MaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers

Cédric Chauve 1 Akbar Rafiey 1 Adrian Davin 2 Celine Scornavacca 3 Philippe Veber 2 Bastien Boussau 2 Gergely Szollosi 4 Vincent Daubin 2 Eric Tannier 2, 5
5 BEAGLE - Artificial Evolution and Computational Biology
LIRIS - Laboratoire d'InfoRmatique en Image et Systèmes d'information, Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive, CarMeN - Cardiovasculaire, métabolisme, diabétologie et nutrition
Abstract : This article has been peer-reviewed and recommended by Peer Community In Evolutionary Biology ( Lateral gene transfers 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 transfer event can be translated into a time constraint between nodes of a phylogeny if the donor and recipient can be identified. When a set of transfers is detected by interpreting the phylogenetic discordance between gene trees and a species tree, the set of all deduced time constraints can be used to rank the species tree, i.e. order totally its internal nodes. Unfortunately lateral gene transfer detection is challenging and current methods produce a significant proportion of false positives. As a result, often, no ranking of the species tree is compatible with the full set of time constraints deduced from predicted transfers. Here we propose a method, implemented in a software called MaxTiC (Maximum Time Consistency), which takes as input a species tree and a series of (possibly inconsistent) time constraints between its internal nodes, weighted by confidence scores. MaxTiC outputs a ranked species tree compatible with a subset of constraints with maximum cumulated confidence score. We extensively tested the method on simulated datasets, under a wide range of conditions that we compare to measures on biological datasets. In most conditions the obtained ranked tree is very close to the real one, confirming the potential of dating the history of life with transfers by maximizing time consistency. MaxTiC is freely available, distributed along with a documentation and several examples:
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Recommended by Peer Community In Evolutionary Biology ( 2017, 〈10.1101/127548〉
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Soumis le : lundi 13 novembre 2017 - 10:57:15
Dernière modification le : mardi 6 novembre 2018 - 15:24:05
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Cédric Chauve, Akbar Rafiey, Adrian Davin, Celine Scornavacca, Philippe Veber, et al.. MaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers. Recommended by Peer Community In Evolutionary Biology ( 2017, 〈10.1101/127548〉. 〈hal-01532738v3〉



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