Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci.
Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci.
复制标题
作者：
B. Rannala;Ziheng Yang
祖先和现代物种的有效种群规模是种群遗传学和人类进化模型中的重要参数。通常使用的方法估计祖先的人口规模，基于计算物种树和推断的基因树之间的不匹配，是高度偏颇的，因为它忽略了基因树重建的不确定性。在这篇文章中，我们开发了一个贝叶斯方法，同时估计物种的分歧时间和当前和祖先的人口规模。该方法使用来自多个基因座的DNA序列数据，并提取关于基因树拓扑结构和合并时间之间的冲突的信息来估计祖先群体的大小。假设物种树的拓扑结构是已知的。一个马尔可夫链蒙特卡罗算法实现整合在不确定的基因树和分支长度（或合并时间）在每个位点，以及物种的分歧时间。该方法可以处理任何物种树，并允许不同基因座处的不同数量的序列。我们将该方法应用于已发表的人类和类人猿的非编码DNA序列。物种形成时间和祖先种群规模的后验估计之间有很强的相关性。使用人类-黑猩猩分歧日期的信息先验，这两个物种的共同祖先的人口规模估计约为20，000，置信区间为95%（8000，40，000）。然而，我们的估计受到模型假设和数据质量的影响。我们认为，可靠的估计还有待更多的数据和更现实的模型。
The effective population sizes of ancestral as well as modern species are important parameters in models of population genetics and human evolution. The commonly used method for estimating ancestral population sizes, based on counting mismatches between the species tree and the inferred gene trees, is highly biased as it ignores uncertainties in gene tree reconstruction. In this article, we develop a Bayes method for simultaneous estimation of the species divergence times and current and ancestral population sizes. The method uses DNA sequence data from multiple loci and extracts information about conflicts among gene tree topologies and coalescent times to estimate ancestral population sizes. The topology of the species tree is assumed known. A Markov chain Monte Carlo algorithm is implemented to integrate over uncertain gene trees and branch lengths (or coalescence times) at each locus as well as species divergence times. The method can handle any species tree and allows different numbers of sequences at different loci. We apply the method to published noncoding DNA sequences from the human and the great apes. There are strong correlations between posterior estimates of speciation times and ancestral population sizes. With the use of an informative prior for the human-chimpanzee divergence date, the population size of the common ancestor of the two species is estimated to be approximately 20,000, with a 95% credibility interval (8000, 40,000). Our estimates, however, are affected by model assumptions as well as data quality. We suggest that reliable estimates have yet to await more data and more realistic models.