Data from: Species tree reconstruction of a poorly resolved clade of salamanders (Ambystomatidae) using multiple nuclear loci

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.