Phyllodactylus benedettii Assembly. Phyllodactylus benedettii

The biodiversity within tropical dry forests (TDF) is astounding and yet poorly cataloged due to inadequate sampling and the presence of cryptic species. In the Mexican TDF, endemic species are common, and the landscape has been continually altered by geologic and anthropogenic changes. To understand how landscape and environmental variables have shaped the population structure of endemic species, we study the recently described species of leaf-toed gecko, Phyllodactylus benedettii, in coastal western Mexico. Using ddRADseq data, we first explore population structure and estimate the number of ancestral populations. Results indicate a high degree of genetic structure with little admixture, and patterns corresponding to both latitudinal and altitudinal gradients. We find that genetic structure cannot be explained purely by geographic distance, and that ecological corridors may facilitate dispersal and gene flow. We then model the spatial distribution of P. benedettii in the TDF through time and find that the coastline has been climatically suitable for the species since the last glacial maximum (LGM). Landscape genetic analyses suggest that the combined influence of isolation by distance (IBD) and isolation by resistance (IBR; forest cover) influence the spatial genetic structure of the species. Overall, our genomic data demonstrate fine-scale population structure in TDF habitat, a complex colonization history, and spatial patterns consistent with both IBD and other ecological factors. These results further highlight the Mexican TDF as a diversity hotspot and suggest that continued anthropogenic changes are likely to impact native fauna.