Comparing Mesolithic and Neolithic genomes using the Eurogenes K36 calculator

[Maciamo]

I have run a Yamna genome as well as the Iron-Age Celtic and Anglo-Saxon Hinxton genomes in the Eurogenes K36 calculator. Now is time to have a look at some Mesolithic and Neolithic Europeans.

Keep in mind that the component names for the Eurogenes K36 admixture are not accurate and do not represent the region of origin, nor even the region where it is the most common today. One of the reasons fro comparing ancient genomes is to try to determine what these components really mean. For more information check the analysis of the K36 components.


Mesolithic Spain (La Braña, C1a2, U5b2c1, c. 5850 BCE)

0.00% Amerindian
0.00% Arabian
0.00% Armenian
10.87% Basque
0.00% Central_African
0.00% Central_Euro
0.00% East_African
0.00% East_Asian
0.00% East_Balkan
0.00% East_Central_Asian
20.37% East_Central_Euro
0.00% East_Med
10.99% Eastern_Euro
33.56% Fennoscandian
0.04% French
0.02% Iberian
0.00% Indo-Chinese
0.00% Italian
0.00% Malayan
0.00% Near_Eastern
0.00% North_African
8.11% North_Atlantic
0.00% North_Caucasian
16.05% North_Sea
0.00% Northeast_African
0.00% Oceanian
0.00% Omotic
0.00% Pygmy
0.00% Siberian
0.00% South_Asian
0.00% South_Central_Asian
0.00% South_Chinese
0.00% Volga-Ural
0.00% West_African
0.00% West_Caucasian
0.00% West_Med

What we see here is a major overlap with the Yamna genome. The components are the same except for the North_Caucasus, Volga-Ural, South-Central_Asian and Amerindian in Yamna and the Basque in Mesolithic Spain. The 17% of North Caucasus and 12% of Central_Asian probably correspond to the teal Armenian-like admixture in Yamna, while the Amerindian and Volga-Ural reflect the Paleolithic Siberian (or ANE) origins of R1a and R1b people, as well as the presence of haplogroup Q1a in the Khvalynsk culture alongside R1a and R1b, and the proximity of N1c tribes in the Volga-Ural region, where population exchange would have taken place during the Khvalynsk and Yamna periods.

This confirms that the East_Central_Euro, Eastern_Euro, Fennoscandian, North_Atlantic and North_Sea components represent Mesolithic admixtures (WHG, SHG, EHG). However the geographic descriptions do not match the actual geographic distributions or prehistoric locations. For example, Spanish La Braña had more Eastern_Euro and Fennoscandian than the Yamna genome from Russia.


Mesolithic Luxembourg (Loschbour, I2a1b, U5b1a, 6100 BCE)

0.00% Amerindian
0.00% Arabian
0.00% Armenian
8.26% Basque
0.00% Central_African
0.00% Central_Euro
0.00% East_African
0.00% East_Asian
0.00% East_Balkan
0.00% East_Central_Asian
20.35% East_Central_Euro
0.00% East_Med
10.17% Eastern_Euro
38.97% Fennoscandian
0.00% French
0.01% Iberian
0.00% Indo-Chinese
0.00% Italian
0.00% Malayan
0.00% Near_Eastern
0.00% North_African
8.99% North_Atlantic
0.00% North_Caucasian
13.25% North_Sea
0.00% Northeast_African
0.00% Oceanian
0.00% Omotic
0.00% Pygmy
0.00% Siberian
0.00% South_Asian
0.00% South_Central_Asian
0.00% South_Chinese
0.00% Volga-Ural
0.00% West_African
0.00% West_Caucasian
0.00% West_Med

This Loschbour sample is very similar to La Braña. They both represent Western European Hunter-Gathers (WHG).


Mesolithic Sweden (Motala6, U5a2, c. 5750 BCE)

0.00% Amerindian
0.00% Arabian
0.00% Armenian
0.00% Basque
0.00% Central_African
5.95% Central_Euro
0.00% East_African
0.00% East_Asian
0.00% East_Balkan
0.00% East_Central_Asian
43.70% East_Central_Euro
0.00% East_Med
2.31% Eastern_Euro
10.01% Fennoscandian
0.00% French
0.00% Iberian
0.00% Indo-Chinese
0.00% Italian
0.00% Malayan
0.00% Near_Eastern
0.00% North_African
19.59% North_Atlantic
0.00% North_Caucasian
18.44% North_Sea
0.00% Northeast_African
0.00% Oceanian
0.00% Omotic
0.00% Pygmy
0.00% Siberian
0.00% South_Asian
0.00% South_Central_Asian
0.00% South_Chinese
0.00% Volga-Ural
0.00% West_African
0.00% West_Caucasian
0.00% West_Med

Another proof that the K36 component names were seriously mislabelled. Mesolithic Scandinavians didn't have a lot of Fennoscandian but rather East_Central_Euro , North_Atlantic and North_Sea. The only difference with the Mesolithic Spaniard above is the absence of 'Basque', which appears to be a specifically SW European Mesolithic component (perhaps associated with mtDNA H1?).


Pitted Ware / Late Mesolithic Sweden (Ajvide58, I2a1, U4d, c. 2400 BCE)

0.73% Amerindian
0.00% Arabian
0.00% Armenian
4.34% Basque
0.00% Central_African
3.69% Central_Euro
0.00% East_African
0.00% East_Asian
0.00% East_Balkan
0.00% East_Central_Asian
17.85% East_Central_Euro
0.00% East_Med
14.34% Eastern_Euro
26.12% Fennoscandian
5.40% French
0.17% Iberian
0.00% Indo-Chinese
0.00% Italian
0.00% Malayan
0.00% Near_Eastern
0.00% North_African
7.92% North_Atlantic
0.00% North_Caucasian
19.45% North_Sea
0.00% Northeast_African
0.00% Oceanian
0.00% Omotic
0.00% Pygmy
0.00% Siberian
0.00% South_Asian
0.00% South_Central_Asian
0.00% South_Chinese
0.00% Volga-Ural
0.00% West_African
0.00% West_Caucasian
0.00% West_Med

This sample is over 3000 years younger than the other Mesolithic samples above. It is contemporary to the last Megalithic cultures in western Europe and Early Bronze Age in central and eastern Europe, as well as in southern Scandinavia (Battle-Axe culture). Yet it does not show any sign of intermingling with either Neolithic farmers or Bronze Age Steppe invaders. Autosomally it is intermediary between WHG (Mesolithic Western Europe) and SHG (Mesolithic Scandinavia). It possess both the French and Central_Euro components found in all later Scandinavians, but absent from WHG and from the Yamna culture.


Early Neolithic European (LBK Stuttgart, T2c1b, c. 5150 BCE)

0.00% Amerindian
1.59% Arabian
0.00% Armenian
0.00% Basque
0.00% Central_African
0.00% Central_Euro
0.00% East_African
0.00% East_Asian
2.66% East_Balkan
0.00% East_Central_Asian
0.00% East_Central_Euro
14.83% East_Med
0.00% Eastern_Euro
0.00% Fennoscandian
0.00% French
16.23% Iberian
0.00% Indo-Chinese
34.79% Italian
0.00% Malayan
0.65% Near_Eastern
2.42% North_African
0.00% North_Atlantic
0.00% North_Caucasian
0.00% North_Sea
0.00% Northeast_African
0.00% Oceanian
0.00% Omotic
0.00% Pygmy
0.00% Siberian
0.00% South_Asian
0.00% South_Central_Asian
0.00% South_Chinese
0.00% Volga-Ural
0.00% West_African
0.00% West_Caucasian
26.82% West_Med


We've got some completely different admixture here, including a bit of Arabian, Near_Eastern and North_African. But the components in this genome match mostly southern European regions in the K36 labels (once again, it doesn't indicate the place of origin).

Let's also check Dodecad K12b

0.00% Gedrosia
0.00% Siberian
3.78% Northwest_African
0.06% Southeast_Asian
54.87% Atlantic_Med
0.23% North_European
0.00% South_Asian
0.00% East_African
10.80% Southwest_Asian
0.00% East_Asian
30.26% Caucasus
0.00% Sub_Saharan


So far the French component is at 0% in Mesolithic, Neolithic and Yamna samples. Where could it have come from? Another distinct Mesolithic population?

[Maciamo]

For the sake of comparison, here is the K36 run for the Mal'ta boy from Siberia, who belonged to Y-haplogroup R* and mt-haplogroup U*.

Palaeolithic Siberia/Baikal (MA1, R*, U*, c. 22,000 BCE)

17.78% Amerindian
0.00% Arabian
0.00% Armenian
0.00% Basque
0.00% Central_African
0.00% Central_Euro
0.00% East_African
0.00% East_Asian
0.00% East_Balkan
0.00% East_Central_Asian
4.67% East_Central_Euro
0.00% East_Med
17.68% Eastern_Euro
21.63% Fennoscandian
0.00% French
0.00% Iberian
0.00% Indo-Chinese
0.00% Italian
0.00% Malayan
0.00% Near_Eastern
0.00% North_African
0.00% North_Atlantic
0.00% North_Caucasian
0.29% North_Sea
0.00% Northeast_African
0.00% Oceanian
0.00% Omotic
0.02% Pygmy
0.00% Siberian
8.75% South_Asian
22.77% South_Central_Asian
0.00% South_Chinese
6.18% Volga-Ural
0.22% West_African
0.00% West_Caucasian
0.00% West_Med


It's pretty much the same components as the Yamna genomes with different proportions (considerably higher Amerindian and South_Asian). But it lacks the North_Caucasus, Central_Euro, North_Atlantic and practically all the North_Sea admixtures.

[Maciamo]

Here is a genome from Late Neolithic Sweden. It is from the Funnelbeaker culture, which actually was seen as a contact zone between Neolithic and Mesolithic populations. It was also hypothesised that Neolithic farmers increasingly reverted to hunting and fishing to get their food as crops failed in the cold climate of Scandinavia. This genomes doesn't show any trace of Mesolithic European except for the Basque component (which could be a hybrid of Neolithic-Mesolithic in itself, and therefore would not necessarily contain any Mesolithic ancestry in this case).

Funnelbeaker (Gökhem7, mtDNA H, c. 3000 BCE Sweden)

Eurogenes K36

0.00% Amerindian
0.00% Arabian
0.00% Armenian
28.21% Basque
0.00% Central_African
0.00% Central_Euro
0.00% East_African
0.00% East_Asian
15.66% East_Balkan
0.00% East_Central_Asian
0.00% East_Central_Euro
0.00% East_Med
0.00% Eastern_Euro
0.00% Fennoscandian
0.00% French
24.60% Iberian
0.00% Indo-Chinese
0.01% Italian
0.00% Malayan
0.00% Near_Eastern
0.00% North_African
0.00% North_Atlantic
0.00% North_Caucasian
0.00% North_Sea
0.00% Northeast_African
0.00% Oceanian
3.60% Omotic
0.00% Pygmy
0.00% Siberian
0.00% South_Asian
0.00% South_Central_Asian
0.00% South_Chinese
0.00% Volga-Ural
0.00% West_African
0.00% West_Caucasian
27.92% West_Med

Running the Dodecad dv3 calculator, this genome shows 8.38% of Northwest_African and 2.14% of Palaeo_African, which are probably reflected in the West_Med and Omotic above, respectively. The rest is 45% West_European and 44.5% Mediterranean.

Using the K12b calculator, Görkhem7 shows 4.77% of Sub_Saharan and 6.75% of Northwest_African. All these African admixtures have completely disappeared in modern Scandinavians, although some of it remained at least until the Late Iron Age.

Just to be sure that this sample is representative, I ran another Funnelbeaker individual.

Funnelbeaker (Gökhem3, mtDNA H1c, c. 3000 BCE Sweden)

Eurogenes K36

0.00% Amerindian 0.00% Arabian
0.00% Armenian
1.82% Basque
0.00% Central_African
0.56% Central_Euro
0.00% East_African
0.00% East_Asian
3.79% East_Balkan
0.00% East_Central_Asian
0.05% East_Central_Euro
0.00% East_Med
0.00% Eastern_Euro
0.00% Fennoscandian
6.78% French
39.24% Iberian
0.00% Indo-Chinese
14.74% Italian
0.00% Malayan
0.00% Near_Eastern
1.36% North_African
0.36% North_Atlantic
0.00% North_Caucasian
6.74% North_Sea
0.00% Northeast_African
0.18% Oceanian
0.00% Omotic
0.00% Pygmy
0.00% Siberian
0.00% South_Asian
0.00% South_Central_Asian
0.00% South_Chinese
0.00% Volga-Ural
0.00% West_African
0.00% West_Caucasian
24.38% West_Med

Gökhem3 show about 14% of Mesolithic European admixture (North_Sea, North_Atlantic, French and Central_Euro). It's interesting because those Mesolithic components include French and Central_Euro, two components that are not found in WHG or in Steppe people and appears to be exclusively central-north Europe (Central Europe and Scandinavia) and could be linked to Y-haplogroup I1, which so far has never been found outside that region before the Germanic migrations of the Iron Age.


Dodecad dv3 (aka K12)


1.96% East_European
38.39% West_European
50.33% Mediterranean
1.19% Neo_African
0.00% West_Asian
0.00% South_Asian
0.00% Northeast_Asian
0.34% Southeast_Asian
0.00% East_African
2.68% Southwest_Asian
4.26% Northwest_African
0.85% Palaeo_African


Whereas Gökhem7 had 10.5% of African admixture, Gökhem3 has 6.3% - lower but still very high.

Dodecad K12b

0.00% Gedrosia
0.00% Siberian
3.94% Northwest_African
0.01% Southeast_Asian
61.16% Atlantic_Med
19.92% North_European
0.34% South_Asian
0.00% East_African
4.36% Southwest_Asian
0.27% East_Asian
8.28% Caucasus
1.73% Sub_Saharan

Same observation here. Gökhem7 had 11.5% of African admixture with the K12b calculator, and Gökhem3 has 5.7%. The Northwest African is always about twice higher than the Sub-Saharan African. The North European is higher, confirming the higher Mesolithic admixture found in K36.

[Maciamo]

Here is a sample from Early Neolithic Hungary.


Alföld Linear Pottery culture (NE1, U5b2c, c. 5200 BCE)

Eurogenes K36

0.00% Amerindian
4.52% Arabian
0.60% Armenian
3.45% Basque
0.00% Central_African
0.00% Central_Euro
0.00% East_African
0.00% East_Asian
5.06% East_Balkan
0.00% East_Central_Asian
0.00% East_Central_Euro
13.65% East_Med
0.00% Eastern_Euro
0.00% Fennoscandian
0.00% French
13.93% Iberian
0.00% Indo-Chinese
32.62% Italian
0.00% Malayan
1.59% Near_Eastern
0.82% North_African
0.00% North_Atlantic
0.00% North_Caucasian
0.00% North_Sea
0.00% Northeast_African
0.00% Oceanian
0.00% Omotic
0.00% Pygmy
0.00% Siberian
0.00% South_Asian
0.00% South_Central_Asian
0.00% South_Chinese
0.00% Volga-Ural
0.00% West_African
0.00% West_Caucasian
23.75% West_Med


Dodecad dv3 (aka K12)

1.58% East_European
18.85% West_European
55.22% Mediterranean
0.15% Neo_African
9.93% West_Asian
0.00% South_Asian
0.00% Northeast_Asian
0.00% Southeast_Asian
0.00% East_African
11.13% Southwest_Asian
3.08% Northwest_African
0.06% Palaeo_African

The only modern population with as much as 55% of Mediterranean are the Sardinians, but they have 11% more West European, 5% less West Asian and 5% less Southwest Asian than this Hungarian Neolithic farmer.

Dodecad K12b

0.00% Gedrosia
0.00% Siberian
2.82% Northwest_African
0.00% Southeast_Asian
49.91% Atlantic_Med
4.66% North_European
0.00% South_Asian
0.00% East_African
12.89% Southwest_Asian
0.00% East_Asian
29.69% Caucasus
0.04% Sub_Saharan

No modern population is similar. At K12b this sample looks like a blend between North Italian and Moroccan Jew.

[Maciamo]

Here are genomes from Mesolithic Karelia and Samara in Russia. Both genomes are very similar and are essentially like Yamna without the North_Caucasian and South_Central_Asian. Both of them nevertheless have 8-10% of Gedrosia at K12b, so not all Gedrosia necessarily comes from the Caucasus or the Iranian plateau.

Mesolithic Samara (I0124, R1b, U5a, c. 5600 BCE)

Eurogenes K36

7.77% Amerindian
0.00% Arabian
0.00% Armenian
0.00% Basque
0.00% Central_African
0.00% Central_Euro
0.00% East_African
0.00% East_Asian
0.00% East_Balkan
0.00% East_Central_Asian
25.82% East_Central_Euro
0.00% East_Med
17.10% Eastern_Euro
35.88% Fennoscandian
0.00% French
0.00% Iberian
0.00% Indo-Chinese
0.00% Italian
0.00% Malayan
0.00% Near_Eastern
0.00% North_African
0.18% North_Atlantic
0.00% North_Caucasian
11.72% North_Sea
0.00% Northeast_African
0.00% Oceanian
0.00% Omotic
0.00% Pygmy
0.00% Siberian
0.00% South_Asian
0.00% South_Central_Asian
0.00% South_Chinese
1.53% Volga-Ural
0.00% West_African
0.00% West_Caucasian
0.00% West_Med


Dodecad dv3 (aka K12)

35.75% East_European
53.50% West_European
0.00% Mediterranean
0.00% Neo_African
0.00% West_Asian
3.59% South_Asian
7.17% Northeast_Asian
0.00% Southeast_Asian
0.00% East_African
0.00% Southwest_Asian
0.00% Northwest_African
0.00% Palaeo_African

Dodecad K12b

10.33% Gedrosia
7.14% Siberian
0.00% Northwest_African
0.00% Southeast_Asian
0.00% Atlantic_Med
82.52% North_European
0.00% South_Asian
0.00% East_African
0.00% Southwest_Asian
0.00% East_Asian
0.00% Caucasus



Mesolithic Karelia (I0061, R1a, C1g, c. 6400 BCE)

Eurogenes K36

13.05% Amerindian
0.00% Arabian
0.00% Armenian
0.00% Basque
0.00% Central_African
0.00% Central_Euro
0.00% East_African
0.00% East_Asian
0.00% East_Balkan
0.00% East_Central_Asian
9.24% East_Central_Euro
0.00% East_Med
23.30% Eastern_Euro
32.82% Fennoscandian
0.00% French
0.00% Iberian
0.00% Indo-Chinese
0.00% Italian
0.00% Malayan
0.00% Near_Eastern
0.00% North_African
6.92% North_Atlantic
0.00% North_Caucasian
5.07% North_Sea
0.00% Northeast_African
0.00% Oceanian
0.00% Omotic
0.00% Pygmy
0.00% Siberian
0.00% South_Asian
0.00% South_Central_Asian
0.00% South_Chinese
9.60% Volga-Ural
0.00% West_African
0.00% West_Caucasian
0.00% West_Med


Dodecad dv3 (aka K12)

33.31% East_European
52.37% West_European
0.00% Mediterranean
0.00% Neo_African
0.00% West_Asian
2.26% South_Asian
11.67% Northeast_Asian
0.29% Southeast_Asian
0.00% East_African
0.00% Southwest_Asian
0.00% Northwest_African
0.10% Palaeo_African


Dodecad K12b

8.62% Gedrosia
11.10% Siberian
0.00% Northwest_African
0.00% Southeast_Asian
0.00% Atlantic_Med
80.13% North_European
0.01% South_Asian
0.00% East_African
0.00% Southwest_Asian
0.00% East_Asian
0.00% Caucasus
0.14% Sub_Saharan

[Maciamo]

Here is a genome from Early Neolithic Hungary. One surprising thing with this genome is that it doesn't show any sign of intermingling with Near Eastern Neolithic newcomers at all. In fact, the skeleton was found to have been tossed with in the village's waste and did not have a proper burial like other village members. This is surely a sign that this was not a member of the community, but an outsider, either a killed enemy or a slave. Therefore, even though this sample is classified as Neolithic, it is representative of a Mesolithic Hungarian.

Körös culture (KO1, I2a, R3, c. 5700 BCE Hungary)

Eurogenes K36

0.00% Amerindian
0.00% Arabian
0.00% Armenian
5.18% Basque
0.00% Central_African
0.01% Central_Euro
0.00% East_African
0.00% East_Asian
0.00% East_Balkan
0.00% East_Central_Asian
29.80% East_Central_Euro
0.00% East_Med
2.86% Eastern_Euro
32.63% Fennoscandian
0.02% French
0.00% Iberian
0.00% Indo-Chinese
0.00% Italian
0.00% Malayan
0.00% Near_Eastern
0.00% North_African
9.98% North_Atlantic
0.00% North_Caucasian
19.54% North_Sea
0.00% Northeast_African
0.00% Oceanian
0.00% Omotic
0.00% Pygmy
0.00% Siberian
0.00% South_Asian
0.00% South_Central_Asian
0.00% South_Chinese
0.00% Volga-Ural
0.00% West_African
0.00% West_Caucasian
0.00% West_Med

This admixture looks identical to a Steppe Proto-Indo-European from Yamna, but without the North_Caucasian and South_Central_Asian components. Like Afanasievo and Yamna it lacks the Central_Euro component, otherwise found in all Mesolithic Scandinavians and Corded Ware people. Like Yamna samples, it also lacks the French component found in Corded Ware and Sintashta. The Eastern_Euro is lower than in Yamna. This sample shows what Mesolithic Steppe people must have been liked autosomally before the arrival of Neolithic cattle herders from the South Caucasus or northern Iran.


Dodecad dv3 (aka K12)


31.67% East_European
67.44% West_European
0.61% Mediterranean
0.13% Neo_African
0.00% West_Asian
0.00% South_Asian
0.00% Northeast_Asian
0.00% Southeast_Asian
0.00% East_African
0.00% Southwest_Asian
0.15% Northwest_African
0.00% Palaeo_African

With a complete lack of Mediterranean and West_Asian, this sample is closest to a modern Finn, although Finns do have 8% of Mediterranean.


Dodecad K12b

0.00% Gedrosia
0.00% Siberian
0.00% Northwest_African
0.12% Southeast_Asian
25.13% Atlantic_Med
74.74% North_European
0.00% South_Asian
0.00% East_African
0.00% Southwest_Asian
0.00% East_Asian
0.00% Caucasus
0.00% Sub_Saharan

Similarly high levels of North_European as modern Finns and Lithuanians, but this KO1 has more Atlantic_Med and lacks the Caucasus and Southwest_Asian found in East Baltic people.

[Maciamo]

Early Neolithic Spain (I0410, R1b-V88, T2c1d, c. 5200 BCE)

Eurogenes K36

0.00% Amerindian
0.00% Arabian
0.00% Armenian
6.61% Basque
0.00% Central_African
0.00% Central_Euro
0.00% East_African
0.00% East_Asian
0.00% East_Balkan
0.00% East_Central_Asian
0.00% East_Central_Euro
0.02% East_Med
0.00% Eastern_Euro
0.00% Fennoscandian
0.00% French
31.06% Iberian
0.00% Indo-Chinese
19.93% Italian
0.00% Malayan
0.00% Near_Eastern
1.15% North_African
0.00% North_Atlantic
0.00% North_Caucasian
0.00% North_Sea
0.00% Northeast_African
0.00% Oceanian
0.00% Omotic
0.00% Pygmy
0.00% Siberian
0.00% South_Asian
0.00% South_Central_Asian
0.00% South_Chinese
0.00% Volga-Ural
0.00% West_African
0.00% West_Caucasian
41.22% West_Med


Dodecad dv3 (aka K12)

0.00% East_European
22.27% West_European
69.29% Mediterranean
0.00% Neo_African
0.02% West_Asian
0.00% South_Asian
0.00% Northeast_Asian
0.00% Southeast_Asian
0.00% East_African
4.72% Southwest_Asian
3.69% Northwest_African
0.01% Palaeo_African

Dodecad K12b

0.00% Gedrosia
0.00% Siberian
2.11% Northwest_African
0.00% Southeast_Asian
77.44% Atlantic_Med
0.00% North_European
0.00% South_Asian
0.00% East_African
5.94% Southwest_Asian
0.00% East_Asian
14.47% Caucasus
0.04% Sub_Saharan