Reference 3 Admixture K=14

Posted by on April 23, 2011

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

Here's the results spreadsheet for K=14.

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

This one I am going to classify as a bad run. The east Asian splits are weird.

Fst divergences between estimated populations for K=14 in the form of an MDS plot.

And the numbers:
C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13
C2 0.109
C3 0.110 0.160
C4 0.239 0.264 0.247
C5 0.107 0.080 0.161 0.267
C6 0.116 0.111 0.176 0.284 0.102
C7 0.132 0.180 0.092 0.265 0.176 0.195
C8 0.189 0.237 0.214 0.335 0.239 0.251 0.237
C9 0.178 0.206 0.154 0.324 0.192 0.229 0.164 0.294
C10 0.217 0.246 0.191 0.373 0.242 0.262 0.229 0.338 0.285
C11 0.209 0.220 0.248 0.350 0.230 0.223 0.272 0.314 0.312 0.344
C12 0.266 0.278 0.307 0.417 0.286 0.281 0.333 0.373 0.374 0.406 0.179
C13 0.143 0.143 0.186 0.287 0.149 0.135 0.209 0.254 0.247 0.278 0.117 0.177
C14 0.364 0.368 0.410 0.528 0.372 0.377 0.437 0.490 0.481 0.514 0.334 0.359 0.283

This is the last plot I am posting in this series of admixture runs since the crossvalidation error is minimized at K=14.

For some reason, Admixture starts acting weird at values of K higher than about 14-15.

Admixture

11 Comments.

  1. Onur April 23, 2011 at 12:13 pm

    Too bad the ADMIXTURE series ended so early.

    • Zack April 25, 2011 at 6:00 am

      Well there will be lots of more focused Admixture runs later.

      My experience with Admixture has been that it starts breaking down around K=12-15.

  2. Garvan April 23, 2011 at 8:29 pm

    Perhaps the data can now be split into different focus areas. It would be nice to see clearer groups emerge in East Asia.

    I think the labeling might not be correct for K=14. I would call C3 East Asian, and split Siberia between C7 & C10.

  3. razib April 23, 2011 at 10:13 pm

    well, if you prune some of the african ones it "frees up" K's.

  4. Vasishta April 24, 2011 at 3:12 am

    I am curious about one thing : How are the Makranis so West Eurasian given their physical appearance, which is quite clearly African influenced? Very interesting..

    • Ez April 24, 2011 at 8:05 am

      There are some Makranis who are clear outliers towards Africans within their population. While most samples are similar to other Pakistanis.

      • Vasishta April 24, 2011 at 9:58 pm

        Most Makranis I've seen (on the internet, admittedly) have something very clearly West African about their countenance. Are these types in abundance simply due to the fact that foreigners are more fascinated by the clearly African-like types rather than the more Baloch/Sub-continental looking types?

    • Zack April 25, 2011 at 6:25 am

      Makranis have some African Admixture but not a whole lot (on average).

  5. Vasishta April 24, 2011 at 10:04 pm

    Also Zack, I want to take this opportunity to thank you for your invaluable efforts. This project, as I predicted at it's early stages has truly been fruitful for enhancing the clarity of South Asian genetic history - Kudos to you! At some point of time, you should get all of this peer reviewed so that you can be 'officially' recognized for your work. Thanks a lot for all of this, it has greatly improved my understanding of subcontinental genetics, too.