Data from: Cryptic diversity and discordance in single-locus species delimitation methods within horned lizards (Phrynosomatidae: Phrynosoma)
Blair, Christopher, Queens College, CUNY
Bryson Jr., Robert W., Burke Museum of Natural History and Culture
Bryson, Robert W., Occidental College, University of Washington
Published Jan 31, 2017 on Dryad.
Cite this dataset
Blair, Christopher; Bryson Jr., Robert W.; Bryson, Robert W. (2017). Data from: Cryptic diversity and discordance in single-locus species delimitation methods within horned lizards (Phrynosomatidae: Phrynosoma) [Dataset]. Dryad. https://doi.org/10.5061/dryad.r7989
Biodiversity reduction and loss continues to progress at an alarming rate, and thus there is widespread interest in utilizing rapid and efficient methods for quantifying and delimiting taxonomic diversity. Single-locus species-delimitation methods have become popular, in part due to the adoption of the DNA barcoding paradigm. These techniques can be broadly classified into tree-based and distance-based methods depending on whether species are delimited based on a constructed genealogy. Although the relative performance of these methods has been tested repeatedly with simulations, additional studies are needed to assess congruence with empirical data. We compiled a large data set of mitochondrial ND4 sequences from horned lizards (Phrynosoma) to elucidate congruence using four tree-based (single-threshold GMYC, multiple-threshold GMYC, bPTP, mPTP) and one distance-based (ABGD) species delimitation models. We were particularly interested in cases with highly uneven sampling and/or large differences in intraspecific diversity. Results showed a high degree of discordance among methods, with multiple-threshold GMYC and bPTP suggesting an unrealistically high number of species (29 and 26 species within the P. douglasii complex alone). The single-threshold GMYC model was the most conservative, likely a result of difficulty in locating the inflection point in the genealogies. mPTP and ABGD appeared to be the most stable across sampling regimes and suggested the presence of additional cryptic species that warrant further investigation. These results suggest that the mPTP model may be preferable in empirical data sets with highly uneven sampling or large differences in effective population sizes of species.
Multiple sequence alignment of unique ND4 haplotypes (220).
Multiple sequence alignment for ABGD analysis of unique haplotypes with singletons removed.
Multiple sequence alignment of 149 ND4 haplotypes (even sampling) after pruning P. platyrhinos sequences.
Multiple sequence alignment for ABGD analysis on the evenly sampled data set with singletons removed.