Microgeographic genomic variation and connectivity in an endangered semiaquatic mammal

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 in recent years, with its populations now largely limited to river headwaters. This restriction to upstream locations highlights the importance of documenting genetic variation and population connectivity in Iberian desmans for effective conservation strategies. While previous studies have revealed phylogeographic structure across the range of the species, gaps remain in our understanding of the microgeographic dynamics that shape genetic exchange within specific geographic regions. This study first combined our newly generated SNP data with previous datasets to further explore genetic structure across the entire Iberian desman distribution using the 115 individuals now available. Due to differences in methodology between our study and previous studies, only 110 SNPs were available for comparison across all individuals. Nevertheless, the analysis with these SNPs confirmed the presence of the five major phylogeographic units previously described and validated the assignment of our newly generated dataset to the Occidental phylogeographic unit. Focusing on our newly generated data, we explored the microgeographic dynamics of this Occidental phylogeographic unit with a higher-resolution genomic dataset (7,604 SNPs, 14 individuals). This analysis provided evidence of isolation-by-distance (IBD), suggesting 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 (Sabor) and between headwaters of this and headwaters from a closely located river (Tua). 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 in upstream areas for maintaining connectivity. Thus, 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 Iberian 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.