The Impact of Cross-Species Gene Flow on Species Tree Estimation
The Impact of Cross-Species Gene Flow on Species Tree Estimation
复制标题
DOI：
10.1101/820019
复制
发表时间：
2019-10
期刊：
影响因子：
--
通讯作者：
Xiyun Jiao;Thomas Flouris;B. Rannala;Ziheng Yang
中科院分区：
文献类型：
--
作者：
Xiyun Jiao;Thomas Flouris;B. Rannala;Ziheng Yang
最近对基因组序列数据的分析表明，跨物种的基因流动在植物和动物中都很常见，这对物种树的推断提出了挑战。我们考察了误导物种树估计所需的基因流水平，包括三个物种以及插曲的渐进式杂交或一个外群和一个内群物种之间的连续迁移。研究了几种物种树估计方法，包括基于最常见的基因树拓扑结构的多数投票方法(使用真实或重建的基因树)，基于物种间平均序列距离(或平均结合时间)的UPGMA方法，以及基于多基因座序列数据的完全似然方法。我们的结果表明，多数投票方法比UPGMA方法对基因流动更有稳健性，并且在假设多物种合并(MSC)模型没有跨物种基因流动的情况下，两者都比似然方法更稳健。如果物种通过短时间间隔的物种形成事件而分化，少量的渗入或迁徙可能会误导物种树方法。基因流动对MSC下的参数的估计表明，冈比亚按蚊非洲蚊子物种复合体是基因流动对物种系统发育产生重大影响的一个例子。
Recent analyses of genomic sequence data suggest cross-species gene flow is common in both plants and animals, posing challenges to species tree inference. We examine the levels of gene flow needed to mislead species tree estimation with three species and either episodic introgressive hybridization or continuous migration between an outgroup and one ingroup species. Several species tree estimation methods are examined, including the majority-vote method based on the most common gene tree topology (with either the true or reconstructed gene trees used), the UPGMA method based on the average sequence distances (or average coalescent times) between species, and the full-likelihood method based on multi-locus sequence data. Our results suggest that the majority-vote method is more robust to gene flow than the UPGMA method and both are more robust than likelihood assuming a multispecies coalescent (MSC) model with no cross-species gene flow. A small amount of introgression or migration can mislead species tree methods if the species diverged through speciation events separated by short time intervals. Estimates of parameters under the MSC with gene flow suggest the Anopheles gambia African mosquito species complex is an example where gene flow greatly impacts species phylogeny.