Pattern of extinction of the woolly mammoth in Beringia.

Extinction of the woolly mammoth in Beringia has long been subject to research and speculation. Here we use a new geo-referenced database of radiocarbon-dated evidence to show that mammoths were abundant in the open-habitat of Marine Isotope Stage 3 (∼45-30 ka). During the Last Glacial Maximum (∼25-20 ka), northern populations declined while those in interior Siberia increased. Northern mammoths increased after the glacial maximum, but declined at and after the Younger Dryas (∼12.9-11.5 ka). Remaining continental mammoths, now concentrated in the north, disappeared in the early Holocene with development of extensive peatlands, wet tundra, birch shrubland and coniferous forest. Long sympatry in Siberia suggests that humans may be best seen as a synergistic cofactor in that extirpation. The extinction of island populations occurred at ∼4 ka. Mammoth extinction was not due to a single cause, but followed a long trajectory in concert with changes in climate, habitat and human presence.

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.