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Thread: Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria[

  1. #471
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    Quote Originally Posted by Kale View Post
    Dang I keep trying a bunch of different starter graphs to test potential deep structure, but a lot of the time it reverts to this. It's super clean but man that is a crazy drift edge for the para-BachoKiro pop.
     

    digraph G {
    size = "7.5,10";
    Root -> South_Africa_2000BPSG [ label = "21" ];
    Root -> OOA1 [ label = "21" ];
    OOA1 -> MotaSG [ label = "140" ];
    OOA1 -> E0 [ label = "33" ];
    E0 -> ZlatyKunSG [ label = "144" ];
    E0 -> E1 [ label = "1" ];
    E1 -> E3_multi1_2x [ label = "2" ];
    E1 -> E1d [ label = "32" ];
    E3_multi1_2 -> E3_multi1_2xy [ label = "11" ];
    E6 -> Tianyuan [ label = "132" ];
    E6 -> E7_g [ label = "9" ];
    W2 -> admixc [ style=dotted, label = "84%" ];
    W2 -> admixj [ style=dotted, label = "65%" ];
    W3 -> Kostenki14 [ label = "131" ];
    W3 -> SunghirSG [ label = "11" ];
    ANE -> Yana_UPSG [ label = "10" ];
    ANE -> MA1SG [ label = "139" ];
    E7_g -> OngeDG_s [ label = "1" ];
    E3_multi1_2x -> E1r [ label = "0" ];
    E3_multi1_2xy -> W2 [ label = "1" ];
    E3_multi1_2xy -> W3 [ label = "3" ];
    OngeDG_s -> admixe [ style=dotted, label = "36%" ];
    E1d -> BachoKiro_IUP [ label = "39" ];
    E1d -> E1dj [ label = "103" ];
    admixw -> E7_gx [ label = "5" ];
    admixe -> OngeDG [ label = "33" ];
    E1dj -> admixw [ style=dotted, label = "15%" ];
    E1dj -> admixc [ style=dotted, label = "16%" ];
    admixc -> GoyetQ116_1 [ label = "133" ];
    E7_gx -> E6 [ label = "3" ];
    E7_gx -> admixj [ style=dotted, label = "35%" ];
    admixj -> ANE [ label = "3" ];
    OngeDG_s -> Japan_Jomon [ label = "44" ];
    E7_g -> PrimorskyKrai_Boisman_MN [ label = "22" ];
    E1r -> E3_multi1_2 [ label = "0" ];
    E3_multi1_2x -> admixw [ style=dotted, label = "85%" ];
    E3_multi1_2 -> Ust_IshimDG [ label = "4" ];
    E1r -> admixe [ style=dotted, label = "64%" ];
    }
    Would it make sense to add some archaics into your model?

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    I think it will just add unnecessary complexity, with archaics added I'd need a new root (which would have to be something deeper, e.g. chimp) and that causes sample quality issues to stick out more.
    With an African root it's pretty much like ignoring anything deeper in the phylogeny. I've run test graphs before with an African root including Australians (because of the Denisovan) and things still turn out normal if you throw in a compensatory near-root edge to account (it even figures out the right % doing this).

    EDIT: So I'm working manually now, looking to the individual F3 residuals to suggest tweaks.
    Started from scratch, it looks like the main residual I've been having is an unaccounted for affinity between East-Asians (PKB, Jomon, Mongolia_N) and Goyet.
    Last edited by Kale; 04-16-2021 at 06:35 PM.
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  5. #473
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    Quote Originally Posted by Kale View Post
    I think it will just add unnecessary complexity, with archaics added I'd need a new root (which would have to be something deeper, e.g. chimp) and that causes sample quality issues to stick out more.
    With an African root it's pretty much like ignoring anything deeper in the phylogeny. I've run test graphs before with an African root including Australians (because of the Denisovan) and things still turn out normal if you throw in a compensatory near-root edge to account (it even figures out the right % doing this).

    EDIT: So I'm working manually now, looking to the individual F3 residuals to suggest tweaks.
    Started from scratch, it looks like the main residual I've been having is an unaccounted for affinity between East-Asians (PKB, Jomon, Mongolia_N) and Goyet.
    Very interesting as always, but why did you place Mota post OOA? Does Mota have Eurasian ancestry?

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    Ignore the names of the nodes in that one, things got shuffled around when I was working automated and I didn't bother to rename them.

    Hmmm check this out. This is the most reasonable way I can currently think to accommodate the weird Goyet <> East Asian interaction. Some sort of para-Ust-Ishim branch.
    Goyet = para-Ust + BK
    East-Asian = Tianyuan + para-Ust
    Kostenki/Sunghir = 'West Eurasian' + para-Ust
    Quite a heavily bottlenecked lineage though, probably could be improved somehow.
    Can anyone think of some archaeological industry that could correspond to such a phenomenon?
     

    digraph G {
    size = "7.5,10";
    Root -> South_Africa_2000BPSG [ label = "13" ];
    Root -> X [ label = "13" ];
    X -> AEA [ label = "16" ];
    AEA -> MotaSG [ label = "140" ];
    AEA -> OOA [ label = "33" ];
    OOA -> OOA1 [ label = "3" ];
    OOA -> ZlatyKunSG [ label = "143" ];
    OOA1 -> pUST [ label = "1" ];
    pUST -> pUST1 [ label = "50" ];
    pUST1 -> pUST2 [ label = "52" ];
    pUST -> Ust_IshimDG [ label = "4" ];
    OOA1 -> IUP [ label = "5" ];
    IUP -> BK1 [ label = "18" ];
    BK2 -> BachoKiro_IUP [ label = "51" ];
    pGOY -> GoyetQ116_1 [ label = "83" ];
    IUP -> E1 [ label = "5" ];
    E1 -> E2 [ label = "1" ];
    E2 -> Tianyuan [ label = "130" ];
    E2 -> E3 [ label = "6" ];
    PKB -> PrimorskyKrai_Boisman_MN [ label = "25" ];
    W1 -> W2 [ label = "8" ];
    W2 -> W3 [ label = "5" ];
    W3 -> Kostenki14 [ label = "131" ];
    pSUN -> SunghirSG [ label = "11" ];
    pANE -> Yana_UPSG [ label = "13" ];
    pONG -> OngeDG [ label = "33" ];
    BK1 -> BK2 [ style=dotted, label = "96%" ];
    pUST2 -> pGOY [ style=dotted, label = "78%" ];
    E3 -> PKB [ style=dotted, label = "92%" ];
    pUST2 -> W1 [ style=dotted, label = "12%" ];
    W3 -> pSUN [ style=dotted, label = "98%" ];
    W2 -> pANE [ style=dotted, label = "75%" ];
    E3 -> pONG [ style=dotted, label = "41%" ];
    X -> BK2 [ style=dotted, label = "4%" ];
    BK1 -> pGOY [ style=dotted, label = "22%" ];
    pUST1 -> PKB [ style=dotted, label = "8%" ];
    OOA1 -> W1 [ style=dotted, label = "88%" ];
    X -> pSUN [ style=dotted, label = "2%" ];
    E1 -> pANE [ style=dotted, label = "25%" ];
    pUST -> pONG [ style=dotted, label = "59%" ];
    }


    EDIT: Here's another with BK1653 added, tones down the bottleneck on the para-Ust lineage quite a bit and I'm liking the proportions better too.
    Might need a slight rework around the Onge area though, Yana+MA1 not quite close enough, Goyet a bit too close (only Z 1.4 residuals each way but I think it's worth a shot).
     

    digraph G {
    size = "7.5,10";
    Root -> South_Africa_2000BPSG [ label = "14" ];
    Root -> X [ label = "14" ];
    X -> AEA [ label = "16" ];
    AEA -> MotaSG [ label = "140" ];
    AEA -> OOA [ label = "33" ];
    OOA -> OOA1 [ label = "2" ];
    OOA -> ZlatyKunSG [ label = "143" ];
    OOA1 -> pUST [ label = "2" ];
    pUST -> pUST1 [ label = "35" ];
    pUST1 -> pUST2 [ label = "17" ];
    pUST -> Ust_IshimDG [ label = "3" ];
    OOA1 -> IUP [ label = "5" ];
    IUP -> BK1 [ label = "6" ];
    BK2 -> BachoKiro_IUP [ label = "62" ];
    pGOY -> pGOY2 [ label = "0" ];
    pGOY2 -> GoyetQ116_1 [ label = "130" ];
    BKG2 -> BachoKiro_Gravettian [ label = "137" ];
    IUP -> E1 [ label = "6" ];
    E1 -> E2 [ label = "1" ];
    E2 -> Tianyuan [ label = "130" ];
    E2 -> E3 [ label = "7" ];
    PKB -> PrimorskyKrai_Boisman_MN [ label = "25" ];
    W1 -> W2 [ label = "2" ];
    W2 -> W3 [ label = "5" ];
    W3 -> Kostenki14 [ label = "131" ];
    pSUN -> SunghirSG [ label = "11" ];
    pANE -> ANE [ label = "3" ];
    ANE -> MA1SG [ label = "139" ];
    ANE -> Yana_UPSG [ label = "10" ];
    pONG -> OngeDG [ label = "33" ];
    BK1 -> BK2 [ style=dotted, label = "96%" ];
    pUST2 -> pGOY [ style=dotted, label = "48%" ];
    pGOY2 -> BKG1 [ style=dotted, label = "74%" ];
    BKG1 -> BKG2 [ style=dotted, label = "97%" ];
    E3 -> PKB [ style=dotted, label = "92%" ];
    pUST2 -> W1 [ style=dotted, label = "40%" ];
    W3 -> pSUN [ style=dotted, label = "98%" ];
    W2 -> pANE [ style=dotted, label = "75%" ];
    E3 -> pONG [ style=dotted, label = "40%" ];
    X -> BK2 [ style=dotted, label = "4%" ];
    BK1 -> pGOY [ style=dotted, label = "52%" ];
    W3 -> BKG1 [ style=dotted, label = "26%" ];
    X -> BKG2 [ style=dotted, label = "3%" ];
    pUST1 -> PKB [ style=dotted, label = "8%" ];
    OOA1 -> W1 [ style=dotted, label = "60%" ];
    X -> pSUN [ style=dotted, label = "2%" ];
    E1 -> pANE [ style=dotted, label = "25%" ];
    pUST -> pONG [ style=dotted, label = "60%" ];
    }


    EDIT: Tried to add Gravettians, it imploded. Not sure why.
    Last edited by Kale; 04-17-2021 at 08:00 PM.
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  8. #475
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    Quote Originally Posted by Kale View Post
    Ignore the names of the nodes in that one, things got shuffled around when I was working automated and I didn't bother to rename them.

    Hmmm check this out. This is the most reasonable way I can currently think to accommodate the weird Goyet <> East Asian interaction. Some sort of para-Ust-Ishim branch.
    Goyet = para-Ust + BK
    East-Asian = Tianyuan + para-Ust
    Kostenki/Sunghir = 'West Eurasian' + para-Ust
    Quite a heavily bottlenecked lineage though, probably could be improved somehow.
    Can anyone think of some archaeological industry that could correspond to such a phenomenon?
     

    digraph G {
    size = "7.5,10";
    Root -> South_Africa_2000BPSG [ label = "13" ];
    Root -> X [ label = "13" ];
    X -> AEA [ label = "16" ];
    AEA -> MotaSG [ label = "140" ];
    AEA -> OOA [ label = "33" ];
    OOA -> OOA1 [ label = "3" ];
    OOA -> ZlatyKunSG [ label = "143" ];
    OOA1 -> pUST [ label = "1" ];
    pUST -> pUST1 [ label = "50" ];
    pUST1 -> pUST2 [ label = "52" ];
    pUST -> Ust_IshimDG [ label = "4" ];
    OOA1 -> IUP [ label = "5" ];
    IUP -> BK1 [ label = "18" ];
    BK2 -> BachoKiro_IUP [ label = "51" ];
    pGOY -> GoyetQ116_1 [ label = "83" ];
    IUP -> E1 [ label = "5" ];
    E1 -> E2 [ label = "1" ];
    E2 -> Tianyuan [ label = "130" ];
    E2 -> E3 [ label = "6" ];
    PKB -> PrimorskyKrai_Boisman_MN [ label = "25" ];
    W1 -> W2 [ label = "8" ];
    W2 -> W3 [ label = "5" ];
    W3 -> Kostenki14 [ label = "131" ];
    pSUN -> SunghirSG [ label = "11" ];
    pANE -> Yana_UPSG [ label = "13" ];
    pONG -> OngeDG [ label = "33" ];
    BK1 -> BK2 [ style=dotted, label = "96%" ];
    pUST2 -> pGOY [ style=dotted, label = "78%" ];
    E3 -> PKB [ style=dotted, label = "92%" ];
    pUST2 -> W1 [ style=dotted, label = "12%" ];
    W3 -> pSUN [ style=dotted, label = "98%" ];
    W2 -> pANE [ style=dotted, label = "75%" ];
    E3 -> pONG [ style=dotted, label = "41%" ];
    X -> BK2 [ style=dotted, label = "4%" ];
    BK1 -> pGOY [ style=dotted, label = "22%" ];
    pUST1 -> PKB [ style=dotted, label = "8%" ];
    OOA1 -> W1 [ style=dotted, label = "88%" ];
    X -> pSUN [ style=dotted, label = "2%" ];
    E1 -> pANE [ style=dotted, label = "25%" ];
    pUST -> pONG [ style=dotted, label = "59%" ];
    }


    EDIT: Here's another with BK1653 added, tones down the bottleneck on the para-Ust lineage quite a bit and I'm liking the proportions better too.
    Might need a slight rework around the Onge area though, Yana+MA1 not quite close enough, Goyet a bit too close (only Z 1.4 residuals each way but I think it's worth a shot).
     

    digraph G {
    size = "7.5,10";
    Root -> South_Africa_2000BPSG [ label = "14" ];
    Root -> X [ label = "14" ];
    X -> AEA [ label = "16" ];
    AEA -> MotaSG [ label = "140" ];
    AEA -> OOA [ label = "33" ];
    OOA -> OOA1 [ label = "2" ];
    OOA -> ZlatyKunSG [ label = "143" ];
    OOA1 -> pUST [ label = "2" ];
    pUST -> pUST1 [ label = "35" ];
    pUST1 -> pUST2 [ label = "17" ];
    pUST -> Ust_IshimDG [ label = "3" ];
    OOA1 -> IUP [ label = "5" ];
    IUP -> BK1 [ label = "6" ];
    BK2 -> BachoKiro_IUP [ label = "62" ];
    pGOY -> pGOY2 [ label = "0" ];
    pGOY2 -> GoyetQ116_1 [ label = "130" ];
    BKG2 -> BachoKiro_Gravettian [ label = "137" ];
    IUP -> E1 [ label = "6" ];
    E1 -> E2 [ label = "1" ];
    E2 -> Tianyuan [ label = "130" ];
    E2 -> E3 [ label = "7" ];
    PKB -> PrimorskyKrai_Boisman_MN [ label = "25" ];
    W1 -> W2 [ label = "2" ];
    W2 -> W3 [ label = "5" ];
    W3 -> Kostenki14 [ label = "131" ];
    pSUN -> SunghirSG [ label = "11" ];
    pANE -> ANE [ label = "3" ];
    ANE -> MA1SG [ label = "139" ];
    ANE -> Yana_UPSG [ label = "10" ];
    pONG -> OngeDG [ label = "33" ];
    BK1 -> BK2 [ style=dotted, label = "96%" ];
    pUST2 -> pGOY [ style=dotted, label = "48%" ];
    pGOY2 -> BKG1 [ style=dotted, label = "74%" ];
    BKG1 -> BKG2 [ style=dotted, label = "97%" ];
    E3 -> PKB [ style=dotted, label = "92%" ];
    pUST2 -> W1 [ style=dotted, label = "40%" ];
    W3 -> pSUN [ style=dotted, label = "98%" ];
    W2 -> pANE [ style=dotted, label = "75%" ];
    E3 -> pONG [ style=dotted, label = "40%" ];
    X -> BK2 [ style=dotted, label = "4%" ];
    BK1 -> pGOY [ style=dotted, label = "52%" ];
    W3 -> BKG1 [ style=dotted, label = "26%" ];
    X -> BKG2 [ style=dotted, label = "3%" ];
    pUST1 -> PKB [ style=dotted, label = "8%" ];
    OOA1 -> W1 [ style=dotted, label = "60%" ];
    X -> pSUN [ style=dotted, label = "2%" ];
    E1 -> pANE [ style=dotted, label = "25%" ];
    pUST -> pONG [ style=dotted, label = "60%" ];
    }


    EDIT: Tried to add Gravettians, it imploded. Not sure why.
    What was the worst Z-score?

  9. #476
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    Would anyone be able to share a pared-down PLINK or ANCESTRYMAP dataset with Zlaty Kun, Bacho Kiro, the other Paleolithic Eurasians, a few high-quality ancient Amerinds like Kennewick, BRA_Sumiduoro, Antilles_Archaic, a few ancient Africans (SAfrica_2000, Mota, Taforalt etc) and Neanderthal?

    I have downloaded the Zlaty Kun fastq files and I see what looks like ancestrymap and PLINK files but I'm a dumbass and cannot figure out how to merge the ANCESTRYMAP files with any of my existing ANCESTRYMAP datasets (one of which contains Bacho Kiro)

    Is there a guide on the forum anywhere explaining how to merge two datasets?

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    Quote Originally Posted by K33 View Post
    Would anyone be able to share a pared-down PLINK or ANCESTRYMAP dataset with Zlaty Kun, Bacho Kiro, the other Paleolithic Eurasians, a few high-quality ancient Amerinds like Kennewick, BRA_Sumiduoro, Antilles_Archaic, a few ancient Africans (SAfrica_2000, Mota, Taforalt etc) and Neanderthal?

    I have downloaded the Zlaty Kun fastq files and I see what looks like ancestrymap and PLINK files but I'm a dumbass and cannot figure out how to merge the ANCESTRYMAP files with any of my existing ANCESTRYMAP datasets (one of which contains Bacho Kiro)

    Is there a guide on the forum anywhere explaining how to merge two datasets?
    You need to use convertf to convert those files to PACKEDANCESTRYMAP and then merge them using plink

    Plink --bfile "File" --bmerge "File2" --indiv-sort f "a combined .fam file" --make-bed --out "yourmergedfile"

    If you have any samples with U as their sex you also need to include --allow-no-sex

    Then you just need to run convertf again to turn it in to a PACKEDANCESTRYMAP file.

    You can then combine the .ind files from the two datasets in the order you combined the .fam files and replace the generated .ind file for your merged dataset.

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    Quote Originally Posted by Mnemonics View Post
    You need to use convertf to convert those files to PACKEDANCESTRYMAP and then merge them using plink

    Plink --bfile "File" --bmerge "File2" --indiv-sort f "a combined .fam file" --make-bed --out "yourmergedfile"

    If you have any samples with U as their sex you also need to include --allow-no-sex

    Then you just need to run convertf again to turn it in to a PACKEDANCESTRYMAP file.

    You can then combine the .ind files from the two datasets in the order you combined the .fam files and replace the generated .ind file for your merged dataset.
    OK so it looks like convertf is part of eigensoft...

    I downloaded eigensoft and after unzipping there is a CONVERTF folder inside... do you run this program out of the R terminal? (I'm using Windows 10, 64 bit)



    My R program is installed on my C:/ drive... the eigensoft package is under D:/EIG-master, Zlaty Kun dataset is under D:/zlaty_kun, my existing (ancestrymap) dataset I want to merge zlaty kun with is D:/Dataset2.

    So I just go into R and type:

    Plink --bfile "D:/zlaty_kun" --bmerge "D:/Dataset2" --indiv-sort f "a combined .fam file" --make-bed --out "yourmergedfile"


    > R says "Error: unexpected string constant in "Plink "D:/zlaty_kun"

    ... what am I missing...

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    You need to compile the Plink and Eigensoft packages first
    Last edited by brauthaz; 04-19-2021 at 03:13 AM.

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    Quote Originally Posted by K33 View Post
    OK so it looks like convertf is part of eigensoft...

    I downloaded eigensoft and after unzipping there is a CONVERTF folder inside... do you run this program out of the R terminal? (I'm using Windows 10, 64 bit)



    My R program is installed on my C:/ drive... the eigensoft package is under D:/EIG-master, Zlaty Kun dataset is under D:/zlaty_kun, my existing (ancestrymap) dataset I want to merge zlaty kun with is D:/Dataset2.

    So I just go into R and type:

    Plink --bfile "D:/zlaty_kun" --bmerge "D:/Dataset2" --indiv-sort f "a combined .fam file" --make-bed --out "yourmergedfile"


    > R says "Error: unexpected string constant in "Plink "D:/zlaty_kun"

    ... what am I missing...
    This is done from the command-line/ outside of R.

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