Maximum likelihood estimation of population growth rates based on the coalescent.
Maximum likelihood estimation of population growth rates based on the coalescent.
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DOI：
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发表时间：
1998-05
期刊：
影响因子：
3.3
通讯作者：
M. Kuhner;Jon A Yamato;J. Felsenstein
中科院分区：
文献类型：
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作者：
M. Kuhner;Jon A Yamato;J. Felsenstein
我们描述了一种方法来共同估计4 Nemu（有效人口规模和中性突变率的四倍）和人口增长率从序列样本使用大都会黑斯廷斯抽样。人口增长（或下降）被假定为指数增长。增长率的估计值偏高，特别是当4 Nemu较低时;由于参数之间的相关性，4 Nemu本身的估计值也略有偏高。这种偏差不能仅仅归因于Metropolis-Hastings抽样，但似乎是估计量的固有属性，预计将出现在任何从系谱结构估计增长率的方法中。与增加来自同一基因座的序列的数量或长度相比，对额外的非连锁基因座进行采样在降低偏倚方面要有效得多。
We describe a method for co-estimating 4Nemu (four times the product of effective population size and neutral mutation rate) and population growth rate from sequence samples using Metropolis-Hastings sampling. Population growth (or decline) is assumed to be exponential. The estimates of growth rate are biased upwards, especially when 4Nemu is low; there is also a slight upwards bias in the estimate of 4Nemu itself due to correlation between the parameters. This bias cannot be attributed solely to Metropolis-Hastings sampling but appears to be an inherent property of the estimator and is expected to appear in any approach which estimates growth rate from genealogy structure. Sampling additional unlinked loci is much more effective in reducing the bias than increasing the number or length of sequences from the same locus.