Testing for positive selection on ftz RCPE and ZE TFBSs.

The test for adaptive selection was carried out using the adaptation of McDonald and Kreitman test [18] suggested in [3], [20]. The numbers between parentheses refer to base substitutions affecting only the cores of TFBSs. In the case of DNase-I footprinting TFBSs and NTFBSs respectively refer to regions of the alignment corresponding or not to the DNase-I footprints reported for D. melanogaster in [29], [39], [40]. For the phylogenetic footprinting, however, TFBSs and NTFBSs respectively refer to regions of the alignment that are either well or badly aligned to D. pseudoobscura orthologs (see Materials and Methods).