Oldest Human Genetic Data Gleaned From 1.8-million-year-old Tooth

Sequencing from a second tooth ‘only’ 800,000 years old provided researchers with key information on the position of the enigmatic Homo antecessor in our evolutionary tree

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Skeletal remains of Homo antecessor
Skeletal remains of Homo antecessorCredit: Prof. Jos Mara Bermdez de Castro

Researchers have recovered the oldest human genetic information to date from two prehistoric teeth, one 1.77 million old and the other 800,000 years in age. The remains are so old they belong to a time that precedes the evolution of modern humans, i.e. Homo sapiens, so technically they are ‘human’ only in the sense that they belong to some of our predecessors in the Homo evolutionary tree.

The older of the two teeth was found in Dmanisi cave in Georgia and belonged to Homo erectus, the first hominin group known to have left Africa and spread throughout Eurasia.

The second tooth was unearthed at a prehistoric site in Spain’s Atapuerca Mountains and belonged to a Homo antecessor, an enigmatic early human with a penchant for cannibalism whose evolutionary relationship to us has been the subject of much debate.

The new research published Wednesday in Nature and led by scientists from the University of Copenhagen has provided a partial answer to that question, revealing that Homo antecessor was not a direct ancestor of Homo sapiens, as had been surmised by some.

Both the analyzed samples precede by hundreds of thousands of years what was until now the oldest sequenced human genome, the 430,000-year-old DNA extracted from the remains of an early Neanderthal that was also found at Atapuerca. 

To achieve this huge leap forward – or actually, backwards – in the study of evolutionary genetics, the scientists used a new method that doesn’t reconstruct ancient DNA but sequences proteins, in this case those found in the dental enamel, the hardest and most durable part of the human body.

The Gran Dolina site in the Atapuerca Mountains , the only source of Homo antecessor boneCredit: Ariel David

Since proteins are built by our cells based on instructions from our nuclear DNA, the amino acid chains that form them represent a sort of mirror image of the nucleotides that form constitute our genetic code, explains Dr. Frido Welker, a molecular anthropologist at the University of Copenhagen.

“Just like DNA sequences, these protein sequences will be slightly different between different people, populations and species in a manner that is determined by their evolution,” Welker tells Haaretz. So by comparing sequences from different prehistoric and modern populations, experts can approximate how closely related these ancient groups are to each other.

The advantage of hunting for proteins instead of DNA is that the latter molecule tends to degrade faster, says Enrico Cappellini a professor at the University of Copenhagen and one the lead authors on the Nature study.

Until now, the oldest animal DNA sequenced has been that of a 700,000-year-old horse and that was only because its remains had been preserved by Canada’s permafrost. By using palaeoproteomics (the study of ancient proteins), the same Danish team has published protein sequences from a 1.77-million-year-old rhino found at Dmanisi, as well as a 1.9-million-year old Gigantopithecus, an extinct great ape from China.

Of course, even this new approach has limits. So if you have nightmares about being chased by a velociraptor in a Jurassic-Park-like scenario, then know we are still very far away from sequencing the proteins – let alone the DNA – of dinosaurs who went extinct 65 million years ago.

In fact, even the 1.77-million-year old protein sequence belonging to the Homo erectus from Dmanisi was too short and damaged to be of much use to the authors of the new study, Welker says. It still stands as the oldest genetic information we have gathered on a human ancestor, but it cannot tell us anything about the evolutionary link between erectus and sapiens.

Digital reconstruction of specimen ATD6-69 from the Homo antecessor collection. Computerized microtomography techniques were used to perform this reconstructionCredit: Prof. Laura Martn-Francs

Close, but no ancestor

The study of the Homo antecessor tooth was, on the other hand, much more revealing.

Remains of this hominin have been found only at that one site in Spain’s Atapuerca Mountains, though some prehistoric stone tools unearthed in France and Britain suggest it may have been present there too between 1.2 and 0.8 million years ago. Very little is known about their behavior, apart from the fact that some of their bones were skillfully butchered, which has been interpreted as the earliest evidence of human cannibalism.

Still, some scholars have theorized that antecessor may have played an outsize role in our evolution.

As hinted by its Latin name, which means predecessor or ancestor, the hypothesis is that this elusive hominin was the last common ancestor of Homo sapiens, Neanderthal and Denisovan, the main hominin groups that inhabited the Earth over the last half-million years. The theory is based on the fact that antecessor shares some features with later hominins, especially a relatively modern-looking face. Also, the time span of antecessor's existence fits well with other studies suggesting that the lineages that eventually led to the evolution of Neanderthals, sapiens and Denisovans split off some time before 750,000 years ago. 

But the Nature study, titled “The dental proteome of Homo antecessor,” does not support this theory. Once the recovered protein sequences were compared to those of other hominins, it became apparent that antecessor could only be a sister group of that mysterious common ancestor we share with Neanderthals and Denisovans.

The Gran Dolina site in the Atapuerca Mountains , the only source of Homo antecessor bonesCredit: Ariel David

“The caveat is that it is difficult to establish how closely related they were to the common ancestor,” Welker tells Haaretz. In other words, we are relatives, but antecessor is not on the same branch as us in the evolutionary tree.

“Personally, I am glad that our ancestors did not diverge from a group of cannibals,” jokes Prof. Israel Hershkovitz, a physical anthropologist from Tel Aviv University.

The recovery of the protein sequences from the erectus and antecessor teeth “is an impressive technical feat,” says Hershkovitz, who did not take part in the study.

Palaeoproteomics allows us to gain insights about earlier times than by using DNA, but it is also a more limited tool that, as the authors stated, can only give us a “best guess” as to the placement of Homo antecessor in relation to later hominin groups, he cautions.

The study’s conclusion that antecessor was a parallel group to one of our distant ancestors does contribute to the growing evidence suggesting that human evolution is anything but a straight line in which one type of hominin evolves into the next one, Welker notes. Research over the last years has shown that our evolutionary history resembles more a tangled bush in which different populations evolved in parallel, coexisted and mixed continuously

Many questions remain unanswered, such as the identity of that missing link between us and our closest evolutionary cousins, the Neanderthals and Denisovans, Welker says. But the newfound ability to glean at least some genetic material from hominin remains that are millions of years old does hint that maybe we will be able to crack that mystery soon, as well as other open questions about our distant origins.

The Sima de los Huesos, or “Bone pit” in the Atapuerca Mountains, where dozens of Neanderthal bodies were foundCredit: Ariel David
The Sima de los Huesos, or “Bone pit” in the Atapuerca Mountains, where dozens of Neanderthal bodies were foundCredit: Ariel David