Dark-Skinned Mesolithic Europeans Mar 4, 2018 18:46:11 GMT
Post by Admin on Mar 4, 2018 18:46:11 GMT
Cheddar Man (UK, Mesolithic)
Eye colour —There is 1 locus (LOC105374875 (formally known as SLC24A4) rs12896399) with low coverage (1x) hence a heterozygote is possible. Prediction includes a range that includes what the 1x coverage found (ancestral G allele) and the possibility of an A derived allele being present.
LOC105374875 rs12896399 LOC105374875 rs12896399
(homozygote GG) (heterozygote GA)
Blue eye 0.564 0.711
Int. eye 0.189 0.143
Brown eye 0.247 0.145
Blue eye 0.564 - 0.711
Int. eye 0.189 - 0.143
Brown eye 0.247 - 0.145
Final prediction: Intermediate (blue/green) eye colour
Explanation: This individual has light or blue/green eye colour, it is not light blue, there are elements of brown/yellow in the eye to give a proposed perceived green colour. Better coverage at the low sequenced marker would clarify this but blue/hazel cannot be ruled out. It is certainly not a brown eyed or clear blue-eyed individual.
Hair colour—There is 1 locus PIGU rs2378249 with low coverage (1x) hence a heterozygote is possible. Prediction is a range that includes what the 1x coverage found, ancestral A allele, but also includes the possibility of a heterozygote being present.
PIGU rs2378249 PIGU rs2378249
(homozygote AA )(heterozygote CA)
Blond 0.014 0.013
Brown 0.719 0.759
Red 0.011 0.023
Black 0.257 0.205
Brown 0.719 – 0.759
Black 0.257 – 0.205
Final Prediction: Dark Brown/Black hair colour
Explanation: The probability value of black is >0.2 so it has an impact on prediction, and will darken the high brown probability. However there are light pigment alleles indicating a lighter shade phenotype. Better coverage at the low sequenced marker would help clarify this. This individual would be perceived as having dark brown hair. Black however cannot be ruled out.
Skin pigmentation—There are 3 loci (BNC2 rs10756819, TYR rs1126809, MC1R rs3212355) missing, and the profile does contain 2 loci (LOC105374875 rs12896399 and PIGU rs2378249) with low coverage (n=1x) hence a heterozygote is possible at those sites. When factoring in possible genotype combinations, a prediction range may be generated. The range consists of assuming the two loci with low coverage are correct as homozygote for their sequenced allele (LOC105374875 rs12896399 G allele and PIGU rs2378249 A allele) and omitting the 3 missing loci from the prediction model as they have no coverage, to including these markers with their ancestral (BNC2 rs10756819-GG, TYR rs1126809-GG, MC1R rs3212355-CC) and also their derived allele counterparts. The following range for skin colour prediction is possible for this individual with these parameters:
ancestral alleles used / derived alleles used
Very Pale 0 0
Pale 0 0
Intermediate 0.394 0.125
Dark 0 0
Dark-Black 0.606 0.875
Very Pale 0
Intermediate 0.394 - 0.125
Dark 0 - 0
Dark-Black 0.606 - 0.875
If we omit the three missing alleles, our tool produces 0.891 and 0.109 probabilities for the intermediate and dark-black category respectively, changing the prediction ranges to 0.891-0.125 and 0.109-0.875. However, note that this completely removes the locus from the prediction model, hence the prediction will not perform optimally (how the prediction model was made), therefore it is best to have some allele present to infer the most probable range for Cheddar Man and we therefore derive the ranges above from the extreme allele constellations only.
Final prediction: Dark/Dark-to-black skin
Explanation: The missing loci certainly impact on this prediction; however utilizing the input of all ancestral alleles is the preferred option over the use of the derived alleles at these loci – hence 0.394 for intermediate and 0.606 for Dark-black would be the most probable profile. That being said a broad range is present in both the intermediate and dark-black categories due to the missing loci. Also this effect, of skipping a skin colour prediction category with regards probability values, tends to be observed more often in admixed individuals. What is important to note is the input of the dark-black prediction is significant on the intermediate category and therefore it is acceptable to propose a dark complexion individual over an intermediate/light prediction even though the intermediate range is large. It is unlikely that this individual has the darkest possible pigmentation, however it cannot be ruled out. Better sequencing coverage would clarify to what degree this individual has a dark complexion.