maanantai 16. marraskuuta 2015

Basic tests with ancient samples using Treemix

Following strictly all instructions given in manual by authors I at first made PCA-plots in two steps.   At first I selected modern populations on what the ancient sample set is to be projected.  So I did a projected plot using SmartPca.

Here is a big view


And here a close-up with impact of all same populations

This looks somewhat different than we have seen in studies.  However I think that my arrangement with modern populations is objective and projected ancient samples should be on right places.  There is some extra effect using more East Asian samples, which makes me wondering what is the history which makes this difference between modern and ancient samples.  It looks like there is in modern Europe a hidden East Asian effect lacking in ancient samples (including so called "steppe populations").

Here is a set of TreeMix results using ancient and modern Europeans.  Some observations on results

-  although the tree itself expresses course from hunter-gatherer and "steppe" populations to early farmers TreeMix gives in some cases extra migrations from ENF to other South European populations.

- during the Bronze and Iron Age migration history in Europe many changes took place.  It looks like Southwestern Finns are closest to original western hunter-gatherers among modern populations.  This is true despite of some eastern influence in Finland.  Even so the drift distance between western hunter-gatherers (Loschbour) and the Finns is almost equal with other modern Europeans.

5 kommenttia:

  1. Can you do those trees with Karelia_HG and Tavastians added in?

    1. Yes I can, but only after processing it and many other ancient samples still being only in Affymetrix specs.

    2. Okies, but if you're not planning to convert the EHG now could you do a couple of these trees again but with Tavastians added. You can throw the Ukrainians in there as well.

    3. I start working with EHG and other samples.

    4. I succeeded in converting Haak's Affy samples to Illumina, hence it could bge possible to repeat that earlier experience with EHG and other Haak's ancient samples, but only using around 50kSNP, which was overlapping between Haak et al. and Estonian BC samples. My database still lacks of ancient Anatolian samples.