The development of high‐throughput sequencing technologies is dramatically increasing the use of single nucleotide polymorphisms (
Molecular ecologists seek to genotype hundreds to thousands of loci from hundreds to thousands of individuals at minimal cost per sample. Current methods, such as restriction‐site‐associated
- NSF-PAR ID:
- 10243960
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- Molecular Ecology Resources
- Volume:
- 16
- Issue:
- 5
- ISSN:
- 1755-098X
- Page Range / eLocation ID:
- p. 1264-1278
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract SNP s) across the field of genetics, but most parentage studies of wild populations still rely on microsatellites. We developed a bioinformatic pipeline for identifyingSNP panels that are informative for parentage analysis from restriction site‐associatedDNA sequencing (RAD seq) data. This pipeline includes options for analysis with or without a reference genome, and provides methods to maximize genotyping accuracy and select sets of unlinked loci that have high statistical power. We test this pipeline on small populations of Mexican gray wolf and bighorn sheep, for which parentage analyses are expected to be challenging due to low genetic diversity and the presence of many closely related individuals. We compare the results of parentage analysis acrossSNP panels generated with or without the use of a reference genome, and betweenSNP s and microsatellites. For Mexican gray wolf, we conducted parentage analyses for 30 pups from a single cohort where samples were available from 64% of possible mothers and 53% of possible fathers, and the accuracy of parentage assignments could be estimated because true identities of parents were known a priori based on field data. For bighorn sheep, we conducted maternity analyses for 39 lambs from five cohorts where 77% of possible mothers were sampled, but true identities of parents were unknown. Analyses with and without a reference genome producedSNP panels with ≥95% parentage assignment accuracy for Mexican gray wolf, outperforming microsatellites at 78% accuracy. Maternity assignments were completely consistent across allSNP panels for the bighorn sheep, and were 74.4% consistent with assignments from microsatellites. Accuracy and consistency of parentage analysis were not reduced when using as few as 284SNP s for Mexican gray wolf and 142SNP s for bighorn sheep, indicating our pipeline can be used to developSNP genotyping assays for parentage analysis with relatively small numbers of loci. -
Abstract Next‐generation sequencing technologies now allow researchers of non‐model systems to perform genome‐based studies without the requirement of a (often unavailable) closely related genomic reference. We evaluated the role of restriction endonuclease (
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