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Cryptic patterns of speciation in cryptic primates: microendemic mouse lemurs and the multispecies coalescent

Species delimitation is ever more critical for assessing biodiversity in threatened regions of the world, with cryptic species and rapid radiations offering two of the greatest challenges, especially when they occur in conjunction. Mouse lemurs (Microcebus) are an example of a rapid, cryptic radiation and here we study five phylogenetic lineages that are found within a restricted geographic area in northeastern Madagascar. To delimit and characterize species diversity we utilize a conceptual framework based on the multispecies coalescent (MSC). Morphometric analyses reveal only minute phenotypic differences among lineages, thus confirming the cryptic nature of taxa. By analyzing genome-wide SNP data, we assess effective population sizes (Ne), divergence times, and patterns of gene flow to inform hypotheses of species delimitation in the context of geographic distribution, ecology and morphological distinction. Differences in Ne have a significant impact on MSC-based species delimitation, particularly with regard to the recently introduced genealogical divergence index (gdi). Lineages with low Ne pass the heuristic gdi test while high Ne lineages fail to delimit a previously recognized species pair. Further, we find that incorporating gene flow into the MSC can greatly affect divergence time estimates. Even so, we are confident that speciation occurred recently and rapidly in this cryptic radiation with reproductive isolation apparent from two areas where divergent lineages occur sympatrically. Finally, we conclude that a previously identified mitochondrial lineage warrants full species status, and provide a species description for this lineage, naming it M. jonahi. Alarmingly, analyses of both whole-genome and RADseq data show a precipitous decline in Ne in this newly described microendemic, thus indicating a high risk of extinction even in the moment of its recognition as a new species.