title: Bone-associated gene evolution and the origin of flight in birds.
abstract: Bones have been subjected to considerable selective pressure throughout vertebrate evolution, such as occurred during the adaptations associated with the development of powered flight. Powered flight evolved independently in two extant clades of vertebrates, birds and bats. While this trait provided advantages such as in aerial foraging habits, escape from predators or long-distance travels, it also imposed great challenges, namely in the bone structure.
  
  
  
  We performed comparative genomic analyses of 89 bone-associated genes from 47 avian genomes (including 45 new), 39 mammalian, and 20 reptilian genomes, and demonstrate that birds, after correcting for multiple testing, have an almost two-fold increase in the number of bone-associated genes with evidence of positive selection (~52.8 %) compared with mammals (~30.3 %). Most of the positive-selected genes in birds are linked with bone regulation and remodeling and thirteen have been linked with functional pathways relevant to powered flight, including bone metabolism, bone fusion, muscle development and hyperglycemia levels. Genes encoding proteins involved in bone resorption, such as TPP1, had a high number of sites under Darwinian selection in birds.
  
  
  
  Patterns of positive selection observed in bird ossification genes suggest that there was a period of intense selective pressure to improve flight efficiency that was closely linked with constraints on body size.
authors.affiliation: CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas, 177, 4050-123, Porto, Portugal.|Abel Salazar Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal.
authors.forename: João Paulo
authors.initials: JP
authors.lastname: Machado
authors.affiliation: Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA, 22630, USA.
authors.forename: Warren E
authors.initials: WE
authors.lastname: Johnson
authors.affiliation: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Volgade 5-7, 1350, Copenhagen, Denmark.
authors.forename: M Thomas P
authors.initials: MT
authors.lastname: Gilbert
authors.affiliation: China National GeneBank, BGI-Shenzhen, Shenzen, 518083, China.|Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100, Copenhagen, Denmark.
authors.forename: Guojie
authors.initials: G
authors.lastname: Zhang
authors.affiliation: Department of Neurobiology Box 3209, Duke University Medical Center, Durham, NC, 27710, USA.|Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
authors.forename: Erich D
authors.initials: ED
authors.lastname: Jarvis
authors.affiliation: Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, 199004, Russia.|Oceanographic Center, 8000 N. Ocean Drive, Nova Southeastern University, Ft Lauderdale, FL, 33004, USA.
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: O'Brien
authors.affiliation: CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas, 177, 4050-123, Porto, Portugal. aantunes@ciimar.up.pt.|Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal. aantunes@ciimar.up.pt.
authors.forename: Agostinho
authors.initials: A
authors.lastname: Antunes
mesh_terms: D000220:Adaptation, Biological; D000818:Animals; D005075:Biological Evolution; D001717:Birds / Q000145:classification / Q000235:genetics*; D049628:Body Size; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D005426:Flight, Animal; D016678:Genome; D023281:Genomics / Q000379:methods; D008322:Mammals / Q000235:genetics; D010012:Osteogenesis / Q000235:genetics*; D010802:Phylogeny; D012641:Selection, Genetic