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Thread: 28 whole-genome from Neolithic and Bronze Age Croatians. Full paper.

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    28 whole-genome from Neolithic and Bronze Age Croatians. Full paper.


    Abstract

    Ancient DNA studies have revealed how human migrations from the Neolithic to the Bronze Age transformed the social and genetic structure of European societies. Present-day Croatia lies at the heart of ancient migration routes through Europe, yet our knowledge about social and genetic processes here remains sparse. To shed light on these questions, we report new whole-genome data for 28 individuals dated to between ~ 4700 BCE–400 CE from two sites in present-day eastern Croatia. In the Middle Neolithic we evidence first cousin mating practices and strong genetic continuity from the Early Neolithic. In the Middle Bronze Age community that we studied, we find multiple closely related males suggesting a patrilocal social organisation. We also find in that community an unexpected genetic ancestry profile distinct from individuals found at contemporaneous sites in the region, due to the addition of hunter-gatherer-related ancestry. These findings support archaeological evidence for contacts with communities further north in the Carpathian Basin. Finally, an individual dated to Roman times exhibits an ancestry profile that is broadly present in the region today, adding an important data point to the substantial shift in ancestry that occurred in the region between the Bronze Age and today.




    Genetic transformations from the Neolithic to Roman times

    In order to understand the genetic affinities of the samples, we performed principal components analysis (PCA) (Methods) by projecting the new shotgun data and published ancient datasets onto the first two principal components constructed from 920 individuals selected from contemporary West Eurasian populations in the Human Origins (HO) dataset30 (Methods, Fig. 2). We also performed model-based clustering analysis in an unsupervised mode with ADMIXTURE (Methods) using 1311 present-day individuals taken from a panel of worldwide populations (Supplementary Fig. S2).
    [QUOTE]The newly-reported individuals fall along the European cline in PCA space, extending between Neolithic agriculturalist and Bronze Age pastoralist populations. Croatia_Pop_MN clusters tightly with other southeast and central European Neolithic and Copper Age individuals, including Copper Age Croatians from Radovanci and Vučedol, who were merged for further analysis into Croatia_North-East_CA, and share similar ADMIXTURE profiles that exhibit a major contribution from Anatolia-related ancestry (Anatolia_N) and a small contribution of Western European hunter-gatherer (WHG)-related ancestry (Supplementary Fig. S2). We also merged Croatia_Pop_MN and Croatia_Osijek_MN to form Croatia_North-East_MN for further analysis, before testing shared drift with other ancient and modern West Eurasian populations with outgroup f3-statistics of the form f3(Croatia_North-East_MN, Test; Mbuti.DG) (Supplementary Fig. S3a-b, Supplementary Table S3, Methods). This group shares most genetic drift with other Neolithic populations from the Balkans and Central Europe, and present-day Sardinians. We then quantified admixture proportions with qpAdm using distal sources of WHG and Anatolia_N to represent Mesolithic hunter-gatherer and Anatolian Neolithic farmer ancestries that are known to have contributed to European genomic diversity (Methods). We were able to model Croatia_North-East_MN as a mixture of 2.4 ± 1% WHG and 97.6 ± 1% Anatolia_N, and even a 100% Anatolia_N model fits the data (p = 0.11), which is congruent with previous studies that show very low WHG introgression in the Balkans and Hungarian Neolithic3,31 (Fig. 3a, Supplementary Fig. S4, Supplementary Table S4). Using Iron Gates hunter-gatherers (Iron_Gates_HG) instead of WHG produced very similar results (Supplementary Table S4). Using DATES (Methods), we estimated the timing of this admixture to between 19 and 42 generations before the contextual date of the samples (Supplementary Fig. S5, Supplementary Table S5, Methods), corresponding to the Early Neolithic. This further supports population continuity during the Middle Neolithic, in contrast to Middle Neolithic populations from central and Western Europe which show additional WHG gene flow during this time31.[/QUOTE]
    We grouped the new Copper Age individual, POP39, with a previously published cladal individual, I3499 (Supplementary Table S2, Supplementary Table S6), who originates from the same site and time period (Croatia_Pop_CA). This group is shifted further up along PC2 and clusters with three previously reported Bronze Age samples from coastal Dalmatia (Croatia_Dal_BA), falling within the wide distribution of Bulgarian and Hungarian Bronze Age genomes and present-day southern Europeans in PCA space (Fig. 2) suggesting the presence of steppe-related ancestry. Indeed, distal admixture modelling with qpAdm estimates a contribution of 71 ± 8% from Anatolia_N and a further 29 ± 8% from Yamnaya_Samara, representing steppe-related ancestry absent in the Neolithic but found widely among Eurasian Copper and Bronze Age populations. (Fig. 3a, Supplementary Fig. S4, Supplementary Fig. S6, Supplementary Table S4). We obtained a feasible two-way admixture model with the more proximal, broadly contemporaneous pre-steppe group Croatia_North-East_CA (64 ± 8%) and Yamnaya_Samara (36 ± 8%) (Fig. 3b, Supplementary Table S4).
    We considered the newly-reported Middle Bronze Age genomes from Jagodnjak (Croatia_Jag_MBA) a single group for further population genetic analysis based on common archaeological context and clustering on the PCA (Fig. 2). We observe a marked shift left along PC1 towards Western and Iron Gates hunter-gatherers, with which it shares the most drift in outgroup f3-statistics (Supplementary Fig. S3, Supplementary Table S3). Distal admixture modelling using sources WHG, Anatolia_N and Yamnaya_Samara confirms a large WHG component in Croatia_Jag_MBA (20 ± 2%), in contrast to Croatia_Pop_CA, and is more than double the fraction estimated for the broadly contemporaneous Dalmatian Bronze Age (Fig. 3a, Supplementary Fig. S4, Supplementary Table S4), also consistent with the significantly positive F4 tests of the form f4(Mbuti.DG, WHG; Croatia_Dal_BA, Croatia_Jag_MBA) (Z = 6.95) (Supplementary Table S7). The Jagodnjak group also harbours slightly greater steppe-related ancestry compared to the preceding Croatia_Pop_CA at 33 ± 5% (see also Supplementary Fig. S6), consistent with previous findings for the Balkan region2. Replacing WHG with Iron_Gates_HG harbours comparable results (Supplementary Table S4). This group falls at the left side of the wide distribution of Bronze Age populations from the Carpathian Basin in PCA space, as well as present-day NW European genomes such as French, suggesting an eastward expansion of the Western Bronze Age signature.

    Genetic transformation following the Bronze Age

    Neither the Jagodnjak nor the Dalmatian Bronze Age groups approximate present-day populations from the region in PCA space, indicating that further significant population changes have since occurred. Our single individual from Popova zemlja, Croatia_Pop_RomanP, provides rare genomic data for Croatia after the Bronze Age33. (Table 1, Fig. 4a, Supplementary Table S1). We find this individual clustering with present-day populations of Croatia, Bulgaria and Romania in PCA and UMAP space (Figs. 2, 3c).We investigated this clustering with f4-statistics and could confirm cladality of this individual with present-day Croatians compared to other ancient and present-day populations in Europe (Supplementary Table S7). We then tested population continuity with qpWave, and found Croatia_RomanP was consistent with forming a genetic clade with present-day Croatians, as well as Bulgarians or Hungarians (p = 0.78 respectively) (Supplementary Table S4). Although based on a single individual who may or may not be representative for the wider population in that time period, this data point indicates that a broadly present-day genetic signature had already formed by Roman times, and any further population turnovers were not as significant as previous ones.



    https://www.nature.com/articles/s41598-021-94932-9



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    As usual G2a, some C and I.

    Two of these, C and I, are found in Mesolithic populations, while G2a is commonly associated with the Neolithicexpansion3. We also detected high mtDNA haplotypic diversity in Jagodnjak, with two males carrying the samedefning mutation for T2b11, while three U subclades and two K subclades, present in Mesolithic populations,are also represented. Y chromosomal haplogroups are restricted to the G2a clade however, four of which belongto the same haplotype G2a2a-Z31430. Te ffh individual lacks a read covering the determining mutation andcan be assigned the next upstream haplotype. Tese shared haplotypes indicate relatedness between individuals,which was further explored with genome-wide kinship analysis.

    https://www.nature.com/articles/s41598-021-94932-9.pdf

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    Interesting to note: No hp E detected in these Croatian samples. These tested people have pretty diverse y-DNA and mtDNA.


    Table 1 Summary information for ancient samples first reported in this paper. Capture data and calibrated radiocarbon dates for POP07 and POP14 were previously reported in2. See Methods and Supplementary Table S1 for further information about data provided in the table.

    From: Reconstructing genetic histories and social organisation in Neolithic and Bronze Age Croatia
    Individual ID Site name, archaeological time period and culture Date range (BCE contextual; calBCE/calCE 95.4% CI calibrated radiocarbon age) Population analysis label Genetic sex # autosomal SNPs overlapping with 1240 K panel mtDNA haplotype Y haplotype
    POP02 Beli Manastir-Popova zemlja Middle Neolithic Sopot 4700–4300 BCE Croatia_Pop_MN F 855,968 K1a
    POP04 M 884,196 H J
    POP05 F 790,411 K1a5
    POP06 F 944,648 K2b1
    POP07 4790–4558 calBCE M 861,721 U5b2b I2a2a
    POP08 4700–4300 BCE F 805,956 U8b1a1
    POP09 F 867,653 K1a4
    POP11 F 865,887 T2b3
    POP12 F 841,209 T2b
    POP13 F 800,065 T2c1d1
    POP14 4763–4536 calBCE F 913,421 N1a1a1
    POP16 4700–4300 BCE F 825,473 N1a1a1a2
    POP19 F 878,975 N1a1a1a3
    POP24 M 795,338 K1a1a I2a2a
    POP27 F 837,294 T2b21
    POP30 M 805,808 T2b11 G2a2a
    POP33 4603–4071 calBCE M 710,341 K1a1 G2a2b2a1a1
    POP35 4584–4458 calBCE M 774,710 J2b1a5 C1a2b
    POP36 4700–4300 BCE M 759,163 H G2a2a
    POP39 Beli Manastir-Popova zemlja Copper Age 2859 – 2502 calBCE Croatia_Pop_CA F 981,784 HV9
    POP23 Beli Manastir-Popova zemlja Roman Period 260–402 calCE Croatia_Pop_RomanP M 962,966 T2f2 R1a1a1b2a2b1
    JAG06 Jagodnjak-Krčevine Middle Bronze Age Southern Transdanubian Encrusted Pottery Culture 1800–1600 BCE Croatia_Jag_MBA M 846,845 T2b11 G2a2a1a2a2a1 ~ 
    JAG34 1879–1642 calBCE M 919,781 K2a G2a2a1a2a2a1 ~ 
    JAG58 1800–1600 BCE M 762,207 T2b11 G2a2a1a2a2a1 ~ 
    JAG78 M 922,257 U5b1b1a G2a2a1a2a2a1 ~ 
    JAG82 M 869,661 U2e1a1 G2a2a1a2a2a1 ~ 
    JAG85 F 734,912 K1b1b1
    JAG93 F 807,256 U5a1g



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    Quote Originally Posted by Hawk View Post
    As usual G2a, some C and I.

    i am not that surprised by the lack of E
    the E was
    more in coastal dalmatia
    ( lets remember the zemunica cave e-L618 case)
    here in this research most of the samples from deep mainland east croatia


    p.s
    it is pretty cool for r1a guys to see this
    in the roman dated sample r1a appear
    maybe a lost slav ( page 4 in the pdf )
    POP23 Beli Manastir-Popovazemlja Roman Period 260–402 calCE Croatia_Pop_RomanP M 962,966 T2f2 R1a1a1b2a2b1

    https://en.wikipedia.org/wiki/Beli_Manastir
    ancestery :
    mostly western jewish here is the overlapp with south europe[U]

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    Quote Originally Posted by Hawk View Post
    As usual G2a, some C and I.
    The one Croatian individual from Roman times was R1a, though. MBA Croatians had lots of WHG ancestry, nearly as much as Baltic people. In contrast, the Middle Neolithic Croatians from the North East had very little WHG genetic input and were nearly 100% ANF. Steppe admixture was among the MBA population around 40%.
    Last edited by real expert; 19-08-21 at 08:35.

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    Quote Originally Posted by real expert View Post
    The one Croatian individual from Roman times was R1b, though. MBA Croatians had lots of WHG ancestry, nearly as much as Baltic people. In contrast, the Middle Neolithic Croatians from the North East had very little WHG genetic input and were nearly 100% ANF. Steppe admixture was among the MBA population around 40%.

    he was r1a - z93 branch apperently

    POP23Beli Manastir-PopovazemljaRoman Period 260–402 calCE Croatia_Pop_RomanP M 962,966 T2f2 R1a1a1b2a2b1

    https://www.yfull.com/tree/R-F1345/


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    Real Expert: Thanks for the link to the paper. I went to the Supplementary information 2 (Sample information Table) and POP7 and POP24 from Middle Neolithic period are both I-M223. So kind of nice to see that in these new samples.

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    Quote Originally Posted by kingjohn View Post
    i am not that surprised by the lack of E
    the E was
    more in coastal dalmatia
    ( lets remember the zemunica cave e-L618 case)
    here in this research most of the samples from deep mainland east croatia


    p.s
    it is pretty cool for r1a guys to see this
    in the roman dated sample r1a appear
    maybe a lost slav ( page 4 in the pdf )
    POP23 Beli Manastir-Popovazemlja Roman Period 260–402 calCE Croatia_Pop_RomanP M 962,966 T2f2 R1a1a1b2a2b1

    https://en.wikipedia.org/wiki/Beli_Manastir
    I don't want to spoil the thread, but you are specifically talking about E-L618/E-V13, there was none to some single wolfs even on coastal areas. The migration toward Danubo-Carpathian basin happened in Middle Bronze Age, upcoming papers will resolve the issue. I mean a quick eye to the whole tree should be self-explanatory that Croatian coast is impossible to be the zero-point origin.

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    Quote Originally Posted by Hawk View Post
    I don't want to spoil the thread, but you are specifically talking about E-L618/E-V13, there was none to some single wolfs even on coastal areas. The migration toward Danubo-Carpathian basin happened in Middle Bronze Age, upcoming papers will resolve the issue. I mean a quick eye to the whole tree should be self-explanatory that Croatian coast is impossible to be the zero-point origin.

    i am talking about E-L618 the ancestor of e-v13
    afcorse i understand e-v13 is more in context in the period of bronze age
    that is what dna point by now ....
    but e-L618 his ancestor was found in this croatian cave ...
    I3948 - Zemunica Cave E-L618* (E1b) N1a1 7860 Croatia - Croatia_Cardial_Neolithic
    i am not expert on this like you

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    I am waiting for the Salento and Jovialis magic.
    A bit sad that there is no L283 in 28 samples, given I would expect it since Maros is far more east than this and it was found there the earliest in Europe. But the autosomal profiles based on abstract kind of give me the hint I have been right.
    As in I was guessing the pre-IE autosomal to be Sardinian like in Balkans and Italy. About Italy I am not so sure anymore, but my gut still leans that way, about Balkans the abstract kind of hints at it. Now time to read this paper.

    Edit: Ok so only 4 Y samples from 2 sites as far as EBA goes. No longer that sad.
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    Generally nothing new since the "Genomic history of Southeast Europe". Bronze age people on the Balkans are not the same as modern and we cant deduce much from single Iron and Rome age results.
    Again no E-V13 and J2b2, the R1a is exclusively Z93. Even G2a is L91 in the Bronze age when we should expect to be under L497 which was considered an Indo-European marker.

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    major info is that G2a2 has been in modern Croatia ( Dalmatia ) for over 2000 years ...............clearly it must be the main marker of Dalmatians
    Fathers mtdna ...... T2b17
    Grandfather mtdna ... T1a1e
    Sons mtdna ...... K1a4p
    Mothers line ..... R1b-S8172
    Grandmother paternal side ... I1-CTS6397
    Wife paternal line ..... R1a-Z282

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    G21-L91 is relatively common in the Southern Balkans (1% from the 5% haplogroup G among Bulgarians), however not sure if any Croat found, unless from Dalmatia region, which had recent migrations from the South.

    https://www.yfull.com/tree/G-L91/

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    Quote Originally Posted by eastara View Post
    Generally nothing new since the "Genomic history of Southeast Europe". Bronze age people on the Balkans are not the same as modern and we cant deduce much from single Iron and Rome age results.
    Again no E-V13 and J2b2, the R1a is exclusively Z93. Even G2a is L91 in the Bronze age when we should expect to be under L497 which was considered an Indo-European marker.
    Everyone that has been up-to-date, even people completely unrelated to each other have suggested a South-Eastern Urnfield expansion in Late Bronze Age for E-V13. I mean, Dienekes 10 years ago mentioned a Late Bronze Age expansion, but he couldn't pin-point the place of origin because of lack of samples.

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    3 members found this post helpful.
    What's interesting is that G2a-U1>L13>Z2022 was found in Middle Neolithic Croatia (alongside PF3147). Nowadays that branch is found mostly around Austria, Bavaria and central Italy, but not in Croatia.

    On the other hand the G2a in MBA Croatia was a typical Neolithic branch close to Ötzi's.

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    5 members found this post helpful.
    This chart clearly shows the Yamna ancestry arriving already in the Copper Age in the Pannonian plain.


    The Roman-age sample had the most Yamna. Considering that he was R1a-Z93, my fist thought was that he could well have been a Sarmatian soldier. However he belonged to the branch Z2124>Z2122>F1345, which is typically found in the Levant and among Ashkenazi Jews, not in the Steppe. But it is also found in Iran, Armenia and the North Caucasus, so the Yamna may be more "Gedrosia". We'll see once we run it in Dodecad K12b.


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    Note that there were 25 more samples in the study that were excluded from the final results, probably because the DNA was too low quality. Only two of them have Y-haplogroups assigned to them and one of them (POP17) is a Copper Age sample that is R1b-L23. (the other one was a Neolithic man belonging to haplogroup C). The Croatian Copper Age ran approximately from 2900 to 2500 BCE, so just prior to the Bell Beaker phenomenon. That makes it one of the oldest R1b-L23 found outside the Yamna or Corded Ware cultures at present. It also confirms that at least some R1b tribes would have taken the Danubian route to reach Central Europe.

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    Quote Originally Posted by Maciamo View Post
    Note that there were 25 more samples in the study that were excluded from the final results, probably because the DNA was too low quality. Only two of them have Y-haplogroups assigned to them and one of them (POP17) is a Copper Age sample that is R1b-L23. (the other one was a Neolithic man belonging to haplogroup C). The Croatian Copper Age ran approximately from 2900 to 2500 BCE, so just prior to the Bell Beaker phenomenon. That makes it one of the oldest R1b-L23 found outside the Yamna or Corded Ware cultures at present. It also confirms that at least some R1b tribes would have taken the Danubian route to reach Central Europe.
    I have the feeling the so called Cetina Culture was R1b-Z2103: https://archeorient.hypotheses.org/8247 and perhaps forerunners of Proto-Illyrians. But this posits a problem since R1b-Z2103 among Albanian has a TMRCA of 1500 ybp and this subclade totally dominates the whole Albanian R1b-Z2103 pool. But it could be that Roman wars, Justinian Plague, Slavic migrations reduced a lot this lineage.

    As a side note, Albanian archeologists like Frano Prendi are of the opinion Illyrian tumuli resemble Cetina tumuli.

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    Finally, an individual dated to Roman times exhibits an ancestry profile that is broadly present in the region today, adding an important data point to the substantial shift in ancestry that occurred in the region between the Bronze Age and today. ( page 1 abstract)
    P.s
    They speak about thr r1a-z93 dude here
    Last edited by kingjohn; 19-08-21 at 14:21.

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    Quote Originally Posted by Maciamo View Post
    Note that there were 25 more samples in the study that were excluded from the final results, probably because the DNA was too low quality. Only two of them have Y-haplogroups assigned to them and one of them (POP17) is a Copper Age sample that is R1b-L23. (the other one was a Neolithic man belonging to haplogroup C). The Croatian Copper Age ran approximately from 2900 to 2500 BCE, so just prior to the Bell Beaker phenomenon. That makes it one of the oldest R1b-L23 found outside the Yamna or Corded Ware cultures at present. It also confirms that at least some R1b tribes would have taken the Danubian route to reach Central Europe.
    Is it possible to see the exact subclade this R1b-L23 sample was, or its autosomal profile? Together with data in where it was found and the age of it.

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    The Roman sample is obviously connected to the Danubian limes. At later stage of the Empire the legionnaires were recruited predominantly in the Eastern parts. After serving their time they were given land in the vicinity and could make blended families with the locals. In this case the haplogroup Ra1-Z2124>Z2122>F1345 may have Anatolian/Middle Eastern origin.

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    Quote Originally Posted by Maciamo View Post
    Note that there were 25 more samples in the study that were excluded from the final results, probably because the DNA was too low quality. Only two of them have Y-haplogroups assigned to them and one of them (POP17) is a Copper Age sample that is R1b-L23. (the other one was a Neolithic man belonging to haplogroup C). The Croatian Copper Age ran approximately from 2900 to 2500 BCE, so just prior to the Bell Beaker phenomenon. That makes it one of the oldest R1b-L23 found outside the Yamna or Corded Ware cultures at present. It also confirms that at least some R1b tribes would have taken the Danubian route to reach Central Europe.
    Quote Originally Posted by Dinko View Post
    Is it possible to see the exact subclade this R1b-L23 sample was, or its autosomal profile? Together with data in where it was found and the age of it.
    For POP17 under "Other IDs" it says: I3499;MathiesonNature2018;capture.data.from.tooth.

    So it's the same one from the previously published study The Genomic History of Southeastern Europe, under which I3499 is labeled from the Vucedol Culture, 2884-2666 calBCE, and is R1b-Z2103+ (could not be classified any deeper).

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    POP04, 4700-4300 BCE, Sopot culture, Middle Neolithic, is most likely under J2a haplogroup, as there is already a J2a-Z6063 from the Sopot Culture from a previous study.

    The lack of J2b-L283 is not surprising, IMHO. I would not expect it to show up in Neolithic Croatia. The Middle Bronze Age samples come from a single site in East Croatia (Osijek). Besides, it's more likely by that time J2b-L283 would be found in the western Balkans, as suggested by the fact that we have I4331 in MBA Dalmatia.

  24. #24
    Regular Member kingjohn's Avatar
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    Quote Originally Posted by Trojet View Post
    POP04, 4700-4300 BCE, Sopot culture, Middle Neolithic, is most likely under J2a haplogroup, as there is already a J2a-Z6063 from the Sopot Culture from a previous study.
    The lack of J2b-L283 is not surprising, IMHO. I would not expect it to show up in Neolithic Croatia. The Middle Bronze Age samples come from a single site in East Croatia (Osijek). Besides, it's more likely by that time J2b-L283 would be found in the western Balkans, as suggested by the fact that we have I4331 in MBA Dalmatia.
    Thanks
    For the link
    I will keep it to a person who i paid
    For his test expecting him to be e1b1b1
    He turn j2a
    P.s
    So those ancient dna link is pretty cool
    Last edited by kingjohn; 20-08-21 at 11:58.

  25. #25
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    more celtic
    Country: France



    1 members found this post helpful.

    Quote Originally Posted by Hawk View Post
    I don't want to spoil the thread, but you are specifically talking about E-L618/E-V13, there was none to some single wolfs even on coastal areas. The migration toward Danubo-Carpathian basin happened in Middle Bronze Age, upcoming papers will resolve the issue. I mean a quick eye to the whole tree should be self-explanatory that Croatian coast is impossible to be the zero-point origin.
    I don't know what worth to give to it, but in ancient Yougoslavija (before breaking off) Montenegro/Cherna Gora was the place of greater variety for Y-E V13 if not the place of denser presence. And this region is not too far from the coastal areas of S-Croatia/Dalmatia, roughly same latitude as Central Bosnija.

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