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 ...即便是针对基因组规模的系统发育数据集开展分析，解析生命之树的深层分化关系依然极具挑战性。担子菌门(Basidiomycota)各亚门间的系统发育关系——涵盖锈菌及其近缘类群柄锈菌亚门(Pucciniomycotina)、黑粉菌及其近缘类群黑粉菌亚门(Ustilaginomycotina)，以及产菇真菌及其近缘类群伞菌亚门(Agaricomycotina)——无论采用传统多基因还是基因组规模的系统发育学分析方法，均呈现出极强的解析抗性。本研究依托多套系统发育组学数据集，通过串联分析与基于基因树的分析手段，探究多种潜在偏倚来源的影响，以解析担子菌门的基部系统发育关系。针对担子菌门基部系统发育关系的推断结果，我们评估了两类核心影响因素：一类为生物学成因（硬多歧支、不完全谱系分选），另一类为未建模进化过程及其效应加剧因子（如快速演化位点与长分支类群）。贝叶斯马尔可夫链蒙特卡洛（Bayesian MCMC）与似然映射分析均有力地拒绝了硬多歧支假说。在串联分析中，快速演化的……