Bastien BOUSSAU Genome scale genotype-phenotype associations along phylogenies
invité par Amaury LAMBERT - Section Écologie et Biologie de l’Évolution
12h30
Le séminaire de Bastien BOUSSAU (Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne) aura lieu dans la salle Favard, IBENS 46 rue d’Ulm 75005 Paris
Summary : Identifying the footprints of selection in coding sequences can inform about the importance and function of individual sites. Analyses of the ratio of nonsynonymous to synonymous substitutions (dN/dS) have been widely used to pinpoint changes in the intensity of selection, but cannot distinguish them from changes in the direction of selection, that is, changes in the fitness of specific amino acids at a given position. We have evaluated several methods that detect changes in directional selection associated to discrete phenotypic changes on a phylogeny, and have found that our method Pelican offers a good trade-off between power and speed, enabling whole genome analyses for hundreds of species (Duchemin et al., MBE 2023, https://doi.org/10.1093/molbev/msac247). In this presentation we present Pelican, show how its performance compares to other state-of-the-art methods, including in the presence of confounding factors such as GC-biased gene conversion and CpG hypermutability, present an extension to handle continuous phenotypes, and demonstrate its use on several phenotypes on a data set of 116 whole genomes from mammals. Overall, we demonstrate that Pelican can analyze large amounts of data to look for genotype-phenotype associations, at the level of individual sites or individual genes, for both discrete and continuous phenotypes. Looking forward, we expect that the use of such phylogenetic approaches on large genomic data sets will be instrumental to annotating gene function across the tree of life.
Webpage : https://lbbe-web.univ-lyon1.fr/fr/annuaires-des-membres/boussau-bastien