Data from: CAnDI: a new tool to investigate conflict in homologous gene trees and explain convergent trait evolution

Phenotypic 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 present a novel conflict identification
program named CAnDI (Conflict And Duplication Identifier), which enables
the analysis of conflict in homologous gene trees rather than inferred
orthologs. We demonstrate that the analysis of conflicts in homologous
trees using CAnDI yields more comparisons than in ortholog trees in six
datasets from across the eukaryotic tree of life. Using the carnivorous
trap of Caryophyllales, a charismatic group of flowering plants, as a case
study we demonstrate that analysing conflict on entire homolog trees can
aid in inferring the genetic basis of trait evolution: by dissecting all
gene relationships within homolog trees, we find genomic evidence that the
molecular basis of the pleisiomorphic mucilaginous sticky trap 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 a LATERAL ORGAN BOUNDARY DOMAIN transcription factor as a
possible candidate for regulating sticky trap development.