Reviewer 2's Review

“This paper tests the hypothesis that the Relish gene, a protein involved in innate immunity, evolves by adaptive evolution in multiple Drosophila lineages. The data does not support the hypothesis that Relish evolves adaptively in all Drosophila lineages suggesting that Relish is not always selected in different lineages. The one quibble I have is that the paper combines McDonald Kreitman (MK) data from three species pairs together for an overall MK test. This is not appropriate because the data are not independent. The more appropriate method would be to map the changes to branches of a Drosophila phylogeny and analyze each branch separately HARVEY, P. H., and M. D. PAGEL, 1991 The Comparative Method in Evolutionary Biology. Oxford University Press, New York.) Alternatively, the combined data and test should be removed.”

n.b. These are the general comments made by the reviewer when reviewing the originally submitted version of this paper. The manuscript was revised before publication. Specific minor points addressed during revision of the paper are not shown.