Data from: Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis

The role of hybridization and subsequent introgression has been demonstrated in an increasing number of species. Recently, Fontaine et al. (2015) conducted a phylogenomic analysis of six members of the Anopheles gambiae species complex. Their analysis revealed a reticulate evolutionary history and pointed to extensive introgression on all four autosomal arms. The study further highlighted the complex evolutionary signals that the co-occurrence of incomplete lineage sorting (ILS) and introgression can give rise to in phylogenomic analyses. While tree-based methodologies were used in the study, phylogenetic networks provide a more natural model to capture reticulate evolutionary histories. In this work, we reanalyze the Anopheles data using a recently devised framework that combines the multispecies coalescent with phylogenetic networks. This framework allows us to capture ILS and introgression simultaneously, and forms the basis for statistical methods for inferring reticulate evolutionary histories. The new analysis reveals a phylogenetic network with multiple hybridization events, some of which differ from those reported in the original study. To elucidate the extent and patterns of introgression across the genome, we devise a new method that quantifies the use of reticulation branches in the phylogenetic network by each genomic region. Applying the method to the mosquito data set reveals the evolutionary history of all the chromosomes. This study highlights the utility of ``network thinking" and the new insights it can uncover, in particular in phylogenomic analyses of large data sets with extensive gene tree incongruence.

越来越多的物种被证实存在杂交及其后续的基因渐渗作用。近期，Fontaine等人（2015）针对冈比亚按蚊（Anopheles gambiae）物种复合体的6个成员开展了系统基因组学分析。其研究结果揭示了一段网状进化历史，并指出四条常染色体臂上均存在广泛的基因渐渗现象。该研究进一步凸显了在系统基因组学分析中，不完全谱系分选（incomplete lineage sorting, ILS）与基因渐渗共同出现时所产生的复杂进化信号。尽管该研究采用了基于物种树的分析方法，但系统发育网络能够提供更自然的建模方式，以捕捉网状进化历史。本研究利用近期提出的结合多物种溯祖（multispecies coalescent）与系统发育网络的分析框架，重新分析了上述冈比亚按蚊数据集。该框架可同时捕捉不完全谱系分选与基因渐渗信号，为推断网状进化历史的统计方法奠定了理论基础。新的分析结果揭示了一个存在多起杂交事件的系统发育网络，其中部分事件与原研究报道的结果存在差异。为阐明全基因组范围内基因渐渗的程度与模式，我们开发了一种新方法，用于量化每个基因组区域对系统发育网络中网状分支的利用情况。将该方法应用于该蚊类数据集后，我们揭示了所有染色体的进化历史。本研究彰显了“网状进化思维”的应用价值，以及其所能带来的全新见解，在存在大量基因树冲突的大型系统基因组学数据集分析中尤为如此。