Population structure in Italy using ancient and modern samples

Salento said:
Antonio 2019 has a table listing the full outliers, R437 and R850 are not on the list, … and they are Scientific Samples :)
Click to expand...
R850 was initially labelled as a Cretan who married a Etruscan and lived with the Rutuli Etruscan tribe..................but I read recently, he was from Greek Corsica ..........somewhere along the line he went to Italy after the Etruscans conquered the Greeks in Corsica.
I will try to find the article
 
Salento said:
thanks, Angela, I understand that some samples look strange, I guess we could omit some samples, … carefully avoiding being biased :)
Click to expand...

There have always been some problems with even academic samples, first and foremost the fact that the requisite ancestry, usually defined as four grandparents from the same area, is self reported. These academics don't act as investigators who go and look up records to make sure that's true.

The only geneticist who I know for a fact did that is Cavalli-Sforza, in his monumental work on the people of the Val Parma and Val Cedra. (I really wish that Stanford would release that raw data; the bloodlines go back to the mid 1500s and before for each sample or they weren't included.)

Then, as we've long known about the TSI sample, some only require 3/4 grandparents to be born in the same area. There has been considerable movement throughout the country since the latter part of the 1800s, especially in areas like Piemonte, Liguria and Lombardia, which were the first to industrialize. So, unless, as in the study on the Peloponnese, care was taken to sample only the elderly, you're going to get some admixed people in the sample in addition to possibly one grandparent. One small study about the Lunigiana studying unparentals didn't ask any questions about ancestry at all! If you showed up for testing, you were in! Talk about a complete waste of time.

One can "check" the list of samples, make it more accurate, in the way that Metspalu did, and Dienekes did, and 23andme did and does, and that is to use a PCA. Samples which fall outside the main cluster are excluded. Of course, you have to have a decent number of samples with which to work. Now, 30 seems a pretty low number for the main cluster of TSI but you see what I mean.

Using this method ensures that no biases are at play, because there is complete transparency. Anyone could duplicate the analysis by just doing a PCA of all the samples.

I'm not by any means trying to influence you guys one way or another as to how to proceed; just giving my two cents about how even academic samples can be misleading.

It's especially visible in groups like the Ashkenazim, where they're so close genetically that they're all "cousins", as 23andme has shown again and again.
 
torzio said:
R850 was initially labelled as a Cretan who married a Etruscan and lived with the Rutuli Etruscan tribe..................but I read recently, he was from Greek Corsica ..........somewhere along the line he went to Italy after the Etruscans conquered the Greeks in Corsica.
I will try to find the article
Click to expand...

You do that. I'm allergic to suppositions and rumor without at least citations, and I don't mean to a post on an amateur site.
 
Jovialis said:
Funny that we have a ton of Greek samples now that show that steppe wasn't a major component. But some people hang their hopes that they will show 50% steppe etc. Thus far there's only one, a woman from the MBA not even from where the Mycenaeans were. But we have only 6 Latin samples, and yet people are confident to call two outliers... why?
Click to expand...

I think you know the answer to your question.

Whether a sample is "autochthonous" to an area is time dependent.

If a sample is buried in the proper context for the time, with the requisite cultural artifacts, i.e. not a slave, a traveling merchant, tourist, pilgrim, etc. and thus seems to have been considered a member of the "tribe", then, in my book, they are exactly that. I mean, one of the, to some people, "suspect" samples, is from the earliest years of the Republic, for goodness' sakes!

Now, if you have a decent enough number of samples to form a cluster on a PCA, and one lists off a bit toward another group, then that is worth noting, for the acceptance and inclusion of people from other groups, if nothing else.

Even then, however, the additional ancestry might be, in the case we're discussing, from another part of Italy, i.e. the Gallic influenced areas north of the Po, or the Greek influenced areas south of Rome.

I keep on coming back to Livy about whom I recently learned quite a bit. He was undoubtedly Gallic admixed, and yet he at numerous times writes of his pride in being a ROMAN. How things have changed in certain parts of the country as some Italians have adopted the values and prejudices of the northerners they once scorned.

So, in those cases, perhaps not completely "Latin" or "Italic" in ancestry, but "Republican Roman" nonetheless.
 
Leopoldo Leone said:
850 and 437 are outliers relative to the main cluster of Etruscans and Italics, even the leaked samples from the Campanian paper show Samnites were akin to Latins and Etruscans.
Though they were outliers in a genetic sense it doesn't seem true to me that they must have been foreigners born outside of Italy (I don't understand why they are labelled "Greeks" here): the Daunian samples show a cline from Latins to Sicily_BA (who we know from the abstract of an upcoming study were similar to Sicily_IA) and, surprise surprise, ORD001 is very close to 437.

I suspect that the "east med" gene flow in the later samples from the Campanian study is due to a mixing of the later arrived Etruscans and Italics and the previous inhabitants, maybe more akin to Sicily_BA (and maybe the "east med" affinity was strengthened by the Greek colonies)
Click to expand...

This issue will be resolved, I believe, with the second half of the Bronze Age samples from mainland southern Italy.
 
The Raveane et al 2022 "Assessing temporal and geographic contacts across the Adriatic Sea through the analysis of genome-wide data from Southern Italy" is now published in the journal Genomics
 
Palermo Trapani said:
The Raveane et al 2022 "Assessing temporal and geographic contacts across the Adriatic Sea through the analysis of genome-wide data from Southern Italy" is now published in the journal Genomics
Click to expand...

Cool! I'll check it out if there is anything different.
 
Jovialis said:
Cool! I'll check it out if there is anything different.
Click to expand...

No problem Jovialis. Razib already has it up on his blog and I saw you made a comment over there pointing out the paper's findings are in line with the Antonio et al 2019 paper. Are any of those samples available to be reviewed, the modern ones that is?
 
"we analysed around 700 South Mediterranean genomes"

These are modern samples, Salento, is there anything you can do to obtain them?

https://www.sciencedirect.com/science/article/pii/S0888754322001501?via%3Dihub#bb0085
 
Jovialis said:
"we analysed around 700 South Mediterranean genomes"

These are modern samples, Salento, is there anything you can do to obtain them?

https://www.sciencedirect.com/science/article/pii/S0888754322001501?via%3Dihub#bb0085
Click to expand...

I'll take a look and then I'll take it from there :)
 
Jovialis said:
"we analysed around 700 South Mediterranean genomes"

These are modern samples, Salento, is there anything you can do to obtain them?

https://www.sciencedirect.com/science/article/pii/S0888754322001501?via%3Dihub#bb0085
Click to expand...

... they have a spreadsheet listing many samples from many papers, it might take a while, ... some might be duplicates of samples we already had.

Code: 
ItalyAbruzzo9_Behar_2013,7.93,0,2.44,0,29.54,16.30,0.05,0.65,11.17,0,31.92,0
ItalyAbruzzo13_Behar_2013,8.46,0,2.77,0,31.93,16.49,0,0,11.85,0,28.50,0
ItalyAbruzzo14_Behar_2013,6.37,0.23,1.17,0.29,30.67,15.60,0,0.42,12.82,0,32.37,0.04
ItalyAbruzzo15_Behar_2013,7.81,0.38,3.26,0,29.22,17.66,0,0,10.76,0,30.91,0
ItalyAbruzzo16_Behar_2013,7.45,0.39,2.50,0.27,28.89,17.92,0,0,10.86,0,31.73,0
ItalyAbruzzo17_Behar_2013,6.78,0.41,2.38,0,29.99,17.91,0.21,0.36,11.98,0,29.97,0
ItalyAbruzzo19_Behar_2013,9.16,0,2.05,0,29.78,17.49,0.01,0,11.99,0.56,28.86,0.10
ItalyAbruzzo20_Behar_2013,8.63,0,2.55,0,28.77,18.04,0,0.36,10.36,0.50,30.79,0
ItalyAbruzzo21_Behar_2013,7.38,0,1.54,0,33.31,16.82,0.28,0.06,11.27,0.11,28.93,0.32
ItalyAbruzzo22_Behar_2013,6.90,0,2.69,0.26,30.81,15.99,0.51,0,9.90,0.49,32.46,0
ItalyAbruzzo23_Behar_2013,6.77,0,2.43,0,28.77,18.94,0,0.04,11.45,0,31.59,0
C-Sicily50_Behar_2013,6.22,0.50,3.62,0,27.78,14.29,0,0.96,12.97,0.12,32.19,1.35
C-Sicily57_Behar_2013,5.88,0.14,4.31,0.30,25.95,15.11,0.24,0.81,13.24,0,34.01,
Ag-Sicily5_Behar_2013,8.11,0,4.73,0,29.88,12.05,0,0.88,11.66,0,32.68,0
Ag-Sicily8_Behar_2013,7.44,0.30,5.18,0.40,27.65,13.74,0.05,0.70,12.31,0,31.71,0.52
E-Sicily18_Behar_2013,4.57,0,4.55,0,28.22,14.85,0.37,0,15.10,0.38,31.41,0.56
W-Sicily1_Behar_2013,7.27,0,4.47,0,28.58,13.24,0,1.03,10.76,0,34.42,0.23
W-Sicily3_Behar_2013,6.69,0.09,4.53,0,28.83,12.64,0,0.47,12.19,0.18,34.27,0.12
W-Sicily4_Behar_2013,6.29,0,3.76,0,31.55,13.88,0,0,12.43,0.46,30.79,0.86
W-Sicily5a_Behar_2013,8.76,0,3.46,0.89,26.50,13.84,0,1.77,11.65,0.13,33.00,0
W-Sicily5b_Behar_2013,4.78,0,3.80,0.83,26.41,15.35,0,0.33,12.18,0,35.60,0.72
W-Sicily7_Behar_2013,5.95,0.23,2.89,0.61,31.36,14.20,0,0,12.77,0.12,31.54,0.33
W-Sicily9_Behar_2013,7.47,0.24,4.26,0,28.88,13.07,0,0.77,14.72,0,30.48,0.10
W-Sicily21_Behar_2013,7.06,0,4.17,0.98,27.98,11.07,0.07,2.67,11.80,0,33.88,0.32
SR23_Busby_2015,4.46,0.74,4.22,1.15,27.25,14.39,0,0.56,12.10,0,35.14,0
SR44_Busby_2015,6.34,0,3.34,0,26.31,16.59,2.66,0,13.18,0,31.58,0
SR48R_Busby_2015,7.10,0.63,3.01,1.31,30.38,15.98,0.27,0,11.62,0,28.51,1.21
SR64_Busby_2015,7.97,0,3.45,0,29.75,13.44,0,2.33,12.10,0,30.48,0.48
TP04_Busby_2015,5.79,0,3.08,0,28.73,18.49,0.78,0.43,11.03,0,30.21,1.46
TP05_Busby_2015,7.76,0,7.31,0,29.40,11.85,0,0,9.38,1.31,32.10,0.89
TP06_Busby_2015,5.05,0,5.42,0.18,29.97,17.93,0,0,9.93,0,30.54,0.98
TP07_Busby_2015,8.32,0.77,5.64,0,26.41,12.48,1.43,2.69,11.62,0,30.64,0
TP08_Busby_2015,4.24,0.57,5.24,0.11,31.12,15.86,0.66,0.70,8.79,0.72,31.22,0.77
TP25_Busby_2015,7.66,0,4.75,1.83,31.62,13.02,0,0,10.63,0,29.49,1
SR60_Busby_2015,5.07,0,5.64,0,27.22,15.93,0,0.20,11.48,0,33.31,1.15
 
Last edited:
Salento said:
... they have a spreadsheet listing many samples from many papers, it might take a while, ... some might be duplicates of samples we already had.
Click to expand...


You're right, for the Italians many are surely duplicates (North Italian/Bergamo HGDP, TSI, Sardinian HGDP... also some south Italian sample is also a duplicate). The new ones are some Greek samples, such as Achea, Argolis, Elis, Corinthia, North Tsakonia, South Tsakonia, Arcadia, Messenia, West Taygetos, East Taygetos, Laconia, Deep Mani.
 
Salento: Buona Domenica. Great work again. I quickly took the coordinates from your post #946 and combined them with the earlier version of the modern Italian samples. I kept only the samples from Abruzzo and Sicily. There are some duplicates but still some new samples. The W-Sicily 7, West-Sicily-4 and TP-25 (Trapani) are all new samples which I get close distances to. The SR48_Bugsby2015r (Syracuse I would assume) is another close match and new one. Seems the Behar 2013 are duplicates and Bugsby 2015 samples are the new ones. Great work again and thanks again for putting these modern academic samples into one database.

Distance to:PalermoTrapani_ANCESTRY
1.79596771W-Sicily7_Behar_2013
1.88369318W-Sicily4_Behar_2013
2.74534151SR64_Busby_2015
2.74534151Siracusa:SR64_LazaridisNat2014
2.88128444Abruzzo:Alp380
2.88513431Ag-Sicily5_Behar_2013
2.88513431Ag-Sicily:5
2.97045451W-Sicily9_Behar_2013
2.97045451W-Sicily:9
3.07784015Abruzzo:Alp090
3.36884253Ag-Sicily8_Behar_2013
3.36884253Ag-Sicily:8
3.47981321C-Sicily50_Behar_2013
3.47981321C-Sicily:50
3.53990113ItalyAbruzzo14_Behar_2013
3.62692707W-Sicily3_Behar_2013
3.62692707W-Sicily:3
3.71638265TP25_Busby_2015
3.81167942Abruzzo:Alp503
3.83469686ItalyAbruzzo9_Behar_2013
4.16391643ItalyAbruzzo22_Behar_2013
4.27519590W-Sicily1_Behar_2013
4.27519590W-Sicily:1
4.36253367SR48R_Busby_2015
4.44958425E-Sicily18_Behar_2013
4.44958425E-Sicily:18
4.90147937ItalyAbruzzo13_Behar_2013
4.97591198ItalyAbruzzo15_Behar_2013
4.97730851ItalyAbruzzo17_Behar_2013
5.01247444W-Sicily21_Behar_2013
5.01247444W-Sicily:21
5.05732143W-Sicily5a_Behar_2013
5.05732143W-Sicily:5a
5.15226164Abruzzo:ALP205
5.28343638Abruzzo:Alp616
5.29267418ItalyAbruzzo16_Behar_2013
5.44095580Abruzzo:Alp162
5.51926626SR60_Busby_2015
5.51926626Siracusa:SR60_LazaridisNat2014
5.56050357Abruzzo:Alp140
5.66633038TP05_Busby_2015
5.66633038Trapani:TP05_LazaridisNat2014
5.66649804C-Sicily57_Behar_2013
5.68560463ItalyAbruzzo19_Behar_2013
5.72960732SR23_Busby_2015
5.73702885ItalyAbruzzo21_Behar_2013
5.74471061TP08_Busby_2015
5.80655664TP07_Busby_2015
5.80655664Trapani:TP07_LazaridisNat2014
5.88855670ItalyAbruzzo20_Behar_2013
5.96341345SR44_Busby_2015
5.98609221TP06_Busby_2015
6.03721790ItalyAbruzzo23_Behar_2013
6.09758149TP04_Busby_2015
6.57307386W-Sicily5b_Behar_2013
6.79867634Abruzzo:ALP161

 
… yes PT, … I’ve been redundant :) though the Abruzzesi were new to us, I suspect? … they belong with previously posted Sicilians, I figure they should be together.
 
Jovialis said:
It would be cool to the new ones if possible.
Click to expand...

the one listed by Pax - I think they are not publicly available or I just couldn’t find them.
Most other Italians would be redundant and similar with the ones we already have, I guess.

… there is another list of Italians using a non linear and different alleles format which we need to figure out how to convert to a standard format.
 
Salento said:
the one listed by Pax - I think they are not publicly available or I just couldn’t find them.
Most other Italians would be redundant and similar with the ones we already have, I guess.
Click to expand...

I will look for them tomorrow; they must have been released, perhaps in a previous study.
 
Pax Augusta said:
You're right, for the Italians many are surely duplicates (North Italian/Bergamo HGDP, TSI, Sardinian HGDP... also some south Italian sample is also a duplicate). The new ones are some Greek samples, such as Achea, Argolis, Elis, Corinthia, North Tsakonia, South Tsakonia, Arcadia, Messenia, West Taygetos, East Taygetos, Laconia, Deep Mani.
Click to expand...

@Salento, indeed, I saw them and I'm going to check them out now. But I was actually referring to these samples in bold.
 
Here are my results using the new additions:

Distance to:Jovialis
1.36923336ItalyAbruzzo15_Behar_2013
1.66129468ItalyAbruzzo16_Behar_2013
1.71953482ItalyAbruzzo20_Behar_2013
1.94663813ItalyAbruzzo9_Behar_2013
2.75210828ItalyAbruzzo22_Behar_2013
2.82391572ItalyAbruzzo23_Behar_2013
3.41641625ItalyAbruzzo17_Behar_2013
3.78219513TP04_Busby_2015
3.97039041ItalyAbruzzo19_Behar_2013
4.28499708TP06_Busby_2015
4.67142377ItalyAbruzzo14_Behar_2013
4.67279360SR48R_Busby_2015
4.77744702ItalyAbruzzo13_Behar_2013
5.08283386Ag-Sicily8_Behar_2013
5.21470996SR64_Busby_2015
5.23111843SR60_Busby_2015
5.24194620C-Sicily50_Behar_2013
5.26858615W-Sicily5a_Behar_2013
5.27725307W-Sicily1_Behar_2013
5.31319113W-Sicily7_Behar_2013
5.41809930W-Sicily4_Behar_2013
5.46488792TP08_Busby_2015
5.47620306SR44_Busby_2015
5.57361642ItalyAbruzzo21_Behar_2013
5.87851172Ag-Sicily5_Behar_2013
 
Here are my results combining the new additions with the previous Italians.

9 out of 10 top matches are Abruzzo, and one Molise. Apulians seem to range all over the South, so it makes sense.

Distance to:Jovialis
1.36923336ItalyAbruzzo15_Behar_2013
1.66129468ItalyAbruzzo16_Behar_2013
1.71953482ItalyAbruzzo20_Behar_2013
1.85132385Molise:pG26_Molise
1.94663813ItalyAbruzzo9_Behar_2013
2.16529444Abruzzo:Alp140
2.71775643Abruzzo:Alp090
2.73558038Abruzzo:Alp616
2.75210828ItalyAbruzzo22_Behar_2013
2.82391572ItalyAbruzzo23_Behar_2013
2.89611809Apulia:cera1
2.91856129Apulia:cera2
3.19426048Umbria:pG06
3.32980480Molise:pG27
3.34511584Apulia:cera8
3.38212951Lazio:NOR28
3.39328749Marche:MarABY030D
3.41641625ItalyAbruzzo17_Behar_2013
3.47597468Marche:MarACO100D
3.49479613Apulia:pu45
3.70070264Abruzzo:Alp503
3.77326119Abruzzo:ALP161
3.78219513TP04_Busby_2015
3.80215728Marche:MarACY030D
3.80621860Apulia:cera9
 
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