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Abstract The development of high‐throughput sequencing technologies is dramatically increasing the use of single nucleotide polymorphisms (SNPs) across the field of genetics, but most parentage studies of wild populations still rely on microsatellites. We developed a bioinformatic pipeline for identifyingSNPpanels that are informative for parentage analysis from restriction site‐associatedDNAsequencing (RADseq) 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 acrossSNPpanels generated with or without the use of a reference genome, and betweenSNPs 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 producedSNPpanels with ≥95% parentage assignment accuracy for Mexican gray wolf, outperforming microsatellites at 78% accuracy. Maternity assignments were completely consistent across allSNPpanels 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 284SNPs for Mexican gray wolf and 142SNPs for bighorn sheep, indicating our pipeline can be used to developSNPgenotyping assays for parentage analysis with relatively small numbers of loci.
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Genomic association with pathogen carriage in bighorn sheep ( Ovis canadensis )
Abstract Genetic composition can influence host susceptibility to, and transmission of, pathogens, with potential population‐level consequences. In bighorn sheep (Ovis canadensis), pneumonia epidemics caused byMycoplasma ovipneumoniaehave been associated with severe population declines and limited recovery across North America. Adult survivors either clear the infection or act as carriers that continually shedM. ovipneumoniaeand expose their susceptible offspring, resulting in high rates of lamb mortality for years following the outbreak event. Here, we investigated the influence of genomic composition on persistent carriage ofM. ovipneumoniaein a well‐studied bighorn sheep herd in the Wallowa Mountains of Oregon, USA. Using 10,605 SNPs generated using RADseq technology for 25 female bighorn sheep, we assessed genomic diversity metrics and employed family‐based genome‐wide association methodologies to understand variant association and genetic architecture underlying chronic carriage. We observed no differences among genome‐wide diversity metrics (heterozygosity and allelic richness) between groups. However, we identified two variant loci of interest and seven associated candidate genes, which may influence carriage status. Further, we found that the SNP panel explained ~55% of the phenotypic variance (SNP‐based heritability) forM. ovipneumoniaecarriage, though there was considerable uncertainty in these estimates. While small sample sizes limit conclusions drawn here, our study represents one of the first to assess the genomic factors influencing chronic carriage of a pathogen in a wild population and lays a foundation for understanding genomic influence on pathogen persistence in bighorn sheep and other wildlife populations. Future research should incorporate additional individuals as well as distinct herds to further explore the genomic basis of chronic carriage.
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- Award ID(s):
- 1716698
- PAR ID:
- 10453772
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Ecology and Evolution
- Volume:
- 11
- Issue:
- 6
- ISSN:
- 2045-7758
- Page Range / eLocation ID:
- p. 2488-2502
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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