Ancient proteins recovered from the enamel of six Homo erectus teeth suggest that East Asian populations of this early human relative exchanged genes with Denisovans about 400,000 years ago. The findings, published in Nature by Qiaomei Fu and colleagues at the Chinese Academy of Sciences, add to growing evidence that human evolution was not a simple succession of isolated species but a network of interbreeding lineages.
For most of the 20th century, human origins were represented as a tree. A central trunk divided into branches, which split into smaller twigs, with each species of human relative, or hominin, occupying a distinct branch.
That was the model I was taught as an undergraduate. Homo sapiens was thought to have appeared in Africa, spread throughout the world and displaced every other human group it encountered.
Neanderthals, Homo erectus and other ancient relatives were treated as evolutionary dead ends: unlucky cousins who left no descendants. Thirty years after I graduated from college, those early lessons have been radically reconsidered.
The story of complete replacement is now clearly wrong, thanks in large part to research such as the study published in Nature by Fu and her colleagues. The paper accomplishes something that seemed impossible just 10 years ago: it extracts important biological information from H. erectus fossils too old to preserve usable DNA.
Proteins preserve a record of ancient contact
Rather than sequencing DNA, the researchers extracted ancient proteins from the enamel of six teeth found at three Chinese sites: Zhoukoudian, where the fossil site known as Peking Man was excavated in the early 20th century; Hexian; and Sunjiadong. All the specimens date to about 400,000 years ago.
Homo erectus is widely considered the first human species to leave Africa. Evidence suggests that it migrated into Eurasia about 2 million years ago, and it became the most geographically widespread of all known human ancestors.
The new research indicates that East Asian H. erectus populations exchanged genes, probably through interbreeding, with Denisovans about 400,000 years ago. Some of that genetic heritage appears to have been passed down to living people in the Philippines, Papua New Guinea and other parts of Southeast Asia.
Tooth enamel is the hardest tissue in the human body, and its proteins can persist long after DNA has been irreversibly degraded. The researchers found that all six specimens shared a previously unknown amino-acid variant. It is a small molecular feature—one altered letter in a protein sequence—that has not been found in any other hominin, living or extinct.
This variant groups the East Asian H. erectus fossils together, supports their identification as a distinct group and helps resolve a long-running debate over whether the rare Hexian fossils were actually H. erectus.
The fossils also share a second variant that is not unique to them. It appears in Denisovans, a mysterious archaic human group known primarily from caves in Siberia.
The corresponding genetic variation occurs in living people at a frequency of 21% in the Philippines and about 1% in India. Its distribution is consistent with the possibility that it entered modern human populations through Denisovan ancestors.
The most reasonable interpretation is that East Asian populations of H. erectus passed the mutation to Denisovans through interbreeding. The Denisovans then passed it on to the ancestors of modern Southeast Asians and Oceanians. This transfer of genetic material from one species to another is known as introgression.
The lineage once thought to be an evolutionary dead end therefore left a small but detectable trace in the genomes of living people—a molecular thread connecting the teeth of Peking Man with people living in Asia today.
A recurring pattern of interbreeding
The importance of the study extends beyond the specific variants and populations it identifies. Its broader implication is that interbreeding among ancient human lineages was not unusual. It was routine.
Every major hominin lineage that researchers have been able to examine genomically shows evidence of admixture. Modern humans outside Africa have about 2% Neanderthal DNA, while Papuans and Indigenous Australians carry an additional 2–5% Denisovan ancestry.
West African populations also carry genetic material from an unidentified ancient lineage. Even the Denisovans themselves likely received gene flow from older and more genetically divergent groups, including, as the new research suggests, H. erectus.
A 2019 review in the American Journal of Physical Anthropology documented at least three separate introgression events involving Denisovan-like populations and the ancestors of people in Southeast Asia and Oceania. Some of those events occurred as recently as 20,000 years ago.
The picture is not of a clean lineage but of a tangled web of contacts and genetic exchanges extending across millions of years.
The implications are far-reaching. The human genome is not the product of a single, unbroken lineage that emerged from Africa. It is a mosaic assembled from contributions by multiple archaic groups, each adapted to its own local environment.
Some Denisovan-derived variants in the Papuan genome, for example, appear to affect immune function. The functional effects of the H. erectus-associated variants identified in the new study are unknown, and their role remains an open question. However, the precedent of other introgressed variants suggests that adaptation to new environments may have been part of the story.
The possibility of undiscovered genetic contributions
The study may be most significant for what it implies about populations researchers have not yet been able to study directly. H. erectus probably survived in Indonesia until 100,000 years ago. Homo floresiensis, a small “hobbit” species, lived on the island of Flores when modern humans arrived. Another human lineage, Homo luzonensis, occupied the Philippines.
None of these populations has yielded DNA, and so far none has produced any molecular data. Were they also absorbed, at least in part, into the populations that replaced them? Genomic evidence from living people has not clearly detected their genetic signals, but until recently the available tools were relatively blunt.
The proteomic approach demonstrated by the new study offers a way forward. If proteins can be recovered from H. erectus enamel after 400,000 years, applying the same method to H. floresiensis or H. luzonensis remains could eventually reveal whether those lineages also contributed to the humans who came after them.
The old metaphor of a tree with a single trunk and separate branches has been quietly replaced in scientific discussions. Human evolution may be better understood as a braided river, with many channels flowing partly together and partly apart while continually exchanging water.
The new study provides further evidence that when ancient human groups disappeared, they left traces of themselves behind.
Source: www.sciencedaily.com
