Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees
Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees
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DOI：
10.1086/318206
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发表时间：
2001-02-01
影响因子：
9.8
通讯作者：
Li, WH
中科院分区：
文献类型：
--
作者：
Chen, FC;Li, WH
为了研究类人猿之间的基因组差异，并估计人类和黑猩猩共同祖先的有效种群规模，我们从人类基因组中选择了53个常染色体非重复DNA片段，并在人、黑猩猩、大猩猩和猩猩中对它们进行了测序。人-黑猩猩对、人-大猩猩对和黑猩猩-大猩猩对的平均序列差异仅为1.24%+/-0.07%、1.62%+/-0.08%和1.63%+/-0.08%。这些估计得到了来自GenBank的更多数据的证实，大大低于之前的估计，之前的估计包括重复序列，而且可能是基于不太准确的序列数据。猩猩与人类、黑猩猩和大猩猩的平均序列差异分别为3.08%+/-0.11%、3.12%+/-0.11%和3.09%+/-0.11%，也大大低于先前的估计。根据GenBank和文献中的大量数据估计了人类亚科之间其他区域的序列差异，其中AlU的差异最大，其次是Y-连锁非编码区、伪基因、常染色体基因间隔区、X-连锁非编码区、同义位点、内含子和非同义位点。从53个片段的串联序列衍生的邻居连接树-长度为24,234bp-支持具有100%自举数值的Homo-Pan支系。然而，当单独分析每个片段时，53个片段中的22个(类似于42%)给出了一棵与物种树不一致的树，这表明人和潘的共同祖先的有效种群规模(Ne)很大。事实上，对53个片段和37个蛋白质编码基因进行简约分析后，估计N-e=52,000到96,000。由于这一估计是根据各种遗传多态数据估计的人类长期有效种群规模(类似于10,000人)的5至9倍，人类谱系显然在与黑猩猩谱系分离后经历了有效种群规模的大幅减少。我们的分析假设了一个分子时钟，这实际上得到了所使用的序列数据的支持。把猩猩的物种形成日期定为1200万到1600万年前，我们得到了人-潘分歧的时间估计为460万到620万年，大猩猩的物种形成日期估计为620万到840万年，这表明大猩猩的分支比人类和黑猩猩的分歧早160万到220万年。
To study the genomic divergences among hominoids and to estimate the effective population size of the common ancestor of humans and chimpanzees, we selected 53 autosomal intergenic nonrepetitive DNA segments from the human genome and sequenced them in a human, a chimpanzee, a gorilla, and an orangutan. The average sequence divergence was only 1.24% +/- 0.07% for the human-chimpanzee pair, 1.62% +/- 0.08% for the human-gorilla pair, and 1.63% +/- 0.08% for the chimpanzee-gorilla pair. These estimates, which were confirmed by additional data from GenBank, are substantially lower than previous ones, which included repetitive sequences and might have been based on less-accurate sequence data. The average sequence divergences between orangutans and humans, chimpanzees, and gorillas were 3.08% +/- 0.11%, 3.12% +/- 0.11%, and 3.09% +/- 0.11%, respectively, which also are substantially lower than previous estimates. The sequence divergences in other regions between hominoids were estimated from extensive data in GenBank and the literature, and Alus showed the highest divergence, followed in order by Y-linked noncoding regions, pseudogenes, autosomal intergenic regions, X-linked noncoding regions, synonymous sites, introns, and nonsynonymous sites. The neighbor-joining tree derived from the concatenated sequence of the 53 segments-24,234 bp in length-supports the Homo-Pan clade with a 100% bootstrap value. However, when each segment is analyzed separately, 22 of the 53 segments (similar to 42%) give a tree that is incongruent with the species tree, suggesting a large effective population size (Ne) of the common ancestor of Homo and Pan. Indeed, a parsimony analysis of the 53 segments and 37 protein-coding genes leads to an estimate of N-e = 52,000 to 96,000. As this estimate is 5 to 9 times larger than the long-term effective population size of humans (similar to 10,000) estimated from various genetic polymorphism data, the human lineage apparently had experienced a large reduction in effective population size after its separation from the chimpanzee lineage. Our analysis assumes a molecular clock, which is in fact supported by the sequence data used. Taking the orangutan speciation date as 12 to 16 million years ago, we obtain an estimate of 4.6 to 6.2 million years for the Homo-Pan divergence and an estimate of 6.2 to 8.4 million years for the gorilla speciation date, suggesting that the gorilla lineage branched off 1.6 to 2.2 million years earlier than did the human-chimpanzee divergence.