Model choice, missing data and taxon sampling impact phylogenomic inference of deep Basidiomycota relationships

Resolving deep divergences in the tree of life is challenging even for analyses of genome-scale phylogenetic datasets. Relationships between Basidiomycota subphyla, the rusts and allies (Pucciniomycotina), smuts and allies (Ustilaginomycotina) and mushroom-forming fungi and allies (Agaricomycotina) were found particularly recalcitrant both to traditional multigene and genome-scale phylogenetics. Here, we address basal Basidiomycota relationships using concatenated and gene-tree based analyses of various phylogenomic datasets to examine the contribution of several potential sources of bias. We evaluate the contribution of biological causes (hard polytomy, incomplete lineage sorting) versus unmodeled evolutionary processes and factors that exacerbate their effects (e.g. fast-evolving sites and long-branch taxa) to inferences of basal Basidiomycota relationships. Bayesian MCMC and likelihood mapping analyses reject the hard-polytomy with confidence. In concatenated analyses, fast-evolving ...