Monday, October 20, 2014

Playing Around with GEDmatch and Ancient DNA

Roberta Estes and her readers at DNAeXplained are having wild fun comparing their DNA to ancient DNA samples uploaded to GEDmatch* by Felix Chandrakamur.  I couldn't resist joining in the fun.

Following her example, I tweaked the Minimum Threshold and the Minimum segment cM sizes (down to 1cM unless otherwise stated) to see if I matched any of the samples.  Those numbers are tweaked to see if there are any DNA matches.  I don't usually mess with GEDmatch's default 700 SNP/7cM, but this DNA is so old there would be no other way to compare.

No one knows yet if these results are meaningful or not, but if people who write about this stuff during the day and lay awake at night obsessing about it are going to compare their DNA to ancient remains, so shall I.

I will compare each ancient DNA sample with me and my parents only at the highest values found (we share much more on each ancient DNA sample at values below).  I just did autosomal comparisons, not X-chromosome.


Clovis Anzick-1 refers to the remains of a toddler who died and was buried in Wilsall, Park, Montana about 12,600 years ago.  This child was a member of the population from which all modern Native Americans descend, particularly those from Mexico and south of Mexico.  NOTE: Since first posting this, the kit number changed to F999919.

Comparing (Christine) and F999913 (Clovis Anzick-1)
Minimum threshold size to be included in total = 400 SNPs
Mismatch-bunching Limit = 200 SNPs
Minimum segment cM to be included in total = 1.0 cM
Chr Start Location            End Location  Centimorgans (cM)                   SNPs
1 159281892               161769805                   4.1                                     406
10 103388824             106662110                   1.6                                     419
Largest segment = 4.1 cM
Total of segments > 1 cM = 5.7 cM

Comparing (Dad) and F999913 (Clovis Anzick-1)
Minimum threshold size to be included in total = 350 SNPs
Mismatch-bunching Limit = 175 SNPs
Minimum segment cM to be included in total = 1.0 cM
Chr Start Location End Location Centimorgans (cM)          SNPs
6 104470668 107607740                    4.7                                 354
10 111327250 114051969                    2.6                                 362
Largest segment = 4.7 cM
Total of segments > 1 cM = 7.3 cM

Comparing (Mom) and F999913 (Clovis Anzick-1)
Minimum threshold size to be included in total = 350 SNPs
Mismatch-bunching Limit = 175 SNPs
Minimum segment cM to be included in total = 1.0 cM
Chr Start Location End Location Centimorgans (cM) SNPs
1 153063519 155385045 2.3 384
2 88322784 99543207 1.6 374
Largest segment = 2.3 cM
Total of segments > 1 cM = 3.9 cM

My Chromosome 1 match is similar to my mom, and my Chromosome 10 match is similar to my dad. Does this point to us being part Native American?  Who knows.


Palaeo-Eskimo 2000 BC is the DNA from a man (now dubbed "Inuk") who died about 4,000 years ago along the shore of Disco Bay in Greenland.

Comparing (Christine) and F999906 (Palaeo-Eskimo 2000 BC)
Minimum threshold size to be included in total = 200 SNPs
Mismatch-bunching Limit = 100 SNPs
Minimum segment cM to be included in total = 1.0 cM
Chr Start Location End Location Centimorgans (cM) SNPs
2 218789542 219868474 1.8 239
Largest segment = 1.8 cM
Total of segments > 1 cM = 1.8 cM

Comparing (Dad) and F999906 (Palaeo-Eskimo 2000 BC)
Minimum threshold size to be included in total = 200 SNPs
Mismatch-bunching Limit = 100 SNPs
Minimum segment cM to be included in total = 1.0 cM
Chr Start Location End Location Centimorgans (cM) SNPs
6 42773468 43799851 2.5 229
12 112727416 113301703 1.1 208
19 15027162 15712229 1.1 265
22 20458678 21923051 3.9 215
Largest segment = 3.9 cM
Total of segments > 1 cM = 8.5 cM

Comparing (Mom) and F999906 (Palaeo-Eskimo 2000 BC)
Minimum threshold size to be included in total = 200 SNPs
Mismatch-bunching Limit = 100 SNPs
Minimum segment cM to be included in total = 1.0 cM
Chr Start Location End Location Centimorgans (cM) SNPs
1 53539560 54409565 1.5 233
6 42721822 43792975 2.5 234
16 1791149 2728282 1.7 206
Largest segment = 2.5 cM
Total of segments > 1 cM = 5.7 cM

I don't appear to match either of my parents' DNA at the highest matching values, although they appear to match each other on their Chromosome 6.


Altai Neanderthal is the DNA that was extracted from a Neanderthal woman's toe bone.  She died in the Altai Mountains in Siberia at least 50,000 years ago.

Comparing (Christine) and F999902 (Altai Neanderthal)
Minimum threshold size to be included in total = 200 SNPs
Mismatch-bunching Limit = 100 SNPs
Minimum segment cM to be included in total = 1.0 cM
Chr Start Location End Location Centimorgans (cM) SNPs
8 20182757 20819443 1.1 236
Largest segment = 1.1 cM
Total of segments > 1 cM = 1.1 cM

Comparing (Dad) and F999902 (Altai Neanderthal)
Minimum threshold size to be included in total = 100 SNPs
Mismatch-bunching Limit = 50 SNPs
Minimum segment cM to be included in total = 1.0 cM
Chr Start Location End Location Centimorgans (cM) SNPs
2 47888491 48685435 1.3 133
2 125902914 126798780 1.0 140
3 20411153 20945046 1.1 139
11 32474646 33371727 1.1 138
21 35719891 36198939 1.1 100
Largest segment = 1.3 cM
Total of segments > 1 cM = 5.6 cM

Comparing (Mom) and F999902 (Altai Neanderthal)
Minimum threshold size to be included in total = 200 SNPs
Mismatch-bunching Limit = 100 SNPs
Minimum segment cM to be included in total = 1.0 cM
Chr Start Location End Location Centimorgans (cM) SNPs
6 31529276 32743927 1.1 222
11 32249953 33344121 1.1 210
Largest segment = 1.1 cM
Total of segments > 1 cM = 2.2 cM

Like Palaeo-Eskimo above, I don't match my parents at the highest values, but they match each other on Chromosome 11.


Denosova is the DNA extracted from a little girl who died at least 30,000 years ago and died and/or was buried in the Denosova Cave in the Altai Mountains in Siberia.

Comparing (Christine) and F999903 (Denisova)
Minimum threshold size to be included in total = 100 SNPs
Mismatch-bunching Limit = 50 SNPs
Minimum segment cM to be included in total = 1.0 cM
Chr Start Location End Location Centimorgans (cM) SNPs
2 155356065 156155492 1.1 109
7 68512715 69604128 1.3 112
8 20182757 20815206 1.0 233
Largest segment = 1.3 cM
Total of segments > 1 cM = 3.4 cM

Comparing (Dad) and F999903 (Denisova)
Minimum threshold size to be included in total = 100 SNPs
Mismatch-bunching Limit = 50 SNPs
Minimum segment cM to be included in total = 1.0 cM
Chr Start Location End Location Centimorgans (cM) SNPs
11 32474646 33347123 1.0 131
Largest segment = 1.0 cM
Total of segments > 1 cM = 1.0 cM

Comparing (Mom) and F999903 (Denisova)
Minimum threshold size to be included in total = 200 SNPs
Mismatch-bunching Limit = 100 SNPs
Minimum segment cM to be included in total = 1.0 cM
Chr Start Location End Location Centimorgans (cM) SNPs
6 31569945 32702306 1.0 213
Largest segment = 1.0 cM
Total of segments > 1 cM = 1.0 cM

None of us seemed to match each other on our highest values.


Linearbandkeramik (LBK) is a sample taken from the remains of a farmer (presumably a man, I can't get more detail) who died in the Stuttgart region about 7,500 years ago.  The German name refers to the Linear Band pottery culture.

Comparing (Christine) and F999916 (Linearbandkeramik)
Minimum threshold size to be included in total = 500 SNPs
Mismatch-bunching Limit = 250 SNPs
Minimum segment cM to be included in total = 3.0 cM
Chr Start Location End Location Centimorgans (cM) SNPs
1 20882387 22912496 3.2 519
1 30050780 31476920 3.3 523
2 217867317 219949518 4.0 519
21 37042588 39041800 3.4 547
Largest segment = 4.0 cM
Total of segments > 3 cM = 13.8 cM

Comparing (Dad) and F999916 (Linearbandkeramik)
Minimum threshold size to be included in total = 500 SNPs
Mismatch-bunching Limit = 250 SNPs
Minimum segment cM to be included in total = 3.0 cM
Chr Start Location End Location Centimorgans (cM)          SNPs
2 217643676 219934637 4.5 555
Largest segment = 4.5 cM
Total of segments > 3 cM = 4.5 cM

Comparing (Mom) and F999916 (Linearbandkeramik)
Minimum threshold size to be included in total = 700 SNPs
Mismatch-bunching Limit = 350 SNPs
Minimum segment cM to be included in total = 3.0 cM
Chr Start Location End Location Centimorgans (cM) SNPs
13 79743931 85588528 3.5 1197
Largest segment = 3.5 cM
Total of segments > 3 cM = 3.5 cM

Since we're predominantly descended from people in Western Europe, it was no surprise that my parents and I are much closer to this ancient person.  I share some this match with my dad on our Chromosome 2.


La Brana-Arintero aka La Brana-1 is from a man who died or was buried about 7,000 years ago in Valdelugueros, León, Spain.  Unlike LBK, La Brana-1 was pre-agricultural, even though he was slightly later.

Comparing (Christine) and F999915 (La Brana-Arintero)
Minimum threshold size to be included in total = 200 SNPs
Mismatch-bunching Limit = 100 SNPs
Minimum segment cM to be included in total = 1.0 cM
Chr Start Location End Location Centimorgans (cM) SNPs
1 63279983 64482048 1.8 205
2 52083107 53498109 1.2 231
2 190278589 192072958 1.9 214
4 89384761 92048466 3.4 276
8 50215053 52688107 1.5 213
9 9347877 10743557 2.5 291
10 109396783 110766205 1.0 205
10 112855667 114042907 1.1 218
12 20867979 21552775 1.2 250
Largest segment = 3.4 cM
Total of segments > 1 cM = 15.6 cM

Comparing (Dad) and F999915 (La Brana-Arintero)
Minimum threshold size to be included in total = 250 SNPs
Mismatch-bunching Limit = 125 SNPs
Minimum segment cM to be included in total = 1.0 cM
Chr Start Location End Location Centimorgans (cM) SNPs
10 22557524 24487606 1.8 256
10 73379996 76482747 1.4 280
12 109031545 111722776 1.3 273
19 43427453 44691915 1.4 257
Largest segment = 1.8 cM
Total of segments > 1 cM = 6.0 cM

Comparing (Mom) and F999915 (La Brana-Arintero)
Minimum threshold size to be included in total = 250 SNPs
Mismatch-bunching Limit = 125 SNPs
Minimum segment cM to be included in total = 1.0 cM
Chr Start Location End Location Centimorgans (cM) SNPs
10 112836288 114332785 1.7 273
12 20766653 21754801 1.6 284
16 1461746 2820106 2.8 265
19 43449630 44951182 1.9 291
Largest segment = 2.8 cM
Total of segments > 1 cM = 8.1 cM

Again, since we are all of Western European ancestry, I expected to have a closer match like this than the first few ancient DNA samples.  My mom had the highest match.  Her ethnicity tests have always revealed a higher than expected amount of Iberian DNA, even though she has no recent Spanish ancestor (I suspect her French Huguenots from the 1600's).  I match her on Chromosome 10.  My dad has Chromosome 10 as well, but on a slightly different span.  Mom and I also share on Chromosome 12.


Mal'ta MA-1 is taken from the arm bone of a 4-year-old boy who died and was buried about 24,000 years ago near the village of Mal'ta, Siberia (near Lake Baikal).  It is considered a link between Europeans and Native Americans.

Comparing (Christine) and F999914 (Malta MA-1)
Minimum threshold size to be included in total = 350 SNPs
Mismatch-bunching Limit = 175 SNPs
Minimum segment cM to be included in total = 1.0 cM
Chr Start Location End Location Centimorgans (cM) SNPs
10 95396719 97209165 1.4 386
Largest segment = 1.4 cM
Total of segments > 1 cM = 1.4 cM

Comparing (Dad) and F999914 (Malta MA-1)
Minimum threshold size to be included in total = 250 SNPs
Mismatch-bunching Limit = 125 SNPs
Minimum segment cM to be included in total = 1.0 cM
Chr Start Location End Location Centimorgans (cM) SNPs
12 20776581 21463245 1.2 289
Largest segment = 1.2 cM
Total of segments > 1 cM = 1.2 cM

Comparing (Mom) and F999914 (Malta MA-1)
Minimum threshold size to be included in total = 300 SNPs
Mismatch-bunching Limit = 150 SNPs
Minimum segment cM to be included in total = 1.0 cM
Chr Start Location End Location Centimorgans (cM) SNPs
2 81275213 84230757 1.3 303
10 95493749 97209165 1.3 367
12 21064601 21931308 1.3 318
Largest segment = 1.3 cM
Total of segments > 1 cM = 3.9 cM

I share Mal'ta on Chromosome 10 with my mother.  My parents share Chromosome 12, which I don't have at my highest level.






*GEDmatch is free to join and their basic utilities far outstrip what you get with Ancestry or Family Tree DNA.  If you join as a paid customer ($10/month) you get some additional fabulous utilities to play with (like Matching Segment Search and Triangulation).  An amazing deal!


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