Species distribution models predict genome-wide polymorphism and gene flow in an endangered amphibian

Species distribution models (SDMs) are widely used to predict habitat suitability but their usefulness and accuracy for inferring population health is still debated. Here, we evaluate whether SDM-derived relative habitat suitability (RHS) predicts genome-wide genetic diversity and connectivity-which are key proxies for population health and the functional integrity of landscapes. We addressed this issue in the Yellow-bellied toad (Bombina variegata), an endangered amphibian species with limited dispersal. We combined hierarchical SDMs, integrating both continental-level bioclimatic data and regional-level landscape variables, with genome-wide SNP data from 404 individuals sampled across 92 sites in southeastern France. We then used a multi-scale modelling framework to test the effect of bioclimatic (BRHS) and landscape (LRHS) habitat suitability on observed heterozygosity and pairwise genetic differentiation, accounting for heterogeneous genetic drift using gravity models. Our results show that both BRHS and LRHS are significant predictors of heterozygosity, with their effects expressed at different spatial scales-11 km and 3 km for BRHS and LRHS, respectively. Connectivity patterns also widely varied depending on scale and were best explained by gravity models integrating LRHS, BRHS, and local heterozygosity, underscoring the combined role of landscape resistance and population size in shaping patterns of genetic differentiation. These findings show that SDMs, when carefully calibrated and interpreted, can provide proxies for genetic diversity and landscape resistance in species with limited dispersal.