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Thread: The genetic prehistory of the Greater Caucasus[preprint Harvard/Jena]

  1. #1121
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    Quote Originally Posted by Michalis Moriopoulos View Post
    "Yamnaya herders from western Asia, four of whom are buried in this grave, started mating with European farmers hundreds of years before launching a major migration into Europe, new DNA evidence indicates."

    Ugh, the Urals and the Caucasus are categorically the standard boundaries between Asia and Europe in modern times, so I don't understand why some science journalists have such a hard time grasping that the Pontic-Caspian Steppe is in Eastern Europe. I can only assume they think it's a more sensational headline. What happened in West Eurasia is already sensational enough without having to get the geography wrong.

    Good point....I posted it for the genetic findings, I didn't get the geographical inaccuracy.

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    Quote Originally Posted by Generalissimo View Post
    Usual garbage from Science News.
    But Anthony’s answer to the « tracer dye theory » is worth the read.

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    Yes, though I wonder how he squares this in his mind with that he said the opposite (cultural expansion via chiefs, no marriage really required) in his major work back when he thought that there was no demic signal of expansion from the Pontic-Caspian steppe in the 2000s.

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    Quote Originally Posted by Eterne View Post
    Yes, though I wonder how he squares this in his mind with that he said the opposite (cultural expansion via chiefs, no marriage really required) in his major work back when he thought that there was no demic signal of expansion from the Pontic-Caspian steppe in the 2000s.
    I think it is quite clear.

    The only interesting part of the paper:

    "Evidence of scant mating between hill-dwelling Maykop farmers and steppe-dwelling Yamnaya herders is “a big surprise,” says archaeologist Volker Heyd of the University of Helsinki, who did not participate in the study. Eastern Europe’s Globular Amphora Culture looks like a good candidate for having mated to some extent with Yamnaya people more than 5,000 years ago, Heyd adds.
    Migrations of some Maykop into Yamnaya territory, accompanied by the transfer of knowledge and language, still happened, Wang’s team suspects. Occasional migrations north through the Caucasus to Yamnaya grasslands fits a scenario in which the ancient homeland of Indo-European language lay among Anatolian farmers, the researchers speculate. If they’re right, they have resolved one of the thorniest issues in the study of languages. But the long-debated origins of Indo-European tongues remain uncertain.

    Maykop people excavated in Yamnaya territory came from a small, isolated population that shows no signs of herder ancestry, contends archaeologist David Anthony of Hartwick College in Oneonta, N.Y. “It just emphasizes that Maykop people chose not to mate with Yamnaya or pre-Yamnaya people.”

    Without regular marriages across the two cultures, Maykop people would not have transferred their language to the Yamnaya, Anthony contends. He considers it likely that Indo-European precursor languages originated among steppe herders."
    Last edited by ffoucart; 02-11-2019 at 12:44 AM.

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  9. #1126
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    For info. I've analysed the BAMs of 4 individuals from Wang: the two Steppe_Eneolithic (PG2001 & PG2004) and two from the Steppe_Maykop (SA6001 &SA6004). As I'm far from being an authorized BAM analyser I cannot guarantee the reliability of the resulting data (reason why I wrote "for info"). That said I confirm with these data the existence of an obvious affinity between the Steppe_Majkop and the UP-Central_Siberia / Amerindian populations:

    D(Steppe_Eneo, Majkop / Kennewick, Mbuti) = -0.0347 Z= -5.824 199707 SNPs

    I tried to duplicate the Wang's qpAdm model for Steppe_Majkop in term of a 3-way (Steppe_Eneo+AG3+Kennewick). Til now the best I got is for SA6001. I'm far from being satisfied, because of the rather low number of SNPs involved, but here it is:

    left pops:
    Maykop6001
    Steppe_EneolithicW
    AfontovaGora3
    Kennewick

    right pops:
    Mota
    Ust_Ishim
    Kostenki14
    MA1
    WHG
    EHG
    CHG
    Iron_Gates_HG
    Iran_N
    West_Siberia_N
    Barcin
    LBK_Austria
    Levant_N
    Clovis

    numsnps used: 58184

    best coefficients: 0.611 0.337 0.051
    Jackknife mean: 0.611084472 0.337255224 0.051660304
    std. errors: 0.040 0.042 0.030

    fixed pat wt dof chisq tail prob
    000 0 11 9.792 0.549198 0.611 0.337 0.051
    001 1 12 12.727 0.389158 0.633 0.367 0.000
    010 1 12 74.716 4.15677e-11 0.856 -0.000 0.144
    100 1 12 178.893 0 0.000 0.887 0.113
    011 2 13 97.433 5.206e-15 1.000 0.000 -0.000
    101 2 13 185.837 0 0.000 1.000 -0.000
    110 2 13 456.992 0 0.000 0.000 1.000
    best pat: 000 0.549198 - -
    best pat: 001 0.389158 chi(nested): 2.936 p-value for nested model: 0.086649
    best pat: 011 5.206e-15 chi(nested): 84.706 p-value for nested model: 3.46278e-20
    En North alom, de North venom
    En North fum naiz, en North manom

    (Roman de Rou, Wace, 1160-1170)

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  11. #1127
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    Nice work, many thanks.

    SA6001 looks like the "top" scorer for ANE / Native American related components based on their ADMIXTURE, so that gives maybe a good "ceiling" for the group.

    It is reassuring that you are getting such a fairly similar fit with a fairly different set of outgroups with more specificity to PGM West Eurasia, and with a single sample rather than the four sample composite. The same main trends are probably driven by the same main outgroups.

    Any possibility of loading West_Siberia_N into the left, rather than right? Also testing with Dali_EBA, Sarazm_Eneo and Botai as candidates. For Dali_EBA and Sarazm in particular there was some suggestion that the Steppe_Eneolithic samples were not actually representing the ancestry of Steppe_Maykop and there was more Central Asian derivation to them (possibly this was based on mtdna, can't remember).

    These are samples Narasimhan (and Damgaard) had, which Wang did not. Getting a feel of whether Botai or West_Siberia_N is closer would be cool as well, though they're close enough that it may only be suggestive, and neither is necessarily as likely an admixing population compared to others (Tersek?).

    Tianyuan and/or ancient East Eurasian samples at Shamanka_N / Lokomotiv_N might be useful in the pright? As ancient samples (so not affected by ancient/modern biases) and closer to an minimally unadmixed ancient East Eurasian set. If you have any of these in your set.

    Also, wondering do PG2001 & PG2004 look identical or different on stats like D(EHG,CHG;X,Outgroup) or D(EHG,CHG;X,Samara_Eneolithic)? The PCA plots suggest that one of the three Steppe_Eneolithic / Piedmont_Eneolithic is a bit more "north" shifted than the others, and ADMIXTURE plots suggest PG2004 is the candidate for this.

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  13. #1128
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    On another note on added elements to the published paper over pre-print, I noticed that their published Fig. 4, based on Supplementary Table 14 (fitting Steppe samples as EHG, CHG, WHG and Anatolian), features a fit for Eneolithic_Steppe and its p-value (which is not in Supplementary Table 14 for whatever reason).

    It seems like Eneolithic_Steppe actually seems to marginally fail to reach the p>0.05 level, as EHG+CHG, with value of only 0.0302.

    This could well just be qpAdm behaving kookily again, but that seems a bit surprising (since EHG+CHG cline looks good in most respects), and I'm not sure why their reviewers didn't question that. The only part of the paper that seems to formally fit Eneolithic_Steppe is actually their qpGraph* with some fairly limited outgroups, and they don't seem to have constructed a high p value model for Eneolithic_Steppe in qpAdm with lots of outgroups.



    *"Our fitted qpGraph model recapitulates the genetic separation between the Caucasus and Steppe groups with the Eneolithic steppe individuals deriving more than 60% of ancestry from EHG and the remainder from a CHG-related basal lineage, whereas the Maykop group received about 86.4% from CHG, 9.6% Anatolian farming related ancestry, and 4% from EHG. The Yamnaya individuals from the Caucasus derived the majority of their ancestry from Eneolithic steppe individuals, but also received about 16% from Globular Amphora-related farmers"

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  15. #1129
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    Quote Originally Posted by Eterne View Post
    On another note on added elements to the published paper over pre-print, I noticed that their published Fig. 4, based on Supplementary Table 14 (fitting Steppe samples as EHG, CHG, WHG and Anatolian), features a fit for Eneolithic_Steppe and its p-value (which is not in Supplementary Table 14 for whatever reason).

    It seems like Eneolithic_Steppe actually seems to marginally fail to reach the p>0.05 level, as EHG+CHG, with value of only 0.0302.

    This could well just be qpAdm behaving kookily again, but that seems a bit surprising (since EHG+CHG cline looks good in most respects), and I'm not sure why their reviewers didn't question that. The only part of the paper that seems to formally fit Eneolithic_Steppe is actually their qpGraph* with some fairly limited outgroups, and they don't seem to have constructed a high p value model for Eneolithic_Steppe in qpAdm with lots of outgroups.



    *"Our fitted qpGraph model recapitulates the genetic separation between the Caucasus and Steppe groups with the Eneolithic steppe individuals deriving more than 60% of ancestry from EHG and the remainder from a CHG-related basal lineage, whereas the Maykop group received about 86.4% from CHG, 9.6% Anatolian farming related ancestry, and 4% from EHG. The Yamnaya individuals from the Caucasus derived the majority of their ancestry from Eneolithic steppe individuals, but also received about 16% from Globular Amphora-related farmers"
    My impression is that they didn’t work too much on Eneolithic Steppe as their purpose was to find an admixture event between Maykop and Yamnaya. And their paper is about the Caucasus, not the Steppe.

    I noted also they didn’t use qpWave on Steppe Eneolithic.

    Also, since the CHG-like admixture found in Steppe Eneolithic is not CHG proper (if we follow them, it’s more basal), they could have think it was worth a proper study.

  16. #1130
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    What else is it supposed to be about? Maikop is the Caucasus.

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