Length Distribution of Ancestral Tracks under a General Admixture Model and Its Applications in Population History Inference

doi:10.1038/srep20048

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	Length Distribution of Ancestral Tracks under a General Admixture Model and Its Applications in Population History Inference
	Ni, Xumin 1; Yang, Xiong 2; Guo, Wei 3; Yuan, Kai 2; Zhou, Ying 2; Ma, Zhiming3 ; Xu, Shuhua 2,4,5
	2016-01-28
发表期刊	SCIENTIFIC REPORTS
ISSN	2045-2322
卷号	6 页码:12
摘要	The length of ancestral tracks decays with the passing of generations which can be used to infer population admixture histories. Previous studies have shown the power in recovering the histories of admixed populations via the length distributions of ancestral tracks even under simple models. We believe that the deduction of length distributions under a general model will greatly elevate the power. Here we first deduced the length distributions under a general model and proposed general principles in parameter estimation and model selection with the deduced length distributions. Next, we focused on studying the length distributions and its applications under three typical special cases. Extensive simulations showed that the length distributions of ancestral tracks were well predicted by our theoretical framework. We further developed a new method, AdmixInfer, based on the length distributions and good performance was observed when it was applied to infer population histories under the three typical models. Notably, our method was insensitive to demographic history, sample size and threshold to discard short tracks. Finally, good performance was also observed when applied to some real datasets of African Americans, Mexicans and South Asian populations from the HapMap project and the Human Genome Diversity Project.
DOI	10.1038/srep20048
语种	英语
资助项目	Strategic Priority Research Program of the Chinese Academy of Sciences (CAS)[XDB13040100] ; National Science Fund for Distinguished Young Scholars[31525014] ; National Natural Science Foundation of China (NSFC)[11426237] ; National Natural Science Foundation of China (NSFC)[91331204] ; National Natural Science Foundation of China (NSFC)[31171218] ; 973 Project[2011CB808000] ; Fundamental Research Funds for the Central Universities[2011JBZ019] ; Science and Technology Commission of Shanghai Municipality[14YF1406800] ; National Excellent Doctoral Dissertation Foundation of PR China[FANEDD 201312] ; National Center for Mathematics and Interdisciplinary Sciences of CAS ; Key Laboratory of Random Complex Structures and Data Science, CAS[2008DP173182] ; National Program for Top-notch Young Innovative Talents of The "Wanren Jihua" Project
WOS研究方向	Science & Technology - Other Topics
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:000368786700001
出版者	NATURE PUBLISHING GROUP
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/21838
专题	应用数学研究所
通讯作者	Ma, Zhiming; Xu, Shuhua
作者单位	1.Beijing Jiaotong Univ, Sch Sci, Dept Math, Beijing 100044, Peoples R China 2.Chinese Acad Sci, Key Lab Computat Biol, Max Planck Independent Res Grp Populat Genom, Shanghai Inst Biol Sci,CAS MPG Partner Inst Compu, Shanghai 200031, Peoples R China 3.Chinese Acad Sci, Acad Math & Syst Sci, Inst Appl Math, Beijing 100190, Peoples R China 4.ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai 200031, Peoples R China 5.Collaborat Innovat Ctr Genet & Dev, Shanghai 200438, Peoples R China
推荐引用方式 GB/T 7714	Ni, Xumin,Yang, Xiong,Guo, Wei,et al. Length Distribution of Ancestral Tracks under a General Admixture Model and Its Applications in Population History Inference[J]. SCIENTIFIC REPORTS,2016,6:12.
APA	Ni, Xumin.,Yang, Xiong.,Guo, Wei.,Yuan, Kai.,Zhou, Ying.,...&Xu, Shuhua.(2016).Length Distribution of Ancestral Tracks under a General Admixture Model and Its Applications in Population History Inference.SCIENTIFIC REPORTS,6,12.
MLA	Ni, Xumin,et al."Length Distribution of Ancestral Tracks under a General Admixture Model and Its Applications in Population History Inference".SCIENTIFIC REPORTS 6(2016):12.