Coalescent Histories on Phylogenetic Networks and Detection of Hybridization Despite Incomplete Lineage Sorting
Coalescent Histories on Phylogenetic Networks and Detection of Hybridization Despite Incomplete Lineage Sorting
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DOI：
10.1093/sysbio/syq084
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发表时间：
2011-03-01
影响因子：
6.5
通讯作者：
Nakhleh, Luay
中科院分区：
文献类型：
--
作者：
Yu, Yun;Cuong Than;Nakhleh, Luay
对越来越多可用的基因组数据的分析继续揭示了杂交的程度及其在不同物种群体进化多样化中的作用。我们通过对系统发育网络上的多位点数据集进行广泛的基于合并的模拟，展示了杂交事件前后的分歧时间如何导致不完整的谱系排序，其基因树不一致特征与杂交所表现出的特征相同。在物种树模型假设下对此类数据进行进化分析可能会错过所有杂交事件，而在物种网络模型假设下进行分析会严重高估杂交事件。这些问题需要在这些情况下进行进化分析的范式转变，从先验假设基因树不一致的单一来源的模型转变为将多个来源整合到统一框架中的模型。我们提出了系统发育网络分支内的合并框架，并展示了如何使用该框架来检测杂交，尽管谱系排序不完整。我们将该模型应用于模拟数据，结果表明，只要参与杂交的物种的分化时间间隔不太小，就可以揭示杂交的特征。我们重新分析了来自 7 个组内酵母菌属物种的 106 个基因座的数据集，文献中已报道了这些物种树没有杂交。我们的分析支持了这一假设，即杂交发生在该群体的进化过程中，解释了数据中的大量不一致。我们的研究结果表明，需要一种综合方法来解决基因树的不一致及其协调。我们的框架将有助于系统地分析杂交发生的基因组数据并阐明其进化作用。
Analyses of the increasingly available genomic data continue to reveal the extent of hybridization and its role in the evolutionary diversification of various groups of species. We show, through extensive coalescent-based simulations of multilocus data sets on phylogenetic networks, how divergence times before and after hybridization events can result in incomplete lineage sorting with gene tree incongruence signatures identical to those exhibited by hybridization. Evolutionary analysis of such data under the assumption of a species tree model can miss all hybridization events, whereas analysis under the assumption of a species network model would grossly overestimate hybridization events. These issues necessitate a paradigm shift in evolutionary analysis under these scenarios, from a model that assumes a priori a single source of gene tree incongruence to one that integrates multiple sources in a unifying framework. We propose a framework of coalescence within the branches of a phylogenetic network and show how this framework can be used to detect hybridization despite incomplete lineage sorting. We apply the model to simulated data and show that the signature of hybridization can be revealed as long as the interval between the divergence times of the species involved in hybridization is not too small. We reanalyze a data set of 106 loci from 7 in-group Saccharomyces species for which a species tree with no hybridization has been reported in the literature. Our analysis supports the hypothesis that hybridization occurred during the evolution of this group, explaining a large amount of the incongruence in the data. Our findings show that an integrative approach to gene tree incongruence and its reconciliation is needed. Our framework will help in systematically analyzing genomic data for the occurrence of hybridization and elucidating its evolutionary role.