Playing with Eigensoft qpAdm

I've been somewhat cautious in using qpAdm, because it looks much easier to use than it actually is.  You can make admixtures, be happy with them, but are your results as reliable as you think?   I am not going to bore you with details and instead make some examples.   Following three examples are made using same references (right file).


Results picked up from detail rows:

Secondly same results selected by the qpAdm:

The EHG stands for East European Hunter-Gatherer
The Belt_Cave Me stands for  Belt_Cave_Mesolithic_LC, the name was truncated during copy-paste operation. 

You can see that in the result of East European Hunter-Gatherer there is definitely something wrong, although the results picked up from detail rows look great. 

Update 1.6.2018 10:35

My answer to Anynyymi/Anonymous is:  yes it works at least for Latvians, but I won't continue making occasional tests with this left model, because I am more ambitious.  It is just not fair to ask for and show occasional results and let them become forgotten.  We need a larger demo.

1.089        0.779712     0.522     0.233     0.245

Update 1.6.2018 11:30

The example below shows the reason why I need more time and don't want to follow any trains of thought outside of my own head and make detailed tests.  Sorry, if I do, it could mislead readers and I just want to dedicate myself to the point here.

The devil lurking behind Botai, WSHG and modern population connections in West Eurasia

I've seen that the West-Siberian Hunter-Gatherer ancestry (WSHG) is in several texts connected to modern day Northeast Europeans  (obviously not by original studies) and now later the same theme is again on topics of new Botai samples.  The Botai was firstly presented by  Damgaard at al. 2018.   But have we one or many explanations for these assumed connections between ancient Siberian-like people and present-day population in Asia and Europe?  Was the connection, mostly even subtle, a result of any migrations or are tests only showing some common ancestry between WSHG/Botai and present-day populations?   I have not seen Damgaard et al. due to the payment wall, but Jeong et al. 2018 gives similar results I have got using f3-statistics.   My tests, as well as Jeong, shows extreme high common drift between Botai samples and ANE and WSHG acts very similarly.  ANE is presented by the Mal`ta child, who lived in Siberia about 24,000 years ago.  F3-statistics show that WSHG and Botai shows high common drift also with EHG (Eastern Hunter-Gatherer), which of course means that EHG can act like a WSHG/Botai proxy to West-Eurasian populations and vice versa.  The EHG ancestry is very common everywhere in Central, Eastern and Northern Europe, but highest in Northeast Europe and in Baltic Sea region.

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 show high common drift for Saamis and Botai samples.  This similarity seems to continue in Finland and Scandinavia,  but in lesser amount  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.

 

 Update 24.5.18 11:30

Here are two updates, the first one listing Botais' top ten of modern populations and the second one the top ten of ancient populations.  I hypothesize of Botais' admixture that is is mainly similar to West-Siberian Hunter Gatherers, with a lump of Eastern Hunter Gatherer admixture, reasoning this by two top matches of ancient populations. Obviously the Eastern Hunter Gatherer admixture ties the result with Fennoscandinavia. The influence between WSHG and EHG is interesting and calls for more study.

  

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 descend:  Possessing 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



 

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.

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.
 

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