The genomic history of the Aegean palatial civilizations.

[Philjames100]

Any idea why these results seem to be different to the PCA and other results?



Figure S4 Genetic affinities between BA Aegeans compared to other present-day Eurasian populations.

For each case, we show the geographic distribution of f3 (warmer colors represent greater sharing between populations X and Y).

Beside each map, we plot the f3 values for the 15 populations that are most closely related to each of the populations in Y.

[Angela]

I actually agree with most what you've said, but you sometimes misunderstand what I try to bring across. Why you, me and others here, are befuddled is the fact, that the skin color prediction doesn't match the accounts of Ancient Greeks about their coloration. Nobody here would be surprised about this result if the Ancient Greeks would claim they were as dark as the Ethiopians or compared themselves to them. Ancient Greeks saw super pale Northern Europeans, moderately dark Egyptians and extremely dark Ethiopians. Hence, they were well aware of all the shades and hues of all kinds of people. They took dark to very dark, and pale to very pale people as an example, to stress their intermediate complexion. Plus, the Greeks talked about their females and Barbarians being pale/white. So, I'm discussing with you and others here because I try to connect the dots, thus make sense out the fact, that there is a discrepancy between the self-description of the Ancient Greeks in terms of their complexion and the result from this study.

I agree, although if you go and look at the Hirisplex examples of their skin shade system, dark is not very dark.

Still, as I said, I agree.

[Angela]

Any idea why these results seem to be different to the PCA and other results?



Figure S4 Genetic affinities between BA Aegeans compared to other present-day Eurasian populations.

For each case, we show the geographic distribution of f3 (warmer colors represent greater sharing between populations X and Y).

Beside each map, we plot the f3 values for the 15 populations that are most closely related to each of the populations in Y.

This is an F3 analysis, not admixture. I provided a link which explains the differences between F3, F4 etc. Given that Log 4 is about 50% steppe, someplace like England or Germany or Norway does make more sense to me.

[Angela]

Why is the word *** censored? "***mentation"

Inviato dal mio POT-LX1T utilizzando Tapatalk

Because the woke idiots have taken control of google and most platforms. Good luck trying to find a paper on population genetics with regard to ***mentation on google. They're censored.

I've switched to Bing, but who knows how long they'll remain sane.

[Philjames100]

This is an F3 analysis, not admixture. I provided a link which explains the differences between F3, F4 etc. Given that Log 4 is about 50% steppe, someplace like England or Germany or Norway does make more sense to me.

So do you think f3 is more accurate in this case?


'Outgroup F3 statistics are a measure of how closely two populations are related with each other... It is thus a similarity measure: The higher the statistic, the more genetically similar A and B are to one another.'

https://compvar-workshop.readthedocs...s/f3stats.html

[Jovialis]

Any idea why these results seem to be different to the PCA and other results?



Figure S4 Genetic affinities between BA Aegeans compared to other present-day Eurasian populations.

For each case, we show the geographic distribution of f3 (warmer colors represent greater sharing between populations X and Y).

Beside each map, we plot the f3 values for the 15 populations that are most closely related to each of the populations in Y.

Here is their genetic distance, which does seem very far.

Distance to:	MBA_Helladic_Logkas:Log04
26.07227071	Scottish
43.55175427	Lithuanian

[Cato]

Because the woke idiots have taken control of google and most platforms. Good luck trying to find a paper on population genetics with regard to ***mentation on google. They're censored.

I've switched to Bing, but who knows how long they'll remain sane.

Thanks

Inviato dal mio POT-LX1T utilizzando Tapatalk

[Jovialis]

Here is their genetic distance, which does seem very far.

Distance to:	MBA_Helladic_Logkas:Log04
26.07227071	Scottish
43.55175427	Lithuanian

Eurogenes K13 shows similar results:

Distance to:	Log04_Helladic-Logkas-MBA
30.98066655	Scottish
42.89642992	Lithuanian

[Jovialis]

Here is Log04 using the Ancient Ethnicities Analyzer sample sets for Dodecad K12b. I have omitted EMBA_Greece, since it is a average with the sample in and of itself in it. I also only used samples prior to the Bronze Age:

Distance to:	MBA_Helladic_Logkas:Log04
4.05551446	49.20% Minoan_Greece_(n=10) + 50.80% Western_Corded_Ware_(n=17)
4.32742922	30.80% Chalcolithic_Anatolia_(n=35) + 69.20% Bell_Beaker_Bavaria/Saxony_(n=20)
4.35235309	28.20% Chalcolithic_Anatolia_(n=35) + 71.80% Bell_Beaker_Poland_(n=6)
4.42282822	57.80% MN_Westphalia_(Megalithic_Wartberg)_(n=6) + 42.20% Chalcolithic_Northwest_Caucasus_(n=3)
4.79227742	55.60% MN_Westphalia_(Megalithic_Wartberg)_(n=6) + 44.40% Kura-Araxes_culture_(n=8)
4.83485120	49.60% Early_Neolithic_Anatolia_(n=7) + 50.40% Western_Corded_Ware_(n=17)
4.84387292	55.60% Minoan_Greece_(n=10) + 44.40% Eastern_Corded_Ware_(n=8)
4.87434178	49.40% Early_Neolithic_Greece_(n=3) + 50.60% Western_Corded_Ware_(n=17)
5.14965055	34.20% Chalcolithic_Anatolia_(n=35) + 65.80% Bell_Beaker_Czechia_(n=15)
5.19833457	55.80% Early_Neolithic_Greece_(n=3) + 44.20% Eastern_Corded_Ware_(n=8)
5.46720224	20.40% Chalcolithic_Anatolia_(n=35) + 79.60% Bell_Beaker_Hungary_(n=6)
5.71054814	47.40% Minoan_Greece_(n=10) + 52.60% Battle-Axe_culture_(n=3)
5.71379690	56.00% Early_Neolithic_Anatolia_(n=7) + 44.00% Eastern_Corded_Ware_(n=8)
5.78136591	31.60% Chalcolithic_North_Levant_(n=6) + 68.40% Bell_Beaker_Bavaria/Saxony_(n=20)
5.79376873	32.60% Chalcolithic_Anatolia_(n=35) + 67.40% Bell_Beaker_Gaul_(n=13)
5.96151263	17.80% Chalcolithic_Northwest_Caucasus_(n=3) + 82.20% Bell_Beaker_Hungary_(n=6)
6.00558714	27.40% Chalcolithic_Azerbaijan_(n=4) + 72.60% Bell_Beaker_Poland_(n=6)
6.02101976	63.80% Pre-Pottery_Neolithic_Anatolia_(n=8) + 36.20% Khvalynsk_culture_(n=3)
6.04999866	35.20% Chalcolithic_North_Levant_(n=6) + 64.80% Bell_Beaker_Czechia_(n=15)
6.38082750	81.00% Bell_Beaker_Hungary_(n=6) + 19.00% Kura-Araxes_culture_(n=8)
6.38690853	34.00% Mesolithic_Volga-Ural_(n=2) + 66.00% Pre-Pottery_Neolithic_Anatolia_(n=8)
6.39897383	59.40% Pre-Pottery_Neolithic_Anatolia_(n=8) + 40.60% Yamna_culture_(n=16)
6.54373606	48.00% Early_Neolithic_Anatolia_(n=7) + 52.00% Battle-Axe_culture_(n=3)
6.55968204	19.40% Chalcolithic_Azerbaijan_(n=4) + 80.60% Bell_Beaker_Hungary_(n=6)
6.60249184	53.60% Bell_Beaker_Netherlands_(n=7) + 46.40% Minoan_Greece_(n=10)

[Jovialis]

Here is Log02 using the same parameters:

Distance to:	MBA_Helladic_Logkas:Log02
2.48578595	28.60% Neolithic_Ukraine_(n=12) + 71.40% Minoan_Greece_(n=10)
2.54935225	29.60% Mesolithic_Baltic_Scandinavia_(SHG)_(n=31) + 70.40% Minoan_Greece_(n=10)
2.67591254	28.40% Mesolithic_Ukraine_(n=7) + 71.60% Minoan_Greece_(n=10)
3.14827590	30.20% Neolithic_Latvia_(n=4) + 69.80% Minoan_Greece_(n=10)
3.37486853	30.20% Neolithic_Lithuania_Narva_culture_(n=4) + 69.80% Minoan_Greece_(n=10)
3.99730565	32.00% Mesolithic_Balkans_HG_(n=43) + 68.00% Minoan_Greece_(n=10)
4.12687861	27.40% Mesolithic_Northwest_Russia_(n=4) + 72.60% Early_Neolithic_Greece_(n=3)
4.22228530	27.40% Mesolithic_Northwest_Russia_(n=4) + 72.60% Minoan_Greece_(n=10)
4.27831093	28.20% Mesolithic_Ukraine_(n=7) + 71.80% Early_Neolithic_Greece_(n=3)
4.46740777	72.00% Early_Neolithic_Anatolia_(n=7) + 28.00% Neolithic_Ukraine_(n=12)
4.51630287	29.00% Mesolithic_Baltic_Scandinavia_(SHG)_(n=31) + 71.00% Early_Neolithic_Anatolia_(n=7)
4.54172493	27.80% Mesolithic_Ukraine_(n=7) + 72.20% Early_Neolithic_Anatolia_(n=7)
4.57468244	71.40% Early_Neolithic_Greece_(n=3) + 28.60% Neolithic_Ukraine_(n=12)
4.79669019	27.80% Mesolithic_Volga-Ural_(n=2) + 72.20% Early_Neolithic_Greece_(n=3)
4.96434435	70.40% Early_Neolithic_Anatolia_(n=7) + 29.60% Neolithic_Lithuania_Narva_culture_(n=4)
5.13790525	29.40% Mesolithic_Baltic_Scandinavia_(SHG)_(n=31) + 70.60% Early_Neolithic_Greece_(n=3)
5.26229683	27.80% Mesolithic_Volga-Ural_(n=2) + 72.20% Minoan_Greece_(n=10)
5.35003628	26.80% Mesolithic_Northwest_Russia_(n=4) + 73.20% Early_Neolithic_Anatolia_(n=7)
5.37347791	66.20% Minoan_Greece_(n=10) + 33.80% Eastern_Corded_Ware_(n=8)
5.38487045	70.60% Early_Neolithic_Anatolia_(n=7) + 29.40% Neolithic_Latvia_(n=4)
5.42140579	48.80% Chalcolithic_North_Levant_(n=6) + 51.20% Bell_Beaker_Czechia_(n=15)
5.48576804	70.00% Early_Neolithic_Greece_(n=3) + 30.00% Neolithic_Latvia_(n=4)
5.57399731	31.40% Mesolithic_Balkans_HG_(n=43) + 68.60% Early_Neolithic_Anatolia_(n=7)
5.60900699	46.80% MN_Westphalia_(Megalithic_Wartberg)_(n=6) + 53.20% Chalcolithic_Anatolia_(n=35)
5.67090951	61.40% Minoan_Greece_(n=10) + 38.60% Western_Corded_Ware_(n=17)

[Jovialis]

Finally, here is the Early Bronze Age Helladic:

Distance to:	EBA_Helladic_Manika:Mik15
1.61010098	92.40% Early_Neolithic_Anatolia_(n=7) + 7.60% Chalcolithic_Iberia_(n=62)
1.62160649	91.20% Early_Neolithic_Anatolia_(n=7) + 8.80% Megalithic_Europe_(n=24)
1.63866104	90.00% Early_Neolithic_Anatolia_(n=7) + 10.00% Chalcolithic_BB_Sardinia_(n=10)
1.65156217	92.00% Early_Neolithic_Anatolia_(n=7) + 8.00% Neolithic_Britain_(n=62)
1.65234286	92.60% Early_Neolithic_Anatolia_(n=7) + 7.40% Bell_Beaker_Iberia_(n=11)
1.67178106	91.00% Early_Neolithic_Anatolia_(n=7) + 9.00% Late_Neolithic_Switzerland_(n=58)
1.72194235	92.00% Early_Neolithic_Anatolia_(n=7) + 8.00% Middle_Late_Neolithic_Spain_(n=12)
1.73119949	90.20% Early_Neolithic_Anatolia_(n=7) + 9.80% Middle_Neolithic_France_(n=19)
1.78939834	92.40% Early_Neolithic_Anatolia_(n=7) + 7.60% Globular_Amphora_culture_(n=6)
1.85073255	85.40% Early_Neolithic_Anatolia_(n=7) + 14.60% Late_Chalcolithic_Baden_culture_(n=14)
1.87866617	4.00% Epipaleolithic_Magreb_(Iberomaurusians)_(n=5) + 96.00% Early_Neolithic_Greece_(n=3)
1.88288829	92.20% Early_Neolithic_Anatolia_(n=7) + 7.80% CA_Remedello_culture_(n=3)
2.02275718	91.20% Early_Neolithic_Anatolia_(n=7) + 8.80% Middle_Neolithic_Sardinia_(n=10)
2.03488753	80.60% Early_Neolithic_Anatolia_(n=7) + 19.40% Early_Neolithic_Starcevo_culture_(n=8)
2.04197772	84.60% Early_Neolithic_Anatolia_(n=7) + 15.40% EN_Alfold_Linear_Pottery_culture_(n=20)
2.04488044	80.00% Early_Neolithic_Anatolia_(n=7) + 20.00% LN_Lengyel_culture_(n=8)
2.05656394	84.60% Early_Neolithic_Anatolia_(n=7) + 15.40% Middle_Neolithic_Sicily_(n=10)
2.05715270	89.40% Early_Neolithic_Anatolia_(n=7) + 10.60% Cucuteni-Trypillian_culture_(n=4)
2.09633678	84.40% Early_Neolithic_Anatolia_(n=7) + 15.60% Middle_Chalcolithic_Hungary_(n=9)
2.10271711	77.80% Early_Neolithic_Anatolia_(n=7) + 22.20% Chalcolithic_Bulgaria_(n=9)
2.13077473	92.00% Early_Neolithic_Anatolia_(n=7) + 8.00% Early_Neolithic_Spain_(n=10)
2.19451927	21.80% Pre-Pottery_Neolithic_Anatolia_(n=8) + 78.20% Early_Neolithic_Anatolia_(n=7)
2.27480436	83.80% Early_Neolithic_Anatolia_(n=7) + 16.20% Early_Neolithic_Italy_(n=10)
2.28583847	95.00% Early_Neolithic_Anatolia_(n=7) + 5.00% MN_Westphalia_(Megalithic_Wartberg)_(n=6)
2.31740703	83.40% Early_Neolithic_Anatolia_(n=7) + 16.60% LN_Tisza-Sopot_culture_(n=11)

[Archetype0ne]

Here is Log02 using the same parameters:

Distance to:	MBA_Helladic_Logkas:Log02
2.48578595	28.60% Neolithic_Ukraine_(n=12) + 71.40% Minoan_Greece_(n=10)
2.54935225	29.60% Mesolithic_Baltic_Scandinavia_(SHG)_(n=31) + 70.40% Minoan_Greece_(n=10)
2.67591254	28.40% Mesolithic_Ukraine_(n=7) + 71.60% Minoan_Greece_(n=10)
3.14827590	30.20% Neolithic_Latvia_(n=4) + 69.80% Minoan_Greece_(n=10)
3.37486853	30.20% Neolithic_Lithuania_Narva_culture_(n=4) + 69.80% Minoan_Greece_(n=10)
3.99730565	32.00% Mesolithic_Balkans_HG_(n=43) + 68.00% Minoan_Greece_(n=10)
4.12687861	27.40% Mesolithic_Northwest_Russia_(n=4) + 72.60% Early_Neolithic_Greece_(n=3)
4.22228530	27.40% Mesolithic_Northwest_Russia_(n=4) + 72.60% Minoan_Greece_(n=10)
4.27831093	28.20% Mesolithic_Ukraine_(n=7) + 71.80% Early_Neolithic_Greece_(n=3)
4.46740777	72.00% Early_Neolithic_Anatolia_(n=7) + 28.00% Neolithic_Ukraine_(n=12)
4.51630287	29.00% Mesolithic_Baltic_Scandinavia_(SHG)_(n=31) + 71.00% Early_Neolithic_Anatolia_(n=7)
4.54172493	27.80% Mesolithic_Ukraine_(n=7) + 72.20% Early_Neolithic_Anatolia_(n=7)
4.57468244	71.40% Early_Neolithic_Greece_(n=3) + 28.60% Neolithic_Ukraine_(n=12)
4.79669019	27.80% Mesolithic_Volga-Ural_(n=2) + 72.20% Early_Neolithic_Greece_(n=3)
4.96434435	70.40% Early_Neolithic_Anatolia_(n=7) + 29.60% Neolithic_Lithuania_Narva_culture_(n=4)
5.13790525	29.40% Mesolithic_Baltic_Scandinavia_(SHG)_(n=31) + 70.60% Early_Neolithic_Greece_(n=3)
5.26229683	27.80% Mesolithic_Volga-Ural_(n=2) + 72.20% Minoan_Greece_(n=10)
5.35003628	26.80% Mesolithic_Northwest_Russia_(n=4) + 73.20% Early_Neolithic_Anatolia_(n=7)
5.37347791	66.20% Minoan_Greece_(n=10) + 33.80% Eastern_Corded_Ware_(n=8)
5.38487045	70.60% Early_Neolithic_Anatolia_(n=7) + 29.40% Neolithic_Latvia_(n=4)
5.42140579	48.80% Chalcolithic_North_Levant_(n=6) + 51.20% Bell_Beaker_Czechia_(n=15)
5.48576804	70.00% Early_Neolithic_Greece_(n=3) + 30.00% Neolithic_Latvia_(n=4)
5.57399731	31.40% Mesolithic_Balkans_HG_(n=43) + 68.60% Early_Neolithic_Anatolia_(n=7)
5.60900699	46.80% MN_Westphalia_(Megalithic_Wartberg)_(n=6) + 53.20% Chalcolithic_Anatolia_(n=35)
5.67090951	61.40% Minoan_Greece_(n=10) + 38.60% Western_Corded_Ware_(n=17)

This might be a dumb question. But does Neolithic Ukraine have any steppe in it?

[Ailchu]

That's because modern Greeks are not that swarthy as people pretend them to be. The same goes for Italians or Spaniards. That said, if the phenotype prediction from this study is 100% correct, that would make BA Greeks a lot darker than regular Middle Easterners or North Africans. If I remember correctly there was a phenotype prediction for individuals from the Roman paper here, and they turned out not be particularly swarthy.

it would be a lot clearer if we had the genotypes. looked through the supplements but couldn't find them. if they were not homozygous for 45A2 their ***mentation probably was darker than regular modern people from near east.

[Jovialis]

This might be a dumb question. But does Neolithic Ukraine have any steppe in it?

Not a dumb question,

They fall between, EHG and WHG.

Steppe has a lot more CHG:



The Neolithic Transition in the Baltic Was Not Driven by Admixture with Early European Farmers - ScienceDirect

[Philjames100]

Eurogenes K13 shows similar results:

Distance to:	Log04_Helladic-Logkas-MBA
30.98066655	Scottish
42.89642992	Lithuanian

What do you think the reason is for the difference between these results and the f3 statistics in the paper?

[Angela]

It's there:

Attachment 12675

Click to enlarge.

[Jovialis]

What do you think the reason is for the difference between these results and the f3 statistics in the paper?

TBH, I am not familiar with that tool. It could be worth e-mailing the author to inquire.

[Philjames100]

It's there:

Attachment 12675

Click to enlarge.

Attachment doesn't work.

[Jovialis]

Attachment doesn't work.

[Duarte]

https://ars.els-cdn.com/content/imag...3706-mmc2.xlsx

[ThirdTerm]

The three BA samples carried SLC24A5 and SLC45A2 typical among modern Europeans today. However, these individuals also carried OCA2, which is common among East Asians, and ASIP, which is associated with darker skin color in African Americans. This may be why the study's authors reached the following conclusion.

Using genotype data, we predicted that Pta08, Kou01, and Log02 most likely had brown eyes, dark brown to black hair, and dark skin (Table S1; STAR Methods). These predictions match the visual representations of male individuals from BA wall paintings of Minoan Crete for hair and eye color. The eye and hair color predictions were similar to those from later periods of the Aegean BA (Lazaridis et al., 2017). Although the overall prediction for all three individuals was of dark skin, they also all carried alleles strongly associated with lighter skin color (rs1426654 in the gene SLC24A5, and rs16891982 in SLC45A2) (Mathieson et al., 2015).

[real expert]

it would be a lot clearer if we had the genotypes. looked through the supplements but couldn't find them. if they were not homozygous for 45A2 their ***mentation probably was darker than regular modern people from near east.

A smart person explained to me how and why the authors predicted the dark skin for the 3 samples.

Looking at the supplements, the studied ones (the EBA Kou01, Pta08 and MBA Log02) are AA on rs1426654 (SLC24A5) but CC and CG (overwhelmingly GG in contemporary Europeans) on rsrs16891982 (SLC45A2). But they checked other alleles that contribute to ***mentation as well, which the HIrisPLex model is based on. Check the Nuclear capture part of the supplement for more information. Either way, I believe that category implies dark-skinned by contemporary pan-European standards, obviously not by global standards.

[Ailchu]

The three BA samples carried SLC24A5 and SLC45A2 typical among modern Europeans today. However, these individuals also carried OCA2, which is common among East Asians, and ASIP, which is associated with darker skin color in African Americans. This may be why the study's authors reached the following conclusion.

if i understand it correctly, looking at the table of genotypes only 1 individual was heterozygous with the derived allele of SLC45A2 associated with light skin. the other 2 were homozygous with the ancestral allele.

[Ailchu]

A smart person explained to me how and why the authors predicted the dark skin for the 3 samples.

i could imagine their skin color might have been similar to what we find in egypt today. if there was still ongoing selection for light skin in greece because of the change in nutrition then it is also likely that there was a similar selection throughout the near east and north africa. so when the ancient greeks compared their skin color to the northern barbarians and the egyptians then probably we should consider that those 2 groups were also darker ***mented than modern ones.

[Gaska]

Phenotyping the ancient world: The physical appearance and ancestry of very degraded samples from a chalcolithic human remains-“Therefore, the aim of the present work was the molecular study of a very critical sample, a Chalcolithic (3480 ± 30 YBP) individual found in Asturias, Northern Iberia, intending to discover a possible geographical ancestry for these remains, and the inference of a group of feasible EVCs (hair, skin and iris ***mentation).Given that ancient DNA is often highly damaged, two different methodologies were used in order to determine the biogeographical ancestry of the individual: mitochondrial DNA (HVR-I and -II) and Single Nucleotide Polymorphisms typing. Despite the antiquity of the samples, the genetic information recovered proved of great value. We could determine that the individual had a European ancestry, blond hair, light skin color and brown eyes. Such outcome reveals that it is possible to obtain not only biogeographical but also phenotypic information from a very critical sample"

This sample comes from the Bronze Age in Asturias (northern Spain) and corresponds exactly to the Griffin warrior dating in Greece. As you can see, this gentleman had fair skin, blond hair and brown eyes, however we have a perfectly preserved mummy from the Argar culture (southeastern Spain) that was buried with his son (4-5 years old). Both have black hair with large braids that reached the waist in the case of the man- During the Bronze Age the phenotypes were very varied but light skin was already a fixed feature for all European regions