Conservation Genetics

, Volume 16, Issue 4, pp 901–913

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

  • Helen R. Taylor
  • Marty D. Kardos
  • Kristina M. Ramstad
  • Fred W. Allendorf
Research Article

Abstract

Pedigrees are frequently recommended for estimating inbreeding coefficients (FPED), 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 FPED 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 FPED by up to 27 % and overestimation of the variance in FPED by up to 182 %. At least 80 % pedigree accuracy was required to produce unbiased estimates of FPED, 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.

Keywords

Inbreeding Pedigree Parentage COLONY Accuracy 

Supplementary material

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Supplementary material 1 (DOCX 16 kb)
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Supplementary material 2 (DOCX 28 kb)
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Supplementary material 3 (DOCX 761 kb)
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Supplementary material 4 (TIFF 307 kb)

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Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Helen R. Taylor
    • 1
    • 3
  • Marty D. Kardos
    • 2
    • 4
  • Kristina M. Ramstad
    • 1
  • Fred W. Allendorf
    • 2
  1. 1.Allan Wilson Centre, School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
  2. 2.Montana Conservation Genetics LabUniversity of MontanaMissoulaUSA
  3. 3.Allan Wilson Centre, Department of AnatomyUniversity of OtagoDunedinNew Zealand
  4. 4.Department of Evolutionary Biology, Evolutionary Biology Centre (EBC)Uppsala UniversityUppsalaSweden

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