Filters








9 Hits in 3.8 sec

SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination

Nicolas Ray, Mathias Currat, Matthieu Foll, Laurent Excoffier
2010 Bioinformatics  
The spatially explicit simulation framework can account for environmental heterogeneity and fluctuations, and it can manage multiple population sources.  ...  SPLATCHE2 is a program to simulate the demography of populations and the resulting molecular diversity for a wide range of evolutionary scenarios.  ...  ACKNOWLEDGEMENTS We thank Daniel Wegmann, Seraina Klopfstein, Samuel Neuenschwander, Grant Hamilton, Guillaume Laval, Pierre Berthier, Stefano Mona and Anna Sramkova for technical help and useful discussions  ... 
doi:10.1093/bioinformatics/btq579 pmid:20956243 fatcat:xffm5pgawrdanepq4dqbfgvdbe

SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal

2019 Bioinformatics  
SPLATCHE3 simulates genetic data under a variety of spatially explicit evolutionary scenarios, extending previous versions of the framework.  ...  The new capabilities include long-distance migration, spatially and temporally heterogeneous short-scale migrations, alternative hybridization models, simulation of serial samples of genetic data and a  ...  Acknowledgements We would like to thank the following people for their help in the development of Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btz311 pmid:31077292 pmcid:PMC6821363 fatcat:4h6yyfdodvazvdndu653idfb3m

Spatial and Temporal Simulation of Human Evolution. Methods, Frameworks and Applications

Macarena Benguigui, Miguel Arenas
2014 Current Genomics  
Here we review the mainly used methods and evolutionary frameworks to perform realistic spatially explicit computer simulations of human evolution.  ...  We finally discuss future implementations to improve current spatially explicit simulations and their derived applications in human evolution.  ...  We thank David A. Liberles, Russell A. Hermansen and Anke Konrad for helpful comments. We thank two reviewers for insightful comments and suggestions.  ... 
doi:10.2174/1389202915666140506223639 pmid:25132795 pmcid:PMC4133948 fatcat:xozxbinvgrh2fnw7mbxi6it65q

popRange: a highly flexible spatially and temporally explicit Wright-Fisher simulator

Kimberly F McManus
2015 Source Code for Biology and Medicine  
Results: This article presents popRange, a forward genetic simulator, which incorporates large-scale genetic data with stochastic spatially and temporally explicit demographic and selective models.  ...  Features such as spatially and temporally variable selection coefficients and demography are incorporated in a highly flexible manner. popRange is implemented as an R package and presented with an example  ...  Carlos Bustamante and Dr. Omar Cornejo for valuable feedback on the simulation framework and manuscript.  ... 
doi:10.1186/s13029-015-0036-4 pmid:25883677 pmcid:PMC4399400 fatcat:cvtfx7tihjdc5iooynluusqnba

Investigating sex-biased migration during the Neolithic transition in Europe, using an explicit spatial simulation framework

R. Rasteiro, P.-A. Bouttier, V. C. Sousa, L. Chikhi
2012 Proceedings of the Royal Society of London. Biological Sciences  
We developed a new individual-based simulation approach to explore the genetic consequences of 45 different scenarios, where we varied the patterns of PMR and admixture between HGs and farmers.  ...  for females and males.  ...  It uses a forward individualrather than backward/coalescent gene-based simulation framework, where the demographic and genetic simulations are carried simultaneously.  ... 
doi:10.1098/rspb.2011.2323 pmid:22298848 pmcid:PMC3350666 fatcat:3fr65vyphbh3hktimrtcqatcam

The genomic impact of historical hybridization with massive mitochondrial DNA introgression

Fernando A. Seixas, Pierre Boursot, José Melo-Ferreira
2018 Genome Biology  
Because invasion and selective sweeps similarly mold variation, population genetics evidence for selection can only be gathered in an explicit demographic framework.  ...  Hybrid incompatibilities and interplay between selection and recombination locally modulate levels of nuclear introgression.  ...  Acknowledgments We thank Liliana Farelo for preparing the DNA samples. Library preparation and sequencing were performed at the Genome Analysis Centre (TGAC, Norwich, presently Earlham Institute).  ... 
doi:10.1186/s13059-018-1471-8 pmid:30056805 pmcid:PMC6065068 fatcat:lsbanoawevgwtnz76cdbu2zplq

Reconstructing Demography and Social Behavior During the Neolithic Expansion from Genomic Diversity Across Island Southeast Asia

François Vallée, Aurélien Luciani, Murray P. Cox
2016 Genetics  
Such questions are ripe for computer modeling.  ...  Using Bayesian inference, model parameters were determined that produce simulations that closely resemble the admixture profiles of 2299 individuals from 84 populations across Island Southeast Asia.  ...  Individual-based models seem particularly well suited to spatially explicit simulations, with the key software in this area, SPLATCHE2 (Ray et al. 2010) , combining forwardin-time simulation of population  ... 
doi:10.1534/genetics.116.191379 pmid:27683274 pmcid:PMC5161281 fatcat:juzvprh2s5gm7nlasd5aj3fgte

Systems Modeling at Multiple Levels of Regulation: Linking Systems and Genetic Networks to Spatially Explicit Plant Populations

James Kitchen, Robin Allaby
2013 Plants  
Sedentism makes plants relevant candidates for spatially explicit modeling that is tied in with dynamical environments.  ...  We propose that in order to fully understand the complexities behind plant adaptation, a system that couples aspects from systems biology with population and landscape genetics is required.  ...  Subsequent simulations could add spatial explicitness, abiotic and biotic factors and GRNs.  ... 
doi:10.3390/plants2010016 pmid:27137364 pmcid:PMC4844292 fatcat:znk6leg5wjdeznmevcyq6azzbi

SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal

Mathias Currat, Miguel Arenas, Claudio S. Quilodràn, Laurent Excoffier, Nicolas Ray
2019
SPLATCHE3 simulates genetic data under a variety of spatially explicit evolutionary scenarios, extending previous versions of the framework.  ...  The new capabilities include longdistance migration, spatially and temporally heterogeneous short-scale migrations, alternative hybridization models, simulation of serial samples of genetic data and a  ...  Brown and David Roessli. Conflict of Interest: none declared.  ... 
doi:10.7892/boris.133890 fatcat:fqfn57j3w5dudnohewd5jbrrbi