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Thread: Dstats and qpAdm with EHG, Samara Eneolithic, and Yamnaya

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    Dstats and qpAdm with EHG, Samara Eneolithic, and Yamnaya

    All relevant Dstats for this conversation can be found here...

    https://drive.google.com/file/d/0B96...ew?usp=sharing

    Here are some interesting ones.

    Karelia HG I0061 appears ENA admixed, to the exclusion of Loschbour and MA1. Motala even appears slightly shifted to ENA. The significance is slightly lower with MA1.

    result: Primate_Gorilla Atayal Loschbour MA1 0.0023 0.356 17489 17410 348143
    result: Primate_Gorilla Atayal Loschbour Motala_HG 0.0059 1.212 20212 19977 451363
    result: Primate_Gorilla Atayal Loschbour Karelia_HG1 0.0155 2.616 21451 20795 442556
    result: Primate_Gorilla Atayal Karelia_HG1 MA1 -0.0126 -1.994 17030 17463 362579
    result: Primate_Gorilla Atayal Loschbour Samara_HG 0.0127 1.849 11173 10893 234692
    result: Primate_Gorilla Atayal Samara_HG MA1 -0.0048 -0.632 8936 9022 192216
    result: Primate_Gorilla Atayal Karelia_HG1 Samara_HG -0.0045 -0.665 11285 11388 255789
    result: Primate_Gorilla Han Loschbour MA1 -0.0001 -0.020 17429 17433 348143
    result: Primate_Gorilla Han Loschbour Motala_HG 0.0034 0.754 20168 20032 451363
    result: Primate_Gorilla Han Loschbour Karelia_HG1 0.0134 2.430 21399 20835 442556
    result: Primate_Gorilla Han Karelia_HG1 MA1 -0.0135 -2.325 17016 17481 362579
    result: Primate_Gorilla Han Loschbour Samara_HG 0.0091 1.405 11121 10920 234692
    result: Primate_Gorilla Han MA1 Samara_HG 0.0030 0.411 9012 8958 192216
    result: Primate_Gorilla Han Karelia_HG1 Samara_HG -0.0048 -0.747 11305 11414 255789

    Some surprises going from Samara HG to Samara Eneolithic. The shift no closer to Kotias than Anatolian Neolithic! Also, there is no difference between Georgians and Armenians, compared to Kotias. The admixing population doesn't seem very CHG specific, but something intermediary between modern Caucasus and CHG. Whether this means a mix of Balkan and CHG will have to be resolved later. Another cause, could be WHG and CHG admixture going into Samara Eneolithic, causing it to look closer to Anatolians and Georgians than it really is.

    result: Samara_HG Samara_Eneolithic Loschbour MA1 0.0031 0.316 6199 6160 143496
    result: Samara_HG Samara_Eneolithic Loschbour Motala_HG -0.0125 -1.723 7345 7531 191030
    result: Samara_HG Samara_Eneolithic Loschbour Kotias 0.0171 1.987 7142 6901 169359
    result: Samara_HG Samara_Eneolithic Loschbour Georgian 0.0202 3.037 8315 7986 192324
    result: Samara_HG Samara_Eneolithic Loschbour Armenian 0.0210 3.170 8310 7968 192324
    result: Samara_HG Samara_Eneolithic Anatolia_Neolithic1 Kotias -0.0001 -0.015 7884 7886 196327
    result: Samara_HG Samara_Eneolithic Georgian Kotias -0.0030 -0.549 7670 7716 196336
    result: Samara_HG Samara_Eneolithic Armenian Kotias -0.0032 -0.581 7772 7822 196336

    Now, going from Samara Eneolithic to Yamnaya, is a different story. While it is not very significant, there is a clear shift away from Anatolians and Georgians, towards Kotias. This could show the influence of Maykop in the Bronze Age.

    result: Samara_Eneolithic Yamnaya_Samara1 Anatolia_Neolithic1 Kotias 0.0121 2.830 15870 15491 359534
    result: Samara_Eneolithic Yamnaya_Samara1 Anatolia_Neolithic1 Satsurblia 0.0052 1.000 12865 12733 291254
    result: Samara_Eneolithic Yamnaya_Samara1 Georgian Kotias 0.0090 2.347 15452 15177 359633
    result: Samara_Eneolithic Yamnaya_Samara1 Georgian Satsurblia 0.0029 0.615 12613 12539 291354
    result: Samara_Eneolithic Yamnaya_Samara1 Armenian Kotias 0.0087 2.259 15643 15374 359633
    result: Samara_Eneolithic Yamnaya_Samara1 Armenian Satsurblia 0.0033 0.691 12684 12600 291354
    result: Samara_Eneolithic Yamnaya_Samara1 LBK_EN1 Kotias 0.0158 3.589 15918 15422 358974
    result: Samara_Eneolithic Yamnaya_Samara1 LBK_EN1 Satsurblia 0.0111 2.085 12977 12692 290752
    result: Samara_Eneolithic Yamnaya_Samara1 Loschbour Kotias 0.0406 6.730 14340 13222 308939
    result: Samara_Eneolithic Yamnaya_Samara1 MA1 Kotias 0.0467 7.571 12337 11237 261327
    result: Samara_Eneolithic Yamnaya_Kalmykia1 Anatolia_Neolithic1 Kotias 0.0129 3.242 15682 15284 354363
    result: Samara_Eneolithic Yamnaya_Kalmykia1 Loschbour Kotias 0.0468 8.632 14267 12992 304798
    result: Samara_Eneolithic Yamnaya_Kalmykia1 MA1 Kotias 0.0413 7.040 12163 11197 257895
    result: Samara_Eneolithic Yamnaya_Kalmykia1 Georgian Kotias 0.0079 2.192 15269 15028 354496
    result: Samara_Eneolithic Yamnaya_Kalmykia1 Georgian Satsurblia 0.0073 1.532 12445 12264 286337
    result: Samara_Eneolithic Yamnaya_Kalmykia1 Armenian Kotias 0.0092 2.513 15467 15185 354496
    result: Samara_Eneolithic Yamnaya_Kalmykia1 Armenian Satsurblia 0.0098 2.039 12555 12311 286337
    result: Samara_Eneolithic Yamnaya_Kalmykia1 LBK_EN1 Kotias 0.0162 3.943 15758 15256 353781
    result: Samara_Eneolithic Yamnaya_Kalmykia1 LBK_EN1 Satsurblia 0.0168 3.175 12830 12405 285677

    Another thing that I am working on involves qpAdm, as well as figuring other ways to see how Samara Eneolithic really relates to Yamnaya. What I am wondering, if this excess WHG that increases the fit is caused by the lack of ENA in the EHG that created Yamnaya. The reason I say this, is the irrelevant branches of R1b and R1a found there and in the HGs. Also, when fixing MA1 as a component, the ENA in EHG does not show up in Yamnaya either. My thinking is that we will find L23 within Sredny Stog, with the split of Z2103 and L51 occurring there. This place, being the real home of IE, and the possibility that some parts of Khavalynsk may have material culture related to those in the west, but may not be involved in the formation and spreading of IE, only to be replaced by cousins to the west.

    Feel free to drop in your own stats and stat requests!

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    Chad, v interesting phenomena indeed! But most of these stats are confounded in one way or another. To prove that the results are really what they seem to imply, we need to exclude other possibilities.

    Quote Originally Posted by Chad Rohlfsen View Post

    Karelia HG I0061 appears ENA admixed, to the exclusion of Loschbour and MA1. Motala even appears slightly shifted to ENA. The significance is slightly lower with MA1.

    result: Primate_Gorilla Atayal Loschbour MA1 0.0023 0.356 17489 17410 348143
    result: Primate_Gorilla Atayal Loschbour Motala_HG 0.0059 1.212 20212 19977 451363
    result: Primate_Gorilla Atayal Loschbour Karelia_HG1 0.0155 2.616 21451 20795 442556
    result: Primate_Gorilla Atayal Karelia_HG1 MA1 -0.0126 -1.994 17030 17463 362579
    result: Primate_Gorilla Atayal Loschbour Samara_HG 0.0127 1.849 11173 10893 234692
    result: Primate_Gorilla Atayal Samara_HG MA1 -0.0048 -0.632 8936 9022 192216
    result: Primate_Gorilla Atayal Karelia_HG1 Samara_HG -0.0045 -0.665 11285 11388 255789
    result: Primate_Gorilla Han Loschbour MA1 -0.0001 -0.020 17429 17433 348143
    result: Primate_Gorilla Han Loschbour Motala_HG 0.0034 0.754 20168 20032 451363
    result: Primate_Gorilla Han Loschbour Karelia_HG1 0.0134 2.430 21399 20835 442556
    result: Primate_Gorilla Han Karelia_HG1 MA1 -0.0135 -2.325 17016 17481 362579
    result: Primate_Gorilla Han Loschbour Samara_HG 0.0091 1.405 11121 10920 234692
    result: Primate_Gorilla Han MA1 Samara_HG 0.0030 0.411 9012 8958 192216
    result: Primate_Gorilla Han Karelia_HG1 Samara_HG -0.0048 -0.747 11305 11414 255789
    As is usual, one has to look at the number of markers as well. The larger the number of markers, the stronger the signal of EHG<--->ENA, so, once the stats with ~10 000 markers are bumped up to the largest ones with 400 000 markers most of the stats will be highly significant it seems.

    These stats imply (Han, Atayal)<--->(Karelia, Samara, Motala) to the exclusion of MA-1 and Loschbour, but this can either be from (Han, Atayal)---->(EHG, SHG) or (Han, Atayal)<----(EHG, SHG), or both. To prove it either way, we need

    Primate_Gorilla Samara_HG Atayal Onge
    Primate_Gorilla Karelia_HG Atayal Onge
    Primate_Gorilla Motala Atayal Onge
    Primate_Gorilla Loschbour Atayal Onge
    Primate_Gorilla MA-1 Atayal Onge

    And we also need to repeat the entire list you just posted previously with Onge instead of Han/Atayal. The significance of the stats may be much reduced, but if the directions and magnitudes are consistent, it implies that there is indeed (ENA)--->(EHG, SHG), while if everything falls back to insignificance with no consistency then instead its probably (EHG, SHG)--->(ENA).


    Quote Originally Posted by Chad Rohlfsen View Post
    Some surprises going from Samara HG to Samara Eneolithic. The shift no closer to Kotias than Anatolian Neolithic! Also, there is no difference between Georgians and Armenians, compared to Kotias. The admixing population doesn't seem very CHG specific, but something intermediary between modern Caucasus and CHG. Whether this means a mix of Balkan and CHG will have to be resolved later. Another cause, could be WHG and CHG admixture going into Samara Eneolithic, causing it to look closer to Anatolians and Georgians than it really is.

    result: Samara_HG Samara_Eneolithic Loschbour MA1 0.0031 0.316 6199 6160 143496
    result: Samara_HG Samara_Eneolithic Loschbour Motala_HG -0.0125 -1.723 7345 7531 191030
    result: Samara_HG Samara_Eneolithic Loschbour Kotias 0.0171 1.987 7142 6901 169359
    result: Samara_HG Samara_Eneolithic Loschbour Georgian 0.0202 3.037 8315 7986 192324
    result: Samara_HG Samara_Eneolithic Loschbour Armenian 0.0210 3.170 8310 7968 192324
    result: Samara_HG Samara_Eneolithic Anatolia_Neolithic1 Kotias -0.0001 -0.015 7884 7886 196327
    result: Samara_HG Samara_Eneolithic Georgian Kotias -0.0030 -0.549 7670 7716 196336
    result: Samara_HG Samara_Eneolithic Armenian Kotias -0.0032 -0.581 7772 7822 196336

    Now, going from Samara Eneolithic to Yamnaya, is a different story. While it is not very significant, there is a clear shift away from Anatolians and Georgians, towards Kotias. This could show the influence of Maykop in the Bronze Age.

    result: Samara_Eneolithic Yamnaya_Samara1 Anatolia_Neolithic1 Kotias 0.0121 2.830 15870 15491 359534
    result: Samara_Eneolithic Yamnaya_Samara1 Anatolia_Neolithic1 Satsurblia 0.0052 1.000 12865 12733 291254
    result: Samara_Eneolithic Yamnaya_Samara1 Georgian Kotias 0.0090 2.347 15452 15177 359633
    result: Samara_Eneolithic Yamnaya_Samara1 Georgian Satsurblia 0.0029 0.615 12613 12539 291354
    result: Samara_Eneolithic Yamnaya_Samara1 Armenian Kotias 0.0087 2.259 15643 15374 359633
    result: Samara_Eneolithic Yamnaya_Samara1 Armenian Satsurblia 0.0033 0.691 12684 12600 291354
    result: Samara_Eneolithic Yamnaya_Samara1 LBK_EN1 Kotias 0.0158 3.589 15918 15422 358974
    result: Samara_Eneolithic Yamnaya_Samara1 LBK_EN1 Satsurblia 0.0111 2.085 12977 12692 290752
    result: Samara_Eneolithic Yamnaya_Samara1 Loschbour Kotias 0.0406 6.730 14340 13222 308939
    result: Samara_Eneolithic Yamnaya_Samara1 MA1 Kotias 0.0467 7.571 12337 11237 261327
    result: Samara_Eneolithic Yamnaya_Kalmykia1 Anatolia_Neolithic1 Kotias 0.0129 3.242 15682 15284 354363
    result: Samara_Eneolithic Yamnaya_Kalmykia1 Loschbour Kotias 0.0468 8.632 14267 12992 304798
    result: Samara_Eneolithic Yamnaya_Kalmykia1 MA1 Kotias 0.0413 7.040 12163 11197 257895
    result: Samara_Eneolithic Yamnaya_Kalmykia1 Georgian Kotias 0.0079 2.192 15269 15028 354496
    result: Samara_Eneolithic Yamnaya_Kalmykia1 Georgian Satsurblia 0.0073 1.532 12445 12264 286337
    result: Samara_Eneolithic Yamnaya_Kalmykia1 Armenian Kotias 0.0092 2.513 15467 15185 354496
    result: Samara_Eneolithic Yamnaya_Kalmykia1 Armenian Satsurblia 0.0098 2.039 12555 12311 286337
    result: Samara_Eneolithic Yamnaya_Kalmykia1 LBK_EN1 Kotias 0.0162 3.943 15758 15256 353781
    result: Samara_Eneolithic Yamnaya_Kalmykia1 LBK_EN1 Satsurblia 0.0168 3.175 12830 12405 285677
    These stats are not confounded. Your case, that the input into the Eneolithic seems to be equidistant from CHG and EEF, seems well-founded.


    Quote Originally Posted by Chad Rohlfsen View Post
    Another thing that I am working on involves qpAdm, as well as figuring other ways to see how Samara Eneolithic really relates to Yamnaya. What I am wondering, if this excess WHG that increases the fit is caused by the lack of ENA in the EHG that created Yamnaya. The reason I say this, is the irrelevant branches of R1b and R1a found there and in the HGs. Also, when fixing MA1 as a component, the ENA in EHG does not show up in Yamnaya either. My thinking is that we will find L23 within Sredny Stog, with the split of Z2103 and L51 occurring there. This place, being the real home of IE, and the possibility that some parts of Khavalynsk may have material culture related to those in the west, but may not be involved in the formation and spreading of IE, only to be replaced by cousins to the west.
    Chad, one of the ways to do this is to add ENA as an admixing population into qpAdm, and look at the infeasible runs, whether or not 'negative ENA' comes up as a possible fit.

    I would like to see the admixture run where ENA appears in EHG and Samara but does not do so in Yamnaya. Can you post it here?

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    Yeah, I have a few qpAdm runs to share tomorrow. I think the stats will change, if we change the ENA pop. There is significant variation within ENA. If the admixing pop into EHG is closer to NE Asian, rather than SE Asian, the numbers change. Would you like me to post ENA variation first?

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    BTW, qpADM picks ENA into EHG.

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    Just a quick bit, before crashing out. MA1 plus WHG was infeasible. Adding ENA, was still infeasible. MA1 plus Han is okay, but a weak fit. The best fit was MA1, Han, and CHG. I'll have Dstats to compare it all as well.

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    ENA variation will be good, thanks!


    Chad, do you mean the qpAdm fits for EHG? CHG--->EHG?
    Huh.

    I do recommend you run the stats as well, if you have the time, so that the proofs are watertight.

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    Oh yeah. If there is EEF input into the Samara Eneolithic, it would explain a lot indeed. I have always been puzzled by how a HG population could make the leap straight into full-fledged pastoralism without going through a semi-sedentary stage at some point.

    There are many cultural innovations, such as notions of private property, tolerance for social stratification and economic inequality, an altered source of prestige among males, or a certain level of long-term orientation and tolerance for drudgery and repetition, which are virtually impossible for HG populations to adapt straight off the bat...

    If there is some degree of population movement, then some of this may be explained.

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    Quote Originally Posted by Chad Rohlfsen View Post

    Another thing that I am working on involves qpAdm, as well as figuring other ways to see how Samara Eneolithic really relates to Yamnaya. What I am wondering, if this excess WHG that increases the fit is caused by the lack of ENA in the EHG that created Yamnaya. The reason I say this, is the irrelevant branches of R1b and R1a found there and in the HGs. Also, when fixing MA1 as a component, the ENA in EHG does not show up in Yamnaya either. My thinking is that we will find L23 within Sredny Stog, with the split of Z2103 and L51 occurring there. This place, being the real home of IE, and the possibility that some parts of Khavalynsk may have material culture related to those in the west, but may not be involved in the formation and spreading of IE, only to be replaced by cousins to the west.

    Feel free to drop in your own stats and stat requests!
    Nice work Chad. All your results make sense within a grand scheme of what we might expect. Perhaps for the last result it could have something due to C-T input.

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    Chad, one last thing, can you include the following stats? Just to check on something I've seen...

    Chimp Mota Onge Syrian
    Chimp Mota Onge BedouinB
    Chimp Mota Onge Anatolia_Neolithic
    Chimp Mota Onge LBK_EN
    Chimp Mota Onge Kotias
    Chimp Mota Onge Pulliyar
    Chimp Mota Onge Paniya

    Chimp Mota Austroasiatic_Ho Syrian
    Chimp Mota Austroasiatic_Ho BedouinB
    Chimp Mota Austroasiatic_Ho Anatolia_Neolithic
    Chimp Mota Austroasiatic_Ho LBK_EN
    Chimp Mota Austroasiatic_Ho Kotias

    Chimp Mota Onge Han
    Chimp Mota Onge Atayal
    Chimp Mota Onge Japanese
    Chimp Mota Onge Oroqen
    Chimp Mota Onge Yakut
    Chimp Mota Onge Ket
    Chimp Mota Onge Karitiana
    Chimp Mota Austroasiatic_Ho Han
    Chimp Mota Austroasiatic_Ho Atayal
    Chimp Mota Austroasiatic_Ho Japanese
    Chimp Mota Austroasiatic_Ho Oroqen
    Chimp Mota Austroasiatic_Ho Yakut
    Chimp Mota Austroasiatic_Ho Ket
    Chimp Mota Austroasiatic_Ho Karitiana

    If you do not have Austroasiatic_Ho, any highly ASI population would do.

    Thanks!
    Last edited by Ryukendo; 01-07-2016 at 07:44 AM.

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    Quote Originally Posted by Ryukendo View Post
    And we also need to repeat the entire list you just posted previously with Onge instead of Han/Atayal. The significance of the stats may be much reduced, but if the directions and magnitudes are consistent, it implies that there is indeed (ENA)--->(EHG, SHG), while if everything falls back to insignificance with no consistency then instead its probably (EHG, SHG)--->(ENA).
    Chimp Karelia_HG Ami Onge -0.0164 -4.036 16194 16735 341554
    Chimp Karelia_HG Atayal Onge -0.0179 -4.221 16185 16774 341554
    Gorilla Karelia_HG Dai Onge -0.0162 -4.088 15043 15538 317554

    Chimp Samara_HG Ami Onge -0.0066 -1.430 9893 10023 206748
    Chimp Samara_HG Atayal Onge -0.0072 -1.489 9890 10034 206748

    Chimp MA1 Ami Onge -0.0032 -0.687 12074 12152 253297
    Chimp MA1 Atayal Onge -0.0009 -0.173 12126 12147 253297

    Looks like (ENA)--->(EHG, SHG) to me.
    Last edited by Kale; 01-07-2016 at 06:24 PM.

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