Hitch-hiking effect – counter reply

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Abstract
A new mutant is neutral while a linked selected locus is segregating and is advantageous while a linked neutral locus is segregating. The selective advantage may exist from the moment of the occurrence of the mutant. Only those mutations which are destined to be fixed in the population are considered. If the majority of gene substitutions by natural selection are of this type with a large initial selective advantage and a rate limited only by the consequent substitutional load, then hitch-hiking has a real effect in reducing heterozygosity at neutral loci. If the population size is very large (this may be contested) such that the product of population size and mutation rate is large, numerous rare alleles (either neutral or deleterious) will be present in the population at each locus and a stable mutation-selection balance reached for deleterious alleles. Then the new advantageous allele will be chosen, in response to environmental changes, from the pre-existing alleles rather than occurring by mutation. Those alleles which were kept for a long period in the population by recurrent mutations, should be more or less in the state of linkage equilibrium, even if their frequencies are small. The alleles here are not meant to be unique at the level of amino acid sequences since there should be many alternatives at the molecular level that respond to the environmental change. There is a constant flow of new advantageous mutants with fairly large selection coefficients through the population. The rate of advantageous gene substitution is independent of environmental changes, population size or even the rate of occurrence of advantageous mutations. Otherwise it would not be possible to explain the uniformity of heterozygosity over many species, since the hitch-hiking effect would be as variable as the effective population size of the actual species. Segregation at the second locus is actively maintained but with selective forces less than those at the first and the effect of hitch-hiking is now much reduced. Thus selectively maintained polymorphisms will protect neutral loci tightly linked to them from the hitch-hiking effects due to loci under directional selection.

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