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    Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting

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    Author
    Yu, Yun; Barnett, R. Matthew; Nakhleh, Luay
    Date
    2013
    Abstract
    Hybridization plays an important evolutionary role in several groups of organisms. A phylogenetic approach to detect hybridization entails sequencing multiple loci across the genomes of a group of species of interest, reconstructing their gene trees, and taking their differences as indicators of hybridization. However, methods that follow this approach mostly ignore population effects, such as incomplete lineage sorting (ILS). Given that hybridization occurs between closely related organisms, ILS may very well be at play and, hence, must be accounted for in the analysis framework. To address this issue, we present a parsimony criterion for reconciling gene trees within the branches of a phylogenetic network, and a local search heuristic for inferring phylogenetic networks from collections of gene-tree topologies under this criterion. This framework enables phylogenetic analyses while accounting for both hybridization and ILS. Further, we propose two techniques for incorporating information about uncertainty in gene-tree estimates. Our simulation studies demonstrate the good performance of our framework in terms of identifying the location of hybridization events, as well as estimating the proportions of genes that underwent hybridization. Also, our framework shows good performance in terms of efficiency on handling large data sets in our experiments. Further, in analyzing a yeast data set, we demonstrate issues that arise when analyzing real data sets. While a probabilistic approach was recently introduced for this problem, and while parsimonious reconciliations have accuracy issues under certain settings, our parsimony framework provides a much more computationally efficient technique for this type of analysis. Our framework now allows for genome-wide scans for hybridization, while also accounting for ILS.
    Citation
    Yu, Yun, Barnett, R. Matthew and Nakhleh, Luay. "Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting." Systematic Biology Advance Access, (2013) Oxford University Press, on behalf of the Society of Systematic Biologists: http://dx.doi.org/10.1093/sysbio/syt037.
    Published Version
    http://dx.doi.org/10.1093/sysbio/syt037
    Keyword
    phylogenetic networks; hybridization; incomplete lineage sorting; coalescent; multi-labeled trees
    Type
    Journal article
    Publisher
    Oxford University Press, on behalf of the Society of Systematic Biologists
    Citable link to this page
    https://hdl.handle.net/1911/71341
    Rights
    This is an author's peer-reviewed final manuscript, as accepted by the publisher.
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    • Computer Science Publications [142]
    • Faculty Publications [5245]

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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