Thursday, March 8, 2012

Afrasans in a Genome-Wide context.

A subset of the Intra-African dataset I have includes Afrasans, or Afroasiatic speakers. Afroasiatic is typically divided into 6 major categories or groups; Semitic, Berber, Egyptian, Chadic, Cushitic and Omotic. A 7th, but nearly extinct group, known as Ongota is contentious, but is by some included as its own branch within the Afroasiatic phylum. All of these Language groups, with the exception of Semitic, are exclusively found in Africa. The 211 Afrasan samples in the dataset belong to 4 or 5 of those groups mentioned, depending on how one accounts for any language shifts (that is shifts within the wider Afrasan phylum) that might have occurred. A rough table is shown below associating the 211 samples with current, and in some cases previously spoken language or language groups of Afroasiatic.

In general, Afroasiatic is thought to have emerged somewhere in the North Eastern section of Africa, anywhere from Ethiopia to Southern Egypt, in the genetic (Autosomal) sense, this area can perhaps be viewed as where such populations inhabiting that area in Africa, lie along a diagonal axis of the C1 vs C3 Intra- African MDSplot (at ~ 34°
from the horizontal), as highlighted below:
MDS plots
After extracting the 211 AA speaking samples from the 1065 sample African Dataset, I performed an MDS Analysis on it as seen below.
Component 1 separates Berber/Semitic/Egyptian speakers from Chadic speakers, with Ethiopian Semitic/Cushitic speakers plotting somewhere in between, but closer to the former in this separation. Component 2, separates Ethiopians+Egyptians from the rest.
Component 3 Separates the Mozabites from the Rest, with Ethiopians again retaining an intermediate position.

Model Based Analysis
The Logical value for a K selection would be 6, i.e. equivalent to the number of known Afroasiatic subgroups, however, since Omotic speakers are not present in the Dataset, I went ahead and run a K=5 unsupervised ADMIXTURE Analysis for the Afrasan Dataset.

The K=5 ADMIXTURE run produced the following FST distances,
The biggest separation for both Axis is for the cluster I nicknamed Cushitic, while the Berber, Semitic and Mozabite clusters appear pretty close, with the Mozabites looking a bit isolated.

The Median proportions for the clusters can be seen below.
The fact that the mozbites formed their own cluster, is intriguing, although one would suspect that inbreeding may play a role, since it can also be seen how the Mozabites cluster away from other North Africans in the 3D MDS plot, almost forming their own group. 

Therefore, to see what this analysis would look like without the Mozabites, I took all 27 of them out, leaving me with 184 AA speaking samples.

I repeated the same analysis as above on the newer Dataset.

MDS Plots
Components 1 and 2 behaved the same way as when the Mozabites were included, Component 3 however, without the Mozabites, separates Berber and Cushitic speakers from the rest to almost the same degree, unlike when the Mozabites were included.

Model Based Analysis
This second iteration of the Afrasan dataset that did not include the Mozabites created a Cushitic, Chadic, Berber and Egyptian clusters, with a 5th cluster which looked like a relic that is present in trace amounts in all the Afrasan samples except the Mada and Hausa. The Egyptian cluster is also found in highland Ethiopians, it also shows a more frequent occurrence of high Standard Deviation relative to all the other clusters;
So the Egyptian cluster looks like it gives less of a linguistic signal than the other clusters, it could potentially be inclusive of a Semitic signal as well as maybe other types of non-Afroasiatic Eurasian affinities.

It would be of great interest to see where Omotic speakears would fit into this analysis.


  1. They were supposed to release some data of Omotic groups (and additional Amhara samples) here under accession #phs000449 but it still hasn't been uploaded. My bet is that in global context they may be somewhere intermediate between the Oromo and Maasai samples, and in regional context they may be quite distinct and perhaps make their own cluster. We'll see.

    1. Yeah, I've been checking on that since you notified me last time, but haven't seen any thing. Do you think it would be in .bed format or some other type, like Behar's Series Matrix files, which is a pain in the .. to import into PLINK. I also hope these 26K SNPs I have would intersect well with the Dataset they would be eventually releasing with out thinning it out too much more....

    2. Usually it's in .ped or .bed format. If this isn't the case I'll find a way to convert it. IIRC, the data was based on the 1 mil illumina chip, so it's going to overlap with most datasets (affymetrix data generally has less dataset overlap).

    3. Well they presumably do have a .ped or .bed format or otherwise they wouldn't have been able to do this:
      "All of the 47 samples had high call rates (> 95%), and the software package PLINK [37] was used to estimate relatedness among individuals"
      I do hope they upload the files in that same format and hopefully sooner rather than later, BTW these are locations and quantities of the samples:

      - 28 male individuals living in the Amhara region in Debele, which is near Debre Birhan
      -nine individuals living in Gieza (the Aari)
      -ten individuals living in Dimeka (the Hamer)

  2. Those look like interesting samples indeed.

    PS. You should check out this new software, perhaps you could try it out on the intra-african dataset:

  3. I've always though it was rather strange that so many genetic studies of North Africans indicate a rather miniscule genetic input from Tropical Africans. Considering people from South the Sahara have consistebtly coexisted with those in the Sahara. The people share a language family (that probably originate in the Horn of Africa) and still the genetic affinity appears small. Any insight into that at all?