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The Altai region of Siberia was inhabited for parts of the Pleistocene by at least two groups of archaic hominins—Denisovans and Neanderthals. Denisova Cave, uniquely, contains stratified deposits that preserve skeletal and genetic evidence of both hominins, artefacts made from stone and other materials, and a range of animal and plant remains. The previous site chronology is based largely on radiocarbon ages for fragments of bone and charcoal that are up to 50,000 years old; older ages of equivocal reliability have been estimated from thermoluminescence and palaeomagnetic analyses of sediments, and genetic analyses of hominin DNA. Here we describe the stratigraphic sequences in Denisova Cave, establish a chronology for the Pleistocene deposits and associated remains from optical dating of the cave sediments, and reconstruct the environmental context of hominin occupation of the site from around 300,000 to 20,000 years ago. Optical dating of sediments from Denisova Cave establishes a chronology for its Pleistocene deposits and the associated artefacts, hominin remains and environmental records, which date to between about 300,000 and 20,000 years ago.

Denisova Cave in southern Siberia is the only site known to have been occupied by Denisovans, Neanderthals and modern humans. The cave consists of three chambers (Main, East and South), with the archaeological assemblages and remains of hominins, fauna and flora recovered from Main and East Chambers being the most thoroughly investigated to date. Here we report the results of analyses of the Palaeolithic artefacts, faunal remains and hominin and mammalian mitochondrial (mt) DNA recovered from renewed excavations in South Chamber. We construct a calendar-year time scale for the stratified Pleistocene deposits from optical dating of the sediments. The timing of hominin occupation and major turnovers in the mtDNA of Denisovans and large mammals largely accords with the patterns detected in Main and East Chambers. Time gaps in those sequences are partly filled by the South Chamber data and the sediment DNA record of Denisovans after 80,000 years ago is more than doubled in size. We combine the sediment dating and DNA records for all three chambers to reveal the whole-of-cave history of this unique site and the climatic conditions experienced by hominins and fauna over the past 300,000 years, including potential changes in habitat suitability for Denisovans and Neanderthals. Here, the authors present mtDNA and chronological data for sediments from excavations in the South Chamber of Denisova Cave, from which they construct a timeline of hominin and faunal occupation that fills stratigraphic gaps in other parts of the cave.

The genus Equus is richly represented in the fossil record, yet our understanding of taxonomic relationships within this genus remains limited. To estimate the phylogenetic relationships among modern horses, zebras, asses and donkeys, we generated the first data set including complete mitochondrial sequences from all seven extant lineages within the genus Equus. Bayesian and Maximum Likelihood phylogenetic inference confirms that zebras are monophyletic within the genus, and the Plains and Grevy's zebras form a well-supported monophyletic group. Using ancient DNA techniques, we further characterize the complete mitochondrial genomes of three extinct equid lineages (the New World stilt-legged horses, NWSLH; the subgenus Sussemionus; and the Quagga, Equus quagga quagga). Comparisons with extant taxa confirm the NWSLH as being part of the caballines, and the Quagga and Plains zebras as being conspecific. However, the evolutionary relationships among the non-caballine lineages, including the now-extinct subgenus Sussemionus, remain unresolved, most likely due to extremely rapid radiation within this group. The closest living outgroups (rhinos and tapirs) were found to be too phylogenetically distant to calibrate reliable molecular clocks. Additional mitochondrial genome sequence data, including radiocarbon dated ancient equids, will be required before revisiting the exact timing of the lineage radiation leading up to modern equids, which for now were found to have possibly shared a common ancestor as far as up to 4 Million years ago (Mya).

A growing number of researchers studying horse domestication come to a conclusion that this process happened in multiple locations and involved multiple wild maternal lines. The most promising approach to address this problem involves mitochondrial haplotype comparison of wild and domestic horses from various locations coupled with studies of possible migration routes of the ancient shepherds. Here, we sequenced complete mitochondrial genomes of six horses from burials of the Ukok plateau (Russia, Altai Mountains) dated from 2.7 to 1.4 thousand years before present and a single late Pleistocene wild horse from the neighboring region (Denisova cave). Sequencing data indicates that the wild horse belongs to an extinct pre-domestication lineage. Integration of the domestic horse data with known Eurasian haplotypes of a similar age revealed two distinct groups: the first one widely distributed in Europe and presumably imported to Altai, and the second one specific for Altai Mountains and surrounding area.

Native cattle breeds represent an important cultural heritage. They are a reservoir of genetic variation useful for properly responding to agriculture needs in the light of ongoing climate changes. Evolutionary processes that occur in response to extreme environmental conditions could also be better understood using adapted local populations. Herein, different evolutionary histories of the world northernmost native cattle breeds from Russia were investigated. They highlighted Kholmogory as a typical taurine cattle, whereas Yakut cattle separated from European taurines approximately 5,000 years ago and contain numerous ancestral and some novel genetic variants allowing their adaptation to harsh conditions of living above the Polar Circle. Scans for selection signatures pointed to several common gene pathways related to adaptation to harsh climates in both breeds. But genes affected by selection from these pathways were mostly different. A Yakut cattle breed-specific missense mutation in a highly conserved NRAP gene represents a unique example of a young amino acid residue convergent change shared with at least 16 species of hibernating/cold-adapted mammals from six distinct phylogenetic orders. This suggests a convergent evolution event along the mammalian phylogenetic tree and fast fixation in a single isolated cattle population exposed to a harsh climate.

This study focuses on expanding knowledge about the genetic diversity of the Altai horse native to Siberia. While studying modern horses from two Altai regions, where horses were subjected to less crossbreeding, we tested the hypothesis, formulated on the basis of morphological data, that the Altai horse is represented by two populations (Eastern and Southern) and that the Mongolian horse has a greater genetic proximity to Eastern Altai horses. Bone samples of ancient horses from different cultures of Altai were investigated to clarify the genetic history of this horse breed. As a genetic marker, we chose hypervariable region I of mitochondrial DNA. The results of the performed phylogenetic and population genetic analyses of our and previously published data confirmed the hypothesis stated above. As we found out, almost all the haplotypes of the ancient domesticated horses of Altai are widespread among modern Altai horses. The differences between the mitochondrial gene pools of the ancient horses of Altai and Mongolia are more significant than between those of modern horses of the respective regions, which is most likely due to an increase in migration processes between these regions after the Early Iron Age.

The MagellanPlus workshop “BlackGate” addressed fundamental questions concerning the dynamic evolution of the Mediterranean–Black Sea (MBS) gateway and its palaeoenvironmental consequences. This gateway drives the Miocene–Quaternary circulation patterns in the Black Sea and governs its present status as the world's largest example of marine anoxia. The exchange history of the MBS gateway is poorly constrained because continuous Pliocene–Quaternary deposits are not exposed on land adjacent to the Black Sea or northern Aegean. Gateway exchange is controlled by climatic (glacio-eustatic-driven sea-level fluctuations) and tectonic processes in the catchment as well as tectonic propagation of the North Anatolian Fault Zone (NAFZ) in the gateway area itself. Changes in connectivity trigger dramatic palaeoenvironmental and biotic turnovers in both the Black Sea and Mediterranean domains. Drilling a Messinian to Holocene transect across the MBS gateway will recover high-amplitude records of continent-scale hydrological changes during glacial–interglacial cycles and allow us to reconstruct marine and freshwater fluxes, biological turnover events, deep biospheric processes, subsurface gradients in primary sedimentary properties, patterns and processes controlling anoxia, chemical perturbations and carbon cycling, growth and propagation of the NAFZ, the timing of land bridges for Africa and/or Asia–Europe mammal migration, and the presence or absence of water exchange during the Messinian salinity crisis. During thorough discussions at the workshop, three key sites were selected for potential drilling using a mission-specific platform (MSP): one on the Turkish margin of the Black Sea (Arkhangelsky Ridge, 400 m b.s.f., metres below the seafloor), one on the southern margin of the Sea of Marmara (North İmrali Basin, 750 m b.s.f.), and one in the Aegean (North Aegean Trough, 650 m b.s.f.). All sites target Quaternary oxic–anoxic marl–sapropel cycles. Plans include recovery of Pliocene lacustrine sediments and mixed marine–brackish Miocene sediments from the Black Sea and the Aegean. MSP drilling is required because the JOIDES Resolution cannot pass under the Bosporus bridges. The wider goals are in line with the aims and scope of the International Ocean Discovery Program (IODP) “2050 Science Framework: Exploring Earth by Scientific Ocean Drilling” and relate specifically to the strategic objectives “Earth's climate system”, “Tipping points in Earth's history”, and “Natural hazards impacting society”.