hwep

hwep performs hypothesis testing for genetic equilibrium and estimates double reduction rates in autopolyploid populations to assess random mating and meiotic behavior.

Key Features:

• Equilibrium Testing in Autopolyploids: Extends equilibrium testing to autopolyploids at any even ploidy level greater than two and accounts for double reduction.
• Estimation of Double Reduction Rates: Provides methods to estimate the rate of double reduction in autopolyploid populations.
• Likelihood Approach: Implements likelihood-based statistical models that incorporate double reduction when evaluating genetic data.
• U-Statistic Minimization Approach: Implements a U-statistic minimization method that generalizes the classical equilibrium χ² test from diploids to polyploids.
• Bootstrap Procedure: Implements a U-statistic-based bootstrap procedure for small sample sizes or uncertain genotypes.
• Genotype Frequency Calculations: Calculates genotype frequencies at equilibrium and predicts changes after one or multiple rounds of random mating given specified double reduction rates.
• Implementation: Implemented in R.

Scientific Applications:

• Equilibrium Testing: Testing for genetic equilibrium and random mating in autopolyploid populations.
• Meiotic Behavior Analysis: Estimating and interpreting double reduction rates to study meiotic processes in autopolyploids.
• Genetic Dynamics Modeling: Modeling genotype-frequency dynamics under random mating and specified double reduction rates.
• Domain Applications: Use in evolutionary biology, plant breeding, and conservation genetics involving polyploid species.

Methodology:

Likelihood-based statistical models, a U-statistic minimization generalizing the equilibrium χ² test for diploids, a U-statistic bootstrap procedure for small samples or uncertain genotypes, and genotype-frequency calculations for predicting changes under random mating with given double reduction rates.