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Thread: Yamna_K6

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    Yamna_K6

    This is just something Davidski is trying out.

    http://eurogenes.blogspot.com/2015/0...rtions-in.html

    Eurogenes K15 and ANE K8 spreadsheets for comparison and reference.

    https://docs.google.com/spreadsheets...gid=1872836177

    https://docs.google.com/spreadsheets...t#gid=74932529

    This test was an unsupervised run. If I'm interpreting Davidski correctly that means when he tried to create ancestor clusters with modern(excluding northeast Euros, Caucasus, and south Asia because of drift) and ancient genomes a pure Yamna cluster appears which most of the Yamna samples almost score 100% in.

    The rest of west Eurasian's ancestry is mostly thrown into two clusters; Middle eastern and pre-Yamna European(prob. very EEF-like). Those two should turn out very similar to each other(ENF+WHG, no ANE?).

    Looks like there's certainly room for a lot of Yamna-like ancestry in Central, south, and west Asia. Kazakhs look like an even mix of Yamna(Ancient Indo Iranians?) and something very east Asian-like(Turks?).

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    Interesting.
    So, at this point, there can be little doubt that Yamnaya went a long way toward creating modern Europe's population.

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    By god this guy will try anything in his power to turn his beloved Northeast Europeans as "Yamna" like as possible. Haak paper says Russians/Lezgians closely followed by Norwegians have second most Yamna DNA after Mordovians.

    But in his work Polish are as Yamna as Norwegians and Lithuanians even more Yamna than Russians. Lezgians who are according to the actual study as close to Yamna as Russians but here appear less Yamna like than 3/4 of any of the European populations. Suprise!

    And why exclude Northeast Europe, Caucasus and South Asia for his ancestral components? Doesn't it turn out how he wants? Going by this Calculator, contrary to Haak paper. Armenians are less than 15% Yamna.

    I quote
    But I'd say this looks like a very reasonable attempt, with more or less comparable results to those published by Haak et al.
    Yup just with the "small" difference that different from the Haak paper suddenly the Northeast Euros turn out more Yamna like than Norwegians. And Lithuanians turn out as much Yamna as Mordovians!! While in the original paper that wasn't the case. This can only be explained that this "calculator" is making populations with more "European genes" appear more Yamna. Explains also why Spaniards here are more Yamna than Turks while in the Haak paper it was the opposite.
    https://drive.google.com/file/d/0B9o...dENTdtZTg/view


    The agenda shines through his work like the sun in the hot summer days. If you can't bring the PIEs to the Baltics, than try to bring the Baltics to PIEs.
    Last edited by Alan; 15-03-15 at 04:56.

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    Alan, Polish weren't tested in Haak 2015. His numbers are very similar to Haak 2015's, they don't have to be identical to be correct.

    You're basing your statement that Lezgins are as close to Yamna as Russians are on one PCA from Haak 2015, that's not nearly enough. I don't think Davidski forced an agenda into this test.

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    Quote Originally Posted by Fire Haired14 View Post
    Alan, Polish weren't tested in Haak 2015. His numbers are very similar to Haak 2015's, they don't have to be identical to be correct.
    Just compare the Yamna ancestry in Lithuanians vs Norwegians and Yamna ancestry in Lithuanians vs Norwegians at the Haak paper. Lithuanians in Eurog. K6 have suddenly significantly more Yamna than Norwegians. He has created a calculator which once again turns all towards Northeast Europeans.

    According to this new "calculator" Armenians are less than 15% Yamna! while according to Haak paper they are ~25% Yamna like. That can only be explained that the number of Yamna ancestry in more "West Asian" admixed populations is pushed down while the number in more "EHG" admixed populations pushed up (suprise that is basically Northeast Europeans).

    You're basing your statement that Lezgins are as close to Yamna as Russians are on one PCA from Haak 2015, that's not nearly enough. I don't think Davidski forced an agenda into this test.
    I am not basing my statement on the PCA map, but the fst distances which are in accordance to the Haak graph.


    page 26
    http://biorxiv.org/content/biorxiv/e...13433.full.pdf

    I also think I know why he used the K6 calculator instead of K8 or K9. It would turn yamna more Central_West Asian like. Thats what even the people under his comment section are speculating.
    Last edited by Alan; 15-03-15 at 04:57.

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    Another thing, didn't he give the word out and make everyone believe that Yamna is 40-45% WHG, 30-35% ANE and 25% ENF, while at the same time his own calculator spit out 35-40/30-35/25/5 (ANE/WHG/ENF/SE)?
    In K8 North Indians appear with less than 3% WHG, suddenly in this K6 calculator they show up with extra WHG (additional to that what might have come from Yamna).
    Last edited by Alan; 14-03-15 at 16:59.

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    Quote Originally Posted by Alan View Post
    Another thing, didn't he give the word out and make everyone believe that Yamna is 40-45% WHG, 30-35% ANE and 25% ENF, while at the same time his own calculator spit out 35/35/25/5 (ANE/WHG/ENF/SE)?

    I don't feel like I can trust his word or work anymore.
    No, that's what others said. It's basically true because the minor we don't know exactly what the minor exotic scores for Yamna mean.

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    Quote Originally Posted by Fire Haired14 View Post
    No, that's what others said. It's basically true because the minor we don't know exactly what the minor exotic scores for Yamna mean.
    What did others said? That Yamna is 40-45% WHG and 30% ANE, while non Yamna sample even reaches 40% (mostly 35%) and some of the samples reach as high as 39% ANE.
    So it's not true. You can't post "assumptions" as "confirmed" facts.

    So if you open a thread with the title "Yamna 25 ENF , 30-35% ANE and 40-45%. Than it deceives people.

    I actually thought he said that because you presented it as if this are the ultimate scores.


    I feel exactly like the guy who asked this
    @David, not to be rude but why are you doing something the researchers have already done?
    Exactly why would you do the work a scientist already has done? Maybe you didn't like the results?

    I simply have lost allot of trust in his work. He puts afford in it, I admit, but there is too often a too strong agenda behind his work.
    Last edited by Alan; 16-03-15 at 01:15.

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    Quote Originally Posted by Alan View Post
    What did others said? That Yamna is 40-45% and 30% ANE, while non Yamna sample even reaches 40% (mostly 35%) and some of the samples reach as high as 39% ANE. So it's not true but more of a bluff. You can't post "assumptions" as "confirmed" facts.

    I actually thought he said that because you presented it as if this are the ultimate scores.


    I feel exactly like the guy who asked this


    Exactly why would you do the work a scientist already has done? Maybe you didn't like the results?

    I simply have lost trust in his work. He puts afford in it, I admit, but his work is too often too biased.
    so he is doctoring his work

    it seems the Haak paper has destroyed his pre-promises ( a year before ) that yamnya would be R1a ...........as you know seven R1b where found
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    Quote Originally Posted by Fire Haired14 View Post
    Alan, Polish weren't tested in Haak 2015. His numbers are very similar to Haak 2015's, they don't have to be identical to be correct.

    You're basing your statement that Lezgins are as close to Yamna as Russians are on one PCA from Haak 2015, that's not nearly enough. I don't think Davidski forced an agenda into this test.
    haak paper is about the ancients............there was no polish in the ancients.

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    Quote Originally Posted by Sile View Post
    so he is doctoring his work

    it seems the Haak paper has destroyed his pre-promises ( a year before ) that yamnya would be R1a ...........as you know seven R1b where found
    ++

    At least someone seems to see through the mask. And now ask yourself again why suddenly Northeast Europeans are scoring more Yamna ancestry than anyone else in Europe. And West and South_Central Asians on average even less than the least Yamna (Spain) like European population.

    David can do great work if it goes in accordence with what he expects and wishes. If he appears to be mistaken on something he does everything in his power to straighten things up as suitable as possible for his own theories and believes.

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    Oh my God Alan just stop it.

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    Where the results conflict with the Haak et al formal stats they're obviously wrong. I don't know how there can even be a debate about it. Even within the results themselves there are glaring inconsistencies. There's been an attempt to get rid of that 50% "Near Eastern" and any "Central Asian" in the Yamnaya Indo-Europeans and to move their center of gravity to certain areas of Europe ever since the results came out. It just took a while.

    Anyone who knows anything at all about these programs and how they work knows that through the choice of K or the selection of references or the samples used you can manipulate the results. I don't know how it could have taken some of you so long to reach these conclusions.

    If there are any actual academics involved in any of this, they should really do some research and re-examine their associations, or they are going to get burnt good and proper.

    Oh, and for the record, I have no dog in the fight; the less Yamnaya my people and I turn out to have the better I'll like it.


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    People are getting mad at Polako! Hahahahaha

    This software can't tell apart Yamna ancestry from indigenous Mesolitich stuff from La Brana swarthoids, so it's completely useless.

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    Quote Originally Posted by Sile View Post
    so he is doctoring his work

    it seems the Haak paper has destroyed his pre-promises ( a year before ) that yamnya would be R1a ...........as you know seven R1b where found
    Seven R1b were found in one location. I'm not saying he doesn't appear to have an agenda, but it seems quite certain to me that R1a was part of the IE expansion. I don't take that admixture stuff too clearly no matter who's doing it. I don't have to be a geneticist to know that it sometimes produces strange results and I think that just illustrates the old saying about any computer calculations: garbage in = garbage out.

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    Quote Originally Posted by Aberdeen View Post
    Seven R1b were found in one location. I'm not saying he doesn't appear to have an agenda, but it seems quite certain to me that R1a was part of the IE expansion. I don't take that admixture stuff too clearly no matter who's doing it. I don't have to be a geneticist to know that it sometimes produces strange results and I think that just illustrates the old saying about any computer calculations: garbage in = garbage out.
    Surely R1a was part of the Yamna expansion. Without doubt for me because Reich said both existed there. Remember he has 50+ samples and only published 6 of them. Means to me some of the other might be R1a too and he is just holding it back for another study to be published.

    Quote Originally Posted by Angela
    Anyone who knows anything at all about these programs and how they work knows that through the choice of K or the selection of references or the samples used you can manipulate the results. I don't know how it could have taken some of you so long to reach these conclusions.
    Gedrosia for example appears only in higher Ks. Now you can imagine yourself why the usage of higher Ks could be contraproductive for him. And the selection of reference populations is so true.

    As I said he has actually great knowledge, but it is useless if you 24/7 use this knowledge to manipulate data and of course People who lose out in these manipulations will be upset most.

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    And also great that in the Comment section people have realized that the Steppe population was replaced by "Polish"(Slavic) like people.

    Goes in accordence with my theory that the original Pontic populations were almost completely replaced by the Slavic expansion(after beeing replaced by the Turkic earlier).

    This is why we nowadays have this gab between, Eastern Europe, the Urals, Central Asia and North Caucasus. It's Altaic admixture in the East and Slavic admixture in the West.
    Last edited by Alan; 16-03-15 at 01:17.

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    Just took a closer look at the scores for the ancient samples. While Oetzi is virtually 100% "Pre-Yamnaya", Stuttgart is only 75% "Pre-Yamnaya"? If she isn't "Pre-Yamnaya" then what is she? All those EEF samples are by definition "Pre-Yamnaya"! Then I thought that perhaps this cluster is supposed to represent Middle Neolithic people just prior to the arrival of the Yamnaya people, but only Oetzi is 100% Pre-Yamnaya, while the other MN sample suddenly has additional "Middle Eastern".

    The whole thing makes so little sense that I'm done giving this "experiment" head room. If someone wants to know the best estimate so far for Yamnaya Indo-European ancestry in modern Europeans, the figures are given in Haak et al, although I think it will change as more ancient samples become available. You're not going to find the numbers in this run.

    To be honest, the whole discussion of this topic is becoming a bit nausea inducing, and I say this as someone who has been following it as an intellectual puzzle for years. At the end of the day, what does it matter who has what percent of Yamnaya ancestry? What does any of this have to do with real life or the real issues confronting all of us?

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    Quote Originally Posted by Angela View Post
    Where the results conflict with the Haak et al formal stats they're obviously wrong. I don't know how there can even be a debate about it. Even within the results themselves there are glaring inconsistencies. There's been an attempt to get rid of that 50% "Near Eastern" and any "Central Asian" in the Yamnaya Indo-Europeans and to move their center of gravity to certain areas of Europe ever since the results came out. It just took a while.
    Everyone who consistently visits Eurogenes blog should know that Yamna-related, pre-Yamna, and Middle Easyerm all carry ENF. Davidski is not trying to make Yamna appear non-ENF just like 23andme isn't trying to make people appear non-ENF by giving percentages in German-French, etc. BTW, the Central Asian component from his K9 is pretty much pure ANE.

    This test isn't meant to measure differnt forms of ancestry in Yamna it's meant to measure Yamna-related ancestry in modern people.

    Quote Originally Posted by Angela View Post
    Anyone who knows anything at all about these programs and how they work knows that through the choice of K or the selection of references or the samples used you can manipulate the results. I don't know how it could have taken some of you so long to reach these conclusions.

    If there are any actual academics involved in any of this, they should really do some research and re-examine their associations, or they are going to get burnt good and proper.

    Oh, and for the record, I have no dog in the fight; the less Yamnaya my people and I turn out to have the better I'll like it.
    You're saying no one should use Ks?

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    Quote Originally Posted by Angela View Post
    Just took a closer look at the scores for the ancient samples. While Oetzi is virtually 100% "Pre-Yamnaya", Stuttgart is only 75% "Pre-Yamnaya"? If she isn't "Pre-Yamnaya" then what is she? All those EEF samples are by definition "Pre-Yamnaya"! Then I thought that perhaps this cluster is supposed to represent Middle Neolithic people just prior to the arrival of the Yamnaya people, but only Oetzi is 100% Pre-Yamnaya, while the other MN sample suddenly has additional "Middle Eastern".

    The whole thing makes so little sense that I'm done giving this "experiment" head room. If someone wants to know the best estimate so far for Yamnaya Indo-European ancestry in modern Europeans, the figures are given in Haak et al, although I think it will change as more ancient samples become available. You're not going to find the numbers in this run.

    To be honest, the whole discussion of this topic is becoming a bit nausea inducing, and I say this as someone who has been following it as an intellectual puzzle for years. At the end of the day, what does it matter who has what percent of Yamnaya ancestry? What does any of this have to do with real life or the real issues confronting all of us?
    Pre-Yamna, Yamna, etc. all the components in this test are simply components just like "West-Med" in K15. Davidski gave them those names because they best represent Yamna, pre-Yamna, etc. ancestry. When he added ancient genomes in his database they created components modern ones couldn't, because they better represent the ancestors of modern people than other modern people.

    No one is(or at least should) taking this as a competition to see who's the most Yamna-descended. That was never the point. Yamna-like people passed on a lot of genes so when researching modern origins they're very much in subject.

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    Quote Originally Posted by Alan View Post
    And also great that in the Comment section people have realized that the Steppe population was replaced by "Polish"(Slavic) like people.

    Goes in accordence with my theory that the original Pontic populations were almost completely replaced by the Slavic expansion(after beeing replaced by the Turkic earlier).

    This is why we nowadays have this gab between, Eastern Europe, the Urals and North Caucasus.
    Yeah, that does appear to be the case. Central Asians look like a mix of Yamna and Siberians, Ural people look like a mix of Yamna, Siberians, and Poles. Obviously Yamna was there before the other two.

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    Seems to me there is obviously a flaw in the three way model: EEF, WHG, ANE.

    1) There's at least two sets of farmers, a more maritime Levant set and another more overland set and the "near eastern" component may be a composite of the two rather than a single component.

    2) There seems to be multiple sources of ANE.

    So whether his alternative is ultimately right or wrong Davidski's tinkering with the model is likely to produce something useful.

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    Quote Originally Posted by Greying Wanderer View Post
    So whether his alternative is ultimately right or wrong Davidski's tinkering with the model is likely to produce something useful.
    sure can, toilet paper is useful too

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    Quote Originally Posted by Sile View Post
    sure can, toilet paper is useful too
    If there are more than three critical components then any model using just the three components is going to be flawed.

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    Quote Originally Posted by Angela View Post
    Just took a closer look at the scores for the ancient samples. While Oetzi is virtually 100% "Pre-Yamnaya", Stuttgart is only 75% "Pre-Yamnaya"? If she isn't "Pre-Yamnaya" then what is she? All those EEF samples are by definition "Pre-Yamnaya"! Then I thought that perhaps this cluster is supposed to represent Middle Neolithic people just prior to the arrival of the Yamnaya people, but only Oetzi is 100% Pre-Yamnaya, while the other MN sample suddenly has additional "Middle Eastern".

    The whole thing makes so little sense that I'm done giving this "experiment" head room. If someone wants to know the best estimate so far for Yamnaya Indo-European ancestry in modern Europeans, the figures are given in Haak et al, although I think it will change as more ancient samples become available. You're not going to find the numbers in this run.

    To be honest, the whole discussion of this topic is becoming a bit nausea inducing, and I say this as someone who has been following it as an intellectual puzzle for years. At the end of the day, what does it matter who has what percent of Yamnaya ancestry? What does any of this have to do with real life or the real issues confronting all of us?
    When a pre Yamna Stuttgart turns out 25% Yamna and the general data is not consistent with the actual study than you know something is wrong here.
    As I said K6 is far too low to even be able to differentiate between farmer and H&G let alone the various farmer and H&G types. K6 only differentiates between "European, Near Eastern, South Asian, Amerindian, East Asian and African." And this is also based on the reference populations you use for it. I assume this might be the reason why some of the EEF genes turn out as Yamna because it can't differentiate between EEF and "West Asian" and probably can't differentiate between pre and post Yamna WHG like ancestry.

    This comes not suprisingly accommodating for Northeast Europeans who lack Gedrosia.
    For example take a look at the Balochi with highest Gedrosia scores. They appear to have only 5%!! Yamna ancestry while anyone surrounding them has suddenly 40%. It almost seems like something "contra West Asian/Gedrosia" is going on in this calculator. And suddenly Northeast Europeans have the top Yamna scores instead of Mordovians, Norwegians, Russians, Lezgians (only Udmurts top them), while strictly taken we could argue that Northeast Europeans have "least" Yamna ancestry because they lack Gedrosia/West Asian which is crucial component among Yamna. This might be the reason why he needed to eradicate this component by using lower Ks

    In order to make Northeast Europeans as "Yamna" like as possible you need to use lower Ks where the components are not specified enough. Even the Haak paper uses at least K16
    page 22 => http://biorxiv.org/content/biorxiv/e...13433.full.pdf

    So how comes someone could thing he can get correct results from a K6 run? Look it can happen that sometimes results get inconsistent I understand that, but I can't believe this is coincidence if it is always Northeast Europeans profiting from this on the cost of Western Asians.

    I am no expert on this field so I can't tell exactly what is wrong, but comparing it with Haak paper, there is definitely something wrong.
    Last edited by Alan; 15-03-15 at 17:19.

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