Most people have seen the ancient skulls of Neanderthals, and images of what our ancient ancestors looked like. They are known for having big noses, protruding brows, larger jaws, and just a generally bigger face than we have today.

In general, this is just something that is accepted by most people and they assume that it is because they lived so long ago that the genetics were quite different. In reality, however, or DNA isn’t that different. Dr. Hannah Long talked about this, saying:

“The Neanderthal genome is 99.7 percent identical to the genome of modern-day humans and the differences between species are likely responsible for altering appearance.”

So, if our genome is 99.7% the same, why did they look so different.

Well, according to a study published in the journal Development, it may be because of the differences in the ‘dark’ region of the genome. This region, which contains what is often called junk DNA, has genetic code that doesn’t have any actual genes. The information here is instructions for things like activating, controlling, and regulating the actual genes.

As much as 98% of all of our DNA falls in this segment of the dark genome though, so it is clearly important.

The team of researchers wanted to know if it could have been some part of the dark genome that caused such dramatic facial differences. They looked at an area known as the enhancer cluster 1.45 (EC 1.45). This is known to regulate a specific gene that is associated with facial development called SOX9.

When there are issues with EC 1.45, it can result in a condition called Pierre Robin sequence, which is where a person has an underdeveloped lower jaw as well as a cleft palate.

To determine if this area of the dark genome may be responsible for the look of the Neanderthal, the team inserted manipulated DNA with different versions of the EC 1.45 into zebrafish. From there, they used fluorescent tags to watch for when the different regions of the DNA were active during the development of embryos. The researchers wrote:

“Strikingly, although differing by only three SNVs [single nucleotide variants], Neanderthal EC1.45 exhibited increased activity during early craniofacial development.”

Dr. Long went on to say:

“We found the enhancer is active in an intriguing population of facial progenitor cells, which contribute to jaw formation. Boosting its activity may have affected expression of the target gene SOX9 during development, perhaps contributing to some of the jaw shape differences seen between modern day humans and fossilized remains from Neanderthals.”

The researchers went on to give zebrafish embryos additional copies of OX9, which ended up causing their jaws to become larger, further supporting their theory.

If you thought that was interesting, you might like to read about a quantum computer simulation that has “reversed time” and physics may never be the same.