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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.

Do we have any idea about the size of the original population, the size of the group which left for Europe, the size of the group's who migrated to central/west Africa?

I had heard that there were several waves of migration towards Europe, do we have a better estimate about this? Wouldn't multiple waves over time provide more diversity?

you can infer sizes from genetic diversity ('effective pop')

for the out of africa group i've seen sizes from 100 to 10,000. i used 1,000 to 10,000 as a likely moderate number, and the range also points to the census size being larger

we can assume that conditional on the size of OoA the other groups were way larger (10x or more). otoh, the main thing i did not explore is that i am now believing that africans themselves especially agriculturalists are 'compounds' of various bottlenecked groups (why west africans are closer to eurasians than they are to khoisan)

It's worth noting that effective population size != actual population size. The former is simply a lower bound on it. If the population is structured enough and in the right ways, the actual size can be orders of magnitude higher. This has been an issue with several supposed bottlenecks within African populations.

the rule of thumb for mammals is Ne is 30% of census size.

i think this is probably an overestimate tbh (assumes poisson distribution of offspring).

I'm not sure that's super applicable to humans. Doesn't it also assume panmixia and non-overlapping generations?

Either way, my understanding is that all indications point to middle and late Pleistocene populations being highly structured and "unusual" as far as standard assumptions go.

Yes. This information is in the article.

> 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.

> 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.

We also know they had negligible genetic impact.

> 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.

You say that like social standing determines who gets to be king. The Nubian pharaohs got their position in the standard way, by conquering Egypt. They weren't native, they took very little interest in their new territory, and they didn't last very long.

There was a well-known Chinese dynasty of Mongol emperors. What do you think the social standing of Mongols in China was before and after that happened?

They did follow the Egyptian religion IIRC and even tangle with Persians

> and even tangle with Persians

Absolutely not. They were gone a hundred years before the beginning of Persia.

My bad, Assyrians