RT Journal Article
SR Electronic
T1 AdmixSim: A Forward-Time Simulator for Various and Complex Scenarios of Population Admixture
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 037135
DO 10.1101/037135
A1 Xiong Yang
A1 Xumin Ni
A1 Ying Zhou
A1 Wei Guo
A1 Kai Yuan
A1 Shuhua Xu
YR 2016
UL http://biorxiv.org/content/early/2016/01/18/037135.abstract
AB Background Population admixture has been a common phenomenon in human, animals and plants, and plays a very important role in shaping individual genetic architecture and population genetic diversity. Inference of population admixture, however, is challenging and typically relies on in silico simulation. We are aware of the lack of a computer tool for such a purpose, especially a simulator is not available for generating data under various and complex admixture scenarios.Results Here we developed a forward-time simulator (AdmixSim) under standard Wright Fisher model, which can simulate admixed populations with: 1) multiple ancestral populations; 2) multiple waves of admixture events; 3) fluctuating population size; and 4) fluctuating admixture proportions. Results of analysis of the simulated data by AdmixSim show that our simulator can fast and accurately generate data resemble real one. We included in AdmixSim all possible parameters that allow users to modify and simulate any kinds of admixture scenarios easily so that it is very flexible. AdmixSim records recombination break points and trace of each chromosomal segment from different ancestral populations, with which users can easily do further analysis and comparative studies with empirical data.Conclusions AdmixSim is expected to facilitate the study of population admixture by providing a simulation framework with flexible implementation of various admixture models and parameters.AbbreviationsAbbreviationExpansionCGFContinuous gene flowGAGradual admixtureHIHybrid isolationLACSLength of ancestral chromosomal segmentPCAPrincipal component analysisPCPrincipal component