Blum Michael G B, Rosenberg Noah A
Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA.
Genetics. 2007 Jul;176(3):1741-57. doi: 10.1534/genetics.106.066233. Epub 2007 Apr 15.
Estimating the number of ancestral lineages of a sample of DNA sequences at time t in the past can be viewed as a variation on the problem of estimating the time to the most recent common ancestor. To estimate the number of ancestral lineages, we develop a maximum-likelihood approach that takes advantage of a prior model of population demography, in addition to the molecular data summarized by the pattern of polymorphic sites. The method relies on a rejection sampling algorithm that is introduced for simulating conditional coalescent trees given a fixed number of ancestral lineages at time t. Computer simulations show that the number of ancestral lineages can be estimated accurately, provided that the number of mutations that occurred since time t is sufficiently large. The method is applied to 986 present-day human sequences located in hypervariable region 1 of the mitochondrion to estimate the number of ancestral lineages of modern humans at the time of potential admixture with the Neanderthal population. Our estimates support a view that the proportion of the modern population consisting of Neanderthal contributions must be relatively small, less than approximately 5%, if the admixture happened as recently as 30,000 years ago.
估计过去某个时间t的DNA序列样本的祖先谱系数量，可以看作是估计最近共同祖先时间问题的一种变体。为了估计祖先谱系的数量，我们开发了一种最大似然方法，该方法除了利用由多态性位点模式总结的分子数据外，还利用了群体人口统计学的先验模型。该方法依赖于一种拒绝采样算法，该算法用于在给定时间t祖先谱系固定数量的情况下模拟条件合并树。计算机模拟表明，只要自时间t以来发生的突变数量足够大，祖先谱系的数量就可以准确估计。该方法应用于位于线粒体高变区1的986条现代人类序列，以估计现代人类在与尼安德特人群体可能发生混合时的祖先谱系数量。我们的估计支持这样一种观点，即如果混合发生在距今3万年前，那么由尼安德特人贡献组成的现代人口比例必然相对较小，不到约5%。
