A genomic baseline for long-term monitoring of economically important aquatic species in the Netherlands
Aquatic species of economic and ecological importance are increasingly threatened by environmental change, yet their genetic diversity and population structure remain poorly characterised, limiting effective conservation and management. To address this gap, we initiated a multi-species genomic monitoring programme in 2022, targeting key marine and freshwater taxa. A total of 2,420 individuals from 104 locations were sampled across six species: turbot (Scophthalmus maximus), zander (Sander lucioperca), European eel (Anguilla anguilla; both glass eel in the marine environment and adult eel in freshwater environments), blue mussel (Mytilus edulis), flat oyster (Ostrea edulis), and Pacific oyster (Magallana gigas). Using genotyping-by-sequencing (GBS) and SNP arrays, we generated genome-wide SNP datasets to assess population structure, genetic diversity, inbreeding, and relatedness. Among fish species, population structure was generally weak, consistent with high connectivity. However, significant variation in genetic diversity and kinship among localities indicates the presence of distinct source populations that may be critical for maintaining adaptive potential and guiding restoration efforts. In bivalves, cultured populations in the Oosterschelde and Waddenzee were genetically homogeneous, whereas wild populations in Grevelingen and Veerse Meer retained distinct genetic signatures, representing important reservoirs of diversity for conservation and breeding. Together, these results provide a genomic baseline for key aquatic species in the Netherlands and demonstrate the value of coordinated, multi-species genomic monitoring. The identification of genetically distinct and diverse populations offers direct guidance for conservation prioritisation, restoration strategies, and the sustainable management of aquatic genetic resources under ongoing environmental change, in the Netherlands but also applied in other national and transnational monitoring contexts.