930,000 years ago, human ancestors were on the verge of extinction? Chinese scientists conduct the first "census" of ancient humans

As a person living in today's society, are you curious about how many human ancestors lived on this blue planet with a population of more than 8 billion people about a million years ago? "930,000 years ago, human ancestors lost about 98.7% of their members in a short period of time and were almost extinct," said Li Haipeng, a researcher at the Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, and his collaborators.

Li Haipeng's research group and Pan Yixuan's research group at the Institute of Brain Functional Genomics at East China Normal University led the creation of a new theoretical method for fast minimal time tracing (FitCoal), and found that humans experienced a sharp population decline during the transition period between the Early and Middle Pleistocene due to drastic changes in the climate and environment. The relevant results were published in the international academic journal Science on September 1.

Estimating the history of human populations within millions of years with an accuracy of “days”

Tracing back the past of life has been an obsession of mankind since ancient times. Li Haipeng told reporters that changes in prehistoric population numbers can comprehensively reflect changes in the climate and environment during that period. "Through the research method of population genetics, we can have a deeper understanding of the formation of modern humans."

However, since hot conditions are not conducive to the preservation of DNA, researchers were unable to extract ancient DNA from the fossils of human ancestors in Africa 300,000 years ago. In order to accurately estimate the history of human populations millions of years ago, the research team created a new theory of population genetics and computational biology - FitCoal.

In fact, FitCoal is both a theoretical framework and a software tool. Input a piece of DNA data of any organism into the software, which researchers call mutation spectrum, and it can give ancestry tracing results. "The analysis results show that FitCoal can accurately estimate the history of human populations within a million years. The accuracy of the intermediate variable required in the calculation process, that is, the mathematical expectation of branch length, is as high as one day, so the error of the estimated population history is extremely small," Li Haipeng introduced the accuracy of FitCoal to reporters in detail.

Although there is no written record of the population size in prehistoric times, the effective population size will affect the ancestry rate of each generation, that is, the probability that two lineages came from the same ancestor in the previous generation. Therefore, human ancestors once left a mark in the population genome, reflecting the size of the population at that time. The older the population history, the weaker the imprint signal that has survived to this day.

In order to accurately interpret the imprint signals left by human ancestors, the research team followed the FitCoal theory for mathematical derivation and obtained an analytical solution for the expected value of the ancestral tree length corresponding to each mutation type (i.e., mutation spectrum) under any population model, and obtained an accurate likelihood value, i.e., the probability of observing the sample mutation spectrum under the conditions of population history. "Therefore, without the need to obtain prior knowledge of population history, FitCoal can automatically and quickly search for the maximum likelihood value, thereby estimating population history and conducting a 'census' of ancient human populations," said Li Haipeng.

From 100,000 to over 1,000, our ancestors were nearly extinct

Based on FitCoal, the research team discovered for the first time that 930,000 years ago, due to the drastic climate changes during the transition period between the Early and Middle Pleistocene, the number of adult human ancestors dropped sharply from nearly 100,000 to 1,280, and this data remained for 117,000 years.

The researchers used two southern African populations from the HGDP-CEPH dataset for further verification. Although the sample size was only 6 and 8 individuals, FitCoal still detected an ancient population bottleneck. This severe ancient population bottleneck coincides with the missing links of African human ancestor fossils, the disappearance of African Homo erectus fossils, the formation of new ancient human species, and the fusion stage of two ancient human chromosomes 2. "The decline in population size during this ancient period reduced the genetic diversity of modern populations by 65.85%, had a profound impact on human life and health, and may have determined the formation of many key phenotypes of modern humans," said Li Haipeng.

Liu Xiaoming, a scholar at the University of South Florida, commented that FitCoal is the most accurate method to date for estimating the history of effective population size. "This method is based on mutation spectrum data and has a series of advantages such as strong adaptability of data form and fast calculation speed. It has very broad application prospects."

Regarding the application of the results, Li Haipeng told reporters that in the future, if you want to understand the historical survival status of an animal, plant or microorganism, you can use FitCoal to trace it. In addition, it can also help reveal the evolution of tumors, the molecular mechanism of rapid growth of brain capacity, and the overall susceptibility of modern people to diabetes. It is reported that the cooperative team has locked on a gene that may be related to human susceptibility to diabetes, and will conduct further in-depth research in the future.