Totalt antall sidevisninger

mandag 9. september 2013

La Braña 1 and modern European variation.

This is a reanalysis of the La Braña's but this time separately. The La Braña 1 matched the 1000 genome reference panel with 129k SNP's. These SNP's was used together with the 288k SNP's from the standard population that match the 1000 genome reference SNP's to impute the missing 129k SNP's from the La Braña as described earlier. These SNP's was then further LD pruned in PLINK to 47k SNP's and then run through the Chromopainter-Finestructure unlinked pipeline using the world panel. The European panel was then later extracted from the Chromopainter output files and run through Finestructure using 38k SNP's.

The heatmap and tree structure below shows somewhat different result than for the composite La Braña individual consisting of both La Braña 1 and La Braña 2. As we can see the La Braña 1 do not completely cluster witht the Finns and Saamis anymore but appears to have a more intermediate position between the Saami-Finnish cluster and the Eastern European cluster.

CC Euro 47k unlinked La Braña 1

This is also reflected in the PCA D1-D2 (horisontal and vertical) where La Braña 1 appears to appear in the middle between the Finnish-Saami cluster and Eastern Europeans.

 CC Euro 47k unlinked La Braña 1 detailed 

CC Euro 47k PCA unlinked D1-D2

CC Euro 47k PCA unlinked D1-D3

The analysis of La Braña 2 will follow later

EDIT 23/9-13

Download individual results

5 kommentarer:

  1. So La Brana 1 resides with the Swedes with a slight tendency towards the Fins? Am I reading this correct? I find this really odd since there are so little U5/U4 in Sweden. Or are the Swedish samples that are similar like La Brana 1 more connected to the north, where the Saami have high numbers U5?

    I keep wondering how this sample of a hunter-gatherer shows such similarity to Swedes whereas mtDNA is said to point to a large population overhaul. It almost seems conflicting data.

    1. I need to do a reanalysis of the La Braña's because I only did the mapping and base quality filtering and not the following contamination filtering. The authors of Chromopainter-Finestructure also recommonds not only base the analysis on one PCA plot alone as there is far more infomration in the data than the PCA plot itself in only two dimensions.

  2. Hi Anders,

    La Brana 1 shows some mediterranean admixture. That could possibly cause it to cluster with Swedes.

    However, this picture below basically shows that the Gokhem funnelbeaker finds are not like current day Swedes.

  3. Try Ancient Kvenland. It is where the Hunter Gatherer's came from in that area.

  4. There really seems to have lived some people by the coast of Botnia Bay that was neither swedes, finns nor sami. Or my ancestry makes no sence at all. A lot of them moved south into modern day Sweden and some moved east to kinsmen in Finland. Some moved to Norway along ancient tradeways over the mountains, and a lot of what was left intermarried with some of the sami in the great wave of new settlements in the 18th Century. The "children" of this settlers were relocated to factories in the South in the 1970th. "Vi flytt int!" -we will not move, was the fruitless slogan of people that faced with unemployment packed up and moved south. Today the North of Sweden are overrepresented on the Swedish haplogroup database. You can look for your children of the "kvens" there. MtDNA H2a1 seems to be one motif. Sadly the YDNA was decimated when so many men from the area were recruited and died as soldiers in the Swedish Army. Men had to be moved up from Sweden to take their places. Well, I hope this DNA business will tell the story political messiness and borders has obscured for to long. Remeber, in the North we litterary walk on water when we need to go somewere. Here winter is coming every year, and we make good use of it. But I can see your problem to get it all together if you think sami, finn and swede are all you have to calculate with in this part of the World.
    Greetings from a Botnia Bay kwinna.