Two Subspecies of Ancestral African Humans Merged To Form Modern Humans

A new paper in Nature argues that genetic signals that have previously been interpreted as signs of archaic admixture in modern humans in Africa, actually reflect a process in which modern humans arose from two distinct gene pools in Africa of sub-species of ancestral modern humans that had a low, but non-zero level of interbreeding between them for hundreds of thousands of years. 

There is a more educated layman oriented description of the paper's findings at the New York Times (paywalled), which is somewhat better than average for NYT science coverage.

a,b, In the two best-fitting parameterizations of early population structure, continuous migration (a) and multiple mergers (b), models that include ongoing migration between stem populations outperform those in which stem populations are isolated. Most of the recent populations are also connected by continuous, reciprocal migration that is indicated by double-headed arrows. These migrations last for the duration of the coexistence of contemporaneous populations with constant migration rates over those intervals. The merger-with-stem-migration model (b, with LL = −101,600) outperformed the continuous-migration model (a, with LL = −115,300). Colours are used to distinguish overlapping branches. The letters a–i represent continuous migration between pairs of populations.

Despite broad agreement that Homo sapiens originated in Africa, considerable uncertainty surrounds specific models of divergence and migration across the continent. Progress is hampered by a shortage of fossil and genomic data, as well as variability in previous estimates of divergence times. 

Here we seek to discriminate among such models by considering linkage disequilibrium and diversity-based statistics, optimized for rapid, complex demographic inference. We infer detailed demographic models for populations across Africa, including eastern and western representatives, and newly sequenced whole genomes from 44 Nama (Khoe-San) individuals from southern Africa. 

We infer a reticulated African population history in which present-day population structure dates back to Marine Isotope Stage 5. The earliest population divergence among contemporary populations occurred 120,000 to 135,000 years ago and was preceded by links between two or more weakly differentiated ancestral Homo populations connected by gene flow over hundreds of thousands of years. Such weakly structured stem models explain patterns 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 genetically and morphologically similar, and that only 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 the variation in previous estimates of divergence times, and argue that studying a range of models is key to making robust inferences about deep history.

Aaron P. Ragsdale, et al., "A weakly structured stem for human origins in Africa" Nature (May 17, 2023) (open access) https://doi.org/10.1038/s41586-023-06055-y

Part of the "Discussion" part of the paper lays out a narrative:

Our inferred models paint a consistent picture of the Middle to Late Pleistocene as a critical period of change, assuming that estimates from the recombination clock accurately relate to geological chronologies. 

During the late Middle Pleistocene, the multiple-merger model indicates three major stem lineages in Africa, tentatively assigned to southern (stem 1S), eastern (stem 1E) and western/central Africa (stem 2). Geographical association was informed by the present population location with the greatest ancestry contribution from each stem. For example, stem 1S contributes 70% to the ancestral formation of the Khoe-San. The extent of the isolation 400 ka between stem 1S, stem 1E and stem 2 suggests that these stems were not proximate to each other. 

Although the length of isolation among the stems is variable across fits, models with a period of divergence, isolation and then a merger event (that is, a reticulation) out-performed models with bifurcating divergence and continuous gene flow.

A population reticulation involves multiple stems that contribute genetically to the formation of a group. One way in which this can happen is through the geographical expansion of one or both stems. For example, if, during MIS 5, either stem 1S from southern Africa moved northwards and thus encountered stem 2, or stem 2 moved from central–western Africa southwards into stem 1S, then we could observe disproportionate ancestry contributions from different stems in contemporary groups. 

We observed two merger events. The first, between stem 1S and stem 2, resulted in the formation of an ancestral Khoe-San population around 120 ka. The second event, between stem 1E and stem 2 about 100 ka, resulted in the formation of the ancestors of eastern and western Africans, including the ancestors of people outside Africa. 

Reticulated models do not have a unique and well-defined basal human population divergence. We suggest conceptualizing the events at 120 ka as the time of most recent shared ancestry among sampled populations. However, interpreting population divergence times in population genetics is always difficult, owing to the co-estimation of divergence time and subsequent migration; methods assuming clean and reticulated splits can infer different split dates. Therefore, in the literature, wide variation exists in estimates of divergence time.

Shifts in wet and dry conditions across the African continent between 140 ka and 100 ka may have promoted these merger events between divergent stems. Precipitation does not neatly track interglacial cycles in Africa, and heterogeneity across regions may mean that the beginning of an arid period in eastern Africa is conversely the start of a wet period in southern Africa. The rapid rise in sea levels during the MIS 5e interglacial might have triggered migration inland away from the coasts, as has been suggested, for example, for the palaeo-Agulhas plain. 

After these merger events, the stems subsequently fractured into subpopulations which persisted over the past 120 ka. These subpopulations can be linked to contemporary groups despite subsequent gene flow across the continent. For example, a genetic lineage sampled in the Gumuz has a probability of 0.7 of being inherited from the ancestral eastern subpopulation 55 ka, compared with a probability of 0.06 of being inherited from the southern subpopulation.

We also find that stem 2 continued to contribute to western Africans during the Last Glacial Maximum (26 ka to 20 ka), indicating that this gene flow probably occurred in western and/or central Africa. Such an interpretation is reinforced by differential migration rates between regions; that is, the gene flow from stem 2 to western Africans is estimated to be five times that of the rate to eastern Africans during this period.