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Founder Effect Allele Retention Probability

· Last updated：2026-08-14

Binomial retention probability 1 − (1−p)^(2N) for an allele among N founders, expected copy number, drift variance, copy-number distribution, and neutral fixation probability. Derived from Mayr 1942, 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 Founder Effect Allele Retention Probability calculator estimates whether an allele with source frequency p is retained among 2N gene copies from N diploid founders. It also reports allele loss probability, expected copy number, drift variance, copy-number distribution, and neutral fixation probability for educational population-genetics analysis.

When to use

  • Estimate the probability that a source-population allele survives a population-founding event.
  • Compare allele retention and loss across different founder counts or source frequencies.
  • Explore how genetic drift affects founder-generation allele frequencies and later neutral fixation.

How it works

  1. 1Enter the number of diploid founders, N, and the allele frequency, p, in the source population.
  2. 2The calculator treats the founding event as binomial sampling across 2N gene copies.
  3. 3It calculates retention as 1 − (1−p)^(2N), loss as (1−p)^(2N), and expected copies as 2Np.
  4. 4The JSON result also includes drift variance, the copy-number distribution, and neutral fixation probability based on the retained copy count.

Use cases

  • Population genetics lessons demonstrating binomial sampling, genetic drift, and founder effects.
  • Conservation genetics comparisons involving small founding populations and rare alleles.
  • Educational analysis of founder mutations and why a retained rare allele can become more common after population isolation.

Examples

1. Pingelap-style founding event: 20 founders and p = 0.05

Population genetics student

Background

A teaching example models a small founding population of approximately 20 diploid founders and an allele with source frequency 0.05.

Problem

Estimate whether the allele is present in the 40 founder gene copies and quantify the expected founding effect.

How to use

Enter 20 for Founder count, 0.05 for Source allele frequency, and 4 for Decimal Places.

{"founderCount":20,"alleleFrequency":0.05,"decimalPlaces":4}

Outcome

The allele has an 87.15% retention probability and a 12.85% loss probability. The expected number of copies is 2.

2. Rare disease allele: 100 founders and p = 0.001

Genetics educator

Background

A rare allele has a source frequency of 0.001 and is sampled by 100 diploid founders, providing 200 founder gene copies.

Problem

Show how a very low source frequency can lead to frequent loss during founding, even when the allele may be amplified by later drift if retained.

How to use

FAQ

What does the founder count represent?

It is the number of diploid founders, N. Together they contribute 2N gene copies to the founding population.

What does source allele frequency mean?

It is the allele frequency p in the source population before founders are sampled, between 0 and 1.

How is allele retention calculated?

Retention is calculated as 1 − (1−p)^(2N), the probability that at least one of the 2N sampled gene copies carries the allele.

What are expected copies?

Expected copies are 2Np, the average number of allele copies predicted among the founders before sampling variation.

Is this calculator intended for clinical or conservation decisions?

No. It is an educational model of neutral founder-effect sampling and should not replace specialist analysis.

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Enter 100 for Founder count, 0.001 for Source allele frequency, and 4 for Decimal Places.

{"founderCount":100,"alleleFrequency":0.001,"decimalPlaces":4}

Outcome

The allele has an 18.14% retention probability and an 81.86% loss probability. The expected number of copies is 0.2.