An integrated model of phenotypic trait changes and site-specific sequence evolution

Levy Karin E, Wicke S, Pupko T, Mayrose I

Research article (journal) | Peer reviewed

Abstract

Recent years have seen a constant rise in the availability of trait data, including morphological features, ecological preferences, and life history characteristics. These phenotypic data provide means to associate genomic regions with phenotypic attributes, thus allowing the identification of phenotypic traits associated with the rate of genome and sequence evolution. However, inference methodologies that analyze sequence and phenotypic data in a unified statistical framework are still scarce. Here, we present TraitRateProp, a probabilistic method that allows testing whether the rate of sequence evolution is associated with a binary phenotypic character trait. The method further allows the detection of specific sequence sites whose evolutionary rate is most noticeably affected following the character transition, suggesting a shift in functional/structural constraints. TraitRateProp is first evaluated in simulations and then applied to study the evolutionary process of plastid plant genomes upon a transition to a heterotrophic lifestyle. To this end, we analyze 20 plastid genes across 85 orchid species, spanning different lifestyles and representing different genera in this large family of flowering plants. Our results indicate higher evolutionary rates following repeated transitions to a heterotrophic lifestyle in all but four of the loci analyzed.

Details about the publication

JournalSystematic Biology
Volume66
Issue6
Page range917-933
StatusPublished
Release year2017 (16/02/2017)
Language in which the publication is writtenEnglish
DOI10.1093/sysbio/syx032
Link to the full texthttps://academic.oup.com/sysbio/article-abstract/doi/10.1093/sysbio/syx032/2978030/An-integrated-model-of-phenotypic-trait-changes?redirectedFrom=fulltext
KeywordsMolecular evolution; genotype-phenotype analysis; evolutionary models; evolutionary biology

Authors from the University of Münster

Wicke, Susann
Group Evolution and Biodiversity of Plants (Prof. Müller)