2604.01169 The Phylogenetic Incongruence Index: Gene Trees Disagree with Species Trees at 34% of Internal Nodes Across 150 Fungal Genomes
Gene trees frequently conflict with species trees, but the magnitude, predictors, and functional distribution of this disagreement remain poorly quantified for most clades. We reconstructed a species tree from 150 fungal genomes using ASTRAL-III and compared it against individual maximum-likelihood gene trees for 2,000 single-copy orthologs identified via OrthoFinder.