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Widespread permafrost thaw is underway as arctic regions warm at twice the rate of the global average. Greenhouse gases (methane and carbon dioxide) released from thawing organic-rich permafrost soils contribute to a positive feedback loop that further accelerates global warming. There is an urgent need to understand the relationship between past permafrost conditions and palaeoclimatic change, to better predict present permafrost response to ongoing and future climate change. Through sulfur isotope analysis (δ34S) of radiocarbon-dated bone collagen samples spanning the last 50,000 years, we have identified what we term a high-magnitude Late Pleniglacial Sulfur Excursion (LPSE) in Eurasia. This anomaly is geographically widespread and several orders of magnitude higher than the sulfur isotope variation previously attributed to changing animal origin or diet alone. We show that a major change in the terrestrial sulfur cycle related to continental-scale environmental processes are, in this context, representing changing permafrost conditions. Sulfur isotope analysis of faunal samples offer an unrivalled prospect of developing high-resolution, tightly chronologically-constrained records of past permafrost change in relation to global climate changes. This would inform on the sensitivity of permafrost to past climate change, enabling constraints to be put on modelled responses of present‐day permafrost to future climate change. More broadly, our findings indicate animal δ34S values may reflect local environmental conditions, complicating the use of δ34S values as a tool for food origin, animal migration, and archaeological palaeodiet and mobility research.

The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located. © 2022, The Author(s). 8028-00005B; IP DKRVO 2019-2023, MK000094862; 220457/Z/20/Z, ERC-2013-StG-337574-UNDEAD, ERC-2019-StG-853272-PALAEOFARM; 075-15-2021-1069; European Molecular Biology Organization, EMBO: 217223/Z/19/Z; Vallee Foundation; Velux Fonden; Wellcome Trust, WT; Francis Crick Institute, FCI: FC001595; Horizon 2020 Framework Programme, H2020: 796877; Medical Research Council, MRC; Natural Environment Research Council, NERC: 210119/Z/18/Z, NE/K003259/1, NE/K005243/1, NE/S00078X/1, NE/S007067/1; Cancer Research UK, CRUK; European Research Council, ERC: 852558; Grantová Agentura České Republiky, GA ČR: 15-06446S; Svenska Forskningsrådet Formas: 2018-01640; Knut och Alice Wallenbergs Stiftelse; Vetenskapsrådet, VR: 681396, BELSPO B2/191/P2/ICHIE; Russian Science Foundation, RSF: 16-18-10265-RNF, 20-17-00033, 21-18-00457-RNF, 310763; Science for Life Laboratory, SciLifeLab; Narodowa Agencja Wymiany Akademickiej, NAWA: PPN/PPO/2018/1/00037 This work was supported by grants to P. Skoglund from the European Research Council (grant no. 852558), the Erik Philip Sörensen Foundation and the Science for Life Laboratory, Swedish Biodiversity Program, made available by support from the Knut and Alice Wallenberg Foundation. A.B., L.S., P. Swali and P. Skoglund were supported by Francis Crick Institute core funding (FC001595) from Cancer Research UK, the UK Medical Research Council and the Wellcome Trust. P. Skoglund was also supported by the Vallee Foundation, the European Molecular Biology Organisation and the Wellcome Trust (217223/Z/19/Z). Computations were supported by SNIC-UPPMAX. We also acknowledge support from Science for Life Laboratory, the Knut and Alice Wallenberg Foundation, the National Genomics Infrastructure funded by the Swedish Research Council and the Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. We thank the Yukon gold mining community and First Nations, including the Tr’ondëk Hwëch’in, for continued support of our palaeontology research in the Yukon Territories, Canada. We thank the Danish National High-Throughput Sequencing Centre and BGI-Europe for assistance in sequencing data generation and the Danish National Supercomputer for Life Sciences–Computerome ( https://computerome.dtu.dk ) for computational resources. We thank National Museum Wales for continued sampling support. M. Germonpré acknowledges support from the Brain.be 2.0 ICHIE project (BELSPO B2/191/P2/ICHIE). M.T.P.G. was supported by the European Research Council (grant no. 681396). M.-H.S.S. was supported by the Velux Foundations through the Qimmeq Project, the Aage og Johanne Louis-Hansens Fond and the Independent Research Fund Denmark (8028-00005B). L.D. acknowledges support from FORMAS (2018-01640). D.W.G.S. received funding for this project from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 796877. M.P. was supported by the Polish National Agency for Academic Exchange–NAWA (grant no. PPN/PPO/2018/1/00037). V.J.S. was supported by the University of Zurich’s University Research Priority Program ‘Evolution in Action: From Genomes to Ecosystems’. This research was done with the participation of ZIN RAS (grant no. 075-15-2021-1069). We are grateful to the museum of the Institute of Plant and Animal Ecology UB RAS (Ekaterinburg, Russia) for provision of samples. R.P.J. and C.O’D. were supported by the Standing Committee for Archaeology of the Royal Irish Academy through the Archaeological Excavation Research Grant Scheme. E.Y.P., P.N. and V.V.P. are supported by the Russian Science Foundation (grant no. 16-18-10265-RNF and 21-18-00457-RNF). Y.V.K. was supported by the Russian Science Foundation (grant no. 20-17-00033). M.H. was supported by the European Research Council (consolidator grant GeneFlow no. 310763). M.L.-G. was supported by the Czech Science Foundation GAČR (grant no. 15-06446S) and institutional financing of the Moravian Museum from the Czech Ministry of Culture (IP DKRVO 2019-2023, MK000094862). L.S. is supported by the Sir Henry Wellcome fellowship (220457/Z/20/Z). We thank Staatliches Museum für Naturkunde Stuttgart for sample access. L.F. and G.L. were supported by European Research Council grants (ERC-2013-StG-337574-UNDEAD and ERC-2019-StG-853272-PALAEOFARM) and Natural Environmental Research Council grants (NE/K005243/1, NE/K003259/1, NE/S007067/1 and NE/S00078X/1). L.F. was also supported by the Wellcome Trust (210119/Z/18/Z). This research was funded in whole, or in part, by the Wellcome Trust (FC001595). For the purpose of open access, the author has applied a CC-BY public copyright licence to any author accepted manuscript version arising from this submission.

Janssens et al. (2021, doi: 10.1002/ar.24624) recently commented on our article (Galeta et al., 2021, doi: 10.1002/ar.24500) regarding the morphological differences between putative Paleolithic dog and Pleistocene wolf crania. The authors argued that these differences reflect the normal population variation of wolves, that some of the cranial measurements used do not reflect morphological changes during domestication, and that our canid dataset was small because we inexplicably omitted several specimens we analyzed in our previous publications. In this commentary, we briefly address the issue of within and between morpho-population variability. The results based on our canid sample suggest that the magnitude of morphological differences between distinct morpho-populations (i.e., recent northern dogs and wolves) is at least twice as large as that observed within morpho-populations (between two groups of recent northern wolves segregated by cluster analysis). The morphological differences between putative Paleolithic dogs and Pleistocene wolves are relatively large, which may indicate that they did not likely represent a single Late Pleistocene morpho-population. Finally, we clarified the rationale behind the composition of our 2021 dataset to show that we did not adjust the list of the analyzed specimens. Although the sample size was small, the randomization analysis published in 2021 confirmed that the unbalanced composition of the reference sample did not affect the reliability of the morphological segregation of putative Paleolithic dogs and Pleistocene wolves.

Lengths, widths, and size proportions (length to width) of the lower carnassial were measured in 45 teeth of the arctic fox and 35 teeth of the red fox from Belgium radiocarbon dated to 46 640–14 120 ka BP. Data the Late Pleistocene foxes from Belgium were compared to 20 ancient and extant populations form Europe, Asia, and North America. The Pleistocene arctic fox from Belgium showed larger carnassial than in all recent samples of this species, whereas the Belgian fossil red foxes were characterized by the carnassial size comparable to that of the recent Siberian red foxes. Both fox species from the Pleistocene of Belgium showed the highest index of the carnassials length to width, which means increase in carnivorous adaptation. We conclude that the higher level of carnivorous specialization reached by the Belgian arctic and red foxes at the end of the Late Pleistocene reflected their scavenging on kills of large carnivores and human hunters (remains of megafauna). Harsh environmental conditions of that period and specific composition of ecosystems led to adapting to a more carnivorous food niche in both foxes.

Background Ancient DNA studies suggest that Late Pleistocene climatic changes had a significant effect on population dynamics in Arctic species. The Eurasian collared lemming (Dicrostonyx torquatus) is a keystone species in the Arctic ecosystem. Earlier studies have indicated that past climatic fluctuations were important drivers of past population dynamics in this species. Results Here, we analysed 59 ancient and 54 modern mitogenomes from across Eurasia, along with one modern nuclear genome. Our results suggest population growth and genetic diversification during the early Late Pleistocene, implying that collared lemmings may have experienced a genetic bottleneck during the warm Eemian interglacial. Furthermore, we find multiple temporally structured mitogenome clades during the Late Pleistocene, consistent with earlier results suggesting a dynamic late glacial population history. Finally, we identify a population in northeastern Siberia that maintained genetic diversity and a constant population size at the end of the Pleistocene, suggesting suitable conditions for collared lemmings in this region during the increasing temperatures associated with the onset of the Holocene. Conclusions This study highlights an influence of past warming, in particular the Eemian interglacial, on the evolutionary history of the collared lemming, along with spatiotemporal population structuring throughout the Late Pleistocene.

Summary Extant Canis lupus genetic diversity can be grouped into three phylogenetically distinct clades: Eurasian and American wolves and domestic dogs.1 Genetic studies have suggested these groups trace their origins to a wolf population that expanded during the last glacial maximum (LGM)1, 2, 3 and replaced local wolf populations.4 Moreover, ancient genomes from the Yana basin and the Taimyr peninsula provided evidence of at least one extinct wolf lineage that dwelled in Siberia during the Pleistocene.35 Previous studies have suggested that Pleistocene Siberian canids can be classified into two groups based on cranial morphology. Wolves in the first group are most similar to present-day populations, although those in the second group possess intermediate features between dogs and wolves.67 However, whether this morphological classification represents distinct genetic groups remains unknown. To investigate this question and the relationships between Pleistocene canids, present-day wolves, and dogs, we resequenced the genomes of four Pleistocene canids from Northeast Siberia dated between >50 and 14 ka old, including samples from the two morphological categories. We found these specimens cluster with the two previously sequenced Pleistocene wolves, which are genetically more similar to Eurasian wolves. Our results show that, though the four specimens represent extinct wolf lineages, they do not form a monophyletic group. Instead, each Pleistocene Siberian canid branched off the lineage that gave rise to present-day wolves and dogs. Finally, our results suggest the two previously described morphological groups could represent independent lineages similarly related to present-day wolves and dogs., Graphical Abstract, Highlights • Pleistocene Siberian wolves represent multiple extinct evolutionary lineages • Pleistocene wolves share ancestry with arctic dogs and some East Asian wolves • A Paleolithic dog specimen is genetically similar to other Pleistocene wolves, Ramos-Madrigal et al. sequence the genomes of four Pleistocene Siberian wolves, two of which have divergent cranial morphologies. These canids represent multiple extinct lineages that dwelled in Siberia >50 ka ago and at least until 14.1 ka ago and that contributed to the genetic ancestry of arctic dogs and some East Asian wolves.

The antiquity of the wolf/dog domestication has been recently pushed back in time from the Late Upper Paleolithic (similar to 14,000 years ago) to the Early Upper Paleolithic (EUP; similar to 36,000 years ago). Some authors questioned this early dog domestication claiming that the putative (EUP) Paleolithic dogs fall within the morphological range of recent wolves. In this study, we reanalyzed a data set of large canid skulls using unbalanced- and balanced-randomized discriminant analyses to assess whether the putative Paleolithic dogs are morphologically unique or whether they represent a subsample of the wolf morpho-population. We evaluated morphological differences between 96 specimens of the 4 a priori reference groups (8 putative Paleolithic dogs, 41 recent northern dogs, 7 Pleistocene wolves, and 40 recent northern wolves) using discriminant analysis based on 5 ln-transformed raw and allometrically size-adjusted cranial measurements. Putative Paleolithic dogs are classified with high accuracies (87.5 and 100.0%, cross-validated) and randomization experiment suggests that these classification rates cannot be exclusively explained by the small and uneven sample sizes of reference groups. It indicates that putative Upper Paleolithic dogs may represent a discrete canid group with morphological signs of domestication (a relatively shorter skull and wider palate and braincase) that distinguish them from sympatric Pleistocene wolves. The present results add evidence to the view that these specimens could represent incipient Paleolithic dogs that were involved in daily activities of European Upper Paleolithic forager groups.

Domestication of horses fundamentally transformed long-range mobility and warfare. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling at Botai, Central Asia around 3500 bc3. Other longstanding candidate regions for horse domestication, such as Iberia and Anatolia, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 bc, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 bc driving the spread of Indo-European languages. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium bc Sintashta culture., The work by G. Boeskorov is done on state assignment of DPMGI SB RAS. This project was supported by the University Paul Sabatier IDEX Chaire d’Excellence (OURASI); Villum Funden miGENEPI research programme; the CNRS ‘Programme de Recherche Conjoint’ (PRC); the CNRS International Research Project (IRP AMADEUS); the France Génomique Appel à Grand Projet (ANR-10-INBS-09-08, BUCEPHALE project); IB10131 and IB18060, both funded by Junta de Extremadura (Spain) and European Regional Development Fund; Czech Academy of Sciences (RVO:67985912); the Zoological Institute ZIN RAS (АААА-А19-119032590102-7); and King Saud University Researchers Supporting Project (NSRSP–2020/2). The research was carried out with the financial support of the Russian Foundation for Basic Research (19-59-15001 and 20-04-00213), the Russian Science Foundation (16-18-10265, 20-78-10151, and 21-18-00457), the Government of the Russian Federation (FENU-2020-0021), the Estonian Research Council (PRG29), the Estonian Ministry of Education and Research (PRG1209), the Hungarian Scientific Research Fund (Project NF 104792), the Hungarian Academy of Sciences (Momentum Mobility Research Project of the Institute of Archaeology, Research Centre for the Humanities); and the Polish National Science Centre (2013/11/B/HS3/03822). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie (grant agreement 797449). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements 681605, 716732 and 834616).

Morphological and genetic evidence put dog domestication during the Paleolithic, sometime between 40,000 and 15,000 years ago, with identification of the earliest dogs debated. We predict that these earliest dogs (referred to herein as protodogs), while potentially difficult to distinguish morphologically from wolves, experienced behavioral shifts, including changes in diet. Specifically, protodogs may have consumed more bone and other less desirable scraps within human settlement areas. Here we apply Dental Microwear Texture Analysis (DMTA) to canids from the Gravettian site of Předmosti (approx. 28,500 BP), which were previously assigned to the Paleolithic dog or Pleistocene wolf morphotypes. We test whether these groups separate out significantly by diet-related variation in microwear patterning. Results are consistent with differences in dietary breadth, with the Paleolithic dog morphotype showing evidence of greater durophagy than those assigned to the wolf morphotype. This supports the presence of two morphologically and behaviorally distinct canid types at this middle Upper Paleolithic site. Our primary goal here was to test whether these two morphotypes expressed notable differences in dietary behavior. However, in the context of a major Gravettian settlement, this may also support evidence of early stage dog domestication. Dental microwear is a behavioral signal that may appear generations before morphological changes are established in a population. It shows promise for distinguishing protodogs from wolves in the Pleistocene and domesticated dogs from wolves elsewhere in the archaeological record.

Domestic dogs (Canis lupus familiaris) are the most variable-sized mammalian species on Earth displaying a 40-fold size difference between breeds(1). Although dogs of variable size are found in the archeological record(2–4), the most dramatic shifts in body size are the result of selection over the last two centuries, as dog breeders selected and propagated phenotypic extremes within closed breeding populations(5). Analyses of over 200 domestic breeds have identified approximately 20 body size genes regulating insulin processing, fatty acid metabolism, TGFβ signaling and skeletal formation(6–10). Of these, Insulin-like Growth Factor 1 (IGF1) predominates, controlling approximately 15% of body size variation between breeds(8). The identification of a functional mutation associated with IGF1 has thus far proven elusive(6,10,11). Here, to identify and elucidate the role of an ancestral IGF1 allele in the propagation of modern canids, we analyzed 1,431 genome sequences from 13 species, including both ancient and modern canids, thus allowing us to define the evolutionary history of both ancestral and derived alleles at this locus. We identified a single variant in an antisense long non-coding RNA (IGF1-AS) that interacts with the insulin-like growth factor-1 (IGF1) gene creating a duplex. While the derived mutation predominates in both modern grey wolves and large domestic breeds, the ancestral allele, which predisposes to small size, was common in small-sized breeds and smaller wild canids. Our analyses demonstrate that this major regulator of canid body size nearly vanished in Pleistocene wolves, before its recent resurgence resulting from human-imposed selection for small-sized breed dogs.

Two canid morphotypes have been proposed for the middle Upper Palaeolithic site of Předmosti (Moravia, Czech Republic): Pleistocene wolf and Palaeolithic dog (Germonpre et al., 2012, 2015; Galeta et al., 2020). In Wilczynski et al. (2020), faunal assemblages from other Upper Palaeolithic Moravian sites were analyzed and those results used to project a similar, which we interpret as flawed, result for Předmosti: that only wild canids were present. We address issues with their methodology and argue that their conclusion, that dogs were not present at any of those studied sites, is based on cursory taphonomic analysis. Further, their projection of these results to Předmosti, an assemblage they did not study, is unsubstantiated, but does highlight the current dearth of taphonomic information that could aid the study of dog domestication. We also point out an important error in their Fig. 1, where the hemimandibles intended to show the natural variability in large canids from Dolni Vĕstonice II and Pavlov I SE, are in fact canid specimens from Předmosti. Since several of these canid specimens have been published by Germonpre et al. (2015), we find it imperative to address this error to ensure these data are correctly referenced in future works.

Frantz, Laurent/0000-0001-8030-3885; Ersmark, Erik/0000-0003-4186-7498; Sjogren, Karl-Goran/0000-0003-1791-3175; Bergstrom, Anders/0000-0002-4096-9268 WOS:000583031800042 PubMed ID: 33122379 Dogs were the first domestic animal, but little is known about their population history and to what extent it was linked to humans. We sequenced 27 ancient dog genomes and found that all dogs share a common ancestry distinct from present-day wolves, with limited gene flow from wolves since domestication but substantial dog-to-wolf gene flow. By 11,000 years ago, at least five major ancestry lineages had diversified, demonstrating a deep genetic history of dogs during the Paleolithic. Coanalysis with human genomes reveals aspects of dog population history that mirror humans, including Levant-related ancestry in Africa and early agricultural Europe. Other aspects differ, including the impacts of steppe pastoralist expansions in West and East Eurasia and a near-complete turnover of Neolithic European dog ancestry. SciLifeLab National Projects; Erik Philip Sorensen Foundation; Francis Crick Institute from Cancer Research UK [FC001595]; UK Medical Research CouncilMedical Research Council UK (MRC); Wellcome TrustWellcome Trust [210119/Z/18/Z]; European Research CouncilEuropean Research Council (ERC) [852558]; Wellcome Trust Investigator awardWellcome Trust [217223/Z/19/Z]; Vallee Foundation; Social Sciences and Humanities Research Council of CanadaSocial Sciences and Humanities Research Council of Canada (SSHRC) [SSHRC IG 435-2014-0075]; State Assignment of the Sobolev Institute of Geology and Mineralogy; ZIN RAS [AAA-A19119032590102-7]; Smithsonian's Peter Buck Postdoctoral Fellowship; AHRC [AH/J001406/1]; SNIC-UPPMAX [b2016004]; UOXF ARC facilityAustralian Research Council; Wolfson College (University of Oxford); ERCEuropean Research Council (ERC) [ERC-2013-StG-337574-UNDEAD]; Natural Environmental Research CouncilNERC Natural Environment Research Council [NE/K005243/1, NE/K003259/1]; NERC Radiocarbon Facility [NF/2016/2/4] Ancient genome sequencing was supported by SciLifeLab National Projects and the Erik Philip Sorensen Foundation (to P.S.). A.B., T.D., and P.S. were supported by the Francis Crick Institute core funding (FC001595) from Cancer Research UK, the UK Medical Research Council, and the Wellcome Trust. P.S. was also supported by the European Research Council (grant no. 852558), a Wellcome Trust Investigator award (217223/Z/19/Z) and the Vallee Foundation. R.J.L. was supported by the Social Sciences and Humanities Research Council of Canada (#SSHRC IG 435-2014-0075). Y.K. was supported by State Assignment of the Sobolev Institute of Geology and Mineralogy. M.S. was supported by ZIN RAS (state assignment no. AAA-A19119032590102-7). A.T.L. was supported by the Smithsonian's Peter Buck Postdoctoral Fellowship. Archaeological work in Serbia was supported by AHRC grant AH/J001406/1. Computations were supported by SNIC-UPPMAX (b2016004) and the UOXF ARC facility. L.F. was supported by the Wellcome Trust (grant 210119/Z/18/Z) and by Wolfson College (University of Oxford). G.L. was supported by the ERC (grant ERC-2013-StG-337574-UNDEAD). G.L. and K.D. were supported by the Natural Environmental Research Council (grants NE/K005243/1 and NE/K003259/1). Dating was supported by the NERC Radiocarbon Facility (NF/2016/2/4).

The cave lion is an extinct felid that was widespread across the Holarctic throughout the Late Pleistocene. Its closest extant relative is the lion (Panthera leo), but the timing of the divergence between these two taxa, as well as their taxonomic ranking are contentious. In this study we analyse 31 mitochondrial genome sequences from cave lion individuals that, through a combination of 14C and genetic tip dating, are estimated to be from dates extending well into the mid-Pleistocene. We identified two deeply diverged and well-supported reciprocally monophyletic mitogenome clades in the cave lion, and an additional third distinct lineage represented by a single individual. One of these clades was restricted to Beringia while the other was prevalent across western Eurasia. These observed clade distributions are in line with previous observations that Beringian and European cave lions were morphologically distinct. The divergence dates for these lineages are estimated to be far older than those between extant lions subspecies. By combining our radiocarbon tip-dates with a split time prior that takes into account the most up-to-date fossil stem calibrations, we estimated the mitochondrial DNA divergence between cave lions and lions to be 1.85 Million ya (95% 0.52– 2.91 Mya). Taken together, these results support previous hypotheses that cave lions existed as at least two subspecies during the Pleistocene, and that lions and cave lions were distinct species.

International audience; Of the most abundant elemental constituents of organic matter, hydrogen has received the least attention due to its exchangeability with ambient water. The development of steam equilibration using two isotopically distinct waters can enable the user to calculate the proportion of exchangeable H and generate a δ2H value of the non-exchangeable H. Three fossil faunal assemblages from Europe were selected in order to investigate collagen δ2H with respect to body mass, diet and to compare chronological periods in the Quaternary. δ15N values in each suite of fauna show trophic level enrichment, a trend which was also observed in δ2H values. In the case of predatory species with lower δ15N values than other carnivore species, the use of hydrogen isotopes could help to infer the consumption of prey with lower δ15N values rather than a significant dietary contribution of plant foods. For example, a cave bear which exhibits low δ2H values are consistent with low δ15N and therefore point to an herbivorous diet and not omnivory. The combination of δ2H, with δ15N and δ13C, from archaeological and ecological studies of humans and fauna could help reconstruct prey preference; which is especially important when trying to distinguish the quantity of marine versus freshwater resources in diets. Relative to dietary influences, climate variability seems to be a minor control on δ2H in the faunal assemblages studied here.

Throughout time, climate changes have caused substantial rearrangements of habitats which have alternately promoted and disfavoured different types of taxa. At first glance, the mountain hare (Lepus timidus) shows the typical hallmarks of a cold-adapted species that has retreated to refugia since the onset of the current Holocene interglacial. In contrary to expectations, however, the species has a high contemporary genetic diversity with no clear differentiation between geographically isolated populations. In order to clarify the phylogeographic history of European mountain hares, we here analysed ancient DNA from the glacial populations that inhabited the previous midlatitude European tundra region. Our results reveal that the Ice Age hares had similar levels of genetic variation and lack of geographic structure as observed today, and the ancient samples were intermingled with modern individuals throughout the reconstructed evolutionary tree. This suggest a temporal genetic continuity in Europe, where the mountain hares were able to keep pace with the rapid changes at the last glacial/interglacial transition, and successfully track their shifting habitat to northern and alpine regions. Further, the temporal demographic analyses showed that the species’ population size in Europe appear to have been tightly linked with palaeoclimatic fluctuations, with increases and declines occurring during periods of global cooling and warming, respectively. Taken together, our results suggest that neither habitat shifts nor demographic fluctuations have had any substantial impact on the genetic diversity of European mountain hares. This remarkable resilience, which contrasts to a majority of previously investigated cold-adapted species, is likely due to its generalist nature which makes it less vulnerable to environmental changes.

The Late Pleistocene site “Troisieme caverne” of Goyet (Belgium) has yielded the broadest set of Neandertal remains in North-Western Europe and is associated with a rich and diverse large mammal assemblage. We reconstructed the dietary ecology at the site using stable isotope tracking (δ 13 C and δ 15 N) of bone collagen. The δ 13 C and δ 15 N values of all species are consistent with those observed in other “mammoth steppe” sites. The relative contribution of potential prey species to the diet of carnivores (including Neandertals) was evaluated using a Bayesian model. The distribution of individuals from herbivorous species and carnivorous ones was determined through cluster analysis in order to identify ecological niches, regardless of the individual species attribution. The Neandertals within the predator guild and the mammoth and reindeer as representatives of the herbivores occupied the most specific and most narrow ecological niches. The “Troisieme caverne” of Goyet can be regarded as a key site for the investigation of Late Pleistocene Neandertal ecology north of the Alps.

Karstic systems have preserved abundant archaeological records with well-represented faunal remains due to their sedimentological and topographical features. These particular localities were intensely exploited and occupied by Neanderthal groups. We focus here on Middle Palaeolithic settlements from the Last Glacial Period (MIS 5d-3), which is characterized by marked climatic variability with colder episodes alternating with more temperate periods. The Ardeche region in south-eastern France and the Meuse Basin in Belgium have recently been the focus of regional studies combining archaeological, geological and chronological data in order to bring to light human land-use and subsistence strategies. These two areas comprise multiple rock shelters and caves with Neanderthal occupations dating from MIS 5d to 3. As well as the obvious traces of occupation by Neanderthals, most sites provide evidence of carnivore occupations (e.g., cave bears, cave hyenas or wolves). Each of these habitation sites presents a specific topography and type of occupation and most of them reveal behavioural homogeneity within their sequences. By comparing data from faunal accumulations in these two related areas, separated by a distance of about one thousand kilometres, we attempt to gain a better understanding of the driving forces behind Neanderthal and animal occupations of karstic networks. Do regional land-use patterns exist in different European karstic localities or can we perceive common features related to the geography and topography of the sites?

Canids from the Upper Paleolithic site of Předmosti are central to debates concerning the domestication of dogs as two morphotypes were identified: Pleistocene wolf and Paleolithic dog (Germonpre et al., 2015a). In Prassack et al. (2020), we set out to determine whether specimens previously parsed into these two groups differed significantly in dental microwear textures, a proxy for diet. We did not assume that one group was comprised of dogs, but hypothesized that if they were, they would likely have consumed more bone, leading to microwear surface textures dominated by pitting. We indeed found significantly higher scales of maximum complexity on second lower molar crushing surfaces of the sample identified as Paleolithic dogs by Germonpre et al. (2015a), consistent with larger pits on average and more bone consumption. These results suggest that the two morphotypes identified by Germonpre et al. (2015a) represent ecologically distinct populations. This is in accord with the interpretation of domestication, but, as we noted, the groups could also represent two distinct wild canid populations with differing diets. Janssens et al. (2021) recently criticized our study, questioning our methods of analysis and claiming bias in our interpretation of results. We reply to their issues here, focusing only on those relevant to Prassack et al. (2020).

Summary Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modern legacy of past equestrian civilizations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN “speed gene,” only rose in popularity within the last millennium. Finally, the development of modern breeding impacted genetic diversity more dramatically than the previous millennia of human management., Graphical Abstract, Highlights • Two now-extinct horse lineages lived in Iberia and Siberia some 5,000 years ago • Iberian and Siberian horses contributed limited ancestry to modern domesticates • Oriental horses have had a strong genetic influence within the last millennium • Modern breeding practices were accompanied by a significant drop in genetic diversity, Genome-wide data from 278 ancient equids provide insights into how ancient equestrian civilizations managed, exchanged, and bred horses and indicate vast loss of genetic diversity as well as the existence of two extinct lineages of horses that failed to contribute to modern domestic animals.

While sequencing ancient DNA (aDNA) from archaeological material is now commonplace, very few attempts to sequence ancient transcriptomes have been made, even from typically stable deposition environments such as permafrost. This is presumably due to assumptions that RNA completely degrades relatively quickly, particularly when dealing with autolytic, nuclease-rich mammalian tissues. However, given the recent successes in sequencing ancient RNA (aRNA) from various sources including plants and animals, we suspect that these assumptions may be incorrect or exaggerated. To challenge the underlying dogma, we generated shotgun RNA data from sources that might normally be dismissed for such study. Here, we present aRNA data generated from two historical wolf skins, and permafrost-preserved liver tissue of a 14,300-year-old Pleistocene canid. Not only is the latter the oldest RNA ever to be sequenced, but it also shows evidence of biologically relevant tissue specificity and close similarity to equivalent data derived from modern-day control tissue. Other hallmarks of RNA sequencing (RNA-seq) data such as exon-exon junction presence and high endogenous ribosomal RNA (rRNA) content confirms our data’s authenticity. By performing independent technical library replicates using two high-throughput sequencing platforms, we show not only that aRNA can survive for extended periods in mammalian tissues but also that it has potential for tissue identification. aRNA also has possible further potential, such as identifying in vivo genome activity and adaptation, when sequenced using this technology., Ancient DNA is known to survive in cold environments for tens of millennia, but it is assumed that ancient RNA could not persist in such a way due to its relative instability. However, this study shows that under permafrost conditions, ancient RNA can survive well enough to show tissue specificity even in mammalian soft tissues.

How modern humans dispersed into Eurasia and Australasia, including the number of separate expansions and their timings, is highly debated [1, 2]. Two categories of models are proposed for the dispersal of non-Africans: (1) single dispersal, i.e., a single major diffusion of modern humans across Eurasia and Australasia [3-5]; and (2) multiple dispersal, i.e., additional earlier population expansions that may have contributed to the genetic diversity of some present-day humans outside of Africa [6-9]. Many variants of these models focus largely on Asia and Australasia, neglecting human dispersal into Europe, thus explaining only a subset of the entire colonization process outside of Africa [3-5, 8, 9]. The genetic diversity of the first modern humans who spread into Europe during the Late Pleistocene and the impact of subsequent climatic events on their demography are largely unknown. Here we analyze 55 complete human mitochondrial genomes (mtDNAs) of hunter-gatherers spanning ∼35,000 years of European prehistory. We unexpectedly find mtDNA lineage M in individuals prior to the Last Glacial Maximum (LGM). This lineage is absent in contemporary Europeans, although it is found at high frequency in modern Asians, Australasians, and Native Americans. Dating the most recent common ancestor of each of the modern non-African mtDNA clades reveals their single, late, and rapid dispersal less than 55,000 years ago. Demographic modeling not only indicates an LGM genetic bottleneck, but also provides surprising evidence of a major population turnover in Europe around 14,500 years ago during the Late Glacial, a period of climatic instability at the end of the Pleistocene.

Efforts to identify Paleolithic dogs or incipient dogs have been based mainly on examination of complete or nearly complete crania. Complete skulls are, however, very rare in the archaeological record. Because canid mandible are far more frequently found in Pleistocene assemblages, the objective of this study is to investigate whether it is possible to differentiate these jaws by metric and osteomorphological methods in two morphotypes: Paleolithic dogs and Pleistocene wolves. This paper is mainly based on the very rich canid assemblage from the Gravettian Předmosti site in the Czech Republic, but also includes a few mandible from several other European Paleolithic sites. This study provides additional evidence of the existence at Předmosti of the two canid morphotypes. The metric data indicate that the mandible of the Paleolithic dogs are shorter than those from Pleistocene wolves in all tested measurements of length, and the carnassial crown length is shorter in Paleolithic dogs compared with the length of this tooth in Pleistocene wolves. Furthermore, in eight of nine indexes, the Paleolithic dogs differ significantly from the Pleistocene wolves. The mandible of Paleolithic dogs differ also in non-metric features from the Pleistocene wolves: they present a high frequency of crowded premolars and backwards-oriented apex of the coronoid. This paper furthermore confirms that Paleolithic dogs occur at two late Upper Paleolithic sites (Eliseevichi, Verholenskaya) where previous studies had indicated their presence. In addition, we document the presence of Paleolithic dogs at another Gravettian site, Kostenki-8.

The Gravettian site of Předmosti I in the central Moravian Plain has yielded a rich and diverse large mammal fauna dated around 25–27,000 14 C years BP (ca. 29,500–31,500 cal BP). This fauna includes numerous carnivores (cave lion, wolf, brown bear, polar fox, wolverine) and herbivores (reindeer, large bovine, red deer, muskox, horse, woolly rhinoceros, woolly mammoth) whose trophic position could be reconstructed using stable isotopic tracking (δ 13 C, δ 15 N, δ 34 S) of bone collagen ( n = 63). Among large canids, two morphotypes, “Pleistocene wolves” and “Palaeolithic dogs”, were considered, and two human bones attributed to the Gravettian assemblage of Předmosti I were also sampled. The trophic system around the Gravettian settlement of Předmosti I showed the typical niche partitioning among herbivores and carnivores seen in other mammoth-steppe contexts. The contribution of the analyzed prey species to the diet of the predators, including humans, was evaluated using a Bayesian mixing model (SIAR). Lions included great amounts of reindeer/muskox and possibly bison in their diet, while Pleistocene wolves were more focused on horse and possibly mammoth. Strong reliance on mammoth meat was found for the human of the site, similarly to previously analyzed individuals from other Gravettian sites in Moravia. Interestingly, the large canids interpreted as “Palaeolithic dogs” had a high proportion of reindeer/muskox in their diet, while consumption of mammoth would be expected from the availability of this prey especially in case of close interaction with humans. The peculiar isotopic composition of the Palaeolithic dogs of Předmosti I may indicate some control of their dietary intake by Gravettian people, who could have use them more for transportation than hunting purpose.

This is a reply to the comments of Morey (2014) on our identification of Palaeolithic dogs from several European Palaeolithic sites. In his comments Morey (2014) presents some misrepresentations and misunderstandings that we remedy here. In contrast to what Morey (2014) propounds, our results suggest that the domestication of the wolf was a long process that started early in the Upper Palaeolithic and that since that time two sympatric canid morphotypes can be seen in Eurasian sites: Pleistocene wolves and Palaeolithic dogs. Contrary to Morey (2014), we are convinced that the study of this domestication process should be multidisciplinary.

Předmostí is one of the most famous Gravettian sites in Central Europe. Its fame is based on a unique human assemblage, sadly largely destroyed during the Second World War, a huge mammoth assemblage and a very rich large canid assemblage. It has been shown previously that mammoth played an important role in the subsistence practices of the Gravettian inhabitants of Předmostí. Detailed analyses of the large canid postcranial material were carried out to investigate whether these canid remains can be assigned to different size groups and whether these remains show evidence of being butchered and consumed by humans. Based on defleshing marks and impact traces on the long bones, it is proposed here that large canids were consumed by the Gravettian inhabitants of Předmostí, thus further elucidating the specific human-large canid relationships that existed during the Upper Palaeolithic.

This protocol provides an efficient DNA extraction and purification of historical museum hides, which potentially have been chemically tanned.

This protocol provides an efficient DNA extraction and purification of ancient bones.

This protocol provides an efficient DNA extraction and purification of ancient sorft tissue.

This single-tube library construction protocol is for degraded DNA using BGISeq-500 sequencing platform.

This single-tube library construction protocol is for degraded DNA using adapters for the Illumina platform.

Ancient DNA research has been revolutionized following the development of ‘Next Generation’ Sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant choice today, mainly because of high production capacities and short read production. Recently a potentially attractive alternative platform for palaeogenomic data generation has been developed, the BGISEQ-500, whose sequence output are comparable with the Illumina series. In this study, we modified the standard BGISEQ-500 library preparation specifically for use on degraded DNA, then directly compared the sequencing performance and data quality of the BGISEQ-500 to the Illumina HiSeq2500 platform, on DNA extracted from eight historic and ancient dog and wolf samples. The data generated was largely comparable between sequencing platforms, with no statistically significant difference observed for parameters including level (p=0.371) and average sequence length (p=0718) of endogenous nuclear DNA, sequence GC content (p=0.311), double-stranded DNA damage rate (p=0.309), and sequence clonality (p=0.093). Small significant differences were found in single strand DNA damage rate (δS, slightly lower for the BGISEQ-500, p=0.011) and the background rate of difference from the reference genome (θ, slightly higher for BGISEQ-500, p=0.012). This may result from the differences in amplification cycles used to PCR amplify the libraries. A significant difference was also observed in the mitochondrial DNA percentages recovered (p=0.018), although we believe this is likely a stochastic effect relating to the extremely low levels of mitochondria that were sequenced from three of the samples with overall very low levels of endogenous DNA. Although we acknowledge our analyses were limited to animal material, our observations suggest that the BGISEQ-500 holds the potential to represent valid and potentially valuable alternative platform for palaeogenomic data generation, that is worthy of future exploration by those interested in the sequencing and analysis of degraded DNA.

This chapter focuses on the mammoth (Mammuthus primigenius) and large canid (wolf (Canis lupus) and/or dog (Canis familiaris)) assemblages recorded at Upper Palaeolithic sites from the Russian Plain and Siberia. It accordingly pursues the following questions: (1) Is the mammoth ubiquitously found in the Upper Palaeolithic sites of Russia?, (2) Are large canids as often present at Siberian sites as they are at sites from the Russian Plain? and (3) Could the high frequency of the mammoth remains in several Upper Palaeolithic assemblages be due to hunting by prehistoric humans? Finally, this essay underlines the need for further studies in this area.

Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range. Our dataset includes 54 previously unpublished mitochondrial genomes and significantly increases the coverage of the Eurasian range of the species. The resulting global phylogeny confirms that the Late Pleistocene mammoth population comprised three distinct mitochondrial lineages that began to diverge ~1.0–2.0 million years ago (Ma). We also find that mammoth mitochondrial lineages were strongly geographically partitioned throughout the Pleistocene. In combination, our genetic results and the pattern of morphological variation in time and space suggest that male-mediated gene flow, rather than large-scale dispersals, was important in the Pleistocene evolutionary history of mammoths.

International audience; The Trou de Chaleux is a cave site located in Belgium. It delivered a rich late Magdalenian material culture constituted mainly of lithic artefacts but also including bone industries and figurative art. This paper presents the results of the analysis of the large collection of bird remains recovered by E. Dupont in 1865, which was yet unstudied from taphonomical and archaeozoological perspectives. In addition to the taxonomic identification,surface alterations were investigated based on a macro- and microscopic analysis, including an analysis of wear traces and elementary composition. Special attention is devoted to the presence of human modifications such as disarticulation or butchering marks, traces of heating, presence of colourants and traces of bone working. The taphonomic history of the bird assemblage is reconstructed and the use of birds by humans characterized, as well as their importance in past human activities. We also discuss evidence for seasonal exploitation and for reconstructingthe local environment and integrate our results with evidence from other Magdalenian assemblages from north-western Europe. At Trou de Chaleux, birds were used for food, as raw material for bone working and for symbolic purposes. The exploitation of avian products was intense, and species have been used for several purposes such as the raven and snowy owl having been exploited both for food and for symbolic reasons. Large bird bones were used as raw material to produce artefacts, but the use-wear analysis did not evidence unambiguous traces related to the use of the objects produced. Despite several limiting factors, the bird material from Trou de Chaleux considerably increases the knowledge of past human exploitation of birds during the late Magdalenian in north-western Europe.

Cave bears are among the most well known extinct Pleistocene mammals. Their biogeography and taxonomy, along with the factors that led to their extinction, have been subject to long-standing controversy. Here, we reconstruct the phylogeography as well as the temporal and spatial population dynamics of cave bears across their range using mitochondrial DNA control region sequences from 77 published as well as 65 new cave bear samples, Our analyses reveal a dramatic loss of genetic diversity in cave bear populations after 30,000 years before present and provide evidence for a range decline from east to west towards the onset of the last glacial maximum. Our results also suggest that the three major haplogroups within cave bears, which may correspond to distinct species, were previously more widespread, with relict populations in remote and alpine areas still harbouring haplotypes that have disappeared from most of their previous range. Applying a phylogenetic dating approach, we estimated the age of the oldest of our samples, originating from the Yana River region in north-eastern Siberia, to be around 178,000 years, which confirms a previous estimate of a Middle Pleistocene age based on its stratigraphic position. Our results extend our knowledge about the evolutionary history of cave bears, but they also show that to unravel the complexities of cave bear evolution future ancient DNA studies on this Pleistocene species will need to go beyond short mitochondrial DNA fragments, including full mitochondrial genomes as well as nuclear DNA sequences.

Spy, a Belgian cave site famous for its Neanderthal remains, contains a wide spectrum of Pleistocene species. Horse, cave hyena, woolly mammoth, woolly rhinoceros and reindeer are the primary taxa. The Spy cave was used alternately by prehistoric humans and Pleistocene carnivores. This study considers whether prehistoric humans or carnivores are responsible for the large number of mammoth remains at the site. It is argued, on the basis of the frequency distribution of the skeletal elements of the mammoth, the age distribution of the mammoth molars, and the diet of the large carnivores and of the prehistoric humans, that the mammoth assemblage of Spy accumulated at the site through the activities of prehistoric humans. On the basis of AMS dates, the stratigraphic position of a number of mammoth molars and the absence of red ochre on the mammoth molars, it was concluded that these prehistoric humans were Neanderthals rather than Anatomically Modern Humans.

Ancient DNA research has been revolutionized following development of next-generation sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant choice today, mainly because of high production capacities and short read production. Recently a potentially attractive alternative platform for palaeogenomic data generation has been developed, the BGISEQ-500, whose sequence output are comparable with the Illumina series. In this study, we modified the standard BGISEQ-500 library preparation specifically for use on degraded DNA, then directly compared the sequencing performance and data quality of the BGISEQ-500 to the Illumina HiSeq2500 platform on DNA extracted from 8 historic and ancient dog and wolf samples. The data generated were largely comparable between sequencing platforms, with no statistically significant difference observed for parameters including level (P = 0.371) and average sequence length (P = 0718) of endogenous nuclear DNA, sequence GC content (P = 0.311), double-stranded DNA damage rate (v. 0.309), and sequence clonality (P = 0.093). Small significant differences were found in single-strand DNA damage rate (δS; slightly lower for the BGISEQ-500, P = 0.011) and the background rate of difference from the reference genome (θ; slightly higher for BGISEQ-500, P = 0.012). This may result from the differences in amplification cycles used to polymerase chain reaction-amplify the libraries. A significant difference was also observed in the mitochondrial DNA percentages recovered (P = 0.018), although we believe this is likely a stochastic effect relating to the extremely low levels of mitochondria that were sequenced from 3 of the samples with overall very low levels of endogenous DNA. Although we acknowledge that our analyses were limited to animal material, our observations suggest that the BGISEQ-500 holds the potential to represent a valid and potentially valuable alternative platform for palaeogenomic data generation that is worthy of future exploration by those interested in the sequencing and analysis of degraded DNA. The authors would like to acknowledge the ERC Consolidator Grant (681396 - Extinction Genomics), the Marie Skłodowska-Curie Actions (H2020-MSCA-ETN-643063 “Microwine”), Danish Council for Independent Research (4005-00107 Wine-ometrics), the Qimmeq project, funded by The Velux Foundations and Aage og Johanne Louis-Hansens Fond, China National GeneBank, and BGI-Shenzhen China for funding. L.F.K.K is supported by an FPI fellowship associated with BFU2014-55090-P (FEDER), T.M.B. is supported by MINECO BFU2014-55090-P (FEDER) and BFU2015-6215-ERC, a U01 MH106874 grant, and the Secretaria d'Universitats i Recerca del Departament d'Economia i Coneixement de la Generalitat de Catalunya.