Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

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. LavoieMeganathan P. Ramakodi, John W. Finger, 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 H 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, David A. Ray

Research output: Contribution to journalArticle

138 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1254449
Number of pages1
JournalScience
Volume346
Issue number6215
DOIs
StatePublished - Dec 12 2014

Fingerprint

Birds
Alligators and Crocodiles
Genome
Dinosaurs
Synteny
Turtles
DNA Transposable Elements
Population Density
Genes
Nucleotides

ASJC Scopus subject areas

  • Medicine(all)

Cite this

Green, R. E., Braun, E. L., Armstrong, J., Earl, D., Nguyen, N., Hickey, G., ... Ray, D. A. (2014). Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science, 346(6215), 1254449. https://doi.org/10.1126/science.1254449

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

In: Science, Vol. 346, No. 6215, 12.12.2014, p. 1254449.

Research output: Contribution to journalArticle

Green, RE, Braun, EL, Armstrong, J, Earl, D, Nguyen, N, Hickey, G, Vandewege, MW, St John, JA, Capella-Gutiérrez, S, Castoe, TA, Kern, C, Fujita, MK, Opazo, JC, Jurka, J, Kojima, KK, Caballero, J, Hubley, RM, Smit, AF, Platt, RN, Lavoie, CA, Ramakodi, MP, Finger, JW, Suh, A, Isberg, SR, Miles, L, Chong, AY, Jaratlerdsiri, W, Gongora, J, Moran, C, Iriarte, A, McCormack, J, Burgess, SC, Edwards, SV, Lyons, EH, Williams, C, Breen, M, Howard, JT, Gresham, CR, Peterson, DG, Schmitz, J, Pollock, DD, Haussler, D, Triplett, EW, Zhang, G, Irie, N, Jarvis, ED, Brochu, CA, Schmidt, CJ, McCarthy, FM, Faircloth, BC, Hoffmann, FG, Glenn, TC, Gabaldón, T, Paten, B & Ray, DA 2014, 'Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs', Science, vol. 346, no. 6215, pp. 1254449. https://doi.org/10.1126/science.1254449
Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G et al. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science. 2014 Dec 12;346(6215):1254449. https://doi.org/10.1126/science.1254449
Green, Richard E. ; Braun, Edward L. ; Armstrong, Joel ; Earl, Dent ; Nguyen, Ngan ; Hickey, Glenn ; Vandewege, Michael W. ; St John, John A. ; Capella-Gutiérrez, Salvador ; Castoe, Todd A. ; Kern, Colin ; Fujita, Matthew K. ; Opazo, Juan C. ; Jurka, Jerzy ; Kojima, Kenji K. ; Caballero, Juan ; Hubley, Robert M. ; Smit, Arian F. ; Platt, Roy N. ; Lavoie, Christine A. ; Ramakodi, Meganathan P. ; Finger, John W. ; Suh, Alexander ; Isberg, Sally R. ; Miles, Lee ; Chong, Amanda Y. ; Jaratlerdsiri, Weerachai ; Gongora, Jaime ; Moran, Christopher ; Iriarte, Andrés ; McCormack, John ; Burgess, Shane C ; Edwards, Scott V. ; Lyons, Eric H ; Williams, Christina ; Breen, Matthew ; Howard, Jason T. ; Gresham, Cathy R. ; Peterson, Daniel G. ; Schmitz, Jürgen ; Pollock, David D. ; Haussler, David ; Triplett, Eric W. ; Zhang, Guojie ; Irie, Naoki ; Jarvis, Erich D. ; Brochu, Christopher A. ; Schmidt, Carl J. ; McCarthy, Fiona M ; Faircloth, Brant C. ; Hoffmann, Federico G. ; Glenn, Travis C. ; Gabaldón, Toni ; Paten, Benedict ; Ray, David A. / Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. In: Science. 2014 ; Vol. 346, No. 6215. pp. 1254449.
@article{8161910e82b84bf88bf686937331f99b,
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.",
author = "Green, {Richard E.} and Braun, {Edward L.} and Joel Armstrong and Dent Earl and Ngan Nguyen and Glenn Hickey and Vandewege, {Michael W.} and {St John}, {John A.} and Salvador Capella-Guti{\'e}rrez and Castoe, {Todd A.} and Colin Kern and Fujita, {Matthew K.} and Opazo, {Juan C.} and Jerzy Jurka and Kojima, {Kenji K.} and Juan Caballero and Hubley, {Robert M.} and Smit, {Arian F.} and Platt, {Roy N.} and Lavoie, {Christine A.} and Ramakodi, {Meganathan P.} and Finger, {John W.} and Alexander Suh and Isberg, {Sally R.} and Lee Miles and Chong, {Amanda Y.} and Weerachai Jaratlerdsiri and Jaime Gongora and Christopher Moran and Andr{\'e}s Iriarte and John McCormack and Burgess, {Shane C} and Edwards, {Scott V.} and Lyons, {Eric H} and Christina Williams and Matthew Breen and Howard, {Jason T.} and Gresham, {Cathy R.} and Peterson, {Daniel G.} and J{\"u}rgen Schmitz and Pollock, {David D.} and David Haussler and Triplett, {Eric W.} and Guojie Zhang and Naoki Irie and Jarvis, {Erich D.} and Brochu, {Christopher A.} and Schmidt, {Carl J.} and McCarthy, {Fiona M} and Faircloth, {Brant C.} and Hoffmann, {Federico G.} and Glenn, {Travis C.} and Toni Gabald{\'o}n and Benedict Paten and Ray, {David A.}",
year = "2014",
month = "12",
day = "12",
doi = "10.1126/science.1254449",
language = "English (US)",
volume = "346",
pages = "1254449",
journal = "Science",
issn = "0036-8075",
publisher = "American Association for the Advancement of Science",
number = "6215",

}

TY - JOUR

T1 - Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

AU - Green, Richard E.

AU - Braun, Edward L.

AU - Armstrong, Joel

AU - Earl, Dent

AU - Nguyen, Ngan

AU - Hickey, Glenn

AU - Vandewege, Michael W.

AU - St John, John A.

AU - Capella-Gutiérrez, Salvador

AU - Castoe, Todd A.

AU - Kern, Colin

AU - Fujita, Matthew K.

AU - Opazo, Juan C.

AU - Jurka, Jerzy

AU - Kojima, Kenji K.

AU - Caballero, Juan

AU - Hubley, Robert M.

AU - Smit, Arian F.

AU - Platt, Roy N.

AU - Lavoie, Christine A.

AU - Ramakodi, Meganathan P.

AU - Finger, John W.

AU - Suh, Alexander

AU - Isberg, Sally R.

AU - Miles, Lee

AU - Chong, Amanda Y.

AU - Jaratlerdsiri, Weerachai

AU - Gongora, Jaime

AU - Moran, Christopher

AU - Iriarte, Andrés

AU - McCormack, John

AU - Burgess, Shane C

AU - Edwards, Scott V.

AU - Lyons, Eric H

AU - Williams, Christina

AU - Breen, Matthew

AU - Howard, Jason T.

AU - Gresham, Cathy R.

AU - Peterson, Daniel G.

AU - Schmitz, Jürgen

AU - Pollock, David D.

AU - Haussler, David

AU - Triplett, Eric W.

AU - Zhang, Guojie

AU - Irie, Naoki

AU - Jarvis, Erich D.

AU - Brochu, Christopher A.

AU - Schmidt, Carl J.

AU - McCarthy, Fiona M

AU - Faircloth, Brant C.

AU - Hoffmann, Federico G.

AU - Glenn, Travis C.

AU - Gabaldón, Toni

AU - Paten, Benedict

AU - Ray, David A.

PY - 2014/12/12

Y1 - 2014/12/12

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84917697073&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84917697073&partnerID=8YFLogxK

U2 - 10.1126/science.1254449

DO - 10.1126/science.1254449

M3 - Article

C2 - 25504731

AN - SCOPUS:84917697073

VL - 346

SP - 1254449

JO - Science

JF - Science

SN - 0036-8075

IS - 6215

ER -