Valid estimates of individual inbreeding coefficients from marker-based pedigrees are not feasible in wild populations with low allelic diversity

Abstract

Pedigrees are frequently recommended for estimating inbreeding coefficients (F PED ), but are error-prone due to missing behavioural data in wild populations. Genetic marker-based pedigrees have been suggested as a remedy to this problem, but their accuracy depends on the number and polymorphism of loci available, and the completeness of population sampling. We used simulations to examine how accuracy of marker-based pedigrees varies with number of loci and sampling regime when allelic diversity is low (2.2–4 alleles per locus in founders), as is often the case in threatened species. We also examined the impact of pedigree errors on the validity of F PED estimated from marker-based pedigrees. Our results indicate that accurate parentage assignments are only feasible if genotypes are available for all individuals that ever existed in the population, and that accuracy does not improve past 40 loci. Errors in marker-based pedigrees resulted in underestimation of F PED by up to 27 % and overestimation of the variance in F PED by up to 182 %. At least 80 % pedigree accuracy was required to produce unbiased estimates of F PED , which were still highly imprecise. Given the degree of sampling required, it is not currently feasible to measure inbreeding in wild populations of threatened species with a pedigree based solely on microsatellite data. Resources may be better directed towards developing more robust genetic tools (whole genome sequencing and large SNP panels) to facilitate direct estimation of inbreeding coefficients without a pedigree. Where this is not possible, long-term monitoring projects will be required to accurately estimate inbreeding coefficients via a combination of behavioural and genetic data.

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Acknowledgments

The authors thank Jinliang Wang for his advice regarding the program COLONY, Kevin Buckley for his assistance with the Victoria University Condor computing platform and Nicola Nelson plus two anonymous reviewers for helpful comments on earlier versions of this manuscript. This study was funded by the Allan Wilson Centre, Victoria University of Wellington, the Centre for Biodiversity and Restoration Ecology, the New Zealand Ministry for Business, Innovation and Employment, and Kaitiaki o Kapiti Trust.

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The authors declare no conflict of interest.

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Correspondence to Helen R. Taylor.

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Taylor, H.R., Kardos, M.D., Ramstad, K.M. et al. Valid estimates of individual inbreeding coefficients from marker-based pedigrees are not feasible in wild populations with low allelic diversity. Conserv Genet 16, 901–913 (2015). https://doi.org/10.1007/s10592-015-0709-1

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Keywords

  • Inbreeding
  • Pedigree
  • Parentage
  • COLONY
  • Accuracy