Addressing gene tree discordance and non-stationarity to resolve a multi-locus phylogeny of the flatfishes (Teleostei: Pleuronectiformes)

Non-homogeneous processes and, in particular, base compositional non-stationarity have long been recognized as a critical source of systematic error. But only a small fraction of current molecular systematic studies methodically examine and effectively account for the potentially confounding effect of non-stationarity. The problem is especially overlooked in multi-locus or phylogenomic scale analyses, in part because no efficient tools exist to accommodate base composition heterogeneity in large data sets. We present a detailed analysis of a data set with 20 genes and 214 taxa to study the phylogeny of flatfishes (Pleuronectiformes) and their position among percomorphs. Most genes vary significantly in base composition among taxa and fail to resolve flatfish monophyly and other emblematic groups, suggesting that non-stationarity may be causing systematic error. We show a strong association between base compositional bias and topological discordance among individual gene partitions and t...