Genetic identification of Slavs in Migration Period Europe using an IBD sharing graph

[Peterski]

Abstract:

https://www.archeologia.uw.edu.pl/archeologia-i-numizmatyka-europy-wschodniej-2/

https://www.archeologia.uw.edu.pl/en/title-4th-scientific-conference-of-the-faculty-of-archaeology-university-of-warsaw-przeszlosc-ma-przyszlosc-the-past-has-a-future/

Leonid Vyazov (Faculty of Science, University of Ostrava, Ostrava, Czech Republic), Gulnaz Sagmanova (Faculty of Science, University of Ostrava, Ostrava, Czech Republic), Olga Flegontova (Faculty of Science, University of Ostrava, Ostrava, Czech Republic), Harald Ringbauer (Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Department of Human Evolutionary Biology, Harvard University, Cambridge, United States), David Reich (Department of Human Evolutionary Biology, Harvard University, Cambridge, United States), Pavel Flegontov (Faculty of Science, University of Ostrava, Ostrava, Czech Republic)

Genetic identification of Slavs in Migration Period Europe using an IBD sharing graph

"Popular methods of genetic analysis relying on allele frequencies such as PCA, ADMIXTURE and qpAdm are not suitable for distinguishing many populations that were important historical actors in the Migration Period Europe. For instance, differentiating Slavic, Germanic, and Celtic people is very difficult relying on these methods, but very helpful for archaeologists given a large proportion of graves with no inventory and frequent adoption of a different culture. To overcome these problems, we applied a method based on autosomal haplotypes. Imputation of missing genotypes and phasing was performed according to a protocol by Rubinacci et al. (2021), and IBD inference was done for ancient Eurasian individuals with data available at >600,000 1240K sites. IBD links for a subset of these individuals were represented as a graph, visualized with a force-directed layout algorithm, and clusters in this graph are inferred with the Leiden algorithm. One of the clusters in the IBD graph emerged that includes nearly all individuals in the dataset annotated archaeologically as “Slavic”. According to PCA a hypothesis for the origin of this population can be proposed: it was formed by admixture of a Baltic-related group with East Germanic people and Sarmatians or Scythians. The individuals belonging to the “Slavic” IBD sharing cluster form a chronological gradient on the PCA plot, with the earliest samples close to the Baltic LBA/EIA group. Later “Slavic” individuals are shifted to the right, closer to Central and Southern Europeans and probably reflecting further admixture of Slavs with local populations during the Migration Period."

[Figaro]

The East Germanic thing is interesting...I’m sure these were not Scandinavian-like people as a whole. Didn’t they have a Balkan component?

[Peterski]

I’m sure these were not Scandinavian-like people as a whole

Why do you think so? So far we have only Swedish-like samples of Goths (Weklice & Kowalewko).

[rothaer]

Why do you think so? So far we have only Swedish-like samples of Goths (Weklice & Kowalewko).

Because a lot of Eastern Germanic areas archeologically visibly got settled from the continental Jastorf culture.

Also, the Eastern Germanic (assumingly Vandal) chieftain from Deutschendorf-Matzdorf (Poprad-Matejovce) in Eastern Slovakia, DA119, is not Scandinavian-like (but Dutch-like).

[Peterski]

Also, the Eastern Germanic (assumingly Vandal) chieftain from Deutschendorf-Matzdorf (Poprad-Matejovce) in Eastern Slovakia, DA119, is not Scandinavian-like (but Dutch-like).

We don't really know if this Poprad sample is Vandal or not.

I am modelled by genetic companies as a mix of Belarusian and Scandinavian. My DNA Tribes for example:

http://i.imgur.com/RbNXQj9.png

[rothaer]

We don't really know if this Poprad sample is Vandal or not.

That's what's implied by the word "assumingly". But him being an Eastern Germanic is not seriously contested.


I am modelled by genetic companies as a mix of Belarusian and Scandinavian. My DNA Tribes for example:

http://i.imgur.com/RbNXQj9.png

In your pic your Germanic is mostly modeled with Denmark, which is not in Scandinavia (Scandinavian Peninsula). I doubt there is at all provided NW Germany for modeling. So the fact that Denmark is chosen doesn't contradict the possibility that NW Germany is the most suitable proxy for your Germanic.

[Peterski]

Some Germanic samples from Slovakia are more Scandinavian-like than Dutch-like:

Distance to: SVK_Tes_Mlynany:R2207
0.02241866 Danish
0.02415170 Dutch
0.03038424 Swedish
0.07688148 Belarusian

[Peterski]

In your pic your Germanic is mostly modeled with Denmark, which is not in Scandinavia (Scandinavian Peninsula).

Denmark is considered part of Scandinavia.

Anyway, Gothic samples from Poland (from Weklice & Kowalewko) are Swedish-like, not Danish-like.

And here is how I get modelled as a mix of Belarusian (assumed Slavs) + Swedish (assumed Goths):

Target: Peterski_scaled
Distance: 2.6692% / 0.02669224
55.2 Belarusian
44.8 Swedish

[rothaer]

Some Germanic samples from Slovakia are more Scandinavian-like than Dutch-like:

Distance to: SVK_Tes_Mlynany:R2207
0.02241866 Danish
0.02415170 Dutch
0.03038424 Swedish
0.07688148 Belarusian

Here also Danish and Dutch come before Swedish, which is the only Scandinavian (Scandinavian Peninsula) reference visible.

[rothaer]

Denmark is considered part of Scandinavia.

Anyway, Gothic samples from Poland (from Weklice & Kowalewko) are Swedish-like, not Danish-like.

And here is how I get modelled as a mix of Belarusian (assumed Slavs) + Swedish (assumed Goths):

Target: Peterski_scaled
Distance: 2.6692% / 0.02669224
55.2 Belarusian
44.8 Swedish

Yes, the assumingly Gutonic samples from Wöklitz/Weklice are Scandinavian-like. Nobody questions that.

As for your modelling it does not imply that combination to be true. I regularly get modelled "untrue". Btw. do you now have more Germanic than me?

[Peterski]

Here also Danish and Dutch come before Swedish, which is the only Scandinavian (Scandinavian Peninsula) reference visible.

:picard1: Denmark is considered part of Scandinavia as well:

http://www.geographicguide.net/europe/maps-europe/scandinavia-map.htm
http://www.vexen.co.uk/countries/files/scandinavia.jpg

[rothaer]

:picard1: Denmark is considered part of Scandinavia as well:

http://www.geographicguide.net/europe/maps-europe/scandinavia-map.htm
http://www.vexen.co.uk/countries/files/scandinavia.jpg

According to that map the biggest Danish island Zealand is also Swedish. :picard1: Scandinavia is a gerographic term that can not seriously be dependent on the shifting many times political southern border of Denmark. I admit that the current usage in English is that fuzzy (and imo wrongly).

[Peterski]

Btw. do you now have more Germanic than me?

Less of West Germanic but probably more of East Germanic.


As for your modelling it does not imply that combination to be true.

When using only ancient samples, I get the same result:

Target: Peterski_scaled
Distance: 2.6188% / 0.02618819
55.2 HUN_Avar_Szolad
44.8 POL_Weklice

https://vahaduo.github.io/vahaduo/

SOURCE:


POL_Weklice:R10618,0.138864,0.137096,0.072784,0.06 137,0.041546,0.0251,0.003525,0.008538,0.007772,-0.005103,-0.002273,-0.004046,-0.011298,-0.010597,0.018458,0.024264,0.017471,0.003421,0.005 279,0.014007,0.000624,0.003462,-0.003328,0.01699,-0.003832
POL_Weklice:R10620,0.129758,0.126941,0.069767,0.05 2972,0.037545,0.013387,0.00329,0.004846,-0.003886,-0.013485,0,0.004196,-0.004906,-0.004266,0.016422,0.006762,0.005346,-0.00152,-0.002263,-0.004127,0.010107,0.003339,0.004683,0.024702,-0.002036
POL_Weklice:R10625,0.129758,0.125926,0.079572,0.07 429,0.048317,0.019522,0.00846,0.01823,0.015748,-0.009476,-0.008282,0.004646,-0.004162,-0.003991,0.008686,0.016839,0.022556,0.003421,0.004 399,0.006628,0.017594,0.011623,-0.002095,-0.001205,0.001078
POL_Weklice:R10626,0.134311,0.127957,0.07203,0.055 879,0.041854,0.023148,0.013161,0.017076,-0.000818,-0.004009,-0.004384,0.012139,-0.00996,0.001239,0.025108,0.000928,-0.008345,0.002407,-0.001634,0.006628,0.004118,0.00136,-0.006902,0.018436,-0.003712
POL_Weklice:R10631,0.129758,0.131003,0.080327,0.06 3308,0.0397,0.023985,0.00188,0.005077,0.006749,-0.011299,-0.008769,0.001199,-0.006541,-0.013074,0.020358,0.005171,-0.00678,0.000507,-0.006536,0.005378,0.009608,-0.000866,-0.006039,0.008555,-0.001557
POL_Weklice:R10633,0.136588,0.129988,0.07731,0.070 737,0.050471,0.024821,0.00423,0.011769,0.01309,-0.00492,-0.005034,0.005995,-0.009663,-0.010872,0.019272,0.025192,0.010822,-0.004054,-0.001508,0.009755,0.019341,0.001113,0.002095,0.002 289,0.002036
POL_Weklice:R10634,0.133173,0.136081,0.071276,0.06 7507,0.041546,0.023706,0.003995,0.015461,0.005931,-0.008018,-0.009906,0.004046,-0.008028,-0.006055,0.021851,0.002652,-0.00665,-0.00228,0.004777,0.001,0.004243,-0.003462,0.00419,0.013255,-0.005389
POL_Weklice:R10636,0.133173,0.118817,0.080704,0.06 8153,0.038161,0.029005,0.003525,0.006692,0.003681,-0.011481,-0.008607,0.003297,-0.001933,-0.002202,0.016015,0.008353,-0.002608,0.001394,0.008045,0.001751,0.000374,0.003 957,0.001479,0.025064,0.001197
POL_Weklice:R11391,0.127482,0.132019,0.065996,0.05 7171,0.044316,0.032072,0.015746,0.010846,-0.003886,-0.016037,-0.003735,0.015886,-0.016204,0.006193,0.023887,0.000398,-0.028163,-0.001647,0.004651,-0.001251,0.017095,0.009027,0.003081,0.012893,0.002 634
HUN_Avar_Szolad:Av2,0.135449,0.128972,0.080704,0.0 63954,0.034776,0.034025,0.006815,0.007615,0.009613 ,-0.02041,-0.001461,-0.005245,0.010852,0.026561,-0.014658,-0.002254,0.002347,0.001267,0.01081,-0.001751,0.001622,-0.002844,0.009613,-0.008314,0.005389

TARGET:


Peterski_scaled,0.133173,0.140143,0.065619,0.05846 3,0.033852,0.022869,0.006815,0.009923,0.000409,-0.018041,-0.003897,-0.001798,0.010109,0.00867,-0.007465,-0.000133,0.002999,0.0019,-0.00088,-0.001251,-0.009982,-0.000742,0.006409,0.006145,-0.002874

[rothaer]

Less of West Germanic but probably more of East Germanic.



When using only ancient samples, I get the same result:

Target: Peterski_scaled
Distance: 2.6188% / 0.02618819
55.2 HUN_Avar_Szolad
44.8 POL_Weklice

https://vahaduo.github.io/vahaduo/

SOURCE:


POL_Weklice:R10618,0.138864,0.137096,0.072784,0.06 137,0.041546,0.0251,0.003525,0.008538,0.007772,-0.005103,-0.002273,-0.004046,-0.011298,-0.010597,0.018458,0.024264,0.017471,0.003421,0.005 279,0.014007,0.000624,0.003462,-0.003328,0.01699,-0.003832
POL_Weklice:R10620,0.129758,0.126941,0.069767,0.05 2972,0.037545,0.013387,0.00329,0.004846,-0.003886,-0.013485,0,0.004196,-0.004906,-0.004266,0.016422,0.006762,0.005346,-0.00152,-0.002263,-0.004127,0.010107,0.003339,0.004683,0.024702,-0.002036
POL_Weklice:R10625,0.129758,0.125926,0.079572,0.07 429,0.048317,0.019522,0.00846,0.01823,0.015748,-0.009476,-0.008282,0.004646,-0.004162,-0.003991,0.008686,0.016839,0.022556,0.003421,0.004 399,0.006628,0.017594,0.011623,-0.002095,-0.001205,0.001078
POL_Weklice:R10626,0.134311,0.127957,0.07203,0.055 879,0.041854,0.023148,0.013161,0.017076,-0.000818,-0.004009,-0.004384,0.012139,-0.00996,0.001239,0.025108,0.000928,-0.008345,0.002407,-0.001634,0.006628,0.004118,0.00136,-0.006902,0.018436,-0.003712
POL_Weklice:R10631,0.129758,0.131003,0.080327,0.06 3308,0.0397,0.023985,0.00188,0.005077,0.006749,-0.011299,-0.008769,0.001199,-0.006541,-0.013074,0.020358,0.005171,-0.00678,0.000507,-0.006536,0.005378,0.009608,-0.000866,-0.006039,0.008555,-0.001557
POL_Weklice:R10633,0.136588,0.129988,0.07731,0.070 737,0.050471,0.024821,0.00423,0.011769,0.01309,-0.00492,-0.005034,0.005995,-0.009663,-0.010872,0.019272,0.025192,0.010822,-0.004054,-0.001508,0.009755,0.019341,0.001113,0.002095,0.002 289,0.002036
POL_Weklice:R10634,0.133173,0.136081,0.071276,0.06 7507,0.041546,0.023706,0.003995,0.015461,0.005931,-0.008018,-0.009906,0.004046,-0.008028,-0.006055,0.021851,0.002652,-0.00665,-0.00228,0.004777,0.001,0.004243,-0.003462,0.00419,0.013255,-0.005389
POL_Weklice:R10636,0.133173,0.118817,0.080704,0.06 8153,0.038161,0.029005,0.003525,0.006692,0.003681,-0.011481,-0.008607,0.003297,-0.001933,-0.002202,0.016015,0.008353,-0.002608,0.001394,0.008045,0.001751,0.000374,0.003 957,0.001479,0.025064,0.001197
POL_Weklice:R11391,0.127482,0.132019,0.065996,0.05 7171,0.044316,0.032072,0.015746,0.010846,-0.003886,-0.016037,-0.003735,0.015886,-0.016204,0.006193,0.023887,0.000398,-0.028163,-0.001647,0.004651,-0.001251,0.017095,0.009027,0.003081,0.012893,0.002 634
HUN_Avar_Szolad:Av2,0.135449,0.128972,0.080704,0.0 63954,0.034776,0.034025,0.006815,0.007615,0.009613 ,-0.02041,-0.001461,-0.005245,0.010852,0.026561,-0.014658,-0.002254,0.002347,0.001267,0.01081,-0.001751,0.001622,-0.002844,0.009613,-0.008314,0.005389

TARGET:


Peterski_scaled,0.133173,0.140143,0.065619,0.05846 3,0.033852,0.022869,0.006815,0.009923,0.000409,-0.018041,-0.003897,-0.001798,0.010109,0.00867,-0.007465,-0.000133,0.002999,0.0019,-0.00088,-0.001251,-0.009982,-0.000742,0.006409,0.006145,-0.002874

You provide only Weklice as Germanic and do then conclude Eastern Germanicness from that?

That source seems pretty Germanic friendly:

Target: rothaer_scaled
Distance: 1.9238% / 0.01923798
64.8 POL_Weklice
35.2 HUN_Avar_Szolad

[Mingle]

According to that map the biggest Danish island Zealand is also Swedish. :picard1: Scandinavia is a gerographic term that can not seriously be dependent on the shifting many times political southern border of Denmark. I admit that the current usage in English is that fuzzy (and imo wrongly).

Scandinavia is a cultural term that always includes all of Denmark.

The word you're looking for is Fennoscandia:
http://www.bodilelmhagen.se/fenno.html

Or Scandinavian Peninsula:
https://www.worldatlas.com/amp/peninsulas/scandinavian-peninsula.html

[rothaer]

Scandinavia is a cultural term that always includes all of Denmark.

The word you're looking for is Fennoscandia:
http://www.bodilelmhagen.se/fenno.html

Or Scandinavian Peninsula:
https://www.worldatlas.com/amp/peninsulas/scandinavian-peninsula.html

The latter. The geographical term Scandinavia equals the Scandinavian Peninsula.

A cultural term Scandinavia is secondary (derived), fuzzy and harms clarity. Like Europe when it is meant as a cultural (or even political) term and detached from the geographical term.

We do have the subject of geography for describing and naming various parts of the surface of the earth. Why refrain from using it when referring to geographical areas?

(I guess that the true reason is ignorance and lack of thoroughness regarding geographical terms by the main part of speakers and that claiming a not perfectly defined "cultural term" is nothing but an excuse for not expressing correctly. I'm not overlooking that eventually the masses will define what is a "correct" "cultural term". But I could just scream and flog'em all. :) )

[Peterski]

Below a map from this publication - locations of individuals from the Slavic IBD cluster older than 500 AD (red dots):

https://i.imgur.com/kgDUQ7b.png

[rothaer]

Below a map from this publication - locations of individuals from the Slavic IBD cluster older than 500 AD (red dots):

https://i.imgur.com/kgDUQ7b.png

This is very interetrsting as is at all that IBD sharing approach. So it's about direct relatedness, you can say. Now, what's unclear to me is whether this approach (being in a cluster that shares IBD segments with early Slavs) gives you any figures for the proportion of Slavic ancestry.

Considering what is stated in the OP the early Slavs could be determined to consist of a Baltic-realted people with some East Germanic and Sarmatian input. This implies to me that small IBD segments from all these three groups are used to assign someone to the "Slavic cluster". Now, is is possible that one or another East Germanic has suffiently many IBD segments to be assigned to that cluster?

[sevruk]

Proto Slavs=Proto Balts

[Peterski]

Among the oldest individuals from the Slavic IBD cluster there are R9673 and R6759 from Viminacium:


SRB_Viminacium:R9673,0.136588,0.126941,0.090132,0. 072675,0.044624,0.030678,0.005405,0.014999,-0.005931,-0.025695,-0.004709,-0.008992,0.016055,0.014175,-0.013572,0.014717,0.026598,-0.004814,-0.001383,0.007379,0.00025,-0.008779,0.002095,-0.005784,-0.000958


SRB_Viminacium:R6759,0.124067,0.119832,0.09164,0.1 01422,0.047701,0.038208,0.01034,0.017768,0.001023,-0.039363,-0.004547,-0.019033,0.038057,0.03592,-0.019137,0.003447,0.014994,-0.007095,-0.00088,0.003126,-0.007736,-0.005935,0.003328,-0.007109,-0.002634

[Dušan]

Among the oldest individuals from the Slavic IBD cluster there are R9673 and R6759 from Viminacium:


SRB_Viminacium:R9673,0.136588,0.126941,0.090132,0. 072675,0.044624,0.030678,0.005405,0.014999,-0.005931,-0.025695,-0.004709,-0.008992,0.016055,0.014175,-0.013572,0.014717,0.026598,-0.004814,-0.001383,0.007379,0.00025,-0.008779,0.002095,-0.005784,-0.000958


SRB_Viminacium:R6759,0.124067,0.119832,0.09164,0.1 01422,0.047701,0.038208,0.01034,0.017768,0.001023,-0.039363,-0.004547,-0.019033,0.038057,0.03592,-0.019137,0.003447,0.014994,-0.007095,-0.00088,0.003126,-0.007736,-0.005935,0.003328,-0.007109,-0.002634

From what century are these 2 samples?

They seems too northern.



Distance to: SRB_Viminacium:R6759
0.03157195 Latvian
0.03182402 Lithuanian_SZ
0.03627177 Lithuanian_RA
0.03687694 Lithuanian_PZ
0.04131605 Lithuanian_VZ
0.04255829 Lithuanian_VA
0.04363796 Estonian
0.04517937 Russian_Pskov
0.04666200 Lithuanian_PA
0.05328828 Belarusian

Distance to: SRB_Viminacium:R9673
0.03203751 Lithuanian_VA
0.03423692 Lithuanian_PA
0.03571393 Lithuanian_RA
0.03604847 Russian_Pskov
0.03857698 Lithuanian_SZ
0.03931255 Estonian
0.04093936 Ukrainian_Rivne
0.04111409 Russian_Kaluga
0.04130789 Latvian
0.04154476 Russian_Tver

[Lemminkäinen]

We don't really know if this Poprad sample is Vandal or not.

I am modelled by genetic companies as a mix of Belarusian and Scandinavian. My DNA Tribes for example:

http://i.imgur.com/RbNXQj9.png

It is possible to make models using different admixture groups, whatever they have. Maybe there was also NW Germans or not. Most important is to know the fit, which tells more than modelling distance. Modelling distance tells how good the fit is by used populations, but not how well the target is modelled by admixture populations. DnaTribes obviously doesn't give any quality indicators.