Thermal evolution of gene expression profiles in Drosophila subobscura

Table 1 ANOVA of relative intensity ratios for gene CG12236.

Source of variation	d.f.	Sum of Squares	Mean Square	F	p-value (parametric)	p-value (permutation)
Temperature (T)	2	1.3882	0.6941	11.475	0.009	0.008
P22 vs. P13	1	1.2829	1.2829	21.210	0.004	0.002
Replicate^a	6	0.3629	0.0605	0.346	0.905
Dye (D)	1	3.5337	3.5337	20.193	< 0.001
T × D	2	0.0392	0.0196	0.112	0.895
Slide^b	24	4.1998	0.1750	11.816	< 0.001
Error^c	36	0.5332	0.0148

Temperature stands for the fixed effects due to thermal selection regime (13, 18 and 22°C), replicate for the random effect of replicated populations (R1, R2 and R3) nested in thermal regime, dye for the fixed effect of cyanine dye Cy3 (green) or Cy5 (red) in the flip dye design, and slide for the random effect of cDNA microarray glass slide nested in thermal regime, replicate and dye.
^a Error term for temperature and for the planned contrast comparing warm- (P22) vs. cold-adapted (P13) populations. ^b Error term for replicate, dye, and temperature × dye interaction. ^c Error term for slide.

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