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

2020 ◽  
Vol 11 ◽  
Author(s):  
Xiong Yang ◽  
Kai Yuan ◽  
Xumin Ni ◽  
Ying Zhou ◽  
Wei Guo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Population Genetic ◽  
Genetic Architecture ◽  
Simulated Data ◽  
Population Admixture ◽  
Common Phenomenon ◽  
Simulation Framework ◽  
Fisher Model ◽  
Break Points

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.

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

2016 ◽  
Author(s):  
Xiong Yang ◽  
Xumin Ni ◽  
Ying Zhou ◽  
Wei Guo ◽  
Kai Yuan ◽  
...  
Keyword(s):  
Population Genetic ◽  
Genetic Architecture ◽  
Simulated Data ◽  
Population Admixture ◽  
Simulation Framework ◽  
Computer Tool ◽  
Background Population ◽  
Fisher Model ◽  
In Silico Simulation ◽  
Break Points

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.

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

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Rui Zhang ◽  
Chang Liu ◽  
Kai Yuan ◽  
Xumin Ni ◽  
Yuwen Pan ◽  
...  
Keyword(s):  
Population Genomics ◽  
Association Studies ◽  
Simulated Data ◽  
Population Admixture ◽  
Simulation Tools ◽  
Fisher Model ◽  
Haplotype Data ◽  
Complex Population ◽  
Complex Scenario ◽  
Local Ancestry Inference

Abstract Background Computer 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. Results We 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. Conclusions AdmixSim 2 is a flexible simulation tool expected to facilitate the study of complex population admixture in various situations.

scholarly journals Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with polynomial functions

2016 ◽  
Author(s):  
Ying Zhou ◽  
Kai Yuan ◽  
Yaoliang Yu ◽  
Xumin Ni ◽  
Pengtao Xie ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Simulated Data ◽  
Population Admixture ◽  
Multiple Wave ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Complex Population ◽  
Important Challenge ◽  
Source Populations ◽  
Admixture Linkage Disequilibrium

AbstractTo infer the histories of population admixture, one important challenge with methods based on the admixture linkage disequilibrium (ALD) is to get rid of the effect of source LD (SLD) which is directly inherited from source populations. In previous methods, only the decay curve of weighted LD between pairs of sites whose genetic distance were larger than a certain starting distance was fitted by single or multiple exponential functions, for the inference of recent single- or multiple-wave of admixture. However, the effect of SLD has not been well defined and no tool has been developed to estimate the effect of SLD on weighted LD decay. In this study, we defined the SLD in the formularized weighted LD statistic under the two-way admixture model, and proposed polynomial spectrum (p-spectrum) to study the weighted SLD and weighted LD. We also found reference populations could be used to reduce the SLD in weighted LD statistic. We further developed a method, iMAAPs, to infer Multiple-wave Admixture by fitting ALD using Polynomial spectrum. We evaluated the performance of iMAAPs under various admixture models in simulated data and applied iMAAPs into analysis of genome-wide single nucleotide polymorphism data from the Human Genome Diversity Project (HGDP) and the HapMap Project. We showed that iMAAPs is a considerable improvement over other current methods and further facilitates the inference of the histories of complex population admixtures.

KERAGAMAN GENETIK INDUK UDANG WINDU DI PERAIRAN SELATAN PANGANDARAN DAN BINUANGEUN, JAWABARAT

2018 ◽  
Vol 5 (3) ◽  
Author(s):  
Ratu Siti Aliah
Keyword(s):  
Genetic Diversity ◽  
Population Genetic ◽  
Gene Locus ◽  
Penaeus Monodon ◽  
12S Rrna ◽  
Brood Stock ◽  
Population Genetic Diversity ◽  
Result Show ◽  
Mtdna Diversity

An evaluation of the Black Tiger Brood Stock (Penaeus monodon) genetic diversity of Pangandaran and Binuangeun was conducted by using the mtDNA diversity of two gene locus of CO I and 12S rRNA to understand their population genetic diversity. The result show that the brood stock of Pangandaran has 17 haplotipe, while from Binuangeun has 13 haplotipe. The result indicated that the genetic diversity of the Balck Tiger brood stock of Pangandaran was higher than thatBinuangeun.Key words : Genetic diversity, Black Tiger brood stock, Pangandaran, Binuangeun

Microsatellite analysis of population genetic diversity in Triplophysa xiangxiensis

2013 ◽  
Vol 37 (1) ◽  
pp. 26 ◽  
Author(s):  
Yanhong YAO ◽  
Lingfu KONG ◽  
Dengqiang WANG ◽  
Wenhui HE ◽  
Li HE ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Genetic ◽  
Microsatellite Analysis ◽  
Population Genetic Diversity

Allozyme variation and an estimate of the inbreeding coefficient in the coffee berry borer, Hypothenemus hampei (Coleoptera: Scolytidae)

1995 ◽  
Vol 85 (1) ◽  
pp. 21-28 ◽  
Author(s):  
Philippe Borsa ◽  
D. Pierre Gingerich
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Population Genetic ◽  
New Caledonia ◽  
Allozyme Variation ◽  
Inbreeding Coefficient ◽  
Hypothenemus Hampei ◽  
Coffee Berry ◽  
Biological Features ◽  
High Degree

AbstractSeven presumed Mendelian enzyme loci (Est-2, Est-3, Gpi, Idh-l, Idh-2, Mdh-2 and Mpi) were characterized and tested for polymorphism in coffee berry borers, Hypothenemus hampei (Ferrari), sampled in Côte d′Ivoire, Mexico and New Caledonia. The average genetic diversity was H = 0.080. Two loci, Mdh-2 and Mpi were polymorphic, and thus usable as genetic markers. The population structure of H. hampei was analysed using Weir & Cockerham's estimators of Wright's F-statistics. A high degree of inbreeding (f = 0.298) characterized the elementary geographic sampling unit, the coffee field. The estimate of gene flow between fields within a country was Nm = 10.6 and that between countries was Nm = 2. The population genetic structure in H. hampei could be related to its known population biological features and history.

scholarly journals Recombination and Gene Conversion in a 170-kb Genomic Region of Arabidopsis thaliana

Genetics ◽  
2002 ◽  
Vol 161 (3) ◽  
pp. 1269-1278 ◽  
Author(s):  
Bernhard Haubold ◽  
Jürgen Kroymann ◽  
Andreas Ratzka ◽  
Thomas Mitchell-Olds ◽  
Thomas Wiehe
Keyword(s):  
Genetic Diversity ◽  
Arabidopsis Thaliana ◽  
Linkage Disequilibrium ◽  
Gene Conversion ◽  
Genomic Sequence ◽  
Genomic Region ◽  
Resistance To Herbivory ◽  
Linkage Disequilibria ◽  
Coalescent Simulations ◽  
The Mean

Abstract Arabidopsis thaliana is a highly selfing plant that nevertheless appears to undergo substantial recombination. To reconcile its selfing habit with the observations of recombination, we have sampled the genetic diversity of A. thaliana at 14 loci of ~500 bp each, spread across 170 kb of genomic sequence centered on a QTL for resistance to herbivory. A total of 170 of the 6321 nucleotides surveyed were polymorphic, with 169 being biallelic. The mean silent genetic diversity (πs) varied between 0.001 and 0.03. Pairwise linkage disequilibria between the polymorphisms were negatively correlated with distance, although this effect vanished when only pairs of polymorphisms with four haplotypes were included in the analysis. The absence of a consistent negative correlation between distance and linkage disequilibrium indicated that gene conversion might have played an important role in distributing genetic diversity throughout the region. We tested this by coalescent simulations and estimate that up to 90% of recombination is due to gene conversion.

scholarly journals Modeling Linkage Disequilibrium and Identifying Recombination Hotspots Using Single-Nucleotide Polymorphism Data

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 2213-2233 ◽  
Author(s):  
Na Li ◽  
Matthew Stephens
Keyword(s):  
Linkage Disequilibrium ◽  
Recombination Rate ◽  
Population Sample ◽  
Simulated Data ◽  
Region Of Interest ◽  
Population Data ◽  
Recombination Rates ◽  
Single Nucleotide ◽  
Recombination Hotspots ◽  
Genomic Regions

AbstractWe introduce a new statistical model for patterns of linkage disequilibrium (LD) among multiple SNPs in a population sample. The model overcomes limitations of existing approaches to understanding, summarizing, and interpreting LD by (i) relating patterns of LD directly to the underlying recombination process; (ii) considering all loci simultaneously, rather than pairwise; (iii) avoiding the assumption that LD necessarily has a “block-like” structure; and (iv) being computationally tractable for huge genomic regions (up to complete chromosomes). We examine in detail one natural application of the model: estimation of underlying recombination rates from population data. Using simulation, we show that in the case where recombination is assumed constant across the region of interest, recombination rate estimates based on our model are competitive with the very best of current available methods. More importantly, we demonstrate, on real and simulated data, the potential of the model to help identify and quantify fine-scale variation in recombination rate from population data. We also outline how the model could be useful in other contexts, such as in the development of more efficient haplotype-based methods for LD mapping.

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