Molecular Biology and Evolution 19:1399-1406 (2002)
© 2002 Society for Molecular Biology and Evolution
Hill-Robertson Interference is a Minor Determinant of Variations in Codon Bias Across Drosophila melanogaster and Caenorhabditis elegans Genomes
,1
*Laboratoire "Biométrie et biologie évolutive," UMR CNRS 5558, Université Claude Bernard Lyon 1, Villeurbanne, France;
Center for the Study of Evolution, University of Sussex, Brighton
According to population genetics models, genomic regions with lower crossing-over rates are expected to experience less effective selection because of Hill-Robertson interference (HRi). The effect of genetic linkage is thought to be particularly important for a selection of weak intensity such as selection affecting codon usage. Consistent with this model, codon bias correlates positively with recombination rate in Drosophila melanogaster and Caenorhabditis elegans. However, in these species, the G+C content of both noncoding DNA and synonymous sites correlates positively with recombination, which suggests that mutation patterns and recombination are associated. To remove this effect of mutation patterns on codon bias, we used the synonymous sites of lowly expressed genes that are expected to be effectively neutral sites. We measured the differences between codon biases of highly expressed genes and their lowly expressed neighbors. In D. melanogaster we find that HRi weakly reduces selection on codon usage of genes located in regions of very low recombination; but these genes only comprise 4% of the total. In C. elegans we do not find any evidence for the effect of recombination on selection for codon bias. Computer simulations indicate that HRi poorly enhances codon bias if the local recombination rate is greater than the mutation rate. This prediction of the model is consistent with our data and with the current estimate of the mutation rate in D. melanogaster. The case of C. elegans, which is highly self-fertilizing, is discussed. Our results suggest that HRi is a minor determinant of variations in codon bias across the genome.
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]
|
|
|
|
 |
|
 A. Heger and C. P. Ponting Variable Strength of Translational Selection Among 12 Drosophila Species Genetics, November 1, 2007; 177(3): 1337 - 1348. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Diaz-Castillo and K. G. Golic Evolution of Gene Sequence in Response to Chromosomal Location Genetics, September 1, 2007; 177(1): 359 - 374. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Jiang, H. Wu, J. Wei, F. Sang, X. Sun, and Z. Lu RF-DYMHC: detecting the yeast meiotic recombination hotspots and coldspots by random forest model using gapped dinucleotide composition features Nucleic Acids Res., July 13, 2007; 35(suppl_2): W47 - W51. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W.-Y. Ko, S. Piao, and H. Akashi Strong Regional Heterogeneity in Base Composition Evolution on the Drosophila X Chromosome Genetics, September 1, 2006; 174(1): 349 - 362. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Marais, P. Nouvellet, P. D. Keightley, and B. Charlesworth Intron Size and Exon Evolution in Drosophila Genetics, May 1, 2005; 170(1): 481 - 485. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Bartolome, X. Maside, S. Yi, A. L. Grant, and B. Charlesworth Patterns of Selection on Synonymous and Nonsynonymous Variants in Drosophila miranda Genetics, March 1, 2005; 169(3): 1495 - 1507. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. D. Singh, P. F. Arndt, and D. A. Petrov Genomic Heterogeneity of Background Substitutional Patterns in Drosophila melanogaster Genetics, February 1, 2005; 169(2): 709 - 722. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Qin, W. B. Wu, J. M. Comeron, M. Kreitman, and W.-H. Li Intragenic Spatial Patterns of Codon Usage Bias in Prokaryotic and Eukaryotic Genomes Genetics, December 1, 2004; 168(4): 2245 - 2260. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. I. Wright, C. B. K. Yau, M. Looseley, and B. C. Meyers Effects of Gene Expression on Molecular Evolution in Arabidopsis thaliana and Arabidopsis lyrata Mol. Biol. Evol., September 1, 2004; 21(9): 1719 - 1726. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Meunier and L. Duret Recombination Drives the Evolution of GC-Content in the Human Genome Mol. Biol. Evol., June 1, 2004; 21(6): 984 - 990. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. I. Jensen-Seaman, T. S. Furey, B. A. Payseur, Y. Lu, K. M. Roskin, C.-F. Chen, M. A. Thomas, D. Haussler, and H. J. Jacob Comparative Recombination Rates in the Rat, Mouse, and Human Genomes Genome Res., April 1, 2004; 14(4): 528 - 538. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Prachumwat, L. DeVincentis, and M. F. Palopoli Intron Size Correlates Positively With Recombination Rate in Caenorhabditis elegans Genetics, March 1, 2004; 166(3): 1585 - 1590. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Bachtrog Protein Evolution and Codon Usage Bias on the Neo-Sex Chromosomes of Drosophila miranda Genetics, November 1, 2003; 165(3): 1221 - 1232. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Andolfatto and J. D. Wall Linkage Disequilibrium Patterns Across a Recombination Gradient in African Drosophila melanogaster Genetics, November 1, 2003; 165(3): 1289 - 1305. [Abstract] [Full Text] [PDF]
|
|