DOI: 10.5061/dryad.2gq14
title: Data from: Species tree reconstruction of a poorly resolved clade of salamanders (Ambystomatidae) using multiple nuclear loci

description: The analysis of diverse data sets can yield different phylogenetic
 estimates that challenge systematists to explain the source of
 discordance. The mole salamanders (family Ambystomatidae) are a classic
 example of this phylogenetic conflict. Previous attempts to resolve the
 ambystomatid species tree using allozymic, morphological, and
 mitochondrial sequence data have yielded different estimates, making it
 unclear which data source best approximates ambystomatid phylogeny and
 which ones yield phylogenetically inaccurate reconstructions. To shed
 light on this conflict, we present the first multi-locus DNA
 sequence-based phylogenetic study of the Ambystomatidae. We utilized a
 range of analyses, including coalescent-based methods of species-tree
 estimation that account for incomplete lineage sorting within a locus and
 concordance-based methods that estimate the number of sampled loci that
 support a particular clade. We repeated these analyses with the removal of
 individual loci to determine if any locus has a disproportionate effect on
 our phylogenetic results. Collectively, these results robustly resolved
 many deep and relatively shallow clades within Ambystoma, including the
 placement of A. gracile and A. talpoideum as the sister clade to a clade
 containing all remaining ambystomatids, and the placement of A. maculatum
 as the sister lineage to all remaining ambystomatids excluding A. gracile
 and A. talpoideum. Both Bayesian coalescent and concordance methods
 produced similar results, highlighting strongly supported branches in the
 species tree. Furthermore, coalescent-based analyses that excluded loci
 produced overlapping species-tree posterior distributions, suggesting that
 no particular locus – including mtDNA – disproportionately contributed to
 our species-tree estimates. Overall, our phylogenetic estimates have
 greater similarity with previous allozyme and mitochondrial sequence-based
 phylogenetic estimates. However, intermediate depths of divergence in the
 ambystomatid species tree remain unresolved, potentially highlighting a
 region of rapid species radiation or a hard polytomy, which limits our
 ability to comment on previous morphologically-based taxonomic groups.
description: AP_DRYADThis contains input and output files generated using BEAST, *BEAST, and MrBayes. "*BEAST Calibration" contains XML files, log files, and species tree posterior distributions generated using a calibrated root for Ambystoma. "*BEAST MCC Trees" contains all MCC trees generated for all non-calibrated analyses using *BEAST. "*BEAST nexus and XML files" contains all XML files and nexus files associated with all non-calibrated analyses using *BEAST. "BEAST (for STEM) XML files" contains the XML files used for tree reconstruction of each locus using BEAST for downstream use in STEM. "BEAST MCC Trees (for STEM)" contains all MCC trees generated in BEAST for downstream use in STEM. "MrBayes Consensus Trees" contains all consensus trees generated using MrBayes. "MrBayes nexus Files" contains all nexus files used for analyses in MrBayes.