Can you believe it? For as long as 117,000 years, the number of adult individuals of human ancestors is only 1280!
Can you believe it? About 930,000 years ago, human ancestors faced a major threat. Drastic climate changes during the transition from the Early to Middle Pleistocene resulted in the loss of approximately 98.7% of their population. They came very close to becoming extinct.
These discoveries come from the collaboration between Li Haipeng’s research group at the Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences and Pan Yixuan’s research group at the Institute of Brain Functional Genomics, East China Normal University. The relevant results were published online in the top international academic journal Science at 2 a.m. Beijing time today (1st).
Caption: Li Haipeng, a researcher at the Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, introduces scientific research results. Photo by Gao Yang
Lack of DNA “forcing” new methods
Many people should remember the big surprise of last year’s Nobel Prize in Physiology or Medicine. Swante Pabo, a researcher who greatly contributed to the study of human evolution and the ancient human genome, achieved a major accomplishment over a decade ago when he published the first sequence of the Neanderthal genome.
The award of this great expert in ancient DNA research also made people wonder: Why do we go back to the past?
Li Haipeng, a researcher at the Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, had the same question in 2013.
The expert explained that studying ancient population sizes helps us understand how climate and environment influenced the formation of modern humans.
Hominid fossils from the past 4 million years demonstrate the gradual evolution of our ancestors into modern humans. The last 1 million years are a crucial phase in human evolution, marking the transition from Homo erectus to modern humans. Research on human groups focuses mainly on the last 100,000 years. This period marks when modern humans migrated out of Africa and populated different parts of the world.
It is impossible to extract ancient DNA from the fossils of African human ancestors 100,000 years ago due to the hot climate in Africa, which is unsuitable for DNA preservation despite the rapid development of ancient DNA sequencing technology. Li Haipeng said.
There are no written records of prehistoric group numbers. Still, the size of each group will impact how likely two lineages are to share a common ancestor in the previous generation. Human ancestors once left imprints in the population genome, reflecting the size of the group at that time. The older the group’s history, the weaker the imprint signal remains.
Researchers developed a new theory called Fast Minimum Time Ancestry (FitCoal) in population genetics and computational biology to understand these signals and estimate the history of ancient human groups.
Install an “eight-fold mirror” for the “census” of ancient human groups.
“Previously, there have been methods that have relatively accurate estimates of group history within 100,000 years. To estimate the group history of millions of years ago, it is necessary to design a new method with high accuracy.” Li Haipeng compared previous methods to aiming a pistol within 100 meters, while FitCoal is like using an “eight-fold scope” that allows you to see targets within a thousand meters.
Using this mathematical theory, we can find the analytical solution for the expected value of the ancestral branch length in any population model. This allows us to calculate the probability of observing the mutation spectrum in a sample and estimate the population history. FitCoal is a tool that can estimate the history of ancient human groups by searching for the most probable values. It does this without prior knowledge and can even conduct a “census” of these groups.
FitCoal was evaluated by researchers to determine its accuracy. They did this using a population history model and analyzing the DNA polymorphic data generated through simulation. The researchers measured the estimated population history’s unbiasedness and 95% confidence interval. They found that FitCoal provided unbiased estimates and had a smaller confidence interval compared to three commonly used methods in the field.
The researchers further analyzed the group history under different conditions through computer simulations, including group blending and natural selection. All results show that FitCoal can accurately estimate the history of human groups within millions of years.
Liu Xiaoming, a professor at the University of South Florida, believes that estimating the history of effective population size using population genetics and evolutionary genomics is the most accurate method. This method is also adaptable to different data formats and has a fast calculation speed. A series of advantages has a very wide range of application prospects.
Researchers examined genome data from 50 human groups obtained from the 1,000 Genomes and HGDP-CEPH genome projects. They discovered that around 930,000 years ago, the ancestors of modern humans underwent an evolutionary change during the transition from the Early to Middle Pleistocene. Due to drastic climate changes, about 98.7% of its members were lost quickly and were almost extinct. The average number of adults over 117,000 years was only 1,280.
“Reviewing the previous research on the history of human effective population size, this bottleneck event is not without trace.” Professor Liu Xiaoming pointed out that this study is a good case of methodology promoting scientific development.
Discovering “ancient things” should inspire the future.
Shanghai scientists have discovered a significant ancient group bottleneck related to the missing link in African human ancestor fossils. This bottleneck also coincides with the disappearance of African Homo erectus fossils and the formation of a new ancient human species. Furthermore, it corresponds to the fusion stage of chromosomes in two ancient human species.
“The decrease in ancient populations has caused a 65.85% reduction in genetic diversity among modern people. This has significantly affected human life and health and likely plays a role in developing important traits in modern humans. Li Haipeng said.
Over 117,000 years, the average adult population was slightly above one thousand. Famine was a plausible possibility. Then scientists will further think about what kind of people can survive in the environment at that time, and can they use energy more efficiently? He further wondered whether the rising obesity rate was related to corresponding genetic mutations. “We have located relevant genes, and future research will target genetic changes.” Li Haipeng says if this hypothesis is true, it could show that everyone can get diabetes, which would challenge what we currently know about the disease. Know.
According to Li Haipeng, this research has several “spillover effects”. It helps understand tumor evolution and uncover the molecular mechanism behind rapid brain growth. Even the history of “thousands of survivors” may be human. The earliest practice of the community of destiny.
Li Lin is an academician of the Chinese Academy of Sciences and the academic director of the Shanghai Institute of Nutrition and Health, which focuses on computational biology. This achievement truly underscores the remarkable skills of this up-and-coming field. Computational biology can be used in various fields, including aiding drug research and development and understanding disease mechanisms. “Life science is one of the most important components of basic research, and computational biology occupies an important place. The Shanghai Institute of Nutrition and Health will maximize the benefits of combining “nutrition, big data, and health” and keep generating excellent research outcomes.Li Lin said.