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..., Comparison of whole homolog trees with ortholog trees for identifying gene tree conflict in six datasets
We compiled six datasets of species trees, ortholog trees, and gene families (homolog trees) from published studies that broadly span the tree of life. We used the species relationships and homolog trees inferred in the initial studies as a basis for each conflict analysis. If available, we used rooted homolog trees from the original study. If the rooted homolog trees were not available, we used the extract_clades.py script from (Yang et al. 2015) to extract them. 
All of the datasets, both homologs and orthologs, were analysed using CAnDI to count the total number of nodes assessed corresponding to each node in the species, where each node was assessed as either conflicting with the species tree or concordant with the species tree. Gene duplication nodes were not counted. 
We extracted 12,172 rooted homologs from the unrooted homologs previously inferred for the plant fami..., , # CAnDI: a new tool to investigate conflict in homologous gene trees and explain convergent trait evolution

[https://doi.org/10.5061/dryad.g4f4qrfzq](https://doi.org/10.5061/dryad.g4f4qrfzq)

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 ...,