Why new genomic data has the potential to rewrite the history of human evolution

Where do we come from? This question has always puzzled mankind. Before the emergence of molecular anthropology, clues to human evolution were mainly studied through fossil specimens. After the emergence of molecular anthropology, DNA became the main means of analyzing human evolution.

From the perspective of zoological classification, we humans belong to the species Homo sapiens, a species that lives on the ground and walks upright. It probably first appeared in Africa about 315,000 years ago. Many zoologists believe that humans are the only surviving members of this evolutionary branch of the genus Homo, but there is a lot of fossil evidence that other humans existed millions of years before us, such as Ardipithecus, Australopithecus, and other Homo species. We humans lived at the same time as at least one other member of the genus Homo, the Neanderthals, who later became extinct.

In addition, we and our ancestors have always lived with other ape-like primates, from modern gorillas to the long-extinct forest apes. It is accepted by anthropologists and biologists around the world that we are related to extinct hominids to some extent, and that we are also related to apes, both living and extinct. However, decades of research on human genome variation has shown that the differences between existing human populations in Africa and a single ancestral population are mainly tree-like models, that is, the current human populations evolved from a common human ancestor. But it is difficult to reconcile this finding with the fossil and archaeological record of humans across the entire African continent.

Our exact evolutionary relationship has been debated ever since the great British naturalist Charles Darwin published his monumental works, On the Origin of Species (1859) and The Descent of Man (1871). Darwin never said, as he is said to have said, that "man is descended from apes." Modern scientists would also refute the popular idea that an extinct species is the 'missing link' between man and apes.

In fact, we and apes may have a common ancestor that existed millions of years ago. This ancestral species does not constitute a "missing link" in a lineage, but rather a node that diverged into different lineages. This ancient primate has not yet been identified, and may never be identified, because the fossil evidence is not entirely clear even in the more evolutionarily related human lineage. This point was already described by Huxley in his article on evolution and biology published in the 1875 edition of the Encyclopedia Britannica. In other words, the goal of completing all the nodes of human evolution is difficult or impossible to achieve in itself.

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The overwhelming fossil evidence suggests that, unlike today, more than one species of our family lived simultaneously throughout much of human history. Specific fossil specimens and species' physical features can now be accurately described, as can the locations where they were found and the times when they lived; however, questions about how species came to exist and why they may have become extinct or evolved into something else can only be hypothesized through scientific speculation, albeit scientifically sound, based on background information gleaned from the localities where the fossils were collected. In inferring specific evolutionary scenarios and filling in gaps in human evolutionary history, researchers must consult a large and diverse body of fossil material, and must do so using sophisticated excavation and recording methods, geochemical dating techniques, and data from other specialized fields such as genetics, ecology and paleoecology, ethology (animal behavior), paleoanthropology, and other multidisciplinary tools.

Molecular Anthropology is a branch of anthropology. It is an emerging interdisciplinary subject that uses molecular analysis of the human genome and DNA genetic information to analyze the origin of humans, ethnic evolution, ancient social and cultural structures, and other multifaceted and multi-level issues. The basic theory is that a certain number of mutations will occur every once in a while when DNA is passed down. Through the occurrence of these mutations, the timeline of evolution and evolutionary branches can be reversed.

The research results of molecular anthropology support the theory that humans walked out of Africa, that is, modern humans living on Earth are all descendants of prehistoric humans who walked out of Africa about 50,000 to 100,000 years ago. Studies on Y-chromosome haplogroups and mitochondrial SNPs show that the ancestors of modern humans settled in East Asia entered the Arabian Peninsula after leaving East Africa, entered Southeast Asia (including Yunnan, my country) along the Indian Ocean coastline, and then gradually expanded to the northern inland areas, that is, the "Southern route" hypothesis of East Asian population migration from south to north. At the same time, there is also a "Northern route" hypothesis, that is, prehistoric humans entered the eastern Mediterranean region from North Africa about 50,000 to 60,000 years ago, and then entered Central Asia and Europe respectively along the east-west direction.

On May 17, 2023, a paper titled "Weak Branch of Human Origin in Africa" ​​was published in the journal Nature, challenging the mainstream view of the single-branch origin of humans and proposing that humans originated from multiple ancestral populations on the African continent, that is, multiple origins. If this theory is confirmed by more subsequent studies, the theory of a single origin of humans will be overturned.

Scientists discovered this new model of human evolution when they examined genetic material from current populations in Africa and compared it with existing fossil evidence of early Homo sapiens populations there. The researchers introduced genomic data from people in East and West Africa, as well as newly sequenced genomes from 44 modern Nama people from southern Africa, into a range of African evolution and migration models proposed in the anthropology and genetics literature. The results showed that the Nama people are an indigenous group with different levels of genetic diversity compared to other modern groups.

Through new model analysis, scientists found that the earliest population differentiation of early humans that can be detected in contemporary humans occurred between 120,000 and 135,000 years ago, when two or more genetically weakly differentiated Homo sapiens populations had been mixed for hundreds of thousands of years. After the population split, people still mixed genes between the parent populations, forming a weak parentage situation. The authors of the article believe that this better explains the genetic differences between individuals and human groups than previous models.

The authors believe that compared with the ancient introgression model, they predict that the fossil remains of coexisting ancestral populations of humans should be genetically and morphologically similar, and that only 1% to 4% of the genetic differentiation in contemporary human populations can be attributed to genetic drift between stem populations. Genetic drift is the random fluctuation of gene frequencies in a small population due to changes in the number of offspring born by individuals with different genotypes. Introgression refers to the repeated backcrossing of the hybrid offspring of two species with their parents, bringing the traits of one parent to the other. The final conclusion is that the stem and branch of human evolution is actually not strong. The ancestors of modern humans are not from a single stem and branch, but from the continuous mixing of genes of two or more ancestors.

The authors suggest that human ancestors from these multiple lineages may have been morphologically similar due to migration between branches, meaning that morphologically distinct hominid fossils such as Homo naledi may not belong to the branch that contributed to the evolution of Homo sapiens.

This theory overturns the previous theory that humans evolved from one stem and branch, that is, the ancestors of humans are not just "Adam" and "Eve", but multiple branches eventually mixed genes. Do you believe that this theory will eventually be confirmed and become the new mainstream theory?

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

Author: Tiangeng

Reviewer: Tao Ning (Associate Researcher, Institute of Biophysics, Chinese Academy of Sciences)

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.