Some of these Neanderthal genes may also help to shape our physical appearance in some way, although figuring out exactly how this ancient DNA translates into bodily characteristics is more complex than it sounds. 

Cracking The Neanderthal Code

In high school biology, most of us are taught about Mendelian genetics, whereby a particular genetic variant – or genotype – goes hand-in-hand with an associated trait, or phenotype. If only this were how things worked in practice, reconstructing a Neanderthal by looking at their DNA would be a simple paint-by-numbers job, with each gene corresponding neatly to a particular color or shape.

In reality, most traits are polygenetic, which means the final outcome is actually the result of multiple genes working together in subtle and complicated ways. As a consequence, it’s often impossible to predict how changing a gene from one variant – or allele – to another will alter a person’s phenotype, even when dealing with modern humans.

“Those things are tough for us to work out from a gene sequence alone, so the way that we work them out is by looking at lots and lots of people and seeing how the people who carry a certain allele differ from people who don’t carry it,” John Hawks, professor of anthropology at the University of Wisconsin–Madison, told IFLScience. 

“We can’t take a genome and use a computer and have it tell us what the phenotype is going to be unless we have lots of people that we’ve looked at who have those genes,” he explained. “And we can’t do that with Neanderthals.”

Given that no one in the last 40,000 years has had the chance to observe a living Neanderthal, there’s no way we can link their genome to their physical appearance.

What we can do, however, is study the Neanderthal sequences in our own DNA and try to figure out how these relate to our physical characteristics. 

Is it likely that Neanderthals had blue eyes? No, I think probably not.

Dr John Hawkes

Pigmentation of the skin, hair, and eyes, for instance, is controlled by the interactions between hundreds of variants in today’s humans. Unfortunately, none of these are directly inherited from Neanderthals, which means we can’t use ourselves as a model for figuring out what our ancient cousins looked like.

Did Neanderthals Have Red Hair?

One characteristic that Neanderthals are speculated to have displayed is red-hairedness. In modern humans, this trait is produced by a mutation that reduces the effectiveness of a gene called MC1R, which controls the production of melanin. Back in 2007, researchers discovered a separate variant of the MC1R gene in two Neanderthals that appeared to hinder its function to a similar degree.

Despite the fact that this variant was not the same as the one that gives modern humans red hair, scientists began to suspect that it might have had the same phenotypic impact. This led to the idea that all Neanderthals were redheads.

Funnily enough, however, this variant has never been found in any of the Neanderthal genomes that have been sequenced since that study came out, suggesting that if it really did exist, it was probably pretty rare. More recently, researchers from the Max Planck Institute for Evolutionary Anthropology analyzed the impact of all the Neanderthal DNA in the modern human genome, including those associated with hair, eye, and skin color.

I don’t think that I would now have any kind of strong prediction about Neanderthals being red haired.

Michael Dannermann

“We looked at variants in modern humans that are associated with red hairedness and asked ‘were any of these brought in from Neanderthal mixture?’” study author Michael Dannemann told IFLScience. “And we could not find a single one.”

Of the more than 20 MC1R variants that affect hair color in people today, none were identified in any of the sequenced Neanderthal genomes, which means that the red hair gene did not exist in Neanderthals. That’s not to say they couldn’t have had their own gene for scarlet locks, but it now seems that all the initial hype around this subject may have been somewhat premature. “I don’t think that I would now have any kind of strong prediction about Neanderthals being red haired,” says Dannemann.

Likewise, the gene OCA2 – which can cause blue or brown eyes in modern humans – has been found in multiple forms in the Neanderthal genome, leading to speculation about sapphire peepers in this ancient hominid. However, the one variant most strongly associated with blue eyes in our own species doesn’t feature in Neanderthal DNA.

“Is it likely that Neanderthals had blue eyes? No, I think probably not,” says Hawks.

In a study published in 2012, researchers attempted to predict the appearance of three Neanderthal individuals based on their genotypes. All three carried multiple genes for different eye colors, but were all determined to have had brown eyes. Intriguingly, one of the trio was predicted to have had red hair, although the authors admit that their confidence in these findings was low, since they couldn’t even reliably guess the eye and hair color of living people from their genomes.

Variety Is The Spice Of Life

“Multiple Neanderthal alleles at different loci contribute to skin and hair color in present-day Europeans, and these Neanderthal alleles contribute to both lighter and darker skin tones and hair color, suggesting that Neanderthals themselves were most likely variable in these traits,” wrote Dannemann and his co-author Janet Kelso in their 2017 study. Like modern humans, then, Neanderthals clearly weren’t all one color, but varied massively in their genetic make-up and phenotypic characteristics.

“We don’t really have any evidence for directional impact that Neanderthal DNA made us lighter or darker skinned, because you can find Neanderthal associations with skin color, but they might go in opposite directions,” says Dannemann. “One makes you actually a little bit lighter-skinned on average, the other one more dark-skinned.”

At first glance, this finding might sound like yet another dead end in our quest to reconstruct the quintessential Neanderthal, but read between the lines and it actually offers some fascinating new insights and fertile ground for speculating about how they may have looked. After all, we know that our own species developed a variety of skin, hair, and eye colors as we migrated out of Africa and encountered new, colder environments around the world. More specifically, lighter forms of pigmentation evolved as populations of Homo sapiens spread further from the equator, where reducing our melanin production allowed us to capture more of the Sun’s ultraviolet light for vitamin D production.

Even in populations with little genetic crossover, this same pigmentation pattern is always observed in direct correlation with latitude. For instance, ancient western Europeans and east Asians living at higher latitudes developed genetic variants for light skin completely independently of one another. “It’s parallel evolution,” explains Hawks. “So there are different genes associated with lighter pigment in China than there are in Europe.”

According to one as yet un-peer-reviewed study, these traits took an incredibly long time to evolve, with light skin only emerging in certain northern European populations in the Iron Age.

Like us, Neanderthals spread over much of the globe, occupying a range of latitudes from north to south. They also existed for considerably longer than we have, giving them plenty of time to develop a wide variety of skin tones. The fact that our own pigmentation genes don’t match theirs means we can’t say for sure what color they were, but it’s not unreasonable to wonder whether they may have shared our tendency to be lighter in the far north and darker in the warmer regions nearer the equator.

We know, for instance, that Neanderthals in different regions became genetically adapted to their environments, with those from higher latitudes evolving sleep patterns that allowed them to rise earlier in the morning. It makes sense, then, to assume that their skin, hair, and eye tones probably became optimized for vitamin D production, only via a different – or parallel – set of genes to our own.

Could Neanderthals have had a stripe?

Dr John Hawks

Unfortunately, there’s a major hole in our data that prevents us from verifying this assumption. “The big missing part is that we have no genomes from Neanderthals from the southern part of their range,” says Hawks. “We have no genomes from Israeli Neanderthals, from Syrian Neanderthals, from Iraqi Neanderthals. So the most interesting piece of pigment variation that might occur because of the range of latitudes we just can’t look at because we don’t have genetics from the southern ones at all.”

Even if we did, the number of unanswered questions around Neanderthal phenotypes would still be massive, given that most of their pigmentation genes weren’t introgressed into modern humans and therefore can’t be seen in action. “If you really want to talk about what I do not know about Neanderthals, I don’t know that their eyes weren’t dark throughout with no whites, like gorilla eyes,” says Hawks. 

In the end, despite having sequenced several high-quality Neanderthal genomes, we still have no way of observing how their DNA manifested itself in all its colorful, fleshy glory. “Maybe the Neanderthals had a very different pattern of graying than we do. Maybe they had a different pattern of hair loss,” ponders Hawks.

“Could Neanderthals have had a stripe? These are all things I don’t know.”