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Coestimation of Gene Trees and Reconciliations Under a Duplication-Loss-Coalescence Model

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Bioinformatics Research and Applications (ISBRA 2017)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 10330))

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Abstract

Accurate gene tree-species tree reconciliation is fundamental to understanding evolutionary processes across species. However, within eukaryotes, the most popular algorithms consider only a restricted set of evolutionary events, typically modeling only duplications and losses or only coalescences. Recent work has unified duplications, losses, and coalescences through an intermediate locus tree; however, the associated reconciliation algorithms assume that the gene tree is known and do not account for gene tree reconstruction error. Here, we demonstrate that independent reconstruction of the gene tree followed by reconciliation substantially degrades accuracy compared to using the true gene tree. To address this challenge, we present DLC-Coestimation, a Bayesian method that simultaneously reconstructs the gene tree and reconciles it with the species tree. We have applied our method on two clades of flies and fungi and demonstrate that it outperforms existing approaches in ortholog, duplication, and loss inference. This work demonstrates the utility of coestimation methods for inferences under joint phylogenetic and population genomic models.

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Acknowledgments

We thank Matthew D. Rasmussen, Ran Libeskind-Hadas, and Mark Huber for helpful comments, feedback, and discussions. This work was supported by funds from the Department of Computer Science and the Dean of Faculty of Harvey Mudd College.

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Authors and Affiliations

  1. Department of Mathematics, Harvey Mudd College, Claremont, CA, USA

    Bo Zhang

  2. Department of Computer Science, Harvey Mudd College, Claremont, CA, USA

    Yi-Chieh Wu

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  1. Bo Zhang
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Correspondence to Yi-Chieh Wu .

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Editors and Affiliations

  1. Georgia State University, Atlanta, Georgia, USA

    Zhipeng Cai

  2. University of Texas at Dallas, Richardson, Texas, USA

    Ovidiu Daescu

  3. Central South University, Changsha, China

    Min Li

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Zhang, B., Wu, YC. (2017). Coestimation of Gene Trees and Reconciliations Under a Duplication-Loss-Coalescence Model. In: Cai, Z., Daescu, O., Li, M. (eds) Bioinformatics Research and Applications. ISBRA 2017. Lecture Notes in Computer Science(), vol 10330. Springer, Cham. https://doi.org/10.1007/978-3-319-59575-7_18

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  • DOI: https://doi.org/10.1007/978-3-319-59575-7_18

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