Simultaneous Bayesian inference of phylogeny and molecular coevolution.

Détails

ID Serval
serval:BIB_AA4DD85D4A30
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
Simultaneous Bayesian inference of phylogeny and molecular coevolution.
Périodique
Proceedings of the National Academy of Sciences of the United States of America
Auteur(s)
Meyer X., Dib L., Silvestro D., Salamin N.
ISSN
1091-6490 (Electronic)
ISSN-L
0027-8424
Statut éditorial
Publié
Date de publication
12/03/2019
Peer-reviewed
Oui
Volume
116
Numéro
11
Pages
5027-5036
Langue
anglais
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Résumé
Patterns of molecular coevolution can reveal structural and functional constraints within or among organic molecules. These patterns are better understood when considering the underlying evolutionary process, which enables us to disentangle the signal of the dependent evolution of sites (coevolution) from the effects of shared ancestry of genes. Conversely, disregarding the dependent evolution of sites when studying the history of genes negatively impacts the accuracy of the inferred phylogenetic trees. Although molecular coevolution and phylogenetic history are interdependent, analyses of the two processes are conducted separately, a choice dictated by computational convenience, but at the expense of accuracy. We present a Bayesian method and associated software to infer how many and which sites of an alignment evolve according to an independent or a pairwise dependent evolutionary process, and to simultaneously estimate the phylogenetic relationships among sequences. We validate our method on synthetic datasets and challenge our predictions of coevolution on the 16S rRNA molecule by comparing them with its known molecular structure. Finally, we assess the accuracy of phylogenetic trees inferred under the assumption of independence among sites using synthetic datasets, the 16S rRNA molecule and 10 additional alignments of protein-coding genes of eukaryotes. Our results demonstrate that inferring phylogenetic trees while accounting for dependent site evolution significantly impacts the estimates of the phylogeny and the evolutionary process.
Mots-clé
Bayes Theorem, Evolution, Molecular, Models, Genetic, Phylogeny, RNA, Ribosomal, 16S/chemistry, RNA, Ribosomal, 16S/genetics, Reproducibility of Results, Software, Bayesian inference, molecular coevolution, phylogeny, tree of life
Pubmed
Web of science
Création de la notice
31/03/2019 16:17
Dernière modification de la notice
20/08/2019 16:14
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