Microgeographic genomic variation and connectivity in an endangered semiaquatic mammal

Background The Iberian desman ( Galemys pyrenaicus ), a semiaquatic mammal endemic to southwestern Europe, is listed as Endangered by the IUCN due to substantial range and population decline. Its restriction to upstream locations highlights the importance of understanding its genetic variation and connectivity for effective conservation strategies. While previous studies have revealed phylogeographic structure across the range of the Iberian desman, gaps remain in our understanding of the microgeographic dynamics that shape genetic exchange within specific geographic regions. Results This study first combined newly generated SNP data with previously available datasets to further explore genetic structure in the Iberian desman across its entire distribution, using a set of 110 SNPs on 115 individuals. This confirmed the presence of five major phylogeographic units. Focusing on the newly generated data, we explored the microgeographic dynamics of the Occidental unit with a higher-resolution genomic dataset (7,604 SNPs, 14 individuals). This analysis provided evidence of isolation-by-distance (IBD), indicating that gene flow decreases with increasing geographic distance and that dispersal occurs primarily over short distances. Focussing on the Douro river system, our genomic clustering results showed both connectivity along the best-sampled river and between headwaters of this river and headwaters from a closely located watershed. Our IBD results were consistent with this: indicating riverine dispersal as well as a combination of riverine and overland dispersal at headwaters. These results highlight the importance of both aquatic and terrestrial corridors at upstream locations for maintaining connectivity. Conclusion Our findings emphasize the critical role of headwater regions in supporting gene flow and preserving genetic diversity in the Iberian desman. Conservation efforts should prioritize the protection and restoration of riparian and terrestrial corridors, particularly in fragmented landscapes, to mitigate isolation and preserve genetic diversity in the desman. This study underscores the value of genomic approaches in conservation and contributes to a deeper understanding of the ecological and evolutionary processes that maintain population connectivity in an endangered species.