Genetics of the Greek Peleponessus

Lazaridis uses in his PCA the other Tuscan samples (Tuscan HGDP) from further south toward Lazio.

https://catalog.coriell.org/0/Sections/Support/NHGRI/ToscaniStatement.aspx?PgId=395

[FONT=&quot]These cell lines and DNA samples were prepared from blood samples collected in a small town near Florence in the Tuscany region of Italy. All of the samples are from unrelated individuals who identified themselves as having at least three out of four Tuscan grandparents.[/FONT]
...

[FONT=&quot]These samples, while not genetically "atypical", do not necessarily represent all Tuscans, nor all Italians, whose population history is complex. The population should not be described merely as "Italian", "Southern European", "European", or "Caucasian", since each of those designators encompasses many populations with many different geographic ancestries. The reference to these samples in the Italian language is preferred.

[/FONT]
https://catalog.coriell.org/0/Sections/Collections/NHGRI/1000Toscani.aspx?PgId=706&coll=HG

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https://catalog.coriell.org/0/Sections/Support/NHGRI/ToscaniStatement.aspx?PgId=395

In regards to TSI, I don't think it can be known which town it comes from exactly. According to the written statement, they chose to refer to it at Citta X. The closest we can know is that it is from a small town near Florence. Moreover, the requirement was 3 out of 4 ancestors from the region of Tuscany.

 
https://catalog.coriell.org/0/Sections/Support/NHGRI/ToscaniStatement.aspx?PgId=395
In regards to TSI, I don't think it can be known which town it comes from exactly. According to the written statement, they chose to refer to it at Citta X. The closest we can know is that it is from a small town near Florence. Moreover, the requirement was 3 out of 4 ancestors from the region of Tuscany.

Thanks for sharing, we've already discussed here about TSI. Probably a minority of Tuscans of TSI are 1/4 mixed, and most likely with southern Italians. Who knows. But TSI is a big sample (more than 100 individuals) and overall the TSI average is a bit more northern-shifted than the Tuscan HGDP average from southern Tuscany. In Tuscany there is even an internal cline.

Anyway Lazarids is using in his PCAs the other sample (Tuscan HGDP) from southern Tuscany towards Lazio. You can even count them: they are 8. While Northern Italians in Lazaridis' PCAs are Bergamo HGDP, they are 13. In the last paper for the the Greeks Lazaridis has also used Greeks from Thessaloniki, Macedonia. I don't know anything about the Albanians, if they are northern or southern Albanians.
 
Thanks for sharing, we've already discussed here about TSI. Probably a minority of Tuscans of TSI are 1/4 mixed, and most likely with southern Italians. Who knows. But TSI is a big sample (more than 100 individuals) and overall the TSI average is a bit more northern-shifted than the Tuscan HGDP average from southern Tuscany. In Tuscany there is even an internal cline.

Anyway Lazarids is using in his PCAs the other sample (Tuscan HGDP) from southern Tuscany towards Lazio. You can even count them: they are 8. While Northern Italians in Lazaridis' PCAs are Bergamo HGDP, they are 13. In the last paper for the the Greeks Lazaridis has also used Greeks from Thessaloniki, Macedonia. I don't know anything about the Albanians, if they are northern or southern Albanians.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440425/#pone.0043759.s002

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Here's an interesting PCA I've retrieved while looking up the TSI sample. However, I can't verify where specifically they come from in those regions yet.

EDIT:

Getting back to Greek genetics, I guess the Mycenaeans would have been within this range.

RHLKGzf.png
 
So many oddities in that pca! Why are some of those north Italians plotting that far south? And are those Italians grouping with the Sardinians half Sardinian (likewise, are those Sardinians they plot with half Italian?)?

Quite a bit of diversity within some of these regions!
 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440425/#pone.0043759.s002
Here's an interesting PCA I've retrieved while looking up the TSI sample. However, I can't verify where specifically they come from in those regions yet.

Old study, I don't know if it was discussed on Eupedia. They mixed many samples of different source (HGDP, HapMap, MESO, GEO-IT...) with some samples collected by themselves. HapMap and TSI are the same thing in that study because TSI was part of the HapMap project. So in the PCA there are likely also TSI samples. But for an unclear reason, Di Gaetano only used 76 out of 114.

I remember little of that study, that of Fiorito seemed more complete. I remember only that the few North and Central Italians who cluster with Southern Italians were seen by Razib and other bloggers as a signature of recent internal Italian migrations. As Fiorito himself admitted a few years later, the first Italian studies had underestimated the impact of migrations and used not very accurate samples.

Here you can find details

08QXVJS.png


Anyway we are too much off-topic, this thread is about the genetics of the Greek Peleponessus, not of Italy.

Angela, can you please move all the last posts about Italy in the Fiorito 2015 or Sazzini thread?

There were two newer Italian papers about the Italian genetics. Sazzini could be of interest to you because includes also Apulians.

Fiorito 2015

http://www.eupedia.com/forum/threads/31707-The-Italian-Genome-Fiorito-et-al-2015

Sazzini 2016

http://www.eupedia.com/forum/thread...se-susceptibility-along-the-Italian-peninsula
 
Getting back to Greek genetics, I guess the Mycenaeans would have been within this range.

Interesting, but I don't think you can do that. Di Gaetano PCA is the scatter plot "of the first two eigenvectors based on 125,799 autosomal SNPs and 1,012 individuals". Not all the PCAs are based on the same. Is the Lazaridis PCA based on the same?


So many oddities in that pca! Why are some of those north Italians plotting that far south? And are those Italians grouping with the Sardinians half Sardinian (likewise, are those Sardinians they plot with half Italian?)? Quite a bit of diversity within some of these regions!

Because not all the northern (and central) Italians used as samples were fully native. This is maybe true also for Sardinians (Sardinians can have partial ancestry from mainland Italy).

Anyway, here is the Fiorito's answer to your question. Fiorito is an Italian geneticist Fiorito who collaborated on the 2012 study posted by Jovialis, and he was the main author of a 2015 update.

the quote comes from the 2015 update

In a previous study, (1) we provided a first overview of the genetic composition of Italians, selecting individuals based on the place of birth only, but we were not able to discriminate between Northern and Central Italians. We observed that a proportion of individuals born in Northern Italy clustered with Southern Italians. This was explained by the internal migration that occurred during the last two generations, when people from Southern Italy left their place of origin looking for better economic opportunities in the North.


(1) Di Gaetano C, Voglino F, Guarrera S et al: An overview of the genetic structure within the Italian population from genome-wide data. PLoS One 2012; 7 : e43759.

The Italian genome reflects the history of Europe and the Mediterranean basin. Available from:
https://www.researchgate.net/public...history_of_Europe_and_the_Mediterranean_basin [accessed Sep 11, 2017].
 
DNA samples were obtained from 49 unrelated volunteers from four different Italian macro-areas (Tuscany, Sicily, Piedmont and Sardinia). Details of the affiliation of the municipalities within the macro-areas mentioned in this work are described in Figure S2.These individuals were grouped according to their birth place, and were selected to have their parents and four grandparents born in the same region. This small sample set is not a random sample of the modern, admixed population, but rather it should approach the historical population structure.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440425/#pone.0043759.s002

It appears this study accounted for the recent internal migrations though.

Edit:
I just saw you recent post now, so I guess they didn't.
 
It appears this study accounted for the recent internal migrations though.

Edit:
I just saw you recent post now, so I guess they didn't.

They obviously didn't (and a birth place doesn't mean anything). They were even forced to admit that.
 
They obviously didn't (and a birth place doesn't mean anything). They were even forced to admit that.

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Why does the TSI sample (*At least 3/4th ancestry near Florence), from a single town have some overlap with Sicilians though? This study is from march 2017. It doesn't look that far off from that 2012 study, at least in regards to the Tuscans.

http://www.nature.com/ejhg/journal/v25/n5/fig_tab/ejhg201718f2.html?foxtrotcallback=true#figure-title

BTW, I'm genuinely curious about this; not trying to beg the question.

Edit: I even see a couple for the other sample Tuscan.

Edit 2: I guess this is not necessarily off-topic, since it was originally in regards to my question to Angela, about Tuscan relation to the Ancient Greeks. Thus its constructive I think. :bigsmile:
 
tNjkWF9.png

Why does the TSI sample (*At least 3/4th ancestry near Florence), from a single town have some overlap with Sicilians though? This study is from march 2017. It doesn't look that far off from that 2012 study, at least in regards to the Tuscans.
http://www.nature.com/ejhg/journal/v25/n5/fig_tab/ejhg201718f2.html?foxtrotcallback=true#figure-title
BTW, I'm genuinely curious about this; not trying to beg the question.
Edit: I even see a couple for the other sample Tuscan.
Edit 2: I guess this is not necessarily off-topic, since it was originally in regards to my question to Angela, about Tuscan relation to the Ancient Greeks. Thus its constructive I think. :bigsmile:


That PCA is from the Greek study, and it's the opposite, it's some Sicilian who goes further north. In that PCA Sicilians range from Peloponnese (in that specific PCA Peloponnesians are south of TSI/central Italians) to south west of TSI average slightly towards Sardinians. Sicily was repopulated in the middle ages after the Norman conquest, even with colonists who were from northern Italy.

TSI in that study overlaps more with Italians, who are north Italians from Lombardy and Venetians. There is even some Venetian who plots in the TSI cluster. Well, I've never seen a Venetian on gedmatch who gets as first population "Tuscan", they are usually even more north-eastern than Lombards.

Once again, ask yourself what a specific PCA represents, not all PCAs are based on the same. Unfortunately the Greek study is not very clear. It seems too interested in showing a similarity between Greeks and Italians to distance themselves from other Balkan peoples.

A Tuscan relation to the Ancient Greeks? Very little, except a very very few Tuscans who could descend from the Mycenaeans/ancient Greeks and a shared neolithic/bronze age mediterranean substratum. From an autosomal point of view when two samples show similar amounts of ancestral components does not imply that these components have exactly the same origin.
 
That PCA is from the Greek study, and it's the opposite, it's some Sicilian who goes further north. In that PCA Sicilians range from Peloponnese (in that specific PCA Peloponnesians are south of TSI/central Italians) to south west of TSI average slightly towards Sardinians. Sicily was repopulated in the middle ages after the Norman conquest, even with colonists who were from northern Italy.

TSI in that study overlaps more with Italians, who are north Italians from Lombardy and Venetians. There is even some Venetian who plots in the TSI cluster. Well, I've never seen a Venetian on gedmatch who gets as first population "Tuscan", they are usually even more north-eastern than Lombards.

Once again, ask yourself what a specific PCA represents, not all PCAs are based on the same. Unfortunately the Greek study is not very clear. It seems too interested in showing a similarity between Greeks and Italians to distance themselves from other Balkan peoples.


A Tuscan relation to the Ancient Greeks? Very little, except a very very few Tuscans who could descend from the Mycenaeans/ancient Greeks and a shared neolithic/bronze age mediterranean substratum. From an autosomal point of view when two samples show similar amounts of ancestral components does not imply that these components have exactly the same origin.

So what you're saying is you doubt the study for this thread?
 
So what you're saying is you doubt the study for this thread?

What I've said, this study seems too interested in showing a similarity between Greeks and Italians to distance themselves from other Balkan peoples. 95% of similarity with the Italians? It seems frankly too high. And why did they not specify who these Italians are? What does "shared ancestry" exactly mean?

And, above all, why did they use in their comparisons only northern Slavic populations (Russians, Polish, Belarussians, Ukranians) and not southern Slavic populations like Bulgarians, Serbs or Macedonians (from Fyrom)?

Obviously there is a similarity between Greeks, Italians and other populations in southern Europe. But the lack of clarity of the study in certain passages of the paper and other details suggest some conclusions are somewhat exaggerated.

Jw4tMNh.jpg
 
What I've said, this study seems too interested in showing a similarity between Greeks and Italians to distance themselves from other Balkan peoples. 95% of similarity with the Italians? It seems frankly too high. And why did they not specify who these Italians are? What does "shared ancestry" exactly mean?

And, above all, why did they use in their comparisons only northern Slavic populations (Russians, Polish, Belarussians, Ukranians) and not southern Slavic populations like Bulgarians, Serbs or Macedonians (from Fyrom)?

Obviously there is a similarity between Greeks, Italians and other populations in southern Europe. But the lack of clarity of the study in certain passages of the paper and other details suggest some conclusions are somewhat exaggerated.

http://www.nature.com/ejhg/journal/v25/n5/fig_tab/ejhg201718f2.html#figure-title

But doesn't the PCA make it clear which Italians they are referring to?
 
Since you say it is clear, is it an average of all the Italian samples? If not, what is it?

In that PCA only northern Italians from Bergamo are labeled as Italians.

So, have some Peloponessians 95% of shared ancestry with northern Italians from Bergamo?


Clearly its inferring the TSI group.

b) PCA analysis of Southern European populations illustrating the close relationship between Peloponneseans Sicilians and Italians (TSI is an Italian population)
http://www.nature.com/ejhg/journal/...1718f2.html?foxtrotcallback=true#figure-title
 
As Pax pointed out, the DeGaetano study is seriously flawed as they only considered place of birth for the samples they themselves collected. I complained to them at the time. I couldn't believe they made such a stupid mistake in a country which has experienced such massive internal migration from south to north. It's virtually useless as a result of that mistake imo because there's no untangling it now.

As for the subject paper, which is what we should be discussing on this thread, they were definitely sloppy in some of the presentation, not carefully labeling which precise groups of Italians were being portrayed in various graphs and tables. That doesn't invalidate the general conclusions at least in so far as Greeks and the southern Italians, at least, are concerned. Also, I'd just point out that similarity does not necessarily imply migration from Mycenaean (or Minoan) Greece, or first millennium BC Greece (from which we have as yet no samples) to Sicily and Southern Italy. It could be the result of similar Neolithic or even early Bronze Age migration from one or more populations to both places. We just won't know until we have samples from the appropriate time periods in Italy, and even then it may be difficult to disentangle it because of the similarities.

As to why there aren't reference samples from the Balkans, we've already discussed it. The purpose of the paper was to debunk Nordicist 19th century speculations that modern Greeks are the result of admixture between "Slavic" populations and recent Near Eastern migrants, both of whom were considered "inferior" peoples by the Nordicists of the time. Regardless, that has nothing to do with comparisons to Italians.

Now, can we get back to the topic?
 
Clearly its inferring the TSI group.

I have read enough studies to say that it's not so clear, Jovialis. They are not saying that Italians in table 2 are TSI only, or TSI + Sicilians.

They are saying that Peloponnesians show a close relationship with Sicilians and Italians (TSI is an Italian population). The words in brackets does not mean what you are trying to prove. They are just explaining what the acronym TSI is, being that TSI is the only Italian sample labeled with an acronym (the other one is IBS, Iberians).
 
I have read enough studies to say that it's not so clear, Jovialis. They are not saying that Italians in table 2 are TSI only, or TSI + Sicilians.

They are saying that Peloponnesians show a close relationship with Sicilians and Italians (TSI is an Italian population). The words in brackets does not mean what you are trying to prove.

You're extremely presumptuous, and rude. I'm merely linking the graphic from the study, and asking questions.
 
The study finds 85-96 percent similarity between the Greeks and south Italians, not Tuscans or north Italains. And the greater difference seems to be from additional Slavic ancestry. If you take a look at the first pca, the Greeks who don't plot with Sicily are more north and closer to the 85 percent figure, again due to additional Slavic.
 

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