To some people ancient history is anything prior to Facebook, for others, it might mean pre-iPod, but this new study uses DNA methylation to look WAY back in time and analyze the beginnings of human evolution (And yes, that’s before the internet was invented).

Using epigenomics to look back into pre-historic times has taught us much about our present, like DNA methylation drives evolutionary differences between men and monkey or how we can exploit evolutionary conservation to detect functional introns. Now an ambitious team lead by Liran Carmel at The Hebrew University of Jerusalem have devised a clever technique to assess ancient hominid methylation patterns in our Neanderthal and Denisovan ‘brethren’.

The researchers used the sands of time as a proxy for ancient DNA methylation. Over centuries cytosine will chemically degrade into different products, like thyamine (C→T) or uracil (C→U), depending on if it was methylated or not (sort of like bisulfite conversion) and these conversion ratios can be determined across the multiple reads from NGS. Here’s what their investigation dug up:

Using this clever hack, the team found that the C→T ratio in archaic humans is highly correlated with measured methylation in modern man.

Taking advantage of these DNA ‘fossils’ the team was able to learn about the differences between modern humans and their Neanderthal and Denisovan relatives.

They found ~2000 DMRs, including substantial differences in the HOXD cluster, which sheds light on the anatomical differences between ancient and modern humans.

The team also noticed the DMRs were significantly enriched in some regions associated with modern disease.

When it comes down to it the study provides new epigenomic insights into our evolution from our closest ancestors, while also opening up a world of possibility for the study of ancient DNA methylation and the evolutionary consequences of epigenetic variation.

Find out more about the fossils in your DNA at Science, April 2014