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Thread: Y-chromosome variability and genetic history of Commons from Northern Italy

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    Moderator Pax Augusta's Avatar
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    Y-chromosome variability and genetic history of Commons from Northern Italy

    Y-chromosome variability and genetic history of Commons from Northern Italy

    Stefania Sarno, Rajiv Boscolo Agostini, Sara De Fanti, Gianmarco Ferri, Silvia Ghirotto, Giorgia Modenini, Davide Pettener, Alessio Boattini

    First published: 10 May 2021 https://doi.org/10.1002/ajpa.24302

    Abstract
    Objectives
    Genetic drift and admixture are driving forces in human evolution, but their concerted impact to population evolution in historical times and at a micro-geographic scale is poorly assessed. In this study we test a demographic model encompassing both admixture and drift to the case of social-cultural isolates such as the so-called “Commons.”
    Materials and methods

    Commons are peculiar institutions of medieval origins whose key feature is the tight relationship between population and territory, mediated by the collective property of shared resources. Here, we analyze the Y-chromosomal genetic structure of four Commons (for a total of 366 samples) from the Central and Eastern Padana plain in Northern Italy.
    Results

    Our results reveal that all these groups exhibit patterns of significant diversity reduction, peripheral/outlier position within the Italian/European genetic space and high frequency of Common-specific haplogroups. By explicitly testing different drift-admixture models, we show that a drift-only model is more probable for Central Padana Commons, while additional admixture (~20%) from external population around the same time of their foundation cannot be excluded for the Eastern ones.
    Discussion

    Building on these results, we suggest central Middle Ages as the most probable age of foundation for three of the considered Commons, the remaining one pointing to late antiquity. We conclude that an admixture-drift model is particularly useful for interpreting the genetic structure and recent demographic history of small-scale populations in which social-cultural features play a significant role.

    [...]

    Here we focus on four more Commons from the Padana Plain in Northern Italy (Figure 1). Two of them (Nonantola and S. Agata Bolognese) are located in the Central Padana Plain (from now on Central Commons), in the same area of the previously mentioned S. Giovanni in Persiceto, with which they also share the denomination of Partecipanza. The remaining two (Grignano Polesine and Massenzatica) are at the Easternmost fringes of the Padana Plain, not far from the Po delta (from now on Eastern Commons).

    [...]

    On that respect, a subtle difference between Central (Nonantola, S. Agata B.) and Eastern (Grignano P., Massenzatica) Commons emerged: Central Commons harbor haplogroups/paragroups that are among the most frequent in Northern Italy, i.e. R-U152* (S. Agata B.) and R-L2 (Nonantola); instead Eastern Commons show high frequencies of more uncommon or rare haplogroups/paragroups in Italy such as R-L51* and T-M70 (Boattini et al., 2013). All these cases can be explained based on the effects of genetic drift, according to which the frequency of some haplogroups may have increased (or decreased) by random fluctuations.

    [...]

    In addition, the case of the Partecipanza of S. Giovanni in Persiceto—where similar patterns where observed, most notably the higher-than-expected frequency of the otherwise rare haplogroup I1-L22—suggested that external admixture could have played a significant role in the genetic history of Commons.


    Last edited by Pax Augusta; 21-05-21 at 22:45.

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    Satyavrata Maciamo's Avatar
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    3 members found this post helpful.
    That kind of study is highly disappointing. I was hoping that they would test deep clades of R1b-U152, but they didn't test any apart from L2! How is that possible? We are in 2021, not in 2011.
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    Quote Originally Posted by Maciamo View Post
    That kind of study is highly disappointing. I was hoping that they would test deep clades of R1b-U152, but they didn't test any apart from L2! How is that possible? We are in 2021, not in 2011.

    not much detail...just..........just 5 ydna types

    Controls and comparison reference populations for the considered haplogroups (R1b-U152, R1b-L51, R1b-L2, G2a-U8, T-M70)


    limiting ourselves to the observation that Grignano P. exhibits an otherwise rare haplogroup, T-M70, which could refer to a Mediterranean background, while R-L51*, which is typical of Massenzatica, is mostly observed in central Europe

    check table 2

    R-U152* 1 12 GP 12 - - 1206.62 +/− 257.25 1280.524 +/− 141.75
    R-U152* 2 10 - - 2541.43 +/− 541.83 3999.52 +/− 415.80 - -
    R-U152* 3 19 NON 11 4714.93 +/− 1005.23 6996.91 +/− 575.771 1016.09 +/− 216.63 1535.75 +/− 206.22
    R-U152* 4 11 SAB 9 2674.84 +/− 570.28 2627.54 +/− 324.46 1040.1 +/− 221.75 1138.26 +/− 163.48
    R-U152* 5 15 SAB 15 - - 520.59 +/− 110.99 594.17 +/− 76.30
    R-U152* 6 15 - - 3139.15 +/− 669.27 4384.90 +/− 278.73 - -
    R-U152* 7 11 - - 3508.49 +/− 748.01 5832.41 +/− 491.53 - -
    R-L51 1 7 - - - - - -
    R-L51 2 16 MA/ME 10 2863.21 +/− 610.44 4457.97 +/− 377.79 1743.77 +/− 371.77 2276.28 +/− 311.76
    R-L51 3 17 - - 2126.93 +/− 453.46 4814.91 +/− 321.75 - -
    R-L2 1 7 GP 6 - - - -
    R-L2 2 9 - - 7405.99 +/− 1578.96 5023.37 +/− 589.37 - -
    R-L2 3 23 - - 3638.76 +/− 775.79 5938.69 +/− 290.09 - -
    R-L2 4 10 NON 10 - - 1135.13 +/− 242.01 996.21 +/− 143.45
    R-L2 5 11 GP 10 678.33 +/− 144.62 687.86 +/− 103.95 700.31 +/− 149.31 721.29 +/− 122.16
    T-M70 1 5 - - - - - -
    T-M70 2 16 GP 15 628.68 +/− 134.03 1946.89 +/− 187.71 562.65 +/− 119.96 792.43 +/− 89.86
    T-M70 3 3 - - - - - -
    G2a-U8 1 9 GP 9 - - 774.65 +/− 165.15 871.71 +/− 136.85
    G2a-U8 2 20 - - 3140.2 +/− 669.49 6764.46 +/− 348.90 - -
    G2a-U8 3 5 GP 5 - - - -
    Fathers mtdna ... T2b17
    Grandfather mtdna ... T1a1e
    Sons mtdna ... K1a4p
    Mum paternal line ... R1b-S8172
    Grandmum paternal side ... I1-CTS6397
    Wife paternal line ... R1a-Z282

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    … Demographic histories of the considered models. “Pop 1” represents a general Italian population; “Pop 2” represents a non-Italian group, source of potential external admixture/introgression :


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    … Y-chromosome diversity indexes in Commons and Controls:


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    … Nonmetric MDS representations of Commons. Controls and reference populations (Italy, left; Europe, right) based on Y-STR data:



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    … there’s a mistake in the image above, … VI stands for Vicenza but it is in purple, … purple = Central-South Italy, but Vicenza is in Veneto - North-East Italy, … maybe they meant to write VT (Viterbo - Lazio) … I think :)

    … see below, I added the full name of the cities:


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    Quote Originally Posted by Maciamo View Post
    That kind of study is highly disappointing. I was hoping that they would test deep clades of R1b-U152, but they didn't test any apart from L2! How is that possible? We are in 2021, not in 2011.
    Apparently the data are not new. From the paper:
    "Y-STRs data for comparison populations were extracted from the literature for both Italy (Boattini et al., 2013) and Europe (Purps et al., 2014), respectively. In addition, comparison data for within-haplogroup comparisons from 16 Euro-Mediterranean populations (329 samples) were also considered and retrieved from Hallast et al. (2015)."

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    Quote Originally Posted by Salento View Post
    … there’s a mistake in the image above, … VI stands for Vicenza but it is in purple, … purple = Central-South Italy, but Vicenza is in Veneto - North-East Italy, … maybe they meant to write VT (Viterbo - Lazio) … I think :)

    … see below, I added the full name of the cities:


    thanks

    Interesting is the G2a-U8 which has links to

    G2a2b (L30, PF3267, S126, U8)
    G-L30 (also G-PF3267, G-S126 or G-U8; G2a2b, previously G2a3) Men who belong to this group but are negative for all its subclades represent a small number today. This haplogroup was found in a Neolithic skeleton from around 5000 BC, in the cemetery of Derenburg Meerenstieg II, Germany, which forms part of the Linear Pottery culture, known in German as Linearbandkeramik (LBK),[12]

    considering that it is Derenburg found with G2a Neolithic ..........near other ancient samples from nearby Karlsdorf neolithic 3 x T1a ydna samples ..........................this would confirm that the G2a, and the T could have moved around Central Europe. Germany and Northern and Central Italy together

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    Intresting thanks for sharing pax augusta
    They could have done better
    Job on the derived branches ....

    P.s
    E-m123 missing completely from commons but occure in 7.14% 3/42 in mesola control group
    https://i.imgur.com/jNHFdIU.png

    But it is not very informative
    E-m123 snp originated in mesolitic
    not expecting for the deep farther downstream like e-L791 and e-m84
    They should have at least anlayse
    It farther for basic e-m34 or e-ft20896
    as maciamo
    Said above we are in 2021 not 2011
    Last edited by kingjohn; 22-05-21 at 14:33.
    https://www.yfull.com/tree/E-FGC7391/

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

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    Quote Originally Posted by Salento View Post
    … there’s a mistake in the image above, … VI stands for Vicenza but it is in purple, … purple = Central-South Italy, but Vicenza is in Veneto - North-East Italy, … maybe they meant to write VT (Viterbo - Lazio) … I think :)

    … see below, I added the full name of the cities:





    VI stands for Vicenza (Veneto), not for Viterbo (Lazio). Samples are from Boattini 2013. The error is in the coloring, not in the initials.





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    Pax, their mistake, …
    … one more thing, Pistoia and … (Tuscany) is Central Italy!

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    Edited

    deleted….

    the Wikipedia page doesn’t make any sense as it contradicts itself.
    Last edited by Salento; 22-05-21 at 18:38.

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    Deleted ……
    Last edited by Salento; 22-05-21 at 18:39.

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    for e-v13 guys....



    NONATOLA


    common 3.70%
    control 3.64%



    GRIGANO P.

    common 6.06%
    control 6.25%


    MASSENZATICA


    common 16%


    MESOLA

    control 7.14%

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    Quote Originally Posted by Salento View Post
    @Torzio, … ???

    … they say: Karsdorf samples are R1b, … a mistake? are they for real? … f a k e News?

    …” I know that I know nothing “ …

    https://en.m.wikipedia.org/wiki/Karsdorf_remains

    someone changed the page 12 days ago .................but chart still have T1a
    There have been hackers on the net changing all T ydna to be somali ....been going on for nearly 2 years


    By his side, I0795 showed higher autosomal admixture frequencies of surrounding populations like Hunter Gatherer Europeans I2a (West Hunter Gatherers) and Aegean-Anatolian Neolithics G2a and H2. However, I0795 have the highest frequency of shared DNA with Upper Paleolithic Neanderthals from Central Europe found in any Early Neolithic population. Further comparisons show that I0795 has similar frequencies like Oase-1 when compared with Vindija Neanderthals. When I0795 and I0797 are compared to Oase-1, they both share a very high percentage of DNA 34% and 18% respectively and I0795 12% with Ostuni1. This could mean that this T1a1 tribe from Karsdorf was closest to Upper Paleolithic Hunter-Gatherers than to Mesolithic haplogroups.

    charts still say T1a


    the third karsdorf T was found by Brandt and Haak



    KAR537

    T1a1- L162

    Brown hair
    Blue eyes
    Pale skin
    The investigated individual 537 is a 184 male with an age at death of around 25-30 years (figure supplementary S1), dated to 5056–185 4959 cal BC (KIA 40357 – 6116 ± 32 BP) (Brandt et al., 2014, Nicklisch, 2017)


    these karsdorf T1a samples along with the 2 x t1a bulgarians from Malek who are the same period could have links with the italians

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    Quote Originally Posted by Salento View Post
    Edited

    deleted….

    the Wikipedia page doesn’t make any sense as it contradicts itself.
    see if these work

    Karsdorf ( 7100yBP - Early Neolithic ) LBK Culture

    I0795 ( 7076 ± 90 yBP )
    House/Phase: S / 2
    Y-DNA: T1a1a2-Y63197 (xBY154289)
    mtDNA: H1 or H1au1b*
    Sr isotope: Native to Unstruttal
    Diet (d13C%0 / d15N%0): -20.0 / 9.0 (highest Animal Protein)
    Age at Death: 45-60
    Death Position: Flexed Left northeast
    Other ID: KAR6/Feature 170/Musm.no. 2006:14423a
    Sample: Tooth / Rib
    Read Pairs:
    Mean Coverage:
    Files: FASTQ / FASTQ&BAM (galaxy) / BAM




    I0797 ( 7087 ± 725 yBP )
    House/Phase: H / 2
    Y-DNA: T1a1a2-Y63197 (xBY154289)
    mtDNA: H46b
    Sr isotope: Native to Unstruttal
    Diet (d13C%0 / d15N%0): -20.2 / 9.1 (highest Animal Protein)
    Age at Death: 24-26
    Death Position: Stretched Dorsal northwest
    Other ID: KAR16a/Feature 611/Musm.no. 2004:26374a
    Sample: Tooth / Rib
    Read Pairs:
    Mean Coverage:
    Files: FASTQ / FASTQ&BAM (galaxy) / BAM



    Kars537 ( 6958 ± 49 yBP )


    House/Phase: O / 2
    Y-DNA: T1a1a2-Y63197 (xBY154289)
    mtDNA: J1c6a
    Sr isotope: Native to Unstruttal ( Rang Group limit )
    Diet (d13C%0 / d15N%0): -19.7 / 8.9 (highest Animal Protein)
    Age at Death: 25–30
    Death Position: Stretched Dorsal southeast
    Other ID: Feature 537 / Museum no 2004:26340a / 14C id KIA-40357
    Sample: Skull
    Read Pairs: 122,568,310
    Mean Coverage: 2.96X
    Virus: Hepatitis B ( HBV )
    Autosomal notes: High CHG
    Files: FASTQ / FASTQ (galaxy) / BAM (FASTQ=>mapped-SAM=>sorted BAM)

    Karsdorf settlement


    https://www.nature.com/articles/nature14317
    doi: https://doi.org/10.1038/nature14317

    https://elifesciences.org/articles/36666
    doi https://doi.org/10.7554/eLife.36666.001

    More research:
    https://www.researchgate.net/publica...ntial_mobility








    Malak Preslavets ( 7600yBP - Mesolithic/Early Neolithic ) Criș Culture

    I0700 ( 7550 ± 200 yBP )

    House: 13
    Y-DNA: T1a1a2-Y63197
    mtDNA: T2e
    Age at Death: Adult
    Death position: Disturbed grave. Perhaps was a flexed burial on the right side
    Sample: Left Femur
    Burial: Cattle bone was discovered next to the feet
    Autosomal notes: The highest EHG+WHG+CHG in the settlement
    Files: FASTQ / FASTQ&BAM (galaxy) / BAM




    I1108 ( 7550 ± 200 yBP )

    House: 4
    Y-DNA: T1a1a2-Y63197
    mtDNA: T2e
    Age at Death: Juvenile
    Death position: Crouched on the right side, with head to west
    Sample: Left Tibia
    Burial: Freshwater mussel shells
    Autosomal notes: The highest EHG+WHG+CHG in the settlement
    Files: FASTQ / FASTQ&BAM (galaxy) / BAM




    Malak Preslavets settlement


    https://www.nature.com/articles/nature25778

    doi: https://doi.org/10.1101/135616









    notice both Karsdorf and Malek also have the G2a-U8 samples found as well

  19. #19
    Regular Member Salento's Avatar
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    … wow, they want to cancel y T history, …

    … I read comments around, it seems as if Ancient y T is an “inconvenient” Haplogroup,
    they call it “Outlier”, as if it doesn’t belong, even though some samples are older than the Mainstream haplogroups from the same place (Neolithic Karsdord - Germany and R850 Ardea Latin - Rome).

    It’s not surprising that new y T posters freak out when they find out their Haplogroup. They come out with these bizarre theories because they think the Rare y T doesn’t belong when it obviously does.

    There is a lot of misinformation around.

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    Quote Originally Posted by Salento View Post
    … wow, they want to cancel y T history, …

    … I read comments around, it seems as if Ancient y T is an “inconvenient” Haplogroup,
    they call it “Outlier”, as if it doesn’t belong, even though some samples are older than the Mainstream haplogroups from the same place (Neolithic Karsdord - Germany and R850 Ardea Latin - Rome).

    It’s not surprising that new y T posters freak out when they find out their Haplogroup. They come out with these bizarre theories because they think the Rare y T doesn’t belong when it obviously does.

    There is a lot of misinformation around.

    don't listen to them
    there is nothing to freak out and to be a shamed off ..
    it is a regular neolithic haplogroup in europe .....
    and you got famous : thomas jefferson

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    Regular Member Salento's Avatar
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    Quote Originally Posted by kingjohn View Post
    don't listen to them
    there is nothing to freak out and to be a shamed off ..
    it is a regular neolithic haplogroup in europe .....
    and you got famous : thomas jefferson
    … I don’t, I’m proud of my rare Haplogroup, … the way I see it ancient y T experienced a catastrophic event, … modern y Ts are the descendants of these tougher than average survivors :)

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    Quote Originally Posted by Salento View Post
    Pax, their mistake, …
    … one more thing, Pistoia and … (Tuscany) is Central Italy!
    It just follows Boattini 2013. Tuscany with Northern Italy according to Y-chromosome.

    "The first group (black squares) is represented by populations from North-Western Italy, including most of the Padana plain and Tuscany. The second group (white squares) includes locations from South-Eastern Italy and the whole Adriatic coast, being represented also in North-Eastern Italy."



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    Quote Originally Posted by Salento View Post
    … I don’t, I’m proud of my rare Haplogroup, … the way I see it ancient y T experienced a catastrophic event, … modern y Ts are the descendants of these tougher than average survivors :)
    I confess that I liked it when you said: I only know that I know nothing. I am in the same situation in relation to my Haplogroup (baseline R1b-L51+ and terminal R1b-DF27+). I am very interested in the controversies regarding my haplogroup too. If there is a chance that my haplogroup will not have a direct relationship with the great Yamna migration to the west, the truth is that I will be very satisfied with that, lol.

  24. #24
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    2 members found this post helpful.
    Thanks Pax and Duarte :)

    @Duarte … the catastrophe inflicted to y T that I mentioned was the R1b (and others) / Yamnaya migration / invasion, … I was being polite to R1b members, … though I’m glad that your Tribe maybe wasn’t part of it :)

    … just theories

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    Quote Originally Posted by Salento View Post
    Thanks Pax and Duarte :)

    @Duarte … the catastrophe inflicted to y T that I mentioned was the R1b (and others) / Yamnaya migration / invasion, … I was being polite to R1b members, … though I’m glad that your Tribe maybe wasn’t part of it :)

    … just theories

    you would know that T was noted as K2 prior to 2008 ...........as it belongs to the K-M9 group with R1a, R1b, N, O, L ............all same family ...........some scholars still use K for T

    a Russian scholar 5 years ago was arguing that it belongs under R1b or R1a as there are only a few snp which seperates T from these

    another wanted to remove it, join it with LT and give LT a new mark .......I think he wanted it as a V

    but, both have also stated that it is 42000 years old .............and the T branch split into 4 group 13500 years ago .............the 4 groups is what we have currently ..............they also said it was initially a pure hunter group

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