Today, researchers announced they have obtained DNA sequences from the earliest human skeletal remains yet, a Spanish fossil from a site known as Sima de los Huesos, or pit of bones. Although the study is undoubtedly a triumph of technology and technique, the results themselves have researchers scratching their heads, since the most closely related DNA has only been found on the opposite side of Eurasia.

The sequencing of DNA from fossil humans has already shaken up our view of the past. The completion of the genome of Neanderthals indicated that they had interbred with modern humans enough to introduce a small bit of their DNA into genomes of any population that left Africa. But sequencing other bones revealed that there was a second group of pre-modern humans in Siberia that also interbred with our ancestors. This group, called the Denisovans, also contributed DNA to our ancestors, but it only appears in groups that migrated into the Pacific.

To confuse matters further, although we have many Neanderthal skeletal remains and a good idea of how they differed from modern humans, so far, all we have of the Denisovans is a couple of teeth. These tell us that their teeth were very large, but little else. Still, the only real question seemed to be how the Denisovans, whom we only know from Siberian remains, ended up getting their DNA carried out into the Pacific.

With the DNA from Sima de los Huesos, there are quite a few more questions now. The cave has extensive remains of both animals and humans that date from over 300,000 years ago. At least 28 individuals have been identified among the remains, and they've been classified as Homo heidelbergensis, a poorly defined grouping that roughly encompasses any pre-modern Eurasian humans who aren't Neanderthals. Nevertheless, there are a few features on the skeletons that suggest they might have been ancestral to Neanderthals.

Getting DNA out of bones that old isn't easy, but Svante Pääbo's group at the Max Planck Institute for Evolutionary Anthropology has been honing its technique on other ancient remains. And in this case, they confirmed they could extract DNA from the samples at the site by obtaining sequences from a cave bear skeleton found there.

That turned out to be a relatively easy task, primarily because they did not have any bears working as technicians in the lab. In contrast, their attempts to amplify ancient human DNA from the bones kept ending up with contamination by modern human DNA. By careful sampling, they determined that the vast majority of ancient DNA fragments were less than 45 base pairs long and had a high frequency of a specific type of damage. (Near the ends, over half of the C residues had been converted to Ts.) So, they set a computer to filter out anything that was over 45 bases and wasn't badly damaged.

With what was left, they managed to reconstruct most of the mitochondrial genome of the individual found in the cave. Then, they were able to compare it to Denisovans, Neanderthals, and modern human populations.

The results are, to say the least, confusing. The Sima de los Huesos individual ended up being most closely related to Denisovans, at least on the DNA level. In fact, it was close enough that it ended up splitting the Neanderthal and Denisovans, which had been considered sister groups based on their full nuclear genomes. And, as noted above, the bones from Sima de los Huesos seemed to have incipient Neanderthal features.

It's also confusing because the DNA provided an independent estimate of the fossil's age, one that placed it at 400,000 years old. That date happens to be before most estimates of when Neanderthals and Denisovans had split into distinct lineages.

The authors consider a number of explanations. One is that the Sima de los Huesos individual is related to the ancestors of Denisovans, but they don't like that idea, since it's hard to see how the two groups could have split and developed distinctive DNA while sharing Western Europe. Another option is that they are related to the common ancestor of both Neanderthals and Denisovans. That seems plausible, but would require the ancestral population to contain two separate mitochondrial DNA lineages, one that ended up in Denisovans, the other in Neanderthals.

Then there are the interbreeding options. Either the Sima de los Huesos population interbred with the Denisovans and provided them with mitochondrial DNA, or some other ancestral population interbred with both of these groups. Given the amount of interbreeding that was going on back then, it's hard to rule these options out.

The only way to get to the bottom of this, Pääbo suggests, is to get the full nuclear genome from these bones. And that is almost certainly an indication that he's currently attempting to do just that.

Nature, 2013. DOI: 10.1038/nature12788 (About DOIs).