The research article posted on July 28, 2026 in non-peer-reviewed bioRxiv, titled Ancient tree-topologies and gene-flow processes among human lineages in Africa, by Gwenna Breton et al. (doi: https://doi.org/10.1101/2024.07.15.603519) looked into the evolution of human beings inside Africa. The authors sampled the genes of different African populations and using AI ("extensive simulations and machine-learning Approximate Bayesian Computation (ABC)"), they compared different models to explain how our species evolved in that continent over the past couple of million years. The paper reports that the best-fitting model is one where "tree-like population histories with long periods of drift separated by short pulses of unidirectional gene-flow better explain the data than continuous gene-flow."
It should be noted that the authors state that their model did so "Without invoking archaic admixture"
The paper notes that instead of repeated migrations of populations, that lead to intermingling, the best models are those with "instantaneous gene-flow processes." This implies that isolated populations co-existed in Africa and time to time they quickly exchanged alleles: " ...our results unambiguously favor an evolutionary history of African lineages ancestral to a variety of Central and Southern African populations where Homo sapiens populations experienced long periods of isolation and drift, followed by short periods of possibly asymmetric gene-flow, which may in turn have induced some reticulations among lineages"
The first modern humans, according to this paper, were the Khoe-San (KS) people who are now found in South Africa and Botswana, they split from a basal lineage between 265,000 and 398,000 yearws ago. Then the rainforest hunter gatherers of Western Africa split from those of Central Africa (called RHG and RHGn, respectively, in the paper), between 127,000 and 190,000 years ago.
These findings differ from those of Ragsdale, A. P. et al., (2023) and the authors note that their dates are olde than the 110,000-135,000 year timeline for the KS split given in that study, and attribute the differenct to Ragsdale et al's use of "very ancient genetic structures, long before Homo sapiens emergence, a feature that is unspecified in our scenarios which considered simply a single ancestral population in which all extant lineages ultimately coalesce."
They agree that there are limitations to their study and that a "large effective population ancestral to all extant populations here investigated" could have existed, and future studeis should look into "very ancient substructures and reticulations within our ancestral population, prior to the original divergence between Southern and Central African populations." The authors also note that "where the ancestors of extant Khoe-San populations lived at that time remains unknown and is nevertheless needed to further elaborate possible scenarios for the causes of the genetic divergence here inferred... similarly as above for the Northern and Southern Khoe-San populations divergence, where the ancestors of extant Eastern and Western Rainforest Hunter-Gatherers lived remains unknown..."
We tend to consider modern Africans as being the same as the ancient ones, those living 100,000 or 200,000 years ago. But, they were not the same. There is a vast space of time of thousands of generations of people during which the genes accumulated mutations, admixing with archaics, and evolving under the pressure of natural selection. The paper recognizes these factors: "... Central African Rainforest Hunter-Gatherer and Southern African Khoe-San populations have had, respectively, extensive time for selection processes, including adaptive introgression processes, to have influenced independently both groups of populations as well as populations within each group separately."
Archaic admixture
The authors state that there is no need to invoke archaic introgression to account for the diversity in the genetic makeup of the Central and South African people. In fact, they "... did not explore possible contributions from unsampled lineages, whether from non-Homo sapiens or from ancient “ghost” human populations, and therefore cannot formally evaluate such possibilities."
But they know that archaics contributed even though they don't say so: they acknowledge that their method can be used to evaluate "scenarios comprising possible contributions from ancient or ghost unsampled populations; where the burden of proof lies on showing that scenarios with archaic admixture fit specific parts of the data significantly better than scenarios without such archaic admixture."
Interestingly, regarding the archaics and their contribution to modern Africans, the authors note that there is no ancient DNA available from ancient African fossils and that this lack of data is a handicap: "In any case, the complexification of scenario-specifications to account for possible past “archaic” or “ancient” introgressions will not fundamentally solve the issue of the current lack of reliable ancient genomic data older than a few hundreds or thousands of years from Sub-Saharan Africa 3,110,111. Indeed, analogously to archaic admixture signals that were identified outside Africa only when ancient DNA data were made available for Neanderthals and Denisovans, we imperatively need to overcome this lack of empirical ancient DNA data in Africa to formally test whether, or not, ancient human or non-human now extinct lineages have significantly contributed to shaping extant African diversity." I am convinced that when hard data is obtained from African fossils, there will be many interesting surprises.
Another finding is that the mixing after long periods of isolation took place around the time of the purported Out of Africa migration of modern humans: "Interestingly, we found strong indications for almost synchronic events of introgressions having occurred during the Last Interglacial Maximum in Africa 73, between ∼85,000 and ∼135,000 years ago... They involved gene-flow between lineages ancestral to Khoe-San populations and ancestors of Rainforest Hunter-Gatherer neighbors on the one hand and, on the other hand, between lineages ancestral to Khoe-San populations and the lineage ancestral to all Rainforest Hunter-Gatherers... we estimated that the instantaneous gene-flow event between the ancestral Rainforest Hunter-Gatherers lineage and that of their extant neighbors seemingly occurred synchronically to the genetic Out-of-Africa. This would imply that possible climatic and ecological shifts at that time may not have only induced population divergences and displacement, but may also have triggered population gene-flow."
This also implies that there was a blending of isolated populations, that contributed diversity to those remaining inside of Africa while another population that migrated out of Africa carried fewer alleles, and less diversity with them (see my post On the Diversity of Africans). It also implies that the Khoisan people were split from the rest, and isolated in Southern Africa with their genetics "enriched" by intermingling with other formerly isolated groups. Did they also interact with archaics like the Homo naledi?
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