Valid estimates of individual inbreeding coefficients from marker-based pedigrees are not feasible in wild populations with low allelic diversity
- 644 Downloads
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.
KeywordsInbreeding Pedigree Parentage COLONY Accuracy
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.
Conflict of interest
The authors declare no conflict of interest.
- Akcay E, Roughgarden J (2007) Extra-pair paternity in birds: review of the genetic benefits. Evol Ecol Res 9:855–868Google Scholar
- Allendorf FW, Luikart G (2007) Conservation and the genetics of populations. Blackwell Publishing, MaldenGoogle Scholar
- Allendorf FW, Ryman N (2002) The role of genetics in population viability analysis. In: Beissinger SR, McCullough DR (eds) Population viability analysis. The Chicago University Press, Chicago, pp 50–85Google Scholar
- Allendorf FW, Luikart G, Aitken SN (2013) Conservation and the genetics of populations, 2nd edn. Wiley-Blackwell Publishing, ChichesterGoogle Scholar
- Colbourne RM, Robertson HA (1997) Successful translocations of little spotted kiwi (Apteryx owenii) between offshore islands of New Zealand. Notornis 44:253–258Google Scholar
- Crow JF, Kimura M (1970) An introduction to population genetics theory. The Blackburn Press, CaldwellGoogle Scholar
- Heather B, Robertson H (2005) The field guide to the Birds of New Zealand. Penguin, AucklandGoogle Scholar
- Malécot G (1948) Les Mathématiques de l’hérédité. Masson et Cie, ParisGoogle Scholar
- Nielsen JF, English S, Goodall-Copestake WP, Wang JL, Walling CA, Bateman AW, Flower TP, Sutcliffe RL, Samson J, Thavarajah NK, Kruuk LEB, Clutton-Brock TH, Pemberton JM (2012) Inbreeding and inbreeding depression of early life traits in a cooperative mammal. Mol Ecol 21:2788–2804PubMedCrossRefGoogle Scholar
- Reid JM, Keller LF, Marr AB, Nietlisbach P, Sardell RJ, Arcese P (2013) Pedigree error due to extra pair reproduction substantially biases estimates of inbreeding depression. Evolution 68(3):802–815Google Scholar
- Robertson HA, Colbourne RM (2004) Survival of little spotted kiwi (Apteryx owenii) on Kapiti Island. Notornis 51:161–163Google Scholar
- Taylor HR (2014) Detecting inbreeding depression in a severely bottlenecked, recovering species: the little spotted kiwi (Apteryx owenii): a thesis submitted to the Victoria University of Wellington in fulfilment of the requirements for the degree of Doctor of Philosophy in Ecology and Biodiversity. Victoria University of WelligtonGoogle Scholar
- R Development Core Team (2013) R: a language and environment for statistical computing. R Foundation for statistical computing, Vienna, AustriaGoogle Scholar
- Therneau T, Atkinson E, Sinnwell J, Matsumoto M, Schaid D, McDonnell S (2011) kinship2: Pedigree functionsGoogle Scholar