Center for Computational and Evolutionary Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
Proc Natl Acad Sci U S A. 2010 May 18;107(20):9264-9. doi: 10.1073/pnas.0913022107. Epub 2010 May 3.
In the absence of recent admixture between species, bipartitions of individuals in gene trees that are shared across loci can potentially be used to infer the presence of two or more species. This approach to species delimitation via molecular sequence data has been constrained by the fact that genealogies for individual loci are often poorly resolved and that ancestral lineage sorting, hybridization, and other population genetic processes can lead to discordant gene trees. Here we use a Bayesian modeling approach to generate the posterior probabilities of species assignments taking account of uncertainties due to unknown gene trees and the ancestral coalescent process. For tractability, we rely on a user-specified guide tree to avoid integrating over all possible species delimitations. The statistical performance of the method is examined using simulations, and the method is illustrated by analyzing sequence data from rotifers, fence lizards, and human populations.
在没有最近物种混合的情况下，跨基因座共享的个体基因树的二分法可以用于推断两个或更多物种的存在。这种通过分子序列数据进行物种划分的方法受到以下事实的限制：个体基因座的系统发育通常解析得很差，并且祖系谱系分选、杂交和其他种群遗传过程会导致基因树的不和谐。在这里，我们使用贝叶斯建模方法来生成物种分配的后验概率，考虑到由于未知基因树和祖系合并过程而导致的不确定性。为了便于处理，我们依赖于用户指定的指导树来避免对所有可能的物种划分进行积分。该方法的统计性能通过模拟进行检验，并通过分析轮虫、围栏蜥蜴和人类种群的序列数据来说明该方法。
