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论文题目: Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with polynomial functions
英文论文题目: Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with polynomial functions
第一作者: Zhou, Y; Yuan, K; Yu, Y; Ni, X; Xie, P; Xing, EP; Xu, S
英文第一作者: Zhou, Y; Yuan, K; Yu, Y; Ni, X; Xie, P; Xing, EP; Xu, S
联系作者: Xu, S (reprint author), Chinese Acad Sci,CAS MPG Partner Inst Computat Biol, Key Lab Computat Biol,320 Yueyang Rd, Shanghai 200031, Peoples R China.
英文联系作者: Xu, S (reprint author), Chinese Acad Sci,CAS MPG Partner Inst Computat Biol, Key Lab Computat Biol,320 Yueyang Rd, Shanghai 200031, Peoples R China.
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发表年度: 2017
卷: 118
期: 5
页码: 503-510
摘要: To infer the histories of population admixture, one important challenge with methods based on the admixture linkage disequilibrium (ALD) is to remove the effect of source LD (SLD), which is directly inherited from source populations. In previous methods, only the decay curve of weighted LD between pairs of sites whose genetic distance were larger than a certain starting distance was fitted by single or multiple exponential functions, for the inference of recent single-or multiple-wave admixture. However, the effect of SLD has not been well defined and no tool has been developed to estimate the effect of SLD on weighted LD decay. In this study, we defined the SLD in the formularized weighted LD statistic under the two-way admixture model and proposed a polynomial spectrum (p-spectrum) to study the weighted SLD and weighted LD. We also found that reference populations could be used to reduce the SLD in weighted LD statistics. We further developed a method, iMAAPs, to infer multiple-wave admixture by fitting ALD using a p-spectrum. We evaluated the performance of iMAAPs under various admixture models in simulated data and applied iMAAPs to the analysis of genome-wide single nucleotide polymorphism data from the Human Genome Diversity Project and the HapMap Project. We showed that iMAAPs is a considerable improvement over other current methods and further facilitates the inference of histories of complex population admixtures.
英文摘要: To infer the histories of population admixture, one important challenge with methods based on the admixture linkage disequilibrium (ALD) is to remove the effect of source LD (SLD), which is directly inherited from source populations. In previous methods, only the decay curve of weighted LD between pairs of sites whose genetic distance were larger than a certain starting distance was fitted by single or multiple exponential functions, for the inference of recent single-or multiple-wave admixture. However, the effect of SLD has not been well defined and no tool has been developed to estimate the effect of SLD on weighted LD decay. In this study, we defined the SLD in the formularized weighted LD statistic under the two-way admixture model and proposed a polynomial spectrum (p-spectrum) to study the weighted SLD and weighted LD. We also found that reference populations could be used to reduce the SLD in weighted LD statistics. We further developed a method, iMAAPs, to infer multiple-wave admixture by fitting ALD using a p-spectrum. We evaluated the performance of iMAAPs under various admixture models in simulated data and applied iMAAPs to the analysis of genome-wide single nucleotide polymorphism data from the Human Genome Diversity Project and the HapMap Project. We showed that iMAAPs is a considerable improvement over other current methods and further facilitates the inference of histories of complex population admixtures.
刊物名称: HEREDITY
英文刊物名称: HEREDITY
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学科: Ecology; Evolutionary Biology; Genetics & Heredity
英文学科: Ecology; Evolutionary Biology; Genetics & Heredity
影响因子: 3.961
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论文类别: Article
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