Remarkable ancient DNA recovery from Sima de los Huesos

This week, Nature published a paper by Meyer et al. looking at the ancient nuclear genome of hominins from Sima de los Huesos in northern Spain.  I heard about this research last fall in a news article about a conference in Europe, and I've been anxious to read the paper, since the results throw an interesting new wrinkle into our understanding of ancient humans.

Sima de los Huesos ('pit of bones') is a fossil site in the Atapuerca Mountains of northern Spain where remains of ancient European hominins have been discovered.  There is much that could be said about the remains (it's a UNESCO World Heritage Site, after all), but I'm most interested in what we call these hominins.  Some have argued that they are Neandertals, but others have claimed that they have traits in common with a group called Homo heidelbergensis.  Originally described in 1908 from a mandible found near Heidelberg, Germany, Homo heidelbergensis was more recently expanded to include the Broken Hill cranium from Zambia along with other specimens from Asia and Europe.  Unfortunately, like many hominin forms, there are precious few specimens of Homo heidelbergensis to ascertain whether it's really distinct from Neanderthals.

Back in 2014, the same research group published a mitochondrial genome from Sima de los Huesos, and it seemed to imply that these bones came from something other than Neandertals.  The mtDNA was most similar to DNA from the Denisovans in Siberia, but here's the tricky part: In hominins, nuclear DNA can tell a different story than the mitochondrial DNA.  We've seen that before in the Denisovans, where their mitochondrial DNA was significantly different from both modern human and Neandertal mtDNA, but their nuclear genome implied that the Denisovans and Neandertals were cousins.  So what would nuclear genomes from Sima hominins tell us?

That's what we found out this week in the new paper by Meyer et al.  The first thing that struck me about their results was how messy the DNA was.  The DNA they recovered was largely microbial contamination (no surprise) and extremely fragmentary (also not that surprising), but their estimate of modern human contamination was as high as 67% for some of the specimens they sequenced.  To try to look at just the original Sima DNA, they looked for sequences that had the telltale signs of deamination, a degradation process that happens to ancient DNA.  When they looked at just the most probable ancient sequences, they still estimated about a 20% contamination rate from modern human DNA.  What's more, they found only about three million nucleotides from the five specimens they examined for DNA.  To put that in perspective, it's a little less than a tenth of one percent of the modern human genome and similarly sparse compared to the Neandertal and Denisovan nuclear genome sequences already available.  So there wasn't much original DNA left in those bones.

Despite these drawbacks, Meyer et al. found that the Sima sequences that are most likely original matched Neandertal sequences more than anything else.  So once again, where the mitochondrial DNA implied that the Sima hominins were something unique and possibly similar to Denisovans, the nuclear genomes identified them as mostly Neandertal.  That's pretty similar to what happened with the Denisovans, where the mitochondrial DNA implied a distant relationship to modern humans and Neandertals, but the nuclear genome showed they were closer to Neandertals than anything else.

What does all this mean?  On the one hand, not much.  It sort of settles what name to put on the hominins from Sima de los Huesos: Neandertal.  If you're interested in that sort of thing (and a lot of you are), then that's good news.  On the other hand, here we have yet another example of something that is basically Neandertal (or a close cousin of Neandertal as with Denisovans) with a very different mitochondrial genome.  I think that's remarkably significant.  In the world of creationism, I have been concerned for some time about how ancient humans like Neandertals and Denisovans fit into the human family tree genetically.  I've argued that it's not an easy fit, and that's not been a very popular opinion.  I take it the preferred tactic is to pooh-pooh the ancient DNA and say it's just contamination.  I find that idea to be untenable for lots of reasons, which leaves me back where I started: How do we fit these funny looking people into our family tree?  The nuclear genomes of Denisovans and Sima hominins suggest that these people might not be that different after all.

With this new nuclear genome sequence from Sima de los Huesos, I think it's about time I started looking more carefully at the genetics of ancient hominins and especially at projected ancestral population sizes.  There's bound to be something really interesting going on there, and there's plenty of DNA to work with.

Meyer et al.  2016.  Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins.  Nature doi:10.1038/nature17405

To read my own take on hominin fossils, don't forget to pick up a copy of What Happened in the Garden.

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