Abstract
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. In silico 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 Drosophila (fly) and Anopheles (mosquito), yet one of their targets, eve, has remained invariant. Our model predicts that stripe 5 in fly disappears and a new posterior stripe is created in mosquito, thus eve stripe modules 3+7 and 4+6 in fly are homologous to 3+6 and 4+5 in mosquito. We can place Clogmia 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 eve.
Highlights
Molecular phylogenies based on protein coding genes have greatly enhanced evolutionary theory, and in favorable cases even allow a reconstruction of the last common ancestral gene or even full evolutionary pathways [1]
We predict a new and different combinatorial logic of stripe formation in mosquito compared to fly, which is fully consistent with development of intermediate species such as moth-fly (Clogmia)
Our simulations further suggest that the dynamics of gene expression in this last common ancestor were similar to other insects, such as wasps (Nasonia)
Summary
Molecular phylogenies based on protein coding genes have greatly enhanced evolutionary theory, and in favorable cases even allow a reconstruction of the last common ancestral gene or even full evolutionary pathways [1]. Gene expression domains can be mapped by in-situ hybridization yet a molecular understanding is limited outside of model organisms. There is considerable need for a computational tool that can take sparse phenotypic information, e.g., broadly defined space-time gene expression, and construct the simplest phylogenetic relationships consistent with data, thereby highlighting interesting events for molecular follow up. The pair-rule genes in turn control the segment polarity genes that are broadly conserved across the arthropods [6]. Mutagenesis and bioinformatics studies have revealed the main DNA motifs controlling the expression of gap and pair-rule genes [7] while systematic quantitative imaging has led to phenomenological models for segmentation dynamics [8, 9]
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