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Comparative Study
. 2005 Feb;169(2):533-8.
doi: 10.1534/genetics.104.036939. Epub 2004 Nov 15.

Evidence for abundant slightly deleterious polymorphisms in bacterial populations

Austin L Hughes  1
Affiliations
Comparative Study

Evidence for abundant slightly deleterious polymorphisms in bacterial populations

Austin L Hughes. Genetics. 2005 Feb.

Abstract

The nearly neutral theory of molecular evolution predicts that slightly deleterious mutations subject to purifying selection are widespread in natural populations, particularly those of large effective population size. To test this hypothesis, the standardized difference between pairwise nucleotide difference and number of segregation sites (corrected for number of sequences) was estimated for 149 population data sets from 84 species of bacteria. This quantity (Tajima's D-statistic) was estimated separately for synonymous (D(syn)) and nonsynonymous (D(non)) polymorphisms. D(syn) was positive in 70% of data sets, and the overall median D(syn) (0.873) was positive. By contrast D(non) was negative in 68% of data sets, and the overall median D(non) (-0.656) was negative. The preponderance of negative values of D(non) is evidence that there are widespread rare nonsynonymous polymorphisms in the process of being eliminated by purifying selection, as predicted to occur in populations with large effective size by the nearly neutral theory. The major exceptions to this trend were seen among surface proteins, particularly those of bacteria parasitic on vertebrates, which included a number of cases of polymorphisms apparently maintained by balancing selection.

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Figures

F<sc>igure</sc> 1.—
Figure 1.—
Median pairwise difference between observed and expected (assuming a Poisson distribution) proportions of codons with zero to three polymorphic nucleotides in the 149 data sets. Tests of the equality of the median proportion observed and the median proportion expected (Wilcoxon signed-rank test) are **P < 0.01 and ***P < 0.001.
F<sc>igure</sc> 2.—
Figure 2.—
Plot of Dnon vs. Dsyn for the 149 data sets. The line is a 45° line. Median Dsyn was significantly greater than median Dnon (Wilcoxon signed-rank test, P < 0.001).
F<sc>igure</sc> 3.—
Figure 3.—
Median values of (A) πS and (B) πN for data sets categorized by parasitism on vertebrates and surface expression of the protein. There was no significant difference among categories with respect to median πS (Kruskal-Wallis test), but median πN differed significantly among categories (Kruskal-Wallis test, P < 0.001).
F<sc>igure</sc> 4.—
Figure 4.—
Median values of (A) Dsyn and (B) Dnon for data sets categorized by parasitism on vertebrates and surface expression of the protein. There was no significant difference among categories with respect to median Dsyn (Kruskal-Wallis test), but median Dnon differed significantly among categories (Kruskal-Wallis test, P < 0.001).
F<sc>igure</sc> 5.—
Figure 5.—
Median percentage of G + C at third-codon positions (GC3) for data sets categorized by parasitism on vertebrates and surface expression of the protein. There was a significant difference among categories with respect to median GC3 (Kruskal-Wallis test, P = 0.004).
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References

    1. Bulmer, M., 1991. The selection-mutation-drift theory of synonymous codon usage. Genetics 129: 897–907. - PMC - PubMed
    1. Faruque, S. M., and J. J. Mekalanos, 2003. Pathogenicity islands and phages in Vibrio cholerae evolution. Trends Microbiol. 11: 505–510. - PubMed
    1. Feil, E. J., J. E. Cooper, H. Grundmann, D. A. Robinson, M. C. Enright et al., 2003. How clonal is Staphylococcus aureus? J. Bacteriol. 185: 3307–3316. - PMC - PubMed
    1. Frank, S. A., 2002 Immunology and Evolution of Infectious Disease. Princeton University Press, Princeton, NJ. - PubMed
    1. Freudenberg-Hua, Y., J. Freudenberg, N. Kluck, S. Cichon, P. Propping et al., 2003. Single nucleotide variation analysis in 65 candidate genes for CNS disorders in a representative sample of the European population. Genome Res. 13: 2271–2276. - PMC - PubMed

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