More than 900,000 years ago, human ancestors almost became extinct?

From an evolutionary perspective, humans are undoubtedly very lucky because we are the only species in the genus Homo of the family Hominidae. Currently, the global population is close to 8 billion. However, a recent study led by Chinese scientists shows that 930,000 years ago, due to drastic climate change, human ancestors may have faced a serious population bottleneck, losing 98.7% of the population in a short period of time, and this bottleneck period lasted for nearly 120,000 years. During this bottleneck period, the average human population was only 1,280 people, and there was a risk of extinction at any time.

Figure 1: The severe population bottleneck experienced by human ancestors during the transition between the Early and Middle Pleistocene (Hu et al., 2023)

This research result was published online in the internationally renowned academic journal Science on August 31, 2023. It was led by Li Haipeng's research group from the Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences and Pan Yixuan's research group from the Institute of Brain Functional Genomics, East China Normal University. Scientists from the Natural History Museum of the University of Florence, the Department of Environmental Biology of the University of Rome, and the University of Texas Health Science Center at Houston also participated in these studies.

Fossil archaeological records show that the history of human evolution can be traced back to 6 million years ago . The ancestors of humans parted ways with the ancestors of chimpanzees, and then went through different stages of development such as Australopithecus, Homo habilis, Homo erectus, and Homo sapiens. Modern Homo sapiens survived the competition and integration with Neanderthals and Denisovans. It is generally believed that 1 million years ago was a critical period in human evolution , but fossil records of this period are extremely rare, and human research history is mainly limited to 300,000 to 100,000 years. With the help of ancient DNA sequencing technology, it is possible to trace back to a more distant human past. However, the climate in Africa 300,000 years ago was hot, and the DNA of human ancestors was difficult to effectively preserve . Therefore, ancient DNA sequencing technology is basically useless in tracing back the human history 300,000 years ago.

The biggest highlight of this study is the invention of a theoretical method that is by far the most accurate in estimating the history of effective population size - Fast Minimum Time Tracing (FitCoal), which can use computers to analyze the spectrum of gene variation in the modern human genome , estimate population history, and conduct a "census" of ancient human populations millions of years ago. In other words, scientists can use the FitCoal method to trace population size changes millions of years ago without the need for fossil records or DNA from ancient humans, thereby gaining a deeper understanding of the formation process of modern humans. This is undoubtedly a major breakthrough. In the previous theoretical framework, only 300,000 to 400,000 years of history could be traced back.

Based on the FitCoal method, researchers analyzed more than 3,000 modern human genome data from 10 African and 40 non-African populations , and discovered for the first time that 930,000 years ago , due to drastic climate changes during the transition period between the Early and Middle Pleistocene, human ancestors lost about 98.7% of their members in a short period of time and were on the verge of extinction. The glacial events of this period caused temperature changes and severe droughts in Africa, which caused the extinction of a large number of species or a reduction in population numbers. The food sources of human ancestors were limited, resulting in a sharp decline in the population of ancient humans and near extinction. Further analysis showed that for as long as 117,000 years, the average number of adult individuals of human ancestors was only 1,280 , and the risk of extinction existed at any time. The two sets of human genome data based on different sources came to similar conclusions.

The researchers evaluated the accuracy of the FitCoal method and found that the method can detect the above-mentioned serious bottleneck of ancient human populations using less than 10 human genome data, and even only 3 African genome data can achieve similar results, indicating that the FitCoal method has high sensitivity . FitCoal has been developed into a software tool by them and placed on the laboratory's website for researchers around the world to download and use.

Researchers speculate that the bottleneck of ancient human populations in the early to middle Pleistocene had a profound impact on the formation of modern humans . This bottleneck may have led to the formation of the Homo sapiens species. One of the key events was that the chromosome 2 of modern humans was formed by the fusion of two small chromosomes, which made the number of chromosomes in humans become 46, while the number of chromosomes in chimpanzees is 48. Since the number of chromosomes of Neanderthals and Denisovans is the same as that of modern humans, it is speculated that the common ancestor of the three was formed during the severe population bottleneck period of ancient humans. At the same time, this bottleneck caused the loss of about 66% of the genetic diversity of modern humans , which may have a significant impact on the health of modern humans.

Interestingly, the period when ancient humans experienced a serious population bottleneck also coincided with major events such as the missing links of African human ancestor fossils and the disappearance of African Homo erectus fossils. It is a great miracle that human ancestors could survive such a long population bottleneck period. Fortunately, about 800,000 years ago, the population of human ancestors recovered rapidly , and its population size increased 20 times, estimated to have reached 27,000 people. Archaeological evidence found in Israel about 790,000 years ago shows that the use of fire may be part of the reason for the population increase. Other factors, such as climate change, may also be the driving force behind the rapid recovery of the population.

References:

Wangjie Hu et al. , Genomic inference of asevere human bottleneck during the Early to Middle Pleistocene transition.Science381,979-984(2023).DOI:10.1126/science.abq7487.

This article is a work supported by Science Popularization China-Starry Sky Project

Author: Tang Bo, PhD Research Librarian in Molecular Biology

Reviewer: Ye Sheng, Professor of Beijing University of Aeronautics and Astronautics

Produced by: China Association for Science and Technology Department of Science Popularization

Producer: China Science and Technology Press Co., Ltd., Beijing Zhongke Xinghe Culture Media Co., Ltd.