Data from: Genetic effects of marine stock enhancement: a case study based on the highly piscivorous Japanese Spanish mackerel

We used a before–after control–impact design to quantify the genetic effects of the large piscivorous Japanese Spanish mackerel (Scomberomorus niphonius) stock enhancement program on wild populations in the Seto Inland Sea. Samples of 1424 wild and 230 hatchery fish collected from 13 sites around Japan were genotyped using five microsatellite markers. A total of 758 wild and 103 hatchery fish were sequenced for the mitochondrial DNA D-loop region. The population structure of Japanese Spanish mackerel was panmictic around Japan. Hatchery fish had significantly lower genetic diversity indices than did wild fish. However, there was no significant change in any of the diversity indices in the Seto Inland Sea, despite the substantial genetic mixing proportion of hatchery-origin genes (7.8%–14.5% from releases in 2001 and 2002), a conclusion supported by simulations. The estimated effective population size was surprisingly small (∼430–970) but stable in the Seto Inland Sea compared with the large census size. A Ryman–Laikre effect was not likely in the Japanese Spanish mackerel.本研究采用前后对照-影响实验设计，量化了大型肉食性日本马鲛（Scomberomorus niphonius）种群增殖放流计划对濑户内海野生种群的遗传影响。研究采集了日本周边13个采样位点的1424尾野生个体与230尾孵化场培育个体，利用5个微卫星标记（microsatellite marker）对其开展基因分型；同时对758尾野生个体与103尾孵化场培育个体的线粒体DNA D-loop区（mitochondrial DNA D-loop region）进行测序。结果显示，日本马鲛的种群结构在日本全域呈现泛交特征；孵化场培育个体的遗传多样性指数显著低于野生个体。尽管2001年与2002年放流的孵化场个体贡献的外源基因在种群中的混合比例达7.8%~14.5%，但濑户内海的各项遗传多样性指数均未出现显著变化，该结论得到了模拟实验的支持。与庞大的实际种群普查数量相比，该海域估算得到的有效种群大小（effective population size）仅为430~970，数值偏小但相对稳定。日本马鲛种群中未出现显著的赖曼-莱克尔效应（Ryman–Laikre effect）。