Table 2. Mean relative expression for all genes assayed in parental species, backcross and X-allele introgressions. Gene expression values in fertile backcross and introgression progeny significantly different from both parental species are shown bolded and marked with an asterisk (post-hoc Scheffe’s test, FDR corrected q< 0.05). Dpb = D. p. bogotana, Dpp = D. p. pseudoobscura, BC_1p = First generation backcross from D. p. pseudoobscura females, BC_1b = First generation backcross from D. p. bogotana females, BC₄ = Fourth generation backcross, F8^y = yellow introgression, F8^y+ = non-yellow introgression, F8^se = sepia introgression, F8^se+ = non-sepia introgression.

	Dpb	Dpp	BC1p	BC1b	BC4	F8y	F8y+	F8se	F8se+
GA13457	−14.95	−11.66	−8.56*	−7.20*	−9.95	−7.27*	−8.67*	−7.97*	−7.08
GA14907	−2.69	−2.30	−1.61	−1.12	−2.94	−1.67	−1.86	−2.00	−1.74
GA15058	−12.10	−7.83	−5.99	−5.43*	−6.02	−8.83	−7.68	−8.40	−8.03
GA15722	−1.33	−2.46	−1.16	−0.94	−0.80	−0.78	−1.54	−2.33	−0.93
GA17870	−4.17	−4.21	−2.18	−2.67	−2.65	−1.49*	−3.27	−3.23	−0.76
GA18484	−8.17	−9.54	−6.08	−5.15*	−8.12	−4.93*	−5.91	−6.35	−5.30
GA18944	−8.62	−8.67	−5.37*	−5.16*	−7.54	−5.08*	−6.02	−6.26	−5.31
GA19543	−7.36	−7.68	−5.14	−4.88	−6.46	−7.00	−5.39	−5.97	−6.83
GA20504	−9.06	−7.68	−5.79	−5.85	−5.87	−10.79	−7.19	−6.59	−12.82
GA21772	−9.68	−9.62	−6.51	−6.78	−8.73	−9.31	−7.61	−7.03	−7.05
GA22690	−8.57	−9.50	−7.79	−7.27	−8.94	−8.79	−7.61	−7.88	−9.62
GA24206	−12.58	−10.15	−6.44*	−6.89*	−7.28*	−9.30	−7.55*	−8.31	−4.90
GA24796	−4.35	−5.49	−3.74	−3.31	−8.34	−3.76	−4.28	−6.02	−4.70
GA25574	−1.31	−0.56	−1.07	−0.20	−2.97	0.17	−1.09	−0.88	−0.93
GA26803	−5.01	−3.52	−3.98	−2.65	−2.89	−5.70	−5.36	−2.73	−3.12
GA27806	−9.58	−7.21	−3.84*	−2.81*	−4.55*	−4.75*	−3.85*	−6.21	−5.25
GA28780	−11.45	−8.13	−4.04*	−3.43*	−4.99*	−5.09*	−3.79*	−4.80*	−13.37
GA30092	−2.09	−1.51	−0.91	0.26	−3.03	0.14	−1.64	−1.88	−2.31
GA30093	−6.97	−3.96	−2.81	−1.35*	−5.14	−1.32*	−2.78	−2.96	−3.50