400,000 Year-Old Human DNA Sequenced: New Technique Enables Researchers To Map Out Oldest Hominin Genes Ever

By Ajit Jha on December 4, 2013 1:44 PM EST

Homo heidelbergensis
DNA from a group of ancient human fossils found in Spain (above), has been determined to be 400,000 years old. (Photo: Javier Trueba, Madrid Scientif)

Sima de los Huesos in Spain is one of the most important paleontology sites in the world. Researchers there have excavated and pieced together 28 skeletons of Middle Pleistocene hominins. There has been some controversy over the ages of fossils found there in recent years: The local research team at La Sima identified the bones as belonging to the species Homo heidelbergensis, a 400,000 year-old human ancestor. But Dr. Chris Stringer, Britain's leading expert on human evolution from the Natural History Museum, claimed that the team was off by 200,000 years, and that the pit is actually filled with Neanderthal remains. A new study, however seems to prove the local research team right.  

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Researchers at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany have successfully sequenced DNA from one of these individualsTheir analysis revealed that the DNA is in fact from a Homo heidelbergensis, and that it bears a close relationship to the mitochondrial genome of Denisovans, extinct relatives of Neanderthals in Asia. Hominins, of course, are a "tribe" that includes all species filed under the Homo genus, including humans. The findings may have anthropologists reconsidering the complex family tree that includes Neanderthals, Denisovans, and the direct ancestors of humans. 

The DNA study of these unique hominins represents a huge breakthrough — until now, sequencing such degraded samples was an impossible endeavor. A team from the Max Planck Institute for Evolutionary Anthropology led by Matthias Meyer joined forces with the team led by Juan Luis Arsuaga to apply new techniques (previously developed to analyze a cave bear fossil) to the recently discovered hominin. The researchers sampled two grams of bone powder from a hominin thigh bone, extracted its DNA, and sequenced the genome of the mitochondria or mtDNA, passed down maternally. Finally, they compared ancient mtDNA with Neanderthals, Denisoans, present day humans, and apes to calculate that the Sima hominin lived about 400,000 years ago. 

Most striking, perhaps, is that this hominin shared a common ancestor with the Denisovans linked to Neanderthals that lived in Asia 700,000 years ago  "The fact that the mtDNA of the Sima de los Huesos hominin shares a common ancestor with Denisovan rather than Neandertal mtDNAs is unexpected since its skeletal remains carry Neandertal derived features," said Meyer in a press release.

There could be two possible explanations to this link. One is that the fossil in question is related to an ancestor of both Neanderthals and Denisovans, or perhaps just the Denisovans — who split off from Neanderthals about 1 million years ago. The other possibility is that Denisova-like mtDNA could have been introduced into the population of Sima hominins or their ancestors from the gene flow from yet another group of hominins — a third group that interbreed with both hominin populations. Either way, it's a complicated family tree that will need to be unravelled. Juan-Luis Arsuaga, the leader of a Spanish team of paleontologists working at the site, thinks further research may clarify genetic relationship between different groups of hominins.

Either way, this study proves that scientists can definitively sequence DNA from human ancestors that are hundreds of thousands of years old, says Svante Pääbo, director at the Max Planck Institute for Evolutionary Anthropology. "This opens prospects to study the genes of the ancestors of Neandertals and Denisovans. It is tremendously exciting," he said.

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