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Extinct cave bears inhabited a large part of Eurasia in a wide diversity of habitats during the Pleistocene. This study investigates via tooth wear analysis the feeding habits of 66 individuals bel...

During the past several decades, the paleoecology of the Mammuthus-Coelodonta Faunal Complex in the Palearctic has been thoroughly explored, especially using stable isotope analysis. Numerous studies have documented high ecological plasticity and regional heterogeneities for this fauna. However, very limited attention has focused on Northeast Asia, at the southeastern edge of the distribution of the mammoth steppe biome. In the present study, we undertook radiocarbon dating, zooarchaeology by mass spectrometry (ZooMS), and stable isotope analysis on the fossil faunas from Yanjiagang Paleolithic site, Northeast (NE) China, and from the Geographical Society Cave in the nearby Russian Far East, to explore the paleoecology of this fauna in this middle-latitude region. Isotopic (δ13C, δ15N) data from these two sites suggested that the woolly mammoth (Mammuthus primigenius) was a grazer feeding on grasses/sedges, while the woolly rhinoceros (Coelodonta antiquitatis) and steppe bison (Bison priscus) utilized a wider range of food resources. All megaherbivores exhibited some ecological plasticity. Meanwhile, the mammal remains from Geographical Society Cave prevalently exhibited lower δ15N values than those from China, indicating variable environments and vegetation in Northeast Asia during MIS 3. Interestingly, through reevaluating the diachronic mammal distribution and ecology based on direct radiocarbon dating and ZooMS, we report the credible presence of Bubalus, typically interpreted as a mild climate faunal element in the Pleistocene, within the Mammuthus-Coelodonta Faunal Complex in Yanjiagang. This emphasizes the unique scenario of this biome in Northeast Asia, where the fauna exhibited sensitivity to synergic effects of climatic oscillations and local geographic traits. After comparing isotopic data of mammoth from different subregions of Asia, we found that NE China displayed both highest δ13C and δ15N values, possibly related to the higher temperature compared to the Arctic regions. This study reveals the characteristics and complexity at the southeastern limit of the range of the mammoth steppe biome and urges more systematic studies within and outside this region.

Lions are one of the world’s most iconic megafauna, yet little is known about their temporal and spatial demographic history and population differentiation. We analyzed a genomic dataset of 20 specimens: two ca. 30,000-y-old cave lions (Panthera leo spelaea), 12 historic lions (Panthera leo leo/Panthera leo melanochaita) that lived between the 15th and 20th centuries outside the current geographic distribution of lions, and 6 present-day lions from Africa and India. We found that cave and modern lions shared an ancestor ca. 500,000 y ago and that the 2 lineages likely did not hybridize following their divergence. Within modern lions, we found 2 main lineages that diverged ca. 70,000 y ago, with clear evidence of subsequent gene flow. Our data also reveal a nearly complete absence of genetic diversity within Indian lions, probably due to well-documented extremely low effective population sizes in the recent past. Our results contribute toward the understanding of the evolutionary history of lions and complement conservation efforts to protect the diversity of this vulnerable species., S.J.O, was supported, in part, by St. Petersburg State University (Genome Russia Grant no. 1.52.1647.2016). T.M.-B. is supported by funding from BFU2017-86471-P (MINECO/FEDER, UE), Howard Hughes International Early Career, Obra Social “La Caixa” and Secretaria d’Universitats i Recerca and Centres de Recerca de Catalunya (CERCA) Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880). We also acknowledge European Research Council (ERC) Consolidator Award 681396-Extinction Genomics to M.T.P.G. and Marie-Sklodowska Curie Fellowship 298820 “SIMBA” to R.B. for their generous funding.

Museum collections are essential for reconstructing and understanding past biodiversity. Many museum specimens are, however, challenging to identify. Museum samples may be incomplete, have an unusual morphology, or represent juvenile individuals, all of which complicate accurate identification. In some cases, inaccurate identification can lead to false biogeographic reconstructions with cascading impacts on paleontological and paleoecological research. Here, we analyzed an unusual Equid mandible found in the Far North of the Taymyr peninsula that was identified morphologically as Equus hemionus, an ancestor of present-day Asiatic wild asses. If correct, this identification represents the only finding of a putative Late Pleistocene hemione in the Arctic region, and is therefore critical to understanding wild ass evolution and paleoecology. To confirm the accuracy of this specimen's taxonomic assignment, we used ancient DNA and mitochondrial hybridization capture to identify and place this specimen in the larger equid phylogeny. We find that the specimen is actually a member of E. caballus, the ancestor of domestic horses. Our study demonstrates the utility of ancient DNA to validate morphological identification, in particular of incomplete, otherwise problematic, or taxonomically unusual museum specimens.

Morphometric and morphotypic variability of the cave bear lower incisors from two different geographic regions (Caucasus and Urals), different stratigraphic periods (Middle and Late Pleistocene), and bearing different mitochondrial haplogroups (kudarensis (Baryshnikov, 1985) and ingressus Rabeder, Hofreiter & Withalm, 2004) was studied. Urals Ursuskanivetz Vereshchagin, 1973 is clearly distinguished from Caucasian U. kudarensis by morphology of the upper and lower incisors. The Urals cave bear exhibits more derived features compared to the Caucasian cave bears. Ursus kanivetz exhibits the largest average size of the lower incisors. The lower incisors of U. kanivetz are clearly distinct from those in U. kudarensis. Also, U.kudarensis specimens display a clear separation from all other groups of cave bears. Morphology of the incisors of the cave bears is clearly different from that of Early Pleistocene U. etruscus G. Cuvier, 1823, as well as from that of recent U. arctos L., 1758 (Rabeder, 1999) and U. maritimus Phipps, 1774. Our results suggest that the incisors of the cave bears are similar to each other and demonstrate a hypocarnivorous adaptation as a major evolution trend in the lineage of Spelearctos group. These adaptation features were perhaps developed in parallel in different lineages of the cave bears (U. spelaeus Rosenmüller, 1794 and U. kanivetz on the one hand and U. kudarensis on the other hand) in the Late Pleistocene.

The Bering Land Bridge (BLB) last connected Eurasia and North America during the Late Pleistocene. Although the BLB would have enabled transfers of terrestrial biota in both directions, it also acted as an ecological filter whose permeability varied considerably over time. Here we explore the possible impacts of this ecological corridor on genetic diversity within, and connectivity among, populations of a once wide-ranging group, the caballine horses (Equus spp.). Using a panel of 187 mitochondrial and eight nuclear genomes recovered from present-day and extinct caballine horses sampled across the Holarctic, we found that Eurasian horse populations initially diverged from those in North America, their ancestral continent, around 1.0–0.8 million years ago. Subsequent to this split our mitochondrial DNA analysis identified two bidirectional long-range dispersals across the BLB ~875–625 and ~200–50 thousand years ago, during the Middle and Late Pleistocene. Whole genome analysis indicated low levels of gene flow between North American and Eurasian horse populations, which probably occurred as a result of these inferred dispersals. Nonetheless, mitochondrial and nuclear diversity of caballine horse populations retained strong phylogeographical structuring. Our results suggest that barriers to gene flow, currently unidentified but possibly related to habitat distribution across Beringia or ongoing evolutionary divergence, played an important role in shaping the early genetic history of caballine horses, including the ancestors of living horses within Equus ferus. © 2021 John Wiley & Sons Ltd 19-05-00477, AAAA-A19-119032590102-7; National Science Foundation, NSF: ARC-1417036; Gordon and Betty Moore Foundation, GBMF: 3804; University of California, Santa Cruz, UCSC; U.S. Bureau of Land Management, BLM; Horizon 2020 Framework Programme, H2020: 681605; Seventh Framework Programme, FP7: IEF-302617; Natural Sciences and Engineering Research Council of Canada, NSERC; Marie Curie; European Research Council, ERC; Svenska Forskningsrådet Formas: 2018-01640; Russian Foundation for Basic Research, РФФИ: 18-04-00327; Knut och Alice Wallenbergs Stiftelse; Vetenskapsrådet, VR; Science for Life Laboratory, SciLifeLab We are grateful to the placer gold mining community, the Tr’ondëk Hwëch’in First Nation, and the Vuntut Gwitchin First Nation for their collaboration and support with our research in Yukon. Tamara Pico, Sarah Crump and Paul Koch provided advice interpreting the palaeoclimate of Beringia. Data generation was supported with funds from NSF ARC-1417036, the Gordon & Betty Moore Foundation (no. 3804) and the American Wild Horse Campaign. A.O.V. was additionally supported by a UCSC Chancellor’s Dissertation Year Fellowship and the CANA Foundation. M.T. and D.G. were supported by the Russian Foundation for Basic Research (project 18-04-00327), and L.E. by a Marie-Curie Intra-European fellowship (FP7, IEF-302617). G.B. is supported by the Federal theme of Zoological Institute of the Russian Academy of Sciences no. AAAA-A19-119032590102-7. S.V. was funded by the Russian Foundation for Basic Research, Grant 19-05-00477. L.D. acknowledges support from FORMAS (project 2018-01640). D.F. was supported by the Natural Science and Engineering Research Council. P.G. and D.M. are supported by the Bureau of Land Management. We acknowledge support from Science for Life Laboratory, the Knut and Alice Wallenberg Foundation, the National Genomics Infrastructure funded by the Swedish Research Council, and Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. L.O. received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement 681605). We are grateful to the placer gold mining community, the Tr?ond?k Hw?ch?in First Nation, and the Vuntut Gwitchin First Nation for their collaboration and support with our research in Yukon. Tamara Pico, Sarah Crump and Paul Koch provided advice interpreting the palaeoclimate of Beringia. Data generation was supported with funds from NSF ARC-1417036, the Gordon & Betty Moore Foundation (no. 3804) and the American Wild Horse Campaign. A.O.V. was additionally supported by a UCSC Chancellor?s Dissertation Year Fellowship and the CANA Foundation. M.T. and D.G. were supported by the Russian Foundation for Basic Research (project 18-04-00327), and L.E. by a Marie-Curie Intra-European fellowship (FP7, IEF-302617). G.B. is supported by the Federal theme of Zoological Institute of the Russian Academy of Sciences no. AAAA-A19-119032590102-7. S.V. was funded by the Russian Foundation for Basic Research, Grant 19-05-00477. L.D. acknowledges support from FORMAS (project 2018-01640). D.F. was supported by the Natural Science and Engineering Research Council. P.G. and D.M. are supported by the Bureau of Land Management. We acknowledge support from Science for Life Laboratory, the Knut and Alice Wallenberg Foundation, the National Genomics Infrastructure funded by the Swedish Research Council, and Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. L.O. received funding from the European Research Council (ERC) under the European Union?s Horizon 2020 research and innovation programme (grant agreement 681605).

Muskox Ovibos moschatus is a Pleistocene relic, which has survived only in North America and Greenland. During the Pleistocene, it was widely distributed in Eurasia and North America. To evaluate its morphological variability through time and space, we conducted an extensive morphometric study of 217 Praeovibos and Ovibos skull remains. The analyses showed that the skulls grew progressively wider from Praeovibos sp. to the Pleistocene O. moschatus, while from the Pleistocene to the recent O. moschatus, the facial regions of the skull turned narrower and shorter. We also noticed significant geographic differences between the various Pleistocene Ovibos crania. Siberian skulls were usually larger than those from Western and Central Europe. Eastern Europeanmuskoxen also exceeded in size those from the other regions of Europe. The large size of Late Pleistocene muskoxen from regions located in more continental climatic regimes was probably associated with the presence of more suitable food resources in steppe-tundra settings. Consistently, radiocarbon-dated records of this species are more numerous in colder periods, when the steppe-tundra was widely spread, and less abundant in warmer periods.

New finds of brown bear (Ursus arctos L., 1758) fossil remains from the territory of Yakutia, namely, skulls and mandibular bones, have been investigated. The new finds are exceptionally large: most dimensions of these specimens exceed those of the present-day brown bears of Yakutia and even the maximal parameters of the largest individuals of the present-day Eurasian subspecies U. a. beringianus and U. a. piscator. Analysis of various data showed that giant brown bears had inhabited northern Yakutia during the Karginian interstadial in the Late Pleistocene.

Morphometric and morphotypic variability of the cave bear upper incisors from two different geographic regions (Caucasus and Urals), different stratigraphic periods (middle and late Pleistocene), and bearing different mitochondrial haplogroups (kudarensis and ingressus) was studied. The specific diet of the cave bears, i.e. hard vegetables, led to noticeable differences between their incisors and the incisors of the brown bear (Ursus arctos). It was found that the upper incisors of the Caucasian cave bears from different stratigraphic periods demonstrate consistent development of their morphology. The late Pleistocene cave bears from the Urals show a greater similarity to the Caucasian cave bears from earlier periods than with the cave bears from later periods. Our results suggest that the incisor morphology has evolved independently in the Caucasian and Ural cave bears as they belong to different phylogenetic lineages and display different ways of adaptation to local environmental conditions.

Palaeogenomes provide the potential to study evolutionary processes in real time, but this potential is limited by our ability to recover genetic data over extended timescales.1 As a consequence, most studies so far have focused on samples of Late Pleistocene or Holocene age, which covers only a small part of the history of many clades and species. Here, we report the recovery of a low coverage palaeogenome from the petrous bone of a ∼360,000 year old cave bear from Kudaro 1 cave in the Caucasus Mountains. Analysis of this genome alongside those of several Late Pleistocene cave bears reveals widespread mito-nuclear discordance in this group. Using the time interval between Middle and Late Pleistocene cave bear genomes, we directly estimate ursid nuclear and mitochondrial substitution rates to calibrate their respective phylogenies. This reveals post-divergence mitochondrial transfer as the dominant factor explaining their mito-nuclear discordance. Interestingly, these transfer events were not accompanied by large-scale nuclear introgression. However, we do detect additional instances of nuclear admixture among other cave bear lineages, and between cave bears and brown bears, which are not associated with mitochondrial exchange. Genomic data obtained from the Middle Pleistocene cave bear petrous bone has thus facilitated a revised evolutionary history of this extinct megafaunal group. Moreover, it suggests that petrous bones may provide a means of extending both the magnitude and time depth of palaeogenome retrieval over substantial portions of the evolutionary histories of many mammalian clades.

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).

Significance Archaeological evidence indicates that domestic pigs arrived in Europe, alongside farmers from the Near East ∼8,500 y ago, yet mitochondrial genomes of modern European pigs are derived from European wild boars. To address this conundrum, we obtained mitochondrial and nuclear data from modern and ancient Near Eastern and European pigs. Our analyses indicate that, aside from a coat color gene, most Near Eastern ancestry in the genomes of European domestic pigs disappeared over 3,000 y as a result of interbreeding with local wild boars. This implies that pigs were not domesticated independently in Europe, yet the first 2,500 y of human-mediated selection applied by Near Eastern Neolithic farmers played little role in the development of modern European pigs., Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.

Westbury et al. reveal the genome-level evolutionary relationships between extinct cave and extant spotted hyena., The genus Crocuta (African spotted and Eurasian cave hyenas) includes several closely related extinct and extant lineages. The relationships among these lineages, however, are contentious. Through the generation of population-level paleogenomes from late Pleistocene Eurasian cave hyena and genomes from modern African spotted hyena, we reveal the cross-continental evolutionary relationships between these enigmatic hyena lineages. We find a deep divergence (~2.5 Ma) between African and Eurasian Crocuta populations, suggesting that ancestral Crocuta left Africa around the same time as early Homo. Moreover, we find discordance between nuclear and mitochondrial phylogenies and evidence for bidirectional gene flow between African and Eurasian Crocuta after the lineages split, which may have complicated prior taxonomic classifications. Last, we find a number of introgressed loci that attained high frequencies within the recipient lineage, suggesting some level of adaptive advantage from admixture.

Palaeogenomes provide the potential to study evolutionary processes in real time⁠, but this potential is limited by our ability to recover genetic data over extended timescales. The Late Pleistocene currently represents the age-limit for temperate-zone palaeogenome retrieval. Consequently, large portions of the evolutionary histories of many organismal clades remain inaccessible for direct genomic investigation. Here, we present the palaeogenome of a 367,000 year old cave bear from Kudaro 1 cave in the Caucasus. Analysis of this genome alongside those of Late Pleistocene representatives almost completely overturns the established view of cave bear evolution based on mitochondrial DNA. The Middle Pleistocene genome further allows us to directly estimate the ursine substitution rate to calibrate our revised nuclear genome phylogeny of Palaearctic bears. This reveals the Middle Pleistocene Transition as a key period in Palaearctic bear evolution, associated with the divergence of the major cave bear lineages, the divergence of brown and polar bears, and the end of gene flow between cave bears and brown bears. With an age encompassing an estimated 23% of the entire evolutionary history of cave bears, the Kudaro 1 genome extends the limit for temperate-zone palaeogenome retrieval well into the Middle Pleistocene.

Over 60% of the modern distribution range of brown bears falls within Russia, yet palaeoecological data from the region remain scarce. Complete modern Russian brown bear mitogenomes are abundant in the published literature, yet examples of their ancient counterparts are absent. Similarly, there is only limited stable isotopic data of prehistoric brown bears from the region. We used ancient DNA and stable carbon (δ13C) and nitrogen (δ15N) isotopes retrieved from five Pleistocene Yakutian brown bears (one Middle Pleistocene and four Late Pleistocene), to elucidate the evolutionary history and palaeoecology of the species in the region. We were able to reconstruct the complete mitogenome of one of the Late Pleistocene specimens, but we were unable to assign it to any of the previously published brown bear mitogenome clades. A subsequent analysis of published mtDNA control region sequences, which included sequences of extinct clades from other geographic regions, assigned the ancient Yakutian bear to the extinct clade 3c; a clade previously identified from Late Quaternary specimens from Eastern Beringia and Northern Spain. Our analyses of stable isotopes showed relatively high δ15N values in the Pleistocene Yakutian brown bears, suggesting a more carnivorous diet than contemporary brown bears from Eastern Beringia.

International audience; Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local Euro-pean wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process. domestication | evolution | gene flow | Neolithic

This article discusses recent finds of Holocene polar bear and walrus from the northern regions of Russia. The ulna of a polar bear was found on Vaygach Island and radiocarbon dated to 1,971 +/- 25 BP (OxA-23631). This calibrates to 430-540 AD, taking into account the marine reservoir effect. The size of the bone is similar to that of a recent Ursus maritimus. The locality of the fossil bone is within the modern species range, which developed about two millennia ago. In 2014 a walrus tusk was found on the coast of New Siberia Island and is radiocarbon dated to 5,065 +/- 35 BP (GrA-62452). This calibrates to 3,510-3,370 BC, taking into account the marine reservoir effect. Its size and morphology are identical to that of an adult male of the subspecies Odobenus rosmarus laptevi. This subspecies populates the eastern parts of the Kara Sea, the entire Laptev Sea and the western parts of the East Siberian Sea. This new discovery could mean that populations of O. rosmarus laptevi inhabited the waters near the New Siberian Islands during the Middle Holocene, and that the present-day coastline of the Siberian Arctic Islands was already formed at that time.

BackgroundResolving the historical biogeography of the leopard(Panthera pardus)is a complex issue, because patterns inferred from fossils and from molecular data lack congruence. Fossil evidence supports an African origin, and suggests that leopards were already present in Eurasia during the Early Pleistocene. Analysis of DNA sequences however, suggests a more recent, Middle Pleistocene shared ancestry of Asian and African leopards. These contrasting patterns led researchers to propose a two-stage hypothesis of leopard dispersal out of Africa: an initial Early Pleistocene colonisation of Asia and a subsequent replacement by a second colonisation wave during the Middle Pleistocene. The status of Late Pleistocene European leopards within this scenario is unclear: were these populations remnants of the first dispersal, or do the last surviving European leopards share more recent ancestry with their African counterparts?ResultsIn this study, we generate and analyse mitogenome sequences from historical samples that span the entire modern leopard distribution, as well as from Late Pleistocene remains. We find a deep bifurcation between African and Eurasian mitochondrial lineages (∼710 Ka), with the European ancient samples as sister to all Asian lineages (∼483 Ka). The modern and historical mainland Asian lineages share a relatively recent common ancestor (∼122 Ka), and we find one Javan sample nested within these.ConclusionsThe phylogenetic placement of the ancient European leopard as sister group to Asian leopards suggests that these populations originate from the same out-of-Africa dispersal which founded the Asian lineages. The coalescence time found for the mitochondrial lineages aligns well with the earliest undisputed fossils in Eurasia, and thus encourages a re-evaluation of the identification of the much older putative leopard fossils from the region. The relatively recent ancestry of all mainland Asian leopard lineages suggests that these populations underwent a severe population bottleneck during the Pleistocene. Finally, although only based on a single sample, the unexpected phylogenetic placement of the Javan leopard could be interpreted as evidence for exchange of mitochondrial lineages between Java and mainland Asia, calling for further investigation into the evolutionary history of this subspecies.

The analysis of bone remains of canids from the Upper-Pleistocene deposits of Geographical Society Cave in Primorskii Territory, Russia, revealed the presence of 4 species: Nyctereutes procyonoides, Canis lupus, Cuon alpinus, and Vulpes vulpes. Their accumulation is associated predominantly with the food activity of larger carnivores (Crocuta ultima, Panthera tigris), which used the cave as a den. No reliable signs of utilization of canids by ancient people were detected.

For the first time, morphometric variation has been studied in metacarpal and metatarsal bones of all known taxa of cave bears, which belong to different molecular genetic groups (deningeri, kudarensis, spelaeus, and ingressus haplotypes). The examined material involves nearly three thousand specimens from 28 localities of Europe, the Urals, Caucasus, and Central Asia. For comparison we used samples of fossil and recent Ursus arctos, as well as U. etruscus, regarded as a common ancestor of brown bears and cave bears. Methods of univariate and multivariate statistical analyses of metapodial bones were employed, providing an opportunity to ascertain the degree of sexual dimorphism in different taxa, the degree of morphological difference between taxa, and to define “size” and “shape” morphospaces for concise description of morphological diversity and classification of cave bears. Our study reveals that, on average, sexual dimorphism is more pronounced in U. arctos and U. kudarensis praekudarensis than in cave bears. Sexual dimorphism of bear metapodia is greater than sexual dimorphism of the skull (Baryshnikov and Puzachenko 2011). The contribution of sexual dimorphism to size of the metapodials is close to a contribution associated with morphological disparity between the bears belonging to different taxa. By the example of two chronosubspecies of Kudaro cave bear: U. kudarensis praekudarensis from Middle Pleistocene and U. k. kudarensis from Late Pleistocene, we succeeded in detecting a decrease of sexual dimorphism over time, which suggests that earlier cave bears inherited a pronounced sexual dimorphism from ancestral taxa. Metacarpal and metatarsal bones of cave bears are easily distinguished from those of U. etruscus and U. arctos, simultaneously demonstrating similarity between cave bears from different genetic groups, involving the species U. kudarensis (the basal taxon for all cave bears, including U. deningeri); some peculiarities of these bones are revealed only in the smaller U. rossicus. The examples have shown the presence (U. k. kudarensis) as well as absence (U. deningeri, U. kanivetz ingressus) of evident spatial (geographical) and temporal patterns in metapodial variability. It is determined that taxa can be better differentiated by metacarpals rather than by metatarsals, because the latter proved to be more “conservative” and less variable over time. It is hypothesized that very rapid modification of metapodial bones occurred at an early stage of evolution of this group, which was presumably a result of occupation of a special ecological niche by cave bears. This study reveals that the size and shape of metacarpal and metatarsal bones did not have an observable link with the taxonomic or evolutionary position of cave bears. At the same time, the clear morphological differences between brown bears and cave bears reflect an early evolutionary divergence between “arctoid” and “spelaeoid” lineages.

Retracing complex population processes that precede extreme population bottlenecks is often impossible based solely on data from living individuals. Such knowledge, however, can be crucial both to elucidate evolutionary histories and to inform appropriate conservation measures. The wisent (Bison bonasus), Europe's largest terrestrial mammal, represents a species that is exemplary for such a population history. Wisent went extinct in the wild within the last century, largely as a result of anthropogenic factors, but were restored by captive breeding starting from a small group of individuals. We investigate patterns of admixture occurring before and after this extinction using low-coverage genomic data from modern individuals, as well as from four historical samples representing two of the original founding lowland wisent and two individuals of the now extinct Caucasian wisent subspecies. Phylogenetic analysis of genomic blocks returns lowland and Caucasian wisent as reciprocally monophyletic across slightly more than half the genomic alignment. Thus, almost half of the complete genomic alignment contradicts the species tree, which is sufficient for whole genome averages to fail to recover the true population history. We also find evidence of admixture between lowland and Caucasian wisent and also, preceding wisent extinction in the wild, between wisent and the cattle/aurochs lineage. In a modern individual that is descended from both lowland wisent and the last surviving Caucasian wisent bull, we are able to not only detect a significant component of Caucasian wisent ancestry, but also to accurately map likely admixed genomic blocks along each chromosome. Overall, our study shows that the evolution of wisent has been substantially more complex than previously thought. We also establish wisent as an exemplary taxon for the study of admixture in wild populations.

Saber-toothed cats (Machairodontinae) are among the most widely recognized representatives of the now largely extinct Pleistocene megafauna. However, many aspects of their ecology, evolution, and extinction remain uncertain. Although ancient-DNA studies have led to huge advances in our knowledge of these aspects of many other megafauna species (e.g., mammoths and cave bears), relatively few ancient-DNA studies have focused on saber-toothed cats [1–3], and they have been restricted to short fragments of mitochondrial DNA. Here we investigate the evolutionary history of two lineages of saber-toothed cats (Smilodon and Homotherium) in relation to living carnivores and find that the Machairodontinae form a well-supported clade that is distinct from all living felids. We present partial mitochondrial genomes from one S. populator sample and three Homotherium sp. samples, including the only Late Pleistocene Homotherium sample from Eurasia [4]. We confirm the identification of the unique Late Pleistocene European fossil through ancient-DNA analyses, thus strengthening the evidence that Homotherium occurred in Europe over 200,000 years later than previously believed. This in turn forces a re-evaluation of its demography and extinction dynamics. Within the Machairodontinae, we find a deep divergence between Smilodon and Homotherium (∼18 million years) but limited diversity between the American and European Homotherium specimens. The genetic data support the hypothesis that all Late Pleistocene (or post-Villafrancian) Homotherium should be considered a single species, H. latidens, which was previously proposed based on morphological data [5, 6]. Paijmans et al. present ancient DNA from some of the most recognized extinct Pleistocene megafauna: the saber-toothed cats. The results elucidate the evolutionary history of these iconic carnivores and provide genetic evidence that saber-toothed cats existed in Europe over 200,000 years later than previously believed., This project received funding from the European Research Council (consolidator grant GeneFlow no. 310763 to M.H.), European Union’s Seventh Framework Programme for research, technological development, and demonstration (grant no. FP7-PEOPLE-2011-IEF-298820 to R.B.), and Lundbeck Foundation (grant no. R52-A5062 to M.L.Z.-M.).

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.

Bone fragments of large anadromous salmon in the Middle Palaeolithic archaeological layers of Kudaro 3 cave (Caucasus) suggested fish consumption by archaic Hominins, such as Neandertals. However, large carnivores such as Asiatic cave bears (Ursus kudarensis) and cave lions (Panthera spelaea) were also found in the cave and could have been responsible for such an accumulation. The diet of these carnivores was evaluated using carbon, nitrogen and sulphur isotopes in faunal bone collagen. The results suggest that anadromous fish were neither part of the diet of either cave bear (vegetarian) or cave lion (predators of herbivores from arid areas) and therefore provide indirect support to the idea that Middle Palaeolithic Hominins, probably Neandertals, were able to consume fish when it was available.

Sequence analyses of the complete brown bear, Ursus arctos, mitochondrial DNA (mtDNA) genome have detected scattered single nucleotide polymorphisms (SNPs) that define distinct mtDNA haplogroups in phylogeographical studies. The degraded DNA in historical samples, such as stuffed or excavated specimens, however, is often not suitable for sequence analyses. To address this problem, we developed an amplified product length polymorphism (APLP) analysis for mtDNA-haplogrouping U. arctos specimens by detecting haplogroup-specific SNPs. We verified the validity and utility of this method by analysing up to 170-year-old skin samples from U. arctos specimens collected widely across continental Eurasia. We detected some of the same haplogroups as those occurring in eastern Hokkaido (Japan) and eastern Alaska in continental Eurasia (the Altai and the Caucasus). Our results show that U. arctos in eastern Hokkaido and eastern Alaska descended from a common ancestor in continental Eurasia, and suggest that U. arctos occupied several refugia in southern Asia during the Last Glacial Maximum. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111, 627-635.

Background Climatic and environmental fluctuations as well as anthropogenic pressure have led to the extinction of much of Europe’s megafauna. The European bison or wisent (Bison bonasus), one of the last wild European large mammals, narrowly escaped extinction at the onset of the 20th century owing to hunting and habitat fragmentation. Little is known, however, about its origin, evolutionary history and population dynamics during the Pleistocene. Results Through ancient DNA analysis we show that the emblematic European bison has experienced several waves of population expansion, contraction, and extinction during the last 50,000 years in Europe, culminating in a major reduction of genetic diversity during the Holocene. Fifty-seven complete and partial ancient mitogenomes from throughout Europe, the Caucasus, and Siberia reveal that three populations of wisent (Bison bonasus) and steppe bison (B. priscus) alternately occupied Western Europe, correlating with climate-induced environmental changes. The Late Pleistocene European steppe bison originated from northern Eurasia, whereas the modern wisent population emerged from a refuge in the southern Caucasus after the last glacial maximum. A population overlap during a transition period is reflected in ca. 36,000-year-old paintings in the French Chauvet cave. Bayesian analyses of these complete ancient mitogenomes yielded new dates of the various branching events during the evolution of Bison and its radiation with Bos, which lead us to propose that the genetic affiliation between the wisent and cattle mitogenomes result from incomplete lineage sorting rather than post-speciation gene flow. Conclusion The paleogenetic analysis of bison remains from the last 50,000 years reveals the influence of climate changes on the dynamics of the various bison populations in Europe, only one of which survived into the Holocene, where it experienced severe reductions in its genetic diversity. The time depth and geographical scope of this study enables us to propose temperate Western Europe as a suitable biotope for the wisent compatible with its reintroduction. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0317-7) contains supplementary material, which is available to authorized users.

To further elucidate the migration history of the brown bears (Ursus arctos) on Hokkaido Island, Japan, we analyzed the complete mitochondrial DNA (mtDNA) sequences of 35 brown bears from Hokkaido, the southern Kuril Islands (Etorofu and Kunashiri), Sakhalin Island, and the Eurasian Continent (continental Russia, Bulgaria, and Tibet), and those of four polar bears. Based on these sequences, we reconstructed the maternal phylogeny of the brown bear and estimated divergence times to investigate the timing of brown bear migrations, especially in northeastern Eurasia. Our gene tree showed the mtDNA haplotypes of all 73 brown and polar bears to be divided into eight divergent lineages. The brown bear on Hokkaido was divided into three lineages (central, eastern, and southern). The Sakhalin brown bear grouped with eastern European and western Alaskan brown bears. Etorofu and Kunashiri brown bears were closely related to eastern Hokkaido brown bears and could have diverged from the eastern Hokkaido lineage after formation of the channel between Hokkaido and the southern Kuril Islands. Tibetan brown bears diverged early in the eastern lineage. Southern Hokkaido brown bears were closely related to North American brown bears.

The two living species of bison (European and American) are among the few terrestrial megafauna to have survived the late Pleistocene extinctions. Despite the extensive bovid fossil record in Eurasia, the evolutionary history of the European bison (or wisent, Bison bonasus) before the Holocene (, This research was supported by the Australian Research Council, the European Commission (PIRSES-GA-2009-247652—BIOGEAST), the Polish National Science Centre (N N304 301940 and 2013/11/B/NZ8/00914), the Danish National Research Foundation (DNRF94), the Marie Curie International Outgoing Fellowship (7th European Community Framework Program—MEDITADNA, PIOF-GA-2011-300854, FP7-PEOPLE) and the Russian Foundation for Basic Research (N 15-04-03882).

Morphological and molecular data suggest the existence of several taxa of cave bears, which were found to belong to three major mitochondrial haplogroups: kudarensis (kudarensis), spelaeus (ladinicus, eremus, spelaeus), and ingressus (uralensis, ingressus, kanivetz). An analysis of craniometrical variability was carried out based on 20 measurements of 279 skulls from 40 European, Ural, and Caucasian localities, in order to investigate morphological similarity/dissimilarity of these taxa in a multivariate approach. The craniometrical analysis divides cave bears into two groups: small cave bears and large cave bears. The group of small bears consists of rossicus/uralensis and ladinicus. In some skull proportions, these taxa display intermediate position between brown and cave bears, i.e. presumably possessing archaic characters of their common ancestor. The group of large bears includes taxa with more specialized skulls. An early radiation within this group is demonstrated by kudarensis which probably ranged across Asia, and deningeri which occupied Europe east to the Ural Mountains. In its craniometrical characters, kanivetz from the Late Pleistocene of the Urals resembles deningeri. Other taxa of large cave bears (spelaeus, ingressus and eremus) reveal further evolution of cranial characters, being similar in the skull proportions. The level of difference between spelaeus and ingressus does not exceed that between subspecies of the recent brown bear, such as Ursus arctos beringianus and U. a. piscator. The examined isolated population of large cave bears from Volga River region (Zhiguli Hills) is similar to ingressus. Thus, based on the craniometrical data, the following species of cave bear are recognized: Ursus kudarensis (with the subspecies U. k. praekudarensis and U. k. kudarensis), U. deningeri (several subspecies), U. rossicus (with subspecies U. r. rossicus and U. r. uralensis), U. ladinicus, U. spelaeus (with subspecies U. s. spelaeus, U. s. eremus, U. s. ingressus, and, provisionally, U. s. kanivetz,).

For a long time, “spelaeoid” (cave-bear-like) bears, Ursus (Spelearctos) spp., were believed to be almost purely European animals. Their geographic range has recently been extended to the east, in southern Siberia, Transbaikalia, Kirghizia, Mongolia and Korea. Two unexpected new findings, presented here in detail, significantly change existing views on the distribution of cave bears; both were found in NorthEastern Siberia, far beyond the Arctic Circle, more than 1500 km to the north-east of the previously accepted range. One of the fossils is a mandible, found near the town of Cherskiy at 68.73 � N, 161.38� E. The analysis of local geology and accompanying mammal fossils suggests that it comes from the Olyorian Fauna (Early to early Middle Pleistocene). Morphologically, the Cherskiy mandible is closest to Ursus savini, a small middle Pleistocene cave bear from the British Cromer Forest-bed Formation, but differs in having a slightly more advanced dentition, and thus it is described as a new subspecies Ursus savini nordostensis. Another newly recognized fossil of the “spelaeoid” bear is an astragalus found at the Oskhordokh site at

Prior to the Holocene, the range of the saiga antelope (Saiga tatarica) spanned from France to the Northwest Territories of Canada. Although its distribution subsequently contracted to the steppes of Central Asia, historical records indicate that it remained extremely abundant until the end of the Soviet Union, after which its populations were reduced by over 95%. We have analysed the mitochondrial control region sequence variation of 27 ancient and 38 modern specimens, to assay how the species' genetic diversity has changed since the Pleistocene. Phylogenetic analyses reveal the existence of two well-supported, and clearly distinct, clades of saiga. The first, spanning a time range from >49 500 C-14 ybp to the present, comprises all the modern specimens and ancient samples from the Northern Urals, Middle Urals and Northeast Yakutia. The second clade is exclusive to the Northern Urals and includes samples dating from between 40 400 to 10 250 C-14 ybp. Current genetic diversity is much lower than that present during the Pleistocene, an observation that data modelling using serial coalescent indicates cannot be explained by genetic drift in a population of constant size. Approximate Bayesian Computation analyses show the observed data is more compatible with a drastic population size reduction (c. 66-77%) following either a demographic bottleneck in the course of the Holocene or late Pleistocene, or a geographic fragmentation (followed by local extinction of one subpopulation) at the Holocene/Pleistocene transition.

New taxonomic study of the “old collection” of Carnivora from Petralona Cave, associated to the well-known hominid skull, housed in the Geology School of the Thessaloniki Aristotle University since 1960, revealed 11 species ( Canis arnensis , Lycaon lycaonoides , Vulpes praeglacialis , Ursus deningeri , U. spelaeus , U. arctos , Pliocrocuta perrieri , Pachycrocuta brevirostris , Crocuta crocuta , Panthera leo spelaea , and Felis silvestris ), which are described in detail. The species composition is typical of the eastern part of the European Mediterranean and may be divided into three biostratigraphic assemblages: early Middle Pleistocene, late Middle Pleistocene and Late Pleistocene.

The causes of the late Pleistocene megafaunal extinctions are still enigmatic. Although the fossil record can provide approximations for when a species went extinct, the timing of its disappearance alone cannot resolve the causes and mode of the decline preceding its extinction. However, ancient DNA analyses can reveal population size changes over time and narrow down potential causes of extinction. Here, we present an ancient DNA study comparing late Pleistocene population dynamics of two closely related species, cave and brown bears. We found that the decline of cave bears started approximately 25,000 years before their extinction, whereas brown bear population size remained constant. We conclude that neither the effects of climate change nor human hunting alone can be responsible for the decline of the cave bear and suggest that a complex of factors including human competition for cave sites lead to the cave bear's extinction.

Lions were the most widespread carnivores in the late Pleistocene, ranging from southern Africa to the southern USA, but little is known about the evolutionary relationships among these Pleistocene populations or the dynamics that led to their extinction. Using ancient DNA techniques, we obtained mitochondrial sequences from 52 individuals sampled across the present and former range of lions. Phylogenetic analysis revealed three distinct clusters: (i) modern lions, Panthera leo; (ii) extinct Pleistocene cave lions, which formed a homogeneous population extending from Europe across Beringia (Siberia, Alaska and western Canada); and (iii) extinct American lions, which formed a separate population south of the Pleistocene ice sheets. The American lion appears to have become genetically isolated around 340,000 years ago, despite the apparent lack of significant barriers to gene flow with Beringian populations through much of the late Pleistocene. We found potential evidence of a severe population bottleneck in the cave lion during the previous interstadial, sometime after 48,000 years, adding to evidence from bison, mammoths, horses and brown bears that megafaunal populations underwent major genetic alterations throughout the last interstadial, potentially presaging the processes involved in the subsequent end-Pleistocene mass extinctions. Wiley Online Library

Until recently, cave bears were believed to have only inhabited Europe. However, recent morphological evidence suggests that cave bears' geographic range extended as far east as Transbaikalia, Eastern Siberia. These Asian cave bears were morphologically distinct from European cave bears. However, how they related to European lineages remains unclear, stressing the need to assess the phylogenetic and phylogeographic relationship between Asian cave bears and their European relatives. In this work, we address this issue using a 227 base-pair fragment of the mitochondrial control region obtained from nine fossil bone samples from eight sites from the Urals, Caucasus, Altai Mountains, Ukraine and Yana River region in Eastern Siberia. Results of the phylogenetic analyses indicate that (i) the cave bear from the Yana River is most closely related to cave bears from the Caucasus region; (ii) the Caucasus/Yana group of bears is genetically very distinct from both European cave bears and brown bears, suggesting that these bears could represent an independent species; and (iii) the Western European cave bear lineage reached at least temporarily to the Altai Mountains, 7000 km east of their known centre of distribution. These results suggest that the diversity of cave bears was greater than previously believed, and that they could survive in a much wider range of ecological conditions than previously assumed. They also agree with recent studies on other extinct and extant species, such as wolves, hyenas and steppe bison, which have also revealed higher genetic and ecological diversity in Pleistocene populations than previously known.

The teeth and bone fragments of Alopex lagopus of early Weichselian age from Mousterian layers of grotto Prolom 2 in Crimea have been studied. The Crimean fossil arctic fox was found to be smaller than the late Weichselian subspecies, A. l. rossicus, from the East European Plain, but it seems to be similar in dimensions to the recent insular subspecies, A. l. spitzbergenensis. From the latter, the Crimean arctic fox differs in the relatively longer carnassial teeth and relatively wider m1. In the Late Pleistocene of Europe, a progressive increase in size of A. lagopus is observed, that makes it possible to recognize two subspecies, stratigraphically replacing one another. The arctic fox from Prolom 2 is presumably referable to the subspecies A. l. meridionalis, while the animals from another Crimean Upper Paleolithic site, Siuren 1, are referred to A. l. fossilis.

We examined morphological variability and evolution of the baculum (os penis) across the Mustelidae through allometric analyses and character mapping. Fifty-four species and 26 genera (including 2 fossil forms) were examined with numerous caniform out-group species. Allometric analyses showed that bacular length is relatively constant across mustelids and caniforms; only a tendency to a slightly shortened baculum in mephitines was observed. Character mapping revealed the ancestral mustelid baculum to be an elongated rod-shaped bone that lacks a urethral groove and possesses a simple, nondistinct distal tip. This form is largely retained in mephitines and, to a lesser degree, in lutrines. From the ancestral condition, it is possible to derive forms with a more complicated head that has projections and openings (e.g., melines, Eira barbara, Galictis, Gulo gulo, Martes) or spoon-shaped and cup-shaped processes (e.g., Ictonyx, Mellivora capensis). Another evolutionary trajectory involves the distal tip of the baculum becoming hook-shaped and the urethral groove well developed (e.g., Mustela, Vormela peregusna). Although the structure of the baculum distinguishes closely related species, many features are derived independently in more distantly related forms. Therefore, bacular structure provides restricted phylogenetic information and should be analyzed in concert with other data sources (e.g., morphology of the basicranial region).