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

  • Miklós Csűrös
  • István Miklós
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3909)

Abstract

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.

Keywords

Horizontal Gene Transfer Gene Content Horizontal Transfer Gene Count Conditional Likelihood 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Miklós Csűrös
    • 1
  • István Miklós
    • 2
  1. 1.Department of Computer Science and Operations ResearchUniversité de MontréalMontréalCanada
  2. 2.Department of Plant Taxonomy and EcologyEötvös Lóránd UniversityHungary

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