A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation.
A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation.
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DOI：
10.1093/genetics/132.2.619
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发表时间：
1992-10
期刊：
影响因子：
3.3
通讯作者：
Alan R. Templeton;K. Crandall;C. Sing
中科院分区：
文献类型：
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作者：
Alan R. Templeton;K. Crandall;C. Sing
我们以前开发了一个分支的方法来确定与显着的表型偏差相关的限制性内切酶图谱或DNA测序定义的单倍型的子集。我们的方法仅限于很少发生重组的DNA片段。在这种情况下，可以从限制性位点或序列数据构建分支图，其代表与观察到的单倍型相关的进化步骤。进化树用于定义嵌套统计设计，以识别与显著表型偏差相关的突变步骤。这一策略背后的核心假设是，任何未被发现的突变引起的表型效应是嵌入在相同的进化历史，是由分支图表示。这种方法的力量取决于人们对用来进行推论的特定分支图的信心。在本文中，我们提出了一种策略，用于估计一组的分支图是一致的，与一个特定的样品的限制性位点或核苷酸序列数据，包括重组的可能性。我们首先评估的限制，简约在构建分支图。一旦确定了这些限制，我们就会构建与这些限制一致的简约和非简约分支图集。我们的估计程序还识别了重组产物的候选单倍型。如果重组是广泛的，我们的算法将DNA区域细分为两个或更多个子部分，每个子部分很少或没有内部重组。我们应用此估计程序的三个数据集，以说明不同程度的分支图的模糊性和重组。
We previously developed a cladistic approach to identify subsets of haplotypes defined by restriction endonuclease mapping or DNA sequencing that are associated with significant phenotypic deviations. Our approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site or sequence data that represents the evolutionary steps that interrelate the observed haplotypes. The cladogram is used to define a nested statistical design to identify mutational steps associated with significant phenotypic deviations. The central assumption behind this strategy is that any undetected mutation causing a phenotypic effect is embedded within the same evolutionary history that is represented by the cladogram. The power of this approach depends upon the confidence one has in the particular cladogram used to draw inferences. In this paper, we present a strategy for estimating the set of cladograms that are consistent with a particular sample of either restriction site or nucleotide sequence data and that includes the possibility of recombination. We first evaluate the limits of parsimony in constructing cladograms. Once these limits have been determined, we construct the set of parsimonious and nonparsimonious cladograms that is consistent with these limits. Our estimation procedure also identifies haplotypes that are candidates for being products of recombination. If recombination is extensive, our algorithm subdivides the DNA region into two or more subsections, each having little or no internal recombination. We apply this estimation procedure to three data sets to illustrate varying degrees of cladogram ambiguity and recombination.