Here’s what you’ll learn when you read this story:

• It used to be nearly impossible to extract genetic material from Homo erectus fossils, but a team of Chinese researchers figured out how to do so without destroying them.
• The researchers used a minimally invasive method to extract proteins from the enamel of H. erectus and Denisovan teeth before analyzing them with mass spectrometry.
• Protein analysis revealed two mutations—one that had previously been unknown, and another that H. erectus passed to modern humans after interbreeding with Denisovans.

In the eerie stillness of a museum gallery, Homo sapiens peer into glass cases with the skulls of their Homo erectus ancestors gazing back at them. Hundreds of thousands of years echo in the shadows of empty eye sockets. Mouths that can no longer speak seem to keep secrets, but in a rare revelation, genetic material from their teeth is telling us more about their past.

H. erectus is thought to have emerged in Africa nearly 2 million years ago. The species later trekked through the Caucasus Mountains and arrived in Asia around 1.6 million years ago, then continued living there until roughly 250,000 years ago. Skeletal remains unearthed mostly in Africa and Asia have provided insights into what these human ancestors looked like, but much of their genetic material has long since degraded, shrouding their origins in mystery. Until now, the only exception to this genetic mystery were peptides extracted from a 1.77-million-year-old tooth found in Dmanisi, Georgia. Previously, the molecular research methods needed to analyze genetic material from these samples would have been too destructive to use with these ancient specimens.

Paleogeneticist Qiaomei Fu, of the Institute of Vertebrate Paleontology and Paleoanthropology (IVPP) at the Chinese Academy of Sciences, wanted to change that with paleoproteomics. She led a team of researchers in the minimally destructive sampling of proteins from the enamel of six H. erectus teeth, all dating to about 400,000 years ago, that were discovered at three different sites in China. A Denisovan tooth from Harbin was also analyzed for comparison. Because the fossils are irreplaceable, Fu used an acid-etching method that recovered molecular information from the tooth enamel without compromising the specimens’ morphological integrity. The team then used two types of mass spectrometry to identify 11 different proteins and hundreds of amino acid positions.

“Understanding the molecular characteristics of this lineage is essential to help us better understand hominin biology throughout the genus Homo,” Fu said in a study recently published in Nature. “Nevertheless, the only molecular data previously recovered from H. erectus comprise peptides extracted from [the Dmanisi tooth]…these sequences lack any single amino acid polymorphisms (SAPs) that can distinguish H. erectus from other human lineages.”

The team couldn't just grind up priceless H. erectus teeth. So they first ran a pilot test on expendable animal fossils from the same sites to see if any proteins survived at all. When those showed positive signals, they applied a gentler acid-etching technique to the hominin teeth—one that dissolves only the surface layer without destroying the specimen—and then analyzed the extracted peptides with mass spectrometry.

When the mass spectrometry findings were further analyzed, a new single amino acid polymorphism (SAP) known as AMBN-A253G was discovered in ameloblastin, a protein necessary for tooth enamel to form. SAPs are positions in a DNA sequence that have nucleotide variations. These can differ between individuals, and if a particular nucleotide isn’t in the same position in more than one percent of a population, that variation is an SAP. Because they can change functions in some proteins, SAPs are needed for evolutionary adaptations. The presence of the AMBN-A253G mutation in all the enamel samples indicates that all six H. erectus individuals belonged the same evolutionary population.

The second mutation identified, AMBN-M273V, was surprising to Fu and her team because it was previously thought to occur only in Denisovans. The researchers believe it was actually passed from H. erectus to Denisovans through admixture, meaning the two groups interbred in East Asia. This variant exists today in some modern human populations from Southeast Asia and Oceania, and was probably inherited by Homo sapiens through introgression from Denisovans. That is, when Denisovans and modern humans interbred, the variant that Denisovans had originally acquired from H. erectus was passed along to H. sapiens. Before this molecular analysis, the relationship between these Chinese H. erectus populations and Denisovans had been unclear based on physical features alone, since paleoanthropologists traditionally classify species by morphology (specifically, the size and shape of bones and teeth) which cannot reveal interbreeding between groups.

“Denisovans received 0.5–8% gene flow from a hominin whose ancestors diverged more than 1[million years ago] from the common lineage ancestral to Neanderthals, Denisovans and modern humans,” the researchers wrote, “and about 15% of these ‘super-archaic’ DNA regions introgressed from Denisovans into Asian and Oceanian individuals.” He thinks this hominin is “linked to Middle Pleistocene H. erectus.”

Maybe those disembodied H. erectus skulls behind glass are silently watching, seeing how far their genes have come since the last of them vanished.