Near Hominin Extinction About 870,000 Years Ago?

I have no doubt that there was a serious bottleneck in hominin populations at roughly the time claimed. But effective population size is a tricky statistic that is further from what people think it means than most people realize, so don't take the absolute magnitude of the bottleneck, or the naive assumptions about the census population of these archaic hominins at this time, too literally. As the New York Times explains:

[O]utside experts said they were skeptical of the novel statistical methods that the researchers used for the study. “It is a bit like inferring the size of a stone that falls into the middle of the large lake from only the ripples that arrive at the shore some minutes later,” said Stephan Schiffels, a population geneticist at Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

The researchers also put too much faith in a model that assumes a single universal mutation rate for genetic evolution, when there is good research to suggest that some parts of the genome evolve at faster rates than other parts of the genome. On the scale of several tens of thousands of generations, those fine points could become important.

Modern humans evolved around 300,000 years ago, and the speciation event that the authors suggests might coincide with this population bottleneck would have given rise to the common ancestor of modern humans, Neanderthals, and Denisovans.

The circumstances driving this 117,000 year period in which hominins may have come close to extinction aren't entirely clear. The editor's summary states:

The model detected a reduction in the population size of our ancestors from about 100,000 to about 1000 individuals, which persisted for about 100,000 years. The decline appears to have coincided with both major climate change and subsequent speciation events.

The paper and its abstract are as follows:

Population size history is essential for studying human evolution. However, ancient population size history during the Pleistocene is notoriously difficult to unravel. 

In this study, we developed a fast infinitesimal time coalescent process (FitCoal) to circumvent this difficulty and calculated the composite likelihood for present-day human genomic sequences of 3154 individuals. 

Results showed that human ancestors went through a severe population bottleneck with about 1280 breeding individuals between around 930,000 and 813,000 years ago. The bottleneck lasted for about 117,000 years and brought human ancestors close to extinction. 

This bottleneck is congruent with a substantial chronological gap in the available African and Eurasian fossil record. Our results provide new insights into our ancestry and suggest a coincident speciation event.

Wangjie Hu et al., "Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition" Science 979-984 (September 1, 2023).

One very basic methodological issue with the speculation that hominins went nearly extinct around 870,000 years ago made by this study, for example, is that genetic information from currently living modern humans showing a population bottleneck only tells us about our direct ancestors. 

As of 870,000 years ago, there was at least one species of the genus Homo, Homo erectus which had already dispersed from Africa to Eurasia. There is good reason to believe that there may have actually been more than one at that point, because the most plausible characterization of Homo floresiensis on the island of Flores in Indonesia and similar archaic hominins in the Philippines, is that this is a more archaic hominin species than Homo erectus.

Therefore, it is possible that these archaic hominin species suffered less severe bottleneck effects somewhere in Eurasia or Oceania that was outside of Africa, which subsequent events, such as the expansion of modern humans, Neanderthals, and Denisovans into Eurasia or later climate catastrophes, or a combination of causes, led to the complete extinction of them at some later time, even though these archaic hominins had weathered the circumstances of 870,000 years ago better than our direct ancestors did.

One can imagine a narrative, for example, in which Homo erectus in Southeast Asia wasn't hit nearly so hard as African Homo erectus around 870,000 years ago, but then was driven to extinction there by the one two punch of the Toba eruption and modern human expansion into Southeast Asia in the wake of that eruption around 70,000 years ago. But, if hominins had gone extinct in Africa, the second prong of this one two punch would have never wiped out Southeast Asian Homo erectus and events might have played out differently. Southeast Asian Homo erectus might have back migrated to Africa 120,000 year or so after Africa experienced the conditions that drove hominins to near extinctions, when those conditions abated.

Further New York Times discussion of the new study (at the same link) notes that:

After decades of fossil hunting, the record of ancient human relatives remains relatively scarce in Africa in the period between 950,000 and 650,000 years ago. The new study offers a potential explanation: there just weren’t enough people to leave behind many remains, Dr. Hu said.

Brenna Henn, a geneticist at the University of California, Davis, who was not involved in the new study, said that a bottleneck was “one plausible interpretation.” But today’s genetic diversity might have been produced by a different evolutionary history, she added.

For example, humans might have diverged into separate populations then come together again. “It would be more powerful to test alternative models,” Dr. Henn said. 

Dr. Hu and his colleagues propose that a global climate shift produced the population crash 930,000 years ago. They point to geological evidence that the planet became colder and drier right around the time of their proposed bottleneck. Those conditions may have made it harder for our human ancestors to find food. 

But Nick Ashton, an archaeologist at the British Museum, noted that a number of remains of ancient human relatives dating to the time of the bottleneck have been found outside Africa. 

If a worldwide disaster caused the human population in Africa to collapse, he said, then it should have made human relatives rarer elsewhere in the world. 

“The number of sites in Africa and Eurasia that date to this period suggests that it only affected a limited population, who may have been ancestors of modern humans,” he said.