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.

Abstract

A chronological framework for the prehistoric cultural complexes of Sakhalin Island is presented based on 160 radiocarbon dates from 74 sites. The earliest 14C-dated site, Ogonki 5, corresponds to the Upper Paleolithic, about 19,500–17,800 BP. According to the 14C data, since about 8800 BP, there is a continuous sequence of Neolithic, Early Iron Age, and Medieval complexes. The Neolithic existed during approximately 8800–2800 BP. Transitional Neolithic-Early Iron Age complexes are dated to about 2800–2300 BP. The Early Iron Age may be dated to about 2500–1300 BP. The Middle Ages period is dated to approximately 1300–300 BP (VII–XVII centuries AD).

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