# Bottleneck Effect Simulator (heterozygosity loss) Expected heterozygosity loss through a population bottleneck: H_final = H₀(1−1/2Nb)^t(1−1/2Nr)^g, retention, inbreeding F, harmonic-mean Ne, and one-generation allele survival. Derived from Wright 1931, Nei et al. 1975, Hartl & Clark 2007, StatPearls. Educational use only. > Canonical page: https://elysiatools.com/en/tools/bottleneck-effect-simulator - **Category:** Education - **Keywords:** bottleneck effect, population bottleneck, genetic drift, heterozygosity loss, effective population size, inbreeding, genetic diversity, conservation genetics, population genetics, genetics ## Overview The Bottleneck Effect Simulator estimates expected heterozygosity after a population bottleneck and recovery period. Enter initial heterozygosity, bottleneck and recovery population sizes, durations, and focal allele frequency to calculate heterozygosity retention, inbreeding coefficient, harmonic-mean effective population size, and one-generation allele survival. ## Inputs - **Initial heterozygosity H₀** (number): Heterozygosity before the bottleneck (0 < H₀ ≤ 1). - **Bottleneck population size** (number): Census size during the bottleneck (Nb). - **Bottleneck generations** (number): Number of generations spent at the bottleneck size (t). - **Recovery population size** (number): Census size after recovery (Nr). - **Recovery generations** (number): Generations spent at the recovery size (g; 0 to skip). - **Focal allele frequency** (number): Frequency p of a focal allele used for the one-generation bottleneck survival estimate. - **Decimal Places** (number) ## When to use - Estimate how a short period of small population size can reduce genetic diversity. - Compare the expected effects of mild and severe bottlenecks across different generation counts. - Use population-genetics examples for teaching genetic drift, inbreeding, and allele loss. ## How it works - Enter the starting heterozygosity H₀, bottleneck size Nb, bottleneck duration t, recovery size Nr, and recovery duration g. - The tool applies H_final = H₀(1−1/2Nb)^t(1−1/2Nr)^g to estimate expected heterozygosity after both periods. - It reports heterozygosity retention, cumulative inbreeding coefficient F, and harmonic-mean effective population size Ne. - Enter a focal allele frequency p to estimate its probability of surviving one bottleneck generation, with results rounded to the selected number of decimal places. ## Use cases - Conservation genetics: estimate diversity loss after a wildlife population crash and subsequent recovery. - Population genetics education: demonstrate how bottleneck size and duration affect heterozygosity and inbreeding. - Comparative analysis: contrast a moderate bottleneck with a severe, prolonged reduction in population size. ## Frequently asked questions ### What does the simulator calculate? It calculates final heterozygosity, retention, inbreeding coefficient, harmonic-mean effective population size, and one-generation survival for a focal allele. ### What is the bottleneck population size? It is the census population size maintained during the bottleneck period, represented as Nb. ### What happens if recovery generations is zero? The recovery phase is skipped, so the result reflects only the specified bottleneck period. ### How is focal allele survival estimated? For allele frequency p, one-generation survival is estimated as 1 − (1−p)^(2Nb). ### Is this a stochastic population simulation? No. It provides deterministic expected values based on the stated formulas and is intended for educational use. ## Related tools - [Amino Acid Composition Analyzer](https://elysiatools.com/en/tools/amino-acid-composition): Per-residue counts and mol%, group tallies, Kyte–Doolittle GRAVY score, and ProtParam MW from a sequence. 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