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

Joshua S. Williams, John H. Niedzwiecki, David W. Weisrock

Research output: Contribution to journalArticlepeer-review

19 Scopus citations


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.

Original languageEnglish
Pages (from-to)671-682
Number of pages12
JournalMolecular Phylogenetics and Evolution
Issue number3
StatePublished - Sep 2013

Bibliographical note

Funding Information:
We thank Jim Demastes, Paul Moler, Greg Pauly, Brad Shaffer, the Louisiana State University Museum of Zoology, and the Museum of Vertebrate Zoology at the University of California, Berkeley for their contribution of tissue samples. We also thank Eric O’Neill, Stephanie Mitchell, Alex Noble, and Ana Mendia for invaluable laboratory assistance. Randal Voss and Paul Hime provided comments that improved this manuscript. We also thank the University of Kentucky Information Technology Department and Center for Computational Sciences for computing time on the Lipscomb High Performance Computing Cluster and for access to other supercomputing resources, and we also thank the Yale University Biomedical High Performance Computing Center for allowing us computing time on the Louise High Performance Computing Cluster (NIH Grants RR19895 and RR029676-01). Funding and support for this work was provided from the University of Kentucky, a Commonwealth of Kentucky NSF EPSCoR Grant (# 0814194) in support of Ecological Genomics training and research, NSF Grant DEB0949532 (to DWW), and a Society of Systematic Biologists Graduate Student Award (to JSW).


  • Ambystoma
  • Bayesian analysis
  • Coalescent analysis
  • Concordance analysis
  • Gene tree
  • Species tree

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics


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