部分自交种群的溯祖理论。
Coalescent theory for a partially selfing population.
作者信息
Fu Y X
机构信息
Human Genetics Center, University of Texas, Houston 77225, USA.
出版信息
Genetics. 1997 Aug;146(4):1489-99. doi: 10.1093/genetics/146.4.1489.
Abstract
A coalescent theory for a sample of DNA sequences from a partially selfing diploid population and an algorithm for simulating such samples are developed in this article. Approximate formulas are given for the expectation and the variance of the number of segregating sites in a sample of k sequences from n individuals. Several new estimators of the important parameters theta = 4N mu and the selfing rate s, where N and mu are, respectively, the effective population size and the mutation rate per sequence per generation, are proposed and their sampling properties are studied.
摘要
本文提出了一种针对部分自交二倍体群体的DNA序列样本的合并理论，以及一种用于模拟此类样本的算法。给出了从n个个体的k个序列样本中分离位点数量的期望和方差的近似公式。提出了几个重要参数theta = 4N mu和自交率s的新估计量，其中N和mu分别是有效群体大小和每代每个序列的突变率，并研究了它们的抽样性质。
相似文献
1
Coalescent theory for a partially selfing population.部分自交种群的溯祖理论。
Genetics. 1997 Aug;146(4):1489-99. doi: 10.1093/genetics/146.4.1489.
2
Estimating effective population size or mutation rate using the frequencies of mutations of various classes in a sample of DNA sequences.利用DNA序列样本中各类突变的频率来估计有效种群大小或突变率。
Genetics. 1994 Dec;138(4):1375-86. doi: 10.1093/genetics/138.4.1375.
3
Bayesian estimation of scaled mutation rate under the coalescent: a sequential Monte Carlo approach.在溯祖模型下缩放突变率的贝叶斯估计：一种序贯蒙特卡罗方法。
BMC Bioinformatics. 2017 Dec 8;18(1):541. doi: 10.1186/s12859-017-1948-6.
4
Coalescent theory for a completely random mating monoecious population.完全随机交配雌雄同体种群的溯祖理论。
Math Biosci. 2007 Feb;205(2):315-24. doi: 10.1016/j.mbs.2006.08.002. Epub 2006 Aug 17.
5
Coalescent patterns in diploid exchangeable population models.二倍体可交换种群模型中的溯祖模式
J Math Biol. 2003 Oct;47(4):337-52. doi: 10.1007/s00285-003-0218-6. Epub 2003 May 15.
6
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.
7
Ancestral inference from haplotypes and mutations.基于单倍型和突变的祖先推断。
Theor Popul Biol. 2018 Jul;122:12-21. doi: 10.1016/j.tpb.2018.04.006. Epub 2018 Apr 25.
8
Incorporating experimental design and error into coalescent/mutation models of population history.将实验设计和误差纳入群体历史的溯祖/突变模型。
Genetics. 2007 Aug;176(4):2335-42. doi: 10.1534/genetics.106.063560. Epub 2007 Jun 11.
9
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.
10
A coalescent-based estimator of admixture from DNA sequences.一种基于溯祖理论的DNA序列混合估计方法。
Genetics. 2006 Jul;173(3):1679-92. doi: 10.1534/genetics.105.054130. Epub 2006 Apr 19.
引用本文的文献
1
Joint identity among loci under mutation and regular inbreeding.突变和规则近亲交配下的基因座共同遗传。
Theor Popul Biol. 2024 Oct;159:74-90. doi: 10.1016/j.tpb.2024.08.002. Epub 2024 Aug 30.
2
Joint inference of evolutionary transitions to self-fertilization and demographic history using whole-genome sequences.利用全基因组序列进行有性生殖到自交进化的联合推断和种群历史分析。
Elife. 2023 May 11;12:e82384. doi: 10.7554/eLife.82384.
3
A Bayesian Approach to Inferring Rates of Selfing and Locus-Specific Mutation.一种推断自交率和基因座特异性突变率的贝叶斯方法。
Genetics. 2015 Nov;201(3):1171-88. doi: 10.1534/genetics.115.179093. Epub 2015 Sep 14.
4
Estimation of parameters of deleterious mutations in partial selfing or partial outcrossing populations and in nonequilibrium populations.部分自交或部分异交群体以及非平衡群体中有害突变参数的估计。
Genetics. 2000 Apr;154(4):1893-906. doi: 10.1093/genetics/154.4.1893.
5
Gustave Malécot, 1911-1998. Population genetics founding father.古斯塔夫·马勒科，1911年 - 1998年。群体遗传学的奠基人。
Genetics. 1999 Jun;152(2):477-84. doi: 10.1093/genetics/152.2.477.
本文引用的文献
1
The coalescent process with selfing.具有自交的溯祖过程。
Genetics. 1997 Jul;146(3):1185-95. doi: 10.1093/genetics/146.3.1185.
2
Estimating long-term mating systems using DNA sequences.利用DNA序列估计长期交配系统。
Genetics. 1996 Feb;142(2):619-27. doi: 10.1093/genetics/142.2.619.
3
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.
4
A phylogenetic estimator of effective population size or mutation rate.有效种群大小或突变率的系统发育估计器。
Genetics. 1994 Feb;136(2):685-92. doi: 10.1093/genetics/136.2.685.
5
Estimating effective population size or mutation rate using the frequencies of mutations of various classes in a sample of DNA sequences.利用DNA序列样本中各类突变的频率来估计有效种群大小或突变率。
Genetics. 1994 Dec;138(4):1375-86. doi: 10.1093/genetics/138.4.1375.
6
Unrooted genealogical tree probabilities in the infinitely-many-sites model.无限多位点模型中的无根系谱树概率。
Math Biosci. 1995 May;127(1):77-98. doi: 10.1016/0025-5564(94)00044-z.
7
Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling.使用Metropolis-Hastings抽样法从序列数据估计有效种群大小和突变率。
Genetics. 1995 Aug;140(4):1421-30. doi: 10.1093/genetics/140.4.1421.
8
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.
9
Inbreeding coefficients and coalescence times.近亲繁殖系数与溯祖时间。
Genet Res. 1991 Oct;58(2):167-75. doi: 10.1017/s0016672300029827.
10
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.
Zotero 插件