Data from: Species discovery and validation in a cryptic radiation of endangered primates: coalescent-based species delimitation in Madagascar's mouse lemurs

Implementation of the coalescent model in a Bayesian framework is an emerging strength in genetically based species delimitation studies. By providing an objective measure of species diagnosis, these methods represent a quantitative enhancement to the analysis of multilocus data, and complement more traditional methods based on phenotypic and ecological characteristics. Recognized as two species 20 years ago, mouse lemurs (genus Microcebus) now comprise more than 20 species, largely diagnosed from mtDNA sequence data. With each new species description, enthusiasm has been tempered with scientific scepticism. Here, we present a statistically justified and unbiased Bayesian approach towards mouse lemur species delimitation. We perform validation tests using multilocus sequence data and two methodologies: (i) reverse-jump Markov chain Monte Carlo sampling to assess the likelihood of different models defined a priori by a guide tree, and (ii) a Bayes factor delimitation test that compares different species-tree models without a guide tree. We assess the sensitivity of these methods using randomized individual assignments, which has been used in bpp studies, but not with Bayes factor delimitation tests. Our results validate previously diagnosed taxa, as well as new species hypotheses, resulting in support for three new mouse lemur species. As the challenge of multiple researchers using differing criteria to describe diversity is not unique to Microcebus, the methods used here have significant potential for clarifying diversity in other taxonomic groups. We echo previous studies in advocating that multiple lines of evidence, including use of the coalescent model, should be trusted to delimit new species. Nuclear and mtDNA lociSequence data files in NEXUS format for all four nuclear and two mtDNA loci used in this study. These files contain the sequence data analyzed in Weisrock et al. (2010) as well as new sequence data from this study.Study Loci.zipLemur Map LocalitiesA list of coordinate information for the localities presented in Figure 1.STRUCTURE AnalysesA folder containing all input and results files for STRUCTURE analyses performed in this study.BPP AnalysesA folder containing all input and results files from BPP analyses. Also included are .xlsx files summarizing the full set of BPP runs.Bayes Factor AnalysesThis folder contains all input and result files associated with *BEAST-based Bayes factor analyses performed in this study. Also included is an .xlsx file summarizing results across all analyses, including HME, sHME, Path Sampling, and Stepping Stone sampling calculations.