cis versus trans effects

Cooley AM, Shefner L, McLaughlin WN, Stewart EE & Wittkopp PJ 2012 The ontogeny of color: developmental origins of divergent pigmentation in Drosophila americana and D. novamexicana. Evol Dev 14:317-325.

• even small and hard-to-detect differences in expression can be biologically meaningful
• we cannot definitively rule out a precise combination of cis- and trans-regulatory changes between species that cause a smaller difference in relative allelic expression in hybrids than between species