A skeleton of a Homo heidelbergensis from Sima de los Huesos, a unique cave site in northern Spain.

Scientists have pieced together the oldest human DNA ever recovered after extracting it from the thigh bone of an individual who died 400,000 years ago.

The research throws up a new riddle in the story of human evolution, because it shows that the ancient Spaniard was related to a mysterious group of early humans from Siberia.

The DNA belonged to a type of human that long pre-dated our own, whose fossils have been found in large numbers at La Sima de los Huesos – the “bone pit” – at Atapuerca in northern Spain.

The ancient cave site has yielded at least 28 skeletons.

Although the species has been classified as Homo heidelbergensis, it also bears traits typical of Neanderthals.

Scientists were able to sequence almost the complete genetic code, or genome, from the creature’s mitochondria, tiny power houses in cells that generate energy and have their own distinct DNA.

Mitochondrial DNA (mtDNA) is passed down only from mothers and can be used to track lineages.

The study revealed a surprise.

Instead of the expected link with the Neanderthals, researchers found genetic similarities with the Denisovans, an enigmatic Eastern Eurasian group from Siberia.

Around 40,000 years ago, Denisovans co-existed alongside Neanderthals and early modern humans, possibly even engaging in interbreeding.

The findings, from a team led by Matthias Meyer at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, appear in the latest edition of the journal Nature.

Commenting on the discovery, British expert Chris Stringer, from London’s Natural History Museum, said: “This unusual finding could be due to at least two different scenarios, both relating to the maternal inheritance of mtDNA and the ease with which it can be lost in a lineage.

“One scenario is that the mtDNA is derived from an ancient population, ancestral to both the Sima fossil population and Denisovans, which has since been lost in lineages in Africa and Western Eurasia.

“A second is that ancestral species interbred in Eurasia, passing over distinctive mtDNA which may have been lost later in the Neanderthal lineage, yet retained in the Denisovan branch.

“Either way, this new finding can help us start to disentangle the relationships of the various human groups known from the last 600,000 years.

“If more mtDNA can be recovered from the Sima ‘population’ of fossils, it may demonstrate how these individuals were related to each other, and how varied their population was.

“Additionally, the recovery of such ancient DNA means that other human fossils from this time period can now be considered for DNA analysis.”

Scientists sampled two grams of bone powder from the fossil.

After sequencing, the DNA was compared with samples from Neanderthals, Denisovans, present-day humans and apes.

The team found evidence that the Spanish human may have shared a 700,000-year-old common ancestor with the Denisovans.

“The fact that the mtDNA of the Sima de los Huesos hominin shares a common ancestor with Denisovan rather than Neanderthal mtDNA is unexpected because its skeletal remains carry Neanderthal-derived features,” Dr Meyer said.

Professor Svante Paabo, director of the Max Planck Institute for Evolutionary Anthropology, said: “Our results show that we can now study DNA from human ancestors that are hundreds of thousands of years old.

“This opens prospects to study the genes of the ancestors of Neandertals and Denisovans. It is tremendously exciting.”