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Angela said:
Are the Spanish HGDP samples included? I always match them better than the French. The HGDP French samples are, of course, not the Southern French ones.

Distance to:Angela
4.72726136Tuscan_HGDP01162
4.77513351North_Italian_HGDP01155
4.96495720Tuscan_HGDP01163
5.14937860Tuscan_HGDP01167
5.51625779North_Italian_HGDP01172
5.76687090Tuscan_HGDP01168
6.22050641North_Italian_HGDP01177
6.45763114Tuscan_HGDP01164
6.47949072Tuscan_HGDP01161
6.54822113Tuscan_HGDP01166
6.55510488North_Italian_HGDP01174
6.88486746North_Italian_HGDP01152
7.02325423Tuscan_HGDP01169
7.57862784North_Italian_HGDP01157
7.70440783North_Italian_HGDP01156
7.73404810North_Italian_HGDP01171
8.49641689North_Italian_HGDP01173
8.52663474North_Italian_HGDP01153
9.30931254North_Italian_HGDP01147
11.09168608North_Italian_HGDP01151
11.83644372North_Italian_HGDP01154
14.50602289French_HGDP00520
16.34482793French_HGDP00536
17.96544461French_HGDP00516
18.22417076French_HGDP00530
Click to expand...

I compared this to the PCA. The samples to which I'm closest in the North Italian cluster are closest to Liguria, which I think is western Liguria and then Emilia, and the samples to which I'm closest in the Tuscan cluster are TSI 130, which is just north of Florence, so it all makes sense as per my known geneaology.

I'm answering so many more questions now that we have all these new calculators using Dienekes K12b.
 
Dodecad is outdated.
 
Salento said:
... you're not up-to-date :)

Most of the dod K12b Ancient are brand new.
Click to expand...

I know the samples are updated.

But, the calculator itself is outdated.
 
Mine, based on #878 coordinates

Distance to: Dodecadk12bStuvanè

4.67986111 Tuscan_HGDP01164
7.03622768 Tuscan_HGDP01163
7.49227602 Tuscan_HGDP01167
8.32751464 North_Italian_HGDP01152
8.76862019 Tuscan_HGDP01162
9.52916051 North_Italian_HGDP01154
9.60292143 Tuscan_HGDP01166
9.80676807 Tuscan_HGDP01161
9.81247166 North_Italian_HGDP01151
9.92054434 North_Italian_HGDP01172
10.00545851 North_Italian_HGDP01147
10.09604378 Tuscan_HGDP01168
10.22485208 North_Italian_HGDP01173
10.25717797 North_Italian_HGDP01157
10.60537600 Tuscan_HGDP01169
11.31080899 North_Italian_HGDP01177
11.32247764 North_Italian_HGDP01174
11.75348459 North_Italian_HGDP01155
12.97706438 North_Italian_HGDP01171
13.02615830 French_HGDP00520
13.71661766 North_Italian_HGDP01153
14.73681784 North_Italian_HGDP01156
16.98823416 French_HGDP00536
17.01347995 French_HGDP00516
18.62697775 French_HGDP00530

Target: Dodecadk12bStuvanè
Distance: 4.3794% / 4.37939048 | ADC: 1x
95.0 Tuscan_HGDP01164
5.0 North_Italian_HGDP01154

Target: Dodecadk12bStuvanè
Distance: 2.2311% / 2.23113672 | ADC: 0.5x
92.8 Tuscan_HGDP01164
5.0 Russian_HGDP00897
2.2 North_Italian_HGDP01154

Target: Dodecadk12bStuvanè
Distance: 1.2939% / 1.29385713 | ADC: 0.25x
86.6 Tuscan_HGDP01164
6.8 Russian_HGDP00889
5.2 North_Italian_HGDP01154
1.4 Bedouin_HGDP00639

Target: Dodecadk12bStuvanè
Distance: 0.0981% / 0.09807429
16.2 North_Italian_HGDP01177
15.6 Druze_HGDP00571
11.0 North_Italian_HGDP01147
7.2 North_Italian_HGDP01172
6.8 French_HGDP00533
5.4 Tuscan_HGDP01164
5.2 French_HGDP00534
4.4 Sardinian_HGDP01073
3.6 French_HGDP00538
3.4 Orcadian_HGDP00806
2.4 Tuscan_HGDP01161
2.0 Druze_HGDP00600
2.0 Russian_HGDP00879
1.8 North_Italian_HGDP01152
1.8 Sardinian_HGDP01066
1.4 Druze_HGDP00564
1.2 Tuscan_HGDP01169
1.0 Adygei_HGDP1382
1.0 French_Basque_HGDP01364
1.0 French_HGDP00520
1.0 Sardinian_HGDP01075
0.8 Sardinian_HGDP00670
0.4 Bedouin_HGDP00631
0.4 Bedouin_HGDP00649
0.4 French_HGDP00532
0.4 Mozabite_HGDP01258
0.4 Orcadian_HGDP00801
0.4 Sardinian_HGDP01068
0.2 Bedouin_HGDP00618
0.2 Bedouin_HGDP00630
0.2 Bedouin_HGDP00651
0.2 Mozabite_HGDP01268
0.2 Mozabite_HGDP01277
0.2 Orcadian_HGDP00797
0.2 Russian_HGDP00885
 
Last edited:
Distance to:RegioX(FTDNA)
3.34049398North_Italian_HGDP01154
5.46777834North_Italian_HGDP01147
5.84171208North_Italian_HGDP01173
6.23531074North_Italian_HGDP01152
6.43469502North_Italian_HGDP01157
6.59252607French_HGDP00520
7.36264898North_Italian_HGDP01172
7.38028455North_Italian_HGDP01151
8.82103735North_Italian_HGDP01174
8.83645291French_HGDP00516
9.28382464North_Italian_HGDP01171
9.56741867French_HGDP00536
9.87954452North_Italian_HGDP01155
9.89127393Tuscan_HGDP01164
10.33679834North_Italian_HGDP01153
10.38911931North_Italian_HGDP01177
10.45358790Tuscan_HGDP01163
10.72101208French_HGDP00530
11.12338977Tuscan_HGDP01167
11.96058527North_Italian_HGDP01156
12.07745420Tuscan_HGDP01162
12.80771252French_HGDP00521
12.81907563French_HGDP00538
13.18837746French_HGDP00525
13.52477726French_HGDP00512


Distance to:RegioX(23andMe)
3.71406785North_Italian_HGDP01154
5.33921343North_Italian_HGDP01147
5.84539135North_Italian_HGDP01173
6.06728110North_Italian_HGDP01152
6.29830930North_Italian_HGDP01157
6.97015064French_HGDP00520
7.01143352North_Italian_HGDP01151
7.12117968North_Italian_HGDP01172
8.67305598North_Italian_HGDP01174
9.18652274North_Italian_HGDP01171
9.20710052French_HGDP00516
9.44976719Tuscan_HGDP01164
9.61240865North_Italian_HGDP01155
9.92362333French_HGDP00536
9.96871607Tuscan_HGDP01163
10.11656068North_Italian_HGDP01177
10.27619579North_Italian_HGDP01153
10.68316433Tuscan_HGDP01167
11.11625387French_HGDP00530
11.59589151Tuscan_HGDP01162
11.80128807North_Italian_HGDP01156
13.26621649French_HGDP00521
13.31208098French_HGDP00538
13.38442752Tuscan_HGDP01166
13.56455307Tuscan_HGDP01168


Distance to:Father(23andMe)
4.13206970North_Italian_HGDP01154
6.38519381French_HGDP00520
7.59313506North_Italian_HGDP01173
7.63840952North_Italian_HGDP01147
8.06409325North_Italian_HGDP01152
8.52505718North_Italian_HGDP01157
8.69483180North_Italian_HGDP01151
8.79691992French_HGDP00516
9.08269233North_Italian_HGDP01172
10.35715212North_Italian_HGDP01174
10.49721868French_HGDP00536
10.62561057Tuscan_HGDP01164
10.81034227North_Italian_HGDP01171
11.33819210Tuscan_HGDP01163
11.41520915French_HGDP00530
11.75150629North_Italian_HGDP01155
11.80270732North_Italian_HGDP01153
11.92562367Tuscan_HGDP01167
12.44428785North_Italian_HGDP01177
12.62221851French_HGDP00521
12.68587403French_HGDP00525
12.77363691French_HGDP00538
13.18273871Tuscan_HGDP01162
13.23869707French_HGDP00529
13.35891837French_HGDP00512


Distance to:Mother(23andMe)
3.56561355North_Italian_HGDP01154
5.49149342North_Italian_HGDP01147
6.98324423North_Italian_HGDP01173
7.09439215North_Italian_HGDP01152
7.31163456North_Italian_HGDP01157
7.31932374French_HGDP00520
7.35930024North_Italian_HGDP01151
8.92560922North_Italian_HGDP01172
9.19806501French_HGDP00516
9.38252631French_HGDP00536
10.57304119North_Italian_HGDP01174
10.62546940French_HGDP00530
11.04452353North_Italian_HGDP01177
11.08752903North_Italian_HGDP01171
11.16357470Tuscan_HGDP01164
11.35544363North_Italian_HGDP01155
12.06674355North_Italian_HGDP01153
12.10793128Tuscan_HGDP01163
12.25920063French_HGDP00538
12.37658273French_HGDP00525
12.73892068Tuscan_HGDP01167
12.87508058French_HGDP00529
13.30596859French_HGDP00521
13.36654780French_HGDP00537
13.49624022French_HGDP00512
 
Progon said:
I know the samples are updated.

But, the calculator itself is outdated.
Click to expand...

There was a thread where Jovialis ran all the Dodecad calculators, Eurogenes Calculators and MDLP calculators using the Ancient Roman Samples and compared those distances and plots to the ones published in the Antonio/Moots et al 2019 Paper. Guess which ones were closest to the academic ones published in the paper.
 
Investigating the source data of the Vahaduo Eurogenes K15 Ancient calculator I was able to verify that there are not many samples from the Iberian Peninsula. I was able to verify the existence of those that are listed below.

Iberia:
Iberia_Pre_BellBeaker_Chalcolithic_ATP16,4.94,38.80,0.01,0.01,56.23,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01
IberiaChalcolithic_I1281,11.39,38.28,0.01,0.01,50.33,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01
IberiaChalcolithic_I1303,2.09,42.04,0.01,0.01,55.87,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01
IberiaMBA_ATP9,17.71,44.44,0.50,0.01,37.36,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01,0.01


Canarias Islands:
Guanche_11,0.01,12.69,0.01,0.01,24.73,0.01,23.27,18.15,0.01,0.01,0.01,0.01,0.19,13.56,7.41
Guanche_5,9.80,16.64,0.09,0.01,29.00,0.01,14.44,14.85,0.01,0.01,0.01,0.01,0.01,1.07,14.12

Out of curiosity I discovered the threads below, respectively created by @Tomenable (Europeans in Zanzibar in 800 CE) and @Ygorcs (Doubts about the "Tanzania_Zanzibar_First Millennium" aDNA sample) where it is discussed how an Iberian European could be found in Zanzibar in 800 CE (I0588_Tanzania_Zanzibar_800AD_outlier_European).

Tomenable said:
I0588 Tanzania Zanzibar, sample published by Pontus Skoglund and dated to 800 AD:

C:\Users\fpess\AppData\Local\Temp\msohtmlclip1\01\clip_image002.jpg


Eurogenes K15 results of this sample:

27834 SNPs used in this evaluation

Admix Results (sorted):

# Population Percent
1 Atlantic 26.89
2 West_Med 26.26
3 North_Sea 24.7
4 East_Med 6.37
5 Baltic 5.24
6 West_Asian 3
7 Red_Sea 2.41
8 Sub-Saharan 2.4
9 Eastern_Euro 1.48
10 Siberian 1.25

Single Population Sharing:

# Population (source) Distance
1 Spanish_Galicia 6.55
2 Portuguese 7.09
3 Spanish_Cantabria 7.34
4 Spanish_Cataluna 7.72
5 Spanish_Castilla_Y_Leon 7.99
6 Spanish_Extremadura 8.15
7 Spanish_Murcia 8.9
8 Spanish_Castilla_La_Mancha 9.69
9 Southwest_French 10.05
10 Spanish_Aragon 10.18
11 Spanish_Valencia 10.25
12 Spanish_Andalucia 10.47
13 French 11.81
14 North_Italian 12.6
15 South_Dutch 16.64
16 French_Basque 17.96
17 West_German 18.29
18 Southwest_English 18.53
19 Tuscan 18.61
20 Southeast_English 20.41

Mixed Mode Population Sharing:

# Primary Population (source) Secondary Population (source) Distance
1 55.1% Orcadian + 44.9% Sardinian @ 4.56
2 60.8% Southwest_English + 39.2% Sardinian @ 5.11
3 55.2% West_Scottish + 44.8% Sardinian @ 5.35
4 55.9% Irish + 44.1% Sardinian @ 5.41
5 58.3% Southeast_English + 41.7% Sardinian @ 5.48
6 59.6% Spanish_Galicia + 40.4% Spanish_Cantabria @ 5.8
7 85.5% Spanish_Galicia + 14.5% French_Basque @ 5.89
8 92% Spanish_Galicia + 8% Sardinian @ 6.11
9 55% North_Dutch + 45% Sardinian @ 6.12
10 73.1% French + 26.9% Sardinian @ 6.18
11 79.4% Spanish_Galicia + 20.6% Spanish_Aragon @ 6.21
12 79.3% Spanish_Galicia + 20.7% Southwest_French @ 6.22
13 83.2% Spanish_Galicia + 16.8% Spanish_Castilla_La_Mancha @ 6.38
14 80.4% Spanish_Galicia + 19.6% Spanish_Cataluna @ 6.47
15 88.9% Spanish_Galicia + 11.1% Spanish_Andalucia @ 6.47
16 88.9% Spanish_Galicia + 11.1% Spanish_Valencia @ 6.48
17 54.5% Portuguese + 45.5% Spanish_Cantabria @ 6.49
18 99.4% Spanish_Galicia + 0.6% Yoruban @ 6.51
19 99.4% Spanish_Galicia + 0.6% Mandenka @ 6.52
20 88% Spanish_Galicia + 12% Spanish_Castilla_Y_Leon @ 6.52

Similarity map:

9ry2D0G.png


Europeans in Zanzibar - eastern coast of Africa - as early as 800 CE ???

This sample is also in Global25.
Click to expand...

Ygorcs said:
I decided to post this doubt of mine here so that someone might perhaps help clarify what's happening with the average population DNA sample named TZA_Zanzibar_FirstMillennium in Global25 datasheets. I have googled to try to find the paper that that sample comes from, but couldn't find it. The issue is that, running the sample into nMonte software to model its ancestry, it's clear that it's just too much of an outlier to be believed: the sample is closest to ancient Iberian samples and, among modern populations, also to Iberians. Okay, I wouldn't be totally surprised by a Portuguese trader/sailor being buried in Zanzibar in the 16th or 17th century (though I still think that would be a real find, as they must've been a tiny minority of the total population), but first millennium? Does anyone have any information about that DNA sample, the study that analyzed and released it, the dating and archaeological circumstances? For now I'll just assume that the labeling was totally wrong and it in fact dates to the last centuries.
Click to expand...

As an experiment, I added the coordinates obtained for this sample in Gedmatch by @Tomenable in the Vahaduo EU K15 Ancient source data and, to my surprise, it became my best ancestral match in the Vahaduo Eurogenes K15 Ancient. Below the results. In calculating the mix, I searched for distances close to that displayed by Gedmatch EU V2 K15 'Mixed Mode Population Sharing - Primary Population + Secondary Population'.
Curious.

Gedmatch EU V2 K15 coordinats:
I0588_Tanzania_Zanzibar_800AD_outlier(European),24.70,26.89,5.24,1.48,26.26,3.00,6.37,2.41,0.00,0.00,1.25,0.00,0.00,0.00,2.40

Distance to:Duarte
6.76977104I0588_Tanzania_Zanzibar_800AD_outlier(European)
8.24704796IA_Prenestina_Colombella_R435
9.21567686IA_Boville_Ernica_R1021
9.48283713Swiss_CHE_IA_SX18
10.20174005IA_Civitavecchia_R474
10.21657477IA_Civitavecchia_R473
10.64023026ScythianMoldova_SCY197
10.64999531RomanSoldier_FN2
11.06359345IA_Ardea_R851
11.28990257IA_Etruscan_Veio_Grotta_Gramiccia_R1015
11.45422193Swiss_DEU_Singen_EBA_MX277
11.65095704France_IA_Jeb8
11.68151531BronzAgeBalkan
12.28918223BronzeAgeDalmatian_I4332
12.30414158IA_Castel_di_Decima_R1016
12.86881502EMBA_Croatia_I4331
13.01338157France_IA_ERS86
13.49124531Swiss_DEU_Singen_EBA_MX283_relMX286
13.53752562Swiss_CHE_EBA_SX20
13.91407201France_IA_NOR4
14.39051771ScythianMoldova_SCY300
14.79033468France_IA_NOR2B6
14.81770563Swiss_DEU_Singen_EBA_MX254_relMX286
15.09151748Vucedol_I3499
15.38797258BronzeAgeEngland_I2462

rIKkhUx.png
 
top 10:
R437 K36 Ancient+ R1 R850 Salento_me :)

... higher distances, ... same Hierarchy as yourDNAportal


mBRmBCF.jpg


id9Fygc.jpg
 
top 10
K36 Ancient: R437 R850 R1

IBuBPrp.jpg



... and Salento_me :grin:

xE7d5CE.jpg
 
Salento said:
top 10
K36 Ancient: R437 R850 R1

IBuBPrp.jpg



... and Salento_me :grin:

xE7d5CE.jpg
Click to expand...

Very interesting, Salento, but what it says to me is that the K15 is terrible for Italians and maybe all Southern Europeans. The fits are much, much worse than with the Dodecad K12b.
 
Duarte said:
@mlukas
Hello mlukas, good evening.
First of all I would like to thank on my behalf and on behalf of the eupedia team all your effort and collaboration in the development of the Dodecad K12b West Eurasia calculator which now is available in the Admixture Studio v2.48 program at www.dnagenics.com


I am making this post just to alert you that I tried to run the calculator 'Dodecad K12b West Eurasia' of dnagenics.com today for two occasions, with the upload of files in both VCF (.txt) and csv (.xlsx) format and the error below was displayed and the admixture has not displayed.

Admixture Calculation started.
SNPs used for the calculation: 160.392
SNPs in calculator: 166.770
Genotype ratio: 96,18%
Elapsed time: 86 seconds
Admixture calculation: 12 - Correct: True
Admixture composition: 12
Start population calculations
Population calculation genomewide
Population file: Dodecad_K12b_V3_Ancient_Commas.txt
Calculate K-Means
Error calculating K-Means: Not enough points. There should be more points than the number K of clusters.
Nome do parâmetro: x
Calculate PCA
Error calculating PCA: Number of outputs should be less than or equal the number of columns in the input data 1.
Nome do parâmetro: value
Calculate N-Monte
Error: Referência de objeto não definida para uma instância de um objeto.
Admixture calculation finished!

Thanks.
Click to expand...
Thank you.
You must contact dnagenics for that. I'm not responsible for this program.
 
Angela said:
Very interesting, Salento, but what it says to me is that the K15 is terrible for Italians and maybe all Southern Europeans. The fits are much, much worse than with the Dodecad K12b.
Click to expand...

... it was out of curiosity :)

I found the K36 ancient coordinates in a folder, I extracted it and reformatted it for compatibility.

I know the order is correct because it matches yourdnaportal website.
 
Salento said:
... it was out of curiosity :)

I found the K36 ancient coordinates in a folder, I extracted it and reformatted it for compatibility.

I know the order is correct because it matches yourdnaportal website.
Click to expand...

K36 has biggest distances from all Eurogenes calculators. It is normal.
 
Salento said:
these are the K36-Ancient coordinates I used ...
Click to expand...

thanks salento (y)

my k36 ancient
like my your dna portal

Distance to:adam
12.65305102EMA_GreekBalkan_AEH_1
13.64229086R850_Iron_Age_Ardea
15.50188053CL30_GreeksouthItalian
16.11039726CL38_GreeksouthItalian
16.98783977CL25_south_Italian
18.04734884CL31_Greek_Balkan
18.62021482CL121__northItalian
19.11710752SZ36_northItalian
19.32573414I7424_Morisco_Andalusia_1500AD
19.37823263R437_Iron_Age_Praeneste
19.66186156i3808_Morisco_Andalusia_1500AD
19.84915615Crimean_Goth_Ker_1
19.85204523SZ32_northItalian
20.04655831SZ43_northItalian
21.69056707EMA_Alpine_STR_310
21.74386580R1_Iron_Age_Protovillanovan_Martinsicuro
22.17985573CL36_northItalian
22.43557220EN_Anatolia_Tepe002
22.65344124MA2198_Anatolia_IA
22.71326925SZ1_GreekBalkan
23.25793413Niederstotzingen_north-Italian_3c
23.37450748CL23_northItalian
23.57039881SZ40_Italian
23.99231752SZ37_Greek_Italian
24.20021488CHL_Armenia_I1632
 
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