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Unionid freshwater mussels exemplify the dramatic loss of biodiversity in freshwater ecosystems, yet genomic data for these ecologically important species remain scarce. Here, we conducted a high\u2010resolution population genomics study of all\n                    <jats:italic>Anodonta<\/jats:italic>\n                    species in Switzerland, with a focus on two species with contrasting reproductive strategies. After generating draft genomes of the hermaphroditic\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>Anodonta cygnea<\/jats:italic>\n                    <\/jats:styled-content>\n                    and the gonochoric\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>Anodonta anatina<\/jats:italic>\n                    <\/jats:styled-content>\n                    , we performed whole\u2010genome resequencing of 421 individuals collected in 31 localities. While\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>A.\u2009anatina<\/jats:italic>\n                    <\/jats:styled-content>\n                    populations followed a metapopulation structure shaped by catchment areas, genetic diversity correlated positively with waterbody size, suggesting greater vulnerability in small ponds compared with large lakes. Inbreeding levels were low; however, effective population sizes were consistently below 100, indicating serious extinction risks. Strong divergence between\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>A.\u2009anatina<\/jats:italic>\n                    <\/jats:styled-content>\n                    populations north and south of the Alps suggests a putative undescribed\n                    <jats:italic>Anodonta<\/jats:italic>\n                    species in the Ticino area. Furthermore, we detected hybridisation between\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>A.\u2009cygnea<\/jats:italic>\n                    <\/jats:styled-content>\n                    and\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>A.\u2009exulcerata<\/jats:italic>\n                    <\/jats:styled-content>\n                    , indicating genomic permeability between these species. In addition, genomic data suggested facultative selfing in\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>A.\u2009cygnea<\/jats:italic>\n                    <\/jats:styled-content>\n                    , leading to a marked reduction in genetic diversity, increased population structure and inbreeding and a decline in effective population size compared to the outcrossing\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>A.\u2009anatina<\/jats:italic>\n                    <\/jats:styled-content>\n                    . Our study underscores that reproductive strategy fundamentally shapes genetic indicators of biodiversity and influences extinction risk; conservation targets should therefore be adapted to the biology of the species of interest. To conclude, we advocate for integrating reproductive mode and genomic data into conservation planning to more accurately assess vulnerability and guide effective action.\n                  <\/jats:p>","DOI":"10.1111\/mec.70066","type":"journal-article","created":{"date-parts":[[2025,8,11]],"date-time":"2025-08-11T11:00:21Z","timestamp":1754910021000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Beyond Genetic Indicators: How Reproductive Mode and Hybridisation Challenge Freshwater Mussel Conservation"],"prefix":"10.1111","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9823-9703","authenticated-orcid":false,"given":"Ellika","family":"Faust","sequence":"first","affiliation":[{"name":"Department of Aquatic Ecology Swiss Federal Institute of Aquatic Science and Technology (Eawag)  D\u00fcbendorf Switzerland"},{"name":"Department of Fish Ecology and Evolution Swiss Federal Institute of Aquatic Science and Technology (Eawag)  Kastanienbaum Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-0148-9782","authenticated-orcid":false,"given":"Julie","family":"Conrads","sequence":"additional","affiliation":[{"name":"Department of Aquatic Ecology Swiss Federal Institute of Aquatic Science and Technology (Eawag)  D\u00fcbendorf Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"Giulio","sequence":"additional","affiliation":[{"name":"Department of Aquatic Ecology Swiss Federal Institute of Aquatic Science and Technology (Eawag)  D\u00fcbendorf Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8537-8659","authenticated-orcid":false,"given":"Claudio","family":"Ciofi","sequence":"additional","affiliation":[{"name":"Department of Biology University of Florence  Sesto Fiorentino (FI) Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0293-171X","authenticated-orcid":false,"given":"Chiara","family":"Natali","sequence":"additional","affiliation":[{"name":"Department of Biology University of Florence  Sesto Fiorentino (FI) Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8078-1788","authenticated-orcid":false,"given":"Philine G. 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