The Genetic Basis of Rapidly Evolving Male Genital Morphology in Drosophila.

We performed genome-wide expression assays comparing gene expression in the Drosophila melanogaster third larval instar genital imaginal disc between males and females. We used microarrays to compare the relative expression levels of five independent male versus female comparisons for each of two different D. melanogaster wild-type strains, Canton-S and Berlin. All microarrays were dual channel direct comparisons of late third larval instar male versus female genital imaginal discs from two Drosophila melanogaster wildtype strains, Canton S and Berlin. For each strain five independent biological samples were analyzed using a dye-swap design (i.e. male samples labeled with Cy5 in three replicates were labeled with Cy3 in the other two replicates in that experimental set).