Gennady F. Baryshnikov

Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA

Whereas evolutionary inferences derived from present-day DNA sequences are by necessity indirect, ancient DNA sequences provide a direct view of past genetic variants. However, base lesions that accumulate in DNA over time may cause nucleotide misincorporations when ancient DNA sequences are replicated. By repeated amplifications of mitochondrial DNA sequences from a large number of ancient wolf remains, we show that C/G-to-T/A transitions are the predominant type of such misincorporations. Using a massively parallel sequencing method that allows large numbers of single DNA strands to be sequenced, we show that modifications of C, as well as to a lesser extent of G, residues cause such misincorporations. Experiments where oligonucleotides containing modified bases are used as templates in amplification reactions suggest that both of these types of misincorporations can be caused by deamination of the template bases. New DNA sequencing methods in conjunction with knowledge of misincorporation processes have now, in principle, opened the way for the determination of complete genomes from organisms that became extinct during and after the last glaciation.

Phylogeography of lions ( Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity

Lions were the most widespread carnivores in the late Pleistocene, ranging from southern Africa to the southern USA, but little is known about the evolutionary relationships among these Pleistocene populations or the dynamics that led to their extinction. Using ancient DNA techniques, we obtained mitochondrial sequences from 52 individuals sampled across the present and former range of lions. Phylogenetic analysis revealed three distinct clusters: (i) modern lions, Panthera leo; (ii) extinct Pleistocene cave lions, which formed a homogeneous population extending from Europe across Beringia (Siberia, Alaska and western Canada); and (iii) extinct American lions, which formed a separate population south of the Pleistocene ice sheets. The American lion appears to have become genetically isolated around 340 000 years ago, despite the apparent lack of significant barriers to gene flow with Beringian populations through much of the late Pleistocene. We found potential evidence of a severe population bottleneck in the cave lion during the previous interstadial, sometime after 48 000 years, adding to evidence from bison, mammoths, horses and brown bears that megafaunal populations underwent major genetic alterations throughout the last interstadial, potentially presaging the processes involved in the subsequent end‐Pleistocene mass extinctions.

Withering Away—25,000 Years of Genetic Decline Preceded Cave Bear Extinction

The causes of the late Pleistocene megafaunal extinctions are still enigmatic. Although the fossil record can provide approximations for when a species went extinct, the timing of its disappearance alone cannot resolve the causes and mode of the decline preceding its extinction. However, ancient DNA analyses can reveal population size changes over time and narrow down potential causes of extinction. Here, we present an ancient DNA study comparing late Pleistocene population dynamics of two closely related species, cave and brown bears. We found that the decline of cave bears started approximately 25,000 years before their extinction, whereas brown bear population size remained constant. We conclude that neither the effects of climate change nor human hunting alone can be responsible for the decline of the cave bear and suggest that a complex of factors including human competition for cave sites lead to the cave bears extinction.

First DNA sequences from Asian cave bear fossils reveal deep divergences and complex phylogeographic patterns

Until recently, cave bears were believed to have only inhabited Europe. However, recent morphological evidence suggests that cave bears’ geographic range extended as far east as Transbaikalia, Eastern Siberia. These Asian cave bears were morphologically distinct from European cave bears. However, how they related to European lineages remains unclear, stressing the need to assess the phylogenetic and phylogeographic relationship between Asian cave bears and their European relatives. In this work, we address this issue using a 227 base‐pair fragment of the mitochondrial control region obtained from nine fossil bone samples from eight sites from the Urals, Caucasus, Altai Mountains, Ukraine and Yana River region in Eastern Siberia. Results of the phylogenetic analyses indicate that (i) the cave bear from the Yana River is most closely related to cave bears from the Caucasus region; (ii) the Caucasus/Yana group of bears is genetically very distinct from both European cave bears and brown bears, suggesting that these bears could represent an independent species; and (iii) the Western European cave bear lineage reached at least temporarily to the Altai Mountains, 7000 km east of their known centre of distribution. These results suggest that the diversity of cave bears was greater than previously believed, and that they could survive in a much wider range of ecological conditions than previously assumed. They also agree with recent studies on other extinct and extant species, such as wolves, hyenas and steppe bison, which have also revealed higher genetic and ecological diversity in Pleistocene populations than previously known.

Ancient DNA sequences point to a large loss of mitochondrial genetic diversity in the saiga antelope (Saiga tatarica) since the Pleistocene

Prior to the Holocene, the range of the saiga antelope (Saiga tatarica) spanned from France to the Northwest Territories of Canada. Although its distribution subsequently contracted to the steppes of Central Asia, historical records indicate that it remained extremely abundant until the end of the Soviet Union, after which its populations were reduced by over 95%. We have analysed the mitochondrial control region sequence variation of 27 ancient and 38 modern specimens, to assay how the species’ genetic diversity has changed since the Pleistocene. Phylogenetic analyses reveal the existence of two well‐supported, and clearly distinct, clades of saiga. The first, spanning a time range from >49 500 14C ybp to the present, comprises all the modern specimens and ancient samples from the Northern Urals, Middle Urals and Northeast Yakutia. The second clade is exclusive to the Northern Urals and includes samples dating from between 40 400 to 10 250 14C ybp. Current genetic diversity is much lower than that present during the Pleistocene, an observation that data modelling using serial coalescent indicates cannot be explained by genetic drift in a population of constant size. Approximate Bayesian Computation analyses show the observed data is more compatible with a drastic population size reduction (c. 66–77%) following either a demographic bottleneck in the course of the Holocene or late Pleistocene, or a geographic fragmentation (followed by local extinction of one subpopulation) at the Holocene/Pleistocene transition.

Vertebrate remains from the Mousterian site of Il'skaya I (northern Caucasus, U.S.S.R.): New analysis and interpretation

Abstract A new analysis of vertebrate remains from the Mousterian open-air site of Ilskaya I was undertaken. The site is located near Krasnodar in the northern Caucasus. The faunal samples available to us were excavated in 1926, 1928, and 1936–1937, and comprise c . 1500 identifiable bones and teeth; mixture of remains from different stratigraphic levels significantly affects the results of the analysis. Steppe bison ( Bison priscus ) dominates the mammalian assemblage (92%), which also includes giant deer, horse, red deer, wolf, hyaena, mammoth, wild ass, corsac, bear, saiga, and dhole. Bird remains (rare for Mousterian open-air sites) include black vulture, magpie, and mallard. Bison is represented by virtually all skeletal parts, although isolated teeth are especially abundant; variations in skeletal-part frequencies primarily reflect weathering effects. Age profiels for bison, obtained from molar crown-height measurements, indicate the predominance of prime-age adults; both males and females appear to be represented, but estimation of sex ratio is problematic. The site was probably occupied during several seasons. The results are discussed within the context of general issues concerning Mousterian subsistence strategy.

Hyenas and hunters: zooarchaeological investigations at Prolom II Cave, Crimea

Prolom II, a stratified archaeological cave deposit in the eastern Crimean Peninsula, Ukraine, dates back to approximately 135 000–60 000 years ago. Stone tool industries from four human occupation levels are characteristic of the Middle Palaeolithic, typically associated with Neanderthals. In addition to the stone tool artifactual material, there is abundant faunal material, including saiga antelope, horse, bison, hyena and bear. This zooarchaeological investigation examined approximately 3500 specimens of animal bones to discern between natural and cultural modifications, and to elucidate human patterns of exploitation of faunal resources in prehistoric subsistence. The high proportion of carnivores, particularly hyena, in the fauna suggest that much of the faunal material is present as a result of non-human agents. Morphological characteristics, such as gnawing marks and punctures, were abundant on most herbivore skeletal elements. Bone destruction patterns were consistent with carnivore and scavenger behaviour, as documented in modern comparative studies. Stone tool cut marks were identifiable under microscopic examination on only six specimens of saiga antelope. The preliminary conclusion is that the site was occupied alternately by carnivores, primarily hyenas and, occasionally, humans. These occupations were probably short-term stays. The deep stratigraphic deposits represent accumulations over long periods of time. We cannot assign more than a few of the faunal specimens to human hunting or modification, despite the large number of stone tools present at the site. The densest and highest frequencies of stone tools occurred in the same levels as the greatest frequencies of hyena bones, which are very unlikely to represent human prey. The human contribution to the faunal assemblage appears to be minimal. The entire collection of bones cannot be used to characterize human subsistence. This is consistent with a growing literature that reassesses the role of humans in the accumulation of animal bones in a variety of archaeological and palaeontological sites. Copyright

MORPHOLOGICAL VARIABILITY AND EVOLUTION OF THE BACULUM (OS PENIS) IN MUSTELIDAE (CARNIVORA)

Abstract We examined morphological variability and evolution of the baculum (os penis) across the Mustelidae through allometric analyses and character mapping. Fifty-four species and 26 genera (including 2 fossil forms) were examined with numerous caniform out-group species. Allometric analyses showed that bacular length is relatively constant across mustelids and caniforms; only a tendency to a slightly shortened baculum in mephitines was observed. Character mapping revealed the ancestral mustelid baculum to be an elongated rod-shaped bone that lacks a urethral groove and possesses a simple, nondistinct distal tip. This form is largely retained in mephitines and, to a lesser degree, in lutrines. From the ancestral condition, it is possible to derive forms with a more complicated head that has projections and openings (e.g., melines, Eira barbara, Galictis, Gulo gulo, Martes) or spoon-shaped and cup-shaped processes (e.g., Ictonyx, Mellivora capensis). Another evolutionary trajectory involves the distal tip of the baculum becoming hook-shaped and the urethral groove well developed (e.g., Mustela, Vormela peregusna). Although the structure of the baculum distinguishes closely related species, many features are derived independently in more distantly related forms. Therefore, bacular structure provides restricted phylogenetic information and should be analyzed in concert with other data sources (e.g., morphology of the basicranial region).

Faunal record identifies Bering isthmus conditions as constraint to end-Pleistocene migration to the New World

Human colonization of the New World is generally believed to have entailed migrations from Siberia across the Bering isthmus. However, the limited archaeological record of these migrations means that details of the timing, cause and rate remain cryptic. Here, we have used a combination of ancient DNA, 14C dating, hydrogen and oxygen isotopes, and collagen sequencing to explore the colonization history of one of the few other large mammals to have successfully migrated into the Americas at this time: the North American elk (Cervus elaphus canadensis), also known as wapiti. We identify a long-term occupation of northeast Siberia, far beyond the species’s current Old World distribution. Migration into North America occurred at the end of the last glaciation, while the northeast Siberian source population became extinct only within the last 500 years. This finding is congruent with a similar proposed delay in human colonization, inferred from modern human mitochondrial DNA, and suggestions that the Bering isthmus was not traversable during parts of the Late Pleistocene. Our data imply a fundamental constraint in crossing Beringia, placing limits on the age and mode of human settlement in the Americas, and further establish the utility of ancient DNA in palaeontological investigations of species histories.

Mousterian hunters of the NW Caucasus: preliminary results of recent investigations

AbstractRecent investigations have produced a group of important new Mousterian sites in the NW Caucasus (Russia). These sites, which range in elevation from 100 to 1350 m above sea level, include Ilskaya II (100 m)) Matuzka Cave (750 m), Barakaevskaya Cave (900 m), and Mezmaiskaya Cave (1350 m). Each contains a large faunal assemblage that, in conjunction with faunal remains excavated earlier from Ilskaya I (100 m) and Dakhovskaya Cave (500 m), constitute a rich source of information on Mousterian paleoecology in this part of Europe. Sites at lower elevations yield remains of mammoths and giant deer; at higher elevations, these taxa are absent but goats and sheep are common. Steppe bison is the most common species in a majority of assemblages, and bone modification and demographic data indicate that it was probably hunted (as opposed to scavenged) by Mousterian groups. Cave bear remains exhibit an inverse relationship to artifacts, and most probably reflect natural mortality. The economic role of mammo...