ArticleScience (New York, N.Y.)2014
Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.
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Article in Science (New York, N.Y.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 194 papers.
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194citing papers in PubMed
54.1field-weighted citation impact, top 1% of its field
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Who cites it
194 citing papers in PubMed, 370 citations in OpenAlex.
- Skeletal pathologies in extant crocodilians as a window into the paleopathology of fossil archosaurs.Anatomical record (Hoboken, N.J. : 2007) · 2026Article
- Genome evolution and long-term demographic history in true crocodiles.G3 (Bethesda, Md.) · 2026Article
- Assessing the Evolutionary Potential of Endangered Populations Using Genomic Analyses of Selection in Ecologically Important Gene Regions.Molecular ecology · 2026Article
- The Vertebrate Genomes Project Phase I: A global reference genome resource.bioRxiv : the preprint server for biology · 2026Article
- Evolution of limb and digit identity genes since the tetrapod ancestor.Nature communications · 2026Article
- Chromosome-level reference genome for the common wall gecko (Tarentola mauritanica) enables comparative and functional studies in geckos.G3 (Bethesda, Md.) · 2026Article
- The genomic basis of independent marine transitions in turtles: convergent episodic adaptation and demographic shifts.Molecular biology and evolution · 2026Article
- TEPEAK: A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations.PLoS computational biology · 2026Article
- Multispecies pangenomes reveal a pervasive influence of population size on structural variation.Science (New York, N.Y.) · 2025Article
- Quaternary Habitat Fluctuations and Demographic Dynamics in Turtles Inferred From Environmental Niche Modelling and Whole Genome Data.Molecular ecology resources · 2025Article
- Review
- Genomes of two Extinct-in-the-Wild reptiles from Christmas Island reveal distinct evolutionary histories and conservation insights.Molecular ecology resources · 2025Article
- Changes in Evolutionary Developmental Control Points in the Amniote Limb May Explain Hyperphalangy.Molecular biology and evolution · 2025Article
- Genomic insights and the conservation potential of captive breeding: The case of Chinese alligator.Science advances · 2025Article
- Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants.bioRxiv : the preprint server for biology · 2025Article
- Chromosome-level reference genome for the medically important Arabian horned viper (Cerastes gasperettii).GigaScience · 2025Article
- Evidence of avian and human influenza A virus infection in farmed Siamese crocodiles (Crocodylus siamensis) in Thailand.PloS one · 2025Article
- Article
- Use of fecal microbiome to understand the impact of housing conditions on metabolic stress responses in farmed saltwater crocodiles (Frontiers in veterinary science · 2025Article
- Resilience of the replacing dentition in adult reptiles.Developmental biology · 2024Review
134 more citing papers are in PubMed but not listed here.
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Authors and funding
55 authors at 20 institutions in 8 countries.
Richard E GreenDepartment of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA. ed@soe.ucsc.edu david.a.ray@ttu.edu.
Edward L BraunDepartment of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
Joel ArmstrongDepartment 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.
Dent EarlDepartment 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.
Ngan NguyenDepartment 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.
Glenn HickeyDepartment 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.
Michael W VandewegeDepartment of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA.
John A St JohnDepartment of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA.
Salvador Capella-GutiérrezBioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain. Universitat Pompeu Fabra, 08003 Barcelona, Spain.
Todd A CastoeDepartment 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.
Colin KernDepartment of Computer and Information Sciences, University of Delaware, Newark, DE 19717, USA.
Matthew K FujitaDepartment of Biology, University of Texas, Arlington, TX 76019, USA.
Juan C OpazoInstituto de Ciencias Ambientales y Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.
Jerzy JurkaGenetic Information Research Institute, Mountain View, CA 94043, USA.
Kenji K KojimaGenetic Information Research Institute, Mountain View, CA 94043, USA.
Juan CaballeroInstitute for Systems Biology, Seattle, WA 98109, USA.
Robert M HubleyInstitute for Systems Biology, Seattle, WA 98109, USA.
Arian F SmitInstitute for Systems Biology, Seattle, WA 98109, USA.
Roy N PlattDepartment 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.
Christine A LavoieDepartment of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA.
Meganathan P RamakodiDepartment 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.
John W FingerDepartment of Environmental Health Science, University of Georgia, Athens, GA 30602, USA.
Alexander SuhInstitute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany. Department of Evolutionary Biology (EBC), Uppsala University, SE-752 36 Uppsala, Sweden.
Sally R IsbergPorosus 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.
Lee MilesFaculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia.
Amanda Y ChongFaculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia.
Weerachai JaratlerdsiriFaculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia.
Jaime GongoraFaculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia.
Christopher MoranFaculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia.
Andrés IriarteDepartamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
John McCormackMoore Laboratory of Zoology, Occidental College, Los Angeles, CA 90041, USA.
Shane C BurgessCollege of Agriculture and Life Sciences, University of Arizona, Tucson, AZ 85721, USA.
Scott V EdwardsDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
Eric LyonsSchool of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.
Christina WilliamsDepartment of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USA.
Matthew BreenDepartment of Molecular Biomedical Sciences, North Carolina State University, Raleigh, NC 27607, USA.
Jason T HowardHoward Hughes Medical Institute, Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.
Cathy R GreshamInstitute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA.
Daniel G PetersonInstitute 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.
Jürgen SchmitzInstitute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany.
David D PollockDepartment of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA.
David HausslerCenter for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA. Howard Hughes Medical Institute, Bethesda, MD 20814, USA.
Eric W TriplettDepartment of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA.
Guojie ZhangChina National GeneBank, BGI-Shenzhen, Shenzhen, China. Center for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
Naoki IrieDepartment of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan.
Erich D JarvisHoward Hughes Medical Institute, Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA.
Christopher A BrochuDepartment of Earth and Environmental Sciences, University of Iowa, Iowa City, IA 52242, USA.
Carl J SchmidtDepartment of Animal and Food Sciences, University of Delaware, Newark, DE 19717, USA.
Fiona M McCarthySchool of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA.
Brant C FairclothDepartment of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90019, USA. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
Federico G HoffmannDepartment 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.
Travis C GlennDepartment of Environmental Health Science, University of Georgia, Athens, GA 30602, USA.
Toni GabaldónBioinformatics 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.
Benedict PatenCenter for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA.
David A RayDepartment 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.
University of California, Santa Cruz · USMississippi State University · USUniversity of Sydney · AUInstitute for Systems Biology · USUniversity of Arizona · USDuke University Hospital · USGenetic Information Research Institute · USNorth Carolina State University · USThe University of Texas at Arlington · USUniversity of Florida · USUniversity of Georgia · USAustral University of Chile · CLCentre for Genomic Regulation · ESChina National GeneBank · CNHarvard University · USInstitució Catalana de Recerca i Estudis Avançats · ESLouisiana State University · USOccidental College · USTexas Tech University · USUniversidad de la República · UY
Funding
GENCODE Resource ProjectU41HG007234 · NHGRI · SANGER INSTITUTE · PI FLICEK, PAUL · 2013 to 2020
$20.3MA Data Coordinating Center for ENCODEU41HG006992 · NHGRI · STANFORD UNIVERSITY · PI CHERRY, J. MICHAEL · 2012 to 2016
$16.6MMaintenance and Development of RepeatMasker and RepeatModelerR01HG002939 · NHGRI · INSTITUTE FOR SYSTEMS BIOLOGY · PI Robert MacDonald Hubley, Arian Fredericus Anthonius Smit · 2003 to 2026
$9.1MEDAC: ENCODE Data Analysis CenterU01HG004695 · NHGRI · EUROPEAN MOLECULAR BIOLOGY LABORATORY · PI BIRNEY, EWAN · 2008 to 2012
$6.4MGenome-wide mutation models to decipher functionR01GM097251 · NIGMS · UNIVERSITY OF COLORADO DENVER · PI POLLOCK, DAVID D · 2012 to 2015
$1.2MHoward Hughes Medical InstituteNHGRI NIH HHS 1U41HG006992-2NHGRI NIH HHS 1U41HG007234-01NHGRI NIH HHS 5U01HG004695NHGRI NIH HHS R01 HG002939NHGRI NIH HHS U01 HG004695NHGRI NIH HHS U41 HG006992NHGRI NIH HHS U41 HG007234NIGMS NIH HHS R01 GM097251
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.
Indexed as
Evolution, MolecularGenomeAlligators and CrocodilesAnimalsBiological EvolutionBirdsConserved SequenceDinosaursDNA Transposable ElementsGenetic VariationMolecular Sequence AnnotationMolecular Sequence DataPhylogenyReptilesSequence AlignmentSequence Analysis, DNADNA Transposable Elements
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