We all make assumptions about how things are, and why they are as they are. We also sometimes have to eat our words.
A great example of that occurred this past week with the announcement that the DNA of "Cheddar Man" had been sequenced. "Cheddar Man" is a 10,000 year old near complete skeleton of a man, found in a cave in 1903 in Somerset County in England. He was about 166 centimeters tall (5 foot 5 and ½ inches) and likely was in his 20's at the time of death. Cheddar Man lived during what's called the Mesolithic Era, often referred to as the middle stone age.
What drew most everyone's attention wasn't the fact that the skeleton's DNA had been sequenced, an absolutely amazing feat in itself. Instead, it was the announcement that the DNA showed he was dark skinned and likely had blue eyes! That will upend a whole lot of things we've assumed about people who lived in Europe in the Stone Age.
Other evidence suggests that humans first appeared in Europe about 45,000 years ago. If Cheddar Man was dark skinned, that means humans lived in northern Europe with dark skin for more than 35,000 years before their skin pigment changed.
That in itself likely upends the long held assumption that the reason northern Europeans had lighter skin and eye color was as an adaptation to higher latitudes and the lack of sunlight. Less sunlight meant that humans were less able to absorb Vitamin D, so skin color adapted over the generations. But the latest evidence now suggests that skin color didn't really change until about 6,000 years ago.
Which means those of us who are Caucasian really are "the new kids on the block"; and we managed to survive quite nicely in Europe for an awfully long time with dark skins.
So just how did the scientists manage to do an entire genetic sequence on a 10,000 year old skeleton, and how did they reach the conclusion about dark skin and blue eyes?
Upon death, DNA begins to break down. You'd think it would have been entirely broken down after 10,000 years. The big break for the geneticists is the fact that Cheddar Man was preserved in a cave. Caves tend to provide the right conditions that could help preserve DNA.
But as previously noted, the skeleton was discovered in 1903, so those advantageous cave conditions ended 115 years ago, more than enough time to cause the DNA to degrade, erasing 10,000 years of preservation. Obviously, the British scientists at the Natural History Museum of London who have been caring for the skeleton over the past century deserve a lot of credit for the fact the DNA survived since 1903.
Cheddar Man's mitochondrial DNA was first tested in 1996 by Dr. Brian Sykes. Mitochondrial DNA is inherited from one's mother. While that was just over 20 years ago, it's a veritable millennium ago in terms of knowledge about DNA. In between, the entire human genome was first sequenced. Sykes, a professor at Oxford University, reportedly obtained the mitochondrial DNA from a molar in Cheddar Man's mouth. His data suggested that Cheddar Man's maternal DNA came from Haplogroup U5. Those with such DNA share it with other ancient humans who lived in Europe.
The latest DNA on Cheddar Man was far more sophisticated than what Sykes did in 1996. The basic technology used is called shotgun sequencing. One of the researchers involved with Cheddar Man was Dr. Selina Brace, a postdoctoral researcher at the Natural History Museum of London. Dr. Brace explained the process used to obtain Cheddar Man's DNA for the full sequencing: "To extract ancient DNA from a human or animal what you're looking for is a dense bone which might have protected the DNA inside it as much as possible.
"We used to use leg bones or teeth as the thick bones and enamel keep DNA quite intact, but in the last two years we've shifted to using the petrous, or inner ear bone, which is the densest bone in the human body ... However it isn't a golden egg. You can still fail to retrieve useful DNA. But if the body was deposited in a good environment, where there was a cool and constant temperature then the petrous bone is a good place to find useful ancient DNA."
A lot of useful DNA. But let's get the main question: just how do the researchers know that Cheddar Man had blue eyes and dark skin? After all, all they have is a skeleton. No flesh. No cave paintings. Certainly no family photos.
Let's first consider Cheddar Man's eye color. You may remember Gregor Mendel, the Augustinian monk from the 19th century who conducted a bunch of experiments with peas. He's the guy who first developed the concept of genetics, including the concept of dominant and recessive genes.
Like me, you probably learned that brown eyes are dominant and blue eyes recessive. It's an idea based upon the assumption that eye color is controlled by a single gene.
Well, it's another idea that has gone out the window. In fact, geneticists have determined that eye color is "polygenic", meaning that it is determined not by a single gene but by multiple genes. Among the genes controlling eye color are OCA2 and HERC2, both located on chromosome 15 (note: humans have 23 pairs of genes); SLC24A4, TYR, and IRF4, all located on chromosome 7; and SLC45A2, located on chromosome 5.
So if there isn't a single gene that causes one to have brown, blue, green or grey eye colors, what causes it? Eye color is actually a function of melanin at the back of the retina. It's composed of a number of different shades. The combination of shades for each person creates distinctive colors for each of us. We simply tend to lump those shades into a handful of colors.
If you know what the different SNP's (single nucleotide polymorphisms) are you can infer the person's actual eye color. In fact, what geneticists have done is to take the actual data for a lot of people, compare it to each person's actual eye color, then figure out a way to predict color based upon the genetic data. They did this using a multinomial regression model.
What the geneticists have determined is that with the six sets of SNP's mentioned above, they can predict eye color to the following level of accuracy:
Brown eyes: 93%
Blue eyes: 91%
Intermediate eye colors: 72%
So based upon the SNP's they found in Cheddar Man's genetic profile, they are about 91% certain that he had blue eyes. Not guaranteed, but very likely.
But why would blue eyes have become a fairly common trait in places like northern Europe? An intriguing theory relates to "the winter blues". Several studies have linked lighter eye color to the ability to overcome seasonal affective disorder (SAD), a major depressive illness. As Dr. Richard Sturm suggested "perhaps those with blue eyes may have been able to withstand the dark, depressing days of the Neolithic European winters better than those with brown eye color?"
So being able to determine Cheddar Man's eye color is interesting, but not many people think the fact that he likely had blue eyes is a big deal. After all, Cheddar Man lived in northern Europe.
Having dark skin in northern Europe is a big deal! So let's consider how the geneticists figured that one out.
Like eye color, skin color is a polygenic trait, meaning there isn't a single gene controlling skin color. In fact, according to the GB Healthwatch, there are a total of 378 genetic loci involved in determining skin color in humans and mice.
So based upon the latest research, humans lived in northern Europe for over 35,000 years with dark skin. Why then would skin have changed color?
It's well known that lighter skin absorbs Vitamin D better than dark skin. It's all been determined that Cheddar Man and his contemporaries were likely lactose intolerant, so they weren't getting needed Vitamin D from the family cow. An alternative theory is that they were getting it from sources such as oily fish.
If Cheddar Man and his contemporaries were getting adequate Vitamin D from a food source, it could explain why they survived at least 35,000 years in a high latitude, low sunlight environment and not have a Vitamin D deficiency.
So if that's the case, why do people like me, a descendent of northern Europeans, have light skin today? What changed? Certainly not the angle of the sun? Not only that, if sunlight was the underlying factor, then why don't Inuit people in Canada and Alaska look like Norweigians?
There are a number of theories. One possible theory is the switch to farming. Remember, Cheddar Man was a hunter gatherer, not a farmer. Once his descendants settled down and started farming, people may have relied less on sources of Vitamin D such as oily fish. And Vitamin D deficiencies probably began appearing, as well as the associated genetic response.
Not proven, but there's the suggestion that a lifestyle change actually was the cause for fair skin to emerge.
So once again, Cheddar Man has changed our understanding of who we humans are, and from where we came, in a very unexpected way. And the story continues to unfold.