polyploid-genotyping

polyploid-genotyping infers genotypes and estimates population genetic parameters for autopolyploid and allopolyploid organisms using genotype likelihoods to model non-standard inheritance patterns.

Key Features:

• Model Development: Provides statistical models tailored for autopolyploids arising from whole-genome duplication (WGD) with potential mixed mating, inbreeding, and double reduction, and for allopolyploids resulting from hybridization with independently segregating subgenomes.
• Genotype Likelihoods: Uses genotype likelihoods to model non-standard inheritance in polyploids and to improve accuracy of genotyping and parameter estimation relative to diploid-focused methods.
• Simulation-Based Validation: Validated by extensive simulations comparing against existing approaches across varying sequencing coverage depths and ploidy levels, demonstrating lower estimation error in genotypes and population genetic parameters, particularly at low coverage.
• Empirical Application: Applied to empirical datasets from published studies to assess performance on real-world polyploid data.

Scientific Applications:

• Population genetics: Enables accurate genotypic analyses and parameter estimation in population genetic studies of polyploid species.
• Evolutionary inference: Supports inference of evolutionary dynamics, biodiversity, and ecological adaptation in polyploid organisms.
• Plant genetics, agriculture, and conservation: Facilitates research and applied studies in plant genetics, crop improvement, and conservation biology where polyploidy is common.

Methodology:

Implements statistical models for autopolyploids and allopolyploids using genotype likelihoods and is validated via extensive simulations across sequencing coverage depths and ploidy levels with comparisons to existing approaches.