使用溯祖方法对两个种群的迁移率和有效种群数量进行最大似然估计。
Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach.
作者信息
Beerli P, Felsenstein J
机构信息
Department of Genetics, University of Washington, Box 357360, Seattle, Washington 98195-7360, USA.
出版信息
Genetics. 1999 Jun;152(2):763-73. doi: 10.1093/genetics/152.2.763.
Abstract
A new method for the estimation of migration rates and effective population sizes is described. It uses a maximum-likelihood framework based on coalescence theory. The parameters are estimated by Metropolis-Hastings importance sampling. In a two-population model this method estimates four parameters: the effective population size and the immigration rate for each population relative to the mutation rate. Summarizing over loci can be done by assuming either that the mutation rate is the same for all loci or that the mutation rates are gamma distributed among loci but the same for all sites of a locus. The estimates are as good as or better than those from an optimized FST-based measure. The program is available on the World Wide Web at http://evolution.genetics. washington.edu/lamarc.html/.
摘要
本文描述了一种估计迁移率和有效种群大小的新方法。它使用基于合并理论的最大似然框架。参数通过Metropolis-Hastings重要性抽样进行估计。在双种群模型中，该方法估计四个参数：每个种群相对于突变率的有效种群大小和移民率。总结位点时，可以假设所有位点的突变率相同，或者假设突变率在位点间呈伽马分布，但位点的所有位点相同。这些估计与基于优化FST的测量方法一样好或更好。该程序可在万维网上获取，网址为http://evolution.genetics.washington.edu/lamarc.html/ 。
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本文引用的文献
1
Segregating sites in Wright's island model.
Theor Popul Biol. 1998 Apr;53(2):166-74. doi: 10.1006/tpbi.1997.1355.
2
Maximum likelihood estimation of population growth rates based on the coalescent.
Genetics. 1998 May;149(1):429-34. doi: 10.1093/genetics/149.1.429.
3
Estimation in an island model using simulation.
Theor Popul Biol. 1996 Dec;50(3):227-53. doi: 10.1006/tpbi.1996.0030.
4
Inferring patterns of migration from gene frequencies under equilibrium conditions.
Genetics. 1996 Dec;144(4):1911-21. doi: 10.1093/genetics/144.4.1911.
5
Estimating gene flow in island populations.
Genet Res. 1996 Apr;67(2):147-58. doi: 10.1017/s0016672300033607.
6
A Hidden Markov Model approach to variation among sites in rate of evolution.
Mol Biol Evol. 1996 Jan;13(1):93-104. doi: 10.1093/oxfordjournals.molbev.a025575.
7
The coalescent in two colonies with symmetric migration.
J Math Biol. 1993;31(8):841-51. doi: 10.1007/BF00168049.
8
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods.
J Mol Evol. 1994 Sep;39(3):306-14. doi: 10.1007/BF00160154.
9
Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling.
Genetics. 1995 Aug;140(4):1421-30. doi: 10.1093/genetics/140.4.1421.
10
Properties of a neutral allele model with intragenic recombination.
Theor Popul Biol. 1983 Apr;23(2):183-201. doi: 10.1016/0040-5809(83)90013-8.
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