Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis
Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis
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DOI：
10.1093/molbev/mss086
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发表时间：
2012-08-01
影响因子：
10.7
通讯作者：
RoyChoudhury, Arindam
中科院分区：
文献类型：
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作者：
Bryant, David;Bouckaert, Remco;RoyChoudhury, Arindam
多物种合并提供了一个优雅的理论框架，用于根据遗传标记估计物种树和物种人口统计数据。然而，多物种合并模型的实际应用受到对每个遗传标记可能的所有基因树进行整合或采样的需要的限制。在这里，我们描述了一种多项式时间算法，该算法直接根据有限位点突变模型下的标记计算物种树的可能性，有效地整合了所有可能的基因树。该方法适用于独立（未连锁）的双等位标记，例如间隔良好的单核苷酸多态性，我们已在 SNAPP 中实现了该方法，SNAPP 是一种马尔可夫链蒙特卡罗采样器，用于推断物种树、分歧日期和种群规模。我们报告了模拟实验的结果以及对 1997 年从 6 个 Ourisia（新西兰本土毛地黄）物种中采样的 69 个个体中扩增的片段长度多态性位点的分析结果。
The multispecies coalescent provides an elegant theoretical framework for estimating species trees and species demographics from genetic markers. However, practical applications of the multispecies coalescent model are limited by the need to integrate or sample over all gene trees possible for each genetic marker. Here we describe a polynomial-time algorithm that computes the likelihood of a species tree directly from the markers under a finite-sites model of mutation effectively integrating over all possible gene trees. The method applies to independent (unlinked) biallelic markers such as well-spaced single nucleotide polymorphisms, and we have implemented it in SNAPP, a Markov chain Monte Carlo sampler for inferring species trees, divergence dates, and population sizes. We report results from simulation experiments and from an analysis of 1997 amplified fragment length polymorphism loci in 69 individuals sampled from six species of Ourisia (New Zealand native foxglove).