Drosophila TFBSs, while for the humans we used Central European (CEU) genotypes sequenced as part of the 1000 Genomes Pilot Project [21] (using a Yoruban population instead of CEU yielded consistent results; not shown). Similar to our findings for the three Drosophila TFs, we observed reduced levels of individual variation at functional binding sites compared to reshuffled motif matches and flanking regions for other Drosophila factors as well as human TFs (Figure 2a). Notably, the significance of this effect was similarly high in Drosophila and humans, despite the fact that the SNP frequency differed approximately 11-fold (2.9% versus 0.25%, respectively), as closely reflected by the 7.5-fold difference in the number of varying TFBSs. This is consistent with the overall differences in the total number of SNPs detected in these two species, likely resulting from their different ancestral effective population sizes [39]. We also observed a significant anti-correlation between variation frequency at motif positions and their information content in both species (Figure 2b).
