Scientists identify ‘ghost’ of a long-extinct relative in humans today

By Katie Hunt, CNN

(CNN) — A prehistoric human known as Homo erectus was the first of our forerunners to leave Africa, crossing continents and ultimately roaming the planet for almost 2 million years. But with scarce genetic material available to study, the species remains a major mystery in human origins.

Now, scientists have retrieved ancient proteins from six teeth unearthed in China that, for the first time, reveal a molecular link between Homo erectus and later human species, including our own: Homo sapiens.

“This is a major step forward in tying together the broken branches of our human evolutionary tree,” said Ryan McRae, a paleoanthropologist at the Smithsonian National Museum of Natural History in Washington, DC, who was not involved in the study. “Homo erectus has long been a bit of an enigma.”

Homo erectus remains have been found in Africa, Asia and Europe; however, obtaining informative molecular data such as DNA has proved challenging given the fossils’ age and poor preservation.

In a study published Wednesday in the scientific journal Nature, Chinese geneticist Fu Qiaomei and her colleagues successfully extracted and analyzed ancient enamel proteins from the teeth unearthed at three sites in China. All the teeth date from around 400,000 years ago.

Proteins, which are made up of sequences of amino acids, are more robust than ancient DNA, a fragile molecule that degrades relatively easily. Proteins contain far less detailed information, but they can still shed some light on a specimen’s evolutionary history.

Fu, a professor at the Institute of Vertebrate Paleontology and Paleoanthropology, part of the Chinese Academy of Sciences in Beijing, and her team used what they described as a new, less invasive technique to study fossils without damaging their morphology.

Rather than drilling, they used acid etching to remove a small sample of enamel from the teeth. The team did not try to recover DNA from the fossils after failing to extract DNA from animal fossils of the same age from the same sites. Fu said it was hard to get DNA, but she would never give up.

Unknown variant discovered

The researchers found that the specimens from the three sites in China shared two amino acid variants, one of which was previously unknown. This finding, the researchers reasoned, suggested the teeth all belonged to the same species.

The second variant had previously been identified in Denisovans, another shadowy species of ancient human, and also in some modern human populations.

That other human species shared this variant suggested that Denisovans had once interbred with Homo erectus, and then, at some later point, Denisovans mated with Homo sapiens, according to the study.

As a result, traces of Denisovan DNA live on in some humans today — something interbreeding geneticists call admixture.

Similarly, modern human populations have some Neanderthal ancestry — a legacy of past interactions with that species that went extinct about 40,000 years ago. Denisovans also interbred with Neanderthals.

Modern human populations in Southeast Asia have the highest Denisovan ancestry, suggesting the two groups once crossed paths there.

‘Ghost lineage’

Geneticists knew that Denisovans had some ancestry from an unknown “ghost lineage” with no DNA match, and Homo erectus was one possible candidate, said Eduard Pop, a research scientist at Naturalis Biodiversity Center in Leiden, Netherlands, via email.

“This study strengthens that link,” said Pop, who is working with researchers to understand if protein information is preserved in Homo erectus fossils found in Indonesia.

“It suggests that East Asian Homo erectus-related populations may have contributed genetically to Denisovans, and through them indirectly to some modern humans,” he said.

“So it fits with a view of human evolution in Asia as a network of populations that sometimes overlapped and interbred, rather than a set of clean, isolated branches.”

From the protein information, the researchers were also able to determine the sex of the fossils — five males and one female — by identifying a sex-specific marker in a tooth enamel gene on the Y chromosome.

Work published in 2020 retrieved proteins from an early Homo erectus fossil found in Dmanisi, Georgia, but, unlike the new study, Pop noted it didn’t reveal any detailed information about how the species sits in relation to other hominins.

The fossils came from three sites in central and northern China: Zhoukoudian, Hexian and Sunjiadong. The country has a long history of the discovery of Homo erectus fossils. In the 1920s and 1930s, hundreds of fossils were excavated from Zhoukoudian, including several skulls. The remains became known as Peking Man. However, the fossils, packed in two wooden crates, went missing during the chaos of World War II.

The tooth from Zhoukoudian used in this latest research was discovered during an excavation from 1949 to 1951, the study noted.

Homo erectus was the earliest human species to have body proportions similar to those of Homo sapiens. They had an upright stance, a large face with a protruding brow and no chin. Fossil evidence for Homo erectus stretches over more than 1.5 million years, far longer than the 400,000 years that Homo sapiens have been around, making the former species by far the longest surviving of all human relatives, according to London’s Natural History Museum.

The new study relied heavily on the hypothesis that Denisovans and Homo erectus interbred, but the Smithsonian’s McRae said an alternative explanation could be possible given that the Homo erectus fossils were 400,000 years old and the oldest known Denisovan fossil included in the study is the Dragon Man cranium, which is 150,000 to 300,000 years old.

“Even at the closest, there is still a 100,000 year gap between the two species, meaning that an ancestor-descendant relationship could be an alternative possibility,” he said via email, suggesting that Denisovans perhaps evolved directly from Homo erectus rather than coexisting.

“Transmission of the amino acid variant through interbreeding is certainly possible, I would even say plausible, but archaeological evidence could help confirm a closer connection between the two groups,” he added.

Fu agreed the information her team gleaned from tooth enamel was not detailed enough to understand how Homo erectus is related to other humans. Only DNA would really provide that granular information, she said. Fu described the study’s finding as a “stone thrown in a pool with a big splash,” opening up new questions for future research.

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