Simulated data were used to explore the consequences for genetic parameter estimates of effects such as negative dam-offspring covariances or additional sire or sire X year variation not accounted for in the estimation models. Extra variation between sires may result from the importation of superior genetic material, favouritism towards the offspring of certain sires or failure to randomise mating groups. The presence of additional sire or sire X year variation equivalent to 6% of the phenotypic variation resulted in negative estimates of approx. -0.5 for the correlation between direct and maternal genetic effects (ram). A similar value of ram was obtained from data generated as offspring = genetic + environmental terms -0.2 * (dam phenotype). This equation's final term has variance 0.04 * Var(dam phenotype), i.e., 4% of the phenotypic variation, but resulted in significant estimates of the permanent environmental effect of dam of the order of 8%. Fitting the dam's phenotypic value as a covariate reduced, but did not always eliminate, the negative estimates of ram, showing the extent to which an effect mediated by dam phenotype is necessarily confounded with genetic effects. If fitted, covariate coefficient estimates for dam phenotype were positive in datasets where no phenotypic dam-offspring relationship was simulated and otherwise negative, but biased.
Robinson, D. L. (1996). Models which might explain negative correlations between direct and maternal genetic effects. Livestock Production Science, 45(2–3), 111–122. https://doi.org/10.1016/0301-6226(96)00002-4