Evidence for abundant slightly deleterious polymorphisms in bacterial populations

被引:66
作者
Hughes, AL [1 ]
机构
[1] Univ S Carolina, Dept Biol Sci, Columbia, SC 29208 USA
关键词
D O I
10.1534/genetics.104.036939
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
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 pair-wise 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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页码:533 / 538
页数:6
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共 39 条
  • [1] [Anonymous], [No title captured]
  • [2] BULMER M, 1991, GENETICS, V129, P897
  • [3] Pathogenicity islands and phages in Vibrio cholerale evolution
    Faruque, SM
    Mekalanos, JJ
    [J]. TRENDS IN MICROBIOLOGY, 2003, 11 (11) : 505 - 510
  • [4] How clonal is Staphylococcus aureus?
    Feil, EJ
    Cooper, JE
    Grundmann, H
    Robinson, DA
    Enright, MC
    Berendt, T
    Peacock, SJ
    Smith, JM
    Murphy, M
    Spratt, BG
    Moore, CE
    Day, NPJ
    [J]. JOURNAL OF BACTERIOLOGY, 2003, 185 (11) : 3307 - 3316
  • [5] Frank S., 2002, IMMUNOLOGY EVOLUTION
  • [6] Single nucleotide variation analysis in 65 candidate genes for CNS disorders in a representative sample of the European population
    Freudenberg-Hua, Y
    Freudenberg, J
    Kluck, N
    Cichon, S
    Propping, P
    Nöthen, MM
    [J]. GENOME RESEARCH, 2003, 13 (10) : 2271 - 2276
  • [7] Genome-wide patterns of nucleotide substitution reveal stringent functional constraints on the protein sequences of thermophiles
    Friedman, R
    Drake, JW
    Hughes, AL
    [J]. GENETICS, 2004, 167 (03) : 1507 - 1512
  • [8] CODON CATALOG USAGE AND THE GENOME HYPOTHESIS
    GRANTHAM, R
    GAUTIER, C
    GOUY, M
    MERCIER, R
    PAVE, A
    [J]. NUCLEIC ACIDS RESEARCH, 1980, 8 (01) : R49 - R62
  • [9] Genetic traces of ancient demography
    Harpending, HC
    Batzer, MA
    Gurven, M
    Jorde, LB
    Rogers, AR
    Sherry, ST
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998, 95 (04) : 1961 - 1967
  • [10] Patterns of sequence divergence in 5′ intergenic spacers and linked coding regions in 10 species of pathogenic bacteria reveal distinct recombinational histories
    Hughes, AL
    Friedman, R
    [J]. GENETICS, 2004, 168 (04) : 1795 - 1803