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Ancient microbial communities of permafrost soils and frozen animal remains represent an archive that has barely been explored. This yet unexplored microbial world is a vast resource that can provide us with new evolutionary insights, metabolic pathways and novel chemistry. Here, we reveal that Actinobacteria isolated from a faecal sample from the intestinal tract of a 28,000-year-old Siberian mammoth are phylogenetically and metabolically distinct from currently known modern siblings. AncientMicromonospora, Oerskovia, Saccharopolyspora, SanguibacterandStreptomycesspecies were successfully revived and their genome sequences resolved. Surprisingly, the genomes of the ancestors show a large phylogenetic distance to strains isolated today and harbour many novel biosynthetic gene clusters that may well represent uncharacterised biosynthetic potential. Metabolic profiles of the strains display production of known molecules like antimycin, conglobatin and macrotetrolides, but the majority of the mass features could not be dereplicated. Our work provides a snapshot into Actinobacteria of the past, yielding unexplored genomic information that is not yet present in current databases.

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. © 2022, The Author(s). 8028-00005B; IP DKRVO 2019-2023, MK000094862; 220457/Z/20/Z, ERC-2013-StG-337574-UNDEAD, ERC-2019-StG-853272-PALAEOFARM; 075-15-2021-1069; European Molecular Biology Organization, EMBO: 217223/Z/19/Z; Vallee Foundation; Velux Fonden; Wellcome Trust, WT; Francis Crick Institute, FCI: FC001595; Horizon 2020 Framework Programme, H2020: 796877; Medical Research Council, MRC; Natural Environment Research Council, NERC: 210119/Z/18/Z, NE/K003259/1, NE/K005243/1, NE/S00078X/1, NE/S007067/1; Cancer Research UK, CRUK; European Research Council, ERC: 852558; Grantová Agentura České Republiky, GA ČR: 15-06446S; Svenska Forskningsrådet Formas: 2018-01640; Knut och Alice Wallenbergs Stiftelse; Vetenskapsrådet, VR: 681396, BELSPO B2/191/P2/ICHIE; Russian Science Foundation, RSF: 16-18-10265-RNF, 20-17-00033, 21-18-00457-RNF, 310763; Science for Life Laboratory, SciLifeLab; Narodowa Agencja Wymiany Akademickiej, NAWA: PPN/PPO/2018/1/00037 This work was supported by grants to P. Skoglund from the European Research Council (grant no. 852558), the Erik Philip Sörensen Foundation and the Science for Life Laboratory, Swedish Biodiversity Program, made available by support from the Knut and Alice Wallenberg Foundation. A.B., L.S., P. Swali and P. Skoglund were supported by Francis Crick Institute core funding (FC001595) from Cancer Research UK, the UK Medical Research Council and the Wellcome Trust. P. Skoglund was also supported by the Vallee Foundation, the European Molecular Biology Organisation and the Wellcome Trust (217223/Z/19/Z). Computations were supported by SNIC-UPPMAX. We also acknowledge support from Science for Life Laboratory, the Knut and Alice Wallenberg Foundation, the National Genomics Infrastructure funded by the Swedish Research Council and the Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. We thank the Yukon gold mining community and First Nations, including the Tr’ondëk Hwëch’in, for continued support of our palaeontology research in the Yukon Territories, Canada. We thank the Danish National High-Throughput Sequencing Centre and BGI-Europe for assistance in sequencing data generation and the Danish National Supercomputer for Life Sciences–Computerome ( https://computerome.dtu.dk ) for computational resources. We thank National Museum Wales for continued sampling support. M. Germonpré acknowledges support from the Brain.be 2.0 ICHIE project (BELSPO B2/191/P2/ICHIE). M.T.P.G. was supported by the European Research Council (grant no. 681396). M.-H.S.S. was supported by the Velux Foundations through the Qimmeq Project, the Aage og Johanne Louis-Hansens Fond and the Independent Research Fund Denmark (8028-00005B). L.D. acknowledges support from FORMAS (2018-01640). D.W.G.S. received funding for this project from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 796877. M.P. was supported by the Polish National Agency for Academic Exchange–NAWA (grant no. PPN/PPO/2018/1/00037). V.J.S. was supported by the University of Zurich’s University Research Priority Program ‘Evolution in Action: From Genomes to Ecosystems’. This research was done with the participation of ZIN RAS (grant no. 075-15-2021-1069). We are grateful to the museum of the Institute of Plant and Animal Ecology UB RAS (Ekaterinburg, Russia) for provision of samples. R.P.J. and C.O’D. were supported by the Standing Committee for Archaeology of the Royal Irish Academy through the Archaeological Excavation Research Grant Scheme. E.Y.P., P.N. and V.V.P. are supported by the Russian Science Foundation (grant no. 16-18-10265-RNF and 21-18-00457-RNF). Y.V.K. was supported by the Russian Science Foundation (grant no. 20-17-00033). M.H. was supported by the European Research Council (consolidator grant GeneFlow no. 310763). M.L.-G. was supported by the Czech Science Foundation GAČR (grant no. 15-06446S) and institutional financing of the Moravian Museum from the Czech Ministry of Culture (IP DKRVO 2019-2023, MK000094862). L.S. is supported by the Sir Henry Wellcome fellowship (220457/Z/20/Z). We thank Staatliches Museum für Naturkunde Stuttgart for sample access. L.F. and G.L. were supported by European Research Council grants (ERC-2013-StG-337574-UNDEAD and ERC-2019-StG-853272-PALAEOFARM) and Natural Environmental Research Council grants (NE/K005243/1, NE/K003259/1, NE/S007067/1 and NE/S00078X/1). L.F. was also supported by the Wellcome Trust (210119/Z/18/Z). This research was funded in whole, or in part, by the Wellcome Trust (FC001595). For the purpose of open access, the author has applied a CC-BY public copyright licence to any author accepted manuscript version arising from this submission.

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.

The woolly mammoth mitochondrial genome (including the Malolyakhovsky mammoth) has been previously sequenced, followed by the annotation of all its genes (MF770243). In this study, based on the Malolyakhovsky mammoth, we describe for the first time the sites of functional significance in the control region of the woolly mammoth mitogenome.

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.

A megaslump at Batagaika, in northern Yakutia, exposes a remarkable stratigraphic sequence of permafrost deposits ~50–80 m thick. To determine their potential for answering key questions about Quaternary environmental and climatic change in northeast Siberia, we carried out a reconnaissance study of their cryostratigraphy and paleoecology, supported by four rangefinder 14C ages. The sequence includes two ice complexes separated by a unit of fine sand containing narrow syngenetic ice wedges and multiple paleosols. Overall, the sequence developed as permafrost grew syngenetically through an eolian sand sheet aggrading on a hillslope. Wood remains occur in two forest beds, each associated with a reddened weathering horizon. The lower bed contains high amounts of Larix pollen (>20%), plus small amounts of Picea and Pinus pumila, and is attributed to interglacial conditions. Pollen from the overlying sequence is dominated by herbaceous taxa (~70%–80%) attributed to an open tundra landscape during interstadial climatic conditions. Of three hypothetical age schemes considered, we tentatively attribute much of the Batagaika sequence to Marine Oxygen Isotope Stage (MIS) 3. The upper and lower forest beds may represent a mid–MIS 3 optimum and MIS 5, respectively, although we cannot discount alternative attributions to MIS 5 and 7.

A partial carcass of an adult woolly mammoth (Mammuthus primigenius) found in 2012 on Maly Lyakhovsky Island presents a new opportunity to retrieve associated anatomical, morphological, and life history data on this important component of Pleistocene biotas. In addition, we address hematological, histological, and microbiological issues that relate directly to quality of preservation. Recovered by staff from North-Eastern Federal University in Yakutsk, this individual is a relatively old female preserving soft tissue of the anteroventral portion of the head, most of both fore-quarters, and the ventral aspect of much of the rest of the body. Both tusks were recovered and subjected to computed tomographic analysis in which annual dentin increments were revealed as cycles of variation in X-ray attenuation. Measurements of annual increment areas (in longitudinal section) display a pulsed pattern of tusk growth showing cycles of growth rate variation over periods of 3-5 years. These intervals are interpreted as calving cycles reflecting regular shifts in calcium and phosphate demand for tusk growth vs. fetal ossification and lactation. Brown liquid associated with the frozen carcass turned out to include remains of hemolyzed blood, and blood samples examined microscopically included white blood cells with preserved nuclei. Muscle tissue from the trunk was unusually well preserved, even at the histological level. Intestinal contents and tissue samples were investigated microbiologically, and several strains of lacticacid bacteria (e.g., Enterococcus faecium, Enterococcus hirae) that are widely distributed as commensal organisms in the intestines of herbivores were isolated. (C) 2017 Elsevier Ltd and INQUA. All rights reserved.

Two female woolly mammoth neonates from permafrost in the Siberian Arctic are the most complete mammoth specimens known. Lyuba, found on the Yamal Peninsula, and Khroma, from northernmost Yakutia, died at ages of approximately one and two months, respectively. Both specimens were CT-scanned, yielding detailed information on the stage of development of their dentition and skeleton and insight into conditions associated with death. Both mammoths died after aspirating mud. Khroma's body was frozen soon after death, leaving her tissues in excellent condition, whereas Lyuba's body underwent postmortem changes that resulted in authigenic formation of nodules of the mineral vivianite associated with her cranium and within diaphyses of long bones. CT data provide the only comprehensive approach to mapping vivianite distribution. Three-dimensional modeling and measurement of segmented long bones permits comparison between these individuals and with previously recovered specimens. CT scans of long bones and foot bones show developmental features such as density gradients that reveal ossification centers. The braincase of Khroma was segmented to show the approximate morphology of the brain; its volume is slightly less (∼2,300 cm3) than that of neonate elephants (∼2,500 cm3). Lyuba's premaxillae are more gracile than those of Khroma, possibly a result of temporal and/or geographic variation but probably also reflective of their age difference. Segmentation of CT data and 3-D modeling software were used to produce models of teeth that were too complex for traditional molding and casting techniques.

Recent palaeogenetic studies indicate a highly dynamic history in collared lemmings (Dicrostonyx spp.), with several demographical changes linked to climatic fluctuations that took place during the last glaciation. At the western range margin of D. torquatus, these changes were characterized by a series of local extinctions and recolonizations. However, it is unclear whether this pattern represents a local phenomenon, possibly driven by ecological edge effects, or a global phenomenon that took place across large geographical scales. To address this, we explored the palaeogenetic history of the collared lemming using a next‐generation sequencing approach for pooled mitochondrial DNA amplicons. Sequences were obtained from over 300 fossil remains sampled across Eurasia and two sites in North America. We identified five mitochondrial lineages of D. torquatus that succeeded each other through time across Europe and western Russia, indicating a history of repeated population extinctions and recolonizations, most likely from eastern Russia, during the last 50 000 years. The observation of repeated extinctions across such a vast geographical range indicates large‐scale changes in the steppe‐tundra environment in western Eurasia during the last glaciation. All Holocene samples, from across the species' entire range, belonged to only one of the five mitochondrial lineages. Thus, extant D. torquatus populations only harbour a small fraction of the total genetic diversity that existed across different stages of the Late Pleistocene. In North American samples, haplotypes belonging to both D. groenlandicus and D. richardsoni were recovered from a Late Pleistocene site in south‐western Canada. This suggests that D. groenlandicus had a more southern and D. richardsoni a more northern glacial distribution than previously thought. This study provides significant insights into the population dynamics of a small mammal at a large geographical scale and reveals a rather complex demographical history, which could have had bottom‐up effects in the Late Pleistocene steppe‐tundra ecosystem.

Librado, Pablo et al., Yakutia is among the coldest regions in the Northern Hemisphere, showing ∼40% of its territory above the Arctic Circle. Native horses are particularly adapted to this environment, with body sizes and thick winter coats minimizing heat loss. We sequenced complete genomes of two ancient and nine present-day Yakutian horses to elucidate their evolutionary origins. We find that the contemporary population descends from domestic livestock, likely brought by early horse-riders who settled in the region a few centuries ago. The metabolic, anatomical, and physiological adaptations of these horses therefore emerged on very short evolutionary time scales. We show the relative importance of regulatory changes in the adaptive process and identify genes independently selected in cold-adapted human populations and woolly mammoths., This work was supported by the Danish Council for Independent Research, Natural Sciences (Grant 4002-00152B); the Danish National Research Foundation (Grant DNRF94); a Marie-Curie Career Integration grant (Grant FP7 CIG-293845); Initiative d'Excellence Chaires d'attractivité, Université de Toulouse (OURASI); and the International Research Group Program (Grant IRG14-08), Deanship of Scientific Research, King Saud University. P.L. was supported by a Villum Fonden Blokstipendier grant (primary investigator: L.O.); H.J. by a Marie-Curie Initial Training Network grant [EUROTAST (Exploring the History, Archeology, and New Genetics of the Transatlantic Slave Trade); Grant FP7 ITN-290344]; C.G. and L.E. by Marie-Curie Intra-European fellowships (FP7-IEF-328024 and FP7 IEF-302617); M. Schubert by a Lundbeck Foundation grant (Grant R52-A5062); M.A.Y. by a National Science Foundation Graduate Research fellowship; M.F. by a Human Frontier Science Program fellowship (LT000320/2014); A.A. by a Villum Fonden Blokstipendier grant; M. Schubert by an NIH grant (Grant R01-GM40282); and J.K. by the Academy of Finland (Grant 286040). Research work on the ancient Yakut population was supported by the French Archaeological Mission in Oriental Siberia (Ministry of Foreign and European Affairs, France), the North-Eastern Federal University (Yakutsk, Sakha Republic), and the Human Adaptation Program of the French Polar Institute Paul Emile Victor [HUMAD MAFSO (Missions Archéologiques Françaises en Sibérie Orientale) 1038].