Green, Richard EBraun, Edward LArmstrong, JoelEarl, DentNguyen, NganHickey, GlennVandewege, Michael WSt John, John ACapella-Gutiérrez, SalvadorCastoe, Todd AKern, ColinFujita, Matthew KOpazo, Juan CJurka, JerzyKojima, Kenji KCaballero, JuanHubley, Robert MSmit, Arian FPlatt, Roy NLavoie, Christine ARamakodi, Meganathan PFinger, John WSuh, AlexanderIsberg, Sally RMiles, LeeChong, Amanda YJaratlerdsiri, WeerachaiGongora, JaimeMoran, ChristopherIriarte, AndrésMcCormack, JohnBurgess, Shane CEdwards, Scott VLyons, EricWilliams, ChristinaBreen, MatthewHoward, Jason TGresham, Cathy RPeterson, Daniel GSchmitz, JürgenPollock, David DHaussler, DavidTriplett, Eric WZhang, GuojieIrie, NaokiJarvis, Erich DBrochu, Christopher ASchmidt, Carl JMcCarthy, Fiona MFaircloth, Brant CHoffmann, Federico GGlenn, Travis CGabaldón, ToniPaten, BenedictRay, David A2015-12-112014-12-12https://hdl.handle.net/10161/11153To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.Alligators and CrocodilesAnimalsBiological EvolutionBirdsConserved SequenceDNA Transposable ElementsDinosaursEvolution, MolecularGenetic VariationGenomeMolecular Sequence AnnotationMolecular Sequence DataPhylogenyReptilesSequence AlignmentSequence Analysis, DNATranscriptomeJournal article1095-9203