A paper by Wangjie Hu published in 2023 in the prestigious journal Science (Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition. Science 381, 979-984 (2023). DOI:10.1126/science.abq7487), reported that our ancestors had a very close shave with extinction.
The article, which of course assumes that the Out Of Africa (OOA) migration is valid, found that non-Africans and Africans split long before the actual migration OOA took place: "African and non-African divergence occurred much earlier than the out-of-Africa dispersal,"
The population leading to modern non-Africans began its decline around 368,000 years ago —368 ky (the range, however is very wide: 176 to 756 kya). This wide range is enough to cover the split that led to the ancestors of Neanderthals and Denisovans.
The bottleneck
The study involved genetics, and infered population sizes, and found a "severe bottleneck" in "each of the 10 African populations" that they sampled, but surprisingly, it was absent in all of the "40 non-African populations." Why would the non-Africans, who are supposed to have split from Africans not carry the signs of the near extinction event? (a simple explanation would be that non-Africans had evolved separately in Eurasia and were not affected by the event, which struck ancient Africans, leaving a direct mark on contemporary Africans. They did not detect direct signals of a near extinction event in non-Africans.
But, the OOA theory can't be questioned, so the authors ran different simulations to find out what was going on. They concluded that the OOA event obscured the signal in non-Africans!!
The paper proposed three different population bottleneck scenarios (I, II, and III). The first (I) agreed with their model of how modern African populations evolved after going through a masive ancient bottleneck. The second secnario (II) was one under which the non-African populations did not go through any bottleneck and it agreed with their model. So then they devised a third scenario (III) which impacted non-Africans with an ancient bottleneck.
But III didn't appear as viable in their model: "However, no ancient severe bottleneck was detected in bottleneck III simulations." So, instead of assuming there was no bottleneck, they concluded that this failure of their model was due to the OOA effect: "[it] indicates that the out-of-Africa dispersal hinders the chance of discovering the ancient severe bottleneck. Furthermore, the ancient severe bottleneck was found to cause a discrepancy in the estimation of the population size between the bottleneck III model and the inferred population size history after the bottleneck was relieved, which suggests a hidden effect of the ancient severe bottleneck on non-African populations." In my opinion, this sounds like they are trying to save the OOA model at all costs.
Their argument was that the OOA event reduced the lineages outside of Africa and erased the genetic evidence of the bottleneck. But, inside Africa, these survived, so all African lineages showed the evidence of the bottleneck (seems like circular reasoning to me!)
With this axiom in mind they used a program called FitCoal and (their explanation seems to be a polite way of saying "we made the data fit our model, cooking the numbers"): "performed an extended FitCoal analysis. To eliminate noise effects resulting from problems such as sequencing or overfitting errors on the inference of population size history, we used the FitCoal-inferred recent population size history as a starting point for size estimation of an ancient population. With this modification, all 19 non-African populations in 1000GP were found to have gone through the severe bottleneck with approximately 1450 individuals between 921 and 785 kyr BP. This result is consistent with that obtained with African populations."
They seem to have shoehorned it into the model, like the bed of Procustes (a Greek fable, where a bandit named Procustes invited people to sleep in his bed, and if they were too long, he cut off their legs, and if they were too short, he'd stretch them on a rack).
Anyway, based on their analysis they concluded that a near extinction event took place 930,000 years ago, and lasted for 117,000 years, which wiped out 98.7% of all humans living at that time. The date makes it take place inside Africa, and it affected the ancestors of thosw who would later evolve into modern humans, Neanderthals and Denisovans. It wiped out genetic diversity ("increas[ing] the inbreeding level of our ancestors, thus contributing to the 65.85% loss in present-day human genetic diversity".)
This near miss was triggered by the ice age in an episode known as the "“0.9 Ma event” (Ma, million years ago)" at that time the ice sheets and sea level variations led to drought, which impacted on vegetation and wildlife.
The dramatic drop in hominin population is the explanation -say the authors- for the lack of fossils during this period (950-650 ky ago) in Africa. However, outside of Africa, Homo erectus thrived, and the Atapuerca hominins also survived. Why? The paper does not provide answers. The authors also suggest that the fusion of chromosome 2 in humans took place during this period leading to the ancestor of Denisovans, Neanderthals, and modern humans.
There was a quick rebound after the near extinction event: "a rapid population recovery was detected in all 10 African populations with a 20-fold increase in size around 813 kyr BP." Tha authors attribute this to the discovery of fire and benign climate.
Closing Comments
Are we overdoing it with genetics and ancient humans? This is like trying to wring blood from a stone.
I wonder if we can extrapolate back in time over a vast period of nearly 950,000 years, and comparing modern human genes of non-Africans and Africans come up with a theory suggesting that a massive near-extinction event took place, which left only 13 out of every 1,000 acient hominins (in Africa) alive, but left those in Eurasia untouched.
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