Genomics outperforms genetics to manage mistakes in fisheries stocking of threatened species.

Hatchery production and fisheries stocking is a widespread and high profile management practice because it allows recreational fisheries to continue in threatened species. Humanmediated transfer of fish across the geographic boundaries of intraspecies lineages or closely related species can cause introgression and outbreeding depression. Hybridization can be difficult to detect due to limited morphological differences among close lineagesand the relatively low power of traditional genetic datasets. Here we showcase the use of genomic techniques to detect admixture of the economically important and threatened golden perch (<i>Macquaria ambigua</i>) in the Murray-Darling Basin, southeast Australia. We detected admixture through a genome-wide dataset of 6,862 single nucleotide polymorphisms (SNPs) across 174 Murray-Darling sourced fish and 15 fish from each of two neighbouring basins: the Lake Eyre and Fitzroy basins. Individuals with partial ancestry from both neighboring basins were detected using genomics throughout the Murray-Darling, suggesting the release of individuals and introgression into the Murray- Darling Basin. Importantly, a traditional microsatellite dataset was unreliable for identifying admixed individuals. The SNP-detected admixed individuals were also found in Murray-Darling impoundments, where fish are solely sourced from government-managed hatcheries, suggesting that some broodstock in hatcheries might have non-endemic ancestry. Stocking programs for golden perch release over one million fingerlings each year, and so could impact the genetic variation in the wild. We advocate for using genomics to check the ancestry of broodstock and for increasing collaboration between managers and academics as done here to better integrate the power of genomics into biodiversity management and conservation.

孵化场繁育与渔业增殖放流是一项应用广泛且备受关注的渔业管理实践，其可保障受威胁物种的休闲渔业活动得以延续。人类介导的鱼类跨种内谱系或近缘物种地理边界的转移，可能引发基因渐渗（introgression）与远交衰退（outbreeding depression）。由于近缘谱系间形态差异有限，且传统遗传数据集的检测效力相对不足，杂交现象往往难以被检出。本研究展示了基因组技术的应用，用于在澳大利亚东南部墨累-达令盆地（Murray-Darling Basin）中检测兼具经济价值且受威胁的黄金鲈（golden perch，学名*Macquaria ambigua*）的遗传混合现象。我们通过一套涵盖6862个全基因组单核苷酸多态性（single nucleotide polymorphisms, SNPs）的数据集完成了遗传混合现象的检测：该数据集包含174尾采自墨累-达令盆地的鱼类，以及分别采自两个邻近流域——艾尔湖流域（Lake Eyre Basin）与菲茨罗伊流域（Fitzroy Basin）的各15尾鱼类。基因组分析显示，墨累-达令盆地全境均存在携带来自两个邻近流域部分祖先血统的个体，这提示存在外来个体放流并引发基因渐渗进入该盆地的情况。值得注意的是，传统微卫星（microsatellite）数据集无法可靠地识别遗传混合个体。通过单核苷酸多态性检测出的遗传混合个体，同样存在于墨累-达令盆地的蓄水水体（impoundments）中——该类水体中的鱼类均源自政府管理的孵化场，这提示部分孵化场的亲鱼（broodstock）可能携带非本地血统。黄金鲈的增殖放流计划每年会放流超100万尾仔鱼（fingerlings），因此可能对野生种群的遗传变异造成影响。我们倡议采用基因组技术检测亲鱼的血统，并推动管理者与学者间的协作（如同本研究所开展的工作），以更好地将基因组技术的优势融入生物多样性管理与保护实践中。