Data from: The multispecies coalescent over-splits species in the case of geographically widespread taxa

Many recent species delimitation studies rely exclusively on limited analyses of genetic data analyzed under the multispecies coalescent (MSC) model, and results from these studies often are regarded as conclusive support for taxonomic changes. However, most MSC-based species delimitation methods have well-known and often unmet assumptions. Uncritical application of these genetic-based approaches (without due consideration of sampling design, the effects of a priori group designations, isolation by distance, cytoplasmic–nuclear mismatch, and population structure) can lead to over-splitting of species. Here, we argue that in many common biological scenarios, researchers must be particularly cautious regarding these limitations, especially in cases of well-studied, geographically variable, and parapatrically-distributed species complexes. We consider these points with respect to a historically controversial species group, the American milksnakes (Lampropeltis triangulum complex), using genetic data from a recent analysis (Ruane et al. 2014; Syst. Biol. 63:231-250). We show that over-reliance on the program BPP, without adequate consideration of its assumptions and of sampling limitations, resulted in over-splitting of species in this study. Several of the hypothesized species of milksnakes instead appear to represent arbitrary slices of continuous geographic clines. We conclude that the best available evidence supports three, rather than seven, species within this complex. More generally, we recommend that coalescent-based species delimitation studies incorporate thorough analyses of geographic variation and carefully examine putative contact zones among delimited species before making taxonomic changes.Supplementary Figure 1: Structurama resultsResults from Structurama analysesFigS1_Structurama.pdfSupplementary Figure 2: consensus gene treesMajority-rule consensus gene trees for 11 nuclear genesFigS2_consensustrees.pdfSupplementary Figure 3: cytb gene treeMaximum clade credibility cytb gene treeFigS3_cytbtree.pdfSupplementary Table 1: BPP resultsResults from BPP analyses for alternative splits of L. gentilis and L. triangulumTableS1.pdfSupplementary Table 2: Lampropeltis taxonomyTaxonomy of Lampropeltis speciesTableS2.pdfOnline Appendix 1Details for Structurama analysesOnline Appendix 2Details for gene tree reconstructionOnline Appendix 3Details for BPP analysesChambersHillis_SuppFilesSupplementary data files associated with all analyses