Saturday, April 20, 2019

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.    

Wednesday, April 17, 2019

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..

Monday, April 1, 2019

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


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.