Can positive selection drown out neutral evolution? That’s what John Hawks claims in response to my post on accelerated evolution. Hawks points out that, rather than looking at the neutral fixation rate (which is equal to the mutation rate, u), we should be more interested in the average time to fixation of a neutral mutation (the product of 4 times the effective population size, 4Ne). On the time scale he’s looking at (40,000 years), neutral evolution shouldn’t really matter because Hawks says that the Ne=100,000, which makes 4Ne>40,000.
Therefore, the majority of new mutations that arose in the past 40,000 years and have fixed (or nearly fixed) in a population should be either beneficial or linked to beneficial mutations. This allows for neutral evolution, however it’s nearly all driven by hitchhiking upon the back of adaptive evolution. But this hypothesis hinges on the assumption that Ne>10,000; this is brought up at Popgen Ramblings in another post critical of the Hawks et al. paper. There’s an important distinction between Ne (the effective population size) and the census population size. Ne is a parameter within population genetics theory that allows us to treat a population as ideal, but it is greatly influenced by the historical demography of a population (especially drastic decreases in population size). So much so that’s it’s not practical to estimate Ne from current population sizes or archaeological data — Ne can only be estimated from population genetic data. The post at Popgen ramblings is skeptical of Hawks et al’s estimate of Ne.
Finally, Hawks paints me as an anti-adaptationist in the tradition of Stephen Jay Gould. This is reminiscent of Larry Moran’s bit where he claims to be a pluralist in the midst of the stark-raving-mad adaptationists. Only the roles are reversed. This time I’m the damn dirty neutralist, whereas I was previously labeled as the gullible adaptationist. I’m having a hard time keeping track of which team I’m on. Maybe that makes me the true pluralist.