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



  

FamilyTreeDna's delivery issues

I ordered my Big-Y kit October 30, 2018 and today I still have no idea about the delivery. I have not either received any explanation from FtDna why I am still waiting for it.  Sure I have asked it.  Expected dates come and go without explanations.  I am disappointed especially because my idea was to open a new blog about Y-DNA and I have now waited for it 185 days.    If I only could have known what I know now I would have had choices  Now I have not. They can keep me hanging as long as it takes.

Detailed Sigtuna Viking Age male haplotypes

I presented in my previous post a new haplotyping process, here.  While preparing a new data base to reprocess all today available Iron Age samples around Baltic Sea, I ran two Sigtuna samples through the haplotyping process.   The sample identified by "84001" was N-L550 and the sample "84005" was I-Z74.   Both results deepened from the results offered by the study.  L550 is a clade known as Scndinavian-Baltic and Z74 is known as Scandinavian-Finnish.  Detailed results and mutations:

L550
Z74

(If pictures are two small to read, please copy them from the screen and paste to some image editing software)

edit 20.2.2019 14:00

After rerunning of the Fastq file of "84005" and reducing the quality, it still being reasonable,  I found a downstream mutation CTS4791, which is according to Yfull a parellel mutation with CTS2208, found mostly from Southern Scandinavia, but also from England.  So the Sigtuna sample 84005 belongs  likely to a very particular Scandinavian-Finnish branch, actually the next level of Z74 diverged to  Norway and to Finland.   The CTS4791 is now the terminal mutation, but even more downstream mutations are possible after new genome scans. 

edit 20.2.2019 14:40

Now the Iron Age Baltic sample DA171 is also checked.   I can't confirm L1025, which is reported on some online services.  I was able to find Z4917, which is now parallelized with L550 in the ISOGG chart.   

Icelandic Vikings like ancient Scandinavians and English Vikings

Recently available data of Icelandic Viking Age samples (study Ancient genomes from Iceland reveal the making of a human population) resemble pretty much Iron Age Scandinavians and also Vikings from UK published in the study

Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum.

Unfortunately this study gives very little idea of the origin of those UK Vikings, but if they were any kind of a mixture of Scandinavians and Britons/Anglo Saxons they could have given something to Icelanders, because British-Scandinavian mixture of Icelanders have been assumed in many studies.  Another question is if Vikings in UK and Iceland represented same Scandinavian migrations, which can be true.  Here is a qpAdm result shoving similarity between these two Viking groups.

 chisq       tail prob       UK-Viking-Age Levaluhta_outlier Scania_IA
 2.767       0.905689      0.307              0.194                   0.498

Y chromosome mutations decoded

Thanks for the mutation map of the newest ISOGG Y-DNA Haplogroup Tree I was now able to decode yDna mutations.  The whole matrix includes over 300000 Y chromosomal SNP's and mutation checks, but it is limited by mutations found in BAM files.  Now tested code fits with the Build 19/37,  but I decoded also the Build 20/38.  I am waiting for my BIG Y and will test the Build 20/38 after it.  Nevetheless, novel mutations are detected as well. My code reads BAM format, but use of FASTQ is also possible if needed.   The second step after decoding BAM files makes matches with ISOGG trees and the result looks like:

This particular result was run using an ancient Kola Peninsula sample BOO002, but my code works with modern samples as well.  So the haplotype is here N1a1a1a1a, in other word N-L392, including also many parallel mutations shown by the ISOGG tree. You can see that some downstream mutations represent other haplogroups, because some downstream mutations exist in several haplogroups.  I am happy with this, but if someone wants to code a tree based on this code, I'll give it (not only data) for a testing purpose. 

Potential pitfall of IBD and other statistics due to homozygous IBD

It is a well known issue that homozygous IBD can lead to erroneous results in many statistics targeting ancestral reckoning, no matter are we trying to find out ancestry using present-day or ancient samples.   Here is a Beagle statistics showing homozygous IBD inside populations using 600000 SNP's.   Results are not  universally applicable, because of low sample numbers, nevertheless they are valid showing the error possibility of ancestral statistics using any selected data. Homozygous IBD can also reveal bad sample selection (unrepresentative selection). It is also good to notice that random individuals can have large homozygous segments near centromere, still showing relatively low overall homozygous IBD, hence a ROH test is not a good method to show inbreeding.