Data from: 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 their inferred trees. Phylogenetic methods applying
non-homogeneous models to accommodate non-stationarity have relatively
minor effect to reduce gene tree discordance, suggesting that available
computer programs applying these methods do not scale up efficiently to
the data set of modest size analysed in this study. By comparing
phylogenetic trees obtained with species tree (STAR) and concatenation
approaches, we show that gene tree discordance in our data set is most
likely due to base compositional biases than to incomplete lineage
sorting. Multi-locus analyses suggest that the combined phylogenetic
signal from all loci in a concatenated data set overcomes systematic
biases induced by non-stationarity at each partition. Finally,
relationships among flatfishes and their relatives are discussed in the
light of these results. We find support for the monophyly of flatfishes
and confirm findings from previous molecular phylogenetic studies
suggesting their close affinity with several carangimorph groups (i.e.,
jack and allies, barracuda, archerfish, billfish and swordfish, threadfin,
moonfish, beach salmon, and snook and barramundi).