More effective purifying selection on RNA viruses than in DNA viruses

Abstract

Analysis of the pattern of nucleotide diversity in 222 independent viral sequence datasets showed the prevalence of purifying selection. In spite of the higher mutation rate of RNA viruses, our analyses revealed stronger evidence of the action of purifying selection in RNA viruses than in DNA viruses. The ratio of nonsynonymous to synonymous nucleotide diversity was significantly lower in RNA viruses than in DNA viruses, indicating that nonsynonymous mutations have been removed at a greater rate (relative to the mutation rate) in the former than in the latter. Moreover, statistics that measure the occurrence of rare polymorphisms revealed significantly a greater excess of rare nonsynonymous polymorphisms in RNA viruses than in DNA viruses but no difference with respect to synonymous polymorphisms. Since rare nonsynonymous polymorphisms are likely to be undergoing the effects of purifying selection acting to eliminate them, this result implies a stronger signature of ongoing purifying selection in RNA viruses than in DNA viruses. Across datasets from both DNA viruses and RNA viruses, we found a negatively allometric relationship between nonsynonymous and synonymous nucleotide diversity; in other words, nonsynonymous nucleotide diversity increased with synonymous nucleotide diversity at a less than linear rate. These findings are most easily explained by the occurrence of slightly deleterious mutations. The fact that the negative allometry was more pronounced in RNA viruses than in DNA viruses provided additional evidence that purifying selection is more effective in the former than in the latter.

Figure 1

Plot of nonsynonymous nucleotide diversity (π_N) vs. synonymous nucleotide diversity (π_S) in 122 independent virus sequence datasets. The line is a 45° line. Sign test of equality of paired π_N and π_S values: P < 0.001.

Figure 2

Plots of (A) mean number of synonymous differences (Ks) vs. the adjusted number of synonymous segregating sites (S*s); and (B) mean number of nonsynonymous differences (Kn) vs. the adjusted number of nonsynonymous segregating sites (S*n) based on 1-substitution codons in 222 virus sequence datasets. In each case, the line is a 45° line. Sign test of the equality of paired Ks and S*n: N.S. Sign test of the equality of paired Kn and S*n: P < 0.001.

Figure 3

Plot on logarithmic axes of nonsynonymous nucleotide diversity (π_N) vs. synonymous nucleotide diversity (π_S) in (A) 76 DNA virus datasets; and (B) 146 RNA virus data sets. In each case, the line is the linear regression of log π_N on log π_S: for DNA viruses, log π_N = -2.15 + 0.788 log π_S (equivalently, π_N = 0.166 π_S ^0.788), R² = 59.2%; P < 0.001); for RNA viruses, log π_N = -3.58 + 0.500 log π_S (equivalently, π_N = 0.028 π_S ^0.500), R² = 33.2%; P < 0.001).

Figure 4

Median ratio of nonsynonymous nucleotide diversity (π_N) to synonymous nucleotide diversity (π_S) in virus sequence datasets classified by virus and host characteristics. Vert. = vertebrate host. NE = non-exposed protein; E = exposed protein. Kruskal-Wallis test for overall difference among medians: P < 0.001. Individual comparisons to E for RNA (Vert., vector): * P < 0.05; ** P < 0.01; *** P < 0.001. Numbers of datasets were as follows: DNA (Vert., no vector): 39 NE, 29 E; RNA (Vert., no vector): 57 NE, 34 E; RNA (Vert., vector) 9 NE, 15 E; RNA (Plant) 13 NE, 18 E.