There are a couple of recent papers on introgression from some quite divergent archaic population into Pygmies ( this also looks to be the case with Bushmen). Among other things, one of those papers discussed the time of the split between African farmers (Bantu) and Pygmies, as determined from whole-genome analysis and the mutation rate. They preferred to use the once-fashionable rate of 2.5 x 10-8 per-site per-generation (based on nothing), instead of the new pedigree-based estimate of about 1.2 x 10-8 (based on sequencing parents and child: new stuff in the kid is mutation). The old fast rate indicates that the split between Neanderthals and modern humans is much more recent than the age of early Neanderthal-looking skeletons, while the new slow rate fits the fossil record – so what’s to like about the fast rate? Thing is, using the slow rate, the split time between Pygmies and Bantu is ~300k years ago – long before any archaeological sign of behavioral modernity (however you define it) and well before the first known fossils of AMH (although that shouldn’t bother anyone, considering the raggedness of the fossil record).

Logically, this means that Pygmies aren’t really modern humans. Or, perhaps, they’re the most divergent of all modern humans. If you want to say that the root stock had capability X in 100,000 BC, and so everyone today must also have capability X (which does not logically follow in any event, but we’re talking anthropologists, so don’t expect much) then Pygmies might not have it. Or if they do, it’s a product of convergent evolution. But of course in the real world the Pygmies have the capabilities that they have: you can’t logic any of them away or conjure new ones into existence.

The bigger picture is that this sure looks like a typical case of backwards reasoning: A implies B, which implies C, and so on, but Z is awful and so A can’t really be true. I don’ think this works, if by “working’, we mean getting the at the truth.