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The Pit of Bones has yielded one of the richest assemblages of human bones from this era
The discovery of DNA in a 400,000-year-old human thigh bone will open up a new frontier in the study of our ancestors. That’s the verdict cast by human evolution experts on an analysis in Nature journal of the oldest human genetic material ever sequenced.
The femur comes from the famed “Pit of Bones” site in Spain, which gave up the remains of at least 28 ancient people. But the results are perplexing, raising more questions than answers about our increasingly complex family tree.
The early human remains from the cave site near the northern Spanish city of Burgos have been painstakingly excavated and pieced together over the course of more than two decades. It has yielded one of the richest assemblages of human bones from this stage of human evolution, in a time called the Middle Pleistocene.
The fossils carry many traits typical of Neanderthals, and either belong to an ancestral species known as Homo heidelbergensis – or, as the British palaeoanthropologist Chris Stringer suggests – are early representatives of the Neanderthal lineage.
But the recent pace of progress in sequencing technology has astonished many scientists: “Years ago, geneticists said they wouldn’t be able to find DNA that was older than 60,000 years old,” said co-author Jose Bermudez de Castro, and a member of the team that excavated the Pit of Bones fossils. “Of course, that wasn’t true. The techniques have advanced hugely.”
The scientists were able to stitch together a near-complete sequence of mitochondrial DNA, or mtDNA (the genetic material contained in the tiny “batteries” that power our cells) from the ancient femur. But comparisons of the genetic code with that from other humans, ancient and modern, yielded a surprise.
Rather than showing a relationship between the Spanish specimens and Neanderthals, which might be expected based their physical features, the mitochondrial DNA was most similar to that found in 40,000 year-old material unearthed thousands of kilometres away at Denisova Cave in Siberia.
The Denisovans were a sister group to the Neanderthals, with distinct genetic characteristics. Identified only by DNA extracted from a tiny finger bone and tooth, they are, as some researchers have remarked, “a genome in search of a fossil” because there are no substantial remains representative of this group.
By using missing mutations in the old DNA sequences, the researchers calculated that the Pit of Bones individual shared a common ancestor with the Denisovans about 700,000 years ago.
Prof Chris Stringer, from London’s Natural History Museum, told BBC News: “We need all the data we can get to build the whole story of human evolution. We can’t just build it from stone tools, we can’t just build it from the fossils. Having the DNA gives us a whole new way of looking at it.”
However, he points out, mtDNA is a small and unusual component of our genetic blueprint, from which only limited conclusions can be drawn. For example, no sign of the interbreeding we now know took place between Neanderthals and modern humans remains in the mtDNA of modern people.
To get the full picture, scientists had to sequence nuclear DNA (that kept in the nuclei of cells) from Neanderthals and compare it with that in present-day populations. Likewise, the true relationships between the Pit people and other ancient populations may only be known if and when nuclear DNA is available.
This will be a challenge given the age of the Spanish fossils, but their good state of preservation – largely a product of the fairly constant temperature inside the cave – gives hope.
“That is our next big thing here, to sequence at least part of the nuclear genome from the individual in the Sima de los Huesos,” Svante Paabo told BBC News.