Tuesday, November 28, 2017

Historical admixture results

I am running historical admixtures using Globetrotter software.  The results will be added to this same blog entry.

Western Volga-Finnic (mainly Mordvas)

time:  36 generations, near 1000 years ago

East_Slavic    0,4867536482
Baltic    0,2887079451
Central_European    0,0570663623
Mongola    0,051551692
East_Volga_Finnic_Chuvash    0,04939485
Mansi_Khanty    0,0270296952
East_Baltic_Finnic    0,0169141037
South_European    0,0098787291
Central_Siberian    0,0073332031
North_Siberian    0,0023436624
North_Baltic-Finnic_G4    0,0015424098
Saami    0,0014836991

East_Volga_Finnic_Chuvash stands for Maris, Chuvashes and Udmurts, East Baltic Finns for Karelians and Vepsians, North Finnic G4 for Ingrians.


West_European    0,6080567694
Baltic    0,203714483
North_Baltic_Finnic_G3    0,092400554
North_Baltic_Finnic_G1    0,0431817267
East_Slavic    0,0387924755
Saami    0,0096464481
North_Siberian    0,0042075434

Globetrotter was not able to infer the admixture date.  Groups North_Baltic_Finnic_G1 and North_Baltic_Finnic_G3 are both Finnish. I modified references from the previous blog entry.  Now the South_Baltic_Finnic is split into Baltic and Finnish portions.


time: 56 generations, around 1500 years ago

East_Baltic_Finnic    0,2279573629
North_Baltic_Finnic_G1    0,1883732327
North_Baltic_Finnic_G3    0,134836117
Basque    0,1242665217
North_Siberian    0,1043483876
West_European    0,0686019039
Central_Siberian    0,0590794466
North_Baltic-Finnic_G4    0,0513959273
Baltic    0,0303972753
East_Volga_Finnic_Chuvash    0,0107438251

Groups North_Baltic_Finnic_G1 and North_Baltic_Finnic_G3 are Finnish, North_Baltic_Finnic_G4 is Ingrian and East_Baltic_Finnic is Karelian+Vepsian.  Basque ancestry was higher that among modern Saamis.

 update 30.11.17

After separating Estonians from the main Baltic group it is possible to test also Estonians.  At first however Finnish results,  Estonians still with Balts.

North Baltic-Finnic, group 1

time: 70,6 generations, near 2000 years ago

Baltic    0,7403595543
Saami    0,1586845132
Mansi_Khanty    0,0874546485
North_Siberian    0,0117447072
Central_Siberian    0,0017565769

Basically this was expected,  the Baltic part (including Estonians) is highest and the rest is composed from Euro-Siberian populations.  What surprises is the Mansi-Khanty part, I would have expected  even more Saami or some Mari-Chuvash -like minor admixture.   However the magnitude is right; three quarters Baltic plus one quarter mixed Euro-Siberians.   2000 years sounds credible, it is near the time of the migration of Baltic Finns to Finland.

North Baltic-Finnic, group 2

time: 43,8 generations,  around 1200 years ago

Baltic    0,6802833838
Scandinavian    0,1470929006
Saami    0,1149188786
Mansi_Khanty    0,0503062607
Central_Siberian    0,0038576149
North_Siberian    0,0035409614

Scandinavian admixture appears around 1200 years ago.  It is impossible to name any exact Scandinavian migration or demographic event in Finland, but the first Swedish crusade can be ruled out.  Scandinavian increases, Baltic and Euro-Siberian decreases.

North Baltic-Finnic, group 3

time: 69 generations, around 1900 years ago

Baltic    0,7973987698
Saami    0,1346869263
Mansi_Khanty    0,0644377493
North_Siberian    0,0032512571
Central_Siberian    0,0002252975

The group 3 is very similar to the group 1, both are Finnish, as well as the group 2.

North Baltic-Finnic, group 4 (Ingrians)

time: 106 generations, around 2900 years ago

Baltic    0,7901064987
Saami    0,1221914423
North_Siberian    0,0845129477
Central_Siberian    0,0031891113

Surprisingly this doesn't look like an East-Finnish migration, which was expected.  It reminds me of an extinct Baltic-Finnic population.

Eastern Baltic-Finnic (Karelians and Vepsians)

time: 43,2 generations, near 1200 years ago

Baltic    0,8118374791
Saami    0,099396225
East_Volga_Finnic_Chuvash    0,0295501283
Mansi_Khanty    0,0263499058
Central_Siberian    0,0214967778
North_Siberian    0,0113694841

Near 1200 years match with the formation of East Baltic-Finnic people.

Estonians with Finnish references

time unclear

Baltic    0,3959754479
East_Slavic    0,3691411424
North_Baltic_Finnic_G1    0,1308129559
West_European    0,0752899347
Basque    0,014077665
Saami    0,0090402024
Mansi_Khanty    0,0037994745
Central_Siberian    0,0018631772

Friday, November 17, 2017

Introductory Globetrotter analysis

Globetrotter is a new software being able to estimate admixtures and also admixture dates. The analysis itself is based on autosomal haplotype data, which is produced by the software Chromopainter, version 2.  My job queue was Plink, Shapeit, CromopainterV2 and Globetrotter.   The Plink format data consisted of 399000 SNPs and 254 individuals over the Eurasian continent.  I liked to have more individuals, but I can use only publicly available data and it is always my restriction.

In the first phase I made a phylogenetic tree using softwares Chromopainter and Finestructure.  Chromopainter was run in two phases, at first to define necessary run parameters and in the second phase generating a tree figure and ancestral matrices.  In the next step individual samples were grouped according to the phylogenetic tree and the result was moved to the following Chromopainter runs preceding Globetrotter analysis.  So there was no handmade grouping and all definitions were done by softwares.



The deep past can't be figured correctly by present day populations.  Names like Finnish, Polish and Eastern_Baltic_Finnic didn't exist thousands years ago and all group names should be understood representing something now unknown.  Another imperfection is that some populations are unmixed.   For example Balts and Basques cannot be defined by any other present day populations, with exception of themselves, which is not clever at all if we want to see ancient migrations.   In those cases there are sure unknown ancient admixtures without present day proxies and for example Balts are figured as East Slavs.


Khanty_Mansi    0.00669230541442569
Saami    0.0318001424720861
Scandinavian    0.0406288973530398
Eastern_Baltic_Finnic    0.372195068297064
South_Baltic_Finnic    0.547727866737746


Basque    0.00627519770432461
West_Europe    0.0203347268787166
Mongola    0.0285387511835476
Nganasan    0.0312587449978488
Irish_Scottish    0.0348178173049934
West_Siberia    0.0372717151545831
Khanty_Mansi    0.058915141944102
Eastern_Volga_Finnic_Chuvash    0.108026814008228
Eastern_Baltic_Finnic    0.120473106582914
Finnish    0.554087984240742


Basque    0.0168485068643567
Southwest_European    0.085582697894791
West_Europe    0.897568795240852


Saami    0.00341643675195708
Nganasan    0.00501267346037914
RushanVanch_Tajikistan    0.00854395216066372
West_Siberia    0.0142527316035022
Irish_Scottish    0.0232322099579794
South_Baltic_Finnic    0.0375544108580537
Baltic    0.0616973387576695
Mongola    0.102871971437878
East_Slavic    0.119214847082816
South_European    0.12153228301688
Eastern_Volga_Finnic_Chuvash    0.184584853664197
Western_Volga_Finnic    0.317983363220266


RushanVanch_Tajikistan    0.00496570412383918
Western_Volga_Finnic    0.00973524498071095
Saami    0.0209045306129885
Scandinavian    0.0314001203298436
Mongola    0.0468217500718522
West_Europe    0.0512201282635752
Eastern_Volga_Finnic_Chuvash    0.322872736453914
West_Siberia    0.510808280436572


Baltic    0.0039132358786016
Saami    0.0040658994834093
South_Baltic_Finnic    0.331326055831535
West_Europe    0.660694808806454

Western Volga-Finnic

West_Siberia    0.001211877430627
Basque    0.00153548108955792
Mongola    0.00217721497484364
Irish_Scottish    0.00441065912271718
Nganasan    0.00489486172279255
Saami    0.00654435392074552
South_Baltic_Finnic    0.00873613821602628
Khanty_Mansi    0.011149101703621
Eastern_Volga_Finnic_Chuvash    0.0443170163661487
Tatar    0.170123511582196
East_Slavic    0.744899783870725


Saami    0.00434883756492699
East_Slavic    0.995651162435073

East Slavs

Western_Volga_Finnic    0.0180131830693537
Mediterranean-East    0.0941857330298036
Central_Europe    0.170383068761459
Baltic    0.717418015139384


Southwest_European 1

South Baltic-Finnic
Saami    0.0015403209540466
Basque    0.00277573750507665
Irish_Scottish    0.00668755305870894
Southwest_European    0.0131644799855559
Eastern_Volga_Finnic_Chuvash    0.0132143162745874
Eastern_Baltic_Finnic    0.0231748074310308
East_Slavic    0.152341012943326
Baltic    0.168097194491377
Scandinavian    0.203236330851964
Finnish    0.415614563156978

East Baltic-Finnic

Nganasan    0.00749839275609302
Khanty_Mansi    0.0101318772456883
Saami    0.0189334364744419
Eastern_Volga_Finnic_Chuvash    0.0341857812007321
Western_Volga_Finnic    0.0445466151938662
Baltic    0.259991450633669
Finnish    0.624712446495509

Finnish admixture dates and proportions.  

date in generations:  69.2367424689291


Khanty_Mansi 0,0290405745
Nganasan 0,0343370651
Saami 0,0360340021
Russian_Pinega 0,0402546721
South_Baltic_Finnic 0,8603336861

The software inferring admixture dates is quite sophisticated and I am still learning how to use it.   Before knowing more about it  I can't comment previous results, they are "as is".