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Thread: Using Global25, how different are the Irish and the English?

  1. #11
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    Quote Originally Posted by sktibo View Post
    Population or target is the row, percentage is the column. So, Wales = 58% UK, 22% Denmark, 1% Sweden, 3% Norway, 1% Poland, 13% Italy, and 2% Finland with this model.
    Thanks, and the columns represent ancients of those countries?

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    Quote Originally Posted by Molfish View Post
    Thanks, and the columns represent ancients of those countries?
    I think they represent moderns, I'm not sure where to find out what they represent with certainty, they may have built their components from ancient samples, but the labels being modern countries indicates to me that these are likely modern reference populations and they are testing these groups against that.

    Fig. S11.14: Population-based admixture estimates based on the spatial median, as described in the
    text. a) estimates of the proportion of ancient populations in modern populations. b) estimates of the
    proportion of ancient populations in ancient samples.

    Not clear if it's using moderns or ancients, as it just says "estimates of the proportion of ancient populations in" and doesn't specify what it was built with.

    Just found this trying to find an answer:

    "Fig. 4: Spatiotemporal patterns of Viking and non-Viking ancestry in Europe during the IA, EVA and VA.

    UK = ‘British-like’ / ‘North Atlantic’ ancient ancestry component. Sweden = ‘Swedish-like’ ancient ancestry component. Denmark = ‘Danish-like’ ancient ancestry component. Norway = ‘Norwegian-like’ ancient ancestry component. Italy = ‘Southern European-like’ ancestry component. See Table S11.2 for statistical tests. The ‘Swedish-like’ ancestry is the highest in present-day Estonia due to the ancient samples from the Salme ship burial, which originated from the Mälaren Valley of Sweden, according to archaeological sources."

    So maybe they did build these with ancient samples. Odd naming system.

    It gave a reference to supplementary figure 11.2. Upon going there, there's a lot more information on this and the answer isn't jumping off the page to me. https://www.biorxiv.org/content/10.1...ntary-material
    Have a look maybe? Page 44.
    Last edited by sktibo; 11-20-2019 at 02:04 AM.
    Paper trail ancestry to the best of my knowledge:
    English (possibly containing some Welsh ancestry) 31.25%, Scottish 17.96%, Scotch-Irish 12.5%, Eastern German 12.5%, Eastern European (Likely Polish possibly including Romanian) 12.5%, French 7.81%, Native American (Saulteaux and Assiniboine) 2.34%, and Colonial American, 3.125%, which cannot be traced with certainty. With certainty, there is Dutch (at least 1.36%) and some English.

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  4. #13
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    Quote Originally Posted by sktibo View Post
    I think they represent moderns, I'm not sure where to find out what they represent with certainty, they may have built their components from ancient samples, but the labels being modern countries indicates to me that these are likely modern reference populations and they are testing these groups against that.

    Fig. S11.14: Population-based admixture estimates based on the spatial median, as described in the
    text. a) estimates of the proportion of ancient populations in modern populations. b) estimates of the
    proportion of ancient populations in ancient samples.

    Not clear if it's using moderns or ancients, as it just says "estimates of the proportion of ancient populations in" and doesn't specify what it was built with.
    Either way, their result for England is quite similar to how I've modelled my mother's data in G25, bearing in mind they didn't source France/West Central Europe.

    https://anthrogenica.com/showthread....l=1#post622823

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    Quote Originally Posted by sktibo View Post
    I think they represent moderns, I'm not sure where to find out what they represent with certainty, they may have built their components from ancient samples, but the labels being modern countries indicates to me that these are likely modern reference populations and they are testing these groups against that.

    Fig. S11.14: Population-based admixture estimates based on the spatial median, as described in the
    text. a) estimates of the proportion of ancient populations in modern populations. b) estimates of the
    proportion of ancient populations in ancient samples.

    Not clear if it's using moderns or ancients, as it just says "estimates of the proportion of ancient populations in" and doesn't specify what it was built with.

    Just found this trying to find an answer:

    "Fig. 4: Spatiotemporal patterns of Viking and non-Viking ancestry in Europe during the IA, EVA and VA.

    UK = ‘British-like’ / ‘North Atlantic’ ancient ancestry component. Sweden = ‘Swedish-like’ ancient ancestry component. Denmark = ‘Danish-like’ ancient ancestry component. Norway = ‘Norwegian-like’ ancient ancestry component. Italy = ‘Southern European-like’ ancestry component. See Table S11.2 for statistical tests. The ‘Swedish-like’ ancestry is the highest in present-day Estonia due to the ancient samples from the Salme ship burial, which originated from the Mälaren Valley of Sweden, according to archaeological sources."

    So maybe they did build these with ancient samples. Odd naming system.

    It gave a reference to supplementary figure 11.2. Upon going there, there's a lot more information on this and the answer isn't jumping off the page to me. https://www.biorxiv.org/content/10.1...ntary-material
    Have a look maybe? Page 44.
    Thanks for all the explanation. I thought the 'Italian' component had to be from samples used in the paper because it's a bizarre choice to use as a southern reference, otherwise.

    The main worry for me in any of these models is their confidence that they can differentiate between British- and Danish-like. This is why I dislike the POBI paper and all of its offspring (there was a Scottish version recently). When (e.g.) Razib quotes from the POBI paper that modelled English as up to 40% Germanic using modern references, I'm annoyed not because I want English and Germans to be separate, but because I don't think it's good science.

    Of course, I made a calculator using modern references but that's a different matter (I'm a crank).

    EDIT: supp. file 03, for anyone else looking. File 02 has archaeological info.

    EDIT2: This is where I start getting confused by DNA papers.

    We used fs2.0.8 (www.paintmychromosomes.com) using the protocol described with the software to paint 1675 modern individuals primarily from across Europe (UK, Italy, Poland, Denmark, Sweden, Finland, Norway, as well as China and Africa) who together form the “modern sample”.
    This isn't really across much of Europe, and UK/Denmark/Norway seems tricky to split, but I'll read on.

    The clustering is strong and perfectly stratified by population label. Each population is characterized by receiving higher ancestry from its own population, implying that each represents a unique aspect of genetic drift.
    I follow so far. Looking at the bottom left of the matrix (fig. S11.2), their ability to isolate falls apart for Denmark and the UK.

    We now use ChromoPainter v2 to paint each ancient sample against each modern sample.
    Seems backwards but I've never read the supplements for this method before, so what do I know?

    In terms of difficult to assign populations, Denmark is one. The individuals which best match a Denmark population also well-match the “UK181_g” population.


    The UK populations contain individuals from the PoBI study and so we can confirm that these are English and hence contains a high proportion of Anglo-Saxon ancestry.
    Where is the science behind this statement? POBI used modern Germans to claim that modern English are Anglo-Saxons. They might well be but this isn't science.

    The “UK61_e” population which is well-matched by the ancient Orkney individuals contains individuals from Scotland and Northern Ireland, whilst “UK_24f” contains individuals from Wales.
    Isn't this all backwards (modern to ancient), or am I wrong again? And why did they think modelling Irish as Italians made any sense? (Rhetorical questions).
    Last edited by Capitalis; 11-20-2019 at 07:38 PM.

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    Quote Originally Posted by Capitalis View Post
    Thanks for all the explanation. I thought the 'Italian' component had to be from samples used in the paper because it's a bizarre choice to use as a southern reference, otherwise.

    The main worry for me in any of these models is their confidence that they can differentiate between British- and Danish-like. This is why I dislike the POBI paper and all of its offspring (there was a Scottish version recently). When (e.g.) Razib quotes from the POBI paper that modelled English as up to 40% Germanic using modern references, I'm annoyed not because I want English and Germans to be separate, but because I don't think it's good science.

    Of course, I made a calculator using modern references but that's a different matter (I'm a crank).

    EDIT: supp. file 03, for anyone else looking. File 02 has archaeological info.

    EDIT2: This is where I start getting confused by DNA papers.



    This isn't really across much of Europe, and UK/Denmark/Norway seems tricky to split, but I'll read on.



    I follow so far. Looking at the bottom left of the matrix (fig. S11.2), their ability to isolate falls apart for Denmark and the UK.



    Seems backwards but I've never read the supplements for this method before, so what do I know?







    Where is the science behind this statement? POBI used modern Germans to claim that modern English are Anglo-Saxons. They might well be but this isn't science.



    Isn't this all backwards (modern to ancient), or am I wrong again? And why did they think modelling Irish as Italians made any sense? (Rhetorical questions).
    The modern population admixture didn't appear to lead to much in the end although it would seem that the Scottish paper K3 is a big improvement. These papers are valuable for the clustering and charts/graphs, but best of all was the K2 using anglo saxon and iron age briton components from the insular Celtic population structure and the genetic drift with icelandic gaels in the Scottish paper. Those are quite informative imo..

    I feel I agree with you that we must be careful when interpreting these charts using modern or seemingly modern components
    Last edited by sktibo; 11-20-2019 at 10:04 PM.
    Paper trail ancestry to the best of my knowledge:
    English (possibly containing some Welsh ancestry) 31.25%, Scottish 17.96%, Scotch-Irish 12.5%, Eastern German 12.5%, Eastern European (Likely Polish possibly including Romanian) 12.5%, French 7.81%, Native American (Saulteaux and Assiniboine) 2.34%, and Colonial American, 3.125%, which cannot be traced with certainty. With certainty, there is Dutch (at least 1.36%) and some English.

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