More than thirty thousand synonymous single-nucleotide-substitutions have occurred in protein-coding genes in the human genome since the human lineage diverged from the chimp lineage ~7 million years ago (Bakewell et al, 2007, p.7490). Since, by definition, synonymous substitutions don’t change the amino acid, these substitutions must be selectively neutral mutations. For neutral mutations, the rate of evolution is simply equal to the point mutation rate U, “irrespective of selection at other linked loci, changes in population size, or almost any other conceivable complication” (Lanfear et al, 2014, p.36). This is problematic because U is approximately 10 to the -8 power for humans, which means that it took about a hundred million generations for each of these substitutions to become fixed in the human genome. Since each generation is more than ten years, a hundred million generations is more than a billion years, which is much longer than the ~7 million years since the human lineage diverged from the chimp lineage. How is this to be reconciled?
Bakewell, M. et al, “More genes underwent positive selection in chimpanzee evolution than in human evolution.” Proceedings of the National Academy of Sciences USA, vol 104, pages 7489–7494, 2007
Lanfear, R. et al, “Population size and the rate of evolution.” Trends in Ecology and Evolution, vol 29, pages 33–40, 2014