Mysterious human ancestor finds its place in our family tree

When it comes to deciphering our ancient family tree, DNA from fossils is the new gold standard. But after about half a million years, even the best-preserved DNA degrades into illegibility, leaving the story of our early evolution shrouded in mystery. A new study of proteins taken from the tooth of an enigmatic human ancestor reveals their rough place in the family tree—and shows how ancient proteins can push beyond the limits of DNA.

The new study is “a landmark paper,” says Mark Collard, an archaeologist at Simon Fraser University who wasn’t involved with the work. “Ancient protein analysis promises to be as exciting as ancient DNA analysis for shedding light on human evolution.”

DNA, made of chains of nucleic acids, can remain embedded inside fossilized bones (and prehistoric “chewing gum”) for up to about 500,000 years, explains Enrico Cappellini, a geneticist at the University of Copenhagen’s Natural History Museum of Denmark. That time frame covers the rise of our species, Homo sapiens, in Africa sometime about 300,000 years ago. But before then, many other kinds of humans roamed Earth, including our close cousins the Neanderthals, and their Siberian kin, the Denisovans. Another early relative is H. antecessor, known chiefly from northern Spain’s Gran Dolina cave.

The physical features of H. antecessor have left anthropologists puzzling over its relationships with other early humans. It has big teeth, as do more primitive members of our genus such as H. erectus, but its face shape is remarkably similar to that of modern humans. Some have argued it could be the last common ancestor of Neanderthals, Denisovans, and H. sapiens. Others argue it is actually a member of H. erectus.

In the new study, Cappellini’s team used mass spectrometry—a technique that can sort out a sample’s chemical composition, including the peptides that make up proteins—to analyze proteins in a sliver of enamel from an 800,000-year-old H. antecessor molar from Gran Dolina. Proteins are much hardier and longer lived than DNA: In just the past 6 months, Cappellini and colleagues have published ancient proteins found in a 1.77-million-year-old rhinoceros and a 1.9-million-year-old primate, Gigantopithecus blacki. But they also contain less genetic information than DNA, and they vary less between species.

Cappellini’s team identified peptide sequences from seven proteins in the ancient tooth enamel—essentially all the proteins found there—including a peptide specific to the Y-chromosome that marks the individual as a male. Next, researchers compared these protein sequences with their equivalents in modern humans, other living apes, Neanderthals, and Denisovans.

The proteins suggest H. antecessor was a close relative of the last common ancestor to humans, Neanderthals, and Denisovans, the researchers report today in Nature . “We see that antecessor falls as a sister group—close, very close—to the branch that leads to us,” Cappellini says.

That solidifies what many suspected, but it’s far from conclusive, says Tim Weaver, an anthropologist at the University of California, Davis, who wasn’t involved in the study. Either way, it offers fantastic proof of the power of proteomics to reveal ancient events in human evolution. “It’s really exciting that we’re starting to get proteins from some of these older fossils,” he says.