Population structure in Italy using ancient and modern samples

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Originally Posted by Pax Augusta

They are all academic samples.

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And? That may be, but if so, the academics didn't check the ancestry of those people carefully enough, because there's no way in hell those two samples are 100% Ashkenazi. The Wales sample is also highly suspect. Maybe the researchers were oblivious to the fact that quite a few Italians settled in Wales.

Therefore, they shouldn't be used. Inclusion in a PCA, for example is going to throw it off.

The Corsican samples should also all be carefully checked, because apparently the researchers didn't give a darn whether some of them were French admixed.

Dienekes always carefully checked each and every sample, academic or not, to make sure it should be included.

No offense to people working on this, of course, but we all want accuracy, I'm sure.

I re-extracted the raw-data (Win and Linux) and ran the Dodecad K12b with a variety of apps.

... test subject WalesL45:

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WalesL45_AdmixtureStudio,6.74,0.5,2.5,0,30.35,29.65,0,0,7.52,1.13,21.6,0
WalesL45_Admix_Linux,6.74,0.50,2.49,0,30.36,29.66,0,0,7.52,1.13,21.60,0
WalesL45_DIYDodecadWin,6.58,0.47,2.36,0.05,30.51,29.44,0.25,0,7.87,1.12,21.34,0
WalesL45_DIYDodecadLinux64,6.58,0.47,2.36,0.05,30.51,29.44,0.25,0,7.87,1.12,21.34,0
WalesL45_DIYDodecadLinux64_10-iteration,6.58,0.46,2.36,0,30.51,29.44,0.24,0,7.87,1.18,21.34,0

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https://i.imgur.com/W9n9Atn.gif

… looks OK, I guess.

Never thought it was your error, Salento, but something must have gone wrong with the selection of that sample.

What are scientific samples? … samples collected from a specific verified area … It doesn’t necessarily mean that those samples must match each other.

The scientific list below has 109 samples collected in Tuscany, … COLLECTED in … Some of the samples on that list do not resemble typical Tuscans.

They made available the block of samples collected in Tuscany, … after that it's up to others which samples to use or not to use or how to label them.


https://i.imgur.com/HSX3FMb.gif

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Originally Posted by Angela

Never thought it was your error, Salento, but something must have gone wrong with the selection of that sample.

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thanks, Angela, I understand that some samples look strange, I guess we could omit some samples, … carefully avoiding being biased :)

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Originally Posted by Angela

And? That may be, but if so, the academics didn't check the ancestry of those people carefully enough, because there's no way in hell those two samples are 100% Ashkenazi. The Wales sample is also highly suspect. Maybe the researchers were oblivious to the fact that quite a few Italians settled in Wales.

Therefore, they shouldn't be used. Inclusion in a PCA, for example is going to throw it off.

The Corsican samples should also all be carefully checked, because apparently the researchers didn't give a darn whether some of them were French admixed.

Dienekes always carefully checked each and every sample, academic or not, to make sure it should be included.

No offense to people working on this, of course, but we all want accuracy, I'm sure.

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I was stating a fact: these are indeed academic samples. They have been dowloaded by academic sites by Salento, who is not responsible at all for their strange results, because outliers and especially mislabeled individuals (who don't fully belong to the label, who may have been born in the place, to which the label refers, to parents who have migrated from elsewhere) are really here and there in the academic sample sets. For many different reasons. This is frequently seen happening, for more than 10 years in academic studies. Sometimes they represent a percentage of the set not large enough to influence the average too much, other times as in the case of Corsicans they represent 25 percent of the individuals, if memory serves me, and influence the average more. There are attentative geneticists who remove them, other geneticists who use them all.

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Originally Posted by Salento

What are scientific samples? … samples collected from a specific verified area … It doesn’t necessarily mean that those samples must match each other.

The scientific list below has 109 samples collected in Tuscany, … COLLECTED in … Some of the samples on that list do not resemble typical Tuscans.

They made available the block of samples collected in Tuscany, … after that it's up to others which samples to use or not to use or how to label them.

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Thanks Salento for that. That's the TSI sample set, it belongs to 1000genomes/HapMap projects. Or rather, TSI is a sample set from the HapMap project shared with 1000genomes.

https://i.imgur.com/GDtfxZe.png

In this sample set there are definitely individuals who are not 100 percent Tuscan, the same people who collected this sample around 2006 or 2007 confirmed this (I also found the date but can't remember it precisely now).

As stated in the project data sheet that I found 4 or 5 years ago and I believe also already published it on Eupedia, TSI is set of individuals based on self reported people with "at least three out of four grandparents who were born in Tuscany."

Aside from the fact that one of the grandparents may be non-Tuscan, even the fact that the other three were simply born in Tuscany (and their full ancestry from the Tuscany is not proven but only self reported) may lead to further inaccuracy.

I think it is the only sample set, but I am really going from memory, of 1000genomes/HapMap projects that does not guarantee that all grandparents are native.

In general, I think that being the sample set really large, there are 117 in all, many are completely Tuscan for real, but obviously not all of them are, and so the most obvious outliers (those that move away from the main cluster) should be removed and in any case not be considered. Again, in the past some geneticists have removed outliers from this sample set, but that doesn't always happen. The Estonian geneticist Metspalu used in his studies a subset of TSI, which he labeled TSI30 (I think based on 21 or 30 individuals from this set chosen by him). Diekenes in his calculators used this specific subset created by Metspalu, TSI30.


Official statement from the TSI HapMap project.

https://i.imgur.com/DsKtT7f.png

I bet R437 wasn't much of an "outlier" if you traveled to the south in the IA. But I guess we just have to wait and see.

INB4 someone mentions Daunians.

These people are late bronze age invaders.

I.e. forgiener/aliens.

I looked at the coordinates of the TSIs big list.
but … the Tuscan and the TSI30 of the original Vahaduo don’t match the updated Vahaduo Tuscan,

… the end result is that the TSIs that match the original don’t match the updated, and the TSIs that match the updated don’t match the original.

Posting the TSIs coordinates would create too much confusion, I think.

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Originally Posted by Salento

I looked at the coordinates of the TSIs big list.
but … the Tuscan and the TSI30 of the original Vahaduo don’t match the updated Vahaduo Tuscan,

… the end result is that the TSIs that match the original don’t match the updated, and the TSIs that match the updated don’t match the original.

Posting the TSIs coordinates would create too much confusion, I think.

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Indeed, agreed.

Samples from most of Italy are missing for the Iron Age. I do not understand why studies on Iron Age Italy presented almost a year ago have not yet come out. However, it is possible that slowly the picture will be clarified.

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Originally Posted by Jovialis

I bet R437 wasn't much of an "outlier" if you traveled to the south in the IA. But I guess we just have to wait and see.

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Antonio 2019 has a table listing the full outliers, R437 and R850 are not on the list, … and they are Scientific Samples :)

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Originally Posted by Salento

Antonio 2019 has a table listing the full outliers, R437 and R850 are not on the list, … and they are Scientific Samples :)

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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?

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Originally Posted by Jovialis

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?

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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)

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Originally Posted by Salento

Antonio 2019 has a table listing the full outliers, R437 and R850 are not on the list, … and they are Scientific Samples :)

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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

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Originally Posted by Salento

thanks, Angela, I understand that some samples look strange, I guess we could omit some samples, … carefully avoiding being biased :)

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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.

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Originally Posted by torzio

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

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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.

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Originally Posted by Jovialis

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?

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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.

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Originally Posted by Leopoldo Leone

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)

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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

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Originally Posted by Palermo Trapani

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

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Cool! I'll check it out if there is anything different.

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Originally Posted by Jovialis

Cool! I'll check it out if there is anything different.

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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

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Originally Posted by Jovialis

"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

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I'll take a look and then I'll take it from there :)