Clusters Galore: African edition

I gathered about 900 individuals from the Dodecad Project and the literature and run Clusters Galore on them. Dodecad Project members were included if any of the following conditions held:

1. They were in the North_African_D, North_African_Jews_D, or East_African_D population
2. They had at least 10% "Northwest African" in the standard K=10 analysis
3. They had at least 10% "West African" in the standard K=10 analysis
4. They had at least 10% "East African" in the stanard K=10 analysis

Integrating among multiple datasets meant that the analysis was done on only 1,871 SNPs, which were however sufficient to infer 28 clusters with 9 PCA dimensions retained.

PCA plots

Below are PCA plots of the first nine dimensions; each dimension is paired with the 1st one to create 8 different scatter plots:

Galore/PCA results

All the results can be found in the spreadsheet, which contains:

• Population Galore results: how many individuals from each population are assigned to each cluster
• Individual Galore results: what is the probability that each ID belongs in each cluster (in %)
• Population PCA results: mean positions of populations in the first 20 principal components
• Individual PCA results: position of individuals in the first 20 principal components.

Some observations

It does appear that within Africa two processes explain most of genetic variation:

1. Variable affiliation with West Eurasians, with North Africans being most West Eurasian-like, followed by some East Africans such as Ethiopians, and then Maasai
2. Contrast between farmers and hunter groups such as the San and Pygmies

With respect to Project participants:

1. All members of East_African_D align with Ethiopians and Ethiopian Jews (cluster #2)
2. All members of North_African_Jews_D align with a major cluster of the Morocco_Jews of Behar et al. (2010) (cluster #3)
3. Members of North_African_D are split over three clusters: most are in the Algeria/Libya/North Morocco cluster #4; one is in the Egyptian cluster #5; three are in the Mozabite/Saharan/"Berber" cluster #7
4. The Other_D participants include many African Americans, as well as some Arabs with some African admixture, etc. Clusters #8 and #10 seems to include many African Americans.

Hopefully this will be useful to project partipants with an African background.