Here are their ethnic backgrounds and the results spreadsheet. Also relevant are the reference I admixture results.
The interesting samples here are the two Iraqi Arabs (HRP0042 & HRP0043) who have some African admixture.
If you can't see the interactive bar chart above, here's a static image.
PS. This was run using Admixture version 1.04.
Here are their ethnic backgrounds and the results spreadsheet. Also relevant are the reference I admixture results.
The interesting samples here are the two Iraqi Arabs (HRP0042 & HRP0043) who have some African admixture.
Also, we finally have a couple of Bengalis (HRP0049 & HRP0050) who have 13% East Asian for this run which is less than Razib's (HRP0002) and his parents' 19-20% but still higher than others.
If you can't see the interactive bar chart above, here's a static image.
PS. This was run using Admixture version 1.04.
You have likely seen the 23andme ancestry painting and probably Doug McDonald's chromosome painting too. This is not quite the same.
Instead of looking at ancestry of segments, I am looking at ancestry of whole chromosomes. My curiosity for this analysis derives from my lovingly homozygous chromosome 9 and a-little-African chromosome 8.
Basically, this is the same Admixture analysis with Reference I dataset and a batch of Harappa project participants, except that instead of using all 22 chromosomes, I ran admixture separately on each chromosome.
Since each chromosome's data was separately processed, the ancestral components inferred for each chromosome are not exactly the same. In practice, at K=4 ancestral components, they stayed reasonably constant, but the errors are larger than the overall autosomal admixture analysis. So you should be wary of assigning significance to minor changes in percentages from chromosome to chromosome. As a rule of thumb, a difference of greater than 5% from the autosomal should be required for you to give it some thought.
I have run the same admixture analysis with K=6 for this group. Once I have analyzed that, I'll write about it. If you guys think it's something worth doing, then I can run the same analysis for the latter batches. Otherwise, we can look directly into proper chromosomal segment painting.
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.
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:
I wish I had a thousand South Asian samples to play with. I wonder how this dendrogram would look in that case.
Here are their ethnic backgrounds and the results spreadsheet. Also relevant are the reference I admixture results.
In case you guys are wondering, the new thing here are the results fro HRP0031 to HRP0040.
If you can't see the interactive charts above, Javascript might be disabled on your browser. Here's a static image for HRP0031 to HRP0040 admixture run.
PS. This was run using Admixture version 1.04.
Here are their ethnic backgrounds and the results spreadsheet. Also relevant are the reference I admixture results.
In case you guys are wondering, the new thing here are the results fro HRP0031 to HRP0040.
PS. This was run using Admixture version 1.04.
Here are their ethnic backgrounds and the results spreadsheet. Also relevant are the reference I admixture results.
In case you guys are wondering, the new thing here are the results fro HRP0031 to HRP0040.
PS. This was run using Admixture version 1.04.
I have improved the Admixture bar charts further. As per your demands, ethnicity information is now available in a table right below the bar plot, in the same order as the bar plot IDs.
Also, you can click on any of the legend color rectangles on the right to sort the bar chart and the table by that ancestral component. Similarly, click on the header row of the table to sort by a column.
I might make some minor tweaks to this one.
Here are their ethnic backgrounds and the results spreadsheet. Also relevant are the reference I admixture results and this batch's results at lower K.
Batch 3 Admixture K=12
If you guys can confirm that the interactive bar chart is working well for you, then this is the last static bar plot.
PS. This was run using Admixture version 1.04.
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