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. (Science, 347, 2015, 1258524) 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 reanalyse 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.

杂交及其后续的基因渐渗（introgression）在越来越多的物种中被证实发挥了关键作用。近期，Fontaine等人（《科学》，347卷，2015年，文章编号1258524）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（phylogenomics）分析。该分析揭示了其网状进化历史，并指出四条常染色体臂上均存在广泛的基因渐渗现象。该研究还进一步强调了在系统基因组学分析中，不完全谱系分选（incomplete lineage sorting, ILS）与基因渐渗共同存在时所产生的复杂进化信号。尽管该研究采用了基于树的分析方法，但系统发育网络（phylogenetic networks）能更自然地建模以还原网状进化历史。本研究采用近期提出的整合多物种溯祖模型（multispecies coalescent）与系统发育网络的分析框架，对上述按蚊数据进行了重新分析。该框架可同时捕捉ILS与基因渐渗信号，为推断网状进化历史的统计方法奠定了基础。本次新分析得到了包含多次杂交事件的系统发育网络，其中部分杂交事件与原始研究的报道存在差异。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使用情况。将该方法应用于该按蚊数据集后，我们得以解析所有染色体的进化历史。本研究凸显了‘网络思维’的应用价值及其所能带来的新认知，尤其针对存在广泛基因树冲突（gene tree incongruence）的大型系统基因组学数据集分析而言。