Regional geography and anthropogenic landscape features shape genetic patterns across populations of the endangered Alcon blue butterfly

Habitat fragmentation and anthropogenic disturbance increasingly threaten species with complex life histories, particularly ecological specialists confined to fragmented habitats. The Alcon blue butterfly ( Phengaris alcon alcon ), an endangered wetland specialist in Switzerland, depends on tightly coupled interactions with specific host plants and ants, making it highly sensitive to landscape change. Here, we combined genome-wide ddRAD sequencing with landscape genetic analyses to assess how geographic distance, environmental structure, and human infrastructure relate to genetic diversity and connectivity across 22 populations in the Swiss lowlands. Population genomic analyses revealed pronounced genetic structure over short spatial scales, with pairwise genetic differentiation ranging from low to very high ( F ST = 0.04–0.44) and clear core–periphery patterns in genetic diversity. Core populations retained higher heterozygosity and evidence of localized gene flow, whereas peripheral populations were more isolated and genetically depauperate. Isolation by distance was significant at the regional scale, confirming geographic distance as a key driver of genetic differentiation. Generalized dissimilarity modeling identified road density and traffic-related disturbance as major predictors of genetic differentiation at broader spatial scales, highlighting the constraining role of anthropogenic barriers on connectivity. Complementary isolation by resistance analysis provided substantially greater support for landscape resistance based on geographic distance and road disturbance rather than for geographic distance alone . Together, our results demonstrate that patterns of genetic variation in P. a. alcon are shaped by the interplay between geographic isolation and anthropogenic landscape barriers, with road and traffic-related effects contributing to genetic fragmentation. Effective conservation will therefore require maintaining and, where possible, restoring dense networks of small wetlands while mitigating barrier effects to preserve connectivity and evolutionary potential.