Razib investigates an unexpected region of South Asian admixture in Daniel MacArthur of GenomesUznzipped, and wonders why this has never been found before, despite the fact that his data was out in the public for a while.
I was surprised about this myself, since I had studied this data when I was starting my ADMIXTURE experiments a couple of years ago. But looking back at that old experiment, it's immediately clear why Dr. MacArthur's column (highlighted) showed no evidence of South Asian admixture at the time: there was no South Asian ancestral population in that reference set!
Naturally, I was curious to see what would turn up if I ran this sample again through my most recent globe13 calculator, which I did using the "bychr" mode of DIYDodecad, which treats each of the 22 autosomes separately:
A clear outlier is indeed shown on chr10 which shows 20.51% "South_Asian" admixture; most of the other chromosomes lack this altogether, so this seems like a legitimate signal of admixture.
I next used the "byseg" mode of DIYDodecad in order to (i) localize this admixture signal within chr10 and study it further. Furthermore, I used the paint_byseg script in order to show how the top-4 components within chr10 varied along the length of the chromosome:
It does appear that a good portion of the first half of chr10 has "South_Asian" ancestry, with the signal close to ~50%, which is a fairly good indication that one half of the diploid genome in this region has this type of ancestry.
Interestingly, the South_Asian signal does not appear "constant" along this portion, but in some of its troughs, the "West_Asian" component shows a corresponding local peak. Now, this might be the case of one really long segment of ancestry which is interpreted sometimes as South_Asian, sometimes as West_Asian by the software, given that the South_Asian component inferred by ADMIXTURE is a composite of West_Asian-like Ancestral North Indians (ANI), and Ancestral South Indians (ASI). But, we can investigate this further by using globe4, which looks at the same chromosome at a lower level of resolution:
So, on balance I would say that there does indeed appear to evidence of South Asian ancestry within chr10 for this sample, and, moreover, this type of South Asian ancestry is probably partly ASI-related.