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Comparing Ancient Greek populations to modern Greeks and Italians

Idontknowwhatimdoing said:
9Fo3o2L.png

[FONT=&quot]
I7QjNRu.png
[/FONT]
Click to expand...
Could you run this model with the Early Iron Age messenia sample?
 
Thanks!

Here's my model with the Yamnaya_Samara average, which is supposed to be more of a standard for Yamna, as I've seen in papers. Though it doesn't seem to bring up the steppe in the case of Cypriots. Maybe it is being subsumed in the ARM BA sample?

pqOz5dq.png


At any rate, I have a favor to ask you.

Here are all of the samples I made averages out of that I am using for this model:

Code: 
Sidon_MBA:ERS1790729_lbancient6404153,8.64,0.24,4.87,0,10.59,0,0.3,2.53,29,0,43.59,0.23
Sidon_MBA:ERS1790730_lbancient6404154,9.7,0,4.69,0.47,14.49,0,0,0.97,26.57,0,42.56,0.55
Sidon_MBA:ERS1790731_lbancient6404155,4,0,6.87,0,15.42,0,0,3.11,30.06,1.97,38.32,0.24
Sidon_MBA:ERS1790732_lbancient6404156,7.64,0,5.13,0,14,0,0,2.81,28.8,0.01,41.26,0.35
Sidon_MBA:ERS1790733-lbancient6404159,7.18,0,3.37,1.97,9.94,0,1.67,2.45,28.41,0,45,0
Corded_Ware:RISE00:Allentoft_2015,10.49,0.15,0,0,31.63,56.79,0.94,0,0,0,0,0
Corded_Ware:RISE1:Allentoft_2015,9.53,2.23,0,0,20.52,67.27,0,0,0,0,0.46,0
Corded_Ware:RISE434:Allentoft_2015,15.93,0,0,0,23.21,60.04,0,0,0,0,0,0.82
Corded_Ware:RISE435:Allentoft_2015,1.49,0,0,0,21.13,68.03,0,0,0,0,9.36,0
Corded_Ware:RISE436:Allentoft_2015,4.85,0,0,0,33.39,44.75,0,0.03,0,3.08,12.21,1.7
Corded_Ware:RISE446:Allentoft_2015,10.44,0,0,0,25.54,64.02,0,0,0,0,0,0
Yamnaya_Samara:I0231:Mathieson_2015,29.21,3.13,0,0,3.94,57.21,2.44,0,0,0,3.33,0.75
Yamnaya_Samara:I0357:Mathieson_2015,30.56,1.4,0,0,7.38,54.65,1.41,0,0,0,4.49,0.12
Yamnaya_Samara:I0370:Mathieson_2015,30.97,3.96,0,0,4.88,57.16,0.12,0,0,0,1.92,0.99
Yamnaya_Samara:I0429:Mathieson_2015,28.47,1.92,0,0,3.71,62.57,0.96,0.21,0,0,1.45,0.7
Yamnaya_Samara:I0438:Mathieson_2015,26.82,1.54,0,0.39,0.6,60.83,1.8,0,0,0,7.77,0.25
Yamnaya_Samara:I0439:Mathieson_2015,24.1,0.47,0,0.94,8.87,55.96,2.12,0,0,0,7.16,0.37
Yamnaya_Samara:I0441:Mathieson_2015,33.85,2.03,0,0.21,1.48,59.11,2.63,0,0,0,0,0.69
Yamnaya_Samara:I0443:Mathieson_2015,29.61,2.46,0,0,3.67,58.66,0.07,0,0,0,4.84,0.69
Yamnaya_Samara:I0444:Mathieson_2015,29.41,1.68,0,0,6.52,59.52,0.6,0.02,0,0,1.07,1.19
Minoan_Zakros_BA:Lazaridis_2022:I14916,0,0,3.51,0,31.15,0,2.37,0,12.57,0,49.61,0.8
Minoan_Lasithi:I0070:Lazaridis_2017,0,0,0.62,0.55,37.53,0,0,0,15.52,0,45.7,0.09
Minoan_Lasithi:I0071:Lazaridis_2017,1.16,0,2.96,0,37.9,0.23,0,0,13.01,0,44.59,0.15
Minoan_Lasithi:I0073:Lazaridis_2017,0,0.05,2.92,0.4,36.38,0,0,0,13.48,0,46.7,0.07
Minoan_Lasithi:I0074:Lazaridis_2017,0.58,0,4.33,0,39.44,0,0,0,12.45,0,43.19,0
Minoan_Lasithi:I9005:Lazaridis_2017,1.52,0,5.68,0,37.33,0,0,0,16.14,0,39.25,0.08
Minoan_Odigitria:I9127:Lazaridis_2017,0,0,0,0,40.33,0,0,1.41,8.2,0,50.06,0
Minoan_Odigitria:I9128:Lazaridis_2017,6.38,2.36,3.13,0,48.96,0,0,0,14.8,1.02,23.34,0
Minoan_Odigitria:I9129:Lazaridis_2017,0,0,4.55,0,44.82,0,0,0,13.21,0,37.43,0
Minoan_Odigitria:I9130:Lazaridis_2017,1.38,0,0.19,0,41.77,0,0,0.28,17.61,0,38.77,0
Minoan_Odigitria:I9131:Lazaridis_2017,5.16,0,0,0,36.32,0,0,0,19.19,0,39.01,0.33
Minoan_Petras_EBA:Pta08:Clemente_2021,0,0,3.85,0.33,34.73,0.38,0.14,0.05,14.68,0.48,43.65,1.72
Anatolian_BA:I2495:Lazaridis_2017,6.07,0,1.17,1.3,27.23,3.79,0,0,14.72,0,43.22,2.51
Anatolian_BA:I2499:Lazaridis_2017,7.88,0.24,1.61,0,26.13,4.81,0,1.72,13.22,0.03,44.36,0
Anatolian_BA:I2683:Lazaridis_2017,8.73,0.62,2.12,0.42,25.19,0.9,0,0,14.26,0,45.14,2.61
ARM_Berkaber_KuraAraxes_EBA:father.or.son.I14343:I14340,24.44,0,0.58,0,3.95,6.71,1.45,0.28,8.53,0,53.16,0.91
ARM_Berkaber_KuraAraxes_EBA:I14339,21.48,0.48,0,0,1.89,8.84,1.84,0,9.12,0,55.96,0.39
ARM_Berkaber_KuraAraxes_EBA:I14341,25.09,0,0,0,5.17,4.52,1.46,0,7.48,0,55.77,0.51
ARM_Berkaber_KuraAraxes_EBA:I14343,27.12,0,0.16,0,6.66,6.72,1.13,0.28,7.55,0,50.25,0.12
ARM_Berkaber_KuraAraxes_EBA:I15132,26.7,0.48,0.23,0,4.59,4.53,0.03,0,10.55,0,51.82,1.08
ARM_Berkaber_KuraAraxes_EBA:I16920,26.45,0,0,0,1.74,8.28,0,0,11.76,0,51.77,0

Would it be possible to replicate my model, and run it in qpADM? I am interested to see how it would behave in that software.
 
If anything, even a G25 version would be interesting to compare as well, provided all of those samples are available. But a qpADM model would be optimal.
 
After some research on Eupedia, the sample's ID should be the following: I19368
 
Jovialis said:
If anything, even a G25 version would be interesting to compare as well, provided all of those samples are available. But a qpADM model would be optimal.
Click to expand...

I'm gonna do all of these another time. I have a lot of stuff to do in the summer. I burned out running models all the time. You can remind me if i forget. I lost my old good references/outgroups for complicated models for modelling Mycenaean admix so i need to figure out which ones are the best to use. Its much easier to make Neolithic models on qpAdm than Mycenaean vs Anatolian etc. Most of the time you get high Standard Errors when you run both Mycenaean and Anatolian on qpAdm because they are too similar. Balkan + Mycenaean + Anatolian are on a cline and Mycenaeans are very related to both, so you get high Standard Errors because qpAdm cant tell the proportions of such related components.
 
I can see that dilemma in modeling, they share much of the same ancestral components.

Also, No rush, maybe I could even find the time to learn qpADM myself from euptor's tutorial . But like yourself, I currently have a lot on my plate.
 
Sure thing:

[TABLE="class: distances"]
[TR]
[TH="align: right"]Distance to:[/TH]
[TH="align: left"]GRC_Palace_of_Nestor_EIA:I19368[/TH]
[/TR]
[TR]
[TD="bgcolor: #E0FF00, align: right"]6.58604037[/TD]
[TD]Smyrna_(n=5)[/TD]
[/TR]
[TR]
[TD="bgcolor: #E7FF00, align: right"]6.78724171[/TD]
[TD]Cyclades_(n=8)[/TD]
[/TR]
[TR]
[TD="bgcolor: #E9FF00, align: right"]6.86629158[/TD]
[TD]Greece_F_(n=5)[/TD]
[/TR]
[TR]
[TD="bgcolor: #F6FF00, align: right"]7.22632687[/TD]
[TD]Argolida:Greek:ARG1_Argos_Argolida[/TD]
[/TR]
[TR]
[TD="bgcolor: #FDFF00, align: right"]7.43273839[/TD]
[TD]Laconia:LAK8_Neapoli_Laconia[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFF400, align: right"]7.81771706[/TD]
[TD]Phokaia:GreecePhokaia60[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFEF00, align: right"]7.98110394[/TD]
[TD]Apulia_(n=230)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFEC00, align: right"]8.06295461[/TD]
[TD]Basilicata_(n=9)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFDC00, align: right"]8.52990090[/TD]
[TD]Crete_(n=21)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFD300, align: right"]8.78163199[/TD]
[TD]Athens_(n=15)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFD200, align: right"]8.81110936[/TD]
[TD]Campania_(n=17)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFD100, align: right"]8.85136665[/TD]
[TD]Ashkenazi_(n=15)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFCD00, align: right"]8.95912648[/TD]
[TD]Calabria_(n=6)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFCA00, align: right"]9.05241957[/TD]
[TD]Molise_(n=2)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFC200, align: right"]9.28975242[/TD]
[TD]Jovialis[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFC000, align: right"]9.36375427[/TD]
[TD]Central_Greece_(n=10)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFBF00, align: right"]9.39218237[/TD]
[TD]Sicily_(n=37)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFA200, align: right"]10.23413050[/TD]
[TD]Abruzzo_(n=19)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FF9500, align: right"]10.63172686[/TD]
[TD]Kos_(n=9)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FF9300, align: right"]10.66344515[/TD]
[TD]Messenia_(n=4)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FF8B00, align: right"]10.89850448[/TD]
[TD]Aitolokarnania:IL4_Douneika_Aitolokarnania[/TD]
[/TR]
[TR]
[TD="bgcolor: #FF7F00, align: right"]11.25989957[/TD]
[TD]Peloponnese_(n=9)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FF6500, align: right"]12.02251538[/TD]
[TD]Lazio_(n=5)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FF5A00, align: right"]12.34731145[/TD]
[TD]Korinthia:KOR42_Kariotika_Korinthia[/TD]
[/TR]
[TR]
[TD="bgcolor: #FF5700, align: right"]12.43650350[/TD]
[TD]Marche_(n=18)
[/TD]
[/TR]
[/TABLE]

d3RFpLx.png


The thing about that sample is, that it may look close to southern Italians on a 2D PCA, but in actuality, it is very different on the Z axis of the 3D PCA.
 
Jovialis said:
Sure thing:

[TABLE="class: distances"]
[TR]
[TH="align: right"]Distance to:[/TH]
[TH="align: left"]GRC_Palace_of_Nestor_EIA:I19368[/TH]
[/TR]
[TR]
[TD="bgcolor: #E0FF00, align: right"]6.58604037[/TD]
[TD]Smyrna_(n=5)[/TD]
[/TR]
[TR]
[TD="bgcolor: #E7FF00, align: right"]6.78724171[/TD]
[TD]Cyclades_(n=8)[/TD]
[/TR]
[TR]
[TD="bgcolor: #E9FF00, align: right"]6.86629158[/TD]
[TD]Greece_F_(n=5)[/TD]
[/TR]
[TR]
[TD="bgcolor: #F6FF00, align: right"]7.22632687[/TD]
[TD]Argolida:Greek:ARG1_Argos_Argolida[/TD]
[/TR]
[TR]
[TD="bgcolor: #FDFF00, align: right"]7.43273839[/TD]
[TD]Laconia:LAK8_Neapoli_Laconia[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFF400, align: right"]7.81771706[/TD]
[TD]Phokaia:GreecePhokaia60[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFEF00, align: right"]7.98110394[/TD]
[TD]Apulia_(n=230)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFEC00, align: right"]8.06295461[/TD]
[TD]Basilicata_(n=9)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFDC00, align: right"]8.52990090[/TD]
[TD]Crete_(n=21)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFD300, align: right"]8.78163199[/TD]
[TD]Athens_(n=15)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFD200, align: right"]8.81110936[/TD]
[TD]Campania_(n=17)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFD100, align: right"]8.85136665[/TD]
[TD]Ashkenazi_(n=15)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFCD00, align: right"]8.95912648[/TD]
[TD]Calabria_(n=6)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFCA00, align: right"]9.05241957[/TD]
[TD]Molise_(n=2)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFC200, align: right"]9.28975242[/TD]
[TD]Jovialis[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFC000, align: right"]9.36375427[/TD]
[TD]Central_Greece_(n=10)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFBF00, align: right"]9.39218237[/TD]
[TD]Sicily_(n=37)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FFA200, align: right"]10.23413050[/TD]
[TD]Abruzzo_(n=19)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FF9500, align: right"]10.63172686[/TD]
[TD]Kos_(n=9)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FF9300, align: right"]10.66344515[/TD]
[TD]Messenia_(n=4)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FF8B00, align: right"]10.89850448[/TD]
[TD]Aitolokarnania:IL4_Douneika_Aitolokarnania[/TD]
[/TR]
[TR]
[TD="bgcolor: #FF7F00, align: right"]11.25989957[/TD]
[TD]Peloponnese_(n=9)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FF6500, align: right"]12.02251538[/TD]
[TD]Lazio_(n=5)[/TD]
[/TR]
[TR]
[TD="bgcolor: #FF5A00, align: right"]12.34731145[/TD]
[TD]Korinthia:KOR42_Kariotika_Korinthia[/TD]
[/TR]
[TR]
[TD="bgcolor: #FF5700, align: right"]12.43650350[/TD]
[TD]Marche_(n=18)
[/TD]
[/TR]
[/TABLE]

d3RFpLx.png


The thing about that sample is, that it may look close to southern Italians on a 2D PCA, but in actuality, it is very different on the Z axis of the 3D PCA.
Click to expand...

Thanks Jovialis.
The extra CHG admixture is interesting. I'm really looking forward to have more iron age sample from archaic and classical era Greece.
 
Jovialis said:
I can see that dilemma in modeling, they share much of the same ancestral components.

Also, No rush, maybe I could even find the time to learn qpADM myself from euptor's tutorial . But like yourself, I currently have a lot on my plate.
Click to expand...

This is common wisdom at Eupedia for a while now and we have warned people against using populations that have a lot of overlap. No problem with EEF and Yamnaya but when starting mixing already admixed populations then you encounter large errors.

Also with regards to giving more weight to uniparentals, there is a very real danger that due to bottlenecks you are reaching the wrong conclusions.
 
bigsnake49 said:
This is common wisdom at Eupedia for a while now and we have warned people against using populations that have a lot of overlap. No problem with EEF and Yamnaya but when starting mixing already admixed populations then you encounter large errors.
Also with regards to giving more weight to uniparentals, there is a very real danger that due to bottlenecks you are reaching the wrong conclusions.
Click to expand...
Look, I've also known that many years. I myself warn people of that, even in this very thread prior. Please do not lecture me. But the aDNA pops. make sense for the region. I still maintain that it is possible to model these groups with BA sources, which is exactly what I have demonstrated. Again this is how papers are done if you haven't noticed.
 
AncIBD will resolve all of these debates. Finally we will have clarity on these issues.
 
Jovialis said:
Look, I've also known that many years. I myself warn people of that, even in this very thread prior. Please do not lecture me. But the aDNA pops. make sense for the region. I still maintain that it is possible to model these groups with BA sources, which is exactly what I have demonstrated. Again this is how papers are done if you haven't noticed.
Click to expand...

I am not lecturing you, I am reinforcing what you have said in the past, you and Angela. and I totally agree with you that we need IBD instead of these least squares models.
 
bigsnake49 said:
I am not lecturing you, I am reinforcing what you have said in the past, you and Angela. and I totally agree with you that we need IBD instead of these least squares models.
Click to expand...
Sorry if I was curt with you.
 
Francesco said:
Thanks Jovialis.
The extra CHG admixture is interesting. I'm really looking forward to have more iron age sample from archaic and classical era Greece.
Click to expand...

From "A genetic probe into the ancient and medieval history of Southern Europe and West Asia". The three samples from Iron age Greek (I thought we had just one) do indeed seem to show higher average CHG admixture. Still to few samples to draw solid conclusions.

 
Francesco said:
From "A genetic probe into the ancient and medieval history of Southern Europe and West Asia". The three samples from Iron age Greek (I thought we had just one) do indeed seem to show higher average CHG admixture. Still to few samples to draw solid conclusions.

Click to expand...

Regarding southern Italy though, the affinity is to Greece_N. Thus it is possible that South Italians may have been insulated from extra CHG migrations that affected Iron Age Greece.
 
Jovialis said:
Regarding southern Italy though, the affinity is to Greece_N. Thus it is possible that South Italians may have been insulated from extra CHG migrations that affected Iron Age Greece.
Click to expand...

But that's not to say it did not impact southern Italy at all. Maybe just less, or more in some areas than others?

I think we do see the legacy of these broader Greek-speaking world migrations more in modern Greeks actually, because most get Minoan_Zakros (about 30% Levant_PPN admixed if I recall), as well we more Kura-Araxes in modern Greeks. Though that may just be how the model makes up for the Corded ware brought in later in the MA. This would need to be resolved by ancIBD.

jdn6qSJ.png


As for where the Greek colonists originated from, Achaean was widely spoken throughout much of the south. That with very little doubt came straight from Northern Peloponnesus.
 
Jovialis said:
I can see that dilemma in modeling, they share much of the same ancestral components.

Also, No rush, maybe I could even find the time to learn qpADM myself from euptor's tutorial . But like yourself, I currently have a lot on my plate.
Click to expand...

I want to re-assert this for all to see, considering the components I've used have a lot of overlap. We can't take these models as gospel.

One day we will be able to rule out populations that do not have IBD (identity by decent) with modern ones.
 
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