Biology Magazine

Oldest Hominin DNA Pinpoints Neanderthal Ancestor

Posted on the 15 March 2016 by Reprieve @EvoAnth

Atapuerca is a Spanish site that sheds a lot of light on human evolution. It contains hundreds of fossils, plus early evidence of religion and cannibalism. Now it's also the source of the oldest hominin DNA ever found.

This DNA is particularly important because it reveals just who the Atapuerca fossils belong to. Scientists had debated whether they were the ancestors of Neanderthals or actually another species.

Previously discovered mitochondrial DNA (mtDNA) from the Atapuerca suggested neither. It indicated that these individuals were actually related to the Denisovans. Which confused everyone, especially me.

Now scientists have retrieved regular DNA from these fossils and it's helping clear up this confusion. And it pinpoints just where these enigmatic hominins fit into the human family tree.

DNA reveals relationship to Neanderthals

Atapuerca is a Spanish site containing dozens of caves. Each of which provides a snapshot into a different part of our (pre)history.

By far the most impressive of these is Sima de los Huesos. Literally translated as "pit of bones", this cave contains dozens of fossils belonging to the human family (aka hominins). Radiometric dating puts the cave at around 400,000 years old; the period Neanderthals began to evolve.

Thus these fossils could represent the ancestors of the Neanderthals, shedding light on how they evolved from the common ancestor that also led to us.

Or they could not. Where these fossils fit in the family tree has long been debated by scientists. On the one hand they do share a lot of similarities with Neanderthals. Some of these features even seem to be not quite as pronounced as they are in the Neanderthals, implying they are the more basal species. This has led many to conclude that they are the ancestors of Neanderthals, but there are some who maintain they aren't. They point to the fact these fossils have several unique characteristics not seen in the Neanderthals as evidence for this position.

Finding DNA would help solve this debate, but the sheer age of the fossils made this seem impossible. You'd be lucky to get DNA more than 50,000 years old; let alone 400,000 years old.

But now a team of researchers have done the seemingly impossible and extracted nuclear DNA from a femur and tooth. This DNA shows marked similarity to later Neanderthals, confirming that they're either their ancestors or at least very closely related to the ancestors.

They also share relatively few similarities with the other hominins living alongside the Neanderthals: humans and Denisovans. Thus the Sima de los Huesos fossils definitely lived after the ancestors of those two groups branched off the Neanderthal group. A split that must have occurred earlier than 400,000 years ago.

Previous mtDNA confuses and surprises (conprises?)

The new DNA data from Sima de los Huesos is particularly interesting because it flat-0ut contradicts previous mitochondrial DNA (mtDNA) data from the same site.

Mitochondrial DNA is DNA from the mitochondria (creative naming by biologists continues to disappoint). Mitochondria are small organelles within your cells that produce much of the energy they need. As such this DNA isn't inherited in the same way as nuclear DNA. Instead of sex and genomes being mixed together, you get whole mitochondria from your mother.

A few years ago this same team was able to recover the oldest ever mtDNA from the site. This revealed the Smia de los Huesos fossils were actually more closely related to the Denisovans than the Neanderthals (although not a direct ancestor of either). This took everyone by surprise because all the anatomical evidence suggested that they should actually be more closely related to the Neanderthals (or at the very least, neither).

In fact, not only did this contradict anatomical data, but geographical information too. Denisovans got their name from the fact they were found in Denisova Cave. Which is on the other side of Europe. No known Denisovan fossils exist between Atapuerca and Denisova. Yet this mtDNA suggests they managed to travel across the entire continent without leaving a shred of evidence behind.

This new nuclear DNA wipes away all this confusion. It reveals a human family tree that makes a lot more sense and is better supported by the evidence.

Which raises the question: why was the mtDNA so odd? The researchers behind these discoveries present two possible options:

  1. The Sima de los Huesos fossils had a lot of differnt mtDNA lineages, including some old ones that may date back to when Denisovans and Neanderthals were the same species. The first study may just have discovered one of these quirky lineages.
  2. The mtDNA recovered from Neanderthals is much newer than Sima de los Huesos. Thus it could have emerged recently, inflating the genetic distance between the two groups. Earlier, most Neanderthals would still have had the "Denisovan" mtDNA.

A troubling trend for mtDNA

Whilst this discovery helps clear up some confusion about human evolution, it also raises some potential problems. There's a reason mtDNA was the first DNA analysed from the site.

This is because each one of your cells has just one copy of your genome. However, it has a lot of mitochondria and thus a lot of mtDNA. This makes it more likely that at least some of the mtDNA would survive. mtDNA also tends to be a lot shorter than regular DNA, so you need to be less lucky to get a complete copy of it.

So, whilst mtDNA doesn't contain all the information of nuclear DNA it's still a favourite of palaeoanthropologists since you're more likely to find some in fossils. For example, whilst we've only been able to sequence a couple of full Neanderthal genomes we've got almost a dozen copies of their mtDNA.

A dozen copies of potentially incorrect data.

Now, to be fair these issues have been known about for some time. For example, the earliest DNA got out of Neanderthals was mtDNA. This said there was no interbreeding with modern humans, which was later found to be false. Thus scientists are used to treating mtDNA with a grain of salt. In fact, I even said as much at the end of the last article on DNA from Sima de los Huseso.

Nevertheless, it was still thought to provide a somewhat reliable picture of the human family tree. But the fact that the two sets of data are so contradictory here suggests that this might not be the case. Outside of specific questions about the history of mtDNA, this sort of information could be worse than useless when it comes to investigating our ancestors. It could be send us barking up the wrong (family) tree.


The oldest DNA ever recovered from a hominin reveals that enigmatic fossils from Atapuerca were actually the ancestors (or closely related to the ancestors) of Neanderthals.


Krings, M., Stone, A., Schmitz, R.W., Krainitzki, H., Stoneking, M. and Pääbo, S., 1997. Neandertal DNA sequences and the origin of modern humans. cell, 90(1), pp.19-30.

Meyer, M., Fu, Q., Aximu-Petri, A., Glocke, I., Nickel, B., Arsuaga, J. L., ... & Pääbo, S. (2013). A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature.

Meyer, M., Arsuaga, J., de Filippo, C., Nagel, S., Aximu-Petri, A., Nickel, B., Martínez, I., Gracia, A., de Castro, J., Carbonell, E., Viola, B., Kelso, J., Prüfer, K. and Pääbo, S. (2016). Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins. Nature.

Prufer, K., Racimo, F., Patterson, N., Jay, F., Sankararaman, S., Sawyer, S., Heinze, A., Renaud, G., Sudmant, P.H., de Filippo, C. and Li, H., 2014. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature, 505(7481), pp.43-49.

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