Impact of amplified fragment length polymorphism size homoplasy on the estimation of population genetic diversity and the detection of selective loci
Impact of amplified fragment length polymorphism size homoplasy on the estimation of population genetic diversity and the detection of selective loci
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DOI：
10.1534/genetics.107.083246
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发表时间：
2008-05-01
期刊：
影响因子：
3.3
通讯作者：
Rolan-Alvarez, Emilio
中科院分区：
文献类型：
--
作者：
Caballero, Armando;Quesada, Humberto;Rolan-Alvarez, Emilio
AFLP标记正在成为进化遗传学、生态学和遗传资源保护领域最流行的遗传分析工具之一。该技术将高信息内容和保真度与进行全基因组扫描的可能性结合起来。然而，该技术的一个潜在问题是具有相同电泳迁移率的手缺乏同源性，即所谓的片段大小同质性。我们进行了一项理论分析，旨在量化 AFLP 同质性对在具有亚种群间迁移的结构化有限种群模型中中性种群内和中性种群间遗传多样性估计的影响。我们还研究了当前使用的方法（DFDIST 软件）的性能，该方法通过比较遗传分化和显性分子标记杂合性来检测选择性位点，以及 AFLP 同质性对其有效性的影响。结果表明，同质性产生的偏差是：（1）高估了决定手存在的等位基因频率，（2）低估了亚群之间的分化程度，以及（3）高估或低估了杂合性，具体取决于标记的等位基因频率。通过减少每个引物组合分析的片段数量，可快速消除同质性的影响。然而，对于每个打印机组合大约 50-100 个片段，预期杂合性（Lip 为 15-25%）可能会出现显着偏差。 DFDIST 软件从显性标记中检测选择性基因座的性能高度依赖于基因组中选择性基因座的数量及其平均效应、分析中选择使用的遗传分化的估计以及用于检测异常值的临界界限概率。总体而言，结果表明应谨慎使用该软件。 AFLP 同质性可使检测选择性位点的能力降低高达 15%。
AFLP markers are becoming one of the most popular tools for genetic analysis in the fields of evolutionary genetics and ecology and conservation of genetic resources. The technique combines a high-information content and fidelity with the possibility of carrying out genomewide scans. However, a potential problem with this technique is the lack of homology of hands with the same electrophoretic mobility, what is known as fragment-size homoplasy. We carried out a theoretical analysis aimed at quantifying the impact of AFLP homoplasy on the estimation of within- and between-neutral population genetic diversity in a model of a Structured finite population with migration among subpopulations. We also investigated the performance of a Currently used method (DFDIST software) to detect selective loci from the comparison between genetic differentiation and heterozygosis of dominant molecular markers, as well as the impact of AFLP homoplasy on its effectiveness. The results indicate that the biases produced by homoplasy are: (1) an overestimation of the frequency of the allele determining the presence of the hand, (2) an underestimation of the degree of differentiation between subpopulations, and (3) an overestimation or underestimation of the heterozygosis, depending on the allele frequency of the markers. The impact of homoplasy is quickly diminished by reducing the number of fragments analyzed per primer combination. However, substantial biases on the expected heterozygosity (Lip to 15-25%) may occur with similar to 50-100 fragments per printer combination. The performance of the DFDIST software to detect selective loci from dominant markers is highly dependent on the number of selective loci in the genome and their average effects, the estimate of genetic differentiation chosen to be used in the analysis, and the critical bound probability used to detect outliers. Overall, the results indicate that the software should be used with caution. AFLP homoplasy can produce a reduction of up to 15% in the power to detect selective loci.