Finnish genetic composition: Iron Age Baltic, Iron Age Germanic and probably Iron Age Saami people

You probably have read my previous post regarding European genetic structures composed by Admixture and Eurasian data.  My aim was to make an admixture analysis free of recent genetic drift.  It gave following admixtures for Southwestern Finns (Finnish, k=10)

- Saami 14%
- Baltic 49%
- Germanic 35%

The post is here.

Now I have tested same admixtures using Iron Age samples and qpAdm.  QpAdm allocates admixtures for given populations, in these tests admixture  populations were Baltic Iron Age, Scanian Iron Age and Levaluhta Iron Age.  Levaluhta consists of five Iron Age remains found from Finnish Bothnia,  Ostrobothnia.  The id of the Scanian IA sample is RISE174 and the Baltic IA sample is DA171.  Although my results are unambiguous, there are some uncertainty regarding the software and given references, and being the first exploring something like this I am curious to see results of professional geneticists.  I simply can't understand why this matter wouldn't interest also researchers.   All samples I use here are publicly available.

Southwest Finns:

chisq       tail prob
1.112       0.992818 

Levaluhta 0.115 
Scania_IA 0.437 
Baltic_IA  0.448

Vepsa:

chisq       tail prob
1.555       0.980354

Levaluhta          0.202 
FIN_Southwest 0.614 
Baltic_IA           0.184
Nganasan        -0.000

and another result of Vepsa

chisq       tail prob
2.734       0.908488
  
Levaluhta          0.000 
FIN_Southwest 0.764 
Baltic_IA            0.164 
Nganasan          0.072


The match is much worse when using present-day Baltic, Germanic and Saami counterparts.

Southwest Finns:

chisq       tail prob
9.270       0.233881

Saami    0.156 
Latvian  0.297 
Swedish 0.548



Outgroups and coverages were

Kostenki14 813405
MA1 625746
WHG 703903
Iron_Gates_HG 884901
EHG 983976
CHG 889688
Ganj_Dareh_N 794892
West_Siberia_N 670626
Anatolia_Neolithic 889986
LBK_EN 880957



Typical SNP coverage of target groups

Vepsa1M 971774
Levaluhta 377788
FIN-Southwest 1102712
Baltic_IA  97311
Scania_IA 373352
Nganasan1M 971774

I have lost some SNP's due to allele mismatches or multiallelic conversion errors in Plink, but the coverage is still reasonable.   Some ancient samples need to be reconverted.

edit 11.12.2018 16:30

Adding Russians from Pinega makes a perfect match for Vepsas.  Not a big surprise.

chisq       tail prob
0.825       0.991377    

FIN-Southwest 0.672    
RusPinega        0.130    
Baltic_IA           0.093    
Levaluhta          0.105