A novel measure of genetic distance for highly polymorphic tandem repeat loci.
A novel measure of genetic distance for highly polymorphic tandem repeat loci.
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DOI：
10.1093/oxfordjournals.molbev.a040268
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发表时间：
1995-09
影响因子：
10.7
通讯作者：
M. Shriver;Li Jin;E. Boerwinkle;Ranjan Deka;E. Ferrell;Ranajit;Chakraborty
中科院分区：
文献类型：
--
作者：
M. Shriver;Li Jin;E. Boerwinkle;Ranjan Deka;E. Ferrell;Ranajit;Chakraborty
遗传距离测量是种群或物种之间关联性的指标，有助于重建这些种群之间的历史和系统发育关系。传统的遗传距离测量被用来分析生化和血清学的多态，这些系统通常表现出有限的变异性。然而，这些传统的遗传距离测量方法不足以分析某些类型的可变数目串联重复序列(VNTR)基因座，这些基因座具有比传统遗传标记更多的等位基因和更高的杂合度水平。在这些基因座观察到的较高杂合性水平上，遗传距离的标准测量是非线性的，并且没有考虑到高变量基因座的突变机制。我们开发了一种遗传距离的测量方法，Dsw，它适用于高度多态的DNA基因座的分析。通过对不同种群的计算机模拟，我们发现Dsw符合线性，其方差在大小上与传统的遗传距离度量相似。对模拟人类种族分化所生成的系统发育树的比较表明，使用DSW方法制备的树的分枝长度与模型树更接近，而不是使用其他方法生成的树。最后，我们利用14个微卫星和STR基因座重建了8个人类群体之间的关系，从而证明了DSW在进化分析中的适用性。使用DSW生成的系统发育树不同于用传统方法构建的树，更好地反映了非洲人和非非洲人之间有充分记录的古代差异。
Genetic distance measures are indicators of relatedness among populations or species and are useful for reconstructing the historic and phylogenetic relationships among such groups. Classical measures of genetic distance were developed to analyze biochemical and serological polymorphisms, systems which generally show limited variability. However, these traditional measures of genetic distance are inadequate for the analysis of certain classes of variable number tandem repeat (VNTR) loci, which have a larger number of alleles and higher levels of heterozygosity than traditional genetic markers. At the higher levels of heterozygosity observed at these loci, the standard measures of genetic distance are nonlinear and do not account for the mutational mechanisms of hypervariable loci. We have developed a measure of genetic distance, DSW, which is appropriate for the analysis of highly polymorphic DNA loci. Using computer simulations of diverging populations, we show that DSW conforms to linearity and that the variance is similar in magnitude to traditional measures of genetic distance. Comparisons of phylogenetic trees derived from the simulated divergence of human racial groups demonstrate that the branch lengths of trees prepared using DSW are more similar to the model tree than those generated using other measures. Finally, we demonstrate the applicability of DSW to evolutionary analysis by reconstructing the relationships among eight human populations using 14 microsatellite and STR loci. The phylogenetic trees generated using DSW are different from trees constructed with traditional measures and better reflect the well-documented ancient divergence of African and non-African populations.