Bones of Ancient Relatives Give Us Epigenetic Clues About Ourselves

Methylation Patterns in Neanderthal and Denisovan Epigenome Give Hints about Modern Human Disease and Appearance

We already know a lot about early modern humans based on scientific evidence collected from our ancestors, gaining clues from migration patterns and remnants left abandoned for ages. However, very little is known about our prehistoric relatives, the Neanderthals and Denisovans, who lived thousands of years before us. With little evidence on hand and even smaller fragments of their DNA to spare, researchers are using epigenetics to give clues about why our archaic cousins differ from us, despite our very similar DNA.

In an article published in Science, researchers from Israel, Germany, and Spain worked to reconstruct the ancient humans’ epigenome from bone fragments, comparing it to the modern human epigenome in attempt to illuminate the differences seen in archaic groups thought to be very similar to ourselves. Using fossilized bone fragments, they reconstructed the entire Neanderthal and Denisovan epigenome, assessing the methylation patterns of early humans and comparing them to our own.

The scientists had to use a process that did not destroy the antiquated DNA, typical to current lab methods. Instead, they focused on one of the nucleotide bases – cytosine – which naturally decays into uracil when unmethylated and thymine when methylated. Measuring cytosine’s rate of decay, the team reconstructed a methylation map of the early humans’ DNA and compared it against the methylation map of modern humans.

What they found was around 2,000 differentially methylated regions (DMRs). This tells us there were 2,000 areas in the genetic code that methylated in a significantly different way when scientists compared the modern and archaic human methylation patterns. Of these DMRs, researchers found that the HOXD cluster was significantly more methylated in the ancient human epigenome than in modern humans, particularly the HOXD9 promoter and HOXD10 gene.

These have been previously linked to the development of body structure. Researchers propose that the change in methylation patterns is associated with the change in physical appearance and bone structure, perhaps epigenetically explaining the elongation of limbs in modern humans compared to the more robust, shorter limbs of our distant relatives.

The team also discovered that the DMRs are more likely to be connected to diseases. That is, in the areas where the degree of methylation differed significantly between the two, modern humans displayed higher methylation in the regions tied closely with disease. This difference may lend support to the relatively recent rise in psychiatric and neurological disorders, giving us further insight into epigenetic consequences for humans.

Researchers suspect that the diseases we are seeing today may only be recent developments, remaining unseen in our distant past. Urging for additional research, the scientists hope to find more pieces to the overwhelming puzzle of our epigenetic past and present.


Source: Learn all about it and read more about their findings here: Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan. Gokhman, D., et al.

Reference: Gemma Tarlach, Epigenetics Helps Explain Early Humans’ Appearances. April 17, 2014

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About Bailey Kirkpatrick 164 Articles
Bailey Kirkpatrick is a science writer with a background in epigenetics and psychology with a passion for conveying scientific concepts to the wider community. She enjoys speculating about the implications of epigenetics and how it might impact our perception of wellbeing and the development of novel preventative strategies. When she’s not combing through research articles, she also enjoys discovering new foods, taking nighttime strolls, and discussing current events over a barrel-aged sour beer or cold-brewed coffee.


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