Saturday, April 18, 2015

Finnish I1, can it descend from pre-Saxon ancestry, part 2

As I mentioned in my previos text, around 28% of Finnish men belong to a certain I1-clade named usually a Bothnian.  The rest 72% consists mostly of N1c1 clades and the rest, below 10% belong mostly to different R haplogroups.  The N1c1 splits roughly into two or three clades:  eastern Karelian, eastern Savonian clades and southern Baltic and Finno-Baltic clades.

The history of Finnish I1 was pretty long unkown and was a target of speculations although many Finns being aware of the Finnish history were able to see more and understand the course of history, actually pretty well (on our Finnish forums treating the Finish history was a member calling himself Moses Leone.  He stated 8 years ago that the Finnish I1 was older than usually supposed and bound to Iron Age migrations).   What we know now more is based on  new Y-chromosome related information.  It shows us hidden history of male ancestral lines thousands years back.  And what can we now say for sure based on the new information? It is the same as many hints have given for us to presume already years ago.  So we don't know now more basics, we only can broaden our knowledge with new facts.

Keeping in mind the Finnish history, not only genetics but also archaeological and linguistic evidences (known already around 200-300 years) it is undeniable that the Bothnian group is closely related to a certain Central European clade, known by the ydna-mutation CTS2208.   Out of touch of this mutation the relation can be confirmed also by STR-statistics.  STR-statistics can give misleading information if used to explain a single individual result more than hundreds years back in time, but statistical results are still valid.  The more we have high classified samples the more history can be plumbed.

I did the following test, you can do it too:

1.  Dowload all I1-L22 (L22 is an upstream mutation for CTS2208, L22>Z74>CTS2208, look here ) from FamilyTreeDna's global I1-project.  Data is available here
2.  Select only samples with 67 markers or more
3.  Select samples randomly from each L22-subclade to have almost equal amounts of samples in each subclade
4.  Run the data using some TMRCA calculator, you can do it for example here
5.  Run the generation table using some PCA- or MDS-software.  PAST works fine on Windows, downloadable here. You can also make phylogenetic trees, if you wish.

Here are my results.

Blue -    Bothnia, corresponds SNP mutation L258
Purple - "pre-Bothnia", mutation L287, negative for L258
Red -     "prepre-Bothnia", "pre-Saxon", mutation CTS2208, negative for L287
Yellow - "preprepre-Bothnia mutation Z74,  negative for CTS2208
Brown - L22-root, samples negative for all downstream mutations
Green -  combined Scandinavian L22-clades


Clusters k3, k4 and k5:

edit 30.4.15

According to the manager of Finnish I1-project the kit 38676 could be CTS2208+, predicted by STR-results and the kit has not yet tested CTS2208.  Assuming this being true we get following PCA-results.  I also added kit numbers and countries for all CTS2208 results.   If I dare to make some conclusions I would say that main Finnish I1-clades descend from a Scandinavian group which rose in Southern Scandinavia during the Bronze Age.  Evaluating more the history I would say that some men migrated from Southern Scandinavia to Finland around 2000 years ago and perhaps later same Scandinavians migrated to England.  English samples are overrepresented due to the US connection.

Saturday, April 11, 2015

Finnish I1, can it descend from pre-Saxon ancestry?

It has gone almost year since I last time visited FtDna's I1-project, being quite tired of the usual pathetic ydna discussion. Now after a little pushed by another Finnish guy I took a look and noticed that the SNP-based phylogenetic tree shows more upstream matches for Finnish Bothnians than a year ago. Most of new matches are from England which obviously mirrors the testing activity more than enything else. Anyway, it looks like the Bothnian I1 descends from something like Anglo-Saxons, but we have to date it, accoring to the clade age (made by Ken Nordtvedt and others), to the time before Anglo-Saxon British migrations.  Here are those connected directly to Bothnians, They form an own class between all other I1 branches and Bothnians.

This information is public and available for anyone from FamilyTreeDna's project page and I don't see any reason to hide kit numbers and names.  I however overwrote all personal information because I am not sure about my right to publish Familytreedna's data.   Anyway it is public, here

 I1-L22 CTS2208 CTS5476 (L22+, Z74+, CTS2208+, CTS5476+
 XXXXXXXXXXXX Topsfield England
 XXXXXXXXXXXX Ryazan Russian Federation
 XXXXXXXXXXXX Glemminge Sweden
 XXXXXXXXXXXX United Kingdom
 XXXXXXXXXXXX Luton Bedfordshire England
 XXXXXXXXXXXX Ephraim England
 XXXXXXXXXXXX New Jersey England
 XXXXXXXXXXXX Ephraim England
 XXXXXXXXXXXX Malderen, Belgium

And here is the beginning of the long Bothnian list. They represent about 28% of all Finnish men.

I1-L22 L258 (L22+, Z74+. CTS2208+, CTS5476+
, L287+. L258+) [ Z133, BY2572, Y8598 available]
XXXXXXXXXXXX Mouhijärvi Finland
XXXXXXXXXXXX Pihlajavesi Finland
XXXXXXXXXXXX Kalajoki Finland

Sunday, April 5, 2015

Comparing ancient and modern Europeans, a special case

Children of Native American and European parents share their parents’ autosomal dna.  Uniparental dna is however inherited without recombination.  The situation is more complex if we imagine an isolated population which started to grow after ancient migrations from 100 Native American men and 100 European women.  After several generations autosomal dna is more mixed. Autosomal dna is after generation also drifted, meaning they have lost something about the original information.  I think that genetic drift is like entropy.  The counterforce for entropy in this case is selection.  Selection resists genetic drift but only in chromosome regions where the selective impact is efficient, in other regions genetic drift goes on.   Uniparental dna doesn't transform similarly.  

What I now portrayed can be tested in practice, we need only two populations showing some common uniparental dna, being on autosomal side far enough from each other to give clear difference and also better if they are enough homogeneous proving isolation.  It is important that populations are not too much mixed. And I have them:  on the other side Sardinians (group 1) and then Finns and  Lithuanians (group 2).  Then we need to know who they were in the beginning. Because we can’t have ancient samples corresponding exactly to history of any modern populations I have used  EN results (European Early Neolithic samples), corresponding to the historical continuity of the group 1.  This historical similarity between Sardinians and EN was shown in Haak et al. 2015, being 91-96%.    

Here we go.  I gathered YDNA and MTDNA distributions from Eupedia and autosomal figures from  Haak et al. 2015.   If my theory is right we should see something like:

  •  autosomal parity between ancient and modern populations in group 1 (Sardinians and EN) is high if both are mostly unmixed.  This is a postulate.

  •  amounts between ancient autosomal dna (EN) and modern uniparental genes (group 2)  roughly match because uniparental genes don’t drift.

  • amounts between modern autosomal genes (group 1, Sardinians) and modern autosomal genes (group 2) don’t match similarly as in previous comparison because autosomal genes have drifted in both populations, in this case around 7000 years, less or more hard to say exactly because we know too little about ancient migrations. 

But this is not a full story.   Trying to make accurate comparison between modern populations usually fails less or more, because we have no fixed reference points.   This happens espacially when using formal admixture softwares.  It happens also in this case when comparing Sardinians and Finns/Lithuanians without using EN as a reference.  Only ancient genomes can be reasonable references, so we actually don't know how much Sardinians and Finns/Lithuanians could match.   

YDNA and MTDA statistics gathered from Eupedia, to download click here.

Comparison between Haak et al. 2015, statistics from page 122 onwards (download here) ,  and now gathered Eupedia numbers:

Finns:  EN 31,5-42,5 %  corresponding to the modern common ydna uniparental with Sardinians 34,5 % (Eupedia numbers)
Lithuanians: EN 33,4-44,2 %  corresponding to the modern common ydna uniparental with Sardinians 38,65 % (Eupedia numbers)

We know that uniparental and autosomal genes correlate and it happens also here. 

For comparison three formal admixture analyses:




Friday, April 3, 2015

Achilles’ heel of admixture analyses.

So many people have made admixture analyses, and got results that are inexplicable if compared to uniparental genes.  Despite of this very obvious observation very few have tried to resolve why this happens.   We can see that for instance the amount and diversity of mitochondrial class H is in obvious contradiction with most admixture analyses.   MtDna H is usually connected to ancient farmer populations, to the first farmers in Europe.  (update 4.4.15: in a long history mtDna H is probably not solely connected to ancient farming, but the question about different results between admixture tests still remains.  Farming in South Europe was probably partly an adaptation, not based on Near-Eastern migrations.  And the H was only indicative, same problems exist with other uniparental genes). But admixture results can show almost zero percent of ancient farmer genes (early farmers’ genes typical for example in Sardinia) and the same population can have MtDna H around 40%.  

How this happens?   The bells should ring between researches’ ears.   If observations contradict it is their duty to find out why.  I have a theory, not only something from thin air, but observations during reading studies and also making some myself.   Studies show that if we use ancient farmer samples from the Neolithic Age we see that uniparental and autosomal results can fit quite well.  But when we make our admixture tests based on present-day samples the difference exists.   So the reason for this contradiction between uniparental and autosomal results is something in terms of sample sets.   This something seems to be the admixture that came among later migrations, after Early European farmers and samples representing them.  It looks that formal admixture tools give much more priority to younger admixtures, more than their quantitative proportion in our genomes shows in reality.   This error is likely caused by the formal admixture methods giving too much attention to what is different and these differences are there because later migrations have smaller expansion area.