Cryptic genetic diversity is a significant challenge for systematists faced with ever-increasing amounts of DNA sequence data. Computationally intensive coalescent-based analyses involving multiple unlinked loci are the only currently viable methods by which to assess the extent to which phenotypically similar populations (or metapopulations) are genetically distinct lineages. Although coalescent-based approaches have been tested extensively via simulations, few empirical studies have examined the impact of prior assumptions and dataset size on the ability to assess genetic isolation (evolutionary independence) using molecular data alone. Here, we consider the efficacy of two coalescent-based approaches (BPP and SpeDeSTEM) for testing the evolutionary independence of cryptic mtDNA haplogroups within three morphologically diagnosable species of Andean mouse opossums (. Thylamys pallidior, T. sponsorius, and T. venustus). Fourteen anonymous nuclear loci, one X-linked nuclear intron, and one mitochondrial gene were analyzed for multiple individuals within each haplogroup of interest. We inferred individual gene trees for each locus and considered all of the nuclear loci jointly in a species-tree analysis. Using only the nuclear loci, we performed "species validation" tests for the cryptic mitochondrial lineages in SpeDeSTEM and BPP. For BPP, we also tested a wide range of prior assumptions, assessed performance of the rjMCMC algorithm, and examined how many loci were necessary to confidently delimit lineages. Results from BPP provided strong support for two independent evolutionary lineages each within T. pallidior, T. sponsorius, and T. venustus, whereas SpeDeSTEM results did not support splitting out mtDNA haplogroups as distinct evolutionary units. For most tests, BPP was robust to prior assumptions, although priors were shown to have an effect on both the strength of lineage recognition among T. venustus haplotypes and on the efficiency of the rjMCMC algorithm. Comparisons of results from datasets with different numbers of loci revealed that some cryptic lineages could be confidently delimited with as few as two loci.
Bibliographical noteFunding Information:
We thank Keith Barker, Courtney Comar, Lorissa Fujishin, and Michael Wells for assistance with laboratory work. Keith Barker, Juan Diaz, Andrew Simons, and anonymous reviewers provided helpful comments on how to improve the manuscript. We are thankful to the many curators and collection managers who loaned tissues that we used in this project, especially Michael Mares and Janet Braun (Sam Noble Museum of Natural History), Joe Cook and Jon Dunnum (Museum of Southwestern Biology), and Bruce Patterson and Bill Stanley (Field Museum of Natural History). This work was supported by the National Science Foundation (Grant Nos. DEB-1110365 to S.A.J. and T.C.G., DEB-0743062 to S.A.J., and DEB-0743039 to R.S.V.), the American Society of Mammalogists, the Society of Systematic Biologists, the Bell Museum of Natural History, and the University of Minnesota.
Copyright 2013 Elsevier B.V., All rights reserved.
- Anonymous loci
- Cryptic species
- Multilocus power analysis
- Species delimitation