Tag Archives: asi - Page 2

Reference 3 Admixture K=11

Continuing with the admixture analysis with our new reference 3 dataset.

Here's the results spreadsheet for K=11.

You can click on the legend to the right of the bar chart to sort by different ancestral components.

You don't know how excited I am to see the Onge (C2) component. Let's compare the Onge component with Reich et al's ASI (Ancestral South Indian):

Reich ASI % Onge Component %
Mala 61.2 39.9
Madiga 59.4 37.9
Chenchu 59.3 38.6
Bhil 57.1 37.5
Satnami 57 36.4
Kurumba 56.8 39.5
Kamsali 55.5 35.5
Vysya 53.8 34.4
Lodi 50.1 31.8
Naidu 49.9 32.1
Tharu 49 32.2
Velama 45.3 28.9
Srivastava 43.6 27.8
Meghawal 39.7 25.4
Vaish 37.4 23.8
Kashmiri-Pandit 29.4 17.6
Sindhi 26.3 13.4
Pathan 23.1 10.6

Let's plot that with a linear regression:

How do you like that?

Now let's take all the reference populations with an Onge component between 10% to 50% and use the equation above to calculate their ASI percentage. The results are in a spreadsheet. There are several populations with an even higher Ancestral South Indian than any of the Reich et al groups, with Paniya being the highest at 67.4%.

Fst divergences between estimated populations for K=11 in the form of an MDS plot.

I guess you might want to see the Fst dendrogram too. Just remember it's not a phylogeny.

And the numbers:

C1 C2 C3 C4 C5 C6 C7 C8 C9 C10
C2 0.165
C3 0.121 0.122
C4 0.090 0.161 0.152
C5 0.071 0.152 0.137 0.048
C6 0.134 0.144 0.067 0.163 0.143
C7 0.184 0.224 0.216 0.179 0.186 0.232
C8 0.210 0.209 0.205 0.235 0.223 0.228 0.286
C9 0.175 0.207 0.139 0.208 0.178 0.141 0.281 0.290
C10 0.261 0.304 0.294 0.257 0.261 0.311 0.123 0.367 0.364
C11 0.150 0.195 0.187 0.143 0.148 0.203 0.059 0.260 0.252 0.133

Dienekes on ANI/ASI

Dienekes has a word of caution about choosing reference populations and admixture results.

Consider a sample of 25 Mexicans from the HapMap and 25 Yoruba from the Hapmap, 25 Iberian Spanish from the 1000 Genomes Project, and 25 Pima from the HGDP as parental populations. We obtain for our Mexican sample:

  • 59.7% European
  • 36.9% "Native American"
  • 3.4% African

Let's run a final experiment with just the Mexicans, Spanish, and Yoruba, i.e., with no Native American samples. At K=3 we obtain:

  • 70% "Native American"
  • 29.7% European
  • 0.4% African

The "Native American" component has increased again! The explanation is simple: as we exclude less admixed Native American groups, Mexicans appear (comparatively) more Native American. The "Native American pole" has shifted, and so has the relative position of populations between them.

In other terms, what is labeled "Native American" in the three experiments is not the same: in the first one it is anchored on the more unadmixed Pima, in the last one in the more admixed Mexicans.

Thus, it seems that unadmixed reference samples are much more useful in getting good results from Admixture.

Then he runs Admixture on the Reich et al dataset for South Asians and tries to estimate the relationship between the Ancestral North Indian percentage computed by Reich et al and his K=2 admixture results on the same data.

Dienekes then included South Asian Dodecad participants in the analysis and ran a K=4 admixture analysis on Reich et al + Dodecad South Asian data, including Yoruba and Beijing Chinese from the HapMap to catch any African or East Asian ancestry.

Here are the admixture results for the reference populations:

The R2 correlation between the West Eurasian admixture component and the Reich et al ANI component is 0.98 which is good. His relationship equation comes out to:

ANI = 0.779*WestEurasian + 39.674

Using this relationship, he calculates the ANI and ASI (Ancestral South Indian) components for Dodecad project members. My results (DOD128) are as follows:

East Eurasian 0.0%
African 3.5%
Ancestral North Indian 75.9%
Ancestral South Indian 20.6%

I should point out that due to my recent Egyptian ancestry, my ANI result is wrong since it's collecting all of the non-African Egyptian in there too.

Also, in the case of Razib, I don't think his East Asian 14.4% should be separated out from his ANI-ASI like that. At least some of it should form part of his ASI percentage in my opinion.

Otherwise, this seems like a very good exercise by Dienekes.