Bottleneck is a program for detecting recent effective population size reductions from allele data frequencies Long Description (required)
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. http://www1.montpellier.inra.fr/CBGP/software/Bottleneck/bottleneck.html
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Summary of Proposed Changes Current Citations/Applications
[Pubmed ID: 8978083 ],
Cornuet JM, Luikart G ,
Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. ,
Genetics ,
12-01-1996 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=8978083, Primary Citation
[Pubmed ID: 29456551 ],
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 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=29456551, , Application
[Pubmed ID: 29497439 ],
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 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=29497439, , Application