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

[real expert]

looking at the frequencies of those genes in modern populations i would guess they were probably intermediate. but those are only very few genes. for example the derived allele of SLC24A5 is at more than 50% frequency in ethiopians and somalis but they aren't really light skinned. i imagine them to have had the skin complexion of modern day north african, levantine populations. those are also almost fixated for SLC24A5. Krause said somewhere that the farmers in europe had the complexion of modern populations from around the mediterranean so the same probably applies to bronze age aegeans.

I agree with you that the BA Aegeans were likely intermediate/olive skinned and not "dark to black". However, the academic paper concluded the opposite. Besides, many Ethio-Semites from Eritrea and North Ethiopia are (when not over-exposed to the sun) often light brown, yellowish. Somalis and Ethiopians from the largest Ethiopian ethnicity, the Oromo, are darker than the Ethio-Semites, though. We have to take into consideration that Horners have varying degrees of Western Eurasian admixture. They have also inherited certain genes for extremely dark skin. For instance, the African component in Somalis/ Ethiopians is largely Dinka-like and the Dinkas are not seldom literally black. Thus, they must have genes that makes them extremely dark even for African standard. When the Egyptians were depicting Nubians with literally black skin, they were not exaggerating.


Here a picture of a Dinka man who is literally black.

One picture of an Ethio-Semitic female from the Tigrinya tribe(Eritrea) with light brown skin tone. The second pic shows an Ethio-Semite women from Ethiopia. Anyway, Ethio-Semites have some additional Arab/Southern Arabian admixture. Bottom line, SLC24A5 has definitely a significant lightening effect.

 

[John Baker]

I've been doing some work on this area and made a rather disturbing discovery. HIrisPlex-S is not only imperfect but severely broken. Has anyone here actually tried testing it with their own DNA?

It gets 2 out three wrong for me. In fact, it doesn't really shift from the default. The only one it gets right is because it's the default of blond hair. I'm not a memory of any poorly surveyed populations or anything so it shouldn't be this inaccurate. I'd expect accuracy issues but not this bad. 23andme gets two out of three right and the one it gets wrong still makes a fairly close prediction.

The tool said I had 95% chance of blue eyes, I have fairly dark brown eyes. It also said I have intermediate skin. Given my family have much of the same genetics, none of these features are very present at all in my relatives. The results I get don't match the manuals statements about accuracy.

I've written about these issues but I can't share links at this point.

I guess search quora for "What-is-the-evidence-that-Cheddar-Man-was-not-black-Scientists-who-sequenced-his-DNA-said-he-had-no-genes-for-light-coloured-skin-He-had-genes-for-skin-colour-consistent-with-Subsaharan-populations" and then look for my answer there.

Someone in this topic said they use HIrisPlex-S. I wonder how they get around the issue. From what I understand, a lot of the problems come from that DNA, being double stranded is ambiguous.

Rather than fully standardising it, G/C and T/A are potentially the same or get confused. I guarantee you bits are getting flipped when people are using these tools.

HIrisPlex-S has a confusing mention of this in the manual:

"*if you are using sequencing data, than you may need to flip strand orientation in your
result before inputting into this prediction model. The only SNP that may cause
confusion and therefore must be converted (from NCBI’s forward orientation) is
rs6119471. All other G/C, A/T SNPs are in the correct orientation for input or are
opposite alleles i.e. SNP G/A, input requests C/T."

Basically, it's got some convention but it's not really telling you exactly when and when not to flip your results.

This is a hidden disaster in genomics. The endian is messed up and it's like someone has encrypted the input with an XOR. You have to jump through a lot of hoops to make sure things are the right way around when comparing. This software probably uses an older convention rather than a standard one. I don't know what scientists are thinking but it's very very hard to work like this.

You can see that it's very likely they didn't read the manual for Cheddar Man. I didn't read the manual fully either until after my analysis. They seem to have gotten ASIP wrong which seems to be important in differentiating east Asian pigmentation from African pigmentation. You fix that and you get brown hair, blue eyes and intermediate skin. However, I can't say that the rest of their alleles are properly matched.

To save me having to do code breaking on this, can someone tell me how you manage to get the alleles in the right orientation each time around?

 

[real expert]

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......

Hi Philjames a bit offtopic. I've read some comments about the Cheddar Man on AG: One user showed cherry picked images of Minoans/ Mycenaeans that were depicted dark to reinforce his claim that the pale depicted Minoans/Mycenaeans(females) were most likely not realistically depicted. He argues for women using makeup like the Geisha from Japan. So according to him only the dark painted Minoans/ Mycenaeans reflect the real phenotype of them BA Aegeans. The thing is that the pale Minoan/ Mycenaean women were not only pale on their face but on their entire body and while working. What this poster also seems not to know is the fact, that some Minoan males were also depicted as pale.

Two pale male Minoans.

Minoan females working

Dark and pale depicted Minoans.

Mycenaeans