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Cited by 359Genomics and Phylogenetic StudiesChromosomal and Genetic VariationsGenome Rearrangement Algorithms

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

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Green, Richard E., Braun, Edward L., Armstrong, Joel, Earl, Dent, Nguyen, Ngan, Hickey, Glenn, Vandewege, Michael W., St. John, John A. +47 more·2014·Science
DOI 10.1126/science.1254449PMC PMC4386873
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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.

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  • Progressive Cactus has been developed over several years and has already been successfully used as an integral component of high-profile comparative genomics projects.

    “Progressive Cactus has been developed over several years, and has already been successfully used as an integral component of high-profile comparative genomics projects16–20.”

    From Progressive Cactus is a multiple-genome aligner for the thousand-genome era (2020) · cites this paper as [16]

    The Materials and Methods section (“Genome alignments and ancestral genome reconstruction”; page unavailable) says progressive-cactus computed the 23-taxon whole-genome alignment, supporting its use as an integral component of this comparative genomics project. The paper does not establish that Progressive Cactus had been developed over several years; its References section cites a 2011 paper on Cactus, but gives no development timeline for Progressive Cactus. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

  • The rate of small indels in any given branch is correlated with the rate of nucleotide substitution.

    “As expected from previous studies16,34, the rate of small indels in any given branch was correlated with the rate of nucleotide substitution (an R2 value of 0.69 for insertions and 0.80 for deletions in avians, and 0.39 and 0.40, respectively, for eutherians)”

    From Progressive Cactus is a multiple-genome aligner for the thousand-genome era (2020) · cites this paper as [16]

    In “Rates of genome evolution in crocodilians, birds, and other reptiles” (page unavailable), the paper reports micro-indel rates relative to substitution rates across several lineages; its Discussion also says crocodilians’ low evolutionary rates extend to micro-indels. This supports a broad association, but the copy does not report a branch-by-branch correlation or establish it for any given branch. (LLM, conf=0.78)

    Experimental — accuracy not yet measured

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Authors
Green, R. E., Braun, E. L., Armstrong, J., Earl, D., Nguyen, N., Hickey, G., Vandewege, M. W., St. John, J. A., Capella-Gutiérrez, S., Castoe, T. A., Kern, C., Fujita, M. K., Opazo, J. C., Jurka, J., Kojima, K. K., Caballero, J., Hubley, R. M., Smit, A. F., Platt, R. N., Lavoie, C. A., Ramakodi, M. P., Finger, J. W., Suh, A., Isberg, S. R., Miles, L., Chong, A. Y., Jaratlerdsiri, W., Gongora, J., Moran, C., Iriarte, A., McCormack, J., Burgess, S. C., Edwards, S. V., Lyons, E., Williams, C., Breen, M., Howard, J. T., Gresham, C. R., Peterson, D. G., Schmitz, J., Pollock, D. D., Haussler, D., Triplett, E. W., Zhang, G., Irie, N., Jarvis, E. D., Brochu, C. A., Schmidt, C. J., McCarthy, F. M., Faircloth, B. C., Hoffmann, F. G., Glenn, T. C., Gabaldón, T., Paten, B., & Ray, D. A.
Affiliations
  • University of California, Santa Cruz (US)
  • University of Florida (US)
  • Mississippi State University (US)
  • Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA.
  • Universitat Pompeu Fabra (ES)
  • The University of Texas at Arlington (US)
  • University of Delaware (US)
  • Austral University of Chile (CL)
  • Genetic Information Research Institute (US)
  • Institute for Systems Biology, Seattle, WA 98109, USA.
  • Institute for Systems Biology (US)
  • University of Georgia (US)
  • Uppsala University (SE)
  • The University of Sydney (AU)
  • Universidad de la República de Uruguay (UY)
  • Occidental College (US)
  • University of Arizona (US)
  • Harvard University (US)
  • North Carolina State University (US)
  • Howard Hughes Medical Institute (US)
  • University of Münster (DE)
  • University of Colorado Anschutz (US)
  • University of Copenhagen (DK)
  • The University of Tokyo (JP)
  • University of Iowa (US)
  • Louisiana State University (US)
  • Institució Catalana de Recerca i Estudis Avançats (ES)
  • Texas Tech University (US)
Corresponding author
  • Green, Richard E.
  • Ray, David A.
ORCID
Venue
Science
Publisher
American Association for the Advancement of Science (AAAS)
Published
2014-12-12
Volume
346
Issue
6215
Pages
1254449-1254449
ISSN
  • 0036-8075 (ISSN-L)
  • 1095-9203
DOI
10.1126/science.1254449
PMC
PMC4386873
OpenAlex
W2170908011
Cited by
359
References
16
Citations by year
2026: 16 · 2025: 19 · 2024: 24 · 2023: 19 · 2022: 17 · 2021: 38 · 2020: 40 · 2019: 47 · 2018: 29 · 2017: 34 · 2016: 36 · 2015: 28 · 2014: 10
FWCI
14.68
Type
journal article
Language
en
Open access
Locations
  • Science (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • Civil War Book Review (submittedVersion)
  • DukeSpace (Duke University) (submittedVersion, cc-by-nc-nd)
  • eScholarship (California Digital Library) (submittedVersion)
  • Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
  • UEA Digital Repository (University of East Anglia) (submittedVersion)
Funders
  • Howard Hughes Medical Institute
  • Japan Society for the Promotion of Science (24570243)
  • National Human Genome Research Institute (U41HG006992, U01HG004695, U41HG007234, R01HG002939)
  • National Institute of General Medical Sciences (R01GM097251)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
Keywords
crocodilians, archosaurs, genome evolution, ancestral genome reconstruction, Alligator mississippiensis, saltwater crocodile, gharial, transposable elements, gene family evolution, chromosomal synteny, heterozygosity, population size reduction, avian genome evolution, dinosaur origin
MeSH terms
Alligators and Crocodiles, Animals, Birds, DNA Transposable Elements, Biological Evolution, Molecular Sequence Data, Phylogeny, Reptiles, Genetic Variation, Sequence Alignment, Genome, Conserved Sequence, Sequence Analysis, DNA, Evolution, Molecular, Dinosaurs, Molecular Sequence Annotation, Transcriptome

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