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Thread: Global25 automated nMonte for South/Central Asian members

  1. #7681
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    Quote Originally Posted by Sapporo View Post
    @ThaYamamoto

    Do you mind doing a normal Global PCA with the individuals you included on the two recent Caucasus - Near Eastern PCA? Or perhaps a South-Central Asian specific PCA with SI tribals, Pamiris and Baloch/Brahui?
    Not exactly what you are asking for, but I did a PCA with Yamamoto's coords and a bunch of South Asian AG users. I posted this before as well.






  2. The Following 4 Users Say Thank You to agent_lime For This Useful Post:

     FrostAssassin0701 (09-15-2020),  ssamlal (09-15-2020),  ThaYamamoto (09-15-2020),  Varun R (09-15-2020)

  3. #7682
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    Quote Originally Posted by MonkeyDLuffy View Post
    Did you run any models by any chance? I am curious how similar are these to other samples, and if it can shed some light on their origins.

    "sample": "bilku",
    "distance": 1.8997,
    "Shahr_I_Sokhta_BA2": 56.5,
    "Krasnoyarsk_MLBA": 20.5,
    "Dzharkutan1_BA": 19,
    "Chokhopani_2700BP": 4


    "sample": ":bilku",
    "distance": 1.9067,
    "Shahr_I_Sokhta_BA3": 50,
    "Bustan_BA_o1": 27,
    "Srubnaya_MLBA": 20,



    with penalty=0

    "sample": ":bilku",
    "distance": 1.7846,
    "Shahr_I_Sokhta_BA2": 55.5,
    "Krasnoyarsk_MLBA": 23.5,
    "Dzharkutan1_BA": 17.5,
    "Chokhopani_2700BP": 3.5

  4. The Following 3 Users Say Thank You to pegasus For This Useful Post:

     Jatt1 (09-20-2020),  MonkeyDLuffy (09-15-2020),  Sapporo (09-15-2020)

  5. #7683
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    @agent_lime

    Am I clustering toward my mother instead of more in between my mother and father? Or is it the dimensions and/or the chip used (they are both on V5 and I am on V3) causing that? You seem to be closer to my father than I am. Though, I'm not sure that would be the case in raw distances.

    In terms of what I was asking for, I was looking for something more in line with what khana has posted in the past or David's South-Central Asian specific G25 PCA (with Pamiris in the top right, Baloch/Brahui in the bottom right and SI tribals in the bottom left).

    Here is an example West Eurasian specific global PCA posted by genica user Michalis Moriopoulos:

    https://i.imgur.com/xvAJLYn.png
    Last edited by Sapporo; 09-15-2020 at 07:19 PM.
    pegasus modeling:
    sample": "Punjabi_Jat:Sapporo_AGUser",
    "fit": 1.1506,
    "IRN_Shahr_I_Sokhta_BA3": 43.33,
    "TKM_Gonur1_BA": 31.67,
    "RUS_Sintashta_MLBA": 25,
    "closestDistances": [

    avatar credit goes out to aaronbee2010

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     Jatt1 (09-20-2020)

  7. #7684
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    Quote Originally Posted by Sapporo View Post
    @ThaYamamoto

    Do you mind doing a normal Global PCA with the individuals you included on the two recent Caucasus - Near Eastern PCA? Or perhaps a South-Central Asian specific PCA with SI tribals (AASI pull), Pamiris (Steppe pull) and Baloch/Brahui (Iran N and BMAC pull)?

    Also, is Kashmiri_Sharika one of the new anthrogenica members? So, a Kashmiri Pandit? Just wondering based on the most Near Eastern shifted NW South Asian cluster Lollybolly, agent_lime and that Kashmiri individual are forming.
    Yeah man I'll try doing that later tonight if I got some time.

    I forgot to edit her name, it's definitely one of the newer users but I'm not sure who till I check my pm's.

    Has tha forum been down for anybody else or just me?

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     Sapporo (09-15-2020)

  9. #7685
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    Quote Originally Posted by pegasus View Post
    "sample": "bilku",
    "distance": 1.8997,
    "Shahr_I_Sokhta_BA2": 56.5,
    "Krasnoyarsk_MLBA": 20.5,
    "Dzharkutan1_BA": 19,
    "Chokhopani_2700BP": 4


    "sample": ":bilku",
    "distance": 1.9067,
    "Shahr_I_Sokhta_BA3": 50,
    "Bustan_BA_o1": 27,
    "Srubnaya_MLBA": 20,



    with penalty=0

    "sample": ":bilku",
    "distance": 1.7846,
    "Shahr_I_Sokhta_BA2": 55.5,
    "Krasnoyarsk_MLBA": 23.5,
    "Dzharkutan1_BA": 17.5,
    "Chokhopani_2700BP": 3.5
    That's some really high east asian

  10. #7686
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    Quote Originally Posted by parasar View Post



    NORTH/CENTRAL EUROPE

    "None of the warriors had the genetic mutation that allows adults to digest milk, an ability known as lactase persistence that’s common in many Europeans.
    Other studies have shown lactase persistence was common in parts of Germany by 500 C.E., and widespread across the region by 1000 C.E. So the gene must have spread before that time, but after the battle just 2000 years earlier. That means that within about 100 generations, the mutation had penetrated populations across Europe. “That’s the strongest selection found in the human genome,” Burger says.
    The finding only deepens the mystery of lactase persistence. In a 2007 study, Burger showed that Europe’s first farmers, living more than 8000 years ago, weren’t lactase persistent either. At the time, he argued that the mutation gradually spread along with the development of agriculture and herding, a theory supported by signs of milking and cheese- and yogurt-making in Stone Age Europe. People able to digest milk, the argument went, would be able to get more calories from their herds than those without, and more of their children would survive to pass on the gene.
    But the Tollense skeletons show that at least 6000 more years went by before the gene for lactase persistence caught on. The DNA results also quash the theory, first proposed in 2015, that the gene for lactase persistence was imported to Western Europe at about 5000 B.C.E. by cow-herding nomads from the steppes of modern-day Ukraine and Russia, the Yamnaya people.
    The results leave scientists more puzzled than ever about exactly when and why Europeans began to drink milk. “Natural genetic drift can’t explain it, and there’s no evidence that it was population turnover either,” says Christina Warinner, a geneticist at Harvard University and the Max Planck Institute for the Science of Human History who was not involved with the study. “It’s almost embarrassing that this is the strongest example of selection we have and we can’t really explain it.”
    Perhaps something about fresh milk helped people ward off disease in the increasingly crowded and pathogen-ridden European towns and villages of the Iron Age and Roman period, Burger speculates. But he admits he’s baffled too. “We have to find a reason why you need this drink.”"

    https://www.sciencemag.org/news/2020...-t-drink-milk#
    Quote Originally Posted by parasar View Post
    The date given for I6561 from radiocarbon is almost as precise as one can get: 4045–3974 calBCE or ~6000 ybp.
    This sample is Y26+ Y2-. The split for Y26 per YFull is: "Y26/M780 formed 4700 ybp, TMRCA 4700 ybp." https://www.yfull.com/tree/R-Y3/
    If so, YFull is off by 27.66% for this line.
    ...

    The earlier reliable LP individual is a Ukrainian Eneolithic individual dated to 5,960 BP [from 1950 AD], as previously noted [30], which presents a mixture of Anatolian farmers and steppe ancestry [30]. During the 5,000–4,000 BP period, we see 3 additional LP individuals in Europe (frequency of the T allele of 3/259 = 1.2%) but no LP individuals in Central Asia (though 0/64 is not significantly different from 3/259, proportion test: p > 0.89). We don’t see any LP individual among those directly affiliated with Yamnaya-associated cultures, but there are not many of them (48 individuals) compared to non-Yamnaya Europeans (and 0/48 is not significantly different from 3/252, proportion test: p = 1).

    Regarding Asia, the earlier reliable LP individual is one from Kazakhstan dated to 3,713 BP. Then, there is a change in dynamic around the Iron Age, with the T allele rising up in frequency between 3,000 BP and present day in Europe (61/198 = 30.8%) while staying low in Central Asia (4/72 = 5.6%) (proportion test: p = 3.6 10−5). In parallel, the T allele emerges in Pakistan, with the first reliable LP individual dated to 2,250 BP.

    In summary, the −13.910*T allele was first seen in Central Europe 5,950 years ago. Given that most samples around that time do not carry evidence for any steppe ancestry, it is difficult to infer whether it originated in Yamnaya-associated cultures or in European farmers. Regardless, the T allele quickly spread across Eurasia during the late Bronze Age (first appearance at 3,713 BP in Central Asia), which is concomitant with the expansion of Yamnaya-associated cultures. This suggests that steppe populations might have contributed to the spread of the T allele across and outside Europe. This hypothesis is further supported by the fact that the −13.910*T allele is currently found at elevated frequency in Europe and North India (Fig 2), the two places where Yamnaya-associated populations are known to have left some genetic legacy [46]. The T allele then strongly increased in frequency in Europe (reaching 31% in average in the 3,000 BP to present day period) while remaining low in Central Asia (6%), likely reflecting differences in selective pressures between populations.

    https://ndownloader.figstatic.com/fi...36/preview.jpg
    https://journals.plos.org/plosbiolog...l.pbio.3000742

    I6561 MathiesonNature2018 5960 Ukraine_EN_o Ukraine M 0
    I5531 OlaldeNature2018 4250 Germany_Bell_Beaker Germany F 0
    I6791 Narasimhan2019 3713 Maitan_MLBA_Alakul Kazakhstan F 0
    I0430 MathiesonNature2015 3675 Russia_Srubnaya_published Russia M 0
    I7719 Narasimhan2019 2250 Saidu_Sharif_H Pakistan F 0

    https://journals.plos.org/plosbiolog...o.3000742.s003

    I7719
    "S2.4.2.2 Saidu Sharif Buddhist monastery, early historic graves in the Swat Valley, Pakistan (n=12)
    Descriptions by Luca M. Olivieri
    These individuals are from one site in the Swat District of the Khyber-Pakhtunkhwa Province of northwestern Pakistan, dated to 400-200 BCE.

    The Buddhist site of Saidu Sharif I was the target of a series of excavations made by the IsMEO Italian Archaeological Mission (with interruptions) between 1963 and 1982 and was directed by D. Faccenna with P. Callieri (and F. Noci) (see more details in ref. (203–205)). A total of 17 single graves were found under the monastery, one was found under the StupaTerrace (Grave 13), another one was found in the area further west, outside the protected archaeological area (Grave 00). The site was explored again by ISMEO in 2011-2015, and 26 166 more graves were documented west of the Stupa Terrace (see more details in ref. (206)).

    A revised chronology, a reconstruction of the extension of the graveyard, as well as a study of the stratigraphy have been recently proposed after a study by the ISMEO Italian Archaeological Mission/ACT-Field School Project (see more details in ref. (206)). Grave architecture and burial features differ from the “Swat Protohistoric Graves” (see above)."

    "Grave 3, single burial, DA-SIM0317-037 (I7719): Context date of 400-200 BCE. Genetically female. Almost complete remains of a 40 to 50 year old morphologically defined as a male (inconsistent with the genetic sex), lying on the right side with the head turned to the right (more information on the grave can be obtained from page 20 of ref. (204))"

  11. #7687
    Quote Originally Posted by Sapporo View Post
    In terms of what I was asking for, I was looking for something more in line with what khana has posted in the past or David's South-Central Asian specific G25 PCA (with Pamiris in the top right, Baloch/Brahui in the bottom right and SI tribals in the bottom left).
    Here is a quick PCA with NW South Asian groups + Tajik and Iranian
    The "distance" in the label is the Euclidean distance to the reference sample, which in this case was set to the "Punjabi Jatt Average"

    The 2D and 3D PCA's are available at

    2D PCA
    3D PCA

    You can use the mouse to pan and zoom in the 3D view to get a better perspective on the distance between the various groups.

    Note that it only takes a couple of minutes to create these PCAs in Genoplot with your personal samples.



    Last edited by GenoPlot; 09-15-2020 at 11:28 PM.
    Explore your Genealogy

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  13. #7688
    Here is a plot for the same populations, this time including a group from the Arabian peninsula to illustrate the relative "pull" towards SW Asia. The reference sample in this PCA is the "Iranian Fars Average" and the size of the markers reflects the Euclidean distance to the reference.

    2D PCA
    3D PCA

    Last edited by GenoPlot; 09-15-2020 at 11:45 PM.
    Explore your Genealogy

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  15. #7689
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    Quote Originally Posted by GenoPlot View Post
    Here is a plot for the same populations, this time including a group from the Arabian peninsula to illustrate the relative "pull" towards SW Asia. The reference sample in this PCA is the "Iranian Fars Average" and the size of the markers reflects the Euclidean distance to the reference.

    2D PCA
    3D PCA

    Great tool! I just wish there was a labeling function.

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     parasar (09-16-2020)

  17. #7690
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    I'm in the process of trying to wrap my head around PCA's and how to interpret them. I'd appreciate if anyone who's planning to plot out PCA's can include me for future runs.

    Here are my coords:
    Kamil_scaled,0.0774,0.004062,-0.108234,0.064277,-0.068628,0.04518,-0.006345,-0.003692,-0.009408,-0.01221,-0.009581,0.003147,-0.005798,-0.00234,0.016151,0.005038,-0.004955,-0.00076,-0.002388,-0.011506,0.001497,-0.007048,-0.001602,-0.001446,0.008861

    Kamil,0.0068,0.0004,-0.0287,0.0199,-0.0223,0.0162,-0.0027,-0.0016,-0.0046,-0.0067,-0.0059,0.0021,-0.0039,-0.0017,0.0119,0.0038,-0.0038,-0.0006,-0.0019,-0.0092,0.0012,-0.0057,-0.0013,-0.0012,0.0074
    G25 Neolithic model

    "sample": "kamil154",
    "distance": 2.3391,
    "Ganj_Dareh_N": 43.5,
    "Barcin_N": 17.5,
    "Simulated_AASI_NW_by_DMXX": 15.5,
    "Karelia_HG": 9,
    "Tyumen_HG": 5,
    "LAO_Hoabinhian": 4,
    "LapaDoSanto_9600BP": 3,
    "GEO_CHG": 2.5

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