Journal Article

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

Jarvis, Erich D., Jaratlerdsiri, Weerachai, Burgess, Shane C., Opazo, Juan C., Haussler, David, Earl, Dent, Jurka, Jerzy, Chong, Amanda Y., Williams, Christina, Finger, John W., Pollock, David D., Suh, Alexander, Braun, Edward L., Armstrong, Joel, Ramakodi, Meganathan P., Gabaldón, Toni, Castoe, Todd A., Kojima, Kenji K., Paten, Benedict, Glenn, Travis C., St. John, John A., Caballero, Juan, Nguyen, Ngan, Gresham, Cathy R., Vandewege, Michael W., Ray, David A., Moran, Christopher, Iriarte, Andrés, Fujita, Matthew K., Gongora, Jaime, Isberg, Sally R., McCarthy, Fiona M., Zhang, Guojie, Peterson, Daniel G., Schmitz, Jürgen, Irie, Naoki, Smit, Arian F., Edwards, Scott V., Kern, Colin, Schmidt, Carl J., Capella-Gutiérrez, Salvador, McCormack, John, Hubley, Robert M., Platt, Roy N., Lyons, Eric, Miles, Lee, Triplett, Eric W., Brochu, Christopher A., Howard, Jason T., Green, Richard E., Faircloth, Brant C., Breen, Matthew, Lavoie, Christine A., Hoffmann, Federico G., Hickey, Glenn

2014

Overview

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.

• Publisher: American Association for the Advancement of Science,The American Association for the Advancement of Science
• Subject: Alligator mississippiensis / alligators / Alligators and Crocodiles - classification / Alligators and Crocodiles - genetics / Animals / Aquatic animals / Aquatic reptiles / Biological Evolution / Birds / Birds - classification / Birds - genetics / Conserved Sequence / Crocodiles / Crocodylus porosus / Dinosaurs / Dinosaurs - classification / Dinosaurs - genetics / DNA Transposable Elements / Evolution / Evolution, Molecular / Evolutionary biology / Fossils / Gavialis gangeticus / Genes / Genetic Variation / Genetics / Genome / Genomes / Genomics / heterozygosity / Karyotypes / Markov chains / Markov Processes / Molecular Sequence Annotation / Molecular Sequence Data / Nucleotides / Phylogeny / Pleistocene / Population number / population size / Reduction / Reptiles / Reptiles - classification / Reptiles - genetics / RESEARCH ARTICLE SUMMARY / Saline water / Sequence Alignment / Sequence Analysis, DNA / Taxa / Transcriptome / transposons / Turtles