Black Skin or Black Hearts?
More popgen nonsense.
Even IF – note IF – the findings and the authors’ conclusions are essentially correct, that does NOT mean that Ancient Europeans were “black” – implying that they were akin to modern sub-Saharan African Negroes or to some other dark-skinned non-European peoples. They were simply darker-skinned European (or proto-Europeans); they were our ancestors, the ancestors of today’s Europeans, albeit before significant skin depigmentation took place. Skin color is not equivalent to race; the identity of a few functional alleles does not determine race. Again, these are the ancestors of today’s Europeans, not any other people, and several phenotypic traits have no bearing on that ancestral relationship nor on current political views on mass migration.
Then we have the fact that these data do not coincide with previous findings, including those on more recent Ancient samples, such as those from Rome.
Then we have the fact that ancient peoples describe themselves and other ancient peoples in was other that what is suggested by these recent breathless accounts, and, most importantly, colored portraits of ancient peoples by ancient peoples, depicting themselves or other ancients, do NOT show them all as dark-skinned “black” people. If Europeans were “black” as recently as 1700 years ago, then what sort of dementia did they have to portray themselves as “white?”
Second one. A bit "dark" but not "black."
There is this famous picture The specimen on the right was “dark” in the sense of modern Middle Easterners, and likely a freedman, the individual on the left is “white” in the modern sense. Neither is “black.”
Ancient Egypt. Male Egyptians out in the sun were shown as brown (not "black"), but Semites and Libyans were depicted as light-skinned, while Sub-Saharans were the only ones shown as "black."
Fair enough, a mix of dark (not “black”) and light is here.
Excerpts (emphasis added) and comments.
Abstract
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.
Indeed. Not the caveats in the last sentence.
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.
Lots of assumption and manipulations.
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…
Half? I thought the breathless reports were saying they were ALL as black as coal?
…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.
Not a very clear or informative abstract. Intentionally so?
As is the case for other complex traits, AI-based algorithms have been designed to predict skin, eye and hair color from DNA information. One of the most widely used test systems, HIrisPlex-S (7–9), infers from 41 SNPs the individual probabilities for three eye, four hair, and five skin color categories. When based on good-quality genomic data, HIrisPlex-S has a low margin of error. However, problems may arise when, regardless of the inferential method used, phenotypes are to be inferred from ancient genomes, usually typed at low coverage.
Yes, these “problems” are well evident when the conclusions do not match any of the ancient depictions, as shown above.
HIrisPlex-S assumes that the allelic and genotypic states of the loci of interest are known, which for many ancient samples is unwarranted. Indeed, directly calling genotypic variants from such data is challenging, because of DNA fragmentation, exogenous contamination, and degradation.
Didn’t read that in any of the breathless accounts. “Challenging?” I thought it was all so definitive?
More often than not, all these factors result in low sequencing depth, which in turn affects the possibility to reliably identify genotypes, and hence phenotypes too. Thus, the robustness of phenotypic prediction methods when applied to ancient samples needs to be validated considering their particular characteristics, as also remarked by Manuel Ferrando-Bernal et al., 2025 (10).
A critical factor, in these cases, is the possibility to take into account genotype uncertainty. In the first part of this paper we compared 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. Then, in the second part of this paper, we applied that protocol to a broad dataset of 348 ancient genomes from Eurasia, thus describing how skin, eye and hair color evolved over the past 45,000 years.
Assumptions and manipulations. Didn’t they consider that there is a problem when the outcome is at odds with how ancient peoples depicted themselves? Wouldn’t they then go back and re-evaluate their methodology?
Results
Starting at 8x the system showed some issues in correctly predicting the true phenotype, especially when the genotypes were defined through the direct approach or imputation method.
“Some issues” – an understatement.
In particular, datasets generated through the imputation method were misassigned almost 100% of times for coverage levels below 8x. This percentage is lower when the direct approach is used, about 30% on average. The probabilistic approach performed slightly better, below a 8x of cover-age the percentage of misassigned dataset is 23% on average.
This analysis highlights how easily the HIrisPlex-S phenotypic estimation procedure fails, if genotypes are called from data with a coverage equal to or lower than 8x, a situation commonly encountered when DNA comes from ancient specimens.
Didn’t read that in any breathless commentaries. “Fails?” So it ain’t so! Where was that in all of the excited media commentary?
Above this coverage threshold, there are no significant differences between the direct, probabilistic and imputation methods; the true phenotype is recovered 100% of times.
Really? How do they know? Photographs of the specimens when alive, hmmmm? How do they know what the “true phenotype” really is, particularly when some of their findings are completely at odds with the historical record (as well as previous data)?
At a genomic coverage level of 8x or lower, conversely, the three methods perform differently. Among them, the probabilistic method is the one that most frequently returns the same phenotype estimated at high coverage. The worst performances are provided by the imputation method, suggesting that the phenotypes inferred obtained through imputation of all missing HIrisPlex-S positions should be considered with caution.
Didn’t read that in any breathless commentaries. Reality is a bit more complex than “you see, we wuz black, bring in dem dere migrants!”"Most frequently returns" - some of their results are completely at odds with the historical record, including the very clear depictions of the ancients made at that time.
If their assumptions of phenotype based on genotype are wrong to begin with, then they are "most frequently" getting more bad results.
Summary of their results:
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 (22).
No surprises for that period.
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 (23).
No surprises for that period either..
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).
Some surprises if true, but what exactly do they mean by “dark” skin phenotype?
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 (Den-mark) 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 Nether-lands, Poland, and Romania), and light skins in Denmark, Great Britain, and Romania (four samples).
Again, even if true, what is “dark” skin?
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 (14), EKA1 from Estonia (24), I2445 from England (14), and SZ1 from Hungary (25).
So? What is “dark?” How dependable are these results?
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 (26) and DA236 from Finland (27).
Dark skin in a total of six samples. Even if true – six? What is “dark?” And why does this NOT match ancient art and is inconsistent with previous studies? Something is “off.”
Did they double check that the ancestry of these samples were really naïve to the regions, particularly for the more recent dates?
However, our downsampling experiments show that it can be safely exploited through the currently available pipeline (direct approach) only when the minimum coverage level at the 41 inferential sites is at least 8x, which is uncommon in ancient samples.
Didn’t read that in any breathless commentaries.
The coverage downsampling procedure we applied on the Ust’-Ishim and SF12 samples proved the probabilistic approach is robust in inferring the true pigmentation trait even at low (below 8x) or very low (1-2x) coverage levels.
Robust? Do they really know?
…therefore the imputation approach should be taken with caution when aiming at phenotypic inference. As is the case when continuous traits are described as discrete, not all phenotypes are inferred with the same level of confidence by HIrisPlex-s (7–9). This is particularly true for the skin phenotypes categories, the limits of which are admittedly somewhat arbitrary.
Didn’t read that in any breathless commentaries. With all the caveats, we see that the story is more complex than the orgasms in the media would lead you to believe.
By a probabilistic approach, we showed that eye, hair and skin color changed substantially through time in Eurasia. It was reasonable to imagine that the first hunting-gathering settlers, who came from warmer climates, had mostly dark pigmentation (2). What was less expected was the long persistence of their phenotypes. We found the first instance of light skin color in the Swedish Mesolithic, but it comes from only one sample in >50. Things changed afterwards, but very slowly, so that only in the Iron Age did the frequency of light skins equal that of dark skins; during much of prehistory, most Europeans were dark-skinned.
They were still Europeans.
Identifying the specific genes responsible for the observed trends is complicated due to the low mean coverage, which often leaves the allelic status at several loci undefined.
Hmmm….so “probabilistic” estimates that do not match historical data coupled with “Identifying the specific genes responsible for the observed trends is complicated…’
Sorry, this is all very “fishy.” I don’t know whether the problem is faulty methodology, bad interpretation, low sample sizes, uncertain sample identities, and/or political bias.
Is it really “black skin” of the ancient samples or “black hearts” or biased reporting by breathless media (apparently not corrected by authors).
I believe that population geneticists should include their political affiliations for the “conflict of interest” statements that typically accompany academic papers.
However, even though I am skeptical about this work, taking all of the ancient human data in toto, the idea that “Ancient civilizations were all founded by blonde/blue Nordics” is ludicrous. I wonder if Europeans today are actually are as light complexioned as they have ever been, instead of the “Ancient Nordics becoming darkened by mongrelization” paradigm.
In summary, let us consider the paradigm “extraordinary claims require extraordinary evidence.”
The idea that a significant fraction of Europeans were “dark-skinned” as recently as the reign of Constatine is completely incompatible with the historical evidence, including how the ancients portrayed themselves. It also goes against previous data, such as from the Antonio et al. Rome paper. It is therefore an extraordinary claim. These authors, with their “probabilistic” manipulations, do NOT provide extraordinary evidence to support their extraordinary claims. I am not convinced.
Of interest, see this. This previous study stated:
Our results identify strong selection for lighter skin pigmentation in groups moving northwards and westwards, consistent with the idea that selection is caused by reduced ultraviolet exposure and resulting vitamin D deficiency. We find that the most strongly selected alleles reached near-fixation several thousand years ago, suggesting that this process was not associated with recent sexual selection as previously proposed62. In the pan-ancestry analysis, we detect strong selection at the SLC45A2 locus (rs35395: C; P = 1.60 × 10−44; s = 0.0215)8,63, with the selected allele (responsible for lighter skin) increasing in frequency from around 13,000 years ago, until plateauing around 2,000 years ago…Both Neolithic farmer- and Steppe-associated ancestries have higher scores for blonde and light brown hair, whereas the hunter-gatherer-associated ancestries have higher scores for dark brown hair and CHG-associated ancestries had the highest score for black hair.
You can see why I am skeptical of the "Europeans were black until 1700 years ago" school of thought.
In final summary, there is much to be skeptical about, re: this paper. Putting aside questions of methodology and politics, the simple reality is that their conclusions – and particularly the breathless way these conclusions have shamelessly been reported in the media – are at odds with everything we know about how ancients portrayed themselves and contemporaries and is inconsistent with previous findings. One could believe that prehistoric Europeans were dark-skinned (which of course does not mean they were “black”) but when the time period overlaps into the historical era, of which we have significant documentation, the whole thing becomes untenable. The Egyptians portrayed Libyan and Semites as light-skinned, why? Because the hot sun drove the Egyptians insane? Greek (including Minoan) vase art was what? Was this more lies and fantasies? The wall art of Pompeii was what? More lies and fantasies? Descriptions of Germans and Gails by Roman authors – what was that? Were the Romans deranged? And of course, from a broad racial-historical standpoint, this all is, as I mentioned above, irrelevant. These were ancestors, regardless of how depigmented they may have been at any point in time.
The skin color issue is akin to the “racial purity” one – where the Left has adopted old tropes from the Right (still pushed by some sweaty fetishists and others) in order to delegitimize race and racial concerns. If one defines race in terms of some absurd and unscientific “purity” standard as per the Old Right and some modern fetishists, then it is easy to delegitimize the reality of biological race by easily disproving “purity.” This is why talk of “purity” is today more often heard from the mocking Left than the sane Right (note “sane” – that fraction thereof). Likewise, conflating race with skin color is another modern leftist trope. It serves two purposed. First, to limit racial differences to the superficial aspect of color (as if there is nothing else) and second, to point to dark-skinned old Europeans, call them “black,” and then say that “blacks have always been part of Europe, so why complain about migrants.” These leftist mendacious distortions could be effectively exposed and dismissed – as I am doing now – by a sane and scientifically informed Right. But sometimes I wonder if “sane and scientifically informed Right” is an oxymoron.