Molecular Biology and Evolution 18:1343-1352 (2001)
© 2001 Society for Molecular Biology and Evolution
The Frequency Distribution of Nucleotide Variation in Drosophila simulans
Section of Evolution and Ecology, University of California at Davis
Patterns of codon bias in Drosophila suggest that silent mutations can be classified into two types: unpreferred (slightly deleterious) and preferred (slightly beneficial). Results of previous analyses of polymorphism and divergence in Drosophila simulans were interpreted as supporting a mutation-selection-drift model in which slightly deleterious, silent mutants make significantly greater contributions to polymorphism than to divergence. Frequencies of unpreferred polymorphisms were inferred to be lower than frequencies of other silent polymorphisms. Here, I analyzed additional D. simulans data to reevaluate the support for these ideas. I found that D. simulans has fixed more unpreferred than preferred mutations, suggesting that this lineage has not been at mutation-selection-drift equilibrium at silent sites. Frequencies of polarized unpreferred polymorphisms are not skewed toward rare alleles. However, frequencies of unpolarized unpreferred codons are lower in high-bias genes than in low-bias genes. This supports the idea that unpreferred codons are borderline deleterious mutations. Purifying selection on silent sites appears to be stronger at twofold-degenerate codons than at fourfold-degenerate codons. Finally, I found that X-linked polymorphisms occur at a higher average frequency than polymorphisms on chromosome arm 3R, even though an average X-linked site is significantly less likely to be polymorphic than an average site on 3R. This result supports a previous analysis of D. simulans indicating different population genetics of X-linked versus autosomal mutations.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  P. R. Haddrill, D. Bachtrog, and P. Andolfatto Positive and Negative Selection on Noncoding DNA in Drosophila simulans Mol. Biol. Evol., September 1, 2008; 25(9): 1825 - 1834. [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]
|
|
|
|
|
|
J. Flowers, E Sezgin, S Kumagai, D. Duvernell, L. Matzkin, P. Schmidt, and W. Eanes Adaptive Evolution of Metabolic Pathways in Drosophila Mol. Biol. Evol., June 1, 2007; 24(6): 1347 - 1354. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. J. Welch Estimating the Genomewide Rate of Adaptive Protein Evolution in Drosophila Genetics, June 1, 2006; 173(2): 821 - 837. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Akashi, W.-Y. Ko, S. Piao, A. John, P. Goel, C.-F. Lin, and A. P. Vitins Molecular Evolution in the Drosophila melanogaster Species Subgroup: Frequent Parameter Fluctuations on the Timescale of Molecular Divergence Genetics, March 1, 2006; 172(3): 1711 - 1726. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. C. Fay and J. A. Benavides Hypervariable Noncoding Sequences in Saccharomyces cerevisiae Genetics, August 1, 2005; 170(4): 1575 - 1587. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. D. Kern and D. J. Begun Patterns of Polymorphism and Divergence from Noncoding Sequences of Drosophila melanogaster and D. simulans: Evidence for Nonequilibrium Processes Mol. Biol. Evol., January 1, 2005; 22(1): 51 - 62. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. D. Shoemaker, K. A. Dyer, M. Ahrens, K. McAbee, and J. Jaenike Decreased Diversity but Increased Substitution Rate in Host mtDNA as a Consequence of Wolbachia Endosymbiont Infection Genetics, December 1, 2004; 168(4): 2049 - 2058. [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]
|
|
|
|
|
|
J. M. Comeron Selective and Mutational Patterns Associated With Gene Expression in Humans: Influences on Synonymous Composition and Intron Presence Genetics, July 1, 2004; 167(3): 1293 - 1304. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Bierne and A. Eyre-Walker The Genomic Rate of Adaptive Amino Acid Substitution in Drosophila Mol. Biol. Evol., July 1, 2004; 21(7): 1350 - 1360. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. B. DuMont, J. C. Fay, P. P. Calabrese, and C. F. Aquadro DNA Variability and Divergence at the Notch Locus in Drosophila melanogaster and D. simulans: A Case of Accelerated Synonymous Site Divergence Genetics, May 1, 2004; 167(1): 171 - 185. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Gravot, M. Huet, and M. Veuille Effect of Breeding Structure on Population Genetic Parameters in Drosophila Genetics, February 1, 2004; 166(2): 779 - 788. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. A. Schlenke and D. J. Begun Natural Selection Drives Drosophila Immune System Evolution Genetics, August 1, 2003; 164(4): 1471 - 1480. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. J. Begun and P. Whitley Molecular Population Genetics of Xdh and the Evolution of Base Composition in Drosophila Genetics, December 1, 2002; 162(4): 1725 - 1735. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. D. Kern, C. D. Jones, and D. J. Begun Genomic Effects of Nucleotide Substitutions in Drosophila simulans Genetics, December 1, 2002; 162(4): 1753 - 1761. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Eyre-Walker Changing Effective Population Size and the McDonald-Kreitman Test Genetics, December 1, 2002; 162(4): 2017 - 2024. [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. M. Comeron and M. Kreitman Population, Evolutionary and Genomic Consequences of Interference Selection Genetics, May 1, 2002; 161(1): 389 - 410. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Hey and R. M. Kliman Interactions Between Natural Selection, Recombination and Gene Density in the Genes of Drosophila Genetics, February 1, 2002; 160(2): 595 - 608. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. J. Begun Protein Variation in Drosophila simulans, and Comparison of Genes from Centromeric Versus Noncentromeric Regions of Chromosome 3 Mol. Biol. Evol., February 1, 2002; 19(2): 201 - 203. [Full Text] [PDF]
|
|