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Thread: Ancient DNA Calculator using Merged-Raw Data

  1. #1
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    Y-DNA haplogroup
    R1b1a1a2b1 (R-F1794)
    MtDNA haplogroup
    H6a1b

    Ethnic group
    Italian
    Country: United States



    3 members found this post helpful.

    Ancient DNA Calculator using Merged-Raw Data

    Ancient DNA Total Shared DNA Compound Segments
    Ajvide 58 2.77% 0.57%
    Altai Neanderthal 1.40% 0.20%
    Australian Aboriginal 7.48% 1.19%
    Bot 15 7.22% 1.06%
    Bot 17 5.85% 1.03%
    BR1 7.33% 1.92%
    BR2 33.86% 23.74%
    Clovis Anzick-1 22.47% 9.78%
    CO1 8.97% 2.46%
    Denisova 1.09% 0.16%
    Gökhem2 4.19% 0.48%
    Hinxton-1 1.82% 0.06%
    Hinxton-2 2.38% 0.17%
    Hinxton-3 3.23% 0.34%
    Hinxton-4 5.42% 0.83%
    Hinxton-5 2.01% 0.03%
    IR1 7.96% 2.65%
    KO1 8.36% 2.38%
    Kostenki 14 13.08% 5.02%
    La Braña Arintero 8.98% 2.21%
    Linearbandkeramik 32.81% 18.77%
    Loschbour 26.39% 13.55%
    Mal'ta 6.48% 1.52%
    Motala12 11.76% 3.54%
    NE1 33.76% 22.58%
    NE5 6.84% 1.33%
    NE6 8.48% 2.15%
    NE7 8.62% 2.16%
    Paleo-Eskimo 9.24% 1.01%
    RISE00 5.21% 1.19%
    RISE150 12.55% 4.53%
    RISE174 12.17% 4.74%
    RISE395 13.58% 5.08%
    RISE479 9.77% 2.80%
    RISE493 24.11% 11.98%
    RISE495 17.56% 7.20%
    RISE496 13.09% 4.16%
    RISE497 20.79% 7.66%
    RISE499 8.06% 2.09%
    RISE500 11.10% 3.02%
    RISE502 8.00% 1.66%
    RISE503 6.58% 1.65%
    RISE504 7.98% 1.69%
    RISE505 22.87% 10.87%
    RISE509 7.29% 1.42%
    RISE511 16.81% 7.05%
    RISE523 13.33% 4.59%
    RISE548 6.94% 1.45%
    RISE552 13.17% 6.62%
    RISE569 7.81% 2.20%
    RISE577 7.22% 1.80%
    RISE601 4.04% 0.35%
    RISE602 4.53% 0.49%
    RISE94 5.71% 1.26%
    RISE97 5.57% 0.84%
    RISE98 21.95% 11.01%
    Ust-Ishim 27.86% 17.09%
    Vi33.16 Neanderthal 0.64% 0.00%
    Vi33.25 Neanderthal 0.67% 0.00%
    Vi33.26 Neanderthal 1.07% 0.00%

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



    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/thread...ogy-Tools-blog
    Last edited by Jovialis; 31-01-19 at 16:20.

  2. #2
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    Y-DNA haplogroup
    R1b1a1a2b1 (R-F1794)
    MtDNA haplogroup
    H6a1b

    Ethnic group
    Italian
    Country: United States



    Ancient DNA Total Shared DNA Compound Segments
    BR2 33.86% 23.74%
    NE1 33.76% 22.58%
    Linearbandkeramik 32.81% 18.77%
    Ust-Ishim 27.86% 17.09%
    Loschbour 26.39% 13.55%
    RISE493 24.11% 11.98%
    RISE505 22.87% 10.87%
    Clovis Anzick-1 22.47% 9.78%
    RISE98 21.95% 11.01%
    RISE497 20.79% 7.66%
    RISE495 17.56% 7.20%
    RISE511 16.81% 7.05%
    RISE395 13.58% 5.08%
    RISE523 13.33% 4.59%
    RISE552 13.17% 6.62%
    RISE496 13.09% 4.16%
    Kostenki 14 13.08% 5.02%
    RISE150 12.55% 4.53%
    RISE174 12.17% 4.74%
    Motala12 11.76% 3.54%
    RISE500 11.10% 3.02%
    RISE479 9.77% 2.80%
    Paleo-Eskimo 9.24% 1.01%
    La Braña Arintero 8.98% 2.21%
    CO1 8.97% 2.46%
    NE7 8.62% 2.16%
    NE6 8.48% 2.15%
    KO1 8.36% 2.38%
    RISE499 8.06% 2.09%
    RISE502 8.00% 1.66%
    RISE504 7.98% 1.69%
    IR1 7.96% 2.65%
    RISE569 7.81% 2.20%
    Australian Aboriginal 7.48% 1.19%
    BR1 7.33% 1.92%
    RISE509 7.29% 1.42%
    Bot 15 7.22% 1.06%
    RISE577 7.22% 1.80%
    RISE548 6.94% 1.45%
    NE5 6.84% 1.33%
    RISE503 6.58% 1.65%
    Mal'ta 6.48% 1.52%
    Bot 17 5.85% 1.03%
    RISE94 5.71% 1.26%
    RISE97 5.57% 0.84%
    Hinxton-4 5.42% 0.83%
    RISE00 5.21% 1.19%
    RISE602 4.53% 0.49%
    Gökhem2 4.19% 0.48%
    RISE601 4.04% 0.35%
    Hinxton-3 3.23% 0.34%
    Ajvide 58 2.77% 0.57%
    Hinxton-2 2.38% 0.17%
    Hinxton-5 2.01% 0.03%
    Hinxton-1 1.82% 0.06%
    Altai Neanderthal 1.40% 0.20%
    Denisova 1.09% 0.16%
    Vi33.26 Neanderthal 1.07% 0.00%
    Vi33.25 Neanderthal 0.67% 0.00%
    Vi33.16 Neanderthal 0.64% 0.00%

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

  3. #3
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    Y-DNA haplogroup
    T1a2 -Z19945
    MtDNA haplogroup
    H12a

    Ethnic group
    Italian
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    1 members found this post helpful.

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

    ANCIENT DNA Total Shar. DNA Comp. Seg.
    Linearbandkeramik 33.12 19.09
    BR2 32.82 19.29
    NE1 32.42 19.32
    Ust-Ishim 27.49 14.80
    Loschbour 25.78 12.82
    RISE493 23.45 11.19
    RISE505 22.13 9.79
    Clovis Anzick-1 21.80 9.22
    RISE98 21.09 9.27
    RISE497 19.08 7.06
    RISE511 17.13 6.07
    RISE495 16.69 5.88
    RISE496 13.27 4.61
    RISE523 12.92 4.68
    RISE174 12.41 4.96
    RISE552 12.09 4.37
    RISE150 11.91 4.80
    RISE395 11.89 4.25
    Kostenki 14 11.60 4.34
    Motala12 11.32 3.62
    RISE500 9.88 3.06
    RISE479 8.69 2.48
    La Braña Arintero 8.55 2.12
    Paleo-Eskimo 8.55 1.39
    RISE499 7.86 2.52
    NE6 7.71 1.72
    NE7 7.68 1.75
    RISE577 7.61 2.20
    IR1 7.28 1.40
    KO1 7.22 1.98
    RISE548 7.19 1.46
    RISE502 7.06 1.58
    NE5 7.02 2.18
    RISE504 7.01 1.87
    RISE503 6.97 1.84
    CO1 6.88 1.73
    RISE569 6.81 1.42
    RISE509 6.57 1.51
    BR1 6.36 0.91
    RISE94 6.33 1.21
    Mal'ta 5.96 1.21
    RISE00 5.84 1.50
    Bot 15 5.53 0.79
    Bot 17 5.51 0.88
    RISE97 5.49 0.95
    Australian Aboriginal 5.39 0.83
    Hinxton-4 5.04 0.74
    RISE602 4.34 0.70
    RISE601 3.81 0.44
    Gökhem2 3.51 0.14
    Hinxton-2 2.56 0.08
    Ajvide 58 2.48 0.18
    Hinxton-3 2.36 0.43
    Hinxton-5 1.88 0.04
    Hinxton-1 1.81 0.27
    Altai Neanderthal 1.48 0.23
    Denisova 0.97 0.03
    Vi33.26 Neanderthal 0.61 0.11
    Vi33.25 Neanderthal 0.40 0.00
    Vi33.16 Neanderthal 0.37 0.08


    Ancient DNA Places of Origin
    http://www.y-str.org/p/ancient-dna.html?m=1
    Last edited by Salento; 29-01-19 at 14:30. Reason: Link to Ancient DNA Places

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    Quote Originally Posted by Salento View Post

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

    ANCIENT DNA Total Shar. DNA Comp. Seg.
    Linearbandkeramik 33.12 19.09
    BR2 32.82 19.29
    NE1 32.42 19.32
    Ust-Ishim 27.49 14.80
    Loschbour 25.78 12.82
    RISE493 23.45 11.19
    RISE505 22.13 9.79
    Clovis Anzick-1 21.80 9.22
    RISE98 21.09 9.27
    RISE497 19.08 7.06
    RISE511 17.13 6.07
    RISE495 16.69 5.88
    RISE496 13.27 4.61
    RISE523 12.92 4.68
    RISE174 12.41 4.96
    RISE552 12.09 4.37
    RISE150 11.91 4.80
    RISE395 11.89 4.25
    Kostenki 14 11.60 4.34
    Motala12 11.32 3.62
    RISE500 9.88 3.06
    RISE479 8.69 2.48
    La Braña Arintero 8.55 2.12
    Paleo-Eskimo 8.55 1.39
    RISE499 7.86 2.52
    NE6 7.71 1.72
    NE7 7.68 1.75
    RISE577 7.61 2.20
    IR1 7.28 1.40
    KO1 7.22 1.98
    RISE548 7.19 1.46
    RISE502 7.06 1.58
    NE5 7.02 2.18
    RISE504 7.01 1.87
    RISE503 6.97 1.84
    CO1 6.88 1.73
    RISE569 6.81 1.42
    RISE509 6.57 1.51
    BR1 6.36 0.91
    RISE94 6.33 1.21
    Mal'ta 5.96 1.21
    RISE00 5.84 1.50
    Bot 15 5.53 0.79
    Bot 17 5.51 0.88
    RISE97 5.49 0.95
    Australian Aboriginal 5.39 0.83
    Hinxton-4 5.04 0.74
    RISE602 4.34 0.70
    RISE601 3.81 0.44
    Gökhem2 3.51 0.14
    Hinxton-2 2.56 0.08
    Ajvide 58 2.48 0.18
    Hinxton-3 2.36 0.43
    Hinxton-5 1.88 0.04
    Hinxton-1 1.81 0.27
    Altai Neanderthal 1.48 0.23
    Denisova 0.97 0.03
    Vi33.26 Neanderthal 0.61 0.11
    Vi33.25 Neanderthal 0.40 0.00
    Vi33.16 Neanderthal 0.37 0.08


    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.

  5. #5
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    Y-DNA haplogroup
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    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

  6. #6
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    1 members found this post helpful.
    Raw Data Version SNPs Used in Evaluation Orcale 1st Single Population Sharing Orcale-4 1st Single Population Sharing
    Merged Raw Data (DIYDodecad Format) 155327 C_Italian @ 6.78 C_Italian_Dodecad @ 7.297379
    Merged Raw Data (23andme Format) 154866 C_Italian @ 6.85 C_Italian_Dodecad @ 7.371545
    AncestryDNA 152095 S_Italian_Sicilian & C_Italian @ 6.97 C_Italian_Dodecad @ 7.504167
    Living DNA 47508 Sicilian @ 4.39 Sicilian_Dodecad @ 4.826463
    23andme (V5) 46844 Sicilian @ 3.89 Sicilian_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.

  7. #7
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    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:










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    1 members found this post helpful.
    Quote Originally Posted by Salento View Post
    Ancient DNA Places of Origin
    http://www.y-str.org/p/ancient-dna.html?m=1
    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 Name Sample Location GEDMatch Sex Y-DNA Mt-DNA Approx. Age by authors My Analysis or Comments
    Altai Neanderthal Denisova Cave, Siberia F999902 F 50,000 years
    Denisova Denisova Cave, Siberia F999903 F 30,000 years
    Palaeo-Eskimo Qeqertarsuaq, Greenland F999906 M Q1a D2a1 4,000 years Palaeo-Eskimo 2000 BC DNA
    Clovis-Anzick-1 Montana, North America F999919 M Q-Z780 D4h3a 12,500 years Matches Living people.
    Mal’ta South - Central Siberia F999914 M R U 24,000 years Matches Living people on X Chromosome.
    La Braña-Arintero León, Spain F999915 M C-V183 U5b2c1 7,000 years Analyzing La Braña-Arintero Ancient DNA
    Motala-12 Östergötland, Sweden F999917 M I-L460 U2e1 7,000 years My Analysis of Motala-12 ancient DNA
    LBK Stuttgart, Germany F999916 F T2c2 7,500 years Matches Living people
    Loschbour Loschbour, Luxembourg F999918 M I-L460 U5b1a 8,000 years Matches Living people
    Ajvide58 Sweden F999924 M I-CTS772 U4d 5000 years Ajvide58 DNA Analysis
    Gökhem2 Sweden F999934 F H1c 5000 years Gökhem2 Ancient DNA Analysis
    Hinxton-2 Cambridgshire, UK F999921 F H2a2b1 1300 years Hinxton-2 Analysis
    Hinxton-3 Cambridgshire, UK F999922 F K1a4a1a2b 1300 years Hinxton-3 Analysis
    Hinxton-4 Cambridgshire, UK F999925 M R-DF25 H1ag1 2000 years Hinxton-4 has X-Matches with living people
    Hinxton-5 Cambridgshire, UK F999926 F H2a2a1 1300 years Hinxton5 Ancient DNA Analysis
    KO1 Tiszaszőlős-Domaháza, Hungary F999931 M I-L68 R3 5650-5780 cal BC Analysis of Neolithic KO1 genome
    NE1 Polgár-Ferenci-hát, Hungary F999937 F U5b2c 5070-5310 cal BC Ancient NE1 Matches living people
    NE5 Kompolt - Kigyósér, Hungary F999927 M C-F3393 J1c 4990-5210 cal BC Ancient Hungarian Genome NE5 Analysis
    NE6 Apc-Berekalja I., Hungary F999932 M C-P255 K1a3a3 4950-5300 cal BC Analysis of Hungarian genome-NE6
    NE7 Apc-Berekalja I., Hungary F999928 M I-L1228 N1a 4360-4490 cal BC Ancient Hungarian genome - NE7
    CO1 Apc-Berekalja I., Hungary F999930 F H 2700-2900 cal BC Analysis of Copper age genome CO1
    BR2 Ludas-Varjú-dűlő, Hungary F999933 M J-M67 K1a1a 1110-1270 cal BC Ancient BR2 matches living people
    IR1 Ludas-Varjú-dűlő, Hungary F999929 M N-M231 G2a1 830-980 cal BC Ancient Hungarian genome - IR1
    Ust'-Ishim Ust'-Ishim, Siberia F999935 M K-M526 R 45,000 years Ust'-Ishim matches with living people!
    Kostenki14 European Russia F999936 M C-V199 U2 38,700-36,200 years Kostenki14 Ancient DNA Analysis
    RISE00 Sope, Estonia F999955 F H5a1 ~2000 years
    RISE94 Viby, Sweden F999956 M K-M1221 K1a2a 4025 years RISE94 has matches with living people
    RISE97 Fredriksberg, Sweden F999945 CT-Y1580 K2a5 3590 years
    RISE98 L Beddinge 56, Sweden F999941 M R-M405 K1b1a 3736 years RISE98 has matches with living people
    RISE150 Przeclawice, Poland F999948 U5a1b1 3469 years RISE150 has matches with living people
    RISE174 Oxie 7, Sweden F999943 W1 1521 years RISE174 has matches with living people
    RISE395 Bol'shekaraganskii, Russia F999949 F U2e1 3540 years RISE395 has matches with living people
    RISE479 Erd 4, Hungary F999944 M I-L1228 T2b ~2000 years
    RISE493 Sabinka 2, Russia F999950 M Q-L712 C4a1c 3214 years RISE493 has matches with living people
    RISE495 Arban 1, Russia F999958 M R-F3105 D4j1
    RISE496 Arban 1, Russia F999959 F U5a1a2a 3070 years
    RISE497 Arban 1, Russia F999957 F-P142 A2f2 ~2000 years RISE497 has matches with living people
    RISE499 Bystrovka, Russia F999952 F H5a1 ~2000 years
    RISE500 Kytmanovo, Russia F999947 F U4d1 ~2000 years
    RISE502 Bystrovka, Russia F999960 F U5a1d 3140 years
    RISE503 Kytmanovo, Russia F999961 U2e2 3328 years
    RISE504 Kytmanovo, Russia F999962 M J-CTS3732 C4a1d 1208 years
    RISE505 Kytmanovo, Russia F999953 U4a1b 3391 years RISE505 has matches with living people
    RISE509 Bateni, Russia F999942 F T2c 4186 years
    RISE511 Bateni, Russia F999967 F J2a2a 4224 years
    RISE523 Kapova cave, Russia F999966 G2a1 3192 years
    RISE548 Temrta IV, Russia F999968 M R-L23 U4 ~2000 years
    RISE552 Ulan IV, Russia F999946 M I-S12195 T2a1a 3940 years RISE552 has matches with living people
    RISE569 Brandysek, Czech Republic F999954 H1af2 ~2000 years
    RISE577 Velke Prilepy, Czech Republic F999951 T2b ~2000 years
    RISE601 Verh-Uimon, Russia F999969 M M8a1 ~2000 years
    RISE602 Sary-Bel, Russia F999965 M J-M410 C4 ~2000 years
    Bot15 Rio Doce, Minas Gerais, Brazil F999963 M C-PH3092 B4a1a1a ~1600 AD
    Bot17 Rio Doce, Minas Gerais, Brazil F999964 M C-Z31878 B4a1a1 ~1600 AD
    Kennewick Man Kennewick, Washington state, USA F999970 M Q-M199 X2a 8358 years

  9. #9
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    Y-DNA haplogroup
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    MtDNA haplogroup
    H12a

    Ethnic group
    Italian
    Country: United States



    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. :)



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    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)


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    1 members found this post helpful.


    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%)

    Last edited by Jovialis; 31-01-19 at 16:14.

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









    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.


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    1 members found this post helpful.
    Well, k36 was made by a blogger so there will be results that are off by a margin or two (or three...)
    mmmmmmmmm dooouuughhhnuuuutz

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    Quote Originally Posted by davef View Post
    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, ...

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    Quote Originally Posted by davef View Post
    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:


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