perjantai 19. tammikuuta 2018

I-CTS2208 update

This is a periodic work I do to confirm where we came from. 

A basic tree connecting the Finnish Bothnian I1-clade (I-L258) to Scandinavian roots, copied from the project "I1 Suomi Finland & N-CTS8565":


 - - - - - - Z74          - 4100 BP
- - - - - - - L813
- - - - - - - - Y30806
- - - - - - - - - BY3474      - 400 BP
- - - - - - - - Y18927
- - - - - - - - - Y21736
- - - - - - - - - - Y20861        - 2100 BP
- - - - - - - - - - - Y23712        - 1650 BP
- - - - - - - CTS2208     - 2900 BP
- - - - - - - - Y20287
- - - - - - - - CTS7676
- - - - - - - - - L287         - 1900 BP

- - - - - - - - - - BY594        - 1450 BP
- - - - - - - - - - L258          - 1700 BP



Corresponding PCA including new CTS2208 samples and locations: 




 

lauantai 13. tammikuuta 2018

Shared IBD in North Europe

One of the most ambiguous thing in genetic genealogy is IBD (identity by descend).   People make easily wrong conclusions by connecting individuals using IBD-segments.  Practically it is impossible to prove common ancestry by a single IBD-segment from Iron Age or earlier.  But it is even worse -  there are many chromosomal areas giving enormously false results.  I have hit with this problem many times, as well as companies on the market selling personal genetic genealogy.  Sometimes fixing the problem has worsened the outcome, rather than fixing it, because the fix in business purpose can have been less factual.

Phasing gives a more reliable result decreasing recombination error, but still the result can be wrong and the result can be useless and the dating error thousands years.   Read for instance Li et al 2014 .   Even in case the individual result is realistic it doesn't tell about the gene flow direction and is useless in searching ancient migrations.  Another issue is the difference between IBD and allelic statistics.   Allelic distances can become really bad for mixed individuals and populations and mostly seen IBD-statistics dealing with origins of whole populations in a long run are mostly false.  I am going to show it, or not, it is your decision.  

I use 800 thousands high coverage SNP's combined from two well-known data sources.  The data was improved by removing bad areas shown in Li et al 2014.   The data was processed by the latest version of Beagle (v. 4.1), using haplotype reference panels from the 1000 genomes project and recombination map from Beagle's own library.  Beagle reports the ancestry likelihood of one IBD-segment of two individual in LOD scores   LOD score 3 means that the probability of common ancestry between two individuals shown by one IBD-segment is 1000:1, which is considered as a strong evidence.   Because my goal was to make statistic between populations rather than individuals I accepted all positive LOD scores.   LOD scores were summed by population pairs and the sum was divided by the product of sample number of both populations, except in intra-populational cases by the product of sample number and sample number - 1.

Because of the small Swedish sample size (only 2) I ran two global PCA-plots, one including Swedish samples and another including Finnish samples,  to make sure that they had not Finnish ancestry.  It was easy done by checking the Asian/Siberian admixture.  Both samples were South-Swedish without for Finns typical eastern admixture and were located among Orcadians, West Slavs etc. (Global PCA with Siberians, East Asians and SSA samples loses nuances in Europe, but shows excellently global differences). This is interesting, because in this case the high Finnish IBD-sharing in Sweden actually means Swedish admixture in Finland, not the Finnish one in Sweden.

My previous blog entries disclosed the Finnish eastward expansion.  Although IBD-segments can't prove the origin of shared ancestry, the result indicates same strong Finnish influence far to the east.  This brought forth the obvious outcome of Swedish and Finnish influence in Northern Russia during the Iron Age.   


Average LOD scores between populations.



   13.1.2018 fixed some colors in matrix and again 16.1.

perjantai 5. tammikuuta 2018

Searching for the Finnish root

We are unlucky people in Finland because the soil in Finland is acidic and destroys all organic remains in one millennium. We will never know the genetic appearance of people who lived here during the first millennium or earlier.  This fact let us speculate about our ancient ancestor and people also do it.  The outcome depends pretty much on beliefs and myths.  I try to bypass the exact solution to this problem by using modern genomes and a retroactive way.  I spit all 99 Finnish samples into 6 groups using Finestructure.  Then I ran each groups against global references using Globetrotter to find out which one of 6 Finnish groups shows the oldest admixture date.  It happened that the oldest Finnish mixture included three genetic elements:  Scandinavians, Estonians and Saamis.  Sound good so far, but it is not simple at all.  Although the Finns are a relatively homogeneous group and removing outliers is quite a simply task, this same doesn't fit with Estonians.  I am kind of sure that many thing happened changing Estonians, for example the Slavic expansion during the first millennium and the demolition of all old kingdoms by devastating German, East Baltic and Slavic armies on the Eastern Baltic coastline in the beginning of the second millennium.  The little can be done, can be done. 


First the test showing the present mixture of the "Finnish root":

Estonian 0,518
Scandinavian 0,415
Saami 0,067


And then the Finnish root after searching for the most obvious admixture date:

59 generation or 1620 years ago
 
Scandinavian 0,730
Estonian 0,164
Saami 0,106




Following results are obtained using Finnish root population

Karelian-Vepsa 44 generations or 1200 years ago
   
Finnish-root 0,698
Baltic 0,154
Mari_Chuvash 0,057
Northeast_Asian 0,024
Mongola 0,015
Central_Siberian 0,013
Saami 0,011


Estonian x generation x years  (unclear) 
           
Baltic 0,644
Finnish-root 0,194
Slavic 0,076
Scandinavian 0,038
Mari_Chuvash 0,028
Saami 0,011


Mordva  29 generations or 800 years  
          
Slavic 0,340
Baltic 0,252
Karelian_Vepsa 0,118
Mari_Chuvash 0,067
West_Europe 0,061
Mongola 0,045
Finnish-root 0,023
Caucasian 0,022
Khanti-Mansi 0,018
Armenian 0,018


Swedish x generation x years (unclear, probably very old, old enough that Finnish-root and Saami didn't yet exist and both designations mean something undetermined)    
           
West_Europe 0,577
Finnish-root 0,147
Saami 0,122
Slavic 0,111
British_Isles3 (Scottish) 0,033
Baltic 0,010


Tatar 30 generations or 825 years ago   
           
Slavic 0,209
Baltic 0,159
Mari_Chuvash 0,152
Balkan 0,093
Mongola 0,085
Karelian_Vepsa 0,065
West_Europe 0,050
Caucasian 0,043
Armenian 0,031
Finnish-root 0,028
Ulchi-Hezhen 0,029
Central_Siberian 0,015
East_Asian 0,011
North_Siberian 0,010

tiistai 26. joulukuuta 2017

Eastward migration of Finns

The origin of Finns is very indisputably from the Migration Period.  Times before it are still unclear as well as the history of  Northeastern Europe in its entirety, including at least Baltic areas and North Russia.  We can talk about Comb Ceramic, Corded Ware, Kiukainen cultures et cetera, but no one can make a true link between Stone Age cultures and the origin of modern Finns and their language and connect them to Finland.  Furthermore, the main stream linguist theory tells that our language came from the Volga basin, but it can't be proven by genetics.  Nothing in our genes links us to the Volga basin, although a large crowd enthusiasts can see it and try to prove it.  Unfortunately for them,  no respected scientific evidence has found to support this idea,  all genetic evidences has been opposite so far.    

Because we know very little about the time before the Migration Period in Finland, let's start from it.  Here are some professional views, made by non-Finnish scientists.  At first a two-piece video document of Swedish production about Baltic Sea Vikings, touching also Finns.

https://www.svtplay.se/video/16169343/ostersjofinnarna/ostersjofinnarna-sasong-1-avsnitt-1

https://www.svtplay.se/video/16169303/ostersjofinnarna/ostersjofinnarna-sasong-1-avsnitt-2?start=auto

What is interesting is how they see the beginning of Finnish settlements.  Six screenshots show how ancient Finnish settlements spread across Southern Finland and continued to the Lake Ladoga.  The presentation doesn't show the whole picture.  Our genes and language imply that they went much further to the east, at least to the Lake Onega in Northern Russia.  There is also an open question about Southern Finland.  Until now scientists have supposed that Southern Finland around our present-day capital town was uninhabited to the Swedish era.  New archaeological finds can change the history and also explain a new straight route from Southwest Finland to Karelia.  Anyway there must have been a southern route to Viking Age Ladogan settlements and Staraja Ladoga/Aldeigjuborg.













The scientific view is clear, the migration flow during the first millennium was from west to east, not from east to west.

Here is another view, a German one from Wikipedia, showing Viking settlements.  No matter how we interpret Vikings, we sure can't consider that all Scandinavians were Vikings, neither all Finns or none of them, but here we have a view about Viking Age settlements linked together.   Note that Ostrobothnia is considered as a Viking settlement.  In some sources it is assumed to have had a Swedish-Saami settlement, disappearing during the Viking Age.








German studies written by Steuer give more information about archeology and evidences about settlements during the Migration period and the Vendel era.

Ring swords



Counterweight of silver scale in the late Viking Age.  It is amazing how many counterweights in purpose to weight silver coins have been found in Finland, especially in comparison to its small population.  The Finnish population was much smaller than the Swedish one and even smaller than in Estonia.  In Estonia it was around three or four times bigger than in Finland.  Only after Northern Crusades the arrangement changed and little by little the number of Finns grew while Estonians suffered from its colony status.

Counterweight



A German book "Die Wikinger", written by Brenda Ralph Lewis, Hildegard Elsner and Nikolai Smirnov locates the heartland of Vikings.



All above was presented as an introduction to my genetic work.  Although the view shown above is anything but perfect and especially some Viking Age settlements can be criticized, it is clear that scientists can't fabricate the history and lie about the migration direction.  It is reasonable to note that my work follows the scientific view.

My new tests are based on 800000 SNP's, 744 samples and globally 104 populations. The data was haplotyped using newest available reference data from the 1000 genomes project and Shapeit software.  Haplotype data was processed using Chromopainter V2 in two steps, the first step to define run parameters, and the result is reported using Globetrotter.  Results show the best present day fit of selected population using all 103 populations as donors.

Finnish samples, 99 individuals from the 1000 genomes project are grouped into four groups using self-reporting of my project members. We see that the Finns can be defined internally with exception of the group 1, which can define other Finnish groups.   Nothing points to migrations from east, even though the data is global. 


Finnish group 1

Finnish2             0,408
Scandinavian      0,262
Finnish3             0,245
Slavic                 0,036
Near-East           0,018
Mari_Chuvash    0,012


Finnish group 2

Finnish4             0,567
Finnish1             0,378
Finnish3             0,054


Finnish group 3

Finnish4             0,783
Finnish2             0,217


Finnish group 4

Finnish3             0,738
Finnish2             0,262



Karelian-Vepsa (Eastern Baltic-Finns)

Finnish4             0,373
Baltic                   0,307
Finnish2             0,212
Mari_Chuvash     0,062
Saami                  0,017



Mordvas


Slavic                  0,516
Tatar                   0,195
Karelian_Vepsa 0,122
Baltic                  0,058
Mari_Chuvash    0,043
Caucasian          0,011


Mari-Chuvash

Tatar                   0,406
Mordva               0,256
Bashkir                0,170
Khanti-Mansi       0,090
North_Siberian   0,018
Karelian_Vepsa 0,013
Tungusic             0,011

  
Scandinavians (academic Swedish samples)

West_Europe    0,573
Finnish2           0,164
Baltic                0,162
Finnish1           0,058
Finnish3           0,031

Finnish 1 includes 26,2%, Finnish2 9,9% and Finnish3 2,1% Swedish ancestry.  


Control results

British Isles 1 (Kent)

British_Isles3    0,487 (Scottish)
West_Europe     0,453
British_Isles2    0,057 (Cornwall)



Bosnia-Hertsegovina Romas

Armenian        0,375
South_Asian    0,224
Balkan             0,195
Slavic              0,122
Near-East       0,021
Caucasian       0,017
Central_Asian 0,017










  

tiistai 28. marraskuuta 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.

Scandinavians

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.

Saami

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

perjantai 17. marraskuuta 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.

Results:



Admixtures

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.

Finns

Khanty_Mansi    0.00669230541442569
Saami    0.0318001424720861
Scandinavian    0.0406288973530398
Eastern_Baltic_Finnic    0.372195068297064
South_Baltic_Finnic    0.547727866737746


Saami

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


Irish

Basque    0.0168485068643567
Southwest_European    0.085582697894791
West_Europe    0.897568795240852


Tatar

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


Khanty-Mansi


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


Scandinavian

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


Baltic

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


Basque

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

admixtures:


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".   







sunnuntai 29. lokakuuta 2017

Tollense Valley Bronze Age battle field, standardized PCA-results

Using the same standardized data we have the following PCA plot, which differs from what we see on plots made using only partly overlapping SNP sets.  I don't see any reason to use Mediterranean samples, because of the small SNP number of some samples.  What we see in general on the plot is that most ancient samples  fall between Germans and Poles.  We see also that Finns, Russians, Poles and Norwegians show genetic drift.  The most Polish ancient sample is WEZ56 and WEZ54 falls inside the British cluster.  Samples WEZ39, WEZ40 and WEZ51 fall somewhat closer Finns, being still Central European. WEZ56 is the most Polish sample in the original study graphics too.