Isochore Evolution in Mammals: A Human-Like Ancestral Structure

Corresponding author: Dominique Mouchiroud, Centre National de la Recherche Scientifique UMR 5558, Biométrie, Génétique et Biologie des Populations, Université Claude Bernard Lyon 1, 43, Boulevard du 11 novembre 1918, 69622 Villeurbanne Cedex, France., mouchi{at}biomserv.univ-lyon1.fr (E-mail).

Communicating editor: G. A. CHURCHILL

Codon usage in mammals is mainly determined by the spatial arrangement of genomic G + C-content, i.e., the isochore structure. Ancestral G + C-content at third codon positions of 27 nuclear protein-coding genes of eutherian mammals was estimated by maximum-likelihood analysis on the basis of a nonhomogeneous DNA substitution model, accounting for variable base compositions among present-day sequences. Data consistently supported a human-like ancestral pattern, i.e., highly variable G + C-content among genes. The mouse genomic structure—more narrow G + C-content distribution—would be a derived state. The circumstances of isochore evolution are discussed with respect to this result. A possible relationship between G + C-content homogenization in murid genomes and high mutation rate is proposed, consistent with the negative selection hypothesis for isochore maintenance in mammals.

This article has been cited by other articles:

				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]

				C. Webber and C. P. Ponting Hotspots of mutation and breakage in dog and human chromosomes Genome Res., December 1, 2005; 15(12): 1787 - 1797. [Abstract] [Full Text] [PDF]

				M. M. Alba and R. Guigo Comparative Analysis of Amino Acid Repeats in Rodents and Humans Genome Res., April 1, 2004; 14(4): 549 - 554. [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 Isochores and tissue-specificity Nucleic Acids Res., September 1, 2003; 31(17): 5212 - 5220. [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]

				M. J. Lercher, N. G. C. Smith, A. Eyre-Walker, and L. D. Hurst The Evolution of Isochores: Evidence From SNP Frequency Distributions Genetics, December 1, 2002; 162(4): 1805 - 1810. [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]

				A. Eyre-Walker, P. D. Keightley, N. G. C. Smith, and D. Gaffney Quantifying the Slightly Deleterious Mutation Model of Molecular Evolution Mol. Biol. Evol., December 1, 2002; 19(12): 2142 - 2149. [Abstract] [Full Text] [PDF]

				J. Castresana Genes on human chromosome 19 show extreme divergence from the mouse orthologs and a high GC content Nucleic Acids Res., April 15, 2002; 30(8): 1751 - 1756. [Abstract] [Full Text] [PDF]

				R. Tarrio, F. Rodriguez-Trelles, and F. J. Ayala Shared Nucleotide Composition Biases Among Species and Their Impact on Phylogenetic Reconstructions of the Drosophilidae Mol. Biol. Evol., August 1, 2001; 18(8): 1464 - 1473. [Abstract] [Full Text] [PDF]

				J. P. Bielawski, K. A. Dunn, and Z. Yang Rates of Nucleotide Substitution and Mammalian Nuclear Gene Evolution: Approximate and Maximum-Likelihood Methods Lead to Different Conclusions Genetics, November 1, 2000; 156(3): 1299 - 1308. [Abstract] [Full Text]