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.
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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.
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.