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Thread: A genetic probe into the ancient and medieval history of Southern Europe and WestAsia

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    Quote Originally Posted by Jovialis View Post
    @Salento & Pax,

    Are you planning on processing and posting the new samples from these three studies in Dodecad K12b Format?
    Hi Pax and Jovialis, I have all the 700+ Coordinates from the Dataset, though when I compared with some of the ENA Bams I got a 0.5 to 2 point distance difference, … I’m not sure which one is more accurate.

    All the results that I’ve seen around are from the Dataset, I think.

    It would take a long time to process 700+ bams, but if you like I can post the Dod k12b coordinates from the Dataset.

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    Quote Originally Posted by Palermo Trapani View Post
    Angela: They are in Dodecad12B: I2478 is from the Vahaduo spreadsheet. The Sicilian Beaker I used the Gedmatch kit seen below. The other 2, I ran a while back and I have the coordinates but I don't have the GEDMATCH Kit that I used. Let me dig, or maybe I got the Kit from a post here. Sicilian_Beaker_I4930 (Kit #TZ9503361)

    Beaker_Northern_Italy:I2478:Olalde_2018,4.97,0,0,0 .15,47.73,28.87,0.74,0,3.49,0.84,12.34,0.86

    Siclian_Beaker_I4930,15.32,6.54,38.77,12.25,22.74, 4.38,0,0,0,0,0,0,0
    Thanks a lot. Just the coordinates for the other two would be great if you have them.


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    Dug into samples of personal interest and found that a parent branch of J-70 (L25) was in Halicarnassus in the Hellenistic period. Lazaridis et al. describe this sample (I3303) as heavily Levantine in the supplementals (great read). There is one sample from above L25 in Imperial Rome-era Apollonia, that’s presented as substantial Mesopotamian (I16584). Above/below L70 branches were found in southwest Anatolia, in a historically Carian/Greek/local Anatolian region (I20787, I20144).

    This obviously is one path to ancient Greek ancestry for modern Greeks and others who are descendants of people who lived in the ancient Greek world. The Fallmerayer types have the burden of disproving each haplogroup branch and its ancestral region/environment.

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    Quote Originally Posted by johen View Post
    I think the wheels of chariots wiped out the languages of CWC and BB (CWC Bohemia line?) 1,600bc and planted new culture.



    south aisa:

    Surely chariot migrated from europe to south Caucasus. And then thunderbolt lord seems to appear late bronze age Karashamb also(now with so many yDNA I ).


    A dagger of the Late Bronze Age, buttons of a mail (14th-13th century B.C.) About 7-8 tombs of warriors with relative military property were discovered in Karashamb.




    Bronze hairpin of the Late Bronze Age; beads bracelet (14th-13th century B.C.)
    https://www.panarmenian.net/eng/details/220791/

    Apa sword in EUROPE:
    https://pbs.twimg.com/media/EENEN_LWsAIzuj4?format=jpg&name=4096x4096

    ST lord dagger:
    https://indo-european.eu/wp-content/...est-steppe.jpg

    andronovo dagger:
    https://www.researchgate.net/profile/Aleksandr-Pilipenko-2/publication/285639978/figure/fig8/AS:[email protected]/a-Daggers-of-Srubno-Andronovo-form-b-Ceramic-pot-with-specific-ornamentation-of-the.png


  5. #105
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    Quote Originally Posted by Angela View Post

    As I pointed out in my first post here above to which I am responding, I think it would be crucial to include Aegean Bronze Age samples, and even more importantly, Aegean Iron Age samples, when or if they have them, and certainly the Greek Marathon sample, and the two Empuries samples, to see if they too could possibly be the source of this signal in Imperial Rome. Sicilian Bronze Age should also be in the mix, and, when we have them, samples from Greek colonists to Southern Italy.
    I would like to add that, if I remember correctly, few samples from Antonio et al. already plot with modern central - southern Italy, so they should eventually be also compared to an hypothetical Iron Age Southern Italic cluster, which we still lack.

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    Greeks and Anatolians of antiquity were too intertwined, you won't be able to separate them.

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    Quote Originally Posted by eupator View Post
    Greeks and Anatolians of antiquity were too intertwined, you won't be able to separate them.
    As far as I know Bronze and Iron age Greece and Anatolia form two different and distinguishable clusters, though, of course, they may be pretty similar to each other.

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    Quote Originally Posted by Leopoldo Leone View Post
    From what I've seen on G25 Anatolia did receive European gene flow, quite of it actually; I suspect they missed it because of their focus on modelling with distal ancestries, whereas it's clear that it is better to use proximal ancestries.
    Overall Greeks in Caria were around 50% Mycenaean-like and 50% Anatolia_BA
    From around the black sea Greeks were 40% Mycenaean-like and 60% Anatolia_BA
    As for Gordion samples, if we take them as "Phrygian", many seem to take around 20-25% Logkas-like ancestry, or 40% Mycenaean-like, but since they are dated in the late hellenistic period (150 BC), I am not sure whether it can be attributed to proto-phrygian ancestry from the Balkans or to Greek ancestry.



    One sample from Palace of Nestor is heavily Anatolian admixed. I agree that Byzantine Western Anatolians probably has significant European admixture from Greek colonies, Thracians, Slavic transplants, Celts and Italic people. Look at Slavic I2a and R1a in there in Maciamo's maps.
    Distance to: GRC_Mycenaean_Palace_of_Nestor_BA:I13517_d
    0.03654511 Greek_Dodecanese
    0.04110671 Italian_Calabria
    0.04146339 Greek_Kos
    0.04271708 Greek_Crete
    0.04305058 Italian_Campania
    0.04383122 Italian_Apulia
    0.04439810 Italian_Basilicata
    0.04479746 Sicilian_East
    0.04774507 Sephardic_Jew
    0.04818263 Italian_Jew
    0.04843735 Romaniote_Jew
    0.04961611 Italian_Molise
    0.04966159 Italian_Abruzzo
    0.05024841 Ashkenazi_Germany
    0.05034152 Cypriot
    0.05158075 Ashkenazi_Poland
    0.05229433 Greek_Izmir
    0.05296337 Greek_Central_Anatolia
    0.05352163 Maltese
    0.05395921 Ashkenazi_Ukraine
    0.05430721 Greek_Cappadocia
    0.05459769 Sicilian_West
    0.05466595 Italian_Lazio
    0.05499461 Ashkenazi_Lithuania
    0.05505034 Ashkenazi_Belarussia

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    You are annoyed because you'd rather have ancient Greeks than Anatolians as ancestors to the imperial Romans but Greeks only separated from Anatolia in the early 20th century, they are intertwined since antiquity and these new samples prove it. The ancient Greeks the West idolizes were in fact Ionics, open a Google map and check were Ionia was.

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    Quote Originally Posted by Angela View Post
    No, it couldn't. They make the difference clear in the paper on Mesopotamia which we haven't yet explored to any great degree.

    For most purposes, CHG and Iran Neo can be used interchangeably. The same is definitely not true of Barcin and Levant PPN.

    https://www.science.org/doi/10.1126/science.abq0762
    Barcin_N and Levant_PPN are more related to each other than CHG and Iran_N are.

    Quote Originally Posted by eupator View Post
    G25 seems biased, when trying to replicate fstat breakdown.

    PCA related problem or ... ?
    This is copy and paste from the paper.



    I guess the percentage of CHG changes significantly (37 to 48%) depending on which EHG component is chosen, whereas on Global25 the percentage of CHG + Iran_N remains steady at 38%.






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    Quote Originally Posted by eupator View Post
    You are annoyed because you'd rather have ancient Greeks than Anatolians as ancestors to the imperial Romans but Greeks only separated from Anatolia in the early 20th century, they are intertwined since antiquity and these new samples prove it. The ancient Greeks the West idolizes were in fact Ionics, open a Google map and check were Ionia was.
    I just said that Anatolia and Greece were, in the Bronze and Iron age, pretty similar, despite being distinguishable from each other (Anatolia lacking the EHG component, for instance). Infact greek colonies on the western coast of Anatolia could have been, as it seems (see the post from Leopoldo Leone), a joining link between the greek world and the Anatolian one, culturally and genetically.

    I just wanted to point out, only for the sake of history, that they are not a monolithic anatolian populations. The samples come from different necropolis, encompassing many different social status, from the richer ones to the poorest: http://www.iitaly.org/magazine/focus...d-ostia-antica. This difference is reflected by the PCA itself, were the "imperial romans" are infact grouped into different clusters.
    Last edited by Francesco; 28-08-22 at 14:17.

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    Quote Originally Posted by Er Monnezza View Post
    Barcin_N and Levant_PPN are more related to each other than CHG and Iran_N are.

    You didn't read the methodology. PPN had to be added because the p-values w/o it were not robust enough. There was Natufian drift that wasn't captured otherwise and the model failed.


    Quote Originally Posted by Er Monnezza View Post
    Barcin_N and Levant_PPN are more related to each other than CHG and Iran_N are.

    I guess the percentage of CHG changes significantly (37 to 48%) depending on which EHG component is chosen, whereas on Global25 the percentage of CHG + Iran_N remains steady at 38%.






    Again you haven't read the methodology, out of the 3 qpAdm models you present only the 3rd one has a robust p-value of 0.221, the middle has 0.0177 and the first barely passable 0.0518. But that's not the point, if you read the supplementary you will see: (We note that the WHG group includes Loschbour, Villabruna, LaBrana1, and Bichon, EHG the two hunter-gatherers from Karelia and one from Samara(2, 18), and CHG two hunter-gatherers from Kotias and Satsurblia caves in Georgia).

    This is a attempt for deflection from the fact the g25 fails to reproduce the official stats. As such it cannot be used to substantiate an opposing (or confirming) claim against the paper.

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    Quote Originally Posted by Francesco View Post
    I just said that Anatolia and Greece were, in the Bronze and Iron age, pretty similar, despite being distinguishable from each other (Anatolia lacking the EHG component, for instance). Infact greek colonies on the western coast of Anatolia could have been, as it seems (see the post from Leopoldo Leone), a joining link between the greek world and the Anatolian one, culturally and genetically.

    I should have made the distinction of "Eastern Romans", I am not referring to the Italian peninsula.

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    Quote Originally Posted by eupator View Post
    I should have made the distinction of "Eastern Romans", I am not referring to the Italian peninsula.

    Ok, There was a misunderstanding. In that case, I agree that anatolians have surely been an important pupulation in the byzantine empire. I don't know if the imperial romans from Antonio couldbe a good proxy for the byzantine empire pupulation, though (maybe yes).

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    Quote Originally Posted by eupator View Post
    You didn't read the methodology. PPN had to be added because the p-values w/o it were not robust enough. There was Natufian drift that wasn't captured otherwise and the model failed.
    Again you haven't read the methodology, out of the 3 qpAdm models you present only the 3rd one has a robust p-value of 0.221, the middle has 0.0177 and the first barely passable 0.0518. But that's not the point, if you read the supplementary you will see: (We note that the WHG group includes Loschbour, Villabruna, LaBrana1, and Bichon, EHG the two hunter-gatherers from Karelia and one from Samara(2, 18), and CHG two hunter-gatherers from Kotias and Satsurblia caves in Georgia).

    This is a attempt for deflection from the fact the g25 fails to reproduce the official stats. As such it cannot be used to substantiate an opposing (or confirming) claim against the paper.

    I won't go into the rest of the post, I'll just say that there are no official statistics, are not comparable to statistics provided, to give an example in another field, by the ECB or another central bank. They are attempts to provide probable statistics by academic studies (which also often produce different results) and are not supervised by an institution that makes them official. The G25 remains what it is, an amateur tool.

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    Quote Originally Posted by Pax Augusta View Post
    I won't go into the rest of the post, I'll just say that there are no official statistics, are not comparable to statistics provided, to give an example in another field, by the ECB or another central bank. They are attempts to provide probable statistics by academic studies (which also often produce different results) and are not supervised by an institution that makes them official. The G25 remains what it is, an amateur tool.

    I was referring to this:

    F-statistics - Wikipedia

    In hindsight, I should have just written fstats.

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    Quote Originally Posted by eupator View Post
    I was referring to this:

    F-statistics - Wikipedia

    In hindsight, I should have just written fstats.
    Got it, Eupator.

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    Quote Originally Posted by Angela View Post
    I have no idea what that means. The R1b carrying Greek speakers were the steppe "invaders" who came down through the Balkans, although they don't seem to have done much "invading" in the sense of establishing a genetic elite. Rather, it seems that they admixed with the locals in a rather egalitarian manner. The culture was a mix of the local culture and the Yamnaya culture.

    It makes sense given the fact that they didn't arrive until after the Early Bronze Age if my memory serves. Greece proper was already highly civilized and densely populated.

    So, we can say good-bye to the Drews theory and the ridiculous Corded Ware theory. The yDna is G, I, and R1b.

    Didn't you read the paper and the supplement? I know it's a lot with three papers and all the supplements, but the weekend is tomorrow, so we can all catch up.
    Getting ready to travel to Greece for my daughter's wedding. Priorities you know...

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    Quote Originally Posted by eupator View Post
    You didn't read the methodology. PPN had to be added because the p-values w/o it were not robust enough. There was Natufian drift that wasn't captured otherwise and the model failed.





    Again you haven't read the methodology, out of the 3 qpAdm models you present only the 3rd one has a robust p-value of 0.221, the middle has 0.0177 and the first barely passable 0.0518. But that's not the point, if you read the supplementary you will see: (We note that the WHG group includes Loschbour, Villabruna, LaBrana1, and Bichon, EHG the two hunter-gatherers from Karelia and one from Samara(2, 18), and CHG two hunter-gatherers from Kotias and Satsurblia caves in Georgia).

    This is a attempt for deflection from the fact the g25 fails to reproduce the official stats. As such it cannot be used to substantiate an opposing (or confirming) claim against the paper.
    You are one of a handful of people that get why PCA based coordinates G25 is never intended to model or be used for genetic distances. PCA/G25 is used for visualize clustering. Of course with PCA you can only see 2 or 3 PCs at a time. The other 22 or 23 PCs are hidden from view.

    That’s why it’s dangerous to put G25 into hands of lay people or amateurs because they either use it to make conclusions or challenge scientific papers and formal statistics. The average Joe is not knowledgeable to know why PCA/G25 can’t be used for genetic distances or modeling so they assume that everything is good especially when they see that PCA/G25 clusters them with their ethnic group. This dupes them into buying into PCA/G25 for modeling and distances and thus a fraud goes undetected!!

    Of course G25 doesn’t use outgroups to distinguish similar ancestries like qpAdm and it doesn’t have p-value to reject models. People think G25 distances is similar. What a joke!

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    Quote Originally Posted by eupator View Post
    You didn't read the methodology. PPN had to be added because the p-values w/o it were not robust enough. There was Natufian drift that wasn't captured otherwise and the model failed.

    Again you haven't read the methodology, out of the 3 qpAdm models you present only the 3rd one has a robust p-value of 0.221, the middle has 0.0177 and the first barely passable 0.0518. But that's not the point, if you read the supplementary you will see: (We note that the WHG group includes Loschbour, Villabruna, LaBrana1, and Bichon, EHG the two hunter-gatherers from Karelia and one from Samara(2, 18), and CHG two hunter-gatherers from Kotias and Satsurblia caves in Georgia).
    Did they put p-values in the paper? I couldn't find anything when I searched.

    Quote Originally Posted by eupator View Post
    This is a attempt for deflection from the fact the g25 fails to reproduce the official stats. As such it cannot be used to substantiate an opposing (or confirming) claim against the paper.
    I know they work differently, but at least Global25 (or any other amateur tool) wouldn't be crazy enough to assign 5% Levant_PPN to I0439 or 12% to I0441.

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    Quote Originally Posted by Angela View Post
    Thanks a lot. Just the coordinates for the other two would be great if you have them.
    Angela: See Post #98 with commentary on all the different kits. Additional commentary :)!, I have a master data sheet that I try to keep current with all ancient Italian samples. I have another file on my hard drive with various Coordinates that I ran personally using GEDMATCH Kit #'s that had all the various coordinates for those Italian and Sicilian Beakers from the various kits. The ones that I had in my maser Ancient Italian data sheet were the ones that were from a Kit that I didn't write the kit down (Before I was at Eupedia in Fall of 2019). Maybe the kit got deleted by the person who extracted the data after they left GEDMATCH.

    But as I noted in post 98, all the coordinates from the various Kits produce results that are in line with the Olade et al 2018 models for the 4 Italian Beakers that they were able to run admixture models for (3 Northern + 1 of the 3 Sicilian Beakers).

    I posted Table S4 from the Supplements of Olade et al 2018 (post #222 in the Southern Arc thread) that has their admixture modeling for the 4 Italian Beakers so you can use as a baseline to compare the results of modeling the 4 Italian Beakers using for example Jovialis's Dodecad 12B K8 model, which produces results very consistent with the Olade et al 2018 modeling.

    Buono Giornata, PT

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    Quote Originally Posted by Er Monnezza View Post
    Did they put p-values in the paper? I couldn't find anything when I searched.
    All of the stuff I mention are included in the methodology in the supplement files.

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    Quote Originally Posted by Ghani View Post
    You are one of a handful of people that get why PCA based coordinates G25 is never intended to model or be used for genetic distances. PCA/G25 is used for visualize clustering. Of course with PCA you can only see 2 or 3 PCs at a time. The other 22 or 23 PCs are hidden from view.

    That’s why it’s dangerous to put G25 into hands of lay people or amateurs because they either use it to make conclusions or challenge scientific papers and formal statistics. The average Joe is not knowledgeable to know why PCA/G25 can’t be used for genetic distances or modeling so they assume that everything is good especially when they see that PCA/G25 clusters them with their ethnic group. This dupes them into buying into PCA/G25 for modeling and distances and thus a fraud goes undetected!!

    Of course G25 doesn’t use outgroups to distinguish similar ancestries like qpAdm and it doesn’t have p-value to reject models. People think G25 distances is similar. What a joke!
    Ghani: You are correct to a point. Principal Components analysis attempts to explain the variation in as few variables as possible (Components). I was taught back in the day to run a principal components on a set of data and keep principal components with an eigen value of 3 or less (appropriate predictor/explanatory variable). All others were not to be included as an explanatory variable.

    The Components are predicted values. These Components (Predicted Values) are then used to model/explain a Target Variable (i.e. Dependent Y variable in OLS Regression Framework). So it has benefits, explaining the Dependent variable in as parsimonious model as possible. Multicollinearity problems are minimized given you have very few X variables which in theory should minimize Multicollinearity problems. Anyone that has run OLS based regression models knows what VIF's (Variance Inflation factors) are or what Condition Indexes are to assess multicollinearity.

    Problems are that the explanatory variables are based on predictions from an entire data set rather than all of the actual observations (data) to measure the independent variables. But a another potential benefit of using only Principal components with eigen values of 3 or less is to minimize overfitting the data, again explain Dependent variable Y with as few components (independent X variables) as possible.

    Of course in genetics research, we can only measure the ancient samples we have. We can't measure what we don't have. It is not like going sample a modern USA city and randomly drawing a sample from the entire population (say Seattle, Saint Louis, New York City, Atlanta) to measure admixture of the various populations living in those cities. We can't go back to ancient Mycenean and Minoan Greece and obtain samples randomly from the population to ensure the data are not skewed one way or the other. So in that sense, the Principal components used to measure ethnicity should be interpreted with "caution" in my opinion. They are not worthless, but one needs to know the limitations of using Principal components based predictors to explain a target variable.

    But in my view, once you have a large enough Sample (N=30 or > ) from a certain ancient culture for a particular time period, you in theory have a large enough sample for central limit theorem to allow for the the data to approximate a standard normal distribution.

    Anyway, my take on it. PCA based regression type analysis is a good tool (using predicted components to explain a Dependent/target variable) but there are limitations to it.

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    Quote Originally Posted by Er Monnezza View Post
    but at least Global25 (or any other amateur tool) wouldn't be crazy enough to assign 5% Levant_PPN to I0439 or 12% to I0441.
    So you think the f-stats results are crazy and the g25 results are sober.

    Interesting, at what point do you guys self-reflect and realize you operate as a cult?

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    Salento provided for me the new samples, and I combined it with the samples from Ancient Rome.

    Here are the results for the two way:

    Distance to: Jovialis
    0.59719201 24.40% HRV_Bezdanjača_BA:I18737 + 75.60% C6:Imperial_Mediterranean:R136_Marcellino_&_Pietro
    0.68840965 26.40% HRV_Cetina_BA:I19027 + 73.60% C6:Imperial_Mediterranean:R136_Marcellino_&_Pietro
    0.71785187 91.80% C6:Medieval_Mediterranean:R973_Tivoli_Palazzo_Cian ti + 8.20% C7:Late_Antiquity_European:R106_Crypta_Balbi
    0.72022100 9.60% HRV_Bezdanjača_BA_brother.I18078.father.I18071:I1 8717 + 90.40% C6:Medieval_Mediterranean:R973_Tivoli_Palazzo_Cian ti
    0.73866716 91.80% C6:Medieval_Mediterranean:R973_Tivoli_Palazzo_Cian ti + 8.20% C7:Medieval_European:R62_Villa_Magna
    0.74241418 93.40% C6:Medieval_Mediterranean:R973_Tivoli_Palazzo_Cian ti + 6.60% C7:Late_Antiquity_European:R31_Mausole_di_Augusto
    0.74683214 93.20% C6:Medieval_Mediterranean:R973_Tivoli_Palazzo_Cian ti + 6.80% C7:Medieval_European:R1286_Cancelleria
    0.74775484 21.80% HRV_Bezdanjača_BA:I18077 + 78.20% C6:Imperial_Mediterranean:R136_Marcellino_&_Pietro
    0.76263032 90.00% C6:Medieval_Mediterranean:R973_Tivoli_Palazzo_Cian ti + 10.00% C7:Late_Antiquity_European:R108_Crypta_Balbi
    0.76413985 90.80% C6:Medieval_Mediterranean:R973_Tivoli_Palazzo_Cian ti + 9.20% C7:Medieval_European:R1220_Cancelleria
    0.77868287 23.60% HRV_Bezdanjača_BA:I18729 + 76.40% C6:Imperial_Mediterranean:R136_Marcellino_&_Pietro
    0.78808210 26.20% HRV_Cetina_BA:I18745 + 73.80% C6:Imperial_Mediterranean:R136_Marcellino_&_Pietro
    0.81738295 13.80% HRV_Bezdanjača_BA:I18087 + 86.20% C6:Medieval_Mediterranean:R973_Tivoli_Palazzo_Cian ti
    0.82114261 7.60% HRV_IA:I5727 + 92.40% C6:Medieval_Mediterranean:R973_Tivoli_Palazzo_Cian ti
    0.83258720 92.00% C6:Medieval_Mediterranean:R973_Tivoli_Palazzo_Cian ti + 8.00% C7:Medieval_European:R1219_Cancelleria
    0.83777954 20.80% HRV_Bezdanjača_BA:I18732 + 79.20% C6:Imperial_Mediterranean:R136_Marcellino_&_Pietro
    0.84330103 15.60% SRB_IA:I16814 + 84.40% C6:Medieval_Mediterranean:R973_Tivoli_Palazzo_Cian ti
    0.85088733 57.40% HRV_Bezdanjača_BA:I18737 + 42.60% TUR_SE_Mardin_RomByz:I4474
    0.85266463 52.20% ALB_Mdv:I14622 + 47.80% C6:Late_Antiquity_Mediterranean:R117_S_Ercolano_Ne cropolis_Ostia
    0.85461046 4.80% MNE_Vrbička_Mes:I16995 + 95.20% C6:Medieval_Mediterranean:R973_Tivoli_Palazzo_Cian ti
    0.86130947 9.00% BGR_Tell_Ezero_EBA:I19461 + 91.00% C6:Medieval_Mediterranean:R973_Tivoli_Palazzo_Cian ti
    0.86203397 21.00% HRV_Trogir_Byz:I15743 + 79.00% C6:Medieval_Mediterranean:R973_Tivoli_Palazzo_Cian ti
    0.88431263 46.40% HRV_Bezdanjača_BA:I18729 + 53.60% TUR_Aegean_Muğla_Stratonikeia_Byz:I20144
    0.88601664 4.40% C1:Mesolithic:R7_Grotta_Continenza + 95.60% C6:Medieval_Mediterranean:R973_Tivoli_Palazzo_Cian ti
    0.89152067 14.60% HRV_Cetina_BA:I18747 + 85.40% C6:Medieval_Mediterranean:R973_Tivoli_Palazzo_Cian ti

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