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.

False correlation between yDna N1c1 and Asian admixture in Finland and Baltic area

Time and again I see people making conclusions between Finnish N1c1 and eastern admixture.   Regardless of the eastern origin of N1c there is not such correlation in Finland.  The reality is even worse for those who cherish this fallacy; if we count also Baltic countries the correlation turns out to be negative.  In Finland alone all male haplogroups have equal level Asian admixture and the only difference comes from the locality, not from the male haplogroup.  Rational person would conclude that the Asian admixture is from a local source.   This is a no-brainer and I don't even need to prove it.  Everyone being familiar with this matter knows it, but it doesn't prevent the biggest Finnish newspaper distributing this urban myth.   Google translation, click here.  

Epilogue.  The fallacy of the eastern origin of Finns results from many things.  I am not interested in other opinions than those bothering Finnish people and researchers, because I don't care much about "public opinions" without scientific basis.  A common idea in Finland, believing in different Finnish origins (Lappeenranta-Vaasa or whatever axis) driven by Finnish "race realists" who inherited opinions from the old Swedish school, is that here in Finland have lived two "races".  Now some Finnish scientists have agreed this and detached themselves from known historic facts.

QpAdm - what it means in practice

As we saw in my previous posts the correlation between fit and standard error is very meaningful.  We saw that the Basques are a loose mixture of East European Steppe  and ancient Iberian people, but they are only far descendants of those two groups and we can't prove that these two are their only ancestor, although they definitely forwarded genes to Basques.  I made similar test showing that the Greeks are distant descendants of Iron Age Anatolians and Bronze Age Balkanians, but again we can't be prove that those two were their only ancestors.  Probably not.

                                Balkans_BronzeAge Anatolia_IA
best coefficients:     0.470                        0.530
Jackknife mean:      0.475197121             0.524802879
std. errors:              0.077                         0.077 

fixed pat  wt  dof     chisq       tail prob
00  0     8    15.062       0.0579554     0.470     0.530

On the other hand,  qpAdm showed that the Finns are very strictly descendants of Iron Age Scanian, Iron Age Baltic and Iron Age Saami people, but we can't prove exact proportions of those thee admixtures, which we saw in high standard errors.  It is easy to understand that admixtures of close populations are not as easy determinable as admixtures of distant populations, because close relatives share much common ancestry.   

But how accurate are results showing very distant ancestry and moderately low standard errors, if the fit is poor?  I tested it.  Following tests show admixtures of Iron Age Saami people in Ostrobothnia Levaluhta.
  

We see that there is only a small difference in admixtures of Iron Age Saamis generated by present-day Finns and Iron Age Scandinavians in conjunction of Bolshoy outlier.  Chisq is high, tail prob. below 0.4, but std. err. only 6% max.  Nothing obliges such a high admixture similarity, because the genetic distance between Finns and Scandinavians is rather high.  Such a similarity is achieved only by a big genetic distant of Bolshoy outlier. 

Another example, although not equally striking.

Chisq is between 10 and 21, tail prob. between 0.006 and 0.24.  FI21 shows best fit.  Std.error is 5% in FI4 and FI12, highest (9%) in case of FI21.