Saami prehistory: Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe

New study preprint reveals that Saami people settled earlier much larger areas in Finland.  The study doesn't give answer how far to the south they lived, but it looks like Saami settlements reached at least the coast of West Finland.  The study discloses also several new samples from Kola Peninsula, oldest ones around 3500 years old.   Two of those Kola samples belong to y-dna N-L392, representing oldest N1-samples so far.  N-L392 is an upstream mutation for the largest Finnish group including Karelians and Savonians.  It is possible that the whole North European N descends from populations that migrated following northeastern route from Siberia and have got the recent genetic shape due genetic bottle necks and assimilations.  This would  be a reasonable explanation until we have other evidences about more southern ancient N.  This is however contradicting with the main stream linguistic theory of the Volga bend origin of Baltic-Finnic languages, assuming a straightforward connection between Finns and their language. One explanation could be that the language came following southern route and was brought toward Estonia by people carrying R1a.

https://www.biorxiv.org/content/biorxiv/early/2018/03/22/285437.full.pdf

edit 25.3.18

A short quote from an Estonian newspaper referring to latest linguistic research:

Eesti Vabariigi aastapäevaks kolme teadusharu koostöös valminud uus seletus läänemeresoome rahvaste tekkest viitab ühe olulise väljarände keskmena Põhja-Eestile, kuhu olid jõudnud Volga äärest teele asunud, teel baltlastega segunenud ja Daugava kaudu praegusesse Eestisse jõudnud väljarändajad.

And here is the Google translation to English, with some syntax corrections:

A new explanation of the formation of Finno-Ugrian peoples, co-written by the three branches of science, points to the emergence of the most significant migration to North Estonia, emigrants embedded on the road from Volga, on their way to the Baltic, and migrated to the present-day Estonia via Daugava (Daugava is in Finnish Väinäjoki and in Estonia Väina jõgi, although Estonians usse also Latvian Daugava.  The beginning "Väinä" (joki=river) can refer to the mythic Finnish hero Väinämöinen, who was the biggest character in the Finnish national epic.  A map figuring Latvia during the Great Northern War around 1700CE, drawn using an original done by Swedish historians: http://www.pohjanprikaatinkilta.fi/PohPr/taistelut/riian%20ymparisto.jpg). 

So the Finno-Ugric migration, later called Baltic-Finnic people,  migrated via Daugava, which is a river in Latvia.  How do we bring together two crucial observations,  the N1-root in Kola Peninsula 3500 years ago and the migration way of Baltic-Finnic people from the Volga region via Latvia and Estonia to Finland, which also happened around 2000-3500 years ago?

https://heureka.postimees.ee/4390183/suur-lugu-postimees-esitleb-kolme-teadusharu-koostoos-sundis-uus-pilt-eestlaste-kujunemisest

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.  

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.  

New Baltic samples in comparison to present-day populations

A large amount of new ancient samples are published 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.

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: 

 

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.

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