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MaxTiC: Fast ranking of a phylogenetic tree by Maximum Time Consistency with lateral gene Transfers

Cédric Chauve, Akbar Rafiey, Adrian A. Davin, Celine Scornavacca, Philippe Veber, Bastien Boussau, Gergely J Szöllősi, Vincent Daubin, Eric Tannier
doi: https://doi.org/10.1101/127548
Cédric Chauve
1Department of Mathematics, Simon Fraser University, Burnaby (BC), Canada
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Akbar Rafiey
1Department of Mathematics, Simon Fraser University, Burnaby (BC), Canada
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Adrian A. Davin
3Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France
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Celine Scornavacca
4Institut des Sciences de l’Evolution, Université de Montpellier, CNRS, IRD, EPHE 34095 Montpellier Cedex 5, France
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Philippe Veber
3Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France
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Bastien Boussau
3Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France
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Gergely J Szöllősi
5MTA-ELTE “Lendulet” Evolutionary Genomics Research Group, Budapest Hungary
6Deptartment of Biological Physics, Eötvos Loránd University, Budapest Hungary
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Vincent Daubin
3Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France
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Eric Tannier
2Inria Grenoble Rhône-Alpes, F-38334 Montbonnot, France
3Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622 Villeurbanne, France
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Abstract

Lateral gene transfers (LGTs) between ancient species contain information about the relative timing of species diversification. Specifically, the ancestors of a donor species must have existed before the descendants of the recipient species. Hence, the detection of a LGT event can be translated into a time constraint between nodes of a phylogeny if donors and recipients can be identified. When a set of LGTs are detected by interpreting the phylogenetic discordance between gene trees and a species tree, the set of all deduced time constraints can be used to order totally the internal nodes and thus produce a ranked tree. Unfortunately LGT detection is still very challenging and all methods produce some proportion of false positives. As a result the set of time constraints is not always compatible with a ranked species tree. We propose an optimization method called MaxTiC (Maximum Time Consistency) for obtaining a ranked species tree that is compatible with a maximum number of time constraints. We give in particular an exact polynomial time method based on dynamic programming to compute an optimal ranked binary tree supposing that a ranked subtree is given and fixed below each of the two children. We turn this principle into a heuristic to solve the general problem and test it on simulated datasets. Under a wide range of conditions, the obtained ranked tree is very close to the real one, confirming the theoretical possibility of dating with transfers by maximizing time consistency.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted April 14, 2017.
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MaxTiC: Fast ranking of a phylogenetic tree by Maximum Time Consistency with lateral gene Transfers
Cédric Chauve, Akbar Rafiey, Adrian A. Davin, Celine Scornavacca, Philippe Veber, Bastien Boussau, Gergely J Szöllősi, Vincent Daubin, Eric Tannier
bioRxiv 127548; doi: https://doi.org/10.1101/127548
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MaxTiC: Fast ranking of a phylogenetic tree by Maximum Time Consistency with lateral gene Transfers
Cédric Chauve, Akbar Rafiey, Adrian A. Davin, Celine Scornavacca, Philippe Veber, Bastien Boussau, Gergely J Szöllősi, Vincent Daubin, Eric Tannier
bioRxiv 127548; doi: https://doi.org/10.1101/127548

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