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New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees

  • Conference paper
Research in Computational Molecular Biology (RECOMB 2009)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 5541))

Abstract

Reconciliation between a set of gene trees and a species tree is the most commonly used approach to infer the duplication and loss events in the evolution of gene families, given a species tree. When a species tree is not known, a natural algorithmic problem is to infer a species tree such that the corresponding reconciliation minimizes the number of duplications and/or losses. In this paper, we clarify several theoretical questions and study various algorithmic issues related to these two problems. (1) For a given gene tree T and species tree S, we show that there is a single history explaining T and consistent with S that minimizes gene losses, and that this history also minimizes the number of duplications. We describe a simple linear-time and space algorithm to compute this parsimonious history, that is not based on the Lowest Common Ancestor (LCA) mapping approach; (2) We show that the problem of computing a species tree that minimizes the number of gene duplications, given a set of gene trees, is in fact a slight variant of a supertree problem; (3) We show that deciding if a set of gene trees can be explained using only apparent duplications can be done efficiently, as well as computing a parsimonious species tree for such gene trees. We also characterize gene trees that can be explained using only apparent duplications in terms of compatible triplets of leaves.

Both authors are supported by grants from NSERC.

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Author information

Authors and Affiliations

  1. Department of Mathematics, Simon Fraser University, Burnaby (BC), Canada

    Cedric Chauve

  2. Département Informatique et Recherche Opérationnelle, Université de Montréal, Montréal (QC), Canada

    Nadia El-Mabrouk

Authors
  1. Cedric Chauve
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  2. Nadia El-Mabrouk
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Editor information

Editors and Affiliations

  1. Computer Science Department, James H. Clark Center, 318 Campus Drive, RM S266, CA 94305-5428,, Stanford, USA

    Serafim Batzoglou

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Chauve, C., El-Mabrouk, N. (2009). New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees. In: Batzoglou, S. (eds) Research in Computational Molecular Biology. RECOMB 2009. Lecture Notes in Computer Science(), vol 5541. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02008-7_4

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  • DOI: https://doi.org/10.1007/978-3-642-02008-7_4

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-02007-0

  • Online ISBN: 978-3-642-02008-7

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