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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 you how to reproduce the 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.


Download the datasheet, plug it into PAST, select all of the columns by clicking on the empty cell above the labels, and go to Multivariate > Ordination > Principal Components. Here's a screen cap of me doing it:

This is what you should end up with. Please note that I also ticked the "convex hulls" box to define the populations from the "group" column in the datasheet.

Here I also ticked the "group labels" box. It's generally a useful feature, even though it makes a mess of the plot in this case due to the large number of populations.

See also...

Global25 workshop 2: intra-European variation

Global25 workshop 3: genes vs geography in Northern Europe

Global25 workshop 4: a neighbour joining tree

Modeling genetic ancestry with Davidski: step by step

Getting the most out of the Global25

Genetic ancestry online store (to be updated regularly)