Reply to Massey: Drift does influence mutation-rate evolution

Although Massey argues that proteome size (P), not the effective population size (N_e), is the primary determinant of mutation-rate evolution (1), nothing in his comment or in his prior work (2) contradicts our conclusions (3).

First, although we noted how the mutation rate/nucleotide site/generation (μ) scales with N_e and P of a species, we did not rank the relative importance of these sources of variation, which are functions of the variance harbored by the samples in an analysis (in this case, for both N_e and P). This issue can be seen easily in figure 2 of Massey (1), where the addition of viruses expands the range of variation in P 100-fold beyond that in our study (3). Massey (1) concludes that P accounts for 94% of the variance in μ among taxa (including viruses), whereas our analysis of cellular species reduces this proportion to ∼41%. Additional caveats to assigning relative levels of causality to the factors driving the evolution of μ are: (i) N_e and P are not phylogenetically independent variables, and (ii) the substantially greater sampling variance for N_e than for P will reduce the slope and correlation of a regression of μ on N_e (3).

Second, Massey (1) argues that a reduced correlation between the mutation rate per cell-division and N_e weakens our proposal that mutation-rate evolution is influenced by drift. No general relationship is expected between the mutation rate per germ-line/cell division (μ_d = μ/x, where x is the number of germ-line cell divisions/generation) and N_e under existing evolutionary theory, which postulates that selection on μ is an indirect effect of linked deleterious mutations, the influence of which is only felt after expression. For a multicellular organism with germ-line sequestration, selection operates on the mutation rate per sexual generation, and we expect the indirect selective effect to be accommodated by reducing μ_d to μ/x (assuming that replication fidelity has not reached its biophysical limits). In principle, multicellularity may impose direct selection on the mutation rate, as somatic mutations have immediate effects (3–5). However, even though high somatic-mutation rates make the direct-selection hypothesis plausible, the limited data are inconsistent with germ-line μ_d scaling with 1/P in multicellular species (when our data are used, the correlation is very close to zero). Because there is variation in x among taxa (which is not proportional to P or N_e), the expectation is that a regression of μ_d on N_e will be weaker than one of μ on N_e, just as found by Massey. Finally, a per cell-division argument does not apply to the mostly unicellular species that we have analyzed, and yet the scaling of μ and N_e is similar in unicellular and multicellular species.

Third, Massey claims that we provide no support for an inverse relationship between μ and P. However, figure 1C in our work (3) shows that μP scales with ∼1/N_e, which is equivalent to saying that μ scales with ∼1/(N_eP).

Although we conclude that the ability of selection to influence μ depends on both the power of drift and the effective target size for deleterious mutations, the importance of proteome-size variation has been made by other authors (2, 6). Should future work with additional key taxa uphold the inverse scaling between μ and N_eP, we will have achieved a fairly general theory for one of the key evolutionary-genetic features of species.