What did modern humans look like during the “Out of Africa” event?

Recently I was having an email exchange with a friend (a prominent public intellectual who is not a scientist), and we were thinking about what “ancestral Africans” looked like. More precisely, the populations which were resident around ~100,000 to ~200,000 years before the present. These are the people who are depicted in paleoanthropology documentaries. Here were some of my major contentions:

1) We don’t know what they looked like
2) They probably were more likely to look like modern Africans than non-Africans
3) But modern Africans are diverse in their looks and we could expect that ancient Africans were too

The neighbor-joining tree above is generated with a naive model of successive bifurcation.

1) Khoisan split off 200,000 years ago
2) Mbuti split off 150,000 years ago
3) Mende split off 100,000 years ago
4) Japanese about 50,000 years ago
5) While Pathan and Basque only 15,000 years ago

The model is wrong in the details. Pathan and Basque have some ancestry is which recently diverged, and much that is deeply diverged. The 15,000 year value is just an average. Similarly, the Khoisan have some Eurasian ancestry. But in the broad sketch it illustrates that some African populations diverged a very long time ago from other groups.

Ancient Africans date to ~200,000 years before the present for all the modern populations. Khoisan to Japanese. You could probably use phylogenetic character reconstruction methods to attempt to infer what ancient Africans looked like…but I’m not sure that it would be useful since modern humans have spread over so many ecologies over such a short span of time.

Outside of Sub-Saharan Africa perhaps on the order of 95% of the ancestry derives from an expansion from a small founder group between 60 and 80 thousand years ago. Removing the “Basal Eurasian” component, groups as diverse as Native Americans, Oceanians and East Asians probably derive their ancestry from a common group which flourished between 50 and 60 thousand years ago (this pulse is the majority of the ancestry of Europeans and South and West Asians as well).

The point here is to illustrate that 50,000 years is definitely sufficient for a great deal of diversity to have emerged in human physical variation. And yet the Khoisan are ~200,000 years diverged from their ancestors within Africa. We actually know that indigenous southern Africans have been selected for lighter pigmentation. We also know that loci associated with pigmentation in modern humans exhibits a lot of variation in Africans, and this variation is likely an ancestral feature of our species.

In sum, the number of generations between ancestral Africans and all modern descendent populations is great enough that I’m not uncertain that we can predict what they look like in anything except their skeletal features. Additionally, most of the history of anatomically modern humans was likely highly structured within Africa. That’s another way of saying that ancient Africans themselves were probably physically diverse.

With all that being said, all things equal ancient Africans probably are more likely to look like modern Africans than modern non-Africans. The main reason is simply that modern Africans occupy the same broad ecological landscape as ancient Africans, and many of our features, from our build to our complexion seem dependent upon environmental pressures. There’s lot of evidence that very light skin is probably a derived characteristic of our species (there are consistent signatures of sweeps around pigmentation loci). And, there is also evidence that some of the archaic introgression into non-Africans may have consequences in our morphology and external physical characteristics. For example, Eurasians seem to have very high frequencies of Neanderthal variants of the keratin gene. This is implicated in hair, skin and nail development.

Addendum: Note that even if we have ancient genomes, polygenic characteristics are still hard to predict. Even today common SNPs only explain a minority of the variation in hair color in Europeans.