Oldest hominin genetic data from more than 2-million-year-old fossils

Genetic data has been extracted from fossilised teeth from an ancient hominin which lived more than two million years ago.

Hominins – humans and our ancient relatives – first emerged in Africa an estimated seven million years ago. The Paranthropus robustus teeth from which the genetic information has been gleaned were found in a South African cave and date back to between 1.8 million and 2.2 million years ago.

It is incredibly difficult for DNA fragments to remain intact after so much time.

The oldest DNA sequenced from a hominin is from a 430,000-year-old Neanderthal specimen in Spain. The oldest DNA found in Africa was only 18,000 years old.

Late last year, DNA fragments recovered from a Siberian mammoth bone became the oldest ever recorded at 2.4 million years old. The DNA strands were better preserved in the cold environment.

But proteins tend to be more resilient. In 2016, researchers obtained protein sequences from ostrich eggshells found in Tanzania that were up to 3.8 million years old.

Proteins record the genetic information that was used to form them.

Up until now, the oldest genetic data from a human ancestor was found in the 800,000-year-old tooth of a cannibal Homo antecessor specimen from Spain and more limited fragments from 1.8-million-year-old Homo erectus fossils from Georgia.

The team that sequenced those fossils from tooth proteins was led by Enrico Cappellini, a protein chemist and associate professor at the University of Copenhagen.

Now, Cappellini has led new research that has broken records yet again. The study is not yet peer-reviewed and is available as a preprint on bioRxiv.

Using mass spectrometry, Cappellini’s team was able to analyse hundreds of amino acids in each sample from the two-million-year-old Paranthropus specimens.

They were even able to determine the biological sex of the four Paranthropus individuals in the South African cave. One protein, amelogenin-Y, is produced by a gene on the Y chromosome and was present in two of the specimens, meaning these were male individuals.

The other two lacked amelogenin-Y, instead sporting the X-chromosome version of the protein, suggesting these were female.

Though limited, the genetic data from the 400 amino acids sequenced allowed the researchers to build a very simple evolutionary tree involving Paranthropus, modern humans (Homo sapiens) and other hominins.

They found that Homo sapiens, Neanderthals and Denisovans are all more closely related to each other than they are to Paranthropus – an unsurprising result. Whether Paranthropus lies directly on the evolutionary lineage which led to modern humans, however, is not clear from the genetic data.

Getting genetic material from such old remains “can be considered a potentially transformative breakthrough for palaeoanthropology,” the authors write.

Queensland University of Technology palaeogenetics expert Dr Sally Wasef, who was not involved in the study, agrees that this technique could open new doors to understand ancient evolutionary lineages.

“Amazingly, protein molecules can preserve some genetic information long beyond the limits of aDNA [ancient DNA]. Ancient proteins might be the only way to answer some genetic questions where we know that our techniques to recover aDNA won’t work,” Wasef says in an email to Cosmos.

“It’s amazing to add even a little information to our knowledge about the early hominin. However, ancient protein is still limited in the information it can provide so far in comparison to aDNA. So, it comes down to what question you want to answer using those hominin remains.”