Evolutionary scrambling at the <i>Drosophila</i> and <i>Anopheles vnd</i> neuroectoderm enhancers (NEEs).

<p>(A) Shown is a phylogenetic tree of the three dipteran species discussed in the study: the sepsid fly <i>Themira putris</i>, the fruitfly <i>Drosophila melanogaster</i>, and the mosquito <i>Anopheles gambiae</i>. The amount of divergence from their latest common ancestors (LCA) is depicted in Millions of years ago (Mya). (B) The <i>Drosophila</i> and <i>Anopheles vnd</i> enhancers still share a common organization of functional binding sites as previously reported <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000276#pgen.1000276-Maizel1" target="_blank">[30]</a>. The colored boxes represent matches to the Dorsal (blue), Twist (green), mu (orange), and Su(H) (red) motifs. Two-dimensional homology plots for the <i>Drosophila</i> and <i>Anopheles vnd</i> enhancers in parallel (C) and anti-parallel (D) orientations reveal spurious blocks of alignment, as would be seen between two DNA sequences chosen randomly. Only two of the motifs shown in (B) (highlighted in green and orange) appear in the plot in (C) as indicated. The anti-parallel two-dimensional plot of these enhancers does not differ qualitatively or quantitatively from the parallel plot. (E–F) Score distributions for (C) and (D), respectively, are quite similar as well. Therefore, it is difficult to rule out organized enhancer elements without extensive sequence inspection.