maanantai 9. tammikuuta 2017

Going ahead with the new data, clustering

My new data makes possible to cluster better samples according to ethnicities. It is now possible to see at least

Middle-Eastern
Abkhasian-Armenian-Georgian-Assyrian
Caucasian
South European
West European
East European
Finnish dwelling zone
Baltic dwelling zone

Unfortunately none of those new sample sources give reasonable South European view, which makes impossible to see inside the Mediterranean area.  With better sampling I probably could create at least Balkan, South-Italian, Iberian and Basque clusters.   It is probably now possible to classify also project individuals by PCA.

Europe, clustered by Saami, Mongolian, South-Asian and Middle-Eastern samples


Zoomed in



Europe, plotted exclusively.  You can see clearly western and eastern clusters, as well as Balts and the Baltic-Finnic group splitting into Scandinavian and East-Slavic relations.   We could see also a clearly distinct Scandinavian group with more proper samples.  Unfortunately the South European picture is fuzzy due to too few samples.  Due to the shortage of samples I narrowed each group down to four samples, except Tuscany to strengthen the southern cluster.  It is very possible that with a larger South European sampling the European west and east would diverge even more than we see now on this plot below.


 





8 kommenttia:

  1. Btw, my blog is a good source for information of European mtDNA. This is a post I made this week. "Finland."

    http://mtdnaatlas.blogspot.com/2017/01/finland.html

    VastaaPoista
    Vastaukset
    1. Great story about our mtdna. I belong to H39, which seems to be around 500-700 years old in Finland and exists at 2 mutation level from me in Europe. Can we say that below 1000 years is Finnish specific. I would say, no.

      Poista
    2. At FtDa I have

      8 full matches, all of Finnish ancestry
      8 at gen. dist. 1, assumed location by surnames
      - 2 German
      - 1 Finnish
      - 5 English or American

      Looking at the map info for MRCA of those at genetic distance 2

      1 Hungary
      1 France
      1 Scotland
      1 Southern Sweden

      Three step mutation on the map

      2 Southern Norway
      1 Germany

      Unfortunately no one of those at one step have given MRCA.

      Poista
  2. To me it seems your PCAs of Europeans using millions of SNPs East Europe+Scandinavia cluster the furthest east because they have the most Yamnaya ancestry? Would you agree? Other analyses using less SNPs though give some Western Europeans like Irish about as much Yamnaya. Are you able do analyses using ancient DNA samples to test if this is correct?

    NorthEast Europe+Scandinavia have the most U5a, U4 which suggests they have more Yamnaya than other Europeans.

    VastaaPoista
    Vastaukset
    1. On the larger two dimensional PCA Scandinavians are drawn by Finns, not by Yamnaya or any other ancient ancestry from anywhere else. On another PCA Scandinavians move between West Europe and Finland.

      Poista
    2. Here are some correlation graphics from rarecoal runs done on the Estonian Biocentre dataset from Pagani et al. 2016 and 1000genomes.

      https://ibb.co/cuuxrF

      Rare allele sharing shows that northern Baltic Finns (Ingrians, Finns, Karelians, Vepsians) mostly descend from a migration of proto-Finnic speakers from Estonia, with a Saami substrate. Exactly as the phylogeny and history of Uralic languages would suggest. Finnic speakers share no significant common ancestry with Mordovians beyond what is shared with other Eastern Europeans.

      Volga-Ural region also experienced recent Turkic-related gene-flow from the east that did not reach Finland or the Baltic (proxied here by both Bashkirs and Altaians). This has been implied by older studies but rare allele sharing makes it plain.

      Poista
    3. We can safely say that Ingrians and Estonians have no Altaian or Bashkir ancestry. Also, we can question the Mordovian-Estonian connection. It is more likely that Estonians have got Baltic admixture, as well as Mordovians, Estonians now locating between Ingrians and Balts. But the Baltic - Volga-Finnic connection is an enigma. Who was first?

      Poista
    4. Who was first depends on whether you're speaking in linguistic or genetic sense. Busby et al. 2015 says the admixture in Mordvas is more recent and from a different source than in Finns (and my Saami-Bashkir/Altaian rare allele comparison proves it).

      Linguistically they are equivalent splits, see the final tree here:
      http://www.elisanet.fi/alkupera/Sukupuu.pdf

      Poista