Abstract
Genetic diversity is a fundamental aspect of biodiversity, yet it is rarely assessed and monitored in conservation practice. 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-resolution population genomics study of all Anodonta species in Switzerland, with a focus on two species with contrasting reproductive strategies. After generating draft genomes of the hermaphroditic Anodonta cygnea and the gonochoric Anodonta anatina, we performed whole-genome resequencing of 421 individuals collected in 31 localities. While A. anatina 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 A. anatina populations north and south of the Alps suggests a putative undescribed Anodonta species in the Ticino area. Furthermore, we detected hybridisation between A. cygnea and A. exulcerata, indicating genomic permeability between these species. In addition, genomic data suggested facultative selfing in A. cygnea, leading to a marked reduction in genetic diversity, increased population structure and inbreeding and a decline in effective population size compared to the outcrossing A. anatina. 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.