GSR: Simulator - BOTTLENECK

Basic Package Attributes
AttributeValue
Title BOTTLENECK
Short Description Bottleneck is a program for detecting recent effective population size reductions from allele data frequencies
Long Description The program BOTTLENECK computes for each population sample and for each locus the distribution of the heterozygosity expected from the observed number of alleles (k), given the sample size (n) under the assumption of mutation-drift equilibrium. This distribution is obtained through simulating the coalescent process of n genes under two possible mutation models, the IAM and the SMM. This enables the computation of the average (Hexp) which is compared to the observed heterozygosity (Hobs, in the sense of Nei's gene diversity) to establish whether there is an heterozygosity excess or deficit at this locus. In addition, the standard deviation (SD) of the mutation-drift equilibrium distribution of the heterozygosity is used to compute the standardized difference for each locus ((Hobs-Hexp)/SD). The distribution obtained through simulation enables also the computation of a P-value for the observed heterozygosity.
Version 1.2.02
Project Started 1999
Last Release 21 years, 8 months ago
Homepagehttp://www1.montpellier.inra.fr/CBGP/software/Bottleneck/bottleneck.html
Citations Cornuet JM, Luikart G, Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data., Genetics, 12-01-1996 [ Abstract, cited in PMC ]
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Last evaluated03-23-2018 (939 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,
VariationsBiallelic Marker, Microsatellite,
Simulation MethodStandard Coalescent (Conditioning by the observed number of alleles),
Input
Data Type
File formatGenepop, Other (Genetix),
Output
Data TypeGenotype or Sequence,
Sequencing Reads
File Format
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesConstant Size, Bottleneck,
Gene Flow
Spatiality
Life Cycle
Mating SystemRandom Mating,
FecundityConstant Number,
Natural Selection
Determinant
Models
Recombination
Mutation ModelsInfinite-allele Model, Stepwise Mutation Model,
Events Allowed
Other
InterfaceCommand-line,
Development
Tested PlatformsWindows,
LanguageOther (Delphi),
License
GSR CertificationApplication,

The following 2 publications are selected examples of applications that used BOTTLENECK.

2018

Souza-Shibatta L, Kotelok-Diniz T, Ferreira DG, Shibatta OA, Sofia SH, de Assumpção L, Pini SFR, Makrakis S, Makrakis MC, Genetic Diversity of the Endangered Neotropical Cichlid Fish (<i>Gymnogeophagus setequedas</i>) in Brazil., Front Genet, 01-01-2018 [Abstract]

Meng JW, He DC, Zhu W, Yang LN, Wu EJ, Xie JH, Shang LP, Zhan J, Human-Mediated Gene Flow Contributes to Metapopulation Genetic Structure of the Pathogenic Fungus <i>Alternaria alternata</i> from Potato., Front Plant Sci, 01-01-2018 [Abstract]


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