Ancient enamel sheds light on extinct giant ape

Scientists have extracted protein fragments from the enamel of a 1.9 million-year-old tooth – the oldest specimen yet to yield ancient proteins.

Their study, published in the journal Nature, doesn’t just solve the mystery of where Gigantopithecus blacki – whose molar was found in Chuifeng Cave in the subtropical south of China – fits into the ape family tree.

It also is a technical tour de force that shows what’s possible in the field of palaeoproteomics. 

In recent years, ancient bones, teeth and even soil have been giving up their secrets in the form of scraps of ancient DNA that have survived the passage of time.

But ancient DNA doesn’t survive forever. The oldest ancient DNA sequences so far date to 700,000 years ago in subpolar specimens.

Closer to the equator, where conditions are hotter and more humid, palaeontologists are hard pressed to find ancient DNA from specimens just a few thousand years old.

This year, ancient proteins have emerged as the new kid on the block in ancient biomolecule research.

Proteins, like DNA, contain strings of building blocks that, when compared between species, can reveal how closely related those species are. Unlike DNA, they stick around for longer.

Earlier this year, Frido Welker, an expert in ancient biomolecules from Denmark’s University of Copenhagen, and colleagues managed to extract proteins from the 1.77-million-year-old tooth enamel of an extinct rhino teeth.

But in that case, the tooth was from the more forgiving temperate climes of Dmanisi, a site in Georgia.

In the current study, Welker and colleagues ground up the enamel and inner dentine core molar of G. blacki’s molar, but without any real expectations. They knew it came from a warmer area with a “worse kind of environment for protein preservation”.

They didn’t have any luck with the dentine, but from the enamel they managed to identify fragments from six proteins, all of which were involved in enamel mineralisation.

Just four partial jawbones, and a few thousand Gigantopithecus teeth, have been dug up from a single region in southern China. Without a skull or other skeletal remains, scientists haven’t been able to figure out where the extinct ape fits in the family tree – or whether it was a great ape at all. 

That’s where the proteins Welker’s team identified come in. 

Comparing them to protein sequences from living great apes, they showed that Gigantopithecus is most closely related to Orangutans. The two species last shared a common ancestor 10–12 million years ago in the Miocene, a time when a burst of new great ape species evolved.

Studying ancient biomolecules is a highly specialised pursuit, requiring clean labs that prevent contamination by the tiniest traces of errant DNA or protein. There are also dedicated algorithms to identify degraded ancient biomolecules and properly analyse the data.

But this study suggests ancient proteins have far more to reveal.

It could be possible to prize proteins from even older specimens, says Welker. “If we have proteins in a subtropical environment at two million years, then at places that are far colder there should then be proteins that are far older.”

Even more tantalising is the prospect of what ancient proteins could reveal about our own ancient relatives.

The tropical islands of southeast Asia have yielded several archaic humans in recent years, including Homo floresiensis from Indonesia, and Homo luzonensis from the Philippines. How exactly these are related to our own species is unclear.

Other remains are simply too fragmentary to pin to a known species.

Ancient proteins could be the key to solving these mysteries. 

“There are all sorts of open questions that we might be able to address now,” says Welker.