1. Let me first say that I’m not a paleontologist or any kind of expert on Cheddar Man (CM). My interest thus far has been somewhat cursory. That said let’s start with the obvious. It isn’t possible to conduct a GWAS on a 9,000 year old skeleton. If they isolated markers from..
2. MC1R and IRF4, than they were able to produce at least partial sequences of C-16 and C-4 using this magical mystery technique. For the sake of argument, lets assume they did. The mutation that created red hair manifests itself in about 8 different alleles in MC1R.
3. The primary pigmentation locus in IRF4 is at rs12203592. The chart below is from an Australian study that shows allelic relationships to skin and hair color. Note there are no dark skin associations. 
4. If UCL was able to sequence the SNPs from SLC24A5, they should be able to do the same with HERC2 and OCA2 because they’re on the same chromosome.
5. mtDNA exhibits more longevity than chromosomal DNA. Viable samples are harvested from Egyptian mummies and old remains all the time so it’s conceivable that UCL could’ve sequenced it to using traditional techniques to identify CM’s mtHaplo.
6. To be clear, the genes we’re discussing exist in everyone. The alleles presented are what control the phenotype for lighter or darker skin. In SLC24A5 the lighter skin locus is the A111T (A) allele homozygous at rs1426654 which decreases melanogenesis;
7. contrast to the ala-111 (G) variant at same marker which increases melanogenesis leading to high skin pigmentation. The (A) allele mutation spread through the European population around 6,000-12,000 years ago. Prior to that, north and west Europeans had darker skin.
8. These associations at SLC24A5 only contribute to a range of 25-35% of total skin pigmentation as you stated in the video indicating that unless other loci can be identified using the 8-Plex System,
9. or through other genes in the melanin pathway not previously stated, (TYRP1, TYR, ALC42A5, POMC, HPS6, TPCN2, etc.) than we should conclude CM’s dark skin has been exaggerated.
10. Nearly every phenotype we know of is more polygenic than was thought just a few years ago. For example, we’ve now identified over 50 SNPs that control eye color alone; the single most important being rs12913832 of HERC2. The (C) allele suppresses OCA2 transcription reducing
11. melanin production in the iris, thus presenting the blue eye phenotype. This mutation was traced back to the northwest region of the Black Sea around 10,000 years ago. As CM is a 9,100 year-old WHG, it’s at least possible that he carried (C)rs12913832 but we won’t know..
12. ..unless UCL releases their sequencing data.
The phylogenetic pathway of L3–>U5 can be found in the link. If these origins are accurate, most of the bifurcations along this chain occurred in Asia or India prior to the inception of U5 in Europe.
en.wikipedia.org/wiki/Human_mit…
The phylogenetic pathway of L3–>U5 can be found in the link. If these origins are accurate, most of the bifurcations along this chain occurred in Asia or India prior to the inception of U5 in Europe.
en.wikipedia.org/wiki/Human_mit…
13. The early U5 clades were known for high resistance to the last LGM conferring survival advantages in cold climates. I’m guessing CM’s extended clade is U5b1(a) as it traces back to Britain during the neolithic.
14. The highest modern-day concentration of U5 is in the Sami people of the circumpolar regions of Scandinavia who are some of the whitest people in the world. For the sake of brevity I eliminated a few references to facts I cited above. I can provide them upon request.
15. If anyone has the 33-marker list released by UCL, please post link. All academics aside, the most pertinent point in this discussion is that whatever the level of melanin production in CM was, it has nothing to do with race. Race is not conferred by genes that produce melanin
