Spatial and Ecological Drivers of Diversification in the World's Southernmost Gecko

Understanding the mechanisms driving genetic differentiation-and ultimately, speciation-is central to evolutionary biology, particularly in widespread species inhabiting environmentally complex landscapes. Homonota darwinii, a member of the H. whitii group, is the southernmost gecko in the world, distributed across the Patagonian Steppe-a vast, heterogeneous landscape with a complex geoclimatic history. This system offers an opportunity to assess the relative roles of geographic distance, environmental variation, and landscape resistance in diversification. We present a comprehensive dataset of > 700 geckos sampled over 20 years across > 1,000,000 km² of southern South America. Using phylogeographic, landscape genomics and coalescent approaches, we examined patterns of population divergence and connectivity. Genomic data revealed geographically consistent groups and admixture in transitional zones. We identified three putative species-level lineages corresponding to regional phylogeographic breaks shared by other taxa. Landscape genomic analyses indicated that isolation-by-environment (IBE), particularly climatic gradients related to aridity, temperature, and seasonality, was the primary driver of genetic divergence. We also identified genomic variants associated with local adaptation. Our results suggest that H. darwinii expanded into the Patagonian Steppe during the Pliocene, with persistence facilitated by adaptations to arid conditions. Within the H. whitii group, we found evidence supporting a hybrid speciation model for Homonota williamsii, involving roughly equal genomic contributions from two H. darwinii genetic groups. This study highlights the interplay of spatial, ecological and historical factors in shaping genetic structure and adaptation. It also provides a framework for taxonomic and conservation initiatives, especially given prior projections of climate-driven population decline in H. darwinii.