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Thread: Ancient genomes reveal structural shifts after the arrival of Steppe-related ancestry

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    Ancient genomes reveal structural shifts after the arrival of Steppe-related ancestry

    Ancient genomes reveal structural shifts after the arrival of Steppe-related ancestry in the Italian Peninsula
    Tina Saupe 26, 27
    Francesco Montinaro 26
    Cinzia Scaggion
    Nicola Carrara
    Toomas Kivisild
    Eugenia D'Atanasio
    Ruoyun Hui
    Anu Solnik
    Ophélie Lebrasseur
    Greger Larson
    Luca Alessandri
    Ilenia Arienzo
    Flavio De Angelis
    Mario Federico Rolfo
    Robin Skeates
    Letizia Silvestri
    Jessica Beckett
    Sahra Talamo
    Andrea Dolfini
    Monica Miari
    Mait Metspalu
    Stefano Benazzi
    Cristian Capelli 26
    Luca Pagani 26
    Christiana L. Scheib 26
    Open Access
    Published:May 10, 2021DOI: https://doi.org/10.1016/j.cub.2021.04.022
    Highlights
    • 22 genomes from Northeastern and Central Italy dated between 3200 and 1500 BCE
    • Arrival of Steppe-related ancestry in the central Italian Peninsula by 1600 BCE
    • Close patrilineal kinship patterns within commingled Chalcolithic cave burials
    • Roman Imperial period had a stronger effect on phenotype shifts than the Bronze Age
    Summary
    Across Europe, the genetics of the Chalcolithic/Bronze Age transition is increasingly characterized in terms of an influx of Steppe-related ancestry. The effect of this major shift on the genetic structure of populations in the Italian Peninsula remains underexplored. Here, genome-wide shotgun data for 22 individuals from commingled cave and single burials in Northeastern and Central Italy dated between 3200 and 1500 BCE provide the first genomic characterization of Bronze Age individuals (n = 8; 0.001–1.2× coverage) from the central Italian Peninsula, filling a gap in the literature between 1950 and 1500 BCE. Our study confirms a diversity of ancestry components during the Chalcolithic and the arrival of Steppe-related ancestry in the central Italian Peninsula as early as 1600 BCE, with this ancestry component increasing through time. We detect close patrilineal kinship in the burial patterns of Chalcolithic commingled cave burials and a shift away from this in the Bronze Age (2200–900 BCE) along with lowered runs of homozygosity, which may reflect larger changes in population structure. Finally, we find no evidence that the arrival of Steppe-related ancestry in Central Italy directly led to changes in frequency of 115 phenotypes present in the dataset, rather that the post-Roman Imperial period had a stronger influence, particularly on the frequency of variants associated with protection against Hansen’s disease (leprosy). Our study provides a closer look at local dynamics of demography and phenotypic shifts as they occurred as part of a broader phenomenon of widespread admixture during the Chalcolithic/Bronze Age transition.

    P.s
    I look at the y haplogroups no E not even the european e-v13

    https://www.cell.com/action/showFull...2821%2900535-2
    https://www.yfull.com/tree/E-FGC7391/

    https://yfull.com/mtree/H3ap/

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    Quote Originally Posted by kingjohn View Post
    Ancient genomes reveal structural shifts after the arrival of Steppe-related ancestry in the Italian Peninsula


    P.s
    I look at the y haplogroups no E not even the european e-v13

    https://www.cell.com/action/showFull...2821%2900535-2

    Thanks kingjohn for linking this interesting paper. I'll take my time to read it in depth. Anyway, it's really weird that after all these papers about Ancient Greece, Rome, BA Europe, etc. the researchers still haven't found e-v13.

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    I quickly skimmed through this study. For those who are interested in the phenotype of Copper and Bronze Age Italians. The authors conclude that CA and BA North and Central Italians were intermediate, thus moderately white with brown eyes and hair. That said, individuals that had dark blond or blond hair with blue eyes were found among Copper Age and Bronze Age Italians, too. Furthermore, the variant rs16891982, linked to darker eyes and hair, decreased in Central Italy after the Copper Age, and in the BA and the post-Roman Republic among the Italian groups. Besides, also interesting to note that J2a was detected in the La Sassa samples from the Chalcolithic period ! As far as I remember the one Etruscan male from the Roman paper was J2a too. In the BA samples R1b-DF90 and R-P312 were found. However, this study had some issues with failed C14 dating.

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    I am almost sure the etruscan was j2b
    But i might be wrong...
    But either it is very cool that they found j2a
    In chl time...
    I think the roman paper you speak about found
    J2a in neolithic italy...
    It look like some branches of j2 made
    To italy pretty early 😎
    So in skin color they are predicted more
    Lighter skin than the aegeans bronze age individuals interesting🤔 thanks for looking at paper and sharing 👍

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    Quote Originally Posted by real expert View Post
    Thanks kingjohn for linking this interesting paper. I'll take my time to read it in depth. Anyway, it's really weird that after all these papers about Ancient Greece, Rome, BA Europe, etc. the researchers still haven't found e-v13.
    It might be wrong, but people believe E-V13 was the core Y-DNA of Eastern Urnfielders who basically even were the pioneers of cremation, Gava-Holigrady derived, Vatin-related cultures.

    There is various reasons to believe they are right.

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    On June 1, E-V13 will show up, wait and see.


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    Great! Finally some Chalcolithic Italian DNA.


    Here are the locations of the samples.



    There are two J2a samples from La Sassa. Both are J2a1-L26 > PF5087 > PF5160 and both date from c. 2840–2500 cal BCE. That branch of J2a is particularly common in the Arabian peninsula today, but is also found in Greece. In Italy, most of the J2-PF5160 today falls under the Z438 > L70 > Z435 clade.

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    Quote Originally Posted by real expert View Post
    Besides, also interesting to note that J2a was detected in the La Sassa samples from the Chalcolithic period ! As far as I remember the one Etruscan male from the Roman paper was J2a too. In the BA samples R1b-DF90 and R-P312 were found. However, this study had some issues with failed C14 dating.
    Nope, Etruscan male was J2b-L283. J2a has been found in the Marche region in the Neolithic period.

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    Quote Originally Posted by Maciamo View Post
    There are two J2a samples from La Sassa. Both are J2a1-L26 > PF5087 > PF5160 and both date from c. 2840–2500 cal BCE. That branch of J2a is particularly common in the Arabian peninsula today, but is also found in Greece. In Italy, most of the J2-PF5160 today falls under the Z438 > L70 > Z435 clade.
    J-PF5160 and especially J-L70 are found all around the Mediterranean, and even in other parts of Europe, yet only Greece is noted here.

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    interesting


    so Broion ( Veneto ) only has R1b and G2a3

    and Marche has I2b and I2d


    the first paper of Covolini de Broion 2017
    https://tel.archives-ouvertes.fr/tel-02063939/document

    Sauveterrian hunter-gatherers in Northern Italy and Southern France
    Evolution and dynamics of lithic technical systems
    Last edited by torzio; 11-05-21 at 07:21.
    Fathers mtdna ... T2b17
    Grandfather mtdna ... T1a1e
    Sons mtdna ... K1a4p
    Mum paternal line ... R1b-S8172
    Grandmum paternal side ... I1-Y33791
    Wife paternal line ... R1a-Z282

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    Here is another one to keep an eye on:



    I wish these samples would be readily available when the papers are published.

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    Quote Originally Posted by Çerç View Post
    J-PF5160 and especially J-L70 are found all around the Mediterranean, and even in other parts of Europe, yet only Greece is noted here.
    I wrote that PF5160 is particularly common in Arabia (Levant included should I add) and Greece. It may be found elsewhere but it is much less common. There is no good data about deep clades of J2 in Turkey, so it's frequency there is hard to tell. Anyway I expect considerable regional differences within Turkey.

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    Quote Originally Posted by real expert View Post
    Anyway, it's really weird that after all these papers about Ancient Greece, Rome, BA Europe, etc. the researchers still haven't found e-v13.
    Not really. This study only has two Bronze Age Y-DNA samples (both R1b-P312, one U152>L2>DF90 and the other one apparently U152 based on the SNP calls). Hardly representative. We would need over 100 samples to get a better idea of whether E-V13 was found among BA and IA Italics.

    If you remember what I wrote in my E-V13 history several years ago, I explained that E-V13 probably came to Italy in 3 waves:

    1) Italic invasion

    2) Greek immigration

    3) Ostrogoths (who had absorbed Balkans people before settling in Italy)

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    To summarise the Y-haplogroups from this study, we've got:

    Neolithic

    One G2 in Lazio

    Chalcolithic

    - Three G2a-L30>CTS2488>F3359 in Veneto.
    - One I2a2a-M223 and one I2a1a-M26 in Romagna (both are typical Megalithic lineages)
    - Two J2a1-L26>PF5160 in Lazio.

    Bronze Age

    Two R1b-U152 in Veneto


    There is also an undated R1 in Broion Veneto.

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    1- As expected, the arrival of the steppe ancestry did not bring anything new to the phenotype of the Chalcolithic and Bronze Age.
    2- Arrival of this autosomal component in small percentages at least 3000 BC-Gattolino, Broion, Iceman, which will surely be related to the so-called warrior ideology (Remedello, steles, copper daggers etc...).
    3-Contrary to what has been previously reported for other Chalcolithic to BA transitions in Europe, we also noted through outgroup f3 tests in form f3 (Italian_CA/Italian_EBA_BA, ancient; Mbuti.DG) that populations associated with Steppe-related ancestry did not leave a male-biased signature in Italy, which, if at all, can instead be seen through the contribution of pre-existing N groups.
    4-steppe ancestry in central italy 400 years later (1.600 BC)

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    So the Appenninic folk already had some steppe ancestry

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    Quote Originally Posted by Maciamo View Post
    Not really. This study only has two Bronze Age Y-DNA samples (both R1b-P312, one U152>L2>DF90 and the other one apparently U152 based on the SNP calls). Hardly representative. We would need over 100 samples to get a better idea of whether E-V13 was found among BA and IA Italics.
    If you remember what I wrote in my E-V13 history several years ago, I explained that E-V13 probably came to Italy in 3 waves:
    1) Italic invasion
    2) Greek immigration
    3) Ostrogoths (who had absorbed Balkans people before settling in Italy)
    You got a point a sample of 22 individuals
    Is not enough....
    But even if e-v13 was present among bronze and iron age italics it doesn't look to be there main branch thats for sure might be rare even among them
    P.s
    About way of enterence of e-v13 to italy
    I agree about point 2 and 3..
    On point 1 time will tell...


    Last edited by kingjohn; 11-05-21 at 14:59.

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    Interesting that their projection for the date of the arrival is later than the Sicilian Bell Beaker. Of course, as they acknowledge, some of their C14 testing failed, and they qualify their conclusions by saying "at least" by their date.

    So, if they're right, I guess it's Polada.

    Interesting steppe percentages: from around 13% to one sample with around 30%. That kind of spread does show it must have been pretty early in their arrival, as the steppe ancestry amounts haven't leveled out. As I've said innumerable times, there just wasn't as much steppe brought into Italy as there was in Central Europe. One reason is the Alps. Much easier to drive your cattle pulled carts and your horse across those nice flat plains of central Europe.

    Looks like people from north of the Alps moved down and mingled with Remedello like people to form Proto-Italics?

    I agree with Maciamo that we can't derive hard and fast conclusions about yDna from 20 samples. It's not like autosomal dna; you need lots of y samples to get a good picture.

    However, as I said above, pretty interesting that there are 2 J2a already in the Chalcolithic, something I have long predicted.

    I also agree with Maciamo's three possibilities for the arrival of the E-V13. I've always personally felt it came later with Greeks and people from the Balkans north of them. As far back as Ralph and Coop they said there was little evidence for admixture after 500 BC (which is already during the time of Greek colonization) except for the Balkans.

    Also, in the interests of fairness, they acknowledge the earlier dated Sicily Bell Beaker, and an older Italian sample in northern Italy, citing Olalde et al.


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    Quote Originally Posted by Maciamo View Post

    If you remember what I wrote in my E-V13 history several years ago, I explained that E-V13 probably came to Italy in 3 waves:

    1) Italic invasion

    2) Greek immigration

    3) Ostrogoths (who had absorbed Balkans people before settling in Italy)

    There are over 600 inscriptions of the Messapic language in Italy, most densely concentrated in the heel. Their distribution is in the image below.

    Messapic was a non-Italic, non-Greek, non-Germanic, language.

    These regions where these inscriptions appear are the regions that are most densely concentrated with E-V13 today. This is modern distribution, so it must be taken with a grain of salt, but nonetheless very relevant to the question of E-V13's entry in Italy.

    I think not considering Messapics is not warranted by the evidence. They are much more likely than Ostrogoths to have brought it.


    From Austrian linguist, who studied paleo-balkan languages and old Albanian, in 2018:


    "Albanian is closely related to Illyrian and Messapic (a language spoken in Southern Italy but originally of Balkan origin)"


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    Some interesting tidbits.

    " most of the N, Chalcolithic, and BA Italian samples available from the literature fall within the EN cluster."

    What the authors call "GEORGIA CHG" begins to appear in northern Italy in the Early Bronze, and then is definitely significantly there in the Bronze Age and the Central Italian Iron Age people, i.e. Italics, Latins, what have you.

    The steady increase, imo, came from the south of the Italian peninsula. Terrible that we have no Bronze and early Iron Age samples from there.

    "
    Italy_Central_M****ithic shares more with Italy_Sardinia_N than with peninsular Italian Chalcolithic. " They should re-read the papers about Sardinia. Everyone should know that they retained more WHG than the mainland.

    "When using two putative sources, all the target BA groups from North and Central Italy presented here support a scenario in which Chalcolithic-like individuals received a contribution of Steppe-related ancestry, possibly through Late N/Chalcolithic groups from the north, such as Germany Bell Beaker, France Middle N, and Italian Chalcolithic sources (Data S3G and S3H)"

    The above is why it would have been helpful to get samples from Northwestern Italy. We have groups flanking around the Alps by taking the route through the Veneto. What about the route through Southern France. Were the Bronze Age Ligures, the original ones, different?

    Maybe I'm missing something, but how could they conclude that "
    populations associated with Steppe-related ancestry did not leave a male-biased signature in Italy, which, if at all, can instead be seen through the contribution of pre-existing N groups, when they only have 20 samples.

    Interesting that like the steppe people, the Chalcolithic people of Italy were patrilocal and practiced female exogamy.

    I wouldn't be so sure about skin ***mentation being lighter in all the samples compared to Greece in the same periods. Note the following:

    "Although these results should be interpreted with caution due to the small sample size, some potentially interesting results emerge. For the variants that are significant in both tests (TLR1 [rs5743618], TNF [rs1800629], HLA [rs3135388], and SLC45A2 [rs16891982]), the signal is driven almost entirely by the post-Roman Republic Central Italy sample group (Cen_postRep), which includes Roman, Late Antiquity, and Medieval individuals.

    See the following for TNF:
    https://www.snpedia.com/index.php/Rs1800629

    For TLR1
    https://www.snpedia.com/index.php/Rs5743618

    For HLA-most important is risk for MS, which is much higher in Northern Europe.
    https://www.snpedia.com/index.php/Rs3135388

    From the authors:

    "There is no detectable difference between the Italian BA samples presented here and the Italian N/Chalcolithic groups, despite the additional Steppe-related ancestry. Three out of four of the variants highlighted here are linked to protection and susceptibility to Hansen’s disease (leprosy). The HLA-related variant (rs3135388), indicated in the susceptibility to physical manifestations of the disease in a Danish medieval population,39
    was significantly different between post-BA Italians and N/Chalcolithic Near East, BA Italians, and Yamnaya. The statistical significance of this variant in this test is probably due to the low frequency of the protective allele in central Italians from the IA onward (Data S6C). Another variant (TNF—rs1800629)66
    also seems to decrease in frequency of the protective allele (Table 3; Data S6C). Both results are consistent with the rise in frequency of this disease in the historical and archaeological record in Europe. The other variant, TLR1 (rs5743618), which has been linked to both protection against leprosy38
    ,67
    and an increased susceptibility to tuberculosis in Asian populations,68
    shows a significant result in the other direction, driven by higher frequency only in the post-Roman Republic Central Italy group (Table 3; Data S6C)."

    Am I interpreting this correctly as indicating that they surfaced in northern Europe but did not come from the steppe since steppe admixed Bronze Age Italians don't carry them or Iron Age Italians either?

    It would be interesting to see if there are more of theem in the Veneto, which had the highest Longobard impact. Anyone know if there are higher levels of MS there than in, say, southern Italy? There are two examples in my family, and lots of allergies, psoriasis, etc., which are also implicated with these "new" alleles.

    The anti-leprosy one, if I'm reading this correctly was a good one though.


    The Yamnaya were responsible for these:
    rs2167079 NR1H3, ACP2 HDL + y Yama versus all except NE_BA
    rs174546 FADS1/FADS2 LDL + y Ita_postBA versus NE_NeoCA and Yama


    They also carried risk alleles for Celiac disease and gluten intolerance but also protective alleles, which makes sense. Celiac disease is more prevalent in northern Europe.

    I've always been a bit confused about these alleles for digestion of starches being claimed to arrive so late and with the Yamnaya. The farmers had been consuming starches quite happily for thousands of years, so obviously they had other alleles which allowed them to do it, even if scientists haven't scoped them out yet.


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    Quote Originally Posted by Johane Derite View Post
    There are over 600 inscriptions of the Messapic language in Italy, most densely concentrated in the heel. Their distribution is in the image below.

    Messapic was a non-Italic, non-Greek, non-Germanic, language.

    These regions where these inscriptions appear are the regions that are most densely concentrated with E-V13 today. This is modern distribution, so it must be taken with a grain of salt, but nonetheless very relevant to the question of E-V13's entry in Italy.

    I think not considering Messapics is not warranted by the evidence. They are much more likely than Ostrogoths to have brought it.


    From Austrian linguist, who studied paleo-balkan languages and old Albanian, in 2018:


    "Albanian is closely related to Illyrian and Messapic (a language spoken in Southern Italy but originally of Balkan origin)"


    Page 1790
    Handbook of Comparative and Historical Indo-European Linguistics
    Joachim Matzinger
    2018




    sound logic you are correct
    that people should also consider that as a possible source
    for spread of e-v13 to italy
    but what would explain the 10% e-v13 in lombardia ?

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    Data Table S6D, tab B is fabulous. You can compare all the Italian samples both to the Near East and Yamnaya for each and every phenotype allele, from starch digestion, to resistance to diseases as well as the ever popular ***mentation.

    Interesting indeed as far as ***mentation goes, as well.

    Copper Age Italians had more SLC45A2 than Yamnaya... 63 versus 44. In fact, it declined in Italy after the arrival of the steppe people. They also had more SLC 24A4 and SLC 24A5.

    For OCA2, it's about even for 3, neither has one of them, and Yamnaya has more of one variety.

    HERC 2 is a little different. One neither has. Yamnaya has more, but they are also present in significant numbers in Copper Age Italy.

    The bizarre thing which I can't explain is that these de-***mentation snps where supposedly the Yamnaya did have higher numbers, like HERC 2 and a few OCA2, went DOWN in Italy after the arrival of the steppe people.

    Did a particularly dark subgroup of steppe admixed people invade Italy in the Bronze Age, or did these researchers also make the mistake of including Sintashta like people, i.e. people who had gone east after picking up de-***mentation snps in Europe?

    Does anyone know?

    Take a look at the prediction sheet, i.e. tab D.

    It makes no sense. People with the de***mentation snps which the Neolithic Italians had could not have had dark to black skin. Shades of the Greek paper! I don't know what group another poster had in mind when he called them "intermediate" in tone.

    Strangely enough, the Northern and Central Italian Neolithic samples are, on the whole, darker than the Sicilian and Sardinian Bronze Age.

    Yamnaya has more positives for some of the many MCIR alleles, but not all.

    Northern Italy Chalcolithic is mixed intermediate and dark to dark to Black. Bronze Age Central and Northern Italy is intermediate, but the ***mentation is mixed in Sicily and Sardinia during the Bronze Age. How people predicted to be a mix of intermediate and dark peoples could "lighten" the Bronze Age is beyond me. Plus, given those snps I don't see how the Yamnaya could have any intermediate people. They don't have most of the skin de***mentation alleles. Perhaps, as I said above, they're including Sintashta samples. Or, the Bell Beakers picked up light skin alleles from a different part of LN Europe.

    As for Iron Age Republican Rome, one sample is dark and one mixed intermediate to dark; the rest are intermediate. Only one of the samples is predicted to have brown/dark blonde hair.

    The Empire is mostly intermediate with some "dark" samples. The first blonde, pale skinned sample shows up during the Empire and then during Antiquity. I would say travelers to Rome.

    Very interesting that Anatolia Neolithic is much lighter than Italian Neolithic. Mixture with WHG? Even the Anatolian AND Jordanian Bronze Age are a mix between Intermediate and dark, like all of Chalcolithic Italy, and Bronze Age Sicily and Sardinia.

    Were the people from the Caucasus bringing the darker phenotypes?

    A lot of certainties overthrown in this paper, and it's clear to me we really don't understand the selection for pale skin and what drove it. What's clear is that it's recent.
    Last edited by Angela; 11-05-21 at 20:04.

  23. #23
    Regular Member Johane Derite's Avatar
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    1 members found this post helpful.
    Quote Originally Posted by kingjohn View Post
    sound logic you are correct
    that people should also consider that as a possible source
    for spread of e-v13 to italy
    but what would explain the 10% e-v13 in lombardia ?
    I agree with Maciamo's reasoning that it probably didn't come all in one group only, and there has already been actual lombards tested
    Positive for ev13, so we know they at least had some. I just think Messapics should be taken into account also. Whether goths brought it or integrated a local lineage i dont know. But i more or less agree that ev13 probably only started expanding big time in late bronze age to early iron age, with maybe a few branches in the balkans spreading a bit earlier (middle bronze age).

  24. #24
    Regular Member Archetype0ne's Avatar
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    Quote Originally Posted by real expert View Post
    I quickly skimmed through this study. For those who are interested in the phenotype of Copper and Bronze Age Italians. The authors conclude that CA and BA North and Central Italians were intermediate, thus moderately white with brown eyes and hair. That said, individuals that had dark blond or blond hair with blue eyes were found among Copper Age and Bronze Age Italians, too. Furthermore, the variant rs16891982, linked to darker eyes and hair, decreased in Central Italy after the Copper Age, and in the BA and the post-Roman Republic among the Italian groups. Besides, also interesting to note that J2a was detected in the La Sassa samples from the Chalcolithic period ! As far as I remember the one Etruscan male from the Roman paper was J2a too. In the BA samples R1b-DF90 and R-P312 were found. However, this study had some issues with failed C14 dating.
    Think it was L283 actually.
    “Man cannot live without a permanent trust in something indestructible in himself, and at the same time that indestructible something as well as his trust in it may remain permanently concealed from him.”

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  25. #25
    Regular Member Archetype0ne's Avatar
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    Quote Originally Posted by blevins13 View Post
    On June 1, E-V13 will show up, wait and see.


    Sent from my ****** using Eupedia Forum
    Are more samples coming out? Or different paper coming out?

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