суббота, 16 марта 2019 г.

Let’s try a formal heuristic approach

I created a massive outgroup f3-statistics matrix, featuring almost 300 ancient and present-day populations and individuals, for the purpose of running unsupervised, or at least semi-supervised, fine scale mixture tests with nMonte. Most of the stats were computed with 400-900K SNPs, which is a lot and should provide plenty of power. The matrix is available in a zip file here.
The results I’m getting with this new setup are very similar to those obtained with the Global25. The main differences, as far as I can see for now, are that the f3 data produce more stable results when modeling very deep ancestry, while the Global25 provides more accuracy when modeling fine scale recent ancestry (probably because it’s better at picking up more recent genetic drift).
Let’s investigate some pertinent issues with the new data using nMonte and PAST. How about we start with these?



– where did Bell Beakers get their steppe ancestry from?
– which Steppe_MLBA group did Indians get their steppe ancestry from?
– do the present-day Irish have any Hallstatt ancestry?
– what is the origin of present-day Basques?
– what is the precise ancestry of Armenia_ChL?
– do the Swat Iron Age samples really lack BMAC ancestry?
– does Anatolia_MLBA really lack steppe ancestry?



Please note that I’m still in the process of incorporating the ancients from the new Olalde et al. paper on the genomic history of Iberia (see here) into the f3 matrix. However, I’ve already updated the Global25 datasheets with most of these samples.



Global 25 datasheet (scaled)
Global 25 pop averages (scaled)
Global 25 datasheet
Global 25 pop averages



By the way, Hajji_Firuz_ChL I2327, from Narasimhan et al. 2018, is now labeled Hajji_Firuz_IA in the above datasheets, because my understanding is that he’s actually from the Iron Age rather than the Chalcolithic period. For background reading about this controversial sample see here and here. I don’t have any more info on this topic; we’ll just have to wait for the formal publication of the Narasimhan et al. manuscript to get all the details. Apparently it’s coming very soon.
See also…
An exceptional burial indeed, but not that of an Indo-European
Maykop: a multi-ethnic layer cake?
Late PIE ground zero now obvious; location of PIE homeland still uncertain, but…

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