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Simple Summary: Global warming at the border of Late Pleistocene-Holocene, around ten thousand years ago caused a dramatic rearrangement of habitats in the Northern Hemisphere. Populations of cold-adapted megafauna species, which were spread over large areas of Eurasia, did not survive it. At the same time, small representatives of this mammoth fauna complex survived, including lemmings and arctic fox, but greatly reduced their distribution northward. However, it is uncertain whether species survived by habitat tracking the elusive tundra, or if they came from other places where they survived warming, and local populations died out without leaving descendants. To answer this, we studied ancient DNA from new fossil remains of arctic foxes from caves in the northern and polar Urals. The data received do not show any connectivity between ancient and modern individuals, supporting the hypothesis of local extinction of arctic fox in the region rather than the tracking habitat hypothesis. These findings are important in light of global climate warming expectations. It is predicted that the most severe effects are expected to occur in high-latitude biomes and the results obtained must be kept in mind when planning conservation policy measures. 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. [ABSTRACT FROM AUTHOR]

The Bering Land Bridge connecting North America and Eurasia was periodically exposed and inundated by oscillating sea levels during the Pleistocene glacial cycles. This land connection allowed the intermittent dispersal of animals, including humans, between Western Beringia (far northeast Asia) and Eastern Beringia (northwest North America), changing the faunal community composition of both continents. The Pleistocene glacial cycles also had profound impacts on temperature, precipitation and vegetation, impacting faunal community structure and demography. While these palaeoenvironmental impacts have been studied in many large herbivores from Beringia (e.g., bison, mammoths, horses), the Pleistocene population dynamics of the diverse guild of carnivorans present in the region are less well understood, due to their lower abundances. In this study, we analyse mitochondrial genome data from ancient brown bears (Ursus arctos; n = 103) and lions (Panthera spp.; n = 39), two megafaunal carnivorans that dispersed into North America during the Pleistocene. Our results reveal striking synchronicity in the population dynamics of Beringian lions and brown bears, with multiple waves of dispersal across the Bering Land Bridge coinciding with glacial periods of low sea levels, as well as synchronous local extinctions in Eastern Beringia during Marine Isotope Stage 3. The evolutionary histories of these two taxa underline the crucial biogeographical role of the Bering Land Bridge in the distribution, turnover and maintenance of megafaunal populations in North America. see also the Perspective by Stephen J. Gaughran and Bridgett vonHoldt [ABSTRACT FROM AUTHOR]

The present phylogeographic pattern of red deer in Eurasia is not only a result of the contraction of their distribution range into glacial refugia and postglacial expansion, but probably also an effect of replacement of some red deer s.l. mtDNA lineages by others during the last 50 000 years. To better recognize this process, we analysed 501 sequences of mtDNA cytochrome b , including 194 ancient and 75 contemporary samples newly obtained for this study. The inclusion of 161 radiocarbon-dated samples enabled us to study the phylogeny in a temporal context and conduct divergence-time estimation and molecular dating. Depending on methodology, our estimate of divergence between Cervus elaphus and Cervus canadensis varied considerably (370 000 or 1.37 million years BP, respectively). The divergence times of genetic lineages and haplogroups corresponded to large environmental changes associated with stadials and interstadials of the Late Pleistocene. Due to the climatic oscillations, the distribution of C. elaphus and C. canadensis fluctuated in north–south and east–west directions. Some haplotypes dated to pre-Last Glacial Maximum periods were not detected afterwards, representing possibly extinct populations. We indicated with a high probability the presence of red deer sensu lato in south-eastern Europe and western Asia during the Last Glacial Maximum. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Just as the domestication of livestock is often cited as a key element in the Neolithic transition to settled, the emergence of large‐scaled reindeer husbandry was a fundamental social transformation for the indigenous peoples of Arctic Eurasia. To better understand the history of reindeer domestication, and the genetic processes associated with the pastoral transition in the Eurasian Arctic, we analyzed archaeological and contemporary reindeer samples from Northwestern Siberia. The material represents Rangifer genealogies spanning from 15,000 years ago to the 18th century, as well as modern samples from the wild Taĭmyr population and from domestic herds managed by Nenetses. The wild and the domestic population are the largest populations of their kind in Northern Eurasia, and some Nenetses hold their domestic reindeer beside their wild cousins. Our analyses of 197 modern and 223 ancient mitochondrial DNA sequences revealed two genetic clusters, which are interpreted as representing the gene pools of contemporary domestic and past wild reindeer. Among a total of 137 different mitochondrial haplotypes identified in both the modern and archaeological samples, only 21 were detected in the modern domestic gene pool, while 11 of these were absent from the wild gene pool. The significant temporal genetic shift that we associate with the pastoral transition suggests that the emergence and spread of reindeer pastoralism in Northwestern Siberia originated with the translocation and subsequent selective breeding of a special type of animal from outside the region. The distinct and persistent domestic characteristics of the haplotype structure since the 18th century suggests little genetic exchange since then. The absence of the typical domestic clade in modern nearby wild populations suggests that the contemporary Nenets domestic breed feature an ancestry from outside its present main distribution, possibly from further South. [ABSTRACT FROM AUTHOR]

Abstract: Aim: The status of geographical units within species and species complexes is debated for many taxa, with many molecular studies failing to detect phenotypically defined subspecies. The history and longevity of geographical patterns are also generally very poorly understood. We examine Holarctic red deer (Cervus elaphus and related forms), incorporating ancient DNA to ask whether the present phylogeography has persisted through climatic perturbations or is a relatively recent phenomenon. Location: Holarctic (Europe, northern Asia and North America). Methods: We obtained 21 modern and 30 Holocene and Late Pleistocene samples, which together with published data resulted in 180 individuals spanning 21 nominal extant and one extinct subspecies. Phylogenetic analyses were carried out on 748‐bp of mitochondrial DNA (cytochrome b and control region). Where possible, the morphology of DNA‐yielding ancient samples was examined to assess subspecies identity. Results: Major clades within the red deer complex are upheld, but subspecies within them receive varying support. The ancient phylogeographical structure conforms in significant part to the modern situation, but some haplogroups no longer survive. Moreover, there have been substantial shifts in geographical ranges through time. Wapitoids spread as far west as Romania in the last glaciation, and elaphoids reached eastward to the Ural Mountains. A possible contact zone between the two lineages stretched from the Urals through the Crimea to Eastern Europe. Main conclusions: Ancient DNA and morphology are strongly complementary in elucidating population history. Through the past 50 kyr, the major lineages of red deer, and some of the subspecies groups within them, have maintained their genetic and morphological integrity and their core geographical distributions, despite range expansions and contractions and likely contact between the haplogroups (with potential for hybridization). [ABSTRACT FROM AUTHOR]

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 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 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. [ABSTRACT FROM AUTHOR]