AdmixSim: A Forward-Time Simulator for Various Complex Scenarios of Population Admixture

doi:10.3389/fgene.2020.601439

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	AdmixSim: A Forward-Time Simulator for Various Complex Scenarios of Population Admixture
	Yang, Xiong 1,2; Yuan, Kai 1,2; Ni, Xumin 3; Zhou, Ying 1,2; Guo, Wei 4; Xu, Shuhua 1,2,5,6,7,8
	2020-12-03
发表期刊	FRONTIERS IN GENETICS
卷号	11 页码:5
摘要	Background: Population admixture is a common phenomenon in humans, animals, and plants, and it plays a very important role in shaping individual genetic architecture and population genetic diversity. Inference of population admixture, however, is very challenging and typically relies on in silico simulation. We are aware of the lack of a computerized tool for such a purpose. A simulator capable of generating data under various complex admixture scenarios would facilitate the study of recombination, linkage disequilibrium, ancestry tracing, and admixture dynamics in admixed populations. We described such a simulator here. Results: We developed a forward-time simulator (AdmixSim) under the standard Wright Fisher model. It can simulate the following admixed populations: (1) multiple ancestral populations; (2) multiple waves of admixture events; (3) fluctuating population size; and (4) admixtures of fluctuating proportions. Analysis of the simulated data by AdmixSim showed that our simulator can quickly and accurately generate data resembling real-world values. We included in AdmixSim all possible parameters that would allow users to modify and simulate any kind of admixture scenario easily, so it is very flexible. AdmixSim records recombination break points and traces of each chromosomal segment from different ancestral populations, with which users can easily perform further analysis and comparative studies with empirical data. Conclusions: AdmixSim facilitates the study of population admixture by providing a simulation framework with the flexible implementation of various admixture models and parameters.
关键词	simulation population admixture genetic ancestry Wright Fisher model admixture model
DOI	10.3389/fgene.2020.601439
收录类别	SCI
语种	英语
资助项目	National Science Fund for Distinguished Young Scholars[31525014] ; National Natural Science Foundation of China (NSFC)[32030020] ; National Natural Science Foundation of China (NSFC)[91731303] ; National Natural Science Foundation of China (NSFC)[31771388] ; National Natural Science Foundation of China (NSFC)[31961130380] ; National Natural Science Foundation of China (NSFC)[31900418] ; National Natural Science Foundation of China (NSFC)[32041008] ; National Natural Science Foundation of China (NSFC)[11801027] ; Chinese Academy of Sciences (CAS)[XDB38000000] ; Chinese Academy of Sciences (CAS)[QYZDJ-SSW-SYS009] ; UK Royal Society-Newton Advanced Fellowship[NAF\R1\191094] ; National Key Research and Development Program[2016YFC0906403] ; Shanghai Municipal Science and Technology Major Project[2017SHZDZX01] ; Fundamental Research Funds for the Central Universities[2020RC001]
WOS研究方向	Genetics & Heredity
WOS类目	Genetics & Heredity
WOS记录号	WOS:000599279200001
出版者	FRONTIERS MEDIA SA
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/57781
专题	中国科学院数学与系统科学研究院
通讯作者	Xu, Shuhua
作者单位	1.Chinese Acad Sci, Key Lab Computat Biol, Shanghai, Peoples R China 2.Chinese Acad Sci, Univ Chinese Acad Sci, Shanghai Inst Nutr & Hlth, Max Planck Soc MPG,Partner Inst Computat Biol, Shanghai, Peoples R China 3.Beijing Jiaotong Univ, Sch Sci, Dept Math, Beijing, Peoples R China 4.Chinese Acad Sci, Acad Math & Syst Sci, Inst Appl Math, Beijing, Peoples R China 5.ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai, Peoples R China 6.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming, Yunnan, Peoples R China 7.Zhengzhou Univ, Henan Inst Med & Pharmaceut Sci, Zhengzhou, Peoples R China 8.Fudan Univ, Collaborat Innovat Ctr Genet & Dev, Shanghai, Peoples R China
推荐引用方式 GB/T 7714	Yang, Xiong,Yuan, Kai,Ni, Xumin,et al. AdmixSim: A Forward-Time Simulator for Various Complex Scenarios of Population Admixture[J]. FRONTIERS IN GENETICS,2020,11:5.
APA	Yang, Xiong,Yuan, Kai,Ni, Xumin,Zhou, Ying,Guo, Wei,&Xu, Shuhua.(2020).AdmixSim: A Forward-Time Simulator for Various Complex Scenarios of Population Admixture.FRONTIERS IN GENETICS,11,5.
MLA	Yang, Xiong,et al."AdmixSim: A Forward-Time Simulator for Various Complex Scenarios of Population Admixture".FRONTIERS IN GENETICS 11(2020):5.