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Pré-Publication, Document De Travail Année : 2017

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

Résumé

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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Dates et versions

hal-01532738 , version 1 (03-06-2017)
hal-01532738 , version 2 (08-10-2017)
hal-01532738 , version 3 (13-11-2017)

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Cédric Chauve, Akbar A Rafiey, Adrian A Davin, Celine Scornavacca, Philippe Veber, et al.. MaxTiC: Fast ranking of a phylogenetic tree by Maximum Time Consistency with lateral gene Transfers. 2017. ⟨hal-01532738v1⟩
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