Bottleneck Effect Simulator (heterozygosity loss)

Bottleneck Effect Simulator (heterozygosity loss) | Online Free Tool | Elysia Tools

Tool usage guide

Learn when to use this tool, what it supports, and how real users apply it.

Key facts

Category: Education
Input types: number
Output type: json
Sample coverage: 4
API ready: Yes

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.

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

1Enter the starting heterozygosity H₀, bottleneck size Nb, bottleneck duration t, recovery size Nr, and recovery duration g.
2The tool applies H_final = H₀(1−1/2Nb)^t(1−1/2Nr)^g to estimate expected heterozygosity after both periods.
3It reports heterozygosity retention, cumulative inbreeding coefficient F, and harmonic-mean effective population size Ne.
4Enter 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.

Examples

1. Northern elephant seal-like bottleneck

Conservation genetics student

Background

A population falls to 20 individuals for five generations, then recovers to 2,000 individuals for ten generations. The starting heterozygosity is 0.5.

Problem

Estimate how much genetic diversity remains after the bottleneck and recovery periods.

How to use

Enter H₀ = 0.5, Nb = 20, t = 5, Nr = 2000, g = 10, and focal allele frequency p = 0.1.

Initial heterozygosity: 0.5; bottleneck size: 20; bottleneck generations: 5; recovery size: 2000; recovery generations: 10; allele frequency: 0.1; decimal places: 4.

Outcome

Final heterozygosity is 0.4394, or 87.89% retained, with F = 0.1211 and harmonic-mean Ne = 29.55. The focal allele's one-generation survival estimate is 98.52%.

2. Severe prolonged bottleneck

Population genetics instructor

Background

A population remains at five individuals for ten generations before recovering to 5,000 individuals for five generations. The starting heterozygosity is 0.5.

Problem

Show how a small population size maintained for several generations can dominate the genetic outcome even after recovery.

FAQ

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.

Initial heterozygosity: 0.5; bottleneck size: 5; bottleneck generations: 10; recovery size: 5000; recovery generations: 5; allele frequency: 0.1; decimal places: 4.

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Learn when to use this tool, what it supports, and how real users apply it.

Key facts

Overview

When to use

How it works

Use cases

Examples

1. Northern elephant seal-like bottleneck

2. Severe prolonged bottleneck

FAQ

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