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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.\n                  <\/jats:p>","DOI":"10.1186\/s12862-025-02460-1","type":"journal-article","created":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T10:18:59Z","timestamp":1761214739000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Microgeographic genomic variation and connectivity in an endangered semiaquatic mammal"],"prefix":"10.1186","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5030-0656","authenticated-orcid":false,"given":"Sara","family":"Sampaio","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7806-4256","authenticated-orcid":false,"given":"Soraia","family":"Barbosa","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4793-4455","authenticated-orcid":false,"given":"Jos\u00e9 A.","family":"Andr\u00e9s","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9703-0171","authenticated-orcid":false,"given":"Lorenzo","family":"Quaglietta","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9269-1181","authenticated-orcid":false,"given":"Steven","family":"Bogdanowicz","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4355-9608","authenticated-orcid":false,"given":"Paulo","family":"Barros","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1319-0769","authenticated-orcid":false,"given":"Michaela","family":"Horn\u00edkov\u00e1","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2569-0768","authenticated-orcid":false,"given":"Joana","family":"Paup\u00e9rio","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4797-0939","authenticated-orcid":false,"given":"Paulo C.","family":"Alves","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7710-5204","authenticated-orcid":false,"given":"Jeremy B.","family":"Searle","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2025,10,23]]},"reference":[{"key":"2460_CR1","doi-asserted-by":"publisher","first-page":"4295","DOI":"10.1111\/mec.15647","volume":"29","author":"CS Mikles","year":"2020","unstructured":"Mikles CS, Aguillon SM, Chan YL, Arcese P, Benham PM, Lovette IJ, et al. 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Mol Ecol. 2017;26:4418\u201333.","journal-title":"Mol Ecol"}],"container-title":["BMC Ecology and Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12862-025-02460-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12862-025-02460-1\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12862-025-02460-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T12:03:11Z","timestamp":1761220991000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcevolbiol.biomedcentral.com\/articles\/10.1186\/s12862-025-02460-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,23]]},"references-count":56,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["2460"],"URL":"https:\/\/doi.org\/10.1186\/s12862-025-02460-1","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-7018148\/v1","asserted-by":"object"}]},"ISSN":["2730-7182"],"issn-type":[{"value":"2730-7182","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,23]]},"assertion":[{"value":"1 July 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 October 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 October 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The Iberian desman individuals from the Douro river system were captured in Bragan\u00e7a, Portugal, during 2015 and 2016 with collection permits No. 663\/2015\/CAPT and No. 548\/2016\/CAPT issued by Instituto da Conserva\u00e7\u00e3o da Natureza e das Florestas (ICNF), the Portuguese national authority regulating nature. The two samples from the Minho river system correspond to tongue tissue of two animals that died on capture in the Serra do Courel with a licence no. 090\/2012, requested as part of the \u2018Scientific Mammalogy Work Camp in Courel - Galicia\u2019, and issued by the Xunta de Galicia, Council of Environment, Territory and Infrastructures, the general directorate of nature conservation. The two samples from the Ulla river system were obtained from the carcasses of specimens collected by ARCEA Xesti\u00f3n de Recursos Naturais S.L. with authorisation from the Xunta de Galicia (the general directorate of natural heritage), permit No. 544\/2012, within the framework of the \u2018Service to study the use of the Iberian desman in the Ulla river basin to determine its spatial use dynamics,\u2019 as part of the LIFE\u2009+\u2009Margall Ulla project (LIFE NAT\/ES\/000514), co-financed with LIFE\u2009+\u2009NATURE & BIODIVERSITY funds, at 49.39% (No. 27\/2012).","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethical approval"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"114"}}