Oldest Hominin DNA Ever Sequenced Challenges Tale of Human Origins

A 400,000-year-old DNA sample taken from a cave in northern Spain muddies science's ideas on the origins of humanity, introducing an entirely new set of problems and questions.

Unearthed at the site known as Sima de los Huesos, the DNA resembles that of an extinct branch of the human family tree known as the Denisovans.

Prior to the study published in the journal Nature, the record for the oldest human DNA ever obtained stretched back just 100,000 years.

According to co-author Matthias Meyer, a geneticist at the Max Planck Institute for Evolutionary Anthropology, the discovery "points to a complex pattern of evolution in the origins of [Neanderthals] and modern humans."

Sima de los Huesos represents the largest collection of hominin fossils dating to the Middle Pleistocene, a period stretching between 781,000-125,000 years ago. In all, the site has turned up at least 28 skeletons.

Previously, the fossils were classified as Homo heidelbergensis, an early human species that lived from roughly 700,000-200,000 years ago and the first early human species to move into colder climates and construct shelters.

Studying the skeleton's DNA was impossible, however, until Meyer and his team succeeded in developing the novel techniques that allowed them to both retrieve and sequence the highly degraded DNA.

Using bone powder from a skeleton's thigh, the researchers extracted its DNA and sequenced the genome of the mitochondria (mtDNA), comparing it to Neanderthals, Denisovans, modern humans and apes.

The results were baffling: Despite the skeleton's apparent Neanderthal-like traits, its DNA revealed it shared a common ancestor with the Denisovans.

The Denisovans were only identified in 2010 when the DNA from a 30,000-year-old finger bone Meyer and his colleagues found in a cave in southern Siberia failed to match any previously known group.

Since the discovery, researchers have uncovered genetic evidence of the group's hybridization with modern human populations among indigenous groups in places such as Australia and New Guinea. Strangely, Denisovan DNA is largely absent in mainland Asia where the fossil was discovered.

An article published in the journal Science in October argues that one explanation for this is the possibility that the mysterious human relatives managed to cross Wallace's Line, an invisible boundary that marks a division in European and Asian mammals to the west, and species of Australian descent to the east. According to Alan Cooper of the University of Adelaide and Christ Stringer of the Natural History Museum in the UK, the human relatives may have then interbred with modern humans moving through the area on their way to Australia and New Guinea.

What this theory does not explain, however, is how Denisovan DNA made its way to the Iberian peninsula, located some 4,000 miles from the site where the finger bone was uncovered and roughly 10,000 miles from Australia.

"It is very odd to find the same mtDNA thousands of miles and hundreds of thousands of years apart," Ed Green, a researcher who participated in the study that first identified Denisovans, told Nature World News in an email. "It demands an explanation and there isn't any clean model that provides it."

According to Beth Shapiro, an associate professor at the University of California, Santa Cruz's Department of Ecology & Evolutionary Biology, one of the most surprising aspects of the new study is just how different the sequence is from any of those belonging to a Neanderthal.

"What if this sequence is not a [Neanderthal] at all, but instead something even older, like Homo erectus?" she said, noting the Homo erectus was geographically far more spread out than Neanderthals, and existed for much longer -- both of which would have contributed to a high degree of genetic diversity.

"If the Denisova mitochondrial genome also came from H. erectus (perhaps via hybridization with an Asian population of erectus), this might explain the close relationship between the Denisova mitochondrial genome, and the [Sima hominin] mitochondrial genome," she said.

Though not an expert on skeletal morphology, Meyer explained in email to Nature World News that, from what he can tell, "it would be a very big surprise if the Sima hominins turned out to be late Homo erectus."

Instead, the researcher believes a more likely explanation may be that the skeletons represent early Neanderthals that may have inherited a small portion of DNA -- including the mitochondrial genome -- from Homo erectus.

"But all of this is speculation," he added.

Regardless of the genome's source, the study marks a major turning point in the field of ancient DNA, Shapiro said, "as it means that there are likely to be many more samples out there that contain recoverable amounts of DNA -- samples that we otherwise might have glossed over or given up on, thinking they were too old, or from a climate that was too warm, for DNA to be preserved."

Going forward, Meyer says he looks forward a follow-up outlining the nuclear genome.

"It is tricky, but I am confident we will get something out."