  Additive genetic variance in natural populations is commonly estimated using
mixed models, in which the covariance of the genetic effects is modeled by a
genetic similarity matrix derived from a dense set of markers. An important but
usually implicit assumption is that the presence of any non-additive genetic
effect only increases the residual variance, and does not affect estimates of
additive genetic variance. Here we show that this is only true for panels of
unrelated individuals. In case there is genetic relatedness, the combination of
population structure and epistatic interactions can lead to inflated estimates
of additive genetic variance.
