The 430,000-year-old DNA comes from mysterious early human fossils found in Spain’s Sima de los Huesos, or “pit of bones”.

The fossils look like they come from ancestors of the Neanderthals, which evolved some 100,000 years later. But a 2013 study found that their mitochondrial DNA is more similar to that of Denisovans (see video, below), who also lived later and thousands of kilometres away, in southern Siberia.

So who were the Sima people – and how are they related to us?

To find out, a team led by Matthias Meyer at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, pieced together parts of the hominin’s nuclear DNA from samples taken from a tooth and a thigh bone.

One of the Sima de los Huesos skeletons – Javier Trueba, Madrid Scientific Films

The results suggest they are more closely related to ancestors of Neanderthals than those of Denisovans – meaning the two groups must have diverged by 430,000 years ago. This is much earlier than the geneticists had expected.

It also alters our own timeline. We know that Denisovans and Neanderthals shared a common ancestor that had split from our modern human lineage. In light of the new nuclear DNA evidence, Meyer’s team suggests this split might have happened as early as 765,000 years ago.

Previous DNA studies had dated this split to just 315,000 to 540,000 years ago, says Katerina Harvati-Papatheodorouat the University of Tubingen in Germany.

But a date of 765,000 years ago actually brings the DNA evidence more in line with some recent fossil interpretations that also suggest an older divergence between modern humans and the ancestor of the Neanderthals and Denisovans.

“I am very happy to see that ideas about the divergence based on ancient DNA and on anatomical studies of the fossil record seem to be converging,” says Aida Gómez-Robles at George Washington University in Washington DC, who was involved in the fossil research.

Tree redrawn?

But if such an ancient split is correct, we might have to redraw parts of our evolutionary tree.

Conventional thinking is that modern humans, Neanderthals and Denisovans all evolved from an ancient hominin called Homo heidelbergensis.

However, H. heidelbergensis didn’t evolve until 700,000 years ago – potentially 65,000 years after the split between modern humans and the Neanderthals and Denisovans.

Instead, another, obscure species called Homo antecessor might now be in the frame as our common ancestor.

This species first appeared more than a million years ago – and its face is very similar to that of modern humans, says Chris Stringer at the Natural History Museum in London.

Further puzzles

“Research must now refocus on fossils from 400,000 to 800,000 years ago to determine which ones might actually lie on the respective ancestral lineages of Neanderthals, Denisovans and modern humans,” he says.

Another puzzle remains. The study confirmed a previous finding that the mitochondrial DNA of the Sima hominin is more similar to Denisovans than to Neanderthals – but no one knows why.

Perhaps there was another unidentified lineage of hominins in Eurasia that interbred with the ancestors of both – but not with the particular group of hominins that evolved into the Neanderthals.

Or, Meyer says, perhaps such mitochondrial DNA was typical of early Neanderthals and Denisovans, and it was only later that Neanderthals acquired different mitochondrial DNA from an African population of “proto-Homo sapiens“.

Journal reference: Nature, DOI: 10.1038/nature17405

Find out more about the oldest human genome dug up in Spain’s pit of bones:

Source: (New Scientist)