a skull in headdress of blue feathers

This new tool will help upend everything we assumed about ancient gender roles

Proteomics, the study of proteins present in our genetic makeup, is a cheaper and easier method than using ancient DNA to determine sex.

A headdress of macaw feathers adorns the 600-year-old skull of a sacrificed child from the Peruvian site of Pampa la Cruz. Archaeologists used proteomics to determine that the key sacrifices at the site, like this individual, were of male children.
Photograph by Becky Hale, National Geographic

A new revelation that the remains of a powerful ancient “man” buried in an elaborate tomb in Spain are actually female is challenging assumptions about the roles of women in early European societies.

But it’s also a vivid example of the game-changing new ways that archaeologists are using the study of proteins that make up the complex biochemistry encoded in cellular DNA.

By examining proteins in organic artifacts like teeth and bones, scientists can now learn details of the DNA that created them—but without having to analyze any actual DNA that may have survived.

Such techniques, called proteomics, have “the capacity to revolutionize archaeology,” says Marta Cintas‑Peña, an archaeologist at the University of Seville and the lead author of a new study that used proteomics to determine the sex of the woman in the tomb.

A lavish tomb—and an unquestioned assumption

The study published today in Scientific Reports describes the discovery of the tomb in 2008 at Valencina de Concepción, a town near Seville in southern Spain.

It lies within a vast burial ground dated to Iberia’s Copper Age, between 4,200 and 5,200 years ago; and it was one of the richest tombs ever found in Spain, with lavish grave goods that included an entire elephant’s tusk, a dagger with a crystal blade, and dozens of mother-of-pearl beads.

Archaeologists at the time suggested the person buried there was a man aged between 17 and 25, based on their assessment of the skeletal remains; the grave goods indicated “he” had held an elite position in society.

But a new examination of the tooth enamel from the individual’s remains shows the presence of proteins made by genes on an X chromosome—but no equivalent proteins made by genes on a Y chromosome. That suggests the person in the tomb was biologically female (XX), and not male (XY).

Cintas-Peña and study senior author Leonardo García Sanjuán, also at the University of Seville, say their new discovery challenges models of prehistoric societies in Iberia that suggest they were led by charismatic men.

But “our study shows this was not necessarily the case,” the researchers say; instead, it seems that women could also be leaders—forcing a rethink of the societal roles of women in Copper Age Iberia and elsewhere.

‘Revolutionizing’ archaeology

While breakthroughs in the study of ancient DNA are enabling archaeologists to extract detailed information from archaeological remains, from sex down to eye color, the process can be expensive and time-consuming, with samples prone to contamination—when there’s actually enough DNA to recover.

Proteomics, on the other hand, can be used to create a partial genetic profile from remains regardless of the presence of DNA in the sample: “It allows you to get a very small genotype from DNA, even when the DNA in a sample is degraded and gone,” says Glendon Parker at the University of California Davis, a pioneer in proteomics who has spent more than a decade researching forensic and archaeological applications.

Parker’s studies also show proteins are often more stable and better preserved in ancient bones and teeth than DNA: “It is always the case that if you have DNA you will have protein,” he says. “But if you have protein, you may not have DNA.”

Using proteomics to determine the sex of human remains is “more effective, cheaper, and faster” than ancient DNA analysis, agree Cintas-Peña and García Sanjuán.

Although the method is only a few years old, it’s already having a scientific impact, they say: “The result we present in the paper confirms the efficiency of the technique.”

Proteomics and ancient DNA

Like the researchers with the Copper Age burial in Spain, being able to determine sex from proteins in human tooth enamel has also been invaluable to Peruvian archaeologist and National Geographic Explorer Gabriel Prieto, who wasn’t involved in the latest study.

He sent teeth from the victims of a mass child sacrifice by the Chimú people of Peru to his co-researcher Parker; the proteins revealed the key sacrifices were male children.

“It really helped us to understand that, at least for this event, boys were the most important sacrificial victims,” Prieto says.

Chimú sacrifices involved hundreds of victims, so ancient DNA analysis would have been prohibitively expensive, even if viable DNA could be found in each set of remains.

And while DNA analysis is ongoing for some of the sacrificial victims, it’s to compliment the proteomics—for example, to show if any of the victims were related. 

“Proteomics and ancient DNA work together,” Prieto says. “But if we have the chance to do the proteomics, then we go with that.”

Proteomics in archaeology—and animals

Besides providing genetic information from animal and human remains, proteomics can also be used to investigate microorganisms that caused ancient diseases such as leprosy or plagues; to identify food residues on ancient pottery; and to determine sources of fibers used in ancient textiles, which could provide insight into ancient trading networks.

Biomolecular archaeologist Michael Buckley at the University of Manchester in the United Kingdom has developed the proteomics of collagen—the main protein in bones—into the Zooarchaeology by Mass Spectrometry (ZooMS) method of determining which animal species a particular bone from an archaeological site came from.

The technique was recently used to show that ivory in a fifth or sixth century English grave came from an African elephant, which implies a previously unknown trade route across the ancient world at that time.

“It’s great that ZooMS is taking off in a big way now,” Buckley says. “One of the most promising aspects is that we’re starting to generate much larger amounts of data and getting much better information about human interactions with animals in the past.”

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