Castelloe J, Templeton A R
Department of Biology, Washington University, St. Louis, Missouri 63130.
Mol Phylogenet Evol. 1994 Jun;3(2):102-13. doi: 10.1006/mpev.1994.1013.
The rooting of intraspecific gene or haplotype trees has proven to be difficult using the traditional techniques of rooting species trees such as outgroups. As an alternative, we apply neutral coalescent theory to the problems of determining the root of an intraspecific gene tree and the relative ages of the haplotypes. By using a recursive equation, exact root probabilities can be calculated for small cladograms and sample sizes. These exact probabilities indicate that root probabilities are not very sensitive to the parameter theta, which is four times the mutation rate times the inbreeding effective size. The exact probabilities also indicate that root probabilities are not very sensitive to the absolute numbers of each haplotype (allele) class, only their relative proportions. The exact method, unfortunately, is not feasible for implementation with larger data sets with present algorithms and computers. However, the exact results suggested a simple heuristic for determining outgroup weights; that is, finding the haplotype that is the oldest in the sample and that can serve as an outgroup for the remainder of the haplotype tree. Computer simulations revealed that these outgroup weights are strongly correlated with actual age and are much better indicators of haplotype age than is the haplotype frequency, another commonly used indicator of relative age.
事实证明，使用诸如外类群等确定物种树根部的传统技术来确定种内基因树或单倍型树的根部是困难的。作为一种替代方法，我们将中性合并理论应用于确定种内基因树根部和单倍型相对年龄的问题。通过使用递归方程，可以为小的分支图和样本量计算精确的根部概率。这些精确概率表明，根部概率对参数θ不是非常敏感，θ是突变率乘以近交有效大小的四倍。精确概率还表明，根部概率对每个单倍型（等位基因）类别的绝对数量不是非常敏感，只对它们的相对比例敏感。不幸的是，对于使用当前算法和计算机处理更大的数据集，精确方法不可行。然而，精确结果提出了一种确定外类群权重的简单启发式方法；也就是说，找到样本中最古老的单倍型，它可以作为单倍型树其余部分的外类群。计算机模拟表明，这些外类群权重与实际年龄密切相关，并且比单倍型频率（另一种常用的相对年龄指标）更能准确指示单倍型年龄。
