Assessing the Impacts of Positive Selection on Coalescent-Based Species Tree Estimation and Species Delimitation
Assessing the Impacts of Positive Selection on Coalescent-Based Species Tree Estimation and Species Delimitation
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DOI：
10.1093/sysbio/syy034
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发表时间：
2018-11-01
影响因子：
6.5
通讯作者：
Castoe, Todd A.
中科院分区：
文献类型：
--
作者：
Adams, Richard H.;Schield, Drew R.;Castoe, Todd A.
严格中性进化的假设是多物种合并模型的基础，并允许推导出基因树分布和合并时间的条件下，一个给定的物种树。在这项研究中，我们进行了计算机模拟，探讨违反这一假设的影响，在特定物种的正选择的形式时，估计物种树，物种界定，并在模型下的合并参数。我们模拟了一系列进化情景下的数据集，这些情景在两个物种形成参数（即，发散时间，选择强度）和实验设计（即，取样的位点数），并纳入物种特异性的正选择发生在一个物种树的分支，以确定多物种的聚结推理选择的影响。我们的研究结果突出了特定的进化情景和参数组合，其中推论可能更多或更少地受到积极选择的影响。在一些极端的情况下，选择可以减少错误的物种界定和增加错误的物种树估计，但这些推论似乎是在很大程度上强大的积极选择的影响下，可能会遇到的经验数据集。
The assumption of strictly neutral evolution is fundamental to the multispecies coalescent model and permits the derivation of gene tree distributions and coalescent times conditioned on a given species tree. In this study, we conduct computer simulations to explore the effects of violating this assumption in the form of species-specific positive selection when estimating species trees, species delimitations, and coalescent parameters under the model. We simulated data sets under an array of evolutionary scenarios that differ in both speciation parameters (i.e., divergence times, strength of selection) and experimental design (i.e., number of loci sampled) and incorporated species-specific positive selection occurring within branches of a species tree to identify the effects of selection on multispecies coalescent inferences. Our results highlight particular evolutionary scenarios and parameter combinations in which inferences may be more, or less, susceptible to the effects of positive selection. In some extreme cases, selection can decrease error in species delimitation and increase error in species tree estimation, yet these inferences appear to be largely robust to the effects of positive selection under many conditions likely to be encountered in empirical data sets.