tiistai 24. maaliskuuta 2015

Estimating ancient genes among present-day European populations, part 3

After adding the Karelian HG things "clicked" in Northeast Europe.  This Ancient Karelian sample is closely related to Yamnaya people, but with less or no European farmer ancestry.  This lack of farmer genes became in new results balanced by additional Hungarian Neolithic farmer genes, especially among northeastern and ancient Corded Ware samples, and as a result chisq  is now pretty much lower in Northeast Europe.   You see on the Excel-sheet also the older chisq for comparison.  It is worth of noticing that both northern hunter-gatherer groups (Scandinavian and Karelian) are necessary to obtain best fits in the north and that my second test proved the western hunter-gatherer (Hungarian neolithic HG) being quite distant for all present-day northern populations, even for some southern ones, like for Basques.

I tried also to find out the lacking piece that could complete certain South European admixtures.  The best fit was obtained among Greeks by adding something like Turkish-Iranian and in a case of Maltese and Sicilians also North African genes (Turkish-Iranian + Tunisian).  It is hard to say exactly for what this Turkish-Iranian stands for, anyway Lebanese, the best Near-Eastern admixture gave a poorer result.

Download new results here.

11 kommenttia:

  1. M. Myllyla,

    I have a quick question for you. Could you tell me how you arrainged your left and right pops for this run? Which pops did you place on the right?

    Thank you!

    VastaaPoista
  2. Hi.
    Do the scores on your spreadsheet correlate in anyway to proportions of admixture ?

    VastaaPoista
  3. Mike, columns from E to I represent admixture proportions. The accuracy depends on chisq and tail propability values, lower chisq is better.

    VastaaPoista
  4. Chad,


    My right is at the base level as simple as

    Mbuti
    Papuan
    She
    Yoruba
    Karitiana

    I have added then more native South or Central Americans, Near Easterners, like Bedouins and I have also named LaBrana1 and Loschbour as "Western_HG" and used it to expand the western effect, because basically western references are quite weak for Europeans. So if you want to test anything to east from Western Europe it could be fine to add them to your right. But this is only a base level and usually I have more references to make necessary finetuning. Usually I have 7 references. The result of adding more populations is not a big effect if you do it in right way and follow instructons. My conclusion is that you must be cautious in addming more references, because results tend to become worse, and authors also warn about using too many references (right populations). I saw also a question about how many admixtures you can use. I have done five at its peak. Authors say that the number of left populations can't be more than right populations.



    VastaaPoista
  5. Is that the order of your right pops? What is the order of the left pops? I'd like to test run this. Thanks!

    VastaaPoista
  6. Chad, yes this was the order. Adding Bedouins:

    BedouinB
    Mbuti
    Papuan
    She
    Yoruba
    Karitiana

    or you can add something else, like

    BedouinB
    Mbuti
    Papuan
    She
    Yoruba
    Western_HG (including Loschbour and LaBrana1)
    Karitiana

    You can't make things wrong until you try to add too many populations. Results vary somewhat, like Yamnaya can have Iranian or Armenian, but you can rank results by statistics.

    Left for example:

    Yamnaya
    Samara_HG
    Karelia_HG
    Iranian
    Armenian
    SwedenSkoglund_MN

    VastaaPoista
  7. @M. Myllylä,

    Are your Hungarian farmers from the Early Neolithic? If so I think you should use Middle Neolithic samples instead. A lot of the extra-hunter gatherer ancestry modern Euros are expressing in your tests, will be absorbed into a Middle Neolithic component.

    VastaaPoista
  8. Krefter, yes they are Early Neolithic. I am planning new tests and when I have something I can also run Middle Neolithic samples. A big issue is however the quality of samples. I don't remember just now how good those Middle Neolithic samples are. The result can be worse than with EN samples if the quality is low.

    VastaaPoista
  9. How does the caucasian hunter gatherer genome fit in the picture? Olenko väärässä vai onko suomalaisten "välimerellinen" perimä suurimmaksi osaksi sitä? EEF komponenttia meissä ei liene paljoakaan.

    -Jouko

    VastaaPoista
    Vastaukset
    1. I have not yet that new sample because, as far as I know, it is not publicly available. I should ask it from the study author. However I think that
      CHG can't explain all common non-WHG and non-EHG ancestry in Western Europe. It is of fourse essential also understand what kind of the history the EEF represents. There is a big difference between ancient EEF samples and the difference of modern South Europeans and(WHG+EHG). So we have a real unknown which is also reported by Haak et al., but often forgotten. I am now busy with other tasks, but sure will come back with CHG.

      Poista

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