Feather development genes and associated regulatory innovation predate the origin of Dinosauria

Mol Biol Evol. 2015 Jan;32(1):23-8. doi: 10.1093/molbev/msu309. Epub 2014 Nov 18.


The evolution of avian feathers has recently been illuminated by fossils and the identification of genes involved in feather patterning and morphogenesis. However, molecular studies have focused mainly on protein-coding genes. Using comparative genomics and more than 600,000 conserved regulatory elements, we show that patterns of genome evolution in the vicinity of feather genes are consistent with a major role for regulatory innovation in the evolution of feathers. Rates of innovation at feather regulatory elements exhibit an extended period of innovation with peaks in the ancestors of amniotes and archosaurs. We estimate that 86% of such regulatory elements and 100% of the nonkeratin feather gene set were present prior to the origin of Dinosauria. On the branch leading to modern birds, we detect a strong signal of regulatory innovation near insulin-like growth factor binding protein (IGFBP) 2 and IGFBP5, which have roles in body size reduction, and may represent a genomic signature for the miniaturization of dinosaurian body size preceding the origin of flight.

Keywords: body size; comparative genomics; dinosaur; enhancer; gene regulation; integument.

Publication types

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

MeSH terms

  • Animals
  • Biological Evolution
  • Birds / anatomy & histology
  • Birds / genetics*
  • Body Size
  • Dinosaurs / anatomy & histology*
  • Dinosaurs / genetics
  • Dinosaurs / growth & development
  • Evolution, Molecular
  • Feathers / growth & development*
  • Feathers / metabolism
  • Genomics / methods*
  • Insulin-Like Growth Factor Binding Protein 2 / genetics
  • Insulin-Like Growth Factor Binding Protein 5 / genetics
  • Keratins / genetics
  • Mutation Rate
  • Phylogeny
  • Regulatory Elements, Transcriptional*


  • Insulin-Like Growth Factor Binding Protein 2
  • Insulin-Like Growth Factor Binding Protein 5
  • Keratins