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Detecting Recent Positive Selection with a Single Locus Test Bipartitioning the Coalescent Tree

文献类型：期刊论文

作者Yang, Zongfeng1,3; Li, Junrui3; Li, Haipeng3; Li, Junrui4; Wiehe, Thomas2; ,
刊名GENETICS
出版日期2018
卷号208期号:2页码:791-805
关键词positive selection adaptation demography
ISSN号0016-6731
DOI10.1534/genetics.117.300401
文献子类Article
英文摘要Many population genomic studies have been conducted in the past to search for traces of recent events of positive selection. These traces, however, can be obscured by temporal variation of population size or other demographic factors. To reduce the confounding impact of demography, the coalescent tree topology has been used as an additional source of information for detecting recent positive selection in a population or a species. Based on the branching pattern at the root, we partition the hypothetical coalescent tree, inferred from a sequence sample, into two subtrees. The reasoning is that positive selection could impose a strong impact on branch length in one of the two subtrees while demography has the same effect on average on both subtrees. Thus, positive selection should be detectable by comparing statistics calculated for the two subtrees. Simulations demonstrate that the proposed test based on these principles has high power to detect recent positive selection even when DNA polymorphism data from only one locus is available, and that it is robust to the confounding effect of demography. One feature is that all components in the summary statistics (Du) can be computed analytically. Moreover, misinference of derived and ancestral alleles is seen to have only a limited effect on the test, and it therefore avoids a notorious problem when searching for traces of recent positive selection.
学科主题Genetics & Heredity
WOS关键词NUCLEOTIDE-SEQUENCE DATA ; SITE FREQUENCY-SPECTRUM ; NATURAL-SELECTION ; PHYLOGENETIC TREES ; NEUTRALITY TESTS ; POPULATION-SIZE ; STATISTICAL TESTS ; DNA POLYMORPHISM ; SNP DATA ; SPURIOUS SIGNATURES
语种英语
WOS记录号WOS:000423563400024
出版者GENETICS SOCIETY AMERICA
版本出版稿
源URL[http://202.127.25.144/handle/331004/648]  
专题中国科学院上海生命科学研究院营养科学研究所
作者单位1.Univ Chinese Acad Sci, Beijing 100049, Peoples R China;
2.Univ Cologne, Inst Genet, D-50674 Cologne, Germany,
3.Chinese Acad Sci, Key Lab Computat Biol, Max Planck Gesell CAS MPG Partner Inst Computat B, Shanghai Inst Biol Sci, Shanghai 200031, Peoples R China;
4.Univ Calif San Francisco, Howard Hughes Med Inst, San Francisco, CA 94143 USA;
推荐引用方式
GB/T 7714		 Yang, Zongfeng,Li, Junrui,Li, Haipeng,et al. Detecting Recent Positive Selection with a Single Locus Test Bipartitioning the Coalescent Tree[J]. GENETICS,2018,208(2):791-805.
APA Yang, Zongfeng,Li, Junrui,Li, Haipeng,Li, Junrui,Wiehe, Thomas,&,.(2018).Detecting Recent Positive Selection with a Single Locus Test Bipartitioning the Coalescent Tree.GENETICS,208(2),791-805.
MLA Yang, Zongfeng,et al."Detecting Recent Positive Selection with a Single Locus Test Bipartitioning the Coalescent Tree".GENETICS 208.2(2018):791-805.

入库方式： OAI收割

来源：上海营养与健康研究所

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