Saturday, June 9, 2018

QpAdm tests, Iron Age Scanian sample RISE174

I've been a long time waiting for ancient Finnish samples and it starts to look  unlikely that I'll ever see them because the Finnish soil is acid and destroys organic material in one millennium.   But don't ever lose hope, it was available all the time from Internet. An old Finnish sample has been available already three years in open data bases.  It was found from the Southern Sweden and was labeled as RISE174, dated 427-611 AD, later Scania_IA.  That is right, we have had three years an ancient Fennoscandinavian sample, common for all Fennoscandinavians and also for many Baltic people, but obviously because it was found from Southern Sweden it's real value was not noticed before.  The reason could also be partly a common prejudice.   I wouldn't be much surprised if Finnish researchers in future will find similar Iron Age samples from Southwestern Finland, if it is possible due to the Finnish soil.  I'll show that present-day Swedes are not much more related to this sample than present-day Finns.  Generally speaking, all qpAdm-results listed below are reliable, although there were many neighboring cultures in the past, being also genetically very similar and in any tests all populations close enough can substitute each other.  

QpAdm results are made using distant ancestral references (the right-file)  to get best possible coverage.  While these results are very reasonable, it is possible to fine-tune all results by using carefully selected less distant references.  So these results are directional.  

All Finnish groups are from the 1000-genomes project and cover full 1MSNP's, as well as all other groups on the second and third plots.  I have seen in my work that testing ancient and modern samples calls for equal coverage of all modern sample groups. 

What kind of Fennoscandinavian was the RISE174/Scania_IA?  Definitely she was not like a present-day Swede, we can see it in following f3-result below and on PCA-plots.  

Next here is a simple PCA-plot, somewhat imperfect one and flat due to a high amount of Asian influence and too few European samples.   This plot shows a new Finnish group, Finnx, and binds it to the Finnish ancestry.  Finnx forms an ordinary Finnish group with less present-day Swedish admixture than typical Southwest Finns, but also less genetic drift than typical East Finns. 

Another plot (vectors 1/2 and 1/3), removed almost all East Asian and Siberian.  There is still a touch East Asian forwarded by South and Central Asians.  It was necessary to remove East and Siberian components to ignore later Siberian admixture in Finland and see the possible Finnx-Scania_IA connection also on PCA.  On the second plot (vectors 1/3) the East Asian is at its least and Scania_IA gives the best match with Finnx. 

 F3-test showing common genetic drift with Scania_IA:


First some European groups in a demonstrative purpose. 

South Italians

Chisq and tail prob:   0.436        0.932651 

Populations:  Beaker_Central_Europe, Iran_LN, Levant_BA
best coefficients:     0.299     0.169     0.531
Jackknife mean:      0.299685849     0.169473438     0.530840713
      std. errors:     0.028     0.032     0.033

North Italians

Chisq and tail prob:   1.738        0.628609

Populations:  Beaker_Central_Europe, Levant_BA, Iran_LN
best coefficients:     0.542     0.416     0.042
Jackknife mean:      0.542422483     0.415568791     0.042008725
      std. errors:     0.019     0.020     0.020


Chisq and tail prob:   1.789        0.774528

Populations:  Beaker_Central_Europe,   Iberia_EN
best coefficients:     0.578     0.422
Jackknife mean:      0.579234989     0.420765011
      std. errors:     0.030     0.030


Chisq and tail prob:   1.101         0.77684

Populations:  Scania_IA, Latvia_MN, Evenk
best coefficients:     0.920     0.092    -0.012
Jackknife mean:      0.918423990     0.093588254    -0.012012243
      std. errors:     0.042     0.042     0.016


Chisq and tail prob:   1.699        0.790857

Populations:  Poltavka, Germany_MN
best coefficients:     0.502     0.498
Jackknife mean:      0.502425062     0.497574938
      std. errors:     0.039     0.039


Chisq and tail prob:   0.642        0.886697

Populations:  Scania_IA, Latvia_MN, Evenk
best coefficients:     0.933     0.052     0.015
Jackknife mean:      0.931374297     0.053427705     0.015197998
      std. errors:     0.039     0.038     0.015


Chisq and tail prob:   0.503        0.973198

Populations:   Sarmatian, Scania_IA
best coefficients:     0.472     0.528
Jackknife mean:      0.475543261     0.524456739
      std. errors:     0.079     0.079


Chisq and tail prob:   1.003          0.9093

Populations:   Latvia_LN, England_N
best coefficients:     0.523     0.477
Jackknife mean:      0.520472837     0.479527163
      std. errors:     0.052     0.052


Chisq and tail prob:    1.647        0.648853 

Populations:    Scania_IA, Latvia_MN, Evenk
best coefficients:     0.851     0.084     0.065
Jackknife mean:      0.849474735     0.085348593     0.065176672
      std. errors:     0.037     0.036     0.014 

Some "what if" analyses:

What if Mordvas are Polish

Chisq and tail prob:    11.941       0.0177937

Populations:    Poltavka, Germany_MN
best coefficients:     0.727     0.273
Jackknife mean:      0.724786064     0.275213936
      std. errors:     0.047     0.047

What if Latvians are Polish

Chisq and tail prob:     9.038       0.0601576

Populations:   Poltavka, Germany_MN
best coefficients:     0.563     0.437
Jackknife mean:      0.562264229     0.437735771
      std. errors:     0.049     0.049

What if Finnx's are Mordva

Chisq and tail prob:    4.728        0.316351

Populations:   Sarmatian, Scania_IA
best coefficients:     0.369     0.631
Jackknife mean:      0.377367376     0.622632624
      std. errors:     0.093     0.093

What if East Finns are Mordvas

Chisq and tail prob:    6.593           0.159

Populations:    Sarmatian, Scania_IA
best coefficients:     0.317     0.683
Jackknife mean:      0.329388055     0.670611945
      std. errors:     0.118     0.118

What if Swedes are Baltic

Chisq and tail prob:    1.867        0.867159

Population:   Scania_IA, Latvia_MN, Evenk
best coefficients,  Jackknife optimisation is negative, 1.000     0.000    -0.000

The results above show the continuum of Scania_IA from Southern Sweden to Russia, to the area where Mordvas live.  Those populations living in eastern and  western areas have however different admixtures, Mordvas lack Baltic middle-neolithic ancestry and show instead late East European Steppe -like admixture, Sarmatians suggesting incursions of the Iranian speakers.  What is also remarkable is that the best Swedish result doesn't include Scania_IA.  This doesn't mean that they have not Iron Age ancestry from Scania and in reality they are really close Scania_IA.  It means only that present-day Swedes are slightly different, own later admixtures and lack of certain older Baltic admixtures.