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).

lauantai 18. toukokuuta 2019

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

Here is a standard admixture analysis using unsupervised admixture method.  Some new samples are removed due to poor quality.  Please note that standard admixture doesn't imply 100% ancestry coverage, rather the best result permitted by given K-value.

Update 18.4.2019 10:40

Another sort order

torstai 16. toukokuuta 2019

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

Soon after my previous post a new study dealt with the same question and published also new data, the study name and link here: The Arrival of Siberian Ancestry Connecting the Eastern Baltic to Uralic Speakers further East.  The study continued on the same theme as so many previous studies connecting the male haplogroup N1c1 with a putative southeastern Baltic Finnic home land, apparently thought to have been in Volga region.  I feel myself somehow embarrassed with this, because I have to be back with this issue so soon.  However, we have no evidences about such linguistic and genetic connection, because we don't know any Volgaic Bronze Age or Early Iron Age populations carrying N1c1, instead of it we know ancient Volgaic samples belonging to male haplogroups R1b, R1a and I2.   But we do have ancient N1c1 samples from the Kola Peninsula and present day N1c1 from the Ural mountain region.  On the contrary to the Volga idea my view is that the N1c1 came to Fennoscandiavia and Baltic regions via Northeastern route.  Without problems it can be demonstrated by using old and new samples from several studies.

The new data was downloaded from Estonian Biocentre.  I found some problems with samples names;  names in the study and data don't match and I was not able to identify all data samples, including two Tatar-like samples, but those samples are less important in this matter.

So the Saami-Finnish path shows an y-axis deviation which I consider as an unknown Fennoscandinavian hunter-gatherer ancestry.

Corresponding admixture analysis is under work and will be published soon.