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Inferring a Duplication, Speciation and Loss History from a Gene Tree (Extended Abstract)

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Comparative Genomics (RECOMB-CG 2007)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 4751))

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Abstract

We consider two questions related to the evolution of gene families. First, given a gene tree for a gene family, can the evolutionary history of this family be explained with only speciation and duplication events, and without gene loss. We show that this question can be answered in linear time, and that such a gene tree induces a single species tree consistent with a history with no loss. We then present a heuristic for the following problem: if a gene tree can not be explained without gene loss, what is the minimum number of losses involved in an evolutionary history of the gene family. We finally evaluate our algorithms on a dataset of plants gene families.

Work supported by grants from NSERC and SFU.

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Authors and Affiliations

  1. Department of Mathematics, Simon Fraser University, 8888 University Drive, V5A 1S6, Burnaby (BC), Canada

    Cedric Chauve

  2. CGL and LaCIM, UQAM, Montréal, Canada

    Cedric Chauve

  3. DIRO, Université de Montréal, CP6128, succ. Centre-Ville, H3C 3J7, Montréal (QC), Canada

    Jean-Philippe Doyon & Nadia El-Mabrouk

Authors
  1. Cedric Chauve
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  2. Jean-Philippe Doyon
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  3. Nadia El-Mabrouk
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Glenn Tesler Dannie Durand

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© 2007 Springer-Verlag Berlin Heidelberg

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Chauve, C., Doyon, JP., El-Mabrouk, N. (2007). Inferring a Duplication, Speciation and Loss History from a Gene Tree (Extended Abstract). In: Tesler, G., Durand, D. (eds) Comparative Genomics. RECOMB-CG 2007. Lecture Notes in Computer Science(), vol 4751. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-74960-8_4

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  • DOI: https://doi.org/10.1007/978-3-540-74960-8_4

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-74959-2

  • Online ISBN: 978-3-540-74960-8

  • eBook Packages: Computer ScienceComputer Science (R0)

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