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Thread: drought of ancient DNA papers on prehistoric Europe/SW Asia

  1. #1271
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    Quote Originally Posted by TuaMan View Post
    I think the potential game changer for tropical or near-tropical locations will be trying to survey as many caves/rock-shelters as possible in these areas (see Shum Laka in Cameroon) and hope you'll be able to dig out some human remains. If I were the head of a university archaeology department I would mandate all faculty, grad students, and post-docs become semi-professional spelunkers.

    Proteomics was also mentioned above, that's another possible work-around. I'm curious though how it compares directly against DNA analysis. With DNA, we can easily tell things like if a person is a Yoruba or Mbuti or a French or a Han or Papuan, or some sort of mix related to any of them. Does proteomics allow for similar granular level analysis as DNA does, or does it only allow for broader inferences?
    I didn't think of that. Good point. There is still hope that we get some DNA out of these regions. Either way I hope we are in for a bunch of surprises.

  2. #1272
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    Some more qpadm.
    Steppe_Piedmont_Eneolithic works with...
    Karelia_HG, Sidelkino, or Arkhangelsk: 29.4-34.5%
    AG3: 10.9-14.4%
    CHG: 54.5-57.7%
    Tail prob: 0.140-0.264
    right = c('Anatolia_Epipaleolithic', 'Iran_GanjDareh_N', 'Taforalt', 'Vanuatu_ancient', 'Taiwan_Hanben_IA', 'Tianyuan', 'Peru_Laramate_900BP', 'MA1.SG', 'Yana_UP.SG', 'Italy_GrottaContinenza_Meso.SG', 'Gravettian', 'BachoKiro_Gravettian', 'GoyetQ116_1', 'Sunghir.SG', 'Kostenki14', 'BachoKiro_IUP', 'Ust_Ishim.DG')
    Probably overloaded with paleo-Euro pops but meh.

    CHG
    Iran_TepeAbdulHosein_N.SG: 59.2 +/- 3.19%
    Anatolia_Epipaleolithic: 28.6 +/- 4.43%
    Karelia_HG: 12.2 +/- 3.13%
    Tail prob: 0.419
    right = c('Iran_GanjDareh_N', 'Taforalt', 'Vanuatu_ancient', 'Taiwan_Hanben_IA', 'Tianyuan', 'Peru_Laramate_900BP', 'AG3', 'MA1.SG', 'Yana_UP.SG', 'Italy_GrottaContinenza_Meso.SG', 'Gravettian', 'BachoKiro_Gravettian', 'GoyetQ116_1', 'Sunghir.SG', 'Kostenki14', 'BachoKiro_IUP', 'Ust_Ishim.DG')
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  4. #1273
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    Quote Originally Posted by Kale View Post
    With two new cool right pops to use and with admixtools2 now, here's revisiting one of my favorite subjects, formation of WHG.
    Right pops: 'Iran_GanjDareh_N', 'CHG.SG', 'Vanuatu_ancient', 'Taiwan_Hanben_IA', 'Tianyuan', 'Peru_Laramate_900BP', 'AG3', 'MA1.SG', 'Yana_UP.SG', 'BachoKiro_Gravettian', 'GoyetQ116_1', 'Sunghir.SG', 'Kostenki14', 'BachoKiro_IUP', 'Ust_Ishim.DG'

    Spain_Azilian and Spain_Chan_Meso.SG both modeled beautifully as 100% ElMiron (Gravettian added to the list of right pops here).
    ElMiron comes out 20.7% Gravettian 79.3% GoyetQ_2
    Portugal_Geometric_Mesolithic and Spain_Granada_HG both work as 100% GoyetQ_2 (again with Gravettian in right pops)

    There's a pretty tight WHG cluster consisting of Bichon.SG, France_Meso (Rochedane & Ranchot88), France_NouvelleAquitaine_Meso.SG, GBR_Meso, Ireland_Mesolithic.SG, Loschbour.DG, Spain_Canes_Meso.SG
    All of them get solid tail probs (between 0.374 and 0.807) except GBR_Meso at 0.065 and Ireland_Mesolithic.SG at 0.046 because both have very low ANE.
    Ancestry proportions in the cluster are between 30.0-40.0% ElMiron, 28.0-37.6% Gravettian, and 26.0-33.8% Steppe_Piedmont_Eneolithic.

    Our oldest HG Villabruna doesn't come out great either, again because of low ANE, just barely passes, using GoyetQ_2 instead of ElMiron to tighten the std. errors
    pop, Piedmont, Gravettian, Goyet, tail prob
    Villabruna 32.0 +/- 3.74 51.0 +/- 6.86 17.0 +/- 7.36 0.078
    What about ITA_Continenza? That sample seems to have the lowest affinity to ANE or Gravettians...

  5. #1274
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    Indeed. Guessing less 'Near Eastern' too to even it out though.
    Italy_GrottaContinenza_Meso.SG
    24.8 +/- 2.96% Piedmont
    56.2 +/- 5.06% Gravettian
    19.0 +/- 5.36% GoyetQ_2
    Tail prob: 0.472
    Collection of 14,000 d-stats: Hidden Content Part 2: Hidden Content Part 3: Hidden Content PM me for d-stats, qpadm, qpgraph, or f3-outgroup nmonte models.

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  7. #1275
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    Given that Alex found a ~4000 year old DF19 in the existing Dutch Beaker samples, maybe there’s more to be learned from what we already have, if only more of an effort was made with samples currently without definitive interpretation. How many more finds are out there?
    R1b>M269>L23>L51>L11>P312>DF19>DF88>FGC11833 >S4281>S4268>Z17112>BY44243

    Ancestors: Francis Cooke (M223/I2a2a) b1583; Hester Mahieu (Cooke) (J1c2 mtDNA) b.1584; Richard Warren (E-M35) b1578; Elizabeth Walker (Warren) (H1j mtDNA) b1583;
    John Mead (I2a1/P37.2) b1634; Rev. Joseph Hull (I1, L1301+ L1302-) b1595; Benjamin Harrington (M223/I2a2a-Y5729) b1618; Joshua Griffith (L21>DF13) b1593;
    John Wing (U106) b1584; Thomas Gunn (DF19) b1605; Hermann Wilhelm (DF19) b1635

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  9. #1276
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    Verifying some f3 outgroup models with qpadm.

    Bulgaria_Smyadovo_EBA (I2175 + I2176)
    Bulgaria_CA 0.558 +/- 0.0357
    Romania_CA.SG (GB1 very WHG-rich) 0.238 +/- 0.0256
    Maikop_Novosvobodnaya 0.203 +/- 0.0291
    Tail: 0.976 (dang!)
    right = c('Anatolia_Barcin_N', 'Levant_N', 'Iran_GanjDareh_N', 'CHG.SG', 'Taforalt', 'Vanuatu_ancient', 'PrimorskyKrai_Boisman_MN', 'Peru_Laramate_900BP', 'Karelia_HG', 'IronGates_Meso1', 'Yamnaya_Samara', 'Ust_Ishim.DG')

    Buyukkaya_ECA
    Anatolia_TepecikCiftlik_N.SG 0.665 +/- 0.0842 7.90
    Caucasus_lowlands_LN 0.335 +/- 0.0842 3.98
    Tail: 0.514
    right = c('Anatolia_Barcin_N', 'Levant_N', 'Iran_GanjDareh_N', 'CHG.SG', 'Taforalt', 'Vanuatu_ancient', 'PrimorskyKrai_Boisman_MN', 'Peru_Laramate_900BP', 'Karelia_HG', 'IronGates_Meso1', 'Yamnaya_Samara', 'Ust_Ishim.DG')

    Greece_Mycenaean
    Greece_Lassithi_Minoan 0.632 +/- 0.0853
    Russia_Mezhovskaya_MLBA.SG 0.142 +/- 0.0287
    Israel_Yehud_IBA 0.226 +/- 0.0961
    Tail: 0.781
    right = c('Anatolia_Barcin_N', 'Levant_N', 'Iran_GanjDareh_N', 'CHG.SG', 'Taforalt', 'Vanuatu_ancient', 'PrimorskyKrai_Boisman_MN', 'Peru_Laramate_900BP', 'Karelia_HG', 'IronGates_Meso1', 'Yamnaya_Samara', 'Ust_Ishim.DG')

    AG3
    MA1.SG 0.788 +/- 0.0678
    UstKyakhta_14KBP 0.0700 +/- 0.0315
    CHG.SG 0.142 +/- 0.0569
    Tail: 0.488
    right = c('Taforalt', 'Anatolia_Epipaleolithic', 'Iran_GanjDareh_N', 'Vanuatu_ancient', 'Taiwan_Hanben_IA', 'Tianyuan', 'Yana_UP.SG', 'Gravettian', 'BachoKiro_Gravettian', 'GoyetQ116_1', 'Sunghir.SG', 'Kostenki14', 'BachoKiro_IUP', 'Ust_Ishim.DG')

    AG3
    MA1.SG 0.941 +/- 0.0339
    UstKyakhta_14KBP 0.0592 +/- 0.0339
    Tail: 0.198
    right = c('Taforalt', 'Anatolia_Epipaleolithic', 'Iran_GanjDareh_N', 'CHG.SG', 'Vanuatu_ancient', 'Taiwan_Hanben_IA', 'Tianyuan', 'Yana_UP.SG', 'Gravettian', 'BachoKiro_Gravettian', 'GoyetQ116_1', 'Sunghir.SG', 'Kostenki14', 'BachoKiro_IUP', 'Ust_Ishim.DG')
    Last edited by Kale; 03-24-2021 at 06:40 AM.
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  11. #1277
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    So apparently ancient DNA from Merovingian times is being tested in Belgium, in Ducth:

    https://merovingerdna.be/

    Some more information in Ducth here, at page 89:

    https://archaeologiamediaevalis.be/d...AM_44-2021.pdf

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  13. #1278
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    Quote Originally Posted by Kale View Post
    Is this the 'wild-woman' Zana and Hvita (Khvit?) of Abkhazia?
    Has there been any update on Zana? Please tell me if there is! I heard she could possibly be basil Eurasian, or even some other human species (heidelbergensis?).

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