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Sunday, August 12, 2018

Global25 workshop 1: that classic West Eurasian plot

In this Global25 workshop I'm going to show how to reproduce, more or less, that classic plot of West Eurasian genetic diversity seen regularly in ancient DNA papers and at this blog (for instance, here). To do this you'll need the datasheet below, which I'll be updating regularly, and the PAST program, which is freely available here.


This is what you'll get if you follow my instructions to the letter. Note the fairly strong correlation with geography. I think this is impressive for so many reasons.

OK, so, download the said datasheet, plug it into PAST, select columns 1 to 8, and go to Multivariate > Ordination > Principal Components. Here's a screen cap of me doing it:

The initial output won't resemble my plot above. So you'll need to place PC2 on the X axis, PC1 on the Y axis, and set the image size to 1206x706. After doing that, you should end up with exactly this:

Then, export the image, flip it horizontally with whatever imaging software that can do the job, and that's it, unless you want to add some labels like I did. Feel free to ask questions and make suggestions in the comments below.

See also...

Global25 workshop 2: intra-European variation

Global25 workshop 3: genes vs geography in Northern Europe

Global25 PAST-compatible datasheets

Modeling genetic ancestry with Davidski: step by step

Genetic ancestry online store (to be updated regularly)