Investigating Phylogenetic Conflict using Homolog Trees reveals the Genetic Basis of Phenotypic Convergence in Carnivorous Sundews

Abstract

AbstractPhenotypic convergence is found across the tree of life, and morphological similarities in distantly related species are often presumed to have evolved independently. However, clarifying the origins of traits has recently highlighted the complex nature of evolution, as apparent convergent features often share similar genetic foundations. Hence, the tree topology of genes that underlie such traits frequently conflicts with the overall history of species relationships. This conflict creates both a challenge for systematists and an exciting opportunity to investigate the rich, complex network of information that connects molecular trajectories with trait evolution. Here we probe the evolutionary history of pleisiomorphic features in the carnivorous Caryophyllales, a charismatic group of flowering plants. Using a novel conflict identification program named CAnDI (Conflict And Duplication Identifier), we dissect all gene relationships within homolog trees and find genomic evidence that the molecular basis of mucilaginous sticky traps was likely present in the ancestor of all carnivorous Caryophyllales. We also show that many genes whose evolutionary trajectories group species with similar trap devices code for proteins contributing to plant carnivory and identify aLATERAL ORGAN BOUNDARY DOMAINgene as a possible regulator of sticky trap development. Our results demonstrate that analysing conflict on homolog trees, rather than pre-identified orthologs, can aid in uncovering the genetic basis of trait evolution.