The oldest genetic data of a human relative found in 2 million year old teeth

Human hominids and their ancient relatives emerged in Africa about seven million years ago. Now researchers have gathered genetic information from an African hominid who lived two million years ago, the oldest data ever recovered.

The protein sequences, described in a preprint posted on the bioRxiv server on July 3¹they come from different Paranthropus robustus tooth fossils found in a South African cave.

This genetic data is the oldest that has been collected from any hominid, taking the genetic record back to previously unthinkable times and places, the scientists say.

It’s a surprising result, says Katerina Douka, an archaeological scientist at the University of Vienna. At that age, the remains have almost turned to stone, she adds.

It’s unclear whether the few sequences that can be recovered from very ancient fossils could help unravel the evolutionary relationships that scientists have debated for decades. No one yet knows how useful it will be, says Beatrice Demarchi, a biomolecular archaeologist at the University of Turin, Italy.

Preserved proteins

Last year, researchers obtained genetic sequences from two-million-year-old permafrost samples from Greenland², setting the record for the oldest discovery of preserved ancient DNA. But DNA degrades faster in warmer climates: Researchers have made heroic efforts to sequence a fragment of the oldest hominid DNA ever recorded: a 400,000-year-old Neanderthal genome, which was found in an underground pit in Spain³.

Move over, DNA: ancient proteins are starting to reveal the history of mankind

Proteins tend to be stronger than DNA, allowing researchers to push the molecular record further back in time. In 2016, the Demarchis team obtained protein sequences from the ostrich (Struthionidaelisten)) eggshells in Tanzania that were up to 3.8 million years old⁴.

Several years later, a team co-led by Enrico Cappellini, a protein chemist at the University of Copenhagen (KU), sequenced tooth proteins from roughly 800,000-year-old remains belonging to a species called homo ancestor in Spain, as well as more limited sequences from 1.8 million years ago Homo erectus georgia fossils⁵.

In the 2023 study, a team led by Cappellini, protein scientist Claire Koenig and molecular biologist Ioannis Pastramanis, both from KU, and molecular biologist Palesa Madupe from the University of Cape Town, sampled four P. robust teeth from Swartkrans cave, 40 kilometers northwest of Johannesburg. Researchers have long debated how these hardy-bodied hominins are related to other ancient human species.

The researchers used a technique called mass spectrometry to analyze hundreds of amino acids in each sample of enamel, the outer mineral layer of teeth.

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A protein they found, called amelogenin-Y, is produced by a gene on the Y chromosome. Its presence in two of the samples allowed the researchers to conclude that the teeth belonged to males. One of these had previously been attributed to a female based on its small size. The other two teeth lacked signs of amelogenin-Y and contained the X-chromosome version of the protein, leading the authors to infer that the specimens were likely female.

About 400 of the same amino acids were sequenced in all four samples. This has allowed the researchers to build a simple evolutionary tree that confirms this homo sapiens, Neanderthals and hominids found in Siberia, called Denisovans, who lived for the past 200,000 years, are all more closely related to each other than they are by two million years in age. Paranthrope. Any other relationship would have been a big surprise, Douka says.

In an enamel protein, the researchers found sequence differences between the Paranthrope remains, potentially reflecting within-species variability.

Potentially transformative

Building an evolutionary tree from the genetic data of such ancient remains may be considered a potentially transformative breakthrough for paleoanthropology, Cappellini and his colleagues write in the preprint. They add that studies of ancient proteins could improve understanding of where creatures like Australopithecus afarensis of which there are many fossil fragments, and the most complete specimen known as Lucy is found in the hominin family tree.

Other scientists say the jury is still out on whether the ancient proteins will help bring consensus to the picture of hominin evolution, which is currently constructed largely from the shapes of bones.

Record breaking ancient DNA found in frozen ground

There is limited variability in enamel proteins, so the 425 amino acids Cappellinis’ team used to build the family tree seem less informative than the first Neanderthal sequences the researchers sequenced in 1997, which included about 360 base pairs of Mitochondrial DNA⁶, which involves a lot of variation, notes Pontus Skoglund, a paleogeneticist at the Francis Crick Institute in London. The shape of bone is probably still a more reliable way of untangling relationships than ancient proteins. There is therefore still a long way to go in ancient evolutionary proteomics.

Demarchi agrees, but is also excited about the possibility of determining the sex of fragmentary fossils, particularly those of animals. It is not uncommon for sex-based size differences to be erroneously attributed to species differences and vice versa: P. robust the fossils were initially attributed to the males of another smaller southern African hominin.

As ancient proteomics expands, the researchers say it will also be instrumental in balancing the benefits with the costs of destructive sampling. Skoglund’s lab is working on nondestructive methods for sifting fossils for their protein content while sparing samples that wouldn’t have yielded good data. It’s important to consider the risk of failure when making decisions about sampling the fossil record, he says.