Three-Dimensional Geometric Morphometric Analysis of Fossil Canid Mandibles and Skulls

Acknowledgements We thank C.P. Klingenberg for critical discussion of methodology. A. Drake and R. Losey were supported by a grant from the Social Sciences and Humanities Research Council of Canada grant (#SSHRC IG 435-2014-0075) and a European Research Council Grant to D. Anderson (#295458). M. Sablin acknowledges participation of ZIN RAS (state assignment № АААА-А17-117022810195-3) to this research. Supplementary information accompanies this paper at doi:10.1038/s41598-017-10232-1Peer reviewedPublisher PD

Ancient DNA Analyses Exclude Humans as the Driving Force Behind Late Pleistocene Musk Ox (Ovibos moschatus) Population Dynamics

The causes of the late Pleistocene megafaunal extinctions are poorly understood. Different lines of evidence point to climate change, the arrival of humans, or a combination of these events as the trigger. Although many species went extinct, others, such as caribou and bison, survived to the present. The musk ox has an intermediate story: relatively abundant during the Pleistocene, it is now restricted to Greenland and the Arctic Archipelago. In this study, we use ancient DNA sequences, temporally unbiased summary statistics, and Bayesian analytical techniques to infer musk ox population dynamics throughout the late Pleistocene and Holocene. Our results reveal that musk ox genetic diversity was much higher during the Pleistocene than at present, and has undergone several expansions and contractions over the past 60,000 years. Northeast Siberia was of key importance, as it was the geographic origin of all samples studied and held a large diverse population until local extinction at approximate to 45,000 radiocarbon years before present (14C YBP). Subsequently, musk ox genetic diversity reincreased at ca. 30,000 14C YBP, recontracted at ca. 18,000 14C YBP, and finally recovered in the middle Holocene. The arrival of humans into relevant areas of the musk ox range did not affect their mitochondrial diversity, and both musk ox and humans expanded into Greenland concomitantly. Thus, their population dynamics are better explained by a non-anthropogenic cause (for example, environmental change), a hypothesis supported by historic observations on the sensitivity of the species to both climatic warming and fluctuations

Population dynamics and range shifts of moose (Alces alces) during the Late Quaternary

Aim: Late Quaternary climate oscillations had major impacts on species distributions and abundances across the northern Holarctic. While many large mammals in this region went extinct towards the end of the Quaternary, some species survived and flourished. Here, we examine population dynamics and range shifts of one of the most widely distributed of these, the moose (Alces alces). Location: Northern Holarctic. Taxon: Moose (A. alces). Methods: We collected samples of modern and ancient moose from across their present and former range. We assessed their phylogeographical relations using part of the mitochondrial DNA in conjunction with radiocarbon dating to investigate the history of A. alces during the last glacial. Results: This species has a relatively shallow history, with the most recent common ancestor estimated at ca. 150–50 kyr. Ancient samples corroborate that its region of greatest diversity is in east Asia, supporting proposals that this is the region of origin of all extant moose. Both eastern and western haplogroups occur in the Ural Mountains during the last glacial period, implying a broader contact zone than previously proposed. It seems that this species went extinct over much of its northern range during the last glacial maximum (LGM) and recolonized the region with climate warming beginning around 15,000 yr bp. The post-LGM expansion included a movement from northeast Siberia to North America via Beringia, although the northeast Siberian source population is not the one currently occupying that area. Main conclusions: Moose are a relatively recently evolved species but have had a dynamic history. As a large-bodied subarctic browsing species, they were seemingly confined to refugia during full-glacial periods and expanded their range northwards when the boreal forest returned after the LGM. The main modern phylogeographical division is ancient, though its boundary has not remained constant. Moose population expansion into America was roughly synchronous with human and red deer expansion. © 2020 The Authors. Journal of Biogeography published by John Wiley & Sons LtdWe warmly thank the following museums, curators and people for access to samples: the late Andrei Sher, Severtsov Institute, Moscow; Andy Currant, Natural History Museum, London; Alfred Gardner, Smithsonian, Washington DC; R. Dale Guthrie, University of Alaska, Fairbanks; John de Vos, National Museum of Natural History (Naturalis), Leiden; Eileen Westwig, American Museum of Natural History, NY; Fyodor Shidlovsky, Ice-Age Museum, Moscow; Tong Haowen, Institute of Vertebrate Palaeontology and Paleoanthropology, Beijing; Mammoth Museum, Yakutsk; Geological Museum, Yakutsk; Paleontological Institute, Moscow; Royal Alberta Museum, Edmonton; Zoological Institute, Saint Petersburg; Museum of the Institute of Plant and Animal Ecology, Ekaterinburg. We thank our Yukon First Nation research partners for their continued support for our work on the ice age fossils of Yukon Territory. We are grateful to the placer gold mining community and the Tr'ond?k Hw?ch'in First Nation for their continued support and partnership with our research in the Klondike goldfields region; and the Vuntut Gwitchin First Nation for their collaboration with research in the Old Crow region. We would also like to thank Shai Meiri for help in drawing the map and useful discussion, Tony Stuart for access to radiocarbon dates, and Iris van Pijlen for laboratory assistance. This research was funded by NERC grant NE/G00269X/1 through the European Union FP7 ERA-NET program BiodivERsA. Funding for AMS dating was provided through NERC/AHRC/ORAU Grant NF/2008/2/15

Grey wolf genomic history reveals a dual ancestry of dogs

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 (Canisfamiliaris) 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 IFT8840,000-30,000 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.Peer reviewe

Species-specific responses of Late Quaternary megafauna to climate and humans

Despite decades of research, the roles of climate and humans in driving the dramatic extinctions of large-bodied mammals during the Late Quaternary remain contentious. We use ancient DNA, species distribution models and the human fossil record to elucidate how climate and humans shaped the demographic history of woolly rhinoceros, woolly mammoth, wild horse, reindeer, bison and musk ox. We show that climate has been a major driver of population change over the past 50,000 years. However, each species responds differently to the effects of climatic shifts, habitat redistribution and human encroachment. Although climate change alone can explain the extinction of some species, such as Eurasian musk ox and woolly rhinoceros, a combination of climatic and anthropogenic effects appears to be responsible for the extinction of others, including Eurasian steppe bison and wild horse. We find no genetic signature or any distinctive range dynamics distinguishing extinct from surviving species, underscoring the challenges associated with predicting future responses of extant mammals to climate and human-mediated habitat change.This paper is in the memory of our friend and colleague Dr. Andrei Sher, who was a major contributor of this study. Dr Sher died unexpectedly, but his major contributions to the field of Quaternary science will be remembered and appreciated for many years to come. We are grateful to Dr. Adrian Lister and Dr. Tony Stuart for guides and discussions. Thanks to Tina B. Brandt, Dr. Bryan Hockett and Alice Telka for laboratory help and samples and to L. Malik R. Thrane for his work on the megafauna locality database. Data taken from the Stage 3 project was partly funded by Grant #F/757/A from the Leverhulme Trust, together with a grant from the McDonald Grants and Awards Fund. We acknowledge the Danish National Research Foundation, the Lundbeck Foundation, the Danish Council for Independent Research and the US National Science Foundation for financial suppor

Widespread horse-based mobility arose around 2200 BCE in Eurasia.

Horses revolutionized human history with fast mobility1. However, the timeline between their domestication and their widespread integration as a means of transport remains contentious2-4. 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 earlier3,5. 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 horses6,7. This supports local horse husbandry before the rise of modern domestic bloodlines

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

Dire wolves were the last of an ancient New World canid lineage

Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America1, 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 Canidae2,3, 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

Comment on “The Earliest Horse Harnessing and Milking”

Comment on "The Earliest Horse Harnessing and Milking" (The earliest use of horses and milking). Alan K. Outrom and his colleagues believe that in Northern Kazakhstan at the Botai settlement was an independent center of domestication of the horse. In contrast, we believe that there were no domestic horses, and the inhabitants of the settlement Botai in the Late Chalcolithic hunted wild horses - tarpan. Bone parameters of Botai horses differ from the parameters of domestic horses of the next historical era - the Bronze Age. Traces on the horses teeth and diastema are not traces of bits, because such bits appeared here only in the early Iron Age