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August 2, 2018

Ancient pigmentation pathways and modern genomics

Filed under: Forensics,Genetics,skin — Razib Khan @ 1:02 am
Piebald horses emerge out of common pigmentation pathways found in humans

Unlike most mammals humans are highly dependent on our sense of sight. This is due to the diurnal nature of many primates. Our ancestors foraged for bright fruit, and so we developed stereoscopic color vision. But eventually the human lineage left the forests of our ancestors, and ventured out to the savanna. We turned our eyes to other uses than detecting fruit, from hunting, to developing a keen eye for art.

Humans are pre-adapted toward color vision

It is not surprising then that humans have had a fixation on the color of our skin and the pelage of our domesticates. Skin is our largest organ, and our complexion is one of the best indicators of ill health.

Additionally, humans have utilized the skin as a canvas upon which to apply tattoos and other coloration so as to indicate group membership. And, as humans from very different geographic regions began to meet each other, any differences in pallor were salient indicators of difference and distinction. Whole people were defined by their color!

In the ancient Near East the Egyptians termed themselves red, while their neighbors to the south were black, and West Asians from the Levant were yellow. Greeks and Arabs distinguished between the ruddy peoples of the north, and the black and brown peoples to the south, with their own ethnicity often defined as being at some sort of equipoise.

Nubians were depicted accurately by the ancient Egyptians

And yet for such an important trait, the genetic elucidation of skin color, and pigmentation more generally, has evaded us until very recently. To be fair, the genetic elucidation of most traits in humans evaded us until the last decade or so, because we did not have genomic tools to explore the whole range of possible genetic sites.

In 2003 the evolutionary biologist Armand Leroi wrote in the afterword of his book Mutants that it was surprising that geneticists were still unclear about what underlay normal variation on the trait of human skin color. This passage was written at an opportune moment. In 2006 a review paper was published, A golden age of pigmentation genetics, which reflected the fact that much had changed since Leroi had written that passage just three years before.

Through analysis of British mixed-race pedigrees geneticists in the 1950s concluded that skin color was controlled by many genes, but that much of the variation was localized to only a few loci. That is, variation on a few genes had a large impact. This means that genomic methods pioneered in the 2000s were well placed to discover the genetic basis of the variation of the trait. If the impact of the mutation was large, then you didn’t need a large sample size to detect it.

75% of the variation in eye color in Europeans is due to one gene

And so they have. Today researchers now know that about half the variation in skin color across populations is due to variation on about ten or so genes. The other half is mostly distributed across the genome. Additionally, they know that the gene that is correlated with blue eye color also effects skin color. Similarly, the gene that causes much of the blondness in Northern Europe is also correlated with skin color. The pigmentation characteristics are usually correlated together. Skin, hair and eyes are all often controlled by the same set of genes.

Though East Asians and Europeans achieve light skin through different mutations, it is also the case that those mutations are found on an overlapping set of genes. Pigmentation pathways are highly conserved in human populations. The wheel is always reinvented in the same way. In fact, the same genes show up over and over across vertebrates.The genetic mutation that results in blonde hair causes the piebald pelage in horses. The mutations associated with red hair in humans are found in the gene that is important in mouse coat color. The gene responsible for much of the difference in pigmentation between Europeans and Africans also has a lightening effect in zebrafish.

There is a great to be done to understanding the genetic basis of many diseases and complex behavioral traits. But with pigmentation genomics has yielded incredible results, producing forensic applications with utility in a wide range of contexts. This is because tens of thousands of years have produced humans who come in all colors, but through simple fine-tuning of the pigmentation pathways which vertebrates had utilized for hundreds of millions of years.

Skin color is a complex topic with numerous historical and anthropological layers. But when it comes to genetics it’s actually surprisingly simple.

You can see your skin, but are you curious about what your genes say about your pigment? Check out Neanderthal by Insitome to learn more!


Ancient pigmentation pathways and modern genomics was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

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