Genomics-enabled mixed-stock analysis uncovers intraspecific migratory complexity and detects unsampled populations in a harvested fish

Population contributions to annual harvests provide key insights to conservation, especially in migratory species that return to specific reproductive areas and may establish genetically distinct populations. In this context, genetic stock identification (GSI) requires reference samples from source populations, yet sampling might be challenging as reproductive areas could be remote and/or unknown. To investigate intraspecific variation in walleye (Sander vitreus) populations harvested in two large lakes in northern Quebec, we used genotyping-by-sequencing data to develop a panel of 336 single nucleotide polymorphisms. We then genotyped 1465 fish and assessed individual migration distances from GPS records. Samples were assigned to a source population using two methods, one requiring allele frequencies of known populations (RUBIAS) and the other without prior knowledge (STRUCTURE). Individual assignments to a known population reached 93% consistency between both methods in the main lake where we identified all five major source populations. However, the analyses also revealed up to three small unsampled populations. Furthermore, populations were characterized by large differences in average migration distance. In contrast, assignment consistency reached 99% in the neighboring lake and walleye were assigned with high confidence to two populations having a similar distribution throughout the lake. The complex population structure and migration patterns in the main lake suggest a more heterogenous habitat and thus, greater potential for local adaptation. This study highlights how combining analytical approaches can inform the robustness of GSI results in a given system and detect intraspecific diversity and complexity relevant for conservation.

年度捕捞的种群贡献可为物种保护提供关键见解，尤其是对于那些返回特定繁殖区域、可能形成遗传分化种群的洄游物种而言。在此背景下，遗传种群识别（genetic stock identification, GSI）需要来自源种群的参考样本，但由于繁殖区域可能偏远甚至未知，采样往往颇具挑战。为研究魁北克北部两座大型湖泊中捕捞的白斑梭鲈（Sander vitreus）种群的种内变异，我们利用测序分型（genotyping-by-sequencing）数据开发了包含336个单核苷酸多态性位点的分型面板。随后我们对1465尾个体进行了基因分型，并基于GPS记录估算了个体的洄游距离。我们采用两种方法将样本归至源种群：一种需要已知种群的等位基因频率（RUBIAS软件），另一种无需预先已知信息（STRUCTURE软件）。在我们已识别全部5个主要源种群的主湖区中，两种方法对已知种群的个体归属判定一致性达93%。但分析结果同时显示，该区域最多存在3个未被采样的小型种群。此外，不同种群的平均洄游距离差异显著。与之形成对比的是，邻近湖泊的归属判定一致性达99%，且该湖中的白斑梭鲈可被高置信度地归为两个种群，二者在湖内的分布范围相似。主湖区复杂的种群结构与洄游模式表明其生境异质性更强，因此种群局部适应的潜力也更高。本研究证实，联合多种分析方法可提升特定系统中GSI结果的稳健性，并检测出与保护相关的种内多样性与种群复杂性。