Despite decades of research, the roles of climate and humans in driving the dramatic extinctions of large-bodied mammals during the Late Quaternary remain contentious. We use ancient DNA, species distribution models and the human fossil record to elucidate how climate and humans shaped the demographic history of woolly rhinoceros, woolly mammoth, wild horse, reindeer, bison and musk ox. We show that climate has been a major driver of population change over the past 50,000 years. However, each species responds differently to the effects of climatic shifts, habitat redistribution and human encroachment. Although climate change alone can explain the extinction of some species, such as Eurasian musk ox and woolly rhinoceros, a combination of climatic and anthropogenic effects appears to be responsible for the extinction of others, including Eurasian steppe bison and wild horse. We find no genetic signature or any distinctive range dynamics distinguishing extinct from surviving species, underscoring the challenges associated with predicting future responses of extant mammals to climate and human-mediated habitat change.

Multidisciplinary study of a key section on the Laptev Sea Coast (Bykovsky Peninsula, east Lena Delta) in 1998-2001 provides the most complete record of Middle and Late Weichselian environments in the East Siberian Arctic. The 40-m high Mamontovy Khayata cliff is a typical Ice Complex section built of icy silts with a network of large syngenetic polygonal ice wedges, and is richly fossiliferous. In combination with pollen, plant macrofossil and mammal fossils, a sequence of ca 70 insect samples provides a new interpretation of the environment and climate of the area between ca 50 and 12 ka. The large number of radiocarbon dates from the section, together with an extensive 14 C database on mammal bones, allows chronological correlation of the various proxies. The Bykovsky record shows how climate change, and the Last Glacial Maximum in particular, affected terrestrial organisms such as insects and large grazing mammals. Both during the presumed ''Karginsky Interstadial'' (MIS 3) and the Sartanian Glacial (MIS 2), the vegetation remained a mosaic arctic grassland with relatively high diversity of grasses and herbs and dominance of xeric habitats: the tundra-steppe type. This biome was supported by a constantly very continental climate, caused by low sea level and enormous extension of shelf land. Variations within the broad pattern were caused mainly by fluctuations in summer temperature, related to global trends but overprinted by the effect of continentality. No major changes in humidity were observed nor were advances of modern-type forest or forest-tundra recorded, suggesting a major revision of the ''Karginsky Interstadial'' paradigm. The changing subtypes of the tundra-steppe environment were persistently favourable for mammalian grazers, which inhabited the shelf lowlands throughout the studied period. Mammal population numbers were lowered during the LGM, especially toward its end, and then flourished in a short, but impressive peak in the latest Weichselian, just before the collapse of the tundra-steppe biome. Throughout MIS 3 and MIS 2, the climate remained very favourable for the aggradation of permafrost. No events of regional permafrost degradation were observed in the continuous Bykovsky sequence until the very end of the Pleistocene. r

Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in previously published frozen bone samples, even though one of the specimens was >50,000 14C years old and another had been stored for 200 years at room temperature. The method therefore sets the stage for molecular-genetic analysis of museum collections.

Ice Complexes, extremely ice-rich permafrost deposits with large ice wedges, are widely distributed in the Arctic region of northeast Siberia. They present excellent archives for the reconstruction of Late Quaternary paleoenvironmental conditions in nonglaciated areas. In 1998, 1999, and 2000 Russian and German scientists worked together on the Bykovsky Peninsula southeast of the Lena Delta in order to investigate the Ice Complex and its associated sediments. Intensive cryolithological and sedimentological studies, Radiocarbon age determinations, paleobotanical studies, micropaleontological investigations, studies of mammal and insect fossils, and stable isotope analyses of ground ice were performed. Radiocarbon data have been obtained from the entire exposed sequence covering approximately the last 60,000 years. The results indicate that compared with modern time the investigated Ice Complex sequence was formed during two cooler and more arid stages of the Late Pleistocene with relatively uniform environmental conditions, separated by a stage with environmental variations and more intensive soil formation caused by climate amelioration. The Late Pleistocene environmental changes were not as strong as those occurring during the Pleistocene/Holocene transition where a sharp break is evident. r

a b s t r a c tLate Quaternary palaeoenvironments of the Siberian Arctic were reconstructed by combining data from several fossil bioindicators (pollen, plant macro-fossils, ostracods, insects, and mammal bones) with sedimentological and cryolithological data from permafrost deposits. The record mirrors the environmental history of Beringia and covers glacial/interglacial and stadial/interstadial climate variations with a focus on the Middle Weichselian interstadial (50-32 kyr BP). The late Pleistocene to Holocene sequence on Kurungnakh Island reflects the development of periglacial landscapes under changing sedimentation regimes which were meandering fluvial during the Early Weichselian, colluvial or proluvial on gently inclined plaines during the Middle and Late Weichselian, and thermokarstaffected during the Holocene. Palaeoecological records indicate the existence of tundra-steppe vegetation under cold continental climate conditions during the Middle Weichselian interstadial. Due to sedimentation gaps in the sequence between 32 and 17 kyr BP and 17 and 8 kyr BP, the Late Weichselian stadial is incompletely represented in the studied outcrops. Nevertheless, by several palaeoecological indications arctic tundra-steppe vegetation under extremely cold-arid conditions prevailed during the late Pleistocene. The tundra-steppe disappeared completely due to lasting paludification during the Holocene. Initially subarctic shrub tundra formed, which later retreated in course of the late Holocene cooling.

The causes of the late Pleistocene megafaunal extinctions are poorly understood. Different lines of evidence point to climate change, the arrival of humans, or a combination of these events as the trigger. Although many species went extinct, others, such as caribou and bison, survived to the present. The musk ox has an intermediate story: relatively abundant during the Pleistocene, it is now restricted to Greenland and the Arctic Archipelago. In this study, we use ancient DNA sequences, temporally unbiased summary statistics, and Bayesian analytical techniques to infer musk ox population dynamics throughout the late Pleistocene and Holocene. Our results reveal that musk ox genetic diversity was much higher during the Pleistocene than at present, and has undergone several expansions and contractions over the past 60,000 years. Northeast Siberia was of key importance, as it was the geographic origin of all samples studied and held a large diverse population until local extinction at ≈45,000 radiocarbon years before present ( 14 C YBP). Subsequently, musk ox genetic diversity reincreased at ca. 30,000 14 C YBP, recontracted at ca. 18,000 14 C YBP, and finally recovered in the middle Holocene. The arrival of humans into relevant areas of the musk ox range did not affect their mitochondrial diversity, and both musk ox and humans expanded into Greenland concomitantly. Thus, their population dynamics are better explained by a nonanthropogenic cause (for example, environmental change), a hypothesis supported by historic observations on the sensitivity of the species to both climatic warming and fluctuations.

The interval since circa 50 Ka has been a period of significant species extinctions among the large mammal fauna. However, the relative roles of an increasing human presence and a synchronous series of complex environmental changes in these extinctions have yet to be fully resolved. Recent analyses of fossil material from Beringia have clarified our understanding of the spatiotemporal pattern of Late Pleistocene extinctions, identifying periods of population turnover well before the last glacial maximum (LGM: circa 21 Ka) or subsequent human expansion. To examine the role of pre-LGM population changes in shaping the genetic structure of an extinct species, we analyzed the mitochondrial DNA of woolly mammoths in western Beringia and across its range. We identify genetic signatures of a range expansion of mammoths, from eastern to western Beringia, after the last interglacial (circa 125 Ka), and then an extended period during which demographic inference indicates no population-size increase. The most marked change in diversity at this time is the loss of one of two major mitochondrial lineages.

We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of mammoth clade II. Analysis of these and 13 recently published mtDNA genomes demonstrates the existence of two apparently sympatric mtDNA clades that exhibit high interclade divergence. The analytical power afforded by the analysis of the complete mtDNA genomes reveals a surprisingly ancient coalescence age of the two clades, Ϸ1-2 million years, depending on the calibration technique. Furthermore, statistical analysis of the temporal distribution of the 14 C ages of these and previously identified members of the two mammoth clades suggests that clade II went extinct before clade I. Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep.mtDNA genome ͉ phylogeny ͉ ancient DNA ͉ next-generation sequencing A lthough ancient DNA analyses offer the potential to tackle a tantalizing range of otherwise unapproachable questions, the actual achievements of the field have been limited by the postmortem degradation of DNA. Even in well preserved specimens from arctic environments, number of specimens and amount of data per specimen are limited. Previous studies to assess the genetic structure of extinct species, including mammoths (1), have had to rely on short sequence intervals that were often only a few hundred nucleotides in length. This has made it difficult to obtain precise estimates of substitution rates and divergence times, particularly for species exhibiting low levels of genetic variation. Additionally, it is possible that the accuracy of these estimates has been compromised by the presence of sequence damage in the form of miscoding lesions, which can introduce significant biases in estimates of evolutionary parameters (2). These problems can be addressed by large-scale sequencing with manifold coverage, which will increase the amount of informative data while filtering out the spurious polymorphisms resulting from sequence damage. This should serve to increase both the precision and accuracy of demographic estimates.