Evolution In Human Pigmentation In Europe

As recently as 2500 years ago, many Europeans were a lot less white. 

The colour of eyes, hair, and skin among Eurasians and Africans is no longer a mystery. The evolution of light skin, hair, and eyes in Eurasia occurred over thousands of years, influenced by natural selection of genes and complex migration, reveals a new preprint study.

“The shift towards lighter pigmentation turned out to be slower than expected, with half of the individuals showing dark or intermediate skin colours well into the Copper and Iron Ages,” wrote the researchers in the study.

Researchers from the University of Ferrara, Italy, have used ancient DNA evidence to understand the natural colour of skin, eyes, and hair in humans from Eurasia. The study analysed DNA samples ranging from 45,000 to 1,700 years old, representing about 34 countries. . . .

[T]he first humans in Eurasia were dark-skinned and dark-haired, originating from warm climates. These darker-skinned humans had more melanin—a pigment that blocks the UV rays the body uses to produce vitamin D—compared to their lighter-skinned kin in the evolutionary cycle. Vitamin D, in turn, is crucial for bone health and strengthening the immune system, as well as aiding calcium absorption and muscle function. . . .

By the Iron Age (1200 BC to 500 BC), light-skinned people became as common as dark-skinned ones, with gene flow being the major driver of change, as noted by the researchers in the study.

The Neolithic farmers from Anatolia, present-day Turkey, “profoundly changed the genetic makeup of populations,” write the researchers, leading to a “population turnover”.

These farmers had two key advantages over the local hunter-gatherers: a stable food supply ensured by farming and animal herding, and a lighter skin tone. A lighter skin tone is better adapted to northern regions where the intensity of UV rays is low, as low melanin content in lighter skin helps produce more vitamin D. These advantages enabled the farmers’ population to grow at a faster rate than the local hunter-gatherers, causing a major shift in the appearance of Europeans.

However, the migration of Neolithic farmers was not the sole cause of the transformation of skin colour in Europe. The researchers have attributed this transformation to a localised process of migration and interbreeding of different isolated populations.

From here.

This excerpt doesn't call out a couple of other significant factors, however, and the analysis seems a bit muddled. And, like many papers in this genre, its technical analysis is strong, but its review of the literature and ability to put their own results in that context is weak.

There was massive population replacement in Europe in the Neolithic era as farmers with ancestors predominantly in Western Anatolia expanded in a southern Cardial Pottery wave and a northern LBK wave surged into Europe starting ca. 6000 BCE in the Southeast, and finishing about 4000 BCE in the Northwest and Southwest. The amount of Mesolithic European hunter-gatherer ancestry was quite modest by the time that this had run its course. So attributing light skin to Anatolian farmer ancestry is problematic. 

The closest modern proxy for Anatolian farmer ancestry is found in the people who are native to Sardinia, depicted below (from here):

Modern Anatolians have had, on average, perhaps 10% Turkic admixture due to events taking place in the Middle Ages, also experienced significant admixture from the Eastern highlands of Iran and the Caucuses during the Copper Age, and some modest Indo-European admixture with Hittite and Greek and Persian invasions from the Bronze Age to the Iron Age. So, modern Anatolians look less like the first farmers of Europe than Sardinians do.

In most Europeans, other than Sardinians and some far northern Scandinavians, this was followed by the significant demographic shift associated with the migration of light skinned, dark eyed Indo-Europeans with ancestral roots in the vicinity of modern day Ukraine to Europe, largely in the Copper Age and Bronze Age, with something close to modern admixtures in place by around the time of Bronze Age collapse in 1200 BCE, prior to the Iron Age. In some places, like the British Isles, the demographic turnover was quite rapid (maybe a century or two) and almost total.

Also, the blue eye pigment mutation that arose once, probably around 4000 BCE in far Northern Europe, probably among some of the last European hunter-gatherers (although a recent discovery suggests that it existed in very low frequencies that mutation rate analysis misses almost twice as long ago), impacted the pigmentation phenotype. As indicated by the quoted material above, they would have been quite dark skinned despite their blue eyes. This does seem to be discussed in the paper itself, even though it isn't really discussed in the article quoted above about the paper.

The modern Northern European pigmentation phenotype didn't really come together until blue eyed Northern European farmers and herders admixed with lighter skinned Indo-Europeans.

The discussion of the paper also seems to understate the importance of human evolution based upon selective fitness, which was definitely an important factor that has been documented in multiple studies of ancient DNA over time, and is ongoing. Pigmentation genes have been some of the stronger sites of selective fitness based evolution in the European gene pool.

Neanderthals would have been lighter skinned than European hunter-gatherers for the entire time that they co-existed in Europe, although light skin and light colored eyes in modern Europeans is not believed to be a product of Neanderthal admixture.

The pre-print and its abstract are as follows:

Light eyes, hair and skins probably evolved several times as Homo sapiens dispersed from Africa. In areas with lower UV radiation, light pigmentation alleles increased in frequency because of their adaptive advantage and of other contingent factors such as migration and drift. However, the tempo and mode of their spread is not known. Phenotypic inference from ancient DNA is complicated, both because these traits are polygenic, and because of low sequence depth. 

We evaluated the effects of the latter by randomly removing reads in two high-coverage ancient samples, the Paleolithic Ust’-Ishim from Russia and the Mesolithic SF12 from Sweden. We could thus compare three approaches to pigmentation inference, concluding that, for suboptimal levels of coverage (<8x), a probabilistic method estimating genotype likelihoods leads to the most robust predictions. 

We then applied that protocol to 348 ancient genomes from Eurasia, describing how skin, eye and hair color evolved over the past 45,000 years. The shift towards lighter pigmentations turned out to be all but linear in time and place, and slower than expected, with half of the individuals showing dark or intermediate skin colors well into the Copper and Iron ages. We also observed a peak of light eye pigmentation in Mesolithic times, and an accelerated change during the spread of Neolithic farmers over Western Eurasia, although localized processes of gene flow and admixture, or lack thereof, also played a significant role.

Silvia Perretti, Maria Teresa Vizzari, Patrícia Santos, Enrico Tassani, Andrea Benazzo, Silvia Ghirotto, Guido Barbujani, "Inference of human pigmentation from ancient DNA by genotype likelihood" bioRxiv (February 12, 2025) https://doi.org/10.1101/2025.01.29.635495

The results section of the paper states, in part::

Paleolithic period

(from approximately 45,000 to 13,000 years ago; 12 samples; 11 typed for eye color, hereafter E, 10 for hair color, hereafter H; 12 for skin color, hereafter S; one of them is the Ust’-Ishim test sample). 

Dark phenotypes are inferred for all traits for almost all the samples analyzed. The only exception is a Russian sample, Kostenki 14, dated to between 38,700 and 36,200 years ago, which exhibits an intermediate skin color.

Mesolithic period

(from approximately 14,000 to 4,000 years ago; 66 samples; 35 E, 63 H, 53 S; one of them is the SF12 test sample). 

Light eye colors are inferred for 11 samples; they come from Northern Europe, France and Serbia. By contrast, all 24 samples from the easternmost regions only display the dark phenotype. In Serbia both phenotypes coexist, one with blue eyes and four with brown eyes. 

61 samples show dark hair phenotypes, with the exception of 1 Swedish and 1 Serbian sample, both showing blonde features. 

Skin color displays a broader range of phenotypes: predominantly dark (43 samples), with regions in Europe also showing intermediate phenotypes (seven samples from Denmark, France, Georgia, Russia, Serbia, and Spain) and the earliest light phenotypes observed in this study (three samples from France and Sweden). 

In this time transect we observe for the first time an individual with inferred blue eyes, blonde hair, and light skin, NEO27, a hunter-gatherer from Sweden who lived approximately 12,000 years ago.

Neolithic period

(from approximately 10,000 to 4,000 years ago; 132 samples, 93 E, 120 H, 93 S). 

We still observe the majority of individuals showing the dark eye phenotype (81 samples), including France, in which we previously found only light phenotype. Both dark and light eye phenotypes are observed in Northern and Central-Eastern Europe, with the light phenotype inferred in 12 samples from Austria, Denmark, Greece, Ireland, Latvia, Serbia, and Sweden. 

Hair color is predicted as dark in almost all samples, with one exception from Austria who has an intermediate phenotype and five from Denmark, Greece, Ireland, and Serbia with light phenotype. Additionally, we observed for the first time in our dataset one sample with red hair, from Turkey. 

The skin phenotype is more variable, with regions in Europe (Portugal, Italy, Austria, Germany, Hungary, Estonia, and Russia) and Western Asia (Iran and Turkey) exhibiting exclusively a dark phenotype, whereas other regions show either both dark and intermediate phenotypes (25 samples exhibit the latter, from Croatia, Denmark, France, Greece, Ireland, Latvia, Malta, Poland, Serbia, Sweden, and Ukraine), or even light skin phenotypes (in five samples from the Czech Republic, Great Britain, Latvia, Sweden, and Ukraine).

Copper Age

(from approximately 6,000 to 3,500 years ago; 42 samples, 31 E, 33 H, 28 S). 

Even during the Copper Age dark phenotypes are prevalent. Most samples, 26, showed dark eyes, with the light phenotype present in five samples from Denmark, Hungary, Italy, and Romania.

Hair phenotypes remain mostly dark, with only one sample showing intermediate hair color (Denmark) and one samples exhibiting light hair color (Romania). 

Skin color is still predominantly dark (17 samples) in Eastern Europe, and the Iberian Peninsula, but intermediate skin tones are observed in Spain, Kazakhstan, and Central Europe (seven samples from Hungary, Italy, the Netherlands, Poland, and Romania), and light skins in Denmark, Great Britain, and Romania (four samples).

Bronze Age

(from approximately 7,000 to 3,000 years ago; 71 samples, 55 E, 64 H, 43 S). 

In this time period we observed an increasing proportion of light eye phenotype. While 39 samples throughout Europe and Asia are still exhibiting dark eyes, 16 samples display a light phenotype. These light phenotypes are still mainly found in Europe, but are also emerging in other regions such as Russia and Jordan, and as far East as Kazakhstan. 

Dark hair phenotypes remain predominant in most of Europe and Asia (49 samples), with intermediate phenotypes present in two samples from Denmark and Hungary. However, there is a greater proportion of light phenotypes (12 samples), specifically in Northern and Central-Eastern Europe, and they appear in Italy, Russia, Jordan, and Kazakhstan. One sample from Greece exhibits red hair. 

Western Europe, Southern Europe, Russia, and Southern Asia still exhibit a higher frequency of dark skin phenotypes (22 samples), but we also observed an increase in intermediate phenotypes in Central Europe and Central-Eastern Europe, as well as their first appearance in Russia (15 samples in total). The light phenotype emerged in six samples from the Czech Republic, Denmark, Estonia, France, Great Britain, and Hungary. 

During this period, we observed an increase in the co-occurrence of estimated blue eyes, blonde hair, and light skin, with four samples exhibiting this combination of phenotypes: I7198 from the Czech Republic, EKA1 from Estonia, I2445 from England, and SZ1 from Hungary.

Iron Age

(from approximately 3,000 to 1,700 years ago; 25 samples, 15 E, 19 H, 11 S). 

In this phase, the dark eye phenotype (10 samples) is present in Great Britain, Spain, and Russia, while the light eye phenotype (3 samples) is found in Denmark and Finland. Italy, and Kazakhstan exhibit both phenotypes. 

Hair remains predominantly dark throughout Europe and Asia (14 samples), with one intermediate phenotype observed in Denmark and four light phenotypes in Denmark, Finland, Italy, and Kazakhstan. 

Skin color analysis shows the dark phenotype (six samples) in Russia, Kazakhstan, and Italy. The intermediate phenotype (three samples) in Denmark, Kazakhstan, and reappears in Spain. The light phenotype (two samples) is still present in Northern Europe. 

A combination of blue eyes, blonde hair, and pale skin is observed in two samples: VK521 from Denmark and DA236 from Finland.