keskiviikko 4. syyskuuta 2019

Ydna haplogroup of the sample RISE175 (Allentoft et al. 2015)

I picked this from Eurogenes.  Studies have usually high quality standards, but older studies also miss many later defined mutations, so my aim is to redefine the haplogroup of this particular ancient sample.  The sample quality is rather poor and only a few mutations can be determined, even when lowering the mapping quality.  Here is a straightforward result:

After filling holes between I1 and I1a2a1a1a2~  we find following levels:  I1a (DF29), I1a2 (S244/Z58), I1a2a (S246/Z59), I1a2a1a (Z62), I1a2a1a1a (S440/Z140, Z141).

Here is a real chance to find oneself in those haplogroups and it would be also nice to know about present-day distributions.

Additionally the result included many candidate mutations published by FamilyTreeDna, which are not yet connected to the tree.  In general, research go on and it would be a good idea to check old samples for new yDna mutation.


tiistai 6. elokuuta 2019

A short overview of Saag et al. 2019 samples

Saag et al. 2019 introduced new ancient East Baltic samples.  I made a short F3-analysis adding some older samples from the Baltic area for a comparison.  The base line consisted of five present-day populations:  Southwestern Finns, Mordvas, Norwegians, Poles and Russians from Pskov.  I didn't want to use modern Balts because they have proved to be unreliable in all f3- and d-statistic, giving high common genetic drift from the westernmost Europe to Ural mountains.  Russians from Pskov do the trick representing much better the Baltic locality.  Balts of course are the most local people, but unfortunately our software toolbox fails with them.   Obviously this has something to do with the high homozygosity and low mixing rate.  So here is the result.  You need to read the original study to interpret sample abbreviations.  In evaluating results it is good to observe that Finns and Mordvas have a Siberian admixture (3-7%) which displaces other ancestral parts and cuts off genetic drift from other ancestral sources.  Accordingly f3- and d-analyses are not able to answer to the questions "where did they come from", the fact that many of us dismiss. 

or download a larger picture here.

perjantai 19. heinäkuuta 2019

Alder analysis dating problems II

After my obvious mistake in parametrization I ran several tests with Alder.  Unfortunately Alder has same problems than Rolloff and trying to estimate regional ancestries and admixture dates is problematic for two main reasons:

- both programs assume only one migration.  If there has been several migrations between populations under test, as it often regionally is,  the spectrum of IBD segments is large and the Admixture-induced Linkage Disequilibrium curve becomes too vague to determine admixture dates.

- in case of obvious one migration the problem is that in some point the results reaches a point where too many segments are "constant" for a long time and those segments don't follow the average recombination rate assumed by Alder.   This leads to a too recent admixture event.  For example, calculating admixture dates for ancient Saami and Nganasan admixture events in Finland gives almost exactly similar curves, pointing out to a fixation of certain IBD segments.

What can I do?  It is possible to pick remote populations and use them as proxies for the assumed admixture event.  For example using Danes instead of Swedes to show North Germanic admixture in Finland.  This is however possible only in cases we already know the prehistory well enough to make this initial setting relevant.

sunnuntai 23. kesäkuuta 2019

Alder analysis dating problems

I have to retract my previous results.  Results were wrong due to a wrong run parameter.  Sorry, I will be soon back.

perjantai 21. kesäkuuta 2019

Finnish ancestry, what we have now ...

is very little.  We really have almost nothing, but even so we can say something.  Actually I am on my summer idle, but will write occasionally.  I have hesitated to publish statistics using sample data released already a year ago by Damgaard et al. 2018, because I didn't want to disturb Finnish researchers who still prepared their own publications (maybe my writings wouldn't disturb -  felt that way anyhow).  But the situation have now changed after several dilettantes have been very active and have broken the silence.  Routinely using f3-statistics we can calculate drift similarity for present-day Finns and inhabitants in Iron Age Fennoscandinavian.  No matter the branch of science we always find out that present-day Finns lived in Finland during that time.  According to f3-statistics the sample closest present-day Finns was the sample named as Levaluhta (Levanluhta) outlier.  I probably will be back sooner or later with this topic, now only shortly:

lauantai 25. toukokuuta 2019

Genetic evidences about Uralic connections between Hungary and Fennoscandinavian Circumpolar region

A new Nature article bundles the history of Hungarians with northern Circumpolar areas.  Indisputable evidences bundle the y-chromosomal group N-L392 and male lineages of these regions together at age around 4800-6400 years ago (clade age 6400 YBP and TMRCA 4800 YBP).  In the light of all available datings and downstream mutations the common origin would have existed not later than around 4000 years ago somewhere between Ural mountains and Ob river in Northern Siberia.   Again, the Hungarian data reveals the same total losing of Siberian autosomal origin that we already have seen in the Baltic region, especially among Balts.  It is still present in Finland and strongest in Northern Fennoscandiavia, diminishing to the south.    Genetic lineages of Hungarians and people in the Baltic Sea region seem to have met in Khanty population (whoever their ancestors were 4000 years ago), read the previously linked Nature article and look at my previous post including an elucidating PCA plot (Uralic path Khanty-Bolshoi).

edit 26.5.2019 11:20

Some typos corrected.  It came into my mind also that the Hungarian N dilemma is not yet proven.  So many times people, like also researchers are, see what they want to see. To prove the Hungarian-Fennoscandinavian uniparental connection we should have wider comparative data available covering frequencies of N in Europe.  It is fascinating to find something like this, but I am afraid that geneticists are too much prone to follow linguistic postulates.  Especially when speaking about the prehistory of Finno-Ugric languages we have had sad history.   So even in the case I like to agree this Hungarian connection, I don't buy it yet, not because I don't believe or I don't like, but I still consider the case doubtful.    

tiistai 21. toukokuuta 2019

The origin of Fennoscandinavian and Baltic N in Kola Peninsula? Part II update 2

Additional data:

After so many studies handling Baltic and Finnic people, I would like to see new Scandinavian research.  We have very few of them.

A few words about methods

Most studies use Nganasans as a Siberian reference despite of the European population being tested.  So, if we consider Nganasans to be closest to Finno-Ugric people, we can mistake with other Europeans, because the relationship between Finns and Nganasans makes them a special case. We may have done a wrong premise in a European wide analysis. Especially, if we assume that N1c1 came to Finland via Norhteastern route, through Kola Peninsula, we should not consider Nganasans as Siberian in general, because it is in that case a special case and cannot represent Siberians in general.  Maybe Ukrainians had some other Siberian connections, we don't know if we use only Siberian references suggested being close only FU-people, in other words Nganasans. Likely Ukrainians have not that admixture, but the method we use has to be neutral.  Do we want to use some edge reference instead of mainline references?  Edge references fit best with population next to the edge.  Another relevant outcome is that the more distant reference groups are from the tested one, the smaller the difference between relative reference groups is when compared to the population under test.  This means that valid Siberian references in same test should give same amount admixture for all tested populations without known Siberian admixture (European references).  If not they are not valid references.  But then, it is totally another issue if we use qpAdm, which tries to use non-relative method, but it is another story.  Let's look it in practice.

I ran a supervised admixture model assigning 10 Siberian groups to 3 West European groups.  The result shows that a genetic connection between Nganasans and West Europeans is possible, despite of the Nganasan tendency to be least admixed Siberians in unsupervised models. Nearest for Nganasans of those three are Germans, followed by Spaniards and English Cornwall is least Nganasan.  The fact is that Admixture is a relative method, which cannot get negative admixture values (qpAdm can).