Figure 3. Evaluating gene–environment mixed mode (G×EMM) and EMMA using simulated datasets.

(A). Comparison of true ${\text{PVE}}_{tot}$ to that estimated from EMMA (left panel) and G×EMM (right panel). Simulations were run with an equal number of samples in each environment ($N_{e1}=N_{e2}$) and with the same value for the environment-specific error terms (${\sigma }_{e1}^2={\sigma }_{e2}^2=1$). (B). Same as (A) but with a 4:1 ratio of samples between environments ($N_{e1}=4\times N_{e2}$). (C). Plot of the true ${\text{PVE}}_{e2}$ vs. the G×EMM estimate of ${\text{PVE}}_{e2}$. Gray points are the results of individual simulations, orange lines denote the median and 95% interquartile range (IQR). The three panels differ in the true proportion of phenotypic variance explained by genetics (PVE) specific to environment 1, ${\text{PVE}}_{e1}\in \{0.2,0.5,0.8\}$. Simulations were run with an equal number of samples in each environment ($N_{e1}=N_{e2}$) and with the same value for the environment-specific error terms (${\sigma }_{e1}^2={\sigma }_{e2}^2=1$). (D). Same as (C) but with a 4:1 ratio of samples between environments ($N_{e1}=4\times N_{e2}$).