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, Zhiming1,3; Xu, Shuhua2,4,5
2016-01-28
发表期刊SCIENTIFIC REPORTS
ISSN2045-2322
卷号6
发表状态已发表
DOI10.1038/srep20048
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.
收录类别SCI
语种英语
资助项目Key Laboratory of Random Complex Structures and Data Science, CAS[2008DP173182]
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
WOS关键词CHROMOSOMAL SEGMENTS ; LIKELIHOOD RATIO ; NEANDERTHAL
原始文献类型Article
引用统计
文献类型期刊论文
条目标识符https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/1937
专题生命科学与技术学院_特聘教授组_徐书华组
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
通讯作者单位生命科学与技术学院
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.
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.
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).
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