Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes

M. Thomas P. Gilbert, Daniela I. Drautz, Arthur M. Lesk, Simon Y.W. Ho, Ji Qi, Aakrosh Ratan, Chih Hao Hsu, Andrei Sher, Love Dalén, Anders Götherström, Lynn P. Tomsho, Snjezana Rendulic, Michael Packard, Paula F. Campos, Tatyana V. Kuznetsova, Fyodor Shidlovskiy, Alexei Tikhonov, Eske Willerslev, Paola Iacumin, Bernard BuiguesPer G.P. Ericson, Mietje Germonpré, Pavel Kosintsev, Vladimir Nikolaev, Malgosia Nowak-Kemp, James R. Knight, Gerard P. Irzyk, Clotilde S. Perbost, Karin M. Fredrikson, Timothy T. Harkins, Sharon Sheridan, Webb Miller, Stephan C. Schuster

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Abstract

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, ≈1-2 million years, depending on the calibration technique. Furthermore, statistical analysis of the temporal distribution of the 14C 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.

Original languageEnglish (US)
Pages (from-to)8327-8332
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume105
Issue number24
DOIs
StatePublished - Jun 17 2008

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    Gilbert, M. T. P., Drautz, D. I., Lesk, A. M., Ho, S. Y. W., Qi, J., Ratan, A., Hsu, C. H., Sher, A., Dalén, L., Götherström, A., Tomsho, L. P., Rendulic, S., Packard, M., Campos, P. F., Kuznetsova, T. V., Shidlovskiy, F., Tikhonov, A., Willerslev, E., Iacumin, P., ... Schuster, S. C. (2008). Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes. Proceedings of the National Academy of Sciences of the United States of America, 105(24), 8327-8332. https://doi.org/10.1073/pnas.0802315105