Table 6.

nested MANOVA results of gene expression analysis of mouthbred juveniles: nested MANOVA to asses effects of maternal challenge, juvenile challenge and their interaction on the relative expression of candidate genes (ΔCt values) in mouthbred juveniles. Female challenge was nested in family. Significant results are marked in bold letters. Results of the univariate posthoc analysis (ANCOVA & Tukey HSD) can be found in Additional file 7: Table S7 and Additional file 8: Table S8

nested MANOVA		All genes					All immune genes					Adaptive genes
Factors	DF	Pillai	F	n Df	d Df	Pr(>F)	Pillai	F	n Df	d Df	Pr(>F)	Pillai	F	n Df	d Df	Pr(>F)
Juvenile Challenge (jC)	2	1.98	5.35	90	4	0.055	1.16	1.11	52	42	0.362	0.37	0.97	18	76	0.497
Maternal Challenge (mC)	1	1.00	2972.31	45	1	0.015	0.86	4.67	26	20	< 0.001	0.28	1.60	9	37	0.152
jC * mC	2	1.92	1.03	90	4	0.571	1.20	1.21	52	42	0.263	0.31	0.77	18	76	0.726
mC in family	4	3.95	6.87	180	16	0.000	2.85	2.20	104	92	< 0.001	1.24	2.01	36	160	0.002
Residuals	45
		All innate IS					Inflammation					Oxidative Stress
Factors	DF	Pillai	F	n Df	d Df	Pr(>F)	Pillai	F	n Df	d Df	Pr(>F)	Pillai	F	n Df	d Df	Pr(>F)
Juvenile Challenge (jC)	2	0.75	1.27	30	64	0.211	0.34	1.72	10	84	0.089	0.19	1.50	6	88	0.188
Maternal Challenge (mC)	1	0.80	8.45	15	31	< 0.001	0.28	3.25	5	41	0.015	0.05	0.68	3	43	0.568
jC * mC	2	0.58	0.88	30	64	0.643	0.25	1.18	10	84	0.318	0.13	1.05	6	88	0.398
mC in family	4	1.90	2.06	60	136	< 0.001	0.50	1.26	20	176	0.212	0.39	1.66	12	135	0.082
Residuals	45
		Various innate IS					Antimicrobial Peptides					Complement Components
Factors	DF	Pillai	F	n Df	d Df	Pr(>F)	Pillai	F	n Df	d Df	Pr(>F)	Pillai	F	n Df	d Df	Pr(>F)
Juvenile Challenge (jC)	2	0.29	1.84	8	86	0.080	0.22	2.84	4	90	0.029	0.77012	1.105	34	60	0.361
Maternal Challenge (mC)	1	0.15	1.88	4	42	0.132	0.06	1.30	2	44	0.283	0.80387	6.992	17	29	< 0.001
jC * mC	2	0.14	0.84	8	86	0.571	0.05	0.59	4	90	0.667	0.64951	0.8487	34	60	0.693
mC in family	4	0.61	2.04	16	180	0.013	0.25	1.58	8	90	0.143	2.19249	2.2833	68	128	< 0.001
Residuals	45
		Epigenetic genes					Developmental genes					Stress related genes
Factors	DF	Pillai	F	n Df	d Df	Pr(>F)	Pillai	F	n Df	d Df	Pr(>F)	Pillai	F	n Df	d Df	Pr(>F)
Juvenile Challenge (jC)	2	0.25	1.19	10	84	0.306	0.23	1.40	8	86	0.208	0.28	1.76	8	86	0.097
Maternal Challenge (mC)	1	0.31	3.73	5	41	0.007	0.16	1.93	4	42	0.122	0.01	0.13	4	42	0.972
jC * mC	2	0.37	1.90	10	84	0.056	0.21	1.27	8	86	0.268	0.19	1.10	8	86	0.374
mC in family	4	0.70	1.88	20	176	0.017	0.54	1.74	16	180	0.042	0.29	0.89	16	180	0.586
Residuals	45
		Metabolism genes					Sex related genes
Factors	DF	Pillai	F	n Df	d Df	Pr(>F)	Pillai	F	n Df	d Df	Pr(>F)
Juvenile Challenge (jC)	2	0.13	1.02	6	88	0.418	0.29179	2.5053	6	88	0.027622
Maternal Challenge (mC)	1	0.17	2.91	3	43	0.045	0.2595	5.0231	3	43	0.004501
jC * mC	2	0.06	0.49	6	88	0.816	0.12935	1.0142	6	88	0.421418
mC in family	4	0.32	1.35	12	135	0.196	0.20872	0.8412	12	135	0.608014
Residuals	45