<link rel="stylesheet" href="//fonts.googleapis.com/css?family=Roboto%3A300%2C400%2C500%2C700%7CRoboto+Slab%3A400%2C700">Oldest hominin DNA pinpoints Neanderthal ancestor - Filthy Monkey Men

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.

One of the fossils from Sima de los Huesos. DNA indicates it's a Neanderthal ancestor

One of the fossils from Sima de los Huesos. DNA indicates it’s a Neanderthal ancestor

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.

The new family tree

The new family tree

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.

The new family tree of humans, Neanderthals and Denisovanns published in Nature

The family tree of humans, Neanderthals and Denisovanns published produced by the mtDNA

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.

A family tree of Neanderthal fossils, produced from Neanderthal mtDNA

A family tree of Neanderthal fossils, produced from Neanderthal mtDNA

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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Wyrd Smythe · 15th March 2016 at 7:26 pm

Their DNA is different because they’re invaders! 🙂

As I understand it, the prevalent theory about the origin of mitochondria is that they were a separate single-cell life form that become symbionts with the single-cell life form that eventually led to the multi-cell animal kingdom. The belief is that, without the energy factory provided by mitochondria, multi-cell life wouldn’t be possible.

Just one of the many interesting chance events (like our Moon) that enabled us to occur!

    Charles A. Bishop · 15th March 2016 at 9:52 pm

    I’ve always found conclusions drawn from mtDNA suspect. For one thing, dates are based on the assumption that mutation rates are constant, and this may not be true. My wife and I were at Atapuerca in September 2015 and one of the researchers said that these fossils were about to be classified as Neanderthal ancestors based on new DNA findings. Now that this evidence is out, the reclassification makes much better sense. But it raises another question. If later Neanderthals and Moderns could produce fertile offspring, it means they weren’t separate species, only separate races. If one accepts this, then what about the 400,000 year old Atapuerca fossils? If like Neanderthals one were to classify them as Archaic Homo sapiens, it would mean that the ancestors of our species are much older than 200,000 years, the date given for our origin in Africa, and also based on mtDNA. Could it be that our species is much older than current models suggest?

      Adam Benton · 17th March 2016 at 2:48 pm

      Trying to define species is a difficult concept to begin with. Trying to do it in fossils is even harder. That’s why so many palaeoanthropologists go for something like the grade system.

        Charles A. Bishop · 17th March 2016 at 3:44 pm

        That is true. But paleo anthropologists often assign new species names to fossils on the basis of very little evidence. These names then remain in use for years and become the source of debates over origins, all mostly in the absence of much new that would confirm their identity or phylogenetic place. I used to worry more about this until an anthropologist friend told me not to be too concerned. Selection will ultimately eliminate bad ideas in the same manner that natural selection operates in the natural world.

        Adam Benton · 17th March 2016 at 3:49 pm

        Often the names become a shorthand for a specific set of fossils; rather than an ironclad concept of species. That’s why there’s so many alternate interpretations.

        Charles A. Bishop · 17th March 2016 at 4:26 pm

        You are right. It is necessary and important to place new finds in meaningful categories. I did not mean to imply that scholars shouldn’t do that. It is the ever increasing number of new species names that bothers me. Discoverers often look for traits that distinguish their fossil from others to show that they have discovered something new, rather than seeing common features that suggest that a fossil belongs to an established taxa. To identify a new species suggests that it has become biologically isolated from other species, and this is very difficult to prove in the absence of good DNA evidence. Such isolation where it occurs can be due either to geographical factors (distance, mountains, rivers, etc.) or to behavioral differences (diet, mating habits, etc.).

Belac · 16th March 2016 at 11:19 pm

While on the subject of neanderthals, what do you think of the Divje Babe flute that some claim is nothing more than a chewed bone?

    Adam Benton · 16th March 2016 at 11:37 pm

    It’s hard to draw conclusions based off a single, contentious example. Until more is discovered I don’t think we can make a prenouncement, one way or the other. However,the paucity of evidence (and the fact that what evidence there is seems so debatable) suggests that it is unlikely; if I had to put my money on it.

      Belac · 17th March 2016 at 1:59 am

      Unlikely that it’s a flute or chewed bone?

        Adam Benton · 17th March 2016 at 2:47 pm

        As I said I’m rather agnostic towards the whole thing, but leaning towards not a flute.

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