Oldest human genome dug up in Spain’s pit of bones

A 400,000-year-old genome from ancient human bone could herald a missing link species – taking us closer than ever to our common ancestor with Neanderthals
DEEP inside the Atapuerca cave system in northern Spain, 30 metres beneath the surface, lies the Sima de los Huesos, or the “pit of bones”. The remains of at least 28 ancient humans have been found at the bottom of this 12-metre-long vertical shaft. Now a thigh bone pulled out of the pit has yielded 400,000-year-old DNA – by far the oldest human DNA ever sequenced.

The results suggest the thigh bone belonged to a previously unknown human species – perhaps even a missing link between the Neanderthals and their mysterious cousins the Denisovans. This, say palaeontologists, brings us closer than ever before to understanding who our own common ancestor with the Neanderthals was.
Video: Pit of bones hides our oldest DNA

The bones at Sima de los Huesos pre-date the origin of Homo sapiens, who appeared around 200,000 years ago, and most closely resemble those of Neanderthals. Fred Spoor of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, calls them “Neanderthals in the making”.

Until now, it had only been possible to sequence the genomes of hominin fossils found in cold climates; DNA breaks down faster in warmer climates like Spain’s. But spurred by the successful sequencing of a 300,000-year-old cave bear genome from the same area, Matthias Meyer, also at the Max Planck Institute in Leipzig, and colleagues decided to give it a go.

They drilled into a hominin thigh bone from the cave and extracted 1.95 grams of material, processed it for DNA, and filtered out a large amount of modern human DNA – the bones had been heavily contaminated as they were removed and handled.

The end result was a near-complete mitochondrial genome – the DNA found inside the organelles that power cells. By comparing it with that of modern humans, chimpanzees and bonobos, plus Neanderthals and Denisovans, Meyer estimated its age at 400,000 years, twice as old as our own species and far older than any hominin genome previously sequenced (Nature, DOI: 10.1038/nature12788). The Neanderthal and Denisovan genomes sequenced in recent years are each around 40,000 years old.

“The genomes we have [up until now] are really very recent,” says Chris Stringer of the Natural History Museum in London. “This takes us at least a few hundred thousand years back, towards our common ancestor with other hominins.”

“This takes us back a few hundred thousand years, to our common ancestor with other hominins”
“This paper is the dream,” says David Reich of Harvard Medical School in Boston, Massachusetts. It is the latest in a series of breakthroughs in ancient DNA, coming just months after the sequencing of the oldest-ever genome, from a 700,000-year-old horse.

Since the Sima de los Huesos hominins look like Neanderthals, and lived in Europe where the Neanderthals would soon dominate, Meyer expected their DNA to look Neanderthal. But to his surprise, it proved quite distinct. It is most closely related to the Denisovans, a species known only from a finger bone and two molars found in a Siberian cave.

“We don’t quite know what to make of it,” says Meyer. “There’s no evidence the Denisovans ranged anywhere near Atapuerca,” says Stringer.

The biggest mystery is how and when our lineage diverged from that of the Neanderthals and Denisovans. Also unclear are the circumstances of the later split between Neanderthals and Denisovans. All we know is that both of these events happened around the time the Sima de los Huesos hominins were living in Spain.

One possibility is that the fossils belong to the common ancestor of Neanderthals and Denisovans, and some of their descendants later headed east and became the Denisovans. “I think that’s the most likely scenario,” says Meyer.

But that doesn’t explain why the Sima de los Huesos bones look so much like Neanderthals, says Stringer. He thinks they were Neanderthal ancestors, and came after the species split from Denisovans. The Neanderthals could easily have lost the mitochondrial genes they shared with Denisovans later on, he says, as mitochondrial DNA is only passed down the female line. “Mitochondrial DNA can be lost if a woman only has sons,” says Stringer.

That means the only way to settle exactly what happened is to sequence a full genome from the Sima de los Huesos fossils. Meyer is working on this now. “It is extremely difficult,” he says.

The Sima de los Huesos genome is particularly exciting because it is from a time that is very close to the origin of our human line. The archaeological evidence suggests these early humans were developing significant new behaviours. On the one hand, they were still using fairly primitive stone tools like a crafted hand axe – nicknamed Excalibur – that was found in the pit. But the bones also suggest more modern traits.

For instance, some believe the pit might have been an early burial site, part of a simple funeral rite. Excalibur could be a tribute to the dead, suggests Stringer.

And the deformed skull of a girl who lived to be around 12 years old, also found in the pit, suggests that the tribe cared for her. “There’s a hint of something human – caring for the disabled,” says Stringer.

Elsewhere in Atapuerca, archaeologists have discovered the remains of an elderly man with severe back problems, who couldn’t have fended for himself. Here, too, the man’s age suggests a community must have protected him.

The possibility of peering into the Sima people’s genes as well as their bones is a huge step forward. A full genome would be invaluable, says Reich. We could find out which of our modern genes were already in place, and which ones had to change to produce modern humans. As Reich puts it: “It’s about what makes us human.”

“A full genome from these bones would tell us which genes had to change to produce modern humans”

A brief history of human fossils

The fossil remains found in Sima de los Huesos, Spain, offer important clues to unravelling the origins of our species (see main story). Here are five other key ancestors.

Lucy Modern humans are descended from the ape-like Australopithecus, which lived in Africa. The most famous specimen is Lucy, a 3.2-million-year-old Australopithecus afarensis found in Ethiopia in 1974. She got her name from The Beatles’ song Lucy in the Sky with Diamonds.

Karabo This 1.9-million-year-old boy was found in South Africa in 2008, alongside an adult female. He belongs to the species Australopithecus sediba, has a mix of ape-like and human-like features, and was named “Answer” by a 17-year-old South African student in a competition.

Turkana Boy An almost complete 1.5-million-year-old Homo erectus fossil was found by Kenya’s Lake Turkana in 1984. The species spread as far as Java, and may be our direct ancestors.

Neanderthal 1 The first recognised Neanderthal was found in 1856 in Germany’s Neander valley. It didn’t get a snappy name, but was the first primitive human identified, and in 1997 became the first to yield DNA.

X-Woman A female finger bone from the Denisova cave in Siberia turned out to belong to a new species when its genome was sequenced in 2010. The Denisovans are most closely related to Neanderthals. Genetics show they roamed as far as Indonesia, where they interbred with modern humans.

This article appeared in print under the headline “Pit of bones hides our oldest DNA”

By Michael MarshallMagazine issue 2946 published 7 December 2013



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