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）标记在每个基因位点上具有多等位基因特性，常被用于鱼类的原产地种群溯源。单核苷酸多态性（Single nucleotide polymorphisms, SNPs）相较STR标记具备诸多技术优势，但通常每个位点仅存在两种等位基因。已有模拟研究表明，独立等位基因数量是预测渔业应用中遗传标记准确率的可靠指标。当前已有的大麻哈鱼STR遗传基线包含数百个等位基因，据此推测，若要使SNP遗传基线的性能媲美此类STR基线，需开发数百个SNP标记。本研究对比了包含349个独立等位基因的15个STR标记体系，与包含66个独立等位基因的61个SNP检测体系，在大麻哈鱼近缘种群溯源中的准确率。结果显示，SNP基线在群体比例分配的平均准确率上略占优势，而在个体溯源分配的准确率上二者表现相当。总体而言，相较微卫星（STR）基线，SNP基线的实际表现远优于基于两者独立等位基因数量所预测的结果。我们认为这一差异源于现有模拟研究未涵盖STR与SNP标记在发现及筛选环节通常采用的不同策略所带来的影响。