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 ...,表型趋同在生命之树的各个类群中广泛存在，远缘物种间的形态相似性通常被认为是独立演化而来。然而，近年来对性状起源的阐明揭示了演化的复杂本质——看似趋同的特征往往共享相似的遗传基础。因此，支撑这些性状的基因的树拓扑结构，常常与物种关系的整体历史存在冲突。这种冲突既为分类学家带来了挑战，也为研究连接分子演化轨迹与性状演化的丰富复杂信息网络提供了极具价值的契机。 在此我们介绍一款全新的冲突识别工具CAnDI（Conflict And Duplication Identifier，冲突与重复识别器），它可针对同源基因树而非推断得到的直系同源基因树开展冲突分析。我们证实，相较于直系同源树分析，利用CAnDI对同源树进行冲突分析可获得更多的比较样本…… 针对六组数据集开展全同源树与直系同源树的比对，以识别基因树冲突。 我们从广泛覆盖生命之树各分支的已发表研究中，构建了六组包含物种树、直系同源树以及基因家族（同源树）的数据集。我们以初始研究中推断得到的物种关系与同源树作为每一次冲突分析的基础。若原始研究中提供了有根同源树，则直接使用；若未提供，则利用杨等（2015）发布的extract_clades.py脚本进行有根化提取。 我们使用CAnDI对所有数据集（包括同源基因与直系同源基因）进行分析，统计对应物种树各节点的评估节点总数，每个评估节点将被判定为与物种树冲突或与物种树一致。基因重复节点不计入统计。 我们从先前为植物类群推断得到的无根同源树中，提取得到12172条有根同源树…… # CAnDI：一款用于探究同源基因树冲突并阐释趋同性状演化的全新工具 [https://doi.org/10.5061/dryad.g4f4qrfzq](https://doi.org/10.5061/dryad.g4f4qrfzq) 在此我们介绍一款全新的冲突识别工具CAnDI（Conflict And Duplication Identifier，冲突与重复识别器），它可针对同源基因树而非推断得到的直系同源基因树开展冲突分析。我们证实，利用CAnDI对来自真核生物生命之树各分支的六组数据集的同源树进行冲突分析，可获得比直系同源树分析更多的比较样本。我们以一类极具吸引力的被子植物类群——石竹目的食肉捕虫结构作为案例研究，证实对全同源树开展冲突分析有助于推断性状演化的遗传基础：通过剖析同源树内的所有基因关系，我们发现基因组证据表明，近祖状粘液粘性捕虫结构的分子基础大概率存在于所有……的祖先类群中。