DOI: 10.5061/dryad.2sc4n
title: Data from: The effects of inference method, population sampling and gene sampling on species tree inferences: an empirical study in slender salamanders (Plethodontidae: Batrachoseps)

description: 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 whether gene and species trees are estimated simultaneously or
 sequentially, and in how gene trees are used to infer the species tree.
 While these methods 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 leverage in
 these different methods, showing 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.
 This leverage is inherent to the mtDNA locus and results from its high
 variation and lower assumed ploidy. This mtDNA leverage may be problematic
 when mtDNA has undergone introgression, as is likely in this dataset. By
 contrast, the leverage of RAG1 in STEM analyses does not reflect
 properties inherent to the locus, but rather results from a gene tree that
 is strongly discordant with all others, and is best explained by
 introgression between distantly related species. Within-species sampling
 was also important, especially in *BEAST analyses, as shown by differences
 in tree topology across 100 subsampled datasets. 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 for Batrachoseps.
description: Jockuschetal_SupplementalFigures_S1-S7pdf file of gene trees for 6 genes (Supplemental Figures S1-S6) and species trees (Supplemental Figure S7) for analyses examining leverage of mitochondrial DNASupplementalFigures_S1-S7.pdfJockuschetal_Supplemental TableS1sample inclusion for replicated subsamplesJockuschetal_SuppTableS1_Final.xlsJockuschetal_89Individual_6Gene_StrictClock_StarBEASTxml file for 89-individuals, 6 genes that produced tree Figure 2a.Jockuschetal_SpeciesTrees_Fig2Tree file, in nexus format, of trees shown in Figure 2. (File contains multiple tree and taxa blocks.)MPEST_BootstrapScriptsThis zipped file unpacks into a folder with R and shell scripts for running MP-EST bootstrap analysesJockuschetal_GeneAlignments_nexusFilesThis zip file contains 6 nexus files, one for each geneJockuschetal_SuppFigS1-S6Trees_nexusFormatThis zip files includes nexus-formatted gene trees shown in Supplemental Figures S1-S6.Jockuschetal_BatrachosepsSpeciesTrees_Primers_SuppTable2Primers used for amplification and sequencing of nuclear genes