It was only a matter of time. In the 1990s scientists started extracting, sequencing and analyzing mitochondrial DNA from Neandertal fossils. In the 2000s they made major advances in obtaining and analyzing ancient nuclear DNA, which is much trickier than mtDNA. In just the past year, paleogeneticists pushed the envelope in sequencing truly ancient DNA, announcing hominin and horse genomes from 400 and 700 thousand years ago, respectively. As I mentioned a few months ago, the burgeoning field of paleogenomics is revealing things about human evolution that could hardly be dreamt of only a few decades ago.

But world of DNA is so much more than just ceaseless sequences of four letters, and the field of ‘epigenetics’ has emerged to investigate the complex way that chemical alterations to DNA structure (not sequence) affect gene expression. Melding epigenetics & paleogenomics, David Gokhmen and colleagues report in Science, “Reconstructing the DNA methylation maps of the Neandertal and the Denisovan.” For a review of what DNA methylation is and does, check out this Scitable overview. In short, DNA methylation is part of the reason why not all of your genes in your genome are expressed at all times throughout your body, even though all of your genes are physically present in all of the cells of your body. Methylation plays an important role in turning genes on or off during development. It’s nuts. Now, the structure of DNA breaks down over time after an animal dies, obscuring original methylation patterns. But the decompositoin process is becoming better understood, including patterns at methylated vs. unmethylated sites. As Gokhmen et al. write, these patterns “may serve as a proxy for the levels of methylation in ancient DNA.”

This brilliant insight allowed Gokhmen and colleagues to identify some 2000 genomic regions in bone cells that differed in methylation between a living human, a Neandertal and a Denisovan (2000 less than 1% of all regions). One such region was the HOXD cluster, which is known to be involved in embryonic limb development. Neandertals and Denisovans were more methylated than humans at the HOXD9 and HOXD10 loci. Whether and how these epigenetic differences might be responsible for anatomical differences between these populations is not at all clear yet. But Neandertals are known to differ from humans in some aspects of arm and leg anatomy – authors point out that Neandertals generally have larger and more robust joints but shorter limbs. They state, “together, these findings suggest that the HOXD cluster might have played a key role in the recent evolution of human limbs.”

Importantly, “Denisovans” are only known from 2 teeth and part of a finger bone, no other limb fossils are known (or at least published) for this ancient population. This leads us to a prediction – if the similarly hypermethylated HOXD sites in Denisova and Neandertals are functionally important, then Denisovan limb fossils, if ever found, should be more like Neandertals than like humans. If this prediction is borne out, this would provide evidence of specifically how HOXD9-10 affect limb development, and how HOXD epigenetic regulation has changed in human evolution. This hypothesis can be tested, but only with the discovery of the right fossils (i.e., genetically attributable to Denisovans). Well, the functional importance of hyper/hypomethylation at these sites could probably also be assessed with transgenic mouse experiments…

There is truly remarkable work being done in paleogenomics – and now paleoepigenomics – which will probably begin to form the basis of some exciting new human evo-devo research.