1. Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Building, University Park, Pennsylvania 16802, USA
2. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, 33 Leninsky Prospect, 119071 Moscow, Russia
3. Zoological Institute, Russian Academy of Sciences, Universitetskaya Naberezhnaya 1, 199034 Saint Petersburg, Russia
4. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California 95064, USA
5. Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
6. 454 Life Sciences, 20 Commercial Street, Branford, Connecticut 06405, USA
7. Roche Diagnostics Corporation, 9115 Hague Road, Indianapolis, Indiana 46250-0414, USA
8. Sperling Foundation, Eugene, Oregon 97405, USA
9. Deceased

Correspondence to: Webb Miller¹Stephan C. Schuster¹ Correspondence and requests for materials should be addressed to W.M. (Email: webb@bx.psu.edu) or S.C.S. (Email: scs@bx.psu.edu).

In 1994, two independent groups extracted DNA from several Pleistocene epoch mammoths and noted differences among individual specimens^{1, 2}. Subsequently, DNA sequences have been published for a number of extinct species. However, such ancient DNA is often fragmented and damaged³, and studies to date have typically focused on short mitochondrial sequences, never yielding more than a fraction of a per cent of any nuclear genome. Here we describe 4.17 billion bases (Gb) of sequence from several mammoth specimens, 3.3 billion (80%) of which are from the woolly mammoth (Mammuthus primigenius) genome and thus comprise an extensive set of genome-wide sequence from an extinct species. Our data support earlier reports⁴ that elephantid genomes exceed 4 Gb. The estimated divergence rate between mammoth and African elephant is half of that between human and chimpanzee. The observed number of nucleotide differences between two particular mammoths was approximately one-eighth of that between one of them and the African elephant, corresponding to a separation between the mammoths of 1.5–2.0 Myr. The estimated probability that orthologous elephant and mammoth amino acids differ is 0.002, corresponding to about one residue per protein. Differences were discovered between mammoth and African elephant in amino-acid positions that are otherwise invariant over several billion years of combined mammalian evolution. This study shows that nuclear genome sequencing of extinct species can reveal population differences not evident from the fossil record, and perhaps even discover genetic factors that affect extinction.

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