A week ago I pointed out that in some visualizations of world wide population variation South Asians & mestizos seem to overlap which each other to a great extent. The reason for this is that both populations can be modeled as admixtures between two separate, but related, populations. Mestizos are the products of pairings between Europeans and indigenous America populations, while South Asians seem to be a stabilized hybrid population which emerged from the fusion of a West Eurasian (closely related to European) and East Eurasian (distantly related to East Asians) populations. The East Eurasian ancestors of South Asians may be distantly related to indigenous American populations, but in a world wide scale the relationship is relatively close (i.e., compared to Europeans vs. indigenous Americans). So when mapped onto a plot of genetic variation incorporating world wide populations South Asians and mestizos naturally resemble each other. That said, a commenter observes:
Great example of how two dimensions lose information. Given how different the two populations are genetically, guarantee that the third component separates them pretty cleanly.