Diversity in populations

Protein-coding genes consist of hundreds or thousands of nucleotides, each of which could mutate to one of three other nucleotides.³ That's not an infinite number of possibilities, but it's pretty large.⁴ It suggests that we could treat every mutation that occurs as if it were completely new, a mutation that has never been seen before and will never be seen again. Does that description ring any bells? Does the infinite alleles model sound familiar? It should, because it exactly fits the situation I've just described.

Having remembered that this situation is well described by the infinite alleles model, I'm sure you'll also remember that we can calculate the equilibrium inbreeding coefficient for the infinite alleles model, i.e.,

$$f = \frac{1}{4N_e\mu + 1} \quad .$$

What's important about this for our purposes, is that to the extent that the infinite alleles model is appropriate for molecular data, then $f$ is the frequency of homozygotes we should see in populations and $1-f$ is the frequency of heterozygotes. So in large populations we should find more diversity than in small ones, which is roughly what we do find. Notice, however, that here we're talking about heterozygosity at individual nucleotide positions,⁵ not heterozygosity of halpotypes.