Population structure in Italy using ancient and modern samples

@PT ... some modern Sicilians unrelated to this thread, ... some lacking the study label.
Code:
TP05_Trapani_LazaridisNat2014,7.76,0,7.31,0,29.40,11.85,0,0,9.38,1.31,32.10,0.89
TP07_Trapani_LazaridisNat2014,8.32,0.77,5.64,0,26.41,12.48,1.43,2.69,11.62,0,30.64,0
SR60_Siracusa_LazaridisNat2014,5.07,0,5.64,0,27.22,15.93,0,0.20,11.48,0,33.31,1.15
SR64_Siracusa_LazaridisNat2014,7.97,0,3.45,0,29.75,13.44,0,2.33,12.10,0,30.48,0.48
C-Sicily50,6.22,0.50,3.62,0,27.78,14.29,0,0.96,12.97,0.12,32.19,1.35
E-Sicily18,4.57,0,4.55,0,28.22,14.85,0.37,0,15.10,0.38,31.41,0.56
W-Sicily1,7.27,0,4.47,0,28.58,13.24,0,1.03,10.76,0,34.42,0.23
W-Sicily3,6.69,0.09,4.53,0,28.83,12.64,0,0.47,12.19,0.18,34.27,0.12
W-Sicily5a,8.76,0,3.46,0.89,26.50,13.84,0,1.77,11.65,0.13,33.00,0
W-Sicily9,7.47,0.24,4.26,0,28.88,13.07,0,0.77,14.72,0,30.48,0.10
W-Sicily21,7.06,0,4.17,0.98,27.98,11.07,0.07,2.67,11.80,0,33.88,0.32
Ag-Sicily5,8.11,0,4.73,0,29.88,12.05,0,0.88,11.66,0,32.68,0
Ag-Sicily8,7.44,0.30,5.18,0.40,27.65,13.74,0.05,0.70,12.31,0,31.71,0.52

Great work once again! Keep it up! We can have all the samples decoded at this rate.
 
@pax I know, what I meant was that now we don't have to use the "updated" Dodecad populations made by apricity users and that racist Italian guy.

Whoever made them are not aberrant anyway, the big picture is more or less the same. To be nitpicky even these samples that come from Raveane 2019 have some problems. One would really have to wonder what is the point of releasing only one Ligurian sample, and not releasing any Piedmontese or Emilan samples. It would also have been helpful if it published information about the exact origin of the various samples. In northeastern Italy, there is quite a difference between the Po Valley, the Pre-Alps, the Alps, and language minorities. Personally, I care about accuracy more than the rest.

In any case, great work, as usual on your part. And a big thank you to Salento.
 
@PT ... some modern Sicilians unrelated to this thread, ... some lacking the study label.
Code:
TP05_Trapani_LazaridisNat2014,7.76,0,7.31,0,29.40,11.85,0,0,9.38,1.31,32.10,0.89
TP07_Trapani_LazaridisNat2014,8.32,0.77,5.64,0,26.41,12.48,1.43,2.69,11.62,0,30.64,0
SR60_Siracusa_LazaridisNat2014,5.07,0,5.64,0,27.22,15.93,0,0.20,11.48,0,33.31,1.15
SR64_Siracusa_LazaridisNat2014,7.97,0,3.45,0,29.75,13.44,0,2.33,12.10,0,30.48,0.48
C-Sicily50,6.22,0.50,3.62,0,27.78,14.29,0,0.96,12.97,0.12,32.19,1.35
E-Sicily18,4.57,0,4.55,0,28.22,14.85,0.37,0,15.10,0.38,31.41,0.56
W-Sicily1,7.27,0,4.47,0,28.58,13.24,0,1.03,10.76,0,34.42,0.23
W-Sicily3,6.69,0.09,4.53,0,28.83,12.64,0,0.47,12.19,0.18,34.27,0.12
W-Sicily5a,8.76,0,3.46,0.89,26.50,13.84,0,1.77,11.65,0.13,33.00,0
W-Sicily9,7.47,0.24,4.26,0,28.88,13.07,0,0.77,14.72,0,30.48,0.10
W-Sicily21,7.06,0,4.17,0.98,27.98,11.07,0.07,2.67,11.80,0,33.88,0.32
Ag-Sicily5,8.11,0,4.73,0,29.88,12.05,0,0.88,11.66,0,32.68,0
Ag-Sicily8,7.44,0.30,5.18,0.40,27.65,13.74,0.05,0.70,12.31,0,31.71,0.52

Salento, a big thank you, great work!

Have you seen these?

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53626


GSM1297338SouthItalian4
GSM1297339SouthItalian5
GSM1297340SouthItalian6
GSM1297341SouthItalian7
GSM1297342SouthItalian8
GSM1297343SouthItalian9
GSM1297344SouthItalian10
GSM1297345SouthItalian11
GSM1297346SouthItalian12
GSM1297347SouthItalian13
GSM1297348SouthItalian14
GSM1297349SouthItalian15
GSM1297350SouthItalian16
GSM1297351SouthItalian17
GSM1297352SouthItalian18
GSM1297335SouthItalian1
GSM1297336SouthItalian2
GSM1297337SouthItalian3

GSM1297438EastSicilian1
GSM1297439EastSicilian2
GSM1297440EastSicilian3
GSM1297441EastSicilian4
GSM1297442EastSicilian5
GSM1297443EastSicilian6
GSM1297444EastSicilian7
GSM1297445EastSicilian8
GSM1297446EastSicilian9
GSM1297447EastSicilian10
GSM1297448WestSicilian1
GSM1297449WestSicilian2
GSM1297450WestSicilian3
GSM1297451WestSicilian4
GSM1297452WestSicilian5
GSM1297453WestSicilian6
GSM1297454WestSicilian7
GSM1297455WestSicilian8
GSM1297456WestSicilian9
GSM1297457WestSicilian10

GSM1297484Greek12
GSM1297485Greek13
GSM1297486Greek14
GSM1297487Greek15
GSM1297488Greek16
GSM1297489Greek17
GSM1297490Greek18
GSM1297491Greek19
GSM1297492Greek20

 
Whoever made them are not aberrant anyway, the big picture is more or less the same. To be nitpicky even these samples that come from Raveane 2019 have some problems. One would really have to wonder what is the point of releasing only one Ligurian sample, and not releasing any Piedmontese or Emilan samples. It would also have been helpful if it published information about the exact origin of the various samples. In northeastern Italy, there is quite a difference between the Po Valley, the Pre-Alps, the Alps, and language minorities. Personally, I care about accuracy more than the rest.

In any case, great work, as usual on your part. And a big thank you to Salento.

I hope even more samples processed will resolve the issues of under sampling and absence of samples.
 
I hope even more samples processed will resolve the issues of under sampling and absence of samples.

Yes, I agree but anyway the picture is already clear. What we need are more ancient samples from prehistoric and protohistoric Italy. So far only a few areas have been covered.
 
Here is the PCA with the new Sicilian samples posted by Salento.

IKFOrpf.png
 
Jovialis: Thanks for the PCA in post #84.
 
I think that many of the samples I posted on #832 are the same samples that @Pax listed on #839, ... the samples were re-named and recycled for another study, ... see below.



ITS is the SouthItalian of Post #839

Code:
ITS2,10.04,0,1.14,0,27.18,15.93,0.93,0,11.33,0.26,33.19,0
ITS4,8.05,0,5.16,0,26.62,12.04,0,0,11.74,0.62,35.77,0
ITS5,5.86,1.35,2.20,0,30.35,16.61,0.65,0.06,11.71,0.58,30.45,0.19
ITS7,9.63,0,2.78,0.45,28.77,16.43,0,0.89,12.03,0,29.02,0


DY1jaN5.gif


mByjhyk.gif


LxgZrU8.gif
 
I think that many of the samples I posted on #832 are the same samples that @Pax listed on #839, ... the samples were re-named and recycled for another study, ... see below.



ITS is the SouthItalian of Post #839

Code:
ITS2,10.04,0,1.14,0,27.18,15.93,0.93,0,11.33,0.26,33.19,0
ITS4,8.05,0,5.16,0,26.62,12.04,0,0,11.74,0.62,35.77,0
ITS5,5.86,1.35,2.20,0,30.35,16.61,0.65,0.06,11.71,0.58,30.45,0.19
ITS7,9.63,0,2.78,0.45,28.77,16.43,0,0.89,12.03,0,29.02,0


DY1jaN5.gif


mByjhyk.gif


LxgZrU8.gif

Great work once again,

Here is a PCA with those new samples. I am fairly close to ITS7, any idea where that one is from?

rxU1d8W.png
 
Great work once again,

Here is a PCA with those new samples. I am fairly close to ITS7, any idea where that one is from?

rxU1d8W.png

ITS7 is from Crispiano, Province of Taranto, ... Puglia :)

ITS2 Naples
ITS4 Naples
ITS5 Salerno
ITS7 Crispiano

zIkl9rl.gif
 
Last edited:
Oxk95sH.png


Here is the PCA with all of the samples organized by region.

You flip this 90 degrees and you essentially get the Italian "boot". It's interesting to see Albanians across the pond plot a little more north than they are geographically. I'm assuming without the Slavic/Gothic input they'd plot with Abruzzo.

GqE5nJ5.png
 
I think that many of the samples I posted on #832 are the same samples that @Pax listed on #839, ... the samples were re-named and recycled for another study, ... see below.

Yes, it is absolutely possible, the samples are very often the same for years that from time to time are renamed in a different way in the studies. When the samples are really new it is specified in the study (also because it takes money to analyze new ones).
 
I have been really thinking lately, remember that one paper stating Albanians and Italians have the highest IBD sharing?
It has been in the back of my mind a lot lately. What it means, that statement, what it says about history. Especially after all the ancient Balkan cluster samples since that paper look modern North Italian like, while most Albanians have Tuscany, Marche and Lombardy as their closest matches bar Central Macedonian Greek.

IIRC, paraphrasing, the paper stated something along the lines Italians share among themselves as much common ancestry with Albanians as between themselves.
What do you guys make of it?
Also, why do Albanians have the greatest resemblance to N. Italians autosomally? One would think given the boot being the closest geographical area, rather South-East Italy would be more so similar.

I really think that one statement went a bit under the radar relatively speaking, and we still have not made enough sense of it.
 
I have been really thinking lately, remember that one paper stating Albanians and Italians have the highest IBD sharing?
It has been in the back of my mind a lot lately. What it means, that statement, what it says about history. Especially after all the ancient Balkan cluster samples since that paper look modern North Italian like, while most Albanians have Tuscany, Marche and Lombardy as their closest matches bar Central Macedonian Greek.

IIRC, paraphrasing, the paper stated something along the lines Italians share among themselves as much common ancestry with Albanians as between themselves.
What do you guys make of it?
Also, why do Albanians have the greatest resemblance to N. Italians autosomally? One would think given the boot being the closest geographical area, rather South-East Italy would be more so similar.

I really think that one statement went a bit under the radar relatively speaking, and we still have not made enough sense of it.

I think that paper was more emphasizing the fact that Italy is a diverse place to the point where any 2 Italians share as many ancestors as they do with an Albanian.

Italy is more like a mini-continent where all sorts of ethnicities lived: Italic, Celtic, Etruscan, Messapians, Greeks, etc... and got homogenized with the Roman Republic/Empire.

Also, why do Albanians have the greatest resemblance to N. Italians autosomally?

Illyrians came from the region ~Hallstatt Culture same as Italics, nothing surprising there. Only difference is that the more south they go, the more EEF-heavy people they mixed with.
 
ITS7 is from Crispiano, Province of Taranto, ... Puglia :)
ITS2 Naples
ITS4 Naples
ITS5 Salerno
ITS7 Crispiano
zIkl9rl.gif
Someone from Puglia, that makes sense. I guess I'm not alone in being Apulian but plotting with Abruzzo and Molise. Our "range" is pan-south Italian.
 
Oxk95sH.png

Here is the PCA with all of the samples organized by region.
@Archetype0ne
To me it looks like Albanians are south Italian-like (Greek-like) + Northeastern European (Slavic). Rather than associated with Northern Italy.
 

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