Richard E Green, Edward L Braun, Joel Armstrong, Dent Earl, Ngan Nguyen, Glenn Hickey, Michael W Vandewege, John A St John, Salvador Capella-Gutiérrez, Todd A Castoe, Colin Kern, Matthew K Fujita, Juan C Opazo, Jerzy Jurka, Kenji K Kojima, Juan Caballero, Robert M Hubley, Arian F Smit, Roy N Platt, Christine A Lavoie, Meganathan P Ramakodi, John W Finger Jr., Alexander Suh, Sally R Isberg, Lee Miles, Amanda Y Chong, Weerachai Jaratlerdsiri, Jaime Gongora, Christopher Moran, Andrés Iriarte, John McCormack, Shane C Burgess, Scott V Edwards, Eric Lyons, Christina Williams, Matthew Breen, Jason T Howard, Cathy R Gresham, Daniel G Peterson, Jürgen Schmitz, David D Pollock, David Haussler, Eric W Triplett, Guojie Zhang, Naoki Irie, Erich D Jarvis, Christopher A Brochu, Carl J Schmidt, Fiona M McCarthy, Brant C Faircloth, Federico G Hoffmann, Travis C Glenn, Toni Gabaldón, Benedict Paten, and and David A Ray, 'Three Crocodilian Genomes Reveal Ancestral Patterns of Evolution among Archosaurs', Science (2014).
To provide context for the diversifications 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 relatively rapid evolution of bird genomes represents an autapomorphy within that clade. 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 new data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.