Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches

Abstract

The estimation of quantitative genetic parameters in wild populations is generally limited by the accuracy and completeness of the available pedigree information. Using relatedness at genomewide markers can potentially remove this limitation and lead to less biased and more precise estimates. We estimated heritability, maternal genetic effects and genetic correlations for body size traits in an unmanaged long-term study population of Soay sheep on St Kilda using three increasingly complete and accurate estimates of relatedness: (i) Pedigree 1, using observation-derived maternal links and microsatellite-derived paternal links; (ii) Pedigree 2, using SNP-derived assignment of both maternity and paternity; and (iii) whole-genome relatedness at 37 037 autosomal SNPs. In initial analyses, heritability estimates were strikingly similar for all three methods, while standard errors were systematically lower in analyses based on Pedigree 2 and genomic relatedness. Genetic correlations were generally strong, differed little between the three estimates of relatedness and the standard errors declined only very slightly with improved relatedness information. When partitioning maternal effects into separate genetic and environmental components, maternal genetic effects found in juvenile traits increased substantially across the three relatedness estimates. Heritability declined compared to parallel models where only a maternal environment effect was fitted, suggesting that maternal genetic effects are confounded with direct genetic effects and that more accurate estimates of relatedness were better able to separate maternal genetic effects from direct genetic effects. We found that the heritability captured by SNP markers asymptoted at about half the SNPs available, suggesting that denser marker panels are not necessarily required for precise and unbiased heritability estimates. Finally, we present guidelines for the use of genomic relatedness in future quantitative genetics studies in natural populations.

Inbreeding depression across the lifespan in a wild mammal population

“…The difference between pedigree and genomic estimates of inbreeding depression reported here is much more pronounced than in a similar comparison focusing on the estimation of heritability and genetic covariances in a study population of Soay sheep on St Kilda, NW Scotland (29). One reason for this is that individuals who lack some ancestry information may have a highly imprecise F ped , while having accurate pedigree relationships with their many (half-)siblings, descendants, and known ancestors.…”

An assessment of the reliability of quantitative genetics estimates in study systems with high rate of extra-pair reproduction and low recruitment

“…Simulation frameworks allow the assessment of power-the probability of detecting an effect given that this effect is true-of a particular dataset or model. In animal models, power is affected by the same factors as precision (Quinn et al, 2006;Morrissey et al, 2007;Bérénos et al, 2014). However, performing a power analysis alone could provide an incomplete picture of the validity of genetic variance estimates.…”

“…Pedigree errors could be particularly common in study systems where extra-pair copulations are important and parental links in pedigrees constructed solely based on social pair observations (that is, social pedigree). Theoretically, the presence of extra-pair paternity (EPP), if not accounted for, can bias downward the heritability estimates, even though evidence so far suggests that this bias is generally small in wild populations (Charmantier and Réale, 2005;Bérénos et al, 2014;Firth et al, 2015; but see Lee and Pollak, 1997 for reports of bias in the animal breeding litterature; see also Walther and Moore, 2005 for a detailed discussion on the concepts of bias, precision and accuracy).…”

Pedigree-based inbreeding coefficient explains more variation in fitness than heterozygosity at 160 microsatellites in a wild bird population

“…The increased availability of high-density molecular markers has generated renewed interest in marker-based estimates of IBD, even in populations for which pedigree data are available (e.g. [16]). This is because, first, genetic markers allow testing for local effects, i.e.…”