Gedmatch calculators on Vahaduo

[vbnetkhio]

Should South_Polish be kept when there is also Polish_Southwest?.

I think it can be deleted, it's probably just one sample and not a real average.

[Peterski]

I think it can be deleted, it's probably just one sample and not a real average.

I don't think so, Davidski collected many Polish samples years ago when he posted as Polako on ABF forum. Probably he made his Eurogenes Polish references based on those.

[Jana]

I get nicely modeled with updated averages:

Target: Stearsolina
Distance: 3.9296% / 3.92961215 | R2P

72.0 Poland_Lemko
28.0 Swiss_French


Target: Stearsolina
Distance: 1.3183% / 1.31834580

59.8 Poland_Lemko
16.6 South_Polish
9.3 French_Basque
9.0 Abhkasian
5.3 Norwegian

Yep, they should be added to the spreadsheet.

[vbnetkhio]

I don't think so, Davidski collected many Polish samples years ago when he posted as Polako on ABF forum. Probably he made his Eurogenes Polish references based on those.

well it's hard to know, but isn't it redundant now that we have more specific Southern Polish averages?

[Komintasavalta]

For Euro K13

Komi,22.39,43.60,3.11,8.46,0.17,0.31,2.39,0.57,15.43,2.56,0.25,0.21,0.54
Sámi_Finland,23.07,47.80,0.02,2.11,0,1.50,0,0.85,21.77,2.22,0.67,0,0
Udmurt,18.51,36.69,0.51,12.56,0.01,0.17,4.09,0.51,23.10,2.89,0.57,0.12,0.29

The Udmurts seem to have the most Iranic type admixture as it is evident in their relatively high West_Asian and South_Asian scores. Though their Y DNA is not very Aryanic.

The extra West_Asian might also account for the excess steppe ancestry in Udmurts. Let's suppose that Udmurts are 75% West Eurasian but 50% steppe, and steppe is considered 100% West Eurasian, so then 66.7% of the West Eurasian ancestry of Udmurts is steppe. But then neither the North_Atlantic or Baltic component has enough steppe for Udmurts.

I think that in K15, the Eastern_Euro component accounts for some of the extra steppe/Iranian/Caucasian ancestry in the VUR, because in K15, Chuvashes have 3.4% West_Asian and Maris have 1.4%:

        North_Sea Atlantic Baltic Eastern_Euro West_Med West_Asian East_Med Red_Sea South_Asian Southeast_Asian Siberian Amerindian Oceanian Northeast_African Sub-Saharan
Chuvash 13.4      5.8      13.5   36.2         0.9      3.4        0.9      0.5     2.0         2.5             17.7     2.4        0.4      0.2               0.3
Erzya   16.8      10.2     27.7   29.1         2.7      3.6        1.1      0.3     1.2         0.5             5.1      1.2        0.0      0.1               0.1
Finnish 29.4      17.4     22.0   18.8         2.5      1.1        0.4      0.1     0.6         0.9             5.3      0.9        0.5      0.1               0.1
Mari    11.4      4.8      11.4   38.4         0.2      1.4        0.2      0.1     3.9         0.8             23.8     2.8        0.3      0.1               0.5

But in K13, Chuvashes have 8.7% West_Asian and Maris have 6.3%:

             North_Atlantic Baltic West_Med West_Asian East_Med Red_Sea South_Asian East_Asian Siberian Amerindian Oceanian Northeast_African Sub-Saharan
Chuvash      14.9           43.1   2.0      8.7        1.3      0.8     2.3         2.7        20.1     2.8        0.4      0.6               0.4
Finnish      34.2           47.7   4.4      2.2        0.6      0.4     0.5         1.0        6.5      0.9        0.8      0.5               0.3
Komi         22.4           43.6   3.1      8.5        0.2      0.3     2.4         0.6        15.4     2.6        0.2      0.2               0.5
Mari         13.2           42.2   1.2      6.3        0.6      0.4     4.4         0.9        26.3     3.3        0.4      0.2               0.7
Mordovian    22.5           47.7   6.9      7.7        3.5      0.7     1.6         1.0        6.1      1.3        0.5      0.2               0.2
Sámi_Finland 23.1           47.8   0.0      2.1        0.0      1.5     0.0         0.8        21.8     2.2        0.7      0.0               0.0
Udmurt       18.5           36.7   0.5      12.6       0.0      0.2     4.1         0.5        23.1     2.9        0.6      0.1               0.3

In K15, the Eastern_Euro component is actually closer to the North_Sea and Atlantic components than to the Baltic component:

FST distance to Eastern_Euro:
0.000 Eastern_Euro
0.020 North_Sea
0.022 Atlantic
0.024 Baltic
0.031 West_Asian
0.032 East_Med
0.038 West_Med
0.056 South_Asian
0.058 Middle_Eastern
0.100 Siberian
0.102 Southeast_Asian
0.108 Northeast_African
0.128 Amerindian
0.142 Sub-Saharan
0.173 Oceanian

In K15, Maris are also closer to the North_Sea and Atlantic components than to the Baltic component:

> t=read.csv("ta/sheet/k15orig",r=1)
> fst=as.matrix(as.dist(read.csv("ta/sheet/k15fst",r=1)))
> mult=as.matrix(t)%*%as.matrix(fst)
> s=sort(mult["Mari",])
> writeLines(paste(sprintf("%.3f",s),names(s)))
3.839 Eastern_Euro
4.607 North_Sea
4.869 Atlantic
4.907 Baltic
5.448 West_Asian
5.556 East_Med
6.344 West_Med
6.457 South_Asian
7.908 Middle_Eastern
7.974 Siberian
9.341 Southeast_Asian
11.905 Northeast_African
12.317 Amerindian
15.075 Sub-Saharan
17.593 Oceanian

Also in this MDS plot of the Eurasian components in K15, Eastern_Euro plots further south than Baltic:

[Jana]

with myheritage raw data I am closest to Lemko, who are white Croat-Vlach mix up

Distance to: Stearsolina

3.88328469 Poland_Lemko
4.43407262 Croat_East
4.48306815 Bosniak_Bosnia
4.58758106 Croat
4.64383462 Croat_North
4.86671347 Hungarian_Alföld
5.52196523 Ukrainian_Carpathian
5.58499776 Moldova_North
5.62725510 Hungarian
5.68233227 Slovenian
5.71636248 Hungarian_North
6.01780691 Hungarian_Transdanubia+Budapest
6.12248316 Croat_South
6.23436444 Croat_West
6.46706270 Bosniak
6.47602502 Slovak
7.03102411 Ukrainian_Galicia
7.04628271 Csángó-Ceangău
7.23221266 Serb_Bosnia
8.14194080 Moldova_Centre
8.30960890 Moldova_average
8.36513000 Romania_Moldavia_North
8.39834508 Hungarian_Transylvania+Székely
8.51442306 Moldova_Ukrainian
8.55248502 Serb_Croatia

Target: Stearsolina
Distance: 2.2453% / 2.24532838 | R2P

94.3 Poland_Lemko
5.7 Ossetian

[rothaer]

A stunning steep cline in distances (with the updated Polish K13):

Distance to: rothaer

4.88755563 German_East
6.75366567 Czech
8.30845954 Sorb_Lusatia
9.43970868 Slovak
9.66557810 Austrian
9.68982456 North-Swedish
9.71481858 Southwest_Finnish
9.77789343 Polish_WarmiaMasuria
9.88799778 Sweden_Svealand_East
10.10652759 Polish_North_Wielkopolska
10.41147924 South_Polish
10.48307684 Polish_Lesser_Poland
10.50438480 Slovenian
10.75786689 Polish_GreaterPoland
11.08615353 Hungarian_North
11.23210132 Polish_Kujawy
11.32514901 Hungarian_Transdanubia+Budapest
11.50077389 German
11.76300557 Polish_Silesia
11.78775636 Croat_North
12.14483429 Hungarian
12.15276923 Swedish
12.21082716 Polish
12.24309193 Ukrainian_Galicia

[Peterski]

"9.77789343 Polish_Masuria
9.77789343 Polish_WarmiaMasuria"

^^^
Duplicates.

[Leto]

The extra West_Asian might also account for the excess steppe ancestry in Udmurts. Let's suppose that Udmurts are 75% West Eurasian but 50% steppe, and steppe is considered 100% West Eurasian, so then 66.7% of the West Eurasian ancestry of Udmurts is steppe. But then neither the North_Atlantic or Baltic component has enough steppe for Udmurts.

I think that in K15, the Eastern_Euro component accounts for some of the extra steppe/Iranian/Caucasian ancestry in the VUR, because in K15, Chuvashes have 3.4% West_Asian and Maris have 1.4%:

        North_Sea Atlantic Baltic Eastern_Euro West_Med West_Asian East_Med Red_Sea South_Asian Southeast_Asian Siberian Amerindian Oceanian Northeast_African Sub-Saharan
Chuvash 13.4      5.8      13.5   36.2         0.9      3.4        0.9      0.5     2.0         2.5             17.7     2.4        0.4      0.2               0.3
Erzya   16.8      10.2     27.7   29.1         2.7      3.6        1.1      0.3     1.2         0.5             5.1      1.2        0.0      0.1               0.1
Finnish 29.4      17.4     22.0   18.8         2.5      1.1        0.4      0.1     0.6         0.9             5.3      0.9        0.5      0.1               0.1
Mari    11.4      4.8      11.4   38.4         0.2      1.4        0.2      0.1     3.9         0.8             23.8     2.8        0.3      0.1               0.5

But in K13, Chuvashes have 8.7% West_Asian and Maris have 6.3%:

             North_Atlantic Baltic West_Med West_Asian East_Med Red_Sea South_Asian East_Asian Siberian Amerindian Oceanian Northeast_African Sub-Saharan
Chuvash      14.9           43.1   2.0      8.7        1.3      0.8     2.3         2.7        20.1     2.8        0.4      0.6               0.4
Finnish      34.2           47.7   4.4      2.2        0.6      0.4     0.5         1.0        6.5      0.9        0.8      0.5               0.3
Komi         22.4           43.6   3.1      8.5        0.2      0.3     2.4         0.6        15.4     2.6        0.2      0.2               0.5
Mari         13.2           42.2   1.2      6.3        0.6      0.4     4.4         0.9        26.3     3.3        0.4      0.2               0.7
Mordovian    22.5           47.7   6.9      7.7        3.5      0.7     1.6         1.0        6.1      1.3        0.5      0.2               0.2
Sámi_Finland 23.1           47.8   0.0      2.1        0.0      1.5     0.0         0.8        21.8     2.2        0.7      0.0               0.0
Udmurt       18.5           36.7   0.5      12.6       0.0      0.2     4.1         0.5        23.1     2.9        0.6      0.1               0.3

In K15, the Eastern_Euro component is actually closer to the North_Sea and Atlantic components than to the Baltic component:

FST distance to Eastern_Euro:
0.000 Eastern_Euro
0.020 North_Sea
0.022 Atlantic
0.024 Baltic
0.031 West_Asian
0.032 East_Med
0.038 West_Med
0.056 South_Asian
0.058 Middle_Eastern
0.100 Siberian
0.102 Southeast_Asian
0.108 Northeast_African
0.128 Amerindian
0.142 Sub-Saharan
0.173 Oceanian

In K15, Maris are also closer to the North_Sea and Atlantic components than to the Baltic component:

> t=read.csv("ta/sheet/k15orig",r=1)
> fst=as.matrix(as.dist(read.csv("ta/sheet/k15fst",r=1)))
> mult=as.matrix(t)%*%as.matrix(fst)
> s=sort(mult["Mari",])
> writeLines(paste(sprintf("%.3f",s),names(s)))
3.839 Eastern_Euro
4.607 North_Sea
4.869 Atlantic
4.907 Baltic
5.448 West_Asian
5.556 East_Med
6.344 West_Med
6.457 South_Asian
7.908 Middle_Eastern
7.974 Siberian
9.341 Southeast_Asian
11.905 Northeast_African
12.317 Amerindian
15.075 Sub-Saharan
17.593 Oceanian

Also in this MDS plot of the Eurasian components in K15, Eastern_Euro plots further south than Baltic:

[img]https://i.ibb.co/XyJqdzm/k15mds.png

Thanks for the long-ass post. I just don't use K15 much, it's usually worse than K13, maybe for Northwestern Europeans it's just as good or even better.
What do we know about the Udmurts? Why would they have more Steppe ancestry than the others in the region? Their Y DNA is homogeneous, 70% N1a or whatever it's called now.

[Komintasavalta]

What do we know about the Udmurts? Why would they have more Steppe ancestry than the others in the region? Their Y DNA is homogeneous, 70% N1a or whatever it's called now.

I don't know if Udmurts have that much steppe in absolute terms, but for example in the qpGraph model in Tambets et al. 2018, Udmurts had 30% Nganasan, 63% Corded Ware, 1% LBK, and 6% EHG, so the proportion of Corded Ware in their non-Nganasan ancestry was around 90%. The proportion of Corded Ware was 62% in Central Russians and 61% in Mordovians, but both obviously had lower Nganasan.

Also in the G25 model below, out of the ancestry of Udmurts that is not from Krasnoyarsk_BA, about 82% is from Yamnaya (but the model doesn't have an EHG source, and maybe Udmurts have extra EHG that is not from Yamnaya):

Target: Udmurt
Sources: GEO_CHG IRN_Ganj_Dareh_N RUS_Krasnoyarsk_BA TUR_Barcin_N Yamnaya_RUS_Samara
Distance: 0.045
62% Yamnaya_RUS_Samara
24% RUS_Krasnoyarsk_BA
14% TUR_Barcin_N