Why I remain a Darwin Skeptic

[glipsnort (Steve Schaffner)]

@Paradigm

I was under the mistaken impression that it was based on difference and an assumption that they all arose in the last ~5 million years.
I was doing an on-line search at the same time and found the following which was helpful: https://www.nature.com/articles/s41467-017-00323-y

As you can see from the introduction to that paper, calculating from the interspecies difference with chimps is one of three main approaches to estimating the mutation rate.

@Paradigm

This paper suggests a figure of about 80 per generation. If we apply this to human lineage and assume a similar or slightly higher figure in chimps (the generation time is a bit shorter) we would expect more than 2% difference (if we assume a split at 5 million years) and looking at point mutations alone.
Has anyone looked at why the difference is smaller than would be expected using these numbers?

There is some discrepancy between estimates from the different methods, but you’ve got the direction wrong. ~80 mutations per generation per person, or 40 mutations/genome copy, is a rate of 1.4e-8 mutations/base-pair/generation. Five million years at 28 years/generation (a currently fashionable estimate, I believe) gives 179,000 generations. Assuming the same generation time for chimps, that would give a total divergence for single base substitutions of 0.5%, which is much lower than the observed 1.2% difference.

A big factor that’s missing here is ancestral variation. The ancestral population had plenty of variation in it, i.e. the time to the most common ancestor of a piece of chimp DNA and the homologous piece of human DNA is substantially longer than the time to the species split. That adds an extra 4Nµ to the divergence, where N is the effective size of the pre-split population. If that was, say, 50,000, that would add an extra 0.28% to the divergence.