Bayesian coalescent inference of past population dynamics from molecular sequences
Bayesian coalescent inference of past population dynamics from molecular sequences
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DOI：
10.1093/molbev/msi103
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发表时间：
2005-05-01
影响因子：
10.7
通讯作者：
Pybus, OG
中科院分区：
文献类型：
--
作者：
Drummond, AJ;Rambaut, A;Pybus, OG
我们介绍贝叶斯天际线图，一种新的方法，估计过去的人口动态，通过时间从一个样本的分子序列，而不依赖于一个预先指定的参数模型的人口历史。我们描述了一个马尔可夫链蒙特卡罗抽样程序，有效地采样的广义天际线图的一个变体，给定的序列数据，并结合这些图，通过时间生成有效的人口规模的后验分布。我们将贝叶斯天际线图应用于模拟数据集，并表明它正确地重建了典型场景下的人口统计历史。最后，我们通过分析两个真实的数据集（埃及的丙型肝炎病毒和白令野牛的线粒体DNA），将贝叶斯天际线图模型与以前的合并方法进行了比较。在对野牛的分析中，我们发现了一个严重但以前未被认识的瓶颈，估计发生在10,000年前，这与阿拉斯加最早的无可争议的大量人类记录和全新世初期北美的巨型动物灭绝相吻合。
We introduce the Bayesian skyline plot, a new method for estimating past population dynamics through time from a sample of molecular sequences without dependence on a prespecified parametric model of demographic history. We describe a Markov chain Monte Carlo sampling procedure that efficiently samples a variant of the generalized skyline plot, given sequence data, and combines these plots to generate a posterior distribution of effective population size through time. We apply the Bayesian skyline plot to simulated data sets and show that it correctly reconstructs demographic history under canonical scenarios. Finally, we compare the Bayesian skyline plot model to previous coalescent approaches by analyzing two real data sets (hepatitis C virus in Egypt and mitochondrial DNA of Beringian bison) that have been previously investigated using alternative coalescent methods. In the bison analysis, we detect a severe but previously unrecognized bottleneck, estimated to have occurred 10,000 radiocarbon years ago, which coincides with both the earliest undisputed record of large numbers of humans in Alaska and the megafaunal extinctions in North America at the beginning of the Holocene.