The evolution of skin pigmentation-associated variation in West Eurasia.

[real expert]

Abstract:

Skin pigmentation is a classic example of a polygenic trait that has experienced directional selection in humans. Genome-wide association studies have identified well over a hundred pigmentation-associated loci, and genomic scans in present-day and ancient populations have identified selective sweeps for a small number of light pigmentation-associated alleles in Europeans. It is unclear whether selection has operated on all of the genetic variation associated with skin pigmentation as opposed to just a small number of large-effect variants. Here, we address this question using ancient DNA from 1,158 individuals from West Eurasia covering a period of 40,000 y combined with genome-wide association summary statistics from the UK Biobank. We find a robust signal of directional selection in ancient West Eurasians on 170 skin pigmentation-associated variants ascertained in the UK Biobank. However, we also show that this signal is driven by a limited number of large-effect variants. Consistent with this observation, we find that a polygenic selection test in present-day populations fails to detect selection with the full set of variants. Our data allow us to disentangle the effects of admixture and selection. Most notably, a large-effect variant at SLC24A5 was introduced to Western Europe by migrations of Neolithic farming populations but continued to be under selection post-admixture. This study shows that the response to selection for light skin pigmentation in West Eurasia was driven by a relatively small proportion of the variants that are associated with present-day phenotypic variation.

The authors pointed out, what was already assumed, that geneticists can‘t really predict the skin colour of very ancient people. Which means, that the very dark (dark brown till black) skin tone concluded for the Cheddar man, is rather speculative. In addition to that neither the Cheddar man, La Brana nor Lola possessed the loci TMEM138, OCA2 and HERC2 associated with the "black" skin pigmentation identified in Sub- Saharan African populations which is a modern, more recent mutation, too.

Relatively dark skin pigmentation in Early Upper Paleolithic Europe would be consistent with those populations being relatively poorly adapted to high-latitude conditions as a result of having recently migrated from lower latitudes. On the other hand, although we have shown that these populations carried few of the light pigmentation alleles that are segregating in present-day Europe, they may have carried different alleles that we cannot now detect. As an extreme example,Neanderthals and the Altai Denisovan individual show genetic scores that are in a similar range to Early Upper Paleolithic individuals (SIAppendix,Table S1), but it is highly plausible that these populations, who lived at high latitudes for hundreds of thousands of years, would have adapted independently to low UV levels. For this reason, we cannot confidently make statements about the skin pigmentation of ancient populations.

source:
https://www.pnas.org/content/118/1/e2009227118

[Anfänger]

Abstract:



The authors pointed out, what was already assumed, that geneticists can‘t really predict the skin colour of very ancient people. Which means, that the very dark (dark brown till black) skin tone concluded for the Cheddar man, is rather speculative. In addition to that neither the Cheddar man, La Brana nor Lola possessed the loci TMEM138, OCA2 and HERC2 associated with the "black" skin pigmentation identified in Sub- Saharan African populations which is a modern, more recent mutation, too.






source:
https://www.pnas.org/content/118/1/e2009227118

It's not speculative, it's just that with the data available today, dark is the most likely skin colour. Maybe they will detect other skin depigmentation genes in the future. The study also show strong selection for the main skin depigmentation genes in Europe, you wouldn't expect selection for these genes if the WHG cluster was light skinned but instead we see selection for light skin AFTER these skin depigmentation genes come into the gene pool of former WHGs, for example SHG or Anatolian farmers.


Very interesting and plausible explanation, starting at about 25:40 :

[real expert]

It's not speculative, it's just that with the data available today, dark is the most likely skin colour. Maybe they will detect other skin depigmentation genes in the future. The study also show strong selection for the main skin depigmentation genes in Europe, you wouldn't expect selection for these genes if the WHG cluster was light skinned but instead we see selection for light skin AFTER these skin depigmentation genes come into the gene pool of former WHGs, for example SHG or Anatolian farmers......

I think you don't get my point. The skin color of the Cheddar man was very likely darker than modern Europeans, which means he was dark-skinned. That being said, he was very likely not dark brown or even black as the involved researchers wanted us to believe. Hence, the Cheddar man was likely rather light brown, thus had a similar skin color, such as Native Americans, the Khoisans or some Indians. Darker than modern pale Europeans doesn’t automatically translate into SSA black- complexion. So, I very much doubt that the Cheddar man had a chocolate or even ebony skin tone, as in the reconstruction. The point is, that the authors exaggerated the swarthiness of the Cheddar man for clickbaits and sensationalism. Controversy sells.

In my opinion a complexion like of these individuals make more sense for the Cheddar man and other WHGs.

7fca71da8b79c35b93ba4d83495ba18a--african-babies-african-children.jpg (511×720) (pinimg.com)

[Anfänger]

I think you don't get my point. The skin color of the Cheddar man was very likely darker than modern Europeans, which means he was dark-skinned. That being said, he was very likely not dark brown or even black as the involved researchers wanted us to believe. Hence, the Cheddar man was likely rather light brown, thus had a similar skin color, such as Native Americans, the Khoisans or some Indians. Darker than modern pale Europeans doesn’t automatically translate into SSA black- complexion. So, I very much doubt that the Cheddar man had a chocolate or even ebony skin tone, as in the reconstruction. The point is, that the authors exaggerated the swarthiness of the Cheddar man for clickbaits and sensationalism. Controversy sells.

In my opinion a complexion like of these individuals make more sense for the Cheddar man and other WHGs.

7fca71da8b79c35b93ba4d83495ba18a--african-babies-african-children.jpg (511×720) (pinimg.com)

You are aware that all of those populations you mentioned have known skin depigmentation genes ? Actually most of them even have the same ones you see in europeans. I don't know why the predicted skin colour of WHGs bothers so many people...

[kingjohn]

Why do people care how a person
Look like if he lived 9000 ybp 🤔

P.s
And yes the farmers were lighter skin than the european hunters, but they did had darker eyes though compare to hunters

[Angela]

Well, the people in those pictures look pretty damn dark to me. A hell of a lot of African Americans are that color, and lighter.

So, what's the big difference. We won't know the exact shade, and I don't see how and why it matters.

All we know is that the WHG didn't have the light pigmentation alleles which have been under selection in Europe since that time, and the farmers did.

[Philjames100]

There are various derived alleles for dark pigmentation found in sub-Saharan Africans and south Asian populations, but not in other Eurasian populations, which apparently weren't taken into account by those claiming that Cheddar Man and other WHGs had dark or very dark skin. Sub-Saharan Africans and south Asian populations also have various other ancestral alleles for dark pigmentation which other Eurasians don't have. So the claim that WHGs would have very dark or black skin because they lacked two alleles SLC24A5 and SLC45A2 doesn't seem to make sense.


“Most alleles associated with light and dark pigmentation in our dataset are estimated to have originated prior to the origin of modern humans ~300 thousand years ago. … our results indicate that both light and dark alleles at MFSD12, DDB1, OCA2, and HERC2 have been segregating inthe hominin lineage for hundreds of thousands of years. Further, the ancestral allele is associated with light pigmentation in approximately half of the predicted causal SNPs ... These observations are consistent with the hypothesis that darker pigmentation is a derived trait.”

Crawford et al. 2017


“The derived rs56203814 and rsl0424065 (T) alleles associated with dark pigmentation are present only in African populations (or those of recent African descent) and are most common in East African populations with Nilo-Saharan ancestry (…)

The derived rs6510760 (A) and rs112332856 (C) alleles (associated with dark pigmentation) are common in all sub-Saharan Africans except the San, as well as in South Asian and Australo-Melanesian populations (…)

The derived rs7948623 (T) allele near TMEM138 (associated with dark pigmentation) is most common in East African Nilo-Saharan populations and is at moderate to high frequency in South Asian and Australo-Melanesian populations.
At SNP rs11230664, within DDB1, the ancestral (C) allele (associated with dark pigmentation) is common in all sub-Saharan African populations, having the highest frequency in East African Nilo-Saharan, Hadza, and San populations (88-96%), and is at moderate to high frequency in South Asian and Australo-Melanesian populations (12 - 66%). The derived (T) allele (associated with light pigmentation) is nearly fixed in European, East Asian, and Native American populations. (…)

The TMRCA of a large number of haplotypes carrying the rs7948623 (A) allele in non-Africans, associated with light pigmentation, is 60 kya, close to the inferred time of the migration of modern humans out of Africa. (…)

The ancestral rs1800404 (C) allele, associated with dark pigmentation, is common in most Africans as well as southern/eastern Asians and Australo-Melanesians, whereas the derived (T) allele, associated with light pigmentation, is most common (frequency >70%) in Europeans and San. Coalescent analysis indicates that the TMRCA (time to most recent common ancestor)of lineages containing the derived (T) allele is 629 kya (95% CI 426-848 kya). (…)

The ancestral rs6497271 (A) allele associated with dark pigmentation is on haplotypes in South Asians and Australo-Melanesians similar or identical to those in Africans, suggesting they are identical by descent. The derived (G) allele associated with light skin pigmentation is most common in Europeans and San and dates to 921 kya (CI: 700 kya-1.3 mya). (…)

Individuals from South Asia and Australo-Melanesia share variants associated with dark pigmentation at MFSD12, DDB1/TMEM138, OCA2 and HERC2 that are identical by descent from Africans. This raises the possibility that other phenotypes shared between Africans and some South Asian and Australo-Melanesian populations may also be due to genetic variants identical by descent from African populations rather than convergent evolution. This observation is consistent with a proposed southern migration route out of Africa ~80 kya. Alternatively, it is possible that light and dark pigmentation alleles segregated in a single African source population and that alleles associated with dark pigmentation were maintained outside of Africa only in the South Asian and Australo-Melanesian populations due to selection.”

Crawford et al. 2017


“The importance of SLC24A5 in explaining pigmentation variation has been magnified due to the relatively low amount of genetic variation in Europe and the reduced phenotypic variation in lightly pigmented populations more broadly. As a result, SLC24A5 and other genes of large effect are repeatedly identified and replicated, especially in studies of admixed populations. (…) reconstructions of Mesolithic and Neolithic pigmentation phenotype using loci common in modern populations should be interpreted with some caution, as it is possible that other as yet unexamined loci may have also influenced phenotype.(…)

A long‐standing question in the evolution of human skin color is whether the darker pigmentation common in populations living in high UVR regions, including Africa, South Asia, and Melanesia, is due to shared ancestral alleles or if darker pigmentation, like lighter pigmentation, has evolved multiple times in recent human history. Crawford et al. (2017) reported that the haplotypes at loci associated with darker pigmentation in several regions of Africa are shared with southern Asian and Australo‐Melanesian populations, supporting a common‐origin model for the evolution of darker skin pigmentation in these populations. The authors also observed that both light and dark alleles at MFSD12, DDB1, OCA2, and HERC2 emerged prior to the origin of modern humans and roughly equal proportions of light and dark alleles are ancestral, suggesting that both types of alleles may have been segregating in early human populations migrating throughout Africa and the rest of the world. This raises the possibility that these loci may explain some of the variation in pigmentation phenotypes observed in equatorial climates outside of Africa. (…)

The derived MFSD12 alleles at rs56203814, a synonymous mutation, and intronic rs10424065 are associated with dark pigmentation and present only in African populations (Crawford et al., 2017). The derived alleles are most common in East African populations with Nilo‐Saharan ancestry while the ancestral alleles are associated with light skin pigmentation and are nearly fixed in East Asians and Europeans. In addition, the San, Ethiopian, and Tanzanian populations with Afro Asiatic ancestry also carry the ancestral alleles. This finding runs strikingly counter to the widely held assumption that ancestral alleles at pigmentation‐associated loci would all be associated with darker pigmentation. In the region of the genome containing TMEM138 and DDB1, variants associated with both lighter and darker skin color have been segregating for up to 600,000 years—well before the evolution of Homo sapiens. The derived, dark pigmentation‐associated allele at rs7948623 in TMEM138 and the derived, light pigmentation‐associated allele at rs11230664 in DDB1 have both undergone directional selection in Africans and non‐Africans. These results by Crawford and colleagues highlight that there are many ways to make enough melanin for a particular UVR regime. Furthermore, phenotypic evidence suggests perhaps a threshold necessity can be met for skin pigmentation and that other factors (sexual selection, drift, etc.) can drive skin to become more darkly pigmented, not just more lightly pigmented.”

Quillen et al 2019

[real expert]

You are aware that all of those populations you mentioned have known skin depigmentation genes ? Actually most of them even have the same ones you see in europeans. I don't know why the predicted skin colour of WHGs bothers so many people...

You don't understand my point. I’m well aware that the posted individuals including the Khoisans carry the canonical Eurasian skin pigmentation gene, SLC24A5. However, just because the WHGs lacked the allele for pale skin found in modern Europeans we can’t automatically assume that they were dark brown or black. Bear in mind, that the WHGs also lacked alleles that cause the skin of SSAs to appear dark brown to nearly black. Hence, Sub-Saharan Africans are not defined merely by the lack of the main skin-lightening gene alleles found in Europeans. Furthermore, there are dozens if not hundreds of gene alleles that code for skin pigmentation, either lightening or darkening it. For instance, a recent study found out that Native Americans or East Asians, have their own skin-lightening allele.

...Now, a new study of the genes of more than 6000 people from five Latin American countries undercuts the simplistic An international team discovered a new genetic variant associated with lighter skin found only in Native American and East Asian populations.

.......So the new variant sheds light on the genes underlying pale skin in East Asia. People at high latitudes in Europe and East Asia seem to have independently evolved lighter skin to produce vitamin D more efficiently with less sunlight, says Nina Jablonski, a biological anthropologist at Pennsylvania State University in University Park (Science, 21 November 2014, p. 934). But, “People have been scratching their heads” about which variants do this in East Asians. Now, researchers know MFSD12 is one. The ancestors of Native Americans presumably carried that variant over the Bering Strait into the Americas.

https://science.sciencemag.org/conte.../6425/333.full

So if Native Americans or East Asians have their own depigmentation genes it can't be rule out that the WHGs had their own too.
By the way, only ignorant or insecure people feel threatened or bothered by the fact that the Cheddar man wasn't lily-white. The irony is that genetically speaking it doesn't really make a difference whether the WHGs were pale or dark. Here is the thing, the issue I have is with the assertion of some authors of the cheddar man paper who pretended that they can predict with high confidence that Cheddar man was dark brown to black. This is not the case. In fact, the only thing they can predict with confidence is that the WHGs were likely darker than the present day pale Europeans. Darker than pale is hell of a range of skin tones and hues. The fact is, that the scientists can't know or be really sure that the Cheddar Man had exactly the same light-skin and dark-skin-related gene alleles that modern people have. He could’ve had a different combination of genes determining a certain skin pigmentation in a manner that doesn’t occur in any modern population. In my opinion, it doesn't make sense for the WHGs to have a complexion that is better suited in hotter places.

Whatever, where there is no certainty people are free to have discourses, to debate or to question certain conclusions of genetic studies. As far as I know this forum was made for all that.

[Anfänger]

You don't understand my point. I’m well aware that the posted individuals including the Khoisans carry the canonical Eurasian skin pigmentation gene, SLC24A5. However, just because the WHGs lacked the allele for pale skin found in modern Europeans we can’t automatically assume that they were dark brown or black. Bear in mind, that the WHGs also lacked alleles that cause the skin of SSAs to appear dark brown to nearly black. Hence, Sub-Saharan Africans are not defined merely by the lack of the main skin-lightening gene alleles found in Europeans. Furthermore, there are dozens if not hundreds of gene alleles that code for skin pigmentation, either lightening or darkening it. For instance, a recent study found out that Native Americans or East Asians, have their own skin-lightening allele.







https://science.sciencemag.org/conte.../6425/333.full

So if Native Americans or East Asians have their own depigmentation genes it can't be rule out that the WHGs had their own too.
By the way, only ignorant or insecure people feel threatened or bothered by the fact that the Cheddar man wasn't lily-white. The irony is that genetically speaking it doesn't really make a difference whether the WHGs were pale or dark. Here is the thing, the issue I have is with the assertion of some authors of the cheddar man paper who pretended that they can predict with high confidence that Cheddar man was dark brown to black. This is not the case. In fact, the only thing they can predict with confidence is that the WHGs were likely darker than the present day pale Europeans. Darker than pale is hell of a range of skin tones and hues. The fact is, that the scientists can't know or be really sure that the Cheddar Man had exactly the same light-skin and dark-skin-related gene alleles that modern people have. He could’ve had a different combination of genes determining a certain skin pigmentation in a manner that doesn’t occur in any modern population. In my opinion, it doesn't make sense for the WHGs to have a complexion that is better suited in hotter places.

Whatever, where there is no certainty people are free to have discourses, to debate or to question certain conclusions of genetic studies. As far as I know this forum was made for all that.

I get your point, see I just wrote with the data available TODAY it´s the most likely and I know that East Asians have their own skin depigmentation genes, that's why wrote that all of those population you mentioned have known genes involved in skin depigmentation. Read the study carefully, there are many genes involved in skin pigmentation BUT it comes down to 5 if i am not mistaken which have a large effect. These 5 show strong selection in Europe. I know from personal experience how large the effect can be. Someone I know has the ancestral allels at SLC24A2 and is just as dark as those in the pictures while someone with the derived allels is pale like an average German. Just one out of the 5 main genes has a huge effect. I agree though there can be unknown genes we don't know of yet but you can say that about any ancient population. Basically phenotype prediction in ancient DNA would be useless if we use this logic with any sample.

It doesn't make much sense for WHGs to be dark IF we don't take into account that they ate a lot of fish. Modern example would be the Inuits they are pretty dark even though they have the East Asian skin depigmentation genes.
The video I posted above has a very plausible explanation, including diet.

By the way, SSA are damn dark. IMHO there isn't much variation in skin colour in Africa. The lightest are probably the Khoisan and they have known westeurasian skin depigmentation genes.

[Angela]

^^Yes, I used to think the Khoi San might have been a good representation of the Africans who left for Eurasia, but then I found out that one of the "Eurasian" depigmentation genes passed down to them from East Africa, so we really don't know. Looking at the Andamanese, however, I would think they were still pretty dark.

The salient fact which has to be answered is why has there been such continuing and ongoing selection for fair skin if WHG were already fair? It wouldn't make sense.

[kingjohn]

If it makes people here feal good
The SHG though were light skin as oposed to the WHG (they did carry the main derived allells)������


In addition to performing this genome-wide scan, we studied the allele frequencies in three pigmentation genes (SLC24A5, SLC45A2, which have a strong effect on skin pigmentation, and OCA2/HERC2, which has a strong effect on eye pigmentation) in which the derived alleles are virtually fixed in northern Europeans today. The differences in allele frequencies of those three loci are among the highest between human populations, suggesting that selection was driving the differences in eye color, skin, and hair pigmentation as part of the adaptation to different environments [50–53]. All of the depigmentation variants at these three genes are in high frequency in SHGs in contrast to both WHGs and EHGs (Fig 4B). We conduct neutral simulations of the allele frequencies in an admixed SHG population to estimate p-values for observing these allele frequencies without selection (S9 Text). The p-values for all three SNPs are lower than 0.2; the combined p-value [54] for all three pigmentation SNPs is 0.028. Therefore, the unique configuration of the SHGs is not fully explained by the fact that SHGs are a mixture of EHGs and WHGs, but could rather be explained by a continued increase of the allele frequencies after the admixture event, likely caused by adaptation to high-latitude environments [50,52].


source:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5760011/

[real expert]

It doesn't make much sense for WHGs to be dark IF we don't take into account that they ate a lot of fish. Modern example would be the Inuits they are pretty dark even though they have the East Asian skin depigmentation genes.
The video I posted above has a very plausible explanation, including diet.

By the way, SSA are damn dark. IMHO there isn't much variation in skin colour in Africa. The lightest are probably the Khoisan and they have known westeurasian skin depigmentation genes.

To me, it is not plausible that researchers took the darkest pigmentation possible for the Cheddar man. It's rather unlikely that he was as dark as modern SSAs or Australo-Melanesians, even if his diet was rich in fish. It's a matter of fact, that higher latitude humans tend to be paler, on average, than lower latitude humans, although they're not as pale as Northern European. Plus, I find a bit disingenuous when people say they don’t care about pigmentation in a forum whom purpose is to discuss anthropology and phenotype. If you don’t care about the pigmentation of ancient populations, fine. But don’t criticize others for being interested in accurate reconstructions of ancient people and wanting to know how they looked like. Bottom line predictions of phenotype are limited. Besides, people are and will be always interested in pigmentation differences, that's why there're plenty genetic studies about the origin of skin color. Nothing wrong with being curious why humans have different pigmentation. You can’t also really blame Europeans/Brits for being puzzled and perplex when hearing that the Cheddar man wasn’t pale as them, since even scientists used to assume that the WHGs had the same shade as modern Europeans.
Other genetic papers showed WHGs with similar complexion as the people I've posted, btw.




Quite different from the Cheddar man- reconstruction.

[real expert]

^^Yes, I used to think the Khoi San might have been a good representation of the Africans who left for Eurasia, but then I found out that one of the "Eurasian" depigmentation genes passed down to them from East Africa, so we really don't know. Looking at the Andamanese, however, I would think they were still pretty dark.

The salient fact which has to be answered is why has there been such continuing and ongoing selection for fair skin if WHG were already fair? It wouldn't make sense.

You have to take this fact into consideration the Andamanese live in tropical places, with the high ultraviolet radiation levels and strong sun exposure. Hence, dark brown to black- skinned populations almost exclusively live near the equator, in tropical areas with intense sunlight: Australia, Melanesia, New Guinea, South Asia, and Africa. So, it makes perfectly sense that the Andamanese, Australian Aborigines or Melanesians didn’t develop light skin. In contrast to that, the Cheddar man lived in a much colder region and in higher latitude. Therefore, I find it rather unrealistic that the researchers gave him the darkest complexion, pigmentation possible, as if he lived in a tropical place.

[MOESAN]

You are aware that all of those populations you mentioned have known skin depigmentation genes ? Actually most of them even have the same ones you see in europeans. I don't know why the predicted skin colour of WHGs bothers so many people...

Search of reality matters, for someones of us!
You are doing your best to not understand or to make people to think you don't understand what Real Expert writes. I understand him very easily...
It's true the pic's he posted are not in themselves a proof of his point. That said differences in pigmentation exists among SSA pop's that are not due to light skinned Europoid intruders in their genomes, and as said Real Expert, the darkerst skins of SSA are due to darkening mutations, so a 'nilotic' black kind of skin is far to be credible for European HG's.

[Anfänger]

Search of reality matters, for someones of us!
You are doing your best to not understand or to make people to think you don't understand what Real Expert writes. I understand him very easily...
It's true the pic's he posted are not in themselves a proof of his point. That said differences in pigmentation exists among SSA pop's that are not due to light skinned Europoid intruders in their genomes, and as said Real Expert, the darkerst skins of SSA are due to darkening mutations, so a 'nilotic' black kind of skin is far to be credible for European HG's.

All SSAs look dark brown or even black(Nilotics) to me except the Khoi san and guys, there are maybe 20-30 threads where we have talked about pigmentation. Most of my posts on this forum are related to pigmentation. You can use the search option, by the way. We have talked about this paper when it was a preprint and now again and when exactly did I say you can't discuss pigmentation or anything else ?! What are we doing right now ? Discussing pigmentation ! If you have problem with Cheddar Mans skin colour go and contact the main genetics. I hope you have serious data that supports your notion of Cheddar Mans skin colour not being that dark because all I hear out of your posts is: "IN MY OPINION HE WASN`T THAT DARK! NO WAY! I DON`T HAVE DATA BUT NEVER EVER THAT DARK!."

Show me data and a plausible explanation and I change the idea of WHGs being dark in a second.

[MOESAN]

All SSAs look dark brown or even black(Nilotics) to me except the Khoi san and guys, there are maybe 20-30 threads where we have talked about pigmentation. Most of my posts on this forum are related to pigmentation. You can use the search option, by the way. We have talked about this paper when it was a preprint and now again and when exactly did I say you can't discuss pigmentation or anything else ?! What are we doing right now ? Discussing pigmentation ! If you have problem with Cheddar Mans skin colour go and contact the main genetics. I hope you have serious data that supports your notion of Cheddar Mans skin colour not being that dark because all I hear out of your posts is: "IN MY OPINION HE WASN`T THAT DARK! NO WAY! I DON`T HAVE DATA BUT NEVER EVER THAT DARK!."

Show me data and a plausible explanation and I change the idea of WHGs being dark in a second.

Wow! Keep cool.
Others than me explained why they THINK (as me, I never said I KNEW) Cheddar man had few chances to be very "black": his geographic place of life, with surely far ancestors already living in Europe latitudes, and I add the fact that we cannot affirm even its African ancestors had a very black skin. NO all SSA people and tribes have not very black skins, even the ones with almost no recent Europoid input, and surveys showed that some mutations in the genome produced darkening over more ancient pops of SS Africa, what supposes some of them were lighter skinned before. I can tell you I see a lot of diverse hues of skin among SSA African: surely not stupid if we consider that skin color is tied to a big extense to latitude hen pop's stay in place a long time.
I have no clue to be precise about Cheddar man, i can only say I doubt it's was black or very dark skinned, what is not to say he had a modern Europoid tone of skin (because he had not our current lightening mutations!
To be serious now, if you have a study that says Cheddar man had the (rare?) darkening mutations foud in SSAfrica, make me know.
On my side I 'll try to find the survey speaking about darkening mutations;

And don't forget to take your pills, or maybe, more gently said, keep cool and drink fresh!

[real expert]

All SSAs look dark brown or even black(Nilotics) to me except the Khoi san and guys, there are maybe 20-30 threads where we have talked about pigmentation. Most of my posts on this forum are related to pigmentation. You can use the search option, by the way. We have talked about this paper when it was a preprint and now again and when exactly did I say you can't discuss pigmentation or anything else ?! What are we doing right now ? Discussing pigmentation ! If you have problem with Cheddar Mans skin colour go and contact the main genetics. I hope you have serious data that supports your notion of Cheddar Mans skin colour not being that dark because all I hear out of your posts is: "IN MY OPINION HE WASN`T THAT DARK! NO WAY! I DON`T HAVE DATA BUT NEVER EVER THAT DARK!."

Show me data and a plausible explanation and I change the idea of WHGs being dark in a second.

Here's the thing, the scientists don't even totally rule out that the Cheddar man could've been fair- skinned. That being said, nobody here argues for the CM being pale, only that he was of intermediate skin complexion, and that the authors made his skin tone a lot darker than he likely was. Keep in mind, that WHGs lived under glacial weather, climate for 20000 years, a skin tone that is more suitable in the tropical regions wouldn’t make sense during the so-called little Ice Age. In addition to that, there was enough time for the WHGs to develop a lighter skin tone than dark brown or black. Furthermore, Loschbour had the same derived variants as Cheddar Man or La Brana but the calculator/algorithm predicted his skin complexion as "intermediate".


FromWiki:

Loschbour man was a hunter-gatherer,and the flint tools used for stalking and killing prey (wild boar and deer) were found by his body. He was one of the last of his kind, soon to be supplanted by new populations more likely to herd rather than hunt—and with paler skins.[3] According to DNA tests reported in 2014, Loschbour man was male,[4] was described as being "a light skinned (white) individual"(intermediate skin with a probability of 90%), brown or black hair (98%), and likely blue eyes (56%).[5] In contrast to 90% of modern Europeans, he was lactose-intolerant.[6] When he died, he was between 34 and 47 years old, 1.6 m (5.2 ft)tall, and weighed between 58 and 62 kg (128–137 lb).[1]

Loschbour man lived over 8,000 years ago, making the skeleton the oldest human remains found in the country.[6] There mains contained Y-DNA of the Haplogroup I2a-M423*.[8] DNA testing (two molars presented good samples) indicates that Western Hunter-Gatherers like Loschbour man "contributed ancestry to all Europeans but not to near-Easterners".

I can't verify it, but a user from anthrogenica wrote this:

He does already have genes that are associated with extremely light skin pigmentation and freckles in modern day Europeans namely IRF4 and he was heterozygous for one of the red hair mutations which in and of itself causes a lot of depigmentation.

He pointed out, that the 10 SNPs panel predicts it to have Black skin based on 4 SNPs; however Loschbour get a vastly different prediction when adding 3 more SNPs in spite of having a similar genetic profile in those SNPs.

Blue-eyed,dark-skinned, earliest modern Briton. - Page 56 (anthrogenica.com)

[real expert]

Search of reality matters, for someones of us!
You are doing your best to not understand or to make people to think you don't understand what Real Expert writes. I understand him very easily...
It's true the pic's he posted are not in themselves a proof of his point. That said differences in pigmentation exists among SSA pop's that are not due to light skinned Europoid intruders in their genomes, and as said Real Expert, the darkerst skins of SSA are due to darkening mutations, so a 'nilotic' black kind of skin is far to be credible for European HG's.

Thanks a lot for understanding what I mean. To make one thing clear, I’m not referring to Anfänger, KJ or Angela here. However, I see this virtue signalling, sanctimonious bunch who insert themselves into discussions about pigmentation of WHGs or other ancient populations, etc. Solely to pride themselves with NOT CARING and not seeing color, thus being superior to those who are genuinely interested in human genetics including pigmentation/phenotype. Hence, whenever people want to point out that the Cheddar man was rather of intermediate, tanned color, academics and those who were full of glee, gotcha moment, and enthusiastically reported that CM was a black man, suddenly pretend like it doesn't matter what shade he was. The fact is, that the black Cheddar man reconstruction got the click-baits and publicity the authors and mass media wanted. So, skin color obviously only matters to certain people when you can “prove“ that ancient European populations were black.

[Anfänger]

Wow! Keep cool.
Others than me explained why they THINK (as me, I never said I KNEW) Cheddar man had few chances to be very "black": his geographic place of life, with surely far ancestors already living in Europe latitudes, and I add the fact that we cannot affirm even its African ancestors had a very black skin. NO all SSA people and tribes have not very black skins, even the ones with almost no recent Europoid input, and surveys showed that some mutations in the genome produced darkening over more ancient pops of SS Africa, what supposes some of them were lighter skinned before. I can tell you I see a lot of diverse hues of skin among SSA African: surely not stupid if we consider that skin color is tied to a big extense to latitude hen pop's stay in place a long time.
I have no clue to be precise about Cheddar man, i can only say I doubt it's was black or very dark skinned, what is not to say he had a modern Europoid tone of skin (because he had not our current lightening mutations!
To be serious now, if you have a study that says Cheddar man had the (rare?) darkening mutations foud in SSAfrica, make me know.
On my side I 'll try to find the survey speaking about darkening mutations;

And don't forget to take your pills, or maybe, more gently said, keep cool and drink fresh!

You guys come and pretend that I tried to shut someones speech or didn't want to discuss pigmentation and then I reply with my opinion about your motivations, I should take my pills, now that's fair and very polite lol. Which pills? I don't take any. Usually people see and judge the world from their own perspective so maybe you should take yours ?



Yes others explained and out of all those only you hadn't had anything useful to say. That's why I am done replying to your answers and I think admins shouldn´t allow personal attacks like yours directed to me.

[Anfänger]

So this is also my last post on this thread.

Yes, WHGs lived for a long time in northern latitudes. That's why it is surprising that they hadn't genes we usually see everywhere around the world involved in skin depigmentation. There are 3 explanation discussed in the video above why it is still likely that WHGs had dark skin. How dark ? Possibly as dark as someone who hasn't got the main skin depigmentation genes ---> dark brown.

This study shows that many genes are involved in skin pigmentation but it comes down to five which a very large effect. We see strong selection for these genes after they come into the gene pool of former WHGs. SHG, Baltic HGs, farmers coming in from Anatolia. You wouldn't expect selection for genes involved in ligther skin if WHGs were light or intermediate because none of the SHGs, Baltics HGs and Anatolian farmers were as light as modern europeans. They were described as light to intermediate. Why are you ignoring this strong sign that there was lighting going on ?

[MOESAN]

You guys come and pretend that I tried to shut someones speech or didn't want to discuss pigmentation and then I reply with my opinion about your motivations, I should take my pills, now that's fair and very polite lol. Which pills? I don't take any. Usually people see and judge the world from their own perspective so maybe you should take yours ?



Yes others explained and out of all those only you hadn't had anything useful to say. That's why I am done replying to your answers and I think admins shouldn´t allow personal attacks like yours directed to me.

I suppose you feels well now? I had the impression I was the attacked person. But some observations of mine were on the general plan, and were not by force centered on you, except the ones concerning your refusal to accept Real Expert valuable arguments.

To show that pigmentation question is not so simple, see under (extracted from it ; bold letters are mine)



Science. Author manuscript; available in PMC 2018 May 17.
Published in final edited form as:
Science. 2017 Nov 17; 358(6365): eaan8433.
Published online 2017 Oct 12. doi: 10.1126/science.aan8433
PMCID: PMC5759959
NIHMSID: NIHMS929213
PMID: 29025994
Loci associated with skin pigmentation identified in African populations

Skin pigmentation is highly variable within Africa. Populations such as the San from southern Africa are almost as lightly pigmented as Asians (1), while the East African Nilo- Saharan populations are the most darkly pigmented in the world (Fig. 1). Most alleles associated with light and dark pigmentation in our dataset are estimated to have originated prior to the origin of modern humans ~300 ky ago (26). In contrast to the lack of variation at MC1R, which is under purifying selection in Africa (61), our results indicate that both light and dark alleles at MFSD12, DDB1, OCA2, and HERC2 have been segregating in the hominin lineage for hundreds of thousands of years (Fig. 4). Further, the ancestral allele is associated with light pigmentation in approximately half of the predicted causal SNPs; Neanderthal and Denisovan genome sequences, which diverged from modern human sequences 804 kya (62), contain the ancestral allele at all loci. These observations are consistent with the hypothesis that darker pigmentation is a derived trait that originated in the genus Homo within the past ~2 million years after human ancestors lost most of their protective body hair, though these ancestral hominins may have been moderately, rather than darkly, pigmented (63, 64). Moreover, it appears that both light and dark pigmentation has continued to evolve over hominid history.
Individuals from South Asia and Australo-Melanesia share variants associated with dark pigmentation at MFSD12, DDB1/TMEM138, OCA2 and HERC2 that are identical by descent from Africans. This raises the possibility that other phenotypes shared between Africans and some South Asian and Australo-Melanesian populations may also be due to genetic variants identical by descent from African populations rather than convergent evolution (65). This observation is consistent with a proposed southern migration route out of Africa ~80 kya (66). Alternatively, it is possible that light and dark pigmentation alleles segregated in a single African source population (13, 48) and that alleles associated with dark pigmentation were maintained outside of Africa only in the South Asian and Australo-Melanesian populations due to selection.

By studying ethnically, genetically, and phenotypically diverse Africans, we identify novel pigmentation loci that are not highly polymorphic in other populations. Interestingly, the loci identified in this study appear to affect multiple phenotypes. For example, DDB1influences pigmentation (42), cellular response to the mutagenic effect of UVR (39) and female fertility (41). Thus, some of the pigmentation-associated variants identified here may be maintained due to pleiotropic effects on other aspects of human physiology.

Have a quiet night.

[Angela]

I'm quite surprised to see what look to me like personal attacks at Anfanger for having a different point of view.

I want that kind of behavior to end right now.

We've discussed this over and over again on God knows how many threads. People's take on it differs; we know that. What is the point of rehashing it over and over again? Why is it so important to convince the people who think he probably "was" dark skinned? And, for God's sake, does it matter what shade of brown he was??? If he was the color of the San it's ok, but not if he was the color of Nigerians or Senegalese (which I doubt for what it's worth)?

I honestly don't get it.

As for my personal opinion, I take the point that the WHG might have had skin lightening genes we don't recognize. Great. The question still remains, as Anfanger succinctly put it: why then did the WHG living in those northern climes select so strongly for genes we KNOW lighten pigmentation. It would be unnecessary, wouldn't it? I haven't seen that addressed at all.

To me that's illogical. If you don't see that and want to believe otherwise, fine, believe what you want.

Just stop beating this topic into the ground. We know what some of you think; you've made it clear in thread after thread. It's no skin off my nose; it's not like it's some unhinged theory like all modern Jews are really Carthaginians.

Also and most important, keep it civil.

[Angela]

I'm quite surprised to see what look to me like personal attacks at Anfanger for having a different point of view.

I want that kind of behavior to end right now.

We've discussed this over and over again on God knows how many threads. People's take on it differs; we know that. What is the point of rehashing it over and over again? Why is it so important to convince the people who think he probably "was" dark skinned? And, for God's sake, does it matter what shade of brown he was??? If he was the color of the San it's ok, but not if he was the color of Nigerians or Senegalese (which I doubt for what it's worth)?

I honestly don't get it.

As for my personal opinion, I take the point that the WHG might have had skin lightening genes we don't recognize. Great. The question still remains, as Anfanger succinctly put it: why then did the WHG living in those northern climes select so strongly for genes we KNOW lighten pigmentation. It would be unnecessary, wouldn't it? I haven't seen that addressed at all.

To me that's illogical. If you don't see that and want to believe otherwise, fine, believe what you want.

Just stop beating this topic into the ground. We know what some of you think; you've made it clear in thread after thread. It's no skin off my nose; it's not like it's some unhinged theory like all modern Jews are really Carthaginians.

Also and most important, keep it civil.

Ed. Some of you also need to refresh your knowledge a bit. As Anfanger explained, different alleles have different effects. We know the ones which have large scale effects. We know that you need a combination of certain high impact alleles to significantly reduce pigmentation in the skin, so a stray small effect allele which shows up in some ancient is, by itself, irrelevant.

The only possibility is that there are unknown skin lightening alleles not currently recognized. You are still left with the problem that if they were already light skinned why have the alleles we do recognize swept through populations in northern latitudes?

[ThirdTerm]

Figure 4 shows that 100% of WHGs had the OCA2/HERC2 gene, which is associated with blue eye color and light skin. However, most studies only link this OCA2/HERC2 gene to blue eyes, concluding that WHGs had blue eyes and dark skin. The OCA2 gene is independently involved in the evolution of light skin pigmentation in East Asia and Europe. Two OCA2 polymorphisms (rs1800414 and rs74653330) have been associated with lighter skin pigmentation in East Asian populations. Aside from three genes associated with light skin in Europe (SLC24A5, SLC45A2 and TYRP1) which began to increase in frequency between 19,000 and 11,000 years ago, OCA2 also showed a potential signal of selection in Europeans and played part in light skin pigmentation in Europe. WHGs had only one depigmentation gene but they were probably as light-skinned as East Asians.


Fig 4. Adaptation to high-latitude environments.

The Scandinavian peninsula was the last part of Europe to be colonized after the Last Glacial Maximum. The migration routes, cultural networks, and the genetic makeup of the first Scandinavians remain elusive and several hypotheses exist based on archaeology, climate modeling, and genetics. By analyzing the genomes of early Scandinavian hunter-gatherers, we show that their migrations followed two routes: one from the south and another from the northeast along the ice-free Norwegian Atlantic coast. These groups met and mixed in Scandinavia, creating a population more diverse than contemporaneous central and western European hunter-gatherers. As northern Europe is associated with cold and low light conditions, we investigated genomic patterns of adaptation to these conditions and genes known to be involved in skin pigmentation. We demonstrate that Mesolithic Scandinavians had higher levels of light pigmentation variants compared to the respective source populations of the migrations, suggesting adaptation to low light levels and a surprising signal of genetic continuity in TMEM131, a gene that may be involved in long-term adaptation to the cold.
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2003703

[MOESAN]

I'm quite surprised to see what look to me like personal attacks at Anfanger for having a different point of view.

I want that kind of behavior to end right now.

Personal attacks at Anfanger? Concerning myself, I posted my opinion and the fact that Anfanger, who very often has good points, did not seem to accept some Real Expert points.
Now, pigmentation matters for me, as everything else, to depict aspects of reality (sometimes supposed reality when speaking about ancient times). But it is not by itself the most important thing, agree. In this thread, I have said what I had to say. I have not tackled every post nor taken a big part in it. Moderating is a good thing, but I have not found in these later posts, any true personal or collective, ethnic, politic, nationalist attacks as we can see in some other threads. Or I ignored them, by nature.
I 'll pass to other threads