Category Archives: Admixture - Page 6

Admixture (Ref3 K=11) HRP0181-HRP0190

Here are the admixture results using Reference 3 for Harappa participants HRP0181 to HRP0190.

You can see the participant results in a spreadsheet as well as their ethnic breakdowns and the reference population results.

Here's our bar chart and table. Remember you can click on the legend or the table headers to sort.

If the above interactive charts are not working, here's a static bar graph.

HRP0181 is half-Punjabi Jatt and half-English and the admixture results are not too different from the average of the reference British and our other Punjabi Jatt participants.

HRP0183, a Khatri, has fairly high European component, less than the Jatts but higher than most other South Asians.

HRP0186 is the most West Asian (and thus least European) of all our Georgian participants.

HRP0188,a Haryana Jatt, has the highest European component (29%) of all South Asians I think. I am surprised at the results for the two Haryana Jatts. I would not have expected their results to be much different from the Punjabi Jatts. If anything, I thought the Haryanavis would be less European than the Punjabis. Now I want to get a few non-Jatt Haryanavi participants. Anybody know someone?

Admixture (Ref3 K=11) HRP0171-HRP0180

Here are the admixture results using Reference 3 for Harappa participants HRP0171 to HRP0180.

You can see the participant results in a spreadsheet as well as their ethnic breakdowns and the reference population results.

Here's our bar chart and table. Remember you can click on the legend or the table headers to sort.

If the above interactive charts are not working, here's a static bar graph.

HRP0171 is our 2nd Tamil Vellalar from Sri Lanka and the results are similar to HRP0169.

HRP0172 has 1/16 Romani ancestry. The Onge component is about 0.4% which could be noise or possibly evidence of a South Asian connection via the Romany.

HRP0174 and HRP0176 are Kerala Nairs.

HRP0175 is a Georgian Svan and pretty similar to HRP0138 (who is Georgian but not sure which local ethnic group).

HRP0177 (Azeri) is a bit more northern European than HRP0083.

HRP0178, our first Punjabi Khatri, has admixture results more like the Punjabi Jatts than Punjabi Brahmins.

HRP0179, who is 7/8 Turkish and 1/8 Kurd, has the highest Siberian component (5%) other than the Kazakh participant.

HRP0180 is our first Pashtun even if he's only half-Pathan (the other half being English). I have heard grumblings on the net about the HGDP Pathans not being representative of the Pashtun tribes. If we use the HGDP Pathans and 1000genomes British averages to estimate HRP0180's recent ancestry, we get 45.5% Pashtun and 54.5% British. So it seems that the HGDP Pathan samples are reasonable for at least this individual.

Admixture (Ref3 K=11) HRP0161-HRP0170

Here are the admixture results using Reference 3 for Harappa participants HRP0161 to HRP0170.

You can see the participant results in a spreadsheet as well as their ethnic breakdowns and the reference population results.

Here's our bar chart and table. Remember you can click on the legend or the table headers to sort.

If the above interactive charts are not working, here's a static bar graph.

HRP0161 is my mom.

HRP0169 is our first 100% Sri Lankan Tamil. Admixture results are close to the other non-Brahmin Tamils.

HRP0170 is a Haryana Jatt whose results match the other Haryana/UP Jatt.

Admixture Ref3 Dendrogram HRP0001-HRP0160

I haven't done any admixture dendrograms in a while, so I thought you guys might be interested.Особенности национального строительства. Стены помещения.

This uses admixture results using Reference 3. As usual, I used complete linkage for the hierarchical clustering.

Let's look at the dendrogram using regular Euclidean distance measure between admixture results.

I also decided to use chi squared distance measure to do the clustering.

PS. Any thoughts on the trees based on two different distance measures?

Admixture (Ref3 K=11) HRP0151-HRP0160

Here are the admixture results using Reference 3 for Harappa participants HRP0151 to HRP0160.

You can see the participant results in a spreadsheet as well as their ethnic breakdowns and the reference population results.

Here's our bar chart and table. Remember you can click on the legend or the table headers to sort.

If the above interactive charts are not working, here's a static bar graph.

There are several interesting participants here. HRP0151 is a quarter Nepalese and his/her results are actually quite odd. The East Asian ancestry shows up as Native American which is possible. I wonder if the quarter Chinese ancestry is not Han but rather some other Chinese ethnicity.

HRP0155 is Sri Lankan Sinhalese and has a lower Onge component than I expected.

HRP0158 is my Dad and has similar results as me (HRP0001).

Admixture: Supervised Zombies Vs Unsupervised

I wanted to see how the supervised ADMIXTURE using zombies performed compared to regular unsupervised ADMIXTURE. Zombies here refers to genomes created using the --simulate option of plink from allele frequencies.

Therefore, I used the allele frequencies computed by Admixture for K=11 ancestral components for Reference 3 to generate 25 zombie individuals per ancestral component.

Using these 275 zombie samples as belonging 100% to one ancestral component, I ran Admixture in supervised mode on the Reference 3 dataset. You can see the population average results here (compare to unsupervised results).

Since I was interested in the difference between the supervised zombie admixture and the unsupervised results, here are the histograms for the difference between the two for all 3,886 samples and each ancestral component. The histogram bins are 0.5% wide.











Most of the results are within the usual error margins. Except for C7 West African component and C10 San/Pygmy component. Those two have larger differences between the unsupervised and supervised zombies approaches. Basically, individuals with West Africans or San/Pygmy ancestry get ~5-8% more West African component in the supervised zombie case with a corresponding decrease in the San/Pygmy component.

Admixture (Ref3 K=11) HRP0141-HRP0150

Here are the admixture results using Reference 3 for Harappa participants HRP0141 to HRP0150.

You can see the participant results in a spreadsheet as well as their ethnic breakdowns and the reference population results.

Here's our bar chart and table. Remember you can click on the legend or the table headers to sort.

If the above interactive charts are not working, here's a static bar graph.

Admixture (Ref3 K=11) HRP0131-HRP0140

Here are the admixture results using Reference 3 for Harappa participants HRP0131 to HRP0140.

You can see the participant results in a spreadsheet as well as their ethnic breakdowns and the reference population results.

Here's our bar chart and table. Remember you can click on the legend or the table headers to sort.

If the above interactive charts are not working, here's a static bar graph.

Admixture (Ref3 K=11) HRP0121-HRP0130

Here are the admixture results using Reference 3 for Harappa participants HRP0121 to HRP0130.

You can see the participant results in a spreadsheet as well as their ethnic breakdowns and the reference population results.

Here's our bar chart and table. Remember you can click on the legend or the table headers to sort.

If the above interactive charts are not working, here's a static bar graph.

Of sensible sematics

One of my met peeves is the confusion which some ethno-linguistic terms can cause. For example, the fact that there were Iranian language speakers on the plains of Ukraine ~2,000 years ago naturally indicates to people that Scythian nomads issued out of Iran northwards. Similarly, the existence of Indo-Aryan Mitanni in what is today Syria also suggests to people that there was a migration of Indians which traversed much of West Asia in a drive toward the Mediterranean from the Indus. Of course our perception of the center of gravity of these ethno-linguistic groups today is a function of historical contingency. If we didn't know much more about Antique and Medieval European history we might posit that the Celtic Galatians of ancient Anatolia were originally from Ireland, based on the contemporary distribution of Celtic languages!

This issue is now cropping up South Asian archaeogenetics. In my opinion the paper Reconstructing Indian population history is probably the most important contribution to the field in a generation. The authors explain technically why a "South Asian" ancestral component falls out of ancestry inference algorithms at the heart of ADMIXTURE, STRUCTURE, or frappe. In short, when you have a population which is a hybrid, but where the hybridization event is very distant in the past, recombination breaks up the signatures of that event (a decay of the linkage disequilibrium between two putative ancestral populations). Additionally, in the Indian case there doesn't seem to be a "pure" population of one of the two ancestral groups, what they termed "Ancestral South Indians" (ASI). The closest reference they found were Onge Andaman Islanders, whose last common ancestors with ASI was on the order of tens of thousands of years in the past. They do have excellent proxies for the other population, "Ancestral North Indians" (ANI). Compared to ASI all West Eurasians can be used as reasonable proxies for ANI.

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