Data from: Using dense locality sampling resolves the subtle genetic population structure of the dispersive fish species Plecoglossus altivelis

In dispersive species with continuous distributions, genetic differentiation between local populations is often absent or subtle and thus difficult to detect. To incorporate such subtle differentiation into management plans, it may be essential to analyse many samples from many localities using adequate numbers of high-resolution genetic markers. Here, we evaluated the usefulness of dense locality sampling in resolving genetic population structure in the ayu (Plecoglossus altivelis), a dispersive fish important in Japanese inland fisheries. Genetic variability in, and differentiation between, ayu populations around the Japan–Ryukyu Archipelago were investigated in 4746 individuals collected from 120 localities by genotyping 12 microsatellite markers. These individuals represented the two subspecies of ayu, namely the Ryukyuan subspecies (Plecoglossus altivelis ryukyuensis) and both amphidromous and landlocked forms of the nominotypical subspecies (P. a. altivelis) along the archipelago. We successfully detected an absence of genetic differentiation within the landlocked form and subtle but significant differentiation and clear geographic patterns of genetic variation among populations of the amphidromous form, which had been considered genetically homogeneous. This suggests that dense locality sampling effectively resolves subtle differences in genetic population structure, reducing stochastic deviation in the detection of genetic differentiation and geographic patterns in local populations of this dispersive species. Resampling analyses based on empirical data sets clearly demonstrate the effectiveness of increasing the number of locality samples for stable and reliable estimations of genetic fixation indices. The genetic population structure observed within the amphidromous form provides useful information for identifying management or conservation units in ayu.

对于具有连续分布的扩散型物种而言，局域种群间的遗传分化往往缺失或极为微弱，因此难以被精准检测。为将这类微弱的遗传分化纳入物种管理方案，通常需采用足量高分辨率遗传标记，对多采样点的大量个体开展遗传分析。本研究以日本内陆渔业重要的扩散型鱼类香鱼（ayu，*Plecoglossus altivelis*）为研究对象，评估了高密度局域采样在解析其遗传群体结构中的应用价值。我们采集了日本-琉球群岛周边120个采样点的4746个香鱼个体，通过对12个微卫星标记（microsatellite markers）进行基因分型，分析了该区域香鱼种群的遗传变异水平及种群间的遗传分化。本次采样的个体涵盖香鱼的两个亚种：琉球亚种（*Plecoglossus altivelis ryukyuensis*），以及分布于该群岛的指名亚种（*P. a. altivelis*）的洄游型与陆封型两种生态型。研究结果显示，陆封型香鱼种群不存在遗传分化；而此前被认为遗传均质的洄游型香鱼种群，实则存在微弱但显著的遗传分化，且呈现出清晰的遗传变异地理格局。这表明高密度局域采样可有效解析扩散型物种局域种群间的细微遗传结构差异，降低遗传分化检测及地理格局分析中的随机偏差。基于经验数据集的重采样分析明确证实，增加采样点数量可实现遗传固定指数（genetic fixation indices）的稳定可靠估计。本次研究在洄游型香鱼种群中揭示的遗传群体结构，可为香鱼的管理单元与保护单元的确定提供重要参考依据。