Multiple refugia, post-glacial dispersal and strong isolation by distance around the Mediterranean Sea: genetic structure of the long-fingered bat (Myotis capaccinii)

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The genetic structure and recent evolutionary history of the long-fingered bat, MyotiscapacciniiBonaparte, 1837, have not previously been investigated across the entire species' range. We combined a maternally inherited mitochondrial marker (cytochrome b) with biparentally inherited nuclear microsatellites from up to 235 individuals from 21 sites, across nine countries. Mitochondrial DNA revealed three major clades: Clade B (Asia Minor) and two sister clades, C1 (Western Europe, likely of Italian/Iberian refugial origin) and C2 (Eastern Europe, likely of Balkan refugial origin). These lineages may reflect major isolation events during quaternary glaciation cycles. Postglacial recolonisation occurred via east–west expansions from these refugia, producing contact zones in the Balkans (B–C2) and possibly Italy (C1–C2). Nuclear markers revealed a highly structured population with strong isolation by distance, shaped both by historical recolonisation routes and by contemporary barriers such as seas (isolating island populations, e.g. Mallorca) and habitat discontinuities (e.g. the Po Basin). However, the mitochondrial structure is not reflected in the nuclear genome. Genetic data support M. capaccinii as a monotypic species, with no evidence for previously described subspecies based on morphological characters or fur colour. Conservation implications are substantial: populations, especially in Western Europe, are declining under habitat degradation and disturbance. The strong population structure and restricted contemporary gene flow highlight the species' vulnerability, underscoring the need to preserve every colony.