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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) lived1-8. 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.

Needles, wood and pollen of Larix, recorded in a peat deposit from Kotelny Island, northern Siberia, indicate the local occurrence of larch around 38 000 cal. a BP, which is during the Middle Pleniglacial (Greenland Interstadial 8) of the Weichselian last glacial period. The pollen record, dominated by Cyperaceae, Poaceae, Betula, Alnus, Salix and Artemisia, indicates steppe-tundra conditions with some shrubs and trees. The distribution of Larix species plays an important role in the reconstruction of climatic conditions during the Weichselian in Siberia. Nowadays Larix does not occur on Kotelny Island and in the present situation the temperature may not be the limiting factor for Larix, but instead the long, snowy winters and the moist tundra vegetation. Our data may contribute to a better understanding of Larix refugia and Weichselian climatic conditions in northern Siberia. [ABSTRACT FROM AUTHOR]

The frozen bodies of a young woolly mammoth ( Mammuthus primigenius), a wild horse ( Equus sp.) and a steppe bison ( Bison priscus) were recently found in the northern Yakutia (northeastern Siberia). All specimens have preserved bones, skin and soft tissues. Whereas the woolly mammoth and the Pleistocene horse were represented by partial frozen bodies, the steppe bison body was recovered in an absolutely complete state. All specimens were found frozen in the permafrost, with some of the tissues mummified. The wild horse and steppe bison are of Holocene age, and the mammoth is of Late Pleistocene age. [ABSTRACT FROM AUTHOR]

The brown bear (Ursus arctos L., 1758) is a widespread bear species inhabiting the forest zone of Eurasia, including the Republic of Yakutia. The association with forest habitats explains why the Pleistocene findings of U. arctos fossils are rare in the northern part of Eastern Siberia, where open steppe-tundra and steppefied landscapes prevailed during the Pleistocene. Fossils of U. arctos that have been found on the territory of Yakutia are dated since the beginning of the Middle Pleistocene. These are mainly the skulls and bones of the postcranial skeleton. In the present study, using comparative morphological analysis, computed tomography, and DNA sequencing, we describe a first mummified carcass of a brown bear individual that inhabited the New Siberian Islands (Northeast Siberia) in the Middle Holocene, approximately 3,500 years BP, which was found in the permafrost of Bolshoy Lyakhovsky Island, Russia, in 2020. [ABSTRACT FROM AUTHOR]

The history and palaeoecology of the steppe bison ( Bison priscus ) remain incompletely understood despite its widespread distribution. Using dental microwear textural analysis (DMTA) and vegetation modelling, we reconstructed the diet and assessed the habitat of steppe bison inhabiting Eurasia and Alaska since the Middle Pleistocene. During the Late Pleistocene, steppe bison occupied a variety of biome types: from the mosaic of temperate summergreen forest and steppe/temperate grassland (Serbia) to the tundra biomes (Siberia and Alaska). Despite the differences in the identified biome types, the diet of steppe bison did not differ significantly among populations in Eurasia. DMTA classified it as a mixed forager in all populations studied. The DMTA of Bb1 bison-a recently identified genetically extinct sister-clade of Bison bonasus -was typical of a highly grazing bovid species and differed from all B. priscus populations. The results of the study temper the common perception that steppe bison were grazers in steppe habitats. The dietary plasticity of the steppe bison was lower when compared with modern European bison and may have played an important role in its extinction, even in the stable tundra biome of eastern Siberia, where it has survived the longest in all of Eurasia., Competing Interests: We declare we have no competing interests., (© 2024 The Author(s).)

Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth's death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale., Competing Interests: Declaration of interests E.L.A., M.T.P.G., and L.D. are on the scientific advisory board of Colossal Biosciences and hold stock options. From 2021 to 2023, M.A.M.-R. received consulting honoraria from Acuity Spatial Genomics. E.L.A. and O.D. are inventors on US provisional patent applications 16/308,386 (E.L.A. and O.D., filed 12/7/2018), 16/247,502 (E.L.A. and O.D., 1/14/2019), and PCT/US2020/064704 (E.L.A., 12/11/2020) by the Baylor College of Medicine and the Broad Institute, relating to the assembly methods in this manuscript., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)