While it is now broadly accepted that Homo sapiens originated within Africa, considerable uncertainty surrounds specific models of divergence and migration across the continent. Progress is hampered by a paucity of fossil and genomic data, as well as variability in prior divergence time estimates. Here we use linkage disequilibrium and diversity-based statistics, optimized for rapid, complex demographic inference to discriminate among such models. We infer detailed demographic models for populations across Africa, including representatives from eastern and western groups, as well as 44 newly whole-genome sequenced individuals from the Nama (Khoe-San). Despite the complexity of African population history, contemporary population structure dates back to Marine Isotope Stage (MIS) 5. The earliest population divergence among contemporary populations occurs 120-135ka, between the Khoe-San and other groups. Prior to the divergence of contemporary African groups, we infer long-lasting structure between two or more weakly differentiated ancestral Homo populations connected by gene flow over hundreds of thousands of years (i.e. a weakly structured stem). We find that weakly structured stem models provide more likely explanations of polymorphism that had previously been attributed to contributions from archaic hominins in Africa. In contrast to models with archaic introgression, we predict that fossil remains from coexisting ancestral populations should be morphologically similar. Despite genetic similarity between these populations, an inferred 1–4% of genetic differentiation among contemporary human populations can be attributed to genetic drift between stem populations. We show that model misspecification explains variation in previous divergence time estimates and argue that studying a suite of models is key to robust inferences about deep history.
Privately some people have been grumbling about models of deep structure between very differentiated populations for a while. They claim this is just a bias in the model specifications because it’s so easy to think of gene flow happening in periodic pulse admixtures. But the reality is that Africa doesn’t seem to have had the same barriers as across Eurasia or between Eurasia and Africa, so how are these deep lineages persisting?
The preprint here shows that the data can fit a different model, one that they find more biologically and paleoanthropologically more reasonable. The discussion has an “out of Africa with total replacement” flavor, but here it is within Africa:
Multiple studies have shown a correspondence between phenotypic differentiation, usually assessed with measurements of the cranium, and genetic differentiation among human populations and between humans and Neanderthals 36,37,38 (see also Section 5.3). This correspondence allows predictions of our model to be related to the fossil record. The fossil record of Africa is sparse during the time period of the stems, but of the available fossils, some are very similar in morphology to contemporary humans (e.g., from Omo Kibish, Ethiopia 39,40), others are similar in some morphological features but not others (e.g., from Jebel Irhoud, Morocco 1,41), and others are very different in morphology (e.g., from Dinaledi, South Africa 42,43). If, as our model predicts, the genetic differences between the stems were comparable to those among contemporary human populations, the most morphologically divergent fossils are unlikely to represent branches that contributed appreciably to contemporary human ancestries.
This result would recenter Omo Kibish from what I can tell.