Ancient genomes provide a tool to investigate the genetic basis of adaptations in extinct organisms. However, the identification of species-specific fixed genetic variants requires the analysis of genomes from multiple individuals. Moreover, the long-term scale of adaptive evolution coupled with the short-term nature of traditional time series data has made it difficult to assess when different adaptations evolved. Here, we analyze 23 woolly mammoth genomes, including one of the oldest known specimens at 700,000 years old, to identify fixed derived non-synonymous mutations unique to the species and to obtain estimates of when these mutations evolved. We find that at the time of its origin, the woolly mammoth had already acquired a broad spectrum of positively selected genes, including ones associated with hair and skin development, fat storage and metabolism, and immune system function. Our results also suggest that these phenotypes continued to evolve during the last 700,000 years, but through positive selection on different sets of genes. Finally, we also identify additional genes that underwent comparatively recent positive selection, including multiple genes related to skeletal morphology and body size, as well as one gene that may have contributed to the small ear size in Late Quaternary woolly mammoths.

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.

Background. The remote location and the difficulty of access of the islands of the Novosibirsk archipelago is one of the reasons for their little study. As a result, many locations of mammoth fauna in this region remain still undescribed and unexplored. The paper describes the bone remains of two representatives of the species «Woolly mammoths» (Mammuthus primigenius Blumenbach, 1799) from the island of Kotelny and Bolshoy Lyakhovsky. The purpose of the work is to determine the habitat time and morphometric features of the found mammoth remains. Material and methods. To achieve this goal, all available morphometric parameters of the finds were measured, followed by a comparison of the obtained data with mammoths found on the mainland. In addition, radiocarbon dating was carried out on the studied samples in Tokyo (Japan). Results. The results of comparing the morphometric parameters of the studied remains with those of the mainland ones showed that the island mammoths were inferior in most parameters, i.e., having an identical individual age, the studied mammoths were not large in size of body. The results of radiocarbon dating correspond to the Karginsky time of the Late Pleistocene. Conclusions. The time of the habitat of the mammoths found on the islands coincides with the time of the existence of the so-called Beringian "bridge", when North America and Eurasia were connected in the area of modern Alaska and Chukotka. At that time, the islands of the Novosibirsk archipelago were part of the mainland. Probably, the small size of these mammoths is due to adaptation to a peculiar method of foraging.

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.

Ancient remains found in permafrost represent a rare opportunity to study past ecosystems. Here, we present an exceptionally well-preserved ancient bird carcass found in the Siberian permafrost, along with a radiocarbon date and a reconstruction of its complete mitochondrial genome. The carcass was radiocarbon dated to approximately 44–49 ka BP, and was genetically identified as a female horned lark. This is a species that usually inhabits open habitat, such as the steppe environment that existed in Siberia at the time. This near-intact carcass highlights the potential of permafrost remains for evolutionary studies that combine both morphology and ancient nucleic acids.

Ancient DNA provides a powerful means to investigate the timing, rate and extent of population declines caused by extrinsic factors, such as past climate change and human activities. One species probably affected by both these factors is the arctic fox, which had a large distribution during the last glaciation that subsequently contracted at the start of the Holocene. More recently, the arctic fox population in Scandinavia went through a demographic bottleneck owing to human persecution. To investigate the consequences of these processes, we generated mitogenome sequences from a temporal dataset comprising Pleistocene, historical and modern arctic fox samples. We found no evidence that Pleistocene populations in mid-latitude Europe or Russia contributed to the present-day gene pool of the Scandinavian population, suggesting that postglacial climate warming led to local population extinctions. Furthermore, during the twentieth-century bottleneck in Scandinavia, at least half of the mitogenome haplotypes were lost, consistent with a 20-fold reduction in female effective population size. In conclusion, these results suggest that the arctic fox in mainland Western Europe has lost genetic diversity as a result of both past climate change and human persecution. Consequently, it might be particularly vulnerable to the future challenges posed by climate change. This article is part of a discussion meeting issue 'The past is a foreign country: how much can the fossil record actually inform conservation?'

The 28,000-year-old remains of a woolly mammoth, named ‘Yuka’, were found in Siberian permafrost. Here we recovered the less-damaged nucleus-like structures from the remains and visualised their dynamics in living mouse oocytes after nuclear transfer. Proteomic analyses demonstrated the presence of nuclear components in the remains. Nucleus-like structures found in the tissue homogenate were histone- and lamin-positive by immunostaining. In the reconstructed oocytes, the mammoth nuclei showed the spindle assembly, histone incorporation and partial nuclear formation; however, the full activation of nuclei for cleavage was not confirmed. DNA damage levels, which varied among the nuclei, were comparable to those of frozen-thawed mouse sperm and were reduced in some reconstructed oocytes. Our work provides a platform to evaluate the biological activities of nuclei in extinct animal species.

The analysis of the spatial-temporal conjugacy of evolution of ice conditions in the Bering Sea with ice conditions in the seas of the East Arctic sector (the Laptev Sea, the East Siberian Sea and the Chukchi Sea) and the Pacific basin (the Sea of Okhotsk and the Sea of Japan) is carried out on the basis of the available information on the ice cover conditions of the seas. The processes of evolution of ice conditions in the water areas of the Bering Sea and the above seas run on, as a rule, in an antiphase to the ice conditions in the adjacent seas. In active development of an ice cover by the seas of the Arctic and Pacific basins it is expected the slowed-down development of ice conditions in the Bering Sea. The Bering Sea can serve as a certain indicator of climatic changes on noted water areas of the East Arctic seas and the Pacific basin seas. However, if the influence of the Arctic on ice conditions of the Bering Sea is quite unambiguous then the influence of the Bering Sea on ice conditions of the Arctic seas, the Chukchi Sea in particular, is more sophisticated. Ice cover growth in the Bering Sea is, as a rule, accompanied by the subsequent ice cover growth in the Chukchi Sea. Positive anomalies of ice cover in the Chukchi Sea (June-November) lead to decrease of ice cover in the Bering Sea (December-May). The direction (sign) of connections between ice processes on water areas Chukchi and Bering of the seas depend on their advance time.

This paper describes the treatment and results of the fixation procedure, extraction, dissection, and data collection of the preserved Late Pleistocene brain of the mummified specimen from permafrost. The partial carcass of the Woolly mammoth (Mammuthus primigenius (Blumenbach 1799)) nicknamed "Yuka" was found in 2010 on the Dmitrii Laptev Sea coast (Northern Yakutia, Russia). It dates to 39,440 -38,850 cal. BP. This fossil presents the unique opportunity to study the preserved brain from permafrost, with well-defined major gross anatomy features of the cerebrum and cerebellum and internal structures revealed by Computed tomography (CT) and Magnetic resonance imaging (MRI). Anatomical description, CT data including volumetry, and results of the histological and electron microscopy study of the specimen are provided. (C) 2014 Elsevier Ltd and INQUA. All rights reserved.

In August 2010, a well-preserved Mammuthus primigenius carcass was found along the coast of Oyogos Yar in the region of the Laptev Sea and the mummy was nicknamed ‘Yuka’. Frozen sediment samples from the area of skull condyles were collected for pollen and plant macrofossil analyses. The results from the palaeobotanical investigation confirmed that the Yuka mammoth lived during the optimum of the Kargin Interstadial (MIS3). The burial place of the mammoth could have been a small shallow freshwater pond with either stagnant or slowly moving water. The vegetation of the Oyogos Yar in MIS3 optimum was probably represented by zonal tundra-steppe combined with mesic-xeric meadows.