Data from: Number of alleles as a predictor of the relative assignment accuracy of STR and SNP baselines for chum salmon

Short tandem repeat (STR) markers, which exhibit many alleles per locus, are commonly used to assign fish to their populations of origin. Single nucleotide polymorphisms (SNPs), which have many technical advantages over STRs, typically exhibit only two alleles per locus. Simulation studies have indicated that number of independent alleles is a good predictor of accuracy of genetic markers for fishery applications. Extant STR baselines for salmon contain hundreds of alleles, and it has been extrapolated that hundreds of SNP markers need to be developed before SNP baselines will compare to these STR baselines. We compared 15 STRs exhibiting 349 independent alleles to 61 SNP assays exhibiting 66 independent alleles for accuracy in assigning to closely related populations of chum salmon. The SNP baseline yielded slightly higher mean accuracies for proportional assignment and comparable accuracies for individual assignment. Overall the SNP baseline performed considerably better, relative to the microsatellite baseline, than predicted based on the number of independent alleles in each baseline. We suggest that this discrepancy is due to the fact that the simulation studies do not capture the impacts of the different strategies commonly employed for discovering and selecting STR and SNP markers.

短串联重复序列（Short Tandem Repeat, STR）标记因每个基因座具有多种等位基因，被广泛应用于鱼类的原产地种群溯源。单核苷酸多态性（Single Nucleotide Polymorphism, SNP）相较STR具备多项技术优势，但每个基因座通常仅存在两种等位基因。已有模拟研究证实，独立等位基因数量是渔业领域遗传标记准确性的可靠预测因子。现有鲑鱼STR基准数据集涵盖数百种等位基因，据推断，需开发数百个SNP标记，方可使SNP基准数据集达到此类STR基准数据集的性能水平。本研究针对将样本溯源至近缘狗鲑（chum salmon）种群的准确性，对比了携带349个独立等位基因的15个STR标记与携带66个独立等位基因的61个SNP检测体系。结果显示，SNP基准数据集在比例归属分析中的平均准确率略高于STR基准，而在个体归属分析中二者准确率相当。总体而言，相较于微卫星（即STR）基准数据集，SNP基准数据集的实际表现远优于基于两类基准独立等位基因数量所预测的结果。我们推测，这一差异源于现有模拟研究未能涵盖开发与筛选STR和SNP标记时常用的不同策略所产生的影响。