So this how I see the evidence stacking up…
- Genome-wide divergence: 500 kya (very strong)
- Introgression: 500-700 kya (very strong)
- HLA exon diversity: uninterpretable because of balancing selection
- HLA introns: uninterpretable because of draft and balancing selection
- HLA exon inter-species variation: possibly in 1 case up to 5 alleles in one locus, and could have been convergence.
- HLA intron inter-species variation: not currently in literature.
I think that #6 is the most important experiment to do, and I encourage it. Even then, however, it would only be one line of evidence. Still, depending on the strength of the results, I’d call it enough. That analysis has not yet been done. The best number, then, is 700-500 kya, with the common ancestors of Sapiens, Neandertals, and Denisovans.
So, my assessment is that there is strong evidence against a bottleneck more recent than 500 kya. More ancient, the evidence has been overstated in the past (see Ayala and Venema) and it is much less clear. It is possible that further work will rule out Gauger’s preferred sole-genetic progenitor scenario. I welcome work to settle this question for good, but in the mean time we do not know from evidence yet. We have testable hypothesis, and a clear research plan. That is it.
I want to add @John_Harshman that I want to get the science right. This is actually a big reason I even have this forum. I want to resolve all objections by legitimate scientists like yourself. I’m committed to taking all your scientific objections very seriously, by either successfully making my case or changing my position.
Feel free to complain if I don’t get to a legitimate point after a week or so, but please don’t jump to conclusions after less than a day, especially late at night when conversations are ending. That is not a reasonable standard.