title: Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.
abstract: To 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.
authors.affiliation: Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. ed@soe.ucsc.edu david.a.ray@ttu.edu.
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authors.initials: RE
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authors.affiliation: Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
authors.forename: Edward L
authors.initials: EL
authors.lastname: Braun
authors.affiliation: Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA.
authors.forename: Joel
authors.initials: J
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authors.affiliation: Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA.
authors.forename: Dent
authors.initials: D
authors.lastname: Earl
authors.affiliation: Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA.
authors.forename: Ngan
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authors.affiliation: Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA.
authors.forename: Glenn
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authors.lastname: Hickey
authors.affiliation: Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA.
authors.forename: Michael W
authors.initials: MW
authors.lastname: Vandewege
authors.affiliation: Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA.
authors.forename: John A
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authors.lastname: St John
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain. Universitat Pompeu Fabra, 08003 Barcelona, Spain.
authors.forename: Salvador
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authors.lastname: Capella-Gutiérrez
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA. Department of Biology, University of Texas, Arlington, TX 76019, USA.
authors.forename: Todd A
authors.initials: TA
authors.lastname: Castoe
authors.affiliation: Department of Computer and Information Sciences, University of Delaware, Newark, DE 19717, USA.
authors.forename: Colin
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authors.lastname: Kern
authors.affiliation: Department of Biology, University of Texas, Arlington, TX 76019, USA.
authors.forename: Matthew K
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authors.lastname: Fujita
authors.affiliation: Instituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.
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authors.affiliation: Genetic Information Research Institute, Mountain View, CA 94043, USA.
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authors.affiliation: Genetic Information Research Institute, Mountain View, CA 94043, USA.
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authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
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authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
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authors.lastname: Hubley
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: Arian F
authors.initials: AF
authors.lastname: Smit
authors.affiliation: Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA.
authors.forename: Roy N
authors.initials: RN
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authors.affiliation: Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA.
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authors.initials: CA
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authors.affiliation: Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA.
authors.forename: Meganathan P
authors.initials: MP
authors.lastname: Ramakodi
authors.affiliation: Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA.
authors.forename: John W
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authors.lastname: Finger
authors.affiliation: Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany. Department of Evolutionary Biology (EBC), Uppsala University, SE-752 36 Uppsala, Sweden.
authors.forename: Alexander
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authors.lastname: Suh
authors.affiliation: Porosus Pty. Ltd., Palmerston, NT 0831, Australia. Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia. Centre for Crocodile Research, Noonamah, NT 0837, Australia.
authors.forename: Sally R
authors.initials: SR
authors.lastname: Isberg
authors.affiliation: Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia.
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authors.affiliation: Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia.
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authors.initials: AY
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authors.affiliation: Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia.
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authors.affiliation: Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia.
authors.forename: Jaime
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authors.lastname: Gongora
authors.affiliation: Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia.
authors.forename: Christopher
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authors.affiliation: Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
authors.forename: Andrés
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authors.affiliation: Moore Laboratory of Zoology, Occidental College, Los Angeles, CA 90041, USA.
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authors.lastname: McCormack
authors.affiliation: College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ 85721, USA.
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authors.initials: SC
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authors.affiliation: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
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authors.initials: SV
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authors.affiliation: School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.
authors.forename: Eric
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authors.lastname: Lyons
authors.affiliation: Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USA.
authors.forename: Christina
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authors.affiliation: Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USA.
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authors.affiliation: Howard Hughes Medical Institute, Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.
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authors.affiliation: Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA.
authors.forename: Cathy R
authors.initials: CR
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authors.affiliation: Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS 39762, USA.
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authors.affiliation: Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany.
authors.forename: Jürgen
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authors.lastname: Schmitz
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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authors.initials: DD
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authors.affiliation: Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA. Howard Hughes Medical Institute, Bethesda, MD 20814, USA.
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authors.affiliation: Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA.
authors.forename: Eric W
authors.initials: EW
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authors.affiliation: China National GeneBank, BGI-Shenzhen, Shenzhen, China. Center for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Guojie
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authors.affiliation: Department of Earth and Environmental Sciences, University of Iowa, Iowa City, IA 52242, USA.
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authors.affiliation: Department of Animal and Food Sciences, University of Delaware, Newark, DE 19717, USA.
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authors.affiliation: School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA.
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authors.initials: BC
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authors.affiliation: Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA.
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authors.affiliation: Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA.
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authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain. Universitat Pompeu Fabra, 08003 Barcelona, Spain. Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain.
authors.forename: Toni
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authors.affiliation: Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA.
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authors.affiliation: Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA. Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA. Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA. ed@soe.ucsc.edu david.a.ray@ttu.edu.
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mesh_terms: D000489:Alligators and Crocodiles / Q000145:classification / Q000235:genetics*; D000818:Animals; D005075:Biological Evolution; D001717:Birds / Q000145:classification / Q000235:genetics*; D017124:Conserved Sequence; D004251:DNA Transposable Elements; D025061:Dinosaurs / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D014644:Genetic Variation; D016678:Genome; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010802:Phylogeny; D012104:Reptiles / Q000145:classification / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D059467:Transcriptome
chemical_list: D004251:DNA Transposable Elements