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GSR: Simulator - BottleSim
| Attribute | Value |
|---|---|
| Title | BottleSim |
| Short Description | a simulation program for changes in genetic diversity during the process of population bottlenecks |
| Long Description | Population bottlenecks reduce genetic diversity and thus cause great concern in conservation biology. Previous theoretical studies often assume discrete generations in projecting declines in genetic diversity caused by bottlenecks. This assumption creates complexities when applying the models to long-lived species with overlapping generations. BottleSim is a program for simulating bottlenecks to estimate the impact on genetic diversity; the novelties include an overlapping-generation model, a wide range of reproductive systems, and flexible population size settings. With these features, BottleSim will be a useful tool for estimating the genetic consequences of bottlenecks, evaluating conservation plans, and performing power analysis. |
| Keywords | population genetics, bottleneck, microsatellite, genetic diversity |
| Version | 2.6 |
| Project Started | 2003 |
| Last Release | 20 years, 10 months ago |
| Homepage | https://github.com/chihhorngkuo/BottleSim |
| Citations | Kuo CH, Janzen FJ, bottlesim: a bottleneck simulation program for long-lived species with overlapping generations, Molecular Ecology Notes, 10-09-2003 [ Abstract ] |
| GSR Certification |  ✔ Accessibility |
| Last evaluated | 03-23-2018 (2213 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | Genotype at Genetic Markers, |
| Variations | Biallelic Marker, Multiallelic Marker, Microsatellite, |
| Simulation Method | Forward-time, Resample Existing Data, |
| Input | |
| Data Type | Other, |
| File format | Program Specific, |
| Output | |
| Data Type | Genotype or Sequence, Diversity Measures, |
| Sequencing Reads | |
| File Format | Genepop, Program Specific, |
| Sample Type | |
| Phenotype | |
| Trait Type | |
| Determinants | |
| Evolutionary Features | |
| Demographic | |
| Population Size Changes | Constant Size, Exponential Growth or Decline, Logistic Growth, Bottleneck, Carrying Capacity, User Defined, |
| Gene Flow | |
| Spatiality | |
| Life Cycle | Overlapping Generation, |
| Mating System | Random Mating, Selfing, Age- or Stage-Specific, |
| Fecundity | Randomly Distributed, |
| Natural Selection | |
| Determinant | |
| Models | |
| Recombination | |
| Mutation Models | |
| Events Allowed | |
| Other | |
| Interface | Command-line, |
| Development | |
| Tested Platforms | Windows, Mac OS X, Linux and Unix, |
| Language | C or C++, |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, Application, Support, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 3
The following 3 publications are selected examples of applications that used BottleSim.
2023
Guinto, D.; Cross, M.; Lipps, G., Jr.; Lee, Y.; Kingsbury, B.; Earl, D.; Dempsey, C.; Hinson, J.; Jordan, M., Conservation Genetic Analysis of Blanding’s Turtles across Ohio, Indiana, and Michigan, Diversity, 10-11-2023 [Abstract]
2022
Zhang S, Lin M, Liu J, Chen J, Liu D, Zhao J, Yao M, A centenary tale: population genetic insights into the introduction history of the oriental fire-bellied toad (Bombina orientalis) in Beijing., BMC Ecol Evol, 10-14-2022 [Abstract]
2004
Kuo CH, Janzen FJ, Genetic effects of a persistent bottleneck on a natural population of ornate box turtles (Terrapene ornata), Conservation Genetics, 08-01-2004 [Abstract]