Bottleneck nearly saw human ancestors die out 900,000 years ago

A genomic model suggests that the population of human ancestors crashed for 117,000 years, nearly spelling the end of the human journey before modern humans even evolved.

According to the research, a severe bottleneck which occurred about 930,000 years ago saw the human ancestor population reduced to just 1,280 breeding individuals. This, they predict, means that about 98.7% of the ancestral population was lost at the beginning of the bottleneck.

This coincides with climate changes which saw a glacial period (Ice Age). Previous research has shown that this long-term glaciation saw marine surface temperatures drop and possible long periods of drought in Africa and Eurasia.

The scientists who produced the model used a new method called FitCoal (fast infinitesimal time coalescent process) to look back through human evolutionary history by analysing the genomic sequences from 3,154 modern humans from today. The participants included people from 10 African and 40 non-African populations.

Their work, part of an international collaboration of scientists from China, Italy and the US, is published in Science.

The ancient “bottleneck was directly found in all 10 African populations, but only a weak signal of the existence of such was detected in all 40 non-African populations,” the authors write.

“The fact that FitCoal can detect the ancient severe bottleneck with even a few sequences represents a breakthrough,” says senior author Dr Yun-Xin Fu, a theoretical population geneticist at University of Texas Health Science Center.

While an estimated 65.85% of current genetic diversity may have been lost due to this bottleneck, it also appears to have contributed to a speciation event which led to modern humans. It appears to have led to the merging of two ancestral chromosomes to form what is currently known as chromosome 2 in modern humans.

This information may point to the last common ancestor between modern humans and our closest relatives, the now extinct Neanderthal and Denisovans.

“If, as seems likely, humans were widespread inside and outside of Africa in the period between about 800-900,000 years … whatever caused the inferred bottleneck was limited in its effects on the wider non-sapiens lineage populations, or any effects were short-lived,” the authors add.

The authors also suggest that this research may help explain an apparent gap in the fossil record of human ancestors in Africa and Eurasia during the middle of the Pleistocene epoch (2.6 million to 12,000 years ago).

“The gap in the African and Eurasian fossil records can be explained by this bottleneck in the Early Stone Age. It coincides with this proposed time period of significant loss of fossil evidence,” says senior author Associate Professor Giorgio Manzi, an anthropologist at Sapienza University of Rome.

However, the authors note that many questions remain unanswered.

“The novel finding opens a new field in human evolution because it evokes many questions, such as the places where these individuals lived, how they overcame the catastrophic climate changes, and whether natural selection during the bottleneck has accelerated the evolution of human brain,” says senior author Dr Yi-Hsuan Pan, from the East China Normal University.

Developments such as the ability to control fire may have contributed to the later rapid population growth 813,000 years ago seen in the model.

“These findings are just the start,” says senior author Professor Li Haipeng, from the Chinese Academy of Sciences. “Future goals with this knowledge aim to paint a more complete picture of human evolution during this Early to Middle Pleistocene transition period, which will in turn continue to unravel the mystery that is early human ancestry and evolution.”