Maximum-likelihood estimation of demographic parameters using the frequency spectrum of unlinked single-nucleotide polymorphisms
Maximum-likelihood estimation of demographic parameters using the frequency spectrum of unlinked single-nucleotide polymorphisms
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DOI：
10.1534/genetics.104.030171
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发表时间：
2004-11-01
期刊：
影响因子：
3.3
通讯作者：
Hudson, RR
中科院分区：
文献类型：
--
作者：
Adams, AM;Hudson, RR
人口统计推断的最大似然法适用于由非连锁单核苷酸多态性（SNP）的频谱组成的数据集。我们使用模拟分析，以探讨两个电源拒绝零假设不变的人口规模和二维和三维的最大似然估计（MLEs）的样本大小和多态位点的数量的影响。需要大量的数据来产生准确的人口推断，特别是对于最近的增长情景。MLE的特性在很大程度上取决于人口假设，因为随着增长开始时间的延长和增长程度的降低，估计数会有所改善。严重的增长会导致对当前人口规模的估计出现向上的偏差，这种偏差随着增长的幅度而增加。一组来自非洲的数据支持温和的古代增长模型，另一组数据与恒定的人口规模和各种增长情景相一致，拒绝超过5倍的增长始于> 36，000年前。对欧洲起源的一组数据的分析表明了一个相互印证的人口历史，85%的人口减少发生在类似于30,000年前。
A maximum-likelihood method for demographic inference is applied to data sets consisting of the frequency spectrum of unlinked single-nucleotide polymorphisms (SNPs). We use simulation analyses to explore the effect of sample size and number of polymorphic sites on both the power to reject the null hypothesis of constant population size and the properties of two- and three-dimensional maximum-likelihood estimators (MLEs). Large amounts of data are required to produce accurate demographic inferences, particularly for scenarios of recent growth. Properties of the MLEs are highly dependent upon the demographic scenario, as estimates improve with a more ancient time of growth onset and smaller degree of growth. Severe episodes of growth lead to an upward bias in the estimates of the current population size, and that bias increases with the magnitude of growth. One data set of African origin supports a model of mild, ancient growth, and another is compatible with both constant population size and a variety of growth scenarios, rejecting greater than fivefold growth beginning >36,000 years ago. Analysis of a data set of European origin indicates a bottlenecked population history, with an 85% population reduction occurring similar to30,000 years ago.