有效种群大小或突变率的系统发育估计器。
A phylogenetic estimator of effective population size or mutation rate.
作者信息
Fu Y X
机构信息
Center for Demographic and Population Genetics, University of Texas, Houston 77225.
出版信息
Genetics. 1994 Feb;136(2):685-92. doi: 10.1093/genetics/136.2.685.
Abstract
A new estimator of the essential parameter theta = 4Ne mu from DNA polymorphism data is developed under the neutral Wright-Fisher model without recombination and population subdivision, where Ne is the effective population size and mu is the mutation rate per locus per generation. The new estimator has a variance only slightly larger than the minimum variance of all possible unbiased estimators of the parameter and is substantially smaller than that of any existing estimator. The high efficiency of the new estimator is achieved by making full use of phylogenetic information in a sample of DNA sequences from a population. An example of estimating theta by the new method is presented using the mitochondrial sequences from an American Indian population.
摘要
在无重组和种群细分的中性赖特 - 费希尔模型下，基于DNA多态性数据开发了一种新的基本参数θ = 4Neμ的估计方法，其中Ne是有效种群大小，μ是每个位点每代的突变率。新估计量的方差仅略大于该参数所有可能无偏估计量的最小方差，且显著小于任何现有估计量。通过充分利用来自一个种群的DNA序列样本中的系统发育信息，实现了新估计量的高效性。使用来自一个美洲印第安人群体的线粒体序列给出了用新方法估计θ的一个例子。
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本文引用的文献
1
Statistical tests of neutrality of mutations.突变中性的统计检验。
Genetics. 1993 Mar;133(3):693-709. doi: 10.1093/genetics/133.3.693.
2
Maximum likelihood estimation of population parameters.总体参数的最大似然估计
Genetics. 1993 Aug;134(4):1261-70. doi: 10.1093/genetics/134.4.1261.
3
Evolutionary relationship of DNA sequences in finite populations.有限种群中DNA序列的进化关系。
Genetics. 1983 Oct;105(2):437-60. doi: 10.1093/genetics/105.2.437.
4
Statistical properties of the number of recombination events in the history of a sample of DNA sequences.DNA序列样本历史中重组事件数量的统计特性。
Genetics. 1985 Sep;111(1):147-64. doi: 10.1093/genetics/111.1.147.
5
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.通过DNA多态性检验中性突变假说的统计方法。
Genetics. 1989 Nov;123(3):585-95. doi: 10.1093/genetics/123.3.585.
6
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.
7
Estimating substitution rates from molecular data using the coalescent.使用溯祖理论从分子数据估计替换率。
Proc Natl Acad Sci U S A. 1992 Jul 1;89(13):5961-5. doi: 10.1073/pnas.89.13.5961.
8
Estimating effective population size from samples of sequences: a bootstrap Monte Carlo integration method.从序列样本估计有效种群大小：一种自助蒙特卡罗积分方法。
Genet Res. 1992 Dec;60(3):209-20. doi: 10.1017/s0016672300030962.
9
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.
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