定向错误的位点对有外类群的中性检验的影响。
Effect of misoriented sites on neutrality tests with outgroup.
作者信息
Baudry Emmanuelle, Depaulis Frantz
机构信息
Laboratoire d'Ecologie, Centre National de la Recherche Scientifique UMR 7625-EPHE, Université Pierre et Marie Curie, 75252 Paris 05, France.
出版信息
Genetics. 2003 Nov;165(3):1619-22. doi: 10.1093/genetics/165.3.1619.
Abstract
Several neutrality tests use outgroups to infer the ancestral and derived states for polymorphism data. However, homoplasy can result in the incorrect inference of the derived variant. We show that empirically derived rates of misorientation strongly influence Fay and Wu's H-test, especially when the sample size is large.
摘要
几种中性检验使用外类群来推断多态性数据的祖先状态和衍生状态。然而，平行进化可能导致对衍生变异的错误推断。我们表明，根据经验得出的方向错误率会强烈影响费伊和吴的H检验，尤其是在样本量较大时。
相似文献
1
Effect of misoriented sites on neutrality tests with outgroup.定向错误的位点对有外类群的中性检验的影响。
Genetics. 2003 Nov;165(3):1619-22. doi: 10.1093/genetics/165.3.1619.
2
Decomposing the Site Frequency Spectrum: The Impact of Tree Topology on Neutrality Tests.分解位点频率谱：树拓扑结构对中性检验的影响。
Genetics. 2017 Sep;207(1):229-240. doi: 10.1534/genetics.116.188763. Epub 2017 Jul 5.
3
A new test for detecting recent positive selection that is free from the confounding impacts of demography.一种新的检测近期正选择的测试方法，该方法不受人口统计学混淆影响。
Mol Biol Evol. 2011 Jan;28(1):365-75. doi: 10.1093/molbev/msq211. Epub 2010 Aug 13.
4
A General Framework for Neutrality Tests Based on the Site Frequency Spectrum.基于碱基分布频谱的中性检验通用框架
Genes (Basel). 2023 Aug 28;14(9):1714. doi: 10.3390/genes14091714.
5
Neutrality tests for sequences with missing data.带有缺失数据的序列的中立性检验。
Genetics. 2012 Aug;191(4):1397-401. doi: 10.1534/genetics.112.139949. Epub 2012 Jun 1.
6
A single-amino-acid change of the gustatory receptor gene, Gr5a, has a major effect on trehalose sensitivity in a natural population of Drosophila melanogaster.味觉受体基因Gr5a的单个氨基酸变化对黑腹果蝇自然种群中海藻糖敏感性有重大影响。
Genetics. 2004 Aug;167(4):1749-58. doi: 10.1534/genetics.104.027045.
7
Context dependence, ancestral misidentification, and spurious signatures of natural selection.上下文依赖性、祖先误认与自然选择的虚假特征
Mol Biol Evol. 2007 Aug;24(8):1792-800. doi: 10.1093/molbev/msm108. Epub 2007 Jun 1.
8
A multilocus sequence survey in Arabidopsis thaliana reveals a genome-wide departure from a neutral model of DNA sequence polymorphism.一项对拟南芥的多位点序列调查显示，全基因组偏离了DNA序列多态性的中性模型。
Genetics. 2005 Mar;169(3):1601-15. doi: 10.1534/genetics.104.033795. Epub 2005 Jan 16.
9
Diversity of the MBL2 gene in various Brazilian populations and the case of selection at the mannose-binding lectin locus.巴西不同人群中MBL2基因的多样性以及甘露糖结合凝集素基因座的选择情况。
Hum Immunol. 2006 Sep;67(9):722-34. doi: 10.1016/j.humimm.2006.05.009. Epub 2006 Jul 10.
10
Postglacial history of a widespread conifer produces inverse clines in selective neutrality tests.冰期后广泛分布的针叶树的历史导致选择中性测试中的反梯度。
Mol Ecol. 2010 Sep;19(18):3857-64. doi: 10.1111/j.1365-294X.2010.04767.x.
引用本文的文献
1
dadi-cli: Automated and distributed population genetic model inference from allele frequency spectra.dadi-cli：基于等位基因频率谱的自动化分布式群体遗传模型推断。
bioRxiv. 2023 Jun 16:2023.06.15.545182. doi: 10.1101/2023.06.15.545182.
2
Interpreting the pervasive observation of U-shaped Site Frequency Spectra.解读普遍存在的 U 型位点频率谱现象。
PLoS Genet. 2023 Mar 23;19(3):e1010677. doi: 10.1371/journal.pgen.1010677. eCollection 2023 Mar.
3
Sweepstakes reproductive success via pervasive and recurrent selective sweeps.通过普遍且反复的选择扫荡来赢得繁殖成功。
Elife. 2023 Feb 20;12:e80781. doi: 10.7554/eLife.80781.
4
Haplotype-based inference of the distribution of fitness effects.基于单体型的适合度效应分布推断。
Genetics. 2022 Apr 4;220(4). doi: 10.1093/genetics/iyac002.
5
Detecting selection using extended haplotype homozygosity (EHH)-based statistics in unphased or unpolarized data.基于扩展单体型纯合度（EHH）统计量的无相位或非极化数据中的选择检测。
PLoS One. 2022 Jan 18;17(1):e0262024. doi: 10.1371/journal.pone.0262024. eCollection 2022.
6
Inferring Genome-Wide Correlations of Mutation Fitness Effects between Populations.推断种群间突变适应度效应的全基因组相关性。
Mol Biol Evol. 2021 Sep 27;38(10):4588-4602. doi: 10.1093/molbev/msab162.
7
Gene flow as a simple cause for an excess of high-frequency-derived alleles.基因流作为高频衍生等位基因过量的一个简单原因。
Evol Appl. 2020 Jun 2;13(9):2254-2263. doi: 10.1111/eva.12998. eCollection 2020 Oct.
8
Adaptive Landscape of Protein Variation in Human Exomes.人类外显子组中蛋白质变异的适应景观。
Mol Biol Evol. 2018 Aug 1;35(8):2015-2025. doi: 10.1093/molbev/msy107.
9
Inferring the Probability of the Derived the Ancestral Allelic State at a Polymorphic Site.推断多态性位点祖先等位基因状态的概率。
Genetics. 2018 Jul;209(3):897-906. doi: 10.1534/genetics.118.301120. Epub 2018 May 16.
10
Detecting Recent Positive Selection with a Single Locus Test Bipartitioning the Coalescent Tree.利用单一位点测试将合并树二分检测近期正选择。
Genetics. 2018 Feb;208(2):791-805. doi: 10.1534/genetics.117.300401. Epub 2017 Dec 7.
本文引用的文献
1
Contrasting evolutionary forces in the Arabidopsis thaliana floral developmental pathway.拟南芥花发育途径中的对比进化力量。
Genetics. 2002 Apr;160(4):1641-50. doi: 10.1093/genetics/160.4.1641.
2
The signature of positive selection at randomly chosen loci.随机选择位点上的正选择特征。
Genetics. 2002 Mar;160(3):1179-89. doi: 10.1093/genetics/160.3.1179.
3
Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels.基因转换和不同的群体历史可能解释多态性与连锁不平衡水平之间的差异。
Am J Hum Genet. 2001 Oct;69(4):831-43. doi: 10.1086/323612. Epub 2001 Aug 29.
4
Estimate of the mutation rate per nucleotide in humans.人类每核苷酸突变率的估计。
Genetics. 2000 Sep;156(1):297-304. doi: 10.1093/genetics/156.1.297.
5
Hitchhiking under positive Darwinian selection.在正向达尔文选择下的搭便车现象。
Genetics. 2000 Jul;155(3):1405-13. doi: 10.1093/genetics/155.3.1405.
6
Nucleotide variation at the CHALCONE ISOMERASE locus in Arabidopsis thaliana.拟南芥查尔酮异构酶基因座的核苷酸变异
Genetics. 2000 Jun;155(2):863-72. doi: 10.1093/genetics/155.2.863.
7
Reduced X-linked nucleotide polymorphism in Drosophila simulans.拟暗果蝇中X连锁核苷酸多态性降低。
Proc Natl Acad Sci U S A. 2000 May 23;97(11):5960-5. doi: 10.1073/pnas.97.11.5960.
8
Contrasting patterns of nucleotide polymorphism at the alcohol dehydrogenase locus in the outcrossing Arabidopsis lyrata and the selfing Arabidopsis thaliana.异交的琴叶拟南芥和自交的拟南芥中乙醇脱氢酶基因座核苷酸多态性的对比模式。
Mol Biol Evol. 2000 Apr;17(4):645-55. doi: 10.1093/oxfordjournals.molbev.a026343.
9
DNA variation in the basic chitinase locus (ChiB) region of the wild plant Arabidopsis thaliana.野生植物拟南芥基本几丁质酶基因座（ChiB）区域的DNA变异
Genetics. 1999 Nov;153(3):1445-53. doi: 10.1093/genetics/153.3.1445.
10
Estimation of the transition/transversion rate bias and species sampling.转换/颠换率偏差估计与物种抽样
J Mol Evol. 1999 Mar;48(3):274-83. doi: 10.1007/pl00006470.
Zotero 插件