The influence of gene-environment interactions on GHR and IGF-1 expression and their association with growth in brook charr, Salvelinus fontinalis (Mitchill)

Table 11 Model selection for individual transcript efficiency using a backwards step-wise procedure.

	iTE_GHR			iTE_IGF-1
Model	Log likelihood	Test	P	Log likelihood	Test	P
iTE ~Env + Sex + EBV·Env + EBV·Sex +Env·Sex +EBV·Env·Sex (1)	-297.317			-436.651
~Env + Sex + EBV·Env + EBV·Sex +Env·Sex (2)	-297.689	1 vs. 2	0.388	-436.657	1 vs. 2	0.906
~Env + Sex + EBV·Env + EBV·Sex (3)	-297.945	2 vs. 3	0.474	-436.897	2 vs. 3	0.489
~Env + Sex + EBV·Env (4)	-298.417	3 vs. 4	0.331	-437.236	3 vs. 4	0.410
~Env + Sex (5)	-302.856	4 vs. 5	0.012	-439.672	4 vs. 5	0.088

Progressively simpler models are subsequently defined by removing terms from previous models beginning with interaction effects (e.g. 1 vs. 2). Nested models were tested evaluated using likelihood ratio tests to select the most parsimonious model. The reported p-values correspond to results of the likelihood ratio tests wherein a value greater than the nominal level of significance (α = 0.05) indicates that removal of the model term does not increase model deviance significantly. The final, parsimonious model that was selected is indicated in bold characters (Env = environment, EBV = EBV group). In the case of iTE_IGF-1, removal of the EBVxEnv term (model 5) resulted in a marginally non-significant likelihood ratio test. However, the interaction term was retained in the final model (model 4 AIC = 890.47), given that its exclusion resulted in a greater penalised likelihood score (model 5 AIC = 891.34).

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