Major role of positive selection in the evolution of conservative segments of Drosophila proteins

Abstract

Slow evolution of conservative segments of coding and non-coding DNA is caused by the action of negative selection, which removes new mutations. However, the mode of selection that affects the few substitutions that do occur within such segments remains unclear. Here, we show that the fraction of allele replacements that were driven by positive selection, and the strength of this selection, is the highest within the conservative segments of Drosophila protein-coding genes. The McDonald-Kreitman test, applied to the data on variation in Drosophila melanogaster and in Drosophila simulans, indicates that within the most conservative protein segments, approximately 72 per cent (approx. 80%) of allele replacements were driven by positive selection, as opposed to only approximately 44 per cent (approx. 53%) at rapidly evolving segments. Data on multiple non-synonymous substitutions at a codon lead to the same conclusion and additionally indicate that positive selection driving allele replacements at conservative sites is the strongest, as it accelerates evolution by a factor of approximately 40, as opposed to a factor of approximately 5 at rapidly evolving sites. Thus, random drift plays only a minor role in the evolution of conservative DNA segments, and those relatively rare allele replacements that occur within such segments are mostly driven by substantial positive selection.

Figure 1.

Results of the McDonald–Kreitman test for the protein segments of different conservatism. The McDonald–Kreitman test was applied to the data on variation within the coding sites among (a–c) 162 individuals of D. melanogaster and (d–f) six individuals of D. simulans, and divergence between these species and the D. yakuba–D. erecta common ancestor. The sites were subdivided into 22 classes of different conservatism of the protein segments that contain them, in the alignment of their orthologues in seven more distant Drosophila species. (a,d) Ratios of the frequencies of the non-synonymous and synonymous substitutions (d_N/d_S, red squares) and polymorphisms (p_N/p_S); analysis was performed for all polymorphisms (cyan circles) and excluding low-frequency polymorphisms (brown triangles). (b,c,e,f) Fraction of positively selected sites α and the rate of adaptive non-synonymous substitutions relative to the rate of synonymous substitutions ω_a for (b,e) all polymorphisms and (c,f) excluding low-frequency polymorphisms. Error bars are 95% CI obtained by non-parametric bootstrapping.

Figure 2.

Clumping of pairs of substitutions at a codon site. Fractions of codons, among codons with two substitutions between the D. simulans–D. sechellia and the D. pseudoobscura–D. persimilis clades, such that these two substitutions occurred in different lineages, for codons residing within segments of different conservatism. Grey bars, non-synonymous substitutions; white bars, synonymous substitutions. The expected value is indicated with a dashed line; error bars are 95% binomial CI.

Figure 3.

Phylogenetic distribution of pairs of non-synonymous substitutions at a codon site. (a) Partial phylogeny of genus Drosophila, with lengths of edges in the units of D_s (adapted from Heger & Ponting [39]); the path to the D. simulans–D. sechellia clade (IV) from its common ancestor with the D. pseudoobscura–D. persimilis clade (I) is coloured. (b) Fractions of codon sites such that the first and the second substitution occurred within particular parts of this path, depending on the conservatism of the segment within which the site resides. For each possible position of the two substitutions relative to the branching-off points of D. ananassae (II) and D. yakuba (III), the two substitutions at a codon site are shown schematically by arrows at the right panel.