The basic formulation of our new inference method is presented. The image depicts a cliff panel, showing a human ancestral population banding together to survive an unknown danger in the dark during an ancient extreme bottleneck. Credit: Shanghai Institute of Nutrition and Health, CAS
A new way to infer ancient population size has revealed a severe bottleneck in human population that has almost eliminated the chance of humanity as we know it today.
The unexplained gap in the African/Eurasian fossil record can now be explained thanks to the team Researchers from China, Italy and the United States. Using a new method called FitCoal (micro-time rapid coalescence), the researchers were able to accurately determine demographic inferences using modern human genomic sequences from 3,154 individuals. These results suggest that early hominid ancestors went through a long and severe bottleneck phase, in which approximately 1,280 individuals were able to maintain the population for approximately 117,000 years. While this research has shed light on some aspects of early to middle Pleistocene ancestors, there are many questions to be answered since this information was revealed.
FitCoal Methodology
A large amount of genomic sequences were analyzed in this study. However, “the fact that FitCoal can detect a severe ancient bottleneck even with a small number of sequences represents a major breakthrough,” says lead author Yun-Xin Fu, a theoretical population geneticist at the University of Texas Health Science Center at Houston.
The researchers will publish their results online at Sciences On August 31, 2023 (US Eastern Time). Results determined using FitCoal to calculate the likelihood of current genome sequences found that early human ancestors experienced a massive loss of life and thus a loss of genetic diversity.
The fossil gap of African hominins and the estimated time period for chromosome fusion are shown on the right. Credit: Science
Interpreting the fossil gap
“The gap in African and Eurasian fossil records can be explained by this bottleneck in the Early Stone Age historically speaking. 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. The suggestion for this decline in hominid populations is mostly climatic: glaciation events at this time led to temperature changes, severe drought, and loss of other organisms. ClassifyIt was likely used as a food source for ancestral humans.
Genetic diversity and human evolution
The ramifications of this suffocation are staggering. An estimated 65.85% of current genetic diversity may have been lost due to this bottleneck in the early to mid-Pleistocene, and a long period of shrinking reproductive populations threatened humanity as we know it today. However, this bottleneck appears to have contributed to a speciation event in which two ancestral chromosomes may converge to form what is currently known as chromosome 2 in modern humans. With this information, the last common ancestor of Denisovans, Neanderthals, and modern humans will likely be discovered (Homo sapiens).
Discover new questions
We all know that once a question is answered, more questions arise.
“The new discovery opens a new field in human evolution because it raises many questions, such as where these individuals lived, how they overcame catastrophic climate changes, and whether natural selection during a bottleneck accelerated the evolution of the human brain,” says the lead author. Yi Hsuan Pan, an evolutionary and functional genomics specialist at East China Normal University (ECNU).
Now that there is reason to believe that ancestral conflict occurred between 930,000 and 813,000 years ago, researchers can continue searching to find answers to these questions and uncover how this small population persisted in difficult and dangerous conditions. Fire control, combined with a shift in climate to be more suitable for human life, may have contributed to the subsequent rapid population increase about 813,000 years ago.
“These findings are just the beginning. Future goals with this knowledge aim to paint a more complete picture of human evolution during this transitional period from the early Pleistocene to the middle Pleistocene, which in turn will continue to unravel the mystery that is the origin and evolution of early humans.” Theoretical population geneticist and scientist Computational Biology at Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences (SINH-CAS).
Reference: “Genomic inference of the severe human bottleneck during the early to middle Pleistocene transition” by Wangji Hu, Ziqian Hao, Pingyuan Du, Fabio Di Vincenzo, Giorgio Manzi, Jialong Cui, Yun-Xin Fu, Yi-Hsuan Pan, and Haiping Li , August 31, 2023, Sciences.
doi: 10.1126/science.abq7487
This research was co-led by Haipeng Li at SINH-CAS and Yi-Hsuan Pan at ECNU. Their collaborators, Fabio Di Vincenzo of the University of Florence, Giorgio Manzi of Sapienza University in Rome, and Yun-Xin Fu of the University of Texas Health Science Center at Houston, made important contributions to the results. The first authors of the paper are Wangjie Hu and Ziqian Hao who used to be students/interns at SINH-CAS and ECNU. They are currently affiliated with the Icahn School of Medicine at Mount Sinai, Shandong First Medical University and Shandong University Academy of Medical Sciences, respectively. Pengyuan Du from SINH-CAS and Jialong Cui from ECNU also contributed to this research.
