Out of Africa's midlife crisis

As a general rule, species start out with fairly high levels of diversity from natural processes of evolution. What happened with the out-of-Africa population is what's known as the founder effect. A small population leaves and becomes reproductively isolated. Whatever diversity can be found in their descendents is largely limited to the diversity that was present in the founding population.

One thing that should be made very clear is that ancient population structures generally don't map neatly to modern cultures or languages. It's best to treat modern terms as labels of convenience.

> I'm confused though by his comments about "our species’ one-time amazing levels of genetic diversity." Overall, he seems to be espousing the idea that "diversity" is something we once had lots of, but have lost over time. Is this true?

"Diversity" can mean a lot of things. In this case, he's referring to the variety of individual alleles. Due to population bottlenecks, most of humanity has reduced variation: for example, at a certain spot in the genome everyone has a T, because everyone who survived the bottleneck happened to have a T there; but in the population that didn't go through the bottleneck, some people have a G instead.

On the other hand, for phenotypical diversity it's not just the set of individual alleles that matters, but their distribution and correlation. For example, let's say height is affected by thousands of genes, for each of which there is an allele that makes you slightly taller and one that makes you slightly shorter, and the combined effect of all these genes is approximately additive.

Then you may have a population A which has both variants for each gene, but they're independently distributed, so everyone is of medium height, with some variance. We also have a population B, which has only one variant left for several of these genes (they have lost diversity!). But B is split into two sub-populations, which differ in the distribution of the remaining height genes: B1 has more tall alleles, and B2 has more short alleles.

Now the average height of B1 is higher than that of A, and the average height of B2 is lower than that of A. You will find very tall people in B1 that you would never see in A, and very short people in B2 that you would also never see in A. So B has more diverse height phenotypes, even though B1 and B2 (even put together!) still have lower genetic diversity than A in terms of the available repertoire of alleles.

> Did the the different tribes of African Bushmen start out as genetically distinct as they are today, or did they start from a common population and diverge over the last 200,000 years?

While groups like the San have a great deal of diversity within the group, they are also distinct from other Hunter Gatherer groups as well. The San are separated from the Hadza by about 110K years, IIRC.

> Were those who left Africa always distinct from those who stayed, or did they change through selection (and interbreeding with Neanderthals and Denisovans) over time?

Yes, those who left Africa were the remnants of a distinct population, separated from the ancestors of sub-Saharan Africans by 40K years when they left Africa 60Kya.

Note that intermixing between those whom we call 'Sub-Saharan' Africans and the "rest of the world" is definitely not new or unique to the 'Western Hemisphere' as OP seems to assume: we know very clearly from Classical written sources and iconography that there were many peoples of 'Sub-Saharan' appearance well north of the Sahara desert, in close contact with Mediterranean and Levantine (thus, clearly "Out of Africa") humans. Even more than this, we know of such 'Sub-Saharan' folks who were very deeply integrated in ancient Mediterranean and Levantine societies, and while these folks were clearly a tiny minority and their distinctive appearance was often remarked upon, this did not hurt their social standing in any sense; there was even a well-known Egyptian dynasty of "Black" pharaohs.

> No introgression with other Sapien populations?

Perhaps indirectly. As he addresses later in the text, it's possible that Denisovans in South East Asia encountered Homo erectus and interbred with them. The Denisovans appear to have more population structure as compared to Neanderthals, and introgression from H. erectus might explain some of it. Considering that South East Asia and Papua New Guinea has the highest Denisovan introgression in modern humans, it's possible that some of that H. erectus ancestry ended up in those of us from East of the Indus.

For what it's worth, I have seen other studies pop up from time to time that claim to have found introgression from some unknown ghost sapien population, but these outliers usually go away by tweaking the parameters.

i talk about introgression in this post https://razib.substack.com/p/here-be-humans

the piece was not exhaustive and meant to be an intro

I've been reading Razib for close to 20 years, and he's never been a great, or even a very good writer. He more than makes up for it with how prolific he is, and I appreciate how frank he is with his theories.

Yep, my take was that the content of this article is brilliant but there is something annoying about the writing at the paragraph level that needs work.

Nobody in their right mind actually thinks placement towards the top of a map actually denotes some kind of hierarchy.

Putting aside the absurd nitpick on the "Sub-" prefix (everyone understands that this refers to "South" and not some position on a hierarchy).

> (riffing on Asia Minor and referring to the fact that that part of the continent is, in fact, a majority of its landmass).

Isn't Asia Minor a bit more than half of Turkey? It's certainly not a majority of all of Asia...

I’ve never heard anyone from the Indian subcontinent complain about this.

I don't think this is an extremely important thing to worry about, but I do think you have a point and I like the term "Africa Major."