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.