR ligands.}, journal = {HLA}, volume = {88}, number = {3}, pages = {87-99}, pmid = {27558013}, issn = {2059-2310}, support = {R01 AI017892/AI/NIAID NIH HHS/United States ; T32 GM007790/GM/NIGMS NIH HHS/United States ; }, mesh = {Alleles ; Databases, Genetic ; Epitopes/chemistry/immunology ; *Ethnic Groups ; Gene Expression ; Gene Frequency ; Genotype ; HLA-A Antigens/classification/*genetics/immunology ; HLA-B Antigens/classification/*genetics/immunology ; HLA-C Antigens/classification/*genetics/immunology ; Haplotypes ; High-Throughput Nucleotide Sequencing ; Humans ; Iran ; Ligands ; *Polymorphism, Genetic ; Receptors, KIR/classification/*genetics/immunology ; Sequence Analysis, DNA ; Terminology as Topic ; }, abstract = {HLA-A, -B and -C alleles of 285 individuals, representing three Iranian Lur populations and one Iranian Kurd population were sequenced completely, yielding human leukocyte antigen (HLA) class I genotypes at high resolution and filling four fields of the official HLA nomenclature. Each population has 87-99 alleles, evenly distributed between the three HLA class I genes, 145 alleles being identified in total. These alleles were already known, named and deposited in the HLA database. The alleles form 316 different HLA A-B-C haplotypes, with each population having between 80 and 112 haplotypes. The four Iranian populations form a related group that is distinguished from other populations, including other Iranians. All four KIR ligands - the A3/11, Bw4, C1 and C2 epitopes - are well represented, particularly Bw4, which is carried by three high-frequency allotypes: HLA-A*24:02, HLA-A*32:01 and HLA-B*51:01. In the Lur and Kurd populations, between 82% and 94% of individuals have the Bw4 epitope, the ligand for KIR3DL1. HLA-B*51:01 is likely of Neandertal origin and associated with Behcet's disease, also known as the Silk Road disease. The Lordegan Lur have the highest frequency of HLA-B*51:01 in the world. This allele is present on 46 Lur and Kurd haplotypes. Present at lower frequency is HLA-B*51:08, which is also associated with Behcet's disease. In the four Iranian populations, 31 haplotypes encode both Bw4(+) HLA-A and Bw4(+) HLA-B, a dual combination of Bw4 epitopes that is relatively rare in other populations, worldwide. This study both demonstrates and emphasizes the value of studying HLA class I polymorphism at highest resolution in anthropologically well-defined populations.}, } @article {pmid27525705, year = {2016}, author = {Villa, P and Soriano, S and Grün, R and Marra, F and Nomade, S and Pereira, A and Boschian, G and Pollarolo, L and Fang, F and Bahain, JJ}, title = {The Acheulian and Early Middle Paleolithic in Latium (Italy): Stability and Innovation.}, journal = {PloS one}, volume = {11}, number = {8}, pages = {e0160516}, pmid = {27525705}, issn = {1932-6203}, mesh = {Animals ; *Archaeology ; Fossils ; Italy ; *Neanderthals ; *Technology ; Tool Use Behavior ; }, abstract = {We present here the results of a technological and typological analysis of the Acheulian and early Middle Paleolithic assemblages from Torre in Pietra (Latium, Italy) together with comparisons with the Acheulian small tools of Castel di Guido. The assemblages were never chronometrically dated before. We have now 40Ar/39Ar dates and ESR-U-series dates, within a geomorphological framework, which support correlations to marine isotope stages. The Acheulian (previously correlated to MIS 9) is now dated to MIS 10 while the Middle Paleolithic is dated to MIS 7. Lithic analyses are preceded by taphonomic evaluations. The Levallois method of the Middle Paleolithic assemblage is an innovation characterized by the production of thin flake blanks without cortex. In contrast, the small tool blanks of the Acheulian were either pebbles or thick flakes with some cortex. They provided a relatively easy manual prehension. The choice of Levallois thin flake blanks in the Middle Paleolithic assemblage suggest that the new technology is most likely related to the emergence of hafting. Accordingly, the oldest direct evidence of hafting technology is from the site of Campitello Quarry in Tuscany (Central Italy) where birch-bark tar, found on the proximal part of two flint flakes, is dated to the end of MIS 7. Nevertheless, a peculiar feature of the Middle Paleolithic at Torre in Pietra is the continuous presence of small tool blanks on pebbles and cores and on thick flake albeit at a much lower frequency than in the older Acheulian industries. The adoption of the new technology is thus characterized by innovation combined with a degree of stability. The persistence of these habits in spite of the introduction of an innovative technique underlies the importance of cultural transmission and conformity in the behavior of Neandertals.}, } @article {pmid27520991, year = {2017}, author = {Isidro, A and Burdeus, JM and Loscos, S and Bara, J and Bosch, J and Gallart, A}, title = {Surgical treatment for an uncommon headache: A gap of 4800 years.}, journal = {Cephalalgia : an international journal of headache}, volume = {37}, number = {11}, pages = {1098-1101}, doi = {10.1177/0333102416665227}, pmid = {27520991}, issn = {1468-2982}, mesh = {Adult ; Animals ; Cervical Atlas/abnormalities ; Headache/*etiology/*surgery ; History, Ancient ; Humans ; Male ; Neanderthals/*abnormalities ; Pseudarthrosis/*complications/*surgery ; Skull Base/abnormalities ; Trephining/*history ; }, abstract = {Background Surgical management of headache due to anomalies in the cervical spine is uncommon, as most cases improve with drugs and/or physical therapy. Case We report two instances of a very uncommon congenital upper cervical spine anomaly due to the presence of a pseudoarthrosis between a unilateral paracondylar process in the base of the skull and an epitransverse process arising from the transverse apophysis (PCP/ETA). The first one corresponds to a male on whom an endoscopic guided puncture was performed, and the second to an adult male from the Neolithic period who showed two cranial trepanations together with the presence of morphine metabolites in both bones and dental calculus. Discussion We draw a parallel between the treatment of two individuals separated by a gap of more than 4800 years: contemporary direct vision of the false joint through a small endoscope, which provides an accurate puncture, and ancient double trepanation with clear signs of bone eburnation.}, } @article {pmid27517578, year = {2016}, author = {Caldararo, N}, title = {Denisovans, Melanesians, Europeans, and Neandertals: The Confusion of DNA Assumptions and the Biological Species Concept.}, journal = {Journal of molecular evolution}, volume = {83}, number = {1-2}, pages = {78-87}, pmid = {27517578}, issn = {1432-1432}, mesh = {Animals ; Biological Evolution ; DNA/genetics ; DNA, Ancient/*analysis ; Fossils ; Hominidae/genetics ; Humans ; Neanderthals/*genetics ; Sequence Alignment/methods ; Sequence Analysis, DNA/methods ; }, abstract = {A number of recent articles have appeared on the Denisova fossil remains and attempts to produce DNA sequences from them. One of these recently appeared in Science by Vernot et al. (Science 352:235-239, 2016). We would like to advance an alternative interpretation of the data presented. One concerns the problem of contamination/degradation of the determined DNA sequenced. Just as the publication of the first Neandertal sequence included an interpretation that argued that Neandertals had not contributed any genes to modern humans, the Denisovan interpretation has considerable influence on ideas regarding human evolution. The new papers, however, confuse established ideas concerning the nature of species, as well as the use of terms like premodern, Archaic Homo, and Homo heidelbergensis. Examination of these problems presents a solution by means of reinterpreting the results. Given the claims for gene transfer among a number of Mid Pleistocene hominids, it may be time to reexamine the idea of anagenesis in hominid evolution.}, } @article {pmid27488556, year = {2017}, author = {de Boer, B}, title = {Evolution of speech and evolution of language.}, journal = {Psychonomic bulletin & review}, volume = {24}, number = {1}, pages = {158-162}, pmid = {27488556}, issn = {1531-5320}, mesh = {Animals ; *Biological Evolution ; Gestures ; Hominidae ; Humans ; *Language ; Music ; Neanderthals ; *Speech ; }, abstract = {Speech is the physical signal used to convey spoken language. Because of its physical nature, speech is both easier to compare with other species' behaviors and easier to study in the fossil record than other aspects of language. Here I argue that convergent fossil evidence indicates adaptations for complex vocalizations at least as early as the common ancestor of Neanderthals and modern humans. Furthermore, I argue that it is unlikely that language evolved separately from speech, but rather that gesture, speech, and song coevolved to provide both a multimodal communication system and a musical system. Moreover, coevolution must also have played a role by allowing both cognitive and anatomical adaptations to language and speech to evolve in parallel. Although such a coevolutionary scenario is complex, it is entirely plausible from a biological point of view.}, } @article {pmid27486223, year = {2016}, author = {Hubbard, TD and Murray, IA and Bisson, WH and Sullivan, AP and Sebastian, A and Perry, GH and Jablonski, NG and Perdew, GH}, title = {Divergent Ah Receptor Ligand Selectivity during Hominin Evolution.}, journal = {Molecular biology and evolution}, volume = {33}, number = {10}, pages = {2648-2658}, pmid = {27486223}, issn = {1537-1719}, support = {R01 ES004869/ES/NIEHS NIH HHS/United States ; R01 ES019964/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Basic Helix-Loop-Helix Transcription Factors/genetics ; Benzo(a)pyrene ; Biological Evolution ; Cytochrome P-450 CYP1A1/genetics ; Cytochrome P-450 CYP1B1/genetics ; DNA/metabolism ; Evolution, Molecular ; Hominidae/*genetics ; Humans ; Ligands ; Neanderthals/*genetics ; Polycyclic Aromatic Hydrocarbons/metabolism ; Receptors, Aryl Hydrocarbon/*genetics ; }, abstract = {We have identified a fixed nonsynonymous sequence difference between humans (Val381; derived variant) and Neandertals (Ala381; ancestral variant) in the ligand-binding domain of the aryl hydrocarbon receptor (AHR) gene. In an exome sequence analysis of four Neandertal and Denisovan individuals compared with nine modern humans, there are only 90 total nucleotide sites genome-wide for which archaic hominins are fixed for the ancestral nonsynonymous variant and the modern humans are fixed for the derived variant. Of those sites, only 27, including Val381 in the AHR, also have no reported variability in the human dbSNP database, further suggesting that this highly conserved functional variant is a rare event. Functional analysis of the amino acid variant Ala381 within the AHR carried by Neandertals and nonhuman primates indicate enhanced polycyclic aromatic hydrocarbon (PAH) binding, DNA binding capacity, and AHR mediated transcriptional activity compared with the human AHR. Also relative to human AHR, the Neandertal AHR exhibited 150-1000 times greater sensitivity to induction of Cyp1a1 and Cyp1b1 expression by PAHs (e.g., benzo(a)pyrene). The resulting CYP1A1/CYP1B1 enzymes are responsible for PAH first pass metabolism, which can result in the generation of toxic intermediates and perhaps AHR-associated toxicities. In contrast, the human AHR retains the ancestral sensitivity observed in primates to nontoxic endogenous AHR ligands (e.g., indole, indoxyl sulfate). Our findings reveal that a functionally significant change in the AHR occurred uniquely in humans, relative to other primates, that would attenuate the response to many environmental pollutants, including chemicals present in smoke from fire use during cooking.}, } @article {pmid27463216, year = {2016}, author = {Taylor, JS and Reimchen, TE}, title = {Opsin gene repertoires in northern archaic hominids.}, journal = {Genome}, volume = {59}, number = {8}, pages = {541-549}, doi = {10.1139/gen-2015-0164}, pmid = {27463216}, issn = {1480-3321}, mesh = {Animals ; Anthropology, Physical ; Base Sequence ; Evolution, Molecular ; Genome, Human ; Hominidae/*genetics ; Humans ; Methyl-CpG-Binding Protein 2/genetics ; Neanderthals/genetics ; Opsins/*genetics ; Phylogeny ; Vision, Ocular/genetics ; }, abstract = {The Neanderthals' northern distribution, hunting techniques, and orbit breadths suggest that they were more active in dim light than modern humans. We surveyed visual opsin genes from four Neanderthals and two other archaic hominids to see if they provided additional support for this hypothesis. This analysis was motivated by the observation that alleles responsible for anomalous trichromacy in humans are more common in northern latitudes, by data suggesting that these variants might enhance vision in mesopic conditions, and by the observation that dim light active species often have fewer opsin genes than diurnal relatives. We also looked for evidence of convergent amino acid substitutions in Neanderthal opsins and orthologs from crepuscular or nocturnal species. The Altai Neanderthal, the Denisovan, and the Ust'-Ishim early modern human had opsin genes that encoded proteins identical to orthologs in the human reference genome. Opsins from the Vindija Cave Neanderthals (three females) had many nonsynonymous substitutions, including several predicted to influence colour vision (e.g., stop codons). However, the functional implications of these observations were difficult to assess, given that "control" loci, where no substitutions were expected, differed from humans to the same extent. This left unresolved the test for colour vision deficiencies in Vindija Cave Neanderthals.}, } @article {pmid27459054, year = {2016}, author = {Lazaridis, I and Nadel, D and Rollefson, G and Merrett, DC and Rohland, N and Mallick, S and Fernandes, D and Novak, M and Gamarra, B and Sirak, K and Connell, S and Stewardson, K and Harney, E and Fu, Q and Gonzalez-Fortes, G and Jones, ER and Roodenberg, SA and Lengyel, G and Bocquentin, F and Gasparian, B and Monge, JM and Gregg, M and Eshed, V and Mizrahi, AS and Meiklejohn, C and Gerritsen, F and Bejenaru, L and Blüher, M and Campbell, A and Cavalleri, G and Comas, D and Froguel, P and Gilbert, E and Kerr, SM and Kovacs, P and Krause, J and McGettigan, D and Merrigan, M and Merriwether, DA and O'Reilly, S and Richards, MB and Semino, O and Shamoon-Pour, M and Stefanescu, G and Stumvoll, M and Tönjes, A and Torroni, A and Wilson, JF and Yengo, L and Hovhannisyan, NA and Patterson, N and Pinhasi, R and Reich, D}, title = {Genomic insights into the origin of farming in the ancient Near East.}, journal = {Nature}, volume = {536}, number = {7617}, pages = {419-424}, pmid = {27459054}, issn = {1476-4687}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; CZD/16/6//Chief Scientist Office/United Kingdom ; /HHMI/Howard Hughes Medical Institute/United States ; 263441//European Research Council/International ; CZD/16/6/4//Chief Scientist Office/United Kingdom ; GM100233/GM/NIGMS NIH HHS/United States ; MC_PC_U127561128//Medical Research Council/United Kingdom ; }, mesh = {Africa, Eastern ; Agriculture/*history ; Animals ; Armenia ; Asia ; Continental Population Groups/*genetics ; DNA/analysis ; Europe ; *Genomics ; History, Ancient ; Human Migration/*history ; Humans ; Hybridization, Genetic/genetics ; Iran ; Israel ; Jordan ; Neanderthals/genetics ; *Phylogeny ; Phylogeography ; Turkey ; }, abstract = {We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 bc, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to greatly reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those of Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.}, } @article {pmid27458909, year = {2016}, author = {Ponce de León, MS and Bienvenu, T and Akazawa, T and Zollikofer, CP}, title = {Brain development is similar in Neanderthals and modern humans.}, journal = {Current biology : CB}, volume = {26}, number = {14}, pages = {R665-6}, doi = {10.1016/j.cub.2016.06.022}, pmid = {27458909}, issn = {1879-0445}, mesh = {Animals ; Biological Evolution ; Brain/anatomy & histology/*growth & development ; Fossils/*anatomy & histology ; Humans ; Neanderthals/anatomy & histology/*growth & development ; Skull/anatomy & histology/*growth & development ; }, abstract = {While the braincase of adult Neanderthals had a similar volume to that of modern humans from the same period, differences in endocranial shape suggest that brain morphology differed between modern humans and Neanderthals. When and how these differences arose during evolution and development is a topic of ongoing research, with potential implications for species-specific differences in brain and cognitive development, and in life history [1,2]. Earlier research suggested that Neanderthals followed an ancestral mode of brain development, similar to that of our closest living relatives, the chimpanzees [2-4]. Modern humans, by contrast, were suggested to follow a uniquely derived mode of brain development just after birth, giving rise to the characteristically globular shape of the adult human brain case [2,4,5]. Here, we re-examine this hypothesis using an extended sample of Neanderthal infants. We document endocranial development during the decisive first two years of postnatal life. The new data indicate that Neanderthals followed largely similar modes of endocranial development to modern humans. These findings challenge the notion that human brain and cognitive development after birth is uniquely derived [2,4].}, } @article {pmid27457544, year = {2016}, author = {Soulier, MC and Morin, E}, title = {Cutmark data and their implications for the planning depth of Late Pleistocene societies.}, journal = {Journal of human evolution}, volume = {97}, number = {}, pages = {37-57}, doi = {10.1016/j.jhevol.2016.05.006}, pmid = {27457544}, issn = {1095-8606}, mesh = {Animals ; *Archaeology ; Bone and Bones ; Food Handling/*methods ; France ; Humans ; Mammals ; Meat ; Neanderthals/*psychology ; *Social Behavior ; *Technology ; }, abstract = {Cutmarks provide empirical evidence for the exploitation of animal resources by past human groups. Their study may contribute substantially to our knowledge of economic behavior, including the procurement of prey and the analysis of butchery sequences. Butchering practices can be investigated using cutmark illustrations recorded on bone templates. In this paper, quantitative data on cutmarks were derived from published and unpublished cutmark drawings for 27 French assemblages dated between the late Middle Paleolithic and the final Upper Paleolithic. The analysis of cutmark data on meaty long bones (humerus, radio-ulna, femur, tibia) highlights strong variations in cutmark length and orientation in the sample that potentially reflect significant shifts in meat processing strategies during the Late Pleistocene. The present study shows that long longitudinal cutmarks are considerably more frequent during the Late Glacial Maximum than in the early Upper Paleolithic. Although the number of studies is small, actualistic data generated in controlled settings indicate that long longitudinal cutmarks are commonly produced during filleting, an activity closely associated with meat preservation, as is the case with drying and smoking. Because they provide information on possible changes in the capacity for anticipation, these results have potentially important implications for the logistical and economic organization of Paleolithic hominins.}, } @article {pmid27429943, year = {2016}, author = {Ko, KH}, title = {Hominin interbreeding and the evolution of human variation.}, journal = {Journal of biological research (Thessalonike, Greece)}, volume = {23}, number = {}, pages = {17}, pmid = {27429943}, issn = {1790-045X}, abstract = {Mitochondrial Eve confirms the "out of Africa" theory, but the evidence also supports interbreeding between Homo sapiens and other hominins: Neanderthals, Denisovans, and Homo heidelbergensis. This article explains how interbreeding between early H. sapiens and archaic hominins occurred. The availability of edible insects in East Asia aided the spread of the unaggressive, highly cooperative Neanderthals, who interbred with H. sapiens in Asia, resulting in a higher admixture of Neanderthal DNA in East Asian populations. Geographical variation in degree of interbreeding between H. sapiens and Neanderthals likely contributed to neurological and behavioral differences in modern humans. Similarly, people with Denisovan genetic admixture were better able to dwell in mountainous regions, allowing their genetic legacy to cross the Himalayas and persist in Southeast Asian and Oceanian H. sapiens. In the Sub-Saharan region, unaffected by Denisovan or Neanderthal interbreeding, H. sapiens interbred with H. heidelbergensis, because high humidity militated against fire-making and allowed the survival of these non-fire-making hominins.}, } @article {pmid27423248, year = {2017}, author = {Miga, KH}, title = {Chromosome-Specific Centromere Sequences Provide an Estimate of the Ancestral Chromosome 2 Fusion Event in Hominin Genomes.}, journal = {The Journal of heredity}, volume = {108}, number = {1}, pages = {45-52}, doi = {10.1093/jhered/esw039}, pmid = {27423248}, issn = {1465-7333}, mesh = {Animals ; *Centromere ; Chromosomes, Human, Pair 2 ; *Chromosomes, Mammalian ; DNA, Satellite ; *Evolution, Molecular ; *Genome ; Genomics/methods ; Hominidae/*genetics ; Humans ; Pan troglodytes/genetics ; }, abstract = {Human chromosome 2 is a product of a telomere fusion of two ancestral chromosomes and loss/degeneration of one of the two original centromeres. Genomic signatures of this event are limited to inverted telomeric repeats at the precise site of chromosomal fusion and to the small amount of relic centromeric sequences that remain on 2q21.2. Unlike the site of fusion, which is enriched for sequences that are shared elsewhere in the human genome, the region of the nonfunctioning and degenerate ancestral centromere appears to share limited similarity with other sites in the human genome, thereby providing an opportunity to study this genomic arrangement in short, fragmented ancient DNA genomic datasets. Here, chromosome-assigned satellite DNAs are used to study shared centromere sequence organization in Denisovan and Neandertal genomes. By doing so, one is able to provide evidence for the presence of both active and degenerate centromeric satellite profiles on chromosome 2 in these archaic genomes, supporting the hypothesis that the chromosomal fusion event took place prior to our last common ancestor with Denisovan and Neandertal hominins and presenting a genomic reference for predicting karyotype in ancient genomic datasets.}, } @article {pmid27405260, year = {2016}, author = {Noback, ML and Samo, E and van Leeuwen, CH and Lynnerup, N and Harvati, K}, title = {Paranasal sinuses: A problematic proxy for climate adaptation in Neanderthals.}, journal = {Journal of human evolution}, volume = {97}, number = {}, pages = {176-179}, doi = {10.1016/j.jhevol.2016.06.003}, pmid = {27405260}, issn = {1095-8606}, mesh = {*Adaptation, Biological ; Animals ; Climate ; Female ; Humans ; Male ; *Neanderthals/anatomy & histology/physiology ; *Paranasal Sinuses/anatomy & histology/physiology ; }, } @article {pmid27389305, year = {2016}, author = {Talamo, S and Hajdinjak, M and Mannino, MA and Fasani, L and Welker, F and Martini, F and Romagnoli, F and Zorzin, R and Meyer, M and Hublin, JJ}, title = {Direct radiocarbon dating and genetic analyses on the purported Neanderthal mandible from the Monti Lessini (Italy).}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {29144}, pmid = {27389305}, issn = {2045-2322}, mesh = {Animals ; DNA, Ancient/*isolation & purification ; *Fossils ; Genetic Testing ; Humans ; Italy ; Mandible/chemistry ; Neanderthals/*genetics ; *Radiometric Dating ; Skull/chemistry ; }, abstract = {Anatomically modern humans replaced Neanderthals in Europe around 40,000 years ago. The demise of the Neanderthals and the nature of the possible relationship with anatomically modern humans has captured our imagination and stimulated research for more than a century now. Recent chronological studies suggest a possible overlap between Neanderthals and anatomically modern humans of more than 5,000 years. Analyses of ancient genome sequences from both groups have shown that they interbred multiple times, including in Europe. A potential place of interbreeding is the notable Palaeolithic site of Riparo Mezzena in Northern Italy. In order to improve our understanding of prehistoric occupation at Mezzena, we analysed the human mandible and several cranial fragments from the site using radiocarbon dating, ancient DNA, ZooMS and isotope analyses. We also performed a more detailed investigation of the lithic assemblage of layer I. Surprisingly we found that the Riparo Mezzena mandible is not from a Neanderthal but belonged to an anatomically modern human. Furthermore, we found no evidence for the presence of Neanderthal remains among 11 of the 13 cranial and post-cranial fragments re-investigated in this study.}, } @article {pmid27381450, year = {2016}, author = {Rougier, H and Crevecoeur, I and Beauval, C and Posth, C and Flas, D and Wißing, C and Furtwängler, A and Germonpré, M and Gómez-Olivencia, A and Semal, P and van der Plicht, J and Bocherens, H and Krause, J}, title = {Neandertal cannibalism and Neandertal bones used as tools in Northern Europe.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {29005}, pmid = {27381450}, issn = {2045-2322}, mesh = {Animals ; Belgium ; *Bone and Bones ; *Cannibalism ; Fossils ; Mortuary Practice ; Neanderthals/genetics/*psychology ; Radiometric Dating ; }, abstract = {Almost 150 years after the first identification of Neandertal skeletal material, the cognitive and symbolic abilities of these populations remain a subject of intense debate. We present 99 new Neandertal remains from the Troisième caverne of Goyet (Belgium) dated to 40,500-45,500 calBP. The remains were identified through a multidisciplinary study that combines morphometrics, taphonomy, stable isotopes, radiocarbon dating and genetic analyses. The Goyet Neandertal bones show distinctive anthropogenic modifications, which provides clear evidence for butchery activities as well as four bones having been used for retouching stone tools. In addition to being the first site to have yielded multiple Neandertal bones used as retouchers, Goyet not only provides the first unambiguous evidence of Neandertal cannibalism in Northern Europe, but also highlights considerable diversity in mortuary behaviour among the region's late Neandertal population in the period immediately preceding their disappearance.}, } @article {pmid27378746, year = {2016}, author = {Kimmel, M and Wojdyła, T}, title = {Genetic demographic networks: Mathematical model and applications.}, journal = {Theoretical population biology}, volume = {111}, number = {}, pages = {75-86}, doi = {10.1016/j.tpb.2016.06.004}, pmid = {27378746}, issn = {1096-0325}, mesh = {*Demography ; Genetic Variation ; *Genetics, Population ; Humans ; *Markov Chains ; *Models, Theoretical ; }, abstract = {Recent improvement in the quality of genetic data obtained from extinct human populations and their ancestors encourages searching for answers to basic questions regarding human population history. The most common and successful are model-based approaches, in which genetic data are compared to the data obtained from the assumed demography model. Using such approach, it is possible to either validate or adjust assumed demography. Model fit to data can be obtained based on reverse-time coalescent simulations or forward-time simulations. In this paper we introduce a computational method based on mathematical equation that allows obtaining joint distributions of pairs of individuals under a specified demography model, each of them characterized by a genetic variant at a chosen locus. The two individuals are randomly sampled from either the same or two different populations. The model assumes three types of demographic events (split, merge and migration). Populations evolve according to the time-continuous Moran model with drift and Markov-process mutation. This latter process is described by the Lyapunov-type equation introduced by O'Brien and generalized in our previous works. Application of this equation constitutes an original contribution. In the result section of the paper we present sample applications of our model to both simulated and literature-based demographies. Among other we include a study of the Slavs-Balts-Finns genetic relationship, in which we model split and migrations between the Balts and Slavs. We also include another example that involves the migration rates between farmers and hunters-gatherers, based on modern and ancient DNA samples. This latter process was previously studied using coalescent simulations. Our results are in general agreement with the previous method, which provides validation of our approach. Although our model is not an alternative to simulation methods in the practical sense, it provides an algorithm to compute pairwise distributions of alleles, in the case of haploid non-recombining loci such as mitochondrial and Y-chromosome loci in humans.}, } @article {pmid27346254, year = {2016}, author = {Laird, MF and Holton, NE and Scott, JE and Franciscus, RG and Marshall, SD and Southard, TE}, title = {Spatial determinants of the mandibular curve of Spee in modern and archaic Homo.}, journal = {American journal of physical anthropology}, volume = {161}, number = {2}, pages = {226-236}, doi = {10.1002/ajpa.23020}, pmid = {27346254}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; Biological Evolution ; Cuspid/*anatomy & histology ; Fossils ; Hominidae/*anatomy & histology ; Humans ; Mandible/*anatomy & histology ; Neanderthals/*anatomy & histology ; }, abstract = {OBJECTIVES: The curve of Spee (COS) is a mesio-distally curved alignment of the canine through distal molar cusp tips in certain mammals including modern humans and some fossil hominins. In humans, the alignment varies from concave to flat, and previous studies have suggested that this difference reflects craniofacial morphology, including the degree of alveolar prognathism. However, the relationship between prognathism and concavity of the COS has not been tested in craniofacially variant populations. We tested the hypothesis that greater alveolar prognathism covaries with a flatter COS in African-American and European-American populations. We further examined this relationship in fossil Homo including Homo neanderthalensis and early anatomically modern Homo sapiens, which are expected to extend the amount of variation in the COS from the extant sample.

METHODS AND MATERIALS: These hypotheses were tested using three-dimensional geometric morphometrics. Landmarks were recorded from the skulls of 166 African-Americans, 123 European-Americans, and 10 fossil hominin mandible casts. Landmarks were subjected to generalized Procrustes analysis, principal components analysis, and two-block partial least squares analysis.

RESULTS: We documented covariation between the COS and alveolar prognathism such that relatively prognathic individuals have a flatter COS. Mandibular data from the fossil hominin taxa generally confirm and extend this correlation across a greater range of facial size and morphology in Homo.

DISCUSSION: Our results suggest that the magnitude of the COS is related to a suite of features associated with alveolar prognathism in modern humans and across anthropoids. We also discuss the implications for spatial interactions between the dental arches.}, } @article {pmid27343769, year = {2016}, author = {Hodgkins, J and Marean, CW and Turq, A and Sandgathe, D and McPherron, SJ and Dibble, H}, title = {Climate-mediated shifts in Neandertal subsistence behaviors at Pech de l'Azé IV and Roc de Marsal (Dordogne Valley, France).}, journal = {Journal of human evolution}, volume = {96}, number = {}, pages = {1-18}, doi = {10.1016/j.jhevol.2016.03.009}, pmid = {27343769}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; Bone and Bones ; *Climate ; Deer ; *Diet ; *Feeding Behavior ; France ; Neanderthals/*physiology ; Reindeer ; }, abstract = {Neandertals disappeared from Europe just after 40,000 years ago. Some hypotheses ascribe this to numerous population crashes associated with glacial cycles in the late Pleistocene. The goal of this paper is to test the hypothesis that glacial periods stressed Neandertal populations. If cold climates stressed Neandertals, their subsistence behaviors may have changed-requiring intensified use of prey through more extensive nutrient extraction from faunal carcasses. To test this, an analysis of Neandertal butchering was conducted on medium sized bovid/cervid remains composed of predominately red deer (Cervus elaphus), reindeer (Rangifer tarandus), and roe deer (Capreolus caprelous) deposited during global warm and cold phases from two French sites: Pech de l'Azé IV (Pech IV, Bordes' excavation) and Roc de Marsal (RDM). Analysis of surface modification on high survival long bones and proximal and middle phalanges demonstrates that skeletal elements excavated from the cold levels (RDM Level 4, Pech IV Level I2) at each cave have more cut marks and percussion marks than elements from the warm levels (RDM Level 9, Pech IV Level Y-Z) after controlling for fragment size. At both sites, epiphyseal fragments are rare, and although this pattern can result from carnivore consumption, carnivore tooth marks are almost nonexistent (<0.1%). Alternatively, processing epiphyseal ends for bone grease may have been a Neandertal survival strategy, and epiphyses were more intensively percussed in cold levels than in warm levels at both RDM and Pech IV. The exploitation of low marrow yield elements such as phalanges does not show a consistent pattern relating to climate, but may have been a general Neandertal behavioral characteristic, suggesting that these hominids were regularly on the edge of sufficient nutrient availability even during interglacials. Overall, the faunal assemblages from Roc de Marsal and Pech IV provide some support for the hypothesis that Neandertals were processing faunal remains more heavily during glacial periods, suggesting a response to increased nutritional stress during colder time periods.}, } @article {pmid27337483, year = {2016}, author = {Abi-Rached, L and Raoult, D}, title = {Paleogenetics and Past Infections: the Two Faces of the Coin of Human Immune Evolution.}, journal = {Microbiology spectrum}, volume = {4}, number = {3}, pages = {}, doi = {10.1128/microbiolspec.PoH-0018-2015}, pmid = {27337483}, issn = {2165-0497}, mesh = {Communicable Diseases/*epidemiology/*immunology ; *Evolution, Molecular ; *Fossils ; Humans ; *Immune System ; Immunogenetics/*methods ; Paleopathology/*methods ; Selection, Genetic ; }, abstract = {With the advent of next-generation sequencing, paleogenetics has considerably expanded over the past few years and notably encompassed the characterization of the genomes of archaic humans who lived more than 30,000 years ago. These paleogenetics investigations have revealed that admixture between modern and archaic humans occurred, with Neanderthals having contributed to 1.5% to 2.1% of modern Eurasian genomes, and Denisovans to 3% to 6% of modern Melanesian genomes and to approximately 0.2% of modern Asian genomes. Although these contributions are modest, they played a major role in shaping immune gene families, such as the HLA class I genes, for which the archaic alleles now represent more than 50% of the alleles in Europe and Asia. Such a high frequency is consistent with these archaic HLA class I variants having been positively selected because of their protective effect against contagious and devastating epidemics, such as those due to the plague agent Yersinia pestis or to Mycobacterium tuberculosis, which is responsible for deadly tuberculosis. While the exact nature of the infectious agents that contributed to the selection of the archaic variants is unknown, we are entering an exciting period in which paleogenetics and paleomicrobiology data can be integrated to generate a clearer picture of how the immune system of modern populations was shaped and the role admixture and epidemics have played in such evolutions.}, } @article {pmid27312187, year = {2016}, author = {Clark, AE}, title = {Time and space in the middle paleolithic: Spatial structure and occupation dynamics of seven open-air sites.}, journal = {Evolutionary anthropology}, volume = {25}, number = {3}, pages = {153-163}, doi = {10.1002/evan.21486}, pmid = {27312187}, issn = {1520-6505}, mesh = {Animals ; Archaeology/*methods ; Fossils ; France ; History, Ancient ; Humans ; Neanderthals ; Occupations/*history ; Spatial Analysis ; Technology/*history ; Tool Use Behavior ; }, abstract = {The spatial structure of archeological sites can help reconstruct the settlement dynamics of hunter-gatherers by providing information on the number and length of occupations. This study seeks to access this information through a comparison of seven sites. These sites are open-air and were all excavated over large spatial areas, up to 2,000 m(2) , and are therefore ideal for spatial analysis, which was done using two complementary methods, lithic refitting and density zones. Both methods were assessed statistically using confidence intervals. The statistically significant results from each site were then compiled to evaluate trends that occur across the seven sites. These results were used to assess the "spatial consistency" of each assemblage and, through that, the number and duration of occupations. This study demonstrates that spatial analysis can be a powerful tool in research on occupation dynamics and can help disentangle the many occupations that often make up an archeological assemblage.}, } @article {pmid27312183, year = {2016}, author = {Churchill, SE and Walker, CS and Schwartz, AM}, title = {Home-range size in large-bodied carnivores as a model for predicting neandertal territory size.}, journal = {Evolutionary anthropology}, volume = {25}, number = {3}, pages = {117-123}, doi = {10.1002/evan.21483}, pmid = {27312183}, issn = {1520-6505}, mesh = {Animals ; Anthropology, Physical ; History, Ancient ; Homing Behavior/*physiology ; Models, Biological ; Neanderthals/*physiology ; Wolves/*physiology ; }, abstract = {Adult human foragers expend roughly 30-60 kcal per km in unburdened walking at optimal speeds.(1,2) In the context of foraging rounds and residential moves, they may routinely travel distances of 50-70 km per week, often while carrying loads.(3) Movement on the landscape, then, is arguably the single most expensive item in the activity budgets of hunter-gatherers. Mobility costs may have been greater still for Neandertals. They had stocky, short-limbed physiques that were energetically costly to move(4) and lived in relatively unproductive Pleistocene environments(5) that may have required greater movement to deal with problems of biodepletion and resource patchiness.(6) But just how mobile were the Neandertals?}, } @article {pmid27304984, year = {2016}, author = {Wallborn, F and Söffler, C and Winkels, P and Hess, M and Engelhardt, P}, title = {[Leishmania infantum induced bone lesions in a dog].}, journal = {Tierarztliche Praxis. Ausgabe K, Kleintiere/Heimtiere}, volume = {44}, number = {4}, pages = {278-282}, doi = {10.15654/TPK-150933}, pmid = {27304984}, issn = {2567-5842}, mesh = {Allopurinol/therapeutic use ; Animals ; Antiprotozoal Agents/therapeutic use ; Bone Diseases, Infectious/diagnosis/drug therapy/pathology/*veterinary ; Dog Diseases/diagnosis/drug therapy/*parasitology/pathology ; Dogs ; Lameness, Animal/parasitology ; Leishmania infantum/*isolation & purification ; Leishmaniasis, Visceral/diagnosis/drug therapy/pathology/*veterinary ; }, abstract = {A 3-year-old Labrador Retriever originating from Spain was presented with a left-sided hind limb lameness for several months. The orthopedic examination revealed a pain response when palpating the left tarsal joint. Radiographic and computed tomographic studies showed polyostotic, aggressive osteolytic bone lesions with mild erosive arthritis. The diagnosis of canine leishmaniasis was confirmed by bone biopsy and the detection of the pathogen by PCR. Three weeks after initiation of therapy with allopurinol, the dog presented no signs of lameness. Eight months after start of therapy, radiographic examination revealed moderate regression of the osteolytic bone lesions.}, } @article {pmid27298468, year = {2016}, author = {Stringer, C}, title = {The origin and evolution of Homo sapiens.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {371}, number = {1698}, pages = {}, pmid = {27298468}, issn = {1471-2970}, mesh = {Africa ; Animals ; *Biological Evolution ; *Fossils ; *Hominidae ; Humans ; Neanderthals ; }, abstract = {If we restrict the use of Homo sapiens in the fossil record to specimens which share a significant number of derived features in the skeleton with extant H. sapiens, the origin of our species would be placed in the African late middle Pleistocene, based on fossils such as Omo Kibish 1, Herto 1 and 2, and the Levantine material from Skhul and Qafzeh. However, genetic data suggest that we and our sister species Homo neanderthalensis shared a last common ancestor in the middle Pleistocene approximately 400-700 ka, which is at least 200 000 years earlier than the species origin indicated from the fossils already mentioned. Thus, it is likely that the African fossil record will document early members of the sapiens lineage showing only some of the derived features of late members of the lineage. On that basis, I argue that human fossils such as those from Jebel Irhoud, Florisbad, Eliye Springs and Omo Kibish 2 do represent early members of the species, but variation across the African later middle Pleistocene/early Middle Stone Age fossils shows that there was not a simple linear progression towards later sapiens morphology, and there was chronological overlap between different 'archaic' and 'modern' morphs. Even in the late Pleistocene within and outside Africa, we find H. sapiens specimens which are clearly outside the range of Holocene members of the species, showing the complexity of recent human evolution. The impact on species recognition of late Pleistocene gene flow between the lineages of modern humans, Neanderthals and Denisovans is also discussed, and finally, I reconsider the nature of the middle Pleistocene ancestor of these lineages, based on recent morphological and genetic data.This article is part of the themed issue 'Major transitions in human evolution'.}, } @article {pmid27274045, year = {2016}, author = {Slatkin, M and Racimo, F}, title = {Ancient DNA and human history.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {23}, pages = {6380-6387}, pmid = {27274045}, issn = {1091-6490}, support = {R01 GM040282/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA Contamination ; *DNA, Ancient ; Fossils ; Genome ; Hominidae/*genetics ; Humans ; }, abstract = {We review studies of genomic data obtained by sequencing hominin fossils with particular emphasis on the unique information that ancient DNA (aDNA) can provide about the demographic history of humans and our closest relatives. We concentrate on nuclear genomic sequences that have been published in the past few years. In many cases, particularly in the Arctic, the Americas, and Europe, aDNA has revealed historical demographic patterns in a way that could not be resolved by analyzing present-day genomes alone. Ancient DNA from archaic hominins has revealed a rich history of admixture between early modern humans, Neanderthals, and Denisovans, and has allowed us to disentangle complex selective processes. Information from aDNA studies is nowhere near saturation, and we believe that future aDNA sequences will continue to change our understanding of hominin history.}, } @article {pmid27274044, year = {2016}, author = {Roebroeks, W and Soressi, M}, title = {Neandertals revised.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {23}, pages = {6372-6379}, pmid = {27274044}, issn = {1091-6490}, mesh = {Animals ; Anthropology, Physical ; Biological Evolution ; Life Style ; *Neanderthals ; }, abstract = {The last decade has seen a significant growth of our knowledge of the Neandertals, a population of Pleistocene hunter-gatherers who lived in (western) Eurasia between ∼400,000 and 40,000 y ago. Starting from a source population deep in the Middle Pleistocene, the hundreds of thousands of years of relative separation between African and Eurasian groups led to the emergence of different phenotypes in Late Pleistocene Europe and Africa. Both recently obtained genetic evidence and archeological data show that the biological and cultural gaps between these populations were probably smaller than previously thought. These data, reviewed here, falsify inferences to the effect that, compared with their near-modern contemporaries in Africa, Neandertals were outliers in terms of behavioral complexity. It is only around 40,000 y ago, tens of thousands of years after anatomically modern humans first left Africa and thousands of years after documented interbreeding between modern humans, Neandertals and Denisovans, that we see major changes in the archeological record, from western Eurasia to Southeast Asia, e.g., the emergence of representational imagery and the colonization of arctic areas and of greater Australia (Sahul).}, } @article {pmid27260176, year = {2016}, author = {Jacobs, Z and Jankowski, NR and Dibble, HL and Goldberg, P and McPherron, SJ and Sandgathe, D and Soressi, M}, title = {The age of three Middle Palaeolithic sites: Single-grain optically stimulated luminescence chronologies for Pech de l'Azé I, II and IV in France.}, journal = {Journal of human evolution}, volume = {95}, number = {}, pages = {80-103}, doi = {10.1016/j.jhevol.2016.03.010}, pmid = {27260176}, issn = {1095-8606}, mesh = {Animals ; *Archaeology ; France ; Geologic Sediments/*analysis ; *Luminescent Measurements ; *Neanderthals ; }, abstract = {Optically stimulated luminescence (OSL) measurements were made on individual, sand-sized grains of quartz from Middle Palaeolithic deposits at three sites (Pech de l'Azé I, II and IV) located close to one another in the Dordogne region of southwest France. We were able to calculate OSL ages for 69 samples collected from these three sites. These ages reveal periods of occupation between about 180 and 50 thousand years ago. Our single-grain OSL chronologies largely support previous age estimates obtained by thermoluminescence dating of burnt flints at Pech IV, electron spin resonance dating of tooth enamel at Pech I, II and IV and radiocarbon dating of bone at Pech I and IV, but provide a more complete picture due to the ubiquitous presence of sand-sized quartz grains used in OSL dating. These complete chronologies for the three sites have allowed us to compare the single-grain ages for similar lithic assemblages among the three sites, to test the correlations among them previously proposed by Bordes in the 1970s, and to construct our own correlative chronological framework for the three sites. This shows that similar lithic assemblages occur at around the same time, and that where a lithic assemblage is unique to one or found at two of the Pech sites, there are no deposits of chronologically equivalent age at the other Pech site(s). We interpret this to mean that, at least for these Pech de l'Azé sites, the Mousterian variants show temporal ordering. Whether or not this conclusion applies to the wider region and beyond, the hypothesis that Mousterian industrial variation is temporally ordered cannot be refuted at this time.}, } @article {pmid27260174, year = {2016}, author = {Rosas, A and Rodriguez-Perez, FJ and Bastir, M and Estalrrich, A and Huguet, R and García-Tabernero, A and Pastor, JF and de la Rasilla, M}, title = {Adult Neandertal clavicles from the El Sidrón site (Asturias, Spain) in the context of Homo pectoral girdle evolution.}, journal = {Journal of human evolution}, volume = {95}, number = {}, pages = {55-67}, doi = {10.1016/j.jhevol.2016.03.005}, pmid = {27260174}, issn = {1095-8606}, mesh = {Animals ; *Biological Evolution ; Clavicle/*anatomy & histology ; Female ; Fossils/*anatomy & histology ; Male ; Neanderthals/*anatomy & histology ; Phylogeny ; Shoulder/anatomy & histology ; Spain ; }, abstract = {We undertook a three-dimensional geometric morphometric (3DGM) analysis on 12 new Neandertal clavicle specimens from the El Sidrón site (Spain), dated to 49,000 years ago. The 3DGM methods were applied in a comparative framework in order to improve our understanding of trait polarity in features related to Homo pectoral girdle evolution, using other Neandertals, Homo sapiens, Pan, ATD6-50 (Homo antecessor), and KNM-WT 15000 (Homo ergaster/erectus) in the reference collection. Twenty-nine homologous landmarks were measured for each clavicle. Variation and morphological similarities were assessed through principal component analysis, conducted separately for the complete clavicle and the diaphysis. On average, Neandertal clavicles had significantly larger muscular entheses, double dorsal curvature, clavicle torsion, and cranial orientation of the acromial end than non-Neandertal clavicles; the El Sidrón clavicles fit this pattern. Variation within the samples was large, with extensive overlap between Homo species; only chimpanzee specimens clearly differed from the other specimens in morphometric terms. Taken together, our morphometric analyses are consistent with the following phylogenetic sequence. The primitive condition of the clavicle is manifest in the cranial orientation of both the acromial and sternal ends. The derived condition expressed in the H. sapiens + Neandertal clade is defined by caudal rotation of both the sternal and acromial ends, but with variation in the number of acromia remaining in a certain cranial orientation. Finally, the autapomorphic Neandertal condition is defined by secondarily acquired primitive cranial re-orientation of the acromial end, which varies from individual to individual. These results suggest that the pace of phylogenetic change in the pectoral girdle does not seem to follow that of other postcranial skeletal features.}, } @article {pmid27260172, year = {2016}, author = {Roussel, M and Soressi, M and Hublin, JJ}, title = {The Châtelperronian conundrum: Blade and bladelet lithic technologies from Quinçay, France.}, journal = {Journal of human evolution}, volume = {95}, number = {}, pages = {13-32}, doi = {10.1016/j.jhevol.2016.02.003}, pmid = {27260172}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; Caves ; *Cultural Evolution ; France ; *Neanderthals ; Technology ; }, abstract = {The discovery of an almost complete Neanderthal skeleton in a Châtelperronian context at Saint-Césaire 35 years ago changed our perspective on the beginning of the Upper Paleolithic in western Europe. Since then, the Châtelperronian has generally been considered a "transitional" industry rather than an Upper or a Middle Paleolithic industry because of its chronological position, and the association of Neanderthal remains with blades, bone tools and personal ornaments. Several competing hypotheses have been proposed to explain the association between Neanderthals and these types of artefacts including post-depositional mixing, acculturation from anatomically modern human populations, or an independent technological evolution by local Neanderthal populations. Quinçay Cave is the only Châtelperronian site where personal ornaments have been found that does not contain an overlying Upper Paleolithic layer. This means that the post-depositional mixing of later elements into the Châtelperronian may not be used as an explanation for the presence of these materials. We report here on a detailed technological analysis of lithic artefacts from the three Châtelperronian layers at Quinçay Cave. We compare our results with the technology of Mousterian blade industries dating to OIS (oxygen isotope stage) 5, the Mousterian of Acheulian Tradition type B, and the Proto-Aurignacian. We show that the Châtelperronian is sufficiently divergent from the Middle Paleolithic to be classified as a fully Upper Paleolithic industry, with a focus on blade and bladelet production. We also show that the Quinçay Châtelperronian includes retouched bladelets that resemble those found in the Proto-Aurignacian, but were produced in a different manner. We argue that a technological convergence cannot account for these behaviors, since the specific type of retouched bladelet associated with the Châtelperronian was also regularly used by Proto-Aurignacian of neighboring regions. We suggest that the idea of retouched bladelets may have diffused from the northern Proto-Aurignacian to the Quinçay Châtelperronian and that the transmission of the morphology of this desired end-product without the transmission of its manufacturing process may point toward a low degree of social intimacy between these groups. We conclude that the apparent paradox of the Châtelperronian is the result of the complexity of interaction between Neanderthal and anatomically modern human groups in western Europe between 45,000 and 40,000 years ago.}, } @article {pmid27251286, year = {2016}, author = {Jaubert, J and Verheyden, S and Genty, D and Soulier, M and Cheng, H and Blamart, D and Burlet, C and Camus, H and Delaby, S and Deldicque, D and Edwards, RL and Ferrier, C and Lacrampe-Cuyaubère, F and Lévêque, F and Maksud, F and Mora, P and Muth, X and Régnier, É and Rouzaud, JN and Santos, F}, title = {Early Neanderthal constructions deep in Bruniquel Cave in southwestern France.}, journal = {Nature}, volume = {534}, number = {7605}, pages = {111-114}, pmid = {27251286}, issn = {1476-4687}, mesh = {Animals ; *Caves ; Construction Industry/history ; Construction Materials/*history ; Facility Design and Construction/history ; Fires/history ; France ; History, Ancient ; *Neanderthals ; }, abstract = {Very little is known about Neanderthal cultures, particularly early ones. Other than lithic implements and exceptional bone tools, very few artefacts have been preserved. While those that do remain include red and black pigments and burial sites, these indications of modernity are extremely sparse and few have been precisely dated, thus greatly limiting our knowledge of these predecessors of modern humans. Here we report the dating of annular constructions made of broken stalagmites found deep in Bruniquel Cave in southwest France. The regular geometry of the stalagmite circles, the arrangement of broken stalagmites and several traces of fire demonstrate the anthropogenic origin of these constructions. Uranium-series dating of stalagmite regrowths on the structures and on burnt bone, combined with the dating of stalagmite tips in the structures, give a reliable and replicated age of 176.5 thousand years (±2.1 thousand years), making these edifices among the oldest known well-dated constructions made by humans. Their presence at 336 metres from the entrance of the cave indicates that humans from this period had already mastered the underground environment, which can be considered a major step in human modernity.}, } @article {pmid27251273, year = {2016}, author = {Soressi, M}, title = {Archaeology: Neanderthals built underground.}, journal = {Nature}, volume = {534}, number = {7605}, pages = {43-44}, pmid = {27251273}, issn = {1476-4687}, mesh = {Animals ; *Caves ; Construction Materials/*history ; *Neanderthals ; }, } @article {pmid27217565, year = {2016}, author = {Weaver, TD and Coqueugniot, H and Golovanova, LV and Doronichev, VB and Maureille, B and Hublin, JJ}, title = {Neonatal postcrania from Mezmaiskaya, Russia, and Le Moustier, France, and the development of Neandertal body form.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {23}, pages = {6472-6477}, pmid = {27217565}, issn = {1091-6490}, mesh = {Animals ; Anthropometry ; Bone and Bones/*anatomy & histology ; Female ; France ; Humans ; Male ; Neanderthals/*anatomy & histology ; Russia ; }, abstract = {Neandertal and modern human adults differ in skeletal features of the cranium and postcranium, and it is clear that many of the cranial differences-although not all of them-are already present at the time of birth. We know less, however, about the developmental origins of the postcranial differences. Here, we address this deficiency with morphometric analyses of the postcrania of the two most complete Neandertal neonates-Mezmaiskaya 1 (from Russia) and Le Moustier 2 (from France)-and a recent human sample. We find that neonatal Neandertals already appear to possess the wide body, long pubis, and robust long bones of adult Neandertals. Taken together, current evidence indicates that skeletal differences between Neandertals and modern humans are largely established by the time of birth.}, } @article {pmid27203426, year = {2016}, author = {Barber, MF and Kronenberg, Z and Yandell, M and Elde, NC}, title = {Antimicrobial Functions of Lactoferrin Promote Genetic Conflicts in Ancient Primates and Modern Humans.}, journal = {PLoS genetics}, volume = {12}, number = {5}, pages = {e1006063}, pmid = {27203426}, issn = {1553-7404}, support = {K99 GM115822/GM/NIGMS NIH HHS/United States ; R01 GM104390/GM/NIGMS NIH HHS/United States ; R01 GM114514/GM/NIGMS NIH HHS/United States ; T32 GM007464/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Antimicrobial Cationic Peptides/genetics/immunology ; Bacteria/*immunology/pathogenicity ; Genetics, Population ; Humans ; Iron/immunology/*metabolism ; Lactoferrin/*genetics/immunology ; Neanderthals/genetics/immunology ; Polymorphism, Genetic ; Primates/genetics/immunology ; Selection, Genetic/*genetics ; }, abstract = {Lactoferrin is a multifunctional mammalian immunity protein that limits microbial growth through sequestration of nutrient iron. Additionally, lactoferrin possesses cationic protein domains that directly bind and inhibit diverse microbes. The implications for these dual functions on lactoferrin evolution and genetic conflicts with microbes remain unclear. Here we show that lactoferrin has been subject to recurrent episodes of positive selection during primate divergence predominately at antimicrobial peptide surfaces consistent with long-term antagonism by bacteria. An abundant lactoferrin polymorphism in human populations and Neanderthals also exhibits signatures of positive selection across primates, linking ancient host-microbe conflicts to modern human genetic variation. Rapidly evolving sites in lactoferrin further correspond to molecular interfaces with opportunistic bacterial pathogens causing meningitis, pneumonia, and sepsis. Because microbes actively target lactoferrin to acquire iron, we propose that the emergence of antimicrobial activity provided a pivotal mechanism of adaptation sparking evolutionary conflicts via acquisition of new protein functions.}, } @article {pmid27178465, year = {2016}, author = {Eichel, KA and Ackermann, RR}, title = {Variation in the nasal cavity of baboon hybrids with implications for late Pleistocene hominins.}, journal = {Journal of human evolution}, volume = {94}, number = {}, pages = {134-145}, doi = {10.1016/j.jhevol.2016.02.007}, pmid = {27178465}, issn = {1095-8606}, support = {P51 OD011133/OD/NIH HHS/United States ; P51 RR013986/RR/NCRR NIH HHS/United States ; P01 HL028972/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Anthropology, Physical ; Biological Evolution ; Female ; Fossils/*anatomy & histology ; Hominidae/*anatomy & histology ; Humans ; *Hybridization, Genetic ; Male ; Nasal Cavity/*anatomy & histology ; Papio/*anatomy & histology/genetics ; Phenotype ; }, abstract = {Hybridization is increasingly proving to be an important force shaping human evolution. Comparisons of both ancient and modern genomes have provided support for a complex evolutionary scenario over the past million years, with evidence for multiple incidents of gene exchange. However, to date, genetic evidence is still limited in its ability to pinpoint the precise time and place of ancient admixture. For that we must rely on evidence of admixture from the skeleton. The research presented here builds on previous work on the crania of baboon hybrids, focusing on the nasal cavity of olive baboons, yellow baboons, and first generation (F1) hybrids. The nasal cavity is a particularly important anatomical region for study, given the clear differentiation of this feature in Neanderthals relative to their contemporaries, and therefore it is a feature that will likely differ in a distinctive manner in hybrids of these taxa. Metric data consist of 45 linear, area, and volume measurements taken from CT scans of known-pedigree baboon crania. Results indicate that there is clear evidence for differences among the nasal cavities of the parental taxa and their F1 hybrids, including a greater degree of sexual dimorphism in the hybrids. There is also some evidence for transgressive phenotypes in individual F1 animals. The greatest amount of shape variation occurs in the anterior bony cavity, the choana, and the mid-nasopharynx. Extrapolating our results to the fossil record, we would expect F1 hybrid fossils to have larger nasal cavities, on average, than either parental taxon, with overall nasal cavity shape showing the most profound changes in regions that are distinct between the parental taxa (e.g., anterior nasal cavity). We also expect size and shape differences to be more pronounced in male F1 hybrids than in females. Because of pronounced anterior nasal cavity differences between Neanderthals and their contemporaries, we suggest that this model might be effective for examining the fossil record of late Pleistocene contact.}, } @article {pmid27140627, year = {2016}, author = {Moorjani, P and Sankararaman, S and Fu, Q and Przeworski, M and Patterson, N and Reich, D}, title = {A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {20}, pages = {5652-5657}, pmid = {27140627}, issn = {1091-6490}, support = {F32 GM115006/GM/NIGMS NIH HHS/United States ; R01 GM100233/GM/NIGMS NIH HHS/United States ; K99 GM111744/GM/NIGMS NIH HHS/United States ; R00 GM111744/GM/NIGMS NIH HHS/United States ; R01 GM083098/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; *Genetic Techniques ; *Genome, Human ; Humans ; Neanderthals/*genetics ; Polymorphism, Single Nucleotide ; Radiometric Dating/*methods ; }, abstract = {The study of human evolution has been revolutionized by inferences from ancient DNA analyses. Key to these studies is the reliable estimation of the age of ancient specimens. High-resolution age estimates can often be obtained using radiocarbon dating, and, while precise and powerful, this method has some biases, making it of interest to directly use genetic data to infer a date for samples that have been sequenced. Here, we report a genetic method that uses the recombination clock. The idea is that an ancient genome has evolved less than the genomes of present-day individuals and thus has experienced fewer recombination events since the common ancestor. To implement this idea, we take advantage of the insight that all non-Africans have a common heritage of Neanderthal gene flow into their ancestors. Thus, we can estimate the date since Neanderthal admixture for present-day and ancient samples simultaneously and use the difference as a direct estimate of the ancient specimen's age. We apply our method to date five Upper Paleolithic Eurasian genomes with radiocarbon dates between 12,000 and 45,000 y ago and show an excellent correlation of the genetic and (14)C dates. By considering the slope of the correlation between the genetic dates, which are in units of generations, and the (14)C dates, which are in units of years, we infer that the mean generation interval in humans over this period has been 26-30 y. Extensions of this methodology that use older shared events may be applicable for dating beyond the radiocarbon frontier.}, } @article {pmid27135931, year = {2016}, author = {Fu, Q and Posth, C and Hajdinjak, M and Petr, M and Mallick, S and Fernandes, D and Furtwängler, A and Haak, W and Meyer, M and Mittnik, A and Nickel, B and Peltzer, A and Rohland, N and Slon, V and Talamo, S and Lazaridis, I and Lipson, M and Mathieson, I and Schiffels, S and Skoglund, P and Derevianko, AP and Drozdov, N and Slavinsky, V and Tsybankov, A and Cremonesi, RG and Mallegni, F and Gély, B and Vacca, E and Morales, MR and Straus, LG and Neugebauer-Maresch, C and Teschler-Nicola, M and Constantin, S and Moldovan, OT and Benazzi, S and Peresani, M and Coppola, D and Lari, M and Ricci, S and Ronchitelli, A and Valentin, F and Thevenet, C and Wehrberger, K and Grigorescu, D and Rougier, H and Crevecoeur, I and Flas, D and Semal, P and Mannino, MA and Cupillard, C and Bocherens, H and Conard, NJ and Harvati, K and Moiseyev, V and Drucker, DG and Svoboda, J and Richards, MP and Caramelli, D and Pinhasi, R and Kelso, J and Patterson, N and Krause, J and Pääbo, S and Reich, D}, title = {The genetic history of Ice Age Europe.}, journal = {Nature}, volume = {534}, number = {7606}, pages = {200-205}, pmid = {27135931}, issn = {1476-4687}, support = {263441//European Research Council/International ; R01 GM100233/GM/NIGMS NIH HHS/United States ; GM100233/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Biological Evolution ; DNA/analysis/genetics/isolation & purification ; Europe ; European Continental Ancestry Group/*genetics/*history ; Female ; Founder Effect ; Genetics, Population ; History, Ancient ; Human Migration/history ; Humans ; *Ice Cover ; Male ; Middle East ; Neanderthals/genetics ; Phylogeny ; Population Dynamics ; Selection, Genetic ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {Modern humans arrived in Europe ~45,000 years ago, but little is known about their genetic composition before the start of farming ~8,500 years ago. Here we analyse genome-wide data from 51 Eurasians from ~45,000-7,000 years ago. Over this time, the proportion of Neanderthal DNA decreased from 3-6% to around 2%, consistent with natural selection against Neanderthal variants in modern humans. Whereas there is no evidence of the earliest modern humans in Europe contributing to the genetic composition of present-day Europeans, all individuals between ~37,000 and ~14,000 years ago descended from a single founder population which forms part of the ancestry of present-day Europeans. An ~35,000-year-old individual from northwest Europe represents an early branch of this founder population which was then displaced across a broad region, before reappearing in southwest Europe at the height of the last Ice Age ~19,000 years ago. During the major warming period after ~14,000 years ago, a genetic component related to present-day Near Easterners became widespread in Europe. These results document how population turnover and migration have been recurring themes of European prehistory.}, } @article {pmid27120938, year = {2016}, author = {Demaeyer, P}, title = {[Not Available].}, journal = {Revue medicale de Bruxelles}, volume = {37}, number = {1}, pages = {52-56}, pmid = {27120938}, issn = {0035-3639}, mesh = {China ; Egypt ; History, Ancient ; History, Medieval ; Humans ; Jews/history ; Judaism/history ; Medicine, Chinese Traditional/history ; Mesopotamia ; Pulmonary Medicine/*history ; }, abstract = {Medicine owes many to Hippocrate, but pneumology traces its origin back to antiquity, from Mesopotamia to ancient Rome. Regarding prehistory: if viscera of this period have not been kept, some bones were. Since Neanderthals, it is then possible to study osteoarticular pathologies (often chronic arthrosis). But no evidence of tuberculosis was found (all thoracic kyphosis are not tuberculosis). Tuberculosis probably appears during the Neolithic age, because of high concentration of population. In ancient times, pneumology was of course not a real medical specialty. However, respiratory illness already constituted a big part of antique medical practice. The purpose of the physician in antiquity was to establish a diagnosis, a prognostic and to propose a treatment. Prognostic revealed to be of great importance in ancient times, since therapeutic efficacy was limited. Contemporary physicians often neglect this part of their practice. In ancient times, physicians also tried to gradually eliminate magic-religious aspects in taking care of the patients. This review will propose a journey from Mesopotamia to ancient Egypt (and its medical papyrus). Very few sources are available concerning medicine in pre-Columbian cultures. However, it is well known that shamans had, besides their religious competences, a great pharmacopoeia. Because of these very few sources, this topic will not be added to this article. Little is known in Europa about chinese medicine before the Jesuit mission in China during the 17th and 18th centuries. Yet, chinese medicine grew in parallel with European's one. Some relevant elements of this medicine will hereafter be shown.}, } @article {pmid27119336, year = {2016}, author = {El Zaatari, S and Grine, FE and Ungar, PS and Hublin, JJ}, title = {Neandertal versus Modern Human Dietary Responses to Climatic Fluctuations.}, journal = {PloS one}, volume = {11}, number = {4}, pages = {e0153277}, pmid = {27119336}, issn = {1932-6203}, mesh = {Animals ; Anthropology, Physical/methods ; Climate ; Diet/methods ; Ecosystem ; Feeding Behavior/*physiology ; Fossils ; Hominidae/physiology ; Humans ; Molar/anatomy & histology ; Neanderthals/*physiology ; Paleodontology/methods ; }, abstract = {The Neandertal lineage developed successfully throughout western Eurasia and effectively survived the harsh and severely changing environments of the alternating glacial/interglacial cycles from the middle of the Pleistocene until Marine Isotope Stage 3. Yet, towards the end of this stage, at the time of deteriorating climatic conditions that eventually led to the Last Glacial Maximum, and soon after modern humans entered western Eurasia, the Neandertals disappeared. Western Eurasia was by then exclusively occupied by modern humans. We use occlusal molar microwear texture analysis to examine aspects of diet in western Eurasian Paleolithic hominins in relation to fluctuations in food supplies that resulted from the oscillating climatic conditions of the Pleistocene. There is demonstrable evidence for differences in behavior that distinguish Upper Paleolithic humans from members of the Neandertal lineage. Specifically, whereas the Neandertals altered their diets in response to changing paleoecological conditions, the diets of Upper Paleolithic humans seem to have been less affected by slight changes in vegetation/climatic conditions but were linked to changes in their technological complexes. The results of this study also indicate differences in resource exploitation strategies between these two hominin groups. We argue that these differences in subsistence strategies, if they had already been established at the time of the first contact between these two hominin taxa, may have given modern humans an advantage over the Neandertals, and may have contributed to the persistence of our species despite habitat-related changes in food availabilities associated with climate fluctuations.}, } @article {pmid27114917, year = {2016}, author = {Pervaiz, N and Abbasi, AA}, title = {Molecular evolution of WDR62, a gene that regulates neocorticogenesis.}, journal = {Meta gene}, volume = {9}, number = {}, pages = {1-9}, pmid = {27114917}, issn = {2214-5400}, abstract = {Human brain evolution is characterized by dramatic expansion in cerebral cortex size. WDR62 (WD repeat domain 62) is one of the important gene in controlling human cortical development. Mutations in WDR62 lead to primary microcephaly, a neurodevelopmental disease characterized by three to four fold reduction in cerebral cortex size of affected individuals. This study analyzes comparative protein evolutionary rate to provide a useful insight into the molecular evolution of WDR62 and hence pinpointed human specific amino acid replacements. Comparative analysis of human WDR62 with two archaic humans (Neanderthals and Denisovans) and modern human populations revealed that five hominin specific amino acid residues (human specific amino acids shared with two archaic humans) might have been accumulated in the common ancestor of extinct archaic humans and modern humans about 550,000-765,000 years ago. Collectively, the data demonstrates an acceleration of WDR62 sequence evolution in hominin lineage and suggests that the ability of WDR62 protein to mediate the neurogenesis has been altered in the course of hominin evolution.}, } @article {pmid27086059, year = {2016}, author = {de-la-Rúa, C and Altuna, J and Hervella, M and Kinsley, L and Grün, R}, title = {Direct U-series analysis of the Lezetxiki humerus reveals a Middle Pleistocene age for human remains in the Basque Country (northern Iberia).}, journal = {Journal of human evolution}, volume = {93}, number = {}, pages = {109-119}, doi = {10.1016/j.jhevol.2016.02.001}, pmid = {27086059}, issn = {1095-8606}, mesh = {Biological Evolution ; Caves ; *Fossils ; Humans ; Humerus ; *Radiometric Dating ; Spain ; }, abstract = {In 1964, a human humerus was found in a sedimentary deposit in Lezetxiki Cave (Basque Country, northern Iberia). The first studies on the stratigraphy, associated mammal faunal remains and lithic implements placed the deposits containing the humerus into the Riss glacial stage. Direct chronometric evidence has so far been missing, and the previous chronostratigraphic framework and faunal dating gave inconsistent results. Here we report laser ablation U-series analyses on the humerus yielding a minimum age of 164 ± 9 ka, corresponding to MIS 6. This is the only direct dating analysis of the Lezetxiki humerus and confirms a Middle Pleistocene age for this hominin fossil. Morphometric analyses suggest that the Lezetxiki humerus has close affinities to other Middle Pleistocene archaic hominins, such as those from La Sima de los Huesos at Atapuerca. This emphasizes the significance of the Lezetxiki fossil within the populations that predate the Neanderthals in south-western Europe. It is thus an important key fossil for the understanding of human evolution in Europe during the Middle Pleistocene, a time period when a great morphological diversity is observed but whose phylogenetic meaning is not yet fully understood.}, } @article {pmid27086057, year = {2016}, author = {Naito, YI and Chikaraishi, Y and Drucker, DG and Ohkouchi, N and Semal, P and Wißing, C and Bocherens, H}, title = {Ecological niche of Neanderthals from Spy Cave revealed by nitrogen isotopes of individual amino acids in collagen.}, journal = {Journal of human evolution}, volume = {93}, number = {}, pages = {82-90}, doi = {10.1016/j.jhevol.2016.01.009}, pmid = {27086057}, issn = {1095-8606}, mesh = {Amino Acids/chemistry ; Animals ; Belgium ; Caves ; *Diet ; Ecosystem ; Food Chain ; *Fossils ; Hyaenidae ; *Neanderthals ; Nitrogen/analysis ; Wolves ; }, abstract = {This study provides a refined view on the diet and ecological niche of Neanderthals. The traditional view is that Neanderthals obtained most of their dietary protein from terrestrial animals, especially from large herbivores that roamed the open landscapes. Evidence based on the conventional carbon and nitrogen isotopic composition of bulk collagen has supported this view, although recent findings based on plant remains in the tooth calculus, microwear analyses, and small game and marine animal remains from archaeological sites have raised some questions regarding this assumption. However, the lack of a protein source other than meat in the Neanderthal diet may be due to methodological difficulties in defining the isotopic composition of plants. Based on the nitrogen isotopic composition of glutamic acid and phenylalanine in collagen for Neanderthals from Spy Cave (Belgium), we show that i) there was an inter-individual dietary heterogeneity even within one archaeological site that has not been evident in bulk collagen isotopic compositions, ii) they occupied an ecological niche different from those of hyenas, and iii) they could rely on plants for up to ∼20% of their protein source. These results are consistent with the evidence found of plant consumption by the Spy Neanderthals, suggesting a broader subsistence strategy than previously considered.}, } @article {pmid27086056, year = {2016}, author = {Skinner, MM and de Vries, D and Gunz, P and Kupczik, K and Klassen, RP and Hublin, JJ and Roksandic, M}, title = {A dental perspective on the taxonomic affinity of the Balanica mandible (BH-1).}, journal = {Journal of human evolution}, volume = {93}, number = {}, pages = {63-81}, doi = {10.1016/j.jhevol.2016.01.010}, pmid = {27086056}, issn = {1095-8606}, mesh = {Anatomic Landmarks ; Animals ; Biological Evolution ; Dental Enamel/anatomy & histology ; Dentin/anatomy & histology ; *Fossils ; Hominidae/*anatomy & histology/*classification ; Humans ; Mandible/*anatomy & histology ; Molar/anatomy & histology ; Tooth Root/anatomy & histology ; }, abstract = {The Middle Pleistocene represents a period of critical importance in human evolution, marked by encephalisation and dental reduction, and increasing diversification of temporally and spatially distributed hominin lineages in Africa, Asia and Europe. New specimens, especially from areas less well represented in the fossil record, can inform the debate on morphological changes to the skeleton and teeth and the phylogenetic course of human evolution during this period. The mandible from the cave of Mala Balanica, Serbia has recently been re-dated to at least 400 ka, and its well-preserved dentition presents an excellent opportunity to characterize molar crown morphology at this time period, and re-examine claims for a lack of Neandertal affinities in the specimen. In this study we employ microtomography to image the internal structure of the mandibular molars (focusing on the morphology of the enamel-dentine junction, or EDJ) of the BH-1 specimen and a comparative sample (n = 141) of Homo erectus sensu lato, Homo neanderthalensis, Pleistocene Homo sapiens, and recent H. sapiens. We quantitatively assess EDJ morphology using 3D geometric morphometrics and examine the expression of discrete dental traits at the dentine surface. We also compare third molar enamel thickness in BH-1 to those of H. neanderthalensis and both Pleistocene and recent H. sapiens, and document previously unreported morphology of the BH-1 premolar and molar roots. Our results highlight the reliability of the EDJ surface for classifying hominin taxa, indicate a primitive dental morphology for BH-1 molars, and confirm a general lack of derived Neandertal features for the Balanica individual. The plesiomorphic character of BH-1 is consistent with several competing models of Middle Pleistocene hominin evolution and provides an important regional and temporal example for reconstructing morphological changes in the mandible and teeth during this time period.}, } @article {pmid27081011, year = {2016}, author = {DeSalle, R}, title = {What do our genes tell us about our past?.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {94}, number = {}, pages = {193-200}, doi = {10.4436/JASS.94032}, pmid = {27081011}, issn = {2037-0644}, mesh = {Animals ; Anthropology, Physical ; *Evolution, Molecular ; Genetic Markers/*genetics ; Genome/*genetics ; Genomics ; Humans ; Neanderthals/*genetics ; Phylogeny ; }, abstract = {The use of DNA sequences to elucidate the history of relationships of organisms is widespread, and focus on our species has been intense. This paper examines some simple aspects of using genetic information to analyze relationships within and amongst humans. Clonal markers (mtDNA and Y chromosomal DNA) have always shown a high degree of structure and robustness when analyzed for hierarchical structure. Results from genome wide phylogenetic structure in many organismal systems suggests instead that recombining genetic elements like the X chromosome and the autosomes will give conflicting information from genome region to genome region. In addition, the evolutionary signal from the different chromosomal regions will show a high degree of incongruence with each other, as do adjacent regions of chromosomes. This incongruence and lack of hierarchical structure is discussed in the context of what we know about human populations and the theoretical underpinnings of tree building based analysis of human populations.}, } @article {pmid27063929, year = {2016}, author = {Houldcroft, CJ and Underdown, SJ}, title = {Neanderthal genomics suggests a pleistocene time frame for the first epidemiologic transition.}, journal = {American journal of physical anthropology}, volume = {160}, number = {3}, pages = {379-388}, doi = {10.1002/ajpa.22985}, pmid = {27063929}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; Communicable Diseases/*genetics/history/*immunology/microbiology ; Evolution, Molecular ; Fossils ; Genome/*genetics/*immunology ; Genomics ; History, Ancient ; Humans ; Neanderthals/*genetics/*immunology ; }, abstract = {High quality Altai Neanderthal and Denisovan genomes are revealing which regions of archaic hominin DNA have persisted in the modern human genome. A number of these regions are associated with response to infection and immunity, with a suggestion that derived Neanderthal alleles found in modern Europeans and East Asians may be associated with autoimmunity. As such Neanderthal genomes are an independent line of evidence of which infectious diseases Neanderthals were genetically adapted to. Sympathetically, human genome adaptive introgression is an independent line of evidence of which infectious diseases were important for AMH coming in to Eurasia and interacting with Neanderthals. The Neanderthals and Denisovans present interesting cases of hominin hunter-gatherers adapted to a Eurasian rather than African infectious disease package. Independent sources of DNA-based evidence allow a re-evaluation of the first epidemiologic transition and how infectious disease affected Pleistocene hominins. By combining skeletal, archaeological and genetic evidence from modern humans and extinct Eurasian hominins, we question whether the first epidemiologic transition in Eurasia featured a new package of infectious diseases or a change in the impact of existing pathogens. Coupled with pathogen genomics, this approach supports the view that many infectious diseases are pre-Neolithic, and the list continues to expand. The transfer of pathogens between hominin populations, including the expansion of pathogens from Africa, may also have played a role in the extinction of the Neanderthals and offers an important mechanism to understand hominin-hominin interactions well back beyond the current limits for aDNA extraction from fossils alone. Am J Phys Anthropol 160:379-388, 2016. © 2016 Wiley Periodicals, Inc.}, } @article {pmid27058445, year = {2016}, author = {Mendez, FL and Poznik, GD and Castellano, S and Bustamante, CD}, title = {The Divergence of Neandertal and Modern Human Y Chromosomes.}, journal = {American journal of human genetics}, volume = {98}, number = {4}, pages = {728-734}, pmid = {27058445}, issn = {1537-6605}, support = {R01 GM090087/GM/NIGMS NIH HHS/United States ; T15 LM007033/LM/NLM NIH HHS/United States ; LM-007033/LM/NLM NIH HHS/United States ; }, mesh = {Animals ; Cadherins/genetics ; Chromosomes, Human, Y/*genetics ; DNA/genetics ; Genetic Variation ; Histone Demethylases/genetics ; Humans ; Male ; Minor Histocompatibility Antigens/genetics ; Mutation, Missense ; Neanderthals/*genetics ; Pan troglodytes/genetics ; Sequence Analysis, DNA ; Spain ; Ubiquitin Thiolesterase/genetics ; }, abstract = {Sequencing the genomes of extinct hominids has reshaped our understanding of modern human origins. Here, we analyze ∼120 kb of exome-captured Y-chromosome DNA from a Neandertal individual from El Sidrón, Spain. We investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the Neandertal lineage as an outgroup to modern human Y chromosomes-including A00, the highly divergent basal haplogroup. We estimate that the time to the most recent common ancestor (TMRCA) of Neandertal and modern human Y chromosomes is ∼588 thousand years ago (kya) (95% confidence interval [CI]: 447-806 kya). This is ∼2.1 (95% CI: 1.7-2.9) times longer than the TMRCA of A00 and other extant modern human Y-chromosome lineages. This estimate suggests that the Y-chromosome divergence mirrors the population divergence of Neandertals and modern human ancestors, and it refutes alternative scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes. The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct. We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to PCDH11Y, TMSB4Y, USP9Y, and KDM5D. Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens. Antigens derived from KDM5D, for example, are thought to elicit a maternal immune response during gestation. It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups.}, } @article {pmid27049965, year = {2016}, author = {Racimo, F and Renaud, G and Slatkin, M}, title = {Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans.}, journal = {PLoS genetics}, volume = {12}, number = {4}, pages = {e1005972}, pmid = {27049965}, issn = {1553-7404}, support = {R01 GM040282/GM/NIGMS NIH HHS/United States ; R01-GM40282/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; Base Sequence ; Computer Simulation ; DNA/*genetics ; *DNA Contamination ; DNA, Mitochondrial/genetics ; Fossils ; *Genetic Drift ; Genetics, Population ; Humans ; Markov Chains ; Monte Carlo Method ; Neanderthals/*genetics ; Sequence Analysis, DNA ; Software ; }, abstract = {When sequencing an ancient DNA sample from a hominin fossil, DNA from present-day humans involved in excavation and extraction will be sequenced along with the endogenous material. This type of contamination is problematic for downstream analyses as it will introduce a bias towards the population of the contaminating individual(s). Quantifying the extent of contamination is a crucial step as it allows researchers to account for possible biases that may arise in downstream genetic analyses. Here, we present an MCMC algorithm to co-estimate the contamination rate, sequencing error rate and demographic parameters-including drift times and admixture rates-for an ancient nuclear genome obtained from human remains, when the putative contaminating DNA comes from present-day humans. We assume we have a large panel representing the putative contaminant population (e.g. European, East Asian or African). The method is implemented in a C++ program called 'Demographic Inference with Contamination and Error' (DICE). We applied it to simulations and genome data from ancient Neanderthals and modern humans. With reasonable levels of genome sequence coverage (>3X), we find we can recover accurate estimates of all these parameters, even when the contamination rate is as high as 50%.}, } @article {pmid27044111, year = {2016}, author = {Varki, A}, title = {Why are there no persisting hybrids of humans with Denisovans, Neanderthals, or anyone else?.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {17}, pages = {E2354}, pmid = {27044111}, issn = {1091-6490}, support = {P01 HL107150/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Fossils ; *Hominidae ; Humans ; *Neanderthals ; }, } @article {pmid27038113, year = {2016}, author = {Harris, K and Nielsen, R}, title = {The Genetic Cost of Neanderthal Introgression.}, journal = {Genetics}, volume = {203}, number = {2}, pages = {881-891}, pmid = {27038113}, issn = {1943-2631}, support = {F32 GM116381/GM/NIGMS NIH HHS/United States ; R01 GM109454/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Evolution, Molecular ; Gene Flow ; Genes, Recessive ; *Genetic Fitness ; *Genetic Load ; Humans ; Hybrid Vigor ; Inbreeding ; Neanderthals/*genetics ; }, abstract = {Approximately 2-4% of genetic material in human populations outside Africa is derived from Neanderthals who interbred with anatomically modern humans. Recent studies have shown that this Neanderthal DNA is depleted around functional genomic regions; this has been suggested to be a consequence of harmful epistatic interactions between human and Neanderthal alleles. However, using published estimates of Neanderthal inbreeding and the distribution of mutational fitness effects, we infer that Neanderthals had at least 40% lower fitness than humans on average; this increased load predicts the reduction in Neanderthal introgression around genes without the need to invoke epistasis. We also predict a residual Neanderthal mutational load in non-Africans, leading to a fitness reduction of at least 0.5%. This effect of Neanderthal admixture has been left out of previous debate on mutation load differences between Africans and non-Africans. We also show that if many deleterious mutations are recessive, the Neanderthal admixture fraction could increase over time due to the protective effect of Neanderthal haplotypes against deleterious alleles that arose recently in the human population. This might partially explain why so many organisms retain gene flow from other species and appear to derive adaptive benefits from introgression.}, } @article {pmid27032491, year = {2016}, author = {Sankararaman, S and Mallick, S and Patterson, N and Reich, D}, title = {The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans.}, journal = {Current biology : CB}, volume = {26}, number = {9}, pages = {1241-1247}, pmid = {27032491}, issn = {1879-0445}, support = {/HHMI/Howard Hughes Medical Institute/United States ; K99 GM111744/GM/NIGMS NIH HHS/United States ; R00 GM111744/GM/NIGMS NIH HHS/United States ; R01 GM100233/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Continental Population Groups/*genetics ; Demography ; Genome, Human ; Humans ; Models, Genetic ; Neanderthals/*genetics ; Time Factors ; }, abstract = {Some present-day humans derive up to ∼5% [1] of their ancestry from archaic Denisovans, an even larger proportion than the ∼2% from Neanderthals [2]. We developed methods that can disambiguate the locations of segments of Denisovan and Neanderthal ancestry in present-day humans and applied them to 257 high-coverage genomes from 120 diverse populations, among which were 20 individual Oceanians with high Denisovan ancestry [3]. In Oceanians, the average size of Denisovan fragments is larger than Neanderthal fragments, implying a more recent average date of Denisovan admixture in the history of these populations (p = 0.00004). We document more Denisovan ancestry in South Asia than is expected based on existing models of history, reflecting a previously undocumented mixture related to archaic humans (p = 0.0013). Denisovan ancestry, just like Neanderthal ancestry, has been deleterious on a modern human genetic background, as reflected by its depletion near genes. Finally, the reduction of both archaic ancestries is especially pronounced on chromosome X and near genes more highly expressed in testes than other tissues (p = 1.2 × 10(-7) to 3.2 × 10(-7) for Denisovan and 2.2 × 10(-3) to 2.9 × 10(-3) for Neanderthal ancestry even after controlling for differences in level of selective constraint across gene classes). This suggests that reduced male fertility may be a general feature of mixtures of human populations diverged by >500,000 years.}, } @article {pmid27020421, year = {2016}, author = {Brown, S and Higham, T and Slon, V and Pääbo, S and Meyer, M and Douka, K and Brock, F and Comeskey, D and Procopio, N and Shunkov, M and Derevianko, A and Buckley, M}, title = {Identification of a new hominin bone from Denisova Cave, Siberia using collagen fingerprinting and mitochondrial DNA analysis.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {23559}, pmid = {27020421}, issn = {2045-2322}, mesh = {Animals ; Antineoplastic Combined Chemotherapy Protocols ; Bone and Bones/*metabolism ; Collagen/analysis/*metabolism ; Cyclophosphamide ; DNA, Mitochondrial/chemistry/classification/*genetics ; Doxorubicin ; Evolution, Molecular ; *Fossils ; Hominidae ; Humans ; Phylogeny ; Podophyllotoxin ; Radiometric Dating ; Sequence Analysis, DNA ; Siberia ; Tandem Mass Spectrometry ; Time Factors ; Vincristine ; }, abstract = {DNA sequencing has revolutionised our understanding of archaic humans during the Middle and Upper Palaeolithic. Unfortunately, while many Palaeolithic sites contain large numbers of bones, the majority of these lack the diagnostic features necessary for traditional morphological identification. As a result the recovery of Pleistocene-age human remains is extremely rare. To circumvent this problem we have applied a method of collagen fingerprinting to more than 2000 fragmented bones from the site of Denisova Cave, Russia, in order to facilitate the discovery of human remains. As a result of our analysis a single hominin bone (Denisova 11) was identified, supported through in-depth peptide sequencing analysis, and found to carry mitochondrial DNA of the Neandertal type. Subsequent radiocarbon dating revealed the bone to be >50,000 years old. Here we demonstrate the huge potential collagen fingerprinting has for identifying hominin remains in highly fragmentary archaeological assemblages, improving the resources available for wider studies into human evolution.}, } @article {pmid26995655, year = {2016}, author = {Árnason, Ú}, title = {The Out of Africa hypothesis and the ancestry of recent humans: Cherchez la femme (et l'homme).}, journal = {Gene}, volume = {585}, number = {1}, pages = {9-12}, doi = {10.1016/j.gene.2016.03.018}, pmid = {26995655}, issn = {1879-0038}, mesh = {Africa ; Animals ; Asia ; *Biological Evolution ; China ; DNA, Mitochondrial/genetics ; Europe ; *Evolution, Molecular ; Female ; *Fossils ; Gene Flow ; Humans ; Male ; Neanderthals/*genetics ; Phylogeny ; }, abstract = {The Out of Africa hypothesis (OOAH) has been a mainstay in the discussion of human evolution since its presentation in the 1980's. However, recent advances in palaeontology and molecular genetics have made it possible to examine the hypothesis in a manner that was inconceivable at the time of its proposal. The palaeontological progress relates to early Homo finds in the Caucasus, Denisova finds in the Altai Mountains and Neanderthal finds in a wide range of localities from the Altai Mountains, the Caucasus, the Levant, Asia Minor, southern and Central Europe and the Iberian Peninsula. The Eurasian location of these finds and recognition of the principle of Last common ancestor (LCA) lend no support to OOAH. The same conclusion is drawn from genomic findings, which (a) have revealed the presence of Denisovan and Neanderthal nuclear DNA, primarily in the genomes of recent Eurasians and (b) have shown genomic introgression from early modern humans into Neanderthals in the Altai Mountains. Similarly, archaeological finds in Sulawesi and the discovery of ≈100,000years old human teeth in southern China constitute strong independent challenges to OOAH. The genomic and palaeogenomic results and the new palaeontological and archaeological discoveries suggest (a) that the ancestors of modern humans had their origin in a Eurasian (largely Asian) biogeographic region which may also have extended into NE Africa, and (b) that the founders of basal African lineages became separated, geographically and genetically, in the westernmost part of this region and spread from there to different parts of the African continent.}, } @article {pmid26989228, year = {2016}, author = {Gibbons, A}, title = {HUMAN EVOLUTION. Five matings for moderns, Neandertals.}, journal = {Science (New York, N.Y.)}, volume = {351}, number = {6279}, pages = {1250-1251}, doi = {10.1126/science.351.6279.1250}, pmid = {26989228}, issn = {1095-9203}, mesh = {Animals ; Asia ; Biological Evolution ; Bone and Bones ; DNA/genetics ; Europe ; Female ; Fossils ; Humans ; Male ; *Mating Preference, Animal ; Neanderthals/*genetics/*psychology ; *Sexual Behavior ; }, } @article {pmid26989198, year = {2016}, author = {Vernot, B and Tucci, S and Kelso, J and Schraiber, JG and Wolf, AB and Gittelman, RM and Dannemann, M and Grote, S and McCoy, RC and Norton, H and Scheinfeldt, LB and Merriwether, DA and Koki, G and Friedlaender, JS and Wakefield, J and Pääbo, S and Akey, JM}, title = {Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals.}, journal = {Science (New York, N.Y.)}, volume = {352}, number = {6282}, pages = {235-239}, doi = {10.1126/science.aad9416}, pmid = {26989198}, issn = {1095-9203}, support = {5R01GM110068/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA/*genetics ; Genetic Variation ; Genome, Human/*genetics ; Humans ; Melanesia ; Neanderthals/*genetics ; Oceanic Ancestry Group/*genetics ; Sequence Analysis, DNA ; }, abstract = {Although Neandertal sequences that persist in the genomes of modern humans have been identified in Eurasians, comparable studies in people whose ancestors hybridized with both Neandertals and Denisovans are lacking. We developed an approach to identify DNA inherited from multiple archaic hominin ancestors and applied it to whole-genome sequences from 1523 geographically diverse individuals, including 35 previously unknown Island Melanesian genomes. In aggregate, we recovered 1.34 gigabases and 303 megabases of the Neandertal and Denisovan genome, respectively. We use these maps of archaic sequences to show that Neandertal admixture occurred multiple times in different non-African populations, characterize genomic regions that are significantly depleted of archaic sequences, and identify signatures of adaptive introgression.}, } @article {pmid26989018, year = {2016}, author = {Gilmore, CC and Weaver, TD}, title = {Comparative perspective on antemortem tooth loss in Neandertals.}, journal = {Journal of human evolution}, volume = {92}, number = {}, pages = {80-90}, doi = {10.1016/j.jhevol.2015.10.011}, pmid = {26989018}, issn = {1095-8606}, mesh = {Animals ; *Anthropology, Physical ; Bayes Theorem ; Europe ; Fossils/*anatomy & histology ; Neanderthals/*anatomy & histology ; Paleodontology ; Tooth Loss/*epidemiology ; }, abstract = {Neandertal specimens with severe antemortem (before death) tooth loss (AMTL) are sometimes interpreted as evidence for human-like behaviors in Neandertals, such as conspecific care or cooking, although it is uncertain whether AMTL frequencies in Neandertals are similar to those in modern humans and exceed those in non-human primates. This study characterizes AMTL (all tooth types) in Neandertals relative to recent human hunter-gatherers and several non-human primate taxa using binomial-normal regression models fit in a Bayesian framework to a sample of 25 Neandertals, 310 recent human hunter-gatherers, 61 chimpanzees, 38 orangutans, and 75 baboons. The probability that a tooth is lost antemortem is modeled to depend on tooth class, taxon, and estimated age at death. Neandertals have odds of AMTL above orangutans and baboons, similar to or somewhat lower than chimpanzees, and below recent humans, if we assume a human-like rate of senescence; or intermediate between chimpanzees and recent humans, if we assume a faster rate of senescence. These findings suggest that Neandertals can only be considered to have frequencies of AMTL above non-human primates if they had more rapid life histories than modern humans. Either Neandertals are not human-like in their life history or their frequency of AMTL. These interpretations are complicated, however, by the substantial inter-population variation in AMTL among recent humans, with some populations having odds of AMTL as low as in non-human primates. These results, together with theoretical considerations, suggest that only high frequencies of AMTL are diagnostic of behavior. Consequently, the behavioral implications of low frequencies of AMTL, such as those found in Neandertals, are ambiguous. Low frequencies in Neandertals could be because they had a low risk of AMTL rather than because they had high mortality from AMTL relative to an average modern human of similar age.}, } @article {pmid26989014, year = {2016}, author = {Mounier, A and Balzeau, A and Caparros, M and Grimaud-Hervé, D}, title = {Brain, calvarium, cladistics: A new approach to an old question, who are modern humans and Neandertals?.}, journal = {Journal of human evolution}, volume = {92}, number = {}, pages = {22-36}, doi = {10.1016/j.jhevol.2015.12.006}, pmid = {26989014}, issn = {1095-8606}, mesh = {Africa ; Animals ; Asia ; Biological Evolution ; Brain/*anatomy & histology ; Europe ; Fossils/*anatomy & histology ; Humans ; Neanderthals/*anatomy & histology ; *Phylogeny ; Skull/*anatomy & histology ; }, abstract = {The evolutionary history of the genus Homo is the focus of major research efforts in palaeoanthropology. However, the use of palaeoneurology to infer phylogenies of our genus is rare. Here we use cladistics to test the importance of the brain in differentiating and defining Neandertals and modern humans. The analysis is based on morphological data from the calvarium and endocast of Pleistocene fossils and results in a single most parsimonious cladogram. We demonstrate that the joint use of endocranial and calvarial features with cladistics provides a unique means to understand the evolution of the genus Homo. The main results of this study indicate that: (i) the endocranial features are more phylogenetically informative than the characters from the calvarium; (ii) the specific differentiation of Neandertals and modern humans is mostly supported by well-known calvarial autapomorphies; (iii) the endocranial anatomy of modern humans and Neandertals show strong similarities, which appeared in the fossil record with the last common ancestor of both species; and (iv) apart from encephalisation, human endocranial anatomy changed tremendously during the end of the Middle Pleistocene. This may be linked to major cultural and technological novelties that had happened by the end of the Middle Pleistocene (e.g., expansion of the Middle Stone Age (MSA) in Africa and Mousterian in Europe). The combined study of endocranial and exocranial anatomy offers opportunities to further understand human evolution and the implication for the phylogeny of our genus.}, } @article {pmid26983523, year = {2016}, author = {Callaway, E}, title = {Oldest ancient-human DNA details dawn of Neanderthals.}, journal = {Nature}, volume = {531}, number = {7594}, pages = {286}, doi = {10.1038/531286a}, pmid = {26983523}, issn = {1476-4687}, mesh = {Animals ; Cell Nucleus/genetics ; DNA/*analysis/genetics ; DNA, Mitochondrial/analysis/genetics ; Evolution, Molecular ; Humans ; Neanderthals/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; Time Factors ; }, } @article {pmid26979798, year = {2016}, author = {Carmody, RN and Dannemann, M and Briggs, AW and Nickel, B and Groopman, EE and Wrangham, RW and Kelso, J}, title = {Genetic Evidence of Human Adaptation to a Cooked Diet.}, journal = {Genome biology and evolution}, volume = {8}, number = {4}, pages = {1091-1103}, pmid = {26979798}, issn = {1759-6653}, support = {F32 DK101154/DK/NIDDK NIH HHS/United States ; F32DK101154/DK/NIDDK NIH HHS/United States ; }, mesh = {Adaptation, Physiological ; Animals ; *Biological Evolution ; *Cooking ; *Diet ; Energy Intake ; Energy Metabolism ; Feeding Behavior ; *Gene Expression Regulation ; Humans ; Liver/metabolism ; Male ; Meat/analysis ; Mice ; Mice, Inbred BALB C ; Neanderthals/genetics/physiology ; Nutrigenomics ; *Selection, Genetic ; Transcriptome ; }, abstract = {Humans have been argued to be biologically adapted to a cooked diet, but this hypothesis has not been tested at the molecular level. Here, we combine controlled feeding experiments in mice with comparative primate genomics to show that consumption of a cooked diet influences gene expression and that affected genes bear signals of positive selection in the human lineage. Liver gene expression profiles in mice fed standardized diets of meat or tuber were affected by food type and cooking, but not by caloric intake or consumer energy balance. Genes affected by cooking were highly correlated with genes known to be differentially expressed in liver between humans and other primates, and more genes in this overlap set show signals of positive selection in humans than would be expected by chance. Sequence changes in the genes under selection appear before the split between modern humans and two archaic human groups, Neandertals and Denisovans, supporting the idea that human adaptation to a cooked diet had begun by at least 275,000 years ago.}, } @article {pmid26976447, year = {2016}, author = {Meyer, M and Arsuaga, JL and de Filippo, C and Nagel, S and Aximu-Petri, A and Nickel, B and Martínez, I and Gracia, A and Bermúdez de Castro, JM and Carbonell, E and Viola, B and Kelso, J and Prüfer, K and Pääbo, S}, title = {Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins.}, journal = {Nature}, volume = {531}, number = {7595}, pages = {504-507}, pmid = {26976447}, issn = {1476-4687}, mesh = {Alleles ; Animals ; DNA, Mitochondrial/genetics ; Fossils ; Genome, Mitochondrial/genetics ; Hominidae/classification/*genetics ; Male ; Neanderthals/classification/genetics ; *Phylogeny ; Sequence Alignment ; Spain ; }, abstract = {A unique assemblage of 28 hominin individuals, found in Sima de los Huesos in the Sierra de Atapuerca in Spain, has recently been dated to approximately 430,000 years ago. An interesting question is how these Middle Pleistocene hominins were related to those who lived in the Late Pleistocene epoch, in particular to Neanderthals in western Eurasia and to Denisovans, a sister group of Neanderthals so far known only from southern Siberia. While the Sima de los Huesos hominins share some derived morphological features with Neanderthals, the mitochondrial genome retrieved from one individual from Sima de los Huesos is more closely related to the mitochondrial DNA of Denisovans than to that of Neanderthals. However, since the mitochondrial DNA does not reveal the full picture of relationships among populations, we have investigated DNA preservation in several individuals found at Sima de los Huesos. Here we recover nuclear DNA sequences from two specimens, which show that the Sima de los Huesos hominins were related to Neanderthals rather than to Denisovans, indicating that the population divergence between Neanderthals and Denisovans predates 430,000 years ago. A mitochondrial DNA recovered from one of the specimens shares the previously described relationship to Denisovan mitochondrial DNAs, suggesting, among other possibilities, that the mitochondrial DNA gene pool of Neanderthals turned over later in their history.}, } @article {pmid26973080, year = {2016}, author = {Ben-Dor, M and Gopher, A and Barkai, R}, title = {Neandertals' large lower thorax may represent adaptation to high protein diet.}, journal = {American journal of physical anthropology}, volume = {160}, number = {3}, pages = {367-378}, doi = {10.1002/ajpa.22981}, pmid = {26973080}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; *Biological Evolution ; Climate ; *Diet ; Dietary Fats ; Dietary Proteins ; Female ; Male ; Neanderthals/anatomy & histology/*physiology ; Pelvis/anatomy & histology/physiology ; Thorax/anatomy & histology/*physiology ; }, abstract = {Humans are limited in their capacity to convert protein into energy. We present a hypothesis that a "bell" shaped thorax and a wide pelvis evolved in Neandertals, at least in part, as an adaptation to a high protein diet. A high protein diet created a need to house an enlarged liver and urinary system in a wider lower trunk. To test the hypothesis, we applied a model developed to identify points of nutritional stress. A ratio of obligatory dietary fat to total animal fat and protein sourced calories is calculated based on various known and estimated parameters. Stress is identified when the obligatory dietary fat ratio is higher than fat content ratios in available prey. The model predicts that during glacial winters, when carbohydrates weren't available, 74%-85% of Neandertals' caloric intake would have had to come from animal fat. Large animals contain around 50% fat calories, and their fat content is diminished during winter, so a significant stressful dietary fat deficit was identified by the model. This deficit could potentially be ameliorated by an increased capability to convert protein into energy. Given that high protein consumption is associated with larger liver and kidneys in animal models, it appears likely that the enlarged inferior section of the Neandertals thorax and possibly, in part, also his wide pelvis, represented an adaptation to provide encasement for those enlarged organs. Behavioral and evolutionary implications of the hypothesis are also discussed. Am J Phys Anthropol 160:367-378, 2016. © 2016 Wiley Periodicals, Inc.}, } @article {pmid26972814, year = {2016}, author = {Wu, XJ and Bruner, E}, title = {The endocranial anatomy of maba 1.}, journal = {American journal of physical anthropology}, volume = {160}, number = {4}, pages = {633-643}, doi = {10.1002/ajpa.22974}, pmid = {26972814}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; *Biological Evolution ; Cephalometry ; China ; Cluster Analysis ; Fossils ; Neanderthals/*anatomy & histology ; Skull/*anatomy & histology ; }, abstract = {OBJECTIVES: Maba 1, a partial cranium from Guandong Province (China) tentatively dated between 300 and 130 ka, has been suggested to display a mosaic of archaic and derived features, including facial affinities with Neandertals. This study aims to evaluate whether Maba 1 shows a derived endocranial phenotype, or if it displays a plesiomorphic braincase morphology.

MATERIALS AND METHODS: We analyzed a set of metric variables on fossil and modern human endocasts using bivariate correlation, principal component analysis, and cluster analyses, to evaluate the morphological affinities of the Maba 1 endocast.

RESULTS: The cranial capacity, estimated at around 1300 cc, and the endocranial proportions of Maba 1 are within the ranges of modern humans, Neandertals and Homo heidelbergensis. However, the frontal lobes are narrow and the parietal areas are short and flattened, as in H. heidelbergensis and H. erectus. Nonetheless, the position of the frontal lobes relative to the orbits, the morphology of the frontal sinus and the curve of the frontal squama are more derived, being similar to Neandertals and modern humans.

CONCLUSIONS: The endocast displays a general archaic morphology, although with some derived features associated with the spatial relationships with the face. A similar admixture was described for other Middle Pleistocene samples, like Sima de los Huesos. Future phylogenetic studies must re-evaluate the facial skeleton to consider whether its features can be considered as related to the Neandertal lineage. Alternatively, they should be interpreted as the result of homoplasy and parallelism within the genus Homo, and may reflect a predominantly Asian variation. Am J Phys Anthropol 160:633-643, 2016. © 2016 Wiley Periodicals, Inc.}, } @article {pmid26966016, year = {2016}, author = {Ghirotto, S and Tassi, F and Barbujani, G and Pattini, L and Hayward, C and Vollenweider, P and Bochud, M and Rampoldi, L and Devuyst, O}, title = {The Uromodulin Gene Locus Shows Evidence of Pathogen Adaptation through Human Evolution.}, journal = {Journal of the American Society of Nephrology : JASN}, volume = {27}, number = {10}, pages = {2983-2996}, pmid = {26966016}, issn = {1533-3450}, support = {295733//European Research Council/International ; GGP14263//Telethon/Italy ; MC_PC_U127561128//Medical Research Council/United Kingdom ; }, mesh = {Animals ; *Evolution, Molecular ; Genetic Loci ; Genetic Markers ; Genetic Variation ; Humans ; Urinary Tract Infections/genetics ; Uromodulin/*genetics ; }, abstract = {Common variants in the UMOD gene encoding uromodulin, associated with risk of hypertension and CKD in the general population, increase UMOD expression and urinary excretion of uromodulin, causing salt-sensitive hypertension and renal lesions. To determine the effect of selective pressure on variant frequency, we investigated the allelic frequency of the lead UMOD variant rs4293393 in 156 human populations, in eight ancient human genomes, and in primate genomes. The T allele of rs4293393, associated with CKD risk, has high frequency in most modern populations and was the one detected in primate genomes. In contrast, we identified only the derived, C allele in Denisovan and Neanderthal genomes. The distribution of the UMOD ancestral allele did not follow the ancestral susceptibility model observed for variants associated with salt-sensitive hypertension. Instead, the global frequencies of the UMOD alleles significantly correlated with pathogen diversity (bacteria, helminths) and prevalence of antibiotic-resistant urinary tract infections (UTIs). The inverse correlation found between urinary levels of uromodulin and markers of UTIs in the general population substantiates the link between UMOD variants and protection against UTIs. These data strongly suggest that the UMOD ancestral allele, driving higher urinary excretion of uromodulin, has been kept at a high frequency because of its protective effect against UTIs.}, } @article {pmid26963222, year = {2016}, author = {Lieberman, P}, title = {The evolution of language and thought.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {94}, number = {}, pages = {127-146}, doi = {10.4436/JASS.94029}, pmid = {26963222}, issn = {2037-0644}, mesh = {Animals ; Anthropology, Physical ; *Biological Evolution ; Cognition/*physiology ; History, Ancient ; Hominidae/*physiology ; Humans ; Language/*history ; *Selection, Genetic ; Speech/physiology ; Theory of Mind/*physiology ; }, abstract = {Language primarily evolved as a vocal medium that transmits the attributes of human culture and the necessities of daily communication. Human language has a long, complex evolutionary history. Language also serves as an instrument of thought since it has become evident that in the course of this process neural circuits that initially evolved to regulate motor control, motor responses to external events, and ultimately talking were recycled to serve tasks such as working memory, cognitive flexibility linguistic tasks such as comprehending distinctions in meaning conveyed by syntax. This precludes the human brain possessing an organ devoted exclusively to language, such as the Faculty of Language proposed by Chomsky (1972, 2012). In essence like Fodor's (1983) modular model, a restatement of archaic phrenological theories (Spurzheim, 1815). The subcortical basal ganglia can be traced back to early anurans. Although our knowledge of the neural circuits of the human brain is at a very early stage and incomplete, the findings of independent studies over the past 40 years, discussed here, have identified circuits linking the basal ganglia with various areas of prefrontal cortex, posterior cortical regions and other subcortical structures. These circuits are active in linguistic tasks such as lexical access, comprehending distinctions in meaning conferred by syntax and the range of higher cognitive tasks involving executive control and play a critical role in conferring cognitive flexibility. The cingulate cortex which appeared in Therapsids, transitional mammal-like reptiles who lived in age of the dinosaurs, most likely enhanced mother-infant interaction, contributing to success in the Darwinian (1859) "Struggle for Existence" - the survival of progeny. They continue to fill that role in present-day mammals as well as being involved in controlling laryngeal phonation during speech and directing attention (Newman & MacLean, 1983; Cummings, 1993". The cerebellum and hippocampus, archaic structures, play role in cognition. Natural selection acting on genetic and epigenetic events in the last 500,000 years enhanced human cognitive and linguistic capabilities. It is clear that human language did not suddenly come into being 70,000 to 100,000 years as Noam Chomsky (Bolhuis et al., 2014) and others claim. The archeological record and analyses of fossil and genetic evidence shows that Neanderthals, who diverged from the human line at least 500,000 years ago possessed some form of language. Nor did the human population suddenly acquire the capability to relate two seemingly unrelated concepts by means of associative learning 100,000 years ago, re-coined "Merge" by Chomsky and his adherents, Merge supposedly is the key to syntax but associative learning, one of the cognitive processes by which children learn languages and the myriad complexities of their cultures, is a capability present in dogs and virtually all animals.}, } @article {pmid26963221, year = {2016}, author = {Schwartz, J}, title = {What constitutes Homo sapiens? Morphology versus received wisdom.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {94}, number = {}, pages = {65-80}, doi = {10.4436/JASS.94028}, pmid = {26963221}, issn = {2037-0644}, mesh = {Adult ; Animals ; *Biological Evolution ; Child, Preschool ; Fetus/anatomy & histology ; History, 19th Century ; History, 20th Century ; History, 21st Century ; History, Ancient ; Hominidae/*anatomy & histology ; Humans ; Mandible/anatomy & histology ; Neanderthals/anatomy & histology ; Skull/*anatomy & histology ; }, abstract = {Although Linnaeus coined Homo sapiens in 1735, it was Blumenbach forty years later who provided the first morphological definition of the species. Since humans were not then allowed to be ante-Diluvian, his effort applied to the genus, as well. After the Feldhofer Grotto Neanderthal disproved this creationist notion, and human-fossil hunting became legitimate, new specimens were allocated either to sapiens or new species within Homo, or even to new species within new genera. Yet as these taxonomic acts reflected the morphological differences between specimens, they failed to address the question: What constitutes H. sapiens? When in 1950 Mayr collapsed all human fossils into Homo, he not only denied humans a diverse evolutionary past, he also shifted the key to identifying its species from morphology to geological age - a practice most paleoanthropologists still follow. Thus, for example, H. erectus is the species that preceded H. sapiens, and H. sapiens is the species into which H. erectus morphed. In order to deal with a growing morass of morphologically dissimilar specimens, the non-taxonomic terms "archaic" (AS) and "anatomically modern" (AMS) were introduced to distinguish between the earlier and later versions of H. sapiens, thereby making the species impossible to define. In attempting to disentangle fact from scenario, I begin from the beginning, trying to delineate features that may be distinctive of extant humans (ES), and then turning to the fossils that have been included in the species. With the exception of Upper Paleolithic humans - e.g. from Cro-Magnon, Dolni Vestonice, Mladeč - I argue that many specimens regarded as AMS, and all those deemed AS, are not H. sapiens. The features these AMS do share with ES suggest the existence of a sapiens clade. Further, restudy of near-recent fossils, especially from southwestern China (∼11-14.5 ka), reinforces what discoveries such as H. floresiensis indicate: "If it's recent, it's not necessarily H. sapiens".}, } @article {pmid26948814, year = {2016}, author = {Burgess, DJ}, title = {Evolutionary genetics: Haunted by the past--modern consequences of Neanderthal DNA.}, journal = {Nature reviews. Genetics}, volume = {17}, number = {4}, pages = {191}, pmid = {26948814}, issn = {1471-0064}, mesh = {Animals ; Disease/*genetics ; Humans ; Neanderthals/*genetics ; }, } @article {pmid26937625, year = {2016}, author = {Schumer, M and Cui, R and Powell, DL and Rosenthal, GG and Andolfatto, P}, title = {Ancient hybridization and genomic stabilization in a swordtail fish.}, journal = {Molecular ecology}, volume = {25}, number = {11}, pages = {2661-2679}, doi = {10.1111/mec.13602}, pmid = {26937625}, issn = {1365-294X}, mesh = {Animals ; *Biological Evolution ; Cyprinodontiformes/classification/*genetics ; Genome ; Genomics ; *Hybridization, Genetic ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {A rapidly increasing body of work is revealing that the genomes of distinct species often exhibit hybrid ancestry, presumably due to postspeciation hybridization between closely related species. Despite the growing number of documented cases, we still know relatively little about how genomes evolve and stabilize following hybridization, and to what extent hybridization is functionally relevant. Here, we examine the case of Xiphophorus nezahualcoyotl, a teleost fish whose genome exhibits significant hybrid ancestry. We show that hybridization was relatively ancient and is unlikely to be ongoing. Strikingly, the genome of X. nezahualcoyotl has largely stabilized following hybridization, distinguishing it from examples such as human-Neanderthal hybridization. Hybridization-derived regions are remarkably distinct from other regions of the genome, tending to be enriched in genomic regions with reduced constraint. These results suggest that selection has played a role in removing hybrid ancestry from certain functionally important regions. Combined with findings in other systems, our results raise many questions about the process of genomic stabilization and the role of selection in shaping patterns of hybrid ancestry in the genome.}, } @article {pmid26922901, year = {2016}, author = {Heyes, PJ and Anastasakis, K and de Jong, W and van Hoesel, A and Roebroeks, W and Soressi, M}, title = {Selection and Use of Manganese Dioxide by Neanderthals.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {22159}, pmid = {26922901}, issn = {2045-2322}, abstract = {Several Mousterian sites in France have yielded large numbers of small black blocs. The usual interpretation is that these 'manganese oxides' were collected for their colouring properties and used in body decoration, potentially for symbolic expression. Neanderthals habitually used fire and if they needed black material for decoration, soot and charcoal were readily available, whereas obtaining manganese oxides would have incurred considerably higher costs. Compositional analyses lead us to infer that late Neanderthals at Pech-de-l'Azé I were deliberately selecting manganese dioxide. Combustion experiments and thermo-gravimetric measurements demonstrate that manganese dioxide reduces wood's auto-ignition temperature and substantially increases the rate of char combustion, leading us to conclude that the most beneficial use for manganese dioxide was in fire-making. With archaeological evidence for fire places and the conversion of the manganese dioxide to powder, we argue that Neanderthals at Pech-de-l'Azé I used manganese dioxide in fire-making and produced fire on demand.}, } @article {pmid26912863, year = {2016}, author = {Simonti, CN and Vernot, B and Bastarache, L and Bottinger, E and Carrell, DS and Chisholm, RL and Crosslin, DR and Hebbring, SJ and Jarvik, GP and Kullo, IJ and Li, R and Pathak, J and Ritchie, MD and Roden, DM and Verma, SS and Tromp, G and Prato, JD and Bush, WS and Akey, JM and Denny, JC and Capra, JA}, title = {The phenotypic legacy of admixture between modern humans and Neandertals.}, journal = {Science (New York, N.Y.)}, volume = {351}, number = {6274}, pages = {737-741}, pmid = {26912863}, issn = {1095-9203}, support = {K22 LM011938/LM/NLM NIH HHS/United States ; U01HG006379/HG/NHGRI NIH HHS/United States ; U01 HG006385/HG/NHGRI NIH HHS/United States ; U01HG004438/HG/NHGRI NIH HHS/United States ; U01 HG006375/HG/NHGRI NIH HHS/United States ; U01 HG004438/HG/NHGRI NIH HHS/United States ; UL1 TR000427/TR/NCATS NIH HHS/United States ; R01LM010685/LM/NLM NIH HHS/United States ; U01HG004610/HG/NHGRI NIH HHS/United States ; U01 HG008657/HG/NHGRI NIH HHS/United States ; U01 HG006382/HG/NHGRI NIH HHS/United States ; R01 LM010685/LM/NLM NIH HHS/United States ; U01HG006382/HG/NHGRI NIH HHS/United States ; U01 HG004603/HG/NHGRI NIH HHS/United States ; R01 GM110068/GM/NIGMS NIH HHS/United States ; 1R01GM114128/GM/NIGMS NIH HHS/United States ; U01HG04603/HG/NHGRI NIH HHS/United States ; T32 EY021453/EY/NEI NIH HHS/United States ; U01HG004609/HG/NHGRI NIH HHS/United States ; U01 HG004609/HG/NHGRI NIH HHS/United States ; U01 HG006389/HG/NHGRI NIH HHS/United States ; U01 HG008672/HG/NHGRI NIH HHS/United States ; U01 HG004599/HG/NHGRI NIH HHS/United States ; U01HG006380/HG/NHGRI NIH HHS/United States ; U01 HG006380/HG/NHGRI NIH HHS/United States ; U01HG008657/HG/NHGRI NIH HHS/United States ; U01HG006388/HG/NHGRI NIH HHS/United States ; R01GM110068/GM/NIGMS NIH HHS/United States ; 5T32EY021453/EY/NEI NIH HHS/United States ; U01HG004608/HG/NHGRI NIH HHS/United States ; U01HG04599/HG/NHGRI NIH HHS/United States ; R01 GM114128/GM/NIGMS NIH HHS/United States ; U01 HG006388/HG/NHGRI NIH HHS/United States ; U01 HG006378/HG/NHGRI NIH HHS/United States ; U01 HG004610/HG/NHGRI NIH HHS/United States ; U01 HG006379/HG/NHGRI NIH HHS/United States ; U01HG006385/HG/NHGRI NIH HHS/United States ; U01HG006378/HG/NHGRI NIH HHS/United States ; 1K22LM011938/LM/NLM NIH HHS/United States ; U01 HG004608/HG/NHGRI NIH HHS/United States ; U01HG006389/HG/NHGRI NIH HHS/United States ; }, mesh = {Alleles ; Animals ; Depression/genetics ; Disease/*genetics ; European Continental Ancestry Group/genetics ; Evolution, Molecular ; Genetic Variation ; Genome, Human ; Haplotypes ; Humans ; Keratosis, Actinic/genetics ; Neanderthals/*genetics ; Phenotype ; }, abstract = {Many modern human genomes retain DNA inherited from interbreeding with archaic hominins, such as Neandertals, yet the influence of this admixture on human traits is largely unknown. We analyzed the contribution of common Neandertal variants to over 1000 electronic health record (EHR)-derived phenotypes in ~28,000 adults of European ancestry. We discovered and replicated associations of Neandertal alleles with neurological, psychiatric, immunological, and dermatological phenotypes. Neandertal alleles together explained a significant fraction of the variation in risk for depression and skin lesions resulting from sun exposure (actinic keratosis), and individual Neandertal alleles were significantly associated with specific human phenotypes, including hypercoagulation and tobacco use. Our results establish that archaic admixture influences disease risk in modern humans, provide hypotheses about the effects of hundreds of Neandertal haplotypes, and demonstrate the utility of EHR data in evolutionary analyses.}, } @article {pmid26912836, year = {2016}, author = {Gibbons, A}, title = {HUMAN EVOLUTION. Neandertal genes linked to modern diseases.}, journal = {Science (New York, N.Y.)}, volume = {351}, number = {6274}, pages = {648-649}, doi = {10.1126/science.351.6274.648}, pmid = {26912836}, issn = {1095-9203}, mesh = {Animals ; Disease/*genetics ; Humans ; Neanderthals/*genetics ; }, } @article {pmid26912479, year = {2016}, author = {Mozzi, A and Forni, D and Clerici, M and Pozzoli, U and Mascheretti, S and Guerini, FR and Riva, S and Bresolin, N and Cagliani, R and Sironi, M}, title = {The evolutionary history of genes involved in spoken and written language: beyond FOXP2.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {22157}, pmid = {26912479}, issn = {2045-2322}, mesh = {Animals ; *Evolution, Molecular ; Forkhead Transcription Factors/*genetics ; Humans ; Language Development Disorders/*genetics ; Membrane Proteins/genetics ; Nerve Tissue Proteins/genetics ; Receptors, Immunologic/genetics ; Selection, Genetic ; Sequence Alignment ; }, abstract = {Humans possess a communication system based on spoken and written language. Other animals can learn vocalization by imitation, but this is not equivalent to human language. Many genes were described to be implicated in language impairment (LI) and developmental dyslexia (DD), but their evolutionary history has not been thoroughly analyzed. Herein we analyzed the evolution of ten genes involved in DD and LI. Results show that the evolutionary history of LI genes for mammals and aves was comparable in vocal-learner species and non-learners. For the human lineage, several sites showing evidence of positive selection were identified in KIAA0319 and were already present in Neanderthals and Denisovans, suggesting that any phenotypic change they entailed was shared with archaic hominins. Conversely, in FOXP2, ROBO1, ROBO2, and CNTNAP2 non-coding changes rose to high frequency after the separation from archaic hominins. These variants are promising candidates for association studies in LI and DD.}, } @article {pmid26898827, year = {2016}, author = {Gokhman, D and Meshorer, E and Carmel, L}, title = {Epigenetics: It's Getting Old. Past Meets Future in Paleoepigenetics.}, journal = {Trends in ecology & evolution}, volume = {31}, number = {4}, pages = {290-300}, doi = {10.1016/j.tree.2016.01.010}, pmid = {26898827}, issn = {1872-8383}, mesh = {Animals ; DNA/genetics ; DNA Methylation ; *Epigenesis, Genetic ; Hominidae/*genetics ; }, abstract = {Recent years have witnessed the rise of ancient DNA (aDNA) technology, allowing comparative genomics to be carried out at unprecedented time resolution. While it is relatively straightforward to use aDNA to identify recent genomic changes, it is much less clear how to utilize it to study changes in epigenetic regulation. Here we review recent works demonstrating that highly degraded aDNA still contains sufficient information to allow reconstruction of epigenetic signals, including DNA methylation and nucleosome positioning maps. We discuss challenges arising from the tissue specificity of epigenetics, and show how some of them might in fact turn into advantages. Finally, we introduce a method to infer methylation states in tissues that do not tend to be preserved over time.}, } @article {pmid26888264, year = {2016}, author = {Hsieh, P and Woerner, AE and Wall, JD and Lachance, J and Tishkoff, SA and Gutenkunst, RN and Hammer, MF}, title = {Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies.}, journal = {Genome research}, volume = {26}, number = {3}, pages = {291-300}, pmid = {26888264}, issn = {1549-5469}, support = {8DP1ES022577-04/DP/NCCDPHP CDC HHS/United States ; R01 HG005226/HG/NHGRI NIH HHS/United States ; 1R01GM113657-01/GM/NIGMS NIH HHS/United States ; F32HG006648/HG/NHGRI NIH HHS/United States ; R01 GM113657/GM/NIGMS NIH HHS/United States ; F32 HG006648/HG/NHGRI NIH HHS/United States ; DP1 ES022577/ES/NIEHS NIH HHS/United States ; }, mesh = {African Continental Ancestry Group/*genetics ; Animals ; *Evolution, Molecular ; Gene Flow ; Gene Frequency ; Genetic Loci ; *Genetics, Population ; *Genome ; *Genome, Human ; *Genomics ; Haplotypes ; Humans ; Linkage Disequilibrium ; Pan paniscus/*genetics ; Polymorphism, Single Nucleotide ; }, abstract = {Comparisons of whole-genome sequences from ancient and contemporary samples have pointed to several instances of archaic admixture through interbreeding between the ancestors of modern non-Africans and now extinct hominids such as Neanderthals and Denisovans. One implication of these findings is that some adaptive features in contemporary humans may have entered the population via gene flow with archaic forms in Eurasia. Within Africa, fossil evidence suggests that anatomically modern humans (AMH) and various archaic forms coexisted for much of the last 200,000 yr; however, the absence of ancient DNA in Africa has limited our ability to make a direct comparison between archaic and modern human genomes. Here, we use statistical inference based on high coverage whole-genome data (greater than 60×) from contemporary African Pygmy hunter-gatherers as an alternative means to study the evolutionary history of the genus Homo. Using whole-genome simulations that consider demographic histories that include both isolation and gene flow with neighboring farming populations, our inference method rejects the hypothesis that the ancestors of AMH were genetically isolated in Africa, thus providing the first whole genome-level evidence of African archaic admixture. Our inferences also suggest a complex human evolutionary history in Africa, which involves at least a single admixture event from an unknown archaic population into the ancestors of AMH, likely within the last 30,000 yr.}, } @article {pmid26886800, year = {2016}, author = {Kuhlwilm, M and Gronau, I and Hubisz, MJ and de Filippo, C and Prado-Martinez, J and Kircher, M and Fu, Q and Burbano, HA and Lalueza-Fox, C and de la Rasilla, M and Rosas, A and Rudan, P and Brajkovic, D and Kucan, Ž and Gušic, I and Marques-Bonet, T and Andrés, AM and Viola, B and Pääbo, S and Meyer, M and Siepel, A and Castellano, S}, title = {Ancient gene flow from early modern humans into Eastern Neanderthals.}, journal = {Nature}, volume = {530}, number = {7591}, pages = {429-433}, pmid = {26886800}, issn = {1476-4687}, support = {R01 GM102192/GM/NIGMS NIH HHS/United States ; GM102192/GM/NIGMS NIH HHS/United States ; U01 MH106874/MH/NIMH NIH HHS/United States ; }, mesh = {Altitude ; Animals ; Bayes Theorem ; Chromosomes, Human, Pair 21/genetics ; Croatia/ethnology ; Gene Flow/*genetics ; Genome, Human/genetics ; Genomics ; Haplotypes/genetics ; Heterozygote ; Humans ; Hybridization, Genetic/genetics ; Neanderthals/*genetics ; Phylogeny ; Population Density ; Siberia ; Spain/ethnology ; Time Factors ; }, abstract = {It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000-65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought.}, } @article {pmid26885854, year = {2016}, author = {Netea, MG and Joosten, LA}, title = {TLRs of Our Fathers.}, journal = {Immunity}, volume = {44}, number = {2}, pages = {218-220}, doi = {10.1016/j.immuni.2016.02.003}, pmid = {26885854}, issn = {1097-4180}, mesh = {Adaptation, Physiological/*genetics ; Animals ; *Haplotypes ; Humans ; Immunity, Innate/*genetics ; Neanderthals/*genetics/*immunology ; Toll-Like Receptors/*genetics ; }, abstract = {Two new studies published in The American Journal of Human Genetics (Dannemann et al., 2016; Deschamps et al., 2016) show that introgression of innate immune genes from Neandertals and Denisovans contributed to the modern genome of European and Asian, but not African, populations, and this might partly explain differences in susceptibility to immune-mediated diseases.}, } @article {pmid26883449, year = {2016}, author = {Marti, A and Folch, A and Costa, A and Engwell, S}, title = {Reconstructing the plinian and co-ignimbrite sources of large volcanic eruptions: A novel approach for the Campanian Ignimbrite.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {21220}, pmid = {26883449}, issn = {2045-2322}, mesh = {Algorithms ; Europe ; *Models, Theoretical ; *Volcanic Eruptions ; Web Browser ; }, abstract = {The 39 ka Campanian Ignimbrite (CI) super-eruption was the largest volcanic eruption of the past 200 ka in Europe. Tephra deposits indicate two distinct plume forming phases, Plinian and co-ignimbrite, characteristic of many caldera-forming eruptions. Previous numerical studies have characterized the eruption as a single-phase event, potentially leading to inaccurate assessment of eruption dynamics. To reconstruct the volume, intensity, and duration of the tephra dispersal, we applied a computational inversion method that explicitly accounts for the Plinian and co-ignimbrite phases and for gravitational spreading of the umbrella cloud. To verify the consistency of our results, we performed an additional single-phase inversion using an independent thickness dataset. Our better-fitting two-phase model suggests a higher mass eruption rate than previous studies, and estimates that 3/4 of the total fallout volume is co-ignimbrite in origin. Gravitational spreading of the umbrella cloud dominates tephra transport only within the first hundred kilometres due to strong stratospheric winds in our best-fit wind model. Finally, tephra fallout impacts would have interrupted the westward migration of modern hominid groups in Europe, possibly supporting the hypothesis of prolonged Neanderthal survival in South-Western Europe during the Middle to Upper Palaeolithic transition.}, } @article {pmid26852814, year = {2016}, author = {Frahm, E and Feinberg, JM and Schmidt-Magee, BA and Wilkinson, KN and Gasparyan, B and Yeritsyan, B and Adler, DS}, title = {Middle Palaeolithic toolstone procurement behaviors at Lusakert Cave 1, Hrazdan valley, Armenia.}, journal = {Journal of human evolution}, volume = {91}, number = {}, pages = {73-92}, doi = {10.1016/j.jhevol.2015.10.008}, pmid = {26852814}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; Armenia ; Caves ; *Cultural Evolution ; Humans ; Neanderthals ; *Technology ; }, abstract = {Strategies employed by Middle Palaeolithic hominins to acquire lithic raw materials often play key roles in assessing their movements through the landscape, relationships with neighboring groups, and cognitive abilities. It has been argued that a dependence on local resources is a widespread characteristic of the Middle Palaeolithic, but how such behaviors were manifested on the landscape remains unclear. Does an abundance of local toolstone reflect frequent encounters with different outcrops while foraging, or was a particular outcrop favored and preferentially quarried? This study examines such behaviors at a finer geospatial scale than is usually possible, allowing us to investigate hominin movements through the landscape surrounding Lusakert Cave 1 in Armenia. Using our newly developed approach to obsidian magnetic characterization, we test a series of hypotheses regarding the locations where hominins procured toolstone from a volcanic complex adjacent to the site. Our goal is to establish whether the cave's occupants procured local obsidian from preferred outcrops or quarries, secondary deposits of obsidian nodules along a river, or a variety of exposures as encountered while moving through the river valley or across the wider volcanic landscape during the course of foraging activities. As we demonstrate here, it is not the case that one particular outcrop or deposit attracted the cave occupants during the studied time intervals. Nor did they acquire obsidian at random across the landscape. Instead, our analyses support the hypothesis that these hominins collected obsidian from outcrops and exposures throughout the adjacent river valley, reflecting the spatial scale of their day-to-day foraging activities. The coincidence of such behaviors within the resource-rich river valley suggests efficient exploitation of a diverse biome during a time interval immediately preceding the Middle to Upper Palaeolithic "transition," the nature and timing of which has yet to be determined for the region.}, } @article {pmid26852813, year = {2016}, author = {Mounier, A and Mirazón Lahr, M}, title = {Virtual ancestor reconstruction: Revealing the ancestor of modern humans and Neandertals.}, journal = {Journal of human evolution}, volume = {91}, number = {}, pages = {57-72}, doi = {10.1016/j.jhevol.2015.11.002}, pmid = {26852813}, issn = {1095-8606}, mesh = {Animals ; *Biological Evolution ; Fossils/*anatomy & histology ; Hominidae/*anatomy & histology ; Humans ; Imaging, Three-Dimensional ; Likelihood Functions ; Neanderthals/anatomy & histology ; Phylogeny ; Skull/*anatomy & histology ; }, abstract = {The timing and geographic origin of the common ancestor of modern humans and Neandertals remain controversial. A poor Pleistocene hominin fossil record and the evolutionary complexities introduced by dispersals and regionalisation of lineages have fuelled taxonomic uncertainty, while new ancient genomic data have raised completely new questions. Here, we use maximum likelihood and 3D geometric morphometric methods to predict possible morphologies of the last common ancestor of modern humans and Neandertals from a simplified, fully resolved phylogeny. We describe the fully rendered 3D shapes of the predicted ancestors of humans and Neandertals, and assess their similarity to individual fossils or populations of fossils of Pleistocene age. Our results support models of an Afro-European ancestral population in the Middle Pleistocene (Homo heidelbergensis sensu lato) and further predict an African origin for this ancestral population.}, } @article {pmid26852812, year = {2016}, author = {Peresani, M and Cristiani, E and Romandini, M}, title = {The Uluzzian technology of Grotta di Fumane and its implication for reconstructing cultural dynamics in the Middle-Upper Palaeolithic transition of Western Eurasia.}, journal = {Journal of human evolution}, volume = {91}, number = {}, pages = {36-56}, doi = {10.1016/j.jhevol.2015.10.012}, pmid = {26852812}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; *Cultural Evolution ; Fossils ; Humans ; Italy ; *Neanderthals ; *Technology ; }, abstract = {From the intricate ensemble of evidence related to the Middle-Upper Palaeolithic transition and the presumed first spread of anatomically modern humans in Europe, the Uluzzian has attracted major attention in the past few years. Although the Uluzzian has been viewed as a supposed product of modern humans settling in Mediterranean Europe, the techno-cultural complex has been the subject of few investigations aiming to clarify its chronology, bone industry, and settlement dynamics. Further, little is known of its technological structure. This article presents the results of an extensive study of the lithic and bone technologies from assemblages recovered at Fumane Cave in the north of Italy. Results confirm that the Uluzzian is a flake-dominated industry that brings together a set of technological innovations. The Levallois is the most used method in the initial phase, which is replaced by more varied flaking procedures and an increase in bladelets and flake-blades. Sidescrapers and points also represent a Mousterian feature in the initial phase, while splintered pieces, backed knives and other Upper Palaeolithic tools increase in the later phase. Our results suggest that the Uluzzian is rooted in the Mousterian lithic technological context and cannot be viewed as a proxy for anatomically modern humans, the carriers of the abrupt cultural changes related to the Aurignacian.}, } @article {pmid26849112, year = {2016}, author = {Zhao, J and Akinsanmi, I and Arafat, D and Cradick, TJ and Lee, CM and Banskota, S and Marigorta, UM and Bao, G and Gibson, G}, title = {A Burden of Rare Variants Associated with Extremes of Gene Expression in Human Peripheral Blood.}, journal = {American journal of human genetics}, volume = {98}, number = {2}, pages = {299-309}, pmid = {26849112}, issn = {1537-6605}, support = {P01 GM099568/GM/NIGMS NIH HHS/United States ; RC2 MH089915/MH/NIMH NIH HHS/United States ; 1-P01-GM0996568/GM/NIGMS NIH HHS/United States ; RC2MH089915/MH/NIMH NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Female ; *Gene Expression ; Gene Expression Profiling ; Gene Frequency ; Genetic Loci ; Genomics ; Genotyping Techniques ; Haplotypes ; Humans ; Linear Models ; Male ; Middle Aged ; *Polymorphism, Single Nucleotide ; Promoter Regions, Genetic ; Reproducibility of Results ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {In order to evaluate whether rare regulatory variants in the vicinity of promoters are likely to impact gene expression, we conducted a novel burden test for enrichment of rare variants at the extremes of expression. After sequencing 2-kb promoter regions of 472 genes in 410 healthy adults, we performed a quadratic regression of rare variant count on bins of peripheral blood transcript abundance from microarrays, summing over ranks of all genes. After adjusting for common eQTLs and the major axes of gene expression covariance, a highly significant excess of variants with minor allele frequency less than 0.05 at both high and low extremes across individuals was observed. Further enrichment was seen in sites annotated as potentially regulatory by RegulomeDB, but a deficit of effects was associated with known metabolic disease genes. The main result replicates in an independent sample of 75 individuals with RNA-seq and whole-genome sequence information. Three of four predicted large-effect sites were validated by CRISPR/Cas9 knockdown in K562 cells, but simulations indicate that effect sizes need not be unusually large to produce the observed burden. Unusually divergent low-frequency promoter haplotypes were observed at 31 loci, at least 9 of which appear to be derived from Neandertal admixture, but these were not associated with divergent gene expression in blood. The overall burden test results are consistent with rare and private regulatory variants driving high or low transcription at specific loci, potentially contributing to disease.}, } @article {pmid26831111, year = {2016}, author = {Gilpin, W and Feldman, MW and Aoki, K}, title = {An ecocultural model predicts Neanderthal extinction through competition with modern humans.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {8}, pages = {2134-2139}, pmid = {26831111}, issn = {1091-6490}, mesh = {Animals ; Cognition ; Competitive Behavior ; *Cultural Evolution ; Ecosystem ; *Extinction, Biological ; Humans ; Models, Psychological ; Models, Theoretical ; Neanderthals/*physiology/*psychology ; Population Density ; Population Growth ; Species Specificity ; }, abstract = {Archaeologists argue that the replacement of Neanderthals by modern humans was driven by interspecific competition due to a difference in culture level. To assess the cogency of this argument, we construct and analyze an interspecific cultural competition model based on the Lotka-Volterra model, which is widely used in ecology, but which incorporates the culture level of a species as a variable interacting with population size. We investigate the conditions under which a difference in culture level between cognitively equivalent species, or alternatively a difference in underlying learning ability, may produce competitive exclusion of a comparatively (although not absolutely) large local Neanderthal population by an initially smaller modern human population. We find, in particular, that this competitive exclusion is more likely to occur when population growth occurs on a shorter timescale than cultural change, or when the competition coefficients of the Lotka-Volterra model depend on the difference in the culture levels of the interacting species.}, } @article {pmid26826668, year = {2016}, author = {Schaefer, NK and Shapiro, B and Green, RE}, title = {Detecting hybridization using ancient DNA.}, journal = {Molecular ecology}, volume = {25}, number = {11}, pages = {2398-2412}, pmid = {26826668}, issn = {1365-294X}, support = {T32 HG008345/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; *DNA, Ancient ; Fossils ; Gene Flow ; Genomics/*methods ; Hominidae/genetics ; Human Migration ; Humans ; *Hybridization, Genetic ; Models, Genetic ; Models, Statistical ; Neanderthals/genetics ; Sequence Analysis, DNA ; }, abstract = {It is well established that related species hybridize and that this can have varied but significant effects on speciation and environmental adaptation. It should therefore come as no surprise that hybridization is not limited to species that are alive today. In the last several decades, advances in technologies for recovering and sequencing DNA from fossil remains have enabled the assembly of high-coverage genome sequences for a growing diversity of organisms, including many that are extinct. Thanks to the development of new statistical approaches for detecting and quantifying admixture from genomic data, genomes from extinct populations have proven useful both in revealing previously unknown hybridization events and informing the study of hybridization between living organisms. Here, we review some of the key recent statistical innovations for detecting ancient hybridization using genomewide sequence data and discuss how these innovations have revised our understanding of human evolutionary history.}, } @article {pmid26819241, year = {2016}, author = {Hejase, HA and Liu, KJ}, title = {Mapping the genomic architecture of adaptive traits with interspecific introgressive origin: a coalescent-based approach.}, journal = {BMC genomics}, volume = {17 Suppl 1}, number = {}, pages = {8}, pmid = {26819241}, issn = {1471-2164}, mesh = {Algorithms ; Animals ; *Chromosome Mapping ; Genetic Loci ; *Genome ; Genome-Wide Association Study ; Genotype ; Humans ; Mice ; Models, Genetic ; Phenotype ; Polymorphism, Single Nucleotide ; }, abstract = {Recent studies of eukaryotes including human and Neandertal, mice, and butterflies have highlighted the major role that interspecific introgression has played in adaptive trait evolution. A common question arises in each case: what is the genomic architecture of the introgressed traits? One common approach that can be used to address this question is association mapping, which looks for genotypic markers that have significant statistical association with a trait. It is well understood that sample relatedness can be a confounding factor in association mapping studies if not properly accounted for. Introgression and other evolutionary processes (e.g., incomplete lineage sorting) typically introduce variation among local genealogies, which can also differ from global sample structure measured across all genomic loci. In contrast, state-of-the-art association mapping methods assume fixed sample relatedness across the genome, which can lead to spurious inference. We therefore propose a new association mapping method called Coal-Map, which uses coalescent-based models to capture local genealogical variation alongside global sample structure. Using simulated and empirical data reflecting a range of evolutionary scenarios, we compare the performance of Coal-Map against EIGENSTRAT, a leading association mapping method in terms of its popularity, power, and type I error control. Our empirical data makes use of hundreds of mouse genomes for which adaptive interspecific introgression has recently been described. We found that Coal-Map's performance is comparable or better than EIGENSTRAT in terms of statistical power and false positive rate. Coal-Map's performance advantage was greatest on model conditions that most closely resembled empirically observed scenarios of adaptive introgression. These conditions had: (1) causal SNPs contained in one or a few introgressed genomic loci and (2) varying rates of gene flow - from high rates to very low rates where incomplete lineage sorting dominated as a primary cause of local genealogical variation.}, } @article {pmid26808112, year = {2016}, author = {Savova, V and Chun, S and Sohail, M and McCole, RB and Witwicki, R and Gai, L and Lenz, TL and Wu, CT and Sunyaev, SR and Gimelbrant, AA}, title = {Genes with monoallelic expression contribute disproportionately to genetic diversity in humans.}, journal = {Nature genetics}, volume = {48}, number = {3}, pages = {231-237}, pmid = {26808112}, issn = {1546-1718}, support = {R01 GM078598/GM/NIGMS NIH HHS/United States ; R01 GM061936/GM/NIGMS NIH HHS/United States ; DP1 GM106412/GM/NIGMS NIH HHS/United States ; R01 GM114864/GM/NIGMS NIH HHS/United States ; GM105857/GM/NIGMS NIH HHS/United States ; U54 LM008748/LM/NLM NIH HHS/United States ; R01 GM61936/GM/NIGMS NIH HHS/United States ; 5DP1 GM106412/DP/NCCDPHP CDC HHS/United States ; R01 GM105857/GM/NIGMS NIH HHS/United States ; R01 MH101244/MH/NIMH NIH HHS/United States ; MH101244/MH/NIMH NIH HHS/United States ; }, mesh = {Alleles ; Animals ; *Gene Expression Regulation ; *Genetic Variation ; Genetics, Population ; Humans ; Neanderthals/genetics ; Pan troglodytes/genetics ; }, abstract = {An unexpectedly large number of human autosomal genes are subject to monoallelic expression (MAE). Our analysis of 4,227 such genes uncovers surprisingly high genetic variation across human populations. This increased diversity is unlikely to reflect relaxed purifying selection. Remarkably, MAE genes exhibit an elevated recombination rate and an increased density of hypermutable sequence contexts. However, these factors do not fully account for the increased diversity. We find that the elevated nucleotide diversity of MAE genes is also associated with greater allelic age: variants in these genes tend to be older and are enriched in polymorphisms shared by Neanderthals and chimpanzees. Both synonymous and nonsynonymous alleles of MAE genes have elevated average population frequencies. We also observed strong enrichment of the MAE signature among genes reported to evolve under balancing selection. We propose that an important biological function of widespread MAE might be the generation of cell-to-cell heterogeneity; the increased genetic variation contributes to this heterogeneity.}, } @article {pmid26806095, year = {2016}, author = {Uhl, A and Reyes-Centeno, H and Grigorescu, D and Kranioti, EF and Harvati, K}, title = {Inner ear morphology of the cioclovina early modern European calvaria from Romania.}, journal = {American journal of physical anthropology}, volume = {160}, number = {1}, pages = {62-70}, doi = {10.1002/ajpa.22938}, pmid = {26806095}, issn = {1096-8644}, mesh = {Anthropology, Physical ; Ear, Inner/*anatomy & histology ; Female ; Humans ; Male ; Principal Component Analysis ; Romania ; Skull/*anatomy & histology ; }, abstract = {OBJECTIVES: The morphology of the human bony labyrinth is thought to preserve a strong phylogenetic signal and to be minimally, if at all, affected by postnatal processes. The form of the semicircular canals is considered a derived feature of Neanderthals and different from the modern human anatomy. Among other hominins, European Middle Pleistocene humans have been found to be most similar to Neanderthals. Early modern humans have been proposed to show a pattern that is distinct, but most similar to that of Holocene people. Here we examine the inner ear structures of the Cioclovina calvaria, one of the earliest reliably dated and relatively complete modern human crania from Europe, in the context of recent and fossil human variation.

MATERIALS AND METHODS: Bony labyrinths were virtually extracted from CT scans of recent Europeans and Cioclovina. Using univariate and multivariate methods, measurements of the semicircular canals were compared with published measurements of other fossil specimens.

RESULTS: Our results show that Cioclovina's inner ear morphology falls within the range of modern variation, with affinities to both Late Pleistocene modern humans and recent Europeans. Using discriminant functions, the sex of the Cioclovina specimen is estimated as male.

DISCUSSION: Results agree with previous work showing that Cioclovina exhibits fully modern cranial morphology.}, } @article {pmid26800015, year = {2016}, author = {Pampush, JD and Daegling, DJ}, title = {The enduring puzzle of the human chin.}, journal = {Evolutionary anthropology}, volume = {25}, number = {1}, pages = {20-35}, doi = {10.1002/evan.21471}, pmid = {26800015}, issn = {1520-6505}, mesh = {Adult ; Animals ; Anthropology, Physical ; Chin/*anatomy & histology/*physiology ; Female ; Hominidae/*anatomy & histology/*physiology ; Humans ; Male ; Marriage ; Neanderthals/anatomy & histology/physiology ; Speech ; }, abstract = {Although modern humans are considered to be morphologically distinct from other living primates because of our large brains, dexterous hands, and bipedal gait, all of these features are found among extinct hominins. The chin, however, appears to be a uniquely modern human trait. Probably because of the chin's exclusivity, many evolutionary scenarios have been proposed to explain its origins. To date, researchers have developed adaptive hypotheses relating chins to speech, mastication, and sexual selection; still others see it as a structural artifact tangentially related to complex processes involving evolutionary retraction of the midfacial skeleton. Consensus has remained elusive, partly because hypotheses purporting to explain how this feature developed uniquely in modern humans are all fraught with theoretical and/or empirical shortcomings. Here we review a century's worth of chin hypotheses and discuss future research avenues that may provide greater insight into this human peculiarity.}, } @article {pmid26767960, year = {2016}, author = {Rodríguez, L and Carretero, JM and García-González, R and Lorenzo, C and Gómez-Olivencia, A and Quam, R and Martínez, I and Gracia-Téllez, A and Arsuaga, JL}, title = {Fossil hominin radii from the Sima de los Huesos Middle Pleistocene site (Sierra de Atapuerca, Spain).}, journal = {Journal of human evolution}, volume = {90}, number = {}, pages = {55-73}, doi = {10.1016/j.jhevol.2015.09.010}, pmid = {26767960}, issn = {1095-8606}, mesh = {Anatomy, Cross-Sectional ; Animals ; Anthropology, Physical ; Female ; Fossils ; Hominidae/*anatomy & histology ; Humans ; Male ; Radius/*anatomy & histology/diagnostic imaging ; Spain ; Tomography, X-Ray Computed ; }, abstract = {Complete radii in the fossil record preceding recent humans and Neandertals are very scarce. Here we introduce the radial remains recovered from the Sima de los Huesos (SH) site in the Sierra de Atapuerca between 1976 and 2011 and which have been dated in excess of 430 ky (thousands of years) ago. The sample comprises 89 specimens, 49 of which are attributed to adults representing a minimum of seven individuals. All elements are described anatomically and metrically, and compared with other fossil hominins and recent humans in order to examine the phylogenetic polarity of certain radial features. Radial remains from SH have some traits that differentiate them from those of recent humans and make them more similar to Neandertals, including strongly curved shafts, anteroposterior expanded radial heads and both absolutely and relatively long necks. In contrast, the SH sample differs from Neandertals in showing a high overall gracility as well as a high frequency (80%) of an anteriorly oriented radial tuberosity. Thus, like the cranial and dental remains from the SH site, characteristic Neandertal radial morphology is not present fully in the SH radii. We also analyzed the cross-sectional properties of the SH radial sample at two different levels: mid-shaft and at the midpoint of the neck length. When standardized by shaft length, no difference in the mid-shaft cross-sectional properties were found between the SH hominins, Neandertals and recent humans. Nevertheless, due to their long neck length, the SH hominins show a higher lever efficiency than either Neandertals or recent humans. Functionally, the SH radial morphology is consistent with more efficient pronation-supination and flexion-extension movements. The particular trait composition in the SH sample and Neandertals resembles more closely morphology evident in recent human males.}, } @article {pmid26767955, year = {2016}, author = {Quam, R and Lorenzo, C and Martínez, I and Gracia-Téllez, A and Arsuaga, JL}, title = {The bony labyrinth of the middle Pleistocene Sima de los Huesos hominins (Sierra de Atapuerca, Spain).}, journal = {Journal of human evolution}, volume = {90}, number = {}, pages = {1-15}, doi = {10.1016/j.jhevol.2015.09.007}, pmid = {26767955}, issn = {1095-8606}, mesh = {Animals ; Anthropology, Physical ; Ear, Inner/*anatomy & histology ; Fossils ; Humans ; Neanderthals/*anatomy & histology ; Spain ; }, abstract = {We performed 3D virtual reconstructions based on CT scans to study the bony labyrinth morphology in 14 individuals from the large middle Pleistocene hominin sample from the site of the Sima de los Huesos (SH) in the Sierra de Atapuerca in northern Spain. The Atapuerca (SH) hominins represent early members of the Neandertal clade and provide an opportunity to compare the data with the later in time Neandertals, as well as Pleistocene and recent humans more broadly. The Atapuerca (SH) hominins do not differ from the Neandertals in any of the variables related to the absolute and relative sizes and shape of the semicircular canals. Indeed, the entire Neandertal clade seems to be characterized by a derived pattern of canal proportions, including a relatively small posterior canal and a relatively large lateral canal. In contrast, one of the most distinctive features observed in Neandertals, the low placement of the posterior canal (i.e., high sagittal labyrinthine index), is generally not present in the Atapuerca (SH) hominins. This low placement is considered a derived feature in Neandertals and is correlated with a more vertical orientation of the ampullar line (LSCm < APA), posterior surface of the petrous pyramid (LSCm > PPp), and third part of the facial canal (LSCm < FC3). Some variation is present within the Atapuerca (SH) sample, however, with a few individuals approaching the Neandertal condition more closely. In addition, the cochlear shape index in the Atapuerca (SH) hominins is low, indicating a reduction in the height of the cochlea. Although the phylogenetic polarity of this feature is less clear, the low shape index in the Atapuerca (SH) hominins may be a derived feature. Regardless, cochlear height subsequently increased in Neandertals. In contrast to previous suggestions, the expanded data in the present study indicate no difference across the genus Homo in the angle of inclination of the cochlear basal turn (COs < LSCm). Principal components analysis largely confirms these observations. While not fully resolved, the low placement of the posterior canal in Neandertals may be related to some combination of absolutely large brain size, a wide cranial base, and an archaic pattern of brain allometry. This more general explanation would not necessarily follow taxonomic lines, even though this morphology of the bony labyrinth occurs at high frequencies among Neandertals. While a functional interpretation of the relatively small vertical canals in the Neandertal clade remains elusive, the relative proportions of the semicircular canals is one of several derived Neandertal features in the Atapuerca (SH) crania. Examination of additional European middle Pleistocene specimens suggests that the full suite of Neandertal features in the bony labyrinth did not emerge in Europe until perhaps <200 kya.}, } @article {pmid26748764, year = {2016}, author = {Williams, FL and Cofran, Z}, title = {Postnatal craniofacial ontogeny in neandertals and modern humans.}, journal = {American journal of physical anthropology}, volume = {159}, number = {3}, pages = {394-409}, doi = {10.1002/ajpa.22895}, pmid = {26748764}, issn = {1096-8644}, mesh = {Adult ; Animals ; Anthropology, Physical ; Anthropometry ; Child ; *Fossils ; Humans ; Mandible/*anatomy & histology ; Neanderthals ; Skull/*anatomy & histology ; }, abstract = {OBJECTIVES: Neandertals and humans are closely related but differ noticeably in adult morphology. Previous work has been equivocal as to the contribution of postnatal growth and development to these differences. Due to disparate preservation, most analyses focus on specific anatomies, reconstructed fossils, or limited sample sizes. The objective of this research is to highlight the importance of postnatal growth in expressing Neandertal-human distinctions in the craniofacial skeleton, using a large and unreconstructed Neandertal sample.

MATERIALS/METHODS: A resampling approach is utilized to compare relative size change in 20 craniofacial dimensions between Neandertals (n = 42) and humans (n = 262). The large number of immature Neandertal samples within and between dental stages provides the necessary variation to test for growth differences. Nested resampling using human-human comparisons assesses the likelihood of observing human-Neandertal growth differences under the null hypothesis of similar ontogenetic variation.

RESULTS: Humans and Neandertals undergo comparable levels of overall size change. However, we identify growth differences for a number of traits, helping explain some of the unique features of this fossil taxon. Nested resampling shows it is unlikely that a Neandertal-like maturation would be observed in a random ontogenetic sample of humans.

DISCUSSION: Growth during adolescence appears to be fundamental in the expression of some Neandertal anatomies. Neandertal upper facial and nasal breadths appear to have expanded rapidly after puberty to account for differences between preadolescents and adults, and Neandertals and humans. Mandibular growth differences may relate to anterior tooth use to process foods and paramastication during Neandertal maturation.}, } @article {pmid26748514, year = {2016}, author = {Dannemann, M and Andrés, AM and Kelso, J}, title = {Introgression of Neandertal- and Denisovan-like Haplotypes Contributes to Adaptive Variation in Human Toll-like Receptors.}, journal = {American journal of human genetics}, volume = {98}, number = {1}, pages = {22-33}, pmid = {26748514}, issn = {1537-6605}, mesh = {Adaptation, Physiological/*genetics ; Animals ; Cell Line ; *Haplotypes ; Humans ; Neanderthals/*genetics ; Polymorphism, Single Nucleotide ; Toll-Like Receptors/*genetics ; }, abstract = {Pathogens and the diseases they cause have been among the most important selective forces experienced by humans during their evolutionary history. Although adaptive alleles generally arise by mutation, introgression can also be a valuable source of beneficial alleles. Archaic humans, who lived in Europe and Western Asia for more than 200,000 years, were probably well adapted to this environment and its local pathogens. It is therefore conceivable that modern humans entering Europe and Western Asia who admixed with them obtained a substantial immune advantage from the introgression of archaic alleles. Here we document a cluster of three Toll-like receptors (TLR6-TLR1-TLR10) in modern humans that carries three distinct archaic haplotypes, indicating repeated introgression from archaic humans. Two of these haplotypes are most similar to the Neandertal genome, and the third haplotype is most similar to the Denisovan genome. The Toll-like receptors are key components of innate immunity and provide an important first line of immune defense against bacteria, fungi, and parasites. The unusually high allele frequencies and unexpected levels of population differentiation indicate that there has been local positive selection on multiple haplotypes at this locus. We show that the introgressed alleles have clear functional effects in modern humans; archaic-like alleles underlie differences in the expression of the TLR genes and are associated with increased [corrected] microbial resistance and increased allergic disease in large cohorts. This provides strong evidence for recurrent adaptive introgression at the TLR6-TLR1-TLR10 locus, resulting in differences in disease phenotypes in modern humans.}, } @article {pmid26748513, year = {2016}, author = {Deschamps, M and Laval, G and Fagny, M and Itan, Y and Abel, L and Casanova, JL and Patin, E and Quintana-Murci, L}, title = {Genomic Signatures of Selective Pressures and Introgression from Archaic Hominins at Human Innate Immunity Genes.}, journal = {American journal of human genetics}, volume = {98}, number = {1}, pages = {5-21}, pmid = {26748513}, issn = {1537-6605}, mesh = {Adaptation, Physiological/genetics ; Animals ; Genome-Wide Association Study ; Humans ; Immunity, Innate/*genetics ; Neanderthals/genetics/*immunology ; Polymorphism, Single Nucleotide ; Selection, Genetic ; }, abstract = {Human genes governing innate immunity provide a valuable tool for the study of the selective pressure imposed by microorganisms on host genomes. A comprehensive, genome-wide study of how selective constraints and adaptations have driven the evolution of innate immunity genes is missing. Using full-genome sequence variation from the 1000 Genomes Project, we first show that innate immunity genes have globally evolved under stronger purifying selection than the remainder of protein-coding genes. We identify a gene set under the strongest selective constraints, mutations in which are likely to predispose individuals to life-threatening disease, as illustrated by STAT1 and TRAF3. We then evaluate the occurrence of local adaptation and detect 57 high-scoring signals of positive selection at innate immunity genes, variation in which has been associated with susceptibility to common infectious or autoimmune diseases. Furthermore, we show that most adaptations targeting coding variation have occurred in the last 6,000-13,000 years, the period at which populations shifted from hunting and gathering to farming. Finally, we show that innate immunity genes present higher Neandertal introgression than the remainder of the coding genome. Notably, among the genes presenting the highest Neandertal ancestry, we find the TLR6-TLR1-TLR10 cluster, which also contains functional adaptive variation in Europeans. This study identifies highly constrained genes that fulfill essential, non-redundant functions in host survival and reveals others that are more permissive to change-containing variation acquired from archaic hominins or adaptive variants in specific populations-improving our understanding of the relative biological importance of innate immunity pathways in natural conditions.}, } @article {pmid26738254, year = {2015}, author = {Magherini, S and Fiore, MG and Chiarelli, B and Serrao, A and Paternostro, F and Morucci, G and Branca, JJ and Ruggiero, M and Pacini, S}, title = {Metopic suture and RUNX2, a key transcription factor in osseous morphogenesis with possible important implications for human brain evolution.}, journal = {Italian journal of anatomy and embryology = Archivio italiano di anatomia ed embriologia}, volume = {120}, number = {1}, pages = {5-20}, pmid = {26738254}, issn = {1122-6714}, mesh = {Amino Acid Sequence ; Animals ; Brain/*embryology ; Core Binding Factor Alpha 1 Subunit/chemistry/*genetics ; Cranial Sutures/*embryology ; Humans ; Molecular Sequence Data ; Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: Overall, the comparative data available on the timing of metopic suture closure in present-day and fossil members of human lineage, as well as great apes, seem to indicate that human brain evolution occurred within a complex network of fetopelvic constraints, which required modification of frontal neurocranial ossification patterns, involving delayed fusion of the metopic suture. It is very interesting that the recent sequencing of the Neanderthal genome has revealed signs of positive selection in the modern human variant of the RUNX2 gene, which is known to affect metopic suture fusion in addition to being essential for osteoblast development and proper bone formation. It is possible that an evolutionary change in RUNX2, affecting aspects of the morphology of the upper body and cranium, was of importance in the origin of modern humans. Thus, to contribute to a better understanding of the molecular evolution of this gene probably implicated in human evolution, we performed a comparative bioinformatic analysis of the coding sequences of RUNX2 in Homo sapiens and other non-human Primates.

RESULTS: We found amino-acid sequence differences between RUNX2 protein isoforms of Homo sapiens and the other Primates examined, that might have important implications for the timing of metopic suture closure.

CONCLUSIONS: Further studies are needed to clear the potential distinct developmental roles of different species-specific RUNX2 N-terminal isoforms. Meantime, our bioinformatic analysis, regarding expression of the RUNX2 gene in Homo sapiens and other non-human Primates, has provided a contribution to this important issue of human evolution.}, } @article {pmid26728717, year = {2016}, author = {Rodriguez-Flores, JL and Fakhro, K and Agosto-Perez, F and Ramstetter, MD and Arbiza, L and Vincent, TL and Robay, A and Malek, JA and Suhre, K and Chouchane, L and Badii, R and Al-Nabet Al-Marri, A and Abi Khalil, C and Zirie, M and Jayyousi, A and Salit, J and Keinan, A and Clark, AG and Crystal, RG and Mezey, JG}, title = {Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations.}, journal = {Genome research}, volume = {26}, number = {2}, pages = {151-162}, pmid = {26728717}, issn = {1549-5469}, mesh = {African Continental Ancestry Group/*genetics ; Animals ; Arabs/*genetics ; Cluster Analysis ; DNA, Mitochondrial/genetics ; European Continental Ancestry Group/*genetics ; Gene Frequency ; *Human Migration ; Humans ; Hybridization, Genetic ; Markov Chains ; Models, Genetic ; Neanderthals/*genetics ; Phylogeny ; Principal Component Analysis ; Qatar ; Sequence Analysis, DNA ; }, abstract = {An open question in the history of human migration is the identity of the earliest Eurasian populations that have left contemporary descendants. The Arabian Peninsula was the initial site of the out-of-Africa migrations that occurred between 125,000 and 60,000 yr ago, leading to the hypothesis that the first Eurasian populations were established on the Peninsula and that contemporary indigenous Arabs are direct descendants of these ancient peoples. To assess this hypothesis, we sequenced the entire genomes of 104 unrelated natives of the Arabian Peninsula at high coverage, including 56 of indigenous Arab ancestry. The indigenous Arab genomes defined a cluster distinct from other ancestral groups, and these genomes showed clear hallmarks of an ancient out-of-Africa bottleneck. Similar to other Middle Eastern populations, the indigenous Arabs had higher levels of Neanderthal admixture compared to Africans but had lower levels than Europeans and Asians. These levels of Neanderthal admixture are consistent with an early divergence of Arab ancestors after the out-of-Africa bottleneck but before the major Neanderthal admixture events in Europe and other regions of Eurasia. When compared to worldwide populations sampled in the 1000 Genomes Project, although the indigenous Arabs had a signal of admixture with Europeans, they clustered in a basal, outgroup position to all 1000 Genomes non-Africans when considering pairwise similarity across the entire genome. These results place indigenous Arabs as the most distant relatives of all other contemporary non-Africans and identify these people as direct descendants of the first Eurasian populations established by the out-of-Africa migrations.}, } @article {pmid26725403, year = {2016}, author = {Janković, I and Ahern, JC and Smith, FH}, title = {On some aspects of Neandertal zygomatic morphology.}, journal = {Homo : internationale Zeitschrift fur die vergleichende Forschung am Menschen}, volume = {67}, number = {2}, pages = {89-99}, doi = {10.1016/j.jchb.2015.12.001}, pmid = {26725403}, issn = {1618-1301}, mesh = {Animals ; Anthropology, Physical ; Biological Evolution ; Europe ; Face/anatomy & histology ; Fossils ; Humans ; Neanderthals/*anatomy & histology ; Paleontology ; Zygoma/*anatomy & histology ; }, abstract = {Neandertals are characterized by a series of well-documented facial characteristics, including midfacial prognathism, large nasal and orbital areas, and a marked supraorbital torus. We provide a comparative morphometric study of another part of this facial complex, the frontal process of the zygomatic. We find that European Neandertals have a distinctly columnar form of the frontal process not found in recent modern humans and most Pleistocene modern humans. Some purportedly modern specimens and specimens pre-dating Neandertals exhibit the same pattern as European Neandertals, while others exhibit the modern human pattern. The columnar form is likely a retention of the ancestral state in Neandertals and the other late Pleistocene specimens that exhibit it, but variation in the pattern seen in early modern humans reveals possible insights into late Pleistocene human evolution.}, } @article {pmid26708102, year = {2016}, author = {Wynn, T and Overmann, K and Coolidge, F}, title = {The false dichotomy: a refutation of the Neandertal indistinguishability claim.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {94}, number = {}, pages = {201-221}, doi = {10.4436/JASS.94022}, pmid = {26708102}, issn = {2037-0644}, mesh = {Animals ; Archaeology ; *Biological Evolution ; *Fossils ; Hominidae ; Humans ; Neanderthals/*anatomy & histology ; *Selection, Genetic ; Skull/anatomy & histology ; }, abstract = {In the debate about the demise of the Neandertal, several scholars have claimed that humanity's nearest relatives were indistinguishable archaeologically, and thus behaviorally and cognitively, from contemporaneous Homo sapiens. They suggest that to hold otherwise is to characterize Neandertals as inferior to H. sapiens, a false dichotomy that excludes the possibility that the two human types simply differed in ways visible to natural selection, including their cognition. Support of the Neandertal indistinguishability claim requires ignoring the cranial differences between the two human types, which have implications for cognition and behavior. Further, support of the claim requires minimizing asymmetries in the quantity and degree of behavioral differences as attested by the archaeological record. The present paper reviews the evidence for cognitive and archaeological differences between the two human types in support of the excluded middle position.}, } @article {pmid26696916, year = {2015}, author = {Irurtzun, A}, title = {The "Globularization Hypothesis" of the Language-ready Brain as a Developmental Frame for Prosodic Bootstrapping Theories of Language Acquisition.}, journal = {Frontiers in psychology}, volume = {6}, number = {}, pages = {1817}, pmid = {26696916}, issn = {1664-1078}, abstract = {In recent research (Boeckx and Benítez-Burraco, 2014a,b) have advanced the hypothesis that our species-specific language-ready brain should be understood as the outcome of developmental changes that occurred in our species after the split from Neanderthals-Denisovans, which resulted in a more globular braincase configuration in comparison to our closest relatives, who had elongated endocasts. According to these authors, the development of a globular brain is an essential ingredient for the language faculty and in particular, it is the centrality occupied by the thalamus in a globular brain that allows its modulatory or regulatory role, essential for syntactico-semantic computations. Their hypothesis is that the syntactico-semantic capacities arise in humans as a consequence of a process of globularization, which significantly takes place postnatally (cf. Neubauer et al., 2010). In this paper, I show that Boeckx and Benítez-Burraco's hypothesis makes an interesting developmental prediction regarding the path of language acquisition: it teases apart the onset of phonological acquisition and the onset of syntactic acquisition (the latter starting significantly later, after globularization). I argue that this hypothesis provides a developmental rationale for the prosodic bootstrapping hypothesis of language acquisition (cf. i.a. Gleitman and Wanner, 1982; Mehler et al., 1988, et seq.; Gervain and Werker, 2013), which claim that prosodic cues are employed for syntactic parsing. The literature converges in the observation that a large amount of such prosodic cues (in particular, rhythmic cues) are already acquired before the completion of the globularization phase, which paves the way for the premises of the prosodic bootstrapping hypothesis, allowing babies to have a rich knowledge of the prosody of their target language before they can start parsing the primary linguistic data syntactically.}, } @article {pmid26681495, year = {2016}, author = {Srinivasan, S and Bettella, F and Mattingsdal, M and Wang, Y and Witoelar, A and Schork, AJ and Thompson, WK and Zuber, V and , and Winsvold, BS and Zwart, JA and Collier, DA and Desikan, RS and Melle, I and Werge, T and Dale, AM and Djurovic, S and Andreassen, OA}, title = {Genetic Markers of Human Evolution Are Enriched in Schizophrenia.}, journal = {Biological psychiatry}, volume = {80}, number = {4}, pages = {284-292}, pmid = {26681495}, issn = {1873-2402}, support = {R01 GM104400/GM/NIGMS NIH HHS/United States ; U24 AG021886/AG/NIA NIH HHS/United States ; U01 AG032984/AG/NIA NIH HHS/United States ; U01 AG016976/AG/NIA NIH HHS/United States ; R01 HL105756/HL/NHLBI NIH HHS/United States ; R01 AG033193/AG/NIA NIH HHS/United States ; U01 MH109514/MH/NIMH NIH HHS/United States ; K24 DK002800/DK/NIDDK NIH HHS/United States ; }, mesh = {*Biological Evolution ; Brain/metabolism ; Genetic Markers/*genetics ; Genetic Predisposition to Disease/*genetics ; Genome-Wide Association Study ; Humans ; Multifactorial Inheritance/genetics ; Polymorphism, Single Nucleotide/*genetics ; Schizophrenia/*genetics/pathology ; }, abstract = {BACKGROUND: Why schizophrenia has accompanied humans throughout our history despite its negative effect on fitness remains an evolutionary enigma. It is proposed that schizophrenia is a by-product of the complex evolution of the human brain and a compromise for humans' language, creative thinking, and cognitive abilities.

METHODS: We analyzed recent large genome-wide association studies of schizophrenia and a range of other human phenotypes (anthropometric measures, cardiovascular disease risk factors, immune-mediated diseases) using a statistical framework that draws on polygenic architecture and ancillary information on genetic variants. We used information from the evolutionary proxy measure called the Neanderthal selective sweep (NSS) score.

RESULTS: Gene loci associated with schizophrenia are significantly (p = 7.30 × 10(-9)) more prevalent in genomic regions that are likely to have undergone recent positive selection in humans (i.e., with a low NSS score). Variants in brain-related genes with a low NSS score confer significantly higher susceptibility than variants in other brain-related genes. The enrichment is strongest for schizophrenia, but we cannot rule out enrichment for other phenotypes. The false discovery rate conditional on the evolutionary proxy points to 27 candidate schizophrenia susceptibility loci, 12 of which are associated with schizophrenia and other psychiatric disorders or linked to brain development.

CONCLUSIONS: Our results suggest that there is a polygenic overlap between schizophrenia and NSS score, a marker of human evolution, which is in line with the hypothesis that the persistence of schizophrenia is related to the evolutionary process of becoming human.}, } @article {pmid26668361, year = {2015}, author = {Stringer, CB and Barnes, I}, title = {Deciphering the Denisovans.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {51}, pages = {15542-15543}, pmid = {26668361}, issn = {1091-6490}, mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*chemistry ; Neanderthals/*genetics ; }, } @article {pmid26667578, year = {2016}, author = {Bermúdez de Castro, JM and Martín-Francés, L and Modesto-Mata, M and Martínez de Pinillos, M and Martinón-Torres, M and García-Campos, C and Carretero, JM}, title = {Virtual reconstruction of the Early Pleistocene mandible ATD6-96 from Gran Dolina-TD6-2 (Sierra De Atapuerca, Spain).}, journal = {American journal of physical anthropology}, volume = {159}, number = {4}, pages = {729-736}, doi = {10.1002/ajpa.22919}, pmid = {26667578}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; Caves ; Female ; Fossils ; Hominidae/*anatomy & histology ; Mandible/*anatomy & histology ; Spain ; Tooth/anatomy & histology ; }, abstract = {OBJECTIVES: In this report, we present a further study of the late Early Pleistocene ATD6-96 human mandible, recovered from the TD6-2 level of the Gran Dolina cave site (Sierra de Atapuerca, northern Spain) and attributed to Homo antecessor.

METHODS: ATD6-96 consists of a left half of a gracile mandible of an adult individual with the premolars and molars in place that is broken at the level of the lateral incisor-canine septum. The present analysis is based on a virtual reconstruction of the whole mandible by means of computed tomography (CT). We have reconstructed the symphysis using information from a modern human sample, as well as from a wide sample composed of several Homo specimens.

RESULTS: This research has allowed us to record new variables with taxonomic and phylogenetic interest. We have estimated the length/width index of the alveolar arcade, as well as the percentage of the arcade length with regard to the total length. The latter confirms that ATD6-96 shares with all African and Asian Homo species a primitive structural pattern, as it was established in previous studies. In constrast, the length/width index of the alveolar arcade in the H. antecessor specimen is close to the mean values of Neandertals and the Atapuerca-Sima de los Huesos hominins.

CONCLUSIONS: H. antecessor is derived regarding the shape of the mandibular alveolar arcade within the genus Homo and points to an early divergence from contemporaneous African populations. Our results also ratify the affinities of H. antecessor with Neanderthals, although the precise relationship with this lineage needs further research.}, } @article {pmid26653207, year = {2015}, author = {Conard, NJ and Serangeli, J and Böhner, U and Starkovich, BM and Miller, CE and Urban, B and Van Kolfschoten, T}, title = {Excavations at Schöningen and paradigm shifts in human evolution.}, journal = {Journal of human evolution}, volume = {89}, number = {}, pages = {1-17}, doi = {10.1016/j.jhevol.2015.10.003}, pmid = {26653207}, issn = {1095-8606}, mesh = {Animals ; *Archaeology ; *Biological Evolution ; Chronology as Topic ; Diet ; Fires ; Germany ; *Hominidae ; Humans ; Social Behavior ; *Tool Use Behavior ; }, abstract = {The exceptional preservation at Schöningen together with a mixture of perseverance, hard work, and sheer luck led to the recovery of unique finds in an exceptional context. The 1995 discovery of numerous wooden artifacts, most notably at least 10 carefully made spears together with the skeletons of at least 20 to 25 butchered horses, brought the debate about hunting versus scavenging among late archaic hominins and analogous arguments about the purportedly primitive behavior of Homo heidelbergensis and Neanderthals to an end. Work under H. Thieme's lead from 1992 to 2008 and results from the current team since 2008 demonstrate that late H. heidelbergensis or early Neanderthals used sophisticated artifacts made from floral and faunal materials, in addition to lithic artifacts more typically recovered at Lower Paleolithic sites. The finds from the famous Horse Butchery Site and two dozen other archaeological horizons from the edges of the open-cast mine at Schöningen provide many new insights into the technology and behavioral patterns of hominins about 300 ka BP during MIS 9 on the Northern European Plain. An analysis of the finds from Schöningen and their contexts shows that the inhabitants of the site were skilled hunters at the top of the food chain and exhibited a high level of planning depth. These hominins had command of effective means of communication about the here and now, and the past and the future, that allowed them to repeatedly execute well-coordinated and successful group activities that likely culminated in a division of labor and social and economic patterns radically different from those of all non-human primates. The unique preservation and high quality excavations have led to a major paradigm shift or "Schöningen Effect" that changed our views of human evolution during the late Lower Paleolithic. In this respect, we can view the behaviors documented at Schöningen as a plausible baseline for the behavioral sophistication of archaic hominins of the late Middle Pleistocene and subsequent periods.}, } @article {pmid26639346, year = {2015}, author = {Lacruz, RS and Bromage, TG and O'Higgins, P and Arsuaga, JL and Stringer, C and Godinho, RM and Warshaw, J and Martínez, I and Gracia-Tellez, A and de Castro, JM and Carbonell, E}, title = {Ontogeny of the maxilla in Neanderthals and their ancestors.}, journal = {Nature communications}, volume = {6}, number = {}, pages = {8996}, pmid = {26639346}, issn = {2041-1723}, support = {K99 DE022799/DE/NIDCR NIH HHS/United States ; R00 DE022799/DE/NIDCR NIH HHS/United States ; }, mesh = {Animals ; Child ; Fossils/anatomy & histology ; Hominidae/anatomy & histology/*growth & development ; Humans ; Male ; Maxilla/anatomy & histology/*growth & development ; Neanderthals ; }, abstract = {Neanderthals had large and projecting (prognathic) faces similar to those of their putative ancestors from Sima de los Huesos (SH) and different from the retracted modern human face. When such differences arose during development and the morphogenetic modifications involved are unknown. We show that maxillary growth remodelling (bone formation and resorption) of the Devil's Tower (Gibraltar 2) and La Quina 18 Neanderthals and four SH hominins, all sub-adults, show extensive bone deposition, whereas in modern humans extensive osteoclastic bone resorption is found in the same regions. This morphogenetic difference is evident by ∼5 years of age. Modern human faces are distinct from those of the Neanderthal and SH fossils in part because their postnatal growth processes differ markedly. The growth remodelling identified in these fossil hominins is shared with Australopithecus and early Homo but not with modern humans suggesting that the modern human face is developmentally derived.}, } @article {pmid26635833, year = {2015}, author = {Mikić, AM}, title = {The First Attested Extraction of Ancient DNA in Legumes (Fabaceae).}, journal = {Frontiers in plant science}, volume = {6}, number = {}, pages = {1006}, pmid = {26635833}, issn = {1664-462X}, abstract = {Ancient DNA (aDNA) is any DNA extracted from ancient specimens, important for diverse evolutionary researches. The major obstacles in aDNA studies are mutations, contamination and fragmentation. Its studies may be crucial for crop history if integrated with human aDNA research and historical linguistics, both general and relating to agriculture. Legumes (Fabaceae) are one of the richest end economically most important plant families, not only from Neolithic onwards, since they were used as food by Neanderthals and Paleolithic modern man. The idea of extracting and analyzing legume aDNA was considered beneficial for both basic science and applied research, with an emphasis on genetic resources and plant breeding. The first reported successful and attested extraction of the legume aDNA was done from the sample of charred seeds of pea (Pisum sativum) and bitter vetch (Vicia ervilia) from Hissar, southeast Serbia, dated to 1,350-1,000 Before Christ. A modified version of cetyltrimethylammonium bromide (CTAB) method and the commercial kit for DNA extraction QIAGEN DNAesy yielded several ng μl(-1) of aDNA of both species and, after the whole genome amplification and with a fragment of nuclear ribosomal DNA gene 26S rDNA, resulted in the detection of the aDNA among the PCR products. A comparative analysis of four informative chloroplast DNA regions (trnSG, trnK, matK, and rbcL) among the modern wild and cultivated pea taxa demonstrated not only that the extracted aDNA was genuine, on the basis of mutation rate, but also that the ancient Hissar pea was most likely an early domesticated crop, related to the modern wild pea of a neighboring region. It is anticipated that this premier extraction of legume aDNA may provide taxonomists with the answers to diverse questions, such as leaf development in legumes, as well as with novel data on the single steps in domesticating legume crops worldwide.}, } @article {pmid26635694, year = {2015}, author = {Hillert, DG}, title = {On the Evolving Biology of Language.}, journal = {Frontiers in psychology}, volume = {6}, number = {}, pages = {1796}, pmid = {26635694}, issn = {1664-1078}, } @article {pmid26630009, year = {2015}, author = {Sawyer, S and Renaud, G and Viola, B and Hublin, JJ and Gansauge, MT and Shunkov, MV and Derevianko, AP and Prüfer, K and Kelso, J and Pääbo, S}, title = {Nuclear and mitochondrial DNA sequences from two Denisovan individuals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {51}, pages = {15696-15700}, pmid = {26630009}, issn = {1091-6490}, mesh = {Animals ; Base Sequence ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*chemistry ; Evolution, Molecular ; Molecular Sequence Data ; Neanderthals/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Denisovans, a sister group of Neandertals, have been described on the basis of a nuclear genome sequence from a finger phalanx (Denisova 3) found in Denisova Cave in the Altai Mountains. The only other Denisovan specimen described to date is a molar (Denisova 4) found at the same site. This tooth carries a mtDNA sequence similar to that of Denisova 3. Here we present nuclear DNA sequences from Denisova 4 and a morphological description, as well as mitochondrial and nuclear DNA sequence data, from another molar (Denisova 8) found in Denisova Cave in 2010. This new molar is similar to Denisova 4 in being very large and lacking traits typical of Neandertals and modern humans. Nuclear DNA sequences from the two molars form a clade with Denisova 3. The mtDNA of Denisova 8 is more diverged and has accumulated fewer substitutions than the mtDNAs of the other two specimens, suggesting Denisovans were present in the region over an extended period. The nuclear DNA sequence diversity among the three Denisovans is comparable to that among six Neandertals, but lower than that among present-day humans.}, } @article {pmid26603101, year = {2016}, author = {Beals, ME and Frayer, DW and Radovčić, J and Hill, CA}, title = {Cochlear labyrinth volume in Krapina Neandertals.}, journal = {Journal of human evolution}, volume = {90}, number = {}, pages = {176-182}, doi = {10.1016/j.jhevol.2015.09.005}, pmid = {26603101}, issn = {1095-8606}, mesh = {Animals ; Anthropology, Physical ; Cochlea/*anatomy & histology ; *Fossils ; Neanderthals/*anatomy & histology ; Tomography, X-Ray Computed ; }, abstract = {Research with extant primate taxa suggests that cochlear labyrinth volume is functionally related to the range of audible frequencies. Specifically, cochlear volume is negatively correlated with both the high and low frequency limits of hearing so that the smaller the cochlea, the higher the normal range of audible frequencies. The close anatomical relationship between the membranous cochlea and the bony cochlear labyrinth allows for the determination of cochlear size from fossil specimens. This study compares Krapina Neandertal cochlear volumes to extant taxa cochlear volumes. Cochlear volumes were acquired from high-resolution computed tomography scans of temporal bones of Krapina Neandertals, chimpanzees, gorillas, and modern humans. We find that Krapina Neandertals' cochlear volumes are similar to modern Homo sapiens and are significantly larger than chimpanzee and gorilla cochlear volumes. The measured cochlear volume in Krapina Neandertals suggests they had a range of audible frequencies similar to the modern human range.}, } @article {pmid26596347, year = {2016}, author = {Racimo, F}, title = {Testing for Ancient Selection Using Cross-population Allele Frequency Differentiation.}, journal = {Genetics}, volume = {202}, number = {2}, pages = {733-750}, pmid = {26596347}, issn = {1943-2631}, support = {R01 GM040282/GM/NIGMS NIH HHS/United States ; R01-GM40282/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; *Alleles ; Animals ; Asian Continental Ancestry Group/genetics ; Computer Simulation ; European Continental Ancestry Group/genetics ; Evolution, Molecular ; *Gene Frequency ; *Genetics, Population ; Genome-Wide Association Study ; Genomics/methods ; Humans ; *Models, Genetic ; Neanderthals/genetics ; ROC Curve ; *Selection, Genetic ; }, abstract = {A powerful way to detect selection in a population is by modeling local allele frequency changes in a particular region of the genome under scenarios of selection and neutrality and finding which model is most compatible with the data. A previous method based on a cross-population composite likelihood ratio (XP-CLR) uses an outgroup population to detect departures from neutrality that could be compatible with hard or soft sweeps, at linked sites near a beneficial allele. However, this method is most sensitive to recent selection and may miss selective events that happened a long time ago. To overcome this, we developed an extension of XP-CLR that jointly models the behavior of a selected allele in a three-population tree. Our method - called "3-population composite likelihood ratio" (3P-CLR) - outperforms XP-CLR when testing for selection that occurred before two populations split from each other and can distinguish between those events and events that occurred specifically in each of the populations after the split. We applied our new test to population genomic data from the 1000 Genomes Project, to search for selective sweeps that occurred before the split of Yoruba and Eurasians, but after their split from Neanderthals, and that could have led to the spread of modern-human-specific phenotypes. We also searched for sweep events that occurred in East Asians, Europeans, and the ancestors of both populations, after their split from Yoruba. In both cases, we are able to confirm a number of regions identified by previous methods and find several new candidates for selection in recent and ancient times. For some of these, we also find suggestive functional mutations that may have driven the selective events.}, } @article {pmid26585747, year = {2015}, author = {Serva, M}, title = {A Stochastic Model for the Interbreeding of Two Populations Continuously Sharing the Same Habitat.}, journal = {Bulletin of mathematical biology}, volume = {77}, number = {12}, pages = {2354-2365}, doi = {10.1007/s11538-015-0127-z}, pmid = {26585747}, issn = {1522-9602}, mesh = {Animals ; Breeding ; Ecosystem ; Extinction, Biological ; *Genetics, Population ; History, Ancient ; Humans ; Mathematical Concepts ; *Models, Genetic ; Neanderthals/genetics ; Stochastic Processes ; }, abstract = {We propose and solve a stochastic mathematical model of general applicability to interbreeding populations which share the same habitat. Resources are limited so that the total population size is fixed by environmental factors. Interbreeding occurs during all the time of coexistence until one of the two population disappears by a random fluctuation. None of the two populations has a selective advantage. We answer the following questions: How long the two populations coexist and how genetically similar they become before the extinction of one of the two? how much the genetic makeup of the surviving population changes by the contribution of the disappearing one? what it is the number of interbreeding events given the observed introgression of genetic material? The model was originally motivated by a paleoanthropological problem concerning the interbreeding of Neanderthals and African modern humans in Middle East which is responsible for the fraction of Neanderthal genes (1-4%) in present Eurasian population.}, } @article {pmid26579858, year = {2015}, author = {Heppt, WJ and Vent, J}, title = {The Facial Profile in the Context of Facial Aesthetics.}, journal = {Facial plastic surgery : FPS}, volume = {31}, number = {5}, pages = {421-430}, doi = {10.1055/s-0035-1567815}, pmid = {26579858}, issn = {1098-8793}, mesh = {Art ; *Esthetics ; Ethnic Groups ; *Face ; Humans ; }, abstract = {Beauty has been an intriguing issue since the evolving of a culture in mankind. Even the Neanderthals are believed to have applied makeover to enhance facial structures and thus underline beauty. The determinants of beauty and aesthetics have been defined by artists and scientists alike. This article will give an overview of the evolvement of a beauty concept and the significance of the facial profile. It aims at sharpening the senses of the facial plastic surgeon for analyzing the patient's face, consulting the patient on feasible options, planning, and conducting surgery in the most individualized way.}, } @article {pmid26567083, year = {2016}, author = {Vyas, DN and Kitchen, A and Miró-Herrans, AT and Pearson, LN and Al-Meeri, A and Mulligan, CJ}, title = {Bayesian analyses of Yemeni mitochondrial genomes suggest multiple migration events with Africa and Western Eurasia.}, journal = {American journal of physical anthropology}, volume = {159}, number = {3}, pages = {382-393}, doi = {10.1002/ajpa.22890}, pmid = {26567083}, issn = {1096-8644}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Africa ; Anthropology, Physical ; Asia, Western ; Bayes Theorem ; Europe ; Genome, Mitochondrial/*genetics ; Haplotypes ; History, Ancient ; *Human Migration ; Humans ; Phylogeny ; Yemen ; }, abstract = {OBJECTIVES: Anatomically, modern humans are thought to have migrated out of Africa ∼60,000 years ago in the first successful global dispersal. This initial migration may have passed through Yemen, a region that has experienced multiple migrations events with Africa and Eurasia throughout human history. We use Bayesian phylogenetics to determine how ancient and recent migrations have shaped Yemeni mitogenomic variation.

MATERIALS AND METHODS: We sequenced 113 mitogenomes from multiple Yemeni regions with a focus on haplogroups M, N, and L3(xM,N) as these groups have the oldest evolutionary history outside of Africa. We performed Bayesian evolutionary analyses to generate time-measured phylogenies calibrated by Neanderthal and Denisovan mitogenomes in order to determine the age of Yemeni-specific clades.

RESULTS: As defined by Yemeni monophyly, Yemeni in situ evolution is limited to the Holocene or latest Pleistocene (ages of clades in subhaplogroups L3b1a1a, L3h2, L3x1, M1a1f, M1a5, N1a1a3, and N1a3 range from 2 to 14 kya) and is often situated within broader Horn of Africa/southern Arabia in situ evolution (L3h2, L3x1, M1a1f, M1a5, and N1a1a3 ages range from 7 to 29 kya). Five subhaplogroups show no monophyly and are candidates for Holocene migration into Yemen (L0a2a2a, L3d1a1a, L3i2, M1a1b, and N1b1a).

DISCUSSION: Yemeni mitogenomes are largely the product of Holocene migration, and subsequent in situ evolution, from Africa and western Eurasia. However, we hypothesize that recent population movements may obscure the genetic signature of more ancient migrations. Additional research, e.g., analyses of Yemeni nuclear genetic data, is needed to better reconstruct the complex population and migration histories associated with Out of Africa.}, } @article {pmid26546309, year = {2015}, author = {Yang, MA and Slatkin, M}, title = {Using Ancient Samples in Projection Analysis.}, journal = {G3 (Bethesda, Md.)}, volume = {6}, number = {1}, pages = {99-105}, pmid = {26546309}, issn = {2160-1836}, support = {R01 GM040282/GM/NIGMS NIH HHS/United States ; R01-GM40282/GM/NIGMS NIH HHS/United States ; }, mesh = {Computer Simulation ; Datasets as Topic ; Demography ; *Genetics, Population ; Genome, Human ; Genomics ; Humans ; *Models, Genetic ; }, abstract = {Projection analysis is a tool that extracts information from the joint allele frequency spectrum to better understand the relationship between two populations. In projection analysis, a test genome is compared to a set of genomes from a reference population. The projection's shape depends on the historical relationship of the test genome's population to the reference population. Here, we explore in greater depth the effects on the projection when ancient samples are included in the analysis. First, we conduct a series of simulations in which the ancient sample is directly ancestral to a present-day population (one-population model), or the ancient sample is ancestral to a sister population that diverged before the time of sampling (two-population model). We find that there are characteristic differences between the projections for the one-population and two-population models, which indicate that the projection can be used to determine whether a test genome is directly ancestral to a present-day population or not. Second, we compute projections for several published ancient genomes. We compare two Neanderthals and three ancient human genomes to European, Han Chinese and Yoruba reference panels. We use a previously constructed demographic model and insert these five ancient genomes to assess how well the observed projections are recovered.}, } @article {pmid26524490, year = {2016}, author = {Rosandić, M and Vlahović, I and Glunčić, M and Paar, V}, title = {Trinucleotide's quadruplet symmetries and natural symmetry law of DNA creation ensuing Chargaff's second parity rule.}, journal = {Journal of biomolecular structure & dynamics}, volume = {34}, number = {7}, pages = {1383-1394}, doi = {10.1080/07391102.2015.1080628}, pmid = {26524490}, issn = {1538-0254}, mesh = {Animals ; Base Composition ; Chromosome Mapping ; Codon ; DNA/*chemistry/*genetics ; Evolution, Molecular ; *G-Quadruplexes ; Genome ; Genomics ; Humans ; *Models, Genetic ; Nucleotides ; *Trinucleotide Repeats ; }, abstract = {For almost 50 years the conclusive explanation of Chargaff's second parity rule (CSPR), the equality of frequencies of nucleotides A=T and C=G or the equality of direct and reverse complement trinucleotides in the same DNA strand, has not been determined yet. Here, we relate CSPR to the interstrand mirror symmetry in 20 symbolic quadruplets of trinucleotides (direct, reverse complement, complement, and reverse) mapped to double-stranded genome. The symmetries of Q-box corresponding to quadruplets can be obtained as a consequence of Watson-Crick base pairing and CSPR together. Alternatively, assuming Natural symmetry law for DNA creation that each trinucleotide in one strand of DNA must simultaneously appear also in the opposite strand automatically leads to Q-box direct-reverse mirror symmetry which in conjunction with Watson-Crick base pairing generates CSPR. We demonstrate quadruplet's symmetries in chromosomes of wide range of organisms, from Escherichia coli to Neanderthal and human genomes, introducing novel quadruplet-frequency histograms and 3D-diagrams with combined interstrand frequencies. These "landscapes" are mutually similar in all mammals, including extinct Neanderthals, and somewhat different in most of older species. In human chromosomes 1-12, and X, Y the "landscapes" are almost identical and slightly different in the remaining smaller and telocentric chromosomes. Quadruplet frequencies could provide a new robust tool for characterization and classification of genomes and their evolutionary trajectories.}, } @article {pmid26499001, year = {2016}, author = {Traynor, S and Gurtov, AN and Hutton Senjem, J and Hawks, J}, title = {Letter to the Editor: Reply to Dunbar et al. (2015).}, journal = {American journal of physical anthropology}, volume = {159}, number = {2}, pages = {361}, doi = {10.1002/ajpa.22880}, pmid = {26499001}, issn = {1096-8644}, mesh = {Animals ; Neanderthals/*anatomy & histology/*physiology ; Orbit/*anatomy & histology ; *Social Behavior ; }, } @article {pmid26498859, year = {2016}, author = {Rangel de Lázaro, G and de la Cuétara, JM and Píšová, H and Lorenzo, C and Bruner, E}, title = {Diploic vessels and computed tomography: Segmentation and comparison in modern humans and fossil hominids.}, journal = {American journal of physical anthropology}, volume = {159}, number = {2}, pages = {313-324}, doi = {10.1002/ajpa.22878}, pmid = {26498859}, issn = {1096-8644}, mesh = {Adult ; Animals ; Anthropology, Physical ; *Fossils ; Humans ; Neanderthals/anatomy & histology ; *Skull/anatomy & histology/blood supply/diagnostic imaging ; Tomography, X-Ray Computed ; }, abstract = {OBJECTIVES: The diploic channels appear to be more developed in humans than in nonhuman primates, suggesting they may be relevant in evolutionary biology. This study is aimed at providing a segmentation procedure for diploic channels and CT analysis, a quantitative description of their variation in modern humans, and paleoanthropological case-studies.

MATERIALS AND METHODS: CT data were used for the 2D and 3D visualization, rendering, and measure, of diploic channels in modern and fossil hominids. We analyzed 20 modern human skulls and three Neanderthals. The effect of different resolution factors was evaluated. A specific protocol was designed to segment the vascular network and localize the main branches, reducing the noise of the cancellous bone.

RESULTS: We provide a quantitative description of the frontal, parietal, and occipital diploic networks in modern humans and in three Neanderthals. There is a correlation in the degree of vascularization among the different vault areas. No side differences can be detected. The diploic network is commonly connected with the meningeal artery at the temporal fossa, with the emissary veins at the occipital bone, and with the venous sinuses at the parieto-occipital areas. The channels are more developed in the parietal areas. The three Neanderthals show a vascular development, which is in the lower range of the modern human variation.

CONCLUSIONS: Modern humans display a large variation in their morphological patterns, being the parietal area the most vascularized. The pattern of the diploic channels may be relevant in anthropology, medicine, and paleontology, taking into account their possible involvement in thermoregulation.}, } @article {pmid26468243, year = {2015}, author = {Weaver, TD and Stringer, CB}, title = {Unconstrained cranial evolution in Neandertals and modern humans compared to common chimpanzees.}, journal = {Proceedings. Biological sciences}, volume = {282}, number = {1817}, pages = {20151519}, pmid = {26468243}, issn = {1471-2954}, mesh = {Animals ; *Biological Evolution ; Fossils ; Genetic Drift ; Humans ; Neanderthals/*anatomy & histology ; Pan troglodytes/*anatomy & histology ; Selection, Genetic ; Skull/*anatomy & histology ; }, abstract = {A variety of lines of evidence support the idea that neutral evolutionary processes (genetic drift, mutation) have been important in generating cranial differences between Neandertals and modern humans. But how do Neandertals and modern humans compare with other species? And how do these comparisons illuminate the evolutionary processes underlying cranial diversification? To address these questions, we used 27 standard cranial measurements collected on 2524 recent modern humans, 20 Neandertals and 237 common chimpanzees to estimate split times between Neandertals and modern humans, and between Pan troglodytes verus and two other subspecies of common chimpanzee. Consistent with a neutral divergence, the Neandertal versus modern human split-time estimates based on cranial measurements are similar to those based on DNA sequences. By contrast, the common chimpanzee cranial estimates are much lower than DNA-sequence estimates. Apparently, cranial evolution has been unconstrained in Neandertals and modern humans compared with common chimpanzees. Based on these and additional analyses, it appears that cranial differentiation in common chimpanzees has been restricted by stabilizing natural selection. Alternatively, this restriction could be due to genetic and/or developmental constraints on the amount of within-group variance (relative to effective population size) available for genetic drift to act on.}, } @article {pmid26466566, year = {2015}, author = {Liu, W and Martinón-Torres, M and Cai, YJ and Xing, S and Tong, HW and Pei, SW and Sier, MJ and Wu, XH and Edwards, RL and Cheng, H and Li, YY and Yang, XX and de Castro, JM and Wu, XJ}, title = {The earliest unequivocally modern humans in southern China.}, journal = {Nature}, volume = {526}, number = {7575}, pages = {696-699}, pmid = {26466566}, issn = {1476-4687}, mesh = {Animals ; Caves ; China ; Europe ; *Fossils ; History, Ancient ; Human Migration/*history ; Humans ; Neanderthals ; Time Factors ; Tooth/*anatomy & histology ; }, abstract = {The hominin record from southern Asia for the early Late Pleistocene epoch is scarce. Well-dated and well-preserved fossils older than ∼45,000 years that can be unequivocally attributed to Homo sapiens are lacking. Here we present evidence from the newly excavated Fuyan Cave in Daoxian (southern China). This site has provided 47 human teeth dated to more than 80,000 years old, and with an inferred maximum age of 120,000 years. The morphological and metric assessment of this sample supports its unequivocal assignment to H. sapiens. The Daoxian sample is more derived than any other anatomically modern humans, resembling middle-to-late Late Pleistocene specimens and even contemporary humans. Our study shows that fully modern morphologies were present in southern China 30,000-70,000 years earlier than in the Levant and Europe. Our data fill a chronological and geographical gap that is relevant for understanding when H. sapiens first appeared in southern Asia. The Daoxian teeth also support the hypothesis that during the same period, southern China was inhabited by more derived populations than central and northern China. This evidence is important for the study of dispersal routes of modern humans. Finally, our results are relevant to exploring the reasons for the relatively late entry of H. sapiens into Europe. Some studies have investigated how the competition with H. sapiens may have caused Neanderthals' extinction (see ref. 8 and references therein). Notably, although fully modern humans were already present in southern China at least as early as ∼80,000 years ago, there is no evidence that they entered Europe before ∼45,000 years ago. This could indicate that H. neanderthalensis was indeed an additional ecological barrier for modern humans, who could only enter Europe when the demise of Neanderthals had already started.}, } @article {pmid26458810, year = {2015}, author = {Renaud, G and Slon, V and Duggan, AT and Kelso, J}, title = {Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA.}, journal = {Genome biology}, volume = {16}, number = {}, pages = {224}, pmid = {26458810}, issn = {1474-760X}, mesh = {Animals ; Base Sequence ; *Consensus Sequence ; *DNA Contamination ; DNA, Mitochondrial/*chemistry ; *Genome, Mitochondrial ; Humans ; Neanderthals/genetics ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {UNLABELLED: Ancient DNA is typically highly degraded with appreciable cytosine deamination, and contamination with present-day DNA often complicates the identification of endogenous molecules. Together, these factors impede accurate assembly of the endogenous ancient mitochondrial genome. We present schmutzi, an iterative approach to jointly estimate present-day human contamination in ancient human DNA datasets and reconstruct the endogenous mitochondrial genome. By using sequence deamination patterns and fragment length distributions, schmutzi accurately reconstructs the endogenous mitochondrial genome sequence even when contamination exceeds 50 %. Given sufficient coverage, schmutzi also produces reliable estimates of contamination across a range of contamination rates.

AVAILABILITY: https://bioinf.eva.mpg.de/schmutzi/ license:GPLv3.}, } @article {pmid26458098, year = {2016}, author = {Dunbar, R and Pearce, E and Stringer, C}, title = {Response to: Traynor et al. "assessing eye orbits as predictors of neandertal group size".}, journal = {American journal of physical anthropology}, volume = {159}, number = {2}, pages = {358-360}, doi = {10.1002/ajpa.22881}, pmid = {26458098}, issn = {1096-8644}, mesh = {Animals ; Neanderthals/*anatomy & histology/*physiology ; Orbit/*anatomy & histology ; *Social Behavior ; }, } @article {pmid26454764, year = {2016}, author = {Weyer, S and Pääbo, S}, title = {Functional Analyses of Transcription Factor Binding Sites that Differ between Present-Day and Archaic Humans.}, journal = {Molecular biology and evolution}, volume = {33}, number = {2}, pages = {316-322}, pmid = {26454764}, issn = {1537-1719}, mesh = {Alleles ; *Binding Sites ; Cell Line ; *Evolution, Molecular ; *Genetic Variation ; Humans ; Polymorphism, Single Nucleotide ; Transcription Factors/*metabolism ; Transcriptional Activation ; }, abstract = {We analyze 25 previously identified transcription factor binding sites that carry DNA sequence changes that are present in all or nearly all present-day humans, yet occur in the ancestral state in Neandertals and Denisovans, the closest evolutionary relatives of humans. When the ancestral and derived forms of the transcription factor binding sites are tested using reporter constructs in 3 neuronal cell lines, the activity of 12 of the derived versions of transcription factor binding sites differ from the respective ancestral variants. This suggests that the majority of this class of evolutionary differences between modern humans and Neandertals may affect gene expression in at least some tissue or cell type.}, } @article {pmid26451479, year = {2015}, author = {Vattathil, S and Akey, JM}, title = {Small Amounts of Archaic Admixture Provide Big Insights into Human History.}, journal = {Cell}, volume = {163}, number = {2}, pages = {281-284}, doi = {10.1016/j.cell.2015.09.042}, pmid = {26451479}, issn = {1097-4172}, mesh = {Animals ; *Biological Evolution ; Genetics, Medical ; Genome, Human ; Hominidae/genetics ; Humans ; Neanderthals/classification/*genetics ; Selection, Genetic ; }, abstract = {Modern humans overlapped in time and space with other hominins, such as Neanderthals and Denisovans, and limited amounts of hybridization occurred. Here, we review recent work that has identified archaic hominin sequence that survives in modern human genomes and what these genomic excavations reveal about human evolutionary history.}, } @article {pmid26441731, year = {2015}, author = {Theofanopoulou, C}, title = {Brain asymmetry in the white matter making and globularity.}, journal = {Frontiers in psychology}, volume = {6}, number = {}, pages = {1355}, pmid = {26441731}, issn = {1664-1078}, abstract = {Recent studies from the field of language genetics and evolutionary anthropology have put forward the hypothesis that the emergence of our species-specific brain is to be understood not in terms of size, but in light of developmental changes that gave rise to a more globular braincase configuration after the split from Neanderthals-Denisovans. On the grounds that (i) white matter myelination is delayed relative to other brain structures and, in humans, is protracted compared with other primates and that (ii) neural connectivity is linked genetically to our brain/skull morphology and language-ready brain, I argue that one significant evolutionary change in Homo sapiens' lineage is the interhemispheric connectivity mediated by the Corpus Callosum. The size, myelination and fiber caliber of the Corpus Callosum present an anterior-to-posterior increase, in a way that inter-hemispheric connectivity is more prominent in the sensory motor areas, whereas "high- order" areas are more intra-hemispherically connected. Building on evidence from language-processing studies that account for this asymmetry ('lateralization') in terms of brain rhythms, I present an evo-devo hypothesis according to which the myelination of the Corpus Callosum, Brain Asymmetry, and Globularity are conjectured to make up the angles of a co-evolutionary triangle that gave rise to our language-ready brain.}, } @article {pmid26441219, year = {2015}, author = {Kivell, TL and Deane, AS and Tocheri, MW and Orr, CM and Schmid, P and Hawks, J and Berger, LR and Churchill, SE}, title = {The hand of Homo naledi.}, journal = {Nature communications}, volume = {6}, number = {}, pages = {8431}, pmid = {26441219}, issn = {2041-1723}, support = {336301//European Research Council/International ; }, mesh = {Animals ; Biological Evolution ; *Fossils ; Gorilla gorilla/anatomy & histology ; Hand/anatomy & histology ; Hand Bones/*anatomy & histology ; Hominidae/*anatomy & histology ; Humans ; Neanderthals/anatomy & histology ; Pan paniscus/anatomy & histology ; Pan troglodytes/anatomy & histology ; Thumb/*anatomy & histology ; Wrist/*anatomy & histology ; }, abstract = {A nearly complete right hand of an adult hominin was recovered from the Rising Star cave system, South Africa. Based on associated hominin material, the bones of this hand are attributed to Homo naledi. This hand reveals a long, robust thumb and derived wrist morphology that is shared with Neandertals and modern humans, and considered adaptive for intensified manual manipulation. However, the finger bones are longer and more curved than in most australopiths, indicating frequent use of the hand during life for strong grasping during locomotor climbing and suspension. These markedly curved digits in combination with an otherwise human-like wrist and palm indicate a significant degree of climbing, despite the derived nature of many aspects of the hand and other regions of the postcranial skeleton in H. naledi.}, } @article {pmid26420257, year = {2015}, author = {Hawkes, N}, title = {Cutting science budget would be "Neanderthal" behaviour, expert says.}, journal = {BMJ (Clinical research ed.)}, volume = {351}, number = {}, pages = {h5217}, doi = {10.1136/bmj.h5217}, pmid = {26420257}, issn = {1756-1833}, mesh = {*Budgets ; Humans ; Research/*economics ; United Kingdom ; }, } @article {pmid26418427, year = {2015}, author = {Ríos, L and Rosas, A and Estalrrich, A and García-Tabernero, A and Bastir, M and Huguet, R and Pastor, F and Sanchís-Gimeno, JA and de la Rasilla, M}, title = {Possible Further Evidence of Low Genetic Diversity in the El Sidrón (Asturias, Spain) Neandertal Group: Congenital Clefts of the Atlas.}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0136550}, pmid = {26418427}, issn = {1932-6203}, mesh = {Animals ; Cervical Atlas/*abnormalities/pathology ; Fossils ; *Genetic Variation ; *Genetics, Population ; Neanderthals/*genetics ; Spain ; }, abstract = {We present here the first cases in Neandertals of congenital clefts of the arch of the atlas. Two atlases from El Sidrón, northern Spain, present respectively a defect of the posterior (frequency in extant modern human populations ranging from 0.73% to 3.84%), and anterior (frequency in extant modern human populations ranging from 0.087% to 0.1%) arch, a condition in most cases not associated with any clinical manifestation. The fact that two out of three observable atlases present a low frequency congenital condition, together with previously reported evidence of retained deciduous mandibular canine in two out of ten dentitions from El Sidrón, supports the previous observation based on genetic evidence that these Neandertals constituted a group with close genetic relations. Some have proposed for humans and other species that the presence of skeletal congenital conditions, although without clinical significance, could be used as a signal of endogamy or inbreeding. In the present case this interpretation would fit the general scenario of high incidence of rare conditions among Pleistocene humans and the specific scenariothat emerges from Neandertal paleogenetics, which points to long-term small and decreasing population size with reduced and isolated groups. Adverse environmental factors affecting early pregnancies would constitute an alternative, non-exclusive, explanation for a high incidence of congenital conditions. Further support or rejection of these interpretations will come from new genetic and skeletal evidence from Neandertal remains.}, } @article {pmid26399483, year = {2015}, author = {Rogers, RL}, title = {Chromosomal Rearrangements as Barriers to Genetic Homogenization between Archaic and Modern Humans.}, journal = {Molecular biology and evolution}, volume = {32}, number = {12}, pages = {3064-3078}, pmid = {26399483}, issn = {1537-1719}, support = {R01 GM040282/GM/NIGMS NIH HHS/United States ; R01-GM40282/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; DNA Transposable Elements ; Evolution, Molecular ; Female ; Fossils ; Gene Flow/genetics ; *Gene Rearrangement ; Genetic Variation ; *Genome, Human ; Hominidae/*genetics ; Humans ; Male ; Neanderthals/*genetics ; Phylogeny ; Polymorphism, Genetic ; Recombination, Genetic/genetics ; Sequence Analysis, DNA ; Y Chromosome ; }, abstract = {Chromosomal rearrangements, which shuffle DNA throughout the genome, are an important source of divergence across taxa. Using a paired-end read approach with Illumina sequence data for archaic humans, I identify changes in genome structure that occurred recently in human evolution. Hundreds of rearrangements indicate genomic trafficking between the sex chromosomes and autosomes, raising the possibility of sex-specific changes. Additionally, genes adjacent to genome structure changes in Neanderthals are associated with testis-specific expression, consistent with evolutionary theory that new genes commonly form with expression in the testes. I identify one case of new-gene creation through transposition from the Y chromosome to chromosome 10 that combines the 5'-end of the testis-specific gene Fank1 with previously untranscribed sequence. This new transcript experienced copy number expansion in archaic genomes, indicating rapid genomic change. Among rearrangements identified in Neanderthals, 13% are transposition of selfish genetic elements, whereas 32% appear to be ectopic exchange between repeats. In Denisovan, the pattern is similar but numbers are significantly higher with 18% of rearrangements reflecting transposition and 40% ectopic exchange between distantly related repeats. There is an excess of divergent rearrangements relative to polymorphism in Denisovan, which might result from nonuniform rates of mutation, possibly reflecting a burst of transposable element activity in the lineage that led to Denisovan. Finally, loci containing genome structure changes show diminished rates of introgression from Neanderthals into modern humans, consistent with the hypothesis that rearrangements serve as barriers to gene flow during hybridization. Together, these results suggest that this previously unidentified source of genomic variation has important biological consequences in human evolution.}, } @article {pmid26392408, year = {2015}, author = {Hu, Y and Ding, Q and He, Y and Xu, S and Jin, L}, title = {Reintroduction of a Homocysteine Level-Associated Allele into East Asians by Neanderthal Introgression.}, journal = {Molecular biology and evolution}, volume = {32}, number = {12}, pages = {3108-3113}, doi = {10.1093/molbev/msv176}, pmid = {26392408}, issn = {1537-1719}, mesh = {Alleles ; Animals ; Asian Continental Ancestry Group/*genetics ; Dipeptidases/*genetics ; Evolution, Molecular ; GPI-Linked Proteins/genetics ; Gene Frequency/genetics ; Haplotypes ; Homocysteine/*genetics ; Humans ; Neanderthals/*genetics ; Phylogeny ; Polymorphism, Single Nucleotide ; Selection, Genetic ; }, abstract = {In this study, we present an analysis of Neanderthal introgression at the dipeptidase 1 gene, DPEP1. A Neanderthal origin for the putative introgressive haplotypes was demonstrated using an established three-step approach. This introgression was under positive natural selection, reached a frequency of >50%, and introduced a homocysteine level- and pigmentation-associated allele (rs460879-T) into East Asians. However, the same allele was also found in non-East Asians, but not from Neanderthal introgression. It is likely that rs460879-T was lost in East Asians and was reintroduced subsequently through Neanderthal introgression. Our findings suggest that Neanderthal introgression could reintroduce an important previously existing allele into populations where the allele had been lost. This study sheds new light on understanding the contribution of Neanderthal introgression to the adaptation of non-Africans.}, } @article {pmid26388184, year = {2015}, author = {Monge, G and Jimenez-Espejo, FJ and García-Alix, A and Martínez-Ruiz, F and Mattielli, N and Finlayson, C and Ohkouchi, N and Sánchez, MC and de Castro, JM and Blasco, R and Rosell, J and Carrión, J and Rodríguez-Vidal, J and Finlayson, G}, title = {Earliest evidence of pollution by heavy metals in archaeological sites.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {14252}, pmid = {26388184}, issn = {2045-2322}, mesh = {Agriculture ; Animals ; Archaeology/*methods ; Caves ; Environmental Monitoring ; Environmental Pollution/*analysis ; Humans ; Industry ; Metals, Heavy/*analysis ; Neanderthals ; Soil/chemistry ; Soil Pollutants/*analysis ; Spain ; }, abstract = {Homo species were exposed to a new biogeochemical environment when they began to occupy caves. Here we report the first evidence of palaeopollution through geochemical analyses of heavy metals in four renowned archaeological caves of the Iberian Peninsula spanning the last million years of human evolution. Heavy metal contents reached high values due to natural (guano deposition) and anthropogenic factors (e.g. combustion) in restricted cave environments. The earliest anthropogenic pollution evidence is related to Neanderthal hearths from Gorham's Cave (Gibraltar), being one of the first milestones in the so-called "Anthropocene". According to its heavy metal concentration, these sediments meet the present-day standards of "contaminated soil". Together with the former, the Gibraltar Vanguard Cave, shows Zn and Cu pollution ubiquitous across highly anthropic levels pointing to these elements as potential proxies for human activities. Pb concentrations in Magdalenian and Bronze age levels at El Pirulejo site can be similarly interpreted. Despite these high pollution levels, the contaminated soils might not have posed a major threat to Homo populations. Altogether, the data presented here indicate a long-term exposure of Homo to these elements, via fires, fumes and their ashes, which could have played certain role in environmental-pollution tolerance, a hitherto neglected influence.}, } @article {pmid26383929, year = {2015}, author = {Gibbons, A}, title = {HUMAN EVOLUTION. Humanity's long, lonely road.}, journal = {Science (New York, N.Y.)}, volume = {349}, number = {6254}, pages = {1270}, doi = {10.1126/science.349.6254.1270-a}, pmid = {26383929}, issn = {1095-9203}, mesh = {Animals ; Cell Nucleus/*genetics ; DNA/*genetics ; *Evolution, Molecular ; Fossils ; Humans ; Neanderthals/*genetics ; Sequence Analysis, DNA ; Spain ; }, } @article {pmid26381860, year = {2016}, author = {Bauer, CC and Bons, PD and Benazzi, S and Harvati, K}, title = {Using elliptical best fits to characterize dental shapes.}, journal = {American journal of physical anthropology}, volume = {159}, number = {2}, pages = {342-347}, doi = {10.1002/ajpa.22866}, pmid = {26381860}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; Fossils ; Humans ; Neanderthals/*anatomy & histology ; Odontometry/*methods ; Paleodontology/*methods ; Tooth Crown/*anatomy & histology ; }, abstract = {A variety of geometric morphometric methods have recently been used to describe dental shape variation in human evolutionary studies. However, the applicability of these methods is limited when teeth are worn or are difficult to orient accurately. Here we show that elliptical best fits on outlines of dental tissues below the crown provide basic size- and orientation-free shape descriptors. Using the dm(2) and M(3) as examples, we demonstrate that these descriptors can be used for taxonomic purposes, such as distinguishing between Neanderthal and recent modern human teeth. We propose that this approach can be a useful alternative to existing methodology.}, } @article {pmid26354411, year = {2015}, author = {Sarah, T and Alia, G and Jess, S and John, H}, title = {Letter to the editor: Reply to Schillaci (2015): "Correlation between multiple variables among extant primates is insufficient for predicting unknown values in extinct hominins".}, journal = {American journal of physical anthropology}, volume = {158}, number = {3}, pages = {524}, doi = {10.1002/ajpa.22784}, pmid = {26354411}, issn = {1096-8644}, mesh = {Animals ; Neanderthals/*anatomy & histology/*physiology ; Orbit/*anatomy & histology ; *Social Behavior ; }, } @article {pmid26331404, year = {2016}, author = {Bailey, SE and Benazzi, S and Buti, L and Hublin, JJ}, title = {Allometry, merism, and tooth shape of the lower second deciduous molar and first permanent molar.}, journal = {American journal of physical anthropology}, volume = {159}, number = {1}, pages = {93-105}, doi = {10.1002/ajpa.22842}, pmid = {26331404}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; Fossils ; Humans ; Molar/*anatomy & histology/pathology ; Neanderthals/*anatomy & histology ; Odontometry ; Tooth Crown/*anatomy & histology/pathology ; Tooth, Deciduous/*anatomy & histology/pathology ; }, abstract = {OBJECTIVES: This study investigates the effect of allometry on the shape of lower dm2 (dm2) and lower M1 (M1) crown outlines and examines whether the trajectory and magnitude of allometric scaling are shared between Neandertals and Homo sapiens.

METHODS: Our sample included 164 specimens: 57 recent H. sapiens, 44 Upper Paleolithic H. sapiens, 17 early H. sapiens, and 46 Neandertals. Of these, 59 represent dm2/M1 pairs from the same individuals. Occlusal photographs were used to obtain crown shapes of dm2s and M1s. Principal components analysis (PCA) of the matrix of shape coordinates was used to explore the pattern of morphological variation across the dm2 and M1 samples. Allometry was investigated by means of the Pearson product-moment correlation coefficient. Two-block partial least squares (2B-PLS) analysis was used to explore patterns of covariation between dm2 and M1 crown outlines of matched individual pairs.

RESULTS: The PCA confirmed significant differences between Neandertal and H. sapiens dm2 and M1 shapes. Allometry accounted for a small but statistically significant proportion of the total morphological variance. The magnitude of the allometric contribution to crown shape was stronger among Neandertals than among H. sapiens. However, we could not reject the null hypothesis that the two species share the same allometric trajectory. The 2B-PLS analysis of the pooled sample of paired individuals revealed a significant correlation in crown shape between dm2 and M1. While Procrustes distances differed significantly between dm2 and M1 in Neandertals, it did not among H. sapiens groups.

CONCLUSIONS: Our results confirm several of the results obtained by a similar study of upper dm2/M1 (dm(2)/M(1)), but there are differences as well. Neandertal dm2/M1 shapes are less derived than those of the dm(2)/M(1). Such differences may support previous studies, which have suggested that different developmental and/or epigenetic factors affect the upper and lower dentitions.}, } @article {pmid26324920, year = {2015}, author = {Arsuaga, JL and Carretero, JM and Lorenzo, C and Gómez-Olivencia, A and Pablos, A and Rodríguez, L and García-González, R and Bonmatí, A and Quam, RM and Pantoja-Pérez, A and Martínez, I and Aranburu, A and Gracia-Téllez, A and Poza-Rey, E and Sala, N and García, N and Alcázar de Velasco, A and Cuenca-Bescós, G and Bermúdez de Castro, JM and Carbonell, E}, title = {Postcranial morphology of the middle Pleistocene humans from Sima de los Huesos, Spain.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {37}, pages = {11524-11529}, pmid = {26324920}, issn = {1091-6490}, mesh = {Animals ; Body Height ; Body Size ; Bone and Bones/anatomy & histology ; *Fossils ; Hominidae/anatomy & histology ; Humans ; Neanderthals/anatomy & histology ; Paleontology ; Phylogeny ; Population Dynamics ; Skull/*anatomy & histology ; Spain ; }, abstract = {Current knowledge of the evolution of the postcranial skeleton in the genus Homo is hampered by a geographically and chronologically scattered fossil record. Here we present a complete characterization of the postcranium of the middle Pleistocene paleodeme from the Sima de los Huesos (SH) and its paleobiological implications. The SH hominins show the following: (i) wide bodies, a plesiomorphic character in the genus Homo inherited from their early hominin ancestors; (ii) statures that can be found in modern human middle-latitude populations that first appeared 1.6-1.5 Mya; and (iii) large femoral heads in some individuals, a trait that first appeared during the middle Pleistocene in Africa and Europe. The intrapopulational size variation in SH shows that the level of dimorphism was similar to modern humans (MH), but the SH hominins were less encephalized than Neandertals. SH shares many postcranial anatomical features with Neandertals. Although most of these features appear to be either plesiomorphic retentions or are of uncertain phylogenetic polarity, a few represent Neandertal apomorphies. Nevertheless, the full suite of Neandertal-derived features is not yet present in the SH population. The postcranial evidence is consistent with the hypothesis based on the cranial morphology that the SH hominins are a sister group to the later Neandertals. Comparison of the SH postcranial skeleton to other hominins suggests that the evolution of the postcranium occurred in a mosaic mode, both at a general and at a detailed level.}, } @article {pmid26308868, year = {2014}, author = {Johansson, S}, title = {The thinking Neanderthals: What do we know about Neanderthal cognition?.}, journal = {Wiley interdisciplinary reviews. Cognitive science}, volume = {5}, number = {6}, pages = {613-620}, doi = {10.1002/wcs.1317}, pmid = {26308868}, issn = {1939-5086}, abstract = {The study of Neanderthal cognition is difficult, because of the archaeological invisibility of cognition, and because of the methodological issues that arise both from that invisibility and from their being close to modern humans. Nevertheless, fair progress has been made in gathering relevant evidence. There is now good evidence that Neanderthals were cognitively sophisticated, displaying many of the cognitive traits that were traditionally regarded as proxies for modern human cognition, notably including language. It can neither be proven nor excluded that they were our cognitive equals, but they were close enough to us, biologically and cognitively, to interbreed successfully and leave a genetic legacy in our DNA. WIREs Cogn Sci 2014, 5:613-620. doi: 10.1002/wcs.1317 CONFLICT OF INTEREST: The author has declared no conflicts of interest for this article. For further resources related to this article, please visit the WIREs website.}, } @article {pmid26294746, year = {2015}, author = {Huerta-Sánchez, E and Casey, FP}, title = {Archaic inheritance: supporting high-altitude life in Tibet.}, journal = {Journal of applied physiology (Bethesda, Md. : 1985)}, volume = {119}, number = {10}, pages = {1129-1134}, doi = {10.1152/japplphysiol.00322.2015}, pmid = {26294746}, issn = {1522-1601}, mesh = {Adaptation, Physiological/*genetics ; *Altitude ; Animals ; Asian Continental Ancestry Group/*genetics ; Demography/methods ; Genetic Association Studies/methods ; Humans ; Neanderthals/*genetics ; Tibet ; }, abstract = {The Tibetan Plateau, often called the roof of the world, sits at an average altitude exceeding 4,500 m. Because of its extreme altitude, the Plateau is one of the harshest human-inhabited environments in the world. This, however, did not impede human colonization, and the Tibetan people have made the Tibetan Plateau their home for many generations. Many studies have quantified their markedly different physiological response to altitude and proposed that Tibetans were genetically adapted. Recently, advances in sequencing technologies led to the discovery of a set of candidate genes which harbor mutations that are likely beneficial at high altitudes in Tibetans. Since then, other studies have further characterized this impressive adaptation. Here, in this minireview, we discuss the progress made since the discovery of the genes involved in Tibetans' adaptation to high altitude with a particular emphasis on describing the series of studies that led us to conclude that archaic human DNA likely contributed to this impressive adaptation.}, } @article {pmid26277304, year = {2015}, author = {Ruebens, K and McPherron, SJ and Hublin, JJ}, title = {On the local Mousterian origin of the Châtelperronian: Integrating typo-technological, chronostratigraphic and contextual data.}, journal = {Journal of human evolution}, volume = {86}, number = {}, pages = {55-91}, doi = {10.1016/j.jhevol.2015.06.011}, pmid = {26277304}, issn = {1095-8606}, mesh = {Animals ; *Fossils ; France ; History, Ancient ; Humans ; Neanderthals/*physiology ; Population Dynamics ; Spain ; Technology/*history/*instrumentation ; Tool Use Behavior ; }, abstract = {Across Europe the period 45-40 ka (thousands of years ago) is associated with several technological changes, including the emergence of the Châtelperronian technocomplex in France and northern Spain. The Châtelperronian, stratigraphically located between the Mousterian and Aurignacian, is characterized by Upper Palaeolithic features, such as volumetric blade reduction, curved backed blades, end-scrapers, bladelets, bone tools and ornaments. Concurrently, repeated, though debated, associations with Neanderthal remains and Mousterian elements suggest a local technological development. Following recent critiques and cumulating technological studies, this paper provides data-driven contextualisations of the Châtelperronian and late Mousterian archaeological records and a primary comparative assessment of a major linking element, backed knives, to re-assess the origin of the Châtelperronian. The results demonstrate the challenging nature of the 50-35 ka record, with many interpretive problems caused by poorly recorded excavations, resulting in only 25 well-contextualised assemblages from the claimed 143 Châtelperronian find spots. These 25 assemblages facilitate more detailed chronostratigraphic and typo-technological assessments and show that the Châtelperronian has a homogenous set of technologies and tools. A similar evaluation of the late Mousterian indicates a wide-ranging late Neanderthal skill set, commonly including laminar blank production and backing. Further, conceptual similarities were noted both in blank selection and edge modification between Mousterian and Châtelperronian backed knives, alongside their near-absence in other, contemporaneous technocomplexes. A Europe-wide contextualisation shows that while the current coarse-grained record still allows for several potential scenarios, the data throughout this paper point towards a most parsimonious model of a Châtelperronian made by Neanderthals, with roots in the late Middle Palaeolithic technological skill set. However, this change seems triggered by early arrivals of modern humans either indirectly, through stimulus diffusion, or directly, after ca. 42 ka. Fully testing this model requires an ongoing focus on site formation and assemblage integrity, alongside in-depth analyses of recently excavated assemblages and existing collections.}, } @article {pmid26274919, year = {2015}, author = {Dutheil, JY and Munch, K and Nam, K and Mailund, T and Schierup, MH}, title = {Strong Selective Sweeps on the X Chromosome in the Human-Chimpanzee Ancestor Explain Its Low Divergence.}, journal = {PLoS genetics}, volume = {11}, number = {8}, pages = {e1005451}, pmid = {26274919}, issn = {1553-7404}, mesh = {Animals ; Chromosomes, Human, X/*genetics ; Female ; Genetic Drift ; Genetic Speciation ; Genetic Variation ; Humans ; Male ; Neanderthals ; Recombination, Genetic ; Selection, Genetic ; Species Specificity ; }, abstract = {The human and chimpanzee X chromosomes are less divergent than expected based on autosomal divergence. We study incomplete lineage sorting patterns between humans, chimpanzees and gorillas to show that this low divergence can be entirely explained by megabase-sized regions comprising one-third of the X chromosome, where polymorphism in the human-chimpanzee ancestral species was severely reduced. We show that background selection can explain at most 10% of this reduction of diversity in the ancestor. Instead, we show that several strong selective sweeps in the ancestral species can explain it. We also report evidence of population specific sweeps in extant humans that overlap the regions of low diversity in the ancestral species. These regions further correspond to chromosomal sections shown to be devoid of Neanderthal introgression into modern humans. This suggests that the same X-linked regions that undergo selective sweeps are among the first to form reproductive barriers between diverging species. We hypothesize that meiotic drive is the underlying mechanism causing these two observations.}, } @article {pmid26261040, year = {2015}, author = {Baird, SJ}, title = {Exploring linkage disequilibrium.}, journal = {Molecular ecology resources}, volume = {15}, number = {5}, pages = {1017-1019}, doi = {10.1111/1755-0998.12424}, pmid = {26261040}, issn = {1755-0998}, mesh = {Computational Biology/*methods ; Genetics, Population/*methods ; *Linkage Disequilibrium ; *Software ; }, abstract = {Linkage disequilibrium (LD, association of allelic states across loci) is poorly understood by many evolutionary biologists, but as technology for multilocus sampling improves, we ignore LD at our peril. If we sample variation at 10 loci in an organism with 20 chromosomes, we can reasonably treat them as 10 'independent witnesses' of the evolutionary process. If instead, we sample variation at 1000 loci, many are bound to be close together on a chromosome. With only one or two crossovers per meiosis, associations between close neighbours decay so slowly that even LD created far in the past will not have dissipated, so we cannot treat the 1000 loci as independent witnesses (Barton). This means that as marker density on genomes increases classic analyses assuming independent loci become mired in the problem of overconfidence: if 1000 independent witnesses are assumed, and that number should be much lower, any conclusion will be overconfident. This is of special concern because our literature suffers from a strong publication bias towards confident answers, even when they turn out to be wrong (Knowles). In contrast, analyses that take into account associations across loci both control for overconfidence and can inform us about LD generating events far in the past, for example human/Neanderthal admixture (Fu et al.). With increased marker density, biologists must increase their awareness of LD and, in this issue of Molecular Ecology Resources, Kemppainen et al. () make software available that can only help in this process: LDna allows patterns of LD in a data set to be explored using tools borrowed from network analysis. This has great potential, but realizing that potential requires understanding LD.}, } @article {pmid26249757, year = {2015}, author = {Amano, H and Kikuchi, T and Morita, Y and Kondo, O and Suzuki, H and Ponce de León, MS and Zollikofer, CPE and Bastir, M and Stringer, C and Ogihara, N}, title = {Virtual reconstruction of the Neanderthal Amud 1 cranium.}, journal = {American journal of physical anthropology}, volume = {158}, number = {2}, pages = {185-197}, doi = {10.1002/ajpa.22777}, pmid = {26249757}, issn = {1096-8644}, abstract = {OBJECTIVES: We describe a new computer reconstruction to obtain complete anatomical information of the ecto- and endocranium from the imperfectly preserved skull of the Neanderthal Amud 1.

MATERIALS AND METHODS: Data were obtained from computed tomography scans of the fossil cranium. Adhesive and plaster were then virtually removed from the original specimen, and the fragments comprising the fossil cranium were separated. These fragments were then mathematically reassembled based on the smoothness of the joints. Both sides of the cranium were reassembled separately, and then aligned based on bilateral symmetry and the distance between the mandibular fossae obtained from the associated mandible. The position of the isolated maxilla was determined based on the position of the mandible that was anatomically articulated to the mandibular fossae. To restore missing basicranial and damaged endocranial regions, the cranium of Forbes' Quarry 1 was warped onto that of La Chapelle-aux-Saints 1, and the resulting composite Neanderthal cranium was then warped onto the reconstructed Amud 1 by an iterative thin-plate spline deformation.

RESULTS: Comparison of the computer reconstruction with the original indicated that the newly reconstructed Amud 1 cranium was slightly shorter and wider in the anteroposterior and mediolateral directions, respectively, suggesting that it was relatively more brachycephalic. The endocranial volume was estimated to be 1,736 cm3 , which was quite similar to the original estimated value of 1,740 cm3 .

DISCUSSION: This new computer reconstruction enables not only measurement of new cranial metrics, but also inclusion of the Amud 1 specimen in three-dimensional geometric morphometric analyses that were previously difficult due to its incompleteness. Am J Phys Anthropol 158:185-197, 2015. © 2015 Wiley Periodicals, Inc.}, } @article {pmid26223605, year = {2015}, author = {Callaway, E}, title = {Neanderthals had outsize effect on human biology.}, journal = {Nature}, volume = {523}, number = {7562}, pages = {512-513}, pmid = {26223605}, issn = {1476-4687}, mesh = {Animals ; Basic Helix-Loop-Helix Transcription Factors/genetics ; *Evolution, Molecular ; Genome-Wide Association Study ; Humans ; Hybridization, Genetic/*genetics ; Mice ; Mutation/*genetics ; Neanderthals/*genetics ; *Phenotype ; Toll-Like Receptors/genetics ; }, } @article {pmid26206078, year = {2015}, author = {Kutzner, A and Pramanik, S and Kim, PS and Heese, K}, title = {All-or-(N)One - an epistemological characterization of the human tumorigenic neuronal paralogous FAM72 gene loci.}, journal = {Genomics}, volume = {106}, number = {5}, pages = {278-285}, doi = {10.1016/j.ygeno.2015.07.003}, pmid = {26206078}, issn = {1089-8646}, mesh = {Animals ; Carrier Proteins/*genetics ; Chromosomes, Human, Pair 1 ; Computer Simulation ; Genes ; Genetic Loci ; Genomics ; Hominidae/genetics ; Humans ; Neanderthals/genetics ; Neoplasm Proteins/*genetics ; Phylogeny ; Proteins ; Segmental Duplications, Genomic ; }, abstract = {FAM72 is a novel neuronal progenitor cell (NPC) self-renewal supporting protein expressed under physiological conditions at low levels in other tissues. Accumulating data indicate the potential pivotal tumourigenic effects of FAM72. Our in silico human genome-wide analysis (GWA) revealed that the FAM72 gene family consists of four human-specific paralogous members, all of which are located on chromosome (chr) 1. Unique asymmetric FAM72 segmental gene duplications are most likely to have occurred in conjunction with the paired genomic neighbour SRGAP2 (SLIT-ROBO Rho GTPase activating protein), as both genes have four paralogues in humans but only one vertebra-emerging orthologue in all other species. No species with two or three FAM72/SRGAP2 gene pairs could be identified, and the four exclusively human-defining ohnologues, with different mutation patterns in Homo neanderthalensis and Denisova hominin, may remain under epigenetic control through long non-coding (lnc) RNAs.}, } @article {pmid26202576, year = {2015}, author = {Nakaoka, H and Inoue, I}, title = {Distribution of HLA haplotypes across Japanese Archipelago: similarity, difference and admixture.}, journal = {Journal of human genetics}, volume = {60}, number = {11}, pages = {683-690}, pmid = {26202576}, issn = {1435-232X}, mesh = {Animals ; Asian Continental Ancestry Group/*genetics ; Evolution, Molecular ; Gene Frequency ; Genetics, Population ; HLA Antigens/*genetics ; Haplotypes ; History, Ancient ; Hominidae/genetics/immunology ; Human Migration/history ; Humans ; Japan ; Linkage Disequilibrium ; Models, Genetic ; Neanderthals/genetics/immunology ; }, abstract = {The human leukocyte antigen (HLA) region is the most polymorphic region in the human genome. The polymorphic nature of the HLA region is thought to have been shaped from balancing selection. The complex migration events during the Out-of-Africa expansion have influenced geographic patterns of HLA allele frequencies and diversities across present-day human populations. Differences in the HLA allele frequency may contribute geographic differences in the susceptibility to many diseases, such as infectious, autoimmune and metabolic diseases. Here we briefly reviewed characteristics of frequency distribution of HLA alleles and haplotypes in Japanese population. A large part of HLA alleles and haplotypes that are common in Japanese are shared with neighboring Asian populations. The differentiations in HLA alleles and haplotypes across Japanese regional populations may provide clues to model for peopling of Japanese Archipelago and for design of genetic association studies. Finally, we introduce recent topics that new HLA alleles derived from ancient admixtures with Neanderthals and Denisovans are thought to have played an important role in the adaptation of modern humans to local pathogens during Out-of-Africa expansion.}, } @article {pmid26196116, year = {2015}, author = {Overmann, KA and Spinapolice, EE and Rios-Garaizar, J and Burke, A and Lorenzo, C and Garofoli, D and Bruner, E and Lozano, M}, title = {Three hands: one year later.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {93}, number = {}, pages = {163-195}, doi = {10.4436/JASS.93015}, pmid = {26196116}, issn = {2037-0644}, mesh = {Animals ; *Brain ; Humans ; *Neanderthals ; *Paleontology ; }, } @article {pmid26156123, year = {2015}, author = {Fish, I and Boissinot, S}, title = {Contrasted patterns of variation and evolutionary convergence at the antiviral OAS1 gene in old world primates.}, journal = {Immunogenetics}, volume = {67}, number = {9}, pages = {487-499}, pmid = {26156123}, issn = {1432-1211}, support = {P51 OD011133/OD/NIH HHS/United States ; P51 RR013986/RR/NCRR NIH HHS/United States ; }, mesh = {2',5'-Oligoadenylate Synthetase/*genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; Disease Resistance/*genetics ; Evolution, Molecular ; Haplotypes/*genetics ; Macaca fascicularis/genetics/immunology ; Macaca mulatta/genetics/immunology ; Papio anubis/genetics/immunology ; Papio papio/genetics/immunology ; Polymorphism, Genetic/*genetics ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The oligoadenylate synthetase 1 (OAS1) enzyme acts as an innate sensor of viral infection and plays a major role in the defense against a wide diversity of viruses. Polymorphisms at OAS1 have been shown to correlate with differential susceptibility to several infections of great public health significance, including hepatitis C virus, SARS coronavirus, and West Nile virus. Population genetics analyses in hominoids have revealed interesting evolutionary patterns. In Central African chimpanzee, OAS1 has evolved under long-term balancing selection, resulting in the persistence of polymorphisms since the origin of hominoids, whereas human populations have acquired and retained OAS1 alleles from Neanderthal and Denisovan origin. We decided to further investigate the evolution of OAS1 in primates by characterizing intra-specific variation in four species commonly used as models in infectious disease research: the rhesus macaque, the cynomolgus macaque, the olive baboon, and the Guinea baboon. In baboons, OAS1 harbors a very low level of variation. In contrast, OAS1 in macaques exhibits a level of polymorphism far greater than the genomic average, which is consistent with the action of balancing selection. The region of the enzyme that directly interacts with viral RNA, the RNA-binding domain, contains a number of polymorphisms likely to affect the RNA-binding affinity of OAS1. This strongly suggests that pathogen-driven balancing selection acting on the RNA-binding domain of OAS1 is maintaining variation at this locus. Interestingly, we found that a number of polymorphisms involved in RNA-binding were shared between macaques and chimpanzees. This represents an unusual case of convergent polymorphism.}, } @article {pmid26154139, year = {2015}, author = {Zilhão, J and Banks, WE and d'Errico, F and Gioia, P}, title = {Analysis of Site Formation and Assemblage Integrity Does Not Support Attribution of the Uluzzian to Modern Humans at Grotta del Cavallo.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0131181}, pmid = {26154139}, issn = {1932-6203}, mesh = {Animals ; Archaeology ; *Fossils ; Geography ; History, Ancient ; Humans ; Italy ; Mandible/*anatomy & histology ; Molar/*anatomy & histology ; Neanderthals/*anatomy & histology ; Radiometric Dating ; Tooth, Deciduous/*anatomy & histology ; }, abstract = {Based on the morphology of two deciduous molars and radiocarbon ages from layers D and E of the Grotta del Cavallo (Lecce, Italy), assigned to the Uluzzian, it has been proposed that modern humans were the makers of this Early Upper Paleolithic culture and that this finding considerably weakens the case for an independent emergence of symbolism among western European Neandertals. Reappraisal of the new dating evidence, of the finds curated in the Taranto Antiquities depot, and of coeval publications detailing the site's 1963-66 excavations shows that (a) Protoaurignacian, Aurignacian and Early Epigravettian lithics exist in the assemblages from layers D and E, (b) even though it contains both inherited and intrusive items, the formation of layer D began during Protoaurignacian times, and (c) the composition of the extant Cavallo assemblages is influenced in a non-negligible manner by the post-hoc assignment of items to stratigraphic units distinct from that of original discovery. In addition, a major disturbance feature affected the 1960s excavation trench down to Mousterian layer F, this feature went unrecognized until 1964, the human remains assigned to the Uluzzian were discovered that year and/or the previous year, and there are contradictions between field reports and the primary anthropological description of the remains as to their morphology and level of provenience. Given these major contextual uncertainties, the Cavallo teeth cannot be used to establish the authorship of the Uluzzian. Since this technocomplex's start date is ca. 45,000 calendar years ago, a number of Neandertal fossils are dated to this period, and the oldest diagnostic European modern human fossil is the <41,400 year-old Oase 1 mandible, Neandertal authorship of the Uluzzian remains the parsimonious reading of the evidence.}, } @article {pmid26137909, year = {2016}, author = {Fraïsse, C and Belkhir, K and Welch, JJ and Bierne, N}, title = {Local interspecies introgression is the main cause of extreme levels of intraspecific differentiation in mussels.}, journal = {Molecular ecology}, volume = {25}, number = {1}, pages = {269-286}, doi = {10.1111/mec.13299}, pmid = {26137909}, issn = {1365-294X}, mesh = {Alleles ; Animals ; Contig Mapping ; *Gene Flow ; *Genetic Speciation ; *Genetics, Population ; Geography ; Mytilus/classification/*genetics ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {Structured populations, and replicated zones of contact between species, are an ideal opportunity to study regions of the genome with unusual levels of differentiation; and these can illuminate the genomic architecture of species isolation, and the spread of adaptive alleles across species ranges. Here, we investigated the effects of gene flow on divergence and adaptation in the Mytilus complex of species, including replicated parental populations in quite distant geographical locations. We used target enrichment sequencing of 1269 contigs of a few kb each, including some genes of known function, to infer gene genealogies at a small chromosomal scale. We show that geography is an important determinant of the genomewide patterns of introgression in Mytilus and that gene flow between different species, with contiguous ranges, explained up to half of the intraspecific outliers. This suggests that local introgression is both widespread and tends to affect larger chromosomal regions than purely intraspecific processes. We argue that this situation might be common, and this implies that genome scans should always consider the possibility of introgression from sister species, unsampled differentiated backgrounds, or even extinct relatives, for example Neanderthals in humans. The hypothesis that reticulate evolution over long periods of time contributes widely to adaptation, and to the spatial and genomic reorganization of genetic backgrounds, needs to be more widely considered to make better sense of genome scans.}, } @article {pmid26136701, year = {2015}, author = {Benítez-Burraco, A and Boeckx, C}, title = {Possible functional links among brain- and skull-related genes selected in modern humans.}, journal = {Frontiers in psychology}, volume = {6}, number = {}, pages = {794}, pmid = {26136701}, issn = {1664-1078}, abstract = {The sequencing of the genomes from extinct hominins has revealed that changes in some brain-related genes have been selected after the split between anatomically-modern humans and Neanderthals/Denisovans. To date, no coherent view of these changes has been provided. Following a line of research we initiated in Boeckx and Benítez-Burraco (2014a), we hypothesize functional links among most of these genes and their products, based on the existing literature for each of the gene discussed. The genes we focus on are found mutated in different cognitive disorders affecting modern populations and their products are involved in skull and brain morphology, and neural connectivity. If our hypothesis turns out to be on the right track, it means that the changes affecting most of these proteins resulted in a more globular brain and ultimately brought about modern cognition, with its characteristic generativity and capacity to form and exploit cross-modular concepts, properties most clearly manifested in language.}, } @article {pmid26119715, year = {2015}, author = {Schillaci, MA}, title = {Body mass as a confounding variable when predicting group size from orbit diameter and neocortex ratio.}, journal = {American journal of physical anthropology}, volume = {158}, number = {1}, pages = {170-171}, doi = {10.1002/ajpa.22781}, pmid = {26119715}, issn = {1096-8644}, mesh = {Animals ; Neanderthals/*anatomy & histology/*physiology ; Orbit/*anatomy & histology ; *Social Behavior ; }, } @article {pmid26104010, year = {2015}, author = {Qin, P and Stoneking, M}, title = {Denisovan Ancestry in East Eurasian and Native American Populations.}, journal = {Molecular biology and evolution}, volume = {32}, number = {10}, pages = {2665-2674}, doi = {10.1093/molbev/msv141}, pmid = {26104010}, issn = {1537-1719}, mesh = {Animals ; Consanguinity ; Gene Flow ; *Genealogy and Heraldry ; Geography ; Hominidae/genetics ; Humans ; Indians, North American/*genetics ; Models, Genetic ; Oceanic Ancestry Group/genetics ; Siberia ; }, abstract = {Although initial studies suggested that Denisovan ancestry was found only in modern human populations from island Southeast Asia and Oceania, more recent studies have suggested that Denisovan ancestry may be more widespread. However, the geographic extent of Denisovan ancestry has not been determined, and moreover the relationship between the Denisovan ancestry in Oceania and that elsewhere has not been studied. Here we analyze genome-wide single nucleotide polymorphism data from 2,493 individuals from 221 worldwide populations, and show that there is a widespread signal of a very low level of Denisovan ancestry across Eastern Eurasian and Native American (EE/NA) populations. We also verify a higher level of Denisovan ancestry in Oceania than that in EE/NA; the Denisovan ancestry in Oceania is correlated with the amount of New Guinea ancestry, but not the amount of Australian ancestry, indicating that recent gene flow from New Guinea likely accounts for signals of Denisovan ancestry across Oceania. However, Denisovan ancestry in EE/NA populations is equally correlated with their New Guinea or their Australian ancestry, suggesting a common source for the Denisovan ancestry in EE/NA and Oceanian populations. Our results suggest that Denisovan ancestry in EE/NA is derived either from common ancestry with, or gene flow from, the common ancestor of New Guineans and Australians, indicating a more complex history involving East Eurasians and Oceanians than previously suspected.}, } @article {pmid26100767, year = {2016}, author = {Hlusko, LJ}, title = {Elucidating the evolution of hominid dentition in the age of phenomics, modularity, and quantitative genetics.}, journal = {Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft}, volume = {203}, number = {}, pages = {3-11}, doi = {10.1016/j.aanat.2015.05.001}, pmid = {26100767}, issn = {1618-0402}, support = {P51 RR013986SUPPORTS/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; *Dentition ; *Genetics ; Hominidae/*physiology ; Humans ; Neanderthals ; Tooth/*anatomy & histology ; }, abstract = {An organism's anatomy is the result of millions of years of interplay between DNA sequence, developmental processes, the environment, and evolutionary forces. The anatomical sciences are consequently highly integrative and interdisciplinary. That said, reaching across all of the relevant disciplines can be a daunting task because scientific publications are produced today at an astounding rate. This manuscript brings together insights from the quantitative genetic analysis of dental variation into the study of human evolutionary odontology within the context of genomics, genetic modularity, and phenomics. It primarily advocates the use of quantitative genetics to not only identify QTLs, but also to assess the patterns of genetic covariance that underlie phenotypic covariance, thereby enabling us to conceptualize phenotypic variation as a reflection of the underlying genetic mechanisms. By highlighting three phenotypes of importance within the study of human evolution (patterning of the dental arcade, enamel thickness, and taurodontism), it is demonstrated how an integrated consideration of quantitative genetics, genomic analyses, and paleontology can bring us to more detailed hypotheses about the evolution of the hominid clade.}, } @article {pmid26098372, year = {2015}, author = {Fu, Q and Hajdinjak, M and Moldovan, OT and Constantin, S and Mallick, S and Skoglund, P and Patterson, N and Rohland, N and Lazaridis, I and Nickel, B and Viola, B and Prüfer, K and Meyer, M and Kelso, J and Reich, D and Pääbo, S}, title = {An early modern human from Romania with a recent Neanderthal ancestor.}, journal = {Nature}, volume = {524}, number = {7564}, pages = {216-219}, pmid = {26098372}, issn = {1476-4687}, support = {R01 GM100233/GM/NIGMS NIH HHS/United States ; GM100233/GM/NIGMS NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; }, mesh = {Alleles ; Animals ; Asian Continental Ancestry Group/genetics ; European Continental Ancestry Group/genetics ; Far East ; *Fossils ; Genome, Human/genetics ; Humans ; Hybridization, Genetic/*genetics ; Indians, North American/genetics ; Male ; Neanderthals/*genetics ; *Phylogeny ; Romania ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {Neanderthals are thought to have disappeared in Europe approximately 39,000-41,000 years ago but they have contributed 1-3% of the DNA of present-day people in Eurasia. Here we analyse DNA from a 37,000-42,000-year-old modern human from Peştera cu Oase, Romania. Although the specimen contains small amounts of human DNA, we use an enrichment strategy to isolate sites that are informative about its relationship to Neanderthals and present-day humans. We find that on the order of 6-9% of the genome of the Oase individual is derived from Neanderthals, more than any other modern human sequenced to date. Three chromosomal segments of Neanderthal ancestry are over 50 centimorgans in size, indicating that this individual had a Neanderthal ancestor as recently as four to six generations back. However, the Oase individual does not share more alleles with later Europeans than with East Asians, suggesting that the Oase population did not contribute substantially to later humans in Europe.}, } @article {pmid26072518, year = {2015}, author = {Hoover, KC and Gokcumen, O and Qureshy, Z and Bruguera, E and Savangsuksa, A and Cobb, M and Matsunami, H}, title = {Global Survey of Variation in a Human Olfactory Receptor Gene Reveals Signatures of Non-Neutral Evolution.}, journal = {Chemical senses}, volume = {40}, number = {7}, pages = {481-488}, pmid = {26072518}, issn = {1464-3553}, support = {DC005782/DC/NIDCD NIH HHS/United States ; }, mesh = {Alleles ; Base Sequence ; DNA/genetics ; *Evolution, Molecular ; Genetic Variation/*genetics ; Humans ; Polymorphism, Single Nucleotide/genetics ; Receptors, Odorant/*genetics ; }, abstract = {Allelic variation at 4 loci in the human olfactory receptor gene OR7D4 is associated with perceptual variation in the sex steroid-derived odorants, androstenone, and androstadienone. Androstadienone has been linked with chemosensory identification whereas androstenone makes pork from uncastrated pigs distasteful ("boar taint"). In a sample of 2224 individuals from 43 populations, we identified 45 OR7D4 single nucleotide polymorphisms. Coalescent modeling of frequency-site-spectrum-based statistics identified significant deviation from neutrality in human OR7D4; individual populations with statistically significant deviations from neutrality include Gujarati, Beijing Han, Great Britain, Iberia, and Puerto Rico. Analysis of molecular variation values indicated statistically significant population differentiation driven mainly by the 4 alleles associated with androstenone perception variation; however, fixation values were low suggesting that genetic structure may not have played a strong role in creating these group divisions. We also studied OR7D4 in the genomes of extinct members of the human lineage: Altai Neandertal and Denisovan. No variants were identified in Altai but 2 were in Denisova, one of which is shared by modern humans and one of which is novel. A functional test of modern human and a synthesized mutant Denisova OR7D4 indicated no statistically significant difference in responses to androstenone between the 2 species. Our results suggest non-neutral evolution for an olfactory receptor gene.}, } @article {pmid26064624, year = {2015}, author = {Diedrich, CG}, title = {'Neanderthal bone flutes': simply products of Ice Age spotted hyena scavenging activities on cave bear cubs in European cave bear dens.}, journal = {Royal Society open science}, volume = {2}, number = {4}, pages = {140022}, pmid = {26064624}, issn = {2054-5703}, abstract = {Punctured extinct cave bear femora were misidentified in southeastern Europe (Hungary/Slovenia) as 'Palaeolithic bone flutes' and the 'oldest Neanderthal instruments'. These are not instruments, nor human made, but products of the most important cave bear scavengers of Europe, hyenas. Late Middle to Late Pleistocene (Mousterian to Gravettian) Ice Age spotted hyenas of Europe occupied mainly cave entrances as dens (communal/cub raising den types), but went deeper for scavenging into cave bear dens, or used in a few cases branches/diagonal shafts (i.e. prey storage den type). In most of those dens, about 20% of adult to 80% of bear cub remains have large carnivore damage. Hyenas left bones in repeating similar tooth mark and crush damage stages, demonstrating a butchering/bone cracking strategy. The femora of subadult cave bears are intermediate in damage patterns, compared to the adult ones, which were fully crushed to pieces. Hyenas produced round-oval puncture marks in cub femora only by the bone-crushing premolar teeth of both upper and lower jaw. The punctures/tooth impact marks are often present on both sides of the shaft of cave bear cub femora and are simply a result of non-breakage of the slightly calcified shaft compacta. All stages of femur puncturing to crushing are demonstrated herein, especially on a large cave bear population from a German cave bear den.}, } @article {pmid26059778, year = {2015}, author = {Chevalier, T and Özçelik, K and de Lumley, MA and Kösem, B and de Lumley, H and Yalçinkaya, I and Taşkiran, H}, title = {The endostructural pattern of a middle pleistocene human femoral diaphysis from the Karain E site (Southern Anatolia, Turkey).}, journal = {American journal of physical anthropology}, volume = {157}, number = {4}, pages = {648-658}, doi = {10.1002/ajpa.22762}, pmid = {26059778}, issn = {1096-8644}, mesh = {Adolescent ; Adult ; Animals ; Anthropology, Physical ; Biological Evolution ; Diaphyses/*anatomy & histology ; Female ; Femur/*anatomy & histology ; Fossils ; Hominidae/*anatomy & histology ; Humans ; Male ; Neanderthals/*anatomy & histology ; Turkey ; Young Adult ; }, abstract = {OBJECTIVE: The human femur from Karain E Cave (Turkey) exhumed from a Mousterian level provided the opportunity to make an incursion into the structural morphology of a late adolescent, or a young adult, femoral shaft from the late Middle Pleistocene of Anatolia.

METHODS: Considering the chrono-ecogeographical context, this study focuses particularly on the endostructural morphological similarities between Karain and Neanderthal fossils.

RESULTS: Comparative analysis shows that some femoral features of the Karain specimen are frequently observed in Neanderthals, in comparison to some Middle Pleistocene Homo and Middle/Upper Paleolithic modern humans. In particular, we note a high degree of circularity and a strong midshaft posteromedial reinforcement of cortical thickness on the medial side. According to the mapping of cortical thickness, this latter feature can be related to the medial spiral distribution pattern of cortical thickness in the mid-proximal shaft, which is present at Karain and in all Neanderthals available for this study. This spiral distribution was not identified in recent modern humans and may be absent from ancient Homo with femoral pilaster.

CONCLUSIONS: The endostructural signature of Karain could indicate a similar biomechanical strain system to that of Neanderthals that could be linked to body shape. However, the presence of posteromedial reinforcement in Berg Aukas may point to an ancestral feature and may be independent of latitude. A larger comparative sample should further clarify the taxonomical, biomechanical, and chrono-ecogeographical origins of the structural femoral features observed in an evolutionary Neanderthal context from MIS 7-9 in Karain.}, } @article {pmid26059551, year = {2015}, author = {Xing, S and Guatelli-Steinberg, D and O'Hara, M and Wu, X and Liu, W and Reid, DJ}, title = {Perikymata distribution in Homo with special reference to the Xujiayao juvenile.}, journal = {American journal of physical anthropology}, volume = {157}, number = {4}, pages = {684-693}, doi = {10.1002/ajpa.22760}, pmid = {26059551}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; China ; Dental Enamel/*anatomy & histology/growth & development ; Hominidae/*physiology ; Neanderthals/anatomy & histology ; Tooth/*anatomy & histology ; }, abstract = {OBJECTIVES: This study investigates where the Xujiayao juvenile (I(1) and C(1)) fits into the array of perikymata distribution patterns found within the genus Homo.

MATERIALS AND METHODS: In addition to the I(1) and the C(1) of the Xujiayao juvenile, this study includes samples of early Homo (H. rudolfensis and H. erectus), Neandertals, early modern humans (Qafzeh), and recent modern humans from Southern Africa, Newcastle (UK), and North America (Inupiaq, AK). Three sets of analyses were undertaken, including a comparison of percentage of perikymata in the cervical half of the crown, repeated measures analysis of the percentage of total perikymata in each decile, and canonical variates analysis using both total perikymata number and the percentage of perikymata in the cervical half of the crown.

RESULTS: The I(1) and C(1) of early Homo and Neandertals have a lower percentage of perikymata in the cervical half of the crown than modern human samples. Repeated measures analysis reveals clear distinctions in the distribution of perikymata between the modern human and fossil samples. Canonical variates analysis suggests greater differences between modern humans and the fossil samples than within the fossil samples, and classifies the Xujiayao teeth among modern humans.

DISCUSSION: The present study further clarifies variation of perikymata distribution patterns within the genus Homo. The perikymata distribution of the Xujiayao juvenile tends to be more similar to that of modern humans than to either early Homo or Neandertals.}, } @article {pmid26053380, year = {2015}, author = {Fregel, R and Cabrera, V and Larruga, JM and Abu-Amero, KK and González, AM}, title = {Carriers of Mitochondrial DNA Macrohaplogroup N Lineages Reached Australia around 50,000 Years Ago following a Northern Asian Route.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0129839}, pmid = {26053380}, issn = {1932-6203}, mesh = {Asia ; Australia ; DNA, Mitochondrial/*genetics ; Ethnic Groups/*genetics ; Evolution, Molecular ; *Genetics, Population ; Haplotypes ; *Heterozygote ; Human Migration ; Humans ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The modern human colonization of Eurasia and Australia is mostly explained by a single-out-of-Africa exit following a southern coastal route throughout Arabia and India. However, dispersal across the Levant would better explain the introgression with Neanderthals, and more than one exit would fit better with the different ancient genomic components discovered in indigenous Australians and in ancient Europeans. The existence of an additional Northern route used by modern humans to reach Australia was previously deduced from the phylogeography of mtDNA macrohaplogroup N. Here, we present new mtDNA data and new multidisciplinary information that add more support to this northern route.

METHODS: MtDNA hypervariable segments and haplogroup diagnostic coding positions were analyzed in 2,278 Saudi Arabs, from which 1,725 are new samples. Besides, we used 623 published mtDNA genomes belonging to macrohaplogroup N, but not R, to build updated phylogenetic trees to calculate their coalescence ages, and more than 70,000 partial mtDNA sequences were screened to establish their respective geographic ranges.

RESULTS: The Saudi mtDNA profile confirms the absence of autochthonous mtDNA lineages in Arabia with coalescence ages deep enough to support population continuity in the region since the out-of-Africa episode. In contrast to Australia, where N(xR) haplogroups are found in high frequency and with deep coalescence ages, there are not autochthonous N(xR) lineages in India nor N(xR) branches with coalescence ages as deep as those found in Australia. These patterns are at odds with the supposition that Australian colonizers harboring N(xR) lineages used a route involving India as a stage. The most ancient N(xR) lineages in Eurasia are found in China, and inconsistently with the coastal route, N(xR) haplogroups with the southernmost geographical range have all more recent radiations than the Australians.

CONCLUSIONS: Apart from a single migration event via a southern route, phylogeny and phylogeography of N(xR) lineages support that people carrying mtDNA N lineages could have reach Australia following a northern route through Asia. Data from other disciplines also support this scenario.}, } @article {pmid26000734, year = {2015}, author = {Kari, L and Hill, KA and Sayem, AS and Karamichalis, R and Bryans, N and Davis, K and Dattani, NS}, title = {Mapping the space of genomic signatures.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0119815}, pmid = {26000734}, issn = {1932-6203}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Models, Theoretical ; }, abstract = {We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. An "image distance" is computed for each pair of graphical representations of DNA sequences, and the distances are visualized as a Molecular Distance Map: Each point on the map represents a DNA sequence, and the spatial proximity between any two points reflects the degree of structural similarity between the corresponding sequences. The graphical representation of DNA sequences utilized, Chaos Game Representation (CGR), is genome- and species-specific and can thus act as a genomic signature. Consequently, Molecular Distance Maps could inform species identification, taxonomic classifications and, to a certain extent, evolutionary history. The image distance employed, Structural Dissimilarity Index (DSSIM), implicitly compares the occurrences of oligomers of length up to k (herein k = 9) in DNA sequences. We computed DSSIM distances for more than 5 million pairs of complete mitochondrial genomes, and used Multi-Dimensional Scaling (MDS) to obtain Molecular Distance Maps that visually display the sequence relatedness in various subsets, at different taxonomic levels. This general-purpose method does not require DNA sequence alignment and can thus be used to compare similar or vastly different DNA sequences, genomic or computer-generated, of the same or different lengths. We illustrate potential uses of this approach by applying it to several taxonomic subsets: phylum Vertebrata, (super)kingdom Protista, classes Amphibia-Insecta-Mammalia, class Amphibia, and order Primates. This analysis of an extensive dataset confirms that the oligomer composition of full mtDNA sequences can be a source of taxonomic information. This method also correctly finds the mtDNA sequences most closely related to that of the anatomically modern human (the Neanderthal, the Denisovan, and the chimp), and that the sequence most different from it in this dataset belongs to a cucumber.}, } @article {pmid25999485, year = {2015}, author = {Gibbons, A}, title = {Human evolution. Ancient DNA pinpoints Paleolithic liaison in Europe.}, journal = {Science (New York, N.Y.)}, volume = {348}, number = {6237}, pages = {847}, doi = {10.1126/science.348.6237.847}, pmid = {25999485}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; DNA/*genetics ; Europe ; *Fossils ; Humans ; *Mandible ; Neanderthals/*genetics ; }, } @article {pmid25982166, year = {2015}, author = {Pääbo, S}, title = {The diverse origins of the human gene pool.}, journal = {Nature reviews. Genetics}, volume = {16}, number = {6}, pages = {313-314}, pmid = {25982166}, issn = {1471-0064}, mesh = {Animals ; *Evolution, Molecular ; Gene Flow ; *Genome, Human ; Humans ; Neanderthals/genetics ; Sequence Analysis, DNA ; }, abstract = {Analyses of the genomes of Neanderthals and Denisovans, the closest evolutionary relatives of present-day humans, suggest that our ancestors were part of a web of now-extinct populations linked by limited, but intermittent or sometimes perhaps even persistent, gene flow.}, } @article {pmid25980758, year = {2015}, author = {Heyes, P and MacDonald, K}, title = {Neandertal energetics: Uncertainty in body mass estimation limits comparisons with Homo sapiens.}, journal = {Journal of human evolution}, volume = {85}, number = {}, pages = {193-197}, doi = {10.1016/j.jhevol.2015.04.007}, pmid = {25980758}, issn = {1095-8606}, mesh = {Animals ; Anthropology, Physical ; Basal Metabolism/*physiology ; Body Size/*physiology ; Energy Metabolism/*physiology ; Female ; Humans ; Locomotion/physiology ; Male ; Neanderthals/*metabolism ; }, } @article {pmid25976251, year = {2015}, author = {Gravina, B and Discamps, E}, title = {MTA-B or not to be? Recycled bifaces and shifting hunting strategies at Le Moustier and their implication for the late Middle Palaeolithic in southwestern France.}, journal = {Journal of human evolution}, volume = {84}, number = {}, pages = {83-98}, doi = {10.1016/j.jhevol.2015.04.005}, pmid = {25976251}, issn = {1095-8606}, mesh = {Animals ; Archaeology ; Diet ; France ; Neanderthals/*physiology ; *Tool Use Behavior ; }, abstract = {Explaining late Middle Palaeolithic industrial variability remains a topic of great interest for researchers focusing on aspects of Neanderthal behavioural complexity and the so-called Middle-to-Upper Paleolithic 'transition.' Several sites in southwestern France figure prominently in these discussions, including the eponymous site of Le Moustier (Dordogne, France), one of the 'key' sequences used in larger anthropological models. Here we present a re-assessment of this important site based on a technological and taphonomic re-evaluation of previously studied collections combined with an analysis of unpublished archaeological material, which includes both lithic and faunal components. Our study produces a very different interpretation of the 'classic' Le Moustier sequence, challenging previous cultural attributions in a way that significantly impacts current debates surrounding the proposed Mousterian of Acheulean Tradition (MTA)--Châtelperronian affiliation. This new interpretation highlights independent changes in lithic technology and subsistence strategies that were previously undetected as well as a novel aspect of Neanderthal raw material use. Finally, we discuss how this new vision has important ramifications for broader issues connected to the definition of late Mousterian techno-complexes, such as the MTA, and the identification of relationships between technology, subsistence, and mobility strategies.}, } @article {pmid25963373, year = {2015}, author = {Racimo, F and Sankararaman, S and Nielsen, R and Huerta-Sánchez, E}, title = {Evidence for archaic adaptive introgression in humans.}, journal = {Nature reviews. Genetics}, volume = {16}, number = {6}, pages = {359-371}, pmid = {25963373}, issn = {1471-0064}, support = {R01HG003229-09/HG/NHGRI NIH HHS/United States ; R01 GM040282/GM/NIGMS NIH HHS/United States ; R01 HG003229/HG/NHGRI NIH HHS/United States ; R01‑GM40282/GM/NIGMS NIH HHS/United States ; K99 GM111744/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Biological/genetics ; Animals ; Evolution, Molecular ; Gene Flow ; Genome, Human ; Haplotypes ; Humans ; Linkage Disequilibrium ; Markov Chains ; *Models, Genetic ; Neanderthals/genetics ; Phylogeny ; Selection, Genetic ; }, abstract = {As modern and ancient DNA sequence data from diverse human populations accumulate, evidence is increasing in support of the existence of beneficial variants acquired from archaic humans that may have accelerated adaptation and improved survival in new environments - a process known as adaptive introgression. Within the past few years, a series of studies have identified genomic regions that show strong evidence for archaic adaptive introgression. Here, we provide an overview of the statistical methods developed to identify archaic introgressed fragments in the genome sequences of modern humans and to determine whether positive selection has acted on these fragments. We review recently reported examples of adaptive introgression, grouped by selection pressure, and consider the level of supporting evidence for each. Finally, we discuss challenges and recommendations for inferring selection on introgressed regions.}, } @article {pmid25957654, year = {2015}, author = {Hartman, G and Hovers, E and Hublin, JJ and Richards, M}, title = {Isotopic evidence for Last Glacial climatic impacts on Neanderthal gazelle hunting territories at Amud Cave, Israel.}, journal = {Journal of human evolution}, volume = {84}, number = {}, pages = {71-82}, doi = {10.1016/j.jhevol.2015.03.008}, pmid = {25957654}, issn = {1095-8606}, mesh = {Animals ; Antelopes/*physiology ; Archaeology ; Carbon Isotopes/analysis ; Dental Enamel/chemistry ; *Diet ; *Homing Behavior ; Israel ; Neanderthals/*physiology ; Oxygen Isotopes/analysis ; Paleontology ; Strontium Isotopes/analysis ; }, abstract = {The Middle Paleolithic site of Amud Cave, Israel, was occupied by Neanderthals at two different time periods, evidenced by two chronologically and stratigraphically distinct depositional sub-units (B4 and B2/B1) during MIS 4 and MIS 3, respectively. The composition of both hunted large fauna and naturally-deposited micromammalian taxa is stable at the site over time, despite a ∼ 10 ky gap between the two occupation phases. However, while gazelle is the most ubiquitous hunted species throughout the occupation, isotopic analysis showed that there is a marked change in Neanderthal hunting ranges between the early (B4) and late (B2/B1) phases. Hunting ranges were reconstructed by comparing oxygen, carbon, and strontium isotopes from gazelle tooth enamel with modern isotope data from the Amud Cave region. This region is characterized by extensive topographic, lithological, and pedological heterogeneity. During the early occupation phase negative oxygen isotope values, low radiogenic (87)Sr/(86)Sr ratios, and low Sr concentrations reveal restricted gazelle hunting in the high elevations west of Amud Cave. In the late occupation phase, hunting ranges became more diverse, but concentrate at low elevations closer to the site. Climatic proxies indicate that conditions were drier in the early occupation phase, which may have pushed gazelle populations into higher, more productive foraging areas. This study showed that Neanderthals adjusted their hunting territories considerably in relation to varying environmental conditions over the course of occupation in Amud Cave. It highlights the utility of multiple isotope analysis in enhancing the resolution of behavioral interpretations based on faunal remains and in reconstructing past hunting behaviors of Paleolithic hominins.}, } @article {pmid25956794, year = {2015}, author = {Glinsky, GV}, title = {Transposable Elements and DNA Methylation Create in Embryonic Stem Cells Human-Specific Regulatory Sequences Associated with Distal Enhancers and Noncoding RNAs.}, journal = {Genome biology and evolution}, volume = {7}, number = {6}, pages = {1432-1454}, pmid = {25956794}, issn = {1759-6653}, mesh = {Animals ; Binding Sites ; Brain/metabolism ; Cell Differentiation ; Chromatin/metabolism ; *DNA Methylation ; Embryonic Stem Cells/*metabolism ; *Enhancer Elements, Genetic ; Evolution, Molecular ; Genome, Human ; Homeodomain Proteins/metabolism ; Humans ; Mice ; Mutation ; Nanog Homeobox Protein ; Nuclear Lamina/genetics ; Primates ; RNA, Long Noncoding/genetics ; RNA, Untranslated/*genetics ; *Regulatory Elements, Transcriptional ; *Retroelements ; Transcription Factors/metabolism ; Transcription, Genetic ; }, abstract = {Despite significant progress in the structural and functional characterization of the human genome, understanding of the mechanisms underlying the genetic basis of human phenotypic uniqueness remains limited. Here, I report that transposable element-derived sequences, most notably LTR7/HERV-H, LTR5_Hs, and L1HS, harbor 99.8% of the candidate human-specific regulatory loci (HSRL) with putative transcription factor-binding sites in the genome of human embryonic stem cells (hESC). A total of 4,094 candidate HSRL display selective and site-specific binding of critical regulators (NANOG [Nanog homeobox], POU5F1 [POU class 5 homeobox 1], CCCTC-binding factor [CTCF], Lamin B1), and are preferentially located within the matrix of transcriptionally active DNA segments that are hypermethylated in hESC. hESC-specific NANOG-binding sites are enriched near the protein-coding genes regulating brain size, pluripotency long noncoding RNAs, hESC enhancers, and 5-hydroxymethylcytosine-harboring regions immediately adjacent to binding sites. Sequences of only 4.3% of hESC-specific NANOG-binding sites are present in Neanderthals' genome, suggesting that a majority of these regulatory elements emerged in Modern Humans. Comparisons of estimated creation rates of novel TF-binding sites revealed that there was 49.7-fold acceleration of creation rates of NANOG-binding sites in genomes of Chimpanzees compared with the mouse genomes and further 5.7-fold acceleration in genomes of Modern Humans compared with the Chimpanzees genomes. Preliminary estimates suggest that emergence of one novel NANOG-binding site detectable in hESC required 466 years of evolution. Pathway analysis of coding genes that have hESC-specific NANOG-binding sites within gene bodies or near gene boundaries revealed their association with physiological development and functions of nervous and cardiovascular systems, embryonic development, behavior, as well as development of a diverse spectrum of pathological conditions such as cancer, diseases of cardiovascular and reproductive systems, metabolic diseases, multiple neurological and psychological disorders. A proximity placement model is proposed explaining how a 33-47% excess of NANOG, CTCF, and POU5F1 proteins immobilized on a DNA scaffold may play a functional role at distal regulatory elements.}, } @article {pmid25921695, year = {2015}, author = {Traynor, S and Gurtov, AN and Senjem, JH and Hawks, J}, title = {Assessing eye orbits as predictors of Neandertal group size.}, journal = {American journal of physical anthropology}, volume = {157}, number = {4}, pages = {680-683}, doi = {10.1002/ajpa.22747}, pmid = {25921695}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; Linear Models ; Neanderthals/*anatomy & histology/*physiology ; Neocortex/anatomy & histology ; Orbit/*anatomy & histology ; *Social Behavior ; }, abstract = {OBJECTIVES: The objective is to investigate the hypothesis that Neandertal eye orbits can predict group size and social cognition as presented by Pearce et al. (Proc R Soc B Biol Sci 280 (2013) 20130168).

MATERIALS AND METHODS: We performed a linear regression of known orbital aperture diameter (OAD), neocortex ratio, and group size among 18 extant diurnal primate species. Our data were derived from Kirk (J Hum Evol 51 (2006) 159-170) and Dunbar (J Hum Evol 22 (1992), 469-493; J Hum Evol 28 (1995) 287-296).

RESULTS: There is a positive correlation between OAD and group size; a positive correlation between neocortex and group size; and a positive correlation between OAD and neocortex size. The strength of the collinearity between OAD and neocortex ratio accounts for any significance of OAD in a model. The model that best accounts for variation in group size is one that includes only neocortex ratio; including OAD does not strengthen the model. OAD accounts for 29 percent of the variation in group size.

DISCUSSION: Larger orbits are correlated with larger group sizes in primates, although not significantly when controlling for neocortex ratio. Moreover, the amount of variation in group size that can be explained by OAD is negligible. The larger orbits of Neandertals compared to the average modern human population do not permit any interpretation of cognitive ability related to group size.}, } @article {pmid25908661, year = {2015}, author = {Conard, NJ and Bolus, M}, title = {Anthropology. Chronicling modern human's arrival in Europe.}, journal = {Science (New York, N.Y.)}, volume = {348}, number = {6236}, pages = {754-756}, doi = {10.1126/science.aab0234}, pmid = {25908661}, issn = {1095-9203}, mesh = {Animals ; *Extinction, Biological ; Humans ; Neanderthals/*classification/*genetics ; *Phylogeny ; }, } @article {pmid25908660, year = {2015}, author = {Benazzi, S and Slon, V and Talamo, S and Negrino, F and Peresani, M and Bailey, SE and Sawyer, S and Panetta, D and Vicino, G and Starnini, E and Mannino, MA and Salvadori, PA and Meyer, M and Pääbo, S and Hublin, JJ}, title = {Archaeology. The makers of the Protoaurignacian and implications for Neandertal extinction.}, journal = {Science (New York, N.Y.)}, volume = {348}, number = {6236}, pages = {793-796}, doi = {10.1126/science.aaa2773}, pmid = {25908660}, issn = {1095-9203}, mesh = {Animals ; Archaeology ; Base Sequence ; DNA, Mitochondrial/analysis/genetics ; Dental Enamel/chemistry ; *Extinction, Biological ; Genome, Mitochondrial/genetics ; Humans ; Incisor/anatomy & histology/chemistry ; Molecular Sequence Data ; Neanderthals/anatomy & histology/*classification/*genetics ; *Phylogeny ; Tooth, Deciduous/anatomy & histology/chemistry ; }, abstract = {The Protoaurignacian culture is pivotal to the debate about the timing of the arrival of modern humans in western Europe and the demise of Neandertals. However, which group is responsible for this culture remains uncertain. We investigated dental remains associated with the Protoaurignacian. The lower deciduous incisor from Riparo Bombrini is modern human, based on its morphology. The upper deciduous incisor from Grotta di Fumane contains ancient mitochondrial DNA of a modern human type. These teeth are the oldest human remains in an Aurignacian-related archaeological context, confirming that by 41,000 calendar years before the present, modern humans bearing Protoaurignacian culture spread into southern Europe. Because the last Neandertals date to 41,030 to 39,260 calendar years before the present, we suggest that the Protoaurignacian triggered the demise of Neandertals in this area.}, } @article {pmid25888025, year = {2015}, author = {Pease, JB and Hahn, MW}, title = {Detection and Polarization of Introgression in a Five-Taxon Phylogeny.}, journal = {Systematic biology}, volume = {64}, number = {4}, pages = {651-662}, doi = {10.1093/sysbio/syv023}, pmid = {25888025}, issn = {1076-836X}, mesh = {Animals ; Classification/*methods ; Computer Simulation ; Data Interpretation, Statistical ; Humans ; Neanderthals/classification ; *Phylogeny ; }, abstract = {When multiple speciation events occur rapidly in succession, discordant genealogies due to incomplete lineage sorting (ILS) can complicate the detection of introgression. A variety of methods, including the [Formula: see text]-statistic (a.k.a. the "ABBA-BABA test"), have been proposed to infer introgression in the presence of ILS for a four-taxon clade. However, no integrated method exists to detect introgression using allelic patterns for more complex phylogenies. Here we explore the issues associated with previous systems of applying [Formula: see text]-statistics to a larger tree topology, and propose new [Formula: see text] tests as an integrated framework to infer both the taxa involved in and the direction of introgression for a symmetric five-taxon phylogeny. Using theory and simulations, we show that the [Formula: see text] statistics correctly identify the introgression donor and recipient lineages, even at low rates of introgression. [Formula: see text] is also shown to have extremely low false-positive rates. The [Formula: see text] tests are computationally inexpensive to calculate and can easily be applied to phylogenomic data sets, both genome-wide and in windows of the genome. In addition, we explore both the principles and problems of introgression detection in even more complex phylogenies.}, } @article {pmid25878134, year = {2015}, author = {Feix, T and Kivell, TL and Pouydebat, E and Dollar, AM}, title = {Estimating thumb-index finger precision grip and manipulation potential in extant and fossil primates.}, journal = {Journal of the Royal Society, Interface}, volume = {12}, number = {106}, pages = {}, pmid = {25878134}, issn = {1742-5662}, mesh = {Animals ; Computer Simulation ; Finger Joint/anatomy & histology/*physiology ; Fingers/anatomy & histology/*physiology ; Fossils/anatomy & histology ; Hand Strength/*physiology ; *Models, Biological ; Motor Skills/*physiology ; Primates/anatomy & histology/*physiology ; Range of Motion, Articular ; }, abstract = {Primates, and particularly humans, are characterized by superior manual dexterity compared with other mammals. However, drawing the biomechanical link between hand morphology/behaviour and functional capabilities in non-human primates and fossil taxa has been challenging. We present a kinematic model of thumb-index precision grip and manipulative movement based on bony hand morphology in a broad sample of extant primates and fossil hominins. The model reveals that both joint mobility and digit proportions (scaled to hand size) are critical for determining precision grip and manipulation potential, but that having either a long thumb or great joint mobility alone does not necessarily yield high precision manipulation. The results suggest even the oldest available fossil hominins may have shared comparable precision grip manipulation with modern humans. In particular, the predicted human-like precision manipulation of Australopithecus afarensis, approximately one million years before the first stone tools, supports controversial archaeological evidence of tool-use in this taxon.}, } @article {pmid25840859, year = {2015}, author = {Gómez-Robles, A and Bermúdez de Castro, JM and Martinón-Torres, M and Prado-Simón, L and Arsuaga, JL}, title = {A geometric morphometric analysis of hominin lower molars: Evolutionary implications and overview of postcanine dental variation.}, journal = {Journal of human evolution}, volume = {82}, number = {}, pages = {34-50}, doi = {10.1016/j.jhevol.2015.02.013}, pmid = {25840859}, issn = {1095-8606}, mesh = {Africa ; Animals ; Asia ; *Biological Evolution ; Classification ; Cuspid/*anatomy & histology ; Europe ; Fossils ; History, Ancient ; Hominidae/*anatomy & histology ; Molar/*anatomy & histology ; }, abstract = {Lower molars have been extensively studied in the context of hominin evolution using classic and geometric morphometric analyses, 2D and 3D approaches, evaluations of the external (outer enamel surface) and internal anatomy (dentine, pulp chamber, and radicular canals), and studies of the crown and root variation. In this study, we present a 2D geometric morphometric analysis of the crown anatomy of lower first, second, and third molars of a broad sample of hominins, including Pliocene and Lower, Middle, and Upper Pleistocene species coming from Africa, Asia, and Europe. We show that shape variability increases from first to second and third molars. While first molars tend to retain a relatively stable 5-cusped conformation throughout the hominin fossil record, second and third molars show marked distal reductions in later Homo species. This trend to distal reduction is similar to that observed in previous studies of premolars and upper second and third molars, and points to a correlated reduction of distal areas across the whole postcanine dentition. Results on lower molar variation, as well as on other postcanine teeth, show certain trends in European Pleistocene populations from the Atapuerca sites. Middle Pleistocene hominins from Sima de los Huesos show Neanderthal affinities and strong dental reduction, especially in the most distal molars. The degree of dental reduction in this population is stronger than that observed in classic Neanderthals. Homo antecessor hominins from Gran Dolina-TD6 have primitive lower teeth that contrast with their more derived upper teeth. The evolutionary implications of these dental affinities are discussed in light of recent paleogenetic studies.}, } @article {pmid25827599, year = {2015}, author = {Young, NM and Winslow, B and Takkellapati, S and Kavanagh, K}, title = {Shared rules of development predict patterns of evolution in vertebrate segmentation.}, journal = {Nature communications}, volume = {6}, number = {}, pages = {6690}, doi = {10.1038/ncomms7690}, pmid = {25827599}, issn = {2041-1723}, mesh = {Alligators and Crocodiles ; Amphibians ; Animals ; Artiodactyla ; *Biological Evolution ; Caniformia ; Carnivora ; Chickens ; Columbidae ; Extremities/*embryology ; Humans ; Models, Anatomic ; Neanderthals ; Primates ; Rodentia ; Somites/*embryology ; Toes/embryology ; }, abstract = {Phenotypic diversity is not uniformly distributed, but how biased patterns of evolutionary variation are generated and whether common developmental mechanisms are responsible remains debatable. High-level 'rules' of self-organization and assembly are increasingly used to model organismal development, even when the underlying cellular or molecular players are unknown. One such rule, the inhibitory cascade, predicts that proportions of segmental series derive from the relative strengths of activating and inhibitory interactions acting on both local and global scales. Here we show that this developmental design rule explains population-level variation in segment proportions, their response to artificial selection and experimental blockade of putative signals and macroevolutionary diversity in limbs, digits and somites. Together with evidence from teeth, these results indicate that segmentation across independent developmental modules shares a common regulatory 'logic', which has a predictable impact on both their short and long-term evolvability.}, } @article {pmid25819346, year = {2015}, author = {Rosas, A and Pérez-Criado, L and Bastir, M and Estalrrich, A and Huguet, R and García-Tabernero, A and Pastor, JF and de la Rasilla, M}, title = {A geometric morphometrics comparative analysis of Neandertal humeri (epiphyses-fused) from the El Sidrón cave site (Asturias, Spain).}, journal = {Journal of human evolution}, volume = {82}, number = {}, pages = {51-66}, doi = {10.1016/j.jhevol.2015.02.018}, pmid = {25819346}, issn = {1095-8606}, mesh = {Animals ; Biological Evolution ; Epiphyses/*anatomy & histology ; Female ; *Fossils ; History, Ancient ; Humerus/*anatomy & histology ; Male ; Neanderthals/*anatomy & histology ; Phylogeny ; Sex Factors ; Spain ; }, abstract = {A new collection of 49,000 year old Neandertal fossil humeri from the El Sidrón cave site (Asturias, Spain) is presented. A total of 49 humeral remains were recovered, representing 10 left and 8 right humeri from adults, adolescents, and a juvenile (not included in the analyses). 3D geometric morphometric (GM) methods as well as classic anthropological variables were employed to conduct a broad comparative analysis by means of mean centroid size and shape comparisons, principal components analysis, and cluster studies. Due to the fragmentary nature of the fossils, comparisons were organized in independent analyses according to different humeral portions: distal epiphysis, diaphysis, proximal epiphysis, and the complete humerus. From a multivariate viewpoint, 3D-GM analyses revealed major differences among taxonomic groups, supporting the value of the humerus in systematic classification. Notably, the Australopithecus anamensis (KP-271) and Homo ergaster Nariokotome (KNM-WT 15000) distal humerus consistently clusters close to those of modern humans, which may imply a primitive condition for Homo sapiens morphology. Australopithecus specimens show a high degree of dispersion in the morphospace. The El Sidrón sample perfectly fits into the classic Neandertal pattern, previously described as having a relatively wide olecranon fossa, as well as thin lateral and medial distodorsal pillars. These characteristics were also typical of the Sima de los Huesos (Atapuerca) sample, African mid-Pleistocene Bodo specimen, and Lower Pleistocene TD6-Atapuerca remains and may be considered as a derived state. Finally, we hypothesize that most of the features thought to be different between Neandertals and modern humans might be associated with structural differences in the pectoral girdle and shoulder joint.}, } @article {pmid25805043, year = {2015}, author = {Gómez-Olivencia, A and Crevecoeur, I and Balzeau, A}, title = {La Ferrassie 8 Neandertal child reloaded: New remains and re-assessment of the original collection.}, journal = {Journal of human evolution}, volume = {82}, number = {}, pages = {107-126}, doi = {10.1016/j.jhevol.2015.02.008}, pmid = {25805043}, issn = {1095-8606}, mesh = {Animals ; Bone and Bones/*anatomy & histology ; Finger Phalanges/anatomy & histology ; *Fossils ; France ; History, Ancient ; Humans ; Infant ; Neanderthals/*anatomy & histology ; *Paleontology ; Pelvic Bones/anatomy & histology ; Ribs/anatomy & histology ; Skull/anatomy & histology ; Spine/anatomy & histology ; }, abstract = {The first evidence of the partial infant Neandertal skeleton La Ferrassie 8 (LF8) was discovered in 1970, although most of the remains were found in 1973 as part of the 1968-1973 work at the site by H. Delporte. This individual and the other Neandertal children from La Ferrassie were published in the early 1980s by J.-L. Heim, and since then LF8 has been regarded as coming from a poorly documented excavation. The recent rediscovery of the box that contained the hominin bones given by Delporte to Heim in the Muséum national d'Histoire naturelle (MNHN) collection provided new fossils and helped to locate LF8 in the site: level M2 in square 1. Two visits to the Musée d'Archéologie nationale et Domaine national de Saint-Germain-en-Laye (MAN) yielded additional fossil remains from both the 1970 and 1973 excavations and resulted in the discovery of all of the notes from the excavation of H. Delporte between 1968 and 1973. Here the new fossil remains (47 after performing all possible refits), representing significant portions of the cranium, mandible, and vertebral column together with fragmentary hand and costal remains, are described. Unsurprisingly, the morphology of the bony labyrinth and of a complete stapes from the nearly complete left temporal show clear Neandertal affinities. Additionally, a complete reassessment of the original LF8 collection has resulted in the identification of several errors in the anatomical determination. Despite the significant increase in the anatomical representation of LF8, the skeletal remains are still limited to the head, thorax, pelvis, and four hand phalanges, with some very fragile elements relatively well preserved. Different hypotheses are proposed to explain this anatomical representation, which can be tested during future fieldwork.}, } @article {pmid25805042, year = {2015}, author = {Lari, M and Di Vincenzo, F and Borsato, A and Ghirotto, S and Micheli, M and Balsamo, C and Collina, C and De Bellis, G and Frisia, S and Giacobini, G and Gigli, E and Hellstrom, JC and Lannino, A and Modi, A and Pietrelli, A and Pilli, E and Profico, A and Ramirez, O and Rizzi, E and Vai, S and Venturo, D and Piperno, M and Lalueza-Fox, C and Barbujani, G and Caramelli, D and Manzi, G}, title = {The Neanderthal in the karst: First dating, morphometric, and paleogenetic data on the fossil skeleton from Altamura (Italy).}, journal = {Journal of human evolution}, volume = {82}, number = {}, pages = {88-94}, doi = {10.1016/j.jhevol.2015.02.007}, pmid = {25805042}, issn = {1095-8606}, mesh = {Animals ; Base Sequence ; *Caves ; DNA/analysis ; *Fossils ; History, Ancient ; Italy ; Molecular Sequence Data ; *Neanderthals ; Paleontology/*methods ; Phylogeny ; Scapula/chemistry ; *Skeleton/chemistry ; }, abstract = {In 1993, a fossil hominin skeleton was discovered in the karst caves of Lamalunga, near Altamura, in southern Italy. Despite the fact that this specimen represents one of the most extraordinary hominin specimens ever found in Europe, for the last two decades our knowledge of it has been based purely on the documented on-site observations. Recently, the retrieval from the cave of a fragment of bone (part of the right scapula) allowed the first dating of the individual, the quantitative analysis of a diagnostic morphological feature, and a preliminary paleogenetic characterization of this hominin skeleton from Altamura. Overall, the results concur in indicating that it belongs to the hypodigm of Homo neanderthalensis, with some phenetic peculiarities that appear consistent with a chronology ranging from 172 ± 15 ka to 130.1 ± 1.9 ka. Thus, the skeleton from Altamura represents the most ancient Neanderthal from which endogenous DNA has ever been extracted.}, } @article {pmid25766902, year = {2015}, author = {Quam, R and Sanz, M and Daura, J and Robson Brown, K and García-González, R and Rodríguez, L and Dawson, H and Rodríguez, RF and Gómez, S and Villaescusa, L and Rubio, Á and Yagüe, A and Ortega Martínez, MC and Fullola, JM and Zilhão, J and Arsuaga, JL}, title = {The Neandertals of northeastern Iberia: new remains from the Cova del Gegant (Sitges, Barcelona).}, journal = {Journal of human evolution}, volume = {81}, number = {}, pages = {13-28}, doi = {10.1016/j.jhevol.2015.02.002}, pmid = {25766902}, issn = {1095-8606}, mesh = {Animals ; Fossils/*anatomy & histology ; Humerus/anatomy & histology ; Male ; Mandible/anatomy & histology ; Neanderthals/*anatomy & histology ; Spain ; Tooth/anatomy & histology ; }, abstract = {The present study describes a new juvenile hominin mandible and teeth and a new juvenile humerus from level V of the GP2 gallery of Cova del Gegant (Spain). The mandible (Gegant-5) preserves a portion of the right mandibular corpus from the M1 distally to the socket for the dc mesially, and the age at death is estimated as 4.5-5.0 years. Gegant-5 shows a single mental foramen located under the dm1/dm2 interdental septum, a relatively posterior placement compared with recent hominins of a similar developmental age. The mental foramen in Gegant-5 is also placed within the lower half of the mandibular corpus, as in the previously described late adolescent/adult mandible (Gegant-1) from this same Middle Paleolithic site. The Gegant-5 canine shows pronounced marginal ridges, a distal accessory ridge, and a pronounced distolingual tubercle. The P3 shows a lingually-displaced protoconid cusp tip and a distal accessory ridge. The P4 shows a slightly asymmetrical crown outline, a continuous transverse crest, a mesially placed metaconid cusp tip, a slight distal accessory ridge, and an accessory lingual cusp. The M1 shows a Y5 pattern of cusp contact and a well-developed and deep anterior fovea bounded posteriorly by a continuous midtrigonid crest. Gegant-4 is the distal portion of a left humerus from a juvenile estimated to be between 5 and 7 years old at death. The specimen shows thick cortical bone. Although fragmentary, the constellation of morphological and metric features indicates Neandertal affinities for these specimens. Their spatial proximity at the site and similar ages at death suggest these remains may represent a single individual. The addition of these new specimens brings the total number of Neandertal remains from the Cova del Gegant to five, and this site documents the clearest evidence for Neandertal fossils associated with Middle Paleolithic stone tools in this region of the Iberian Peninsula.}, } @article {pmid25760648, year = {2015}, author = {Radovčić, D and Sršen, AO and Radovčić, J and Frayer, DW}, title = {Evidence for Neandertal jewelry: modified white-tailed eagle claws at Krapina.}, journal = {PloS one}, volume = {10}, number = {3}, pages = {e0119802}, pmid = {25760648}, issn = {1932-6203}, mesh = {Animals ; Anthropology, Cultural ; Archaeology ; Croatia ; Eagles/anatomy & histology/classification ; *Fossils ; *Hoof and Claw ; *Neanderthals ; }, abstract = {We describe eight, mostly complete white-tailed eagle (Haliaëtus [Haliaeetus] albicilla) talons from the Krapina Neandertal site in present-day Croatia, dating to approximately 130 kyrs ago. Four talons bear multiple, edge-smoothed cut marks; eight show polishing facets and/or abrasion. Three of the largest talons have small notches at roughly the same place along the plantar surface, interrupting the proximal margin of the talon blade. These features suggest they were part of a jewelry assemblage, --- the manipulations a consequence of mounting the talons in a necklace or bracelet. An associated phalanx articulates with one of the talons and has numerous cut marks, some of which are smoothed. These white-tailed eagle bones, discovered more than 100 years ago, all derive from a single level at Krapina and represent more talons than found in the entire European Mousterian period. Presence of eight talons indicates that the Krapina Neandertals acquired and curated eagle talons for some kind of symbolic purpose. Some have argued that Neandertals lacked symbolic ability or copied this behavior from modern humans. These remains clearly show that the Krapina Neandertals made jewelry well before the appearance of modern humans in Europe, extending ornament production and symbolic activity early into the European Mousterian.}, } @article {pmid25758009, year = {2015}, author = {Webb, AE and Gerek, ZN and Morgan, CC and Walsh, TA and Loscher, CE and Edwards, SV and O'Connell, MJ}, title = {Adaptive Evolution as a Predictor of Species-Specific Innate Immune Response.}, journal = {Molecular biology and evolution}, volume = {32}, number = {7}, pages = {1717-1729}, pmid = {25758009}, issn = {1537-1719}, mesh = {Adaptation, Physiological/*genetics ; Amino Acids/metabolism ; Animals ; *Biological Evolution ; Genetics, Population ; Humans ; Immunity, Innate/*genetics ; Mice ; Phylogeny ; Protein Structure, Tertiary ; Selection, Genetic ; Species Specificity ; Toll-Like Receptor 3/chemistry ; }, abstract = {It has been proposed that positive selection may be associated with protein functional change. For example, human and macaque have different outcomes to HIV infection and it has been shown that residues under positive selection in the macaque TRIM5α receptor locate to the region known to influence species-specific response to HIV. In general, however, the relationship between sequence and function has proven difficult to fully elucidate, and it is the role of large-scale studies to help bridge this gap in our understanding by revealing major patterns in the data that correlate genotype with function or phenotype. In this study, we investigate the level of species-specific positive selection in innate immune genes from human and mouse. In total, we analyzed 456 innate immune genes using codon-based models of evolution, comparing human, mouse, and 19 other vertebrate species to identify putative species-specific positive selection. Then we used population genomic data from the recently completed Neanderthal genome project, the 1000 human genomes project, and the 17 laboratory mouse genomes project to determine whether the residues that were putatively positively selected are fixed or variable in these populations. We find evidence of species-specific positive selection on both the human and the mouse branches and we show that the classes of genes under positive selection cluster by function and by interaction. Data from this study provide us with targets to test the relationship between positive selection and protein function and ultimately to test the relationship between positive selection and discordant phenotypes.}, } @article {pmid25683122, year = {2015}, author = {Kim, BY and Lohmueller, KE}, title = {Selection and reduced population size cannot explain higher amounts of Neandertal ancestry in East Asian than in European human populations.}, journal = {American journal of human genetics}, volume = {96}, number = {3}, pages = {454-461}, pmid = {25683122}, issn = {1537-6605}, mesh = {Alleles ; Animals ; Asian Continental Ancestry Group/*genetics ; European Continental Ancestry Group/*genetics ; Genetics, Population ; Genome ; Humans ; Neanderthals/*genetics ; *Population Density ; }, abstract = {It has been hypothesized that the greater proportion of Neandertal ancestry in East Asians than in Europeans is due to the fact that purifying selection is less effective at removing weakly deleterious Neandertal alleles from East Asian populations. Using simulations of a broad range of models of selection and demography, we have shown that this hypothesis cannot account for the higher proportion of Neandertal ancestry in East Asians than in Europeans. Instead, more complex demographic scenarios, most likely involving multiple pulses of Neandertal admixture, are required to explain the data.}, } @article {pmid25683119, year = {2015}, author = {Vernot, B and Akey, JM}, title = {Complex history of admixture between modern humans and Neandertals.}, journal = {American journal of human genetics}, volume = {96}, number = {3}, pages = {448-453}, pmid = {25683119}, issn = {1537-6605}, support = {R01 GM110068/GM/NIGMS NIH HHS/United States ; 1R01GM110068/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Asian Continental Ancestry Group/genetics ; European Continental Ancestry Group/genetics ; Gene Flow ; *Genetics, Population ; Genome ; Humans ; Models, Genetic ; Neanderthals/*genetics ; }, abstract = {Recent analyses have found that a substantial amount of the Neandertal genome persists in the genomes of contemporary non-African individuals. East Asians have, on average, higher levels of Neandertal ancestry than do Europeans, which might be due to differences in the efficiency of purifying selection, an additional pulse of introgression into East Asians, or other unexplored scenarios. To better define the scope of plausible models of archaic admixture between Neandertals and anatomically modern humans, we analyzed patterns of introgressed sequence in whole-genome data of 379 Europeans and 286 East Asians. We found that inferences of demographic history restricted to neutrally evolving genomic regions allowed a simple one-pulse model to be robustly rejected, suggesting that differences in selection cannot explain the differences in Neandertal ancestry. We show that two additional demographic models, involving either a second pulse of Neandertal gene flow into the ancestors of East Asians or a dilution of Neandertal lineages in Europeans by admixture with an unknown ancestral population, are consistent with the data. Thus, the history of admixture between modern humans and Neandertals is most likely more complex than previously thought.}, } @article {pmid25681013, year = {2015}, author = {Estalrrich, A and Rosas, A}, title = {Division of labor by sex and age in Neandertals: an approach through the study of activity-related dental wear.}, journal = {Journal of human evolution}, volume = {80}, number = {}, pages = {51-63}, doi = {10.1016/j.jhevol.2014.07.007}, pmid = {25681013}, issn = {1095-8606}, mesh = {Animals ; Belgium ; Female ; *Fossils ; France ; *Gender Identity ; Male ; Neanderthals/*psychology ; Paleodontology ; Sex Factors ; Spain ; *Tooth Wear ; }, abstract = {The analysis of activity-related dental wear patterns in prehistoric anatomically modern humans and modern hunter-gatherers has shown sex differences attributable to a gendered division of labor. Neandertals are known to have extensive anterior dental wear related to the use of their front teeth as a tool. In this study we analyze the i) cultural striations (scratches on the labial surface of the anterior teeth with a cut-mark morphology), and ii) dental chipping (ante-mortem microfracture involving enamel or both enamel and dentine) in 19 Neandertal individuals from the l'Hortus (France), Spy (Belgium), and El Sidrón (Spain) sites, and compare the characteristics of those traits with the age and sex estimation for the individuals and among samples. The study reveals that all individuals have cultural striations, but those detected on the adult females are longer than the striations found in adult males. Regarding the distribution of dental chipping, the prevalence of this trait is higher in the maxillary dentition of males whereas females have the majority of dental chipping on their mandibular teeth. The differences detected on the overall activity-related dental wear pattern denote a difference or a division of labor by age and sex in Neandertals while using the mouth as a third hand, i.e., in activities other than the provisioning of food, and provide new evidence for the lifestyle of this Pleistocene fossil human species.}, } @article {pmid25631427, year = {2015}, author = {Callaway, E}, title = {Neanderthals gain human neighbour.}, journal = {Nature}, volume = {517}, number = {7536}, pages = {541}, doi = {10.1038/517541a}, pmid = {25631427}, issn = {1476-4687}, mesh = {Animals ; Breeding/history ; Europe ; *Fossils ; History, Ancient ; Humans ; Israel ; *Neanderthals/genetics ; Skull/anatomy & histology ; Time Factors ; }, } @article {pmid25631406, year = {2015}, author = {}, title = {Human history defies easy stories.}, journal = {Nature}, volume = {517}, number = {7536}, pages = {527}, doi = {10.1038/517527a}, pmid = {25631406}, issn = {1476-4687}, mesh = {Animals ; *Biological Evolution ; *Fossils ; Humans ; Israel ; Neanderthals/genetics ; *Skull/anatomy & histology ; }, } @article {pmid25629628, year = {2015}, author = {Hershkovitz, I and Marder, O and Ayalon, A and Bar-Matthews, M and Yasur, G and Boaretto, E and Caracuta, V and Alex, B and Frumkin, A and Goder-Goldberger, M and Gunz, P and Holloway, RL and Latimer, B and Lavi, R and Matthews, A and Slon, V and Mayer, DB and Berna, F and Bar-Oz, G and Yeshurun, R and May, H and Hans, MG and Weber, GW and Barzilai, O}, title = {Levantine cranium from Manot Cave (Israel) foreshadows the first European modern humans.}, journal = {Nature}, volume = {520}, number = {7546}, pages = {216-219}, pmid = {25629628}, issn = {1476-4687}, mesh = {Africa/ethnology ; Animals ; *Caves ; Europe/ethnology ; *Fossils ; Humans ; Israel ; Neanderthals/anatomy & histology/physiology ; *Phylogeny ; Skull/*anatomy & histology ; }, abstract = {A key event in human evolution is the expansion of modern humans of African origin across Eurasia between 60 and 40 thousand years (kyr) before present (bp), replacing all other forms of hominins. Owing to the scarcity of human fossils from this period, these ancestors of all present-day non-African modern populations remain largely enigmatic. Here we describe a partial calvaria, recently discovered at Manot Cave (Western Galilee, Israel) and dated to 54.7 ± 5.5 kyr bp (arithmetic mean ± 2 standard deviations) by uranium-thorium dating, that sheds light on this crucial event. The overall shape and discrete morphological features of the Manot 1 calvaria demonstrate that this partial skull is unequivocally modern. It is similar in shape to recent African skulls as well as to European skulls from the Upper Palaeolithic period, but different from most other early anatomically modern humans in the Levant. This suggests that the Manot people could be closely related to the first modern humans who later successfully colonized Europe. Thus, the anatomical features used to support the 'assimilation model' in Europe might not have been inherited from European Neanderthals, but rather from earlier Levantine populations. Moreover, at present, Manot 1 is the only modern human specimen to provide evidence that during the Middle to Upper Palaeolithic interface, both modern humans and Neanderthals contemporaneously inhabited the southern Levant, close in time to the likely interbreeding event with Neanderthals.}, } @article {pmid25620980, year = {2014}, author = {Benítez-Burraco, A}, title = {Biological noise and H2A.Z: a promising connection for language.}, journal = {Frontiers in genetics}, volume = {5}, number = {}, pages = {463}, pmid = {25620980}, issn = {1664-8021}, } @article {pmid25613885, year = {2015}, author = {Skinner, MM and Stephens, NB and Tsegai, ZJ and Foote, AC and Nguyen, NH and Gross, T and Pahr, DH and Hublin, JJ and Kivell, TL}, title = {Human evolution. Human-like hand use in Australopithecus africanus.}, journal = {Science (New York, N.Y.)}, volume = {347}, number = {6220}, pages = {395-399}, doi = {10.1126/science.1261735}, pmid = {25613885}, issn = {1095-9203}, mesh = {Animals ; Archaeology ; *Biological Evolution ; Hominidae/anatomy & histology ; Humans ; Metacarpal Bones/*anatomy & histology ; Metacarpus/*anatomy & histology/physiology ; Neanderthals/anatomy & histology ; Posture ; Thumb/*anatomy & histology/physiology ; }, abstract = {The distinctly human ability for forceful precision and power "squeeze" gripping is linked to two key evolutionary transitions in hand use: a reduction in arboreal climbing and the manufacture and use of tools. However, it is unclear when these locomotory and manipulative transitions occurred. Here we show that Australopithecus africanus (~3 to 2 million years ago) and several Pleistocene hominins, traditionally considered not to have engaged in habitual tool manufacture, have a human-like trabecular bone pattern in the metacarpals consistent with forceful opposition of the thumb and fingers typically adopted during tool use. These results support archaeological evidence for stone tool use in australopiths and provide morphological evidence that Pliocene hominins achieved human-like hand postures much earlier and more frequently than previously considered.}, } @article {pmid25602066, year = {2015}, author = {Hublin, JJ and Neubauer, S and Gunz, P}, title = {Brain ontogeny and life history in Pleistocene hominins.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1663}, pages = {20140062}, pmid = {25602066}, issn = {1471-2970}, mesh = {Animals ; *Biological Evolution ; Brain/*embryology/*growth & development ; *Fossils ; *Hominidae ; Humans ; Organ Size ; Paleontology ; Species Specificity ; }, abstract = {A high level of encephalization is critical to the human adaptive niche and emerged among hominins over the course of the past 2 Myr. Evolving larger brains required important adaptive adjustments, in particular regarding energy allocation and life history. These adaptations included a relatively small brain at birth and a protracted growth of highly dependent offspring within a complex social environment. In turn, the extended period of growth and delayed maturation of the brain structures of humans contribute to their cognitive complexity. The current palaeoanthropological evidence shows that, regarding life history and brain ontogeny, the Pleistocene hominin taxa display different patterns and that one cannot simply contrast an 'ape-model' to a 'human-model'. Large-brained hominins such as Upper Pleistocene Neandertals have evolved along their own evolutionary pathway and can be distinguished from modern humans in terms of growth pattern and brain development. The life-history pattern and brain ontogeny of extant humans emerged only recently in the course of human evolution.}, } @article {pmid25581429, year = {2015}, author = {Do, R and Balick, D and Li, H and Adzhubei, I and Sunyaev, S and Reich, D}, title = {No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans.}, journal = {Nature genetics}, volume = {47}, number = {2}, pages = {126-131}, pmid = {25581429}, issn = {1546-1718}, support = {R01 GM078598/GM/NIGMS NIH HHS/United States ; R01MH101244/MH/NIMH NIH HHS/United States ; R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 HG006399/HG/NHGRI NIH HHS/United States ; HG006399/HG/NHGRI NIH HHS/United States ; GM100233/GM/NIGMS NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; R01 GM105857/GM/NIGMS NIH HHS/United States ; R01GM078598/GM/NIGMS NIH HHS/United States ; R01 MH101244/MH/NIMH NIH HHS/United States ; }, mesh = {African Continental Ancestry Group/*genetics ; Amino Acid Substitution ; Animals ; Computer Simulation ; European Continental Ancestry Group/*genetics ; Gene Frequency ; Genetic Variation ; Genetics, Population ; Genome, Human/*genetics ; Humans ; Models, Genetic ; Mutation ; Neanderthals/*genetics ; Selection, Genetic/*physiology ; }, abstract = {Non-African populations have experienced size reductions in the time since their split from West Africans, leading to the hypothesis that natural selection to remove weakly deleterious mutations has been less effective in the history of non-Africans. To test this hypothesis, we measured the per-genome accumulation of nonsynonymous substitutions across diverse pairs of populations. We find no evidence for a higher load of deleterious mutations in non-Africans. However, we detect significant differences among more divergent populations, as archaic Denisovans have accumulated nonsynonymous mutations faster than either modern humans or Neanderthals. To reconcile these findings with patterns that have been interpreted as evidence of the less effective removal of deleterious mutations in non-Africans than in West Africans, we use simulations to show that the observed patterns are not likely to reflect changes in the effectiveness of selection after the populations split but are instead likely to be driven by other population genetic factors.}, } @article {pmid25575941, year = {2015}, author = {Rogers, AR and Bohlender, RJ}, title = {Bias in estimators of archaic admixture.}, journal = {Theoretical population biology}, volume = {100C}, number = {}, pages = {63-78}, doi = {10.1016/j.tpb.2014.12.006}, pmid = {25575941}, issn = {1096-0325}, abstract = {This article evaluates bias in one class of methods used to estimate archaic admixture in modern humans. These methods study the pattern of allele sharing among modern and archaic genomes. They are sensitive to "ghost" admixture, which occurs when a population receives archaic DNA from sources not acknowledged by the statistical model. The effect of ghost admixture depends on two factors: branch-length bias and population-size bias. Branch-length bias occurs because a given amount of admixture has a larger effect if the two populations have been separated for a long time. Population-size bias occurs because differences in population size distort branch lengths in the gene genealogy. In the absence of ghost admixture, these effects are small. They become important, however, in the presence of ghost admixture. Estimators differ in the pattern of response. Increasing a given parameter may inflate one estimator but deflate another. For this reason, comparisons among estimators are informative. Using such comparisons, this article supports previous findings that the archaic population was small and that Europeans received little gene flow from archaic populations other than Neanderthals. It also identifies an inconsistency in estimates of archaic admixture into Melanesia.}, } @article {pmid25563409, year = {2015}, author = {Perry, GH and Kistler, L and Kelaita, MA and Sams, AJ}, title = {Insights into hominin phenotypic and dietary evolution from ancient DNA sequence data.}, journal = {Journal of human evolution}, volume = {79}, number = {}, pages = {55-63}, doi = {10.1016/j.jhevol.2014.10.018}, pmid = {25563409}, issn = {1095-8606}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; DNA/analysis/genetics ; DNA Copy Number Variations ; Feeding Behavior/*physiology ; Fossils ; Genetic Variation ; Genomics ; Hominidae/*genetics/*physiology ; Humans ; Molecular Sequence Data ; Myosin Heavy Chains/genetics ; Neanderthals ; Paleontology ; Phenotype ; Receptors, G-Protein-Coupled/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Nuclear genome sequence data from Neandertals, Denisovans, and archaic anatomically modern humans can be used to complement our understanding of hominin evolutionary biology and ecology through i) direct inference of archaic hominin phenotypes, ii) indirect inference of those phenotypes by identifying the effects of previously-introgressed alleles still present among modern humans, or iii) determining the evolutionary timing of relevant hominin-specific genetic changes. Here we review and reanalyze published Neandertal and Denisovan genome sequence data to illustrate an example of the third approach. Specifically, we infer the timing of five human gene presence/absence changes that may be related to particular hominin-specific dietary changes and discuss these results in the context of our broader reconstructions of hominin evolutionary ecology. We show that pseudogenizing (gene loss) mutations in the TAS2R62 and TAS2R64 bitter taste receptor genes and the MYH16 masticatory myosin gene occurred after the hominin-chimpanzee divergence but before the divergence of the human and Neandertal/Denisovan lineages. The absence of a functional MYH16 protein may explain our relatively reduced jaw muscles; this gene loss may have followed the adoption of cooking behavior. In contrast, salivary amylase gene (AMY1) duplications were not observed in the Neandertal and Denisovan genomes, suggesting a relatively recent origin for the AMY1 copy number gains that are observed in modern humans. Thus, if earlier hominins were consuming large quantities of starch-rich underground storage organs, as previously hypothesized, then they were likely doing so without the digestive benefits of increased salivary amylase production. Our most surprising result was the observation of a heterozygous mutation in the first codon of the TAS2R38 bitter taste receptor gene in the Neandertal individual, which likely would have resulted in a non-functional protein and inter-individual PTC (phenylthiocarbamide) taste sensitivity variation, as also observed in both humans and chimpanzees.}, } @article {pmid25563407, year = {2015}, author = {Bastir, M and García-Martínez, D and Estalrrich, A and García-Tabernero, A and Huguet, R and Ríos, L and Barash, A and Recheis, W and de la Rasilla, M and Rosas, A}, title = {The relevance of the first ribs of the El Sidrón site (Asturias, Spain) for the understanding of the Neandertal thorax.}, journal = {Journal of human evolution}, volume = {80}, number = {}, pages = {64-73}, doi = {10.1016/j.jhevol.2014.10.008}, pmid = {25563407}, issn = {1095-8606}, mesh = {Adult ; Animals ; *Biological Evolution ; *Fossils ; Humans ; Neanderthals/*anatomy & histology ; Ribs/*anatomy & histology ; Spain ; Thorax/anatomy & histology ; }, abstract = {Reconstructing the morphology of the Neanderthal rib cage not only provides information about the general evolution of human body shape but also aids understanding of functional anatomy and energetics. Despite this paleobiological importance there is still debate about the nature and extent of variations in the size and shape of the Neandertal thorax. The El Sidrón Neandertals can be used to contribute to this debate, providing new costal remains ranging from fully preserved and undistorted ribs to highly fragmented elements. Six first ribs are particularly well preserved and offer the opportunity to analyze thorax morphology in Neandertals. The aims of this paper are to present this new material, to compare the ontogenetic trajectories of the first ribs between Neandertals and modern humans, and, using geometric morphometrics, to test the hypothesis of morphological integration between the first rib and overall thorax morphology. The first ribs of the El Sidrón adult Neandertals are smaller in centroid size and tend to be less curved when compared with those of modern humans, but are similar to Kebara 2. Our results further show that the straightening of the first ribs is significantly correlated with a straightening of the ribs of the upper thorax (R = 0.66; p < 0.0001) in modern humans, suggesting modularity in the upper and lower thorax units as reported in other hominins. It also supports the hypothesis that the upper thorax of Neandertals differs in shape from modern humans with more anteriorly projecting upper ribs during inspiration. These differences could have biomechanical consequences and account for stronger muscle attachments in Neandertals. Different upper thorax shape would also imply a different spatial arrangement of the shoulder girdle and articulation with the humerus (torsion) and its connection to the upper thorax. Future research should address these inferences in the context of Neandertal overall body morphology.}, } @article {pmid25556237, year = {2015}, author = {Lin, YL and Pavlidis, P and Karakoc, E and Ajay, J and Gokcumen, O}, title = {The evolution and functional impact of human deletion variants shared with archaic hominin genomes.}, journal = {Molecular biology and evolution}, volume = {32}, number = {4}, pages = {1008-1019}, pmid = {25556237}, issn = {1537-1719}, mesh = {Alleles ; Animals ; *Evolution, Molecular ; Genetic Variation ; *Genome ; Hominidae/*genetics ; Humans ; *Sequence Deletion ; }, abstract = {Allele sharing between modern and archaic hominin genomes has been variously interpreted to have originated from ancestral genetic structure or through non-African introgression from archaic hominins. However, evolution of polymorphic human deletions that are shared with archaic hominin genomes has yet to be studied. We identified 427 polymorphic human deletions that are shared with archaic hominin genomes, approximately 87% of which originated before the Human-Neandertal divergence (ancient) and only approximately 9% of which have been introgressed from Neandertals (introgressed). Recurrence, incomplete lineage sorting between human and chimp lineages, and hominid-specific insertions constitute the remaining approximately 4% of allele sharing between humans and archaic hominins. We observed that ancient deletions correspond to more than 13% of all common (>5% allele frequency) deletion variation among modern humans. Our analyses indicate that the genomic landscapes of both ancient and introgressed deletion variants were primarily shaped by purifying selection, eliminating large and exonic variants. We found 17 exonic deletions that are shared with archaic hominin genomes, including those leading to three fusion transcripts. The affected genes are involved in metabolism of external and internal compounds, growth and sperm formation, as well as susceptibility to psoriasis and Crohn's disease. Our analyses suggest that these "exonic" deletion variants have evolved through different adaptive forces, including balancing and population-specific positive selection. Our findings reveal that genomic structural variants that are shared between humans and archaic hominin genomes are common among modern humans and can influence biomedically and evolutionarily important phenotypes.}, } @article {pmid25551383, year = {2014}, author = {Xing, S and Martinón-Torres, M and Bermúdez de Castro, JM and Zhang, Y and Fan, X and Zheng, L and Huang, W and Liu, W}, title = {Middle Pleistocene hominin teeth from Longtan Cave, Hexian, China.}, journal = {PloS one}, volume = {9}, number = {12}, pages = {e114265}, pmid = {25551383}, issn = {1932-6203}, mesh = {Animals ; Archaeology ; *Caves ; China ; Evolution, Molecular ; *Fossils ; Hominidae/*anatomy & histology ; Image Processing, Computer-Assisted ; Tooth/*anatomy & histology/diagnostic imaging ; X-Ray Microtomography ; }, abstract = {Excavations at the Longtan Cave, Hexian, Anhui Province of Eastern China, have yielded several hominin fossils including crania, mandibular fragments, and teeth currently dated to 412 ± 25 ka. While previous studies have focused on the cranial remains, there are no detailed analyses of the dental evidence. In this study, we provide metric and morphological descriptions and comparisons of ten teeth recovered from Hexian, including microcomputed tomography analyses. Our results indicate that the Hexian teeth are metrically and morphologically primitive and overlap with H. ergaster and East Asian Early and mid-Middle Pleistocene hominins in their large dimensions and occlusal complexities. However, the Hexian teeth differ from H. ergaster in features such as conspicuous vertical grooves on the labial/buccal surfaces of the central incisor and the upper premolar, the crown outline shapes of upper and lower molars and the numbers, shapes, and divergences of the roots. Despite their close geological ages, the Hexian teeth are also more primitive than Zhoukoudian specimens, and resemble Sangiran Early Pleistocene teeth. In addition, no typical Neanderthal features have been identified in the Hexian sample. Our study highlights the metrical and morphological primitive status of the Hexian sample in comparison to contemporaneous or even earlier populations of Asia. Based on this finding, we suggest that the primitive-derived gradients of the Asian hominins cannot be satisfactorily fitted along a chronological sequence, suggesting complex evolutionary scenarios with the coexistence and/or survival of different lineages in Eurasia. Hexian could represent the persistence in time of a H. erectus group that would have retained primitive features that were lost in other Asian populations such as Zhoukoudian or Panxian Dadong. Our study expands the metrical and morphological variations known for the East Asian hominins before the mid-Middle Pleistocene and warns about the possibility that the Asian hominin variability may have been taxonomically oversimplified.}, } @article {pmid27325709, year = {2015}, author = {Pääbo, S}, title = {Dorcas Cummings Lecture.}, journal = {Cold Spring Harbor symposia on quantitative biology}, volume = {80}, number = {}, pages = {291-294}, doi = {10.1101/sqb.2015.80.030171}, pmid = {27325709}, issn = {1943-4456}, mesh = {Animals ; DNA/genetics ; Fossils ; Genetic Variation ; Genome, Mitochondrial ; Humans ; Neanderthals/*genetics ; }, } @article {pmid25535354, year = {2015}, author = {Chirchir, H and Kivell, TL and Ruff, CB and Hublin, JJ and Carlson, KJ and Zipfel, B and Richmond, BG}, title = {Recent origin of low trabecular bone density in modern humans.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {2}, pages = {366-371}, pmid = {25535354}, issn = {1091-6490}, mesh = {Adult ; Animals ; *Biological Evolution ; Body Size ; Bone Density/*physiology ; Bone and Bones/anatomy & histology/diagnostic imaging ; Extremities/anatomy & histology ; Female ; Fossils ; Hominidae/*anatomy & histology/*physiology ; Humans ; Imaging, Three-Dimensional ; Male ; Neanderthals/anatomy & histology/physiology ; Pan troglodytes/anatomy & histology/physiology ; Pongo pygmaeus/anatomy & histology/physiology ; Primates/anatomy & histology/physiology ; X-Ray Microtomography ; }, abstract = {Humans are unique, compared with our closest living relatives (chimpanzees) and early fossil hominins, in having an enlarged body size and lower limb joint surfaces in combination with a relatively gracile skeleton (i.e., lower bone mass for our body size). Some analyses have observed that in at least a few anatomical regions modern humans today appear to have relatively low trabecular density, but little is known about how that density varies throughout the human skeleton and across species or how and when the present trabecular patterns emerged over the course of human evolution. Here, we test the hypotheses that (i) recent modern humans have low trabecular density throughout the upper and lower limbs compared with other primate taxa and (ii) the reduction in trabecular density first occurred in early Homo erectus, consistent with the shift toward a modern human locomotor anatomy, or more recently in concert with diaphyseal gracilization in Holocene humans. We used peripheral quantitative CT and microtomography to measure trabecular bone of limb epiphyses (long bone articular ends) in modern humans and chimpanzees and in fossil hominins attributed to Australopithecus africanus, Paranthropus robustus/early Homo from Swartkrans, Homo neanderthalensis, and early Homo sapiens. Results show that only recent modern humans have low trabecular density throughout the limb joints. Extinct hominins, including pre-Holocene Homo sapiens, retain the high levels seen in nonhuman primates. Thus, the low trabecular density of the recent modern human skeleton evolved late in our evolutionary history, potentially resulting from increased sedentism and reliance on technological and cultural innovations.}, } @article {pmid25514948, year = {2014}, author = {Johansson, S}, title = {Neanderthals did speak, but FOXP2 doesn't prove it.}, journal = {The Behavioral and brain sciences}, volume = {37}, number = {6}, pages = {558-9; discussion 577-604}, doi = {10.1017/S0140525X13004068}, pmid = {25514948}, issn = {1469-1825}, mesh = {*Animal Communication ; Animals ; *Biological Evolution ; *Communication ; Humans ; Primates/*physiology ; Speech/*physiology ; }, abstract = {Ackermann et al. treat both genetic and paleoanthropological data too superficially to support their conclusions. The case of FOXP2 and Neanderthals is a prime example, which I will comment on in some detail; the issues are much more complex than they appear in Ackermann et al.}, } @article {pmid25509854, year = {2013}, author = {Maliarchuk, BA}, title = {[Mutation process in the protein-coding genes of human mitochondrial genome in context of evolution of the genus].}, journal = {Molekuliarnaia biologiia}, volume = {47}, number = {6}, pages = {927-933}, pmid = {25509854}, issn = {0026-8984}, mesh = {Animals ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Genome, Human/*genetics ; *Genome, Mitochondrial ; Humans ; Mutation/*genetics ; Neanderthals ; Polymorphism, Genetic ; }, abstract = {The human mitochondrial genome, although it has a small size, is characterized by high level of variation, non-uniformly distributed in groups of nucleotide positions that differ in the degree of variability. Considering the mutation process in human mtDNA relative to the mitochondrial genomes of the genus Homo-neandertals, denisova hominin and other primate species, it appears that more than half (56.5%) variable positions in the human mtDNA protein-coding genes are characterized by back (reverse) mutations to the pre-H. sapiens state of mitochondrial genome. It has been found that hypervariable nucleotide positions show a minimal proportion of specific to H. sapiens mutations, and, conversely, a high proportion of mutations (both nucleotide and amino acid substitutions), leading to the loss of Homo-specific variants of polymorphisms. Most often, polymorphisms specific to H. sapiens arise in result of single forward mutations and disappear mainly due to multiple back mutations, including those in the mutational "hotspots".}, } @article {pmid25498601, year = {2014}, author = {Marean, CW}, title = {The origins and significance of coastal resource use in Africa and Western Eurasia.}, journal = {Journal of human evolution}, volume = {77}, number = {}, pages = {17-40}, doi = {10.1016/j.jhevol.2014.02.025}, pmid = {25498601}, issn = {1095-8606}, mesh = {*Adaptation, Physiological ; Africa ; Animals ; *Biological Evolution ; Europe ; *Feeding Behavior ; *Geologic Sediments ; Hominidae ; Humans ; Mollusca ; Paleontology ; *Shellfish ; }, abstract = {The systematic exploitation of marine foods by terrestrial mammals lacking aquatic morphologies is rare. Widespread ethnographic and archaeological evidence from many areas of the world shows that modern humans living on coastlines often ratchet up the use of marine foods and develop social and technological characteristics unusual to hunter-gatherers and more consistent with small scale food producing societies. Consistent use of marine resources often is associated with reduced mobility, larger group size, population packing, smaller territories, complex technologies, increased economic and social differentiation, and more intense and wide-ranging gifting and exchange. The commitment to temporally and spatially predictable and dense coastal foods stimulates investment in boundary defense resulting in inter-group conflict as predicted by theory and documented by ethnography. Inter-group conflict provides an ideal context for the proliferation of intra-group cooperative behaviors beneficial to the group but not to the altruist (Bowles, 2009). The origins of this coastal adaptation marks a transformative point for the hominin lineage in Africa since all previous adaptive systems were likely characterized by highly mobile, low-density, egalitarian populations with large territories and little boundary defense. It is important to separate occasional uses of marine foods, present among several primate species, from systematic and committed coastal adaptations. This paper provides a critical review of where and when systematic use of coastal resources and coastal adaptations appeared in the Old World by a comparison of the records from Africa and Europe. It is found that during the Middle Stone Age in South Africa there is evidence that true coastal adaptations developed while there is, so far, a lack of evidence for even the lowest levels of systematic coastal resource use by Neanderthals in Europe. Differences in preservation, sample size, and productivity between these regions do not explain the pattern.}, } @article {pmid25487326, year = {2015}, author = {Sánchez-Quinto, F and Lalueza-Fox, C}, title = {Almost 20 years of Neanderthal palaeogenetics: adaptation, admixture, diversity, demography and extinction.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1660}, pages = {20130374}, pmid = {25487326}, issn = {1471-2970}, mesh = {Adaptation, Biological/*genetics ; Animals ; *Biological Evolution ; DNA, Mitochondrial/genetics ; *Extinction, Biological ; Fossils ; *Genetic Variation ; Genetics, Population ; Genomics/*methods/trends ; *Hybridization, Genetic ; Neanderthals/*genetics ; Population Dynamics ; }, abstract = {Nearly two decades since the first retrieval of Neanderthal DNA, recent advances in next-generation sequencing technologies have allowed the generation of high-coverage genomes from two archaic hominins, a Neanderthal and a Denisovan, as well as a complete mitochondrial genome from remains which probably represent early members of the Neanderthal lineage. This genomic information, coupled with diversity exome data from several Neanderthal specimens is shedding new light on evolutionary processes such as the genetic basis of Neanderthal and modern human-specific adaptations-including morphological and behavioural traits-as well as the extent and nature of the admixture events between them. An emerging picture is that Neanderthals had a long-term small population size, lived in small and isolated groups and probably practised inbreeding at times. Deleterious genetic effects associated with these demographic factors could have played a role in their extinction. The analysis of DNA from further remains making use of new large-scale hybridization-capture-based methods as well as of new approaches to discriminate contaminant DNA sequences will provide genetic information in spatial and temporal scales that could help clarify the Neanderthal's-and our very own-evolutionary history.}, } @article {pmid25481629, year = {2015}, author = {Yravedra, J and Cobo-Sánchez, L}, title = {Neanderthal exploitation of ibex and chamois in southwestern Europe.}, journal = {Journal of human evolution}, volume = {78}, number = {}, pages = {12-32}, doi = {10.1016/j.jhevol.2014.10.002}, pmid = {25481629}, issn = {1095-8606}, mesh = {Animals ; Environment ; Geologic Sediments ; *Goats ; Neanderthals/*physiology ; Paleontology ; Predatory Behavior/*physiology ; Rupicapra ; Seasons ; Spain ; }, abstract = {There is increasing evidence that Neanderthals had a diverse and flexible diet. They exploited a wide range of resources from large proboscideans to small animals like turtles, rabbits, and marine species. Here, we discuss the importance of ibex and chamois in Neanderthal hunting strategies. The exploitation of both animals has traditionally been regarded as typical of Homo sapiens hunting behavior but was not a feature of Neanderthal behavior, which was thought to have focused on other kinds of game like deer, horses or large bovids. Our analysis of an extensive sample of Middle Paleolithic sites with faunal remains in the Iberian Peninsula reveals that Iberian ibex and chamois were frequently present throughout this period. Statistical analyses allowed us to assess the conditions that might have favored the presence or absence of these animals in the sites, while the taphonomic analyses enabled us to address the issue of whether ibex and chamois were indeed hunted by Neanderthals in the Iberian Peninsula. Our results indicate a better representation of both species in rocky and mountainous areas. The taphonomy of some sites reveals that chamois and ibex were hunted by Neanderthals, who showed great adaptive capacities to a wide variety of environments, including mountainous habitats. In contrast, other sites with favorable ecological conditions for ibex and chamois where these animals were not exploited by Neanderthals, who chose to hunt other species like deer, horses or aurochs, suggest behavioral complexity and large versatility.}, } @article {pmid25467111, year = {2015}, author = {Sams, AJ and Hawks, J and Keinan, A}, title = {The utility of ancient human DNA for improving allele age estimates, with implications for demographic models and tests of natural selection.}, journal = {Journal of human evolution}, volume = {79}, number = {}, pages = {64-72}, pmid = {25467111}, issn = {1095-8606}, support = {R01 GM108805/GM/NIGMS NIH HHS/United States ; R01GM108805/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anthropology, Physical ; DNA/analysis/*genetics ; Europe ; *Evolution, Molecular ; Genetics, Population/*methods ; Humans ; Male ; Neanderthals/*genetics ; Selection, Genetic ; }, abstract = {The age of polymorphic alleles in humans is often estimated from population genetic patterns in extant human populations, such as allele frequencies, linkage disequilibrium, and rate of mutations. Ancient DNA can improve the accuracy of such estimates, as well as facilitate testing the validity of demographic models underlying many population genetic methods. Specifically, the presence of an allele in a genome derived from an ancient sample testifies that the allele is at least as old as that sample. In this study, we consider a common method for estimating allele age based on allele frequency as applied to variants from the US National Institutes of Health (NIH) Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project. We view these estimates in the context of the presence or absence of each allele in the genomes of the 5300 year old Tyrolean Iceman, Ötzi, and of the 50,000 year old Altai Neandertal. Our results illuminate the accuracy of these estimates and their sensitivity to demographic events that were not included in the model underlying age estimation. Specifically, allele presence in the Iceman genome provides a good fit of allele age estimates to the expectation based on the age of that specimen. The equivalent based on the Neandertal genome leads to a poorer fit. This is likely due in part to the older age of the Neandertal and the older time of the split between modern humans and Neandertals, but also due to gene flow from Neandertals to modern humans not being considered in the underlying demographic model. Thus, the incorporation of ancient DNA can improve allele age estimation, demographic modeling, and tests of natural selection. Our results also point to the importance of considering a more diverse set of ancient samples for understanding the geographic and temporal range of individual alleles.}, } @article {pmid25454779, year = {2015}, author = {Smith, GM}, title = {Neanderthal megafaunal exploitation in Western Europe and its dietary implications: a contextual reassessment of La Cotte de St Brelade (Jersey).}, journal = {Journal of human evolution}, volume = {78}, number = {}, pages = {181-201}, doi = {10.1016/j.jhevol.2014.10.007}, pmid = {25454779}, issn = {1095-8606}, mesh = {Animals ; Diet ; *Ecology ; Europe ; Feeding Behavior/*physiology ; Fossils ; France ; Geologic Sediments ; Neanderthals/*physiology ; Paleontology ; Perissodactyla ; Ursidae ; Wolves ; }, abstract = {The recurrent presence at Middle Palaeolithic sites of megafaunal remains, such as mammoth, elephant and rhinoceros, together with isotope analyses signalling meat as a prominent protein source, have been used to argue that these species played a central role in Neanderthal diet. Key to this model are the bone heap horizons from La Cotte de St Brelade (Jersey), which were previously interpreted as game drive debris resulting from systematic Neanderthal hunting. However, this hypothesis has never been rigorously tested, neither at a site-scale, incorporating taphonomic and contextual data, nor at a wider European scale. First, this paper provides a contextual reassessment of the faunal remains from La Cotte to fully understand Neanderthal behaviour at the site. Second, a comparative database of 30 well-published Middle Palaeolithic sites with megafauna permits a data-driven, broader spatial (European) and diachronic assessment of the role of megafauna in Neanderthal subsistence behaviour. Results suggest initial Neanderthal occupation at La Cotte was intensive although through time site visits became more infrequent, as highlighted by a reduction in cultural debris concurrent with a rise in carnivore presence. While mammoths, just as other large mammals and occasionally carnivores, were clearly butchered at this locality, their acquisition and role in Neanderthal diet remains ambiguous. Broader comparisons across Western Europe indicate a main focus on a range of large herbivores, with only a minor, opportunistic, role for megafauna. Whilst stable isotope analysis suggests that Neanderthal diet was meat-oriented, zooarchaeological data do not support the inference that megafauna were the major contributor of meat.}, } @article {pmid25447821, year = {2015}, author = {Adel, S and Kakularam, KR and Horn, T and Reddanna, P and Kuhn, H and Heydeck, D}, title = {Leukotriene signaling in the extinct human subspecies Homo denisovan and Homo neanderthalensis. Structural and functional comparison with Homo sapiens.}, journal = {Archives of biochemistry and biophysics}, volume = {565}, number = {}, pages = {17-24}, doi = {10.1016/j.abb.2014.10.012}, pmid = {25447821}, issn = {1096-0384}, mesh = {Animals ; Databases, Genetic ; Genome, Human/*physiology ; Humans ; Leukotrienes/*genetics/metabolism ; Lipoxygenases/*genetics/metabolism ; Neanderthals/*genetics/metabolism ; Signal Transduction/*genetics ; Species Specificity ; }, abstract = {Mammalian lipoxygenases (LOXs) have been implicated in cell differentiation and in the biosynthesis of pro- and anti-inflammatory lipid mediators. The initial draft sequence of the Homo neanderthalensis genome (coverage of 1.3-fold) suggested defective leukotriene signaling in this archaic human subspecies since expression of essential proteins appeared to be corrupted. Meanwhile high quality genomic sequence data became available for two extinct human subspecies (H. neanderthalensis, Homo denisovan) and completion of the human 1000 genome project provided a comprehensive database characterizing the genetic variability of the human genome. For this study we extracted the nucleotide sequences of selected eicosanoid relevant genes (ALOX5, ALOX15, ALOX12, ALOX15B, ALOX12B, ALOXE3, COX1, COX2, LTA4H, LTC4S, ALOX5AP, CYSLTR1, CYSLTR2, BLTR1, BLTR2) from the corresponding databases. Comparison of the deduced amino acid sequences in connection with site-directed mutagenesis studies and structural modeling suggested that the major enzymes and receptors of leukotriene signaling as well as the two cyclooxygenase isoforms were fully functional in these two extinct human subspecies.}, } @article {pmid25440134, year = {2014}, author = {Rubini, M and Cerroni, V and Festa, G and Sardella, R and Zaio, P}, title = {A revision of hominin fossil teeth from Fontana Ranuccio (Middle Pleistocene, Anagni, Frosinone, Italy).}, journal = {Journal of human evolution}, volume = {77}, number = {}, pages = {204-216}, doi = {10.1016/j.jhevol.2014.09.002}, pmid = {25440134}, issn = {1095-8606}, mesh = {Animals ; Biological Evolution ; Dental Pulp Cavity/anatomy & histology ; *Fossils ; Geologic Sediments ; Hominidae/*anatomy & histology ; Humans ; Italy ; Paleodontology ; Tooth/*anatomy & histology ; Tooth Root/anatomy & histology ; }, abstract = {The Fontana Ranuccio hominin teeth (FR, Latium, Italy) are dated to the Middle Pleistocene. In previous studies these teeth were classified as two lower (left and right) second molars, one lower left central incisor and a badly worn incisor crown, the exact position of which could not be determined. In 2012 these remains were acquired by the Anthropological Service of S.B.A.L. (Italian Ministry of Culture) and for this reason re-analysed. In a thorough revision we have reassessed them both morphologically and dimensionally as two lower (left and right) first molars, one lower left lateral incisor and a possible upper left canine. The comparison with penecontemporaneous and diachronic samples shows that the Fontana Ranuccio teeth are morphologically similar to Atapuerca-Sima de los Huesos, Arago XIII and Neanderthal samples.}, } @article {pmid25439708, year = {2014}, author = {Mateos, A and Goikoetxea, I and Leonard, WR and Martín-González, JÁ and Rodríguez-Gómez, G and Rodríguez, J}, title = {Neandertal growth: what are the costs?.}, journal = {Journal of human evolution}, volume = {77}, number = {}, pages = {167-178}, doi = {10.1016/j.jhevol.2014.09.003}, pmid = {25439708}, issn = {1095-8606}, mesh = {Animals ; Basal Metabolism/*physiology ; Body Height/physiology ; Body Temperature Regulation/physiology ; Body Weight/physiology ; Child ; Child, Preschool ; Energy Metabolism ; Female ; Humans ; Infant ; Male ; Neanderthals/*growth & development ; }, abstract = {Energetic approaches have been increasingly used to address key issues in Neandertal palaeoecology and palaeobiology. Previous research has focused exclusively on the energy requirements of adults and highlights the high energy demands of these individuals compared with modern humans. Less attention has been paid to the energy requirements of sub-adult Neandertals, even though this age group could provide clues for a better understanding of Neandertal life history. Accordingly, herein, we estimate the energy costs of maintenance and growth in Neandertal infants and children from one to six years of age and compare these costs with values for modern humans. Statural growth models for two modern human populations (Beasain and Evenki) and an average Neandertal model population are used to establish weight growth models. In turn, these models of body weight growth are used to estimate key components of energetic variables (basal metabolic rate, total energy expenditure, energy of growth and daily energy requirements). Between three and six years of age, Neandertal children have slightly lower basal and growth energy costs than do modern humans of the same age, due primarily to their smaller body mass and slower growth rates. The reduction in energy allocated to growth is likely the result of metabolic adaptations to other somatic factors and thermal stress. Data from contemporary human infants and children suggest that even mild cold stress increases non-shivering thermogenesis, thus elevating metabolic needs by 50% or more. These results suggest that thermal stress likely played a strong role in shaping the delayed developmental patterns and lower energy allocated to growth during early life in Neandertals relative to Homo sapiens.}, } @article {pmid25413709, year = {2015}, author = {Hofreiter, M and Paijmans, JL and Goodchild, H and Speller, CF and Barlow, A and Fortes, GG and Thomas, JA and Ludwig, A and Collins, MJ}, title = {The future of ancient DNA: Technical advances and conceptual shifts.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {37}, number = {3}, pages = {284-293}, doi = {10.1002/bies.201400160}, pmid = {25413709}, issn = {1521-1878}, mesh = {Animals ; DNA/*genetics/isolation & purification ; DNA Damage ; Genome ; *High-Throughput Nucleotide Sequencing ; Humans ; Multilocus Sequence Typing ; Temperature ; }, abstract = {Technological innovations such as next generation sequencing and DNA hybridisation enrichment have resulted in multi-fold increases in both the quantity of ancient DNA sequence data and the time depth for DNA retrieval. To date, over 30 ancient genomes have been sequenced, moving from 0.7× coverage (mammoth) in 2008 to more than 50× coverage (Neanderthal) in 2014. Studies of rapid evolutionary changes, such as the evolution and spread of pathogens and the genetic responses of hosts, or the genetics of domestication and climatic adaptation, are developing swiftly and the importance of palaeogenomics for investigating evolutionary processes during the last million years is likely to increase considerably. However, these new datasets require new methods of data processing and analysis, as well as conceptual changes in interpreting the results. In this review we highlight important areas of future technical and conceptual progress and discuss research topics in the rapidly growing field of palaeogenomics.}, } @article {pmid25407444, year = {2015}, author = {Fiorenza, L and Benazzi, S and Henry, AG and Salazar-García, DC and Blasco, R and Picin, A and Wroe, S and Kullmer, O}, title = {To meat or not to meat? New perspectives on Neanderthal ecology.}, journal = {American journal of physical anthropology}, volume = {156 Suppl 59}, number = {}, pages = {43-71}, doi = {10.1002/ajpa.22659}, pmid = {25407444}, issn = {1096-8644}, mesh = {Animals ; Dental Calculus/pathology ; Europe ; *Feeding Behavior ; *Fossils ; Isotopes/analysis ; *Meat ; *Neanderthals/anatomy & histology/physiology ; Paleopathology ; Technology ; Tooth Wear/pathology ; }, abstract = {Neanderthals have been commonly depicted as top predators who met their nutritional needs by focusing entirely on meat. This information mostly derives from faunal assemblage analyses and stable isotope studies: methods that tend to underestimate plant consumption and overestimate the intake of animal proteins. Several studies in fact demonstrate that there is a physiological limit to the amount of animal proteins that can be consumed: exceeding these values causes protein toxicity that can be particularly dangerous to pregnant women and newborns. Consequently, to avoid food poisoning from meat-based diets, Neanderthals must have incorporated alternative food sources in their daily diets, including plant materials as well.}, } @article {pmid25407030, year = {2015}, author = {Benazzi, S and Nguyen, HN and Kullmer, O and Hublin, JJ}, title = {Exploring the biomechanics of taurodontism.}, journal = {Journal of anatomy}, volume = {226}, number = {2}, pages = {180-188}, pmid = {25407030}, issn = {1469-7580}, mesh = {Animals ; Biomechanical Phenomena/physiology ; Dental Pulp Cavity/*abnormalities/physiopathology ; Dental Stress Analysis/methods ; Finite Element Analysis ; Mastication/physiology ; Neanderthals/*physiology ; Stress, Physiological/physiology ; Tooth Abnormalities/*physiopathology ; }, abstract = {Taurodontism (i.e. enlarged pulp chamber with concomitant apical displacement of the root bi/trifurcation) is considered a dental anomaly with relatively low incidence in contemporary societies, but it represents a typical trait frequently found in Neandertal teeth. Four hypotheses can be envisioned to explain the high frequency in Neandertals: adaptation to a specific occlusal loading regime (biomechanical advantage), adaptation to a high attrition diet, pleiotropic or genetic drift effects. In this contribution we used finite element analysis (FEA) and advanced loading concepts based on macrowear information to evaluate whether taurodontism supplies some dental biomechanical advantages. Loads were applied to the digital model of the lower right first molar (RM1) of the Neandertal specimen Le Moustier 1, as well as to the digital models of both a shortened and a hyper-taurodontic version of Le Moustier RM1 . Moreover, we simulated a scenario where an object is held between teeth and pulled in different directions to investigate whether taurodontism might be useful for para-masticatory activities. Our results do not show any meaningful difference among all the simulations, pointing out that taurodontism does not improve the functional biomechanics of the tooth and does not favour para-masticatory pulling activities. Therefore, taurodontism should be considered either an adaptation to a high attrition diet or most likely the result of pleiotropic or genetic drift effects. Finally, our results have important implications for modern dentistry during endodontic treatments, as we observed that filling the pulp chamber with dentine-like material increases tooth stiffness, and ultimately tensile stresses in the crown, thus favouring tooth failure.}, } @article {pmid25388672, year = {2015}, author = {Fukase, H and Kondo, O and Ishida, H}, title = {Size and placement of developing anterior teeth in immature Neanderthal mandibles from Dederiyeh Cave, Syria: implications for emergence of the modern human chin.}, journal = {American journal of physical anthropology}, volume = {156}, number = {3}, pages = {482-488}, doi = {10.1002/ajpa.22665}, pmid = {25388672}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; Caves ; Chin/*anatomy & histology ; Humans ; Incisor/*anatomy & histology ; Mandible/*anatomy & histology ; Neanderthals/*anatomy & histology ; Syria ; }, abstract = {Evolutionary and functional significance of the human chin has long been explored from various perspectives including masticatory biomechanics, speech, and anterior tooth size. Recent ontogenetic studies have indicated that the spatial position of internally forming anterior teeth partially constrains adult mandibular symphyseal morphology. The present study therefore preliminarily examined the size and placement of developing anterior teeth in immature Neanderthal mandibles of Dederiyeh 1 and 2, compared with similarly-aged modern humans (N = 16) and chimpanzees (N = 7) whose incisors are comparatively small and large among extant hominids, respectively. The Dederiyeh 1 mandible is described as slightly presenting a mental trigone and attendant mental fossa, whereas Dederiyeh 2 completely lacks such chin-associated configurations. Results showed that, despite symphyseal size being within the modern human range, both Dederiyeh mandibles accommodated overall larger anterior dentition and displayed a remarkably wide bicanine space compared to those of modern humans. Dederiyeh 2 had comparatively thicker deciduous incisor roots and more enlarged permanent incisor crypts than Dederiyeh 1, but both Dederiyeh individuals exhibited a total dental size mostly intermediate between modern humans and chimpanzees. These findings potentially imply that the large deciduous/permanent incisors collectively distended the labial alveolar bone, obscuring an incipient mental trigone. It is therefore hypothesized that the appearance of chin-associated features, particularly of the mental trigone and fossa, can be accounted for partly by developmental relationships between the sizes of the available mandibular space and anterior teeth. This hypothesis must be, however, further addressed with more referential samples in future studies.}, } @article {pmid25378462, year = {2014}, author = {Seguin-Orlando, A and Korneliussen, TS and Sikora, M and Malaspinas, AS and Manica, A and Moltke, I and Albrechtsen, A and Ko, A and Margaryan, A and Moiseyev, V and Goebel, T and Westaway, M and Lambert, D and Khartanovich, V and Wall, JD and Nigst, PR and Foley, RA and Lahr, MM and Nielsen, R and Orlando, L and Willerslev, E}, title = {Paleogenomics. Genomic structure in Europeans dating back at least 36,200 years.}, journal = {Science (New York, N.Y.)}, volume = {346}, number = {6213}, pages = {1113-1118}, doi = {10.1126/science.aaa0114}, pmid = {25378462}, issn = {1095-9203}, mesh = {DNA/*genetics/history ; Europe ; European Continental Ancestry Group/*genetics/history ; Fossils ; Genome, Human/*genetics ; Genomics ; History, Ancient ; Humans ; Male ; Siberia ; }, abstract = {The origin of contemporary Europeans remains contentious. We obtained a genome sequence from Kostenki 14 in European Russia dating from 38,700 to 36,200 years ago, one of the oldest fossils of anatomically modern humans from Europe. We find that Kostenki 14 shares a close ancestry with the 24,000-year-old Mal'ta boy from central Siberia, European Mesolithic hunter-gatherers, some contemporary western Siberians, and many Europeans, but not eastern Asians. Additionally, the Kostenki 14 genome shows evidence of shared ancestry with a population basal to all Eurasians that also relates to later European Neolithic farmers. We find that Kostenki 14 contains more Neandertal DNA that is contained in longer tracts than present Europeans. Our findings reveal the timing of divergence of western Eurasians and East Asians to be more than 36,200 years ago and that European genomic structure today dates back to the Upper Paleolithic and derives from a metapopulation that at times stretched from Europe to central Asia.}, } @article {pmid25369936, year = {2014}, author = {Brower, CS and Rosen, CE and Jones, RH and Wadas, BC and Piatkov, KI and Varshavsky, A}, title = {Liat1, an arginyltransferase-binding protein whose evolution among primates involved changes in the numbers of its 10-residue repeats.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {46}, pages = {E4936-45}, pmid = {25369936}, issn = {1091-6490}, support = {R56 DK039520/DK/NIDDK NIH HHS/United States ; R01 GM031530/GM/NIGMS NIH HHS/United States ; R01 DK039520/DK/NIDDK NIH HHS/United States ; DK039520/DK/NIDDK NIH HHS/United States ; R37 DK039520/DK/NIDDK NIH HHS/United States ; GM031530/GM/NIGMS NIH HHS/United States ; }, mesh = {Alternative Splicing ; Amino Acid Sequence ; Aminoacyltransferases/*metabolism ; Animals ; Arginine/metabolism ; Base Sequence ; Chromosome Mapping ; *Evolution, Molecular ; Exons/genetics ; Gene Expression ; Humans ; Ligands ; Mice/*genetics ; Molecular Sequence Data ; Primates/*genetics ; Protein Binding ; Protein Isoforms/metabolism ; Protein Processing, Post-Translational ; Proteolysis ; Recombinant Fusion Proteins/metabolism ; Sequence Alignment ; Sequence Homology ; Species Specificity ; *Tandem Repeat Sequences ; }, abstract = {The arginyltransferase Ate1 is a component of the N-end rule pathway, which recognizes proteins containing N-terminal degradation signals called N-degrons, polyubiquitylates these proteins, and thereby causes their degradation by the proteasome. At least six isoforms of mouse Ate1 are produced through alternative splicing of Ate1 pre-mRNA. We identified a previously uncharacterized mouse protein, termed Liat1 (ligand of Ate1), that interacts with Ate1 but does not appear to be its arginylation substrate. Liat1 has a higher affinity for the isoforms Ate1(1A7A) and Ate1(1B7A). Liat1 stimulated the in vitro N-terminal arginylation of a model substrate by Ate1. All examined vertebrate and some invertebrate genomes encode proteins sequelogous (similar in sequence) to mouse Liat1. Sequelogs of Liat1 share a highly conserved ∼30-residue region that is shown here to be required for the binding of Liat1 to Ate1. We also identified non-Ate1 proteins that interact with Liat1. In contrast to Liat1 genes of nonprimate mammals, Liat1 genes of primates are subtelomeric, a location that tends to confer evolutionary instability on a gene. Remarkably, Liat1 proteins of some primates, from macaques to humans, contain tandem repeats of a 10-residue sequence, whereas Liat1 proteins of other mammals contain a single copy of this motif. Quantities of these repeats are, in general, different in Liat1 of different primates. For example, there are 1, 4, 13, 13, 17, and 17 repeats in the gibbon, gorilla, orangutan, bonobo, neanderthal, and human Liat1, respectively, suggesting that repeat number changes in this previously uncharacterized protein may contribute to evolution of primates.}, } @article {pmid25341783, year = {2014}, author = {Fu, Q and Li, H and Moorjani, P and Jay, F and Slepchenko, SM and Bondarev, AA and Johnson, PL and Aximu-Petri, A and Prüfer, K and de Filippo, C and Meyer, M and Zwyns, N and Salazar-García, DC and Kuzmin, YV and Keates, SG and Kosintsev, PA and Razhev, DI and Richards, MP and Peristov, NV and Lachmann, M and Douka, K and Higham, TF and Slatkin, M and Hublin, JJ and Reich, D and Kelso, J and Viola, TB and Pääbo, S}, title = {Genome sequence of a 45,000-year-old modern human from western Siberia.}, journal = {Nature}, volume = {514}, number = {7523}, pages = {445-449}, pmid = {25341783}, issn = {1476-4687}, support = {R01-GM40282/GM/NIGMS NIH HHS/United States ; F32 GM115006/GM/NIGMS NIH HHS/United States ; R01 GM100233/GM/NIGMS NIH HHS/United States ; R01 GM040282/GM/NIGMS NIH HHS/United States ; K99 GM104158/GM/NIGMS NIH HHS/United States ; K99-GM104158/GM/NIGMS NIH HHS/United States ; GM100233/GM/NIGMS NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; }, mesh = {Alleles ; Animals ; Chromosomes, Human, Pair 12/genetics ; Diet ; Evolution, Molecular ; *Fossils ; Genome, Human/*genetics ; Humans ; Hybridization, Genetic/genetics ; Male ; Molecular Sequence Data ; Mutation Rate ; Neanderthals/genetics ; Phylogeny ; Population Density ; Population Dynamics ; Principal Component Analysis ; Sequence Analysis, DNA ; Siberia ; }, abstract = {We present the high-quality genome sequence of a ∼45,000-year-old modern human male from Siberia. This individual derives from a population that lived before-or simultaneously with-the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000-13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 × 10(-9) to 0.6 × 10(-9) per site per year, a Y chromosomal mutation rate of 0.7 × 10(-9) to 0.9 × 10(-9) per site per year based on the additional substitutions that have occurred in present-day non-Africans compared to this genome, and a mitochondrial mutation rate of 1.8 × 10(-8) to 3.2 × 10(-8) per site per year based on the age of the bone.}, } @article {pmid25341767, year = {2014}, author = {Callaway, E}, title = {Oldest-known human genome sequenced.}, journal = {Nature}, volume = {514}, number = {7523}, pages = {413}, doi = {10.1038/514413a}, pmid = {25341767}, issn = {1476-4687}, mesh = {Animals ; *Fossils ; Genome, Human/*genetics ; History, Ancient ; Human Migration/history ; Humans ; Hybridization, Genetic ; Neanderthals/genetics ; Siberia/ethnology ; }, } @article {pmid25340175, year = {2014}, author = {Castro-Chavez, F}, title = {File Compression and Expansion of the Genetic Code by the use of the Yin/Yang Directions to find its Sphered Cube.}, journal = {Journal of biodiversity, bioprospecting and development}, volume = {1}, number = {1}, pages = {}, pmid = {25340175}, support = {T32 HL007812/HL/NHLBI NIH HHS/United States ; }, abstract = {OBJECTIVE: The objective of this article is to demonstrate that the genetic code can be studied and represented in a 3-D Sphered Cube for bioinformatics and for education by using the graphical help of the ancient "Book of Changes" or I Ching for the comparison, pair by pair, of the three basic characteristics of nucleotides: H-bonds, molecular structure, and their tautomerism.

METHODS: The source of natural biodiversity is the high plasticity of the genetic code, analyzable with a reverse engineering of its 2-D and 3-D representations (here illustrated), but also through the classical 64-hexagrams of the ancient I Ching, as if they were the 64-codons or words of the genetic code.

RESULTS: In this article, the four elements of the Yin/Yang were found by correlating the 3×2=6 sets of Cartesian comparisons of the mentioned properties of nucleic acids, to the directionality of their resulting blocks of codons grouped according to their resulting amino acids and/or functions, integrating a 384-codon Sphered Cube whose function is illustrated by comparing six brain peptides and a promoter of osteoblasts from Humans versus Neanderthal, as well as to Negadi's work on the importance of the number 384 within the genetic code.

CONCLUSIONS: Starting with the codon/anticodon correlation of Nirenberg, published in full here for the first time, and by studying the genetic code and its 3-D display, the buffers of reiteration within codons codifying for the same amino acid, displayed the two long (binary number one) and older Yin/Yang arrows that travel in opposite directions, mimicking the parental DNA strands, while annealing to the two younger and broken (binary number zero) Yin/Yang arrows, mimicking the new DNA strands; the graphic analysis of the of the genetic code and its plasticity was helpful to compare compatible sequences (human compatible to human versus neanderthal compatible to neanderthal), while further exploring the wondrous biodiversity of nature for educational purposes.}, } @article {pmid25339238, year = {2015}, author = {Macias, ME and Churchill, SE}, title = {Functional morphology of the Neandertal scapular glenoid fossa.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {298}, number = {1}, pages = {168-179}, doi = {10.1002/ar.23072}, pmid = {25339238}, issn = {1932-8494}, mesh = {Adaptation, Physiological/physiology ; Animals ; *Biological Evolution ; Biomechanical Phenomena/physiology ; Glenoid Cavity/*anatomy & histology/*physiology ; Humans ; Imaging, Three-Dimensional ; Locomotion/physiology ; *Mathematics ; Neanderthals/*anatomy & histology/*physiology ; Pan troglodytes/anatomy & histology/physiology ; Pongo/anatomy & histology/physiology ; Principal Component Analysis ; }, abstract = {Neandertals and Homo sapiens are known to differ in scapular glenoid fossa morphology. Functional explanations may be appropriate for certain aspects of glenoid fossa morphology; however, other factors--e.g., allometry, evolutionary development--must be addressed before functional morphology is considered. Using three-dimensional geometric morphometrics, shape of the scapular glenoid fossa was compared among Neandertals, early and recent modern humans, chimpanzees, orangutans, Australopithecus afarensis, and Au. sediba. Permutation analysis revealed that side, sex, and lifestyle did not correlate with shape. Of the features we found to differ between groups, anterior glenoid rim morphology and fossa curvature did not correlate with the aforementioned shape variables; thus, a functional explanation is appropriate for these components of glenoid fossa shape. Shared morphology among recent humans and chimpanzees (to the exclusion of Neandertals and orangutans) suggests independent forces contributing to these morphological configurations. Potential explanations include adaptations to habitual behavior and locomotor adaptations in the scapulae of recent humans and chimpanzees; these explanations are supported by clinical and experimental literature. The absence of these morphological features in Neandertals may support the lack of these selective forces on their scapular glenoid fossa morphology.}, } @article {pmid25329008, year = {2015}, author = {Xing, S and Martinón-Torres, M and Bermúdez de Castro, JM and Wu, X and Liu, W}, title = {Hominin teeth from the early Late Pleistocene site of Xujiayao, Northern China.}, journal = {American journal of physical anthropology}, volume = {156}, number = {2}, pages = {224-240}, doi = {10.1002/ajpa.22641}, pmid = {25329008}, issn = {1096-8644}, mesh = {Animals ; China ; *Fossils ; History, Ancient ; Hominidae/*anatomy & histology ; Paleodontology ; Tooth/*anatomy & histology ; }, abstract = {It is generally accepted that from the late Middle to the early Late Pleistocene (∼340-90 ka BP), Neanderthals were occupying Europe and Western Asia, whereas anatomically modern humans were present in the African continent. In contrast, the paucity of hominin fossil evidence from East Asia from this period impedes a complete evolutionary picture of the genus Homo, as well as assessment of the possible contribution of or interaction with Asian hominins in the evolution of Homo sapiens and Homo neanderthalensis. Here we present a comparative study of a hominin dental sample recovered from the Xujiayao site, in Northern China, attributed to the early Late Pleistocene (MIS 5 to 4). Our dental study reveals a mosaic of primitive and derived dental features for the Xujiayao hominins that can be summarized as follows: i) they are different from archaic and recent modern humans, ii) they present some features that are common but not exclusive to the Neanderthal lineage, and iii) they retain some primitive conformations classically found in East Asian Early and Middle Pleistocene hominins despite their young geological age. Thus, our study evinces the existence in China of a population of unclear taxonomic status with regard to other contemporary populations such as H. sapiens and H. neanderthalensis. The morphological and metric studies of the Xujiayao teeth expand the variability known for early Late Pleistocene hominin fossils and suggest the possibility that a primitive hominin lineage may have survived late into the Late Pleistocene in China.}, } @article {pmid25324463, year = {2015}, author = {Fiorenza, L}, title = {Reconstructing diet and behaviour of Neanderthals from Central Italy through dental macrowear analysis.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {93}, number = {}, pages = {119-133}, doi = {10.4436/JASS.93002}, pmid = {25324463}, issn = {2037-0644}, mesh = {Animals ; Caves ; Diet/history ; Feeding Behavior/*physiology ; Female ; Fossils ; History, Ancient ; Italy ; Male ; Neanderthals/*physiology ; Paleontology ; Tooth Wear/*pathology ; }, abstract = {Neanderthals have been traditionally considered at the top of the food chain with a diet mostly consisting of animal proteins. New findings challenged this view and suggested that Neanderthals living in areas with more favourable climatic conditions exploited various food sources, including plant materials. In this study, the attention is focused on dental macrowear of Neanderthals from Central Italy, whose diet has been largely unexplored. Three-dimensional digital models of teeth have been examined through occlusal fingerprint analysis (OFA), a method used to understand how wear facets are formed. The results show a close similarity between the specimens of Saccopastore 1 and 2, with a wear pattern that indicates the use of diverse sources of food, but with a predominance of animal proteins. On the other hand, the specimens of Guattari 2 and 3 display a slightly different dental wear from each other, which probably reflects the chronological sequence of the Guattari Cave. It appears that at the end of the marine isotope stage (MIS)5 the occupants of this cave consumed marginally more plant foods, while during MIS 3 they relied more on animal proteins. Finally, a close look at the Saccopastore maxillary molars reveals the presence of a distinct type of wear that has been previously described in some Neanderthals and early Homo sapiens from Near East, and it provides additional information about the culture and lifestyle of these Pleistocene human populations.}, } @article {pmid25295956, year = {2014}, author = {Faivre, JP and Maureille, B and Bayle, P and Crevecoeur, I and Duval, M and Grün, R and Bemilli, C and Bonilauri, S and Coutard, S and Bessou, M and Limondin-Lozouet, N and Cottard, A and Deshayes, T and Douillard, A and Henaff, X and Pautret-Homerville, C and Kinsley, L and Trinkaus, E}, title = {Middle pleistocene human remains from Tourville-la-Rivière (Normandy, France) and their archaeological context.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e104111}, pmid = {25295956}, issn = {1932-6203}, mesh = {Animals ; Archaeology ; *Fossils ; France ; Hominidae/*anatomy & histology ; Humans ; }, abstract = {Despite numerous sites of great antiquity having been excavated since the end of the 19th century, Middle Pleistocene human fossils are still extremely rare in northwestern Europe. Apart from the two partial crania from Biache-Saint-Vaast in northern France, all known human fossils from this period have been found from ten sites in either Germany or England. Here we report the discovery of three long bones from the same left upper limb discovered at the open-air site of Tourville-la-Rivière in the Seine Valley of northern France. New U-series and combined US-ESR dating on animal teeth produced an age range for the site of 183 to 236 ka. In combination with paleoecological indicators, they indicate an age toward the end of MIS 7. The human remains from Tourville-la-Rivière are attributable to the Neandertal lineage based on morphological and metric analyses. An abnormal crest on the left humerus represents a deltoid muscle enthesis. Micro- and or macro-traumas connected to repetitive movements similar to those documented for professional throwing athletes could be origin of abnormality.}, } @article {pmid25282273, year = {2014}, author = {Fornai, C and Benazzi, S and Svoboda, J and Pap, I and Harvati, K and Weber, GW}, title = {Enamel thickness variation of deciduous first and second upper molars in modern humans and Neanderthals.}, journal = {Journal of human evolution}, volume = {76}, number = {}, pages = {83-91}, doi = {10.1016/j.jhevol.2014.05.013}, pmid = {25282273}, issn = {1095-8606}, mesh = {Animals ; Dental Enamel/*diagnostic imaging ; Fossils/diagnostic imaging ; Humans ; Molar/*diagnostic imaging ; *Neanderthals ; Tooth Wear/diagnostic imaging ; Tooth, Deciduous/*diagnostic imaging ; X-Ray Microtomography ; }, abstract = {Enamel thickness and dental tissue proportions have been recognized as effective taxonomic discriminators between Neanderthal and modern humans teeth. However, most of the research on this topic focused on permanent teeth, and little information is available for the deciduous dentition. Moreover, although worn teeth are more frequently found than unworn teeth, published data for worn teeth are scarce and methods for the assessment of their enamel thickness need to be developed. Here, we addressed this issue by studying the 2D average enamel thickness (AET) and 2D relative enamel thickness (RET) of Neanderthal and modern humans unworn to moderately worn upper first deciduous molars (dm(1)s) and upper second deciduous molars (dm(2)s). In particular, we used 3D μCT data to investigate the mesial section for dm(1)s and both mesial and buccal sections for dm(2)s. Our results confirmed previous findings of an Neanderthal derived condition of thin enamel, and thinner enamel in dm(1)s than dm(2)s in both Neanderthal and modern humans. We demonstrated that the Neanderthal 2D RET indices are significantly lower than those of modern humans at similar wear stages in both dm(1)s and dm(2)s (p < 0.05). The discriminant analysis showed that using 2D RET from dm(1) and dm(2) sections at different wear stages up to 93% of the individuals are correctly classified. Moreover, we showed that the dm(2) buccal sections, although non-conventionally used, might have an advantage on mesial sections since they distinguish as well as mesial sections but tend to be less worn. Therefore, the 2D analysis of enamel thickness is suggested as a means for taxonomic discrimination between modern humans and Neanderthal unworn to moderately worn upper deciduous molars.}, } @article {pmid25279839, year = {2015}, author = {Bermúdez de Castro, JM and Quam, R and Martinón-Torres, M and Martínez, I and Gracia-Téllez, A and Arsuaga, JL and Carbonell, E}, title = {The medial pterygoid tubercle in the Atapuerca Early and Middle Pleistocene mandibles: evolutionary implications.}, journal = {American journal of physical anthropology}, volume = {156}, number = {1}, pages = {102-109}, doi = {10.1002/ajpa.22631}, pmid = {25279839}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; Biological Evolution ; *Fossils ; Hominidae/*anatomy & histology ; Humans ; Mandible/*anatomy & histology ; Neanderthals/*anatomy & histology ; }, abstract = {Numerous studies have attempted to identify the presence of uniquely derived (autoapomorphic) Neandertal features. Here, we deal with the medial pterygoid tubercle (MTP), which is usually present on the internal face of the ascending ramus of Neandertal specimens. Our study stems from the identification of a hypertrophied tubercle in ATD6-96, an Early Pleistocene mandible recovered from the TD6 level of the Atapuerca-Gran Dolina site and attributed to Homo antecessor. Our review of the literature and study of numerous original fossil specimens and high quality replicas confirm that the MTP occurs at a high frequency in Neandertals (ca. 89%) and is also present in over half (ca. 55%) of the Middle Pleistocene Sima de los Huesos (SH) hominins. In contrast, it is generally absent or minimally developed in other extinct hominins, but can be found in variable frequencies (
METHODS: This study was a review of skeletal and ethnographic evidence for menopause and postreproductive life in humans' distant past, hypotheses for the evolution of menopause and long postreproductive life, variation in age at menopause with focus on childhood environments, and the study of variation in symptom experience across populations.

RESULTS: Longevity, rather than capacity for menopause, sets humans apart from other primates. Skeletal evidence demonstrates that some Neanderthals and archaic Homo sapiens lived to the age at menopause and that at least one third of women in traditional foraging populations live beyond menopause. The evolutionary reasons for why women experience a long postreproductive life continue to be debated. A developmental perspective suggests that early childhood may be a critical time for the environment to irreversibly influence the number of oocytes or rate of follicular atresia and, ultimately, age at menopause. A comparative perspective examines symptom experience at midlife through participant observation, qualitative interviews, and quantitative instruments to gain a holistic understanding of the meaning, experience, and sociocultural context of menopause.

CONCLUSIONS: An evolutionary perspective suggests that menopause is not a recent phenomenon among humans. A developmental perspective focuses on the influence of early childhood on ovarian function. A comparative perspective expands clinical norms and provides knowledge about the range of human variations.}, } @article {pmid25216347, year = {2014}, author = {Chene, G and Tardieu, AS and Trombert, B and Amouzougan, A and Lamblin, G and Mellier, G and Coppens, Y}, title = {A species' Odyssey: evolution of obstetrical mechanics from Australopithecus Lucy to nowadays.}, journal = {European journal of obstetrics, gynecology, and reproductive biology}, volume = {181}, number = {}, pages = {316-320}, doi = {10.1016/j.ejogrb.2014.08.027}, pmid = {25216347}, issn = {1872-7654}, mesh = {Animals ; Biological Evolution ; *Biomechanical Phenomena ; Female ; Gorilla gorilla/anatomy & histology ; Hominidae/*anatomy & histology ; Humans/anatomy & histology ; *Labor, Obstetric ; Neanderthals/anatomy & histology ; Pan troglodytes/anatomy & histology ; Pelvic Bones ; Pelvimetry ; Pongo/anatomy & histology ; Pregnancy ; }, abstract = {OBJECTIVE: Study of obstetrical mechanics of Australopithecus Lucy, Homo neanderthalensis and Homo erectus relative to modern Homo sapiens and the Catarrhines.

STUDY DESIGN: The material comprised a total of 360 pelves: 3 fossil pelves reconstructed using casts (Australopithecus afarensis Lucy or AL 288-1, Homo erectus KNM-WT 15000, H. neanderthalensis or Kebara 2), 305 female modern adult pelves and 52 female Catarrhine pelves (29 gorillas, 18 chimpanzees, 5 orang-utans). All these pelves were reconstructed in order to carry out 11 pelvimetric measurements. Each measurement was carried out twice and by two different operators.

RESULTS: The pelvis of Lucy was platypelloid at each pelvic plane. The pelvic inlet of H. neanderthalensis was anteroposteriorly oval whereas the midplane and the outlet were transversely oval. The pelvis of H. erectus was globally round. In modern women, the inlet was transversely oval. The pelvic midplane and outlet were anteroposteriorly oval. In the great apes, the shape of all three pelvic planes was anteroposteriorly oval. The discriminating value of the various pelvimetry measurements place Australopithecus Lucy, H. neanderthalensis Kebara 2, and H. erectus KNM-WT 15000 close to modern humans and less similar to the great apes.

CONCLUSION: Obstetrical mechanics evolved from dystocic delivery with a transverse orientation in Australopithecus to delivery with a modern human-like rotational birth and an increase in the anteroposterior diameters in H. erectus, H. neanderthalensis and modern H. sapiens.}, } @article {pmid25214705, year = {2014}, author = {Pearce, E and Moutsiou, T}, title = {Using obsidian transfer distances to explore social network maintenance in late Pleistocene hunter-gatherers.}, journal = {Journal of anthropological archaeology}, volume = {36}, number = {}, pages = {12-20}, pmid = {25214705}, issn = {0278-4165}, support = {295663//European Research Council/International ; }, abstract = {Social behaviour is notoriously difficult to study archaeologically and it is unclear how large the networks of prehistoric humans were, or how they remained connected. Maintaining social cohesion was crucial for early humans because social networks facilitate cooperation and are imperative for survival and reproduction. Recent hunter-gatherer social organisation typically comprises a number of nested layers, ranging from the nuclear family through to the ~1500-strong ethnolinguistic tribe. Here we compare maximum obsidian transfer distances from the late Pleistocene with ethnographic data on the size of the geographic areas associated with each of these social grouping layers in recent hunter-gatherers. The closest match between the two is taken to indicate the maximum social layer within which contact could be sustained by Pleistocene hominins. Within both the (sub)tropical African and Subarctic biomes, the maximum obsidian transfer distances for Pleistocene modern humans (~200km and ~400km respectively) correspond to the geographic ranges of the outermost tribal layer in recent hunter-gatherers. This suggests that modern humans could potentially sustain the cohesion of their entire tribe at all latitudes, even though networks are more dispersed nearer the poles. Neanderthal obsidian transfer distances (300km) indicate that although Neanderthal home ranges are larger than those of low latitude hominins, Neanderthals travelled shorter distances than modern humans living at the same high latitudes. We argue that, like modern humans, Neanderthals could have maintained tribal cohesion, but that their tribes were substantially smaller than those of contemporary modern humans living in similar environments. The greater time taken to traverse the larger modern human tribal ranges may have limited the frequency of their face-to-face interactions and thus necessitated additional mechanisms to ensure network connectivity, such as the exchange of symbolic artefacts including ornaments and figurines. Such cultural supports may not have been required to the same extent by the Neanderthals due to their smaller tribes and home ranges.}, } @article {pmid25211913, year = {2014}, author = {Wong, K}, title = {The 1 percent difference. Genome comparisons reveal the DNA that distinguishes Homo sapiens from its kin.}, journal = {Scientific American}, volume = {311}, number = {3}, pages = {100}, pmid = {25211913}, issn = {0036-8733}, mesh = {Animals ; DNA/*analysis ; Gorilla gorilla/genetics ; Humans ; Neanderthals/genetics ; Pan paniscus/genetics ; Pan troglodytes/genetics ; *Sequence Alignment ; }, } @article {pmid25211907, year = {2014}, author = {de Waal, F}, title = {One for all.}, journal = {Scientific American}, volume = {311}, number = {3}, pages = {68-71}, pmid = {25211907}, issn = {0036-8733}, mesh = {Animals ; Behavior, Animal ; *Biological Evolution ; *Cooperative Behavior ; Humans ; Neanderthals ; Primates ; }, } @article {pmid25211901, year = {2014}, author = {}, title = {Where we came from.}, journal = {Scientific American}, volume = {311}, number = {3}, pages = {40-41}, pmid = {25211901}, issn = {0036-8733}, mesh = {Animals ; *Biological Evolution ; Humans ; Neanderthals ; *Pedigree ; }, } @article {pmid25211900, year = {2014}, author = {Wong, K}, title = {The human saga evolution rewritten. Awash in fresh insights, scientists have had to revise virtually every chapter of the human story.}, journal = {Scientific American}, volume = {311}, number = {3}, pages = {36-39}, pmid = {25211900}, issn = {0036-8733}, mesh = {Animals ; *Biological Evolution ; Caves ; Fossils ; Humans/genetics ; Neanderthals/genetics ; South Africa ; }, } @article {pmid25209431, year = {2015}, author = {Zanolli, C}, title = {Molar crown inner structural organization in Javanese Homo erectus.}, journal = {American journal of physical anthropology}, volume = {156}, number = {1}, pages = {148-157}, doi = {10.1002/ajpa.22611}, pmid = {25209431}, issn = {1096-8644}, mesh = {Animals ; Anthropology, Physical ; Dental Enamel/anatomy & histology ; Dentin/anatomy & histology ; Hominidae/*anatomy & histology ; Indonesia ; Molar/*anatomy & histology ; Tooth Crown/*anatomy & histology ; }, abstract = {This contribution investigates the inner organizational pattern (tooth tissue proportions and enamel-dentine junction morphology) of seven Homo erectus permanent molar crowns from the late Lower-early Middle Pleistocene Kabuh Formation of the Sangiran Dome (Central Java, Indonesia). The previous study of their external characteristics confirmed the degree of time-related structural reduction occurred in Javanese H. erectus, and also revealed a combination of nonmetric features which are rare in the Lower and early Middle Pleistocene dental record, but more frequently found in recent humans. In accordance with their outer occlusal morphology, the specimens exhibit a set of derived internal features, such as thick to hyperthick enamel, an incomplete expression of the crest patterns at the enamel-dentine junction (EDJ) level, a sharp EDJ topography. As a whole, these features differ from those expressed in some penecontemporaneous specimens/samples representing African H. erectus/ergaster and H. heidelbergensis, as well as in Neanderthals, but occur in recent human populations. Further research in virtual dental paleoanthropology to be developed at macroregional scale would clarify the polarity and intensity of the intermittent exchanges between continental and insular Southeast Asia around the Lower to Middle Pleistocene boundary, as well as should shed light on the still poorly understood longitudinal evolutionary dynamics across continental Asia.}, } @article {pmid25200886, year = {2015}, author = {Lorenzo, C and Pablos, A and Carretero, JM and Huguet, R and Valverdú, J and Martinón-Torres, M and Arsuaga, JL and Carbonell, E and Bermúdez de Castro, JM}, title = {Early Pleistocene human hand phalanx from the Sima del Elefante (TE) cave site in Sierra de Atapuerca (Spain).}, journal = {Journal of human evolution}, volume = {78}, number = {}, pages = {114-121}, doi = {10.1016/j.jhevol.2014.08.007}, pmid = {25200886}, issn = {1095-8606}, mesh = {Animals ; Biological Evolution ; *Caves ; Finger Phalanges/*anatomy & histology ; *Fossils ; Hominidae/*anatomy & histology ; Spain ; }, abstract = {In this study, a new Early Pleistocene proximal hand phalanx (ATE9-2) from the Sima del Elefante cave site (TE - Sierra de Atapuerca, Spain), ascribed to Homo sp., is presented and comparatively described in the context of the evolution of the genus Homo. The ATE9-2 specimen is especially important because of the paucity of hand bones in the human fossil record during the Early Pleistocene. The morphological and metrical analyses of the phalanx ATE9-2 indicate that there are no essential differences between it and comparator fossil specimens for the genus Homo after 1.3 Ma (millions of years ago). Similar to Sima de los Huesos and Neandertal specimens, ATE9-2 is a robust proximal hand phalanx, probably reflecting greater overall body robusticity in these populations or a higher gracility in modern humans. The age of level TE9 from Sima del Elefante and morphological and metrical studies of ATE9-2 suggest that the morphology of the proximal hand phalanges and, thus, the morphology of the hand could have remained stable over the last 1.2-1.3 Ma. Taking into account the evidence recently provided by a metacarpal from Kaitio (Kenya) from around 1.42 Ma, we argue that modern hand morphology is present in the genus Homo subsequent to Homo habilis.}, } @article {pmid25197076, year = {2014}, author = {Rodríguez-Vidal, J and d'Errico, F and Giles Pacheco, F and Blasco, R and Rosell, J and Jennings, RP and Queffelec, A and Finlayson, G and Fa, DA and Gutiérrez López, JM and Carrión, JS and Negro, JJ and Finlayson, S and Cáceres, LM and Bernal, MA and Fernández Jiménez, S and Finlayson, C}, title = {A rock engraving made by Neanderthals in Gibraltar.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {37}, pages = {13301-13306}, pmid = {25197076}, issn = {1091-6490}, support = {249587//European Research Council/International ; }, mesh = {Animals ; Caves ; *Engraving and Engravings ; *Geologic Sediments ; Gibraltar ; Humans ; Imaging, Three-Dimensional ; *Neanderthals ; Weather ; }, abstract = {The production of purposely made painted or engraved designs on cave walls--a means of recording and transmitting symbolic codes in a durable manner--is recognized as a major cognitive step in human evolution. Considered exclusive to modern humans, this behavior has been used to argue in favor of significant cognitive differences between our direct ancestors and contemporary archaic hominins, including the Neanderthals. Here we present the first known example of an abstract pattern engraved by Neanderthals, from Gorham's Cave in Gibraltar. It consists of a deeply impressed cross-hatching carved into the bedrock of the cave that has remained covered by an undisturbed archaeological level containing Mousterian artifacts made by Neanderthals and is older than 39 cal kyr BP. Geochemical analysis of the epigenetic coating over the engravings and experimental replication show that the engraving was made before accumulation of the archaeological layers, and that most of the lines composing the design were made by repeatedly and carefully passing a pointed lithic tool into the grooves, excluding the possibility of an unintentional or utilitarian origin (e.g., food or fur processing). This discovery demonstrates the capacity of the Neanderthals for abstract thought and expression through the use of geometric forms.}, } @article {pmid25190608, year = {2014}, author = {Ségurel, L and Quintana-Murci, L}, title = {Preserving immune diversity through ancient inheritance and admixture.}, journal = {Current opinion in immunology}, volume = {30}, number = {}, pages = {79-84}, doi = {10.1016/j.coi.2014.08.002}, pmid = {25190608}, issn = {1879-0372}, mesh = {Animals ; Evolution, Molecular ; Genome ; Genome-Wide Association Study ; Humans ; Models, Immunological ; Selection, Genetic/*immunology ; }, abstract = {The progress of genomic technologies is allowing researchers to scan the genomes of different species for the occurrence of natural selection at an unprecedented level of resolution. These studies show that genes involved in immune processes are preferential targets of different forms of selection, some of which act to preserve immune diversity over time. Recent work in humans shows that this can be achieved either by inheriting advantageous immune variation from distant ancestral species, through long-term balancing selection, or by acquiring novel selected alleles through admixture with extinct hominins such as Neanderthals or Denisovans. These studies collectively increase our knowledge of immune genes for which maintaining the functional diversity has conferred a strong selective advantage for host survival.}, } @article {pmid25172957, year = {2014}, author = {Racimo, F and Kuhlwilm, M and Slatkin, M}, title = {A test for ancient selective sweeps and an application to candidate sites in modern humans.}, journal = {Molecular biology and evolution}, volume = {31}, number = {12}, pages = {3344-3358}, pmid = {25172957}, issn = {1537-1719}, support = {R01 GM040282/GM/NIGMS NIH HHS/United States ; R01-GM40282/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bayes Theorem ; *Evolution, Molecular ; Genome, Human ; Humans ; *Models, Genetic ; Neanderthals/genetics ; Polymorphism, Single Nucleotide ; Selection, Genetic ; }, abstract = {We introduce a new method to detect ancient selective sweeps centered on a candidate site. We explored different patterns produced by sweeps around a fixed beneficial mutation, and found that a particularly informative statistic measures the consistency between majority haplotypes near the mutation and genotypic data from a closely related population. We incorporated this statistic into an approximate Bayesian computation (ABC) method that tests for sweeps at a candidate site. We applied this method to simulated data and show that it has some power to detect sweeps that occurred more than 10,000 generations in the past. We also applied it to 1,000 Genomes and Complete Genomics data combined with high-coverage Denisovan and Neanderthal genomes to test for sweeps in modern humans since the separation from the Neanderthal-Denisovan ancestor. We tested sites at which humans are fixed for the derived (i.e., nonchimpanzee allele) whereas the Neanderthal and Denisovan genomes are homozygous for the ancestral allele. We observe only weak differences in statistics indicative of selection between functional categories. When we compare patterns of scaled diversity or use our ABC approach, we fail to find a significant difference in signals of classic selective sweeps between regions surrounding nonsynonymous and synonymous changes, but we detect a slight enrichment for reduced scaled diversity around splice site changes. We also present a list of candidate sites that show high probability of having undergone a classic sweep in the modern human lineage since the split from Neanderthals and Denisovans.}, } @article {pmid25170982, year = {2014}, author = {Duggan, AT and Stoneking, M}, title = {Recent developments in the genetic history of East Asia and Oceania.}, journal = {Current opinion in genetics & development}, volume = {29}, number = {}, pages = {9-14}, doi = {10.1016/j.gde.2014.06.010}, pmid = {25170982}, issn = {1879-0380}, mesh = {Animals ; DNA, Mitochondrial/chemistry/genetics ; Far East ; Genome, Human/*genetics ; *Human Migration ; Humans ; Neanderthals/*genetics ; Oceania ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {Recent developments in our understanding of the genetic history of Asia and Oceania have been driven by technological advances. Specifically, our understanding of the past has been augmented by: genome sequences from ancient hominins and ancient modern humans; more comprehensive studies of existing populations (e.g., complete mtDNA genome sequences and genome-wide data) and the development of new statistics and analytical methods to interpret the abundance of new data. We review some of the new discoveries since we entered the age of archaic and modern genomics and how they have changed our understanding of the settlement and subsequent population dynamics in Asia and the Pacific.}, } @article {pmid25156452, year = {2014}, author = {Márquez, S and Pagano, AS and Delson, E and Lawson, W and Laitman, JT}, title = {The nasal complex of Neanderthals: an entry portal to their place in human ancestry.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {297}, number = {11}, pages = {2121-2137}, doi = {10.1002/ar.23040}, pmid = {25156452}, issn = {1932-8494}, mesh = {*Adaptation, Physiological/physiology ; Animals ; Female ; Humans ; Male ; Nasal Cavity/*anatomy & histology/physiology ; Neanderthals/*anatomy & histology/physiology ; Nose/anatomy & histology/physiology ; *Phylogeny ; }, abstract = {Neanderthals are one of the most intensely studied groups of extinct humans, as aspects of their phylogeny and functional morphology remain controversial. They have long been described as cold adapted but recent analyses of their nasal anatomy suggest that traits formerly considered adaptations may be the result of genetic drift. This study performs quantitative and qualitative analysis of aspects of the nasal complex (NC) in Neanderthals and other later Pleistocene fossils from Europe and Africa. A geographically diverse sample of modern human crania was used to establish an anatomical baseline for populations inhabiting cold and tropical climates. Nasofrontal angle, piriform aperture dimensions, and relative maxillary sinus volume were analyzed along with qualitative features of the piriform aperture rim. Results indicate that Neanderthals and other later Pleistocene Homo possessed NC's that align them with tropical modern humans. Thus comparison of Neanderthal nasal morphology with that of modern humans from cold climates may not be appropriate as differences in overall craniofacial architecture may constrain the narrowing of the piriform apertures in Neanderthals. They retain primitively long, low crania, large maxillary sinuses, and large piriform aperture area similar to mid-Pleistocene Homo specimens such as Petralona 1 and Kabwe 1. Adaptation to cold climate may have necessitated other adaptations such as bony medial projections at the piriform aperture rim and, potentially, midfacial prognathism. Nasal complex components of the upper respiratory tract remain a critical but poorly understood area that may yet offer novel insight into one of the greatest continuing controversies in paleoanthropology.}, } @article {pmid25150897, year = {2014}, author = {Wilson, L and Browne, CL}, title = {Change in raw material selection and subsistence behaviour through time at a Middle Palaeolithic site in southern France.}, journal = {Journal of human evolution}, volume = {75}, number = {}, pages = {28-39}, doi = {10.1016/j.jhevol.2013.12.018}, pmid = {25150897}, issn = {1095-8606}, mesh = {Animals ; Feeding Behavior/*physiology ; *Fossils ; France ; Geologic Sediments ; History, Ancient ; Neanderthals/*physiology ; Technology ; Tool Use Behavior ; }, abstract = {We apply a resource selection model to the lithic assemblages from 11 archaeological layers at a Middle Palaeolithic site in southern France, the Bau de l'Aubesier. The model calculates how to weight each of 10 variables in order to best match the proportions of raw materials from various potential sources in the lithic assemblages. We then combine the variables into two sets of five each, those related to the characteristics of the raw materials themselves, and those related to the sources and the terrain around them. Running the model with each subset shows that the terrain variables always provide a better match to raw material use than do the raw material variables taken by themselves, but the best model is always the overall (10-variable) model. This means that terrain is most important in every case, but raw material properties also matter. Comparing the percentage contributions of each subset within the overall model, however, shows a clear change in emphasis in the upper layers versus the lower layers of the site. In the lower six layers, the percent contribution of the terrain variables is always greater than that of the raw material variables, but in the upper five layers the reverse is true: terrain still matters, but raw material becomes more important. We also look at faunal and basic tool typological data, which show a progressive change through time, as smaller prey become more important (and large prey less so), and tools and cores proportionally less abundant in the assemblag