Homo naledi, an early human species found in South Africa. Photo: National Geographic

New analysis of DNA from a collection of bones found in Spain – the oldest human DNA of its kind studied – could help write the history of early humankind.

The research, published on Monday in the journal Nature, focuses on hominins from the Sima de los Huesos ("pit of bones") site in Spain. They were found back in the '90s, but scientists haven't settled on their genetic origin. Now, by managing to extract some truly ancient nuclear DNA, researchers believe they've shown that the 430,000-year-old bones belonged to Neanderthal ancestors, or at least close relatives.

That's not an entirely new idea. A recent study pointed out striking physiological similarities between these Sima hominins and Neanderthals, our close cousins. Neanderthals emerged only about 40,000 years ago, but researchers suggested the 28 hominins found in the pit of bones might belong to the species Homo heidelbergensis, which lived in the right place and time and was thought to be an ancestor of Neanderthals.

Then the plot thickened: DNA analysis published in 2013 suggested the Sima hominins were more closely related to Denisovans – a less-understood lineage of human.

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But this isn't just another he-said-she-said DNA tale. The 2013 study analysed mitochondrial DNA (mtDNA), which is easier to recover from ancient bones. But it doesn't tell the whole story. It's a small molecule of DNA found in the mitochondria of each cell – the cell's power plant. When an egg and a sperm meet, only the egg cell holds on to its mtDNA – so while a person's nuclear DNA will paint a unique portrait of their genetic lineage, mtDNA extracted from the same individual will show an identical copy made straight down the maternal line, save for any mutations that have been picked up along the way.

While the new study confirms that the Sima hominins do have mtDNA that loops them in with the Denisovans, it also shows the nuclear DNA is consistent with that you'd find in a Neanderthal ancestor.

The results suggest Neanderthals and Denisovans diverged a good 400,000 years back, giving the Sima lineage time to pick up a new set of mtDNA as the generations went on – one that would match Neanderthals as we know them.

And based on the DNA analysis, the researchers believe Neanderthals and Homo sapiens may have split from their last common ancestor more than 600,000 years ago, which is a few hundred thousand years earlier than previously assumed.

"Research must now refocus on fossils from 400,000 to 800,000 years ago to determine which ones might actually lie on the respective ancestral lineages of Neanderthals, Denisovans and modern humans," Chris Stringer of the Natural History Museum in London, who wasn't involved in the study, told New Scientist.

In other words, the new study poses more questions than it answers. Theories on the early days and interwoven family ties of humanity – already poorly understood – might be in need of a major overhaul. But while these proto-Neanderthals may have scientists scratching their heads for some time, the analysis of their long-sought DNA shows how far scientific techniques have come in just a few decades.