File:Multidimensional scaling components discriminating genetic clusters in Africa.png

English: Multidimensional scaling components discriminating genetic clusters in Africa.

We used multidimensional scaling (MDS) to discriminate clusters of genetic variation within Africa and neighboring regions. MDS was applied to the pairwise, individual identity-by-state (IBS) matrix of 279,500 SNPs using PLINK 1.07 software. The top three MDS components were plotted together using R 2.11.1. A) In axis one is plotted dimension 1 and in axis two is plotted dimension 2. B) In axis one is plotted dimension 1 and in axis two is plotted dimension 3. Population colors match Figure B (k = 8), with the exception that the Fulani group was highlighted as a distinct population, indicated in light green. North African populations are all indicated in turquoise except for Tunisians that are shown in dark blue.

Our North African population samples are clearly differentiated from other African populations. MDS component 1 separates sub-Saharan Africans from populations that currently reside outside of Africa (OOA), and the North African populations cluster closest to the Near Eastern Qatari. A subset of individuals are intermediate between the North and sub-Saharan African samples. MDS component 2 differentiates western from eastern sub-Saharan Africans (Figure A). MDS component 3 differentiates populations thought to have a high degree of autochthonous ancestry (i.e. Tunisian Berbers and Saharawi) from populations outside of Africa. Interestingly, the MDS component 3 appears to be largely independent of the amount of sub-Saharan ancestry (Figure B) and North Africans are dispersed along the MDS component 3 axis, with the Tunisian Berbers occupying the extreme end of this gradient.