Zack Ajmal has been taking his Reference 3 data set for a stroll over at the Harappa Ancestry Project. Or, more accurately, he's been driving his computer to crunch up ADMIXTURE results ascending up a later of K's. Because it is the Harappa Ancestry Project Zack's populations are overloaded a touch on South Asians. He managed to get a hold of the data set from Reconstructing Indian History. If you will recall this paper showed that the South Asian component which falls out of ancestry structure inference algorithms may actually be a stabilized hybrid of two ancient populations, "Ancestral North Indian" (ANI) and "Ancestral South Indian" (ASI). ANI are a population which can be compared pretty easily to other West Eurasians. There are no "pure" groups of ASI, but the indigenous peoples of the Andaman Islands are the closest, having diverged from the mainland ASI populations tens of thousands of years ago. At K = 11, that is, 11 inferred ancestral populations, Zack seems to have now stumbled onto the patterns which one would expect from this hybrid model of South Asians. Let me quote him:
Now let’s take all the reference populations with an Onge component between 10% to 50% and use the equation above to calculate their ASI percentage. The results are in a spreadsheet. There are several populations with an even higher Ancestral South Indian than any of the Reich et al groups, with Paniya being the highest at 67.4%.
The r-squared between % ASI and % Onge, an Andaman group, is 0.994. That means 99.4% of the variation in the former can be explained by variation of the latter. The % ASI is consistently higher than Onge. Why? The last common ancestors of Andaman Islanders and the ASI diverged on the order of tens of thousands of years ago. Dienekes observed ADMIXTURE needs good reference populations, and the Onge have been so long diverged from the last common ancestor with the mainland ASI populations that it's not a perfect proxy for this ancient group. But it seems that the underestimate is systematically biased in the same direction, so that explains the good fit between the two trends. Zack naturally generated a pairwise matrix of Fsts between these inferred ancestral populations. Remember, the value within Fst shows the proportion of the genetic variance in the two populations which can be partitioned across them, but not within them. So it's a rough measure of genetic distance. Here's the matrix. I've renamed some populations:
S AsianAndamanE AsianSW AsianEuropeanSiberianW AfricanPapuanAmerindianKhoisan/PygmyE African
