1. The annual release of hatchery-bred larvae into naturally reproducing fish populations (enhancement stocking) is used commonly to increase native populations of fish where recruitment is presumably limited. Despite the widespread practice of enhancement stocking, its efficacy and sustainability are seldom monitored.
2. We used 1264 amplified fragment length polymorphism markers from 23 vendace Coregonus albula populations in northern Germany to determine whether stocking from external sources contributes to the catch in target populations and leads to hybridization between native and stocked fish. We examined the effects of historical factors as well as recent stocking effects by combined analysis of population-based equilibrium between migration and drift (IBD) and individual-based assessments of parentage and hybridization using Bayesian methods.
3. Stocking success and hybridization rates differed between north-east and north-west German lakes and corresponded negatively to geographical and genetic distances between source and target populations. When populations were compared with and without stocked individuals, we calculated that stocking reduced pairwise genetic distances by c. 11%.
4. Lakes stocked with genetically similar fish exhibited direct recapture rates of 4% and increased levels of hybridization, leading to genetic homogenization. For lakes in which a genetically more distant source was stocked, recapture rates of stocked fish were 0% and hybridization was lower, with target populations remaining genetically distinct.
5. Synthesis and applications. Our results show that stocking from a genetically similar source can disrupt historical genetic differentiation and, possibly, local adaptation, whereas stocking from a genetically distant source only marginally contributed to the native populations and led to no detectable homogenization. The fitness disadvantage of fish stocked from distant sources therefore appears to form a natural impediment to genetic homogenization.