Oldest known human DNA found

Researchers investigating the Sima de los Huesos (‘pit of bones’), an underground cave in the Sierra de Atapuerca in northern Spain, have extracted and analysed mitochondrial DNA (mtDNA) from the femur of a 400,000-year-old hominin, an ancient human. DNA this old had until recently been retrieved only from the permafrost.

The team from Germany’s Max Planck Institute for Evolutionary Anthropology, led by Matthias Meyer, have developed a new technique for retrieving and sequencing highly degraded ancient DNA. They joined forces with Spanish palaeontologist Juan-Luis Arsuaga, leader of the group which has excavated at least 28 of the hominin skeletons over the past 20 years.

The thigh bone of a 400,000-year-old hominin from Sima de los Huesos, Spain, was excavated by Arsuaga and his team. Credit: Javier Trueba, Madrid Scientific Films.

The researchers sampled 2 g of bone powder from a hominin thigh bone. They extracted its DNA and sequenced the genome of the mitochondrial DNA, a small part of the genome that is passed down along the maternal line and occurs in many copies per cell. The researchers then compared this ancient mtDNA with Neanderthals, Denisovans, present-day humans and apes.

From the missing mutations in the old DNA sequences, the researchers calculated that the hominin lived about 400,000 years ago and shared a common ancestor with the Denisovans, an extinct group from Asia related to the Neanderthals, about 700,000 years ago. Meyer said this was “unexpected since its skeletal remains carry Neanderthal-derived features”.

Skeleton of a Homo heidelbergensis from Sima de los Huesos, a unique cave site in Northern Spain. Credit: Javier Trueba, Madrid Scientific Films.

Considering their age and their features, the Sima hominins were likely related to the population ancestral to both Neanderthals and Denisovans. Another possibility is that gene flow from yet another group of hominins brought the Denisova-like mtDNA into the Sima hominins or their ancestors.

As studies of ancient hominin DNA have previously been limited to the Late Pleistocene period, the new research is helping to expand our understanding of the genetics of human evolution to at least 200,000 years back in time to the Middle Pleistocene. Juan-Luis Arsuaga, director of the Center for Research on Human Evolution and Behaviour in Madrid, said the researchers’ “unexpected result points to a complex pattern of evolution in the origin of Neanderthals and modern humans”.

The Sima de los Huesos hominins lived approximately 400,000 years ago during the Middle Pleistocene. Credit: Javier Trueba, Madrid Scientific Films.

Arsuaga added that he hopes “more research will help clarify the genetic relationships of the hominins from Sima de los Huesos to Neanderthals and Denisovans”. The researchers are currently pursuing this goal by focusing on retrieving DNA from more individuals from the site and on retrieving nuclear DNA sequences. In future they may go even further back, with the institute’s director, Svante Pääbo, saying their results open “prospects to study the genes of the ancestors of Neanderthals and Denisovans”.

The research has been published in the journal Nature.

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