As parental strains, S and Strong-R of these two crosses were highly homozygous in responding to the resistance trait, these two crosses were considered as a replicates.
The converted SAGE library could be considered as a technical replicate.
Moreover, in the case of using our system for menu selection, chord interaction along with action windows can be considered as a virtually replicated menu interface, since every user can select from a (virtually positioned) menu in a position that is useful for him/her.
Therefore, data from each transect line at each site were pooled and analyzed at the site rather than transect level, with each of the 62 sites considered as an independent replicate.
The PhyML version 3.1 [ 36] was used to reconstruct ML trees for each gene with bootstrap replicates of 100 which is generally considered as a reasonable number of replicates.
Sex, insecticide treatment and parental temperature regime were entered as fixed factors, and replicate, considered as a random factor, was nested within parental temperature regime.
As fixed effects for the model we entered "color morph" and "δC" (without interaction) and each morph pair ("evolutionary replicate") was considered as a random effect under the assumption of a common slope for each morph pair.
An expression increase in adaxial petals of 1.5-times or above in at least two biological replicates was considered as a differential expression and consequently as a further corroboration of RNA-Seq data.
Replicate (within parental temperature regime) was considered as a random factor.
