Data for: Spatial and temporal genetic variation in an exploited reef fish: The effects of exploitation on cohort genetic structure

Many coral reef fishes are fished, often resulting in detrimental genetic effects; however, reef fishes often show unpredictable patterns of genetic variation, which potentially mask the effects of fishing. Our goals were to characterize spatial and temporal genetic variation and determine the effects of fishing on an exploited reef fish, Plectropomus leopardus, Lacepède (the common coral trout). To determine population structure, we genotyped 417 Great Barrier Reef coral trout from four populations sampled in two years (1996 and 2004) at nine microsatellite loci. To test for exploitation effects, we additionally genotyped 869 individuals from a single cohort (ages 3-5) across eight different reefs, including fished and control populations. Genetic structure differed substantially in the two sampled years, with only one year exhibiting isolation by distance. Thus, genetic drift likely plays a role in shaping population genetic structure in this species. Although we found no loss of genetic diversity associated with exploitation, our relatedness patterns show that pulse fishing likely affects populations. Additionally, genetic structure in the cohort samples likely reflected spatial variation in recruitment contributing to genetic structure at the population level. Overall, we show that fishing does impact coral reef fishes, highlighting the importance of repeated widespread sampling to accurately characterize the genetic structure of reef fishes, as well as the power of analysing cohorts to avoid the impacts of recruitment-related genetic swamping. The high temporal and spatial variability in genetic structure, combined with possible selection effects, will make conservation/management of reef fish species complex.

许多珊瑚礁鱼类均面临捕捞压力，常引发有害的遗传效应；然而，礁栖鱼类的遗传变异模式往往难以预测，这可能会掩盖捕捞带来的影响。本研究的目标是解析空间与时间维度上的遗传变异特征，并明确捕捞对被开发的礁栖鱼类豹纹鳃棘鲈（Plectropomus leopardus, Lacepède，俗称珊瑚鳟）的影响。为明确种群结构，研究团队对大堡礁海域的417尾珊瑚鳟进行了基因分型，这些样本采自2个年份（1996年与2004年）的4个种群，检测位点为9个微卫星（microsatellite）位点。为验证捕捞开发的影响，研究团队额外对869尾来自单一龄组（3~5龄）的个体进行了基因分型，这些个体采自8个不同的礁体，涵盖捕捞种群与对照种群。两个采样年份的种群遗传结构存在显著差异，仅其中一个年份呈现出距离隔离效应。由此推测，遗传漂变可能在该物种种群遗传结构的塑造中发挥了作用。尽管未发现与捕捞开发相关的遗传多样性丧失现象，但亲缘关系分析结果表明，脉冲式捕捞可能会对种群产生影响。此外，龄组样本中的遗传结构，大概率反映了补充过程的空间变异，而这类变异会在种群层面促成遗传结构的形成。综上，本研究证实捕捞确实会对珊瑚礁鱼类产生影响，这凸显了开展大范围重复采样以精准解析礁栖鱼类遗传结构的重要性，同时也证明了通过分析龄组样本，能够规避与补充相关的遗传淹没效应带来的干扰。种群遗传结构存在较高的时空变异性，加之可能存在的选择效应，将使得礁栖鱼类的保护与管理工作更为复杂。