Isolation and Connectivity: Population Structure of an Ectomycorrhizal Truffle in the Fragmented Mountain Landscape of the Madrean Sky Island Archipelago.

The impact of climate change induced habitat fragmentation on plant species and populations has been studied in numerous systems, but far less is known about how these processes shaped the population structure and demographic history of fungal symbionts. Here, we investigate the population structure and demographic history of ectomycorrhizal fungus Rhizopogon salebrosus, a symbiont of Pinus species, across the Madrean Sky Islands Archipelago (MSIA) of southern Arizona and northern Sonora. Rhizopogon salebrosus produces truffle-like sporocarps and depends on small mammals for spore dispersal. Using genome-wide data from sporocarps and bioassay-derived root tips sampled across seven mountain ranges, we assessed patterns of genetic structure, divergence, and connectivity across this fragmented landscape. We identified strong geographic structuring consistent with island-like population differentiation, accompanied by rare signals of admixture. Genetic divergence among populations increased with geographic distance, and demographic inference supports long-term isolation associated with historical habitat fragmentation, with limited recent gene flow among islands. Together, these results highlight the lasting influence of past climate-driven landscape dynamics on fungal population structure and emphasize the role of geographic isolation in shaping the evolutionary history of symbiotic fungi in montane systems.