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Title: 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, Fontaineet al. (Science, 347, 2015, 1258524) conducted a phylogenomic analysis of six members of theAnopheles gambiaespecies 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 theAnophelesdata using a recently devised framework that combines the multispecies coalescent with phylogenetic networks. This framework allows us to captureILSand 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.

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Date Published:
Journal Name:
Molecular Ecology
Page Range / eLocation ID:
p. 2361-2372
Medium: X
Sponsoring Org:
National Science Foundation
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