Background
Native fish populations in the Murray-Darling Basin have declined since European colonisation. Many species, including the iconic Murray cod (Maccullochella peelii) and golden perch (Macquaria ambigua), now depend on intensive management activities such as stocking. The Murray-Darling Basin Plan was developed to balance human water needs against environmental requirements, with native fish population recovery serving as a key measure of success. FishGen (Murray-Darling Basin Fisheries Genetic Resources Program) was initially established to evaluate environmental flow outcomes by distinguishing hatchery-stocked from wild-bred fish. However, FishGen has evolved beyond this original scope, and now provides critical support for genetic management of hatchery broodstock, informing breeding strategies that minimise inbreeding, and offering insights into stocked fish movement patterns to support adaptive fisheries management across the Basin.
Methods
FishGen employs a genomic approach to managing Basin-scale stocking activities, involving genotyping of both hatchery broodstock and wild-caught samples. The comprehensive database currently comprises 9,973 samples from hatchery and wild populations, including 6,056 genotyped at thousands of genome-wide single nucleotide polymorphism (SNP) markers. We use parentage analyses to identify stocked fish by assigning wild-caught juveniles to hatchery parents. Kinship and individual inbreeding analyses assess relatedness and inbreeding levels amongst hatchery broodstock, enabling recommendations for breeding strategies that maximise genetic diversity. Spatial analyses calculate minimum distances between inferred stocking locations and eventual sampling locations of identified stocked fish to infer movement patterns.
Results
To date, 226 wild-caught juveniles have been assigned at least one hatchery parent, with numbers expected to increase as more broodstock are genotyped. Moderate numbers of related and inbred hatchery broodstock were identified, and hatchery-specific recommendations are expected to significantly improve genetic diversity and health of stocked fish. Initial movement analyses indicated stocked fish are moving substantial distances (up to 360 km).
Conclusion
FishGen demonstrates the value of long-term genomic monitoring for conservation and fisheries management. This multi-institutional, collaborative project is improving native fish genetic health by informing hatchery practices, adaptive stocking strategies, and conservation policy, while helping optimise environmental water management in the Murray-Darling Basin. Long-term genetic monitoring continuation is crucial for maintaining sustainable, diverse native fish populations under changing environmental conditions.