Monthly Archives: March 2011 - Page 6

Harappa and Reference I Dendrograms

Posted by on March 1, 2011 7 comments

Looking at the Harappa dendrogram and the dendrogram for reference I, I thought I would combine them to see where our project participants fit.

Then I got more curious. I wanted to see a similarity tree of all the samples in reference I (2,654) plus the 40 Harappa participants I have processed till now. That came out to be such a huge tree it was impossible to save it in a way to be legible. Finally I compromised by selecting only the South Asian samples from the Reference I dataset and putting them together with the Harappa data. Unfortunately, that doesn't give the Iranian and European-admixed participants any information. I'll have to analyze those separately.

Anyway, here's the South Asian Admixture Dendrogram in PDF format. That means you can search for "HRP" to find all the project members, which is why I like PDF in this case better than an image.

Note that Singapore Indians are such a good stand-in for South Indians.

Harappa Admixture Dendrogram

Posted by on March 1, 2011 18 comments

Using the ancestral component percentages from the Admixture run at K=12 for Harappa Project participants, we can calculate the pairwise Euclidean distance between them. These distances can be used to create complete linkage (i.e. furthest neighbor) hierarchical clustering, which you see below.

Note that this is not a phylogeny. It just visualizes the closeness of your admixture results to others.

Thus in terms of admixture results, the Punjabis mostly cluster together along with the Rajasthani (HRP0033), except for my family (HRP0001 and HRP0035) who cluster (not so closely) with the Sindhi-Balochi guy (HRP0039) likely due to the Southwest Asian and African components.

Interestingly, the Bihari Brahmin (HRP0003) is very different from the Bihari Kayastha participant (HRP0032). The Caribbean Indian samples (HRP0027 & HRP0028) cluster with the Bihari Kayastha, so we can't really say for sure where from India their ancestors originated from.

The South Indian Brahmin samples seem to vary consistently from the non-Brahmin ones.

The Iranians cluster closely except for the Khorasanian HRP0034 and Assyrian HRP0010. The Assyrian Iranian sample is actually closer to the Iraqi/Egyptian Jewish sample (HRP0037) than to other Iranians.

The participants with recent European admixture cluster very loosely with each other. Other techniques will need to be used to pinpoint their specific South Asian origins.

If we make a cut at about 0.3 on this tree, we get 3 South Asian clusters:

  • the Northwest of South Asia
  • South Indian Brahmins, Bihari Brahmin, UP Brahmin
  • South Indian non-Brahmin, Bihari non-Brahmin, Bengalis, Caribbean Indians

I wish I had a thousand South Asian samples to play with. I wonder how this dendrogram would look in that case.