qpAdm tour of Europe: Mesolithic to Neolithic transition

For a while now I’ve been trying to work out a way to model present-day Europeans with qpAdm as a mixture of Neolithic and Mesolithic populations. It hasn’t been easy, because often what works for some Europeans doesn’t work for others. But I’ve finally figured it out. The trick is to account for Siberian, East Asian and Sub-Saharan ancestry, by including the Nganasan from Siberia, Onge from the Andaman Islands, and Yoruba from West Africa, respectively, as reference pops. Below is the spreadsheet with the results and outgroups. Judging by the chisq and tail prob, most of the fits aren’t spectacular, but as far as I can tell, they work. Moreover, in the entire analysis not a single standard error reached 2%. Based on my experience with qpAdm, that’s a remarkable thing for such a complex analysis, and I think it suggests that the reference populations are relevant. Interestingly, while, as expected, the Nganasan-related admixture peaks in far Northern Europe, the Onge-related ancestry is, perhaps surprisingly, most pronounced in Southern Europe. Any ideas why? My thoughts on that here.

Update 014/01/2017: If you guys want to reproduce my analysis, but you don’t have the same dataset, which is more than likely, you should be able to get very similar results using the full Human Origins dataset. Try these reference pops and outgroups.

pleft

Barcin_Neolithic

Caucasus_HG (Kotias)

Eastern_HG (Karelia_HG x2, Samara_HG)

Nganasan

Onge

Western_HG (Hungary_HG, Iberia_HG, Loschbour)

Yoruba (from the HGDP) pright

AG3-MA1

Chukchi

Han

Karitiana

Kostenki14

Levant_Neolithic

Mbuti (Mbuti.DG x3 from Fu et al.)

Papuan

Satsurblia

Ust_Ishim

Villabruna

If you’re seeing “infeasible”, then remove the redundant reference population that might be causing problems, usually Yoruba or Nganasan, and run again. If it’s still not working, then maybe your dataset is just too different in some way, perhaps with not enough markers (there should be around 200K SNPs available for these runs). See also… qpAdm tour of Europe: the Bronze Age invasion Source Eurogenes Blog