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GSR: Simulator - CDPOP
| Attribute | Value |
|---|---|
| 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 | 7 years, 8 months ago |
| Homepage | https://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 Certification |  ✔ Accessibility |
| Last evaluated | 12-29-2017 (2297 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Genotype at Genetic Markers, Diploid DNA Sequence, Sex Chromosomes, Mitochondrial DNA, |
| Variations | Biallelic Marker, Multiallelic Marker, Single Nucleotide Variation, Microsatellite, |
| Simulation Method | Forward-time, |
| Input | |
| Data Type | Allele 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 format | Genepop, STRUCTURE, Program Specific (Cdpop specific formatted genotypes can be used to start simulations and a provided format is given in documentation.), Other, |
| Output | |
| Data Type | Genotype 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 Reads | Other (Various other statastics in output file include, mean and standard deviations for dispersal distances and mate distances, mean and standard ), |
| File Format | Genepop, 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 Changes | Constant 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 Flow | Stepping 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 Cycle | Discrete Generation Model, Age structured, Overlapping Generation, |
| Mating System | Random Mating, Monogamous, Polygamous, Selfing, Age- or Stage-Specific, Assortative or Disassortative, |
| Fecundity | Constant Number, Randomly Distributed, Influenced by Environment, |
| Natural Selection | |
| Determinant | Single-locus, Multi-locus, Fitness of Offspring, Environmental Factors, |
| Models | Directional Selection, Balancing Selection, Multi-locus models, Epistasis, Disruptive, Frequency-Dependent, |
| Recombination | Uniform, |
| Mutation Models | Two-allele Mutation Model, k-Allele Model, Stepwise Mutation Model, |
| Events Allowed | Varying Demographic Features (Can change landscape at given generations. the dispersal kernel varies spatial depending on the landscape.), Population Events, Varying Genetic Features, |
| Other | |
| Interface | Command-line, Graphical User Interface, Script-based (Python), |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, |
| Language | Python, |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 28
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]