Conservation strategy insights for three protected Phengaris butterflies combining genetic and landscape analyses

Biodiversity loss is accelerating globally, with insects among the most affected taxa. Wetlands, crucial ecosystems providing essential services, have experienced significant decline due to agricultural intensification and habitat destruction. These changes threaten species that rely on wetland habitats, such as the Phengaris butterflies, which exhibit complex ecological dependencies on specific host plants and ant species. Their populations are structured into metapopulations, where connectivity between habitat patches plays a crucial role in species persistence. This study focuses on population genomics and landscape analysis of three Phengaris species (P. alcon, P. nausithous, P. teleius) in the Bugey Mountain Massif, France, with the aim of developing a conservation strategy. Using ddRAD sequencing, we analyzed genetic diversity, population structure, and gene flow across multiple localities, revealing distinct population clusters with varying degrees of connectivity. Despite some populations exhibiting high genetic diversity levels, others demonstrate low heterozygosity and signs of genetic isolation, emphasizing conservation concerns. Migration estimates and resistance mapping further identified key dispersal corridors and isolated patches requiring targeted interventions. Our findings support metapopulation conservation strategies that prioritize maintaining connectivity, enhancing degraded patches, and identifying new potential habitats. By combining genomic and landscape data, we propose an evidence-based approach to conservation planning, facilitating adaptive management for Phengaris species. This study provides a practical framework for habitat restoration and corridor management in fragmented ecosystems, ensuring long-term species resilience in rapidly changing landscapes.