Tag: India genomics

Visualization of genetic distances, part n

By Razib Khan | April 21, 2011 4:56 pm

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:

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CATEGORIZED UNDER: Genetics, Genomics

Genetics as the myth buster: Indian edition

By Razib Khan | March 28, 2011 1:17 pm

Whenever Zack Ajmal posts a new update to the Harappa Ancestry Project he appends some data to his ethnic database. This sends me to Wikipedia, because how many people are supposed to know what a “Muslim Rawther” means? Well, if you are a Muslim Rawther, and perhaps from Southern India, you would. But South Asian ethno-linguistic categories and hierarchies are notoriously Byzantine, and I have difficulty making sense of them. This isn’t too surprising in my case, as my family’s background is relatively mixed in the very recent past (e.g., Hindus and Muslims, and people of various caste backgrounds), so we’re not the sort who can go at length about our pure ancestry and all that stuff. Unfortunately, Wikipedia isn’t always useful, because the people editing the entries on particular South Asian ethnic groups are often people from those ethnic groups, so you get a lot of extraneous information, and a particular slant on how awesome and high achieving the group (also, sometimes there’s funny stuff about how notoriously good looking that particular caste!). On occasion there are other sources which are informative. For example, Zack has several individuals from the Tamil Nadar caste. I know a little about this group because 1) I have a friend whose family is Nadar (he’s American, so saying he’s an American Nadar is pretty worthless), 2) The New York Times profiled the group last fall.

When Zack noted that a group termed Tamil Vishwakarma had submitted entries, I went to Wikipedia. That was the first time I’d heard of the group. This is what I found:

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CATEGORIZED UNDER: Genetics, Genomics

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