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Wednesday, July 16, 2014

Model yourself as a mixture of ancient genomes

Update 12/05/2015: 4mix: four-way mixture modeling in R


This is really easy and should work well for most personal genomics customers (ie. those of European ancestry and with data files from 23andMe, FTDNA and AncestryDNA).

First of all, make sure you have your Eurogenes K15 ancestry proportions from GEDmatch. Then do the following:

- download the 4 Ancestors Oracle (here)

- download the Eurogenes ancient genomes datasheet (here)

- place everything into the same directory

- double click of the 4 Ancestors Oracle icon (the big red number 4)

- select the Eurogenes K15 ancient genomes datasheet

- type your Eurogenes K15 ancestry proportions into the fields provided

- hit the go button and let it rip

I'm not sure I'm allowed to upload the 4 Ancestors Oracle online, but I couldn't find the original link, so let's assume for the time being that I am. In any case, many thanks to Alexandr Burnashev for this great tool.

You'll also find some modern populations in the datasheet. They're there so that users with ancestry from outside of Europe don't end up with ridiculous results.

Obviously, you can edit the datasheet to explore more options by removing or adding individuals and populations. A spreadsheet of Eurogenes K15 population averages is available here. The oracle settings can also be tweaked in a couple of ways to fine tune the results.

If the calculator crashes, try replacing the periods with commas in both the datasheet and your ancestry proportions.

Please keep checking this post, because I'll attempt to update the datasheet at the link above every time a new ancient genome is published and has enough markers available to be tested with the Eurogenes K15. Eventually we might end up with a tool that covers most of the continents and many periods of history and prehistory.

I've done similar analyses of a variety of ancient genomes. For instance, StoraFörvar11, or SfF11, from Mesolithic Sweden came out 3/4 La Brana-1 and 1/4 MA-1, which translates to 3/4 Western European Hunter-Gatherer (WHG) and 1/4 Ancient North Eurasian (ANE), and lines up well with results reported recently for Swedish hunter-gatherers in scientific literature. You can see the full analysis StoraFörvar11 and a couple of other ancient genomes at the links below.

Analysis of Mesolithic Swedish forager StoraFörvar11

More ancient genomes from Sweden: Pitted Ware forager Ajvide58 and TRB farm girl Gokhem2

I'm still trying to answer a whole lot of e-mails so I won't be monitoring this post for a while. But please feel free to share your results and any tips you might have in the comments below.