Ancient tooth protein suggests Homo erectus may have left a genetic legacy in today’s humans

As an undergraduate, I was told that Homo sapiens was one of the offshoots that emerged in Africa, spread around the world, and replaced every hominin it encountered.

Neanderthals, Homo erectus, and other ancient relatives all hit evolutionary dead ends—unlucky close relatives who left no descendants. In the 30 years since I left university, those early courses have now been completely revised.

This neat alternative story is now completely false, thanks in large part to research published this week in the journal Nature by Fu Qiaomei of the Chinese Academy of Sciences and colleagues.

The paper achieves something that seemed impossible just a decade ago: it recovers meaningful biological information from Homo erectus fossils that are too old for DNA.

Rather than extracting ancient proteins from genetic sequences, the team extracted ancient proteins from the enamel of six teeth from three Chinese sites—Zhoukoudian, Hexian, and Sunjiadong—all dating back about 400,000 years ago.

Homo erectus is widely believed to be the first hominin to leave Africa. There is evidence that this species migrated into Eurasia nearly two million years ago. It remains the most geographically distributed human ancestor ever.

The new study shows that Homo erectus exchanged genes with the Denisovans of East Asia about 400,000 years ago.

The study shows that it now appears that some of this genetic heritage was passed on to living people in the Philippines, Papua New Guinea and throughout Southeast Asia.

Tooth enamel is the hardest tissue in the body, and its proteins can survive long enough for DNA to degrade beyond recovery. What the team found among these proteins was surprising. All six samples had a previously unknown amino acid variation—a tiny molecular signature, a change of one letter in a protein sequence that has never been seen in any other ancient human, living or dead.

This variant brings these East Asian Homo erectus together into a unique group, confirms their identity and resolves a long-standing debate over whether the unusual Hexian fossil is Homo erectus. However, the second variation they share is not unique to Homo erectus.

It also appears among the Denisovans – a mysterious group of ancient humans who lived primarily in a cave in Siberia. The corresponding genetic variant occurs in 21% of living people in the Philippines and about 1% in India, a distribution pattern consistent with what we would expect if it entered modern humans through the Denisovan lineage.

The most reasonable explanation is that Homo erectus populations in East Asia passed this mutation to the Denisovans through interbreeding, and the Denisovans later passed it on to the ancestors of modern Southeast Asians and Oceanians. This transfer of genetic material from one species to another is called introgression.

It turns out that a lineage we once thought was a dead end leaves behind tiny but detectable traces in living human genomes—a molecular thread connecting the teeth of Peking Man to living humans in Asia.

repeating pattern

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But the significance of today’s paper goes far beyond the specific variants or specific populations involved. What it does show is that interbreeding between ancient human lineages was not uncommon. This is routine.

Every major ancient human lineage we’ve been able to examine genome-wide shows admixture. Modern humans outside Africa carry about 2% Neanderthal DNA. Papuans and Aboriginal Australians also have 2% to 5% Denisovan ancestry.

West African populations carry genetic traits from unknown ancient ancestry. As today’s study further highlights, even the Denisovans themselves received gene flow from older, more divergent creatures, possibly Homo erectus.

A 2019 review in the American Journal of Physical Anthropology documented at least three different episodes of introgression of Denisovan-like humans into ancestors in Southeast Asia and Oceania, some of which occurred 20,000 years ago.

The picture is not one of a clean lineage, but of an intricate network of contacts and exchanges stretching over millions of years.

The impact is far-reaching. Our genome is not the product of a single complete lineage from Africa. They are a mosaic made up of contributions from multiple ancient groups, each adapted to their own regional context.

For example, some Denisovan-derived variants in the Papuan genome appear to affect immune function. The Homo erectus -derived variant discovered today has unknown functional consequences—it remains an open question—but precedent for the introgression of other genetic variants suggests that adaptation to new environments may be part of the story.

ghost population

Perhaps most interesting are the implications of this new paper for all the populations we can’t yet study. Homo erectus existed in Indonesia until about a hundred thousand years ago. When modern humans arrived on Flores, Homo floresiensis was a small “hobbit” species. Another human lineage, Homo Luzon, occupied the Philippines.

None of these populations produced DNA, and to this day, none has produced any molecular data. Were they also absorbed (at least partially) into the human group that replaced them?

To date, genomic evidence from living humans has not clearly detected their signal, but the tools available until recently were blunt instruments.

The proteomic approach demonstrated in today’s paper offers a way forward. If proteins can be recovered from 400,000-year-old Homo erectus tooth enamel, applying the same method to the Floresian and Luzon material may eventually reveal whether these lineages also contributed to the humans that followed them.

The old metaphor of a tree—one trunk branching off into different species—has been quietly superseded in the scientific literature. This process is best thought of as a braided river, with many channels partly together and partly apart, constantly exchanging water.

The new study reaffirms that when ancient humans disappeared, they left their traces behind. SKS

SKS

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