Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes

被引：128

作者：

Gilbert, M. Thomas P. ^{[1
]}

Drautz, Daniela I. ^{[2
]}

Lesk, Arthur M. ^{[2
]}

Ho, Simon Y. W. ^{[3
]}

Qi, Ji ^{[2
]}

Ratan, Aakrosh ^{[2
]}

Hsu, Chih-Hao ^{[2
]}

Sher, Andrei ^{[4
]}

Dalen, Love ^{[5
]}

Gotherstrom, Anders ^{[6
]}

Tomsho, Lynn P. ^{[2
]}

Rendulic, Snjezana ^{[2
]}

Packard, Michael ^{[2
]}

Campos, Paula F. ^{[1
]}

Kuznetsova, Tatyana V. ^{[7
]}

Shidlovskiy, Fyodor ^{[8
]}

Tikhonov, Alexei ^{[9
]}

Willerslev, Eske ^{[1
]}

Iacumin, Paola ^{[10
]}

Buigues, Bernard

Ericson, Per G. P. ^{[11
]}

Germonpre, Mietje ^{[12
]}

Kosintsev, Pavel ^{[13
]}

Nikolaev, Vladimir ^{[14
]}

Nowak-Kemp, Malgosia ^{[15
]}

Knight, James R. ^{[16
]}

Irzyk, Gerard P. ^{[16
]}

Perbost, Clotilde S. ^{[16
]}

Fredrikson, Karin M. ^{[17
]}

Harkins, Timothy T. ^{[17
]}

Sheridan, Sharon ^{[17
]}

Miller, Webb ^{[2
]}

Schuster, Stephan C. ^{[2
]}

机构：

[1] Univ Copenhagen, Ctr Ancient Genet, DK-2100 Copenhagen, Denmark

[2] Penn State Univ, Ctr Comparat Genom & Bioinformat, University Pk, PA 16802 USA

[3] Australian Natl Univ, Sch Bot & Zool, Ctr Macroevolut & Macroecol, Canberra, ACT 0200, Australia

[4] Russian Acad Sci, Severtsov Inst Ecol & Evolut, Moscow 119071, Russia

[5] Ctr UCM ISCIII Evoluc & Comportamiento Humanos, Madrid 28029, Spain

[6] Uppsala Univ, Evolut Biol Ctr, Dept Evolut Biol, S-75236 Uppsala, Sweden

[7] Moscow MV Lomonosov State Univ, Fac Geol, Dept Paleontol, Moscow 119991, Russia

[8] All Russian Exihibit Ctr, Ice Age Museum, Moscow 129223, Russia

[9] Russian Acad Sci, Inst Zool, St Petersburg 199034, Russia

[10] Univ Parma, Dept Earth Sci, I-43100 Parma, Italy

[11] Swedish Museum Nat Hist, Dept Vertebrate Zool, S-10405 Stockholm, Sweden

[12] Royal Belgian Inst Nat Sci, Dept Palaeontol, B-1000 Brussels, Belgium

[13] Russian Acad Sci, Urals Branch, Inst Plant & Anim Ecol, Ekaterinburg 620144, Russia

[14] Russian Acad Sci, Dept Glaciol, Inst Geog, Moscow 109017, Russia

[15] Univ Oxford, Museum Nat Hist, Oxford OX1 3PW, England

[16] 454 Life Sci, Branford, CT 06405 USA

[17] Roche Diagnost Corp, Indianapolis, IN 46250 USA

来源：

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | 2008年 / 105卷 / 24期

关键词：

mtDNA genome; phylogeny; ancient DNA; next-generation sequencing;

D O I：

10.1073/pnas.0802315105

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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

引用

页码：8327 / 8332

页数：6

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