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Thread: Modelling Admixture with PCA

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    Modelling Admixture with PCA

    I'm opening this thread for postings of admixture proportions from a PCA. I already have a thread for posting admixture proportions from D-stats, here.

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    David Wesolski at Eurogenes, has created a global PCA with 50 dimensions. Normal PCAs only have 2 dimensions. His PCA has so many dimensions it is impossible for our eyes to comprehend it. He posted the locations of all the global samples in all 50 dimensions, to use to produce admixture results.

    I've been playing around with Europe, and the results are 100% consistent with everything we've seen before.

    Here are some results.
    Population Yamnaya_Samara Loschbour Sweden_MN D statistic
    Czech 51 4 45 0.0097
    Belarusian 55 13 32 0.0172
    Lithuanian 56 21 23 0.0177
    Norwegian 49 7 44 0.0082
    Andronovo 73 3 24 0.0105


    Population Cypriot Hungary_CA Mozabite Yamnaya_Samara D statistic
    Italian_Bergamo 10 66 0 24 0.0148
    Italian_EastSicilian 48 37 2 13 0.0096
    Italian_Tuscan 30 48 0 22 0.0109
    Italian_WestSicilian 46 37 2 15 0.0098


    Population Cypriot Iberia_Chalcolithic Mozabite Yamnaya_Samara D statistic
    Spanish_Andalucia 22 51 3 24 0.0081
    Spanish_Aragon 13 60 1 26 0.0079
    Spanish_Baleares 20 50 1 29 0.0094
    Spanish_Cantabria 12 58 1 29 0.0079
    Spanish_Castilla_la_Mancha 20 55 0 25 0.009
    Spanish_Castilla_y_Leon 15 51 7 27 0.0091
    Spanish_Cataluna 15 52 3 30 0.0103
    Spanish_Extremadura 18 48 6 28 0.0102
    Spanish_Galicia 18 49 5 28 0.0081
    Spanish_Murcia 19 52 3 26 0.0078
    Spanish_Pais_Vasco 0 70 0 30 0.0117
    Spanish_Valencia 17 55 1 27 0.0086

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    Quote Originally Posted by Fire Haired14 View Post
    Spanish_Pais_Vasco 0 70 0 30 0.0117
    Yamnaya is unusually high for Basques. Probably because there is much Loschbour in Yamna?

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    It's also too high for Spaniards, and for the same reason.

    Also, this doesn't tell us anything about the gene flows that formed the Spanish and the Italians; there was no migration of "Cypriots" into those countries at the kind of levels which would be required to get these kinds of admixture results.

    I'm not even sure that it's accurate for northern Europeans. The Yamnaya percentage might be inflated by high WHG/EHG genes that were absorbed as the actual Yamnaya type people moved across Europe.


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    Quote Originally Posted by Angela View Post
    I'm not even sure that it's accurate for northern Europeans. The Yamnaya percentage might be inflated by high WHG/EHG genes that were absorbed as the actual Yamnaya type people moved across Europe.
    Yes, except that WHG in Basques as in Sardinians came mostly with EEF farmers, not Yamnaya people.

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    Quote Originally Posted by Angela View Post
    It's also too high for Spaniards, and for the same reason.

    Also, this doesn't tell us anything about the gene flows that formed the Spanish and the Italians; there was no migration of "Cypriots" into those countries at the kind of levels which would be required to get these kinds of admixture results.

    I'm not even sure that it's accurate for northern Europeans. The Yamnaya percentage might be inflated by high WHG/EHG genes that were absorbed as the actual Yamnaya type people moved across Europe.
    Yamnaya admixture wasn't already studied in a peer review paper as Haak (2015)?



    Quote Originally Posted by Fire Haired14 View Post
    David Wesolski at Eurogenes, has created a global PCA with 50 dimensions. Normal PCAs only have 2 dimensions. His PCA has so many dimensions it is impossible for our eyes to comprehend it. He posted the locations of all the global samples in all 50 dimensions, to use to produce admixture results.

    I've been playing around with Europe, and the results are 100% consistent with everything we've seen before.

    Here are some results.
    Population Yamnaya_Samara Loschbour Sweden_MN D statistic
    Czech 51 4 45 0.0097
    Belarusian 55 13 32 0.0172
    Lithuanian 56 21 23 0.0177
    Norwegian 49 7 44 0.0082
    Andronovo 73 3 24 0.0105


    (...)
    The source? A link?

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    Quote Originally Posted by Pax Augusta View Post
    Yamnaya admixture wasn't already studied in a peer review paper as Haak (2015)?




    Indeed, and by a more sophisticated method than a simple Admixture run.

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    Quote Originally Posted by Pax Augusta View Post
    Yamnaya admixture wasn't already studied in a peer review paper as Haak (2015)?

    The source? A link?
    These results were created by amateurs, using the same tools academics use.

    Quote Originally Posted by Angela View Post
    It's also too high for Spaniards, and for the same reason.

    Also, this doesn't tell us anything about the gene flows that formed the Spanish and the Italians; there was no migration of "Cypriots" into those countries at the kind of levels which would be required to get these kinds of admixture results.

    I'm not even sure that it's accurate for northern Europeans. The Yamnaya percentage might be inflated by high WHG/EHG genes that were absorbed as the actual Yamnaya type people moved across Europe.
    Yamnaya has hardly any or no WHG. WHG and EHG behave in significantly differnt ways in PCA and D-stats. Trust me, Iberia Middle Neolithic/Copper age, provides all the WHG Iberians need. Actually it gives too much, which is why they need Cypriot admixture. Cypriot are a proxy for unsampled Near Eastern ancestors of mostly Southern Europe, but also Central Europe. When you see the basically the same results from two completely differnt methods(PCA and D-stats), you got to admit, there's something legitimate about the results.

    In 500 BC, if they discovered DNA, someone would have figured out Europeans are mostly Sycthian+Sardinian. It wouldn't mean, Europeans literally had Sycthian and Sardinian ancestry, but that they have ancestors who were similar to Sycthians and Sardinians. We're in a similar situation in 2000 AD, with Cypriots and Southern Europe.

    Quote Originally Posted by Angela View Post
    Indeed, and by a more sophisticated method than a simple Admixture run.
    They used the exact same method as D-stat admixture. They tested the relatedness of test populations to outgroups, then modeled modern test populations as a mixture of ancient ones. I think they used F-stats instead D-stats(don't know the difference between the two), but it's the same idea.

    Haak 2015.
    We estimate mixture proportions using a method thatgives unbiased estimates even without an accurate model for the relationships between the
    test populations and the outgroup populations (SI9).

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    @Everyone,

    There's no doubt Steppe admixture is significant for Spain and Italy. 20-30% from the Pontic-Caspein Steppe, not Ukraine where they had EEF admixture, is reasonable. When you model Spain and Italy, as Steppe+WHG+EEF, you still get 20-30% Steppe, but a bad fit(because they need Cypriot or something similar).

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    Quote Originally Posted by Fire Haired14 View Post
    @Everyone,

    There's no doubt Steppe admixture is significant for Spain and Italy. 20-30% from the Pontic-Caspein Steppe, not Ukraine where they had EEF admixture, is reasonable. When you model Spain and Italy, as Steppe+WHG+EEF, you still get 20-30% Steppe, but a bad fit(because they need Cypriot or something similar).
    I have my doubts
    có che un pòpoło no 'l defende pi ła só łéngua el xe prónto par èser s'ciavo

    when a people no longer dares to defend its language it is ripe for slavery.

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    Here are better results. I used the nMonte system instead of 4mix. nMonte, breaks down percentages to decimals.

    Anatolia_Neolithic Yamnaya_Samara Loschbour Cypriot @ D Cycles
    Italian_Tuscan 42.6 25.5 6.4 25.5 0.007143 100
    Scottish_Argyll 28.85 39.6 21.75 9.8 0.009478 100


    Iberia Iberia_Chalcolithic Bell_Beaker_Germany Cypriot @ D
    Spanish_Aragon 39.6 45.9 14.9 0.006734
    Basque_Spanish 61.8 38.2 0 0.018822


    Italy Iceman_MN Bell_Beaker_Germany Cypriot @ D
    Italian_Bergamo 29.45 48.6 21.95 0.008345
    Italian_Tuscan 16 42.25 41.75 0.007458
    Italian_WestSicilian 12.7 29.75 57.55 0.010929
    Anatolia_Neolithic Yamnaya_Samara Loschbour @ D Cycles
    Scottish_Argyll 36.1 44.25 19.65 0.009592 100
    Italian_Tuscan 61.45 37.55 1 0.008183 100
    Hungary_BA 41.4 32.9 25.7 0.013439 100

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    I don't doubt that there is steppe admixture in southern Europe. Just results from yDna indicate that this is the case, and, as has been pointed out, it was found through the extensive modeling presented in Haak et al.

    What I'm questioning is the amount, which seems about right for certain groups and pretty off for others (I highly doubt that the Basques are 70% Yamnaya related). I'm also questioning modeling groups using a mixture of ancient and modern genomes. In this particular case, Cypriots have their own particular population history and admixture. Throwing them into the mix may be altering the other percentages in ways we can't really predict.

    Why not just wait for aDna? It won't be long.

    Oh, and last I heard there are problems with the use and interpretation of Dstats, and we have that from the people who know the most about them, like Patterson. All these methods have their limitations. We have to try to take into account the results from all of the tools at our disposal, not constantly proclaim that this is the definitive tool and these are the only correct conclusions.

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    Quote Originally Posted by Angela View Post
    I don't doubt that there is steppe admixture in southern Europe. Just results from yDna indicate that this is the case, and, as has been pointed out, it was found through the extensive modeling presented in Haak et al.

    What I'm questioning is the amount, which seems about right for certain groups and pretty off for others (I highly doubt that the Basques are 70% Yamnaya related). I'm also questioning modeling groups using a mixture of ancient and modern genomes.
    Basque came out 30% Yamnaya. BTW, what makes Basque unique in these tests(D-stats, ADMIXTURE, PCA) is they lack the Near Eastern-signal other Iberians and French have. They have as much Steppe admixture.



    Quote Originally Posted by Angela View Post
    In this particular case, Cypriots have their own particular population history and admixture. Throwing them into the mix may be altering the other percentages in ways we can't really predict.
    In D-stats, Cypriots unique history isn't expressed. This is because there are no Near Eastern-outgroups. Cypriots relationship to non-West Eurasian outgroups, European HGs, and CHG, is basically the same as Anatolia_Neolithic. The only difference is Cypriot isn't as close to EEF outgroups as Anatolia_Neolithic is. So, Cypriot is like EEF but not EEF.

    Using simple math, you can suck out a zombie ancestor out of test populations. So, for Georgians and Mozabite I did this. Georgian's non-CHG side in D-stats, behaves similar to Cypriot. Mozabite's non-African side, behaves similar to Cypriot. So, Cypriot in D-stats with the outgroups used, is like a pure Near Eastern. They're not EEF or CHG, and they don't appear to have exotic admixture(African, East Asian, South Asian, Steppe). That's why I use them as a Near Eastern ancestor proxy for South Europe.

    In other methods, Lebanese or Turkish work better than Cypriot for South Europe. In D-stats however Cypriots work better.

    Quote Originally Posted by Angela View Post
    Why not just wait for aDna? It won't be long.

    Oh, and last I heard there are problems with the use and interpretation of Dstats, and we have that from the people who know the most about them, like Patterson. All these methods have their limitations. We have to try to take into account the results from all of the tools at our disposal, not constantly proclaim that this is the definitive tool and these are the only correct conclusions.
    I'm impatient. It's been a year since any big ancient DNA paper was published. I've used D-stats, PCA, and ADMIXTURE(not just ANE K8, but also old ones based on moderns), and have gotten the same results.

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    Quote Originally Posted by Fire Haired14 View Post
    Basque came out 30% Yamnaya. BTW, what makes Basque unique in these tests(D-stats, ADMIXTURE, PCA) is they lack the Near Eastern-signal other Iberians and French have. They have as much Steppe admixture.





    In D-stats, Cypriots unique history isn't expressed. This is because there are no Near Eastern-outgroups. Cypriots relationship to non-West Eurasian outgroups, European HGs, and CHG, is basically the same as Anatolia_Neolithic. The only difference is Cypriot isn't as close to EEF outgroups as Anatolia_Neolithic is. So, Cypriot is like EEF but not EEF.

    Using simple math, you can suck out a zombie ancestor out of test populations. So, for Georgians and Mozabite I did this. Georgian's non-CHG side in D-stats, behaves similar to Cypriot. Mozabite's non-African side, behaves similar to Cypriot. So, Cypriot in D-stats with the outgroups used, is like a pure Near Eastern. They're not EEF or CHG, and they don't appear to have exotic admixture(African, East Asian, South Asian, Steppe). That's why I use them as a Near Eastern ancestor proxy for South Europe.

    In other methods, Lebanese or Turkish work better than Cypriot for South Europe. In D-stats however Cypriots work better.



    I'm impatient. It's been a year since any big ancient DNA paper was published. I've used D-stats, PCA, and ADMIXTURE(not just ANE K8, but also old ones based on moderns), and have gotten the same results.
    was'nt there a recent paper indicating the Balkan E haplogroup origins as Cyprus and they had a lot of EEF ................IIRC , these 2 major E Haplogroups came into cyprus vis the northern levant

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    Quote Originally Posted by Fire Haired14 View Post
    Here are better results. I used the nMonte system instead of 4mix. nMonte, breaks down percentages to decimals.
    To be honest all these results seem to change too much.

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    Quote Originally Posted by Angela View Post
    I don't doubt that there is steppe admixture in southern Europe. Just results from yDna indicate that this is the case, and, as has been pointed out, it was found through the extensive modeling presented in Haak et al.

    What I'm questioning is the amount, which seems about right for certain groups and pretty off for others (I highly doubt that the Basques are 70% Yamnaya related). I'm also questioning modeling groups using a mixture of ancient and modern genomes. In this particular case, Cypriots have their own particular population history and admixture. Throwing them into the mix may be altering the other percentages in ways we can't really predict.

    Why not just wait for aDna? It won't be long.

    Oh, and last I heard there are problems with the use and interpretation of Dstats, and we have that from the people who know the most about them, like Patterson. All these methods have their limitations. We have to try to take into account the results from all of the tools at our disposal, not constantly proclaim that this is the definitive tool and these are the only correct conclusions.


    I agree. All these methods give us, internally, some respective weights of "componants" between populations, not absolute %s, these last ones varying in every run.. And as you I dont like too much thses groupings of different ages reference populations. The results, taken with caution, can tell something about global ancient affinities but very little about History of populations moves (who. when?).

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    I 'm not so astonished by the respectable supposed weight of "Yamnaya" or "steppic" among Basques (and Iberians at a lower level). Looking at diverse studies admixtures and PCA's and Y-haplos, I see some imput come from North in Iberia, even if some proximity can be explained by the partly remaining WHG imput, not so completely different from a element (HG) among "steppic" people. But I admit I don't manage too well all these D-stats and Co...

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    Quote Originally Posted by MOESAN View Post


    I agree. All these methods give us, internally, some respective weights of "componants" between populations, not absolute %s, these last ones varying in every run.. And as you I dont like too much thses groupings of different ages reference populations.
    The reason the scores change is the differnt ancestors are made up of the same older components. Cypriot and EEF are made up of a lot of the same stuff. Cypriot can swallow some EEF and vice versa. I explained to Anegla why in D-stats(not PCA), Cypriot is a good Near Eastern proxy. Their unique recent history has no affect.

    Quote Originally Posted by MOESAN View Post
    The results, taken with caution, can tell something about global ancient affinities but very little about History of populations moves (who. when?).
    You've got to understand the genetic diversity in West Eurasia 10,000 years ago was much greater than it is today. Modern day Europeans are all a fusion of the same Holocene era populations. We can differentiate differnt ethnic ancestries in Europe today, but no population in Europe has accumulated 1,000s of years of unique evolution, like Holocene era West Eurasians had.

    In these tests, the main sources of diversity in Europe, are differnt ratios of ancestry from the same Holocene era populations. Local ethnic and region ancestry has hardly any affect. There's really no difference between English and Czech or Tuscan and Spanish, even though they have no ethnic or regional connections. We can't identify the exact ethnic or regional origin, of the people who migrated into Spain and Italy after 3000 BC. However, with genomes from Spain and Italy dating 3000 BC, we can get a good idea what large genetic groupings the people migrated into both places after 3000 BC were apart of. We can't get ethnic/regional/cultural/etc information, because it makes a small affect on DNA.

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    Look at these results. This is a totally unbiased approach, to find what changed in Spain, Italy, Greece, Norway, and Turkey after 3000 BC. I used people who lived in their regions in 3000 BC, other Europeans from 3000 BC(Yamnaya), and all modern non-Europeans as possible ancestors. For Italy and Spain, I only used moderns from the same regions as the 3000 BC genomes are from.

    Iceman_MN Yamnaya_Samara Adygei Cypriot Mozabite BedouinB Druze @ D
    Bergamo 60.85 27.4 5.45 4 2.3 0 0 0.011837
    Tuscan 42.9 25.7 0 30.3 0.3 0.15 0.65 0.009941

    Norway.
    Sweden_MN Yamnaya_Samara Chechen Mozabite BedouinB @ D
    Norway 47.1 52.15 0.3 0.25 0.2 0.011449

    Spain.
    Iberia_Chalcolithic Yamnaya_Samara Adygei Cypriot Mozabite Chechen Druze @ D
    Cantabria 59.05 28.1 2.55 8.25 1.25 0.15 0.65 0.007823

    Greece.
    Anatolia_Neolithic Yamnaya_Samara Adygei Cypriot Druze Abkhasian Armenian Druze Georgian Kotias Lebanese Palestinian
    Greek 52.7 36.35 2.75 7.65 0.55 0 0 0.55 0 0 0 0 0.007823
    Turkish 25.2 0 0 0 0 13.25 4.5 8.3 27.1 16.85 1.15 3.65 0.01017

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    Quote Originally Posted by Fire Haired14 View Post
    Look at these results. This is a totally unbiased approach, to find what changed in Spain, Italy, Greece, Norway, and Turkey after 3000 BC. I used people who lived in their regions in 3000 BC, other Europeans from 3000 BC(Yamnaya), and all modern non-Europeans as possible ancestors. For Italy and Spain, I only used moderns from the same regions as the 3000 BC genomes are from.

    Iceman_MN Yamnaya_Samara Adygei Cypriot Mozabite BedouinB Druze @ D
    Bergamo 60.85 27.4 5.45 4 2.3 0 0 0.011837
    Tuscan 42.9 25.7 0 30.3 0.3 0.15 0.65 0.009941

    Norway.
    Sweden_MN Yamnaya_Samara Chechen Mozabite BedouinB @ D
    Norway 47.1 52.15 0.3 0.25 0.2 0.011449

    Spain.
    Iberia_Chalcolithic Yamnaya_Samara Adygei Cypriot Mozabite Chechen Druze @ D
    Cantabria 59.05 28.1 2.55 8.25 1.25 0.15 0.65 0.007823

    Greece.
    Anatolia_Neolithic Yamnaya_Samara Adygei Cypriot Druze Abkhasian Armenian Druze Georgian Kotias Lebanese Palestinian
    Greek 52.7 36.35 2.75 7.65 0.55 0 0 0.55 0 0 0 0 0.007823
    Turkish 25.2 0 0 0 0 13.25 4.5 8.3 27.1 16.85 1.15 3.65 0.01017

    clearly this makes sense.........just looking at Bergamo and Tuscan you can see the North-Caucasus association with Bergamo and the cypriot association with the Tuscans

    good job

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    Quote Originally Posted by Sile View Post
    clearly this makes sense.........just looking at Bergamo and Tuscan you can see the North-Caucasus association with Bergamo and the cypriot association with the Tuscans

    good job
    And the Mozabite with Bergamo, just lol. I still think that all these results change too much to be plausible. Not to mention that always the same samples have been tested and I think it's unuseful if you don't use exactly the same reference populations. There is no historical association between Tuscans and Cypriots.

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    @Fire Haired.

    I found these in the Eurogenes comments. Fire Haired, have you made ​​them?

    ANE K8.
    Tuscan: 29.75% MN10, 36.45% German Bell Beaker, 33.8% Cypriot: 0.006936
    D-stats.
    Tuscan: 32.25% MN10, 32.25% German Bell Beaker, 35.5% Near East(26.6% Turksih, 8.9% Georgian): 0.003571
    Eurogenes K15
    Tuscan: 28.95% Otzi, 36.45% Irish, 34.6% Near East (20.45% Leban_Christain, 6.15% Georgian, 4.15% Samartian, 3.85% Palestinian): 0.008142

    ANE K8
    West Sicilian: 16% MN10, 22% German Bell Beaker, 58% Cypriot, 4% Mozabite: 0.001823
    D-stats.
    West Sicilian: 14.1% MN10, 20.85% German Bell Beaker, 60.6% Near East(44.55% Cypriot, 16.05% Turkish), 4.45% Mozabite: 0.00211
    Eurogenes K15
    South_Italian: 20.9% Otzi, 16.35% Irish, 61.05% Near East(29.75% Cypriot, 22.75% Leban_Druze, 8.55% Georgian): 0.00376

    ANE K8
    Central_Greek: 27.5% MN5, 29.75% BeloRussian, 42.5% Near East(21.4% Georgian_Laz, 21.1% Cypriot): 0.002436
    D-stats.
    Greek1: 23.8% MN5, 37.85% BeloRussian, 38.35% Near East(16.3% Cypriot, 13% Turkish, 9.05% Georgian): 0.00164

    ANE K8
    Spain_Aragon: 54.85% MN30, 31.1% German Bell Beaker, 13.55% Near East(5.3% Cypriot, 8.25% Turkish), 0.5% Mozabite: 0.008961
    D stats
    Spain_Aragon: 36.6% MN20, 38.2% German Bell Beaker, 23.5% Turkish, 1.7% Mozabite: 0.004955
    Eurogenes K15
    Spain_Aragon: 37.35% Spain_MN, 47.2% Irish, 15.28% Near East(9.15% Leban_Druze, 6.3% Palestinian): 0.018645

  23. #23
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    1 members found this post helpful.
    Quote Originally Posted by MOESAN View Post
    I 'm not so astonished by the respectable supposed weight of "Yamnaya" or "steppic" among Basques (and Iberians at a lower level). Looking at diverse studies admixtures and PCA's and Y-haplos, I see some imput come from North in Iberia, even if some proximity can be explained by the partly remaining WHG imput, not so completely different from a element (HG) among "steppic" people. But I admit I don't manage too well all these D-stats and Co...
    You are right, "steppic" or "Yamnaya" (=Bell-Beaker?) is not absent in Basques. But it is still lower than elsewhere. Sardinians are the ones who don't have any significant "steppe".
    And yes steppe people where partly WHG (being part of EHG) for sure.

  24. #24
    Elite member Fire Haired14's Avatar
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    Quote Originally Posted by Pax Augusta View Post
    And the Mozabite with Bergamo, just lol. I still think that all these results change too much to be plausible. Not to mention that always the same samples have been tested and I think it's unuseful if you don't use exactly the same reference populations.
    The results change, because there's 50 differnt variables. You can't expect every little decimal to be exactly correct. Yes, there's incorrect 1% Mozabite score, but that doesn't disqualify all the results. Trust me, these results are 90% correct. You'll see them in studies in the next few years, once we get ancient DNA from Spain and Italy.

    Quote Originally Posted by Pax Augusta View Post
    There is no historical association between Tuscans and Cypriots.
    Put yourself in the perspective of someone in 500 BC. There's no historical association between Romans and Sycthians. Yet, it's clear Romans have ancestry from Sycthian-like people.

    99.99999% of human history was in pre-history. Writing has existed for a short period and till recently had limited ability to tell us about genetics/history of people movements. Written history in Italy starts shortly before 0 AD. Still, written documents from Italy from before 0 AD don't tell us a lot about the people who lived there. Before that Italy is in pre-history. There were certainly people from West Asia who migrated into Italy, between 2000 BC and 0 AD.

  25. #25
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    Quote Originally Posted by ElHorsto View Post
    Yes, except that WHG in Basques as in Sardinians came mostly with EEF farmers, not Yamnaya people.
    This work is showing EEF type "WHG" as "real" WHG and Cypriot is eating up some EEF too. The EEF percentages are too low and the Yamna genes are too high in some populations.


    I haven't seen any perfect calculator out so far. Be it Eurogenes, Gedrosia or puntDNAL. Partyl because of personal reasons of the creators and partly because it is hard to find a perfect working solution.
    Bell_Beaker is not steppic. Bell Beaker is an Late_Neolithic/Bronze Age phenomenon of Central Europe.

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