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

Abstract

Assignment of parentage with molecular markers is most difficult when the true parents have close relatives in the adult population. Here, we present an efficient solution to that problem by extending simple exclusion approaches to parentage analysis with single nucleotide polymorphic markers (SNPs). We augmented the previously published homozygote opposite test (hot), which counts mismatches due to the offspring and candidate parent having different homozygous genotypes, with an additional test. In this case, parents homozygous for the same SNP are incompatible with heterozygous offspring (i.e., "Homozygous Identical Parents, Heterozygous Offspring are Precluded": hiphop). We tested this approach in a cooperatively breeding bird, the superb fairy-wren, Malurus cyaneus, where rates of extra-pair paternity are exceptionally high, and where paternity assignment is challenging because breeding males typically have first-order adult relatives in their neighbourhood. Combining the tests and conditioning on the maternal genotype with a set of 1376 autosomal SNPs always allowed us to distinguish a single most likely sire from his relatives, and also to identify cases where the true sire must have been unsampled. In contrast, if just the hot test was used, we failed to identify a single most-likely sire in 2.5% of cases. Resampling enabled us to create guidelines for the number of SNPs required when first-order relatives coexist in the mating pool. Our method, implemented in the R package hiphop, therefore provides unambiguous parentage assignments even in systems with complex social organisation. We also identified a suite of Z-and W-linked SNPs that always identified sex correctly.

A sex skew in life-history research: the problem of missing males

“…miniaturization of GPS tags, methods for better distinguishing between GPS tag failure and animal death [104]) make it increasingly possible to collect demographic data in the field. Reduced costs mean that next-generation sequencing is increasingly accessible as a means of assigning paternity (but see [105]) and new tools are being developed to analyse paternity from single-nucleotide polymorphic markers [106]. These approaches may help us understand why the sexes live, reproduce and die at different tempos, and these data may have applied impacts for the health of managed populations and predicting population responses to environmental change.…”

Male‐specific nocturnal song functions similarly to day song in a diurnal bird species

“…We further filtered the autosomal SNPs to retain 1000 high‐quality autosomal SNPs, which improved computing time while retaining a sufficient sample to confidently assign relatedness (Huisman, 2017). To filter, we followed the approach of Cockburn et al (2021). The resulting DArT sequences were compared to previously sequenced bird species by Diversity Arrays, Canberra, using a basic local alignment search tool (BLAST) to estimate the location of the identified SNPs on the chromosome (species: yellow robin, Eopsaltria australis , zebra finch, Taeniopygia guttata and superb fairy‐wren, Malurus cyanueus ) (Fan et al, 2013).…”

Hybridization decreases native cutthroat trout reproductive fitness

“…Sites were further thinned to include only one site (randomly chosen) within each 10,000 bp window. We identified parent–offspring relationships using hiphop (Cockburn et al, 2021). Correct parent–offspring assignments were determined visually as per the hiphop vignette.…”

“…Sites were further thinned to include only one site (randomly chosen) within each 10,000 bp window. We identified parent-offspring relationships using hiphop (Cockburn et al, 2021).…”