How did the Finnish population transformed into something but Russian didn't

Ruling now out the strict allele data I am going to make an informal comparison regarding my experience about FamilyTreeDna's new service named myOrigins.

In a big view we already saw how the populational structure follows paternal haplogroups. Look here.  But how autosomal and ydna match overally? I think that considerably well in Western Europe and Southern Europe, but quite poorly in Scandinavia, Russia and Finland.

Let' look closer.  British Isles are the most western country on both ydna and autosomal maps excluding Basques who also belong to the top R1b owners.   In some locations British men are homogeneously R1b.

Some ethnicities in Balkan Peninsula with their high I2 are also easily distinguished.

The third distinguishable group consists of Finno-Ugrian and Finnic people in Russia and Finland.

The centre is populated by Germans, French and generally by Central Europeans being very close each other also by Fst figures.  Another mainline group consists of Southeast European, including also Balkan Peninsula in general.

All those groups show similarity between autosomal and uniparental inheritances as far as I have noticed.

But when we go to the countries populated by R1a, I1 and N1c1 men in Northern Europe the picture starts to look blurry.  Some Ydna statistics first.  All numbers are from Eupedia's Ydna statistics, except Finnish numbers which are from T. Lappalainen et al. 2006.  It is still the newest study about Finnish paternal haplogroups.   I used this study regarding Finns because Eupedia doesn't give the east-west distrubution in Finland.  However I checked that given numbers are in-line at country level.


Regional percents per haplogroup:

After taking notice of the similarities and differences between haplogroups let's look at the autosomal side.  I collected these figures from online forums and the numbers are not absolutely trustworthy, but give us guidelines.  FamilyTreeDna only can give true country averages regarding their service.  Anyway, I am not cheating, this is what cool numbers say.

After those numeric figures let's put things together.

While in Scandinavia the haplogroup I is obviously the backbone of European Northlands (read the preprint of Lazaridis et. al and what it says about ancient genomes in Sweden), it in Finland turns to North Circumpolar, even though Ostrobothnians have more I1 than Scandinavians ( Scandinavia : 34,25%, Ostrobothnia: 47%).   On the other hand in Russia the N1c1 has minimum effect on the autosomal results;  in Russia the N proportion is 23% and in Otrobothnia 29%.  However the autosomal result is very different, North Circumpolar 15,4% in Russia and 80,6% in Western Finland including Ostrobothnia. Russians still share the common genetic history with their western Slavic origin in a great deal.  I can see many explanations for this different genetic transformation in Finland and Russia, as also in case of Finland compared to Scandinavia, but it is hard to see how it could be confirmed by genetic data.  

Just keep in mind that I only make assumptions about how the autosomal and paternal genes are connected, but I am not the only one making this.  In fact most of present-day academic researchers writing studies and amateur researchers making online blogs suppose same and there is good reasons to do it.   In principle there are only three basic ways to deviate from the autosomal ancestry once in our ancestral past bound with uniparental inheritance:  1) mixing which is detected also by changes in uniparental heritage, 2) random mutations and 3) genetic drift.  Genetic drift is connected to locality and time.   The way we can estimate it includes dating of the uniparental heritage.  Without reliable datings it is like witch work, cooking magic soup.

It seems to be very little continuity between Ydna and autosomal in Finland.  But several studies show that either maternal haplogroups in Finland can't be the reason for unexpected results, for contradicting results between uniparental and autosomal inheritances in Northern Europe ought to be other reasons.  Studies prove that mitochondrial inheritance in Finland is partucarly southern and also western and only some specific and uncommon mitochondrial lines found mainly in Northern Finland imply northeastern origin.

Conclusions

My conclusion is that there is no reasonable conclusions that could explain what we see.  

FamilyTreeDna released a new Population Finder, now myOrigins

Meanwhile waiting for those 11 Scandinavian ancient genomes I take an overview about the new Population Finder, now named newly as myOrigins.  This is only  a short view while waiting for more results and comments and I'll do completer review after having more experience.

So Familytreedna has released a new population finder, which is meant to be able to find your ancestry.    Looking at first results it looks like being uncertain and gives obviously false ancestries.  Unfortunately they seem to have fallen into the same mistake which 23andme did in their first effort with Ancestry Composition.  It looks like Ftdna has gone even further regarding the Finnish ancestry.  The overfitting is apparently  reaching a new record.  Finns don't have anymore regular Scandinavian admix, only very infrequently.  They are either 100% Finns (rarely according now available results)  or Finns with significant Slavic, French and British admixture.   I would consider around 10% or more Central European or British ancestry meaningful in Finland.  I collected results now availabe on online forums and first results are here.  But first you can read and learn what they write about new population clusters:

https://www.familytreedna.com/learn/ftdna/myorigins-population-clusters/



Then first Finnish results.   Shortly main clusters and where they peak:

1. North circumpolar - in Northeastern Finland excluding proper Lapland
2. European coastal plain - in Switzerland and France
3. European coastal islands - in UK
4. Transural Peneplain - in East and Central European Slavic region
5. European Northlands - In Southern Norway (inlands)

Finnish result show evident Central European and British origins, which is absolutely new information and doesn't fit with the known history of Swedish migration to Finland, with other ideas and known information about the Finnish history. 

Thanks and I hope happy summertime to all

Thanks you for following my blog.  I decided to pause while more ancient wide genome results are publicly available.   Just now there is coming several new studies with new ancient samples and I don't see it worthwhile to repeat same analyses.  But when more these samples become available it will be possible to make some improvements because I have some ideas how to avoid uncertainty and distortion in results regarding Finnish history.     

Iberian caveman from La Braña

Finally I got downloaded the ancient La Braña genome.  It is publicly available from the NCBI sequence read archive.  I refined it by GATK, a program reading genome sequences and calling SNPs.  A bit over 1 million SNPs were called,  over 100k overlapped with  the 1M Illumina set used by 23andme, but only 20 kSNP’s overlapped with my standard LD-pruned set.  It is less than  some other projects have been able to reach, but still usable, although some amount of inaccuracy is seen in individual results.  The big view and locations of populations on MDS-plots  are still very correct.   

Playing around with PCA, which I have used earlier,  I found it being poorly applicable in this case and I moved to MDS.   It was obvious that the LaBrana1 sample being something different than any present-day population didn’t share as much common SNP-level principal components with them as MDS can retrieve using genetic distances. 

Comparing to other online results shows some similarity and also differences.  What made me pondering was the obvious Asian affinity of LaBrana1 shown on the Eurasian plot.   This Asian affinity was shown around at the same level with most eastern Russians, like most eastern samples from Vologda and most eastern Mordvins.  This is very close what I have seen achieved by some other projects, but surprisingly Lazaridis et al.  didn’t show Asian affinity for LaBrana1.   Unfortunately he didn’t inform us about the amount of SNPs used on his PCA-plot (or I didn't find it), but the study tells that only a 10 kSNP overlapping set was obtained for LaBrana1 and even less for some other ancient samples.  But maybe I am wrong.   Maybe I know more after testing  other ancient WHG samples. 

MDS plottings and IBS-statistics show closest similarity with Northern European populations.   My data lacks of Basques, so I can’t say how close the LaBrana1 they might be.  In general South Europeans are more distant for LaBrana1 than North Europeans and Near Easteners are even more distant.   The closest population at average IBS-level was Western/Southwestern Finns,  but the difference to Estonians and Lithuanians was quite small. 

European MDS

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Eurasian MDS

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IBS-statistics for top ten individuals

Estonian            0.8101938

Lithuanian          0.8101357

FI0007              0.8099396

Belorussian         0.8098805

SC0001              0.8098763

Estonian            0.8098527

Lithuanian          0.8097566

FI0005              0.8096651

Lithuanian          0.809652

Russian             0.8094852

IBS average statistics including all population from my extended European data set (East and North Asians excluded)

 

Estonians, the genetic comparison

I succeeded to download 13 Estonian samples from the study “Upper Palaeolithic Siberiangenome reveals dual ancestry of Native Americans “  released by Estonian Biocenter.   After the qualification I had 11 samples, two was removed due to being too close relatives with other samples.   I have only a few comments about the Finestructure, otherwise I only hope you enjoy the results.

• the Finestructure analysis is based on IBS-similarity.
• I removed Lithuanians from the Finestructure run because they show very high national IBS-similarity and it distorts results in the aggregate mode.  This happens although the aggregate level is quite low in my analysis.   This means practically that Estonians are compared to Slavs (Belarussians).
• processes using MCMC-aggregate features usually change individual results and usually you can’t compare individual results on Finestructure matrixes.  To see individual results you have to look the raw data matrix, not the aggregate matrix, but in my run the difference between raw and aggregate is very small.   In this context I refer to my previous analyses and to the effects of young isolations, they tend to distort aggregated results.
• as also in my previous Finestructure analysis, the South European result seems to be somewhat inaccurate, but Northern Europe looks quite good. 
• the tree result on the matrix seems to imply more differences than similarities between samples.  So for example the Finns on the matrix are split into two or three groups.   It is at least for me impossible to estimate the balance of similarities and differences between individuals and populations in existing software analyzing tools.   It is strongly up to the selected tools, and accordingly to the authors, how similarities and differences are weighted.   Some authors prefer similarities, even in case it is very small, and disregard differences.  This can be seen by comparing results and analyzing tools.   This question is interesting and reminds of the complex history of each population and used data which can be inadequate. 

PCA world

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PCA extended Europe

Dimensions 1 and 2:

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Dimensions 1 and 3:

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PCA Europe

Dimensions 1 and 2:

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Dimensions 1 and 3:

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Finestructure

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Looking closer: The Finnish cluster in Europe

New PCA's

A new PCA analysis including only Europeans.   The first plot including dimensions 1 and 2 shows for Finns East European and Scandinavian affinities, more precisely for the Eastern Finns the East European affinity closer eastern Vologda samples and the Western Finns match closer western Vologda samples and Belarussians.    Scandinavian affinity on second dimension looks quite constant for all Finns.   This result could mean that the common affinity between Finns and Scandinavians is older than the present genetic shape of these populations (Finns and Scandinavians) and the difference in the East European affinity among Finns idicates also different origins for Eastern and Western Finns in Eastern Europe. This explanation is supported also by the position of Scandinavian and some CEU samples who seem to diverge from Central Europeans toward Finns (dimension 2). The second plot, showing dimensions 1 and 3, confirms the East European affinity of Finns.  Scandinavians keep their position near Central Europeans. 

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Retesting Finestructure

I have a new interesting experiment with Finestructure.   I played with it a couple years ago testing it several days and found some problems.  It seemed to exaggerate young and small isolated populations by increasing their similarities with other populations in straight relation to the shared haplotypes within the isolation.  This effect is a bit difficult to describe exactly by words although testing revealed it certainly. After seeing this problem I decided to give up with Finestructure.  Maybe the problem was partially in Chromopainter and it’s data selections.   Now, in my new experiment I used IBS data as an input to the Finestructure.  The authors of Finestructure claim that IBS data is much worse than the data generated by Chromopainter.  My results show that IBS data gives fair good results, better than in my previous tests with Chromopainter data which was pretty much distorted by the problem I described above.   Pretty much testing ought to be done before this can be proved stone cold, and even then many readers will not believe me now, so just now it is enough for me to know this.   I think that the effect is basically the same I have seen so many times in population genetic tests;   many analyses “infer” that most homogeneous populations, owning highest shared genome similarity, are root populations.  This means that those analyses often select typical genetic features from most homogeneous subpopulations.  But this is a big mistake; in many cases the most homogeneous subpopulation is younger than the root population, the one they once diverged from.     In other words:  the portrait doesn’t come better by increasing contrast, because we likely will lose nuances and sometimes also profile resembles the neighbor.    
  

So I spent a little time more with testing and I think that I found a way to avoid the false gene pumping between populations described above.   Definitely, this test done with IBS-data looks very clean.   Some problems can be seen in sorting out Mediterranean populations, but in Northern and Eastern Europe the grouping result is amazing.   The Finns cluster with Northern Russians, which is of course right and follows the known history.  Northwest Russia was the homeland for many Finnic speaking groups before the russification took place.    Tree model can’t figure simultaneously the Finns belonging also to the Fennoscandinavian group.    

The graphic shows also affinities between individuals.

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