Phylogenetic detection of protein sites associated with continuous traits

Comparative genomic data can be used to look for substitutions in coding sequences that are associated with the variation of a particular phenotypic trait. A few statistical methods have been proposed to do so for phenotypes represented by discrete values. For continuous traits, no such statistical approach has been proposed, and researchers have resorted to sensible but uncharacterized criteria. Here, we investigate a phylogenetic model for coding sequences where amino acid preferences at a site are given by a continuous function of a quantitative trait. This function is inferred from the amino acids and the trait values in extant species and requires inferred point estimates of ancestral values of the trait at internal nodes. For detecting sites whose evolution is associated with this trait, we use a significance test against the hypothesis that amino acid preference does not depend on the trait. This procedure is compared to simpler strategies on simulated alignments. It displays an increased recall for low false positive rates, which is of special importance for performing whole-genome scans. This comes however at a much higher computational cost, and we suggest using a simple test to filter promising candidate sites. We then revisit a dataset of alignments for 62 species of mammals, using longevity as a phenotypic trait. We apply our method to three protein families that have previously been proposed to display sites associated with variation in lifespan in mammals. Using a graphical representation extracted from the detailed phylogenetic analysis of candidate sites, we suggest that the evidence for this in the sequence data alone is weak. The proposed method has been added to our Pelican software. It is available at https://gitlab.in2p3.fr/phoogle/pelican and can now be used with both discrete and continuous phenotypes to search for sites associated with phenotypic variation, on data sets with thousands of alignments.