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Thread: Makin a map of EEF, WHG and ANE admixtures in Europe. Please post your data.

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    Quote Originally Posted by Fire Haired14 View Post
    Many theories which today are mainstream Polako believed in when they were not backed up by academic papers. He is looking at real modern and ancient people's DNA, making real tests, has experience, etc. He doesn't claim to be the hurting yourself because papers about a single subject don't come out oftenly, and they are restricted from coming up with new ideas. A blog like Polako's allows constant exchange of ideas, constant experimentation, and is less restricted than the academic world but probably isn't much less equipped.
    No its complete shizz;

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    6 out of 8 members found this post helpful.
    I have been busy lately, but managed time to make a map of the EEF.




    It would be nice to have some data for North Africa (besides Egypt) and Kazakhstan.


    There is some conflicting data between the Lazaridis paper and the Eurogenes data based on the K13 admixtures. For example Lazaridis found that the Spaniards and the Basques had respectively 80% and 71% of EEF, while Eurogenes has 66-69% and 59%. Another odd difference is for Sardinians who have respectively 81% and 90%.

    Percentages for other regions seem much more similar in the two sets of data though (e.g. Orcadians are both at 45%, Belarussians are at 40% vs 42%, Estonains at 32% vs 33%, Tuscans at 75% vs 78%, Hungarians 56% vs 52%, etc.).

    I had to split some countries in two regions when the data was borderline between Lazaridis and Eurogenes. For example Bulgaria has values of 71% and 68%, Greece 79% and 82%, Scotland 39% and 45%...


    I had to extrapolate a bit for some regions based on other data (Dodecad, Y-DNA).

    There was no data for Montenegro or Macedonia, so I used to the same average as for Albania, Kosovo and southern Bulgaria.

    In the Volga region, I assumed that the Tatars had more Neolithic farmer ancestry than their Chuvash and Mordvin neighbours, because they have considerably higher Near Eastern Y-DNA and Dodecad admixture.

    In Scandinavia, individual data showed less than 40% of EEF in northern Sweden. Since the mountainous border between Norway and Sweden has substantial levels of mixed Saami-Scandinavian ancestry, it makes more sense if that region is more similar to northern Sweden.

    I am not going to explain my reasoning for every single region, but nothing is arbitrary.
    Last edited by Maciamo; 18-06-14 at 09:25.
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    The "calculator business" is a mess!

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    0 out of 1 members found this post helpful.

    Smile

    Quote Originally Posted by Nobody1 View Post
    No its complete shizz;

    Are 23andme or Geno 2.0 credible?

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    Quote Originally Posted by Maciamo View Post
    I have been busy lately, but managed time to make a map of the EEF.




    It would be nice to have some data for North Africa (besides Egypt) and Kazakhstan.

    There is some conflicting data about Spain (67-69% or 80% ?) and the Basques (59% or 71% ?). I had to extrapolate a bit for some regions based on other data (Dodecad, Y-DNA).
    Looks great. I was going to buy decent drawing/graphics program to make nice maps. At the moment I have only Windows 7 Paint to use, good only for something crud like in post #2.
    Be wary of people who tend to glorify the past, underestimate the present, and demonize the future.

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    1 out of 1 members found this post helpful.
    Quote Originally Posted by Maciamo View Post
    I have been busy lately, but managed time to make a map of the EEF.




    It would be nice to have some data for North Africa (besides Egypt) and Kazakhstan.

    There is some conflicting data about Spain (67-69% or 80% ?) and the Basques (59% or 71% ?). I had to extrapolate a bit for some regions based on other data (Dodecad, Y-DNA).
    I may be reading the map incorrectly because I am slightly color blind, but the colors don't seem to correspond to the peer reviewed, published academic data from Lazaridis et al.

    If the academic data isn't used then perhaps, since it will undoubtedly be picked up by the internet, it might be a good idea to provide information on it stating that it is based on a blogger's data and not that from an academic paper.


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    Quote Originally Posted by Maciamo View Post
    I have been busy lately, but managed time to make a map of the EEF.




    It would be nice to have some data for North Africa (besides Egypt) and Kazakhstan.

    There is some conflicting data about Spain (67-69% or 80% ?) and the Basques (59% or 71% ?). I had to extrapolate a bit for some regions based on other data (Dodecad, Y-DNA).
    It is a very nice looking map, but I think people on this forum should make their own personal maps with written down percentages. Much of this is pure guessing, and people need to understand EEF absorbs related forms of middle eastern ancestry and is about 20% WHG.
    Last edited by Fire Haired14; 18-06-14 at 00:53.

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    Please check again my post with the map above. I have explained in more details how I made the map. I have also modified a bit the hues for Iberia using averages of Lazaridis et al. and Eurogenes.

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    Quote Originally Posted by John Doe View Post
    EEF-WHG-ANE results (rounded to full numbers):

    EEF 88
    WHG 5
    ANE 7




    Any interpretation will be welcomed.

    This calculator is obsolete for West Asians (such as N. Caucasians, Druze or Cypriots) and the Jewish, Eastern Mediterranean and Iberian (non-Basque) scores are quite off as well.

    MfA, at anthrogenica, optimised the excel file, the results are more in line with those the authors obtained (you can compare with the paper's extended data file).

    You can download it here:

    https://docs.google.com/spreadsheet/...=sharing#gid=0

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    Quote Originally Posted by Semitic Duwa View Post
    This calculator is obsolete for West Asians (such as N. Caucasians, Druze or Cypriots) and the Jewish, Eastern Mediterranean and Iberian (non-Basque) scores are quite off as well.

    MfA, at anthrogenica, optimised the excel file, the results are more in line with those the authors obtained (you can compare with the paper's extended data file).

    You can download it here:

    https://docs.google.com/spreadsheet/...=sharing#gid=0

    Alright, here are my results from that:

    Results (rounded):
    Near East 84
    ANE 16

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    Quote Originally Posted by John Doe View Post
    Alright, here are my results from that:

    Results (rounded):
    Near East 84
    ANE 16
    Pretty much in line with other Ashkenazi results, it's always around ~85% Near East & ~15% ANE.

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    Quote Originally Posted by Semitic Duwa View Post
    Pretty much in line with other Ashkenazi results, it's always around ~85% Near East & ~15% ANE.
    Okay thanks, can you please answer my 2 questions on the thread "The Jewish people, where are they from?".

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    Quote Originally Posted by John Doe View Post
    Okay thanks, can you please answer my 2 questions on the thread "The Jewish people, where are they from?".
    I'll do that ASAP, unfortunately I'm a busy man.

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    Quote Originally Posted by Semitic Duwa View Post
    I'll do that ASAP, unfortunately I'm a busy man.

    Thanks, I understand. :)

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    My result, all Norwegian back to the middle of the 17. century, when I connect to a few Danes, Finns, Germans and Dutch:
    EEF: 42,57355725
    WHG: 40,99924797
    ANE: 16,42719478

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    My father's result:
    EEF 41,18706
    WHG 42,03763
    ANE 16,77531

    My maternal uncle's result:
    EEF 43,9539
    WHG 39,98378
    ANE 16,06232

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    What does the ANE represent? Does it represent the PIE admixture of West Eurasians?

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    1 out of 1 members found this post helpful.
    Quote Originally Posted by John Doe View Post
    What does the ANE represent? Does it represent the PIE admixture of West Eurasians?
    If the PIE urheimat is in the Samara Culture of the Volga, then we should soon know the proportion of ANE in them because the Reich group is working on a paper about them.

    http://en.wikipedia.org/wiki/Samara_culture

    https://mcidublin.conference-service...tractID=814052

    Genotyping of 390,000 SNPs in more than forty 3,000-9,000 year old humans from the ancient Russian steppe
    David Reich 1 ,2, Nadin Rohland1 ,2, Swapan Mallick1 ,2, Iosif Lazaridis1, Eadaoin Harney1, Susanne Nordenfelt1, Qiaomei Fu3, Matthias Meyer3, Dorcas Brown4, David Anthony4, Nick Patterson2
    1Harvard Medical School, Boston, MA, USA, 2Broad Institute of Harvard and MIT, Cambridge, MA, USA, 3Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, 4Hartwick College, Oneonta, NY, USA
    A central challenge in ancient DNA research is that for many bones that contain genuine DNA, the great majority of molecules in sequencing libraries are microbial. Thus, it has been impractical to carry out whole genome analyses of substantial numbers of ancient individuals. We report a strategy for in-solution capture of ancient DNA from approximately 390,000 single nucleotide polymorphism (SNP) targets, adapting a method of Fu et al. PNAS 2013 who enriched a 40,000 year old DNA sample for the entire chromosome 21. Of the SNPs targets, the vast majority overlap the Affymetrix Human Origins array, allowing us to compare the ancient samples to a database of more than 2,700 present-day humans from 250 groups.
    We applied the SNP capture as well as mitochondrial genome enrichment to a series of 65 bones dating to between 3,000-9,000 years ago from the Samara district of Russia in the far east of Europe, a region that has been suggested to be part of the Proto-Indo-European homeland. We successfully extracted nuclear data from 10-90% of targeted SNPs for more than 40 of the samples, and for all of these samples also obtained complete mitochondrial genomes. We report three key findings:

    • Samples from the Samara region possess Ancient North Eurasian (ANE) admixture related to a recently published 24,000 year old Upper Paleolithic Siberian genome. This contrasts with both European agriculturalists and with European hunter-gatherers from Luxembourg and Iberia who had little such ancestry (Lazaridis et al. arXiv.org 2013). This suggests that European steppe groups may have been be implicated in the dispersal of ANE ancestry across Europe where it is currently pervasive.
    • The mtDNA composition of the steppe population is primarily West Eurasian, in contrast with northwest Russian samples of this period (Der Sarkissian et al. PLoS Genetics 2013) where an East Eurasian presence is evident.
    • Samara experienced major population turnovers over time: early samples (>6000 years) belong primarily to mtDNA haplogroups U4 and U5, typical of European hunter-gatherers but later ones include haplogroups W, H, T, I, K, J.

    We report modeling analyses showing how the steppe samples may relate to ancient and present-day DNA samples from the rest of Europe, the Caucasus, and South Asia, thereby clarifying the relationship of steppe groups to the genetic, archaeological and linguistic transformations of the late Neolithic and Bronze ages.

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    Quote Originally Posted by Angela View Post
    If the PIE urheimat is in the Samara Culture of the Volga, then we should soon know the proportion of ANE in them because the Reich group is working on a paper about them.

    http://en.wikipedia.org/wiki/Samara_culture

    https://mcidublin.conference-service...tractID=814052

    Genotyping of 390,000 SNPs in more than forty 3,000-9,000 year old humans from the ancient Russian steppe
    David Reich 1 ,2, Nadin Rohland1 ,2, Swapan Mallick1 ,2, Iosif Lazaridis1, Eadaoin Harney1, Susanne Nordenfelt1, Qiaomei Fu3, Matthias Meyer3, Dorcas Brown4, David Anthony4, Nick Patterson2
    1Harvard Medical School, Boston, MA, USA, 2Broad Institute of Harvard and MIT, Cambridge, MA, USA, 3Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, 4Hartwick College, Oneonta, NY, USA
    A central challenge in ancient DNA research is that for many bones that contain genuine DNA, the great majority of molecules in sequencing libraries are microbial. Thus, it has been impractical to carry out whole genome analyses of substantial numbers of ancient individuals. We report a strategy for in-solution capture of ancient DNA from approximately 390,000 single nucleotide polymorphism (SNP) targets, adapting a method of Fu et al. PNAS 2013 who enriched a 40,000 year old DNA sample for the entire chromosome 21. Of the SNPs targets, the vast majority overlap the Affymetrix Human Origins array, allowing us to compare the ancient samples to a database of more than 2,700 present-day humans from 250 groups.
    We applied the SNP capture as well as mitochondrial genome enrichment to a series of 65 bones dating to between 3,000-9,000 years ago from the Samara district of Russia in the far east of Europe, a region that has been suggested to be part of the Proto-Indo-European homeland. We successfully extracted nuclear data from 10-90% of targeted SNPs for more than 40 of the samples, and for all of these samples also obtained complete mitochondrial genomes. We report three key findings:

    • Samples from the Samara region possess Ancient North Eurasian (ANE) admixture related to a recently published 24,000 year old Upper Paleolithic Siberian genome. This contrasts with both European agriculturalists and with European hunter-gatherers from Luxembourg and Iberia who had little such ancestry (Lazaridis et al. arXiv.org 2013). This suggests that European steppe groups may have been be implicated in the dispersal of ANE ancestry across Europe where it is currently pervasive.
    • The mtDNA composition of the steppe population is primarily West Eurasian, in contrast with northwest Russian samples of this period (Der Sarkissian et al. PLoS Genetics 2013) where an East Eurasian presence is evident.
    • Samara experienced major population turnovers over time: early samples (>6000 years) belong primarily to mtDNA haplogroups U4 and U5, typical of European hunter-gatherers but later ones include haplogroups W, H, T, I, K, J.

    We report modeling analyses showing how the steppe samples may relate to ancient and present-day DNA samples from the rest of Europe, the Caucasus, and South Asia, thereby clarifying the relationship of steppe groups to the genetic, archaeological and linguistic transformations of the late Neolithic and Bronze ages.
    I'm expecting samples from Samara to be >90% ANE when they come from around 6,000 years ago. Mixing with farmers would bring it down to 75-50% around 4,000 years ago. In these proportions they've entered Europe as IE. Will see soon.

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    Quote Originally Posted by Angela View Post
    If the PIE urheimat is in the Samara Culture of the Volga, then we should soon know the proportion of ANE in them because the Reich group is working on a paper about them.

    http://en.wikipedia.org/wiki/Samara_culture

    https://mcidublin.conference-service...tractID=814052

    Genotyping of 390,000 SNPs in more than forty 3,000-9,000 year old humans from the ancient Russian steppe
    David Reich 1 ,2, Nadin Rohland1 ,2, Swapan Mallick1 ,2, Iosif Lazaridis1, Eadaoin Harney1, Susanne Nordenfelt1, Qiaomei Fu3, Matthias Meyer3, Dorcas Brown4, David Anthony4, Nick Patterson2
    1Harvard Medical School, Boston, MA, USA, 2Broad Institute of Harvard and MIT, Cambridge, MA, USA, 3Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, 4Hartwick College, Oneonta, NY, USA
    A central challenge in ancient DNA research is that for many bones that contain genuine DNA, the great majority of molecules in sequencing libraries are microbial. Thus, it has been impractical to carry out whole genome analyses of substantial numbers of ancient individuals. We report a strategy for in-solution capture of ancient DNA from approximately 390,000 single nucleotide polymorphism (SNP) targets, adapting a method of Fu et al. PNAS 2013 who enriched a 40,000 year old DNA sample for the entire chromosome 21. Of the SNPs targets, the vast majority overlap the Affymetrix Human Origins array, allowing us to compare the ancient samples to a database of more than 2,700 present-day humans from 250 groups.
    We applied the SNP capture as well as mitochondrial genome enrichment to a series of 65 bones dating to between 3,000-9,000 years ago from the Samara district of Russia in the far east of Europe, a region that has been suggested to be part of the Proto-Indo-European homeland. We successfully extracted nuclear data from 10-90% of targeted SNPs for more than 40 of the samples, and for all of these samples also obtained complete mitochondrial genomes. We report three key findings:

    • Samples from the Samara region possess Ancient North Eurasian (ANE) admixture related to a recently published 24,000 year old Upper Paleolithic Siberian genome. This contrasts with both European agriculturalists and with European hunter-gatherers from Luxembourg and Iberia who had little such ancestry (Lazaridis et al. arXiv.org 2013). This suggests that European steppe groups may have been be implicated in the dispersal of ANE ancestry across Europe where it is currently pervasive.
    • The mtDNA composition of the steppe population is primarily West Eurasian, in contrast with northwest Russian samples of this period (Der Sarkissian et al. PLoS Genetics 2013) where an East Eurasian presence is evident.
    • Samara experienced major population turnovers over time: early samples (>6000 years) belong primarily to mtDNA haplogroups U4 and U5, typical of European hunter-gatherers but later ones include haplogroups W, H, T, I, K, J.

    We report modeling analyses showing how the steppe samples may relate to ancient and present-day DNA samples from the rest of Europe, the Caucasus, and South Asia, thereby clarifying the relationship of steppe groups to the genetic, archaeological and linguistic transformations of the late Neolithic and Bronze ages.

    So does this mean the 16% ANE I get from the calculator come from a PIE/Ural source?

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    Quote Originally Posted by John Doe View Post
    So does this mean the 16% ANE I get from the calculator come from a PIE/Ural source?

    I'm already on record that I don't trust the "calculator" results very much, since they conflict with the Lazaridis et al results, for some groups substantially so, and have wide confidence margins, but I suppose you could take it as a rough estimate of your ANE contribution.

    When the results from the Samara people come in, we'll know much more, but I personally think the ANE is probably a signature of the movement of steppe peoples into Europe. It might also be partly a signature of hunter gatherers from the far north east, since a bit of ANE shows up in those people as well.

    Ed. For Ashkenazim, it's a different calculation. People in the Near East have ANE too, and so do South Asians, but I don't think we yet know when it arrived, or with whom. Perhaps some of it came with IE people, but perhaps some of it came before. I'm afraid we still have a lot to learn.

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    Quote Originally Posted by Angela View Post
    I'm already on record that I don't trust the "calculator" results very much, since they conflict with the Lazaridis et al results, for some groups substantially so, and have wide confidence margins, but I suppose you could take it as a rough estimate of your ANE contribution.

    When the results from the Samara people come in, we'll know much more, but I personally think the ANE is probably a signature of the movement of steppe peoples into Europe. It might also be partly a signature of hunter gatherers from the far north east, since a bit of ANE shows up in those people as well.

    Ed. For Ashkenazim, it's a different calculation. People in the Near East have ANE too, and so do South Asians, but I don't think we yet know when it arrived, or with whom. Perhaps some of it came with IE people, but perhaps some of it came before. I'm afraid we still have a lot to learn.
    I suppose you're right, until we'll know for certain, I guess it remains uncertain why East Mediterraneans have around 15% ANE.

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    Quote Originally Posted by John Doe View Post
    I suppose you're right, until we'll know for certain, I guess it remains uncertain why East Mediterraneans have around 15% ANE.
    The ANE in modern Middle Eastern people could be partly Turkish in origin, but that wouldn't show up in members of the Jewish diaspora who left the Middle East before the coming of the Turks.

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    Quote Originally Posted by Aberdeen View Post
    The ANE in modern Middle Eastern people could be partly Turkish in origin, but that wouldn't show up in members of the Jewish diaspora who left the Middle East before the coming of the Turks.
    Since Jews are a pre Islamic East Mediterranean group it's unlikely that their ANE admixture came from the Turks who invaded Western Asia about 1,000 years after the destruction of the temple. Therefore this ANE admixture probably came from somewhere else, but I guess this puzzle is yet to be solved.

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    1 out of 1 members found this post helpful.
    Quote Originally Posted by Aberdeen View Post
    The ANE in modern Middle Eastern people could be partly Turkish in origin, but that wouldn't show up in members of the Jewish diaspora who left the Middle East before the coming of the Turks.

    ANE is present in all of Western and South Asia. It is more of an Indo_European or Proto_Caucasic signature. An evidence for this is that ANE reaches it's higest frequency among Iranic and Caucasic groups of Western Asia.

    ANE reaches levels of 25% in North Caucasus.
    Last edited by Alan; 01-07-14 at 17:06.

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