Ancient DNA Calculator using Merged-Raw Data

Jovialis

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Points
113
Ethnic group
Italian
Y-DNA haplogroup
R-PF7566 (R-Y227216)
mtDNA haplogroup
H6a1b7
Ancient DNATotal Shared DNACompound Segments
Ajvide 582.77%0.57%
Altai Neanderthal1.40%0.20%
Australian Aboriginal7.48%1.19%
Bot 157.22%1.06%
Bot 175.85%1.03%
BR17.33%1.92%
BR233.86%23.74%
Clovis Anzick-122.47%9.78%
CO18.97%2.46%
Denisova1.09%0.16%
Gökhem24.19%0.48%
Hinxton-11.82%0.06%
Hinxton-22.38%0.17%
Hinxton-33.23%0.34%
Hinxton-45.42%0.83%
Hinxton-52.01%0.03%
IR17.96%2.65%
KO18.36%2.38%
Kostenki 1413.08%5.02%
La Braña Arintero8.98%2.21%
Linearbandkeramik32.81%18.77%
Loschbour26.39%13.55%
Mal'ta6.48%1.52%
Motala1211.76%3.54%
NE133.76%22.58%
NE56.84%1.33%
NE68.48%2.15%
NE78.62%2.16%
Paleo-Eskimo9.24%1.01%
RISE005.21%1.19%
RISE15012.55%4.53%
RISE17412.17%4.74%
RISE39513.58%5.08%
RISE4799.77%2.80%
RISE49324.11%11.98%
RISE49517.56%7.20%
RISE49613.09%4.16%
RISE49720.79%7.66%
RISE4998.06%2.09%
RISE50011.10%3.02%
RISE5028.00%1.66%
RISE5036.58%1.65%
RISE5047.98%1.69%
RISE50522.87%10.87%
RISE5097.29%1.42%
RISE51116.81%7.05%
RISE52313.33%4.59%
RISE5486.94%1.45%
RISE55213.17%6.62%
RISE5697.81%2.20%
RISE5777.22%1.80%
RISE6014.04%0.35%
RISE6024.53%0.49%
RISE945.71%1.26%
RISE975.57%0.84%
RISE9821.95%11.01%
Ust-Ishim27.86%17.09%
Vi33.16 Neanderthal0.64%0.00%
Vi33.25 Neanderthal0.67%0.00%
Vi33.26 Neanderthal1.07%0.00%

BR2 and NE1 are my highest percentages of similarity, which makes sense:

X61fEEf.png


https://www.pnas.org/content/113/2/368

I combined my 23andme (V5), AncestryDNA, LivingDNA, and Genographic Project Helix 2.0 raw data into one file of 1,200,808 SNPs, using DNAkit Studio. Above are results from an ancient DNA calculator that Wheal posted on here a while ago. Utilizing the combined raw data made a significant difference with this calculator, compared to using the 650k SNPs from 23andme V5. However, I also uploaded the combined raw data to Gedmatch Genesis, and observed only a slight difference in the results. I had even converted the 1.2 million SNPs in DIYDodecad format, for a Dodecad K12b run; and the results were mostly similar to the 650k SNP runs.

If you're interested in combining your raw data, here is where I found the tool:

https://wilhelmhgenealogy.wordpress.com/dna-kit-studio/

As for the Ancient DNA calculator, it is found here:

http://www.y-str.org/2014/12/ancient-calculator.html

Here is the original thread on the ancient DNA calculator:

https://www.eupedia.com/forum/threads/36704-On-line-calculator-from-Genetic-Geneology-Tools-blog
 
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Ancient DNATotal Shared DNACompound Segments
BR233.86%23.74%
NE133.76%22.58%
Linearbandkeramik32.81%18.77%
Ust-Ishim27.86%17.09%
Loschbour26.39%13.55%
RISE49324.11%11.98%
RISE50522.87%10.87%
Clovis Anzick-122.47%9.78%
RISE9821.95%11.01%
RISE49720.79%7.66%
RISE49517.56%7.20%
RISE51116.81%7.05%
RISE39513.58%5.08%
RISE52313.33%4.59%
RISE55213.17%6.62%
RISE49613.09%4.16%
Kostenki 1413.08%5.02%
RISE15012.55%4.53%
RISE17412.17%4.74%
Motala1211.76%3.54%
RISE50011.10%3.02%
RISE4799.77%2.80%
Paleo-Eskimo9.24%1.01%
La Braña Arintero8.98%2.21%
CO18.97%2.46%
NE78.62%2.16%
NE68.48%2.15%
KO18.36%2.38%
RISE4998.06%2.09%
RISE5028.00%1.66%
RISE5047.98%1.69%
IR17.96%2.65%
RISE5697.81%2.20%
Australian Aboriginal7.48%1.19%
BR17.33%1.92%
RISE5097.29%1.42%
Bot 157.22%1.06%
RISE5777.22%1.80%
RISE5486.94%1.45%
NE56.84%1.33%
RISE5036.58%1.65%
Mal'ta6.48%1.52%
Bot 175.85%1.03%
RISE945.71%1.26%
RISE975.57%0.84%
Hinxton-45.42%0.83%
RISE005.21%1.19%
RISE6024.53%0.49%
Gökhem24.19%0.48%
RISE6014.04%0.35%
Hinxton-33.23%0.34%
Ajvide 582.77%0.57%
Hinxton-22.38%0.17%
Hinxton-52.01%0.03%
Hinxton-11.82%0.06%
Altai Neanderthal1.40%0.20%
Denisova1.09%0.16%
Vi33.26 Neanderthal1.07%0.00%
Vi33.25 Neanderthal0.67%0.00%
Vi33.16 Neanderthal0.64%0.00%

For better clarity, here are the percentages, highest-to-lowest for Total Shared DNA.
 

Merged Megafile, same RawData mix as Above. (1.201.500 SNPs)

ANCIENT DNATotal Shar. DNAComp. Seg.
Linearbandkeramik33.1219.09
BR232.8219.29
NE132.4219.32
Ust-Ishim27.4914.80
Loschbour25.7812.82
RISE49323.4511.19
RISE50522.139.79
Clovis Anzick-121.809.22
RISE9821.099.27
RISE49719.087.06
RISE51117.136.07
RISE49516.695.88
RISE49613.274.61
RISE52312.924.68
RISE17412.414.96
RISE55212.094.37
RISE15011.914.80
RISE39511.894.25
Kostenki 1411.604.34
Motala1211.323.62
RISE5009.883.06
RISE4798.692.48
La Braña Arintero8.552.12
Paleo-Eskimo8.551.39
RISE4997.862.52
NE67.711.72
NE77.681.75
RISE5777.612.20
IR17.281.40
KO17.221.98
RISE5487.191.46
RISE5027.061.58
NE57.022.18
RISE5047.011.87
RISE5036.971.84
CO16.881.73
RISE5696.811.42
RISE5096.571.51
BR16.360.91
RISE946.331.21
Mal'ta5.961.21
RISE005.841.50
Bot 155.530.79
Bot 175.510.88
RISE975.490.95
Australian Aboriginal5.390.83
Hinxton-45.040.74
RISE6024.340.70
RISE6013.810.44
Gökhem23.510.14
Hinxton-22.560.08
Ajvide 582.480.18
Hinxton-32.360.43
Hinxton-51.880.04
Hinxton-11.810.27
Altai Neanderthal1.480.23
Denisova0.970.03
Vi33.26 Neanderthal0.610.11
Vi33.25 Neanderthal0.400.00
Vi33.16 Neanderthal0.370.08


Ancient DNA Places of Origin
http://www.y-str.org/p/ancient-dna.html?m=1
 
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Merged Megafile, same RawData mix as Above. (1.201.500 SNPs)

ANCIENT DNATotal Shar. DNAComp. Seg.
Linearbandkeramik33.1219.09
BR232.8219.29
NE132.4219.32
Ust-Ishim27.4914.80
Loschbour25.7812.82
RISE49323.4511.19
RISE50522.139.79
Clovis Anzick-121.809.22
RISE9821.099.27
RISE49719.087.06
RISE51117.136.07
RISE49516.695.88
RISE49613.274.61
RISE52312.924.68
RISE17412.414.96
RISE55212.094.37
RISE15011.914.80
RISE39511.894.25
Kostenki 1411.604.34
Motala1211.323.62
RISE5009.883.06
RISE4798.692.48
La Braña Arintero8.552.12
Paleo-Eskimo8.551.39
RISE4997.862.52
NE67.711.72
NE77.681.75
RISE5777.612.20
IR17.281.40
KO17.221.98
RISE5487.191.46
RISE5027.061.58
NE57.022.18
RISE5047.011.87
RISE5036.971.84
CO16.881.73
RISE5696.811.42
RISE5096.571.51
BR16.360.91
RISE946.331.21
Mal'ta5.961.21
RISE005.841.50
Bot 155.530.79
Bot 175.510.88
RISE975.490.95
Australian Aboriginal5.390.83
Hinxton-45.040.74
RISE6024.340.70
RISE6013.810.44
Gökhem23.510.14
Hinxton-22.560.08
Ajvide 582.480.18
Hinxton-32.360.43
Hinxton-51.880.04
Hinxton-11.810.27
Altai Neanderthal1.480.23
Denisova0.970.03
Vi33.26 Neanderthal0.610.11
Vi33.25 Neanderthal0.400.00
Vi33.16 Neanderthal0.370.08


Ancient DNA Places of Origin
http://www.y-str.org/p/ancient-dna.html?m=1

I did a one-to-one comparison between BR2 vs my old raw data, and my newly merged raw data, and saw slight improvements on Chromosomes 1, 15, 16, 17, and 22. There were less "Large gap between adjacent SNPs " lines in the validity of segments. I also noticed 166169 SNP were used in the old raw data, and 469849 were used in the merged data.
 
The magnitude of the results difference between my files is small, but the distance of the populations (@​) is closer with the Combine Files.

A comparison:


MDLP K11 - 4 Populations

23andme V5:

1 Armenia_MLBA + Bell_Beaker + British_Roman + Tyrolean_Iceman_EN @ 2.320581
2 Armenia_MLBA + Bell_Beaker + British_Roman + Europe_EN @ 2.441416
3 Armenia_LBA + Bell_Beaker + British_Roman + Hungary_EN @ 2.604989

Megafile:
1 Armenia_MLBA + Bell_Beaker + British_Roman + Salzmuende_MN @ 1.501243
2 Armenia_MLBA + Bell_Beaker + Levant_BA + Remedello_BA @ 1.564589
3 Armenia_Chalcolithic + Bell_Beaker + British_Roman + Hungary_CA @ 1.651155
 
Raw Data VersionSNPs Used in EvaluationOrcale 1st Single Population SharingOrcale-4 1st Single Population Sharing
Merged Raw Data (DIYDodecad Format)155327C_Italian @ 6.78C_Italian_Dodecad @ 7.297379
Merged Raw Data (23andme Format)154866C_Italian @ 6.85C_Italian_Dodecad @ 7.371545
AncestryDNA152095S_Italian_Sicilian & C_Italian @ 6.97C_Italian_Dodecad @ 7.504167
Living DNA47508Sicilian @ 4.39Sicilian_Dodecad @ 4.826463
23andme (V5)46844Sicilian @ 3.89Sicilian_Dodecad @ 4.251447


Here are my oracle and oracle-4 1st single population approximations on Dodecad K12b, for each version of raw data I have. The merged raw data in DIYDodecad format used the most SNPs in the evaluation. Nevertheless, the difference is only minor.
 
1 S_Italian_Sicilian_Dodecad on both. (I only uploaded the 23v5 and the Combo, just so I can test it. I usually del...)

Up and down, the sum of your 5 result could average my 5 regional pop. sharing:

NjZtnZc.jpg








 

Interesting when running them through Gedmatch Genesis. For example, Denisova and Altai Neaderthal is considered overwhelmingly, or totally "Sub-Saharan African" in the calculators I've run it on. Goes to show the various components people are broken down into on gedmatch are essentially meaningless.

Sample NameSample LocationGEDMatchSexY-DNAMt-DNAApprox. Age by authorsMy Analysis or Comments
Altai NeanderthalDenisova Cave, SiberiaF999902F50,000 years
DenisovaDenisova Cave, SiberiaF999903F30,000 years
Palaeo-EskimoQeqertarsuaq, GreenlandF999906MQ1aD2a14,000 yearsPalaeo-Eskimo 2000 BC DNA
Clovis-Anzick-1Montana, North AmericaF999919MQ-Z780D4h3a12,500 yearsMatches Living people.
Mal’taSouth - Central SiberiaF999914MRU24,000 yearsMatches Living people on X Chromosome.
La Braña-ArinteroLeón, SpainF999915MC-V183U5b2c17,000 yearsAnalyzing La Braña-Arintero Ancient DNA
Motala-12Östergötland, SwedenF999917MI-L460U2e17,000 yearsMy Analysis of Motala-12 ancient DNA
LBKStuttgart, GermanyF999916FT2c27,500 yearsMatches Living people
Loschbour Loschbour, LuxembourgF999918MI-L460U5b1a8,000 yearsMatches Living people
Ajvide58SwedenF999924MI-CTS772U4d5000 yearsAjvide58 DNA Analysis
Gökhem2SwedenF999934FH1c5000 yearsGökhem2 Ancient DNA Analysis
Hinxton-2Cambridgshire, UKF999921FH2a2b11300 yearsHinxton-2 Analysis
Hinxton-3Cambridgshire, UKF999922FK1a4a1a2b1300 yearsHinxton-3 Analysis
Hinxton-4Cambridgshire, UKF999925MR-DF25H1ag12000 yearsHinxton-4 has X-Matches with living people
Hinxton-5Cambridgshire, UKF999926FH2a2a11300 yearsHinxton5 Ancient DNA Analysis
KO1Tiszaszőlős-Domaháza, HungaryF999931MI-L68R35650-5780 cal BCAnalysis of Neolithic KO1 genome
NE1Polgár-Ferenci-hát, HungaryF999937FU5b2c5070-5310 cal BCAncient NE1 Matches living people
NE5Kompolt - Kigyósér, HungaryF999927MC-F3393J1c4990-5210 cal BCAncient Hungarian Genome NE5 Analysis
NE6Apc-Berekalja I., HungaryF999932MC-P255K1a3a34950-5300 cal BCAnalysis of Hungarian genome-NE6
NE7Apc-Berekalja I., HungaryF999928MI-L1228N1a4360-4490 cal BCAncient Hungarian genome - NE7
CO1Apc-Berekalja I., HungaryF999930FH2700-2900 cal BCAnalysis of Copper age genome CO1
BR2Ludas-Varjú-dűlő, HungaryF999933MJ-M67K1a1a1110-1270 cal BCAncient BR2 matches living people
IR1Ludas-Varjú-dűlő, HungaryF999929MN-M231G2a1830-980 cal BCAncient Hungarian genome - IR1
Ust'-IshimUst'-Ishim, SiberiaF999935MK-M526R45,000 yearsUst'-Ishim matches with living people!
Kostenki14European RussiaF999936MC-V199U238,700-36,200 yearsKostenki14 Ancient DNA Analysis
RISE00Sope, EstoniaF999955FH5a1~2000 years
RISE94Viby, SwedenF999956MK-M1221K1a2a4025 yearsRISE94 has matches with living people
RISE97Fredriksberg, SwedenF999945CT-Y1580K2a53590 years
RISE98L Beddinge 56, SwedenF999941MR-M405K1b1a3736 yearsRISE98 has matches with living people
RISE150Przeclawice, PolandF999948U5a1b13469 yearsRISE150 has matches with living people
RISE174Oxie 7, SwedenF999943W11521 yearsRISE174 has matches with living people
RISE395Bol'shekaraganskii, RussiaF999949FU2e13540 yearsRISE395 has matches with living people
RISE479Erd 4, HungaryF999944MI-L1228T2b~2000 years
RISE493Sabinka 2, RussiaF999950MQ-L712C4a1c3214 yearsRISE493 has matches with living people
RISE495Arban 1, RussiaF999958MR-F3105D4j1
RISE496Arban 1, RussiaF999959FU5a1a2a3070 years
RISE497Arban 1, RussiaF999957F-P142A2f2~2000 yearsRISE497 has matches with living people
RISE499Bystrovka, RussiaF999952FH5a1~2000 years
RISE500Kytmanovo, RussiaF999947FU4d1~2000 years
RISE502Bystrovka, RussiaF999960FU5a1d3140 years
RISE503Kytmanovo, RussiaF999961U2e23328 years
RISE504Kytmanovo, RussiaF999962MJ-CTS3732C4a1d1208 years
RISE505Kytmanovo, RussiaF999953U4a1b3391 yearsRISE505 has matches with living people
RISE509Bateni, RussiaF999942FT2c4186 years
RISE511Bateni, RussiaF999967FJ2a2a4224 years
RISE523Kapova cave, RussiaF999966G2a13192 years
RISE548Temrta IV, RussiaF999968MR-L23U4~2000 years
RISE552Ulan IV, RussiaF999946MI-S12195T2a1a3940 yearsRISE552 has matches with living people
RISE569Brandysek, Czech RepublicF999954H1af2~2000 years
RISE577Velke Prilepy, Czech RepublicF999951T2b~2000 years
RISE601Verh-Uimon, RussiaF999969MM8a1~2000 years
RISE602Sary-Bel, RussiaF999965MJ-M410C4~2000 years
Bot15Rio Doce, Minas Gerais, BrazilF999963MC-PH3092B4a1a1a~1600 AD
Bot17Rio Doce, Minas Gerais, BrazilF999964MC-Z31878B4a1a1~1600 AD
Kennewick ManKennewick, Washington state, USAF999970MQ-M199X2a8358 years
 
Our top 3 Ancient pop. Oracle:

Top 5 EUtest Single Pop. (4 Anc.)

LBK (Linearbandkeramik)
1 Sardinian @ 17.501347

2 Tuscan @ 29.172617
3 South_Italian_&_Sicilian @ 31.322887
4 North_Italian @ 31.634396
5 GR @ 33.166294

BR2
1 AT @ 8.063127
2 FR @ 9.528506
3 West_&_Central_German @ 11.630827
4 HU @ 12.531700
5 NL @ 12.625481

NE1

1 Sardinian @ 23.157549
2 Tuscan @ 26.121943
3 South_Italian_&_Sicilian @ 26.975130
4 GR @ 28.661140
5 North_Italian @ 28.932219


Obviously I could have chosen other options ​and get different results. :)


 
Comparing myself with the above LBK and NE1 (EUtest).
I’m not that different from them except for one.

Using 1 population approximation:

1 South_Italian_&_Sicilian @ 8.562772
2 GR @ 8.642689
3 AJ @ 11.292471
4 Tuscan @ 16.543209
5 North_Italian @ 22.591982




(Screenshot)

46M36xy.jpg
 
JaJ7z5j.png


Above are the Dodecad k12b results for BR2, NE1, and LBK. Below are mine, they look like it could be LBK or NE1 with additional "North_Europe", and "Gedrosia".

The BR2 shows some gedrosia too. Other Modern European populations get gedrosia as well (example: Argyll 13.1%, Orcadian 12%, Irish 11.91%, English 10.62%, British_Isles 9.50% French 8.08%, French_Basque 9.80%, Mixed Germanics 10.7%, CEU30 10.60%)

IYqcfQG.png
 
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K36 Map of Similarity Rate: NE1, LBK (Linearbandkeramik), BR2

IHfKHbv.jpg


kQWKrjS.jpg


dm8eoEv.jpg




This is my map, I'm reclutant to believe it, I think that the reds are too far away from each other, and that should have been only 1 red halfway between, right in to Puglia.

aDkByvb.jpg
 
Well, k36 was made by a blogger so there will be results that are off by a margin or two (or three...)
 
Well, k36 was made by a blogger so there will be results that are off by a margin or two (or three...)

True, but we use what we can.
That said, it took me forever to do all of that.

... aniway, and I thought it was cold last week, ... :petrified:
 
Well, k36 was made by a blogger so there will be results that are off by a margin or two (or three...)

My K36 Map It’s starting to make a lot of sense now.
Rome and Greece. Who knows, the Blogger could be a Genius too, or not.
a Wider view:

oGx4Q0R.jpg
 

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