Adams Rachel I, Brown Kyle M, Hamilton Matthew B
Georgetown University, Department of Biology, Reiss Sciences Building 406, 37th and O Streets NW, Washington, DC 20057-1229 USA.
Mol Ecol. 2004 Sep;13(9):2579-88. doi: 10.1111/j.1365-294X.2004.02256.x.
Microsatellite allelic states are determined by electrophoretic sizing of polymerase chain reaction fragments to define electromorphs. Numerous studies have documented that identical microsatellite electromorphs are potentially heterogeneous at the DNA sequence level, a phenomenon called electromorph size homoplasy. Few studies have examined the impact of electromorph size homoplasy on estimates of population genetic parameters. We investigated the frequency of microsatellite electromorph size homoplasy for 12 loci in the tropical tree Corythophora alta and 11 loci in the anadromous fish Morone saxatilis by sequencing 14-23 homozygotes per locus sampled from multiple populations for a total of 453 sequences. Sequencing revealed no homoplasy for M. saxatilis loci. Seven C. alta loci exhibited homoplasy, including single and compound repeat motifs both with and without interruptions. Between 12.5 and 42.9% of electromorphs sampled per locus showed size homoplasy. Two methods of correction for homoplasy in C. alta generally produced little or no change in single-locus estimates of RST, except for two loci in which some additional differentiation among populations was revealed. Twelve-locus estimates of RST (including the seven loci corrected for homoplasy) were slightly greater than estimates from uncorrected data, although the 95% confidence intervals overlapped. The frequency of methodological errors such as clerical mistakes or sample mislabelling per genotype scored was estimated at 5.4 and 7.3% for C. alta and M. saxatilis, respectively. Simulations showed that the increase in RST produced by homoplasy correction was only slightly larger than variation in RST estimates expected to be caused by methodological errors.
微卫星等位基因状态通过聚合酶链反应片段的电泳大小测定来确定，以定义电形态。大量研究表明，相同的微卫星电形态在DNA序列水平上可能是异质的，这种现象称为电形态大小同塑性。很少有研究考察电形态大小同塑性对群体遗传参数估计的影响。我们通过对从多个群体中每个位点采样的14 - 23个纯合子进行测序，共获得453个序列，研究了热带树木高柯氏豆12个位点和溯河产卵鱼类条纹鲈11个位点的微卫星电形态大小同塑性频率。测序结果显示条纹鲈位点没有同塑性。高柯氏豆的7个位点表现出同塑性，包括有和没有中断的单重复和复合重复基序。每个位点采样的电形态中有12.5%至42.9%表现出大小同塑性。高柯氏豆中两种校正同塑性的方法通常在RST的单位点估计中几乎没有或没有产生变化，除了两个位点，在这两个位点中揭示了群体间一些额外的分化。RST的12位点估计值（包括校正了同塑性的7个位点）略高于未校正数据的估计值，尽管95%置信区间重叠。对于高柯氏豆和条纹鲈，每个基因型评分中诸如文书错误或样本错误标记等方法错误的频率分别估计为5.4%和7.3%。模拟表明，同塑性校正导致的RST增加仅略大于预期由方法错误引起的RST估计值的变化。
