title: Testing for Independence between Evolutionary Processes.
abstract: Evolutionary events co-occurring along phylogenetic trees usually point to complex adaptive phenomena, sometimes implicating epistasis. While a number of methods have been developed to account for co-occurrence of events on the same internal or external branch of an evolutionary tree, there is a need to account for the larger diversity of possible relative positions of events in a tree. Here we propose a method to quantify to what extent two or more evolutionary events are associated on a phylogenetic tree. The method is applicable to any discrete character, like substitutions within a coding sequence or gains/losses of a biological function. Our method uses a general approach to statistically test for significant associations between events along the tree, which encompasses both events inseparable on the same branch, and events genealogically ordered on different branches. It assumes that the phylogeny and themapping of branches is known without errors. We address this problem from the statistical viewpoint by a linear algebra representation of the localization of the evolutionary events on the tree.We compute the full probability distribution of the number of paired events occurring in the same branch or in different branches of the tree, under a null model of independence where each type of event occurs at a constant rate uniformly inthephylogenetic tree. The strengths andweaknesses of themethodare assessed via simulations;we then apply the method to explore the loss of cell motility in intracellular pathogens.
authors.affiliation: UMR7138 "Evolution Paris-Seine" UPMC-CNRS Bât A, 4ème étage, porte 414, Case 5 7 quai Saint Bernard, 75252 Paris Cedex 05; Atelier de BioInformatique - MNHN Boite Courier 50 Batiment 139 - RdC 45 rue Buffon, 75005 Paris; Smile "Stochastic Models for the Inference of Life Evolution" Center for Interdisciplinary Research in Biology Collège de France 11, place Marcelin Berthelot 75231 Paris Cedex 05; kaderbehdenna@gmail.com.
authors.forename: Abdelkader
authors.initials: A
authors.lastname: Behdenna
authors.affiliation: Atelier de BioInformatique - MNHN Boite Courier 50 Batiment 139 - RdC 45 rue Buffon, 75005 Paris; Enzymologie De L'arn Bât B - 2ème étage 7, quai St Bernard Boîte courrier 60 75252 Paris Cedex 05;
authors.forename: Joël
authors.initials: J
authors.lastname: Pothier
authors.affiliation: Institut Pasteur, Microbial Evolutionary Genomics 25-28 Rue du Docteur Roux 75015, Paris; UMR 3525 - CNRS - Institut Pasteur Génétique des génomes 25-28 rue du Docteur Roux, Site Fernbach 75724 Paris Cedex 15;
authors.forename: Sophie S
authors.initials: SS
authors.lastname: Abby
authors.affiliation: Smile "Stochastic Models for the Inference of Life Evolution" Center for Interdisciplinary Research in Biology Collège de France 11, place Marcelin Berthelot 75231 Paris Cedex 05; Laboratoire de Probabilités & Modèles Aléatoires UPMC Univ Paris 06 Case courrier 188 4, Place Jussieu 75252 Paris Cedex 05;
authors.forename: Amaury
authors.initials: A
authors.lastname: Lambert
authors.affiliation: UMR7138 "Evolution Paris-Seine" UPMC-CNRS Bât A, 4ème étage, porte 414, Case 5 7 quai Saint Bernard, 75252 Paris Cedex 05; Atelier de BioInformatique - MNHN Boite Courier 50 Batiment 139 - RdC 45 rue Buffon, 75005 Paris; Smile "Stochastic Models for the Inference of Life Evolution" Center for Interdisciplinary Research in Biology Collège de France 11, place Marcelin Berthelot 75231 Paris Cedex 05;
authors.forename: Guillaume
authors.initials: G
authors.lastname: Achaz
mesh_terms: D005075:Biological Evolution; D002965:Classification / Q000379:methods*; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D010802:Phylogeny; D011336:Probability
keywords: Coevolution; phylogeny; statistical test.