The oldest human DNA sequences

The oldest human DNA sequences

The first analysis of nuclear DNA from Sima de los Huesos hominins, conducted by researchers of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, provides evidence of their relationship to Neanderthals.

The Sima de los Huesos, or the Pit of Bones, is a cave site in the Sierra de Atapuerca of northern Spain, dated to around 430,000 years ago. It preserves a large collection of fossils attributed to an enigmatic species — the Sima de los Huesos hominin. The site has been excavated continuously since 1984. After thirty years, archaeologists have recovered nearly 7,000 fossils corresponding to all skeletal regions of at least 28 individuals.

Previous analyses of the hominins in 2013 showed that their mitochondrial DNA was distantly related to Denisovans, extinct relatives of  Neanderthals in Asia. MtDNA is found in the mitochondria, energy-producing structures which are located outside the cell nucleus, and is therefore only maternally inherited. It's also more abundant in cells than is nuclear DNA.

The relation to Denisovans was unexpected, since the skulls found at the Sima de los Huesos site have the beginnings of a prominent brow ridge as well as other traits typical of Neanderthals. Until now it has been unclear how the 400,000-year-old individuals were related to Neanderthals and Denisovans who lived until about 40,000 years ago. Dr. Matthias Meyer and his team have recently succeeded in sequencing nuclear DNA from the fossils, a challenging task as the extremely old DNA is degraded to very short fragments. Nuclear DNA can tell a different story than mtDNA and the results now show that the Sima de los Huesos hominins were indeed early Neanderthals.


As with previous findings, the research also confirmed that the mitochondrial DNA of the Spanish hominins is more closely related to Denisovans than to Neanderthals. Who they were remains a mystery, and finding out the answer to this query has the potential to provide a huge insight into human evolution and how early human ancestors interacted with their extinct relatives. It is possible that there are many extinct human populations that scientists have yet to discover.

"Sima de los Huesos is currently the only non-permafrost site that allow us to study DNA sequences from the Middle Pleistocene, the time period preceding 125,000 years ago," says Matthias Meyer. "The recovery of a small part of the nuclear genome from the Sima de los Huesos hominins is not just the result of our continuous efforts in pushing for more sensitive sample isolation and genome sequencing technologies," Meyer adds. "This work would have been much more difficult without the special care that was taken during excavation."

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Juan-Luis Arsuaga of the Universidad Complutense de Madrid, who led the excavations at Sima de los Huesos for three decades, said: "We have hoped for many years that advances in molecular analysis techniques would one day aid our investigation of this unique assembly of fossils. We have thus removed some of the specimens with clean instruments and left them embedded in clay to minimise alterations of the material that might take place after excavation."

The nuclear DNA sequences recovered from two specimens secured in this way show that they belong to the Neanderthal evolutionary lineage and are more closely related to Neanderthals than to Denisovans. This finding indicates that the population divergence between Denisovans and Neanderthals had already occurred by 430,000 years ago when the Sima de los Huesos hominins lived. According to Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology "these results provide important anchor points in the timeline of human evolution. They are consistent with a rather early divergence of 550,000 to 750,000 years ago of the modern human lineage from archaic humans."

Based on previously discovered ancient DNA and fossil evidence, scientists generally agreed that humans’ direct ancestors shared a common ancestor with Neanderthals (Homo neanderthalensis) and Denisovans (Homo denisova) that lived in Africa about half a million years ago. Homo sapiens evolved in Africa about 200,000 years ago and expanded from Africa into Asia and Europe. They then interbred not only with Neanderthals, but with Denisovans, too. Later, both the Denisovans and Neanderthals became extinct.

More information: Human origins: Not that simple

Researchers conducting the first-ever genomic study of indigenous Australians have indeed found evidence of a single 'out of Africa' migration for modern humans about 72,000 years ago. The study confirmed a long-standing claim that indigenous Australians and Papuans are descended directly from the first people to inhabit the continent some 50,000 years ago, which makes the Aboriginal civilization the oldest on the planet.

Intriguingly, the scientists uncovered genetic evidence that points to the existence of an unknown human species, likely a distant relative of Denisovans, that interbred with anatomically modern humans as they migrated through Africa. There is evidence that the highest presence of Denisovan admixture is in Oceanian populations (see image on top), followed by many Southeast Asian populations.

Researchers should now be looking for a population, dating from 1.2 million to 800,000 years ago, that was discovered in northern Spain in 1994. If such specimens, known as Homo antecessor, can be found in Africa or the Middle East, they are the strongest candidate for the common ancestor.




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