The influence of locus number and information content on species delimitation: an empirical test case in an endangered Mexican salamander

Paul M. Hime, Scott Hotaling, Richard E. Grewelle, Eric M. O'Neill, S. Randal Voss, H. Bradley Shaffer, David W. Weisrock

Research output: Contribution to journalArticlepeer-review

30 Scopus citations


Perhaps the most important recent advance in species delimitation has been the development of model-based approaches to objectively diagnose species diversity from genetic data. Additionally, the growing accessibility of next-generation sequence data sets provides powerful insights into genome-wide patterns of divergence during speciation. However, applying complex models to large data sets is time-consuming and computationally costly, requiring careful consideration of the influence of both individual and population sampling, as well as the number and informativeness of loci on species delimitation conclusions. Here, we investigated how locus number and information content affect species delimitation results for an endangered Mexican salamander species, Ambystoma ordinarium. We compared results for an eight-locus, 137-individual data set and an 89-locus, seven-individual data set. For both data sets, we used species discovery methods to define delimitation models and species validation methods to rigorously test these hypotheses. We also used integrated demographic model selection tools to choose among delimitation models, while accounting for gene flow. Our results indicate that while cryptic lineages may be delimited with relatively few loci, sampling larger numbers of loci may be required to ensure that enough informative loci are available to accurately identify and validate shallow-scale divergences. These analyses highlight the importance of striking a balance between dense sampling of loci and individuals, particularly in shallowly diverged lineages. They also suggest the presence of a currently unrecognized, endangered species in the western part of A. ordinarium's range.

Original languageEnglish
Pages (from-to)5959-5974
Number of pages16
JournalMolecular Ecology
Issue number23
StatePublished - Dec 1 2016

Bibliographical note

Funding Information:
We thank Brian and Shonna Storz for their efforts in the field to sample A. ordinarium across its range. This study was greatly improved through discussions with participants of a Species Delimitation Workshop at the National Institute of Mathematical and Biological Synthesis, and through additional discussions with Laura Kubatko and Tara Pelletier. The design and implementation of phrapl analyses were greatly aided through discussions with phrapl workshop participants at the Ohio State University. We thank the University of Kentucky Center for Computational Sciences and Lipscomb High Performance Computing Cluster, as well as Jeramiah Smith, for access to supercomputing resources. We thank Sebastian Voitel for providing a photograph of A. ordinarium. We also thank associate editor Bryan Carstens and two anonymous reviewers for valuable comments that improved the final manuscript. This research was supported by the National Science Foundation through awards DEB-1257648 and DEB-1457832 (to HBS), DEB-0949532 (to DWW and EMO), and DEB-1355000 (to DWW). This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. 3048109801 to PMH. SH was supported by a University of Kentucky Department of Biology Gertrude Flora Ribble Fellowship.

Publisher Copyright:
© 2016 John Wiley & Sons Ltd


  • Ambystoma
  • Trans-Mexican Volcanic Belt
  • approximate likelihood
  • population structure
  • singular value decomposition
  • speciation

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics


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