Scientists have identified the oldest "nuclear DNA" from a human, revealing that it originated from an early representative of the Neanderthal lineage. The nuclear DNA was retrieved from the ancient "Pit of Bones," known as "Sima de los Huesos" in Spanish, a site in Spain with remains that are around 400,000 years old, although their relationship to Neanderthals and other human relatives has been debated.

Pieces of nuclear DNA represent the main genetic map of an organism and are collectively referred to as the genome. Located in the nuclei of ours cells, genetic sampling and sequencing technologies of these genetic remnants can help us uncover the missing links in our evolutionary lines.

After examination of the specimens, the team revealed that the 28 individuals buried in the 13-meter-deep cave were closely related to Neanderthals, supporting initial reports that pointed in this direction when results pointed to a Denisovan link. 

"Sima de los Huesos is currently the only non-permafrost site that allows us to study DNA sequences from the Middle Pleistocene, the time period preceding 125,000 years ago," said Matthias Meyer, who participated in the research.

The mitochondrial DNA (mDNA) analyses revealed a Denisovan relationship in one individual in the study, supporting the findings from the previous study. This led the scientists to believe that the mDNA observed in later Neanderthals were the results of a migration from Africa, leading to the replacement of the mDNA types in the Pit of Bones people.

The findings shed light on the ancient divergence of modern humans (Homo sapiens) and Neanderthals from a common ancestor.

"There has been continuing debate about how deep in time the Neanderthal-sapiens split was, with estimates ranging from about 800,000 years to 300,000 years," said Chris Stringer from London's Natural History Museum, who did not participate in the current study. "I have recently favored a split time of about 400,000, and have argued for many years that the widespread species H. heidelbergensis at about 500,000 was probably their last common ancestor."

"These results provide important anchor points in the timeline of human evolution," concluded Svante Pääbo, co-author of the study. "They are consistent with a rather early divergence of 550,000 to 750,000 years ago of the modern human lineage from archaic humans".

The findings were published in the March 14 issue of Nature.