A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination.
A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination.
复制标题
对表型关联与从限制性内切核酸酶作图推断的单倍型进行分支分析。
DOI：
10.1093/genetics/134.2.659
复制
发表时间：
1993
期刊：
影响因子：
3.3
通讯作者：
Sing,CF
中科院分区：
文献类型：
--
作者：
Templeton,AR;Sing,CF
我们之前开发了一种基于分支理论的分析策略，以识别与显着表型偏差相关的单倍型子集。我们最初的方法仅限于很少发生重组的DNA片段。在这种情况下，可以从限制性位点数据构建分支图，以估计所观察到的单倍型彼此相关的进化步骤。然后使用进化树来定义用于识别与显著表型偏差相关的突变步骤的嵌套统计设计。这一策略背后的核心假设是，负责特定表型效应的突变嵌入在进化史中，由分支图表示。这种方法的力量取决于进化树在描绘DNA区域进化历史方面的准确性。这种准确性可以减少重组和估计的分支图拓扑结构的不确定性。在以前的论文中，我们提出了一种算法，用于估计一组可能的claudgram和重组事件。在本文中，我们提出了一个算法，用于定义一个嵌套的统计设计下的分支图的不确定性和重组。给定巢式设计，可以使用巢式方差分析（对于单倍体或纯合菌株）或排列检验（对于异交二倍体基因区域）来检查表型关联。在本文中，我们还扩展了这种分析策略，包括分类表型，除了定量表型。使用果蝇数据集的一些工作的例子。这些例子说明，有一些重组实际上可以增强生物学推论，可能来自分支分析。特别地，重组可用于将物理定位分配给负责显著表型效应的突变的给定亚区。
We previously developed an analytical strategy based on cladistic theory to identify subsets of haplotypes that are associated with significant phenotypic deviations. Our initial approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site data to estimate the evolutionary steps that interrelate the observed haplotypes to one another. The cladogram is then used to define a nested statistical design for identifying mutational steps associated with significant phenotypic deviations. The central assumption behind this strategy is that a mutation responsible for a particular phenotypic effect is embedded within the evolutionary history that is represented by the cladogram. The power of this approach depends on the accuracy of the cladogram in portraying the evolutionary history of the DNA region. This accuracy can be diminished both by recombination and by uncertainty in the estimated cladogram topology. In a previous paper, we presented an algorithm for estimating the set of likely claodgrams and recombination events. In this paper we present an algorithm for defining a nested statistical design under cladogram uncertainty and recombination. Given the nested design, phenotypic associations can be examined using either a nested analysis of variance (for haploids or homozygous strains) or permutation testing (for outcrossed, diploid gene regions). In this paper we also extend this analytical strategy to include categorical phenotypes in addition to quantitative phenotypes. Some worked examples are presented using Drosophila data sets. These examples illustrate that having some recombination may actually enhance the biological inferences that may derived from a cladistic analysis. In particular, recombination can be used to assign a physical localization to a given subregion for mutations responsible for significant phenotypic effects.
登录
查看更多内容
果蝇中酯酶 6 的限制性位点多态性与酶活性变异之间的关联。
影响因子：
3.3
作者：
A. Y. Game;J. Oakeshott
通讯作者：
J. Oakeshott
影响因子：
3.3
作者：
Alan R. Templeton;K. Crandall;C. Sing
通讯作者：
Alan R. Templeton;K. Crandall;C. Sing
影响因子：
6.9
作者：
Koch, KE;Wu, Y;Xu, J
通讯作者：
Xu, J
DOI：
--
发表时间：
1984
期刊：
影响因子：
--
作者：
T. Yamazaki;Y. Matsuo;Yasuhisa Inouei;Yasubumi Matsuo
通讯作者：
Yasubumi Matsuo
线粒体DNA多态性统计分析：chi 2与小样本问题。
影响因子：
10.7
作者：
D. Roff;P. Bentzen
通讯作者：
P. Bentzen