Updated plots:
The motivation for these plots is that different kinds of mutation happen at different rates, which means that we should see more of some kinds of genetic variant than other kinds, if the genetic variants are the result of previous mutations. What’s shown in the plots are different classes of single-base differences and how frequently they occur in a human population. The details of the different classes are explained in a blog post by me, here.
I have made the plots for two different frequency bins; that is, one plot show variants that are rare in the human population (0.5% to 1.0%) and the other variants that are common (40% to 50%). (I pulled the variants for the different frequencies when @evograd was preparing this post.) According to the model that is the subject of this thread, rare variants are all the result of recent mutations, and should show the characteristic pattern expected of mutations – which they do. In the same model, however, most high frequency variants were created along with the original couple – but they also show exactly the same pattern, which is what we would expect if the human lineage is older than 500,000 years and high frequency variants are also the result of mutations.