Deep intraspecific divergence in Drosophila meridionalis, a cactophilic member of the New World Drosophila repleta group

Abstract Pleistocene climatic changes have impacted on population demography and divergence in neotropical biomes. However, the extent of these impacts differs with regard to biological group, time and geography. Here, we evaluate how palaeoclimatic changes may have influenced the population dynamics of species associated with xeric environments in South America. To this end, we analysed the population structure and established a phylogeographical hypothesis for Drosophila meridionalis, a cactophilic member of the D. repleta group. We used several different statistical analyses based on a molecular dataset composed of the mitochondrial cytochrome C oxidase subunit I from 196 individuals and the X-linked period gene from 84 individuals. We also quantified the morphological variation in the aedeagus of 217 individuals using geometric morphometry. Our molecular and morphological analysis showed that D. meridionalis is structured in two phyletic and geographically structured lineages, one with an inland distribution (ESU-Group A) and another found along the Brazilian coastline (ESU-Group BC). The latter is composed of two allopatric subgroups. The estimated start of D. meridionalis diversification was during the Pleistocene. The causal effect of palaeoclimatic changes that occurred during the Pleistocene is the likely explanation for the structure seen in D. meridionalis. Our results suggest that historical events differentially affected the population dynamics of D. meridionalis in both spatial and temporal dimensions.