Spatiotemporal variation in habitat suitability predicts genomic diversity and structure in a Western Ghats endemic Tarantula ( Thrigmopoeus truculentus )

Physical barriers are well known to restrict gene flow and generate population structure, yet what drives genetic differentiation in the absence of such barriers remains less understood. In these cases, long-term climatic fluctuations may shape genomic variation by altering habitat connectivity through time. The Western Ghats mountains in Peninsular India, marked by high endemism and in-situ radiations, provide a compelling natural laboratory to understand how historical climate change can shape genetic diversity. While the role of topographic barriers in generating diversity in this landscape is well documented, the influence of paleoclimatic processes has rarely been examined, especially from a genomic perspective. Here, we combine genome-wide SNPs and ecological niche modelling with present and past climatic data to test the role of elevation, geographic distance, environment and paleohabitat dynamics in shaping the genetic diversity and structure in a wet-adapted tarantula species endemic mostly to the central Western Ghats. Despite overall genomic admixture and continuity, populations show little north–south structuring, and genetically distinct central populations. Paleoclimate projections from the present to the Last Glacial Maximum reveal that northern and southern regions maintained stable habitat suitability for Thrigmopoeus , whereas central regions experienced high temporal variability. Linear mixed models identify historical stability of suitable habitats as the strongest predictor of genetic structure. Central populations occupying historically unstable habitats also show reduced heterozygosity, elevated inbreeding, and smaller historical effective population sizes. These results demonstrate that, even in the absence of physical barriers, long-term climate dynamics can generate and maintain fine-scale, within-species genetic diversity.