Analyses of Iron and Bronze Age Bulgarian(Thracian?) genomes

[Scholarios]

Forgive me if this has been posted already. Did a search for "Thracians" and didn't see it.

Below are the results of analyses of four Iron and Bronze Age Bulgarian genomes.

This paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3824117/) gives the following descriptions of the four samples:

Sample P192-1 was found at the site of a pit sanctuary near Svilengrad, Bulgaria, excavated between 2004 and 2006. The pits are associated with the Thracian culture and date to the Early Iron Age (800–500 BC) based on pottery found in the pits. A total of 67 ritual pits, including 16 pits containing human skeletons or parts of skeletons, were explored during the excavations. An upper wisdom tooth from an adult male was used for DNA analysis.

Sample T2G2 was found in a Thracian tumulus (burial mound) near the village of Stambolovo, Bulgaria. Two small tumuli dating to the Early Iron Age (850–700 BC) were excavated in 2008. A canine tooth from an inhumation burial of a child (c.12 years old) inside a dolium was used for DNA analysis.

Sample V2 was found in a flat cemetery dating to the Late Bronze Age (1500–1100 BC) near the village of Vratitsa, Bulgaria. Nine inhumation burials were excavated between 2003 and 2004. A molar from a juvenile male (age 16–17) was used for DNA analysis.

Sample K8 was found in the Yakimova Mogila Tumulus, which dates to the Iron Age (450–400 BC), near Krushare, Bulgaria. An aristocratic inhumation burial containing rich grave goods was excavated in 2008. A molar from one individual, probably male, was used for DNA analysis.

These samples include both human DNA and DNA from environmental contaminants such as bacteria and fungi, which introduces a great deal of noise into the data. The very small number of SNPs for these samples also contributes to the noise in the data. This noise shows up in the results below as Negroid or Mongoloid admixture.

In spite of the noise, a few things can be learned. The two samples from the Thracian tumuli, T2G2 and K8, and the Bronze Age sample V2 had significant amounts of the K12b Gedrosia component. The amounts of the Gedrosia component seen in these samples are much larger than the 1.5–3.3% of the Gedrosia component seen in Bulgarians today. Note that the Gedrosia component is associated with R1b but not with R1a.

All of the samples have significantly more of the dv3 West European component than the dv3 East European component. Note that Thracians were typically described by ancient writers as having blue eyes and red hair, and that red hair is a predominantly Western European trait.

[Scholarios]

P192-1

globe4

90.47% European
9.53% African
0.00% Amerindian
0.00% Asian
globe10

85.37% Atlantic_Baltic
10.34% Palaeo_African
4.29% West_Asian
0.00% Amerindian
0.00% Australasian
0.00% East_Asian
0.00% Neo_African
0.00% Siberian
0.00% South_Asian
0.00% Southern
globe13

45.10% Mediterranean
42.11% North_European
9.71% Palaeo_African
3.08% West_Asian
0.00% Amerindian
0.00% Arctic
0.00% Australasian
0.00% East_African
0.00% East_Asian
0.00% Siberian
0.00% South_Asian
0.00% Southwest_Asian
0.00% West_African
K7b

75.63% Atlantic_Baltic
16.32% Southern
4.11% African
3.94% West_Asian
0.00% East_Asian
0.00% Siberian
0.00% South_Asian
K10a

48.93% Atlantic_Baltic
44.15% Mediterranean
6.91% Palaeoafrican
0.00% East_Asian
0.00% Red_Sea
0.00% Siberian
0.00% South_Asian
0.00% Southeast_Asian
0.00% Sub_Saharan
0.00% West_Asian
K12b

45.82% Caucasus
26.87% Atlantic_Med
21.68% North_European
2.36% Sub_Saharan
2.01% Northwest_African
1.26% Siberian
0.00% East_African
0.00% East_Asian
0.00% Gedrosia
0.00% South_Asian
0.00% Southeast_Asian
0.00% Southwest_Asian
dv3

42.86% Mediterranean
19.81% West_European
19.50% West_Asian
9.70% East_European
7.77% Northeast_Asian
0.36% Northwest_African
0.00% East_African
0.00% Neo_African
0.00% Palaeo_African
0.00% South_Asian
0.00% Southeast_Asian
0.00% Southwest_Asian
MDLP World-22

32.35% Austronesian
27.04% Atlantic_Mediterranean_Neolithic
17.80% North-East-European
15.94% Indo-Iranian
6.88% Samoedic
0.00% Arctic-Amerind
0.00% East-Siberean
0.00% East-South-Asian
0.00% Indian
0.00% Indo-Tibetan
0.00% Melanesian
0.00% Mesoamerican
0.00% Near_East
0.00% North-Amerind
0.00% North-European-Mesolithic
0.00% North-Siberean
0.00% Paleo-Siberian
0.00% Pygmy
0.00% South-African
0.00% South-America_Amerind
0.00% Sub-Saharian
0.00% West-Asian
Old World 26

15.97% Sardinian
14.70% Finnish
10.85% Palestinian
9.94% Dai
7.98% Yakut
7.27% Gujarati
7.14% Naxi
6.57% Yoruba
6.39% Kenya-Bantu
5.06% Mbuti-Pygmy
2.96% Archaic
1.90% Biaka-Pygmy
1.62% Kalash
0.95% She
0.50% Melanesian
0.16% Japanese
0.00% Basque
0.00% Bedouin
0.00% Brahui
0.00% Burusho
0.00% Druze
0.00% Lahu
0.00% Mandenka
0.00% Mozabite
0.00% Papuan
0.00% San
T2G2

globe4

76.67% European
23.32% African
0.01% Amerindian
0.00% Asian
globe10

53.38% West_Asian
20.22% Atlantic_Baltic
17.12% Palaeo_African
9.28% Australasian
0.00% Amerindian
0.00% East_Asian
0.00% Neo_African
0.00% Siberian
0.00% South_Asian
0.00% Southern
globe13

51.47% West_Asian
15.94% North_European
11.78% Palaeo_African
8.80% East_African
7.12% Australasian
4.89% Arctic
0.00% Amerindian
0.00% East_Asian
0.00% Mediterranean
0.00% Siberian
0.00% South_Asian
0.00% Southwest_Asian
0.00% West_African
K7b

60.48% West_Asian
23.69% African
14.49% South_Asian
1.33% Atlantic_Baltic
0.00% East_Asian
0.00% Siberian
0.00% Southern
K10a

35.95% West_Asian
15.13% Atlantic_Baltic
15.01% Palaeoafrican
14.33% South_Asian
13.64% Mediterranean
3.14% East_Asian
2.81% Sub_Saharan
0.00% Red_Sea
0.00% Siberian
0.00% Southeast_Asian
K12b

54.44% Gedrosia
19.46% Sub_Saharan
13.43% Atlantic_Med
11.30% South_Asian
1.34% Caucasus
0.03% East_Asian
0.00% East_African
0.00% North_European
0.00% Northwest_African
0.00% Siberian
0.00% Southeast_Asian
0.00% Southwest_Asian
dv3

51.27% West_Asian
33.26% West_European
7.63% Neo_African
6.95% Southeast_Asian
0.89% Palaeo_African
0.01% South_Asian
0.00% East_African
0.00% East_European
0.00% Mediterranean
0.00% Northeast_Asian
0.00% Northwest_African
0.00% Southwest_Asian
MDLP World-22

Insufficient SNPs
Old World 26

18.90% Finnish
14.14% Kenya-Bantu
12.32% Yoruba
10.35% Gujarati
8.43% Yakut
7.03% Palestinian
6.90% Archaic
6.71% Mbuti-Pygmy
6.70% Dai
4.18% Naxi
2.72% Biaka-Pygmy
1.21% Kalash
0.18% Bedouin
0.17% San
0.04% She
0.00% Basque
0.00% Brahui
0.00% Burusho
0.00% Druze
0.00% Japanese
0.00% Lahu
0.00% Mandenka
0.00% Melanesian
0.00% Mozabite
0.00% Papuan
0.00% Sardinian
V2

globe4

58.89% European
20.61% Asian
11.91% African
8.59% Amerindian
globe10

43.70% Atlantic_Baltic
24.26% West_Asian
12.27% East_Asian
11.29% Neo_African
8.47% Australasian
0.00% Amerindian
0.00% Palaeo_African
0.00% Siberian
0.00% South_Asian
0.00% Southern
globe13

39.58% North_European
27.22% West_Asian
12.61% West_African
12.60% East_Asian
7.56% Australasian
0.42% Arctic
0.00% Amerindian
0.00% East_African
0.00% Mediterranean
0.00% Palaeo_African
0.00% Siberian
0.00% South_Asian
0.00% Southwest_Asian
K7b

44.14% West_Asian
28.34% Atlantic_Baltic
18.46% African
5.72% East_Asian
3.34% Siberian
0.00% South_Asian
0.00% Southern
K10a

60.73% Atlantic_Baltic
16.10% Sub_Saharan
10.95% West_Asian
6.53% East_Asian
5.68% Southeast_Asian
0.01% Siberian
0.00% Mediterranean
0.00% Palaeoafrican
0.00% Red_Sea
0.00% South_Asian
K12b

44.15% North_European
20.14% Sub_Saharan
15.06% Gedrosia
9.62% Siberian
7.67% Caucasus
3.35% Southeast_Asian
0.01% East_Asian
0.00% Atlantic_Med
0.00% East_African
0.00% Northwest_African
0.00% South_Asian
0.00% Southwest_Asian
dv3

42.02% West_Asian
37.17% West_European
11.74% Neo_African
5.15% Southeast_Asian
3.93% East_European
0.00% East_African
0.00% Mediterranean
0.00% Northeast_Asian
0.00% Northwest_African
0.00% Palaeo_African
0.00% South_Asian
0.00% Southwest_Asian
MDLP World-22

46.09% North-East-European
22.90% Sub-Saharian
16.90% West-Asian
8.74% Mesoamerican
5.37% South-America_Amerind
0.00% Arctic-Amerind
0.00% Atlantic_Mediterranean_Neolithic
0.00% Austronesian
0.00% East-Siberean
0.00% East-South-Asian
0.00% Indian
0.00% Indo-Iranian
0.00% Indo-Tibetan
0.00% Melanesian
0.00% Near_East
0.00% North-Amerind
0.00% North-European-Mesolithic
0.00% North-Siberean
0.00% Paleo-Siberian
0.00% Pygmy
0.00% Samoedic
0.00% South-African
Old World 26

23.45% Sardinian
19.42% Finnish
17.05% Gujarati
8.80% Yoruba
6.84% Basque
6.75% Yakut
6.35% She
5.73% Kenya-Bantu
3.36% Archaic
1.13% San
0.75% Melanesian
0.37% Bedouin
0.00% Biaka-Pygmy
0.00% Brahui
0.00% Burusho
0.00% Dai
0.00% Druze
0.00% Japanese
0.00% Kalash
0.00% Lahu
0.00% Mandenka
0.00% Mbuti-Pygmy
0.00% Mozabite
0.00% Naxi
0.00% Palestinian
0.00% Papuan
K8

globe4

97.86% European
1.65% Amerindian
0.49% African
0.00% Asian
globe10

46.81% West_Asian
36.90% Atlantic_Baltic
13.62% Southern
2.68% Palaeo_African
0.00% Amerindian
0.00% Australasian
0.00% East_Asian
0.00% Neo_African
0.00% Siberian
0.00% South_Asian
globe13

39.15% West_Asian
36.95% Mediterranean
20.05% North_European
2.99% Palaeo_African
0.85% Southwest_Asian
0.00% Amerindian
0.00% Arctic
0.00% Australasian
0.00% East_African
0.00% East_Asian
0.00% Siberian
0.00% South_Asian
0.00% West_African
K7b

46.44% Atlantic_Baltic
36.25% West_Asian
17.30% Southern
0.00% African
0.00% East_Asian
0.00% Siberian
0.00% South_Asian
K10a

47.35% Atlantic_Baltic
32.21% West_Asian
18.41% Mediterranean
2.02% Palaeoafrican
0.00% East_Asian
0.00% Red_Sea
0.00% Siberian
0.00% South_Asian
0.00% Southeast_Asian
0.00% Sub_Saharan
K12b

32.79% Atlantic_Med
29.27% Gedrosia
17.54% North_European
17.50% Caucasus
2.90% Northwest_African
0.00% East_African
0.00% East_Asian
0.00% Siberian
0.00% South_Asian
0.00% Southeast_Asian
0.00% Southwest_Asian
0.00% Sub_Saharan
dv3

39.88% West_European
24.25% East_European
14.34% West_Asian
12.79% Mediterranean
5.86% South_Asian
2.87% Palaeo_African
0.01% Northwest_African
0.00% East_African
0.00% Neo_African
0.00% Northeast_Asian
0.00% Southeast_Asian
0.00% Southwest_Asian
MDLP World-22

75.04% Atlantic_Mediterranean_Neolithic
9.27% Melanesian
9.00% West-Asian
6.68% South-African
0.02% North-East-European
0.00% Arctic-Amerind
0.00% Austronesian
0.00% East-Siberean
0.00% East-South-Asian
0.00% Indian
0.00% Indo-Iranian
0.00% Indo-Tibetan
0.00% Mesoamerican
0.00% Near_East
0.00% North-Amerind
0.00% North-European-Mesolithic
0.00% North-Siberean
0.00% Paleo-Siberian
0.00% Pygmy
0.00% Samoedic
0.00% South-America_Amerind
0.00% Sub-Saharian
Old World 26

35.08% Finnish
20.05% Yakut
17.38% Basque
10.37% Bedouin
6.09% Gujarati
4.40% Yoruba
3.70% Archaic
2.44% Mbuti-Pygmy
0.47% Naxi
0.01% Kalash
0.00% Biaka-Pygmy
0.00% Brahui
0.00% Burusho
0.00% Dai
0.00% Druze
0.00% Japanese
0.00% Kenya-Bantu
0.00% Lahu
0.00% Mandenka
0.00% Melanesian
0.00% Mozabite
0.00% Palestinian
0.00% Papuan
0.00% San
0.00% Sardinian
0.00% She

[Arch Hades]

Check out this ADMIXTURE run, P192-1 and K8 seem to be a lot like modern Italians and French.

http://i1067.photobucket.com/albums/u431/ArchHades/Genetic%20maps%20and%20distance%20tables/ThracianADMIXTUREruncomparison.jpg~original

Unfortunate though no Balkan Slavs were sampled for the modern populations for a compare and contrast, Would have loved to see Serbs, Bulgarians, FYROMians etc compared to them...my money would be on them being closer.

LINK (http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004353#pgen-1004353-g001)

[Scholarios]

And Apparently, the research paper reports that the K8 individual, who was found in a royal type grave has such a strange genome due to modern DNA contamination. The individual found in a pit appears much more West Asian- leading some to posit some kind of elite dominance theory as usual.


The first individual (P192-1) was excavated from a pit sanctuary near Svilengrad, Bulgaria, dated to 800–500 BCE. The other individual (K8) was found in the Yakimova Mogila Tumulus in southeastern Bulgaria, dated to 450–400 BCE.

...

For the Thracian individuals from Bulgaria, no clear pattern emerges. While P192-1 still shows the highest proportion of Sardinian ancestry, K8 more resembles the HG individuals, with a high fraction of Russian ancestry.

...

Interestingly, this individual [K8] was excavated from an aristocratic inhumation burial containing rich grave goods, indicating a high social standing, as opposed to the other individual, who was found in a pit [15]. However, the DNA damage pattern of this individual does not appear to be typical of ancient samples (Table S4 in [15]), indicating a potentially higher level of modern DNA contamination.

http://z5.ifrm.com/30470/13/0/p1191905/journal_pgen_1004353_t001.png

http://z5.ifrm.com/30470/13/0/p1191904/journal_pgen_1004353_g003.png

http://z5.ifrm.com/30470/13/0/p1191906/journal_pgen_1004353_g01.png

[Scholarios]

Check out this ADMIXTURE run, P192-1 and K8 seem to be a lot like modern Italians and French.

http://i1067.photobucket.com/albums/u431/ArchHades/Genetic%20maps%20and%20distance%20tables/ThracianADMIXTUREruncomparison.jpg~original

Unfortunate though no Balkan slavs were sampled for the modern populations for a compare and contrast, Would have loved to see Serbs, Bulgarians, FYROMians etc compared to them...my money would be on them being closer.

LINK (http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004353#pgen-1004353-g001)

I bet they would too. Too bad the research isnt really based as much around proving continuity as finding patterns between ancient dna and prehistoric migrations. Also, it's always kind of hard to compare ancient to modern dna because the collection method is so different. On the other hand, the Minoan mtdna stuff was pretty amazing- matching closest with modern Cretans from Lasithi.

[Arch Hades]

There doesn't seem to be that much of a difference in that ADMIXTURE run between K-8 and P192-1...despite what the authors wrote. I don't think it's necessarily contaminated.

About a 10% difference in the frequencies in components, probably typical variation you'd find over the same ethnicity in different regions over a few hundred year separation.

[Kale]

http://z5.ifrm.com/30470/13/0/p1191905/journal_pgen_1004353_t001.png

Wow that's a terrible number of SNPS. 1/3 to 1/4 of La Brana? The two La Brana individuals were being merged together in many projects due to THEM not having enough SNPs. No wonder there's so much randomness in those autosomal breakdowns.

[Arch Hades]

P192-1

globe13

45.10% Mediterranean
42.11% North_European
9.71% Palaeo_African
3.08% West_Asian
0.00% Amerindian
0.00% Arctic
0.00% Australasian
0.00% East_African
0.00% East_Asian
0.00% Siberian
0.00% South_Asian
0.00% Southwest_Asian
0.00% West_African


K8

globe13

39.15% West_Asian
36.95% Mediterranean
20.05% North_European
2.99% Palaeo_African
0.85% Southwest_Asian
0.00% Amerindian
0.00% Arctic
0.00% Australasian
0.00% East_African
0.00% East_Asian
0.00% Siberian
0.00% South_Asian
0.00% West_African




? Well these runs by Genetiker can't be right. Look at the differences between the two, yet compare the differences in the ADMIXTURE run from the actual study I pasted. A 40% West Asian count for K8 yet a 3% for P192-1 ?

http://genetiker.wordpress.com/2014/06/11/analyses-of-iron-and-bronze-age-bulgarian-genomes/

[Kale]

P192-1

globe13

45.10% Mediterranean
42.11% North_European
9.71% Palaeo_African
3.08% West_Asian
0.00% Amerindian
0.00% Arctic
0.00% Australasian
0.00% East_African
0.00% East_Asian
0.00% Siberian
0.00% South_Asian
0.00% Southwest_Asian
0.00% West_African


K8

globe13

39.15% West_Asian
36.95% Mediterranean
20.05% North_European
2.99% Palaeo_African
0.85% Southwest_Asian
0.00% Amerindian
0.00% Arctic
0.00% Australasian
0.00% East_African
0.00% East_Asian
0.00% Siberian
0.00% South_Asian
0.00% West_African




? Well these runs by Genetiker can't be right. Look at the differences between the two, yet compare the differences in the ADMIXTURE run from the actual study I pasted. A 40% West Asian count for K8 yet a 3% for P192-1 ?

http://genetiker.wordpress.com/2014/06/11/analyses-of-iron-and-bronze-age-bulgarian-genomes/

Low SNPS will do that. The uniparental markers were definitely interesting, and maybe if they can get some data on specific genes that would be nice, but in terms of pure autosomal count, I doubt these genomes are much useful for anything.

[Artek]

There doesn't seem to be that much of a difference in that ADMIXTURE run between K-8 and P192-1...despite what the authors wrote. I don't think it's necessarily contaminated.

About a 10% difference in the frequencies in components, probably typical variation you'd find over the same ethnicity in different regions over a few hundred year separation.
That's what I think as well. Also, given a huge difference in status, it should've been a typical phenomenon for conqueror elites to be at least slightly different genetically from the people they've ruled.