Genetic footprints of Quaternary climatic fluctuations on the endangered Tuco-tuco-das-dunas (Ctenomys flamarioni)

The biogeographic history of a species results from responses to past and current processes, and understanding those responses at both temporal scales is essential. We explored phylogeographic and current genetic variation structure in Ctenomys flamarioni—a subterranean rodent that inhabits a small region of the coastal plain of Brazil—and contrasted the roles of “present-day niche suitability” versus “historical climate stability” to understand current and past intraspecific genetic diversity. We used both mitochondrial DNA sequences (concatenated Cytb and D-loop, n = 78) and nuclear DNA (9 microsatellites loci, n = 154) molecular markers for individuals across the entire distribution of the species. We used phylogeographic trees, Bayesian clustering, and haplotype networks to explore genetic variation and diversity. We correlated genetic diversity with measures of current niche suitability and potential areas of Late Quaternary paleostability. Phylogeographic patterns confirmed low levels of genetic diversity structured at different hierarchical levels. We also found a weak but significant pattern of isolation by distance, indicating that geographical distance partially modulates genetic differences among populations. We also observed a positive correlation between genetic diversity and climate paleostability for microsatellites at local and regional scales. However, we found no significant association between genetic diversity and niche suitability for microsatellites at local or regional scales. We observed several signatures of bottleneck and population expansion at different geographic scales. Our results suggest that Quaternary climatic fluctuations—acting together with habitat suitability and other contemporary factors—played a fundamental role in elucidating the evolutionary history of the species—including patterns of historical dispersal, and current patterns of habitat occupation and genetic structure. In addition, based on our molecular and environmental data sets from the across the range of the species and considering the restricted endemism of C. flamarioni, we emphasize the urgency of conservation actions to protect this endangered species.