In a post below I regenerated the HGDP PCA plot you’ve probably seen around, except that I added my parents (and a few HapMap populations) into the plot. The PCA below was basically a visualization of the two largest independent dimensions of genetic variance in the data set. It wasn’t to scale, as the vertical African vs. non-African dimension is somewhat greater than the horizontal west vs. east dimension in magnitude. But, I argued that the positioning of my parents was deceptive as to their heritage. In the comments John Emerson offers a hypothesis to salvage the possibility that the PCA is telling us something informative about my parents’ relationship to the Uyghurs:
Was there ever an endogenous Mughal group in South Asia? If both your parents distantly came from that group, even though assimilated to the local populations for a few generations, the Uighur connection would be unremarkable.
Combing the plot I generated with the historical information this is an eminently plausible model. But we need to consider what the PCA is showing us. The position of my parents’ is a reflection of their average genetic variance in relation to two …