title: Feather development genes and associated regulatory innovation predate the origin of Dinosauria.
abstract: 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.
authors.affiliation: Department of Developmental Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA.
authors.forename: Craig B
authors.initials: CB
authors.lastname: Lowe
authors.affiliation: Department of Geological Sciences, University of Texas at Austin, Austin TX.
authors.forename: Julia A
authors.initials: JA
authors.lastname: Clarke
authors.affiliation: Department of Natural History, Royal Ontario Museum, Toronto, and Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada (Deceased).
authors.forename: Allan J
authors.initials: AJ
authors.lastname: Baker
authors.affiliation: Center for Biomolecular Science and Engineering, University of California, Santa Cruz.
authors.forename: David
authors.initials: D
authors.lastname: Haussler
authors.affiliation: Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA sedwards@fas.harvard.edu.
authors.forename: Scott V
authors.initials: SV
authors.lastname: Edwards
mesh_terms: D000818:Animals; D005075:Biological Evolution; D001717:Birds / Q000033:anatomy & histology / Q000235:genetics*; D049628:Body Size; D025061:Dinosaurs / Q000033:anatomy & histology* / Q000235:genetics / Q000254:growth & development; D019143:Evolution, Molecular; D005241:Feathers / Q000254:growth & development* / Q000378:metabolism; D023281:Genomics / Q000379:methods*; D018971:Insulin-Like Growth Factor Binding Protein 2 / Q000235:genetics; D018975:Insulin-Like Growth Factor Binding Protein 5 / Q000235:genetics; D007633:Keratins / Q000235:genetics; D059645:Mutation Rate; D010802:Phylogeny; D050436:Regulatory Elements, Transcriptional
chemical_list: D018971:Insulin-Like Growth Factor Binding Protein 2; D018975:Insulin-Like Growth Factor Binding Protein 5; D007633:Keratins
keywords: body size; comparative genomics; dinosaur; enhancer; gene regulation; integument