Whole-Genome Shotgun Sequencing of Mitochondria from Ancient Hair Shafts

M. Thomas P. Gilbert,^1* Lynn P. Tomsho,² Snjezana Rendulic,² Michael Packard,² Daniela I. Drautz,² Andrei Sher,³ Alexei Tikhonov,⁴ Love Dalén,⁵ Tatyana Kuznetsova,⁶ Pavel Kosintsev,⁷ Paula F. Campos,¹ Thomas Higham,⁸ Matthew J. Collins,⁹ Andrew S. Wilson,¹⁰ Fyodor Shidlovskiy,¹¹ Bernard Buigues,¹² Per G. P. Ericson,¹³ Mietje Germonpré,¹⁴ Anders Götherström,¹⁵ Paola Iacumin,¹⁶ Vladimir Nikolaev,¹⁷ Malgosia Nowak-Kemp,¹⁸ Eske Willerslev,¹ James R. Knight,¹⁹ Gerard P. Irzyk,¹⁹ Clotilde S. Perbost,¹⁹ Karin M. Fredrikson,²⁰ Timothy T. Harkins,²⁰ Sharon Sheridan,²⁰ Webb Miller,^2* Stephan C. Schuster^2*

Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in previously published frozen bone samples, even though one of the specimens was >50,000 ¹⁴C years old and another had been stored for 200 years at room temperature. The method therefore sets the stage for molecular-genetic analysis of museum collections.

¹ Centre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark.
² Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, 310 Wartik Building, University Park, PA 16802, USA.
³ Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 33 Leninsky Prospect, Moscow 119071, Russia.
⁴ Zoological Institute, Russian Academy of Sciences, Universitetskaya Naberezhnaya, St. Petersburg 199034, Russia.
⁵ Centro UCM-ISCIII de Evolución y Comportamiento Humanos, c/Sinesio Delgado 4, 28029 Madrid, Spain.
⁶ Department of Paleontology, Faculty of Geology, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119992, Russia.
⁷ Institute of Plant and Animal Ecology, The Urals Branch of the Russian Academy of Sciences, 202 8th of March Street, Ekaterinburg 620144, Russia.
⁸ Research Laboratory for Archaeology and the History of Art, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK.
⁹ Departments of Biology and Archaeology, BioArch, University of York, York YO10 5YW, UK.
¹⁰ Department of Archaeological Sciences, University of Bradford, Bradford BD7 1DP, UK.
¹¹ The Ice Age Museum, All-Russia Exhibition Centre, pavilion 71, Moscow 129223, Russia.
¹² 2 Avenuedela Pelouse, F-94160 Saint Mandé, France.
¹³ Department of Vertebrate Zoology, Swedish Museum of Natural History, Post Office Box 50007, S-10405, Stockholm, Sweden.
¹⁴ Department of Palaeontology, Royal Belgian Institute of Natural Sciences, Vautierstraat 29, 1000 Brussels, Belgium.
¹⁵ Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.
¹⁶ Department of Earth Sciences, University of Parma, Parco Area delle Scienze 157/A, 43100 Parma, Italy.
¹⁷ Department of Glaciology, Institute of Geography, Russian Academy of Science, 29 Staromonetny Pereulok, Moscow 109017, Russia.
¹⁸ Oxford University Museum of Natural History, Parks Road, Oxford OX1 3PW, UK.
¹⁹ 454 LifeSciences, 20 Commercial Street, Branford, CT 06405, USA.
²⁰ Roche Diagnostics Corporation, 9115 Hague Road, Indianapolis, IN 46250–0414, USA.

^* These authors contributed equally to this work.

To whom correspondence should be addressed. E-mail: webb{at}bx.psu.edu (W.M.); scs{at}bx.psu.edu (S.C.S.)

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