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Length Distribution of Ancestral Tracks under a General Admixture Model and Its Applications in Population History Inference
Ni, Xumin1; Yang, Xiong2; Guo, Wei3; Yuan, Kai2; Zhou, Ying2; Ma, Zhiming3; Xu, Shuhua2,4,5
2016-01-28
Source PublicationSCIENTIFIC REPORTS
ISSN2045-2322
Volume6Pages:12
AbstractThe 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.
DOI10.1038/srep20048
Language英语
Funding ProjectStrategic 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 Research AreaScience & Technology - Other Topics
WOS SubjectMultidisciplinary Sciences
WOS IDWOS:000368786700001
PublisherNATURE PUBLISHING GROUP
Citation statistics
Cited Times:7[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.amss.ac.cn/handle/2S8OKBNM/21838
Collection应用数学研究所
Affiliation1.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
Recommended Citation
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.
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