tiistai 22. toukokuuta 2018

F3-analysis of Botai-culture gives contradicting results

The Botai culture was an ancient culture which lived around 3500 BC in Kazakhstan.

https://en.wikipedia.org/wiki/Botai_culture

Some researches state that horses were domesticated by this culture. The recent study, Damgaard at al. 2018, published three samples of Botai culture.  There has been some discussion about a genetic link between present-day Saami  and Botai people, seen by IBD-segments on public Gedmatch service.   IBD-statistics however has a shortcoming in analyzing ancient samples, because a) IBD-segments become mostly random after around 1500 years and b) ancient samples has usually too low quality to form usable IBD-segments.  However,  my f3-statistics so high common drift for Saamis and Botai samples.  This similarity seems to continue in Finland and Scandinavia,  but not in Mongolia, which probably means an artificial effect between Saamis and Botai samples, generated by a coincidentally similar admixture of Siberian and ancient Steppe cultures in both populations.

torstai 3. toukokuuta 2018

Homozygosity by descent figures in Eurasia

This is not aimed to be an overall test including all Eurasian populations. Basically I have included only some samples covering over 400000 markers.   In some cases sample sizes were limited by too few individual per population and I dropped all population including less than 3 samples.  Even this is absolutely too little to get steady results.  It is also possible that some sample groups are poorly gathered and don't represent given population ideally.  Anyway this test gives a general view about existing homozygosity by descend in Eurasia.  The definition of Homozygosity by descendPossessing two genes at a given locus that are descended from a single source, such as may occur in inbreeding or in consanguineous mating.  

If my readers are interesting in seeing larger data and more populations, for example East Asians, Africans and Americans, I can rerun this test.   

Results are generated by Beagle software.



Update 3.5. 19:15   Fixed Turkish sample size and LOD-scores
Update 3.5.  20:47  Removed Turkish results, because some individuals showed excessive homozygosity



 


tiistai 24. huhtikuuta 2018

The naked truth about Dstat and Nganasan ancestry in Europe, updated

Maybe you are already bored of this issue, but I have to return to it, because it is so crazy and studies still use Nganasans to prove historical events in Europe.  It is also important to correct false conclusions.

In following tests I compare Nganasans, Native Americans, Europeans and some Asian populations and I prove that tests using Dstat and Nganasans are the craziest folly I have seen in population genetics.    My results imply that Nganasans went through a genetic drift during thousands years losing almost all ANE (Ancient North Eurasian) ancestry.  ANE is commonly found everywhere in Western and Northern Eurasian  and Native American people.   It is possible that they later got some genes from early Uralic speakers and albeit of the all  homogeneity they show in simplified comparisons the latest admixture event they have.



Update 26.4.18 10:20

After testing all available Siberians and their ANE/ENA ratios I found that actually Ket-people share highest drift with Finns, much more than Nganasans.  What probably is misleading people with Nganasans is that when comparing to other Siberians, the Finns share proportionally more drift with Nganasans than for example Lithuanians.  Still Lithuanians share more drift with Ket people than Finns with Nganasans.   My reckoning about this is that we (Finns) have received two Siberian migrations, the first one occurred when the Uralic language was brought to the Baltic Sea region and the second one via northeastern route and was forwarded by Saami people.





sunnuntai 15. huhtikuuta 2018

Is the Nganasan ancestry of Uralic speakers proven?

Lamnidis et al. 2018 preprint shows that all tested Uralic speakers except Hungarians show highest genetic drift with Nganasans.  Maybe, but it is not a piece of cake to prove, because Nganasans actually act like a proxy population for all North and East Asians.   Here is the original Dstat-table from the preprint


We see that Saamis, Finns, Russians (obviously North Russians) and Mordovians show positive drift with Nganasans.   But if we compare Nganasans to Beijing Chinese we see that also Altaians, Bengalis, Mongolians and Hazaras have more drift with Nganasans than with Chinese people. 



It is easy to find out the problem,  we have serious problems in using such a small inbred population as a reference, for example Hazaras should have Mongolian ancestry, but statistics  shows more Nganasan than Mongolian drift.

 Lithuanian     Hazara    Mongola      Mbuti     -0.0618   -21.006  50384  57016 890006
 Lithuanian     Hazara    Ngan           Mbuti     -0.0624   -17.118  50494  57211 890006

Nevertheless, in my opinion the Asian admixture in Finland is North Asian, but wrong conclusions are always possible when we have more that two variables.
 

torstai 22. maaliskuuta 2018

Saami prehistory: Ancient Fennoscandian genomes reveal origin and spread of Siberian ancestry in Europe

New study preprint reveals that Saami people settled earlier much larger areas in Finland.  The study doesn't give answer how far to the south they lived, but it looks like Saami settlements reached at least the coast of West Finland.  The study discloses also several new samples from Kola Peninsula, oldest ones around 3500 years old.   Two of those Kola samples belong to y-dna N-L392, representing oldest N1-samples so far.  N-L392 is an upstream mutation for the largest Finnish group including Karelians and Savonians.  It is possible that the whole North European N descends from populations that migrated following northeastern route from Siberia and have got the recent genetic shape due genetic bottle necks and assimilations.  This would  be a reasonable explanation until we have other evidences about more southern ancient N.  This is however contradicting with the main stream linguistic theory of the Volga bend origin of Baltic-Finnic languages, assuming a straightforward connection between Finns and their language. One explanation could be that the language came following southern route and was brought toward Estonia by people carrying R1a.

https://www.biorxiv.org/content/biorxiv/early/2018/03/22/285437.full.pdf

edit 25.3.18

A short quote from an Estonian newspaper referring to latest linguistic research:

Eesti Vabariigi aastapäevaks kolme teadusharu koostöös valminud uus seletus läänemeresoome rahvaste tekkest viitab ühe olulise väljarände keskmena Põhja-Eestile, kuhu olid jõudnud Volga äärest teele asunud, teel baltlastega segunenud ja Daugava kaudu praegusesse Eestisse jõudnud väljarändajad.

And here is the Google translation to English, with some syntax corrections:

A new explanation of the formation of Finno-Ugrian peoples, co-written by the three branches of science, points to the emergence of the most significant migration to North Estonia, emigrants embedded on the road from Volga, on their way to the Baltic, and migrated to the present-day Estonia via Daugava (Daugava is in Finnish Väinäjoki and in Estonia Väina jõgi, although Estonians usse also Latvian Daugava.  The beginning "Väinä" (joki=river) can refer to the mythic Finnish hero Väinämöinen, who was the biggest character in the Finnish national epic.  A map figuring Latvia during the Great Northern War around 1700CE, drawn using an original done by Swedish historians: http://www.pohjanprikaatinkilta.fi/PohPr/taistelut/riian%20ymparisto.jpg). 

So the Finno-Ugric migration, later called Baltic-Finnic people,  migrated via Daugava, which is a river in Latvia.  How do we bring together two crucial observations,  the N1-root in Kola Peninsula 3500 years ago and the migration way of Baltic-Finnic people from the Volga region via Latvia and Estonia to Finland, which also happened around 2000-3500 years ago?

https://heureka.postimees.ee/4390183/suur-lugu-postimees-esitleb-kolme-teadusharu-koostoos-sundis-uus-pilt-eestlaste-kujunemisest

perjantai 9. maaliskuuta 2018

New ancient samples on PCA

I ran 2500 samples, each representing 900000 SNP's using Eigensoft's SmartPCA with the parameter "lsqproject", which is designed to correct missing data of ancient samples.   The manual states:

lsqproject:  YES
PCA projections is carried out by solving least squares equations rather than an orthogonal projection step.  This is approriate if PCs are calculated using samples with little missing data but it is desired to project samples with much missing data onto the top PCs.


Next I computed eigenvector averages for all populations in order to make the output more readable.  So each symbol represents up to around 20 samples. Corresponding eigenvalues are 13.858230 and 10.064209.

The result:






It should be easy to discover different historical events, for example the Blatterhole_MN, which was a distinct group and solely its own kind with zero steppe admixture, holding probably 60% ancient farmer and 40% western hunter-gatherer ancestry.  

lauantai 10. helmikuuta 2018

New Baltic samples on PCA plots

I have made two PCA plots using new Baltic samples published by Mittnik et al. 2018, but as far as I can see with a different approach.  On my plots modern populations are placed at first hand on grounds of ancient samples, giving, in my humble opinion, a historically correct approach.  I have also standardized  sample sizes of modern populations to minimize the effects of modern genetic drift, which of course, if exists, will lead to comparison error due to irrelevant PCA-components.  Thirdly I have here two regional view; Eurasian and European.  The Asian effect on the Eurasian picture is pronounced in certain modern populations implying Asian admixture events after the Bronze Age Europe.


Eurasian picture:


Close-up of Eurasian picture:



European picture:


edit 10.2.2018

On the Eurasian picture the first dimension (X) represents East-Asian and Siberian maximums and the second one (Y) represents ancient farmer maximum.  So the picture isn't relevant for checking dimensions inside present-day Europe.  It is easy to understand that the flat left represents Asian/Siberian minimum regardless of later European structures.  Similarly the the vertical axis represents variation between ancient farmers and hunter-gatherers rather than structures inside present-day Europe.   The third picture (Europeans only) represents historically correct variation between ancient farmers and hunter-gatherers and exclusively to these variations ancient Steppe populations.