Bottleneck Heterozygosity Loss
Project heterozygosity loss over a constant-size diploid bottleneck.
Description
A diploid bottleneck can reduce heterozygosity through drift.
A diploid bottleneck can reduce heterozygosity through drift. A constant-size model compounds the retained fraction across generations.
Project heterozygosity loss over a constant-size diploid bottleneck.
When to use Bottleneck Heterozygosity Loss
Use this for the following task: Project heterozygosity loss over a constant-size diploid bottleneck.
Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
How to use Bottleneck Heterozygosity Loss and understand its results
- Prepare the observed records or explicit model parameters requested below. Keep probabilities as fractions and paired records aligned.
- Enter initialHeterozygosity, bottleneckDiploidSize, generations using the field table, then run the tool.
- Read retainedHeterozygosity, lossFraction. Interpret flags, units, ordering and placeholder values using the rules below.
- Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.
| Input field | Meaning | Value type and bounds | Requirement |
|---|---|---|---|
| initialHeterozygosity | Initial heterozygosity | number | Required |
| bottleneckDiploidSize | Bottleneck diploid size | integer | Required |
| generations | Generations | integer | Required |
Use initial heterozygosity in [0,1], positive integer bottleneck size and nonnegative integer generations. Apply the retention factor.1
retainedFraction=(1−1/(2N))^generations; retainedH=initialH×fraction; lossFraction=1−fraction This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| retainedHeterozygosity | Retained heterozygosity | number |
| lossFraction | Loss fraction | number |
{
"input": {
"initialHeterozygosity": 0.5,
"bottleneckDiploidSize": 2,
"generations": 2
},
"output": {
"retainedHeterozygosity": 0.28125,
"lossFraction": 0.4375
}
}Limitations and assumptions
LossFraction is relative loss, not the absolute heterozygosity difference. Mutation, migration and population-size variation are excluded.
The tool evaluates supplied observations or a declared model. It does not establish the biological cause of an observed pattern. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.
Alternative or Complementary methods
Choose Inbreeding Accumulation for this operation: Project accumulated inbreeding using an explicit initial coefficient and constant effective size. For a complementary task, use Population FST for this operation: Compute heterozygosity-based FST from population allele frequencies and explicit weights.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Bottleneck Heterozygosity Loss — tool.io
Similar or alternative tools
- Inbreeding Accumulation
Project accumulated inbreeding using an explicit initial coefficient and constant effective size.
- Population FST
Compute heterozygosity-based FST from population allele frequencies and explicit weights.