Royer-Carenzi, M. | Search bioRxiv

bioRxiv2019

Testing for correlation between traits under directional evolution

Being confounding factors, directional trends are likely to make two quantitative traits appear as spuriously correlated. By determining the probability distributions of independent contrasts when traits evolve following Brownian motions with linear trends, we show that the standard independent contrasts can not be used to test for correlation in this situation. We propose a multiple regression approach which corrects the bias caused by directional evolution.\n\nWe show that our approach is equivalent to performing a Phylogenetic Generalized Least Squares (PGLS) analysis with tip times as covariables by providing a new and more general proof of the equivalence between PGLS and independent contrasts methods.\n\nOur approach is assessed and compared with three previous correlation tests on data simulated in various situations and overall outperforms all the other methods. The approach is next illustrated on a real dataset to test for correlation between hominin cranial capacity and body mass.

evolutionary biology↗

bioRxiv2017

Detecting Molecular Basis Of Phenotypic Convergence

Convergence is the process by which several species independently evolve similar traits. This evolutionary process is not only strongly related to fundamental questions such as the predictability of evolution and the role of adaptation, its study also may provide new insights about genes involved in the convergent character. We focus on this latter question and aim to detect molecular basis of a given phenotypic convergence. After pointing out a number of concerns about detection methods based on ancestral reconstruction, we propose a novel approach combining an original measure of the extent to which a site supports a phenotypic convergence, with a statistical framework for selecting genes from the measure of their sites. First, our measure of \"convergence level\" outperforms two previous ones in distinguishing simulated convergent sites from non-convergent ones. Second, by applying our detection approach to the well-studied case of convergent echolocation between dolphins and bats, we identified a set of genes which is very significantly annotated with audition-related GO-terms. This result constitutes an indirect evidence that genes involved in a phenotypic convergence can be identified with a genome-wide approach, a point which was highly debated, notably in the echolocation case (the latest articles published on this topic were quite pessimistic). Our approach opens the way to systematic studies of numerous examples of convergent evolution in order to link (convergent) phenotype to genotype.

evolutionary biology↗