Heritability estimation
We estimated narrow-sense heritability (h2 ) as
the amount of additive genetic variance divided by the total phenotypic
variance (i.e., the sum of the different variance components). Because
the model was fitted with binary data, all variance estimates of the
model were calculated on a latent scale. It is possible to measure
heritability on either the latent trait scale or the observed
data-scale, the selection of which depends on inferences being made .
Heritability on the latent scale was estimated as\(h^{2}=\frac{V_{A}}{V_{A}+\ V_{\text{SE}}+\ V_{e}}\), where\(V_{A}\) is the additive genetic variance, \(V_{\text{SE}}\) is the
variance associated with shared environment, and \(V_{e}\ \)is the
residual variance, which was fixed at 1. In this case, we also estimated
heritability on the observed data-scale, as this provides parameter
estimates which are directly interpretable in relation to the ecology of
the species whilst incorporating other factors (i.e., fixed effects and
residual variance) which may influence the probability of contracting
chlamydia. To convert parameter estimates, we used the
QGglmm package in R . This package uses estimates of
additive genetic variance, phenotypic variance (sum of all random
effects variance + residual variance) and the intercept and converts
them to the data-scale, thereby allowing for the calculation of
heritability on this scale. We repeated this process for all random
effect variances, thus measuring the proportion of phenotypic variance
attributed to either shared environment effects or maternal effects
(hereafter referred to as intra-class coefficient (ICC)).