So I decided to run the South Asian samples data which I had earlier done PCA/MClust on through ChromoPainter and fineSTRUCTURE.
Here is the coancestry matrix among the 715 participants visualized as a heat map.
fineSTRUCTURE can use this coancestry matrix to classify individuals into clusters, 52 in this case (compared to 38 using PCA and MClust). You can check the cluster assignments in a spreadsheet.
Note that I have named the clusters. That's just a shorthand so we don't have to refer to them by cluster number. Instead I used the population with the largest number of individuals in a cluster to label that cluster.
Here's the cluster-level coancestry heat map.
And the pairwise coincidence:
And finally PCA plots for the first 10 dimensions from fineSTRUCTURE.