Predicting Ancestral Segmentation Phenotypes from Drosophila to Anopheles Using <i>In Silico</i> Evolution

<div><p>Molecular evolution is an established technique for inferring gene homology but regulatory DNA turns over so rapidly that inference of ancestral networks is often impossible. <i>In silico</i> evolution is used to compute the most parsimonious path in regulatory space for anterior-posterior patterning linking two Dipterian species. The expression pattern of gap genes has evolved between <i>Drosophila</i> (fly) and <i>Anopheles</i> (mosquito), yet one of their targets, <i>eve</i>, has remained invariant. Our model predicts that stripe 5 in fly disappears and a new posterior stripe is created in mosquito, thus <i>eve</i> stripe modules 3+7 and 4+6 in fly are homologous to 3+6 and 4+5 in mosquito. We can place <i>Clogmia</i> on this evolutionary pathway and it shares the mosquito homologies. To account for the evolution of the other pair-rule genes in the posterior we have to assume that the ancestral Dipterian utilized a dynamic method to phase those genes in relation to <i>eve</i>.</p>