Lynch M, Milligan B G
Department of Biology, University of Oregon, Eugene 97403.
Mol Ecol. 1994 Apr;3(2):91-9. doi: 10.1111/j.1365-294x.1994.tb00109.x.
Recent advances in the application of the polymerase chain reaction make it possible to score individuals at a large number of loci. The RAPD (random amplified polymorphic DNA) method is one such technique that has attracted widespread interest. The analysis of population structure with RAPD data is hampered by the lack of complete genotypic information resulting from dominance, since this enhances the sampling variance associated with single loci as well as induces bias in parameter estimation. We present estimators for several population-genetic parameters (gene and genotype frequencies, within- and between-population heterozygosities, degree of inbreeding and population subdivision, and degree of individual relatedness) along with expressions for their sampling variances. Although completely unbiased estimators do not appear to be possible with RAPDs, several steps are suggested that will insure that the bias in parameter estimates is negligible. To achieve the same degree of statistical power, on the order of 2 to 10 times more individuals need to be sampled per locus when dominant markers are relied upon, as compared to codominant (RFLP, isozyme) markers. Moreover, to avoid bias in parameter estimation, the marker alleles for most of these loci should be in relatively low frequency. Due to the need for pruning loci with low-frequency null alleles, more loci also need to be sampled with RAPDs than with more conventional markers, and some problems of bias cannot be completely eliminated.
聚合酶链反应应用方面的最新进展使得对个体在大量基因座上进行评分成为可能。随机扩增多态性DNA（RAPD）方法就是这样一种引起广泛关注的技术。由于显性导致缺乏完整的基因型信息，利用RAPD数据进行群体结构分析受到阻碍，因为这会增加与单个基因座相关的抽样方差，并在参数估计中引入偏差。我们给出了几个群体遗传参数（基因和基因型频率、群体内和群体间杂合度、近亲繁殖程度和群体细分以及个体亲缘关系程度）的估计量及其抽样方差的表达式。虽然对于RAPD来说似乎不可能有完全无偏的估计量，但我们提出了几个步骤，以确保参数估计中的偏差可以忽略不计。与共显性（RFLP、同工酶）标记相比，当依赖显性标记时，为达到相同程度的统计功效，每个基因座大约需要多抽样2至10倍的个体。此外，为避免参数估计中的偏差，这些基因座中大多数的标记等位基因频率应相对较低。由于需要剔除具有低频无效等位基因的基因座，与使用更传统的标记相比，使用RAPD时也需要抽样更多的基因座，并且一些偏差问题无法完全消除。
