Tuesday, September 27, 2016

ANI, ASI, etc.

CIP wrote in the comments to the previous post about the 2016 Reich paper:
This is in accord with the conventional view that Europeans and Asians probably separated after leaving Africa in the Middle East. East Asians then separated from South Asians in India and Amerindians and related groups separated from East Asians much later.
Guest wrote in the comments about the 2009 Reich paper:
One, the ‘Ancestral North Indians’ (ANI), is genetically close to Middle Easterners, Central Asians, and Europeans, whereas the other, the ‘Ancestral South Indians’ (ASI), is as distinct from ANI and East Asians as they are from each other. By introducing methods that can estimate ancestry without accurate ancestral populations, we show that ANI ancestry ranges from 39–71% in most Indian groups, and is higher in traditionally upper caste and Indo-European speakers. Groups with only ASI ancestry may no longer exist in mainland India. However, the indigenous Andaman Islanders are unique in being ASI-related groups without ANI ancestry.
Guest wrote this in another comment:
You are confusing the ANI and Indians who currently live in the North. All Indians studied in the Reich paper (except Andamese) are mixtures of ANI and ASI, and consequently more related to each other than to outside groups like West Eurasians. The two papers are quite consistent, and David Reich is an author on both papers.

My response:

The 2009 paper has a diagram like this (my diagram is not to scale, but is topologically correct):

What does the 2016 paper tell us?  It tells us that all Indians (all the mixtures of ANI and ASI) are neighbor-joining closer to a group that includes East Asians and Amerindians; and in line with the CIP comment above, the chart should look like (topologically, but not to scale):

East Asian and Amerindian form a group.  While per 2016, all mixtures of ANI and ASI are closer to this group than to Europeans, I'm not moving ASI from its position in the 2009 paper.  

I think it is remarkable that the 2016 paper seems to state that
1. All mixtures of ANI + ASI are closer to the (East Asian + Amerindian) group than to European.

2. India has definitely had mixing with peoples from its west, whereas India has been reproductively isolated from the Amerindians for more than 14,000 years.  Despite this, Indians (all ANI, ASI mixtures) are closer to (East Asian, Amerindian).   It seems that the mixing simply does not show up on the resolution of the 2016 chart.
Remember, the neighbor-joining algorithm creates a group of all (ANI, ASI) mixtures.   It creates a group of (East Asians, Amerindians).  It creates a group of various {Europeans}.  And it then chooses to group the (ANI, ASI) mixtures with the (East Asian, Amerindians) group, and not with the {Europeans}  group. Note that in the groups mentioned in the 2016 paper,  Pathans are around 71% ANI, Madiga around 32% ANI.
3.  Certainly, the topology above can be drawn equivalently in many ways.  It can be drawn putting ANI just to the right of {Europeans}, to make ANI appear to be close to {Europeans}.  But ANI {32%-71%} is closer to {East Asian, Amerindian} than to {Europeans}.  That is the only way to read the 2016 paper, and that is how I have drawn the diagram, so as not to mislead.

4.  The last point is why don't people create charts like this?

What happened to the Europeans? 
Well, in the 2009 paper, what happened to the East Asians?  One can include Europeans as the dashed line below - notice that it is a very non-Eurocentric way of drawing exactly the same topology.

The answer is that the geneticists are, in my opinion, making some assumptions about history, largely because of the Indo-European language hypothesis, and perhaps because of the Colin Renfrew-ish hypothesis of a population explosion of the from-the-west-bringers-of-agriculture to India.

The 2009 and 2016 papers are not inconsistent.  But the 2009 paper exhibits the assumption geneticists make, not based on their own science, but from a particular reading of history.

PS: Since the commenters in my previous post simply don't get the point: suppose for arguments' sake, ANI was identical to European.  Then the 29%-68% ASI mix in the Indian groups would distance the Indian groups from European.   But it is surprising that the entire set of {European=ANI, ASI} mixes is closer to {East Asian, Amerindian} than to European.  
Based on historical biases, we should have expected Pathan, Balochi, Makrani to first form a group with Iranian, and so on. Sorry, they don't.  Even the Hazara, Shia and Persian-language speaking, are not close to the Iranian.   Likewise with the Tajik, who speak a Persian language (though the Tajik are largely Sunni).

Culture, language and genes are rather disjoint.