Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland.
Swiss Institute of Bioinformatics (SIB), Switzerland.
Mol Biol Evol. 2018 Feb 1;35(2):504-517. doi: 10.1093/molbev/msx307.
Reticulate species evolution, such as hybridization or introgression, is relatively common in nature. In the presence of reticulation, species relationships can be captured by a rooted phylogenetic network, and orthologous gene evolution can be modeled as bifurcating gene trees embedded in the species network. We present a Bayesian approach to jointly infer species networks and gene trees from multilocus sequence data. A novel birth-hybridization process is used as the prior for the species network, and we assume a multispecies network coalescent prior for the embedded gene trees. We verify the ability of our method to correctly sample from the posterior distribution, and thus to infer a species network, through simulations. To quantify the power of our method, we reanalyze two large data sets of genes from spruces and yeasts. For the three closely related spruces, we verify the previously suggested homoploid hybridization event in this clade; for the yeast data, we find extensive hybridization events. Our method is available within the BEAST 2 add-on SpeciesNetwork, and thus provides an extensible framework for Bayesian inference of reticulate evolution.
网状种系进化，如杂交或基因渗入，在自然界中较为常见。在存在网状进化的情况下，种系关系可以通过有根系统发生网络来捕获，而直系同源基因进化可以建模为嵌入在种系网络中的分支基因树。我们提出了一种贝叶斯方法，可从多基因序列数据中共同推断种系网络和基因树。一个新的出生-杂交过程被用作种系网络的先验，我们假设嵌入的基因树具有多物种网络合并先验。我们通过模拟验证了我们的方法从后验分布中正确抽样的能力，从而可以推断出种系网络。为了量化我们方法的功效，我们重新分析了来自云杉和酵母的两个大型基因数据集。对于三个密切相关的云杉，我们验证了该分支中先前提出的同倍体杂交事件；对于酵母数据，我们发现了广泛的杂交事件。我们的方法可在 BEAST 2 附加的 SpeciesNetwork 中使用，因此为贝叶斯推断网状进化提供了一个可扩展的框架。
