I was inferring genetic traits of ancient individuals, among them the “Cheddar Man”, whose pigmentation phenotype I thought was well established from his genotype.

However, most of the 58 trait markers I was checking for could not be called reliably (with MAPQ ≥30 and base quality ≥30). Most markers had no reads at all, several others were supported by only a single read. This included markers like HERC2/OCA2 rs12913832 for eye colour, likewise SLC24A5 and SLC45A2 used to infer skin pigmentation.

So I switched to Loschbour, who was broadly from the same Mesolithic horizon, because the published genome has about 22x coverage, which makes him a very suitable candidate for this type of analysis.

Appearance and some genetic traits of the Loschbour individual

Eye colour: likely blue

Loschbour was G/G at rs12913832, with all 21 reads supporting G. This strongly implies blue eyes.

Hair colour and texture

Hair colour

The HIrisPlex hair-colour markers were well covered, with 9 to 23 reads per site.

The major MC1R red-hair variants rs1805007, rs1805008, and rs1805009 were absent, likewise the blond-derived allele at KITLG rs12821256. Loschbour was also ancestral C/C at SLC45A2 rs16891982. Together, these results favor dark hair.

In the 2014 HIrisPlex analysis reported in “Ancient human genomes suggest three ancestral populations for present-day Europeans”, the probability of dark hair was 97.8%: 57.9% for black and 41.3% for brown. A later HIrisPlex-S reanalysis in “Ancient genomes indicate population replacement in Early Neolithic Britain” (2019) inferred probabilities of 53.2% for brown hair and 46.3% for black.

Hair texture

At TCHH rs11803731, Loschbour was heterozygous:

The T allele has been associated with a greater likelihood of straight hair.

The derived EDAR V370A allele, associated with thick straight hair and several other traits in East Asian populations, was absent.

Beard density

The beard-density markers showed mixed tendencies.

Skin pigmentation

Loschbour carried the ancestral state at both SLC24A5 rs1426654 and SLC45A2 rs16891982, with strong read support: 20/20 reads for SLC24A5 and 17/17 reads for SLC45A2.

The derived alleles, which Loschbour did not have, are associated with lighter pigmentation in later Western Eurasians. Two markers, however, are not enough to reconstruct Loschbour’s exact skin tone.

A published HIrisPlex-S analysis incorporating a larger set of pigmentation variants instead assigned Loschbour an 89.3% probability of having an “intermediate” skin-tone.

For comparison, I applied the scoring method used by the YSEQ Phenotype Predictor to the phenotype markers. Since I no longer had the BAM at this point, I could only score the markers I had already extracted. Using the nine available markers resulted in scores of 38.2% Light/pale, 37.2% Moderate and 24.6% Dark/olive.

Freckling: possible

Loschbour was homozygous T/T at IRF4 rs12203592. The T allele at this marker has been strongly associated with freckling and increased sun sensitivity among Europeans.

Height: shorter stature

I also analysed the genome using the PGS002804 polygenic score for height (based on the Yengo et al. height score).

The score uses 1,099,005 variants. For Loschbour:

• 1,089,338 variants had confident genotype calls (call rate of 99.12%).
• The usable reads had a mean depth of 20.3×.
• Matching these calls against the 1000 Genomes reference panel left 1,083,087 variants for the comparison.

Loschbour’s matched raw height PGS was 0.9671. In comparison with 503 present-day Europeans from the 1000 Genomes Project, this was 3.23 standard deviations below the mean. No individual in that panel had a lower score.

Relative to this present-day European reference panel, the score points to a strong genetic tendency toward shorter adult stature.

His skeleton has been estimated at approximately 1.60 m (5′3″) tall, which is in line with the polygenic height score.

ABO blood group

rs8176719: the O-frameshift

Eight high-quality reads covered this site, all with the GRCh37 reference/deletion state, supporting the frameshift allele resulting in blood group O.

A/B-discriminating markers

Neither marker carried the common B variant.

Therefore, Loschbour was very likely blood group O, with an O/O genotype.

Rhesus blood group

The mean sequencing depth across RHD and RHCE was:

RHD mean depth  = 3.988×
RHCE mean depth = 7.840×

RHD / RHCE = 0.509

Using the common whole-genome sequencing copy-number approximation,

(RHD coverage / RHCE coverage) × 2

the estimated RHD copy number is:

≈ 1.02 copies

Several RHD exons also had sequence coverage. The estimated copy number of about one fits an RHD-hemizygous genotype: one chromosome with RHD and one without it.

This means Loschbour was probably RhD-positive, with possibly a D/d configuration.

Other common Rh antigens

At the major C/c-associated marker in RHCE (rs676785), all 13 reads carried G, supporting the c state.

At rs609320, the 9 C and 4 G reads indicate E/e heterozygosity.

Thus, the probable Rh phenotype is D+ C− c+ E+ e+. This is less certain than the type O result.

Other inferred traits

Lactose digestion

At MCM6/LCT rs4988235, Loschbour lacked the lactase-persistence allele, with 19 reads supporting the non-persistence state. rs182549 likewise carried the non-persistence variant. Together, these markers indicate lactase non-persistence.

Earwax and apocrine secretion (ABCC11 rs17822931)

Loschbour lacked the ABCC11 variant responsible for dry earwax and reduced apocrine secretion. The expected phenotype is therefore wet-type earwax with normal apocrine secretion.

Bitter-taste perception

All three TAS2R38 markers had good coverage. The result is consistent with relatively strong sensitivity to bitter compounds.

Conclusion

These results support several commonly reported traits in Loschbour, including light eyes, dark hair, lactase non-persistence, and blood group O.

For skin pigmentation, the ancestral SLC24A5 and SLC45A2 states alone would suggest relatively darker pigmentation, but broader analyses seem to place Loschbour closer to an intermediate category.