Punjabi and What?

Looking at the admixture analysis for my Harappa Ancestry Project, I count 6 Punjabis (not including my sister and I). Let’s average those six and compare them to me and my sister.

Ancestral Pop Average Punjabi Me My sister NSA1 NSA2
South Asian 46% 38% 35% 7% 7%
Balochistan/Caucasus 35% 35% 34% 32% 30%
Kalash 5% 5% 2% -1% 0%
Southeast Asian 1% 0% 1% 1% 1%
Southwest Asian 0% 10% 12% 43% 40%
European 11% 6% 7% -7% 0%
Papuan 0% 0% 1% 2% 2%
Northeast Asian 0% 0% 0% 0% 0%
Siberian 2% 2% 2% 4% 3%
Eastern Bantu 0% 0% 0% 0% 0%
West African 0% 1% 2% 6% 6%
East African 0% 3% 3% 12% 11%

As you can see, the major difference between the Punjabis and me is my Southwest Asian and African percentages.

Now, I know that a quarter of my ancestry is not South Asian. So let’s try to estimate the admixture percentages for that ancestry. Being three-quarters Punjabi (I think), let’s average my sister’s and my results and then subtract 3/4th of the average Punjabi results from them. Then, multiply by 4 and you get NSA1 in the table above, which is supposedly my non-South-Asian ancestor.

Since some of the percentages are negative, I set those to zero and rescaled all the others so that they summed to 100%. That is NSA2.

I computed the average admixture results for a bunch of reference populations. Let’s compare NSA1 and NSA2 to those populations.

The top five populations most similar to NSA1 are:

  1. Yemenese
  2. Jordanians
  3. Palestinian
  4. Egyptians
  5. Syrians

For NSA2, we get the same five populations but the Egyptians and Palestinians exchange places.

This shows roughly that my quarter ancestry is most likely from the Middle East region of Egypt, Arabia or the Levant.

Let’s look at it another way. If I know that I have Punjabi and Egyptian ancestry, I can use the average Punjabi and average Egyptian admixture percentages to calculate my percentage of both ancestries since that has to sum to 100%. So:

Zack = p * Punjabi + (1-p) * Egyptian

And we solve for p using least squares.

I got 81.3% Punjabi for myself and 75.8% for my sister. On average, that’s 78.5% Punjabi and 21.5% Egyptian, which is pretty close to our genealogical information.

Harappa Clustering

As I had computed the admixture percentages for myself, my sister and other participants in my Harappa Ancestry Project, I decided to do some clustering analysis on them to see which persons clustered together. The resulting tree for a hierarchical clustering is as follows. It shows which persons are the most similar.

I am HRP0001 and my sister is HRP0035. As expected, we cluster together and then with a half-Sindhi half-Balochi guy and finally with all the Punjabis.

Since I have a lot of reference populations in my data, I did the same cluster analysis using the average admixture results for each reference analysis. Here’s the section of the tree containing my sister and me.

This time we cluster with the Bene Israel, a Jewish tribe from Bombay, India, though our similarity with them is not that great. Then with the Punjabis, Sindhis and Pathan.

Doing the same analysis with individual samples from my references,

A weak clustering with Burusho!

If I use PCA (Principal Component Analysis) results to compute hierarchical clusters, you can see that I am an outlier among the South Asian participants.

If you look at my PCA coordinates, you’ll realize that among the 365 South Asians I used in the analysis, I am one of the five complete outliers.

However, when I use model-based clustering on the PCA results, I end up in a really weird, loose cluster (CL9) with a Kashmiri, 5/21 Balochis, 2 Bene Israel Jews, 3/23 Brahui, 1/25 Burusho, 8/17 Makranis, 2/21 Pathans and 3/22 Sindhis. This is mostly a group of outliers and those who have some African admixture.

My Harappa Project Results

I have been blogging up a storm on Harappa Ancestry Project with more than 50 posts since I last linked to it.

Let’s see what I have found out about myself there. Here are the admixture results for me and my sister:

Me My sister
South Asian 37.9% 34.8%
Balochistan/Caucasus 34.7% 34.2%
Southwest Asian 9.8% 12.3%
European 5.9% 7.2%
Kalash 4.5% 2.3%
East African 3.1% 3.0%
West African 1.4% 1.8%
Siberian 2.4% 1.8%
Papuan 0.2% 1.0%
Northeast Asian 0.2% 0.3%
Southeast Asian 0.0% 1.3%
Eastern Bantu 0.0% 0.0%

You can see the results of all the participants in a spreadsheet or in a nice interactive bar chart. I am HRP0001 and my sister is HRP0035.

Interestingly, both McDonald and 23andme ancestry painting show my sister to have more African admixture than me, but here I have about the same East African as her and even her West African percentage is only a tiny bit higher.

To figure out what these ancestral populations mean, do read the post about the reference population analysis.

Harappa Ancestry Project Update

I have got 25 participants to the Harappa Ancestry Project now. But we still need more especially from the Hindi belt.

I have been detailing the datasets I am using:

I have also started admixture analysis of the reference populations and first batch of project participants.

Harappa Project New Site

As several people had asked, I have set up a separate website for the Harappa Ancestry Project at http://www.harappadna.org/.

I am keeping a link to the new site on the top menu bar here titled Harappa DNA.

I might also crosspost some items from the project here.

I have also set up a Facebook page for the Harappa Ancestry Project. Please like it on Facebook so I can get a nice short name for the Facebook page URL.

I have received several samples and will be reporting some analysis results soon. However, I do need lots of participants, so please spread the word.

Cross-posted at Harappa Ancestry Project.

Harappa Ancestry Project

I have become interested (some would say obsessed) with genetics recently. I wrote about getting my DNA test done and there’s a lot more about my own results that I plan to bore you with.

One fun application of genetic testing is inferring ancestry: Which ancestral group are you descended from? Can we estimate the admixture of the different population groups you are descended from?

Most DNA testing companies provide information about ancestry and genetic genealogy has taken off. With several genome databases (HapMap, HGDP, etc) and software (like plink, admixture, Structure) publicly available, the days of the genome bloggers are here. And I am trying to be the latest one.

In starting this project, I have been inspired by the Dodecad Ancestry Project by Dienekes Pontikos and Eurogenes Ancestry Project by David Wesolowski. The catalyst for this project was my friend Razib who I bug whenever I need to talk genetics.

What is Harappa Ancestry Project?
It is a project to analyze (autosomal) genetic data of participants of South Asian origin for the purpose of providing detailed ancestry information. So the focus of the project is on South Asians: Indians, Pakistanis, Bangladeshis and Sri Lankans.

The project will collect 23andme raw genetic data from participants to better understand the ancestry relationships of different South Asian ethnicities.

I have named it after Harappa, an archaeological site of the Indus Valley Civilization in Punjab, Pakistan.

Participation
People of South Asian origin, or from neighboring countries, are eligible to participate. The list of countries of origin I am accepting are as follows:

  • Afghanistan
  • Bangladesh
  • Bhutan
  • Burma
  • India
  • Iran
  • Maldives
  • Nepal
  • Pakistan
  • Sri Lanka
  • Tibet

Right now, I am only accepting raw data samples from people who have tested with 23andme.

Please do not send samples from close relatives. I define close relatives as 2nd cousins or closer. If you have data from yourself and your parents, it might be better to send the samples from your parents (assuming they are not related to each other) and not send your own sample.

If you are unsure if you are eligible to participate, please send me an email (harappa@zackvision.com) to inquire about it before sending off your raw data.

What to send?
Please send your All DNA raw data text file (zipped is better) downloaded from 23andme to harappa@zackvision.com along with ancestral background information about you and all four of your grandparents. Background information would include where they were born, mother tongue, caste/community to which they belonged, etc. Please provide as much ancestry information as possible and try to be specific. Do especially include information about any ancestry from outside South Asia.

Data Privacy
The raw genetic data and ancestry information that you send me will not be shared with anyone.

Your data will be used only for ancestry analysis. No analysis of physical or health/medical traits will be performed.

The individual ancestry analysis published on this blog will be done using an ID of the form HRPnnnn known to only you and me.

What do you get?
All results of ancestry analysis (individual and group) will be posted on this blog under the Harappa Ancestry Project category. This will include admixture analysis as well as clustering into population groups etc.

I suggest you read about Dienekes’ analysis on South Asians for an idea about what to expect.

You can access all blog posts related to this project from the Harappa Ancestry Project link on the navigation menu on every page of my website. You can also subscribe to the project feed.