Predicting Ancestral Segmentation Phenotypes from Drosophila to Anopheles Using In Silico Evolution

PLoS Genet. 2016 May 26;12(5):e1006052. doi: 10.1371/journal.pgen.1006052. eCollection 2016 May.

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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Anopheles / genetics*
  • Computer Simulation
  • Drosophila melanogaster / genetics*
  • Evolution, Molecular*
  • GTPase-Activating Proteins / genetics*
  • Gene Expression Regulation, Developmental
  • In Situ Hybridization
  • Phylogeny

Substances

  • GTPase-Activating Proteins

Grants and funding

This work was supported by the Simons Investigator mathematical modelling of biological systems, https://www.simonsfoundation.org to PF, the National Science Foundation grant PHY-1502151 http://www.nsf.gov/ to EDS, the Fonds de Recherche du Québec Nature et Technologies, Programe Nouveaux Chercheurs http://www.frqnt.gouv.qc.ca/accueil to PF, and the Natural Science and Engineering Research Council of Canada, Undergraduate Summer Research Award http://www.nserc-crsng.gc.ca/index_eng.asp to PT. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.