Abstract
Variation in the mitochondrial DNA transcriptional control region sequence was investigated in wild and hatchery‐released red sea bream Pagrus major from Kagoshima Bay, where an extensive hatchery‐release programme has been conducted for >30 years. The programme has successfully augmented commercial catches in the bay (released juveniles have been produced from the captive broodstock, repeatedly used over multiple generations). Samples were also obtained from outside the bay, where limited stocking has occurred. Genetic diversity indices measured as number of haplotypes, haplotype richness, haplotype diversity and nucleotide diversity were lower in hatchery‐released fish than in wild fish. Genetic differences in wild fish from the bay, especially in the inner bay, compared with fish from outside the bay were detected in terms of decreased genetic diversity indices and changed haplotype frequencies. Unbiased population pair‐wise F ST estimates based on an empirical Bayesian method, however, revealed low genetic differentiation between samples from the bay and its vicinity. Mixed stock identification analyses estimated the proportion of hatchery‐released fish in wild populations in the inner and central bays at 39·0 and 8·7%, respectively, although the precision of the estimates was very low because of the small genetic differentiation between populations and relatively small sample sizes. Hence, the long‐term extensive hatchery release programme has affected the genetic diversity of wild populations in the bay; however, the genetic effects were low and appeared to remain within the bay.