hiphop

hiphop implements an enhanced exclusion approach for parentage assignment using single nucleotide polymorphism (SNP) markers to resolve paternity among closely related candidate parents in socially complex populations.

Key Features:

• Enhanced Exclusion Approach: Builds on the homozygote opposite test (hot) and introduces the "Homozygous Identical Parents, Heterozygous Offspring are Precluded" (hiPhOp) criterion to identify mismatches between offspring and candidate parents.
• Comprehensive Parentage Analysis: Integrates hiPhOp with hot and conditions on maternal genotypes to distinguish a single most likely sire from closely related candidates using a set of 1,376 autosomal SNPs, applicable where extra-pair paternity and complex social structures occur.
• Resampling for SNP Guidelines: Employs resampling techniques to establish guidelines on the number of SNPs required when first-order relatives are present in the mating pool.
• Identification of Sex-linked SNPs: Identifies Z- and W-linked SNPs that reliably determine sex.

Scientific Applications:

• Avian molecular ecology: Enables accurate paternity assignment in species with high rates of extra-pair paternity and complex social organization.
• Case study — Malurus cyaneus (superb fairy-wren): Applied to resolve paternity and relatedness in superb fairy-wrens, a system with frequent extra-pair paternity and close kin among potential parents.

Methodology:

Computational methods explicitly include the homozygote opposite test (hot), the hiPhOp exclusion criterion, conditioning on maternal genotypes, resampling to evaluate SNP set sizes, and identification of Z- and W-linked SNPs, applied to a dataset of 1,376 autosomal SNPs.