Molecular Biology and Evolution, Vol 16, 1521-1527, Copyright © 1999 by Society for Molecular Biology and Evolution
S Hughes, D Zelus and D Mouchiroud
The genomes of warm-blooded vertebrates are characterized by a strong
heterogeneity in base composition, with GC-rich and GC-poor isochores. The
GC content of sequences, especially in third codon positions, is highly
correlated with that of the isochore they are embedded in. In amphibian and
fish genomes, GC-rich isochores are nearly absent. Thus, it has been
proposed that the GC increase in a part of mammalian and avian genomes
represents an adaptation to homeothermy. To test this selective hypothesis,
we sequenced marker protein genes in two cold- blooded vertebrates, the
Nile crocodile Crocodylus niloticus (10 genes) and the red-eared slider
Trachemys scripta elegans (6 genes). The analysis of base composition in
third codon position of this original data set shows that the Nile
crocodile and the turtle also exhibit GC- rich isochores, which rules out
the homeothermy hypothesis. Instead, we propose that the GC increase
results from a mutational bias that took place earlier than the adaptation
to homeothermy in birds and before the turtle/crocodile divergence.
Surprisingly, the isochore structure appears very similar between the
red-eared slider and the Nile crocodile than between the chicken and the
Nile crocodile. This point questions the phylogenetic position of turtles
as a basal lineage of extant reptiles. We also observed a regular molecular
clock in the Archosauria, which enables us, by using a more extended data
set, to confirm Kumar and Hedges's dating of the bird-crocodile split.
ORIGINAL ARTICLE
Warm-blooded isochore structure in Nile crocodile and turtle
Laboratoire de Biometrie et Biologie Evolutive, Universite Claude Bernard, Villeurbanne, France. hughes@biomserv.univ-lyon1.fr
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  C. L. Organ, R. G. Moreno, and S. V. Edwards Three tiers of genome evolution in reptiles Integr. Comp. Biol., October 1, 2008; 48(4): 494 - 504. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. L. Chojnowski and E. L. Braun Turtle isochore structure is intermediate between amphibians and other amniotes Integr. Comp. Biol., October 1, 2008; 48(4): 454 - 462. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. K. Bag, S. Paul, S. Ghosh, and C. Dutta Reverse Polarization in Amino acid and Nucleotide Substitution Patterns Between Human Mouse Orthologs of Two Compositional Extrema DNA Res, September 25, 2007; (2007) dsm015v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Z. Wang, T. Miyake, S. V. Edwards, and C. T. Amemiya Tuatara (Sphenodon) Genomics: BAC Library Construction, Sequence Survey, and Application to the DMRT Gene Family J. Hered., November 1, 2006; 97(6): 541 - 548. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. H. Press and H. Robins Isochores Exhibit Evidence of Genes Interacting With the Large-Scale Genomic Environment Genetics, October 1, 2006; 174(2): 1029 - 1040. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. T. Webster, E. Axelsson, and H. Ellegren Strong Regional Biases in Nucleotide Substitution in the Chicken Genome Mol. Biol. Evol., June 1, 2006; 23(6): 1203 - 1216. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Astarita, B. C. Rourke, J. B. Andersen, J. Fu, J. H. Kim, A. F. Bennett, J. W. Hicks, and D. Piomelli Postprandial increase of oleoylethanolamide mobilization in small intestine of the Burmese python (Python molurus) Am J Physiol Regulatory Integrative Comp Physiol, May 1, 2006; 290(5): R1407 - R1412. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. van Rheede, T. Bastiaans, D. N. Boone, S. B. Hedges, W. W. de Jong, and O. Madsen The Platypus Is in Its Place: Nuclear Genes and Indels Confirm the Sister Group Relation of Monotremes and Therians Mol. Biol. Evol., March 1, 2006; 23(3): 587 - 597. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Kudla, A. Helwak, and L. Lipinski Gene Conversion and GC-Content Evolution in Mammalian Hsp70 Mol. Biol. Evol., July 1, 2004; 21(7): 1438 - 1444. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. F. Arndt, D. A. Petrov, and T. Hwa Distinct Changes of Genomic Biases in Nucleotide Substitution at the Time of Mammalian Radiation Mol. Biol. Evol., November 1, 2003; 20(11): 1887 - 1896. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. E. Vinogradov DNA helix: the importance of being GC-rich Nucleic Acids Res., April 1, 2003; 31(7): 1838 - 1844. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. A. Ream, G. C. Johns, and G. N. Somero Base Compositions of Genes Encoding {alpha}-Actin and Lactate Dehydrogenase-A from Differently Adapted Vertebrates Show No Temperature-Adaptive Variation in G + C Content Mol. Biol. Evol., January 1, 2003; 20(1): 105 - 110. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Duret, M. Semon, G. Piganeau, D. Mouchiroud, and N. Galtier Vanishing GC-Rich Isochores in Mammalian Genomes Genetics, December 1, 2002; 162(4): 1837 - 1847. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Duret and L. D. Hurst The Elevated GC Content at Exonic Third Sites Is Not Evidence Against Neutralist Models of Isochore Evolution Mol. Biol. Evol., May 1, 2001; 18(5): 757 - 762. [Abstract] [Full Text]
|
|
|
|
|
|
K. J. Fryxell and E. Zuckerkandl Cytosine Deamination Plays a Primary Role in the Evolution of Mammalian Isochores Mol. Biol. Evol., September 1, 2000; 17(9): 1371 - 1383. [Abstract] [Full Text] [PDF]
|
|