A new method of inferring ancient population size revealed a severe bottleneck in the human population which almost wiped out the chance for humanity as we know it today.

An unexplained gap in the African/Eurasian fossil record may now be explained thanks to a team of researchers from China, Italy and the United States. Using a novel method called FitCoal (fast infinitesimal time coalescent process), the researchers were able to accurately determine demographic inferences by using modern-day human genomic sequences from 3,154 individuals. These findings indicate that early human ancestors went through a prolonged, severe bottleneck in which approximately 1,280 breeding individuals were able to sustain a population for about 117,000 years. While this research has illuminated some aspects of our early to middle Pleistocene ancestors, many more questions remain to be answered since this information was uncovered.

A high extinction risk of our ancestor decoded by a new inference method. Core formula of the new inference method. The image depicts a cliff painting, illustrating the population of human ancestor pull together to survive the unknown danger in the darkness during the ancient severe bottleneck. [IMAGE: SINH]

The ancient human population bottleneck and the Out-of-Africa dispersal. The African hominin fossil gap and the estimated time period of chromosome fusion are shown on the right. [IMAGE: SCIENCE]

A large amount of genomic sequences were analyzed in this study. However, “the fact that FitCoal can detect the ancient severe bottleneck with even a few sequences represents a breakthrough,” says senior author Fu Yun-Xin, a theoretical population geneticist at the University of Texas Health Science Center at Houston.

Researchers will publish their findings in Science on September 1, 2023 (America Eastern Standard Time). The results determined using FitCoal to calculate the likelihood for present-day genome sequences indicate that early human ancestors experienced extreme loss of life and therefore, loss of genetic diversity.

“The gap in the African and Eurasian fossil records can be explained by this bottleneck in the Early Stone Age as chronological. It coincides with this proposed time period of significant loss of fossil evidence,” says senior author Giorgio Manzi, an anthropologist at Sapienza University of Rome. Reasons suggested for this downturn in human ancestral population are mostly climatic: glaciation events around this time lead to changes in temperatures, severe droughts, and loss of other species, potentially used as food sources for ancestral humans.

An estimated 65.85 percent of current genetic diversity may have been lost due to this bottleneck in the early to middle Pleistocene era, and the prolonged period of minimal numbers of breeding individuals threatened humanity as we know it today. However, this bottleneck seems to have contributed to a speciation event where two ancestral chromosomes may have converged to form what is currently known as chromosome 2 in modern humans. With this information, the last common ancestor has potentially been uncovered for the Denisovans, Neanderthals, and modern humans (Homo sapiens). However, we all know that once a question is answered, more questions arise.

“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 the human brain,” says senior author Pan Yi-Hsuan, an evolutionary and functional genomics at East China Normal University (ECNU).

Now that there is reason to believe an ancestral struggle occurred between 930,000 and 813,000 years ago, researchers can continue digging to find answers to these questions and reveal how such a small population persisted in assumably tricky and dangerous conditions. The control of fire, as well as the climate shifting to be more hospitable for human life, could have contributed to a later rapid population increase around 813,000 years ago.

“These findings are just the start. 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,” says senior author Li Haipeng, a theoretical population geneticist and computational biologist at the Shanghai Institute of Nutrition and Health (SINH) of the Chinese Academy of Sciences (CAS).

This research was jointly led by Li Haipeng at CAS’s SINH and Pan Yi-Hsuan at ECNU. Their collaborators, Fabio Di Vincenzo at the University of Florence, Giogio Manzi at Sapienza University of Rome, and Fu Yun-Xin at the University of Texas Health Science Center at Houston, have made important contribution to the findings. The research was first-authored by Hu Wangjie and Hao Ziqian who used to be students/interns at CAS’s SINH and ECNU. They are currently affiliated with the Icahn School of Medicine at Mount Sinai, and Shandong First Medical University & Shandong Academy of Medical Sciences, respectively. Du Pengyuan at CAS’s SINH, and Cui Jialong at ECNU also contributed to this research.

The National Natural Science Foundation of China, Strategic Priority Research Program of the Chinese Academy of Sciences, the National Key Research and Development Project, the National Institute of Health, the Education Bureau of Jinan and Shandong First Medical University, the Key Laboratory of Brain Functional Genomics at East China Normal University, the Shanghai Institute of Nutrition and Health of the Chinese Academy of Sciences, the China Postdoctoral Science Foundation, Shandong Provincial Natural Science Foundation and the Shandong Provincial Postdoctoral Innovation Talent Support Program all made this research possible.

Source: Shanghai Institute of Nutrition and Health,

Chinese Academy of Sciences