Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes

doi:10.1073/pnas.0802315105

Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes

^aCentre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark;
^cCenter for Comparative Genomics and Bioinformatics, Pennsylvania State University, 310 Wartik Building, University Park, PA 16802;
^dCentre for Macroevolution and Macroecology, School of Botany and Zoology, Australian National University, Canberra ACT 0200, Australia;
^eSevertsov Institute of Ecology and Evolution, Russian Academy of Sciences, 33 Leninsky Prospect, Moscow 119071, Russia;
^fCentro UCM-ISCIII de Evolución y Comportamiento Humanos, c/Sinesio Delgado 4, 28029 Madrid, Spain;
^gDepartment of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, S-752 36 Uppsala, Sweden;
^hDepartment of Paleontology, Faculty of Geology, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119991, Russia;
ⁱThe Ice Age Museum, All-Russia Exhibition Centre, Pavilion 71, Moscow 129223, Russia;
^jZoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, St. Petersburg 199034, Russia;
^kDepartment of Earth Sciences, University of Parma, Parco Area delle Scienze 157/A, 43100 Parma, Italy;
^l2 Avenue de la Pelouse, F-94160 St. Mandé, France;
^mDepartment of Vertebrate Zoology, Swedish Museum of Natural History P.O. Box 50007, S-104 05 Stockholm, Sweden;
ⁿDepartment of Palaeontology, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, 1000 Brussels, Belgium;
^oInstitute of Plant and Animal Ecology, Urals Branch of the Russian Academy of Sciences, 202 8th of March Street, Ekaterinburg 620144, Russia;
^pInstitute of Geography, Russian Academy of Science, Department of Glaciology, 29 Staromonetny per., Moscow 109017, Russia;
^qOxford University Museum of Natural History, Parks Road, Oxford OX1 3PW, United Kingdom;
^r454 Life Sciences, 20 Commercial Street, Branford, CT 06405; and
^sRoche Diagnostics Corporation, 9115 Hague Road, Indianapolis, IN 46250-0414

Edited by Francisco J. Ayala, University of California, Irvine, CA, and approved April 17, 2008 (received for review March 7, 2008)

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.

Footnotes

^bTo whom correspondence may be addressed. E-mail: mtpgilbert{at}gmail.com, webb{at}bx.psu.edu, or scs{at}bx.psu.edu
Author contributions: M.T.P.G., W.M., and S.C.S. contributed equally to this work; M.T.P.G., A.S., W.M., and S.C.S. designed research; M.T.P.G., D.I.D., L.P.T., S.R., M.P., P.F.C., W.M., and S.C.S. performed research; A.S., T.V.K., F.S., A.T., E.W., P.I., B.B., P.G.P.E., M.G., P.K., V.N., M.N.-K., J.R.K., G.P.I., C.S.P., K.M.F., T.T.H., and S.S. contributed new reagents/analytic tools; M.T.P.G., D.I.D., A.M.L., S.Y.W.H., J.Q., A.R., C.-H.H., A.S., L.D., A.G., L.P.T., S.R., M.P., P.F.C., T.V.K., F.S., A.T., E.W., P.I., B.B., P.G.P.E., M.G., P.K., V.N., M.N.-K., W.M., and S.C.S. analyzed data; and M.T.P.G., A.M.L., S.Y.W.H., A.S., L.D., A.G., W.M., and S.C.S. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. EU153446, EU153448, EU153450, EU153451, and EU153453).
This article contains supporting information online at www.pnas.org/cgi/content/full/0802315105/DCSupplemental.
Freely available online through the PNAS open access option.