Estimating the number of ancestral lineages using a maximum-likelihood method based on rejection sampling
Estimating the number of ancestral lineages using a maximum-likelihood method based on rejection sampling
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DOI：
10.1534/genetics.106.066233
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发表时间：
2007-07-01
期刊：
影响因子：
3.3
通讯作者：
Rosenberg, Noah A.
中科院分区：
文献类型：
--
作者：
Blum, Michael G. B.;Rosenberg, Noah A.
估计过去时间 t 的 DNA 序列样本的祖先谱系数量可以被视为估计最近共同祖先时间问题的变体。为了估计祖先谱系的数量，除了通过多态位点模式总结的分子数据之外，我们还开发了一种最大似然方法，该方法利用了先前的人口统计模型。该方法依赖于拒绝采样算法，该算法是为了在时间 t 给定固定数量的祖先谱系的情况下模拟条件合并树而引入的。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，就可以准确估计祖先谱系的数量。该方法适用于位于线粒体高变区 1 的 986 个现代人类序列，以估计现代人类在可能与尼安德特人种群混合时的祖先谱系数量。我们的估计支持这样一种观点，即如果这种混合发生在 3 万年前，那么由尼安德特人贡献的现代人口比例一定相对较小，不到 5%。
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 similar to 5%, if the admixture happened as recently as 30,000 years ago.