The origin of Fennoscandinavian and Baltic N in Kola Peninsula? Part II

Soon after my previous post a new study dealt with the same question and published also new data, the study name and link here: The Arrival of Siberian Ancestry Connecting the Eastern Baltic to Uralic Speakers further East.  The study continued on the same theme as so many previous studies connecting the male haplogroup N1c1 with a putative southeastern Baltic Finnic home land, apparently thought to have been in Volga region.  I feel myself somehow embarrassed with this, because I have to be back with this issue so soon.  However, we have no evidences about such linguistic and genetic connection, because we don't know any Volgaic Bronze Age or Early Iron Age populations carrying N1c1, instead of it we know ancient Volgaic samples belonging to male haplogroups R1b, R1a and I2.   But we do have ancient N1c1 samples from the Kola Peninsula and present day N1c1 from the Ural mountain region.  On the contrary to the Volga idea my view is that the N1c1 came to Fennoscandiavia and Baltic regions via Northeastern route.  Without problems it can be demonstrated by using old and new samples from several studies.

The new data was downloaded from Estonian Biocentre.  I found some problems with samples names;  names in the study and data don't match and I was not able to identify all data samples, including two Tatar-like samples, but those samples are less important in this matter.

So the Saami-Finnish path shows an y-axis deviation which I consider as an unknown Fennoscandinavian hunter-gatherer ancestry.

Corresponding admixture analysis is under work and will be published soon. 

The origin of Fennoscandinavian and Baltic N in Kola Peninsula?

I made several attempts to find downstream mutations of ancient Kola Peninsula samples BOO002 and BOO004.  Only those two belong to male remains and are tested L392, in my tests L392 is also the terminal mutation.  Both belong to the same terminal mutation and have no downstream mutations.  Yfull gives age estimates for L392:  formed 6400 ybp, TMRCA 4800 ybp.  Those two male samples were published by Lamnidis et al. 2018 and the age estimate was 3473 ± 87 calBP.  So there have to be 4800-around 3500=1300 years difference between estimates of the whole clade (by TMRCA) and Kola Peninsula sample ages, indicating migrations and/or  founder effects. Considering this we can say that Kola samples are not so far from the TMRCA estimate of all L392 samples, including all downstreams. But because Kola samples have not downstream mutations, we have to consider them as belonging to the forefather clade of all living people carrying mutation L392.  I made a migration model based on this assumption.   


N-L1026/L392 formed 6400 ybp, TMRCA 4800 ybp
-  N-VL29 formed 4100 ybp, TMRCA 3600 ybp
--   N-BY33087 formed 1750 ybp, TMRCA 950 ybp 
        id:YF11696FIN [FI-ES]
---     N-BY33088 formed 950 ybp, TMRCA 950 ybp 
           id:YF14404RUS [RU-NGR]
           id:YF11830FIN [FI-IS]

We see that VL29, which is one of main European branches of N, is only 1200 years younger than the upstream branch in Kola Peninsula.   You can click the branch name to see more details on Yfull pages.  We also see that there has obviously been a founder effect in Russia and Finland.  Nevertheless, 1200-1300 years is the same time gap than we saw between the estimate of the L392 and pure L392's in Kola Peninsula.  It is only a short leap from  L392 to VL29, where ever it happened, but why not from the arctic zone to the boreal forest. 

Another downstrean branch of L392:


N-Z1936 formed 4800 ybp, TMRCA 4300 ybp

This obviously can be considered as a straightforward downstream of L392, particularly because Z1936 mostly exists in the neighborhood of Kola Peninsula. 

--   N-Z1934 formed 4300 ybp, TMRCA 4300 ybp
         id:YF15740RUS [RU-MOW]

---    N-Z1928 formed 4300 ybp, TMRCA 3300 ybp


----    N-Z1925 formed 3300 ybp, TMRCA 3000 ybp

-----      N-Y29767 formed 3000 ybp, TMRCA 600 ybp
             id:YF08170SWE [SE-BD]
             id:YF04765SWE [SE-BD]
-----      N-Y62904 formed 3000 ybp, TMRCA 1200 ybp
             id:YF12523FIN [FI-LS] 
             id:YF06892FIN [FI-OL]

The more we go down the branch Z1936, the more it becomes purely Finnish and shows clade ages below 2000 years, meaning an obvious local founder effect.

It is also possible that another pure L392 lived southward and was the origin of the East European migration, but we have no evidence so far.   Considering the question of how the Siberian admixture of the L392 branch disappeared in some North European regions, we have several explanations.  The first explanation is due to getting more mixed.  This is supported by the fact that even recently the Siberian admixture becomes stronger in the north and disappears in the south.  Another explanation is that the original L392 was not Siberian at all, but then we have to search evidences how the Siberian admixture reached Fennoscandinavia and even the westernmost Scandinavia in the north, if not by arctic migrations via Kola Peninsula (including L392 and other northeast migrants).  So if we are not happy with one L392 and one Siberian and we still try to find alternatives we could have two distinct L392 migrations, one via Kola and another from east to the Baltic Sea, then we could have three distinct migrations of L392, one to Kola, second to Estonia to explain Baltic Finns and third to explain Balts.  Sound like a slippery slope. 

If the Kola postulate is right, then we obviously had two southward migrations:  one from Kola to Scandinavia and Western Finland through the Baltic Sea, ending up to the shores of Baltic region, another from Kola to White Sea Region, Karelia and Eastern Finland.  


You can browse the data by clicking the branch id's above or going to the Yfull straight here.  




 

Some issues with the new Harvard 1000 Genomes data

After downloading and testing the Reich Lab data labeled 1240K/5081 individuals I found some issues with the included 1000 Genomes data.  It looks like everything else is OK and the issue applies to 1000 Genomes only.   I prepared a replacing data using the original project data and results are fine.   I am very grateful of all new ancient samples, but have to inform about this.  The issue probably doesn't become revealed on PCAs using global data, only in local European analyses.    

Iron Age Finns not cultural followers of Estonian Tarand culture

It seems to me that Iron Age Finns, despite of belonging partly to the same Y-Dna with Estonians, were not same people with them by cultural means. It happens that almost all burials in the famous Luistari graveyard are much more like Christian inhumations, differing from the Finnic habit described in Estonia and Kama Volga (Tarand graves).  Besides burials in Luistari another meaningful, but smaller graveyard, Pappilanmäki, from the same era and situating only 14 km from Luistari, gives more cultural hints.  Pappilanmäki, meaning "vicarage hill" (after crusades churches were usually placed to sacred pagan places to destroy the power of pagan gods)  is culturally even more famous than Luistari, although more destroyed, obviously because it was a sacred place of Finnish pagans. 

Google translator is now much better than it was a couple years ago and I can now publish texts that were earlier inconceivable gibberish.  A Google translation of a Finnish newspaper with research references.

A popular article in a  local newspaper Turun Sanomat, on 2nd Feb 2008:

"Turun Sanomat reported 16.1. docent Kari Uotila's archaeological research conducted in Eura and their new perspectives. The news asked why in the Iron Age, the rich Eura fell into a "backward" in the Middle Ages. New research will bring some light to the matter, but the answer can be considered with the current data.

Eura and Köyliö are known for 50-550 AD. quite poorly. The reason was that  deads were not buried with their equipment. But there was a big change at the beginning of the Meroving era (550-800) when the rich body cemeteries of the region were born: the metal parts of the suit and accessories remained abundant in their graves.

Such cemeteries, mostly genealogical, are known from the upper reaches of Eurajoki, Kauttua to the Eura Church. They were buried until the mid-12th century, when the Eura parish embraced Christianity and moved to church burials.

The cemetery also spread to Köyliö Island, Huittinen, Yläne and also called Säkylä. When the dead in the rest of the country were buried by incineration, the southern part of Ala-Satakunta formed a separate inhumation cemetery until the entire cemetery institution - the line line Laitila-Kokemäki-Ikaalinen-Jämsä-Mikkeli - began to move to the influence of Christian inhumation.

An early burial in Eura.

The Finnish institution experienced a strong social and cultural upheaval during the Meroving period, having lived to some extent in the shadow of the coastal Proto-Scandinavian settlement. The villages apparently began to be organized as parishes - the parish is a linguistic term - and apart from the Eura region, it took on a cremation ground burial, a cremation into stone ground (in my opinion Tarand graves).

Metallic materials increased and became enriched with new weapons and jewelery everywhere, in Eura. From its findings, Pappilanmäki's silver-handled and gold-plated ring sword (about 650-750) is the pride of the whole of Finland, and glorious is also the sword of the same cemetery, decorated with silver-plated Christian silver plots, from the Crusade period.  Figuring this, in the burial place of Pappilanmäki was buried the chiefdom of the parish. (My comment:  ring sword finds are ultimately rare in the world, 80 pieces overall and 14 of those in Finland).

The burial of Eura was a subject of long-awaited research. It was early recognized that its inhumation burials, sometimes in rows, corresponded to well-known burial mounds in the Central European Germanic areas since the 400s.

Without Christianity, these clearly showed the effect of Christianity. Therefore, in the early 1950s, Professor Aarne Äyräpää described the Eura region inhumation trunks as remote Christian. The problem was how this kind of funeral was rooted in Finland when there was hardly any evidence of it elsewhere in the Baltic Sea region? 

Influences on the Central European Germans

Finland already had connections to Central Europe around 500, which was a time of new state formation. They appear here in finds of the continental European shield bosses. Connections continued at the beginning of the Meroving, where several spear types came from Central Europe, including the long-necked barbed angons, the late shapes of the legions of the legionnaires, the slits.

Shields were also renewed. The starting point for the Central European shields was the development of a skilled "Finnish shield boss", which was named after Helmer Salmo, a genius researcher and classifier at Meroving.

When such spears and shield bosses were not known elsewhere in the Baltic Sea, they had to show direct links to Central Europe. But the merchandise they were not, which is why I ended up on the idea that they came with Germanic druhtinaz(es),  who served as mercenaries (my comment.  This is an outcome that is today almost banned, therefore all finds reminding us of Germanic connections before Swedes are also almost banned).

A similar explanation fits into Ala-Satakunta's inhumation burials: some of the mercenaries embraced the Germanic semi-Christian faith and conception of life and proclaimed it after returning home. Thus, a semi-Christian foothold  was formed in Ala-Satakunta, and as incredible as it seems,

The Eura Luistari Grand Cemetery seems to have been established as an early Christian cemetery. When the same change in burial practices occurred in the 1000s elsewhere in Finland, it is interpreted as a Christian feature; why should we think differently here?


The military organization developed Satakunta

Apparently, the European touch left a third trace, an organization called the hundredth (my definition centurion ~ Satakunta). The hunredth institution is old in Europe. It is from Rome from the 5th or 4th century BC, from the Central European Germans from the 1st century, from the franc and Alemans of the 500s, the Anglo-Saxons from the next century, from Central Sweden maybe from the 400s (Gerhard Hafström), Novgorod and Mongols from the Middle Ages.

Satakunta was a troop of 100 men everywhere, and also areas for lifting their arms, in Sweden, to equip the fleet. Analogy and logic require us to conclude that the Finnish Satakunta was also established as a 100-man military area.

Satakunta is a translation loan from the Germanic Hundertschaft or the Proto-Scandinmavian hundare, but I understand that in Finnish, it shows that one hundred (Satakunta) were organized on their own. It later became the province of Satakunta"

Because of the obvious and severe dispute in term of Finnish history across times and researchers, or preferably saying due to the Finnish tradition of being aggressive or speechless and refusing to admit facts if they are against own prejudices, I also refuse to comment this article, to avoid being misled.  But I am going on to add historic overviews additionally to genetic analyses, because all serious academic researchers are in my opinion welcome to be published in English and the Google translate makes it now possible.  Traditionally, before the '80th, the research in Finland was written in Finnish or German, lately in Finnish and English..

Processing y-chromosomal bam-file

After getting my own bam-file I found out that in some cases the quality set of FamilyTreDna is too high and in some cases the result of the online browser is difficult to explain.  So here is a simple job to reprocess y-chromosomal bam-files:  

bcftools mpileup  -Ou --ignore-RG -f assembly38.fasta in.bam | bcftools call  -Ou -m --ploidy 1 | bcftools filter -e 'QUAL<80'  > out.vcf

You can change the QUAL parameter if you wish to alter the quality level of the output (VCF-file). All you need is to download bcftools, compile it and download the human genome assembly version 38 (assembly38.fasta).
 
You can also trim your Bam-file using following command:

./bam trimbam in.bam out.bam -L n1 -R n2 -c, where

n1 is integer representing left side cutting of bases and n2 right side cutting (conversely for reverse reads).  C is optional and perform soft cutting.  More about trimbam here.

I have tested this and compared to the original VCF made by FamilyTreDna.  Using this utility is worthwhile especially if you are searching downstream mutations that for some reason are not available in your provider's data.

I made also a conversion selecting all mutated variants and connecting them to publicly available variant names (named variants) and ISOGG haplotree.  It is however a bit tricky job and calls for more detailed instructions and I don't publish it.  All named ISOGG variants introduced by FamilyTreeDna are listed here and on following pages.

The VCF specification

edit

Instructions for installing BCFTOOLS on Ubuntu, search "install bcftools ubuntu" by Google.

edit 02.04.2019 14:00

It looks like VCF quality scores are highly dependent on the sample number and I added the read depth to the filtering phase.  You can modify both,  QUAL and DP.  I see this dependency mostly as a positive thing, but in some cases also a drawback.  I also filtered indels out.  

 bcftools mpileup  -Ou --ignore-RG -f assembly38.fasta in.bam | bcftools call  -Ou -mv -V indels --ploidy 1 | bcftools filter -i 'QUAL>80 & DP>5'  > var.flt.vcf

edit 10.4.2029 13:10

Scripts above don't work with ancient dna, they work only with high quality modern samples. 

My BIG Y is ready!

Last Monday it happened, the BIG Y is here after 199 days, just right to be a gift for my 70th birthday!  In my opinion FamilyTreeDna gives much value for money, although they should compensate somehow stumbling in delivery.

Here are some examples showing what you get.  The block diagram is one of the most resourceful apparatus, because it defines my genetic distance by using still unnamed variants.  Here is how it looks:

My match names are erased, but clicking names on your own BIG Y site you see numbers telling how many still unnamed variants differ between you and named kits.

Here the difference is 11 variants and using average mutation rate, 150 years, we can obtain 11/2*150=825 years.   This is an estimation and I need more matches to increase reliability.   
 
It is essential to know the number of unnamed variants, because most youngest markers are unnamed, in my case all younger than 1200 years.  So if you are interested in genealogy, you need to know those markers just now.

Another powerful tool is the chromosome browsing tool, because the read depth varies and FamilyTreeDna tells only the average read depth of their service, not individually.  In some cases it happens that some crucial markers show too few reads and are therefor marked "low quality".   But using chromosome browsing you can see more and rescue your results!  If you are familiar with genetics you can calculate the quality level checking data inside downloadable VCF and  BAM files.  In my case quality scores of BY35383 are for derived allele 24.0287 Phred and the RMS base quality 31.5945 Phred, those values based on FamilyTreeDna's VCF file (Phred conversion to decimal numbers, Wikipedia).  Being even more familiar with genetics you can process the BAM file and pick more information, because the results depends on many run parameter set usually to serve average cases.   Probably you will find out that the probability of those "low quality" variants is 99.9% or even better.  This can save your day if you are genealogist. Two examples here show the difference between high and low quality cases:

Iron Age Finns in Southwestern Finland belonged to N-haplogroup

A new article taking place before the study tells that at least four of around twenty samples in a southwestern Iron Age cemetery (Luistari) belonged to the male haplogroup N and no other haplogroups existed.  If we assume an even distribution between females and males, we can say that at least four of ten males carried haplogroup N.  The probability for all ten being N is very high and suggests about quite a dense local population.  The article doesn't give information about detailed haplotypes, so we can't figure the origin or populational connections.   Ten of twenty samples got maternal haplogroups, some showed eastern and some western kinship.  A bit mysteriously the article suggests that maternal haplogroups have more similarity with modern eastern and northern Finns than with modern western or southwestern Finns.  Does this mean that present-day western Finns migrated later?  Or does this mean that Iron Age Finns married women from eastern and northern parts of the country?   Researchers were able to specify some phenotypic details of four men and one woman. They all were blond.   Three of N samples showed mutations linked to the disease Dupuytren's contracture, also called in Scandinavia as "Viking disease".  This is a huge amount, even if we suggest N=20.  Did the Vikings belong to the haplogroup N?

Article 

Luistari is a large Iron Age cemetery in Finland with a lot material artifacts like jewellery and weapons and significant even in an European scale including over 1300 burials.

Luistari