So you're right - it's a summary of allele methods, including PSMC, interspersed with the discussion on LD, and then back to a special case of an allele method with the use of PSMC on single genomes.I'm sorry, but that wasn't my reading of the passage. As I say, it seems to me that the passage in italics is about a method based on allele counts, (explicitly not including PSMC). It seems to be describing the kind of study you mention in your "Part I" blog:
So, a bottleneck to two individuals would leave an enduring mark on our genomes – and one part of that mark would be a severe reduction in the number of alleles we have - down to a maximum of four alleles at any given gene. Humans, however, have a large number of alleles for many genes – famously, there are hundreds of alleles for some genes involved in immune system function. These alleles take time to generate, because the mutation rate in humans is very low. This high allele diversity is thus the first indication that we did not pass through a severe population bottleneck, but rather a relatively mild one (estimated, as we have discussed, at about 10,000 individuals by current methods).Clearly you have a study in mind that supports the passage in italics and also this paragraph from your blog. All I am requesting is that you share the reference with me. Sorry if I am starting to sound like a broken record!