Data from: The effects of inference method, population sampling and gene sampling on species tree inferences: an empirical study in slender salamanders (Plethodontidae: Batrachoseps)

Species tree methods are now widely used to infer the relationships among species from multi-locus datasets. Many methods have been developed, which differ in how gene trees are used to infer the species tree. While these methods all perform well on simulated data, less is known about what impacts their performance on empirical data. We used a dataset including five nuclear genes and one mitochondrial gene for 22 species of Batrachoseps to compare the effects of method of analysis, within-species sampling and gene sampling on species tree inferences. For this dataset, the choice of inference method had the largest effect on the species tree topology. Exclusion of individual loci had large effects in *BEAST and STEM, but not in MP-EST. Different loci carried the greatest weight in these different methods, suggesting that the causes of their disproportionate effects differ. Even though substantial information was present in the nuclear loci, the mitochondrial gene dominated the *BEAST species tree. If loci with disproportionate impacts also violate the assumption of these species tree methods that all discordance is due to incomplete lineage sorting, then analyses may be positively misled. The potential for this problem is expected to be especially pervasive with animal mitochondrial loci, which are both typically far more variable than nuclear loci and highly subject to introgression. Within-species sampling was also important, as shown by differences in tree topology across 100 subsampled datasets. *BEAST showed high levels of variation in nodal support across these subsamples (ranging from <5-95% for some focal nodes). Despite the sensitivity of the species tree methods to multiple factors, five species groups, the relationships among these, and some relationships within them, are generally consistently resolved.