Dataset for: Smith et al., Phylogenomic analysis of the parrots of the world distinguishes artifactual from biological sources of gene tree discordance

Gene tree discordance is expected in phylogenomic trees and biological
processes are often invoked to explain it. However, heterogeneous levels
of phylogenetic signal among individuals within datasets may cause
artifactual sources of topological discordance. We examined how the
information content in tips and subclades impacts topological discordance
in the parrots (Order: Psittaciformes), a diverse and highly threatened
clade of nearly 400 species. Using ultraconserved elements from 96% of the
clade's species-level diversity, we estimated concatenated and
species trees for 382 ingroup taxa. We found that discordance among tree
topologies was most common at nodes dating between the late Miocene and
Pliocene, and often at the taxonomic level of genus. Accordingly, we used
two metrics to characterize information content in tips and assess the
degree to which conflict between trees was being driven by lower quality
samples. Most instances of topological conflict and non-monophyletic
genera in the species tree could be objectively identified using these
metrics. For subclades still discordant after tip-based filtering, we used
a machine learning approach to determine whether phylogenetic signal or
noise was the more important predictor of metrics supporting the
alternative topologies. We found that when signal favored one of the
topologies, noise was the most important variable in poorly performing
models that favored the alternative topology. In sum, we show that
artifactual sources of gene tree discordance, which are likely a common
phenomenon in many datasets, can be distinguished from biological sources
by quantifying the information content in each tip and modeling which
factors support each topology.