Molecular Biology and Evolution 19:728-735 (2002)
© 2002 Society for Molecular Biology and Evolution
Genome Evolution and Developmental Constraint in Caenorhabditis elegans
Department of Organismic and Evolutionary Biology, Harvard University
It has been hypothesized that evolutionary changes will be more frequent in later ontogeny than early ontogeny because of developmental constraint. To test this hypothesis, a genomewide examination of molecular evolution through ontogeny was carried out using comparative genomic data in Caenorhabditis elegans and Caenorhabditis briggsae. We found that the mean rate of amino acid replacement is not significantly different between genes expressed during and after embryogenesis. However, synonymous substitution rates differed significantly between these two classes. A genomewide survey of correlation between codon bias and expression level found codon bias to be significantly correlated with mRNA expression (rs = -0.30 and P < 10-131) but does not alone explain differences in dS between classes. Surprisingly, it was found that genes expressed after embryogenesis have a significantly greater number of duplicates in both the C. elegans and C. briggsae genomes (P < 10-20 and P < 10-13) when compared with early-expressed and nonmodulated genes. A similarity in the distribution of duplicates of nonmodulated and early-expressed genes, as well as a disproportionately higher number of early pseudogenes, lend support to the hypothesis that this difference in duplicate number is caused by selection against gene duplicates of early-expressed genes, reflecting developmental constraint. Developmental constraint at the level of gene duplication may have important implications for macroevolutionary change.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  A. D. Cutter, A. Dey, and R. L. Murray Evolution of the Caenorhabditis elegans Genome Mol. Biol. Evol., June 1, 2009; 26(6): 1199 - 1234. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. H. Thomas Genome evolution in Caenorhabditis Brief Funct Genomic Proteomic, June 23, 2008; (2008) eln022v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Yang and R. Nielsen Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage Mol. Biol. Evol., March 1, 2008; 25(3): 568 - 579. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. D. Cutter, J. D. Wasmuth, and M. L. Blaxter The Evolution of Biased Codon and Amino Acid Usage in Nematode Genomes Mol. Biol. Evol., December 1, 2006; 23(12): 2303 - 2315. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. D. Cutter, M.-A. Felix, A. Barriere, and D. Charlesworth Patterns of Nucleotide Polymorphism Distinguish Temperate and Tropical Wild Isolates of Caenorhabditis briggsae Genetics, August 1, 2006; 173(4): 2021 - 2031. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. He and J. Zhang Higher Duplicability of Less Important Genes in Yeast Genomes Mol. Biol. Evol., January 1, 2006; 23(1): 144 - 151. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. M. Good and M. W. Nachman Rates of Protein Evolution Are Positively Correlated with Developmental Timing of Expression During Mouse Spermatogenesis Mol. Biol. Evol., April 1, 2005; 22(4): 1044 - 1052. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. D. Cutter and S. Ward Sexual and Temporal Dynamics of Molecular Evolution in C. elegans Development Mol. Biol. Evol., January 1, 2005; 22(1): 178 - 188. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. I. Castillo-Davis, D. L. Hartl, and G. Achaz cis-Regulatory and Protein Evolution in Orthologous and Duplicate Genes Genome Res., August 1, 2004; 14(8): 1530 - 1536. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J.-V. Chamary and L. D. Hurst Similar Rates but Different Modes of Sequence Evolution in Introns and at Exonic Silent Sites in Rodents: Evidence for Selectively Driven Codon Usage Mol. Biol. Evol., June 1, 2004; 21(6): 1014 - 1023. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. I. Castillo-Davis, F. A. Kondrashov, D. L. Hartl, and R. J. Kulathinal The Functional Genomic Distribution of Protein Divergence in Two Animal Phyla: Coevolution, Genomic Conflict, and Constraint Genome Res., May 1, 2004; 14(5): 802 - 811. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Mitreva, J. P. McCarter, J. Martin, M. Dante, T. Wylie, B. Chiapelli, D. Pape, S. W. Clifton, T. B. Nutman, and R. H. Waterston Comparative Genomics of Gene Expression in the Parasitic and Free-Living Nematodes Strongyloides stercoralis and Caenorhabditis elegans Genome Res., February 1, 2004; 14(2): 209 - 220. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. E. Winter, L. Goodstadt, and C. P. Ponting Elevated Rates of Protein Secretion, Evolution, and Disease Among Tissue-Specific Genes Genome Res., January 1, 2004; 14(1): 54 - 61. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. dos Reis, L. Wernisch, and R. Savva Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome Nucleic Acids Res., December 1, 2003; 31(23): 6976 - 6985. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. D. Cutter, B. A. Payseur, T. Salcedo, A. M. Estes, J. M. Good, E. Wood, T. Hartl, H. Maughan, J. Strempel, B. Wang, et al. Molecular Correlates of Genes Exhibiting RNAi Phenotypes in Caenorhabditis elegans Genome Res., December 1, 2003; 13(12): 2651 - 2657. [Abstract] [Full Text] [PDF]
|
|