Ancestral population sizes and species divergence times in the primate lineage on the basis of intron and BAC end sequences
Ancestral population sizes and species divergence times in the primate lineage on the basis of intron and BAC end sequences
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DOI：
10.1007/s00239-004-2639-2
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发表时间：
2004-10-01
影响因子：
3.9
通讯作者：
Klein, J
中科院分区：
文献类型：
--
作者：
Satta, Y;Hickerson, M;Klein, J
应用两种最大似然法对20个不同基因座的内含子序列进行了研究，估计了6个灵长类物种(人、黑猩猩、大猩猩、猩猩、东半球猴和新大陆猴的代表)的祖先种群的有效规模和物种分化时间。核苷酸替换和基因内重组的比率异质性检查发现了五个异常的基因座(ODC1、GHR、HBE、INS和HBG)。在灵长类进化的主要分歧中，祖先的多态估计在0.21%到0.96%之间。当非洲类人猿和亚洲类人猿分化时，就会出现一种异常低的多态性。然而，考虑到灵长类祖先的世代时间可能很短，我们得出的结论是，灵长类祖先的种群规模并不比现存人类的种群规模小。此外，在假设人类和黑猩猩之间存在600万年(MYR)分歧的情况下，人类与大猩猩、猩猩、东半球猴子和新大陆猴子的分歧时间估计分别为7.2、18、34和65 MYR前，这通常比传统估计的时间要早。除内含子序列外，在人类和这些数据集之间使用了另外三个同源序列数据集，包括58,156个随机BAC末端序列(BES)，结果表明，核苷酸替换率每年低至每个位点0.6-0.8×10(-9)，祖先多态程度为0.33-0.51%。如此低的替换率和较短的世代时间，相对较高的多态程度表明，在人类和黑猩猩共同的祖先谱系中，有效种群规模相当大。
The effective sizes of ancestral populations and species divergence times of six primate species (humans, chimpanzees, gorillas, orangutans, and representatives of Old World monkeys and New World monkeys) are estimated by applying the two-species maximum likelihood (ML) method to intron sequences of 20 different loci. Examination of rate heterogeneity of nucleotide substitutions and intragenic recombination identifies five outrageous loci (ODC1, GHR, HBE, INS, and HBG). The estimated ancestral polymorphism ranges from 0.21 to 0.96% at major divergences in primate evolution. One exceptionally low polymorphism occurs when African and Asian apes diverged. However, taking into consideration the possible short generation times in primate ancestors, it is concluded that the ancestral population size in the primate lineage was no smaller than that of extant humans. Furthermore, under the assumption of 6 million years (myr) divergence between humans and chimpanzees, the divergence time of humans from gorillas, orangutans, Old World monkeys, and New World monkeys is estimated as 7.2, 18, 34, and 65 myr ago, respectively, which are generally older than traditional estimates. Beside the intron sequences, three other data sets of orthologous sequences are used between the human and the these data sets including 58,156 random BAC end sequences (BES) shows that the nucleotide substitution rate is as low as 0.6-0.8 x 10(-9) per site per year and the extent of ancestral polymorphism is 0.33-0.51%. With such a low substitution rate and short generation time, the relatively high extent of polymorphism suggests a fairly large effective population size in the ancestral lineage common to humans and chimpanzees.