Solís-Lemus Claudia, Ané Cécile
Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.
PLoS Genet. 2016 Mar 7;12(3):e1005896. doi: 10.1371/journal.pgen.1005896. eCollection 2016 Mar.
Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their genetic material. While a great deal of research has flourished into the inference of phylogenetic trees, statistical methods to infer phylogenetic networks are still limited and under development. The main disadvantage of existing methods is a lack of scalability. Here, we present a statistical method to infer phylogenetic networks from multi-locus genetic data in a pseudolikelihood framework. Our model accounts for incomplete lineage sorting through the coalescent model, and for horizontal inheritance of genes through reticulation nodes in the network. Computation of the pseudolikelihood is fast and simple, and it avoids the burdensome calculation of the full likelihood which can be intractable with many species. Moreover, estimation at the quartet-level has the added computational benefit that it is easily parallelizable. Simulation studies comparing our method to a full likelihood approach show that our pseudolikelihood approach is much faster without compromising accuracy. We applied our method to reconstruct the evolutionary relationships among swordtails and platyfishes (Xiphophorus: Poeciliidae), which is characterized by widespread hybridizations.
系统发育网络对于表示通过边扩展的生命之树是必要的，这些边代表诸如水平基因转移、杂交或基因流等事件。并非所有物种都遵循其遗传物质垂直遗传的模式。虽然关于系统发育树推断的大量研究蓬勃发展，但推断系统发育网络的统计方法仍然有限且仍在发展中。现有方法的主要缺点是缺乏可扩展性。在这里，我们提出了一种在伪似然框架下从多位点遗传数据推断系统发育网络的统计方法。我们的模型通过合并模型考虑不完全谱系分选，并通过网络中的网状节点考虑基因的水平遗传。伪似然的计算快速且简单，并且它避免了全似然的繁重计算，而全似然对于许多物种来说可能是难以处理的。此外，四重奏水平的估计具有易于并行化的额外计算优势。将我们的方法与全似然方法进行比较的模拟研究表明，我们的伪似然方法在不影响准确性的情况下要快得多。我们应用我们的方法来重建剑尾鱼和孔雀鱼（剑尾鱼属：花鳉科）之间的进化关系，其特点是广泛杂交。
