Reliability assessment of null allele detection: inconsistencies between and within different methods

Microsatellite loci are widely used in population genetic studies, but the presence of null alleles may lead to biased results. Here, we assessed five methods that indirectly detect null alleles and found large inconsistencies among them. Our analysis was based on 20 microsatellite loci genotyped in a natural population of Microtus oeconomus sampled during 8 years, together with 1200 simulated populations without null alleles, but experiencing bottlenecks of varying duration and intensity, and 120 simulated populations with known null alleles. In the natural population, 29% of positive results were consistent between the methods in pairwise comparisons, and in the simulated data set, this proportion was 14%. The positive results were also inconsistent between different years in the natural population. In the null-allele-free simulated data set, the number of false positives increased with increased bottleneck intensity and duration. We also found a low concordance in null allele detecti...微卫星位点（microsatellite loci）被广泛应用于群体遗传学研究，但无效等位基因（null alleles）的存在可能导致研究结果产生偏倚。本研究对五种间接检测无效等位基因的方法进行了评估，发现各方法间存在较大差异。本分析基于8年间采样获得的根田鼠（Microtus oeconomus）自然种群的20个微卫星位点基因分型数据，同时纳入1200个无无效等位基因但经历不同时长与强度种群瓶颈的模拟种群，以及120个携带已知无效等位基因的模拟种群。在自然种群中，两两比较的阳性结果里仅有29%在各方法间保持一致；而在模拟数据集内，该占比仅为14%。自然种群的阳性结果在不同采样年份间也存在不一致性。在无无效等位基因的模拟数据集里，假阳性数量随种群瓶颈强度与时长的增加而上升。本研究还发现无效等位基因检测的一致性程度较低……