New records of Holocene polar bear and walrus (Carnivora) in the Russian Arctic

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

Evolutionary history and palaeoecology of brown bear in North-East Siberia re-examined using ancient DNA and stable isotopes from skeletal remains

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

Evolutionary History of Saber-Toothed Cats Based on Ancient Mitogenomics

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.)

Diversity of muskox Ovibos moschatus (Zimmerman, 1780) (Bovidae, Mammalia) in time and space based on cranial morphometry

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

Historical biogeography of the leopard (Panthera pardus) and its extinct Eurasian populations

Background: Resolving 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? Results: In 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. Conclusions: The 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 origins and spread of domestic horses from the Western Eurasian steppes

This is the final version. Available on open access from Nature Research via the DOI in this recordData availability: All collapsed and paired-end sequence data for samples sequenced in this study are available in compressed fastq format through the European Nucleotide Archive under accession number PRJEB44430, together with rescaled and trimmed bam sequence alignments against both the nuclear and mitochondrial horse reference genomes. Previously published ancient data used in this study are available under accession numbers PRJEB7537, PRJEB10098, PRJEB10854, PRJEB22390 and PRJEB31613, and detailed in Supplementary Table 1. The genomes of ten modern horses, publicly available, were also accessed as indicated in their corresponding original publications57,61,85-87.NOTE: see the published version available via the DOI in this record for the full list of authorsDomestication 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 BC. 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

Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

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 con-tribution 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

Morphometry of upper cheek teeth of cave bears (Carnivora, Ursidae)

Univariate and multivariate statistics were applied to analyse the morphometrical variability of 4920 upper cheek teeth (P4, M1 and M2) of cave bears from 123 geographical sites (180 samples) of different Pliocene – Pleistocene ages. The analysed specimens included those belonging to the big cave bears Ursus kudarensis, U. deningeri, U. spelaeus (three subspecies) and U. kanivetz (including U. ingressus), as well as the small cave bear U. rossicus. The information‐theoretical parameters (Shannon entropy and orderliness (Von Foerster, 1960: On self‐organizing systems and their environments. In Self‐Organizing Systems, 31–50. Pergamon Press, London) were used to estimate tooth diversity in different teeth, different taxa and in selected local chrono‐populations. Multivariate allometry coefficients (Klingenberg, 1996: Multivariate allometry. In Advances in Morphometrics, 23‐49. Plenum Press, New York) were used to describe the relationships of different ‘parts’ of a tooth and to compare allometric patterns amongst species or selected local samples. A multivariate analysis showed a significant overlap of the size/shape parameter ranges in deningeroid and spelaeoid bears within morphological spaces. Within the cave bear lineage, the Deninger\u27s bear has the greatest morphological diversity index (entropy) of all the teeth overall, and the lowest diversity is observed in the final taxon of this lineage – U. kanivetz (=ingressus). The P4 and M2 diversity showed multidirectional correlations with elevation above sea level amongst several ‘local’ populations of Late Pleistocene cave bears. The morphological disparities between the studied taxa are in close agreement with the distances in the available schemes of genetic differentiation based on ancient mitochondrial DNA. The split of U. kudarensis and U. deningeri has a good bootstrap support, which corresponds to the hypothesis about their parallel evolution. The small cave bear U. rossicus is placed between U. arctos and U. deningeri. The phylogenetic signal is more pro

Craniometrical variability in the cave bears (Carnivora, Ursidae): Multivariate comparative analysis

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,)