Monday, September 18, 2017

Ancient IBD/cM matrix analysis offer


I've had a few requests from personal genomics customers to stick their files into an Identity-by-Descent/cM matrix like the one at the link below. Also please check out the accompanying comments thread for ideas of what can be done with the output.

A Bronze Age dominion from the Atlantic to the Altai

I can do this for USD $15 per individual. The deadline for sending through the data files (which, in this run, can only be from 23andMe, Ancestry or FTDNA) is this time Tuesday.

I'll send out the results to each participant over e-mail. However, participants are encouraged to post their results in the comments thread below so that they can be discussed and analyzed further.

Update 20/09/2017: The analysis is underway. Please don't send any more data files. If there's enough interest, I'll do another run soon.

Update 22/09/2017: I've just sent out the results to the participants in the form of two text files titled "ancients_only" and "full_column". The former is a matrix of overall shared haplotype tracts in centimorgans (cM) that includes the user and 65 ancient genomes, and the latter a list of haplotype tracts, also in cM, shared between the user and well over 3000 public samples.

So what can we do with these files? For one, we can look at them, because simply eyeballing these sorts of stats can be very informative. Sorting the data in some way and calculating population averages might help with that.

The "ancients_only" file can be used for slightly more advanced analyses. For instance, below is a Neighbor joining graph produced with the Past 3 program (freely available here). I simply loaded my "ancients_only" file into Past 3, selected all of the columns and rows, and then did this: Multivariate > Clustering > Neighbor joining. Note that I cluster on the same branch as Slav_Bohemia, and this makes perfect sense considering my Polish ancestry. By the way, I dropped Oetzi from this run because he was behaving strangely, which is not unusual for low coverage genomes. Click on the image and open in a new tab for a better view.

Indeed, Past 3 can do a lot of interesting things with matrix files; anything from linear models to rotating three dimensional plots. If you'd like to repeat the linear models from my above linked to blog post, then choose the relevant two columns in your matrix and go Model > Generalized Linear Model. You should see something like this.


Moreover, a matrix with the 3000+ public samples can be gotten here and combined, in part or in whole, with your other files so that you can analyze yourself alongside a larger number of individuals.

79 comments:

  1. Should have these done on Thursday, unless something comes up.

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  2. I'll have both to you in about 7-8 hours.

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  3. Yeah, that's fine. I'm starting in about 24 hours.

    ReplyDelete
  4. Hey Davidski, when are the Tanzanian South-Cushitic pastoralist genomes being published?

    And have you heard of any Neolithic and Paleolithic genomes from Northeast Africa yet? Especially the Nubia?

    Thanks. And this is a great project.

    ReplyDelete
  5. @David

    Will you also check ancients? In other words, will you check if Iran Chalcolithic shares with Yamnaya rather than others? I mean, it may settle a huge number of debates, or at least give a hint at where to look.

    ReplyDelete
  6. @Lathan

    No idea when the African genomes are coming out. The paper is probably in peer review now.

    @epoch

    Iran_ChL genomes are pseudo-haploid. Can't run them in this.

    ReplyDelete
  7. @David

    O, I see. Not everything can be used for this.

    Another thing, probably slightly OT. I came across this remark from Nick Patterson in the "Early Slavs from Bohemia" thread:

    "This kind of thing is inevitable. There can be lab mixups of various types or reburials (so a body winds up in deeper strata). This is a reason that I am nervous about making heavy inference from samples that are outliers in a population.
    a) Outlier might be of real interest
    b) Or the sample has an atypical history
    c) Or something is wrong.

    Often hard to tell. The Reich lab is carbon dating more and more samples though this is expensive!"

    http://eurogenes.blogspot.com/2017/05/two-early-slavs-from-bohemia.html?showComment=1495222388871#c5890778235093582920

    From what I read in the Sup Info of Mathieson 2015 they did not mention carbon dating of the remains, only of the site. Do you know how sure we can be that the Khvalynsk outlier actually is a Khvalynsk sample?

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  8. Do you know how sure we can be that the Khvalynsk outlier actually is a Khvalynsk sample?

    He wasn't actually marked as an outlier in any papers to date.

    But I don't know how his archaeological affiliation was determined exactly and whether it was a high confidence call. You might need to ask Nick Patterson about that.

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  9. @David - But I don't know how his archaeological affiliation was determined exactly and whether it was a high confidence call. You might need to ask Nick Patterson about that.

    You mean getting hit over the head and dumped into a ditch isn't specific to one culture? :3

    I'm afraid I'll have to sit this out. Family health crisis unfortunately. Next time.

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  10. @All

    The analysis is underway. Please don't send any more data files. If there's enough interest, I'll do another run soon.

    ReplyDelete
  11. Hi, this is my matrix. Now it remains to know its meaning. Comments!

    https://drive.google.com/file/d/0B1HxVzk_qIwzd3pqbFFCSVFDSjg/view?usp=sharing

    Thank you

    David

    ReplyDelete
  12. OK, I sent out the output files not long ago and updated the blog post with some ideas and instructions. Check out my Neighbor joining tree!

    https://2.bp.blogspot.com/-ue-j4khjt_U/WcUcpe1vBeI/AAAAAAAAGGA/gH_4xNlXy_oBBr-6SeS9TP8W9hh8GYRQwCLcBGAs/s1600/David_W_Neighbor_joining_tree.png

    Also, Matt, if you're reading this, here's the matrix with over 3,000 public samples.

    https://drive.google.com/file/d/0B8XSV9HEoqpFOUVQd1lfejREYlk/view?usp=sharing

    ReplyDelete
  13. @ Davidski

    Thanks for your work.
    My results

    AAA_Helgenes
    AAB_Sintashta_RISE395 16.7517755
    AAB_Roman_Britain_6DRIF-22 12.372527
    AAB_Unetice_RISE577 11.72396279
    AAB_Unetice_RISE150 11.3984053
    AAB_Anglo_Saxon_NO3423 10.795745
    AAB_Portugal_LNCA_DolmenAnsiao96B 10.53239
    AAB_Afanasievo_RISE511 9.507238
    AAB_Nordic_IA_RISE174 8.849702
    AAB_Mezhovskaya_RISE523 8.82688
    AAC_Karasuk_outlier_RISE502 8.078086
    AAB_Yamnaya_Kalmykia_RISE552 6.857887
    AAB_Spain_LNCA_ATP2 5.91294
    AAB_Yamnaya_Kalmykia_RISE548 5.791653
    AAB_Nordic_LN_RISE98 5.679253
    AAC_Altai_IA_RISE602 5.554495
    AAB_Portugal_MBA_TV3831 5.52035
    AAB_Spain_LNCA_Matojo 5.059983
    AAB_Ireland_EBA_Rathlin2_RSK1 4.916634
    AAB_Portugal_MN_LugarCanto42 4.45519
    AAB_Ireland_EBA_Rathlin1_RM127 4.422253
    AAB_Hungary_IA_IR1 4.419994
    AAB_Slav_Bohemia_RISE569 4.37205
    AAB_Hungary_HG_I1507 4.371752
    AAC_Karasuk_outlier_RISE495 3.959117
    AAB_Ireland_MN_Ballynahatty_BA64 3.826798
    AAC_Karasuk_outlier_RISE493 3.643144
    AAB_Satsurblia_SATP 3.613877
    AAB_Portugal_MBA_TV32032 3.594428
    AAB_Roman_Britain_6DRIF-3 3.533179
    AAB_Hungary_BA_RISE479 3.44839
    AAB_Greece_LN_Pal7 3.179656
    AAB_Roman_Britain_6DRIF-18 3.03813
    AAB_Hungary_N_I1506 2.985472
    AAB_Iberia_EN_CB13 2.903345
    AAC_Altai_IA_RISE601 2.63249
    AAB_Karasuk_RISE496 2.53847
    AAB_Motala_HG_Motala12 2.36684
    AAB_Anatolia_N_Bar31 2.350238
    AAB_LBK_Stuttgart 1.977932
    AAB_Sweden_MN_Gok2 1.85787
    AAB_Karasuk_RISE499 1.84502
    AAB_Bichon_Bichon 1.84386
    AAB_Portugal_MN_LugarCanto41 1.766666
    AAB_Greece_LN_Klei10 1.67404
    AAB_Portugal_LNCA_CovaMoura9B 1.63677
    AAB_Portugal_MBA_MonteGato104 1.557905
    AAB_Hungary_N_I1495 1.5414
    AAB_Greece_EN_Rev5 1.52268
    AAB_Roman_Britain_6DRIF-21 1.486628
    AAB_Andronovo_RISE500 1.11802
    AAB_Hungary_BA_I1504 0.85747
    AAB_Anatolia_N_Bar8 0
    AAB_Andronovo_RISE505 0
    AAB_Hungary_CA_I1497 0
    AAB_Hungary_N_I1496 0
    AAB_Kotias_KK1 0
    AAB_LaBrana1_LaBrana1 0
    AAB_Loschbour_Loschbour 0
    AAB_Oetzi_Oetzi 0
    AAB_Pitted_Ware_Ajv58 0
    AAB_Portugal_LNCA_CabecoArruda122A 0
    AAB_Portugal_LNCA_CovaMoura364 0
    AAB_Portugal_MN_LugarCanto44 0
    AAB_Roman_Britain_outlier_3DRIF-26 0
    AAB_Spain_LNCA_ATP16 0
    AAC_Altai_IA_RISE504 0
    AAC_Karasuk_outlier_RISE497 0







    ReplyDelete
  14. I'm American, 7/8th Norwegian by descent.

    Top modern matches, averaged:


    RussiaNW 10.3628055
    Norwegian 8.5535599
    Utah_Scandinav 8.292284163
    Saami 7.2426796
    Finnish 6.643150417
    Utah_German 6.054027664
    Orcadian 5.65797413
    Russian_North 5.088347215
    English_Kent 5.083618765
    Estonian 4.835378524
    Cornwall 4.822076878
    Utah_USA 4.469781414

    Only two Russian Northwest and three Saami samples, but there seems to be a real connection. I score as about 2% Siberian on ADMIXTURE calculators, so it makes sense. Two of my three closest individual matches were to Chuvash.

    Ancient individual matches:

    AAB_Unetice_RISE150 13.442742
    AAB_Nordic_LN_RISE98 12.851084
    AAB_Yamnaya_Kalmykia_RISE548 11.005777
    AAC_Karasuk_outlier_ 9.004888
    AAB_Karasuk_RISE499 8.809091
    AAB_Roman_Britain_6DRIF 8.637628
    AAB_Ireland_EBA_Rathlin 8.606186
    AAB_Andronovo_RISE505 8.247044
    AAB_Ireland_EBA_Rathlin2 _ 7.941592
    AAB_Andronovo_RISE500 7.14226013
    AAB_Greece_LN_Pal7 6.834963


    Small samples, so I don't know whether to make a big deal out of these results. My closest matches are to an Unetice Pole from around 1800 B.C. and an R1b Swede from around 2100 B.C. The other Unetice sample was a dud, so I suspect that with enough data I would turn out closest to the Neolithic Scandinavians.

    ReplyDelete
  15. English, East Anglian:

    AAB_Afanasievo_RISE511 9.232964
    AAB_Anatolia_N_Bar31 0
    AAB_Anatolia_N_Bar8 1.973855
    AAB_Andronovo_RISE500 10.2060098
    AAB_Andronovo_RISE505 0
    AAB_Anglo_Saxon_NO3423 6.5713445
    AAB_Bichon_Bichon 0.7067
    AAB_Greece_EN_Rev5 0
    AAB_Greece_LN_Klei10 0
    AAB_Greece_LN_Pal7 1.76034
    AAB_Hungary_BA_I1504 2.36881
    AAB_Hungary_BA_RISE479 0
    AAB_Hungary_CA_I1497 1.625764
    AAB_Hungary_HG_I1507 0.96928
    AAB_Hungary_IA_IR1 3.5563518
    AAB_Hungary_N_I1495 4.272295
    AAB_Hungary_N_I1496 0
    AAB_Hungary_N_I1506 2.866862
    AAB_Iberia_EN_CB13 2.802699
    AAB_Ireland_EBA_Rathlin1_RM127 8.597182
    AAB_Ireland_EBA_Rathlin2_RSK1 12.52403
    AAB_Ireland_MN_Ballynahatty_BA64 3.387557
    AAB_Karasuk_RISE496 3.698784
    AAB_Karasuk_RISE499 20.6952997
    AAB_Kotias_KK1 0
    AAB_LaBrana1_LaBrana1 1.4578
    AAB_LBK_Stuttgart 2.12978
    AAB_Loschbour_Loschbour 2.608912
    AAB_Mezhovskaya_RISE523 1.075
    AAB_Motala_HG_Motala12 3.683518
    AAB_Nordic_IA_RISE174 7.2245
    AAB_Nordic_LN_RISE98 3.9755169
    AAB_Oetzi_Oetzi 1.97706
    AAB_Pitted_Ware_Ajv58 2.346145
    AAB_Portugal_LNCA_CabecoArruda122A 10.801202
    AAB_Portugal_LNCA_CovaMoura364 0
    AAB_Portugal_LNCA_CovaMoura9B 2.56866
    AAB_Portugal_LNCA_DolmenAnsiao96B 0
    AAB_Portugal_MBA_MonteGato104 1.462675
    AAB_Portugal_MBA_TV32032 0
    AAB_Portugal_MBA_TV3831 4.378157
    AAB_Portugal_MN_LugarCanto41 2.63479973
    AAB_Portugal_MN_LugarCanto42 6.89848067
    AAB_Portugal_MN_LugarCanto44 1.71684
    AAB_Roman_Britain_6DRIF-18 5.6299293
    AAB_Roman_Britain_6DRIF-21 1.767712
    AAB_Roman_Britain_6DRIF-22 4.019409
    AAB_Roman_Britain_6DRIF-3 3.682746
    AAB_Roman_Britain_outlier_3DRIF-26 1.15846
    AAB_Satsurblia_SATP 0
    AAB_Sintashta_RISE395 2.696899
    AAB_Slav_Bohemia_RISE569 1.920134
    AAB_Spain_LNCA_ATP16 4.232946
    AAB_Spain_LNCA_ATP2 1.889402
    AAB_Spain_LNCA_Matojo 3.6635848
    AAB_Sweden_MN_Gok2 0
    AAB_Unetice_RISE150 6.551865
    AAB_Unetice_RISE577 2.46105
    AAB_Yamnaya_Kalmykia_RISE548 8.7826224
    AAB_Yamnaya_Kalmykia_RISE552 1.41141
    AAC_Altai_IA_RISE504 2.04188
    AAC_Altai_IA_RISE601 0
    AAC_Altai_IA_RISE602 0
    AAC_Karasuk_outlier_RISE493 4.347327
    AAC_Karasuk_outlier_RISE495 1.184342
    AAC_Karasuk_outlier_RISE497 0
    AAC_Karasuk_outlier_RISE502 1.737628

    ReplyDelete
  16. @ Davidski, cheers for the shoutout. The size of that matrix is really at or beyond the limits of what I can do with averaging out with the spreadsheet method I use (or at least, it maybe takes longer than i have patience for ;) ) but thanks.

    ReplyDelete
  17. @ Matt,

    I'm sure everyone would be okay with you using our data for graphing. You're free to use mine, for sure. I'll have my stuff up here soon.

    ReplyDelete
  18. Euro-mutt

    Ancients:

    AAB_Nordic_LN_RISE98 15.1803537
    AAC_Karasuk_outlier_RISE502 12.14899901
    AAB_Yamnaya_Kalmykia_RISE548 11.939083
    AAB_Afanasievo_RISE511 11.718604
    AAB_Unetice_RISE150 10.876749
    AAB_Andronovo_RISE505 10.424346
    AAB_Karasuk_RISE499 9.91026
    AAB_Yamnaya_Kalmykia_RISE552 9.335215
    AAB_Sintashta_RISE395 7.3357957
    AAB_Anglo_Saxon_NO3423 7.138464
    AAB_Ireland_EBA_Rathlin1_RM127 6.914043
    AAB_Roman_Britain_6DRIF-22 6.540072
    AAB_Ireland_EBA_Rathlin2_RSK1 6.033046
    AAB_Andronovo_RISE500 5.982405
    AAB_Portugal_MBA_TV32032 5.855381
    AAB_Portugal_MN_LugarCanto42 5.715064
    AAB_Sweden_MN_Gok2 5.332439
    AAB_Hungary_CA_I1497 5.1534879
    AAB_Hungary_BA_I1504 5.109243
    AAB_Roman_Britain_6DRIF-3 5.09514
    AAC_Altai_IA_RISE504 4.871235
    AAB_Pitted_Ware_Ajv58 4.278134
    AAB_Portugal_MBA_MonteGato104 4.19162144
    AAB_Spain_LNCA_Matojo 4.089124
    AAB_Karasuk_RISE496 3.6737917
    AAC_Altai_IA_RISE601 3.475469
    AAC_Karasuk_outlier_RISE493 3.366392
    AAB_Unetice_RISE577 3.302024
    AAB_Nordic_IA_RISE174 3.085825
    AAB_Mezhovskaya_RISE523 3.060812
    AAB_Ireland_MN_Ballynahatty_BA64 3.020314
    AAB_Portugal_MN_LugarCanto41 2.9059
    AAB_Roman_Britain_6DRIF-18 2.860906
    AAB_Loschbour_Loschbour 2.730059
    AAB_Spain_LNCA_ATP16 2.66654813
    AAB_LBK_Stuttgart 2.572323
    AAB_Hungary_N_I1495 2.54884
    AAC_Altai_IA_RISE602 2.4768
    AAB_Greece_EN_Rev5 2.354084
    AAB_Motala_HG_Motala12 2.008695
    AAB_Hungary_HG_I1507 1.899536
    AAB_Portugal_MN_LugarCanto44 1.856754
    AAB_Hungary_BA_RISE479 1.837311
    AAB_Greece_LN_Pal7 1.82286
    AAB_Bichon_Bichon 1.759274
    AAB_Roman_Britain_6DRIF-21 1.58591
    AAB_Greece_LN_Klei10 1.52577
    AAB_Spain_LNCA_ATP2 1.39874
    AAB_Slav_Bohemia_RISE569 1.378009
    AAB_Satsurblia_SATP 1.282883
    AAB_Portugal_LNCA_CovaMoura364 1.266809
    AAB_Hungary_IA_IR1 1.06789
    AAB_Portugal_LNCA_CabecoArruda122A 1.056011
    AAB_Portugal_LNCA_CovaMoura9B 0.986935
    AAB_Oetzi_Oetzi 0.75436
    AAB_Portugal_LNCA_DolmenAnsiao96B 0.580779
    AAB_Anatolia_N_Bar31 0.28784
    AAB_Anatolia_N_Bar8 0
    AAB_Hungary_N_I1496 0
    AAB_Hungary_N_I1506 0
    AAB_Iberia_EN_CB13 0
    AAB_Kotias_KK1 0
    AAB_LaBrana1_LaBrana1 0
    AAB_Portugal_MBA_TV3831 0
    AAB_Roman_Britain_outlier_3DRIF-26 0
    AAC_Karasuk_outlier_RISE495 0
    AAC_Karasuk_outlier_RISE497 0

    ReplyDelete
  19. Top 100 modern individuals:

    Utah_USA_NA11891 23.4682238
    Latvian_GS000035027 19.5256044
    English_Cornwall_HG00249 16.433908
    Utah_Scandinavian_NA07346 14.635498
    Utah_German_NA12239 14.4500472
    Utah_German_NA07022 14.125439
    Mari_mari3 12.778314
    Russian_North_HGDP00891 12.629419
    Orcadian_HG00125 12.290583
    Orcadian_HGDP00800 11.930816
    Orcadian_HG00124 11.640142
    Utah_USA_NA12145 11.291805
    Orcadian_HGDP00804 11.195737
    English_Cornwall_HG00263 10.948266
    English_Kent_HG01334 10.86301
    Norwegian_NOR101 10.77167783
    French_HGDP00538 10.7579804
    Belarusian_GS000014324 10.299699
    Estonian_ee68 10.293421
    Slovakian_Slovakia222 10.2055053
    French_HGDP00528 10.150875
    English_Kent_HG00128 10.087612
    Serbian_Serbia_Serbia19_GSM1424665 10.058413
    Italian_Tuscan_NA20509 9.891118
    Spanish_Castilla_Y_Leon_HG01506 9.807251
    Estonian_ee86 9.7524262
    Utah_USA_NA12154 9.624001
    Estonian_ee144 9.438562
    Orcadian_HG00100 9.334663
    Moksha_mordovia5 9.269123
    Sicilian_West_WestSicilian10H 9.221184
    Ukrainian_West_GS000035178 9.1698148
    Finnish_HG00364 9.135117
    Ukrainian_East_UkrBel618 9.036228
    Ashkenazi_Jew_ashkenazy1e 9.012637
    Orcadian_HG00117 8.919005
    Ashkenazi_Jew_ashkenazy7e 8.86112
    French_HGDP00513 8.760578
    Komi_GS000035018 8.7295794
    English_Cornwall_HG00256 8.669854
    Spanish_Baleares_HG01670 8.6602
    Utah_USA_NA12283 8.444657
    Slovakian_Slovakia118 8.415299
    Croatian_GSM1841131 8.410251
    Utah_USA_NA12749 8.3990729
    Utah_Scandinavian_NA12249 8.379915
    English_Cornwall_HG00259 8.353
    Russian_North_HGDP00887 8.286039
    Utah_USA_NA12044 8.284005
    English_Cornwall_HG00250 8.231026
    Utah_USA_NA12282 8.21636
    Norwegian_NOR126 8.200352
    Orcadian_HG00102 8.165127
    English_Kent_HG00141 8.156837
    Utah_USA_NA12546 8.077786
    Bulgarian_Bulgaria5 8.020719
    Latvian_GS000016903 7.947704
    English_Kent_HG00146 7.937961
    Bosnian_Bosnian_4_GSM1424660 7.884202
    Vepsa_GS000035244 7.878328
    Spanish_Spain10 7.859405
    Polish_Polish16H 7.804417
    Slovenian_Slovenian_14 7.77683557
    English_Cornwall_HG00235 7.740439
    Serbian_Serbian_Serbia9_GSM1424683 7.701269
    Romanian_Romania6 7.686074
    English_Cornwall_HG00245 7.6763593
    Utah_USA_NA12342 7.547523
    Spanish_Baleares_HG01613 7.53747269
    French_HGDP00531 7.5274779
    Sephardic_Jew_sephardic5tur 7.498313
    Macedonian_Macedonian2_GSM1424618 7.488779
    Spanish_Galicia_HG01705 7.4170548
    Lithuanian_lithuania3 7.410625
    Estonian_ee66 7.381807
    English_Cornwall_HG00234 7.331173
    English_Cornwall_HG00264 7.309364
    Utah_USA_NA12748 7.299198
    Basque_French_HGDP01367 7.28241
    Utah_USA_NA12045 7.240136
    Estonian_ee45 7.1686808
    French_HGDP00525 7.165268
    Spanish_Castilla_La_Mancha_HG01746 7.1598775
    Utah_USA_NA12340 7.148583
    Estonian_ee50 7.140646
    English_Kent_HG00157 7.11687
    Lithuanian_lithuania6 7.103729
    Kosovar_Kosovo12_GSM1424631 7.099791
    Utah_British_NA12005 7.078816
    Hazara_HGDP00112 7.072089
    Estonian_ee136 7.047731
    Ashkenazi_Jew_ashkenazy9e 7.042993
    Slovenian_Slovenian188 6.999963
    Orcadian_HG00108 6.995197
    Norwegian_NOR107 6.977914
    Basque_French_HGDP01379 6.908994
    Russian_North_HGDP00901 6.899245
    Latvian_latvian54H7 6.8962537
    Croatian_GSM1841115 6.885017
    Ukrainian_West_GS000035175 6.8425


    ReplyDelete
  20. Top 75 modern pop averages:

    Komi 6.4815982
    Tatar_Mishar 6.227453
    Utah_Scandinavian 6.18233262
    Utah_German 5.81818997
    Latvian 5.78009412
    Utah_USA 5.5298965
    Norwegian 5.29431744
    Polish 5.21782346
    Orcadian 5.08637953
    Ingrian 4.93772933
    English_Cornwall 4.81405562
    Estonian 4.28759346
    English_Kent 4.2115799
    Ukrainian_West 4.13614942
    Ukrainian_East 4.113382
    Spanish_Baleares 4.0551462
    Utah_British 4.03981567
    French 3.95409879
    Finnish 3.84986767
    Vepsa 3.76677485
    Belarusian 3.70539261
    Spanish_Castilla_La_Mancha 3.68616588
    Swedish 3.6024675
    Slovenian 3.58938705
    Slovakian 3.53558898
    Ashkenazi_Jew 3.45085688
    Spanish_Canarias 3.24010165
    Russian_North 3.22359826
    Hungarian 3.20907621
    Moksha 3.1870786
    Saami 3.18459067
    Tatar_Kryashen 3.1266269
    Lithuanian 3.03784985
    Serbian 3.03708617
    Romanian 2.96786836
    Bosnian 2.8723482
    Tabasaran 2.77484367
    Russian_Northwest 2.759969
    Mari 2.74862285
    Montenegrin 2.66877436
    Ukrainian_North 2.659621
    Russian_West 2.628892
    Croatian 2.62389354
    Azeri 2.6129104
    Basque_French 2.61282453
    German 2.57363567
    Spanish_Valencia 2.56562889
    Spanish_Castilla_Y_Leon 2.51982362
    Spanish_Cataluna 2.5122776
    Mansi 2.49427491
    Spanish_Cantabria 2.47494925
    Spanish_Aragon 2.40970858
    Macedonian 2.40772307
    Erzya_mordovia 2.34740533
    Spanish 2.27055123
    Udmurd 2.23056375
    Chuvash 2.20894819
    Spanish_Andalucia 2.1904231
    Kosovar 2.12828778
    Greenlander_West 2.0854406
    Bashkir 2.03821524
    Kabardin 1.99343567
    Spanish_Murcia 1.97721267
    Italian_Tuscan 1.94721122
    Hazara_Afghanistan 1.90979333
    Cossack_Kuban 1.8445
    Greek_Macedonia 1.79308271
    Scottish_Argyll 1.73305925
    Bulgarian 1.72939025
    Spanish_pais_Vasco 1.6621105
    Spanish_Extremadura 1.6221965
    Spanish_Galicia 1.6128731
    Italian_Bergamo 1.60662101
    Cossack_Ukrainian 1.5517655
    Moroccan_Jew 1.5394192

    ReplyDelete
  21. West Ukrainian culturally for 250 years paper trail.

    "Ancients" above 5.0
    AAB_Ireland_EBA_Rathlin1_RM127 13.1556885
    AAB_Hungary_IA_IR1 9.87608
    AAB_Unetice_RISE150 8.919633
    AAB_Unetice_RISE577 7.762798
    AAB_Andronovo_RISE505 7.653074
    AAB_Ireland_EBA_Rathlin2_RSK1 7.16609
    AAB_Hungary_HG_I1507 7.023542
    AAB_Nordic_IA_RISE174 6.709605
    AAB_Afanasievo_RISE511 6.353592
    AAC_Karasuk_outlier_RISE502 6.105593
    AAB_Hungary_BA_RISE479 5.91144
    AAB_Portugal_MBA_TV32032 5.860841

    "Moderns" above 16.0
    Croatian_GSM1841121 22.940375
    Slovakian_Slovakia411 21.47469428
    Estonian_ee147 20.3318413
    Estonian_GS000017209 19.5201645
    Russian_North_HGDP00885 19.340754
    Estonian_ee78 19.247257
    Polish_Polish10H 19.190638
    Lithuanian_lithuania9 18.685255
    Ukrainian_West_UkrLv240 18.537329
    Ukrainian_North_Ukraine136 18.468432
    Estonian_a39 18.309442
    Belarusian_GS000014324 18.236673
    Ukrainian_West_GS000035178 18.127011
    Ukrainian_West_UkrLv215 18.001162
    Latvian_latvian54H7 17.9410166
    Mozabite_HGDP01273 17.905884
    Ukrainian_East_UkrBel736 17.866116
    Slovakian_Slovakia256 17.604307
    Belarusian_belorus7 17.385669
    Polish_Polish12H 17.3128468
    Ukrainian_North_UkrainePol19 16.905952
    Ukrainian_East_UkrBel733 16.8683653
    Russian_West_GS000016819 16.845141
    Russian_North_HGDP00882 16.8322631
    Latvian_latvian22J5 16.716382
    Karelian_GS000035149 16.4635504
    Polish_Polish9H 16.111341

    ReplyDelete
  22. Now top Moderns

    Basque_French_HGDP01380 17.721878
    Spanish_Valencia_HG01776 14.859439
    English_Cornwall_HG00160 13.506335
    English_Kent_HG00152 13.192521
    Utah_Scandinavian_NA07346 12.043676
    French_HGDP00519 11.449055
    Estonian_GS000017199 10.875242
    Utah_USA_NA12145 10.681289
    English_Cornwall_HG00245 10.6283624
    Vepsa_GS000016971 10.563117
    French_HGDP00537 10.332528
    Orcadian_HG00102 10.044597
    Orcadian_HG00121 9.9740582
    Polish_Polish11H 9.893548
    Lithuanian_GS000016904 9.841885
    English_Kent_HG00145 9.703207
    Russian_North_HGDP00896 9.440439
    Slovakian_Slovakia222 9.416012
    Russian_North_HGDP00886 9.3189804
    English_Cornwall_HG00263 9.106229
    Orcadian_HG00107 9.033685
    Moksha_mordovia14 9.0278884
    Utah_Scandinavian_NA12248 8.94535
    Italian_Tuscan_NA20766 8.92634
    Utah_USA_NA12749 8.847244
    Avar_GS000014407 8.806463
    Bosnian_Bosnian_13_GSM1424654 8.702346
    French_HGDP00535 8.70054022
    Italian_Tuscan_HGDP01162 8.659078
    Estonian_ee78 8.628335
    Greenlander_East_GSM558768 8.366382
    Norwegian_NOR106 8.344245
    Utah_USA_NA12341 8.334125
    Utah_USA_NA11893 8.286903
    Sardinian_HGDP00673 8.2761015
    Utah_USA_NA12264 8.272402
    Spanish_Castilla_Y_Leon_HG01612 8.26236
    Russian_Central_GS000035242 8.207584
    Spanish_Baleares_HG01631 8.183449
    Hungarian_GS000016901 8.168986
    Scottish_Argyll_HG00104 8.098118
    Utah_German_NA07345 8.087358
    Utah_British_NA11920 8.028522
    Italian_Tuscan_NA20813 8.00725
    Serbian_Serbian_Serbia7_GSM1424682 7.9656198
    French_HGDP00517 7.9191949
    Lithuanian_lithuania6 7.909469
    English_Cornwall_HG00259 7.80104
    Orcadian_HG00114 7.751608
    English_Kent_HG00130 7.649591
    English_Kent_HG01334 7.616478
    Estonian_GS000017206 7.512956
    Colombian_GSM531114 7.50871
    Utah_USA_NA12342 7.504915
    Latvian_latvian58C6 7.502672
    Italian_Tuscan_NA20527 7.455373
    Utah_USA_NA12282 7.421038
    Russian_North_HGDP00903 7.397888
    Gujarati_NA20904 7.394681
    French_HGDP00529 7.3924
    Norwegian_NOR111 7.283133
    English_Kent_HG00143 7.275521
    French_HGDP00511 7.274362
    Slovakian_Slovakia425 7.261354
    Romanian_Romania12 7.261317
    Orcadian_HGDP00803 7.243577
    Utah_German_NA11830 7.230943
    Orcadian_HG00109 7.22228
    English_Kent_HG00129 7.193687
    Utah_USA_NA12056 7.146905
    Basque_French_HGDP01378 7.088122
    Spanish_Spanish20H 7.018347
    Estonian_GS000017208 6.989605
    Macedonian_Macedonian7_GSM1424624 6.987235
    Serbian_Serbian_Serbia5_GSM1424679 6.943076
    Utah_USA_NA11881 6.931813
    Sephardic_Jew_sephardic14bul 6.915986
    Bulgarian_Bulgarian10H 6.855414
    Greenlander_West_GSM558777 6.847348
    English_Cornwall_HG00256 6.83909
    Romanian_Romania4 6.827662
    Russian_West_GS000016796 6.781069
    Utah_USA_NA11919 6.759878
    Spanish_Galicia_HG01707 6.751144
    English_Kent_HG00127 6.747961
    Ashkenazi_Jew_ashkenazy10e 6.738469
    Lithuanian_GS000016905 6.723337
    Latvian_latvian58C8 6.703595

    ReplyDelete
  23. Ancients:

    AAB_Spain_LNCA_ATP2 12.154296
    AAB_Unetice_RISE150 9.608421
    AAB_Anglo_Saxon_NO3423 9.3617289
    AAB_Spain_LNCA_Matojo 8.606585
    AAB_Nordic_LN_RISE98 7.6308697
    AAB_Spain_LNCA_ATP16 7.18066
    AAB_Portugal_MN_LugarCanto44 6.754815
    AAB_Portugal_MBA_MonteGato104 6.68850484
    AAB_Portugal_MBA_TV32032 6.5379326
    AAB_Portugal_LNCA_CovaMoura364 6.4564237
    AAB_LaBrana1_LaBrana1 6.397674
    AAB_Ireland_MN_Ballynahatty_BA64 6.161949
    AAB_Ireland_EBA_Rathlin2_RSK1 5.90511
    AAB_Nordic_IA_RISE174 5.69514
    AAB_Andronovo_RISE500 5.566669
    AAB_Anatolia_N_Bar8 5.382943
    AAB_Roman_Britain_6DRIF-21 5.336766
    AAB_Portugal_LNCA_CovaMoura9B 5.151194
    AAB_Andronovo_RISE505 4.884776
    AAB_Bichon_Bichon 4.807908
    AAB_Roman_Britain_6DRIF-18 3.87896
    AAB_Portugal_MN_LugarCanto42 3.523487
    AAB_Portugal_MN_LugarCanto41 3.516834
    AAC_Karasuk_outlier_RISE502 3.464467
    AAB_Yamnaya_Kalmykia_RISE552 3.452883
    AAB_Mezhovskaya_RISE523 3.275702
    AAB_Loschbour_Loschbour 3.243495
    AAB_Slav_Bohemia_RISE569 3.219847
    AAB_Motala_HG_Motala12 3.217487
    AAB_Hungary_CA_I1497 3.188648
    AAB_LBK_Stuttgart 2.9066
    AAB_Ireland_EBA_Rathlin1_RM127 2.805886
    AAC_Karasuk_outlier_RISE495 2.775052
    AAB_Hungary_N_I1496 2.510278
    AAB_Hungary_BA_I1504 2.44784
    AAB_Iberia_EN_CB13 2.417861
    AAC_Altai_IA_RISE601 2.407046
    AAC_Karasuk_outlier_RISE493 2.368364
    AAB_Yamnaya_Kalmykia_RISE548 2.339761
    AAB_Greece_EN_Rev5 2.28117
    AAB_Karasuk_RISE496 2.276359
    AAB_Hungary_N_I1506 2.17003
    AAB_Oetzi_Oetzi 2.157042
    AAB_Roman_Britain_6DRIF-22 2.140597
    AAB_Anatolia_N_Bar31 2.082461
    AAB_Hungary_N_I1495 2.02615
    AAC_Altai_IA_RISE602 1.9552
    AAB_Afanasievo_RISE511 1.949347
    AAB_Karasuk_RISE499 1.933334
    AAB_Unetice_RISE577 1.9324181
    AAB_Hungary_IA_IR1 1.91747
    AAB_Portugal_LNCA_CabecoArruda122A 1.74305
    AAB_Portugal_MBA_TV3831 1.73546
    AAB_Portugal_LNCA_DolmenAnsiao96B 1.711982
    AAB_Roman_Britain_6DRIF-3 1.585151
    AAB_Hungary_BA_RISE479 1.36846
    AAB_Greece_LN_Klei10 1.32308
    AAB_Greece_LN_Pal7 1.21711

    Top 40 moderns:

    Basque_French_HGDP01363 9.88102
    Spanish_Valencia_HG01605 9.8416581
    Moroccan_Moroccan12H 9.6163749
    Spanish_Aragon_HG01676 9.53385
    Basque_French_HGDP01373 9.514234
    Spanish_Extremadura_HG01510 9.429952
    Spanish_Cataluna_HG01536 9.247764
    Ukrainian_East_GS000035174 8.9539541
    Utah_USA_NA12413 8.939456
    Spanish_Cataluna_HG01537 8.69123
    English_Cornwall_HG00237 8.655676
    Basque_French_HGDP01375 8.651864
    Montenegrin_Montenegro7_GSM1424640 8.637771
    Mozabite_HGDP01259 8.494754
    Peruvian_HG02302 8.485347
    Basque_French_HGDP01367 8.45435
    Spanish_Spanish20H 8.332209
    German_GS000016891 8.297376
    Puerto_Rican_GSM531210 8.0924
    Spanish_Spanish24H 8.070807
    Basque_French_HGDP01371 7.988825
    Italian_South_SouthItalian4H 7.9041092
    Jordanian_Jordan646 7.819715
    Moroccan_Moroccan14H 7.810098
    Estonian_ee68 7.749795
    Basque_French_HGDP01365 7.728534
    English_Cornwall_HG00259 7.58315
    Scottish_Argyll_HG00103 7.500374
    Italian_Tuscan_HGDP01168 7.4880377
    Utah_Scandinavian_NA07346 7.433837
    Spanish_Murcia_HG01617 7.396799
    Colombian_GSM531127 7.306737
    Spanish_Castilla_La_Mancha_HG01504 7.2744332
    Karelian_GS000016970 7.2304023
    Basque_French_HGDP01377 7.1713424
    Tunisian_Tunisian8H 7.136262
    Spanish_Valencia_HG01779 7.076908
    Hungarian_hungary20 7.041261
    Basque_French_HGDP01364 7.021052
    Spanish_Castilla_Y_Leon_HG01783 7.018113

    ReplyDelete
  24. Graphics:

    - Oetzi - Rabai

    https://drive.google.com/file/d/0B1HxVzk_qIwzZU1IVEVaVkRzS0E/view?usp=sharing

    - Tree (Neighbour_joining_clustering)

    https://drive.google.com/file/d/0B1HxVzk_qIwzWjE4STQwRzJ3WGs/view?usp=sharing

    Thanks for you work, David!

    Regards

    ReplyDelete
  25. My results: (Ancients)

    AAB_Andronovo_RISE500 17,145621
    AAB_Roman_Britain_6DRIF-22 15,995595
    AAB_Yamnaya_Kalmykia_RISE548 11,343428
    AAB_Afanasievo_RISE511 10,296394
    AAB_Ireland_EBA_Rathlin2_RSK1 8,8230396
    AAB_Nordic_IA_RISE174 8,101785
    AAB_Andronovo_RISE505 7,780931
    AAB_Roman_Britain_6DRIF-3 6,933925
    AAB_Pitted_Ware_Ajv58 6,68318
    AAB_Mezhovskaya_RISE523 6,510341
    AAB_Roman_Britain_6DRIF-18 6,508469
    AAC_Karasuk_outlier_RISE502 6,016296
    AAB_Slav_Bohemia_RISE569 5,785742
    AAB_Yamnaya_Kalmykia_RISE552 5,752832
    AAB_Portugal_MN_LugarCanto41 5,44168
    AAB_Nordic_LN_RISE98 4,919167
    AAB_Spain_LNCA_ATP2 4,674716
    AAB_Ireland_EBA_Rathlin1_RM127 4,477305
    AAB_Portugal_LNCA_CabecoArruda122A 4,3234563
    AAB_Iberia_EN_CB13 4,3009722
    AAB_Portugal_LNCA_CovaMoura9B 3,934942
    AAB_Hungary_N_I1506 3,876037
    AAB_Unetice_RISE577 3,814262
    AAB_Sintashta_RISE395 3,734422
    AAB_Portugal_MBA_TV32032 3,591087
    AAB_Karasuk_RISE496 3,57491
    AAC_Karasuk_outlier_RISE495 3,45846
    AAB_Karasuk_RISE499 3,23068
    AAB_Anglo_Saxon_NO3423 3,151901
    AAB_Portugal_MN_LugarCanto44 2,841017
    AAB_Ireland_MN_Ballynahatty_BA64 2,83384
    AAB_Hungary_HG_I1507 2,83234
    AAC_Altai_IA_RISE602 2,299445
    AAB_Spain_LNCA_ATP16 2,297892
    AAB_Portugal_LNCA_CovaMoura364 2,20875
    AAB_Sweden_MN_Gok2 2,18115
    AAB_Satsurblia_SATP 2,1234
    AAB_Anatolia_N_Bar31 2,12068
    AAB_Roman_Britain_6DRIF-21 2,11004
    AAB_LaBrana1_LaBrana1 1,97584
    AAB_Portugal_MBA_MonteGato104 1,88084
    AAB_Loschbour_Loschbour 1,65013
    AAB_Unetice_RISE150 1,57885
    AAB_Greece_LN_Klei10 1,56901
    AAB_Portugal_MN_LugarCanto42 1,49954
    AAB_Spain_LNCA_Matojo 1,402323
    AAB_Kotias_KK1 1,327316
    AAB_Portugal_MBA_TV3831 1,32433
    AAB_Anatolia_N_Bar8 1,12844
    AAB_LBK_Stuttgart 1,0844441
    AAB_Hungary_BA_RISE479 0,881237
    AAC_Altai_IA_RISE504 0,808801
    AAB_Bichon_Bichon 0,5946
    AAB_Greece_EN_Rev5 0
    AAB_Greece_LN_Pal7 0
    AAB_Hungary_BA_I1504 0
    AAB_Hungary_CA_I1497 0
    AAB_Hungary_IA_IR1 0
    AAB_Hungary_N_I1495 0
    AAB_Hungary_N_I1496 0
    AAB_Motala_HG_Motala12 0
    AAB_Oetzi_Oetzi 0
    AAB_Portugal_LNCA_DolmenAnsiao96B 0
    AAB_Roman_Britain_outlier_3DRIF-26 0
    AAC_Altai_IA_RISE601 0
    AAC_Karasuk_outlier_RISE493 0
    AAC_Karasuk_outlier_RISE497 0

    ReplyDelete
  26. Top 50 Modern matches:

    English_Kent_HG00141 27,7478522
    Utah_German_NA12239 24,446229
    English_Kent_HG00138 19,730626
    Estonian_ee59 17,001032
    English_Kent_HG00152 14,469127
    Orcadian_HG00110 14,255506
    French_HGDP00514 14,071683
    Utah_German_NA12057 13,181542
    English_Kent_HG00145 12,76463
    English_Cornwall_HG00243 12,7308841
    Orcadian_HG00121 12,458477
    English_Kent_HG00151 12,333112
    Ashkenazi_Jew_ashkenazy7e 12,188303
    Bulgarian_Bulgarian10H 12,1013928
    Orcadian_HGDP00800 12,076324
    English_Kent_HG00135 11,845454
    Montenegrin_Montenegro21_GSM1424649 11,75365949
    Utah_USA_NA11881 11,709575
    English_Kent_HG00139 11,3820507
    English_Cornwall_HG00263 11,37624
    Spanish_Pais_Vasco_HG01521 11,282587
    Utah_German_NA07000 10,976353
    English_Kent_HG00146 10,969149
    French_HGDP00538 10,92928
    Croatian_GSM1841126 10,85597
    Norwegian_NOR111 10,724372
    Estonian_ee105 10,65209731
    Utah_USA_NA12234 10,448183
    Estonian_GS000017209 10,292224
    English_Kent_HG00142 10,28596
    English_Cornwall_HG00251 10,1338139
    Utah_German_NA12716 10,1221904
    Utah_USA_NA12749 10,094053
    Utah_USA_NA11995 10,086597
    French_HGDP00537 10,019936
    Utah_USA_NA11892 9,9801962
    English_Kent_HG00128 9,908737
    Utah_USA_NA12056 9,875564
    Belarusian_belorus5 9,833302
    Lithuanian_lithuania5 9,735358
    Russian_North_HGDP00889 9,636861
    Orcadian_HGDP00810 9,6295
    Ukrainian_West_UkrLv228 9,569684
    Norwegian_NOR108 9,5295761
    Utah_British_NA12827 9,289007
    Orcadian_HG00123 9,287136
    Cossack_Ukrainian_GS000035238 9,263278
    Belarusian_belorus7 9,248209
    Norwegian_NOR106 9,242999

    ReplyDelete
  27. My ancients are easy to interpret. Among the top 11 I have three samples from Roman Britain Driffield Terrace.
    As I am South_Dutch/Belgian, it seems plausible that they had a lot of Belgae ancestry.

    AAB_Roman_Britain_6DRIF-3 21,333273
    AAB_Yamnaya_Kalmykia_RISE548 14,08972
    AAB_Roman_Britain_6DRIF-21 13,231303
    AAB_Unetice_RISE577 13,140402
    AAB_Ireland_EBA_Rathlin2_RSK1 11,2042198
    AAB_Sintashta_RISE395 10,910651
    AAB_Anglo_Saxon_NO3423 10,792951
    AAB_Nordic_IA_RISE174 9,276697
    AAB_Portugal_MN_LugarCanto42 8,6604467
    AAB_Ireland_MN_Ballynahatty_BA64 8,619298
    AAB_Roman_Britain_6DRIF-22 8,25345
    AAB_Karasuk_RISE496 6,6589617
    AAB_Afanasievo_RISE511 5,93304
    AAB_Andronovo_RISE505 5,835642
    AAB_Hungary_BA_I1504 5,50697
    AAB_Yamnaya_Kalmykia_RISE552 4,90714
    AAB_Unetice_RISE150 4,7994111
    AAB_Portugal_LNCA_DolmenAnsiao96B 4,765008
    AAB_Portugal_MBA_MonteGato104 4,4965848
    AAB_Portugal_MBA_TV3831 4,3699011
    AAC_Karasuk_outlier_RISE495 4,2248325
    AAB_Nordic_LN_RISE98 4,205276
    AAB_Motala_HG_Motala12 4,084636
    AAB_Portugal_MN_LugarCanto44 4,053803
    AAB_Loschbour_Loschbour 4,0308263
    AAB_Iberia_EN_CB13 3,995065
    AAB_LaBrana1_LaBrana1 3,920796
    AAB_Portugal_LNCA_CabecoArruda122A 3,9081
    AAB_Spain_LNCA_ATP16 3,61109
    AAB_Andronovo_RISE500 3,59557
    AAB_Oetzi_Oetzi 3,46608
    AAB_Hungary_CA_I1497 3,350283
    AAC_Altai_IA_RISE504 3,268279
    AAB_Hungary_N_I1506 3,087775
    AAB_Bichon_Bichon 3,0437467
    AAB_Karasuk_RISE499 2,754702
    AAB_Roman_Britain_6DRIF-18 2,753474
    AAB_Ireland_EBA_Rathlin1_RM127 2,665477
    AAC_Karasuk_outlier_RISE493 2,5583
    AAB_Slav_Bohemia_RISE569 2,381255
    AAB_Hungary_BA_RISE479 2,299432
    AAB_Portugal_MN_LugarCanto41 2,229835
    AAB_LBK_Stuttgart 2,156556
    AAB_Hungary_HG_I1507 2,07099
    AAC_Altai_IA_RISE602 2,054522
    AAB_Pitted_Ware_Ajv58 1,9885
    AAB_Mezhovskaya_RISE523 1,96248
    AAB_Spain_LNCA_Matojo 1,86028
    AAB_Kotias_KK1 1,6344
    AAC_Karasuk_outlier_RISE502 1,5817364
    AAB_Portugal_MBA_TV32032 1,3784922
    AAB_Sweden_MN_Gok2 1,137183
    AAA_Ger_Huijbregts_Ger_Huijbregts 1
    AAB_Greece_LN_Pal7 0,968163
    AAB_Anatolia_N_Bar31 0
    AAB_Anatolia_N_Bar8 0
    AAB_Greece_EN_Rev5 0
    AAB_Greece_LN_Klei10 0
    AAB_Hungary_IA_IR1 0
    AAB_Hungary_N_I1495 0
    AAB_Hungary_N_I1496 0
    AAB_Portugal_LNCA_CovaMoura364 0
    AAB_Portugal_LNCA_CovaMoura9B 0
    AAB_Roman_Britain_outlier_3DRIF-26 0
    AAB_Satsurblia_SATP 0
    AAB_Spain_LNCA_ATP2 0
    AAC_Altai_IA_RISE601 0
    AAC_Karasuk_outlier_RISE497 0

    ReplyDelete
  28. What DNA test do I need to take to have to have this done?( I've only had the full sequence MtDNA test) I'm interested in the comparison with ancient populations. When do you plan to do this again? Thanks! (......even though my MtDNA is post-LBK, I have a lot of German ancestry from Venne and those women were GAC & LBK)

    ReplyDelete
  29. @jv

    You need an autsomal data file from FTDNA, Ancestry or 23andMe. They usually go for around $100 these days.

    ReplyDelete
    Replies
    1. Thank you. I will order from FTDNA as I have my MtDNA account with them. COULD you please give me your opinion regarding my MtDNA lineage? ANY idea when MtDNA H6a1 entered the PC Steppe? Do you think H6a1 was in the pre-Yamnaya populations? Also, did she come from Mesolithic Iran/Caucasus? Maybe the Zarzian Culture? I can trace the line H6 from Israel 4000 BCE to H6a1a Esperstedt , Germany 2300 BCE Schnurkeramikkultur,1800 BCE Netherlands Glockenbecherkultur and H6a1a 1800 BCE Srubna Culture Samara, Russia. Thank you

      Delete
  30. "I simply loaded my "ancients_only" file into Past 3, selected all of the columns and rows, and then did this: Multivariate > Clustering > Neighbor joining. Note that I cluster on the same branch as Slav_Bohemia, and this makes perfect sense considering my Polish ancestry. By the way, I dropped Oetzi from this run because he was behaving strangely, which is not unusual for low coverage genomes. Click on the image and open in a new tab for a better view."

    This didn't seem to work for me. When I clicked after "Neighbour joining" I was told that the first two rows (in effect since I had to experiment with removals. Anything less than these two rows as a whole was constantly termed erroneous) were errors. When I removed them I did get a result, but the clusters included only the ancient samples and not my figures.

    ReplyDelete
  31. I'm a NW European, but I also clustered with Slav Bohemia on the neighbor joining tree.

    ReplyDelete
  32. I'm a NW European, but I also clustered with Slav Bohemia on the neighbor joining tree.

    This does happen occasionally, probably because Slav_Bohemia is the most recent ancient genome in the analysis. Different clustering methods might show different results as well.

    ReplyDelete
  33. @Davidski,

    Should I use an ancient or a relevant average modern population for the Generalized Linear Model?

    ReplyDelete
  34. With the 3000+ samples list, I haven't been able to do much, but thought the following PCA exercise may be of interest to some:

    Part1:

    a) Separated all the samples by population grouping*: https://pastebin.com/v4d4Bm5b

    b) Take a list of populations which have reasonably high levels of total sharing with the ancients (including some West Eurasians as well that don't): https://pastebin.com/Cvyx2Udu

    (My cutoff is pretty arbitrary here)

    c) Then after getting that list, using just the ancients as columns and modern people as rows, produce a PCA:

    Result is this: https://ibb.co/jPTHJk

    Each population's label sits at the centre of where its dots (individual samples) plot - and there's a lot of variation within each population here.

    First PC1 separates populations which are generally high tract length sharers with the ancients from populations which are low. This dimension spans the British Isles+Norway on the positive end, as the highest sharers cumulatively with all ancients, down to Near East on the negative with very little sharing. Most of the rest of Europe about 50-75% the distance from the Near East to BI on this dimension.

    (A point of interest to me is that the British Isles is distinct here from populations who generally look to have similar proportions of WHG:Anatolian:Steppe, like Slovakian or German, and overlap heavily with one another. This does not mean that they have more ancient European ancestry or something but is due to the ancients including BI ancients and generally from the whole region from Iberia->Germany, and more likely to be specifically ancestral.).

    Second PC2 then splits populations with relatively high Iberia farmer sharing and lower Steppe and Karasuk (e.g. most extreme Sardinian) sharing on the other from populations who are the reverse (e.g. most extreme Kets).

    * For an alternative list of population groupings: https://pastebin.com/TCbjTbiJ. I've merged a lot of the populations here, to make it easier for me to run averages.

    ReplyDelete
  35. Part 2: So, variations on that PCA above:

    A) Removing row populations who have high sharing with Karasuk, and pretty low sharing with Iberia_EN (e.g. Kets etc.) - https://ibb.co/cnmHZQ, https://ibb.co/fhrvM5, https://ibb.co/hJnPEQ

    That gives a more decompressed look at the variation in the European populations without hugely changing the PCs.

    (Population list: https://pastebin.com/D2pwKHBB)

    B) Modified A) by removing column ancients from the Iron Age (Roman Britain, Anglo Saxon, Slav Bohemia) - https://ibb.co/gTYEW5, https://ibb.co/cctEW5

    Removed in case the preponderance of Iron Age to CE samples from Britain were swelling up the BI position in PC1. Does appear to have reduced that effect, however the graph is mostly the same, so this shape doesn't only or mainly come from that.

    C) Modified B) by removing column ancients from the Irish EBA as well : https://ibb.co/n4geyk, https://ibb.co/jkbCJk

    Flattens things out once again, however again, no major changes.

    Going back to A) though, if we do include the Iron Age populations and go to PC3: https://ibb.co/jR9or5, and loadings there: https://ibb.co/enQiPQ
    This PC3 splits a tendency on the posistive end to share CM with the most recent ancestors of Eastern European - HungaryBA and Slav Bohemia - from a more general set of affinities to the ancients in general on the negative end of the PC. Once decent quality samples from the largely Steppe_EMBA+Narva Baltic_BA population are available, I expect they would also load heavily on the positive end of a similar PC.

    Contrasting the position of the Tajik populations (and apparently Uralic speaking Udmurds) are also pretty interesting here, fitting relatively close to Eastern Europe in the overall structure of PC1 and PC2, due to both having relatively high steppe related CM sharing and lower CM sharing with ancient Iberians and North-Central Bronze Age Europeans... and then very distinct in PC3 because, of course, not sharing these more recent ancestors from late Bronze Age to late Iron Age / CE with present day Eastern European people.

    ReplyDelete
  36. Part 2: So, variations on that PCA above:

    A) Removing row populations who have high sharing with Karasuk, and pretty low sharing with Iberia_EN (e.g. Kets etc.) - https://ibb.co/cnmHZQ, https://ibb.co/fhrvM5, https://ibb.co/hJnPEQ

    That gives a more decompressed look at the variation in the European populations without hugely changing the PCs.
    (Population list: https://pastebin.com/D2pwKHBB)

    B) Modified A) by removing column ancients from the Iron Age (Roman Britain, Anglo Saxon, Slav Bohemia) - https://ibb.co/gTYEW5, https://ibb.co/cctEW5

    Removed in case the preponderance of Iron Age to CE British samples were swelling up the BI position in PC1. Does appear to have reduced that effect, however the graph is mostly the same, so this shape doesn't only or mainly come from that.

    ReplyDelete
  37. Part 3:

    C) Modified B) by removing column ancients from the Irish EBA as well : https://ibb.co/n4geyk, https://ibb.co/jkbCJk

    Flattens things out once again, however again, no major changes.

    Going back to A) though, if we do include the Iron Age populations and go to PC3: https://ibb.co/jR9or5, and loadings there: https://ibb.co/enQiPQ

    This PC3 splits a tendency on the posistive end to share CM with the most recent ancestors of Eastern European - HungaryBA and Slav Bohemia - from a more general set of affinities to the ancients in general on the negative end of the PC.

    Once decent quality samples from the largely Steppe_EMBA+Narva Baltic_BA population are available, I expect they would also be part of loading heavily on the positive end of a similar PC.

    Contrasting the position of the Tajik populations and apparently Uralic Udmurds are also pretty interesting here, fitting relatively close to Eastern Europe in the overall structure of PC1 and PC2, due to having relatively high steppe related CM sharing and lower CM sharing with ancient Iberians and North-Central Bronze Age Europeans... and then very distinct in PC3 because, of course, due to not sharing these more recent ancestors from late Bronze Age to late Iron Age / CE with present day Eastern European people.

    (At Davidski, sorry, an earlier version of this got trapped in your anti-link spam filter, so please delete that if you see).

    ReplyDelete
  38. One last thing also, same as above, using just Bronze Age or later ancients as columns:

    PC1 / PC2: https://ibb.co/mAFiPQ (PC1: high Bronze Age or later sharing vs lower BA or later sharing, PC2: East vs West Bronze Age)

    PC1 / PC3: https://ibb.co/mAFiPQ (PC3: Bronze Age or later ancestors or recent Eastern Europe vs other Bronze Age or later)

    PC2 / PC3: https://ibb.co/jbnf4Q

    Loadings: https://ibb.co/hYHf4Q

    (Fewer columns so slightly more noise in position of populations with low n).

    ReplyDelete
  39. Had some time to use run population averages, just with the ancient individuals as columns for now:

    1. Grouped Ancients as rows, individual ancients as columns: https://pastebin.com/YAVpGj0P

    2. Grouped moderns as rows, individual ancients as columns: https://pastebin.com/YAVpGj0P

    (Not sure if this is worthwhile or if you all have already run / got population averages.)

    Anyway, some graphics based on 2. above: https://imgur.com/a/7F24w
    All pretty self explanatory

    (Btw, I think the method of running an average I have here may be slightly better than the one I used before, which I'm as sure about now. Apologies, folks who used that data).

    ReplyDelete
  40. @jv

    I don't know much about H6a1a.

    But I'd say that you should be able to track the entry of your lineage into Central Europe with precision within a few years as many more ancient mito genomes are sequenced.

    ReplyDelete
  41. These are my ordered non-zero ancients

    AAB_Sintashta_RISE395 13.468412
    AAB_Unetice_RISE577 12.097242
    AAB_Yamnaya_Kalmykia_RISE552 9.746889
    AAB_Ireland_EBA_Rathlin1_RM127 8.557313
    AAB_Unetice_RISE150 8.12866
    AAB_Hungary_BA_RISE479 8.10181
    AAC_Karasuk_outlier_RISE502 7.581374
    AAB_Karasuk_RISE499 7.27049671
    AAB_Yamnaya_Kalmykia_RISE548 6.908238
    AAB_Greece_EN_Rev5 6.541456
    AAB_Ireland_MN_Ballynahatty_BA64 6.416608
    AAB_Afanasievo_RISE511 5.768278
    AAB_Sweden_MN_Gok2 5.752744
    AAB_Anglo_Saxon_NO3423 5.715692
    AAB_Loschbour_Loschbour 5.132116
    AAB_Andronovo_RISE505 4.88297887
    AAB_Roman_Britain_6DRIF-3 4.785061
    AAB_LBK_Stuttgart 4.7076274
    AAB_Hungary_N_I1496 4.68666
    AAB_Portugal_LNCA_CovaMoura364 4.29161105
    AAB_Bichon_Bichon 4.206344
    AAB_Ireland_EBA_Rathlin2_RSK1 4.093057
    AAB_Portugal_MN_LugarCanto42 3.977782
    AAB_Pitted_Ware_Ajv58 3.85059
    AAB_Nordic_LN_RISE98 3.594694
    AAB_Roman_Britain_6DRIF-22 3.346546
    AAB_Roman_Britain_6DRIF-18 3.0715997
    AAC_Altai_IA_RISE601 2.831298
    AAB_Anatolia_N_Bar31 2.707102
    AAB_Karasuk_RISE496 2.69625
    AAB_Mezhovskaya_RISE523 2.6578239
    AAB_Portugal_MBA_MonteGato104 2.589931
    AAB_Portugal_MN_LugarCanto41 2.429286
    AAB_Greece_LN_Klei10 2.4218
    AAB_Slav_Bohemia_RISE569 2.31379
    AAB_Portugal_MN_LugarCanto44 2.30726
    AAB_Greece_LN_Pal7 2.176416
    AAB_Roman_Britain_outlier_3DRIF-26 2.084594
    AAB_Portugal_LNCA_CabecoArruda122A 2.03082
    AAB_Satsurblia_SATP 1.863605
    AAC_Karasuk_outlier_RISE493 1.791589
    AAB_Hungary_IA_IR1 1.78818
    AAB_Roman_Britain_6DRIF-21 1.702548
    AAB_Oetzi_Oetzi 1.675735
    AAB_Spain_LNCA_ATP2 1.590423
    AAC_Altai_IA_RISE602 1.56451
    AAB_Iberia_EN_CB13 1.451491
    AAB_Andronovo_RISE500 1.439435
    AAB_Hungary_CA_I1497 1.390123
    AAB_Hungary_N_I1495 1.374484
    AAB_Portugal_LNCA_DolmenAnsiao96B 1.32424
    AAB_Anatolia_N_Bar8 1.305
    AAB_Kotias_KK1 1.264201
    AAC_Karasuk_outlier_RISE495 1.24146
    AAB_Hungary_BA_I1504 1.120406
    AAB_Portugal_MBA_TV3831 0.893657
    AAB_Portugal_LNCA_CovaMoura9B 0.726186

    ReplyDelete
  42. A lot of the results posted here make sense. Iberia Chalcolithic and modern Spain matching with a Spaniard, Nordin_LN with Norwegian, Roman Britain for England and NW France. But if one's ancestry is so mixed I doubt this test is of much use. Interestingly, Yamnaya seems to keep popping up for NW Euros. We'd have to see other European results to see if this is a legitimate correlation.

    @David,

    Could something like this resolve genealogical relationships between Olalde and Mathiesons's ancient genomes? Like who was North Bell Beaker's Neolithic ancestor?

    @jv,

    This is the age estimate I get for H6a1.

    H 15ky
    ---H6 12ky
    ------H6a 10ky
    ---------H6a1 10ky
    ------------H6a1a 6ky
    ------------H6a1b 8ky

    "Steppe" could have formed between 5000 and 4000 BC which several thousand years after these age estimates. I'm thinking H6a1 had already formed and expanded in the Caucasus before coming onto the Steppe.

    ReplyDelete
  43. @ Samuel Andrews

    Yes, my results as NW French and Norman make sense
    Old Britons, Nordic and Anglo-Saxons are at the top of my list.

    AAB_Sintashta_RISE395 16.7517755
    AAB_Roman_Britain_6DRIF-22 12.372527
    AAB_Unetice_RISE577 11.72396279
    AAB_Unetice_RISE150 11.3984053
    AAB_Anglo_Saxon_NO3423 10.795745
    AAB_Portugal_LNCA_DolmenAnsiao96B 10.53239
    AAB_Afanasievo_RISE511 9.507238
    AAB_Nordic_IA_RISE174 8.849702
    AAB_Mezhovskaya_RISE523 8.82688
    AAC_Karasuk_outlier_RISE502 8.078086
    AAB_Yamnaya_Kalmykia_RISE552 6.857887

    ReplyDelete
  44. So had a go at calculating population averages for length CM sharing.

    It does seem that they vary hugely between population, going from 3806(!) in Nganasan down to 2 in Cypriot. Values are huge in modern Siberians, even by comparison to Bronze Age and HG ancients. Some of these groups are compromised of relatively close relatives, particularly the small Siberian groups - surprised me that these were way high than Karitiana who look very drifted in Fst scores, and isolated maritime Oceanian populations.

    Europeans generally have very short or average sharing averages within populations (which makes sense for huge and admixing populations) in the range of 2 - 20. There are some clear outliers in Russian Central (288) and Cossack Ukrainian (162) who may have been sampled from relatively close relatives (not close enough like first order relatives to distort unlinked PCA, but close enough to have a high excess of sharing here).

    The sheer diversity of value sizes looks to make it impossible just to run a PCA on these. Even in neighbour joining, the branch length differences are huge. Using lengths is super sensitive to very recent shared relatedness, which can be significant in panels where they're only screening out very close relatives (because it's not important to the work they're doing), or it's not possible to do that because the populations are so small. (This is why chunkcounts can be more useful for PCA in some circumstances than the length information?).

    Anyway, here's 1) the .CSV of all pop averages so anyone's free to try with PAST3 though: https://file.io/mNsALZ

    Also 2), here's a .CSV modern groups for rows and grouped ancient averages for columns:

    https://file.io/0dK6fy

    Some more graphs with the ancients as columns and moderns as rows, using group averages in rows and columns, which smooths out a lot that is much noisier with row and column individuals:

    https://imgur.com/a/8mwv6
    https://imgur.com/a/YyckG

    ReplyDelete
  45. How would this work compared to running 100 SNPs and 3 cM against these samples in Gedmatch?

    Also, with phased SNP array data, many of the smaller segments tend to vanish. That's not "IBS vs. IBD", just "unphased data and faulty results".


    There's another interesting thing you can do, too:
    Use the DNA.land ~39 million imputed SNPs instead of the typical arrays.

    We've uploaded to Bar8 from Barcin NW Anatolia c. 8300 BP (no relatives; educational attainment: 14.7 years You have attended college ;) ) and WC1 from Wezmeh Cave, Iran (no relatives either; 13.8 years You have attended college :D ) so I can download the VCF files and make them available, although I think already these have excellent coverage at the typical 1.2 million combined SNP array chip SNPs. (That includes the Affymetrix Human Origins Array as well as the Illumina chips.)


    Do we really know the IBD segments at the whole genome sequence level that constitute "WHG, Anatolian Neolithic, Iranian Neolithic" etc.?

    What do we know about IBD between some of these high-coverage ancient whole genomes and modern whole genome sequences, for example from the 1K Genomes and the SGDP? Does this look the same as IBD using the "minimal set' of SNPs? What about very rare alleles?

    Also how about using the Southern and Eastern African aDNA samples, and also waiting for the aDNA North Africans?

    ReplyDelete
  46. This is probably more of a haplotype test than an IBD test, but whatever it is, it's more informative for fine scale ancestry than using unlinked markers (thus, much better than IBS, for example), and indeed very accurate. The accuracy of the output can be seen in these PCA.

    http://eurogenes.blogspot.com.au/2014/08/haplotype-based-pca-of-west-eurasia-and.html

    Also, unlike IBD tests elsewhere, there is a lot of already integrated output, so users don't have to ask other users for their results, or try to run reference samples themselves, to put their own results into a context.

    However, I really can't just add ancient samples from different sources. It's best if all of the ancient samples are genotyped and prepped in exactly the same way.

    ReplyDelete
  47. I ran 2 Generalized Linear Models with the Anglo-Saxon and the Nordic IA RISE174. It looks like I share somewhat more ancestry with EBA Steppe peoples.

    Anglo-Saxon

    https://drive.google.com/file/d/0B-tlHcv5HwZBdEVnTTJha1p5N0k/view?usp=sharing

    Nordic IA

    https://drive.google.com/file/d/0B-tlHcv5HwZBTWhmNUZWaVJjVVk/view?usp=sharing

    ReplyDelete
  48. Please note that I'll be doing another run at the end of next month. It'll be exactly the same as the last one, so no point doing it again for anyone who's already done it.

    Interestingly, what I found is that this test is very good at picking up not only minor Ashkenazi ancestry, but also minor Sephardic Jewish ancestry, so if anyone is interested in exploring this possibility then taking part in this exercise should be very useful.

    ReplyDelete
  49. Possibly of interest (not sure if anyone read the other posts): I was having a look again at the matrix of group averages.

    Using the simple matrix of averages produces PCA and neighbour joining which don't show very much. Or rather they do show structure, but because the Nganasan and ancient related dimensions are so high, other structure is very small in the PCA / Neighbour Joining:

    So: https://imgur.com/a/NcOwS

    Thinking about this, I carried out a square root transformation of the matrix. That would make the covariance between large (e.g. at most extreme Nganasan) and small dimensions (at most extreme, Cypriot) a lot more even.

    Running PCA and Neighbour Joining on the square root of the average shared CM matrix:

    https://imgur.com/a/qevWQ

    This gives something which is more reflective of deep structure and less dominated by the recent structure.

    This process, using the square root of the matrix / CM may be useful if you want to look at a slightly different balance of the recent and ancient structure (downside is that this isn't really interpretable in the same straightforward way).

    (Various graphs using the square root of shared CM: https://imgur.com/a/XhLG3).

    ReplyDelete
  50. Here are my anicents:

    AAB_Afanasievo_RISE511 2.09049

    AAB_Anatolia_N_Bar31 0

    AAB_Anatolia_N_Bar8 0.97035

    AAB_Andronovo_RISE500 4.512618

    AAB_Andronovo_RISE505 6.612144

    AAB_Anglo_Saxon_NO3423 7.49012

    AAB_Bichon_Bichon 0

    AAB_Greece_EN_Rev5 0

    AAB_Greece_LN_Klei10 1.683009

    AAB_Greece_LN_Pal7 3.26847974

    AAB_Hungary_BA_I1504 6.296164

    AAB_Hungary_BA_RISE479 1.82977

    AAB_Hungary_CA_I1497 1.023273

    AAB_Hungary_HG_I1507 3.463794

    AAB_Hungary_IA_IR1 0

    AAB_Hungary_N_I1495 2.465896

    AAB_Hungary_N_I1496 0

    AAB_Hungary_N_I1506 3.62879

    AAB_Iberia_EN_CB13 3.682671

    AAB_Ireland_EBA_Rathlin1_RM127 8.88122

    AAB_Ireland_EBA_Rathlin2_RSK1 7.1050328

    AAB_Ireland_MN_Ballynahatty_BA64 3.161594

    AAB_Karasuk_RISE496 4.10343

    AAB_Karasuk_RISE499 3.2259

    AAB_Kotias_KK1 0

    AAB_LaBrana1_LaBrana1 0

    AAB_LBK_Stuttgart 2.9941529

    AAB_Loschbour_Loschbour 2.933235

    AAB_Mezhovskaya_RISE523 11.743162

    AAB_Motala_HG_Motala12 0

    AAB_Nordic_IA_RISE174 3.050938

    AAB_Nordic_LN_RISE98 13.4329

    AAB_Oetzi_Oetzi 0

    AAB_Pitted_Ware_Ajv58 0

    AAB_Portugal_LNCA_CabecoArruda122A 0.87258

    AAB_Portugal_LNCA_CovaMoura364 1.21213

    AAB_Portugal_LNCA_CovaMoura9B 2.92982

    AAB_Portugal_LNCA_DolmenAnsiao96B 1.796368

    AAB_Portugal_MBA_MonteGato104 1.615219

    AAB_Portugal_MBA_TV32032 6.447425

    AAB_Portugal_MBA_TV3831 0

    AAB_Portugal_MN_LugarCanto41 0

    AAB_Portugal_MN_LugarCanto42 3.16183

    AAB_Portugal_MN_LugarCanto44 4.03809

    AAB_Roman_Britain_6DRIF-18 7.89825

    AAB_Roman_Britain_6DRIF-21 4.011221

    AAB_Roman_Britain_6DRIF-22 5.06692

    AAB_Roman_Britain_6DRIF-3 9.356601

    AAB_Roman_Britain_outlier_3DRIF-26 0

    AAB_Satsurblia_SATP 0

    AAB_Sintashta_RISE395 6.449945

    AAB_Slav_Bohemia_RISE569 4.428073

    AAB_Spain_LNCA_ATP16 2.3384

    AAB_Spain_LNCA_ATP2 2.183731

    AAB_Spain_LNCA_Matojo 2.818434

    AAB_Sweden_MN_Gok2 5.690385

    AAB_Unetice_RISE150 4.736982

    AAB_Unetice_RISE577 7.486465

    AAB_Yamnaya_Kalmykia_RISE548 12.847587

    AAB_Yamnaya_Kalmykia_RISE552 8.945287

    AAC_Altai_IA_RISE504 0

    AAC_Altai_IA_RISE601 2.60782

    AAC_Altai_IA_RISE602 0

    AAC_Karasuk_outlier_RISE493 0

    AAC_Karasuk_outlier_RISE495 5.870795

    AAC_Karasuk_outlier_RISE497 0

    AAC_Karasuk_outlier_RISE502 6.4392894

    ReplyDelete
  51. Top to 5.
    Modern Matches
    (only included top of English and left out Utah)

    Estonian_ee14 20.519316
    Estonian_ee147 17.7388588
    Hungarian_GS000016901 15.0727931
    English_Kent_HG00131 12.5047673
    English_Cornwall_HG00254 12.2043229
    Norwegian_NOR111 11.9545958
    English_Cornwall_HG00233 11.673633
    Orcadian_HG00117 11.3710984
    Orcadian_HG00110 10.9251329
    Estonian_GS000017199 10.246228
    Russian_North_HGDP00881 9.658181
    Finnish_GS000016894 9.645945
    Macedonian_Macedonian19_GSM1424617 9.518464
    Orcadian_HG00115 9.275291
    English_Cornwall_HG00234 9.272401.3255389
    Hungarian_hungary7 9.948052
    Orcadian_HG00123 9.03231
    Slovakian_Slovakia150 9.0809014
    Chuvash_Chuvash11 8.726197
    Slovakian_Slovakia429 8.668007
    Russian_North_HGDP00894 8.6256213
    Mari_GS000014331 8.596761
    English_Cornwall_HG00252 8.299781
    Ukrainian_East_UkrBel618 8.14323
    Ukrainian_East_GS000035121 8.1435916
    Romanian_Romania13 8.146691
    Adygei_HGDP01384 7.9683
    Russian_North_HGDP00896 7.932111
    Belarusian_belorus7 7.605246
    Erzya_mordovia11 7.485887
    Scottish_Argyll_HG00103 7.27218
    Ukrainian_East_GS00003512 8.1435916
    Romanian_Romania13 8.146691
    French_HGDP00530 7.873901
    English_Cornwall_HG00261 7.905423
    Spanish_Extremadura_HG01531 7.712461
    Spanish_Spanish33H 7.705787
    Spanish_Murcia_HG01756 7.758243
    Erzya_mordovia11 7.485887
    Ukrainian_North_GS000013755 7.377048
    Spanish_Galicia_HG01704 6.829332
    Polish_Polish16H 6.786185
    English_Cornwall_HG00260 6.652127
    Polish_Polish11H 6.584474
    rench_HGDP00527 6.5892593
    Serbian_Bosnia_Serbian_B-H9_GSM1424669 6.540832
    Montenegrin_Montenegro1_GSM1424636 6.503154
    Chuvash_Chuvash13 6.431465
    Latvian_latvian58C8 6.412131
    Swedish_GS000035240 6.408373
    Spanish_Valencia_HG01607 6.356098
    Greenlander_West_GSM558765 6.30466
    Estonian_ee136 6.336066
    Estonian_ee72 6.263758
    French_HGDP00511 6.254699
    Spanish_Spanish34H 6.083324
    Puerto_Rican_GSM531197 6.0123951
    Spanish Aragon_HG01676 6.389606
    Adygei_HGDP01383 6.227883
    Norwegian_NOR148 6.0034178
    Bosnian_Bosnian_8_GSM1424664 5.9583
    Belarusian_GS000035241 5.951467
    Basque_French_HGDP01377 5.559201
    Tajik_Ishkasim_GS000016189 5.85127345
    English_Cornwall_HG00256 5.841081
    Kyrgyz_GS000016191 5.820921
    Spanish_Cantabria_HG01513 5.808557
    French_HGDP00516 5.666612
    Lithuanian_lithuania2 5.575585
    Armenian_Martuni_594711 5.485525
    Uzbek_uzbek88 5.406702
    Greenlander_West_GSM558764 5.404897
    BedouinA_HGDP00635 5.313244
    Croatian_GSM1841134 5.152686375
    Chuvash_Chuvash6 5.090122
    Selkup_selkup2 5.0563243

    ReplyDelete
  52. The final run is underway.

    Please note that the results should be ready on Sunday or Monday.

    ReplyDelete
  53. The output files from the latest run have been sent out to the participants. Please let me know if you didn't get your files yet (though check your junk mail folder first).

    Also please let me know if there's something wrong with your files, like columns or rows missing or the wrong name in your files.

    This was the last IBD/haplotype run for a while. I might do more next year, or not.

    ReplyDelete
  54. By the way, the full matrix with the reference samples is located here. It shouldn't be much different from the matrix of the same type from the previous run.

    https://drive.google.com/file/d/0B9o3EYTdM8lQNG5SSE1Vb3pDdW8/view?usp=sharing

    ReplyDelete
  55. Thanks David,

    My mother,
    All her known ancestry is Norman

    Ancients

    AAB_Nordic_LN_RISE98 11.551827
    AAB_Ireland_EBA_Rathlin2_RSK1 11.36062
    AAC_Karasuk_outlier_RISE502 10.6204245
    AAB_Roman_Britain_6DRIF-22 9.507771
    AAB_Unetice_RISE150 9.316421
    AAB_Roman_Britain_6DRIF-18 7.837079
    AAB_Yamnaya_Kalmykia_RISE548 6.850959
    AAB_Sintashta_RISE395 6.5188689
    AAB_Afanasievo_RISE511 6.303805
    AAB_Portugal_MBA_TV3831 6.12366
    AAB_Anglo_Saxon_NO3423 5.948935
    AAB_Hungary_HG_I1507 5.841674
    AAB_Nordic_IA_RISE174 5.657935
    AAB_Mezhovskaya_RISE523 4.63648
    AAB_Roman_Britain_6DRIF-21 4.546093
    AAB_Hungary_N_I1496 4.178912
    AAB_Karasuk_RISE496 3.868711
    AAB_Andronovo_RISE505 3.66838
    AAB_Yamnaya_Kalmykia_RISE552 3.569872
    AAB_Spain_LNCA_ATP16 3.517192
    AAB_Hungary_N_I1506 3.499324
    AAB_Greece_LN_Klei10 3.459601
    AAC_Altai_IA_RISE602 3.309373
    AAB_Unetice_RISE577 3.15992
    AAB_Greece_LN_Pal7 3.144392
    AAB_Ireland_EBA_Rathlin1_RM127 3.10218
    AAB_Andronovo_RISE500 3.042733
    AAB_Anatolia_N_Bar8 2.342066
    AAB_Portugal_MBA_TV32032 2.340929
    AAB_Hungary_BA_RISE479 2.3243
    AAB_Karasuk_RISE499 2.27123
    AAB_Anatolia_N_Bar31 2.1949
    AAB_Roman_Britain_6DRIF-3 2.16941
    AAB_Bichon_Bichon 2.107768
    AAB_Loschbour_Loschbour 2.02534
    AAB_Spain_LNCA_ATP2 1.97691
    AAB_Portugal_MN_LugarCanto42 1.77719
    AAB_Ireland_MN_Ballynahatty_BA64 1.750724
    AAB_Iberia_EN_CB13 1.61539
    AAB_Greece_EN_Rev5 1.552122
    AAB_Hungary_N_I1495 1.531179
    AAC_Altai_IA_RISE601 1.496901
    AAB_LBK_Stuttgart 1.42724
    AAB_Portugal_MN_LugarCanto41 1.364218
    AAC_Karasuk_outlier_RISE493 1.324791
    AAB_LaBrana1_LaBrana1 1.28351
    AAB_Sweden_MN_Gok2 1.20004
    AAB_Hungary_CA_I1497 1.08945
    AAB_Portugal_LNCA_DolmenAnsiao96B 0.96788
    AAB_Portugal_MN_LugarCanto44 0.903419
    AAB_Portugal_MBA_MonteGato104 0.88338
    AAB_Portugal_LNCA_CovaMoura364 0.61828
    AAB_Hungary_BA_I1504 0
    AAC_Karasuk_outlier_RISE495 0
    AAB_Hungary_IA_IR1 0
    AAB_Motala_HG_Motala12 0
    AAB_Portugal_LNCA_CovaMoura9B 0
    AAB_Portugal_LNCA_CabecoArruda122A 0
    AAB_Spain_LNCA_Matojo 0
    AAB_Kotias_KK1 0
    AAB_Pitted_Ware_Ajv58 0
    AAB_Slav_Bohemia_RISE569 0
    AAC_Altai_IA_RISE504 0
    AAB_Satsurblia_SATP 0
    AAB_Oetzi_Oetzi 0
    AAB_Roman_Britain_outlier_3DRIF-26 0
    AAC_Karasuk_outlier_RISE497 0

    ReplyDelete
  56. Now Moderns above 7


    Orcadian_HG00110 14.475241
    Orcadian_HG00109 13.08115
    Utah_Scandinavian_NA12248 12.972287
    Chechen_ch55 12.888375
    Vepsa_GS000017632 12.786198
    Orcadian_HG00107 11.624195
    Dominican_GSM531142 11.5226677
    Hungarian_hungary7 11.409546
    Lithuanian_GS000035040 11.152151
    English_Cornwall_HG00251 11.113924
    French_HGDP00514 10.944773
    Slovenian_Slovenian90 10.9402787
    English_Kent_HG00127 10.8937
    Greenlander_East_GSM558768 10.8694002
    Utah_Scandinavian_NA12875 10.806613
    Utah_USA_NA12275 10.71548
    Utah_British_NA12489 10.458613
    Orcadian_HG00096 10.363046
    Utah_German_NA12057 10.281102
    Ukrainian_East_UkrBel620 10.251536
    English_Cornwall_HG00242 10.144187
    Utah_USA_NA12341 10.05134
    French_HGDP00519 9.753802
    English_Kent_HG00137 9.665715
    English_Kent_HG01334 9.633953
    Italian_Tuscan_NA20805 9.565043
    Slovakian_Slovakia411 9.562743
    Orcadian_HG00113 9.480361
    Orcadian_HGDP00796 9.477838
    English_Cornwall_HG00239 9.369001
    Moksha_mordovia14 9.0111432
    Spanish_Baleares_HG01632 8.982559
    Palestinian_HGDP00745 8.946666
    Erzya_mordovia6 8.861311
    Estonian_ee86 8.71597
    Spanish_Cataluna_HG01762 8.69219
    English_Kent_HG00151 8.651964
    Spanish_Cantabria_HG01679 8.55852
    Belarusian_GS000014324 8.551554
    French_HGDP00529 8.521487
    English_Cornwall_HG00252 8.495404
    Utah_British_NA11920 8.4112019
    Utah_USA_NA11891 8.3302408
    Scottish_Argyll_HG00104 8.291267
    Orcadian_HG00125 8.27623
    Spanish_Baleares_HG01631 8.267177
    Greenlander_West_GSM558765 8.242225
    English_Cornwall_HG00232 8.155716
    Estonian_ee14 8.147503
    Spanish_Castilla_Y_Leon_HG01500 7.971709
    English_Kent_HG00130 7.877634
    Macedonian_Macedonian9_GSM1424626 7.740696
    French_HGDP00534 7.7207352
    Spanish_Pais_Vasco_HG01521 7.71403339
    French_HGDP00535 7.713748
    Norwegian_NOR146 7.71291
    English_Kent_HG00155 7.707903
    Orcadian_HG00102 7.656243
    Utah_British_NA12348 7.636785
    Erzya_mordovia10 7.63597
    Italian_Tuscan_HGDP01168 7.520678
    Orcadian_HG00114 7.512968
    Finnish_HG00351 7.494633
    Spanish_Murcia_HG01618 7.47731354
    Chechen_ch174 7.441028
    Russian_North_HGDP00898 7.4019605
    French_HGDP00537 7.277731
    Estonian_ee114 7.241416
    Utah_USA_NA12282 7.235981
    Utah_Scandinavian_NA07346 7.233114
    Spanish_Pais_Vasco_HG01519 7.22833
    Utah_German_NA11930 7.207485
    Orcadian_HG00100 7.181038
    Utah_British_NA12827 7.152068
    Saami_GS000035025 7.144601
    Spanish_Cataluna_HG01761 7.13986
    Italian_Bergamo_HGDP01156 7.1188428
    Italian_Bergamo_HGDP01153 7.116374
    Tatar_GS000013705 7.108236
    Hungarian_hungary20 7.06185
    Orcadian_HGDP00810 7.004754

    ReplyDelete
  57. Circassian Adyghe

    moderns
    Balkar_bal26‎ ‎9.017191‎
    Abkhasian_abh107‎ ‎8.914848‎
    Balkar_GS000016171‎ ‎8.789937‎
    North_Ossetian_NorthOssetia11‎ ‎8.7586‎
    Makrani_HGDP00134‎ ‎8.75695‎
    Kabardin_GS000014412‎ ‎8.6799006‎
    Georgian_mg31‎ ‎8.631912‎
    North_Ossetian_NorthOssetia1‎ ‎8.497878‎
    Nogai_nogay6‎ ‎8.433705‎
    Georgian_mg64‎ ‎8.346976‎
    AAB_Yamnaya_Kalmykia_RISE552‎ ‎8.241516‎
    Kumyk_kumyks1‎ ‎8.031223‎
    Adygei_HGDP01398‎ ‎76.218498‎
    North_Ossetian_GS000014414‎ ‎7.911181‎
    Estonian_ee105‎ ‎7.79478‎
    Balkar_GS000016172‎ ‎7.664233‎
    Nogai_nogay8‎ ‎7.64884‎
    Abkhasian_abh60‎ ‎7.64253‎
    Balkar_bal42‎ ‎7.635583‎
    Turkish_tur306‎ ‎7.4717939‎
    AAB_Afanasievo_RISE511‎ ‎7.445641‎
    Kumyk_kumyks4‎ ‎7.30400485‎
    Nogai_nogay15‎ ‎7.260375‎
    Chechen_ch126‎ ‎7.172894‎
    Georgian_mg27‎ ‎7.06318‎

    ancients
    AAB_Yamnaya_Kalmykia_RISE552‎ ‎8.241516‎
    AAB_Afanasievo_RISE511‎ ‎7.445641‎
    AAB_Karasuk_RISE499‎ ‎5.049705‎
    AAB_Yamnaya_Kalmykia_RISE548‎ ‎5.0456434‎
    AAB_Mezhovskaya_RISE523‎ ‎3.745081‎
    AAB_Portugal_LNCA_CabecoArruda122A ‎3.384766‎
    AAB_Roman_Britain_6DRIF-18‎ ‎3.368252‎
    AAB_Unetice_RISE577‎ ‎3.219513‎
    AAB_Iberia_EN_CB13‎ ‎2.717782‎
    AAB_Kotias_KK1‎ ‎2.519078‎
    AAB_Greece_LN_Pal7‎ ‎2.376812‎
    AAB_Nordic_IA_RISE174‎ ‎2.36579‎
    AAB_Ireland_EBA_Rathlin1_RM127‎ ‎2.123369‎
    AAB_Sintashta_RISE395‎ ‎2.08358‎
    AAB_Portugal_MBA_TV3831‎ ‎2.049955‎
    AAB_Satsurblia_SATP ‎2.03391‎
    AAB_Ireland_EBA_Rathlin2_RSK1‎ ‎1.886384‎
    AAB_Motala_HG_Motala12‎ ‎1.88183‎
    AAB_Pitted_Ware_Ajv58‎ ‎1.734875‎
    AAB_Hungary_CA_I1497‎ ‎1.515327‎
    AAB_Unetice_RISE150‎ ‎1.311231‎
    AAC_Karasuk_outlier_RISE502‎ ‎1.28715‎
    AAB_Portugal_LNCA_CovaMoura9B ‎1.22925‎
    AAB_Portugal_LNCA_DolmenAnsiao96B ‎1.148459‎
    AAB_Spain_LNCA_Matojo ‎1.078616‎
    AAC_Altai_IA_RISE602‎ ‎0.935903‎
    AAB_Hungary_IA_IR1‎ ‎0.927924‎
    AAB_Roman_Britain_6DRIF-22‎ ‎0.602789‎

    ReplyDelete
  58. Jewish Sefarad from Turkey (Me)

    moderns
    Spanish_Spanish24H 9.991606
    Sephardic_Jew_sephardic8tur 9.918591
    Spanish_Spanish18H 9.868333
    Spanish_Castilla_Y_Leon_HG01501 9.8666046
    Sephardic_Jew_sephardic4tur 9.864239
    English_Kent_HG00139 9.774871
    Turkmen_Turkm1820Y 9.58592
    Moroccan_Jew_Morocco_Jew_10 9.50789
    Ashkenazi_Jew_ashkenazy1w 9.39209
    Peruvian_HG01991 9.31654
    Ukrainian_West_UkrLv215 9.23544
    Sephardic_Jew_sephardic2tur 9.059313
    Sephardic_Jew_sephardic6tur 9.041601
    Utah_USA_NA11891 8.8929337
    French_HGDP00516 8.782844
    Spanish_Pais_Vasco_HG01519 8.7425607
    Bulgarian_Bulgaria6 8.613353
    Moroccan_Jew_Morocco_Jew_7 8.516483
    Sephardic_Jew_sephardic3tur 8.361968
    Moroccan_Jew_Morocco_Jew_5 8.0205982
    Sephardic_Jew_sephardic9tur 7.749657
    Orcadian_HG00097 7.676
    Italian_Tuscan_NA20800 7.62498
    Ecuadorian_GSM531181 7.574185
    Ashkenazi_Jew_ashkenazy4w 7.4173
    Croatian_GSM1841122 7.379854
    Bulgarian_Bulgarian14H 7.30099
    Ecuadorian_GSM531178 7.13125774
    Ashkenazi_Jew_ashkenazy8e 7.063417
    AAB_Portugal_LNCA_CabecoArruda122A 7.0109527

    ancients
    AAB_Portugal_LNCA_CabecoArruda122A 7.0109527
    AAB_Portugal_MN_LugarCanto44 5.4031474
    AAB_Andronovo_RISE505 4.807191
    AAB_Anatolia_N_Bar31 4.694531
    AAB_Yamnaya_Kalmykia_RISE552 4.676614
    AAB_Karasuk_RISE499 4.5973472
    AAB_Roman_Britain_6DRIF-22 4.340499
    AAB_Portugal_LNCA_CovaMoura364 4.323923
    AAB_Andronovo_RISE500 3.892618
    AAB_Roman_Britain_outlier_3DRIF-26 3.620717
    AAB_Nordic_IA_RISE174 3.357168
    AAB_Karasuk_RISE496 3.340335
    AAB_Portugal_LNCA_DolmenAnsiao96B 3.30771
    AAB_Hungary_BA_RISE479 3.233344
    AAB_Bichon_Bichon 3.142946
    AAB_Spain_LNCA_ATP2 3.118091
    AAB_Ireland_MN_Ballynahatty_BA64 2.897273
    AAB_Ireland_EBA_Rathlin2_RSK1 2.629605
    AAB_Nordic_LN_RISE98 2.553524
    AAB_Spain_LNCA_Matojo 2.378144
    AAB_Hungary_IA_IR1 2.237071
    AAB_Hungary_CA_I1497 2.07952
    AAB_Anatolia_N_Bar8 1.86913
    AAB_Kotias_KK1 1.79867
    AAB_LaBrana1_LaBrana1 1.6793519
    AAC_Karasuk_outlier_RISE502 1.45563
    AAB_Afanasievo_RISE511 1.441771
    AAB_Greece_LN_Klei10 1.412242
    AAB_Portugal_MN_LugarCanto41 1.405098
    AAB_Roman_Britain_6DRIF-3 1.363847
    AAC_Karasuk_outlier_RISE495 1.35078
    AAB_Portugal_LNCA_CovaMoura9B 1.317029
    AAB_Unetice_RISE577 1.29087
    AAB_Mezhovskaya_RISE523 1.22446
    AAB_Slav_Bohemia_RISE569 1.199362
    AAB_Oetzi_Oetzi 1.14137096
    AAB_Hungary_N_I1506 1.12275
    AAB_Greece_LN_Pal7 0.90698
    AAB_Portugal_MBA_MonteGato104 0.86474
    AAB_Roman_Britain_6DRIF-18 0.719853
    AAB_Hungary_HG_I1507 0.661819
    AAC_Karasuk_outlier_RISE493 0.57908

    ReplyDelete
  59. Thank you, David. Now to share:

    First, my mother, who is Turkish from Konya province:

    Ancients:
    AAB_Andronovo_RISE500 6.42408
    AAB_Yamnaya_Kalmykia_RISE552 5.278317
    AAB_Unetice_RISE150 5.12841
    AAC_Karasuk_outlier_RISE493 4.331857
    AAB_Afanasievo_RISE511 3.380824
    AAB_Nordic_IA_RISE174 3.324351
    AAB_Slav_Bohemia_RISE569 3.121997
    AAB_Iberia_EN_CB13 3.1094142
    AAB_Unetice_RISE577 2.767068
    AAB_Andronovo_RISE505 2.253122
    AAB_Greece_LN_Klei10 1.92386
    AAB_Portugal_MBA_TV3831 1.919169
    AAB_Karasuk_RISE496 1.8745
    AAB_Anglo_Saxon_NO3423 1.82043
    AAB_Portugal_MBA_MonteGato104 1.76354
    AAB_Karasuk_RISE499 1.74112
    AAB_Pitted_Ware_Ajv58 1.72317
    AAB_Loschbour_Loschbour 1.62675
    AAB_Roman_Britain_6DRIF-3 1.579112
    AAB_Anatolia_N_Bar8 1.52354
    AAC_Karasuk_outlier_RISE495 1.234356
    AAC_Altai_IA_RISE602 1.233702
    AAB_Portugal_LNCA_CovaMoura9B 1.18412
    AAB_Kotias_KK1 1.17528
    AAB_Motala_HG_Motala12 1.136066
    AAC_Karasuk_outlier_RISE502 1.10671
    AAB_Portugal_LNCA_CabecoArruda122A 1.051965
    AAB_Portugal_MN_LugarCanto44 1.013606
    AAB_Anatolia_N_Bar31 0.869125
    AAB_Roman_Britain_6DRIF-22 0.645181

    Moderns above 5

    Adygei_HGDP01403 20.257358
    UAE_UAE8H 9.589406
    Armenian_Gavar_594276 9.534454
    Lezgin_lez36 8.937939
    Chuvash_Chuvash2 8.042364
    Nenets_Tundra_GS000016161 7.8317198
    Montenegrin_Montenegro1_GSM1424636 7.741284
    Armenian_Dprabak_594262 7.615005
    Dolgan_Dolgan3840 7.307762
    Yukaghir_Yukagir5 6.985219
    Dolgan_Dolgan2 6.9719976
    Kirghiz_KirgizKGN71 6.971676
    Abkhasian_abh74 6.91966
    Armenian_arm23 6.62113
    Slovenian_Slovenian188 6.158294
    Russian_North_HGDP00879 6.092113
    Azeri_GS000013742 6.091424
    Buryat_buryat26 5.955876
    Nogai_nogay3 5.868947
    Tabasaran_GS000014421 5.852775
    Yakut_HGDP00946 5.7739889
    Armenian_Chambarak_591328 5.724905
    Turkish_tur20 5.7244615
    Kazakh_Kazakh34cp 5.418473
    Nganassan_Nganassan12 5.361141
    Greek_Peloponnese_GreecePelop4 5.27383
    Moldavian_GS000016900 5.245368
    Armenian_Chambarak_591320 5.208148
    Slovakian_Slovakia218 5.203969
    Turkmen_GS000035120 5.177666
    Balkar_bal115 5.1171949
    Lithuanian_lithuania8 5.088057
    Polish_Polish12H 5.059424
    Yemenite_Jew_Yemen_Jew_8 5.039334
    Polish_Polish8H 5.028475

    ReplyDelete
  60. Now, my father, who is also from Konya province, near a village on the Karaman border:

    Ancients:

    AAB_Ireland_EBA_Rathlin1_RM127 4.7023287
    AAB_Yamnaya_Kalmykia_RISE552 4.202706
    AAB_Roman_Britain_6DRIF-22 3.975372
    AAB_Nordic_IA_RISE174 3.78104
    AAB_Karasuk_RISE499 3.744172
    AAB_Slav_Bohemia_RISE569 3.503353
    AAB_Hungary_BA_I1504 3.490808
    AAB_Portugal_LNCA_CabecoArruda122A 3.366632
    AAB_Afanasievo_RISE511 3.218045
    AAB_Roman_Britain_6DRIF-18 3.07996
    AAB_Portugal_MBA_MonteGato104 2.83521
    AAB_Greece_LN_Klei10 2.807088
    AAB_Portugal_LNCA_CovaMoura9B 2.784958
    AAB_Hungary_IA_IR1 2.578737
    AAB_Hungary_N_I1506 2.526664
    AAB_Hungary_N_I1496 2.380193
    AAB_Anatolia_N_Bar31 2.31071
    AAB_Portugal_MBA_TV32032 2.227
    AAB_Sintashta_RISE395 2.13554
    AAB_Portugal_LNCA_CovaMoura364 1.98638
    AAB_Iberia_EN_CB13 1.962123
    AAB_Greece_EN_Rev5 1.66943
    AAB_Hungary_BA_RISE479 1.598346
    AAB_LBK_Stuttgart 1.55689
    AAB_Anglo_Saxon_NO3423 1.47606
    AAB_Hungary_HG_I1507 1.41522
    AAB_Anatolia_N_Bar8 1.412246
    AAB_Andronovo_RISE500 1.046159
    AAB_Satsurblia_SATP 1.021313
    AAB_Kotias_KK1 0.96273

    Moderns above 5:

    Mongolian_GS000035236 8.571368
    Bulgarian_Bulgarian8H 8.490846
    Hungarian_GS000016902 8.1575322
    Bosnian_Bosnian_8_GSM1424664 8.13567
    Mordovian_GS000015874 7.691629
    Italian_Bergamo_HGDP01177 7.16786
    Hazara_HGDP00119 7.033922
    Serbian_Serbian_Serbia2_GSM1424676 6.601477
    Bulgarian_Bulgaria5 6.589201
    Assyrian_GS000013750 6.404038
    Hungarian_hungary10 6.37783
    Lebanese_Druze_981 6.292318
    Croatian_GSM1841126 6.194472
    Utah_German_NA12144 6.192405
    Armenian_Lebanon_1369 5.994606
    Ukrainian_West_GS000035177 5.9425353
    Yakut_HGDP00957 5.887503
    Armenian_Lebanon_752 5.82123
    North_Ossetian_NorthOssetia14 5.7873648
    Armenian_Lebanon_987 5.738021
    Spanish_Spanish17H 5.630353
    Evenk_evenk14 5.619151
    Russian_North_HGDP00899 5.617099
    Estonian_ee53 5.613946
    Utah_USA_NA12154 5.593913
    Kalash_HGDP00285 5.583187
    Armenian_Lebanon_1278 5.582825
    Kumyk_Kumyk22 5.577164
    BedouinA_HGDP00639 5.472095
    Pathan_HGDP00214 5.458734
    English_Cornwall_HG00243 5.442521
    Armenian_Dprabak_594264 5.287463
    Russian_North_HGDP00882 5.280798
    Armenian_armenia102 5.268501
    Italian_Bergamo_HGDP01153 5.169909
    English_Kent_HG00129 5.16099
    Buryat_GS000022093 5.068622
    Russian_North_HGDP00903 5.014713
    Bulgarian_Bulgaria33 5.0077091

    ReplyDelete
  61. And, now, my father in law, who is Iranian Azeri from a village north of Tabriz:

    Ancients:

    AAB_Hungary_IA_IR1 5.834071
    AAC_Karasuk_outlier_RISE495 4.251577
    AAB_Roman_Britain_6DRIF-18 3.258722
    AAB_Kotias_KK1 3.03509
    AAC_Altai_IA_RISE601 2.77634
    AAB_Ireland_EBA_Rathlin2_RSK1 2.73472
    AAB_Nordic_LN_RISE98 2.73472
    AAB_Portugal_MBA_MonteGato104 2.454019
    AAB_Karasuk_RISE499 2.30782
    AAB_Hungary_BA_RISE479 2.178168
    AAC_Karasuk_outlier_RISE493 2.156091
    AAB_Andronovo_RISE505 1.9842
    AAB_Hungary_N_I1496 1.96231
    AAB_Iberia_EN_CB13 1.79143
    AAB_Greece_EN_Rev5 1.734624
    AAB_Satsurblia_SATP 1.713895
    AAC_Altai_IA_RISE504 1.71109
    AAB_Portugal_LNCA_DolmenAnsiao96B 1.65593
    AAB_Portugal_MBA_TV32032 1.573096
    AAB_Roman_Britain_6DRIF-21 1.386672
    AAB_Roman_Britain_6DRIF-22 1.36676
    AAB_Hungary_CA_I1497 1.2746
    AAB_Portugal_MN_LugarCanto44 1.26624
    AAB_Yamnaya_Kalmykia_RISE548 1.25957
    AAC_Altai_IA_RISE602 1.09614
    AAB_LaBrana1_LaBrana1 0.771773
    AAB_Yamnaya_Kalmykia_RISE552 0.15665

    Moderns above 5:

    English_Kent_HG00154 17.273723
    Balkar_GS000016170 13.75133
    Lezgin_lez52 9.305623
    Chechen_ch174 8.5985468
    Armenian_Dprabak_594258 7.068226
    Armenian_Chambarak_591322 7.013583
    Armenian_Lebanon_752 6.784362
    Yakut_HGDP00956 6.697956
    Iranian_iran3 6.6785995
    Armenian_Yegvard_594215 6.674042
    Armenian_Dprabak_594265 6.427722
    Ashkenazi_Jew_ashkenazy8e 6.396128
    Greek_Greek10H 6.345505
    Georgian_mg5 6.2420195
    Finnish_GS000016894 6.167029
    Uzbek_usb1 6.136495
    Makrani_HGDP00146 6.042303
    Armenian_armenia293 5.93247419
    Assyrian_GS000013751 5.92488
    Nogai_nogay10 5.88076
    Macedonian_Macedonian14_GSM1424615 5.86220794
    Slovakian_Slovakia94 5.83819
    Armenian_Lebanon_1879 5.825038
    Armenian_Lebanon_223 5.82465
    Abkhasian_abh53 5.821655
    Serbian_Serbian_Serbia7_GSM1424682 5.67931
    Indian_Singapore_SGVP00269 5.662798
    Iranian_iran4 5.650865
    Abkhasian_abh41 5.605775
    Greek_Greek16H 5.57198893
    French_HGDP00511 5.363605
    Armenian_Chambarak_591413 5.352352
    Balkar_bal22 5.33844
    Italian_Tuscan_NA20540 5.3380612
    Mozabite_HGDP01264 5.284681
    Armenian_Lebanon_243 5.280737
    Croatian_GSM1841132 5.2310321
    Italian_Tuscan_NA20521 5.220965
    North_Ossetian_GS000014414 5.197427
    Italian_South_SouthItalian6H 5.051291
    Macedonian_Macedonian8_GSM1424625 5.0353017

    ReplyDelete
  62. And, here is what happens when two admixed Central Anatolian Turks and an Iranian Azeri are placed in a neighbor-join tree based on ancients and moderns altogether:

    https://drive.google.com/open?id=1xDSEu4KpL01tLpidcZ4AIBD1iOyO9P6j

    They all appear to be within the Iranian cluster, with my father on the border between the Iranians and an ancient British Roman outlier...

    ReplyDelete
  63. David:

    I more closely viewed the Mongolian to whom my father appears related (more than his relation to other moderns in your list). Looking at the Full matrix you have uploaded, that Mongolian is very different from the others and appears surely Tuvan. Here are the top 20 individuals to whom Mongolian_GS000035236 is related most closely in your Full list:

    Tuvinian_GS000016175 79.9454025
    Tuvinian_tuva8 67.437609
    Altaian_altai13 64.7527042
    Tuvinian_tuva15 59.831656
    Tuvinian_GS000017247 53.8523694
    Tuvinian_tuva5 51.753942
    Altaian_altai9 48.5079602
    Altaian_GS000016174 45.5866025
    Tuvinian_tuva9 45.5314287
    Altaian_altai11 45.0043075
    Tuvinian_tuva12 44.608433
    Tuvinian_tuva1 44.411097
    Tuvinian_tuva16 42.0453904
    Altaian_GS000020512 40.6437589
    Tuvinian_tuva10 40.551704
    Altaian_altai2 40.1731328
    Buryat_Buryat4 39.9861632
    Tuvinian_tuva2 39.32236367
    Tuvinian_GS000016968 39.29450269
    Nganassan_Nganassan1 38.2807902

    It is further notable that *none* of the other individuals who are classified as Mongolian in your Full list have any value above 25 for any of the Altaians and Tuvinians, mostly staying below 15 (only with some Buryats they share more than 30). So, anyway, Mongolian_GS000035236 is really more Tuvinian.

    ReplyDelete
  64. Might be. I just keep the labels that they come with.

    ReplyDelete
  65. Fair enough.

    Also, I checked out the English_Kent_HG00154 individual who appears curiously similar to my Iranian Azeri father-in-law.

    There is something interesting going on with Kent folk as they seem to be *very* similar to some ancients. The particular Kentian to whom my father in law appears similar has the following ancient relations:

    AAB_Andronovo_RISE505 17.7070789
    AAB_Nordic_LN_RISE98 15.381119
    AAB_Anglo_Saxon_NO3423 14.215199
    AAB_Yamnaya_Kalmykia_RISE548 12.6967519
    AAB_Sintashta_RISE395 11.938612
    AAB_Roman_Britain_6DRIF-21 11.344539
    AAB_Ireland_EBA_Rathlin1_RM127 10.455916

    ReplyDelete
  66. Not sure if that's meaningful unless your father-in-law himself shares at least a few cM with this English Kent individual.

    ReplyDelete
  67. @David:
    That's the point -- my father-in-law shares 17.27 cM with that Kent individual (the most he shares with anyone in your list). That's why I checked him out.

    ReplyDelete
  68. OK, I see. This individual from Kent might have some minor but recent ancestry from western Asia. Lots of people settled in London an surrounds from a lot of different places during the past 200 years or so.

    Then again, this might just be the result of an unusual accumulation of ancient segments from the Bronze Age steppe and even Neolithic western Asia.

    ReplyDelete
  69. Hmm.. Well, I don't see anyone Western Asian in that Kentian's top 120 "closest relations" list -- not even any Caucasus folks, though my father-in-law is clearly most related to Caucasus people. The only kind of interesting thing that is clear from that Kentian's list (aside from the ancients) is the Kentian's obvious Finno-Ugric ancestry (Karelians, Saami, Erzya Mordvins, Estonians, Finns, Mari, Vepsa, ...). And, an Uyghur at 8cM overlap too is kind of interesting...

    I have to look at the 2 and 3 hop neighborhoods to learn more (if there is more information to be gained).

    ReplyDelete
  70. would anyone consider 3cm hits as potential evidence of jewish ancestry?? as i know its a bit low

    ReplyDelete
  71. @MomOfZoha

    I had a closer look at that shared cM between your father in law and the sample from Kent. It's actually a single hit, so probably a cold spot. But at first glance, your father in law does show a lot of shared segments with Northern Europeans.

    @Hyper500

    If you have Jewish ancestry you'll share some cM with all or almost all of the Ashkenazi and Sephardi samples in this analysis.

    So if you're seeing a few zeros between you and the Ashkenazi and Sephardi samples in the cM column, then chances are you don't have any Jewish ancestry.

    ReplyDelete
  72. @David:
    Interesting, thanks for checking. My husband's family name means "from Karabagh" as they are known to have migrated from Karabagh upon the Russo-Persian war a couple centuries ago, and the name is shared by both Azeris and Armenians of Iran. Certainly, some of his ancestors' relations would have stayed in the Russian empire.

    By the way, do you have the shared segment information (locations and lengths) stored for that matrix, or did you recalculate it?

    ReplyDelete
  73. I have the segment information, but it's too bulky to edit and send over to each participant. I'd need some sort of script to extract the info for each individual. Don't have anything like that yet.

    ReplyDelete
  74. Ok, I appreciate if you do not delete it (I'm guessing time is more valuable to you than space).

    ReplyDelete
  75. I don't plan on deleting the raw output for a while, in case someone wants to check something.

    ReplyDelete
  76. This comment has been removed by the author.

    ReplyDelete

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