Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequencing errors
Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequencing errors
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DOI：
10.1093/molbev/msn148
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发表时间：
2008-09-01
影响因子：
10.7
通讯作者：
Yang, Ziheng
中科院分区：
文献类型：
--
作者：
Burgess, Ralph;Yang, Ziheng
估计人类和类人猿共同祖先的种群参数对于理解我们的进化史非常重要。特别是，对人类-黑猩猩共同祖先的种群规模的推断可能会揭示这两个物种分离的过程，以及人类种群在其早期进化史上是否经历了严重的规模缩减。本研究采用Rannala and Yang（2003）的贝叶斯方法进行祖先推断。基于多位点DNA序列的物种分化时间和祖先种群大小的贝叶斯估计。遗传学，164:1645-1656)扩展，以适应基因座之间的可变突变率和随机的物种特异性测序错误。该模型被用于分析人类、黑猩猩、大猩猩、猩猩和猕猴的15000个中性位点（7.4 Mb）的全基因组数据集。我们对类人猿谱系的有效种群规模进行了可靠而精确的估计，该谱系可以追溯到大约30万年前的颈猿类分化时期。结果表明，在整个类人猿谱系中，祖先种群比现代人类大5-10倍。这些估计对于使用的先验和关于重组的模型假设是稳健的。人类和黑猩猩之间异常低的X染色体差异不能用男性突变偏差的变异或当前的杂交和渐渗模型来解释。相反，我们的参数估计与人类-黑猩猩物种形成的简单瞬时过程一致，但显示出人类-黑猩猩共同祖先特有的X染色体有效种群大小的显著减少，可能是由于在两个物种分离之前对X染色体进行了选择性扫描。
Estimation of population parameters for the common ancestors of humans and the great apes is important in understanding our evolutionary history. In particular, inference of population size for the human-chimpanzee common ancestor may shed light on the process by which the 2 species separated and on whether the human population experienced a severe size reduction in its early evolutionary history. In this study, the Bayesian method of ancestral inference of Rannala and Yang (2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics. 164:1645-1656) was extended to accommodate variable mutation rates among loci and random species-specific sequencing errors. The model was applied to analyze a genome-wide data set of similar to 15,000 neutral loci (7.4 Mb) aligned for human, chimpanzee, gorilla, orangutan, and macaque. We obtained robust and precise estimates for effective population sizes along the hominoid lineage extending back similar to 30 Myr to the cercopithecoid divergence. The results showed that ancestral populations were 5-10 times larger than modern humans along the entire hominoid lineage. The estimates were robust to the priors used and to model assumptions about recombination. The unusually low X chromosome divergence between human and chimpanzee could not be explained by variation in the male mutation bias or by current models of hybridization and introgression. Instead, our parameter estimates were consistent with a simple instantaneous process for human-chimpanzee speciation but showed a major reduction in X chromosome effective population size peculiar to the human-chimpanzee common ancestor, possibly due to selective sweeps on the X prior to separation of the 2 species.