ChromoPainter & fineSTRUCTURE on a South Asian data set

Over at Harappa DNA Zack ran ChromoPainter/fineStructure on his South Asian data set and posted the results. The new method immediately makes a few things clear: 1) The "South Asians" in the HGDP data set that's been used for so long are rather on the inbred side, and relatively genetically distinct as far as South Asian populations go. It goes to illustrate the importance of finely calibrating geographic coverage, and the consequences of the "Permit Raj." 2) Some of the Gujarati individuals in the HapMap also shake out as a moderately tight group (the square in the middle of the graphic above). Not too surprising, but rather striking. Another illustration of the importance of selecting representative and informative populations for any given region. 3) In the clustering spreadsheet Zack found that my parents aligned with a Brahmin from trans-Himalaya India and some Indians from Singapore, all notable for clear East ...