Neolithic Anatolia-Kinship Patterns

[real expert]

To those that are interested in phenotype prediction, in that study they found an Anatolian farmer with blond hair from 10, 000 years ago. Plus, people with pale to very pale skin tone were also found, although with low likely-hood. In terms of the obtained probabilities for pale to to very pale complexion, these findings stand in contrast to the CA/BA Italian and Aegean study.

Inferring phenotypic traits and inbreeding for Aşıklı-128

Phenotypic traits

We analyzed a number of functional SNPs (e.g., lactose tolerance, skin pigmentation, eye color) in the high coverage genome of Aşıklı-128. We restricted the analysis to this one individual with the highest coverage (5× ) to avoid excessive amounts of missing data. SNPs associated with phenotypes of interest were called from the BAM file using the samtools mpileup function143
and filtering with a mapping quality and a base quality lower than 30, as described in van de Loosdrecht et al. (2018).166
We retrieved the alleles associated with predicting skin, eye and hair color166
and computed the probability of skin, eye and hair shade for the Aşıklı-128 individual using the tool HIrisPlex (http://hirisplex.erasmusmc.nl/). Probabilities of 0.968, 0.019 and 0.009 for having intermediate, very pale and pale skin color were obtained respectively, including a high probability of having light hair color (> 0.99). Regarding the eye color prediction, probabilities of 0.547, 0.338 and 0.115 were obtained for brown, blue and intermediate color, respectively.
We further analyzed derived allele variants in the MCM6 gene associated with lactose tolerance in Europeans (rs4988235),167
Africans (rs41456145, rs145946881)168
,169
and Middle Easterners (rs41380347)168
,169
for the Aşıklı-128 individual. Aşıklı-128 shows a homozygous ancestral genotype for these SNP positions, as reported in previous studies that propose the appearance of the lactose tolerance allele much later than the Neolithic.23
,170
Thus, Aşıklı-128 individual was likely lactose intolerant and could not digest milk as an adult.

https://www.cell.com/current-biology/fulltext/S0960-9822(21)00423-1

 

[Alpakut]

Dodecad G13:

Anatolian_N:Ash002,2.69,0.59,0,0,18.16,0,56.31,0,0,14.96,4.78,0,2.51
Anatolian_N:Ash033,0,0,0,2.35,34.69,0,43.17,0,0.41,19.37,0.01,0,0
Anatolian_N:Ash040,0,0,3.58,0,18.28,0,58.15,0,0,15.64,3.82,0,0.53
Anatolian_N:Ash128,0.41,0,4.48,0.14,15.31,0.62,51.91,0.38,0,16.09,10.38,0,0.27
Anatolian_N:Ash129,0,0,2.03,0.34,15.16,1.32,57.54,0.31,0,15.99,7.32,0,0
Anatolian_N:Ash131,0,0,0,0.82,14.33,0,60.92,0,0.67,15.93,6.55,0.79,0
Anatolian_N:Ash133,0,0,2.04,0,15.87,0.61,54.87,0.5,0.03,14.14,11.35,0,0.58
Anatolian_N:Ash136,0,0,5.52,0,17.24,0,54.38,0,0.13,14.35,8.37,0,0
Anatolian_N:CCH144,0,0,0.7,0.78,24.42,0,45.84,1.18,0,26.72,0.36,0,0
Anatolian_N:CCH163,1.62,0,0.57,0,22.29,0,56.07,0,0,11.05,8.39,0,0
Anatolian_N:CCH285,0,0,3.22,0,19.16,0,60.51,0,0,13.45,3.66,0,0
Anatolian_N:CCH289,0,0,1.48,0,25.78,0,52.54,3.12,0.27,16.81,0,0,0
Anatolian_N:CCH290,0,0,1.35,0,12.46,0,67.95,0,2.35,15.22,0.67,0,0
Anatolian_N:CCH294,0,0,1.89,0,23.58,0,53.3,0.11,0.79,18.69,0,0,1.64
Anatolian_N:CCH311,0,0,2.25,0,19.61,0,53.79,0,0,19.34,5.01,0,0
Anatolian_N:cth006,0,0,0,2.46,37.04,0,47.46,1.01,0,11.27,0.75,0,0
Anatolian_N:cth217,0,0,0,0.7,26.06,0,54.31,0.08,0,14.26,4.59,0,0
Anatolian_N:cth728,1.96,0.19,0,1.8,20.17,0,56.42,1.13,0,17,1.33,0,0
Anatolian_N:cth739,0,0,2.45,0.14,20.48,0,55,0.66,1.68,18.95,0,0,0.65
Anatolian_N:cth747,0,0,1.2,0,23.56,0.92,46.37,0,0,22.58,5.37,0,0
Anatolian_N:cth842,0,0,0,0,22.08,0,57.71,0,3.58,12.41,3.25,0,0.96
Anatolian_N:pch034,0,0,1.35,0.79,23.75,0,49.25,1.09,0,18.07,5.71,0,0
[COLOR=#333333]Anatolian_N_(n=22),0.011363636,0.284090909,3.279090909,0.5,38.97363636,0.557727273,0,0.724090909,13.525,0.167727273,40.91318182,1.062272727
[/COLOR]

Can you generate Vahaduo codes for this? The average of all 22 sample would also be enough. Would be really great.

 

[Salento]

… please delete, wrong thread