Cyaniris semiargus ddRADseq raw sequences

Historical climatic oscillations and geographic barriers have profoundly shaped genetic diversity and speciation across Europe, particularly within glacial refugia. The widespread butterfly Cyaniris semiargus (Mazarine blue) provides a striking example of such divergence, especially in its southernmost populations, which are fragmented across montane and coastal habitats. Using genome-wide ddRADseq data and environmental analyses, we investigated the genetic structure, gene flow, and ecological differentiation of C. semiargus across the western Palearctic, with a focus on its isolated southern populations. Our results reveal four deeply diverged genetic lineages within the Iberian Peninsula and North Africa. These lineages exhibit strong genetic structure, ecological specialization, and minimal gene flow, consistent with allopatric divergence strengthened by local adaptation. Coastal populations show host plant specialization and adaptation to milder and more stable climates, while montane lineages persist in climatically extreme refugia. Interestingly, another lineage in the Peloponnese is following similar high-altitude climatic selective pressures. Together, these findings point to parallel processes of ecological speciation across both montane and coastal environments. Adopting a conservative taxonomic approach, albeit reflecting their evolutionary and conservation significance, we recognize these four lineages as subspecies. Our study highlights the role of glacial refugia, habitat specialization, and ecological divergence in driving biodiversity, and underscores the urgent need for lineage-specific conservation measures.