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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 [] per individual. Please e-mail the data and money (via PayPal) to []. 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.

78 comments:

Davidski said...

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

Chad Rohlfsen said...

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

Davidski said...

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

Lathan The Great said...

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.

epoch2013 said...

@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.

Davidski said...

@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.

epoch2013 said...

@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?

Davidski said...

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.

Ryan said...

@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.

Davidski said...

@All

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

David Rabaez said...

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

Davidski said...

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

Helgenes50 said...

@ 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







Derek said...

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.

Paul Brooker said...

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

Matt said...

@ 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.

Chad Rohlfsen said...

@ 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.

Chad Rohlfsen said...

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

Chad Rohlfsen said...

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


Chad Rohlfsen said...

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

Dmytro said...

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

Helgenes50 said...

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

David Rabaez said...

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

David Rabaez said...

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

Tesmos said...

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

Tesmos said...

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

huijbregts said...

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

jv said...

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)

Davidski said...

@jv

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

jv said...

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

Dmytro said...

"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.

Derek said...

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

Davidski said...

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.

Tesmos said...

@Davidski,

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

Davidski said...

Why not try both?

Matt said...

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.

Matt said...

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.

Matt said...

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.

Matt said...

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).

Matt said...

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).

Matt said...

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).

Davidski said...

@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.

KVN said...

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

Samuel Andrews said...

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.

Helgenes50 said...

@ 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

Chad Rohlfsen said...

What Norwegian?

Matt said...

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

Open Genomes said...

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?

Davidski said...

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.

Tesmos said...

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

Davidski said...

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.

Matt said...

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).

Gabriel Opi said...

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

Gabriel Opi said...

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

Davidski said...

The final run is underway.

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

Davidski said...

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.

Davidski said...

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

Helgenes50 said...

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

Helgenes50 said...

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

Alper Romano said...

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

Alper Romano said...

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

MomOfZoha said...

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

MomOfZoha said...

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

MomOfZoha said...

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

MomOfZoha said...

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...

MomOfZoha said...

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.

Davidski said...

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

MomOfZoha said...

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

Davidski said...

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

MomOfZoha said...

@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.

Davidski said...

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.

MomOfZoha said...

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).

Hyper500 said...

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

Davidski said...

@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.

MomOfZoha said...

@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?

Davidski said...

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.

MomOfZoha said...

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

Davidski said...

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