Patagonian monsters: November 2026

Sunday, November 8, 2026

On a near miss extinction of hominins

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.

Saturday, November 7, 2026

Coxcatlán Cave, Mexico: 33 ky human presence

I am just back from a short but well deserved vacation with our children, their partners, and our grandchildren. Sharing quality time with the family is, in my opinion, one of the best things one can do. It is a pity that life is so short!

But, getting down to the subject of my blog, I'd like to share a paper🞿 published in 2021, that reported ancient pre-Clovis dates of more than 30,000 years ago, for a site in Mexico.

🞿 This is the paper: Somerville AD, Casar I, Arroyo-Cabrales J. New AMS Radiocarbon Ages from the Preceramic Levels of Coxcatlan Cave, Puebla, Mexico: A Pleistocene Occupation of the Tehuacan Valley? Latin American Antiquity. 2021;32(3):612-626. doi:10.1017/laq.2021.26

The site is known as Coxcatlan Cave, and it is located in the state of Puebla, in Mexico (Google map), roughly 320 km (200 mi.) southeast of Mexico City. It was discovered in the 1960s by the American archaeologist Richard Stockton MacNeish (1918-2001). MacNeish found remains of a plant known as teosintle (or teocintle), Zea perennis, a wild variety that is an ancient ancestor of maize, that later domesticated, producing modern maize. These remains were between 7,000 and 8,700 years old.

The cave is set in Tehuacan Valley, and was occupied by humans over a period spanning more than ten thousand years. The most recent groups, in the cave's upper sediment layers, were the nomads who gathered teosinte, that later became farmers.

But, what is really interesting is found in the oldest, deepest layers of the cave. These were analyzed by Somerville et al and dated using accelerated mass spectrometry radiocarbon dating techniques. They were expecting them to be not older than 12,000 yers BP, but instead, they were much older: "[the] bones from the Ajuereado phase zones at the base of the cave yielded surprisingly old ages that range from 33,448 to 28,279 cal BP, a time prior to the Last Glacial Maximum. Because these early ages are many thousands of years older than current models estimate for the peopling of the Americas, they require reassessments of the artifacts and ecofacts excavated from these early zones." A conflict with the orthodox viewpoint of a recent peopling of America!

The oldest layers are known as the Ajuereado level, which has two phases, "Early" and "Later", each of them is composed of different "Zones".

The oldest zone of the Early phase contained crude stone tools: "Minimally worked blades, end-scrapers, and choppers are present" as well as "Pleistocene fauna" while the more recent 10,000 to 14,500 year-old layers of the "Later" Ajuereado phase had more advanced stone tools ("bifacial projectile points; that is, Lerma and Abasolo points" and modern animal remains.

Old Dates

The authors measured dates of bones from the Early Ajuereado phase zones. And found them to be "much older than anticipated", they were 33,228 to 28,279 cal BP years old.

The Early phase produced a lot of lepus (rabbit species, like the jackrabbit) bones, that had been cracked open by humans, they show cut marks, and had also been cooked: There was charcoal and also "crude" stone tools and flakes.

The tools were manmade, as they were composed of flint, which is not found in the rocks of the cave, implying that the stone was brought to the cave from an external quarry. The authors point out that " ... a material external to the cave, makes it difficult to dismiss them as cultural artifacts."

This is at odds with the accepted dates for the peopling of America, but the tools, bones, and fire clearly indicate an early date for the presence of humans at Coxcatlán:

"Because many of the stone tools associated with these early levels are only minimally worked and the antiquity of the ages places these stratigraphic layers many thousands of years before traditional hypotheses posit the arrival of humans in North America, the identity of these objects as tools remains questionable. Nevertheless, the observations that the faunal remains appear to have been processed by humans, that the stone tools are made from flint, and that several stone tools exhibit retouching provide support for the notion of a pre-LGM occupation of Coxcatlan Cave during the Early Ajuereado phase. The radiocarbon ages produced from this study mandate a careful reconsideration of the materials recovered from these zones, including a close inspection of the chipped-stone tools and an analysis of faunal material to document breakage patterns, cut marks, and thermal alterations. The results of this study and those of future reanalyses have important implications for our understanding of several important issues in the archaeology of the New World, including the peopling of the Americas, the timing and causes of the megafaunal extinctions, and the origins of agriculture."

In support for an early presence of humans in this region, the paper cites Mirambell, Lorena, 1994 Los primeros pobladores del actual territorio mexicano. In Historia antigua de México, edited by Manzanilla, Linda R. and Luján, Leonardo López, pp. 177–208. Instituto Nacional de Antropología e Historia, Mexico City. Mirambell mentioned the site at Rancho La Amapola with dates ranging from 45,000 to 25,000 cal. radiocarbon years BP, which produced "a chipped-stone discoidal scraper and Pleistocene faunal bones, including a broken and utilized horse tibia."

Comments

This is an extremely old date. At least 15,000 years older than any site in America. In my opinion, the crude tools of the Early Ajuereado phase are evidence of a more primitive group of humans in the area. These humans mastered fire, made stone tools, and coexisted with the megafauna. The Later Ajuereado phase is 10,000 to 14,500 years old, and represents a more sophisticated group of humans (different tools).

Could this indicate an original group of humans (Denisovans or Neanderthals?) in America 30,000 years ago, replaced by a more recent wave of migrants (Homo sapiens) some 15,000 years ago?

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