From Gene Trees to Species Trees through a Supertree Approach

Authors:
Celine Scornavacca;Vincent Berry;Vincent Ranwez
Affiliations:
Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS), Université Montpellier II, CC 064 - 34095 and Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier ...;Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM,UMR 5506, CNRS), Université Montpellier II 161, rue Ada, Montpellier Cedex 5, France 34392;Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS), Université Montpellier II, CC 064 - 34095
Venue:
LATA '09 Proceedings of the 3rd International Conference on Language and Automata Theory and Applications
Year:
2009

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Abstract

Gene trees are leaf-labeled trees inferred from molecular sequences. Due to duplication events arising in genome evolution, gene trees usually have multiple copies of some labels, i.e. species. Inferring a species tree from a set of multi-labeled gene trees (MUL trees) is a well-known problem in computational biology. We propose a novel approach to tackle this problem, mainly to transform a collection of MUL trees into a collection of evolutionary trees, each containing single copies of labels. To that aim, we provide several algorithmic building stones and describe how they fit within a general species tree inference process. Most algorithms have a linear-time complexity, except for an FPT algorithm proposed for a problem that we show to be intractable.