perjantai 9. maaliskuuta 2018

New ancient samples on PCA

I ran 2500 samples, each representing 900000 SNP's using Eigensoft's SmartPCA with the parameter "lsqproject", which is designed to correct missing data of ancient samples.   The manual states:

lsqproject:  YES
PCA projections is carried out by solving least squares equations rather than an orthogonal projection step.  This is approriate if PCs are calculated using samples with little missing data but it is desired to project samples with much missing data onto the top PCs.

Next I computed eigenvector averages for all populations in order to make the output more readable.  So each symbol represents up to around 20 samples. Corresponding eigenvalues are 13.858230 and 10.064209.

The result:

It should be easy to discover different historical events, for example the Blatterhole_MN, which was a distinct group and solely its own kind with zero steppe admixture, holding probably 60% ancient farmer and 40% western hunter-gatherer ancestry.  

lauantai 10. helmikuuta 2018

New Baltic samples on PCA plots

I have made two PCA plots using new Baltic samples published by Mittnik et al. 2018, but as far as I can see with a different approach.  On my plots modern populations are placed at first hand on grounds of ancient samples, giving, in my humble opinion, a historically correct approach.  I have also standardized  sample sizes of modern populations to minimize the effects of modern genetic drift, which of course, if exists, will lead to comparison error due to irrelevant PCA-components.  Thirdly I have here two regional view; Eurasian and European.  The Asian effect on the Eurasian picture is pronounced in certain modern populations implying Asian admixture events after the Bronze Age Europe.

Eurasian picture:

Close-up of Eurasian picture:

European picture:

edit 10.2.2018

On the Eurasian picture the first dimension (X) represents East-Asian and Siberian maximums and the second one (Y) represents ancient farmer maximum.  So the picture isn't relevant for checking dimensions inside present-day Europe.  It is easy to understand that the flat left represents Asian/Siberian minimum regardless of later European structures.  Similarly the the vertical axis represents variation between ancient farmers and hunter-gatherers rather than structures inside present-day Europe.   The third picture (Europeans only) represents historically correct variation between ancient farmers and hunter-gatherers and exclusively to these variations ancient Steppe populations.  

keskiviikko 7. helmikuuta 2018

New Baltic samples in comparison to present-day populations

A large amount of new ancient samples is publishes by Mittnik et al 2018.
I compared those samples against modern local populations using F3-statistics (qp3Pop) using Chimp as the outgroup to eliminate even smallest impact of African/Near Eastern gene flow after the OOA event.   F3-scores were divided by a constant value giving results below 10.

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.

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.


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


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


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