Reich Lab's new Admixtools version 3 includes a new admixture calculator based on f4-statistics. So here is my first effort to find out our Neolithic genetic admixtures. This test is based on three European Neolithic sample groups: Yamnaya culture samples, Neolithic farmer samples from Hungary and Neolithic hunter-gatherer samples from Southern Scandinavia. East-Asian samples were used additionally to find out possible Northeastern migrations.
So I had four admixture groups. It wasn't enough, it became soon obvious that South Europeans had a fifth admixture dimension. I tried to solve the problem and fit Near-Eastern samples to the model, because my previous test with Mixmapper showed a later Near-Eastern admixture in South Europe. But at this time it didn't succeed. Sure there is a solution and I'll try to find it later. Just now some South European results show poor accuracy due to this unknown admixture proportion. Best fit was obtained in Ukrainian, Belarussian, Cornwall and Basque results. Results show elevated amounts of East Asian, which was the case also in Haak et al. The reason is either in low-quality ancient samples or in the method itself.
This new tool is exciting because it makes estimates fast and seems to have less problems caused by genetic drift, which are typical for admixture analyses. But I have work to do to learn pros and cons.
Download Excel-file here.
edit 20.03.15 Sardinian and Sicilian row names corrected.
edit 21.03.15 I did preliminary tests using HungaryGamba_HG, aka KO1, instead of Scandinavian hunter-gatherers. KO1 was a hunter-gatherer found from Hungarian plain and lived around 5000 years ago and the genome is around as old as the Swedish hunter-gatherer Ajv58 used in my earlier test with other Scandinavian samples from the same period.
The result implies that KO1 shares less common ancestry with Yamnaya, Scandinavian obviously much more than KO1. Replacing Scandinavian HGs by KO1 led to much higher Yamnaya and lower hunter-gatherer admixtures everywhere where the sum admixture of Yamnaya and Scandinavian HG was highest. I am working with this but have not just now time to complete my tests.
edit 21.03.15 Sorry about erroneous test, now corrected (underlined). To be in a hurry is not a good thing.