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    Inference of reticulate evolutionary histories by maximum likelihood: the performance of information criteria

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    Author
    Park, Hyun Jung; Nakhleh, Luay
    Date
    2012
    Abstract
    Background: Maximum likelihood has been widely used for over three decades to infer phylogenetic trees from molecular data. When reticulate evolutionary events occur, several genomic regions may have conflicting evolutionary histories, and a phylogenetic network may provide a more adequate model for representing the evolutionary history of the genomes or species. A maximum likelihood (ML) model has been proposed for this case and accounts for both mutation within a genomic region and reticulation across the regions. However, the performance of this model in terms of inferring information about reticulate evolution and properties that affect this performance have not been studied. Results: In this paper, we study the effect of the evolutionary diameter and height of a reticulation event on its identifiability under ML. We find both of them, particularly the diameter, have a significant effect. Further, we find that the number of genes (which can be generalized to the concept of "non-recombining genomic regions") that are transferred across a reticulation edge affects its detectability. Last but not least, a fundamental challenge with phylogenetic networks is that they allow an arbitrary level of complexity, giving rise to the model selection problem. We investigate the performance of two information criteria, the Akaike Information Criterion (AIC) and the Bayesian Information Criterion (BIC), for addressing this problem. We find that BIC performs well in general for controlling the model complexity and preventing ML from grossly overestimating the number of reticulation events. Conclusion: Our results demonstrate that BIC provides a good framework for inferring reticulate evolutionary histories. Nevertheless, the results call for caution when interpreting the accuracy of the inference particularly for data sets with particular evolutionary features.
    Citation
    Park, Hyun Jung and Nakhleh, Luay. "Inference of reticulate evolutionary histories by maximum likelihood: the performance of information criteria." BMC Bioinformatics, 13, no. Suppl 19 (2012) BioMed Central: S12. https://doi.org/10.1186/1471-2105-13-S19-S12.
    Published Version
    https://doi.org/10.1186/1471-2105-13-S19-S12
    Type
    Journal article
    Publisher
    BioMed Central
    Citable link to this page
    https://hdl.handle.net/1911/70724
    Rights
    This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
    Link to License
    https://creativecommons.org/licenses/by/2.0/
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    • Computer Science Publications [154]
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    Managed by the Digital Scholarship Services at Fondren Library, Rice University
    Physical Address: 6100 Main Street, Houston, Texas 77005
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    Site Map