Visualizing European genetic variation: looking at dimensions which aren’t so boring

By Razib Khan | February 14, 2013 2:40 am

Yesterday I re-ran Plink with a narrower European-biased data set, and generated some MDS plots. I only had a few Asian and African populations, mostly so that I could replicate the standard dimensions 1 and 2, producing the classic “v-shape” which you’ve seen before. But what’s more interesting are lower coordinates. They may not capture as much of the variation in the distance matrix, but illustrate important dynamics. I haven’t used the directlabels package yet, so right now the labels are still imperfect. I’m giving black text as well as colored text. Also, here’s the original data (as in MDS results, not the raw data).

MORE ABOUT: Human Genetics
  • Davidski

    I think this is worth a mention here. One of my project members did this PCA ages go based on ADMIXTURE results from the Jtest.

    From here:

    The interesting thing about it is that it not only shows how the populations cluster across the first two dimensions, but also their main ADMIXTURE “ancestral” components.

    For instance, the Irish (IE), Cornish and Western Scots (Scottish) cluster very close to the Central and Eastern English here (labeled as just English), but its interesting to note that the former three are part of the light blue cluster, along with the French (FR) and Basques, while the English part of the dark blue cluster, along with the Dutch and the Western Germans (labeled as NL and DE).

    So I think this is a nice way of visualizing how these populations relate to each other on a couple of different levels. In other words, the plot still shows ancient relationships between them that have been erased by isolation-by-distance on PCAs, at least across the first two dimensions anyway.

    This guy did plenty of other plots based on the same data, including spinning 3D animations, but I don’t have them here right now.


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About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at


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