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）标记每个位点携带多个等位基因，目前被广泛应用于鱼类个体的种群归源分析。单核苷酸多态性（Single nucleotide polymorphisms, SNPs）虽相较于STRs具备多项技术优势，但每个位点通常仅存在两种等位基因。已有模拟研究表明，独立等位基因数量可有效预测遗传标记在渔业应用中的分型准确性。当前已有的鲑鱼STR基准数据集包含数百个等位基因，据此可推断，需开发数百个SNP标记，方能使SNP基准数据集的性能比肩上述STR基准数据集。本研究针对大麻哈鱼（chum salmon）的近缘种群归源准确性，对比了包含349个独立等位基因的15个STR标记与包含66个独立等位基因的61个SNP检测体系的性能表现。在比例归源分析中，SNP基准数据集的平均准确性略高于STR基准数据集；而在个体归源分析中，二者的准确性相当。整体而言，相较于微卫星基准数据集，SNP基准数据集的实际性能远超基于二者独立等位基因数量所预测的结果。本研究认为，该差异源于现有模拟研究未纳入STR与SNP标记在发现及筛选流程中所采用的不同策略所产生的影响。