@article {pmid39395415,
year = {2024},
author = {de Flamingh, A and Gnoske, TP and Kerbis Peterhans, JC and Simeonovski, VA and Gitahi, N and Mwebi, O and Agwanda, BR and Catchen, JM and Roca, AL and Malhi, RS},
title = {Compacted hair in broken teeth reveals dietary prey of historic lions.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.09.029},
pmid = {39395415},
issn = {1879-0445},
abstract = {With recent advances, nuclear genome data for phylogenomic analyses can now be sequenced from minuscule quantities of DNA[1] and from specimens that are more than a million years old.[2] DNA analysis from hair is a well-established approach[3] widely used in forensic science[4] and wildlife conservation.[5] Hair samples can be effectively decontaminated[6] and can be used to identify the mammalian species from which the hair was shed.[7][,][8] We aimed to use advances optimized for degraded DNA to systematically identify dietary prey species from hair compacted in the teeth of two Tsavo lions that lived during the 1890s in Kenya (see description of samples in the STAR Methods and Patterson[9] and Kerbis Peterhans and Gnoske[10] for background on the Tsavo "man-eaters"). Analysis of hair DNA identified giraffe, human, oryx, waterbuck, wildebeest, and zebra as prey and also identified hair that originated from lion. DNA preservation allowed for analyses of complete mitogenome profiles of zebra, giraffe, and lion. Giraffe mitogenomes are phylogeographically partitioned, and we found that the lions ate at least two individuals that belong to a subspecies of Masai giraffe (Giraffa tippelskirchi tippelskirchi) typically found in southeast Kenya. The lion mitogenome from a hair sample was identical to the Tsavo lion endogenous mitogenome and most closely matched other East African lions from Kenya and Tanzania. Our approach enables a better understanding of the hunting behaviors, diets, and ecology of historical individuals, populations, and species and holds promise for extinct populations and species.},
}

@article {pmid39390557,
year = {2024},
author = {Sawyer, S and Gelabert, P and Yakir, B and Llanos-Lizcano, A and Sperduti, A and Bondioli, L and Cheronet, O and Neugebauer-Maresch, C and Teschler-Nicola, M and Novak, M and Pap, I and Szikossy, I and Hajdu, T and Moiseyev, V and Gromov, A and Zariņa, G and Meshorer, E and Carmel, L and Pinhasi, R},
title = {Improved detection of methylation in ancient DNA.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {261},
pmid = {39390557},
issn = {1474-760X},
abstract = {Reconstructing premortem DNA methylation levels in ancient DNA has led to breakthrough studies such as the prediction of anatomical features of the Denisovan. These studies rely on computationally inferring methylation levels from damage signals in naturally deaminated cytosines, which requires expensive high-coverage genomes. Here, we test two methods for direct methylation measurement developed for modern DNA based on either bisulfite or enzymatic methylation treatments. Bisulfite treatment shows the least reduction in DNA yields as well as the least biases during methylation conversion, demonstrating that this method can be successfully applied to ancient DNA.},
}

@article {pmid39383567,
year = {2024},
author = {Wu, Y and Ma, Q and Han, B and Shen, Y and Wen, S},
title = {Familial hypodontia in bronze age Northwest China (1046-771BC).},
journal = {Archives of oral biology},
volume = {169},
number = {},
pages = {106104},
doi = {10.1016/j.archoralbio.2024.106104},
pmid = {39383567},
issn = {1879-1506},
abstract = {OBJECTIVE: This research aimed to report hypodontia cases in a Middle Bronze Age high-tier cemetery in China and test the possible hereditary behind hypodontia by performing kinship tests on those individuals.

DESIGN: In this study, dental anomalies were observed on a human skeletal sample (n = 45) uncovered from Yaoheyuan, China. Ancient DNA analysis was subsequently employed on a subsample of the Yaoheyuan individuals (n = 15), including individuals observed hypodontia and individuals randomly sampled from the cemetery for preliminary investigation on the cemetery demography. Kinship estimation tests (READ, TKGWV2, KIN, and F3 test) were subsequently employed.

RESULTS: The Yaoheyuan elite population had a prevalence (n = 7, 15 %) of tooth agenesis in either the maxilla or mandible, with one to two teeth missing. All missing teeth were incisors, except for one individual missing maxillary second molar. Preliminary ancient DNA results indicate that several kinship groups existed among interred individuals, including those with hypodontia, indicating the hereditary origin of these cases.

CONCLUSIONS: The prevalence of hypodontia observed on site is high compared to that in both modern East Asian populations and archaeological samples in the Chinese population. The preliminary kinship analysis suggests a case of familial hypodontia. Ancient DNA analysis should be thoroughly conducted in future studies to understand the genetic markers contributing to those hypodontia cases among the Yaoheyuan individuals.},
}

@article {pmid39357284,
year = {2024},
author = {Fuchs, J and García-Tabernero, A and Rosas, A and Camus, H and Metz, L and Slimak, L and Zanolli, C},
title = {The dentition of a new adult Neanderthal individual from Grotte Mandrin, France.},
journal = {Journal of human evolution},
volume = {196},
number = {},
pages = {103599},
doi = {10.1016/j.jhevol.2024.103599},
pmid = {39357284},
issn = {1095-8606},
abstract = {Grotte Mandrin is located in the middle Rhône River Valley, in Mediterranean France, and has yielded 11 Pleistocene archeological and paleoanthropological layers (ranging from the oldest layer J to the youngest layer B) dating from Marine Isotope Stage (MIS) 5 to MIS 3. We report here the nearly complete dentition of an adult Neanderthal individual, nicknamed 'Thorin,' associated to the last phase of the Post-Neronian II, in layer B2 (∼44.50-42.25 ka). A previous paleogenetic analysis revealed that Thorin is a male individual and that he shows a deep genetic divergence with other penecontemporaneous Neanderthals from western Europe that possibly occurred ∼105 ka. The 31 teeth of Thorin (including two distomolars) are described and analyzed using microcomputed tomography imaging and are compared with other Neanderthals and modern humans. Based on direct observation and measurements on the fossil remains, and using microtomographic imaging, tooth wear, nonmetric characters, crown dimensions, and dental tissue proportions were investigated, and the shape of the enamel-dentine junction of the M[2], M2, and M3 was analyzed by geometric morphometrics. Our results indicate that Thorin's teeth show dental characteristics typical of MIS 5-3 Neanderthals. It is also the first time that the presence of two distomolars is reported in a Neanderthal individual, a trait that is rare among modern human populations. Combined with the genetic peculiarities of this individual, the results of the present study imply either a process of morphological convergence among the latest Neanderthal groups or an underestimation of the genetic variability of recent Neanderthal groups.},
}

@article {pmid39345259,
year = {2024},
author = {Wu, X and Ding, B and Nie, L and Zhong, C and Liu, P and Liang, J and Wang, L and Gao, X and Wei, J and Zhou, Y},
title = {Genomic insights into the complex demographic history and inbreeding phenomena during Zhou Dynasty on the Central Plains of China.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1471740},
pmid = {39345259},
issn = {1664-302X},
abstract = {In the Central Plains of China during the Zhou Dynasty (1046-256 BCE), the social hierarchy gradually solidified, accompanied by frequent wars and the phenomena of multicultural and multi-ethnic integration. These social phenomena collectively influenced the population's genetic structure at that time. However, our understanding of the genetic history of this period remains largely unknown owing to limited ancient DNA studies. In this study, we successfully obtained 11 ancient genomes from the Guanzhuang site during the Zhou Dynasty on the central plain of China. Our findings revealed remarkable genetic continuity with the Neolithic populations of the Yellow River Basin and emphasized genetic diversity through the analysis of uniparental genetic markers. Population structure analysis further confirmed the genetic similarity between the Guanzhuang population and ancient populations of the Yellow River Basin and indicated genetic exchanges with ancient populations from surrounding regions. Intriguingly, signs of inbreeding within the Guanzhuang community cast doubt on the stringent enforcement of the contemporary marital regulations against consanguineous marriages within the same surname or clan. These revelations significantly enhance our insight into the complex interplay of ancient demography and societal organization, concurrently presenting a genetic perspective to view the complex evolution of Chinese civilization's multiethnic.},
}

@article {pmid39343094,
year = {2024},
author = {Wei, X and Zhang, M and Min, R and Jiang, Z and Xue, J and Zhu, Z and Yuan, H and Li, X and Zhao, D and Cao, P and Liu, F and Dai, Q and Feng, X and Yang, R and Wu, X and Hu, C and Ma, M and Liu, X and Wan, Y and Yang, F and Zhou, R and Kang, L and Dong, G and Ping, W and Wang, T and Miao, B and Bai, F and Zheng, Y and Liu, Y and Yang, MA and Wang, W and Bennett, EA and Fu, Q},
title = {Neolithic to Bronze Age human maternal genetic history in Yunnan, China.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2024.09.013},
pmid = {39343094},
issn = {1673-8527},
abstract = {Yunnan in southwest China is a geographically and ethnically complex region at the intersection of southern China and Southeast Asia, and a focal point for human migrations. To clarify its maternal genetic history, we generated 152 complete mitogenomes from 17 Yunnan archaeological sites. Our results reveal distinct genetic histories segregated by geographical regions. Maternal lineages of ancient populations from northwestern and northern Yunnan exhibit closer affinities with past and present-day populations from northern East Asia and Tibet, providing important genetic evidence for the migration and interaction of populations along the Tibetan-Yi corridor since the Neolithic. Between 5500 to 1800 years ago, central Yunnan populations maintained their internal genetic relationships, including a 7000-year-old basal lineage of the rare and widely dispersed haplogroup M61. At the Xingyi site, changes in mitochondrial DNA haplogroups occurred between the Late Neolithic and Bronze Age, with haplogroups shifting from those predominant in the Yellow River region to those predominant in coastal southern China. These results highlight the high diversity of Yunnan populations during the Neolithic to Bronze Age.},
}

@article {pmid39333293,
year = {2024},
author = {Petrova, TV and Panitsina, VA and Bodrov, SY and Abramson, NI},
title = {The mitochondrial genome of the critically endangered enigmatic Kazakhstani endemic Selevinia betpakdalaensis (Rodentia: Gliridae) and its phylogenetic relationships with other dormouse species.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {22259},
pmid = {39333293},
issn = {2045-2322},
support = {075-15-2021-1069//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2021-1069//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2021-1069//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2021-1069//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {Animals ; *Phylogeny ; *Genome, Mitochondrial ; Endangered Species ; Rodentia/genetics/classification ; },
abstract = {Dormice (family Gliridae) are an ancient group of rodents. It was fully dominant in the Oligocene and Early Miocene, and its current diversity is represented by a few extant species. A Kazakhstani endemic, the desert dormouse Selevinia betpakdalaensis is one of the most enigmatic dormouse species. Lack of genetic data has not allowed Selevinia to be included in previous molecular phylogenetic analyses. In the current study, we report the first genetic data on S. betpakdalaensis as well as mitochondrial genomes of Myomimus roachi and Glirulus japonicus (retrieved from museum specimens) and a mitogenome of Graphiurus murinus (assembled from SRA data). The assembled mitochondrial genomes were combined with available mitochondrial data from GenBank to reconstruct the mitochondrial phylogeny of Gliridae. Taking into account a distortion of the phylogeny as a result of an analysis of the saturated third codon position, we obtained for the first time a resolved phylogeny of the family. The first split within Gliridae was estimated as an average of 34.6 Mya, whereas divergence time of subfamilies Graphiurinae and Glirinae was assessed at 32.67 Mya. The phylogenetic analysis confirmed the relationship (previously shown based on cranial and mandibular morphology) between Selevinia and the Myomimus.},
}

Animals
*Phylogeny
*Genome, Mitochondrial
Endangered Species
Rodentia/genetics/classification

@article {pmid39326418,
year = {2024},
author = {Liu, Y and Miao, B and Li, W and Hu, X and Bai, F and Abuduresule, Y and Liu, Y and Zheng, Z and Wang, W and Chen, Z and Zhu, S and Feng, X and Cao, P and Ping, W and Yang, R and Dai, Q and Liu, F and Tian, C and Yang, Y and Fu, Q},
title = {Bronze Age cheese reveals human-Lactobacillus interactions over evolutionary history.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.08.008},
pmid = {39326418},
issn = {1097-4172},
abstract = {Despite the long history of consumption of fermented dairy, little is known about how the fermented microbes were utilized and evolved over human history. Here, by retrieving ancient DNA of Bronze Age kefir cheese (∼3,500 years ago) from the Xiaohe cemetery, we explored past human-microbial interactions. Although it was previously suggested that kefir was spread from the Northern Caucasus to Europe and other regions, we found an additional spreading route of kefir from Xinjiang to inland East Asia. Over evolutionary history, the East Asian strains gained multiple gene clusters with defensive roles against environmental stressors, which can be a result of the adaptation of Lactobacillus strains to various environmental niches and human selection. Overall, our results highlight the role of past human activities in shaping the evolution of human-related microbes, and such insights can, in turn, provide a better understanding of past human behaviors.},
}

@article {pmid39322456,
year = {2024},
author = {Hou, J and Guan, X and Xia, X and Lyu, Y and Liu, X and Mazei, Y and Xie, P and Chang, F and Zhang, X and Chen, J and Li, X and Zhang, F and Jin, L and Luo, X and Sinding, MS and Sun, X and Achilli, A and Migliore, NR and Zhang, D and Lenstra, JA and Han, J and Fu, Q and Liu, X and Zhang, X and Chen, N and Lei, C and Zhang, H},
title = {Evolution and legacy of East Asian aurochs.},
journal = {Science bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.scib.2024.09.016},
pmid = {39322456},
issn = {2095-9281},
abstract = {Aurochs (Bos primigenius), once widely distributed in Afro-Eurasia, became extinct in the early 1600 s. However, their phylogeography and relative contributions to domestic cattle remain unknown. In this study, we analyzed 16 genomes of ancient aurochs and three mitogenomes of ancient bison (Bison priscus) excavated in East Asia, dating from 43,000 to 3,590 years ago. These newly generated data with previously published genomic information on aurochs as well as ancient/extant domestic cattle worldwide through genome analysis. Our findings revealed significant genetic divergence between East Asian aurochs and their European, Near Eastern, and African counterparts on the basis of both mitochondrial and nuclear genomic data. Furthermore, we identified evidence of gene flow from East Asian aurochs into ancient and present-day taurine cattle, suggesting their potential role in facilitating the environmental adaptation of domestic cattle.},
}

@article {pmid39314480,
year = {2024},
author = {Akbari, A and Barton, AR and Gazal, S and Li, Z and Kariminejad, M and Perry, A and Zeng, Y and Mittnik, A and Patterson, N and Mah, M and Zhou, X and Price, AL and Lander, ES and Pinhasi, R and Rohland, N and Mallick, S and Reich, D},
title = {Pervasive findings of directional selection realize the promise of ancient DNA to elucidate human adaptation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.09.14.613021},
pmid = {39314480},
issn = {2692-8205},
abstract = {We present a method for detecting evidence of natural selection in ancient DNA time-series data that leverages an opportunity not utilized in previous scans: testing for a consistent trend in allele frequency change over time. By applying this to 8433 West Eurasians who lived over the past 14000 years and 6510 contemporary people, we find an order of magnitude more genome-wide significant signals than previous studies: 347 independent loci with >99% probability of selection. Previous work showed that classic hard sweeps driving advantageous mutations to fixation have been rare over the broad span of human evolution, but in the last ten millennia, many hundreds of alleles have been affected by strong directional selection. Discoveries include an increase from ∼0% to ∼20% in 4000 years for the major risk factor for celiac disease at HLA-DQB1 ; a rise from ∼0% to ∼8% in 6000 years of blood type B; and fluctuating selection at the TYK2 tuberculosis risk allele rising from ∼2% to ∼9% from ∼5500 to ∼3000 years ago before dropping to ∼3%. We identify instances of coordinated selection on alleles affecting the same trait, with the polygenic score today predictive of body fat percentage decreasing by around a standard deviation over ten millennia, consistent with the "Thrifty Gene" hypothesis that a genetic predisposition to store energy during food scarcity became disadvantageous after farming. We also identify selection for combinations of alleles that are today associated with lighter skin color, lower risk for schizophrenia and bipolar disease, slower health decline, and increased measures related to cognitive performance (scores on intelligence tests, household income, and years of schooling). These traits are measured in modern industrialized societies, so what phenotypes were adaptive in the past is unclear. We estimate selection coefficients at 9.9 million variants, enabling study of how Darwinian forces couple to allelic effects and shape the genetic architecture of complex traits.},
}

@article {pmid39305897,
year = {2024},
author = {Zampirolo, G and Holman, LE and Sawafuji, R and Ptáková, M and Kovačiková, L and Šída, P and Pokorný, P and Pedersen, MW and Walls, M},
title = {Tracing early pastoralism in Central Europe using sedimentary ancient DNA.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.08.047},
pmid = {39305897},
issn = {1879-0445},
abstract = {Central European forests have been shaped by complex human interactions throughout the Holocene, with significant changes following the introduction of domesticated animals in the Neolithic (∼7.5-6.0 ka before present [BP]). However, understanding early pastoral practices and their impact on forests is limited by methods for detecting animal movement across past landscapes. Here, we examine ancient sedimentary DNA (sedaDNA) preserved at the Velký Mamuťák rock shelter in northern Bohemia (Czech Republic), which has been a forested enclave since the early Holocene. We find that domesticated animals, their associated microbiomes, and plants potentially gathered for fodder have clear representation by the Late Neolithic, around 6.0 ka BP, and persist throughout the Bronze Age into recent times. We identify a change in dominant grazing species from sheep to pigs in the Bronze Age (∼4.1-3.0 ka BP) and interpret the impact this had in the mid-Holocene retrogressions that still define the structure of Central European forests today. This study highlights the ability of ancient metagenomics to bridge archaeological and paleoecological methods and provide an enhanced perspective on the roots of the "Anthropocene."},
}

@article {pmid39300260,
year = {2024},
author = {Gretzinger, J and Gibbon, VE and Penske, SE and Sealy, JC and Rohrlach, AB and Salazar-García, DC and Krause, J and Schiffels, S},
title = {9,000 years of genetic continuity in southernmost Africa demonstrated at Oakhurst rockshelter.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {39300260},
issn = {2397-334X},
abstract = {Southern Africa has one of the longest records of fossil hominins and harbours the largest human genetic diversity in the world. Yet, despite its relevance for human origins and spread around the globe, the formation and processes of its gene pool in the past are still largely unknown. Here, we present a time transect of genome-wide sequences from nine individuals recovered from a single site in South Africa, Oakhurst Rockshelter. Spanning the whole Holocene, the ancient DNA of these individuals allows us to reconstruct the demographic trajectories of the indigenous San population and their ancestors during the last 10,000 years. We show that, in contrast to most regions around the world, the population history of southernmost Africa was not characterized by several waves of migration, replacement and admixture but by long-lasting genetic continuity from the early Holocene to the end of the Later Stone Age. Although the advent of pastoralism and farming substantially transformed the gene pool in most parts of southern Africa after 1,300 BP, we demonstrate using allele-frequency and identity-by-descent segment-based methods that the ‡Khomani San and Karretjiemense from South Africa still show direct signs of relatedness to the Oakhurst hunter-gatherers, a pattern obscured by recent, extensive non-Southern African admixture. Yet, some southern San in South Africa still preserve this ancient, Pleistocene-derived genetic signature, extending the period of genetic continuity until today.},
}

@article {pmid39294129,
year = {2024},
author = {Bozzi, D and Neuenschwander, S and Cruz Dávalos, DI and Sousa da Mota, B and Schroeder, H and Moreno-Mayar, JV and Allentoft, ME and Malaspinas, AS},
title = {Towards predicting the geographical origin of ancient samples with metagenomic data.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21794},
pmid = {39294129},
issn = {2045-2322},
mesh = {Humans ; *DNA, Ancient/analysis ; *Metagenomics/methods ; *Metagenome ; Geography ; Microbiota/genetics ; },
abstract = {Reconstructing the history-such as the place of birth and death-of an individual sample is a fundamental goal in ancient DNA (aDNA) studies. However, knowing the place of death can be particularly challenging when samples come from museum collections with incomplete or erroneous archives. While analyses of human DNA and isotope data can inform us about the ancestry of an individual and provide clues about where the person lived, they cannot specifically trace the place of death. Moreover, while ancient human DNA can be retrieved, a large fraction of the sequenced molecules in ancient DNA studies derive from exogenous DNA. This DNA-which is usually discarded in aDNA analyses-is constituted mostly by microbial DNA from soil-dwelling microorganisms that have colonized the buried remains post-mortem. In this study, we hypothesize that remains of individuals buried in the same or close geographic areas, exposed to similar microbial communities, could harbor more similar metagenomes. We propose to use metagenomic data from ancient samples' shotgun sequencing to locate the place of death of a given individual which can also help to solve cases of sample mislabeling. We used a k-mer-based approach to compute similarity scores between metagenomic samples from different locations and propose a method based on dimensionality reduction and logistic regression to assign a geographical origin to target samples. We apply our method to several public datasets and observe that individual samples from closer geographic locations tend to show higher similarities in their metagenomes compared to those of different origin, allowing good geographical predictions of test samples. Moreover, we observe that the genus Streptomyces commonly infiltrates ancient remains and represents a valuable biomarker to trace the samples' geographic origin. Our results provide a proof of concept and show how metagenomic data can also be used to shed light on the place of origin of ancient samples.},
}

Humans
*DNA, Ancient/analysis
*Metagenomics/methods
*Metagenome
Geography
Microbiota/genetics

@article {pmid39292210,
year = {2024},
author = {Atağ, G and Waldman, S and Carmi, S and Somel, M},
title = {An explanation for the sister repulsion phenomenon in Patterson's f-statistics.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyae144},
pmid = {39292210},
issn = {1943-2631},
support = {772390//H2020 ERC Consolidator/ ; 952317//H2020-WIDESPREAD-05-2020 TWINNING/ ; //Scientific and Technological Research Council of Turkey (TÜBİTAK)/ ; },
abstract = {Patterson's f-statistics are among the most heavily utilized tools for analyzing genome-wide allele frequency data for demographic inference. Beyond studying admixture, f3- and f4-statistics are also used for clustering populations to identify groups with similar histories. However, previous studies have noted an unexpected behavior of f-statistics: multiple populations from a certain region systematically show higher genetic affinity to a more distant population than to their neighbors, a pattern that is mismatched with alternative measures of genetic similarity. We call this counter-intuitive pattern "sister repulsion". We first present a novel instance of sister repulsion, where genomes from Bronze Age East Anatolian sites show higher affinity toward Bronze Age Greece rather than each other. This is observed both using f3- and f4-statistics, contrasts with archaeological/historical expectation, and also contradicts genetic affinity patterns captured using principal components analysis or multidimensional scaling on genetic distances. We then propose a simple demographic model to explain this pattern, where sister populations receive gene flow from a genetically distant source. We calculate f3- and f4-statistics using simulated genetic data with varying population genetic parameters, confirming that low-level gene flow from an external source into populations from 1 region can create sister repulsion in f-statistics. Unidirectional gene flow between the studied regions (without an external source) can likewise create repulsion. Meanwhile, similar to our empirical observations, multidimensional scaling analyses of genetic distances still cluster sister populations together. Overall, our results highlight the impact of low-level admixture events when inferring demographic history using f-statistics.},
}

@article {pmid39291130,
year = {2024},
author = {Song, G and Wang, Y and Ruan, Q and Cai, DE},
title = {The ancient mitochondrial genome of a Siberian roe deer (Capreolus pygargus) from Jartai Pass Site in Xinjiang, China, and its phylogenetic relationships.},
journal = {Mitochondrial DNA. Part B, Resources},
volume = {9},
number = {9},
pages = {1232-1236},
pmid = {39291130},
issn = {2380-2359},
abstract = {The ancient mitochondrial genome of a Siberian roe deer (Capreolus pygargus) coded as NJ26S from Jartai Pass Site was obtained by high throughput sequencing. The damage pattern demonstrated the authenticity and reliability of the ancient DNA data. The length of the mitogenome was 16,357 bp, which contained 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region. The total base composition of the mitochondrial genome is 28.17% A, 25.01% T, 11.89% G, 19.72% C, and 15.21% missing data with an AT composition of 53.18%. A maximum-likelihood phylogenetic tree was recovered including other roe deer sequences under the TIM2 + I + G4 model. This study presents molecular evidence indicating the presence of Capreolus pygargus in the Xinjiang Uygur Autonomous Region in China more than 3,000 years ago.},
}

@article {pmid39280844,
year = {2024},
author = {Modina, SA and Kusliy, MA and Malikov, DG and Molodtseva, AS},
title = {Phylogeography of the woolly mammoth (Mammuthus primigenius) in the Minusinsk Depression of southern Siberia in the Late Pleistocene.},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {28},
number = {5},
pages = {571-577},
doi = {10.18699/vjgb-24-63},
pmid = {39280844},
issn = {2500-0462},
abstract = {To date, a number of studies have been published on the phylogenetics of woolly mammoths (Mammuthus primigenius), ranging from analyses of parts of the mitochondrial genome to studies of complete nuclear genomes. However, until recently nothing was known about the genetic diversity of woolly mammoths in southern Siberia, in the Minusinsk Depression in particular. Within the framework of this effort, libraries for high-throughput sequencing of seven bone samples of woolly mammoths were obtained, two-round enrichment using biotinylated probes of modern mtDNA of Elephas maximus immobilised on magnetic microspheres and sequencing with subsequent bioinformatic analysis were carried out. Phylogenetic reconstructions showed the presence of all studied mammoths in clade I, which expanded its range. The assignment of mammoth mitotypes in the Minusinsk Depression to different clusters within clade I may indicate a sufficiently high diversity of their gene pool. Phylogeographic reconstructions revealed a genetic proximity of mitochondrial lineages of Late Pleistocene mammoths of the Minusinsk Depression and other regions of eastern Siberia and estimated their divergence time in the range of 100-150 thousand years ago, which indicates active migrations of woolly mammoths over vast territories of eastern Siberia in the late Middle Pleistoceneearly Late Pleistocene.},
}

@article {pmid39279684,
year = {2024},
author = {Pan, J and Liu, X and Baca, M and Calvière-Tonasso, L and Schiavinato, S and Chauvey, L and Tressières, G and Perdereau, A and Aury, JM and Oliveira, PH and Wincker, P and Abdykanova, A and Arsuaga, JL and Bayarsaikhan, J and Belinskiy, AB and Carbonell, E and Davoudi, H and Lira Garrido, J and Gilbert, AS and Hermes, T and Warinner, C and Kalmykov, AA and Lordkipanidze, D and Mackiewicz, P and Mohaseb, AF and Richter, K and Sayfullaev, N and Shapiro, B and Shnaider, S and Southon, J and Stefaniak, K and Summers, GD and van Asperen, EN and Vanishvili, N and Hill, EA and Kuznetsov, P and Reinhold, S and Hansen, S and Mashkour, M and Berthon, R and Taylor, WTT and Houle, JL and Hekkala, E and Popović, D and Orlando, L},
title = {Genome-wide population affinities and signatures of adaptation in hydruntines, sussemiones and Asian wild asses.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17527},
doi = {10.1111/mec.17527},
pmid = {39279684},
issn = {1365-294X},
support = {101027750//European Union's Horizon 2020 research and innovation programme/ ; 101062645//European Union's Horizon 2020 research and innovation programme/ ; //Agricultural Science and Technology Innovation Program (ASTIP-05)/ ; //CNRS and University Paul Sabatier (AnimalFarm IRP)/ ; //Spanish Ministerio de Educación, Cultura y Deporte (Archaeological Projects Abroad 2017)/ ; //Wroclaw Centre of Biotechnology programme ('The Leading National Research Center [KNOW]')/ ; 681605//HORIZON EUROPE European Research Council/ ; 834616//HORIZON EUROPE European Research Council/ ; 101071707//HORIZON EUROPE European Research Council/ ; ANR-10-INBS-09//Agence Nationale pour la Recherche/ ; 19-78-10053//Russian Science Foundation/ ; 22-18-00194//Russian Science Foundation/ ; },
abstract = {The extremely rich palaeontological record of the horse family, also known as equids, has provided many examples of macroevolutionary change over the last ~55 Mya. This family is also one of the most documented at the palaeogenomic level, with hundreds of ancient genomes sequenced. While these data have advanced understanding of the domestication history of horses and donkeys, the palaeogenomic record of other equids remains limited. In this study, we have generated genome-wide data for 25 ancient equid specimens spanning over 44 Ky and spread across Anatolia, the Caucasus, Central Asia and Mongolia. Our dataset includes the genomes from two extinct species, the European wild ass, Equus hydruntinus, and the sussemione Equus ovodovi. We document, for the first time, the presence of sussemiones in Mongolia and their survival around ~3.9 Kya, a finding that should be considered when discussing the timing of the first arrival of the domestic horse in the region. We also identify strong spatial differentiation within the historical ecological range of Asian wild asses, Equus hemionus, and incomplete reproductive isolation in several groups yet considered as different species. Finally, we find common selection signatures at ANTXR2 gene in European, Asian and African wild asses. This locus, which encodes a receptor for bacterial toxins, shows no selection signal in E. ovodovi, but a 5.4-kb deletion within intron 7. Whether such genetic modifications played any role in the sussemione extinction remains unknown.},
}

@article {pmid39278943,
year = {2024},
author = {Sun, Y and Lorenzen, ED and Westbury, MV},
title = {Late Pleistocene polar bear genomes reveal the timing of allele fixation in key genes associated with Arctic adaptation.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {826},
pmid = {39278943},
issn = {1471-2164},
support = {37352//Villum Fonden/ ; 9064-00025B//Danmarks Frie Forskningsfond/ ; },
mesh = {*Ursidae/genetics ; Animals ; Arctic Regions ; *Alleles ; *Genome ; Adaptation, Physiological/genetics ; Evolution, Molecular ; Selection, Genetic ; },
abstract = {The polar bear (Ursus maritimus) occupies a relatively narrow ecological niche, with many traits adapted for cold temperatures, movement across snow, ice and open water, and for consuming highly lipid-dense prey species. The divergence of polar bears from brown bears (Ursus arctos) and their adaptation to their Arctic lifestyle is a well-known example of rapid evolution. Previous research investigating whole genomes uncovered twelve key genes that are highly differentiated between polar and brown bears, show signatures of selection in the polar bear lineage, and are associated with polar bear adaptation to the Arctic environment. Further research suggested fixed derived alleles in these genes arose from selection on both standing variation and de novo mutations in the evolution of polar bears. Here, we reevaluate these findings based on a larger and geographically more representative dataset of 119 polar bears and 135 brown bears, and assess the timing of derived allele fixation in polar bears by incorporating the genomes of two Late Pleistocene individuals (aged 130-100,000 years old and 100-70,000 years old). In contrast with previous results, we found no evidence of derived alleles fixed in present-day polar bears within the key genes arising from de novo mutation. Most derived alleles fixed in present-day polar bears were also fixed in the Late Pleistocene polar bears, suggesting selection occurred prior to 70,000 years ago. However, some derived alleles fixed in present-day polar bears were not fixed in the two Late Pleistocene polar bears, including at sites within APOB, LYST, and TTN. These three genes are associated with cardiovascular function, metabolism, and pigmentation, suggesting selection may have acted on different loci at different times.},
}

*Ursidae/genetics
Animals
Arctic Regions
*Alleles
*Genome
Adaptation, Physiological/genetics
Evolution, Molecular
Selection, Genetic

@article {pmid39268685,
year = {2024},
author = {Scheib, CL and Hui, R and Rose, AK and D'Atanasio, E and Inskip, SA and Dittmar, J and Cessford, C and Griffith, SJ and Solnik, A and Wiseman, R and Neil, B and Biers, T and Harknett, SJ and Sasso, S and Biagini, SA and Runfeldt, G and Duhig, C and Evans, C and Metspalu, M and Millett, MJ and O'Connell, TC and Robb, JE and Kivisild, T},
title = {Low Genetic Impact of the Roman Occupation of Britain in Rural Communities.},
journal = {Molecular biology and evolution},
volume = {41},
number = {9},
pages = {},
doi = {10.1093/molbev/msae168},
pmid = {39268685},
issn = {1537-1719},
support = {2000368/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; //St John's College, Cambridge/ ; PRG243//Estonian Research Council/ ; 2014-2020.4.01.16-0030//European Union through the European Regional Development Fund/ ; 2014-2020.4.01.15-0012//European Regional Development Fund/ ; },
mesh = {Humans ; United Kingdom ; *Human Migration ; *Rural Population ; History, Ancient ; DNA, Ancient/analysis ; Genetics, Population ; },
abstract = {The Roman period saw the empire expand across Europe and the Mediterranean, including much of what is today Great Britain. While there is written evidence of high mobility into and out of Britain for administrators, traders, and the military, the impact of imperialism on local, rural population structure, kinship, and mobility is invisible in the textual record. The extent of genetic change that occurred in Britain during the Roman military occupation remains underexplored. Here, using genome-wide data from 52 ancient individuals from eight sites in Cambridgeshire covering the period of Roman occupation, we show low levels of genetic ancestry differentiation between Romano-British sites and indications of larger populations than in the Bronze Age and Neolithic. We find no evidence of long-distance migration from elsewhere in the Empire, though we do find one case of possible temporary mobility within a family unit during the Late Romano-British period. We also show that the present-day patterns of genetic ancestry composition in Britain emerged after the Roman period.},
}

Humans
United Kingdom
*Human Migration
*Rural Population
History, Ancient
DNA, Ancient/analysis
Genetics, Population

@article {pmid39262445,
year = {2023},
author = {Borry, M and Forsythe, A and Andrades Valtueña, A and Hübner, A and Ibrahim, A and Quagliariello, A and White, AE and Kocher, A and Vågene, ÅJ and Bartholdy, BP and Spurīte, D and Ponce-Soto, GY and Neumann, G and Huang, IT and Light, I and Velsko, IM and Jackson, I and Frangenberg, J and Serrano, JG and Fumey, J and Özdoğan, KT and Blevins, KE and Daly, KG and Lopopolo, M and Moraitou, M and Michel, M and van Os, M and Bravo-Lopez, MJ and Sarhan, MS and Dagtas, ND and Oskolkov, N and Smith, OS and Lebrasseur, O and Rozwalak, P and Eisenhofer, R and Wasef, S and Ramachandran, SL and Vanghi, V and Warinner, C and Fellows Yates, JA},
title = {Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT.},
journal = {F1000Research},
volume = {12},
number = {},
pages = {926},
doi = {10.12688/f1000research.134798.2},
pmid = {39262445},
issn = {2046-1402},
mesh = {*Metagenomics/methods ; Humans ; *Metadata ; High-Throughput Nucleotide Sequencing/methods ; Software ; Metagenome ; Computational Biology/methods ; DNA, Ancient/analysis ; },
abstract = {BACKGROUND: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.org) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications.

METHODS: Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate rapid data filtering and downloading of ancient metagenomic data, as well as improving automated metadata curation and validation for AncientMetagenomeDir.

RESULTS: AncientMetagenomeDir was extended to include standardised metadata of over 6000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community.

CONCLUSIONS: Together, both standardised metadata reporting and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.},
}

*Metagenomics/methods
Humans
*Metadata
High-Throughput Nucleotide Sequencing/methods
Software
Metagenome
Computational Biology/methods
DNA, Ancient/analysis

@article {pmid39261697,
year = {2024},
author = {Thompson, B and Petrić Howe, N},
title = {Ancient DNA debunks Rapa Nui 'ecological suicide' theory.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/d41586-024-02963-9},
pmid = {39261697},
issn = {1476-4687},
}

@article {pmid39261696,
year = {2024},
author = {Callaway, E},
title = {Famed Pacific island's population 'crash' debunked by ancient DNA.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {39261696},
issn = {1476-4687},
}

@article {pmid39261607,
year = {2024},
author = {Schiffels, S and Nägele, K},
title = {Rapa Nui's population history rewritten using ancient DNA.},
journal = {Nature},
volume = {633},
number = {8029},
pages = {290-291},
pmid = {39261607},
issn = {1476-4687},
}

@article {pmid39261501,
year = {2024},
author = {Canesin, LEC and Vilaça, ST and Oliveira, RRM and Al-Ajli, F and Tracey, A and Sims, Y and Formenti, G and Fedrigo, O and Banhos, A and Sanaiotti, TM and Farias, IP and Jarvis, ED and Oliveira, G and Hrbek, T and Solferini, V and Aleixo, A},
title = {A reference genome for the Harpy Eagle reveals steady demographic decline and chromosomal rearrangements in the origin of Accipitriformes.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {19925},
pmid = {39261501},
issn = {2045-2322},
support = {316531/2023-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 316532/2023-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 309243/2023-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Animals ; *Genome ; *Eagles/genetics ; Female ; DNA Transposable Elements/genetics ; Phylogeny ; Evolution, Molecular ; Retroelements/genetics ; Genomics/methods ; },
abstract = {The Harpy Eagle (Harpia harpyja) is an iconic species that inhabits forested landscapes in Neotropical regions, with decreasing population trends mainly due to habitat loss, and currently classified as vulnerable. Here, we report on a chromosome-scale genome assembly for a female individual combining long reads, optical mapping, and chromatin conformation capture reads. The final assembly spans 1.35 Gb, with N50scaffold equal to 58.1 Mb and BUSCO completeness of 99.7%. We built the first extensive transposable element (TE) library for the Accipitridae to date and identified 7,228 intact TEs. We found a burst of an unknown TE ~ 13-22 million years ago (MYA), coincident with the split of the Harpy Eagle from other Harpiinae eagles. We also report a burst of solo-LTRs and CR1 retrotransposons ~ 31-33 MYA, overlapping with the split of the ancestor to all Harpiinae from other Accipitridae subfamilies. Comparative genomics with other Accipitridae, the closely related Cathartidae and Galloanserae revealed major chromosome-level rearrangements at the basal Accipitriformes genome, in contrast to a conserved ancient genome architecture for the latter two groups. A historical demography reconstruction showed a rapid decline in effective population size over the last 20,000 years. This reference genome serves as a crucial resource for future conservation efforts towards the Harpy Eagle.},
}

Animals
*Genome
*Eagles/genetics
Female
DNA Transposable Elements/genetics
Phylogeny
Evolution, Molecular
Retroelements/genetics
Genomics/methods

@article {pmid39235046,
year = {2024},
author = {de la Fuente Castro, C and Cortés, C and Raghavan, M and Castillo, D and Castro, M and Verdugo, RA and Moraga, M},
title = {The genomic and cultural diversity of the Inka Qhapaq hucha ceremony in Chile and Argentina.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae196},
pmid = {39235046},
issn = {1759-6653},
abstract = {The South American archaeological record has ample evidence of the socio-cultural dynamism of human populations in the past. This has also been supported through the analysis of ancient genomes, by showing evidence of gene flow across the region. While the extent of these signals is yet to be tested, the growing number of ancient genomes allows for more fine-scaled hypotheses to be evaluated. In this study, we assessed the genetic diversity of individuals associated with the Inka ritual, Qhapaq hucha. As part of this ceremony, one or more individuals were buried with Inka and local-style offerings on mountain summits along the Andes, leaving a very distinctive record. Using paleogenomic tools, we analyzed three individuals: two newly-generated genomes from El Plomo Mountain (Chile) and El Toro Mountain (Argentina), and a previously published genome from Argentina (Aconcagua Mountain). Our results reveal a complex demographic scenario with each of the individuals showing different genetic affinities. Furthermore, while two individuals showed genetic similarities with present-day and ancient populations from the southern region of the Inka empire, the third individual may have undertaken long-distance movement. The genetic diversity we observed between individuals from similar cultural contexts supports the highly diverse strategies the Inka implemented while incorporating new territories. More broadly, this research contributes to our growing understanding of the population dynamics in the Andes by discussing the implications and temporality of population movements in the region.},
}

@article {pmid39233501,
year = {2024},
author = {Pavlova, SV and Romanenko, SA and Matveevsky, SN and Kuksin, AN and Dvoyashov, IA and Kovalskaya, YM and Proskuryakova, AA and Serdyukova, NA and Petrova, TV},
title = {Supernumerary Chromosomes Enhance Karyotypic Diversification of Narrow-Headed Voles of the Subgenus Stenocranius (Rodentia, Mammalia).},
journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution},
volume = {},
number = {},
pages = {},
doi = {10.1002/jez.b.23273},
pmid = {39233501},
issn = {1552-5015},
support = {//This study was supported by Russian Science Foundation (Grant 22-24-00513)./ ; },
abstract = {The subgenus Stenocranius contains two cryptic species: Lasiopodomys gregalis (subdivided into three allopatrically distributed and genetically well-isolated lineages A, B, and C) and Lasiopodomys raddei. To identify karyotype characteristics of this poorly studied cryptic species complex, we used comparative cytogenetic analysis of 138 individuals from 41 localities in South Siberia and Mongolia. A detailed description of the L. raddei karyotype and of the L. gregalis lineage С karyotype is presented for the first time. The A chromosome complement of all examined narrow-headed voles consisted of 2n = 36 and a fundamental number of autosomal arms (FNa) of 50. Between species, patterns of differential staining were similar, though additional C-heterochromatic blocks were found in L. gregalis lineages; Ag-positive nucleolar organizers and ribosomal DNA (rDNA) clusters are located on eight and nine acrocentric pairs, respectively. No B chromosomes (Bs) were found in the Early Pleistocene relic L. raddei, while one to five small heterochromatic acrocentric Bs were detected in all L. gregalis lineages; the number and frequency of Bs varied considerably within lineages, but no intraindividual variation was observed. In both species, telomeric repeats were visualized at termini of all chromosomes, including Bs. The number and localization of rDNA clusters on Bs varied among B-carriers. Immunodetection of several meiotic proteins indicated that meio-Bs are transcriptionally inactive and have a pattern of meiotic behavior similar to that of sex chromosomes (some homology of Bs to sex chromosomes is supposed). The nature, mechanisms of inheritance and stability of Bs in L. gregalis require further investigation.},
}

@article {pmid39222521,
year = {2024},
author = {Garcia-Heras, J},
title = {The Discovery of Common Chromosome Aneuploidies with Medical Implications Through Innovative Analysis of Ancient DNA (aDNA).},
journal = {Journal of the Association of Genetic Technologists},
volume = {50},
number = {3},
pages = {96-99},
pmid = {39222521},
issn = {1523-7834},
abstract = {Two recent studies that re-examined through novel approaches previous shotgun sequencing data from prehistoric/historic Europeans uncovered several autosomal and sex chromosome aneuploidies (Anastasiadou et al., 2024; Rohrlach et al., 2024). These disorders, which are common in contemporary humans, were trisomies 18 and 21, Klinefelter syndrome (47,XXY), 47,XYY syndrome, and mosaic Turner syndrome X/XX. These discoveries about prehistoric/historic occurrence of constitutional chromosomal syndromes with high clinical significance in modern medical genetics are an important breakthrough. They contribute to a more comprehensive genetic delineation of past human populations and give impetus to perform more historic/prehistoric studies to discover other contemporary genetic disorders. A molecular profiling of ancient DNA (aDNA) from human remains added to anthropological and archaeological data may also give a broader picture of the social and historical contexts of individuals who were affected by genetic diseases. These advances in the detection of chromosome aneuploidies and previous discoveries of current monogenic syndromes in archaic hominins also highlight the possibility of detecting other genetic diseases of present-day occurrence in our ancestors. As a result, it might be feasible to delineate the evolutionary history of modern genetic diseases, establishing a timeline of their emergence, patterns of mutations, putative mechanisms of selection, and genomic mechanisms involved.},
}

@article {pmid39215552,
year = {2024},
author = {Laval, G and Patin, E and Quintana-Murci, L and Kerner, G},
title = {Deep estimation of the intensity and timing of natural selection from ancient genomes.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14015},
doi = {10.1111/1755-0998.14015},
pmid = {39215552},
issn = {1755-0998},
abstract = {Leveraging past allele frequencies has proven to be key for identifying the impact of natural selection across time. However, this approach suffers from imprecise estimations of the intensity (s) and timing (T) of selection, particularly when ancient samples are scarce in specific epochs. Here, we aimed to bypass the computation of allele frequencies across arbitrarily defined past epochs and refine the estimations of selection parameters by implementing convolutional neural networks (CNNs) algorithms that directly use ancient genotypes sampled across time. Using computer simulations, we first show that genotype-based CNNs consistently outperform an approximate Bayesian computation (ABC) approach based on past allele frequency trajectories, regardless of the selection model assumed and the number of available ancient genotypes. When applying this method to empirical data from modern and ancient Europeans, we replicated the reported increased number of selection events in post-Neolithic Europe, independently of the continental subregion studied. Furthermore, we substantially refined the ABC-based estimations of s and T for a set of positively and negatively selected variants, including iconic cases of positive selection and experimentally validated disease-risk variants. Our CNN predictions support a history of recent positive and negative selection targeting variants associated with host defence against pathogens, aligning with previous work that highlights the significant impact of infectious diseases, such as tuberculosis, in Europe. These findings collectively demonstrate that detecting the footprints of natural selection on ancient genomes is crucial for unravelling the history of severe human diseases.},
}

@article {pmid39191285,
year = {2024},
author = {Arzelier, A and De Belvalet, H and Pemonge, MH and Garberi, P and Binder, D and Duday, H and Deguilloux, MF and Pruvost, M},
title = {Ancient DNA sheds light on the funerary practices of late Neolithic collective burial in southern France.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2029},
pages = {rspb20241215},
doi = {10.1098/rspb.2024.1215},
pmid = {39191285},
issn = {1471-2954},
support = {DFG-HA-5407/4-1//Deutsche Forschungsgemeinschaft/ ; ANR22-CE27-0012, ANR15-CE27-0001, ANR17-FRAL-0010//Agence Nationale de la Recherche/ ; },
mesh = {*DNA, Ancient/analysis ; France ; Humans ; *Burial/history ; *Archaeology ; Male ; Bayes Theorem ; Female ; History, Ancient ; },
abstract = {The Aven de la Boucle (Corconne, Gard, southern France) is a karst shaft used as a collective burial between 3600 and 2800 cal BCE. The site encompasses the skeletal remains of approximately 75 individuals comprising a large majority of adult individuals, represented by scattered and commingled remains. To date, few studies have explored the potential of ancient DNA to tackle the documentation of Neolithic collective burials, and the funerary selection rules within such structures remain largely debated. In this study, we combine genomic analysis of 37 individuals with archaeo-anthropological data and Bayesian modelling of radiocarbon dates. Through this multidisciplinary approach, we aim to characterize the identity of the deceased and their relationships, as well as untangle the genetic diversity and funerary dynamics of this community. Genomic results identify 76% of male Neolithic individuals, suggesting a marked sex-biased selection. Available data emphasize the importance of biological relatedness and a male-mediated transmission of social status, as the affiliation to a specific male-lineage appears as a preponderant selection factor. The genomic results argue in favour of 'continuous' deposits between 3600 and 2800 BCE, carried out by the same community, despite cultural changes reflected by the ceramic material.},
}

*DNA, Ancient/analysis
France
Humans
*Burial/history
*Archaeology
Male
Bayes Theorem
Female
History, Ancient

@article {pmid39169089,
year = {2024},
author = {Oberreiter, V and Gelabert, P and Brück, F and Franz, S and Zelger, E and Szedlacsek, S and Cheronet, O and Cano, FT and Exler, F and Zagorc, B and Karavanić, I and Banda, M and Gasparyan, B and Straus, LG and Gonzalez Morales, MR and Kappelman, J and Stahlschmidt, M and Rattei, T and Kraemer, SM and Sawyer, S and Pinhasi, R},
title = {Maximizing efficiency in sedimentary ancient DNA analysis: a novel extract pooling approach.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {19388},
pmid = {39169089},
issn = {2045-2322},
support = {1111111//Research Platform MINERVA, University of Vienna/ ; CA19141-8d068698//COST iNEAL STSM Grant/ ; NECEM, HRZZ-IP-2019-04-6649//Hrvatska Zaklada za Znanost/ ; No. 101042570//European Research Council (ERC) MicroStratDNA project/ ; M3108-G//Austrian Science Fund/ ; },
mesh = {*DNA, Ancient/analysis ; *Geologic Sediments ; Humans ; Animals ; Archaeology/methods ; Fossils ; High-Throughput Nucleotide Sequencing/methods ; Hominidae/genetics ; Europe ; Africa ; },
abstract = {In the last few decades, the field of ancient DNA has taken a new direction towards using sedimentary ancient DNA (sedaDNA) for studying human and mammalian population dynamics as well as past ecosystems. However, the screening of numerous sediment samples from archaeological sites remains a time-consuming and costly endeavor, particularly when targeting hominin DNA. Here, we present a novel high-throughput method that facilitates the fast and efficient analysis of sediment samples by applying a pooled testing approach. This method combines multiple extracts, enabling early parallelization of laboratory procedures and effective aDNA screening. Pooled samples with detectable aDNA signals undergo detailed analysis, while empty pools are discarded. We have successfully applied our method to multiple sediment samples from Middle and Upper Paleolithic sites in Europe, Asia, and Africa. Notably, our results reveal that an aDNA signal remains discernible even when pooled with four negative samples. We also demonstrate that the DNA yield of double-stranded libraries increases significantly when reducing the extract input, potentially mitigating the effects of inhibition. By embracing this innovative approach, researchers can analyze large numbers of sediment samples for aDNA preservation, achieving significant cost reductions of up to 70% and reducing hands-on laboratory time to one-fifth.},
}

*DNA, Ancient/analysis
*Geologic Sediments
Humans
Animals
Archaeology/methods
Fossils
High-Throughput Nucleotide Sequencing/methods
Hominidae/genetics
Europe
Africa

@article {pmid39165395,
year = {2024},
author = {Armbrecht, L and Bolch, CJS and Paine, B and Cooper, A and McMinn, A and Woodward, C and Hallegraeff, G},
title = {Recovering sedimentary ancient DNA of harmful dinoflagellates accumulated over the last 9000 years off Eastern Tasmania, Australia.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae098},
pmid = {39165395},
issn = {2730-6151},
abstract = {Harmful algal blooms (HABs) have had significant adverse impacts on the seafood industry along the Tasmanian east coast over the past 4 decades. To investigate the history of regional HABs, we performed analyses of sedimentary ancient DNA (sedaDNA) in coastal sediments up to ~9000 years old collected inshore and offshore of Maria Island, Tasmania. We used metagenomic shotgun sequencing and a hybridisation capture array ("HABbaits1") to target three harmful dinoflagellate genera, Alexandrium, Gymnodinium, and Noctiluca. Bioinformatic and DNA damage analyses verified the authenticity of the sedaDNA sequences. Our results show that dinoflagellates of Alexandrium genera have been present off eastern Tasmania during the last ~8300 years, and we sporadically detected and unambiguously verified sequences of Gymnodinium catenatum that were present offshore up to ~7600 years ago. We also recovered sedaDNA of the fragile, soft-bodied Noctiluca scintillans with increased relative abundance since 2010, consistent with plankton surveys. This study enabled us to identify challenges of sedaDNA sequence validation (in particular for G. catenatum, a microreticulate gymnodinoid species) and provided guidance for the development of tools to monitor past and present HAB species and improvement of future HAB event predictions.},
}

@article {pmid39159385,
year = {2024},
author = {Tian, Y and Koncz, I and Defant, S and Giostra, C and Vyas, DN and Sołtysiak, A and Pejrani Baricco, L and Fetner, R and Posth, C and Brandt, G and Bedini, E and Modi, A and Lari, M and Vai, S and Francalacci, P and Fernandes, R and Steinhof, A and Pohl, W and Caramelli, D and Krause, J and Izdebski, A and Geary, PJ and Veeramah, KR},
title = {The role of emerging elites in the formation and development of communities after the fall of the Roman Empire.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {36},
pages = {e2317868121},
doi = {10.1073/pnas.2317868121},
pmid = {39159385},
issn = {1091-6490},
support = {856453//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; 426551838//Deutsche Forschungsgemeinschaft (DFG)/ ; 2018/31/G/HS3/01159//Narodowe Centrum Nauki (NCN)/ ; },
mesh = {Humans ; *Archaeology ; *Roman World/history ; Italy ; History, Medieval ; Human Migration/history ; History, Ancient ; },
abstract = {Elites played a pivotal role in the formation of post-Roman Europe on both macro- and microlevels during the Early Medieval period. History and archaeology have long focused on their description and identification based on written sources or through their archaeological record. We provide a different perspective on this topic by integrating paleogenomic, archaeological, and isotopic data to gain insights into the role of one such elite group in a Langobard period community near Collegno, Italy dated to the 6-8th centuries CE. Our analysis of 28 newly sequenced genomes together with 24 previously published ones combined with isotope (Sr, C, N) measurements revealed that this community was established by and organized around a network of biologically and socially related individuals likely composed of multiple elite families that over time developed into a single extended pedigree. The community also included individuals with diverse genetic ancestries, maintaining its diversity by integrating newcomers and groups in later stages of its existence. This study highlights how shifts in political power and migration impacted the formation and development of a small rural community within a key region of the former Western Roman Empire after its dissolution and the emergence of a new kingdom. Furthermore, it suggests that Early Medieval elites had the capacity to incorporate individuals from varied backgrounds and that these elites were the result of (political) agency rather than belonging to biologically homogeneous groups.},
}

Humans
*Archaeology
*Roman World/history
Italy
History, Medieval
Human Migration/history
History, Ancient

@article {pmid39158588,
year = {2024},
author = {Van Emmenis, L},
title = {Sarah Gaffen: I thrive on turning my vision for the lab into reality.},
journal = {The Journal of experimental medicine},
volume = {221},
number = {9},
pages = {},
doi = {10.1084/jem.20241418},
pmid = {39158588},
issn = {1540-9538},
mesh = {Humans ; History, 20th Century ; History, 21st Century ; *Interleukin-17/metabolism ; Autoimmunity ; },
abstract = {Sarah Gaffen, PhD, is a professor of medicine and rheumatology and holds the Gerald P. Rodnan endowed chair at the University of Pittsburgh. Her lab explores the biological function of IL-17 and its receptor in the context of fungal host defense and autoimmunity. We spoke to Sarah about where her interest in cytokines began, the importance of saying no in your career, and her interest in paleogenetics.},
}

Humans
History, 20th Century
History, 21st Century
*Interleukin-17/metabolism
Autoimmunity

@article {pmid39151011,
year = {2024},
author = {Rathmann, H and Vizzari, MT and Beier, J and Bailey, SE and Ghirotto, S and Harvati, K},
title = {Human population dynamics in Upper Paleolithic Europe inferred from fossil dental phenotypes.},
journal = {Science advances},
volume = {10},
number = {33},
pages = {eadn8129},
doi = {10.1126/sciadv.adn8129},
pmid = {39151011},
issn = {2375-2548},
mesh = {Humans ; *Fossils ; Europe ; *Phenotype ; *Tooth/anatomy & histology ; *Population Dynamics ; Bayes Theorem ; Archaeology ; },
abstract = {Despite extensive archaeological research, our knowledge of the human population history of Upper Paleolithic Europe remains limited, primarily due to the scarce availability and poor molecular preservation of fossil remains. As teeth dominate the fossil record and preserve genetic signatures in their morphology, we compiled a large dataset of 450 dentitions dating between ~47 and 7 thousand years ago (ka), outnumbering existing skeletal and paleogenetic datasets. We tested a range of competing demographic scenarios using a coalescent-based machine learning Approximate Bayesian Computation (ABC) framework that we modified for use with phenotypic data. Mostly in agreement with but also challenging some of the hitherto available evidence, we identified a population turnover in western Europe at ~28 ka, isolates in western and eastern refugia between ~28 and 14.7 ka, and bottlenecks during the Last Glacial Maximum. Methodologically, this study marks the pioneering application of ABC to skeletal phenotypes, paving the way for exciting future research avenues.},
}

Humans
*Fossils
Europe
*Phenotype
*Tooth/anatomy & histology
*Population Dynamics
Bayes Theorem
Archaeology

@article {pmid39149515,
year = {2024},
author = {Rbbani, G and Murshed, R and Siriyappagouder, P and Sharko, F and Nedoluzhko, A and Joshi, R and Galindo-Villegas, J and Raeymaekers, JAM and Fernandes, JMO},
title = {Embryonic temperature has long-term effects on muscle circRNA expression and somatic growth in Nile tilapia.},
journal = {Frontiers in cell and developmental biology},
volume = {12},
number = {},
pages = {1369758},
doi = {10.3389/fcell.2024.1369758},
pmid = {39149515},
issn = {2296-634X},
abstract = {Embryonic temperature has a lasting impact on muscle phenotype in vertebrates, involving complex molecular mechanisms that encompass both protein-coding and non-coding genes. Circular RNAs (circRNAs) are a class of regulatory RNAs that play important roles in various biological processes, but the effect of variable thermal conditions on the circRNA transcriptome and its long-term impact on muscle growth plasticity remains largely unexplored. To fill this knowledge gap, we performed a transcriptomic analysis of circRNAs in fast muscle of Nile tilapia (Oreochromis niloticus) subjected to different embryonic temperatures (24°C, 28°C and 32°C) and then reared at a common temperature (28°C) for 4 months. Nile tilapia embryos exhibited faster development and subsequently higher long-term growth at 32°C compared to those reared at 28°C and 24°C. Next-generation sequencing data revealed a total of 5,141 unique circRNAs across all temperature groups, of which 1,604, 1,531, and 1,169 circRNAs were exclusively found in the 24°C, 28°C and 32°C groups, respectively. Among them, circNexn exhibited a 1.7-fold (log2) upregulation in the 24°C group and a 1.3-fold (log2) upregulation in the 32°C group when compared to the 28°C group. Conversely, circTTN and circTTN_b were downregulated in the 24°C groups compared to their 28°C and 32°C counterparts. Furthermore, these differentially expressed circRNAs were found to have multiple interactions with myomiRs, highlighting their potential as promising candidates for further investigation in the context of muscle growth plasticity. Taken together, our findings provide new insights into the molecular mechanisms that may underlie muscle growth plasticity in response to thermal variation in fish, with important implications in the context of climate change, fisheries and aquaculture.},
}

@article {pmid39146937,
year = {2024},
author = {Du, P and Zhu, K and Wang, M and Sun, Z and Tan, J and Sun, B and Sun, B and Wang, P and He, G and Xiong, J and Huang, Z and Meng, H and Sun, C and Xie, S and Wang, B and Ge, D and Ma, Y and Sheng, P and Ren, X and Tao, Y and Xu, Y and Qin, X and Allen, E and Zhang, B and Chang, X and Wang, K and Bao, H and Yu, Y and Wang, L and Ma, X and Du, Z and Guo, J and Yang, X and Wang, R and Ma, H and Li, D and Pan, Y and Li, B and Zhang, Y and Zheng, X and Han, S and Jin, L and Chen, G and Li, H and Wang, CC and Wen, S},
title = {Genomic dynamics of the Lower Yellow River Valley since the Early Neolithic.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.07.063},
pmid = {39146937},
issn = {1879-0445},
abstract = {The Yellow River Delta played a vital role in the development of the Neolithic civilization of China. However, the population history of this region from the Neolithic transitions to the present remains poorly understood due to the lack of ancient human genomes. This especially holds for key Neolithic transitions and tumultuous turnovers of dynastic history. Here, we report genome-wide data from 69 individuals dating to 5,410-1,345 years before present (BP) at 0.008 to 2.49× coverages, along with 325 present-day individuals collected from 16 cities across Shandong. During the Middle to Late Dawenkou period, we observed a significant influx of ancestry from Neolithic Yellow River farmers in central China and some southern Chinese ancestry that mixed with local hunter-gatherers in Shandong. The genetic heritage of the Shandong Longshan people was found to be most closely linked to the Dawenkou culture. During the Shang to Zhou Dynasties, there was evidence of genetic admixture of local Longshan populations with migrants from the Central Plain. After the Qin to Han Dynasties, the genetic composition of the region began to resemble that of modern Shandong populations. Our genetic findings suggest that the middle Yellow River Basin farmers played a role in shaping the genetic affinity of neighboring populations in northern China during the Middle to Late Neolithic period. Additionally, our findings indicate that the genetic diversity in the Shandong region during the Zhou Dynasty may be linked with their complex ethnicities.},
}

@article {pmid39140291,
year = {2024},
author = {de la Fuente, J},
title = {Catastrophic selection: the other side of the coin.},
journal = {Annals of medicine},
volume = {56},
number = {1},
pages = {2391014},
doi = {10.1080/07853890.2024.2391014},
pmid = {39140291},
issn = {1365-2060},
mesh = {Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Antimicrobial Peptides/pharmacology ; Machine Learning ; Drug Resistance, Bacterial ; Proteomics/methods ; },
abstract = {Recently, a machine learning molecular de-extinction paleoproteomic approach was used to recover inactivated antimicrobial peptides to overcome the challenges posed by antibiotic-resistant pathogens. The authors showed the possibility of identifying lost molecules with antibacterial capacity, but the other side of the coin associated with catastrophic selection should be considered for the development of new pharmaceuticals.},
}

Humans
*Anti-Bacterial Agents/pharmacology/therapeutic use
Antimicrobial Peptides/pharmacology
Machine Learning
Drug Resistance, Bacterial
Proteomics/methods

@article {pmid39136992,
year = {2024},
author = {Skovrind, M and Louis, M and Ferguson, SH and Glazov, DM and Litovka, DI and Loseto, L and Meschersky, IG and Miller, MM and Petr, M and Postma, L and Rozhnov, VV and Scott, M and Westbury, MV and Szpak, P and Friesen, TM and Lorenzen, ED},
title = {Elucidating the sustainability of 700 y of Inuvialuit beluga whale hunting in the Mackenzie River Delta, Northwest Territories, Canada.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {34},
pages = {e2405993121},
doi = {10.1073/pnas.2405993121},
pmid = {39136992},
issn = {1091-6490},
support = {37352//Villum Fonden YIP+/ ; 9064-00025B//Independent research fund, Sapre Aude/ ; CF23-1061//Carlsberg Foundation Semper Ardens Accelerate/ ; 435-2012-0641//Canadian Government | Social Sciences and Humanities Research Council of Canada (SSHRC)/ ; 61914//Polar Continental Shelf Program/ ; 62816//Polar Continental Shelf Program/ ; 000//Aurora Research Institute (ARI)/ ; },
mesh = {Animals ; *Beluga Whale/genetics ; Northwest Territories ; Female ; Male ; Hunting ; Nitrogen Isotopes/analysis ; Carbon Isotopes/analysis ; DNA, Mitochondrial/genetics ; Inuit ; },
abstract = {Beluga whales play a critical role in the subsistence economies and cultural heritage of Indigenous communities across the Arctic, yet the effects of Indigenous hunting on beluga whales remain unknown. Here, we integrate paleogenomics, genetic simulations, and stable δ[13]C and δ[15]N isotope analysis to investigate 700 y of beluga subsistence hunting in the Mackenzie Delta area of northwestern Canada. Genetic identification of the zooarchaeological remains, which is based on radiocarbon dating, span three time periods (1290 to 1440 CE; 1450 to 1650 CE; 1800 to 1870 CE), indicates shifts across time in the sex ratio of the harvested belugas. The equal number of females and males harvested in 1450 to 1650 CE versus more males harvested in the two other time periods may reflect changes in hunting practices or temporal shifts in beluga availability. We find temporal shifts and sex-based differences in δ[13]C of the harvested belugas across time, suggesting historical adaptability in the foraging ecology of the whales. We uncovered distinct mitochondrial diversity unique to the Mackenzie Delta belugas, but found no changes in nuclear genomic diversity nor any substructuring across time. Our findings indicate the genomic stability and continuity of the Mackenzie Delta beluga population across the 700 y surveyed, indicating the impact of Inuvialuit subsistence harvests on the genetic diversity of contemporary beluga individuals has been negligible.},
}

Animals
*Beluga Whale/genetics
Northwest Territories
Female
Male
Hunting
Nitrogen Isotopes/analysis
Carbon Isotopes/analysis
DNA, Mitochondrial/genetics
Inuit

@article {pmid39135339,
year = {2024},
author = {Tseng, YH and Kuo, LY and Borokini, I and Fawcett, S},
title = {The role of deep hybridization in fern speciation: Examples from the Thelypteridaceae.},
journal = {American journal of botany},
volume = {},
number = {},
pages = {e16388},
doi = {10.1002/ajb2.16388},
pmid = {39135339},
issn = {1537-2197},
abstract = {PREMISE: Hybridization is recognized as an important mechanism in fern speciation, with many allopolyploids known among congeners, as well as evidence of ancient genome duplications. Several contemporary instances of deep (intergeneric) hybridization have been noted, invariably resulting in sterile progeny. We chose the christelloid lineage of the family Thelypteridaceae, recognized for its high frequency of both intra- and intergeneric hybrids, to investigate recent hybrid speciation between deeply diverged lineages. We also seek to understand the ecological and evolutionary outcomes of resulting lineages across the landscape.

METHODS: By phasing captured reads within a phylogenomic data set of GoFlag 408 nuclear loci using HybPhaser, we investigated candidate hybrids to identify parental lineages. We estimated divergence ages by inferring a dated phylogeny using fossil calibrations with treePL. We investigated ecological niche conservatism between one confirmed intergeneric allotetraploid and its diploid progenitors using the centroid, overlap, unfilling, and expansion (COUE) framework.

RESULTS: We provide evidence for at least six instances of intergeneric hybrid speciation within the christelloid clade and estimate up to 45 million years of divergence between progenitors. The niche quantification analysis showed moderate niche overlap between an allopolyploid species and its progenitors, with significant divergence from the niche of one progenitor and conservatism to the other.

CONCLUSIONS: The examples provided here highlight the overlooked role that allopolyploidization following intergeneric hybridization may play in fern diversification and range and niche expansions. Applying this approach to other fern taxa may reveal a similar pattern of deep hybridization resulting in highly successful novel lineages.},
}

@article {pmid39078618,
year = {2024},
author = {Vaughn, AH and Nielsen, R},
title = {Fast and Accurate Estimation of Selection Coefficients and Allele Histories from Ancient and Modern DNA.},
journal = {Molecular biology and evolution},
volume = {41},
number = {8},
pages = {},
pmid = {39078618},
issn = {1537-1719},
mesh = {*Selection, Genetic ; Humans ; *DNA, Ancient/analysis ; *Models, Genetic ; *Gene Frequency ; Likelihood Functions ; Markov Chains ; Algorithms ; Evolution, Molecular ; Alleles ; Computer Simulation ; },
abstract = {We here present CLUES2, a full-likelihood method to infer natural selection from sequence data that is an extension of the method CLUES. We make several substantial improvements to the CLUES method that greatly increases both its applicability and its speed. We add the ability to use ancestral recombination graphs on ancient data as emissions to the underlying hidden Markov model, which enables CLUES2 to use both temporal and linkage information to make estimates of selection coefficients. We also fully implement the ability to estimate distinct selection coefficients in different epochs, which allows for the analysis of changes in selective pressures through time, as well as selection with dominance. In addition, we greatly increase the computational efficiency of CLUES2 over CLUES using several approximations to the forward-backward algorithms and develop a new way to reconstruct historic allele frequencies by integrating over the uncertainty in the estimation of the selection coefficients. We illustrate the accuracy of CLUES2 through extensive simulations and validate the importance sampling framework for integrating over the uncertainty in the inference of gene trees. We also show that CLUES2 is well-calibrated by showing that under the null hypothesis, the distribution of log-likelihood ratios follows a χ2 distribution with the appropriate degrees of freedom. We run CLUES2 on a set of recently published ancient human data from Western Eurasia and test for evidence of changing selection coefficients through time. We find significant evidence of changing selective pressures in several genes correlated with the introduction of agriculture to Europe and the ensuing dietary and demographic shifts of that time. In particular, our analysis supports previous hypotheses of strong selection on lactase persistence during periods of ancient famines and attenuated selection in more modern periods.},
}

*Selection, Genetic
Humans
*DNA, Ancient/analysis
*Models, Genetic
*Gene Frequency
Likelihood Functions
Markov Chains
Algorithms
Evolution, Molecular
Alleles
Computer Simulation

@article {pmid39135108,
year = {2024},
author = {Alaçamlı, E and Naidoo, T and Güler, MN and Sağlıcan, E and Aktürk, Ş and Mapelli, I and Vural, KB and Somel, M and Malmström, H and Günther, T},
title = {READv2: advanced and user-friendly detection of biological relatedness in archaeogenomics.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {216},
pmid = {39135108},
issn = {1474-760X},
support = {P21-0266//Riksbankens Jubileumsfond/ ; 772390//HORIZON EUROPE European Research Council/ ; },
abstract = {The advent of genome-wide ancient DNA analysis has revolutionized our understanding of prehistoric societies. However, studying biological relatedness in these groups requires tailored approaches due to the challenges of analyzing ancient DNA. READv2, an optimized Python3 implementation of the most widely used tool for this purpose, addresses these challenges while surpassing its predecessor in speed and accuracy. For sufficient amounts of data, it can classify up to third-degree relatedness and differentiate between the two types of first-degree relatedness, full siblings and parent-offspring. READv2 enables user-friendly, efficient, and nuanced analysis of biological relatedness, facilitating a deeper understanding of past social structures.},
}

@article {pmid39114968,
year = {2024},
author = {Moriano, J and Leonardi, O and Vitriolo, A and Testa, G and Boeckx, C},
title = {A multi-layered integrative analysis reveals a cholesterol metabolic program in outer radial glia with implications for human brain evolution.},
journal = {Development (Cambridge, England)},
volume = {},
number = {},
pages = {},
doi = {10.1242/dev.202390},
pmid = {39114968},
issn = {1477-9129},
support = {2021-SGR-313; FI-SDUR 2020//Generalitat de Catalunya/ ; PID2019-107042GB-I00//Ministerio de Ciencia e Innovacion/ ; },
abstract = {The definition of molecular and cellular mechanisms contributing to brain ontogenetic trajectories is essential to investigate the evolution of our species. Yet their functional dissection at an appropriate level of granularity remains challenging. Capitalizing on recent efforts that have extensively profiled neural stem cells from the developing human cortex, we develop an integrative computational framework to perform (i) trajectory inference and gene regulatory network reconstruction, (ii) (pseudo)time-informed non-negative matrix factorization for learning the dynamics of gene expression programs, and (iii) paleogenomic analysis for a higher-resolution mapping of derived regulatory variants in our species in comparison to our closest relatives. We provide evidence for cell type-specific regulation of gene expression programs during indirect neurogenesis. In particular, our analysis uncovers a key role for a cholesterol program in outer radial glia, regulated by zinc-finger transcription factor KLF6. A cartography of the regulatory landscape impacted by Homo sapiens-derived variants reveals signals of selection clustering around regulatory regions associated with GLI3, a well-known regulator of radial glial cell cycle, and impacting KLF6 regulation. Our study contributes to the evidence of significant changes in metabolic pathways in recent human brain evolution.},
}

@article {pmid39114174,
year = {2024},
author = {Civáň, P and Fricano, A and Russell, J and Pont, C and Özkan, H and Kilian, B and Brown, TA},
title = {Genetic erosion in domesticated barley and a hypothesis of a North African centre of diversity.},
journal = {Ecology and evolution},
volume = {14},
number = {8},
pages = {e70068},
pmid = {39114174},
issn = {2045-7758},
abstract = {Barley is one of the founder crops of the Neolithic transition in West Asia. While recent advances in genomics have provided a rather detailed picture of barley domestication, there are contradictory views on how the domestication process affected genetic diversity. We set out to revisit this question by integrating public DNA sequencing data from ancient barley and wide collections of extant wild and domesticated accessions. Using two previously overlooked approaches - analyses of chloroplast genomes and genome-wide proportions of private variants - we found that the barley cultivated six millennia ago was genetically unique and more diverse when compared to extant landraces and cultivars. Moreover, the chloroplast genomes revealed a link between the ancient barley, an obscure wild genotype from north-eastern Libya, and a distinct population of barley cultivated in Ethiopia/Eritrea. Based on these results, we hypothesize past existence of a wider North African population that included both wild and cultivated types and suffered from genetic erosion in the past six millennia, likely due to a rapid desertification that ended the Holocene African humid period. Besides providing clues about the origin of Ethiopian landraces, the hypothesis explains the post-domestication loss of diversity observed in barley. Analyses of additional samples will be necessary to resolve the history of African barley and its contribution to the extant cultivated gene pool.},
}

@article {pmid39113775,
year = {2024},
author = {Furness, LH and Kersten, O and Boilard, A and Keith-Diagne, L and Brito, C and Barrett, JH and Kitchener, A and Sabin, R and Lavery, S and Plön, S and Star, B},
title = {Population structure of Dugong dugon across the Indo-Pacific revealed by historical mitogenomes.},
journal = {Royal Society open science},
volume = {11},
number = {8},
pages = {240599},
pmid = {39113775},
issn = {2054-5703},
abstract = {Sirenia, an iconic marine taxon with a tropical and subtropical worldwide distribution, face an uncertain future. All species are designated 'Vulnerable' to extinction by the IUCN. Nonetheless, a comprehensive understanding of geographic structuring across the global range is lacking, impeding our ability to highlight particularly vulnerable populations for conservation priority. Here, we use ancient DNA to investigate dugong (Dugong dugon) population structure, analysing 56 mitogenomes from specimens comprising the known historical range. Our results reveal geographically structured and distinct monophyletic clades characterized by contrasting evolutionary histories. We observe deep-rooted and divergent lineages in the East (Indo-Pacific) and obtain new evidence for the relatively recent dispersal of dugongs into the western Indian Ocean. All populations are significantly differentiated from each other with western populations having approximately 10-fold lower levels of genetic variation than eastern Indo-Pacific populations. Additionally, we find a significant temporal loss of genetic diversity in western Indian Ocean dugongs since the mid-twentieth century, as well as a decline in population size beginning approximately 1000 years ago. Our results add to the growing body of evidence that dugong populations are becoming ever more susceptible to ongoing human action and global climate change.},
}

@article {pmid39105137,
year = {2024},
author = {de Vos, JM and Streiff, SJR and Bachelier, JB and Epitawalage, N and Maurin, O and Forest, F and Baker, WJ},
title = {Phylogenomics of the pantropical Connaraceae: revised infrafamilial classification and the evolution of heterostyly.},
journal = {Plant systematics and evolution = Entwicklungsgeschichte und Systematik der Pflanzen},
volume = {310},
number = {4},
pages = {29},
pmid = {39105137},
issn = {0378-2697},
abstract = {UNLABELLED: Connaraceae is a pantropical family of about 200 species containing lianas and small trees with remarkably diverse floral polymorphisms, including distyly, tristyly, homostyly, and dioecy. To date, relationships within the family have not been investigated using a targeted molecular phylogenetic treatment, severely limiting systematic understanding and reconstruction of trait evolution. Accordingly, their last infrafamilial classification was based only on morphological data. Here, we used phylogenomic data obtained using the Angiosperms353 nuclear target sequence capture probes, sampling all tribes and almost all genera, entirely from herbarium specimens, to revise infrafamilial classification and investigate the evolution of heterostyly. The backbone of the resulting molecular phylogenetic tree is almost entirely resolved. Connaraceae consists of two clades, one containing only the African genus Manotes (4 or 5 species), which we newly recognize at the subfamily level. Vegetative and reproductive synapomorphies are proposed for Manotoideae. Within Connaroideae, Connareae is expanded to include the former Jollydoreae. The backbone of Cnestideae, which contains more than half of the Connaraceae species, remains incompletely resolved. Reconstructions of reproductive system evolution are presented that tentatively support tristyly as the ancestral state for the family, with multiple parallel losses, in agreement with previous hypotheses, plus possible re-gains. However, the great diversity of stylar polymorphisms and their phylogenetic lability preclude a definitive answer. Overall, this study reinforces the usefulness of herbarium phylogenomics, and unlocks the reproductive diversity of Connaraceae as a model system for the evolution of complex biological phenomena.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00606-024-01909-y.},
}

@article {pmid39098141,
year = {2024},
author = {Golob, A and Kravanja, P and Concato, M and Leskovar, T and Zupanič Pajnič, I},
title = {Searching for alternative high DNA-yielding bone types for DNA analysis of aged skeletal remains.},
journal = {Forensic science international},
volume = {362},
number = {},
pages = {112184},
doi = {10.1016/j.forsciint.2024.112184},
pmid = {39098141},
issn = {1872-6283},
abstract = {The petrous bone contains significantly higher amounts of DNA than any other human bone. Because of highly destructive sampling and because it is not always part of the recovered remains, the need for alternative sources of DNA is important. To identify additional optimal bone types, petrous bones were compared to femurs, tali, and calcanei sampled from 66 adult skeletons from two distinct modern-era Christian cemeteries. An extraction method employing full demineralization was used to obtain DNA, real-time PCR quantification to ascertain DNA quantity and degradation, and a commercial forensic short tandem repeats (STR) PCR amplification kit to determine genetic profiles. Statistical analysis was performed to explore the differences in DNA yield, DNA degradation, and success of STR amplification. A systematic studies exploring intra-skeletal variability in DNA preservation including various excavation sites differing by time period and geographical position are rare, and the second part of the investigation was based on a comparison of both archaeological sites, which allowed us to compare the effect of different post-mortem intervals and environmental conditions on DNA preservation. The older burial site in Črnomelj was active between the 13th and 18th century, whereas the more recent Polje burial was in use from the 16th to 19th century, creating different temporal and geographical environments. Results for the Črnomelj burial site revealed that the petrous bone outperformed all other bone types studied, except the calcaneus. At the Polje archeological site calcanei, tali, and femurs yielded the same STR typing success as petrous bones. The results obtained highlight the importance of careful bone sample selection for DNA analysis of aged skeletal remains. In addition to petrous bones, calcanei were found to be an alternative source of DNA when older burial sites are investigated. When more recent burial sites are processed, calcanei, tali, and femurs should be sampled besides petrous bones, not only because they exhibited good performance, but also because of easier sampling and easier grinding in the case of trabecular bones. This study contributes valuable insights into the potential use of various skeletal types as a source of DNA for investigation of aged skeletal remains, and it offers practical implications for forensic and archaeological investigations.},
}

@article {pmid39091721,
year = {2024},
author = {Gyuris, B and Vyazov, L and Türk, A and Flegontov, P and Szeifert, B and Langó, P and Mende, BG and Csáky, V and Chizhevskiy, AA and Gazimzyanov, IR and Khokhlov, AA and Kolonskikh, AG and Matveeva, NP and Ruslanova, RR and Rykun, MP and Sitdikov, A and Volkova, EV and Botalov, SG and Bugrov, DG and Grudochko, IV and Komar, O and Krasnoperov, AA and Poshekhonova, OE and Chikunova, I and Sungatov, F and Stashenkov, DA and Zubov, S and Zelenkov, AS and Ringbauer, H and Cheronet, O and Pinhasi, R and Akbari, A and Rohland, N and Mallick, S and Reich, D and Szécsényi-Nagy, A},
title = {Long shared haplotypes identify the Southern Urals as a primary source for the 10th century Hungarians.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39091721},
issn = {2692-8205},
abstract = {During the Hungarian Conquest in the 10th century CE, the early medieval Magyars, a group of mounted warriors from Eastern Europe, settled in the Carpathian Basin. They likely introduced the Hungarian language to this new settlement area, during an event documented by both written sources and archaeological evidence. Previous archaeogenetic research identified the newcomers as migrants from the Eurasian steppe. However, genome-wide ancient DNA from putative source populations has not been available to test alternative theories of their precise source. We generated genome-wide ancient DNA data for 131 individuals from candidate archaeological contexts in the Circum-Uralic region in present-day Russia. Our results tightly link the Magyars to people of the Early Medieval Karayakupovo archaeological horizon on both the European and Asian sides of the southern Urals. Our analyes show that ancestors of the people of the Karayakupovo archaeological horizon were established in the Southern Urals by the Iron Age and that their descendants persisted locally in the Volga-Kama region until at least the 14th century.},
}

@article {pmid39088604,
year = {2024},
author = {Kukutai, T and Black, A},
title = {CARE-ing for Indigenous nonhuman genomic data - rethinking our approach.},
journal = {Science (New York, N.Y.)},
volume = {385},
number = {6708},
pages = {eadr2493},
doi = {10.1126/science.adr2493},
pmid = {39088604},
issn = {1095-9203},
mesh = {Animals ; Biological Evolution ; *Birds/genetics ; DNA, Ancient/analysis ; *Fossils ; *Genome ; *Genomics/ethics ; New Zealand ; Sequence Analysis, DNA ; },
abstract = {Earlier this year, an international group of scientists published a paper in ScienceAdvances on the draft genome of the little bush moa (Anomalopteryx didiformis), one of about nine species of extinct flightless birds endemic to Aotearoa (New Zealand). The genome was sequenced from the ancient DNA of a "poorly provenanced" fossil bone acquired by the Royal Ontario Museum. It held important clues about the moa's evolutionary history and aspects of its biology.},
}

Animals
Biological Evolution
*Birds/genetics
DNA, Ancient/analysis
*Fossils
*Genome
*Genomics/ethics
New Zealand
Sequence Analysis, DNA

@article {pmid39086419,
year = {2024},
author = {Farhud, DD and Azari, M and Rahbar, M},
title = {Tracking of Infectious Diseases and Deadly Injuries through Signs Observed in Excavated Human Skeletons of 2000 BC/Iron Age in Iran.},
journal = {Iranian journal of public health},
volume = {53},
number = {7},
pages = {1598-1611},
pmid = {39086419},
issn = {2251-6093},
abstract = {BACKGROUND: Throughout history, many wars have occurred for various reasons, and many empires and kings have fallen or many people killed by wars. Wars were not always due to the conquest of the country. in the Iron Age, societies were governed by tribes at the head of the tribe, and war was only for to seize property, slaves, and food. Our research area is the same period as the Medes Kingdom, which included the union of small, large tribes, wars between tribes existed in that period, and their signs can be seen on the remains of the people of that period.

METHODS: Our research is related to human remains from Sagezabad cemetery, Qazvin plain, which dates back to 2000 BC (Iron Age 2 and 3) in Iran.

RESULTS: The blows on the remains were very serious and caused death. We have discussed how to kill by "considering the injured body".

CONCLUSION: Our investigation of how people were killed in war based on injury marks and bullet holes in bones, and simulating those injuries to body tissues and organs also, people who had bone cuts from the war and survived and had bone repair and died due to lack of nutrients and infection were also discussed.},
}

@article {pmid39080329,
year = {2024},
author = {Boggi, B and Sharpen, JDA and Taylor, G and Drosou, K},
title = {A novel integrated extraction protocol for multi-omic studies in heavily degraded samples.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {17477},
pmid = {39080329},
issn = {2045-2322},
mesh = {Animals ; Brain/metabolism ; DNA/isolation & purification ; Genomics/methods ; Lipids/analysis ; Metabolomics/methods ; *Multiomics/methods ; Proteins/isolation & purification/metabolism ; Proteomics/methods ; Swine ; },
abstract = {The combination of multi-omic techniques, such as genomics, transcriptomics, proteomics, metabolomics and epigenomics, has revolutionised studies in medical research. These techniques are employed to support biomarker discovery, better understand molecular pathways and identify novel drug targets. Despite concerted efforts in integrating omic datasets, there is an absence of protocols that integrate all four biomolecules in a single extraction process. Here, we demonstrate for the first time a minimally destructive integrated protocol for the simultaneous extraction of artificially degraded DNA, proteins, lipids and metabolites from pig brain samples. We used an MTBE-based approach to separate lipids and metabolites, followed by subsequent isolation of DNA and proteins. We have validated this protocol against standalone extraction protocols and show comparable or higher yields of all four biomolecules. This integrated protocol is key to facilitating the preservation of irreplaceable samples while promoting downstream analyses and successful data integration by removing bias from univariate dataset noise and varied distribution characteristics.},
}

Animals
Brain/metabolism
DNA/isolation & purification
Genomics/methods
Lipids/analysis
Metabolomics/methods
*Multiomics/methods
Proteins/isolation & purification/metabolism
Proteomics/methods
Swine

@article {pmid39078610,
year = {2024},
author = {Nagel, AA and Flouri, T and Yang, Z and Rannala, B},
title = {Bayesian Inference Under the Multispecies Coalescent with Ancient DNA Sequences.},
journal = {Systematic biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/sysbio/syae047},
pmid = {39078610},
issn = {1076-836X},
abstract = {Ancient DNA (aDNA) is increasingly being used to investigate questions such as the phylogenetic relationships and divergence times of extant and extinct species. If aDNA samples are sufficiently old, expected branch lengths (in units of nucleotide substitutions) are reduced relative to contemporary samples. This can be accounted for by incorporating sample ages into phylogenetic analyses. Existing methods that use tip (sample) dates infer gene trees rather than species trees, which can lead to incorrect or biased inferences of the species tree. Methods using a multispecies coalescent (MSC) model overcome these issues. We developed an MSC model with tip dates and implemented it in the program bpp. The method performed well for a range of biologically realistic scenarios, estimating calibrated divergence times and mutation rates precisely. Simulations suggest that estimation precision can be best improved by prioritizing sampling of many loci and more ancient samples. Incorrectly treating ancient samples as contemporary in analyzing simulated data, mimicking a common practice of empirical analyses, led to large systematic biases in model parameters, including divergence times. Two genomic datasets of mammoths and elephants were analyzed, demonstrating the method's empirical utility.},
}

@article {pmid39067763,
year = {2024},
author = {Bragazzi, NL and Del Rio, D and Mayer, EA and Mena, P},
title = {We are what, when, and how we eat: the evolutionary impact of dietary shifts on physical and cognitive development, health, and disease.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {100280},
doi = {10.1016/j.advnut.2024.100280},
pmid = {39067763},
issn = {2156-5376},
abstract = {"We are what, when, and how we eat": the evolution of human dietary habits mirrors the evolution of humans themselves. Key developments in human history, such as the advent of stone tool technology, the shift to a meat-based diet, control of fire, advancements in cooking and fermentation techniques, the domestication of plants and animals, have significantly influenced human anatomical, physiological, social, cognitive, and behavioral changes. Advancements in scientific methods, such as the analysis of microfossils like starch granules, plant-derived phytoliths, and coprolites, have yielded unprecedented insights into past diets. Nonetheless, the isolation of ancient food matrices remains analytically challenging. Future technological breakthroughs and a more comprehensive integration of paleogenomics, paleoproteomics, paleoglycomics, and paleometabolomics will enable a more nuanced understanding of early human ancestors' diets, which holds the potential to guide contemporary dietary recommendations and tackle modern health challenges, with far-reaching implications for human well-being, and ecological impact on the planet.},
}

@article {pmid39050717,
year = {2024},
author = {Monnereau, A and Ughi, A and Orecchioni, P and Hagan, R and Talbot, HM and Nikita, E and Hamilton, D and Le Roux, P and Molinari, A and Carver, M and Craig, OE and Speller, CF and Alexander, MM and Wales, N},
title = {Multi-proxy bioarchaeological analysis of skeletal remains shows genetic discontinuity in a Medieval Sicilian community.},
journal = {Royal Society open science},
volume = {11},
number = {7},
pages = {240436},
pmid = {39050717},
issn = {2054-5703},
abstract = {The medieval period in Sicily was turbulent, involving successive regime changes, from Byzantine (Greek Christian), Aghlabid (Sunni Muslim), Fatimid (Shī'a Muslim), to Normans and Swabians (Latin Christian). To shed new light on the local implications of regime changes, we conducted a multidisciplinary analysis of 27 individuals buried in adjacent Muslim and Christian cemeteries at the site of Segesta, western Sicily. By combining radiocarbon dating, genome-wide sequencing, stable and radiogenic isotopic data, and archaeological records, we uncover genetic differences between the two communities but find evidence of continuity in other aspects of life. Historical and archaeological evidence shows a Muslim community was present by the 12th century during Norman governance, with the Christian settlement appearing in the 13th century under Swabian governance. A Bayesian analysis of radiocarbon dates from the burials finds the abandonment of the Muslim cemetery likely occurred after the establishment of the Christian cemetery, indicating that individuals of both faiths were present in the area in the first half of the 13th century. The biomolecular results suggest the Christians remained genetically distinct from the Muslim community at Segesta while following a substantially similar diet. This study demonstrates that medieval regime changes had major impacts beyond the political core, leading to demographic changes while economic systems persisted and new social relationships emerged.},
}

@article {pmid39044634,
year = {2024},
author = {Rivera Rosas, DE and Geraldi, NR and Glud, RN and Oguri, K and Haond, SA and Duarte, CM},
title = {A sedimentary DNA record of the Atacama Trench reveals biodiversity changes in the most productive marine ecosystem.},
journal = {Global change biology},
volume = {30},
number = {7},
pages = {e17412},
doi = {10.1111/gcb.17412},
pmid = {39044634},
issn = {1365-2486},
support = {JP20H02013//Japan Society for the Promotion of Science/ ; 669947//ERC Advanced Grant "Benthic diagenesis and microbiology of hadal trenches"/ ; DNRF145//Danmarks Grundforskningsfond/ ; //King Abdullah University of Science and Technology/ ; },
mesh = {*Geologic Sediments/analysis ; *Biodiversity ; *DNA, Environmental/analysis ; *RNA, Ribosomal, 18S/genetics ; *Ecosystem ; Chile ; Animals ; DNA Barcoding, Taxonomic ; Eukaryota/genetics ; Aquatic Organisms/genetics ; },
abstract = {The hadopelagic environment remains highly understudied due to the inherent difficulties in sampling at these depths. The use of sediment environmental DNA (eDNA) can overcome some of these restrictions as settled and preserved DNA represent an archive of the biological communities. We use sediment eDNA to assess changes in the community within one of the world's most productive open-ocean ecosystems: the Atacama Trench. The ecosystems around the Atacama Trench have been intensively fished and are affected by climate oscillations, but the understanding of potential impacts on the marine community is limited. We sampled five sites using sediment cores at water depths from 2400 to ~8000 m. The chronologies of the sedimentary record were determined using [210]Pbex. Environmental DNA was extracted from core slices and metabarcoding was used to identify the eukaryote community using two separate primer pairs for different sections of the 18S rRNA gene (V9 and V7) effectively targeting pelagic taxa. The reconstructed communities were similar among markers and mainly composed of chordates and members of the Chromista kingdom. Alpha diversity was estimated for all sites in intervals of 15 years (from 1842 to 2018), showing a severe drop in biodiversity from 1970 to 1985 that aligns with one of the strongest known El Niño events and extensive fishing efforts during the time. We find a direct impact of sea surface temperature on the community composition over time. Fish and cnidarian read abundance was examined separately to determine whether fishing had a direct impact, but no direct relation was found. These results demonstrate that sediment eDNA can be a valuable emerging tool providing insight in historical perspectives on ecosystem developments. This study constitutes an important step toward an improved understanding of the importance of environmental and anthropogenic drivers in affecting open and deep ocean communities.},
}

*Geologic Sediments/analysis
*Biodiversity
*DNA, Environmental/analysis
*RNA, Ribosomal, 18S/genetics
*Ecosystem
Chile
Animals
DNA Barcoding, Taxonomic
Eukaryota/genetics
Aquatic Organisms/genetics

@article {pmid39028337,
year = {2024},
author = {Çubukcu, H and Kılınç, GM},
title = {Evaluation of genotype imputation using Glimpse tools on low coverage ancient DNA.},
journal = {Mammalian genome : official journal of the International Mammalian Genome Society},
volume = {},
number = {},
pages = {},
pmid = {39028337},
issn = {1432-1777},
abstract = {Ancient DNA provides a unique frame for directly studying human population genetics in time and space. Still, since most of the ancient genomic data is low coverage, analysis is confronted with a low number of SNPs, genotype uncertainties, and reference-bias. Here, we for the first time benchmark the two distinct versions of Glimpse tools on 120 ancient human genomes from Eurasia including those largely from previously under-evaluated regions and compare the performance of genotype imputation with de facto analysis approaches for low coverage genomic data analysis. We further investigate the impact of two distinct reference panels on imputation accuracy for low coverage genomic data. We compute accuracy statistics and perform PCA and f4-statistics to explore the behaviour of genotype imputation on low coverage data regarding (i)two versions of Glimpse, (ii)two reference panels, (iii)four post-imputation filters and coverages, as well as (iv)data type and geographical origin of the samples on the analyses. Our results reveal that even for 0.1X coverage ancient human genomes, genotype imputation using Glimpse-v2 is suitable. Additionally, using the 1000 Genomes merged with Human Genome Diversity Panel improves the accuracy of imputation for the rare variants with low MAF, which might be important not only for ancient genomics but also for modern human genomic studies based on low coverage data and for haplotype-based analysis. Most importantly, we reveal that genotype imputation of low coverage ancient human genomes reduces the genetic affinity of the samples towards human reference genome. Through solving one of the most challenging biases in data analysis, so-called reference bias, genotype imputation using Glimpse v2 is promising for low coverage ancient human genomic data analysis and for rare-variant-based and haplotype-based analysis.},
}

@article {pmid39026955,
year = {2024},
author = {Worth, JRP and Kikuchi, S and Kanetani, S and Takahashi, D and Aizawa, M and Marchuk, EA and Choi, HJ and Polezhaeva, MA and Sheiko, VV and Ueno, S},
title = {Chloroplast genome-based genetic resources via genome skimming for the subalpine forests of Japan and adjacent regions.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e11584},
pmid = {39026955},
issn = {2045-7758},
abstract = {The Japanese subalpine zone is dominated by an ecologically important forest biome, subalpine coniferous forest, constituting a distinct assemblage of cold-tolerant angiosperm and conifer species. While being relatively intact compared to other forest biomes in Japan, subalpine coniferous forests are under significant threat from deer browsing, global warming and small population size effects. However, there is a severe lack of genetic resources available for this biome's major constituent plant species. This study aimed to develop chloroplast genome-based genetic resources for 12 widespread subalpine tree and shrub species (7 angiosperms and 5 conifers) via genome skimming of whole-genomic DNA using short reads (100-150 bp in length). For 10 species, whole chloroplast genomes were assembled via de novo-based methods from 4 to 10 individuals per species sampled from across their ranges in Japan and, for non-Japanese endemic species, elsewhere in northeast Asia. A total of 566 single nucleotide polymorphisms for Japanese samples and 768 for all samples (varying from 2 to 202 per species) were identified which were distributed in geographically restricted lineages in most species. In addition, between 9 and 58 polymorphic simple sequence repeat regions were identified per species. For two Ericaceae species (Rhododendron brachycarpum and Vaccinium vitis-idaea) characterised by large chloroplast genomes, de novo assembly failed, but single nucleotide polymorphisms could be identified using reference mapping. These data will be useful for genetic studies of species taxonomic relationships, investigating phylogeographic patterns within species, developing chloroplast-based markers for conservation genetic studies and has potential application for studies of environmental and ancient DNA.},
}

@article {pmid39018301,
year = {2024},
author = {Del Papa, M and De Los Reyes, M and Poiré, DG and Rascovan, N and Jofré, G and Delgado, M},
title = {Anthropic cut marks in extinct megafauna bones from the Pampean region (Argentina) at the last glacial maximum.},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0304956},
pmid = {39018301},
issn = {1932-6203},
mesh = {*Fossils ; Animals ; Argentina ; *Bone and Bones/anatomy & histology ; Humans ; *Extinction, Biological ; Xenarthra/anatomy & histology ; Paleontology ; Archaeology ; },
abstract = {The initial peopling of South America is a topic of intense archaeological debate. Among the most contentious issues remain the nature of the human-megafauna interaction and the possible role of humans, along with climatic change, in the extinction of several megamammal genera at the end of the Pleistocene. In this study, we present the analysis of fossil remains with cutmarks belonging to a specimen of Neosclerocalyptus (Xenarthra, Glyptodontidae), found on the banks of the Reconquista River, northeast of the Pampean region (Argentina), whose AMS 14C dating corresponds to the Last Glacial Maximum (21,090-20,811 cal YBP). Paleoenvironmental reconstructions, stratigraphic descriptions, absolute chronological dating of bone materials, and deposits suggest a relatively rapid burial event of the bone assemblage in a semi-dry climate during a wet season. Quantitative and qualitative analyses of the cut marks, reconstruction of butchering sequences, and assessments of the possible agents involved in the observed bone surface modifications indicate anthropic activities. Our results provide new elements for discussing the earliest peopling of southern South America and specifically for the interaction between humans and local megafauna in the Pampean region during the Last Glacial Maximum.},
}

*Fossils
Animals
Argentina
*Bone and Bones/anatomy & histology
Humans
*Extinction, Biological
Xenarthra/anatomy & histology
Paleontology
Archaeology

@article {pmid39013011,
year = {2024},
author = {Williams, MP and Flegontov, P and Maier, R and Huber, CD},
title = {Testing Times: Disentangling Admixture Histories in Recent and Complex Demographies using ancient DNA.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyae110},
pmid = {39013011},
issn = {1943-2631},
abstract = {Our knowledge of human evolutionary history has been greatly advanced by paleogenomics. Since the 2020s, the study of ancient DNA has increasingly focused on reconstructing the recent past. However, the accuracy of paleogenomic methods in resolving questions of historical and archaeological importance amidst the increased demographic complexity and decreased genetic differentiation remains an open question. We evaluated the performance and behavior of two commonly used methods, qpAdm and the f3-statistic, on admixture inference under a diversity of demographic models and data conditions. We performed two complementary simulation approaches - firstly exploring a wide demographic parameter space under four simple demographic models of varying complexities and configurations using branch-length data from two chromosomes - and secondly, we analyzed a model of Eurasian history composed of 59 populations using whole-genome data modified with ancient DNA conditions such as SNP ascertainment, data missingness, and pseudo-haploidization. We observe population differentiation is the primary factor driving qpAdm performance. Notably, whilst complex gene-flow histories influence which models are classified as plausible, they do not reduce overall performance. Under conditions reflective of the historical period, qpAdm most frequently identifies the true model as plausible amongst a small candidate set of closely related populations. To increase the utility for resolving fine-scaled hypotheses, we provide a heuristic for further distinguishing between candidate models that incorporates qpAdm model P-values and f3-statistics. Finally, we demonstrate a significant performance increase for qpAdm using whole-genome branch-length f2-statistics, highlighting the potential for improved demographic inference that could be achieved with future advancements in f-statistic estimations.},
}

@article {pmid39009303,
year = {2024},
author = {Shen, Q and Wu, Z and Zan, J and Yang, X and Guo, J and Ji, Z and Wang, B and Liu, Y and Mao, X and Wang, X and Zou, X and Zhou, H and Peng, Y and Ma, H and He, H and Bai, T and Xu, M and Wen, S and Jin, L and Zhang, Q and Wang, CC},
title = {Ancient genomes illuminate the demographic history of Shandong over the past two millennia.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2024.07.008},
pmid = {39009303},
issn = {1673-8527},
abstract = {Shandong province, located in the Lower Yellow River, is one of the birthplaces of ancient Chinese civilization. However, the comprehensive genetic histories of this region have remained largely unknown until now due to a lack of ancient human genomes. Here, we present 21 ancient genomes from Shandong dating from the Warring States period to the Jin-Yuan Dynasties. Unlike the early Neolithic samples from Shandong, the historical samples are most closely related to post-Late Neolithic populations of the Middle Yellow River Basin, suggesting a population turnover in Shandong from the Neolithic Age to the Historical era. In addition, we detect a close genetic affinity between the historical samples in Shandong and present-day Han Chinese, showing long-term genetic stability in Han Chinese at least since the Warring States period.},
}

@article {pmid39009302,
year = {2024},
author = {Yu, Y and Yang, X and Liu, D and Du, P and Meng, H and Huang, Z and Xiong, J and Ding, Y and Ren, X and Allen, E and Wang, H and Han, S and Jin, L and Wang, CC and Wen, S},
title = {Ancient genomic analysis of a Chinese hereditary elite from the Northern and Southern Dynasties.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2024.07.009},
pmid = {39009302},
issn = {1673-8527},
abstract = {China's Northern and Southern Dynasties period (3[rd]-6[th] centuries AD) marked a significant era of ethnic integration in northern China. However, previous ancient DNA studies have primarily focused on northern ethnic groups, with limited research on the genetic formation of the hereditary elite family, especially considering their abundant archaeological record and clear material identity. In this study, we obtained the ancient genome of a hereditary elite family, Gao Bin (, 503-572 AD), at 0.6473-fold coverage with 475132 single-nucleotide polymorphisms (SNPs) on the 1240k panel. His mitochondrial haplogroup belonged to Z4 and Y-haplogroup to O1a1a2b-F2444*. The genetic profile of Gao Bin was most similar to that of the northern Han Chinese. He could be modelled as deriving all his ancestry from Late Neolithic to Iron Age Yellow River farmers without influence from Northeast Asia, Korea, or the Mongolian Plateau. Our study sheds light on the genetic formation of hereditary elite families in the context of the Southern and Northern Dynasties ethnic integration.},
}

@article {pmid39002897,
year = {2024},
author = {Du, S and Chen, J and Li, J and Qian, W and Wu, S and Peng, Q and Liu, Y and Pan, T and Li, Y and Hadi, SS and Tan, J and Yuan, Z and Wang, J and Tang, K and Wang, Z and Wen, Y and Dong, X and Zhou, W and Ruiz-Linares, A and Shi, Y and Jin, L and Liu, F and Zhang, M and Wang, S},
title = {A multi-ancestry GWAS meta-analysis of facial features and its application in predicting archaic human features.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2024.07.005},
pmid = {39002897},
issn = {1673-8527},
abstract = {Facial morphology, a complex trait influenced by genetics, holds great significance in evolutionary research. However, due to limited fossil evidence, the facial characteristics of Neanderthals and Denisovans have remained largely unknown. In this study, we conducted a large-scale multi-ethnic meta-analysis of Genome-Wide Association Study (GWAS), including 9674 East Asians and 10,115 Europeans, quantitatively assessing 78 facial traits using 3D facial images. We identified 71 genomic loci associated with facial features, including 21 novel loci. We developed a facial polygenic score (FPS) that enables the prediction of facial features based on genetic information. Interestingly, the distribution of FPSs among populations from diverse continental groups exhibited significant correlations with observed facial features. Furthermore, we applied the FPS to predict the facial traits of seven Neanderthals and one Denisovan using ancient DNA, and aligned predictions with the fossil records. Our results suggested that Neanderthals and Denisovans likely shared similar facial features, such as a wider but shorter nose and a wider endocanthion distance. The decreased mouth width was characterized specifically in Denisovan. The integration of genomic data and facial trait analysis provides valuable insights into the evolutionary history and adaptive changes in human facial morphology.},
}

@article {pmid38996487,
year = {2024},
author = {Sandoval-Velasco, M and Dudchenko, O and Rodríguez, JA and Pérez Estrada, C and Dehasque, M and Fontsere, C and Mak, SST and Khan, R and Contessoto, VG and Oliveira Junior, AB and Kalluchi, A and Zubillaga Herrera, BJ and Jeong, J and Roy, RP and Christopher, I and Weisz, D and Omer, AD and Batra, SS and Shamim, MS and Durand, NC and O'Connell, B and Roca, AL and Plikus, MV and Kusliy, MA and Romanenko, SA and Lemskaya, NA and Serdyukova, NA and Modina, SA and Perelman, PL and Kizilova, EA and Baiborodin, SI and Rubtsov, NB and Machol, G and Rath, K and Mahajan, R and Kaur, P and Gnirke, A and Garcia-Treviño, I and Coke, R and Flanagan, JP and Pletch, K and Ruiz-Herrera, A and Plotnikov, V and Pavlov, IS and Pavlova, NI and Protopopov, AV and Di Pierro, M and Graphodatsky, AS and Lander, ES and Rowley, MJ and Wolynes, PG and Onuchic, JN and Dalén, L and Marti-Renom, MA and Gilbert, MTP and Aiden, EL},
title = {Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.},
journal = {Cell},
volume = {187},
number = {14},
pages = {3541-3562.e51},
doi = {10.1016/j.cell.2024.06.002},
pmid = {38996487},
issn = {1097-4172},
support = {R35 GM147467/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Mammoths/genetics ; *Genome/genetics ; Female ; *Skin ; Elephants/genetics ; Chromatin/genetics ; Fossils ; DNA, Ancient/analysis ; Mice ; Humans ; X Chromosome/genetics ; },
abstract = {Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth's death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.},
}

Animals
*Mammoths/genetics
*Genome/genetics
Female
*Skin
Elephants/genetics
Chromatin/genetics
Fossils
DNA, Ancient/analysis
Mice
Humans
X Chromosome/genetics

@article {pmid38996465,
year = {2024},
author = {Sawchuk, EA and Sirak, KA and Manthi, FK and Ndiema, EK and Ogola, CA and Prendergast, ME and Reich, D and Aluvaala, E and Ayodo, G and Badji, L and Bird, N and Black, W and Fregel, R and Gachihi, N and Gibbon, VE and Gidna, A and Goldstein, ST and Hamad, R and Hassan, HY and Hayes, VM and Hellenthal, G and Kebede, S and Kurewa, A and Kusimba, C and Kyazike, E and Lane, PJ and MacEachern, S and Massilani, D and Mbua, E and Morris, AG and Mutinda, C and M'Mbogori, FN and Reynolds, AW and Tishkoff, S and Vilar, M and Yimer, G},
title = {Charting a landmark-driven path forward for population genetics and ancient DNA research in Africa.},
journal = {American journal of human genetics},
volume = {111},
number = {7},
pages = {1243-1251},
pmid = {38996465},
issn = {1537-6605},
mesh = {Humans ; *DNA, Ancient/analysis ; *Genetics, Population ; Africa ; Genomics ; Black People/genetics ; },
abstract = {Population history-focused DNA and ancient DNA (aDNA) research in Africa has dramatically increased in the past decade, enabling increasingly fine-scale investigations into the continent's past. However, while international interest in human genomics research in Africa grows, major structural barriers limit the ability of African scholars to lead and engage in such research and impede local communities from partnering with researchers and benefitting from research outcomes. Because conversations about research on African people and their past are often held outside Africa and exclude African voices, an important step for African DNA and aDNA research is moving these conversations to the continent. In May 2023 we held the DNAirobi workshop in Nairobi, Kenya and here we synthesize what emerged most prominently in our discussions. We propose an ideal vision for population history-focused DNA and aDNA research in Africa in ten years' time and acknowledge that to realize this future, we need to chart a path connecting a series of "landmarks" that represent points of consensus in our discussions. These include effective communication across multiple audiences, reframed relationships and capacity building, and action toward structural changes that support science and beyond. We concluded there is no single path to creating an equitable and self-sustaining research ecosystem, but rather many possible routes linking these landmarks. Here we share our diverse perspectives as geneticists, anthropologists, archaeologists, museum curators, and educators to articulate challenges and opportunities for African DNA and aDNA research and share an initial map toward a more inclusive and equitable future.},
}

Humans
*DNA, Ancient/analysis
*Genetics, Population
Africa
Genomics
Black People/genetics

@article {pmid38993187,
year = {2023},
author = {Meng, XY and Wang, QL and Shi, MJ and Zhang, HY},
title = {Historical Pathogen-Driven Selection May Contribute to Contemporary Ethnic Difference in Bladder Cancer Susceptibility.},
journal = {Bladder cancer (Amsterdam, Netherlands)},
volume = {9},
number = {3},
pages = {211-216},
pmid = {38993187},
issn = {2352-3735},
abstract = {BACKGROUND: The rationale for ethnic differences in bladder cancer (BCa) susceptibility is an important open question. In this study, we raised the hypothesis that the APOBEC3-rs1014971 variant associated with BCa risk and APOBEC-mutagenesis probably contribute to ethnic differences.

METHODS: We calculated the ethnicity-stratified 5-year age-adjusted incidence rates of BCa using the US SEER database. We performed somatic mutational-signature analyses and compared the APOBEC-related mutational contribution across BCa tumors in patients of different ethnicities. We analyzed the allele frequency distribution of APOBEC3-related rs1014971 in contemporary populations of different ethnicities and in ancient human genomes. We also analyzed the natural selection profiles and ages of the investigated SNPs.

RESULTS: We validated the ethnic difference in BCa risk using US SEER data, revealing Caucasians to be at >2-fold greater risk than Asians / Pacific islanders. In contemporary populations, we observed a coherent ethnic distribution in terms not only of the allele frequency of APOBEC3-related rs1014971, but also the mutational contribution of APOBEC-mediated mutagenesis in BCa tumors. Population genetics and ancient genome analyses further suggested that the diverse ethnic distribution of rs1014971 could be rooted in human evolution.

CONCLUSIONS: It is possible that APOBEC3-related rs1014971 is involved in the different BCa incidence across ethnic groups, and this difference is potentially derived from human evolution. Our findings suggested an evolutionary link between contemporary population-level variations in malignancy susceptibility and pathogen-driven selection in the past, not unlike previously reported cases of certain autoimmune and metabolic disorders.},
}

@article {pmid38987254,
year = {2024},
author = {Bergström, A},
title = {Improving data archiving practices in ancient genomics.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {754},
pmid = {38987254},
issn = {2052-4463},
mesh = {*Genomics ; Humans ; *DNA, Ancient/analysis ; Animals ; Metadata ; },
abstract = {Ancient DNA is producing a rich record of past genetic diversity in humans and other species. However, unless the primary data is appropriately archived, its long-term value will not be fully realised. I surveyed publicly archived data from 42 recent ancient genomics studies. Half of the studies archived incomplete datasets, preventing accurate replication and representing a loss of data of potential future use. No studies met all criteria that could be considered best practice. Based on these results, I make six recommendations for data producers: (1) archive all sequencing reads, not just those that aligned to a reference genome, (2) archive read alignments too, but as secondary analysis files, (3) provide correct experiment metadata on samples, libraries and sequencing runs, (4) provide informative sample metadata, (5) archive data from low-coverage and negative experiments, and (6) document archiving choices in papers, and peer review these. Given the reliance on destructive sampling of finite material, ancient genomics studies have a particularly strong responsibility to ensure the longevity and reusability of generated data.},
}

*Genomics
Humans
*DNA, Ancient/analysis
Animals
Metadata

@article {pmid38986104,
year = {2024},
author = {Jordan, B},
title = {[Ancient DNA speaks].},
journal = {Medecine sciences : M/S},
volume = {40},
number = {6-7},
pages = {563-565},
doi = {10.1051/medsci/2024070},
pmid = {38986104},
issn = {1958-5381},
mesh = {Humans ; *DNA, Ancient/analysis ; Sequence Analysis, DNA/methods ; Pedigree ; },
abstract = {Many human DNA sequences have been obtained from ancient remains dating back from several millennia. However, these have low coverage and may contain many errors; this has limited their usefulness for many analyses, in particular the search for Identical By Descent (IBD) segments that is very powerful for detection of kinship. A new method, using imputation from database data and sophisticated statistical analysis, proves able to detect IBD segments (and thus parenthood) in low-quality DNA sequences from individuals linked only by sixth degree parenthood, opening a whole new field of investigation using ancient DNA.},
}

Humans
*DNA, Ancient/analysis
Sequence Analysis, DNA/methods
Pedigree

@article {pmid38981530,
year = {2024},
author = {Goldstein, ST and Mueller, NG and Janzen, A and Ogola, C and Dal Martello, R and Fernandes, R and Li, S and Iminjili, V and Juengst, S and Odera Otwani, A and Sawchuk, EA and Wang, K and Ndiema, E and Boivin, N},
title = {Early agriculture and crop transitions at Kakapel Rockshelter in the Lake Victoria region of eastern Africa.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2026},
pages = {20232747},
doi = {10.1098/rspb.2023.2747},
pmid = {38981530},
issn = {1471-2954},
support = {//Max-Planck-Institut für Menschheitsgeschichte/ ; },
mesh = {*Crops, Agricultural ; Kenya ; *Archaeology ; *Agriculture ; Animals ; Radiometric Dating ; Africa, Eastern ; },
abstract = {The histories of African crops remain poorly understood despite their contemporary importance. Integration of crops from western, eastern and northern Africa probably first occurred in the Great Lakes Region of eastern Africa; however, little is known about when and how these agricultural systems coalesced. This article presents archaeobotanical analyses from an approximately 9000-year archaeological sequence at Kakapel Rockshelter in western Kenya, comprising the largest and most extensively dated archaeobotanical record from the interior of equatorial eastern Africa. Direct radiocarbon dates on carbonized seeds document the presence of the West African crop cowpea (Vigna unguiculata (L.) Walp) approximately 2300 years ago, synchronic with the earliest date for domesticated cattle (Bos taurus). Peas (Pisum sativum L. or Pisum abyssinicum A. Braun) and sorghum (Sorghum bicolor (L.) Moench) from the northeast and eastern African finger millet (Eleusine coracana (L.) Gaertn.) are incorporated later, by at least 1000 years ago. Combined with ancient DNA evidence from Kakapel and the surrounding region, these data support a scenario in which the use of diverse domesticated species in eastern Africa changed over time rather than arriving and being maintained as a single package. Findings highlight the importance of local heterogeneity in shaping the spread of food production in sub-Saharan Africa.},
}

*Crops, Agricultural
Kenya
*Archaeology
*Agriculture
Animals
Radiometric Dating
Africa, Eastern

@article {pmid38976766,
year = {2024},
author = {Souilmi, Y and Wasef, S and Williams, MP and Conroy, G and Bar, I and Bover, P and Dann, J and Heiniger, H and Llamas, B and Ogbourne, S and Archer, M and Ballard, JWO and Reed, E and Tobler, R and Koungoulos, L and Walshe, K and Wright, JL and Balme, J and O'Connor, S and Cooper, A and Mitchell, KJ},
title = {Ancient genomes reveal over two thousand years of dingo population structure.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {30},
pages = {e2407584121},
pmid = {38976766},
issn = {1091-6490},
support = {CE170100015//Department of Education and Training | Australian Research Council (ARC)/ ; DP210101960//Department of Education and Training | Australian Research Council (ARC)/ ; FL140100260//Department of Education and Training | Australian Research Council (ARC)/ ; 2021/GNT2011277//DHAC | National Health and Medical Research Council (NHMRC)/ ; },
mesh = {Animals ; Australia ; *Genome ; Dogs/genetics ; Wolves/genetics ; DNA, Ancient/analysis ; Genetics, Population ; },
abstract = {Dingoes are culturally and ecologically important free-living canids whose ancestors arrived in Australia over 3,000 B.P., likely transported by seafaring people. However, the early history of dingoes in Australia-including the number of founding populations and their routes of introduction-remains uncertain. This uncertainty arises partly from the complex and poorly understood relationship between modern dingoes and New Guinea singing dogs, and suspicions that post-Colonial hybridization has introduced recent domestic dog ancestry into the genomes of many wild dingo populations. In this study, we analyzed genome-wide data from nine ancient dingo specimens ranging in age from 400 to 2,746 y old, predating the introduction of domestic dogs to Australia by European colonists. We uncovered evidence that the continent-wide population structure observed in modern dingo populations had already emerged several thousand years ago. We also detected excess allele sharing between New Guinea singing dogs and ancient dingoes from coastal New South Wales (NSW) compared to ancient dingoes from southern Australia, irrespective of any post-Colonial hybrid ancestry in the genomes of modern individuals. Our results are consistent with several demographic scenarios, including a scenario where the ancestry of dingoes from the east coast of Australia results from at least two waves of migration from source populations with varying affinities to New Guinea singing dogs. We also contribute to the growing body of evidence that modern dingoes derive little genomic ancestry from post-Colonial hybridization with other domestic dog lineages, instead descending primarily from ancient canids introduced to Sahul thousands of years ago.},
}

Animals
Australia
*Genome
Dogs/genetics
Wolves/genetics
DNA, Ancient/analysis
Genetics, Population

@article {pmid38969261,
year = {2024},
author = {Wang, M and Chen, H and Luo, L and Huang, Y and Duan, S and Yuan, H and Tang, R and Liu, C and He, G},
title = {Forensic investigative genetic genealogy: expanding pedigree tracing and genetic inquiry in the genomic era.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgg.2024.06.016},
pmid = {38969261},
issn = {1673-8527},
abstract = {Genetic genealogy provides crucial insights into the complex biological relationships within contemporary and ancient human populations by analyzing shared alleles and chromosomal segments that are identical by descent, to understand kinship, migration patterns, and population dynamics. Within forensic science, forensic investigative genetic genealogy (FIGG) has gained prominence by leveraging next-generation sequencing technologies and population-specific genomic resources, opening new investigative avenues. In this review, we synthesize current knowledge, underscore recent advancements, and discuss the growing role of FIGG in forensic genomics. FIGG has been pivotal in revitalizing dormant inquiries and offering new genetic leads in numerous cold cases. Its effectiveness relies on the extensive SNP profiles contributed by individuals from diverse populations to specialized genomic databases. Advances in computational genomics and the growth of human genomic databases have spurred a profound shift in the application of genetic genealogy across forensics, anthropology, and ancient DNA studies. As the field progresses, FIGG is evolving from a nascent practice into a more sophisticated and specialized discipline, shaping the future of forensic investigations.},
}

@article {pmid38965340,
year = {2024},
author = {Gibbon, VE and Thompson, JC and Alves, S},
title = {Informed proxy consent for ancient DNA research.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {815},
pmid = {38965340},
issn = {2399-3642},
mesh = {Humans ; *Informed Consent ; *DNA, Ancient/analysis ; },
abstract = {We argue for implementation of informed proxy or relational autonomy consent in human aDNA research, where the deceased may be represented by living people the research affects. Embracing the underlying principles and process of informed proxy consent has the potential to transform research by (1) enriching outcomes by learning from and collaborating with interested and affected persons; (2) empowering people potentially impacted by research to stipulate evidence for information flow; (3) guarding researchers against actual or perceived violations by providing a common set of guidelines; and (4) highlighting the essential nature of long-term consultation and community partnerships to research outcome success.},
}

Humans
*Informed Consent
*DNA, Ancient/analysis

@article {pmid38963678,
year = {2024},
author = {Coppola Bove, L and Kirkpatrick, CL and Vigil-Escalera Guirado, A and Botella López, MC and Bos, KI},
title = {A morphological and molecular approach to investigating infectious disease in early medieval Iberia: The necropolis of La Olmeda (Palencia, Spain).},
journal = {American journal of biological anthropology},
volume = {},
number = {},
pages = {e24994},
doi = {10.1002/ajpa.24994},
pmid = {38963678},
issn = {2692-7691},
support = {805268/ERC_/European Research Council/International ; //Erasmus+ Traineeship Program Scholarship/ ; //Junta de Andalucía and SEPIE/ ; 756-2023-0246//Social Sciences and Humanities Research Council of Canada Postdoctoral Fellowship/ ; },
abstract = {OBJECTIVE: Here we investigate infectious diseases that potentially contribute to osteological lesions in individuals from the early medieval necropolis of La Olmeda (6th-11th c. CE) in North Iberia.

MATERIALS AND METHODS: We studied a minimum number of 268 individuals (33 adult females; 38 adult males, 77 unknown/indeterminate sex; and 120 non-adults), including articulated and commingled remains. Individuals with differential diagnoses suggesting chronic systemic infectious diseases were sampled and bioinformatically screened for ancient pathogen DNA.

RESULTS: Five non-adults (and no adults) presented skeletal evidence of chronic systemic infectious disease (1.87% of the population; 4.67% of non-adults). The preferred diagnoses for these individuals included tuberculosis, brucellosis, and malaria. Ancient DNA fragments assigned to the malaria-causing pathogen, Plasmodium spp., were identified in three of the five individuals. Observed pathology includes lesions generally consistent with malaria; however, additional lesions in two of the individuals may represent hitherto unknown variation in the skeletal manifestation of this disease or co-infection with tuberculosis or brucellosis. Additionally, spondylolysis was observed in one individual with skeletal lesions suggestive of infectious disease.

CONCLUSIONS: This study sheds light on the pathological landscape in Iberia during a time of great social, demographic, and environmental change. Genetic evidence challenges the hypothesis that malaria was absent from early medieval Iberia and demonstrates the value of combining osteological and archaeogenetic methods. Additionally, all of the preferred infectious diagnoses for the individuals included in this study (malaria, tuberculosis, and brucellosis) could have contributed to the febrile cases described in historical sources from this time.},
}

@article {pmid38960861,
year = {2024},
author = {Dolenz, S and van der Valk, T and Jin, C and Oppenheimer, J and Sharif, MB and Orlando, L and Shapiro, B and Dalén, L and Heintzman, PD},
title = {Unravelling reference bias in ancient DNA datasets.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {7},
pages = {},
pmid = {38960861},
issn = {1367-4811},
support = {2021.0048//Knut and Alice Wallenberg Foundation/ ; },
mesh = {*DNA, Ancient/analysis ; Humans ; *Sequence Analysis, DNA/methods ; Software ; Animals ; Sequence Alignment/methods ; Computational Biology/methods ; Algorithms ; },
abstract = {MOTIVATION: The alignment of sequencing reads is a critical step in the characterization of ancient genomes. However, reference bias and spurious mappings pose a significant challenge, particularly as cutting-edge wet lab methods generate datasets that push the boundaries of alignment tools. Reference bias occurs when reference alleles are favoured over alternative alleles during mapping, whereas spurious mappings stem from either contamination or when endogenous reads fail to align to their correct position. Previous work has shown that these phenomena are correlated with read length but a more thorough investigation of reference bias and spurious mappings for ancient DNA has been lacking. Here, we use a range of empirical and simulated palaeogenomic datasets to investigate the impacts of mapping tools, quality thresholds, and reference genome on mismatch rates across read lengths.

RESULTS: For these analyses, we introduce AMBER, a new bioinformatics tool for assessing the quality of ancient DNA mapping directly from BAM-files and informing on reference bias, read length cut-offs and reference selection. AMBER rapidly and simultaneously computes the sequence read mapping bias in the form of the mismatch rates per read length, cytosine deamination profiles at both CpG and non-CpG sites, fragment length distributions, and genomic breadth and depth of coverage. Using AMBER, we find that mapping algorithms and quality threshold choices dictate reference bias and rates of spurious alignment at different read lengths in a predictable manner, suggesting that optimized mapping parameters for each read length will be a key step in alleviating reference bias and spurious mappings.

AMBER is available for noncommercial use on GitHub (https://github.com/tvandervalk/AMBER.git). Scripts used to generate and analyse simulated datasets are available on Github (https://github.com/sdolenz/refbias_scripts).},
}

*DNA, Ancient/analysis
Humans
*Sequence Analysis, DNA/methods
Software
Animals
Sequence Alignment/methods
Computational Biology/methods
Algorithms

@article {pmid38957694,
year = {2024},
author = {Mousavi-Derazmahalleh, M and Haue, N and Kanstrup, M and Laursen, JT and Lukehurst, SS and Kveiborg, J and Allentoft, ME},
title = {Far away from home? Ancient DNA shows the presence of bicolored shrew (Crocidura leucodon) in Bronze Age Denmark.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e11680},
pmid = {38957694},
issn = {2045-7758},
abstract = {An excavation of an Early Iron Age village near Aalborg in Denmark uncovered the jaws and skull fragments from a small mammal that were morphologically identified to the genus Crocidura (white-toothed shrews). Three Crocidura species are known from prehistoric continental Europe but none of them are distributed in Scandinavia, which is why this surprising finding warranted further analyses. The bone was radiocarbon-dated to 2840-2750 calibrated years before present (cal. BP), corresponding to the Late Bronze Age and hence earlier than the Iron Age archeological context in which it was found. Using highly optimized ancient DNA protocols, we extracted DNA from one tooth and shotgun-sequenced the sample to reconstruct a near-complete mitochondrial reference genome (17,317 bp, 32.6× coverage). Phylogenetic analyses determined this specimen as a bicolored shrew (Crocidura leucodon) but with a phylogenetic position basal to the clade of known sequences from this species. The confirmation of Crocidura presence in Denmark by the Late Bronze Age sheds new light on the prehistoric natural history of Scandinavia. We discuss the implications of this finding from both zoo-archeological and ecological perspectives. Furthermore, the mitochondrial genome reconstructed in this study offers a valuable resource for future research exploring the genetic makeup and evolutionary history of Eurasian shrew populations.},
}

@article {pmid38957308,
year = {2024},
author = {Çokoğlu, SS and Koptekin, D and Fidan, FR and Somel, M},
title = {Investigating food production-associated DNA methylation changes in paleogenomes: Lack of consistent signals beyond technical noise.},
journal = {Evolutionary applications},
volume = {17},
number = {7},
pages = {e13743},
pmid = {38957308},
issn = {1752-4571},
abstract = {The Neolithic transition introduced major diet and lifestyle changes to human populations across continents. Beyond well-documented bioarcheological and genetic effects, whether these changes also had molecular-level epigenetic repercussions in past human populations has been an open question. In fact, methylation signatures can be inferred from UDG-treated ancient DNA through postmortem damage patterns, but with low signal-to-noise ratios; it is thus unclear whether published paleogenomes would provide the necessary resolution to discover systematic effects of lifestyle and diet shifts. To address this we compiled UDG-treated shotgun genomes of 13 pre-Neolithic hunter-gatherers (HGs) and 21 Neolithic farmers (NFs) individuals from West and North Eurasia, published by six different laboratories and with coverage c.1×-58× (median = 9×). We used epiPALEOMIX and a Monte Carlo normalization scheme to estimate methylation levels per genome. Our paleomethylome dataset showed expected genome-wide methylation patterns such as CpG island hypomethylation. However, analyzing the data using various approaches did not yield any systematic signals for subsistence type, genetic sex, or tissue effects. Comparing the HG-NF methylation differences in our dataset with methylation differences between hunter-gatherers versus farmers in modern-day Central Africa also did not yield consistent results. Meanwhile, paleomethylome profiles did cluster strongly by their laboratories of origin. Using larger data volumes, minimizing technical noise and/or using alternative protocols may be necessary for capturing subtle environment-related biological signals from paleomethylomes.},
}

@article {pmid38948161,
year = {2024},
author = {Özdoğan, KT and Gelabert, P and Hammers, N and Altınışık, NE and de Groot, A and Plets, G},
title = {Archaeology meets environmental genomics: implementing sedaDNA in the study of the human past.},
journal = {Archaeological and anthropological sciences},
volume = {16},
number = {7},
pages = {108},
pmid = {38948161},
issn = {1866-9557},
abstract = {Sedimentary ancient DNA (sedaDNA) has become one of the standard applications in the field of paleogenomics in recent years. It has been used for paleoenvironmental reconstructions, detecting the presence of prehistoric species in the absence of macro remains and even investigating the evolutionary history of a few species. However, its application in archaeology has been limited and primarily focused on humans. This article argues that sedaDNA holds significant potential in addressing key archaeological questions concerning the origins, lifestyles, and environments of past human populations. Our aim is to facilitate the integration of sedaDNA into the standard workflows in archaeology as a transformative tool, thereby unleashing its full potential for studying the human past. Ultimately, we not only underscore the challenges inherent in the sedaDNA field but also provide a research agenda for essential enhancements needed for implementing sedaDNA into the archaeological workflow.},
}

@article {pmid38946459,
year = {2024},
author = {Özkan, M and Gürün, K and Yüncü, E and Vural, KB and Atağ, G and Akbaba, A and Fidan, FR and Sağlıcan, E and Altınışık, EN and Koptekin, D and Pawłowska, K and Hodder, I and Adcock, SE and Arbuckle, BS and Steadman, SR and McMahon, G and Erdal, YS and Bilgin, CC and Togan, İ and Geigl, EM and Götherström, A and Grange, T and Özer, F and Somel, M},
title = {The first complete genome of the extinct European wild ass (Equus hemionus hydruntinus).},
journal = {Molecular ecology},
volume = {33},
number = {14},
pages = {e17440},
doi = {10.1111/mec.17440},
pmid = {38946459},
issn = {1365-294X},
support = {772390//European Research Council Consolidator Grant H2020/ ; 952317//European Commission Horizon 2020 TWINNING Programme/ ; 117Z991//Türkiye Bilimsel ve Teknolojik Araştırma Kurumu/ ; },
mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Haplotypes/genetics ; *Phylogeny ; *Gene Flow ; Equidae/genetics ; Genome, Mitochondrial ; Extinction, Biological ; Fossils ; Genetics, Population ; Genetic Variation ; },
abstract = {We present palaeogenomes of three morphologically unidentified Anatolian equids dating to the first millennium BCE, sequenced to a coverage of 0.6-6.4×. Mitochondrial DNA haplotypes of the Anatolian individuals clustered with those of Equus hydruntinus (or Equus hemionus hydruntinus), the extinct European wild ass, secular name 'hydruntine'. Further, the Anatolian wild ass whole genome profiles fell outside the genomic diversity of other extant and past Asiatic wild ass (E. hemionus) lineages. These observations suggest that the three Anatolian wild asses represent hydruntines, making them the latest recorded survivors of this lineage, about a millennium later than the latest observations in the zooarchaeological record. Our mitogenomic and genomic analyses indicate that E. h. hydruntinus was a clade belonging to ancient and present-day E. hemionus lineages that radiated possibly between 0.6 and 0.8 Mya. We also find evidence consistent with recent gene flow between hydruntines and Middle Eastern wild asses. Analyses of genome-wide heterozygosity and runs of homozygosity suggest that the Anatolian wild ass population may have lost genetic diversity by the mid-first millennium BCE, a possible sign of its eventual demise.},
}

Animals
*DNA, Mitochondrial/genetics
*Haplotypes/genetics
*Phylogeny
*Gene Flow
Equidae/genetics
Genome, Mitochondrial
Extinction, Biological
Fossils
Genetics, Population
Genetic Variation

@article {pmid38942016,
year = {2024},
author = {Dehasque, M and Morales, HE and Díez-Del-Molino, D and Pečnerová, P and Chacón-Duque, JC and Kanellidou, F and Muller, H and Plotnikov, V and Protopopov, A and Tikhonov, A and Nikolskiy, P and Danilov, GK and Giannì, M and van der Sluis, L and Higham, T and Heintzman, PD and Oskolkov, N and Gilbert, MTP and Götherström, A and van der Valk, T and Vartanyan, S and Dalén, L},
title = {Temporal dynamics of woolly mammoth genome erosion prior to extinction.},
journal = {Cell},
volume = {187},
number = {14},
pages = {3531-3540.e13},
doi = {10.1016/j.cell.2024.05.033},
pmid = {38942016},
issn = {1097-4172},
mesh = {Animals ; *Mammoths/genetics ; *Extinction, Biological ; *Genome/genetics ; *Mutation ; Siberia ; Phylogeny ; Evolution, Molecular ; Time Factors ; },
abstract = {A number of species have recently recovered from near-extinction. Although these species have avoided the immediate extinction threat, their long-term viability remains precarious due to the potential genetic consequences of population declines, which are poorly understood on a timescale beyond a few generations. Woolly mammoths (Mammuthus primigenius) became isolated on Wrangel Island around 10,000 years ago and persisted for over 200 generations before becoming extinct around 4,000 years ago. To study the evolutionary processes leading up to the mammoths' extinction, we analyzed 21 Siberian woolly mammoth genomes. Our results show that the population recovered quickly from a severe bottleneck and remained demographically stable during the ensuing six millennia. We find that mildly deleterious mutations gradually accumulated, whereas highly deleterious mutations were purged, suggesting ongoing inbreeding depression that lasted for hundreds of generations. The time-lag between demographic and genetic recovery has wide-ranging implications for conservation management of recently bottlenecked populations.},
}

Animals
*Mammoths/genetics
*Extinction, Biological
*Genome/genetics
*Mutation
Siberia
Phylogeny
Evolution, Molecular
Time Factors

@article {pmid38932149,
year = {2024},
author = {Ferreira, RC and Alves, GV and Ramon, M and Antoneli, F and Briones, MRS},
title = {Reconstructing Prehistoric Viral Genomes from Neanderthal Sequencing Data.},
journal = {Viruses},
volume = {16},
number = {6},
pages = {},
pmid = {38932149},
issn = {1999-4915},
support = {20/08943-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 311154/2021-2//National Council for Scientific and Technological Development/ ; },
mesh = {Animals ; *Neanderthals/genetics/virology ; *Genome, Viral ; *DNA, Ancient/analysis ; Evolution, Molecular ; DNA, Viral/genetics ; Sequence Analysis, DNA/methods ; Humans ; Phylogeny ; DNA Viruses/genetics/classification/isolation & purification ; Fossils/virology ; },
abstract = {DNA viruses that produce persistent infections have been proposed as potential causes for the extinction of Neanderthals, and, therefore, the identification of viral genome remnants in Neanderthal sequence reads is an initial step to address this hypothesis. Here, as proof of concept, we searched for viral remnants in sequence reads of Neanderthal genome data by mapping to adenovirus, herpesvirus and papillomavirus, which are double-stranded DNA viruses that may establish lifelong latency and can produce persistent infections. The reconstructed ancient viral genomes of adenovirus, herpesvirus and papillomavirus revealed conserved segments, with nucleotide identity to extant viral genomes and variable regions in coding regions with substantial divergence to extant close relatives. Sequence reads mapped to extant viral genomes showed deamination patterns of ancient DNA, and these ancient viral genomes showed divergence consistent with the age of these samples (≈50,000 years) and viral evolutionary rates (10[-5] to 10[-8] substitutions/site/year). Analysis of random effects showed that the Neanderthal mapping to genomes of extant persistent viruses is above what is expected by random similarities of short reads. Also, negative control with a nonpersistent DNA virus does not yield statistically significant assemblies. This work demonstrates the feasibility of identifying viral genome remnants in archaeological samples with signal-to-noise assessment.},
}

Animals
*Neanderthals/genetics/virology
*Genome, Viral
*DNA, Ancient/analysis
Evolution, Molecular
DNA, Viral/genetics
Sequence Analysis, DNA/methods
Humans
Phylogeny
DNA Viruses/genetics/classification/isolation & purification
Fossils/virology

@article {pmid38929847,
year = {2024},
author = {Puga, M and Serrano, JG and García, EL and González Carracedo, MA and Jiménez-Canino, R and Pino-Yanes, M and Karlsson, R and Sullivan, PF and Fregel, R},
title = {El Hierro Genome Study: A Genomic and Health Study in an Isolated Canary Island Population.},
journal = {Journal of personalized medicine},
volume = {14},
number = {6},
pages = {},
pmid = {38929847},
issn = {2075-4426},
support = {D0886501//Swedish Research Council/ ; PID2021-123080NB-I00//Spanish Ministry of Science, Innovation, and Universities/ ; RYC-2015-17205//Spanish Ministry of Science, Innovation, and Universities/ ; },
abstract = {El Hierro is the smallest and westernmost island of the Canary Islands, whose population derives from an admixture of different ancestral components and that has been subjected to genetic isolation. We established the "El Hierro Genome Study" to characterize the health status and the genetic composition of ~10% of the current population of the island, accounting for a total of 1054 participants. Detailed demographic and clinical data and a blood sample for DNA extraction were obtained from each participant. Genomic genotyping was performed with the Global Screening Array (Illumina). The genetic composition of El Hierro was analyzed in a subset of 416 unrelated individuals by characterizing the mitochondrial DNA (mtDNA) and Y-chromosome haplogroups and performing principal component analyses (PCAs). In order to explore signatures of isolation, runs of homozygosity (ROHs) were also estimated. Among the participants, high blood pressure, hypercholesterolemia, and diabetes were the most prevalent conditions. The most common mtDNA haplogroups observed were of North African indigenous origin, while the Y-chromosome ones were mainly European. The PCA showed that the El Hierro population clusters near 1000 Genomes' European population but with a shift toward African populations. Moreover, the ROH analysis revealed some individuals with an important portion of their genomes with ROHs exceeding 400 Mb. Overall, these results confirmed that the "El Hierro Genome" cohort offers an opportunity to study the genetic basis of several diseases in an unexplored isolated population.},
}

@article {pmid38927726,
year = {2024},
author = {Zhu, S and Zhang, N and Zhang, J and Shao, X and Guo, Y and Cai, D},
title = {Ancient Mitochondrial Genomes Provide New Clues in the History of the Akhal-Teke Horse in China.},
journal = {Genes},
volume = {15},
number = {6},
pages = {},
pmid = {38927726},
issn = {2073-4425},
support = {NO.17ZDA221//Major Project of the National Social Science Foundation of China/ ; NO.2020YFC1521606//National Key Research and Development Program of China/ ; NO. 2022M722460//Project funded by China Postdoctoral Science Foundation/ ; NO. 2022CXTD17//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Animals ; Horses/genetics ; *Genome, Mitochondrial/genetics ; China ; *DNA, Ancient/analysis ; *Haplotypes ; DNA, Mitochondrial/genetics ; Phylogeny ; History, Ancient ; High-Throughput Nucleotide Sequencing ; Domestication ; },
abstract = {This study analyzed ancient DNA from the remains of horses unearthed from the Shihuyao tombs. These were found to date from the Han and Tang Dynasties in Xinjiang (approximately 2200 to 1100 years ago). Two high-quality mitochondrial genomes were acquired and analyzed using next-generation sequencing. The genomes were split into two maternal haplogroups, B and D, according to a study that included ancient and contemporary samples from Eurasia. A close genetic affinity was observed between the horse of the Tang Dynasty and Akhal-Teke horses according to the primitive horse haplotype G1. Historical evidence suggests that the ancient Silk Road had a vital role in their dissemination. Additionally, the matrilineal history of the Akhal-Teke horse was accessed and suggested that the early domestication of the breed was for military purposes.},
}

Animals
Horses/genetics
*Genome, Mitochondrial/genetics
China
*DNA, Ancient/analysis
*Haplotypes
DNA, Mitochondrial/genetics
Phylogeny
History, Ancient
High-Throughput Nucleotide Sequencing
Domestication

@article {pmid38927608,
year = {2024},
author = {Di Stefano, B and Zupanič Pajnič, I and Concato, M and Bertoglio, B and Calvano, MG and Sorçaburu Ciglieri, S and Bosetti, A and Grignani, P and Addoum, Y and Vetrini, R and Introna, F and Bonin, S and Previderè, C and Fattorini, P},
title = {Evaluation of a New DNA Extraction Method on Challenging Bone Samples Recovered from a WWII Mass Grave.},
journal = {Genes},
volume = {15},
number = {6},
pages = {},
pmid = {38927608},
issn = {2073-4425},
support = {no available//Comunità di Lussino, Trieste, Italy/ ; },
mesh = {Humans ; *Bone and Bones/chemistry ; World War II ; DNA Fingerprinting/methods ; Forensic Genetics/methods ; Microsatellite Repeats/genetics ; DNA/genetics/isolation & purification ; DNA, Ancient/analysis ; },
abstract = {Bones and teeth represent a common finding in ancient DNA studies and in forensic casework, even after a long burial. Genetic typing is the gold standard for the personal identification of skeletal remains, but there are two main factors involved in the successful DNA typing of such samples: (1) the set-up of an efficient DNA extraction method; (2) the identification of the most suitable skeletal element for the downstream genetic analyses. In this paper, a protocol based on the processing of 0.5 g of bone powder decalcified using Na2EDTA proved to be suitable for a semi-automated DNA extraction workflow using the Maxwell[®] FSC DNA IQ™ Casework Kit (Promega, Madison, WI, USA). The performance of this method in terms of DNA recovery and quality was compared with a full demineralisation extraction protocol based on Qiagen technology and kits. No statistically significant differences were scored according to the DNA recovery and DNA degradation index (p-values ≥ 0.176; r ≥ 0.907). This new DNA extraction protocol was applied to 88 bone samples (41 femurs, 19 petrous bones, 12 metacarpals and 16 molars) allegedly belonging to 27 World War II Italian soldiers found in a mass grave on the isle of Cres (Croatia). The results of the qPCR performed by the Quantifiler Human DNA Quantification kit showed values above the lowest Limit of Quantification (lLOQ; 23 pg/µL) for all petrous bones, whereas other bone types showed, in most cases, lower amounts of DNA. Replicate STR-CE analyses showed successful typing (that is, >12 markers) in all tests on the petrous bones, followed by the metacarpals (83.3%), femurs (52.2%) and teeth (20.0%). Full profiles (22/22 autosomal markers) were achieved mainly in the petrous bones (84.2%), followed by the metacarpals (41.7%). Stochastic amplification artefacts such as drop-outs or drop-ins occurred with a frequency of 1.9% in the petrous bones, whereas they were higher when the DNA recovered from other bone elements was amplified (up to 13.9% in the femurs). Overall, the results of this study confirm that petrous bone outperforms other bone elements in terms of the quantity and quality of the recovered DNA; for this reason, if available, it should always be preferred for genetic testing. In addition, our results highlight the need for accurate planning of the DVI operation, which should be carried out by a multi-disciplinary team, and the tricky issue of identifying other suitable skeletal elements for genetic testing. Overall, the results presented in this paper support the need to adopt preanalytical strategies positively related to the successful genetic testing of aged skeletal remains in order to reduce costs and the time of analysis.},
}

Humans
*Bone and Bones/chemistry
World War II
DNA Fingerprinting/methods
Forensic Genetics/methods
Microsatellite Repeats/genetics
DNA/genetics/isolation & purification
DNA, Ancient/analysis

@article {pmid38926415,
year = {2024},
author = {Austin, RM and Honap, TP and Mann, AE and Hübner, A and DeGaglia, CMS and Warinner, C and Zuckerman, MK and Hofman, CA},
title = {Metagenomic and paleopathological analyses of a historic documented collection explore ancient dental calculus as a diagnostic tool.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {14720},
pmid = {38926415},
issn = {2045-2322},
support = {Pre-doctoral Fellowship//Smithsonian Institution, National Museum of Natural History, United States/ ; NSF BCS-1643318//National Science Foundation, United States/ ; NSF BCS-1643318//National Science Foundation, United States/ ; NSF BCS-1643318//National Science Foundation, United States/ ; },
mesh = {*Dental Calculus/microbiology/history ; Humans ; *Metagenomics/methods ; *Paleopathology/methods ; *Tuberculosis/diagnosis/microbiology ; *Mycobacterium tuberculosis/genetics/isolation & purification ; DNA, Bacterial/genetics ; Male ; Treponema pallidum/genetics/isolation & purification ; Syphilis/diagnosis/microbiology/history ; Female ; Adult ; Metagenome/genetics ; Middle Aged ; },
abstract = {Dental calculus is a microbial biofilm that contains biomolecules from oral commensals and pathogens, including those potentially related to cause of death (CoD). To assess the utility of calculus as a diagnostically informative substrate, in conjunction with paleopathological analysis, calculus samples from 39 individuals in the Smithsonian Institution's Robert J. Terry Collection with CoDs of either syphilis or tuberculosis were assessed via shotgun metagenomic sequencing for the presence of Treponema pallidum subsp. pallidum and Mycobacterium tuberculosis complex (MTBC) DNA. Paleopathological analysis revealed that frequencies of skeletal lesions associated with these diseases were partially inconsistent with diagnostic criteria. Although recovery of T. p. pallidum DNA from individuals with a syphilis CoD was elusive, MTBC DNA was identified in at least one individual with a tuberculosis CoD. The authenticity of MTBC DNA was confirmed using targeted quantitative PCR assays, MTBC genome enrichment, and in silico bioinformatic analyses; however, the lineage of the MTBC strain present could not be determined. Overall, our study highlights the utility of dental calculus for molecular detection of tuberculosis in the archaeological record and underscores the effect of museum preparation techniques and extensive handling on pathogen DNA preservation in skeletal collections.},
}

*Dental Calculus/microbiology/history
Humans
*Metagenomics/methods
*Paleopathology/methods
*Tuberculosis/diagnosis/microbiology
*Mycobacterium tuberculosis/genetics/isolation & purification
DNA, Bacterial/genetics
Male
Treponema pallidum/genetics/isolation & purification
Syphilis/diagnosis/microbiology/history
Female
Adult
Metagenome/genetics
Middle Aged

@article {pmid38916350,
year = {2024},
author = {Sankaranarayanan, G and Kodiveri Muthukaliannan, G},
title = {Exploring antimicrobial resistance determinants in the Neanderthal microbiome.},
journal = {Microbiology spectrum},
volume = {12},
number = {8},
pages = {e0266223},
pmid = {38916350},
issn = {2165-0497},
abstract = {UNLABELLED: This study aimed to investigate the presence of antimicrobial resistance determinants (ARDs) in the Neanderthal microbiome through meticulous analysis of metagenomic data derived directly from dental calculus and fecal sediments across diverse Neanderthal sites in Europe. Employing a targeted locus mapping approach followed by a consensus strategy instead of an assembly-first approach, we aimed to identify and characterize ARDs within these ancient microbial communities. A comprehensive and redundant ARD database was constructed by amalgamating data from various antibiotic resistance gene repositories. Our results highlighted the efficacy of the KMA tool in providing a robust alignment of ancient metagenomic reads to the antibiotic resistance gene database. Notably, the KMA tool identified a limited number of ARDs, with only the 23S ribosomal gene from the dental calculus sample of Neanderthal remains at Goyet Troisieme Caverne exhibiting ancient DNA (aDNA) characteristics. Despite not identifying ARDs with typical ancient DNA damage patterns or negative distance proportions, our findings suggest a nuanced identification of putative antimicrobial resistance determinants in the Neanderthal microbiome's genetic repertoire based on the taxonomy-habitat correlation. Nevertheless, our findings are limited by factors such as environmental DNA contamination, DNA fragmentation, and cytosine deamination of aDNA. The study underscores the necessity for refined methodologies to unlock the genomic assets of prehistoric populations, fostering a comprehensive understanding of the intricate dynamics shaping the microbial landscape across history.

IMPORTANCE: The results of our analysis demonstrate the challenges in identifying determinants of antibiotic resistance within the endogenous microbiome of Neanderthals. Despite the comprehensive investigation of multiple studies and the utilization of advanced analytical techniques, the detection of antibiotic resistance determinants in the ancient microbial communities proved to be particularly difficult. However, our analysis did reveal the presence of some authentic ancient conservative genes, indicating the preservation of certain genetic elements over time. These findings raise intriguing questions about the factors influencing the presence or absence of antibiotic resistance in ancient microbial communities. It could be speculated that the spread of current antibiotic resistance, which has reached alarming levels in modern times, is primarily driven by anthropogenic factors such as the widespread use and misuse of antibiotics in medical and agricultural practices.},
}

@article {pmid38913897,
year = {2024},
author = {Sasso, S and Saag, L and Spros, R and Beneker, O and Molinaro, L and Biagini, SA and Lehouck, A and Van De Vijver, K and Hui, R and D'Atanasio, E and Kushniarevich, A and Kabral, H and Metspalu, E and Guellil, M and Ali, MQA and Geypen, J and Hoebreckx, M and Berk, B and De Winter, N and Driesen, P and Pijpelink, A and Van Damme, P and Scheib, CL and Deschepper, E and Deckers, P and Snoeck, C and Dewilde, M and Ervynck, A and Tambets, K and Larmuseau, MHD and Kivisild, T},
title = {Capturing the fusion of two ancestries and kinship structures in Merovingian Flanders.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {27},
pages = {e2406734121},
pmid = {38913897},
issn = {1091-6490},
support = {NA//agentschap Onroerend Erfgoed Archeologie syntheseproject/ ; G0A4521N//Fonds Wetenschappelijk Onderzoek (FWO)/ ; STG/18/021//KU Leuven start-up grant/ ; ZKD6488 C24M/19/075//KU Leuven BOF-C24/ ; NA//EWI-Vlaanderen citizien science project "MamaMito"/ ; PRG1027//Estonian Research fundation grant/ ; NA//Sapienza University Rome fellowship/ ; },
mesh = {Humans ; History, Medieval ; *Pedigree ; Belgium ; Burial/history ; Genetics, Population/methods ; Female ; Male ; DNA, Ancient/analysis ; England ; Human Migration ; Archaeology ; Netherlands ; Genome, Human ; },
abstract = {The Merovingian period (5th to 8th cc AD) was a time of demographic, socioeconomic, cultural, and political realignment in Western Europe. Here, we report the whole-genome shotgun sequence data of 30 human skeletal remains from a coastal Late Merovingian site of Koksijde (675 to 750 AD), alongside 18 remains from two Early to Late Medieval sites in present-day Flanders, Belgium. We find two distinct ancestries, one shared with Early Medieval England and the Netherlands, while the other, minor component, reflecting likely continental Gaulish ancestry. Kinship analyses identified no large pedigrees characteristic to elite burials revealing instead a high modularity of distant relationships among individuals of the main ancestry group. In contrast, individuals with >90% Gaulish ancestry had no kinship links among sampled individuals. Evidence for population structure and major differences in the extent of Gaulish ancestry in the main group, including in a mother-daughter pair, suggests ongoing admixture in the community at the time of their burial. The isotopic and genetic evidence combined supports a model by which the burials, representing an established coastal nonelite community, had incorporated migrants from inland populations. The main group of burials at Koksijde shows an abundance of >5 cM long shared allelic intervals with the High Medieval site nearby, implying long-term continuity and suggesting that similarly to Britain, the Early Medieval ancestry shifts left a significant and long-lasting impact on the genetic makeup of the Flemish population. We find substantial allele frequency differences between the two ancestry groups in pigmentation and diet-associated variants, including those linked with lactase persistence, likely reflecting ancestry change rather than local adaptation.},
}

Humans
History, Medieval
*Pedigree
Belgium
Burial/history
Genetics, Population/methods
Female
Male
DNA, Ancient/analysis
England
Human Migration
Archaeology
Netherlands
Genome, Human

@article {pmid38912151,
year = {2024},
author = {Farhud, DD and Azari, M and Rahbar, M},
title = {Oral Infections in Ancient Human Skulls in 2000 BC/Iron Age, Iran.},
journal = {Iranian journal of public health},
volume = {53},
number = {5},
pages = {1115-1127},
pmid = {38912151},
issn = {2251-6093},
abstract = {BACKGROUND: Oral infections have been seen in humans since ancient times. Excessive penetration of this infection can cause human death. Most of these infections are gum cysts and abscesses. The cyst creates large hard lumps in the gums, which is causes loose, and protruding teeth and abscesses, causing cavities in the jawbone and teeth. In this article, we have discussed for this infectious disease in 4000 - year - old ancient humans from Qazvin Province, Iran. The bone remains of our research are related to Sagezabad ancient cemetery in Qazvin plain.

METHODS: We tried to use reliable international atlases to get detailed information about ancient oral infections. The bones were extracted from the 2019 excavation of the Ghara Tappe area of Sagezabad for the Iron Age 2[nd] and 3[rd] Qazvin plains of Iran. This cemetery belongs to the period of the Medes Kingdom (pre - Achaemenian kingdom) in Iran.

RESULTS: We have discussed one of the ancient cemeteries with a large number of ancient populations. In this cemetery, there are signs of war and infectious diseases on the bones, which can be clearly seen. We have specially mentioned the abscess as the cause of oral infection from Sagezabad cemetery.

CONCLUSION: Oral infection existed in Iran since 2000 BC. Of course, this infection was common in ancient times and even Paleolithic period, like Homo Heidelbergensis.},
}

@article {pmid38903121,
year = {2024},
author = {Bougiouri, K and Aninta, SG and Charlton, S and Harris, A and Carmagnini, A and Piličiauskienė, G and Feuerborn, TR and Scarsbrook, L and Tabadda, K and Blaževičius, P and Parker, HG and Gopalakrishnan, S and Larson, G and Ostrander, EA and Irving-Pease, EK and Frantz, LAF and Racimo, F},
title = {Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38903121},
issn = {2692-8205},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {The multi-millenia long history between dogs and humans has placed them at the forefront of archeological and genomic research. Despite ongoing efforts including the analysis of ancient dog and wolf genomes, many questions remain regarding their geographic and temporal origins, and the microevolutionary processes that led to the diversity of breeds today. Although ancient genomes provide valuable information, their use is hindered by low depth of coverage and post-mortem damage, which inhibits confident genotype calling. In the present study, we assess how genotype imputation of ancient dog and wolf genomes, utilising a large reference panel, can improve the resolution provided by ancient datasets. Imputation accuracy was evaluated by down-sampling high coverage dog and wolf genomes to 0.05-2x coverage and comparing concordance between imputed and high coverage genotypes. We measured the impact of imputation on principal component analyses and runs of homozygosity. Our findings show high (R[2]>0.9) imputation accuracy for dogs with coverage as low as 0.5x and for wolves as low as 1.0x. We then imputed a dataset of 90 ancient dog and wolf genomes, to assess changes in inbreeding during the last 10,000 years of dog evolution. Ancient dog and wolf populations generally exhibited lower inbreeding levels than present-day individuals. Interestingly, regions with low ROH density maintained across ancient and present-day samples were significantly associated with genes related to olfaction and immune response. Our study indicates that imputing ancient canine genomes is a viable strategy that allows for the use of analytical methods previously limited to high-quality genetic data.},
}

@article {pmid38891676,
year = {2024},
author = {Abdelmanova, AA and Deniskova, TE and Kharzinova, VR and Chinarov, RY and Boronetskaya, OI and Sölkner, J and Brem, G and Ai, H and Huang, L and Trukhachev, VI and Zinovieva, NA},
title = {Tracing the Dynamical Genetic Diversity Changes of Russian Livni Pigs during the Last 50 Years with the Museum, Old, and Modern Samples.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {11},
pages = {},
pmid = {38891676},
issn = {2076-2615},
support = {23-46-00014//Russian Science Foundation/ ; },
abstract = {The pig industry is usually considered an intensive livestock industry, mainly supported by hybrid breeding between commercial pig breeds. However, people's pursuit of a more natural environment and higher meat quality has led to an increasing demand for eco-friendly and diverse pig feeding systems. Therefore, the importance of rearing and conserving local pig breeds is increasing. The Livni pig is a local breed with good adaptability to the environmental and fodder conditions in central Russia. In this study, we aimed to analyze the genetic diversity and population structure of Livni pigs using whole-genome single nucleotide polymorphism (SNP) data. We utilized the Porcine GGP HD BeadChip on genotype samples from old (n = 32, 2004) and modern (n = 32, 2019) populations of Livni pigs. For the museum samples of Livni pigs (n = 3), we extracted DNA from their teeth, performed genomic sequencing, and obtained SNP genotypes from the whole-genome sequences. SNP genotypes of Landrace (n = 32) and Large White (n = 32) pigs were included for comparative analysis. We observed that the allelic richness of Livni pigs was higher than those of Landrace and Large White pigs (AR = 1.775-1.798 vs. 1.703 and 1.668, respectively). The effective population size estimates (NE5 = 108 for Livni pigs, NE5 = 59 for Landrace and Large White pigs) confirmed their genetic diversity tendency. This was further supported by the length and number of runs of homozygosity, as well as the genomic inbreeding coefficient (almost twofold lower in Livni pigs compared to Landrace and Large White pigs). These findings suggest that the Livni pig population exhibits higher genetic diversity and experiences lower selection pressure compared to commercial pig populations. Furthermore, both principal component and network tree analyses demonstrated a clear differentiation between Livni pigs and transboundary commercial pigs. The TreeMix results indicated gene flow from Landrace ancestors to Livni pigs (2019) and from Large White ancestors to Livni pigs (2004), which was consistent with their respective historical breeding backgrounds. The comparative analysis of museum, old, and modern Livni pigs indicated that the modern Livni pig populations have preserved their historical genomic components, suggesting their potential suitability for future design selection programs.},
}

@article {pmid38886480,
year = {2024},
author = {Laffranchi, Z and Zingale, S and Indra, L and Coia, V and Salazar García, DC and Paladin, A and Kaeser, MA and Delley, G and Szidat, S and Lösch, S and Zink, A and Milella, M},
title = {Geographic origin, ancestry, and death circumstances at the Cornaux/Les Sauges Iron Age bridge, Switzerland.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {12180},
pmid = {38886480},
issn = {2045-2322},
support = {10531FL_197103 / 1//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; Funding Decree n.9/2021//Autonomous Province of Bolzano-Alto Adige - Department of Innovation, Research, University and Museums/ ; CIDEGENT/2019/061//Generalitat Valenciana/ ; },
mesh = {Humans ; Switzerland ; Male ; History, Ancient ; Adult ; Female ; *Archaeology ; Fossils ; Bone and Bones ; Radiometric Dating ; },
abstract = {Cornaux/Les Sauges (Switzerland, Late Iron Age) revealed remnants of a wooden bridge, artifacts, and human and animal skeletal remains. The relationship between the collapsed structure and the skeletal material, whether it indicates a potential accident or cultural practices, remains elusive. We evaluate the most plausible scenario for Cornaux based on osteological, taphonomic, isotopic, and paleogenomic analysis of the recovered individuals. The latter amount to at least 20 individuals, mostly adult males. Perimortem lesions include only blunt force traumas. Radiocarbon data fall between the 3rd and 1st c. BCE, although in some cases predating available dendrochronological estimates from the bridge. Isotopic data highlight five to eight nonlocals. No close genetic relatedness links the analyzed skeletons. Paleogenomic results, the first for Iron Age Switzerland, point to a genetic affinity with other Central and Western European Iron Age groups. The type of skeletal lesions supports an accidental event as the more plausible explanation. Radiocarbon data and the demographic structure of the sample may suggest a sequence of different events possibly including executions and/or sacrifices. Isotopic and paleogenomic data, while not favoring one scenario over the other, do support earlier interpretations of the last centuries BCE in Europe as a dynamic period from a biocultural perspective.},
}

Humans
Switzerland
Male
History, Ancient
Adult
Female
*Archaeology
Fossils
Bone and Bones
Radiometric Dating

@article {pmid38885310,
year = {2024},
author = {Wang, M and Huang, Y and Liu, K and Wang, Z and Zhang, M and Yuan, H and Duan, S and Wei, L and Yao, H and Sun, Q and Zhong, J and Tang, R and Chen, J and Sun, Y and Li, X and Su, H and Yang, Q and Hu, L and Yun, L and Yang, J and Nie, S and Cai, Y and Yan, J and Zhou, K and Wang, C and , and Zhu, B and Liu, C and He, G},
title = {Multiple Human Population Movements and Cultural Dispersal Events Shaped the Landscape of Chinese Paternal Heritage.},
journal = {Molecular biology and evolution},
volume = {41},
number = {7},
pages = {},
pmid = {38885310},
issn = {1537-1719},
support = {82202078//National Natural Science Foundation of China/ ; 23&ZD203//Major Project of the National Social Science Foundation of China/ ; },
mesh = {Humans ; *Human Migration ; China ; *Asian People/genetics ; Male ; *Chromosomes, Human, Y/genetics ; DNA, Ancient/analysis ; Paternal Inheritance ; Phylogeny ; East Asian People ; },
abstract = {Large-scale genomic projects and ancient DNA innovations have ushered in a new paradigm for exploring human evolutionary history. However, the genetic legacy of spatiotemporally diverse ancient Eurasians within Chinese paternal lineages remains unresolved. Here, we report an integrated Y-chromosome genomic database encompassing 15,563 individuals from both modern and ancient Eurasians, including 919 newly reported individuals, to investigate the Chinese paternal genomic diversity. The high-resolution, time-stamped phylogeny reveals multiple diversification events and extensive expansions in the early and middle Neolithic. We identify four major ancient population movements, each associated with technological innovations that have shaped the Chinese paternal landscape. First, the expansion of early East Asians and millet farmers from the Yellow River Basin predominantly carrying O2/D subclades significantly influenced the formation of the Sino-Tibetan people and facilitated the permanent settlement of the Tibetan Plateau. Second, the dispersal of rice farmers from the Yangtze River Valley carrying O1 and certain O2 sublineages reshapes the genetic makeup of southern Han Chinese, as well as the Tai-Kadai, Austronesian, Hmong-Mien, and Austroasiatic people. Third, the Neolithic Siberian Q/C paternal lineages originated and proliferated among hunter-gatherers on the Mongolian Plateau and the Amur River Basin, leaving a significant imprint on the gene pools of northern China. Fourth, the J/G/R paternal lineages derived from western Eurasia, which were initially spread by Yamnaya-related steppe pastoralists, maintain their presence primarily in northwestern China. Overall, our research provides comprehensive genetic evidence elucidating the significant impact of interactions with culturally distinct ancient Eurasians on the patterns of paternal diversity in modern Chinese populations.},
}

Humans
*Human Migration
China
*Asian People/genetics
Male
*Chromosomes, Human, Y/genetics
DNA, Ancient/analysis
Paternal Inheritance
Phylogeny
East Asian People

@article {pmid38883810,
year = {2024},
author = {Pathak, AK and Simonian, H and Ibrahim, IAA and Hrechdakian, P and Behar, DM and Ayub, Q and Arsanov, P and Metspalu, E and Yepiskoposyan, L and Rootsi, S and Endicott, P and Villems, R and Sahakyan, H},
title = {Human Y chromosome haplogroup L1-M22 traces Neolithic expansion in West Asia and supports the Elamite and Dravidian connection.},
journal = {iScience},
volume = {27},
number = {6},
pages = {110016},
pmid = {38883810},
issn = {2589-0042},
abstract = {West and South Asian populations profoundly influenced Eurasian genetic and cultural diversity. We investigate the genetic history of the Y chromosome haplogroup L1-M22, which, while prevalent in these regions, lacks in-depth study. Robust Bayesian analyses of 165 high-coverage Y chromosomes favor a West Asian origin for L1-M22 ∼20.6 thousand years ago (kya). Moreover, this haplogroup parallels the genome-wide genetic ancestry of hunter-gatherers from the Iranian Plateau and the Caucasus. We characterized two L1-M22 harboring population groups during the Early Holocene. One expanded with the West Asian Neolithic transition. The other moved to South Asia ∼8-6 kya but showed no expansion. This group likely participated in the spread of Dravidian languages. These South Asian L1-M22 lineages expanded ∼4-3 kya, coinciding with the Steppe ancestry introduction. Our findings advance the current understanding of Eurasian historical dynamics, emphasizing L1-M22's West Asian origin, associated population movements, and possible linguistic impacts.},
}

@article {pmid38881417,
year = {2024},
author = {Green, MH},
title = {The Pandemic Arc: Expanded Narratives in the History of Global Health.},
journal = {Journal of the history of medicine and allied sciences},
volume = {},
number = {},
pages = {},
doi = {10.1093/jhmas/jrae008},
pmid = {38881417},
issn = {1468-4373},
abstract = {Using the examples of plague, smallpox, and HIV/AIDS, the present essay argues for the benefits of incorporating the evolutionary histories of pathogens, beyond visible epidemic spikes within human populations, into our understanding of what pandemics actually are as epidemiological phenomena. The pandemic arc - which takes the pathogen as the defining "actor" in a pandemic, from emergence to local proliferation to globalization - offers a framework capable of bringing together disparate aspects not only of the manifestations of disease but also of human involvement in the pandemic process. Pathogens may differ, but there are common patterns in disease emergence and proliferation that distinguish those diseases that become pandemic, dispersed through human communities regionally or globally. The same methods of genomic analysis that allow tracking the evolutionary development of a modern pathogen such as SARS-CoV-2 also allow us to trace pandemics into the past. Reconstruction of these pandemic arcs brings new elements of these stories into view, recovering the experiences of regions and populations hitherto overlooked by Eurocentric narratives. This expanded global history of infectious diseases, in turn, lays a groundwork for reconceiving what ambitions a truly global health might aim for.},
}

@article {pmid38871872,
year = {2024},
author = {Callaway, E},
title = {Ancient DNA from Maya ruins tells story of ritual human sacrifices.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {38871872},
issn = {1476-4687},
}

@article {pmid38870299,
year = {2024},
author = {Curry, A},
title = {Sacrificed Maya boys tied to myth of 'Hero Twins'.},
journal = {Science (New York, N.Y.)},
volume = {384},
number = {6701},
pages = {1160-1161},
doi = {10.1126/science.adr0288},
pmid = {38870299},
issn = {1095-9203},
mesh = {Female ; Humans ; Male ; *DNA, Ancient ; History, Ancient ; *Twins/history ; Child ; *Ceremonial Behavior ; *Civilization/history ; },
abstract = {Ancient DNA shows continuity between living and ancient Maya communities.},
}

Female
Humans
Male
*DNA, Ancient
History, Ancient
*Twins/history
Child
*Ceremonial Behavior
*Civilization/history

@article {pmid38845985,
year = {2024},
author = {Tejero, JM and Cheronet, O and Gelabert, P and Zagorc, B and Álvarez-Fernández, E and Arias, P and Averbouh, A and Bar-Oz, G and Barzilai, O and Belfer-Cohen, A and Bosch, MD and Brück, F and Cueto, M and Dockner, M and Fullola, JM and Gárate, D and Giannakoulis, M and González, C and Jakeli, N and Mangado, X and Meshveliani, T and Neruda, P and Nigst, P and Ontañón, R and Shemer, M and Šimková, PG and Tapia, J and Sánchez de la Torre, M and Schwab, C and Weber, G and Pinhasi, R},
title = {Cervidae antlers exploited to manufacture prehistoric tools and hunting implements as a reliable source of ancient DNA.},
journal = {Heliyon},
volume = {10},
number = {11},
pages = {e31858},
pmid = {38845985},
issn = {2405-8440},
abstract = {Antler is one of the primary animal raw materials exploited for technical purposes by the hunter-gatherer groups of the Eurasian Upper Palaeolithic (UP) all over the ecological range of deers, and beyond. It was exhaustively employed to produce one of the most critical tools for the survival of the UP societies: hunting weapons. However, antler implements can be made from diverse deer taxa, with different ecological requirements and ethological behaviours. Identifying the antler's origin at a taxonomic level is thus essential in improving our knowledge of humans' functional, practical and symbolic choices, as well as the human-animal interface during Prehistoric times. Nevertheless, palaeogenetics analyses have focused mainly on bone and teeth, with genetic studies of antler generally focused on modern deer conservation. Here we present the results of the first whole mitochondrial genome ancient DNA (aDNA) analysis by means of in-solution hybridisation capture of antlers from pre-Holocene archaeological contexts. We analysed a set of 50 Palaeolithic and Neolithic (c. 34-8ka) antler and osseous objects from South-Western Europe, Central Europe, South-Western Asia and the Caucasus. We successfully obtained aDNA, allowing us to identify the exploited taxa and demonstrate the archaeological relevance of those finds. Moreover, as most of the antlers were sampled using a minimally-invasive method, further analyses (morphometric, technical, genetic, radiometric and more) remain possible on these objects.},
}

@article {pmid38830089,
year = {2024},
author = {Fordham, DA and Brown, SC and Canteri, E and Austin, JJ and Lomolino, MV and Haythorne, S and Armstrong, E and Bocherens, H and Manica, A and Rey-Iglesia, A and Rahbek, C and Nogués-Bravo, D and Lorenzen, ED},
title = {52,000 years of woolly rhinoceros population dynamics reveal extinction mechanisms.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {24},
pages = {e2316419121},
pmid = {38830089},
issn = {1091-6490},
support = {DP180102392//Department of Education and Training | Australian Research Council (ARC)/ ; },
mesh = {Animals ; *Extinction, Biological ; *Perissodactyla ; *Population Dynamics ; *Fossils ; Ecosystem ; DNA, Ancient/analysis ; Paleontology ; },
abstract = {The extinction of the woolly rhinoceros (Coelodonta antiquitatis) at the onset of the Holocene remains an enigma, with conflicting evidence regarding its cause and spatiotemporal dynamics. This partly reflects challenges in determining demographic responses of late Quaternary megafauna to climatic and anthropogenic causal drivers with available genetic and paleontological techniques. Here, we show that elucidating mechanisms of ancient extinctions can benefit from a detailed understanding of fine-scale metapopulation dynamics, operating over many millennia. Using an abundant fossil record, ancient DNA, and high-resolution simulation models, we untangle the ecological mechanisms and causal drivers that are likely to have been integral in the decline and later extinction of the woolly rhinoceros. Our 52,000-y reconstruction of distribution-wide metapopulation dynamics supports a pathway to extinction that began long before the Holocene, when the combination of cooling temperatures and low but sustained hunting by humans trapped woolly rhinoceroses in suboptimal habitats along the southern edge of their range. Modeling indicates that this ecological trap intensified after the end of the last ice age, preventing colonization of newly formed suitable habitats, weakening stabilizing metapopulation processes, triggering the extinction of the woolly rhinoceros in the early Holocene. Our findings suggest that fragmentation and resultant metapopulation dynamics should be explicitly considered in explanations of late Quaternary megafauna extinctions, sending a clarion call to the fragility of the remaining large-bodied grazers restricted to disjunct fragments of poor-quality habitat due to anthropogenic environmental change.},
}

Animals
*Extinction, Biological
*Perissodactyla
*Population Dynamics
*Fossils
Ecosystem
DNA, Ancient/analysis
Paleontology

@article {pmid38813936,
year = {2024},
author = {Arsuaga, JL and Martínez, I and Gracia-Téllez, A and Carretero, JM and Esquivel, A and García, N and Lorenzo, C and Quam, R and Aramburu, A and Sala, N and Trueba, J},
title = {How the Sima de los Huesos was won.},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {307},
number = {7},
pages = {2225-2245},
doi = {10.1002/ar.25509},
pmid = {38813936},
issn = {1932-8494},
support = {PID2021-122355NB-C31 supported by MCIN/AEI/10.1303//Government of Spain/ ; //Cátedra de Otoacústica Evolutiva y Paleoantropología (HM Hospitales-Universidad de Alcalá)/ ; EPU-INV-UAH/2022/006//Universidad de Alcalá/ ; },
mesh = {Humans ; *Fossils ; Animals ; *Biological Evolution ; Female ; Male ; Hominidae/anatomy & histology ; Spain ; },
abstract = {Although the first discovery of a human fossil in the Sima de los Huesos took place in 1976, systematic excavations did not begin there until 1984. Since then, this site has been continuously excavated in month-long camps. The site is dated by different radiometric techniques to between 430,000 and 300,000 years ago. Until the 2023 campaign, just over 7000 human fossils have been recovered, constituting the largest collection of fossils prior to Homo sapiens ever discovered. The fossils correspond to a minimum of 29 individuals of both sexes and different ages at death, from preadolescents to a specimen of advanced age. Comparative anatomy and ancient DNA studies both suggest that this is a population closely related to Homo neanderthalensis. The great variety and extraordinary quality of the fossils recovered have allowed us to carry out a series of investigations that have greatly increased our knowledge about the evolution of Homo in the Middle Pleistocene. Among the most important discoveries, it has been possible to establish body size and proportions, the confirmation that the origin of the accumulation of human fossils was of an anthropic nature, that those past humans took care of disabled individuals and who were capable of having an oral language almost as complex and efficient as that of our own species.},
}

Humans
*Fossils
Animals
*Biological Evolution
Female
Male
Hominidae/anatomy & histology
Spain

@article {pmid38806487,
year = {2024},
author = {Bagnasco, G and Marzullo, M and Cattaneo, C and Biehler-Gomez, L and Mazzarelli, D and Ricciardi, V and Müller, W and Coppa, A and McLaughlin, R and Motta, L and Prato, O and Schmidt, F and Gaveriaux, F and Marras, GB and Millet, MA and Madgwick, R and Ballantyne, R and Makarewicz, CA and Trentacoste, A and Reimer, P and Mattiangeli, V and Bradley, DG and Malone, C and Esposito, C and Breslin, EM and Stoddart, S},
title = {Bioarchaeology aids the cultural understanding of six characters in search of their agency (Tarquinia, ninth-seventh century BC, central Italy).},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {11895},
pmid = {38806487},
issn = {2045-2322},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Italy ; Humans ; *Archaeology ; History, Ancient ; Male ; DNA, Ancient/analysis ; Female ; },
abstract = {Etruria contained one of the great early urban civilisations in the Italian peninsula during the first millennium BC, much studied from a cultural, humanities-based, perspective, but relatively little with scientific data, and rarely in combination. We have addressed the unusual location of twenty inhumations found in the sacred heart of the Etruscan city of Tarquinia, focusing on six of these as illustrative, contrasting with the typical contemporary cremations found in cemeteries on the edge of the city. The cultural evidence suggests that the six skeletons were also distinctive in their ritualization and memorialisation. Focusing on the six, as a representative sample, the scientific evidence of osteoarchaeology, isotopic compositions, and ancient DNA has established that these appear to show mobility, diversity and violence through an integrated bioarchaeological approach. The combination of multiple lines of evidence makes major strides towards a deeper understanding of the role of these extraordinary individuals in the life of the early city of Etruria.},
}

Italy
Humans
*Archaeology
History, Ancient
Male
DNA, Ancient/analysis
Female

@article {pmid38798346,
year = {2024},
author = {Fine, AG and Steinrücken, M},
title = {A novel expectation-maximization approach to infer general diploid selection from time-series genetic data.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38798346},
issn = {2692-8205},
support = {R01 GM146051/GM/NIGMS NIH HHS/United States ; },
abstract = {Detecting and quantifying the strength of selection is a main objective in population genetics. Since selection acts over multiple generations, many approaches have been developed to detect and quantify selection using genetic data sampled at multiple points in time. Such time series genetic data is commonly analyzed using Hidden Markov Models, but in most cases, under the assumption of additive selection. However, many examples of genetic variation exhibiting non-additive mechanisms exist, making it critical to develop methods that can characterize selection in more general scenarios. Thus, we extend a previously introduced expectation-maximization algorithm for the inference of additive selection coefficients to the case of general diploid selection, in which heterozygote and homozygote fitnesses are parameterized independently. We furthermore introduce a framework to identify bespoke modes of diploid selection from given data, as well as a procedure for aggregating data across linked loci to increase power and robustness. Using extensive simulation studies, we find that our method accurately and efficiently estimates selection coefficients for different modes of diploid selection across a wide range of scenarios; however, power to classify the mode of selection is low unless selection is very strong. We apply our method to ancient DNA samples from Great Britain in the last 4,450 years, and detect evidence for selection in six genomic regions, including the well-characterized LCT locus. Our work is the first genome-wide scan characterizing signals of general diploid selection.},
}

@article {pmid38796876,
year = {2024},
author = {Psonis, N and Vassou, D and Nafplioti, A and Tabakaki, E and Pavlidis, P and Stamatakis, A and Poulakakis, N},
title = {Identification of the 18 World War II executed citizens of Adele, Rethymnon, Crete using an ancient DNA approach and low coverage genomes.},
journal = {Forensic science international. Genetics},
volume = {71},
number = {},
pages = {103060},
doi = {10.1016/j.fsigen.2024.103060},
pmid = {38796876},
issn = {1878-0326},
mesh = {Humans ; *DNA, Ancient/analysis ; *World War II ; Male ; Greece ; *DNA Fingerprinting ; Skull ; Genome, Human ; Forensic Anthropology ; Whole Genome Sequencing ; },
abstract = {In the Battle of Crete during the World War II occupation of Greece, the German forces faced substantial civilian resistance. To retribute the numerous German losses, a series of mass executions took place in numerous places in Crete; a common practice reported from Greece and elsewhere. In Adele, a village in the regional unit of Rethymnon, 18 male civilians were executed and buried in a burial pit at the Sarakina site. In this study, the first one conducted for a conflict that occurred in Greece, we identified for humanitarian purposes the 18 skulls of the Sarakina victims, following a request from the local community of Adele. The molecular identification of historical human remains via ancient DNA approaches and low coverage whole genome sequencing has only recently been introduced. Here, we performed genome skimming on the living relatives of the victims, as well as high throughput historical DNA analysis on the skulls to infer the kinship degrees among the victims via genetic relatedness analyses. We also conducted targeted anthropological analysis to successfully complete the identification of all Sarakina victims. We demonstrate that our methodological approach constitutes a potentially highly informative forensic tool to identify war victims. It can hence be applied to analogous studies on degraded DNA, thus, paving the path for systematic war victim identification in Greece and beyond.},
}

Humans
*DNA, Ancient/analysis
*World War II
Male
Greece
*DNA Fingerprinting
Skull
Genome, Human
Forensic Anthropology
Whole Genome Sequencing

@article {pmid38795367,
year = {2024},
author = {Larsson, MNA and Morell Miranda, P and Pan, L and Başak Vural, K and Kaptan, D and Rodrigues Soares, AE and Kivikero, H and Kantanen, J and Somel, M and Özer, F and Johansson, AM and Storå, J and Günther, T},
title = {Ancient Sheep Genomes Reveal Four Millennia of North European Short-Tailed Sheep in the Baltic Sea Region.},
journal = {Genome biology and evolution},
volume = {16},
number = {6},
pages = {},
pmid = {38795367},
issn = {1759-6653},
support = {2017-05267//Vetenskapsrådet/ ; P21-0266//Riksbankens Jubileumsfond/ ; CTS 18:129//Carl Tryggers Stiftelse för Vetenskaplig Forskning/ ; //Knut and Alice Wallenberg Foundation/ ; //National Academic Infrastructure for Supercomputing in Sweden/ ; //Swedish National Infrastructure for Computing/ ; },
mesh = {Animals ; *Genome ; Sheep/genetics ; Genetic Variation ; Sheep, Domestic/genetics ; DNA, Ancient/analysis ; },
abstract = {Sheep are among the earliest domesticated livestock species, with a wide variety of breeds present today. However, it remains unclear how far back this diversity goes, with formal documentation only dating back a few centuries. North European short-tailed (NEST) breeds are often assumed to be among the oldest domestic sheep populations, even thought to represent relicts of the earliest sheep expansions during the Neolithic period reaching Scandinavia <6,000 years ago. This study sequenced the genomes (up to 11.6X) of five sheep remains from the Baltic islands of Gotland and Åland, dating from the Late Neolithic (∼4,100 cal BP) to historical times (∼1,600 CE). Our findings indicate that these ancient sheep largely possessed the genetic characteristics of modern NEST breeds, suggesting a substantial degree of long-term continuity of this sheep type in the Baltic Sea region. Despite the wide temporal spread, population genetic analyses show high levels of affinity between the ancient genomes and they also exhibit relatively high genetic diversity when compared to modern NEST breeds, implying a loss of diversity in most breeds during the last centuries associated with breed formation and recent bottlenecks. Our results shed light on the development of breeds in Northern Europe specifically as well as the development of genetic diversity in sheep breeds, and their expansion from the domestication center in general.},
}

Animals
*Genome
Sheep/genetics
Genetic Variation
Sheep, Domestic/genetics
DNA, Ancient/analysis