A month ago I asked for a Malagasy genotype. Almost immediately I received a response from someone that was 33% Malagasy. More recently I have sent a genotyping kit to someone who is Malagasy. Those results should come in within a month or so. But a few days ago I received a contact from a person of the Merina ethnic group of highland Madagascar. So of course I ran their data. Here are the technical logistics. I wanted to look at their genotype through an African and a Southeast Asian lens. So I created an African loaded data set with 400,000 markers. Unfortunately the Southeast Asian data set I have has only 56,000 markers, and only 18,000 in common with this genotype. I ran ADMIXTURE on the former data set, K 2 to K 11. But at only 18,000 markers I think there just isn't enough to run ADMIXTURE and make inferences of the grain which I want to make. So I ran EIGENSOFT to generate PCA's. I did this for the African data set too. From dimension 1 to dimension 10. I uploaded all the files to Google Docs. You can look at the Southeast Asian weighted PCA's there. I'm not going to post them. The Asian ancestry of the Merina individual does look to be similar to that of Malays. What you'd expect. Below are K = 10 and PC's 1 and 4.
The African ancestry of this individual is not exotic at all, and aligns with what we saw in the ~33% Malagasy individual.