u/NationalEconomics369

The individual I15499 only has 45k snps, so this model has high errors of 10%. I wonder if someone can create a passing model with low error despite the snp count. Dinka + Nuerat passes, but Dinka + Egypt TIP fails. Its interesting since for the kulubnarti nubians, Egypt TIP gives passing models more than Nuerat

https://www.nature.com/articles/s41598-022-25384-y/figures/4

I linked the Kadruka study which mentioned that Kadruka and Kenya_EPN form a clade relative to the samples used in panel B.  f4(Sudan_Kadruka1_4000BP, Kenya_EarlyPastoral_N; population X, Chimp) informs us whether X shares more alleles with Kadruka or Kenya EPN, if the |Z| is less than 3 according to the study then there is no detectable preference and population X shares an equivalent amount of genetic drift with Kadruka and Kenya EPN. In this case for Kadruka the Z is less than 3 for all samples, so it forms a clade with Kenya EPN relative to the tested populations in X.

Replicating the same test for this sample - f₄(Serbia_Roman_oAfr - I15499, Kenya EPN; X, Chimp), the absolute value Z for all runs was less than 3 where X was a list of the following https://pastes.io/4hdy6upQ . Results were the same when replacing Kenya EPN with Elmenteitan. Meaning that Kenya EPN and I15499 form a clade.

I tested if I15499 forms a clade with modern samples from the Horn , it does form a clade with Eritreans but does not form a clade with Somali for 4 samples with the |Z| < 3 threshold. Those 4 samples (Jordan PPNB, Israel MLBA, Natufian, Anatolia Neolithic) share more alleles with I15499 than with Somali. This individual had the haplogroups L2a1 and E-V32 both of which are very common in the Horn.

qpadm right left pops: https://pastes.io/xNIIxEJg

I noticed that there are several groups with similar levels of Cushitic admixture and they are all fairly close to each other genetically, yet they all look very different from each other.

In my opinion,

Southern/Eastern Nilotes with Cushitic admixture (Kalenjin, Maasai, Samburu, Datooga) show an equal influence of both Cushitic and Nilotic in appearance

Kunama show a bias towards unadmixed Nilotes but some can show a minor Cushitic influence

Tutsi and Hima show a bias towards Cushitic in appearance

I may be wrong and the reality is that they all look very similar to each other excluding outliers, but curious on others opinions here

Son I’m crying

PGS (polygenic score) predicts where you'll fall on a given trait (like height) compared to others, based on a bunch of genetic variants added together.

For this graph, i used the Yengo 2022 study, which captures ~40% of height variance in Europeans and applied it to East Africans

From the paper:

>In out-of-sample estimation and prediction, the 12,111 SNPs (or all SNPs in the HapMap 3 panel) account for 40% (45%) of phenotypic variance in populations of European ancestry but only around 10–20% (14–24%) in populations of other ancestries.

caveat here is that since I'm using the Human Origins (HO) dataset, it only covers a little over a third of the SNPs used in that study. So this graph really only captures a small percent of height variance in these populations. For Ancients in the 2nd image, I imputed since their coverage was not uniform like HO.

PGS are also typically least predictive in African populations, but I've found the results line up well with recorded heights in these groups. Graph is normed on the average of my dataset, so interpret Z = 0 as avg.

How to read

• Y-axis (PGS Z-score): Each individual's genetic predisposition for height, standardized so that 0 = the overall sample mean. Positive values = genetically predicted to be taller than avg
• X-axis: Populations, sorted left-to-right from lowest to highest median PGS.
• Box plots: Median (center line), interquartile range (box, 25-75th percentile), and whiskers (range excluding outliers).
• Dots: Individual samples.

Paternally dominated by E-V12(includes E-V32) and T-L208, but the maternal side was more diverse

R was the 'elite' cemetery. those buried there lived about 9 years longer than the S group and had more elaborate grave goods/burials

Interestingly, the lower class cemetery had more diverse ydna

Study: https://www.nature.com/articles/s41467-021-27356-8.pdf