Data from: Ecological disturbance influences adaptive divergence despite high gene flow in golden perch (Macquaria ambigua): implications for management and resilience to climate change

Populations that are adaptively divergent but maintain high gene flow may have greater resilience to environmental change as gene flow allows the spread of alleles that have already been tested elsewhere. In addition, populations naturally subjected to ecological disturbance may already hold resilience to future environmental change. Confirming this necessitates ecological genomic studies of high dispersal, generalist species. Here we perform one such study on golden perch (Macquaria ambigua) in the Murray-Darling Basin (MDB), Australia using a genome-wide SNP dataset. The MDB spans across arid to wet and temperate to sub-tropical environments, with low to high ecological disturbance in the form of low to high hydrological variability. We found high gene flow across the basin and three populations with low neutral differentiation. Genotype-environment association analyses detected adaptive divergence predominantly linked to an arid region with highly variable riverine flow, and candidate loci included functions related to fat storage, stress and molecular or tissue repair. The high connectivity of golden perch in the MDB will likely allow locally adaptive traits in its most arid and hydrologically variable environment to spread and be selected in localities that are predicted to become arid and hydrologically variable in future climates. High connectivity in golden perch is likely due to their generalist life history and efforts of fisheries management. Our study adds to growing evidence of adaptation in the face of gene flow, and highlights the importance of considering ecological disturbance and adaptive divergence in biodiversity management.

尽管存在适应性分化但仍维持高水平基因流的种群，对环境变化的适应力往往更强——因为基因流能够促进已在其他环境中经受考验的等位基因在种群间传播。此外，天然经受生态扰动的种群，往往已具备应对未来环境变化的适应潜力。要验证这一观点，需针对高扩散能力的泛化物种开展生态基因组学研究。本研究便以澳大利亚墨累-达令盆地（Murray-Darling Basin, MDB）的黄金鲈（*Macquaria ambigua*）为研究对象，基于全基因组单核苷酸多态性（Single Nucleotide Polymorphism, SNP）数据集开展相关分析。墨累-达令盆地涵盖了从干旱到湿润、从温带到亚热带的多种生境类型，水文动态变异程度跨度极大，对应着程度不等的生态扰动。研究结果显示，该流域内种群间基因流水平整体较高，且存在三个中性遗传分化程度极低的种群类群。基因型-环境关联分析（Genotype-Environment Association Analysis）结果表明，适应性分化主要与水文动态变异极强的干旱区域相关；候选位点所关联的基因功能涉及脂肪储存、应激响应以及分子或组织修复相关通路。墨累-达令盆地内黄金鲈的高种群连通性，或将使得其在最干旱且水文动态变异最强的生境中演化出的本地适应性性状，能够在未来气候预测中将趋于干旱且水文动态变异加剧的区域快速传播并受到正向选择。黄金鲈种群的高连通性，大概率源于其泛化的生活史策略以及渔业管理部门的保护管理举措。本研究为“基因流背景下仍可发生适应性分化”这一论点补充了新的实证依据，同时强调了在生物多样性管理中纳入生态扰动与适应性分化考量的重要性。