Yaroslav V. Kuzmin

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.

A 33,000-Year-Old Incipient Dog from the Altai Mountains of Siberia: Evidence of the Earliest Domestication Disrupted by the Last Glacial Maximum

Background Virtually all well-documented remains of early domestic dog (Canis familiaris) come from the late Glacial and early Holocene periods (ca. 14,000–9000 calendar years ago, cal BP), with few putative dogs found prior to the Last Glacial Maximum (LGM, ca. 26,500–19,000 cal BP). The dearth of pre-LGM dog-like canids and incomplete state of their preservation has until now prevented an understanding of the morphological features of transitional forms between wild wolves and domesticated dogs in temporal perspective. Methodology/Principal Finding We describe the well-preserved remains of a dog-like canid from the Razboinichya Cave (Altai Mountains of southern Siberia). Because of the extraordinary preservation of the material, including skull, mandibles (both sides) and teeth, it was possible to conduct a complete morphological description and comparison with representative examples of pre-LGM wild wolves, modern wolves, prehistoric domesticated dogs, and early dog-like canids, using morphological criteria to distinguish between wolves and dogs. It was found that the Razboinichya Cave individual is most similar to fully domesticated dogs from Greenland (about 1000 years old), and unlike ancient and modern wolves, and putative dogs from Eliseevichi I site in central Russia. Direct AMS radiocarbon dating of the skull and mandible of the Razboinichya canid conducted in three independent laboratories resulted in highly compatible ages, with average value of ca. 33,000 cal BP. Conclusions/Significance The Razboinichya Cave specimen appears to be an incipient dog that did not give rise to late Glacial – early Holocene lineages and probably represents wolf domestication disrupted by the climatic and cultural changes associated with the LGM. The two earliest incipient dogs from Western Europe (Goyet, Belguim) and Siberia (Razboinichya), separated by thousands of kilometers, show that dog domestication was multiregional, and thus had no single place of origin (as some DNA data have suggested) and subsequent spread.

Radiocarbon reservoir correction ages in the peter the Great Gulf, Sea of Japan, and eastern coast of the Kunashir, Southern Kuriles (northwestern Pacific)

The radiocarbon reservoir age correction values (R) for the Russian Far East are estimated as 370+ or -26 yr for the northwestern Sea of Japan, and 711+ or -46 yr for the southern Kurile Islands.

Dates are not just data : Paleolithic settlement patterns in siberia derived from radiocarbon records

The large radiocarbon database now established for Paleolithic sites in Siberia and the Russian Far East can be used to build up a picture of relative population size in these regions. We consider the time period of ca. 46,000 to 12,000 B.P. for which we have assembled and critically studied 437 radiocarbon dates. All dates from individual sites that fall within 1,000 14C years are considered as a single event and called occupation episode. The results of our analysis show that the number of 14C dates until ca. 28,000 B.P. is small and increases at ca. 28,000–20,000 B.P, and dates decrease in frequency for the ca. 20,000–16,000 B.P. time range. It is after ca. 16,000 B.P. that we see a substantial rise in the number of 14C dates. In terms of the relative size of Siberian Paleolithic populations based on the frequency of occupation episodes, population density was small until ca. 36,000 B.P. Subsequently, population size increased gradually at ca. 36,000–16,000 B.P., and the growth rate became almost exponential at ca. 16,000–12,000 B.P. The number of occupations from ca. 20,000 to 18,000 B.P. did not decrease, running counter to arguments that Siberia was completely or considerably depopulated during the Last Glacial Maximum.

Chronology of the earliest pottery in East Asia: progress and pitfalls

The origin of pottery is among the most important questions in Old World archaeology. The author undertakes a critical review of radiocarbon dates associated with the earliest pottery-making and eliminates a number of them where the material or its context are unreliable. Using those that survive this process of ‘chronometric hygiene’, he proposes that food-containers made of burnt clay originated in East Asia in the Late Glacial, c. 13 700-13 300 BP, and appeared in three separate regions, in Japan, China and far eastern Russia, at about the same time.

Radiocarbon Chronology of the Siberian Paleolithic

We have compiled 462 C-14 determinations for 120 Paleolithic and Mesolithic sites from Siberia and the Russian Far East. The Mousterian sites are dated to ca. 46,000–28,500 BP. The Middle–Upper Paleolithic transition dates to ca. 43,300–28,500 BP. Although there are a few earlier sites, most of the Upper Paleolithic sites are dated to the time interval between ca. 34,000 BP and 10,000 BP. The earlier Upper Paleolithic stage is characterized by macroblade technology and is radiocarbon-dated to ca. 34,000–20,000 BP. The earliest microblade technology occurs in the late stage of the Upper Paleolithic, dated to ca. 23,000–20,000 BP, but the majority of microblade sites is dated to ca. 20,000–11,000 BP. The Final Paleolithic (Mesolithic) sites date to ca. 12,000–6000 BP. At ca. 13,000–11,000 BP, the earliest Neolithic appeared in both the Russian Far East (Amur River basin) and the Transbaikal. The Paleolithic–Neolithic transition occurred ca. 13,000–6000 BP.

Radiocarbon-based chronology of the Paleolithic in Siberia and its relevance to the peopling of the New World.

The territory of Siberia is of crucial importance for the study of early human dispersal and the peopling of the New World. A Siberian Paleolithic Radiocarbon Database has been compiled. The Database allows us to compile a chronological framework for human colonization of Northern Asia. There are 446 (super 14) C dates for 13 Middle and 111 Upper Paleolithic sites older than around 12,000 BP. Seventeen percent of the dates were obtained by the accelerator mass spectrometry (AMS) technique, and the remaining 83% are conventional. From the viewpoint of the spatial distribution of the (super 14) C-dated sites, the majority of these are located at the Yenisey River Basin, Transbaikal, and the Altai Mountains. The general outline of the Upper Paleolithic colonization of Siberia is given here. The earliest traces of modern human occupation are dated to around 43,000-39,000 BP in the southern part of Siberia. It seems that by around 13,000 BP, almost all of northern Asia, including the extreme northeastern Siberia had been colonized by modern humans. We discuss some controversial problems that have provoked heated debates in current Russian archaeology. Notable among these are the surprisingly early AMS dates for the Early Upper Paleolithic, the age of the Dyuktai culture of Yakutia, the problem of human presence in Siberia at the time of the Last Glacial Maximum (20,000-18,000 BP), and the timing of the initial settling of the Chukchi Peninsula and northeastern Siberia.

RADIOCARBON DATE FREQUENCY AS AN INDEX OF INTENSITY OF PALEOLITHIC OCCUPATION OF SIBERIA: DID HUMANS REACT PREDICTABLY TO CLIMATE OSCILLATIONS?

Upper Paleolithic humans occupied southern Siberia by about 43,00038,000 BP (14C yr), and afterward continued to live there despite the very cold climate. If climatic conditions limited expansion of the colonizing population in northern Siberia, the Paleolithic ecumene should have contracted during the coldest episodes within the last 40,000 yr, and fewer 14C-dated sites should be known from those periods. In fact, the human population seems to have remained stable or even expanded during cold periods. Comparison of calibrated 14C dates for Siberian occupations with Greenland ice cores fails to demonstrate a simple correlation between climatic fluctuations and the dynamics of human colonization and persistence in Siberia between about 36,000 and 12,000 BP. Cold climate does not appear to have posed any significant challenge to humans in Siberia in the Late Pleistocene, and a supposed Last Glacial Maximum hiatus in population dynamics seems illusory.

A REVIEW OF THE EVIDENCE FOR EXTINCTION CHRONOLOGIES FOR FIVE SPECIES OF UPPER PLEISTOCENE MEGAFAUNA IN SIBERIA

A review of the radiocarbon chronology of some late Upper Pleistocene mammals from Siberia is presented. Previously published data has been supplemented by new 14C dates for 5 species (woolly mammoth, woolly rhinoceros, bison, horse, and muskox) to reconstruct chronological extinction patterns. The final extinction of woolly rhinoceros and bison in Siberia can be dated to approximately 11,000-9700 BP, but some megafaunal species (woolly mammoth, horse, and muskox) survived into the Late Holocene, about 3700-2200 BP.

Two Islands in the Ocean: Prehistoric Obsidian Exchange between Sakhalin and Hokkaido, Northeast Asia

ABSTRACT Obsidian exchange patterns were studied on Sakhalin Island which connects Japan with mainland Asia. One hundred-eighty-two specimens of obsidian, including 157 artifacts from 75 sites on Sakhalin, ranging in age from the early Upper Paleolithic (ca. 19,400-17,800 RYBP) to the Okhotsk cultural complex (ca. 1400-800 RYBP), and 25 geological samples from Hokkaido Island (Japan), were examined by neutron activation analysis. Geochemical data suggest that all the obsidian artifacts from known sources found in Sakhalin archaeological sites were brought from Hokkaido sources. Widespread use of Hokkaido obsidian by Sakhalin inhabitants shows that long-distance contacts and exchange have taken place in Northeast Asia since at least the Upper Paleolithic. Although this obsidian transport could have been land-based during the Pleistocene, people had to use watercraft to cross La Pérouse Strait during the past 10,000 years. The distance of raw material transport was about 250-300 km in the early Upper Paleolithic, but increased up to 1000 km by the end of the Upper Paleolithic, the Neolithic, and later periods.