torstai 31. toukokuuta 2018

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.

torstai 24. toukokuuta 2018

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.

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.

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.


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