KMS Of Academy of mathematics and systems sciences, CAS
| AdmixSim: A Forward-Time Simulator for Various Complex Scenarios of Population Admixture | |
| Yang, Xiong1,2; Yuan, Kai1,2; Ni, Xumin3; Zhou, Ying1,2; Guo, Wei4; Xu, Shuhua1,2,5,6,7,8 | |
| 2020-12-03 | |
| Source Publication | FRONTIERS IN GENETICS
 |
| Volume | 11Pages:5 |
| Abstract | 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. |
| Keyword | simulation population admixture genetic ancestry Wright Fisher model admixture model |
| DOI | 10.3389/fgene.2020.601439 |
| Indexed By | SCI |
| Language | 英语 |
| Funding Project | 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 Research Area | Genetics & Heredity |
| WOS Subject | Genetics & Heredity |
| WOS ID | WOS:000599279200001 |
| Publisher | FRONTIERS MEDIA SA |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.amss.ac.cn/handle/2S8OKBNM/57781 |
| Collection | 中国科学院数学与系统科学研究院 |
| Corresponding Author | Xu, Shuhua |
| Affiliation | 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 |
| Recommended Citation 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. |
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