GSR: Simulator - CDPOP

Basic Package Attributes
AttributeValue
Title CDPOP
Short Description CDPOP is a landscape genetics tool for simulating the emergence of spatial genetic structure in populations resulting from specified landscape processes governing organism movement behavior.
Long Description CDPOP (Cost Distance POPulations) is an individual-based simulator of gene flow in complex landscapes to explain observed population responses and provide a foundation for landscape genetics. It models genetic exchange among spatially located individuals as a function of individual-based movement through mating and dispersal, incorporating population dynamics and the all factors that affect the frequency of an allele in a population (mutation, gene flow, genetic drift, and selection). User’s initially specify individual locations, environmental conditions governing gene flow, spatially-explicit fitness landscapes governing selection, and various genic configurations, and CDPOP models divergence through time as function of individual-based movement, breeding and dispersal as functions of the given landscape surfaces.
Version 1.0 or later
Project Started 2010
Last Release 4 years, 2 months ago
Homepagehttps://github.com/ComputationalEcologyLab/CDPOP
Citations Landguth EL, Cushman SA, cdpop: A spatially explicit cost distance population genetics program., Mol Ecol Resour, 01-01-2010 [ Abstract, cited in PMC ]
GSR CertificationGSR-certified

Accessibility
Documentation
Application
Support

Last evaluated12-29-2017 (1022 days ago)
Author verificationThe basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator.
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataGenotype at Genetic Markers, Diploid DNA Sequence, Sex Chromosomes, Mitochondrial DNA,
VariationsBiallelic Marker, Multiallelic Marker, Single Nucleotide Variation, Microsatellite,
Simulation MethodForward-time,
Input
Data TypeAllele Frequencies (Example format file provided with documentation), Empirical (Known data can be used to start simulations and example format is provide with documentation for known genotypes.),
File formatGenepop, STRUCTURE, Program Specific (Cdpop specific formatted genotypes can be used to start simulations and a provided format is given in documentation.), Other,
Output
Data TypeGenotype or Sequence, Demographic (An output file is provided for each generation run with various demographic parameters, including birth sizes, migration sizes, death number), Mutation (Given in the output file.), Diversity Measures (Given in the output file.), Fitness (If selection was initialized, then the frequency information for the alleles at the loci under selection will be shown in the output file.),
Sequencing ReadsOther (Various other statastics in output file include, mean and standard deviations for dispersal distances and mate distances, mean and standard ),
File FormatGenepop, STRUCTURE, Program Specific (A general option included, as well as cdpop formatted data), Other (Genalex),
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size (The population will remain constant if all open habitat locations are filled, which is a function of vital rates and the ability of an indiv), Exponential Growth or Decline (The population cannot grow exponentially, but it can decline exponentially.), Logistic Growth, Bottleneck, Carrying Capacity (Set at the beginning of the simulations.),
Gene FlowStepping Stone Models, Island Models, Continent-Island Models, Sex or Age-Specific Migration Rates, Influenced by Environmental Factors, Admixed Population (Not directly, but could be simulated with different areas of the genotype), Other (Individuals move as a probabilistic function of their environment (e.g., as habitat fragmentation increases)),
Spatiality
Life CycleDiscrete Generation Model, Age structured, Overlapping Generation,
Mating SystemRandom Mating, Monogamous, Polygamous, Selfing, Age- or Stage-Specific, Assortative or Disassortative,
FecundityConstant Number, Randomly Distributed, Influenced by Environment,
Natural Selection
DeterminantSingle-locus, Multi-locus, Fitness of Offspring, Environmental Factors,
ModelsDirectional Selection, Balancing Selection, Multi-locus models, Epistasis, Disruptive, Frequency-Dependent,
RecombinationUniform,
Mutation ModelsTwo-allele Mutation Model, k-Allele Model, Stepwise Mutation Model,
Events AllowedVarying Demographic Features (Can change landscape at given generations. the dispersal kernel varies spatial depending on the landscape.), Population Events, Varying Genetic Features,
Other
InterfaceCommand-line, Graphical User Interface, Script-based (Python),
Development
Tested PlatformsWindows, Mac OS X, Linux and Unix,
LanguagePython,
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation, Application, Support,

The following 28 publications are selected examples of applications that used CDPOP.

2017

Shirk AJ, Landguth EL, Cushman SA, A comparison of individual-based genetic distance metrics for landscape genetics., Mol Ecol Resour, 11-01-2017

Stucki S, Orozco-terWengel P, Forester BR, Duruz S, Colli L, Masembe C, Negrini R, Landguth E, Jones MR, Bruford MW, Taberlet P, et al., High performance computation of landscape genomic models including local indicators of spatial association., Mol Ecol Resour, 09-01-2017

Creech TG, Epps CW, Landguth EL, Wehausen JD, Crowhurst RS, Holton B, Monello RJ, Simulating the spread of selection-driven genotypes using landscape resistance models for desert bighorn sheep., PLoS One, 01-01-2017

Shirk AJ, Landguth EL, Cushman SA, A comparison of regression methods for model selection in individual-based landscape genetic analysis., Mol Ecol Resour, 08-10-2017

Stucki S, Orozco-terWengel P, Forester BR, Duruz S, Colli L, Masembe C, Negrini R, Landguth E, Jones MR, Bruford MW, Taberlet P, et al., High performance computation of landscape genomic models including local indicators of spatial association., Mol Ecol Resour, 09-01-2017 [Abstract]

Shirk AJ, Landguth EL, Cushman SA, A comparison of individual-based genetic distance metrics for landscape genetics., Mol Ecol Resour, 11-01-2017 [Abstract]

Creech TG, Epps CW, Landguth EL, Wehausen JD, Crowhurst RS, Holton B, Monello RJ, Simulating the spread of selection-driven genotypes using landscape resistance models for desert bighorn sheep., PLoS One, 01-01-2017 [Abstract]

Shirk AJ, Landguth EL, Cushman SA, A comparison of regression methods for model selection in individual-based landscape genetic analysis., Mol Ecol Resour, 08-10-2017 [Abstract]

2016

Cushman SA, Landguth EL, Spatially Heterogeneous Environmental Selection Strengthens Evolution of Reproductively Isolated Populations in a Dobzhansky-Muller System of Hybrid Incompatibility., Front Genet, 01-01-2016

Forester BR, Jones MR, Joost S, Landguth EL, Lasky JR, Detecting spatial genetic signatures of local adaptation in heterogeneous landscapes., Mol Ecol, 01-01-2016

Smith AL, Landguth EL, Bull CM, Banks SC, Gardner MG, Driscoll DA, Dispersal responses override density effects on genetic diversity during post-disturbance succession., Proc Biol Sci, 03-30-2016

Zeller KA, Creech TG, Millette KL, Crowhurst RS, Long RA, Wagner HH, Balkenhol N, Landguth EL, Using simulations to evaluate Mantel-based methods for assessing landscape resistance to gene flow., Ecol Evol, 06-01-2016

Forester BR, Jones MR, Joost S, Landguth EL, Lasky JR, Detecting spatial genetic signatures of local adaptation in heterogeneous landscapes., Mol Ecol, 01-01-2016 [Abstract]

Smith AL, Landguth EL, Bull CM, Banks SC, Gardner MG, Driscoll DA, Dispersal responses override density effects on genetic diversity during post-disturbance succession., Proc Biol Sci, 03-30-2016 [Abstract]

Zeller KA, Creech TG, Millette KL, Crowhurst RS, Long RA, Wagner HH, Balkenhol N, Landguth EL, Using simulations to evaluate Mantel-based methods for assessing landscape resistance to gene flow., Ecol Evol, 06-01-2016 [Abstract]

Cushman SA, Landguth EL, Spatially Heterogeneous Environmental Selection Strengthens Evolution of Reproductively Isolated Populations in a Dobzhansky-Muller System of Hybrid Incompatibility., Front Genet, 01-01-2016 [Abstract]

2015

Landguth EL, Johnson NA, Cushman SA, Clusters of incompatible genotypes evolve with limited dispersal., Front Genet, 01-01-2015

Landguth EL, Johnson NA, Cushman SA, Clusters of incompatible genotypes evolve with limited dispersal., Front Genet, 01-01-2015 [Abstract]

2014

Landguth EL, Schwartz M., Evaluating sample allocation and effort in detecting population differentiation for discrete and continuously distributed individuals, Conservation Genetics, 08-01-2014

Cooke GM, Landguth EL, Beheregaray LB, Riverscape genetics identifies replicated ecological divergence across an Amazonian ecotone., Evolution, 07-01-2014

Cooke GM, Landguth EL, Beheregaray LB, Riverscape genetics identifies replicated ecological divergence across an Amazonian ecotone., Evolution, 07-01-2014 [Abstract]

Beheregaray LB, Cooke GM, Chao NL, Landguth EL, Ecological speciation in the tropics: insights from comparative genetic studies in Amazonia., Front Genet, 01-01-2014 [Abstract]

2013

Jones MR, Forester BR, Teufel AI, Adams RV, Anstett DN, Goodrich BA, Landguth EL, Joost S, Manel S, Integrating landscape genomics and spatially explicit approaches to detect loci under selection in clinal populations., Evolution, 12-01-2013 [Abstract]

2012

Landguth EL, Cushman SA, Johnson NA, Simulating natural selection in landscape genetics., Mol Ecol Resour, 03-01-2012 [Abstract]

Blair C, Weigel DE, Balazik M, Keeley AT, Walker FM, Landguth E, Cushman S, Murphy M, Waits L, Balkenhol N, A simulation-based evaluation of methods for inferring linear barriers to gene flow., Mol Ecol Resour, 09-01-2012 [Abstract]

2010

Cushman SA, Landguth EL, Spurious correlations and inference in landscape genetics., Mol Ecol, 09-01-2010 [Abstract]

Landguth EL, Cushman SA, Schwartz MK, McKelvey KS, Murphy M, Luikart G, Quantifying the lag time to detect barriers in landscape genetics., Mol Ecol, 10-01-2010 [Abstract]

Landguth EL, Cushman SA, Murphy MA, Luikart G, Relationships between migration rates and landscape resistance assessed using individual-based simulations., Mol Ecol Resour, 09-01-2010 [Abstract]


Propose changes to this simulator