ploidyinfer

ploidyinfer infers individual ploidy levels and estimates allele frequencies from codominant genetic marker data in organisms with polysomic inheritance by modeling genotypic probabilities that include double-reduction.

Key Features:

• Model-based estimation: Uses genotypic probabilities of polysomic inheritance with double-reduction to estimate allele frequencies from allelic phenotypes derived from codominant genetic markers.
• Expectation-maximization algorithm: Employs an expectation-maximization algorithm to estimate allele frequencies and model parameters while explicitly accounting for null alleles, false alleles, negative amplifications, and self-fertilization.
• Posterior probability assignment: Computes posterior probabilities to assign individuals to ploidy levels, providing a probabilistic framework for ambiguous genotypes.

Scientific Applications:

• Plant genetics and breeding: Determine ploidy levels and allele frequencies in polyploid plant species to inform breeding decisions and evolutionary analyses.
• Population genetics: Assess within- and among-population variation in ploidy and allele frequency distributions in taxa with polysomic inheritance.
• Genomic research: Infer ploidy and allele frequency parameters from genetic marker datasets to support studies of polyploid genome architecture.

Methodology:

Uses an expectation-maximization algorithm to estimate allele frequencies and model parameters under a genotypic-probability model of polysomic inheritance that incorporates double-reduction and accounts for genotyping errors, and computes posterior probabilities for ploidy assignment.