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本文引用的文献

1
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.一种通过核苷酸序列比较研究来估计碱基替换进化速率的简单方法。
J Mol Evol. 1980 Dec;16(2):111-20. doi: 10.1007/BF01731581.
2
Extensive mitochondrial diversity within a single Amerindian tribe.单个美洲印第安部落内广泛的线粒体多样性。
Proc Natl Acad Sci U S A. 1991 Oct 1;88(19):8720-4. doi: 10.1073/pnas.88.19.8720.
3
Estimating effective population size from samples of sequences: inefficiency of pairwise and segregating sites as compared to phylogenetic estimates.从序列样本估计有效种群大小：与系统发育估计相比，成对比较和分离位点方法的低效性
Genet Res. 1992 Apr;59(2):139-47. doi: 10.1017/s0016672300030354.
4
On the number of segregating sites in genetical models without recombination.关于无重组遗传模型中的分离位点数。
Theor Popul Biol. 1975 Apr;7(2):256-76. doi: 10.1016/0040-5809(75)90020-9.

使用Metropolis-Hastings抽样法从序列数据估计有效种群大小和突变率。

Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling.

作者信息

Kuhner M K, Yamato J, Felsenstein J

机构信息

Department of Genetics, University of Washington, Seattle 98195-7360, USA.

出版信息

Genetics. 1995 Aug;140(4):1421-30. doi: 10.1093/genetics/140.4.1421.

DOI:10.1093/genetics/140.4.1421
PMID:7498781
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC1206705/
Abstract

We present a new way to make a maximum likelihood estimate of the parameter 4N mu (effective population size times mutation rate per site, or theta) based on a population sample of molecular sequences. We use a Metropolis-Hastings Markov chain Monte Carlo method to sample genealogies in proportion to the product of their likelihood with respect to the data and their prior probability with respect to a coalescent distribution. A specific value of theta must be chosen to generate the coalescent distribution, but the resulting trees can be used to evaluate the likelihood at other values of theta, generating a likelihood curve. This procedure concentrates sampling on those genealogies that contribute most of the likelihood, allowing estimation of meaningful likelihood curves based on relatively small samples. The method can potentially be extended to cases involving varying population size, recombination, and migration.

摘要

我们提出了一种基于分子序列的群体样本对参数4Nμ（有效群体大小乘以每个位点的突变率，即θ）进行最大似然估计的新方法。我们使用Metropolis-Hastings马尔可夫链蒙特卡罗方法，以与它们相对于数据的似然性和相对于合并分布的先验概率的乘积成比例的方式对谱系进行采样。必须选择一个特定的θ值来生成合并分布，但生成的树可用于评估其他θ值下的似然性，从而生成似然曲线。该过程将采样集中在那些贡献大部分似然性的谱系上，从而能够基于相对较小的样本估计有意义的似然曲线。该方法有可能扩展到涉及群体大小变化、重组和迁移的情况。