Sequencing the nuclear genome of the extinct woolly mammoth
Sequencing the nuclear genome of the extinct woolly mammoth
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DOI：
10.1038/nature07446
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发表时间：
2008-11-20
期刊：
影响因子：
64.8
通讯作者：
Schuster, Stephan C.
中科院分区：
文献类型：
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作者：
Miller, Webb;Drautz, Daniela I.;Schuster, Stephan C.
1994年，两个独立的研究小组从几只更新世猛犸象身上提取了DNA，并注意到个体标本之间的差异（1,2）。随后，一些灭绝物种的DNA序列被公布出来。然而，这种古老的DNA往往是碎片化和受损的(3)，迄今为止的研究通常集中在短线粒体序列上，从未得到任何核基因组的一小部分。在这里，我们描述了来自几个猛犸象标本的41.7亿个碱基（Gb）序列，其中33亿个碱基（80%）来自长毛猛犸象（Mammuthus primigenius）基因组，从而构成了一套广泛的来自灭绝物种的全基因组序列。我们的数据支持先前的报告(4)，即大象基因组超过4gb。据估计，猛犸象和非洲象之间的分化率是人类和黑猩猩之间的一半。观察到的两个特定猛犸象之间核苷酸差异的数量大约是其中一个猛犸象与非洲象之间核苷酸差异的八分之一，对应于猛犸象之间1.5 - 2.0 Myr的差异。估计大象和猛犸象同源氨基酸差异的概率为0.002，对应于每个蛋白质大约有一个残基。研究人员发现，猛犸象和非洲象在氨基酸位置上存在差异，而这些差异在几十亿年的哺乳动物共同进化过程中是不变的。这项研究表明，灭绝物种的核基因组测序可以揭示化石记录中不明显的种群差异，甚至可能发现影响灭绝的遗传因素。
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 damaged(3), 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(4) 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.