Recent analyses of genomic sequence data suggest cross-species gene flow is common in both plants and animals, posing challenges to species tree estimation. 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 based on gene tree topologies is more robust to gene flow than the UPGMA method based on coalescent times and both are more robust than likelihood assuming a multispecies coalescent (MSC) model with no cross-species gene flow. Comparison of the continuous migration model with the episodic introgression model suggests that a small amount of gene flow per generation can cause drastic changes to the genetic history of the species and mislead species tree methods, especially if the species diverged through radiative speciation events. Estimates of parameters under the MSC with gene flow suggest that African mosquito species in the Anopheles gambia species complex constitute such an example of extreme impact of gene flow on species phylogeny.

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跨物种基因流对物种树估计的影响

最近对基因组序列数据的分析表明，跨物种基因流在植物和动物中都很常见，这对物种树的估计提出了挑战。我们检查了误导三个物种的物种树估计所需的基因流水平，以及外群物种和一个内群物种之间的间歇性渐进杂交或连续迁移。检查了几种物种树估计方法，包括基于最常见基因树拓扑结构（使用真实或重建的基因树）的多数投票方法，基于平均序列距离（或平均合并时间）之间的 UPGMA 方法。种，以及基于多位点序列数据的全似然法。我们的结果表明，基于基因树拓扑的多数投票方法比基于聚结时间的 UPGMA 方法对基因流更稳健，并且两者都比假设没有跨物种基因流的多物种聚结（MSC）模型的可能性更稳健. 连续迁移模型与情景基因渗入模型的比较表明，每代少量的基因流会导致物种遗传历史发生剧烈变化并误导物种树方法，特别是如果物种通过辐射物种形成事件发生分化。使用基因流对 MSC 下的参数进行估计表明，冈比亚按蚊物种复合体中的非洲蚊子物种构成了基因流对物种系统发育的极端影响的一个例子。