Evolutionary inferences about quantitative traits are affected by underlying genealogical discordance

BioRxiv : the Preprint Server for Biology
Fábio K MendesMatthew W Hahn

Abstract

Modern phylogenetic methods used to study how traits evolve often require a single species tree as input, and do not take underlying gene tree discordance into account. Such approaches may lead to errors in phylogenetic inference because of hemiplasy - the process by which single changes on discordant trees appear to be homoplastic when analyzed on a fixed species tree. Hemiplasy has been shown to affect inferences about discrete traits, but it is still unclear whether complications arise when quantitative traits are analyzed. In order to address this question and to characterize the effect of hemiplasy on traits controlled by a large number of loci, we present a multispecies coalescent model for quantitative traits evolving along a species tree. We demonstrate theoretically and through simulations that hemiplasy decreases the expected covariances in trait values between more closely related species relative to the covariances between more distantly related species. This effect leads to an overestimation of a trait's evolutionary rate parameter, to a decrease of the trait's phylogenetic signal, and to increased false positive rates in comparative methods such as the phylogenetic ANOVA. We also show that hemiplasy affects discre...Continue Reading

Related Concepts

Complication
Biological Evolution
Genes
Trees (plant)
Genetic Loci
Simulation
Analysis
Lymphatic Tree
Phylogenetic Analysis
Comparative Study Research

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