Data from: Analyzing contentious relationships and outlier genes in phylogenomics

Recent studies have demonstrated that conflict is common among gene trees
in phylogenomic studies, and that less than one percent of genes may
ultimately drive species tree inference in supermatrix analyses. Here, we
examined two datasets where supermatrix and coalescent-based species trees
conflict. We identified two highly influential “outlier” genes in each
dataset. When removed from each dataset, the inferred supermatrix trees
matched the topologies obtained from coalescent analyses. We also
demonstrate that, while the outlier genes in the vertebrate dataset have
been shown in a previous study to be the result of errors in orthology
detection, the outlier genes from a plant dataset did not exhibit any
obvious systematic error and therefore may be the result of some
biological process yet to be determined. While topological comparisons
among a small set of alternate topologies can be helpful in discovering
outlier genes, they can be limited in several ways, such as assuming all
genes share the same topology. Coalescent species tree methods relax this
assumption but do not explicitly facilitate the examination of specific
edges. Coalescent methods often also assume that conflict is the result of
incomplete lineage sorting (ILS). Here we explored a framework that allows
for quickly examining alternative edges and support for large phylogenomic
datasets that does not assume a single topology for all genes. For both
datasets, these analyses provided detailed results confirming the support
for coalescent-based topologies. This framework suggests that we can
improve our understanding of the underlying signal in phylogenomic
datasets by asking more targeted edge-based questions.