Data from: Application of genomic offsets to inform freshwater fisheries management under climate change

<b>Abstract</b><br/><p>Genomic tools are becoming increasingly necessary for mitigating biodiversity loss and guiding management decisions in the context of climate change. Freshwater fish species are particularly susceptible to the impacts of changing environments, including kokanee, the resident form of sockeye salmon (<em>Oncorhynchus nerka</em>), which has already been negatively impacted by increases in extreme temperature throughout its distribution. A previous study using whole genome resequencing of wild kokanee stocks identified 1412 environmentally-associated SNPs and demonstrated genomic offset, a measure of climate vulnerability, to be significantly correlated with higher increases in extreme warm temperatures across much of the species’ range in western Canada. Here, we aimed to operationalize this information for fisheries management by first developing a Genotyping-in-Thousands by sequencing (GT-seq) panel populated exclusively with environment-associated SNPs. We then evaluated the robustness of the GT-seq panel relative to the signal in the whole genome resequencing baseline, and demonstrated a novel application of donor and recipient importance (DI/RI) analysis to inform recreational fisheries stocking decisions. We found that a reduced GT-seq panel of 616 SNPs exhibited a significant positive correlation with those calculated from the full set of 1412 SNPs across the climate change scenarios tested; similar results were obtained when adding new reference populations not included in the original whole genome resequencing baseline. The DI/RI analysis revealed clear spatial trends, with populations situated in the warmest regions of southern interior British Columbia (Canada) having the highest probability for successful translocations to different recipient locations to the north. Similarly, candidate recipient lakes for stocking at the centre of the distribution had higher recipient importance values than those located towards the eastern and western range peripheries. Although further refinement is required, pairing targeted genotyping with genomic offset and DI/RI predictions holds great promise for informing freshwater fisheries management moving forward.</p>

<b>摘要</b><br/>&lt;p&gt;在气候变化背景下，基因组工具对于减缓生物多样性丧失、辅助管理决策的必要性与日俱增。淡水鱼类尤其易受环境变化影响，其中包括陆封型红大马哈鱼（<em>Oncorhynchus nerka</em>）——即红大马哈鱼的陆封种群，其整个分布范围均已因极端高温频次增加而受到负面影响。此前一项针对野生陆封红大马哈鱼种群开展全基因组重测序的研究，共鉴定出1412个环境关联单核苷酸多态性位点（Single Nucleotide Polymorphisms, SNPs），并证实基因组偏移（genomic offset，一种气候脆弱性量化指标）与加拿大西部该物种大部分分布区内的极端高温增幅呈显著正相关。本研究旨在将上述研究成果应用于渔业管理实践，首先开发了一套仅包含环境关联SNPs的测序千样本基因分型（Genotyping-in-Thousands by sequencing, GT-seq）分型面板。随后，本研究针对该GT-seq分型面板相对于全基因组重测序基线数据集的信号稳健性开展了评估，并首次将供体与受体重要性（Donor and Recipient Importance, DI/RI）分析应用于休闲渔业放流决策辅助。研究发现，在本次测试的所有气候变化情景下，包含616个SNPs的精简GT-seq分型面板，其计算得到的基因组偏移结果与基于全部1412个SNPs的计算结果呈显著正相关；在加入原始全基因组重测序基线数据集未涵盖的新增参考种群后，也得到了相似的结果。DI/RI分析结果显示出清晰的空间格局：加拿大不列颠哥伦比亚省南部内陆极端高温区域的种群，向北部不同接收地点成功移殖的概率最高。同样，分布中心区域拟作为放流接收点的湖泊，其受体重要性值高于分布范围东西两侧边缘区域的接收点。尽管仍需进一步优化，但将靶向基因分型与基因组偏移及DI/RI预测相结合的研究思路，为未来淡水渔业管理决策提供了极具潜力的辅助方案。&lt;/p&gt;