I'd be remiss to not mention this paper from Hopi Hoekstra's group after I previously discussed the anti-evo-devo paper she wrote with Jerry Coyne. The premise of the paper from Hoekstra and Coyne is that Sean Carroll overplays the importance of cis-regulatory changes in the evolution of form. Well, Hoekstra and colleagues mapped the genes responsible for natural coat color variation in subspecies of a beach mouse. They isolated two QTLs, and they identified one candidate gene for each. One candidate gene contains a substitution in a protein coding region, while the other gene has no change in protein coding sequence, but it has different expression in the two ecomorphs.
What does this all mean? First of all, protein coding changes do contribute to important morphological evolution -- the population with the derived amino acid mutation lives in a beach habitat, and it has adapted to this habitat with a lighter coat color. Second, expression changes are also important. Hoekstra and Coyne were not arguing that cis-regulatory changes are not important, but that they aren't as important as Coyne Carroll makes them out to be.
The paper was published in PLoS Biology, so it's free to download if you'd like to read it.
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In the last sentence
do you mean "...aren't as important as Carroll makes them out to be"?
Yes, Kevin, I do. I can't keep their names straight. Thanks.