HIPHOP: improved paternity assignment among close relatives using a simple exclusion method for biallelic markers

TY - JOUR

T1 - HIPHOP: improved paternity assignment among close relatives using a simple exclusion method for biallelic markers

AU - Cockburn, Andrew

AU - Peñalba, Joshua V.

AU - Jaccoud, Damian

AU - Kilian, Andrzej

AU - Brouwer, Lyanne

AU - Double, Michael C.

AU - Margraf, Nicolas

AU - Osmond, Helen L.

AU - Kruuk, Loeske E. B.

AU - van de Pol, Martijn

N1 - 7284, AnE; Data archiving: data archived in NCBI (no NIOO data)

PY - 2021

Y1 - 2021

N2 - 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.

AB - 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.

KW - international

KW - Plan_S-Compliant_NO

U2 - 10.1111/1755-0998.13389

DO - 10.1111/1755-0998.13389

M3 - Article

SN - 1755-098X

VL - 21

SP - 1850

EP - 1865

JO - Molecular Ecology Resources

JF - Molecular Ecology Resources

IS - 6

ER -