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

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    Author
    Wen, Dingqiao; Yu, Yun; Hahn, Matthew W.; Nakhleh, Luay
    Date
    2016
    Abstract
    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.
    Citation
    Wen, Dingqiao, Yu, Yun, Hahn, Matthew W., et al.. "Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis." Molecular Ecology, 25, no. 11 (2016) Wiley: 2361-2372. https://doi.org/10.1111/mec.13544.
    Published Version
    https://doi.org/10.1111/mec.13544
    Keyword
    Anopheles gambiae; hybridization; incomplete lineage sorting; introgression; phylogenetic networks
    Type
    Journal article
    Publisher
    Wiley
    Citable link to this page
    https://hdl.handle.net/1911/97399
    Rights
    This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by Wiley.
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    Home | FAQ | Contact Us | Privacy Notice | Accessibility Statement
    Managed by the Digital Scholarship Services at Fondren Library, Rice University
    Physical Address: 6100 Main Street, Houston, Texas 77005
    Mailing Address: MS-44, P.O.BOX 1892, Houston, Texas 77251-1892
    Site Map