Inferring a duplication, speciation and loss history from a gene tree

Authors:
Cedric Chauve;Jean-Philippe Doyon;Nadia El-Mabrouk
Affiliations:
Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada and CGL and LaCIM, UQAM, Montréal, Canada;DIRO, Université de Montréal, Montréal, QC, Canada;DIRO, Université de Montréal, Montréal, QC, Canada
Venue:
RECOMB-CG'07 Proceedings of the 2007 international conference on Comparative genomics
Year:
2007

Citing 5
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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.