AdmixSim 2: a forward-time simulator for modeling complex population admixture

Rui Zhang,Shuhua Xu,Chang Liu,Yuwen Pan,Kai Yuan,Xumin Ni

doi:10.1186/s12859-021-04415-x

Abstract

BackgroundComputer simulations have been widely applied in population genetics and evolutionary studies. A great deal of effort has been made over the past two decades in developing simulation tools. However, there are not many simulation tools suitable for studying population admixture.ResultsWe here developed a forward-time simulator, AdmixSim 2, an individual-based tool that can flexibly and efficiently simulate population genomics data under complex evolutionary scenarios. Unlike its previous version, AdmixSim 2 is based on the extended Wright-Fisher model, and it implements many common evolutionary parameters to involve gene flow, natural selection, recombination, and mutation, which allow users to freely design and simulate any complex scenario involving population admixture. AdmixSim 2 can be used to simulate data of dioecious or monoecious populations, autosomes, or sex chromosomes. To our best knowledge, there are no similar tools available for the purpose of simulation of complex population admixture. Using empirical or previously simulated genomic data as input, AdmixSim 2 provides phased haplotype data for the convenience of further admixture-related analyses such as local ancestry inference, association studies, and other applications. We here evaluate the performance of AdmixSim 2 based on simulated data and validated functions via comparative analysis of simulated data and empirical data of African American, Mexican, and Uyghur populations.ConclusionsAdmixSim 2 is a flexible simulation tool expected to facilitate the study of complex population admixture in various situations.

Highlights

Computer simulations have been widely applied in population genetics and evolutionary studies
Recombination, and mutation To validate the basic functions of our simulator, we used admixture models of three typical admixed populations (African Americans, Mexicans, and Uyghurs) which are of 2, 3, and 4 distinct ancestral originations, respectively (Additional file 4: Table S1)
The results of principal component analysis (PCA) and admixture analysis were largely concordant between simulated data and empirical data, indicating the simulated data by AdmixSim 2 are a satisfactory alternative on a global level

Summary

Introduction

Computer simulations have been widely applied in population genetics and evolutionary studies. Among forward-time simulators, some possess functions to simulate a process of population admixture directly, such as admix’em [12], SELAM [13], SLiM [14,15,16], simuPOP, fwdpp [17], and forqs [18] They are flexible and computationally efficient in fields of their respective designing objectives and workable on other demographic scenarios. We introduce a highly flexible and user-friendly forward-time simulation tool called AdmixSim 2 It allows simulating real sequence data in a series of complex admixture processes with various evolutionary driving forces including de novo mutation, drift, recombination, and natural selection. The source code of AdmixSim 2 is freely available at https://www.picb.ac.cn/PGG/resource.php or https://github.com/Shuhua-Group/AdmixSim

Results

Discussion

Conclusion