hiphop: Improved paternity assignment among close relatives using a simple exclusion method for biallelic markers

Area of Science:

• Genetics
• Evolutionary Biology
• Behavioral Ecology

Background:

• Parentage assignment using molecular markers is challenging when candidate parents have close relatives in the population.
• Extra-pair paternity is common in cooperatively breeding birds like the superb fairy-wren, complicating paternity analysis.

Purpose of the Study:

• To develop and test an efficient method for parentage assignment using single nucleotide polymorphic markers (SNPs) in populations with related individuals.
• To improve the accuracy and reliability of parentage analysis in complex social systems.

Main Methods:

• Augmented the homozygote opposite test (hot) with a new test, Homozygous Identical Parents, Heterozygous Offspring are Precluded (hiphop).
• Utilized 1376 autosomal SNPs for parentage assignment in superb fairy-wrens (Malurus cyaneus).
• Developed guidelines for the number of SNPs required based on resampling.

Main Results:

• The combined hot and hiphop method, conditioned on maternal genotype, successfully distinguished the most likely sire from relatives in all cases.
• Using only the hot test resulted in failure to identify a single most-likely sire in 2.5% of cases.
• Identified Z- and W-linked SNPs that accurately determined sex.

Conclusions:

• The hiphop method provides unambiguous parentage assignments, even in species with complex social structures and high rates of extra-pair paternity.
• The developed SNP-based approach enhances the resolution of parentage analysis in challenging ecological contexts.
• The R package 'hiphop' offers a robust tool for genetic parentage assignment.