Let’s consider another excerpt from Eugene Koonin’s recent paper, “Darwinian evolution in the light of genomics” (Nucleic Acids Research, 2009, 1–24). I’m going to soon highlight some very significant, yet subtle points, that would seem to follow from this excerpt that outlines the difference between two types of selection. So check it out (emphasis is added):
According to the neutral theory, a substantial majority of the mutations that are fixed in the course of evolution are selectively neutral so that fixation occurs via random drift. A corollary of this theory is that gene sequences evolve in an approximately clock-like manner (in support of the original molecular clock hypothesis of Zuckerkandl and Pauling) whereas episodic beneficial mutations subject to natural selection are sufficiently rare to be safely disregarded for a quantitative description of the evolutionary process. Of course, the neutral theory should not be taken to mean that selection is unimportant for evolution. What the theory actually maintains is that the dominant mode of selection is not the Darwinian positive selection of adaptive mutations, but stabilizing, or purifying selection that eliminates deleterious mutations while allowing fixation of neutral mutations by drift (17).
Subsequent studies refined the theory and made it more realistic in that, to be fixed, a mutation needs not to be literally neutral but only needs to exert a deleterious effect that is small enough to escape efficient elimination by purifying selection—the modern ‘nearly neutral’ theory (38). Which mutations are ‘seen’ by purifying selection as deleterious critically depends on the effective populations’ size: in small populations, drift can fix even mutations with a significant deleterious effect (16).
Importantly, in the later elaborations of the neutral theory, Kimura and others realized that mutations that were (nearly) neutral at the time of fixation were not indifferent to evolution. On the contrary, such mutations comprised the pool of variation that can be tapped into by natural selection under changed conditions, a phenomenon that could be potentially important for macroevolution (17,41).