Tavaré S, Balding D J, Griffiths R C, Donnelly P
Department of Mathematics, University of Southern California, Los Angeles 90089-1113, USA.
Genetics. 1997 Feb;145(2):505-18. doi: 10.1093/genetics/145.2.505.
The paper is concerned with methods for the estimation of the coalescence time (time since the most recent common ancestor) of a sample of intraspecies DNA sequences. The methods take advantage of prior knowledge of population demography, in addition to the molecular data. While some theoretical results are presented, a central focus is on computational methods. These methods are easy to implement, and, since explicit formulae tend to be either unavailable or unilluminating, they are also more useful and more informative in most applications. Extensions are presented that allow for the effects of uncertainty in our knowledge of population size and mutation rates, for variability in population sizes, for regions of different mutation rate, and for inference concerning the coalescence time of the entire population. The methods are illustrated using recent data from the human Y chromosome.
本文关注的是用于估计种内DNA序列样本的合并时间（自最近共同祖先以来的时间）的方法。这些方法除了利用分子数据外，还利用了种群统计学的先验知识。虽然给出了一些理论结果，但核心重点是计算方法。这些方法易于实现，而且由于显式公式往往不可用或没有启发性，所以在大多数应用中它们也更有用且信息更丰富。文中还介绍了一些扩展内容，这些扩展考虑了我们对种群大小和突变率的认识存在不确定性的影响、种群大小的变异性、不同突变率区域的影响以及关于整个种群合并时间的推断。文中使用来自人类Y染色体的最新数据对这些方法进行了说明。
