Research in Computational Molecular Biology

Volume 3909 of the series Lecture Notes in Computer Science pp 206-220

A Probabilistic Model for Gene Content Evolution with Duplication, Loss, and Horizontal Transfer

  • Miklós CsűrösAffiliated withDepartment of Computer Science and Operations Research, Université de Montréal
  • , István MiklósAffiliated withDepartment of Plant Taxonomy and Ecology, Eötvös Lóránd University

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We introduce a Markov model for the evolution of a gene family along a phylogeny. The model includes parameters for the rates of horizontal gene transfer, gene duplication, and gene loss, in addition to branch lengths in the phylogeny. The likelihood for the changes in the size of a gene family across different organisms can be calculated in O(N+hM 2) time and O(N+M 2) space, where N is the number of organisms, h is the height of the phylogeny, and M is the sum of family sizes. We apply the model to the evolution of gene content in Proteobacteria using the gene families in the COG (Clusters of Orthologous Groups) database.