It is common to distinguish between Africans and non-Africans, with the former being much more genetically diverse than the latter. But, the real “gap” in human origins seems to be between the really old Africans (“Paleoafricans”) and the rest (“Afrasians”).
The Paleoafrican element is entirely confined to Africa, while the Afrasian one is found in both Africa and Eurasia. Indeed, modern humans can be entirely split into two groups: (i) a group of “pure” Afrasians which includes all non-Africans, and (ii) a group of Afrasian-Paleoafricans which includes all non-Caucasoid Africans. Human groups of entirely Paleoafrican origin, unhybridized with the younger Afrasians are no longer in existence.
Today, a preprint with very sophisticated computational methods of data analysis was posted, Ancient admixture into Africa from the ancestors of non-Africans. The figure to the right shows the proportion of deep “Eurasian” admixture into each major Sub-Saharan African population. Basically this preprint very formally breaks down the high likelihood that Dienekes’ model outlined in the mid-aughts was correct. Even back in 2008, there was an mtDNA phylogeny and coalescence that aligned well with his hypothesis: The Dawn of Human Matrilineal Diversity. Finally, there is the fact Y haplogroup E is dominant among non-hunter-gatherers in Africa, and it is within the “Eurasian-clade” DE.
The abstract of the new preprint makes the genome-wide results pretty clearly in alignment with the older uniparental evidence, as well as some interesting twists that one can infer from population genomics:
Genetic diversity across human populations has been shaped by demographic history, making it possible to infer past demographic events from extant genomes. However, demographic inference in the ancient past is difficult, particularly around the out-of-Africa event in the Late Middle Paleolithic, a period of profound importance to our species’ history. Here we present SMCSMC, a Bayesian method for inference of time-varying population sizes and directional migration rates under the coalescent-with-recombination model, to study ancient demographic events. We find evidence for substantial migration from the ancestors of present-day Eurasians into African groups between 40 and 70 thousand years ago, predating the divergence of Eastern and Western Eurasian lineages. This event accounts for previously unexplained genetic diversity in African populations, and supports the existence of novel population substructure in the Late Middle Paleolithic. Our results indicate that our species’ demographic history around the out-of-Africa event is more complex than previously appreciated.
The reason I put “Basal Eurasian” in the headline is that this is the “ghost population” postulated by the Reich group researchers in the first half of the teens to account for the fact that Mesolithic European hunter-gatherers seem to share more genetically with people such as Oceanians and Han Chinese in some ways that European “first farmers.” More precisely, the early West Asian farmer groups seem to be a mix of a population that is distinct as the “first branch” of non-African humanity, “Basal Eurasians”, and people related to West Eurasian Mesolithic hunter-gatherers. The latter place West Asians in the clade with Pleistocene Europeans and early Siberians, as a “western” group, while the former means that West Asians have ancestry that is more distant to Papuans and Amerindians than Mesolithic European hunter-gatherers.
Another thing that notable about Basal Eurasians is there is some circumstantial evidence that this population did not undergo much admixture with Neanderthals. This is important because the authors above report that the dominant signal of admixture between “40 and 70 thousand years ago” didn’t contribute Neanderthal admixture. Additionally, there’s the symmetrical distance from Han and European, which means that the gene-flow predates that divergence. Europeans have some Basal Eurasian admixture, so the symmetry might imply that this admixture is even basal to the Basal Eurasians (a Lazaridis et al. preprint suggests that there might be such a thing), though I’m not sure they have the statistical power to ascertain this. Rather, whatever this back-migration was, it probably doesn’t extend to a population beyond the Near East, and, it was probably just a bit before the massive “Out of Africa” break that happened ~55,000 years ago and is synchronous with Neanderthal admixture that we currently detect.
There are some things to reflect on in light of these data. First, crazy ideas sometimes are true. Reading Dienekes’ 2005 post today is not that exciting. It is quite plausible, perhaps right even. But in 2005 it seemed crazy. The “dogma” of a tree-like phylogeny and explosive “Out-of-Africa” event all over the world was pretty strong then. It was a robust prior and hard to entertain alternative models. But science advances, so here we are.
Second, terms like “Eurasian” and “African” do a little too much work. The ancestral lineages that we are thinking of here may not have been geographically where we assume using the geographical term. There is a good amount of evidence that the ancestors of the non-African lineage went through a protracted bottleneck. But we don’t know where this bottleneck occurred. We call it “non-African,” but perhaps the bottleneck occurred in Kenya? We don’t know. The bottleneck includes Basal Eurasians, so it predated Neanderthal admixture, and the massive radiation ~55-60,000 years ago. The most likely region is probably the Levant and Arabia. Sub-Saharan Africa seems to be lacking the geographic barriers such as a mega-desert or bodies to water to sustain barriers to gene-flow for thousands of years. But “most likely” does not mean overwhelmingly likely.
Preprints like the one above fill in a lot of general dynamics, but I think ancient DNA is going to be necessary to nail down the model tightly.
What can we expect? Honestly, we don’t know, but here is my general sense of what ancient DNA + better methods + more compute time (look at all the simulations!) + non-genetic information (paleontology, paleoclimate, paleo-everything) might tell us. Below is my best guess outline…
- Proto-modern humans diversified in Africa 100 to 200 thousand years ago.
- One branch related to eastern modern humans becomes isolated from other populations 75 to 100 thousand years ago
- This branch is ancestral “non-Africans.” They are probably located in the southern Near East
- But, in southeast Asia, there are other earlier expansions of modern human-related groups, which have mixed with local hominins
- The expansion of the primary non-African group means that most of the signal of earlier Asian “moderns” is gone, though perhaps some of them are responsible for the Denisovan and other archaic signals
- At the same time that the non-basal non-Africans are pushing east, the basal non-Africans are pushing west. The admixture between Basal Eurasians and African hunter-gatherers of various sorts results in the emergence of what we term Africans qua Africans. My working assumption is that the non-African ancestry in hunter-gatherer populations is due to continuous gene-flow from the primary synthetic groups
- Archaic admixture everywhere there were earlier human groups
As Iain Mathieson once said, the story of the last few hundred thousand years is the collapse of old structure.