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

  • Cedric Chauve
  • Nadia El-Mabrouk
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5541)


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.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Cedric Chauve
    • 1
  • Nadia El-Mabrouk
    • 2
  1. 1.Department of MathematicsSimon Fraser UniversityBurnaby (BC)Canada
  2. 2.Département Informatique et Recherche OpérationnelleUniversité de MontréalMontréal (QC)Canada

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