Monday, April 23, 2012
Eurogenes ADMIXTURE utilities at Gedmatch
Update 27/11/2013: I've made the new K13 the default Eurogenes admix test at GEDmatch. It seems to hit the spot for most people. See here.
Update 11/10/2012: The Jtest and EUtest are now available at GEDmatch, and these have superseded most of my tests offered there, except those that include Amerindian references samples. Also, the Jtest and EUtest come with a variety of "Oracle" ethnic matching tools. For more info see here.
Update 07/05/2012: Eurogenes' Gedmatch ADMIXTURE ancestry test guide.
Gedmatch now features a series of ancestry tests based on my experiments with the ADMIXTURE software. The K9 to K12 are basically part of a single package, and specifically designed for people with majority of their recent ancestry from north of the Alps and Carpathians. However, the K9 will be useful for many other individuals too. Then there's the K12b, the K13, and a new version of my Hunter-Gatherer vs. Farmer test. The latter two should work well for people from all over the globe.
The K9 to K13, K12b and Hunter-Gatherer vs. Farmer tests don't suffer from the usual "calculator effect", whereby project members get somewhat different scores from non-members of exactly the same ancestry. In other words, all results are directly comparable, and I encourage all users to swap notes vigorously. However, it's important to understand that you won't see dramatic differences in the levels of the inta-North European components. That's because they're largely based on very similar allele frequencies, and separated by low Fst (genetic) distances. Indeed, note the progression from one North European cluster at K9, to four at K12 (North Sea, South Baltic, Volga-Ural and Western European). Generally speaking, the four northern clusters at K12 can be thought of as a subset of the K9 cluster.
Thus, if you're looking for a fairly clean cut summation of your ancestry, then use the results from K9 or the Hunter-Gatherer vs. Farmer tests, where genetic differentiation between the clusters is greatest. But I think the K10 to K13 are more useful as chromosome paintings, and that's precisely because they're not as clean cut. As a result, much of your genome won't be covered in just one color, but in a mosaic of colors. Studying these patterns at local level, and cross checking the information with other results, like Ancestry Finder data from 23andMe, might be a useful way of pinpointing segments from very specific parts of Europe.
Below is my K12 chromosome painting. Yes, it's kind of noisy, but in fact, it's also very informative. I can spot some very close correlations with my Ancestry Finder results. It's not only matching single segments, but whole clusters of segments. Actually, here's an idea: download all the paintings, from K9 to K12, and then view them like an animation using the default Windows image viewer. It's interesting to see how the North Euro cluster breaks up into four different clusters.