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Using an ethnoarcheological perspective we examine Nenets site formation, seasonality and landscape usage in controlling reindeer herds in a complex system of more than 20 abandoned campsites and other sites of interest over 100 km and a time-span of several decades. We establish a chronology based on more than 150 expiration dates from imported food items, supported by additional seasonal evidence such as presence/absence of newborn reindeer, hearths and other artifacts. We separated the sites into five stages and compared the patterns of change, especially from 1986 to 2003 as the road and railroad connecting the Yamal gas mining fields were constructed nearby. We find that the impact of road and rail construction is reflected in the increase of imported goods upon its completion. [ABSTRACT FROM AUTHOR]

Dogs have been essential to life in the Siberian Arctic for over 9,500 y, and this tight link between people and dogs continues in Siberian communities. Although Arctic Siberian groups such as the Nenets received limited gene flow from neighboring groups, archaeological evidence suggests that metallurgy and new subsistence strategies emerged in Northwest Siberia around 2,000 y ago. It is unclear if the Siberian Arctic dog population was as continuous as the people of the region or if instead admixture occurred, possibly in relation to the influx of material culture from other parts of Eurasia. To address this question, we sequenced and analyzed the genomes of 20 ancient and historical Siberian and Eurasian Steppe dogs. Our analyses indicate that while Siberian dogs were genetically homogenous between 9,500 to 7,000 y ago, later introduction of dogs from the Eurasian Steppe and Europe led to substantial admixture. This is clearly the case in the Iamal-Nenets region (Northwestern Siberia) where dogs from the Iron Age period (~2,000 y ago) possess substantially less ancestry related to European and Steppe dogs than dogs from the medieval period (~1,000 y ago). Combined with findings of nonlocal materials recovered from these archaeological sites, including glass beads and metal items, these results indicate that Northwest Siberian communities were connected to a larger trade network through which they acquired genetically distinctive dogs from other regions. These exchanges were part of a series of major societal changes, including the rise of large-scale reindeer pastoralism ~800 y ago. [ABSTRACT FROM AUTHOR]

Body size is correlated with many critical behavioral and developmental patterns in carnivores, including domestic dogs. The body masses and bite forces of archaeological dog remains from Siberia and the Russian Far East were estimated to make inferences regarding their behaviors and capacitis. The dogs date from ∼10,000–100 cal. BP and derive from archaeological sites spanning from steppe environments in the south to tundra regions of the northern Arctic. The dogs exhibit a four-fold difference in body mass, ranging from 7.6 to 32.5 kg, but have a mean body mass of only 16.4 kg. Bite forces are around only half those of modern wolves, indicating that the dogs had greatly reduced abilities to grasp and masticate prey and food items. The dogs exhibit a slight decrease in body size through time, perhaps due to human selection or greater survival rates for smaller individuals in human-dominated food environments. Dog body size variance within individual archaeological sites was as high as in a sample of modern wolves from throughout the study area, suggesting little strict human control over body size. No correlation was found between body size and site latitude, suggesting that Bergmann's rule does not hold for these canids. Human shelters may provide a buffer against low temperatures that might favour larger body sizes at high latitudes. About 90% of the analyzed dogs have estimated body masses less than 21.5 kg, suggesting most were best adapted for procuring prey smaller than themselves—the dogs were not capable of taking down larger prey without the assistance of humans. Estimated dog body masses cannot eliminate the possibility that many of the animals were used for pulling sleds, and nearly all were capable of packing modest loads on their backs. Livestock guarding dogs are not well-evidenced by the body mass data, but herding dogs are a possibility in all of the pastoral or agricultural settings analyzed. Image 1 • Body masses and bite forces were estimated for 199 archaeological dog remains from Siberia and the Russian Far East. • The dogs' body masses range from 7.6 to 32.5 kg, with a mean of 16.4 kg. • The dogs' bite forces are around half those of modern wolves. • The dogs exhibit a slight decrease in body size through time. • Many of the dogs were of sufficient size to pull sleds, and all could have carried packs. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Seven species of red-toothed shrews (Sorex araneus, Sorex isodon, Sorex tundrensis, Sorex caecutiens, Sorex minutus, Sorex minutissimus, Neomys fodiens), white-toothed shrews (Crocidura sp.), moles (Talpa sp.) and hedgehogs (Erinaceus sp.) were found in Late Pleistocene and Holocene deposits of the southern part of the western slope of the Ural Mountains. In the Late Pleistocene and Early Holocene deposits, the red-toothed shrews were dominated by S. tundrensis. This species disappeared from the area by the Late Holocene, when S. araneus became the predominant species. Smaller mandibular sizes have been registered for S. araneus in the Middle and Late Holocene, as compared to the sizes of older samples. The morphometric criteria have been established for a species differential diagnosis of the Late Pleistocene – Early Holocene mandibular samples of S. araneus and S. tundrensis , found in local deposits of the southern Pre-Urals area studied. • Bones of insectivorous mammals (10 taxons) were found in the deposits of caves and grottoes in the southern Pre-Urals. • Sorex tundrensis was dominant species in the Late Pleistocene and Early Holocene deposits. • Fossil Sorex araneus and Sorex tundrensis are well differentiated by three morphometric parameters. • Temporal variability was traced within the samples of mandibles of Sorex araneus. [ABSTRACT FROM AUTHOR]

Domestication has particular salience in archaeology, and numerous recent theoretical papers describe this process as a set of evolutionary, ongoing, social, and material relationships between humans and select other species. In contrast, analytical papers on the domestication of dogs nearly always involve a search for their origins as marked by changes in genes and morphologies. This article explores this contrast through the examination of dog remains from the Iron Age Ust’-Polui site in the western Siberian Arctic. Many of the numerous dogs represented at this site were killed and probably consumed when young, likely as part of sacrifices. Others at the site were intentionally buried. Ust’-Polui also contains abundant evidence of advanced dog sledding, including probable harness parts and portions of several complex sleds. Sacrificing and otherwise killing dogs is a domestication practice, as these activities are a form of selective breeding. Domestication of dogs at Ust’-Polui and elsewhere is more than selective breeding, as it is enabled and dependent upon specific landscapes, built things, and other species. At Ust’-Polui these at a minimum included a rich local environment, sleds and harness swivels, and freshwater fish, all of which intertwined in making the particular domestic relationships at the site possible. [ABSTRACT FROM AUTHOR]

Red deer (Cervus elaphus) is one of the species that is rather wide spread and survived across Europe over the Holocene. The analyses of carbon and nitrogen stable isotopes in bone collagen of ungulate remains have been applied in paleoecological studies as environmental and dietary indicators. In this study we present the carbon and nitrogen stable isotope compositions of previously radiocarbon-dated red deer bone samples (N = 68) found in Central, Southern and Eastern Europe and Asia and aligned to one of two species: European red deer (Cervus elaphus) and wapiti (Cervus canadensis). We showed that the values of carbon and nitrogen stable isotope ratios of European red deer and wapiti overlapped. Among all analysed independent factors (determined for the locality and time period relevant for each of the analysed samples), the variability of δ 13C values in European red deer dated to the Holocene is best explained by forest cover and mean July temperature, and variability of δ 15N values by the mean July temperature, annual precipitation and altitude. Additionally, combining the results of the present study with isotopic data on European red deer collected from published sources, we revealed that the values of δ 13C and of δ 15N in C. elaphus bones changed according to environmental oscillations that took place in Europe over the last 50 000 years. We concluded that red deer shifted their feeding habitats in relation to changing environmental conditions, for example, forest expansion during the climate warming, and in the mid to later Holocene in response to deforestation caused by human activity and the spread of agriculture. We also found out that red deer reacted in varied ways to changing local conditions in different regions of Europe. Modern individuals of C. elaphus had the lowest δ 13C values among all analysed specimens, so they probably inhabited the most densely forested areas in comparison to other European red deer populations during the last 50 000 years. • δ 13C and δ 15N values of ancient red deer and wapiti bones have been analysed. • We showed that δ 13C and δ 15N in deer fluctuated with environmental changes in Europe. • The values of δ 13C and δ 15N of red deer and wapiti overlapped. • Forest cover and July temperature influenced δ 13C values within Holocene deer bones. • Temperature, precipitation and altitude shaped δ 15N values within Holocene deer bones. [ABSTRACT FROM AUTHOR]

Remarkable and intriguing is the discovery of Desman remains in Sed'yu-1 (Komi Republic, Russia) in the far northeast of Europe; finds that are dated to the Bølling Interstadial. Mammalian communities including desman are dominated by the Siberian lemming. A review of Lateglacial desman finds in Europe and the Urals as well as the contemporaneous mammalian communities in northeastern European are presented and the possible migration ways desmans used during the Lateglacial expansion are discussed. [ABSTRACT FROM AUTHOR]

We present the high-quality genome sequence of a ∼45,000-year-old modern human male from Siberia. This individual derives from a population that lived before-or simultaneously with-the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000-13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 × 10−9 to 0.6 × 10−9 per site per year, a Y chromosomal mutation rate of 0.7 × 10−9 to 0.9 × 10−9 per site per year based on the additional substitutions that have occurred in present-day non-Africans compared to this genome, and a mitochondrial mutation rate of 1.8 × 10−8 to 3.2 × 10−8 per site per year based on the age of the bone. [ABSTRACT FROM AUTHOR]

The widespread extinctions of large mammals at the end of the Pleistocene epoch have often been attributed to the depredations of humans; here we present genetic evidence that questions this assumption. We used ancient DNA and Bayesian techniques to reconstruct a detailed genetic history of bison throughout the late Pleistocene and Holocene epochs. Our analyses depict a large diverse population living throughout Beringia until around 37,000 years before the present, when the population's genetic diversity began to decline dramatically. The timing of this decline correlates with environmental changes associated with the onset of the last glacial cycle, whereas archaeological evidence does not support the presence of large populations of humans in Eastern Beringia until more than 15,000 years later. [ABSTRACT FROM AUTHOR]

This study describes a non-destructive method that can be used to estimate the age of archaeological dog remains involving tooth pulp cavity closure ratios. This technique was first developed in wildlife management and zoology for wild carnivores. For the first time, we develop this technique for dogs by utilizing a modern sample of 751 teeth roots from 106 animals with known life histories. The method involves measuring widths of teeth roots and their pulp cavities by means of X-ray images, and then calculating the ratios of pulp cavity infilling for each tooth. The method is developed for upper and lower canines and the distal and mesial roots of the mandibular M1. Our assessments demonstrate that upper and lower canines are most strongly correlated with age, followed by the mesial and distal roots of the mandibular M1. The method is useful for assigning specimens to relative age categories, and proved most reliable with younger individuals. We illustrate the applicability of the method by analyzing 369 teeth roots from 77 archaeological dogs from the Iron Age Ust'-Polui site in Arctic Siberia. Previously, ageing of the dog remains at this site involved only assessments of dental eruption patterns and long bone epiphysis fusion. The overall age estimation results from Ust'-Polui produced a mortuary profile dominated by juveniles and prime age adults, suggesting a regional preference for dogs of these age groups in sacrifices. • Pulp cavity closure ratios are utilized for age estimation in dogs. • Procedure is non-destructive and provides relative age estimates. • Ageing method is applied to upper and lower canines and mandibular M1. • Pulp cavity closure ratios of canines have strongest correlation with age. • Method is applied to dog teeth from the Ust'-Polui site in Arctic Siberia. [ABSTRACT FROM AUTHOR]

Climatic oscillations are considered primary factors influencing the distribution of various life forms on Earth. Large species adapted to cold climates are particularly vulnerable to extinction due to climate changes. In our study, we investigated whether temperature increase since the Late Pleistocene and the contraction of environmental niche during the Holocene were the main factors contributing to the decreasing range of moose (Alces alces) in Europe. We also examined whether there were significant differences in environmental conditions between areas inhabited by moose in Europe and Asia, that could support the division of moose into western and eastern forms, as suggested by genetic and morphological data. We analysed environmental conditions in the locations of 655 subfossil and modern moose occurrences over the past 50,000 years in Eurasia. We found that the most limiting climatic factor for the moose distribution since the Late Pleistocene was July temperature. More than 90 % of moose records were found in areas where mean summer temperature was below 19 °C, with July temperatures showing over 3 times narrower interquartile range compared to January temperatures. We identified significant differences in environmental conditions between areas inhabited by the European and Asiatic moose. In Europe, the species occurred in regions with milder climates, higher primary productivity, and more frequently within forest biomes compared to Asiatic individuals. The moose range shifted more in the west-east than in the south-north direction during the Holocene climate warming in Europe. We conclude that although the area of suitable moose habitat has increased since 12-8 ka years BP, as demonstrated by environmental niche modeling, the retreat of A. alces in large areas of Europe was likely caused by anthropogenic landscape change (e.g., deforestation) and overhunting by humans during the late Holocene rather than by climate warming during the Pleistocene to Holocene transition., Competing Interests: Declaration of competing interest Due to the Ukrainian laws established since the Russian invasion in February 2022, Ukrainian scientists employed in the Ukrainian institutions are not allowed to be included as co-authors in the same papers with Russian researchers. That is why the name of professor Bogdan Ridush from the Yuriy Fedkovych Chernivtsi National University in Ukraine, who participated in this study, based on his request, has been excluded from the list of authors and moved to the Acknowledgements., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

Now extinct, the aurochs (Bos primigenius) was a keystone species in prehistoric Eurasian and North African ecosystems, and the progenitor of cattle (Bos taurus), domesticates that have provided people with food and labour for millennia 1 . Here we analysed 38 ancient genomes and found 4 distinct population ancestries in the aurochs-European, Southwest Asian, North Asian and South Asian-each of which has dynamic trajectories that have responded to changes in climate and human influence. Similarly to Homo heidelbergensis, aurochsen first entered Europe around 650 thousand years ago 2 , but early populations left only trace ancestry, with both North Asian and European B. primigenius genomes coalescing during the most recent glaciation. North Asian and European populations then appear separated until mixing after the climate amelioration of the early Holocene. European aurochsen endured the more severe bottleneck during the Last Glacial Maximum, retreating to southern refugia before recolonizing from Iberia. Domestication involved the capture of a small number of individuals from the Southwest Asian aurochs population, followed by early and pervasive male-mediated admixture involving each ancestral strain of aurochs after domestic stocks dispersed beyond their cradle of origin., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Horses revolutionized human history with fast mobility 1 . However, the timeline between their domestication and their widespread integration as a means of transport remains contentious 2-4 . Here we assemble a collection of 475 ancient horse genomes to assess the period when these animals were first reshaped by human agency in Eurasia. We find that reproductive control of the modern domestic lineage emerged around 2200 BCE, through close-kin mating and shortened generation times. Reproductive control emerged following a severe domestication bottleneck starting no earlier than approximately 2700 BCE, and coincided with a sudden expansion across Eurasia that ultimately resulted in the replacement of nearly every local horse lineage. This expansion marked the rise of widespread horse-based mobility in human history, which refutes the commonly held narrative of large horse herds accompanying the massive migration of steppe peoples across Europe around 3000 BCE and earlier 3,5 . Finally, we detect significantly shortened generation times at Botai around 3500 BCE, a settlement from central Asia associated with corrals and a subsistence economy centred on horses 6,7 . This supports local horse husbandry before the rise of modern domestic bloodlines., (© 2024. The Author(s).)

Western Eurasia witnessed several large-scale human migrations during the Holocene 1-5 . Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes-mainly from the Mesolithic and Neolithic periods-from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a 'great divide' genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 BP, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 BP, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a 'Neolithic steppe' cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations., (© 2024. The Author(s).)

Despite the high level of interest, the population history of arctic foxes during the Late Pleistocene and Holocene remains poorly understood. Here we aimed to fill gaps in the demographic and colonization history of the arctic fox by analyzing new ancient DNA data from fossil specimens aged from 50 to 1 thousand years from the Northern and Polar Urals, historic DNA from museum specimens from the Novaya Zemlya Archipelago and the Taymyr Peninsula and supplementing these data by previously published sequences of recent and extinct arctic foxes from other regions. This dataset was used for reconstruction of a time-calibrated phylogeny and a temporal haplotype network covering four time intervals: Late Pleistocene (ranging from 30 to 13 thousand years bp), Holocene (ranging from 4 to 1 thousand years bp), historical (approximately 150 years), and modern. Our results revealed that Late Pleistocene specimens showed no genetic similarity to either modern or historical specimens, thus supporting the earlier hypothesis on local extinction rather than habitat tracking.

The taxonomic status of the now likely extirpated Korean Peninsula wolf has been extensively debated, with some arguing it represents an independent wolf lineage, Canis coreanus . To investigate the Korean wolf's genetic affiliations and taxonomic status, we sequenced and analysed the genomes of a Korean wolf dated to the beginning of the 20th century, and a captive wolf originally from the Pyongyang Central Zoo. Our results indicated that the Korean wolf bears similar genetic ancestry to other regional East Asian populations, therefore suggesting it is not a distinct taxonomic lineage. We identified regional patterns of wolf population structure and admixture in East Asia with potential conservation consequences in the Korean Peninsula and on a regional scale. We find that the Korean wolf has similar genomic diversity and inbreeding to other East Asian wolves. Finally, we show that, in contrast to the historical sample, the captive wolf is genetically more similar to wolves from the Tibetan Plateau; hence, Korean wolf conservation programmes might not benefit from the inclusion of this specimen., (© 2023 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Research on the evolution of dog foraging and diet has largely focused on scavenging during their initial domestication and genetic adaptations to starch-rich food environments following the advent of agriculture. The Siberian archaeological record evidences other critical shifts in dog foraging and diet that likely characterize Holocene dogs globally. By the Middle Holocene, body size reconstruction for Siberia dogs indicates that most were far smaller than Pleistocene wolves. This contributed to dogs' tendencies to scavenge, feed on small prey, and reduce social foraging. Stable carbon and nitrogen isotope analysis of Siberian dogs reveals that their diets were more diverse than those of Pleistocene wolves. This included habitual consumption of marine and freshwater foods by the Middle Holocene and reliance on C 4 foods by the Late Holocene. Feeding on such foods and anthropogenic waste increased dogs' exposure to microbes, affected their gut microbiomes, and shaped long-term dog population history.

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) lived 1-8 . 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).)

Domestication of horses fundamentally transformed long-range mobility and warfare 1 . However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling 2-4 at Botai, Central Asia around 3500 BC 3 . Other longstanding candidate regions for horse domestication, such as Iberia 5 and Anatolia 6 , 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 7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 BC 8,9 driving the spread of Indo-European languages 10 . This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium BC Sintashta culture 11,12 ., (© 2021. The Author(s).)

Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America 1 , yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae 2,3 , there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently.

Because of their role in immune defense against pathogens, major histocompatibility complex (MHC) genes are useful in evolutionary studies on how wild vertebrates adapt to their environments. We investigated the molecular evolution of MHC class I (MHCI) genes in four closely related species of Eurasian badgers, genus Meles. All four species of badgers showed similarly high variation in MHCI sequences compared to other Carnivora. We identified 7-21 putatively functional MHCI sequences in each of the badger species, and 2-7 sequences per individual, indicating the existence of 1-4 loci. MHCI exon 2 and 3 sequences encoding domains α1 and α2 exhibited different clade topologies in phylogenetic networks. Non-synonymous nucleotide substitutions at codons for antigen-binding sites exceeded synonymous substitutions for domain α1 but not for domain α2, suggesting that the domains α1 and α2 likely had different evolutionary histories in these species. Positive selection and recombination seem to have shaped the variation in domain α2, whereas positive selection was dominant in shaping the variation in domain α1. In the separate phylogenetic analyses for exon 2, exon 3, and intron 2, each showed three clades of Meles alleles, with rampant trans-species polymorphism, indicative of the long-term maintenance of ancestral MHCI polymorphism by balancing selection.

Understanding extinction events requires an unbiased record of the chronology and ecology of victims and survivors. The rhinoceros Elasmotherium sibiricum, known as the 'Siberian unicorn', was believed to have gone extinct around 200,000 years ago-well before the late Quaternary megafaunal extinction event. However, no absolute dating, genetic analysis or quantitative ecological assessment of this species has been undertaken. Here, we show, by accelerator mass spectrometry radiocarbon dating of 23 individuals, including cross-validation by compound-specific analysis, that E. sibiricum survived in Eastern Europe and Central Asia until at least 39,000 years ago, corroborating a wave of megafaunal turnover before the Last Glacial Maximum in Eurasia, in addition to the better-known late-glacial event. Stable isotope data indicate a dry steppe niche for E. sibiricum and, together with morphology, a highly specialized diet that probably contributed to its extinction. We further demonstrate, with DNA sequencing data, a very deep phylogenetic split between the subfamilies Elasmotheriinae and Rhinocerotinae that includes all the living rhinoceroses, settling a debate based on fossil evidence and confirming that the two lineages had diverged by the Eocene. As the last surviving member of the Elasmotheriinae, the demise of the 'Siberian unicorn' marked the extinction of this subfamily.

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 (<11.7 thousand years ago (kya)) remains a mystery. We use complete ancient mitochondrial genomes and genome-wide nuclear DNA surveys to reveal that the wisent is the product of hybridization between the extinct steppe bison (Bison priscus) and ancestors of modern cattle (aurochs, Bos primigenius) before 120 kya, and contains up to 10% aurochs genomic ancestry. Although undetected within the fossil record, ancestors of the wisent have alternated ecological dominance with steppe bison in association with major environmental shifts since at least 55 kya. Early cave artists recorded distinct morphological forms consistent with these replacement events, around the Last Glacial Maximum (LGM, ∼21-18 kya).