Publication Date:
2008-11-21
Description:
In 1994, two independent groups extracted DNA from several Pleistocene epoch mammoths and noted differences among individual specimens. Subsequently, DNA sequences have been published for a number of extinct species. However, such ancient DNA is often fragmented and damaged, 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 reports 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.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miller, Webb -- Drautz, Daniela I -- Ratan, Aakrosh -- Pusey, Barbara -- Qi, Ji -- Lesk, Arthur M -- Tomsho, Lynn P -- Packard, Michael D -- Zhao, Fangqing -- Sher, Andrei -- Tikhonov, Alexei -- Raney, Brian -- Patterson, Nick -- Lindblad-Toh, Kerstin -- Lander, Eric S -- Knight, James R -- Irzyk, Gerard P -- Fredrikson, Karin M -- Harkins, Timothy T -- Sheridan, Sharon -- Pringle, Tom -- Schuster, Stephan C -- HG002238/HG/NHGRI NIH HHS/ -- England -- Nature. 2008 Nov 20;456(7220):387-90. doi: 10.1038/nature07446.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Building, University Park, Pennsylvania 16802, USA. webb@bx.psu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19020620" target="_blank"〉PubMed〈/a〉
Keywords:
Africa
;
Animals
;
Cell Nucleus/*genetics
;
Conserved Sequence/genetics
;
Elephants/anatomy & histology/*genetics
;
*Evolution, Molecular
;
*Extinction, Biological
;
Female
;
*Fossils
;
Genome/*genetics
;
*Genomics
;
Hair/metabolism
;
Humans
;
India
;
Male
;
Phylogeny
;
Sequence Analysis, DNA/*methods
Print ISSN:
0028-0836
Electronic ISSN:
1476-4687
Topics:
Biology
,
Chemistry and Pharmacology
,
Medicine
,
Natural Sciences in General
,
Physics
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