Genome-wide diversity and Pinna rudis admixture reveal Thau lagoon as a conservation reservoir for the collapsing fan mussel Pinna nobilis

The conservation of Pinna nobilis increasingly depends on the Thau lagoon population, which has remained demographically stable and largely escaped the mass mortality events (MMEs) that have devastated open-sea populations across the Mediterranean. Here we assess the genetic diversity in the Thau and Diane lagoons (France), and characterize the genome-wide admixture with Pinna rudis . Mitochondrial diversity in Thau, especially at protein-coding genes, closely mirrors that previously documented in open-sea populations, while comparisons of historical and contemporary samples reveal differences in 16S rRNA haplotype composition that are consistent with recent erosion of mitochondrial diversity. Extended mitochondrial and nuclear SNP data confirm and refine earlier evidence of successive historical population expansions. We also report the first evidence of mitochondrial heteroplasmy in P. nobilis , identified in an individual carrying both P. nobilis and P. rudis mitogenomes. In contrast, all five confirmed F1 hybrids retained only P. nobilis mitogenomes, indicating asymmetric mitochondrial inheritance during hybridization. Nuclear genomic analyses revealed low but widespread admixture with P. rudis , consistent with a history of limited yet persistent gene flow. Candidate introgressed regions were enriched for genes involved in innate immune recognition and signalling, apoptosis, cell adhesion, extracellular matrix organization, and proteostasis, identifying pathways potentially relevant to host resilience that warrant functional investigation. However, the absence of complete disease resistance among admixed individuals indicates that any potential contribution of these regions to disease resilience is likely to be modest and context dependent. These results show that P. nobilis retains substantial evolutionary potential despite its recent demographic collapse, and that the standing genetic diversity and admixture preserved in the Thau lagoon could constitute valuable resources for conservation. Future studies linking genomic variation with individual infection outcomes will be essential to determine whether the identified candidate variants directly contribute to disease tolerance and resistance.