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Thread: The Italian Genome-Fiorito et al 2015

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    The Italian Genome-Fiorito et al 2015

    This is one of the papers I've been waiting for, and it's behind a pay wall. Oh well...

    The Italian genome reflects the history of Europe and the Mediterranean basin
    http://www.nature.com/ejhg/journal/vaop/ncurrent/suppinfo/ejhg2015233s1.html?url=/ejhg/journal/vaop/ncurrent/abs/ejhg2015233a.html


    "Abstract

    Recent scientific literature has highlighted the relevance of population genetic studies both for disease association mapping in admixed populations and for understanding the history of human migrations. Deeper insight into the history of the Italian population is critical for understanding the peopling of Europe. Because of its crucial position at the centre of the Mediterranean basin, the Italian peninsula has experienced a complex history of colonization and migration whose genetic signatures are still present in contemporary Italians. In this study, we investigated genomic variation in the Italian population using 2.5 million single-nucleotide polymorphisms in a sample of more than 300 unrelated Italian subjects with well-defined geographical origins. We combined several analytical approaches to interpret genome-wide data on 1272 individuals from European, Middle Eastern, and North African populations. We detected three major ancestral components contributing different proportions across the Italian peninsula, and signatures of continuous gene flow within Italy, which have produced remarkable genetic variability among contemporary Italians. In addition, we have extracted novel details about the Italian population’s ancestry, identifying the genetic signatures of major historical events in Europe and the Mediterranean basin from the Neolithic (e.g., peopling of Sardinia) to recent times (e.g., ‘barbarian invasion’ of Northern and Central Italy). These results are valuable for further genetic, epidemiological and forensic studies in Italy and in Europe."

    I really love no information abstracts, don't you? :)


    This is the link to the Supplementary Info:
    http://www.nature.com/ejhg/journal/v...g2015233a.html

    I've gone through it all and I have some thoughts, but it's too late to get into it now. :) I'll just say that although it's better than the Busby effort, some of the choices are still obscure to me, and at least in the supplement there is no clarity as to the direction of the gene flow. Maybe if I can get my hands on the actual paper it will seem clearer, but I also get the feeling, as I did with the Busby paper, that I'm back to a time five years or more in the past before Lazaridis et al or Haak et al and Allentoft et al.

    To get started, nothing really new on the PCA front except that Armenians are so removed from other Near Easterners. Turks as well to a certain extent. :
    PCA from the Italian Genome Paper-2015.jpgPCA from the Italian Genome Paper-2015.jpg

    There's also a graphic on Italian variation. The general cline is as expected, except that Calabrians (Reggio Calabria) are south of some of the Sicilians. That may have to do with the samples chosen for Sicily, which are Trapani and Ragusa. I doubt that there'd be much difference between Reggio and, say, Messina, but some Sicilian posters might know better. Also, there are some samples floating out of the expected cline in north and central Italy. This may have to do with the fact that there has been a certain amount of intermarriage across provincial lines in northern and central Italy starting around the end of the 19th century. I can't see anything in the supplement as to their standards for sample inclusion. Not that it would make much difference, but I don't know why they would have chosen Ferrara for Emilia Romagna.

    Italian variation-The Italian Genome Paper 2015.jpg
    Last edited by Angela; 12-11-15 at 16:14. Reason: To correct link


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    I just made a thread for the same study. Can you delete it?

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    The study attempted to date the North African and Middle Eastern DNA among Italians. The summary of the results is found in the file entitled "Supplementary Information". For Northern Italians it is given as being from late Roman times (about 1400 years ago), and for Southern Italians it is given as medieval (about 1000 years ago). The admixture in Central Italians is said to be older, going from back before Etruscan times (about 3000 years ago) to Roman times (about 1800 years ago.) They also attempted to date the Northern/Central European DNA in North Italy, they estimated it to Roman times (about 1700 years ago.)

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    This confirm again that Sicily is genetically close to mainlander southern Italians.
    Sicilians and mainlander Southern Italian phenotype galleries.

    http://italicroots.lefora.com/topic/1111/Re-Groups-of-Sicilians
    http://italicroots.lefora.com/topic/375/Southern-italians-how-we-really-look

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    Quote Originally Posted by Hauteville View Post
    This confirm again that Sicily is genetically close to mainlander southern Italians.
    Yes, indeed. That's the same thing that the dodecad analyses showed years ago, but which some doubted.

    I also found it interesting that there is still some minor variation in Sicily. If you go through the supplementary info section's graphics, in particular the Admixture ones, you can see it. I have to think about it some more but I wonder if it is a northwest versus southeast difference given the two areas where they chose to sample. The Boattini et al studies showed more Northern and Central European yDna in the northwest than elsewhere on the island if I remember correctly.

    It's impossible to know how much variation there might be in Calabria if you go down to a fine enough resolution, because they only sampled in Reggio Calabria.

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    The samples are both from North West Sicily (Trapani) and far South East (Ragusa), Basilicata's samples are from both Matera and Potenza. It's quite interesting the position of Latium judging on the fact that on Behar et al Abruzzo samples were distant to Tuscany while the ones from Latium are very close to them. They are from Viterbo who are very close to Tuscany geographically and it was a very Etruscan area.

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    This is Fire-Haired's comment from a duplicate thread he started.


    New Study, Italian diversity: Mostly Geography

    The paper is under paywall but there's lots of useful information in the Supplementary information. I made lots of notes from it I'll share later. Basically all the tests, IBD, ADMIXTURE, and PCA, say Italian genetic diversity correlates with geography. There's lots of good info in this study.


    I think there was an old study way back which found Italy is one of the most genetically diverse countries in Europe. A good question is: How old could this diversity be and what caused it? My guess is the diversity goes back to at least the pre-Roman Iron age, if people for the most part have stayed in their own regions since then.


    IMO, Italy received immigration from North of the Alps and East Mediterranean after the Copper age, and the populations in Italy before that were "EEF" with little WHG-admixture. We'll need ancient DNA to know the population history.
    Last edited by Angela; 12-11-15 at 22:17.

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    It would be nice to have new ancient samples from everywhere of Italy other than Otzi and Remedello.

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    Quote Originally Posted by Angela View Post




    Fire Haired:

    New Study, Italian diversity: Mostly Geography


    The paper is under paywall but there's lots of useful information in the Supplementary information. I made lots of notes from it I'll share later. Basically all the tests, IBD, ADMIXTURE, and PCA, say Italian genetic diversity correlates with geography. There's lots of good info in this study.


    I think there was an old study way back which found Italy is one of the most genetically diverse countries in Europe. A good question is: How old could this diversity be and what caused it? My guess is the diversity goes back to at least the pre-Roman Iron age, if people for the most part have stayed in their own regions since then.


    IMO, Italy received immigration from North of the Alps and East Mediterranean after the Copper age, and the populations in Italy before that were "EEF" with little WHG-admixture. We'll need ancient DNA to know the population history.


    Good insights, Fire-Haired.

    I think the paper you're referring to is Ralph and Coop et al. It's not that old; it's 2013! :)

    Years ago, Dienekes said that Italian genetics could be explained by a Neolithic substratum that covered the whole area, and then migrations from the north that had a disproportionate effect from north to south, and migrations from the east and south-east that had a disproportionate effect from south to north, created the cline and the clusters we see today. It sounded about right then and it sounds about right now.

    The devil is in the details, however, and it looks like ancient dna is going to be necessary to flesh them out. Certainly, this type of Alder analysis, also attempted by Busby and Hellenthal, just isn't cutting it, although I think this one is better, both because they show a wide variety of possible mixes (none of which are going to be accurate, of course, because they're using modern populations, but still a variety), and they're giving a range of dates, which means it's easier to tie some of this to actual historical events.

    What actually happened, in Italy as in most places in Europe, although perhaps more in Italy, is that there were layers of migrations impacting the same areas that came from the same parts of the world, and Alder can't sort them out. The same thing happened with Iberia. It couldn't sort out if the SSA and North African came in the Mesolithic, the Paleolithic or the Moorish era. The yDna and mtDna paper that just came out that used highly resolved subclades actually did a better job, in my opinion.
    Last edited by Angela; 12-11-15 at 16:18. Reason: grammar

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    Quote Originally Posted by Hauteville View Post
    The samples are both from North West Sicily (Trapani) and far South East (Ragusa), Basilicata's samples are from both Matera and Potenza. It's quite interesting the position of Latium judging on the fact that on Behar et al Abruzzo samples were distant to Tuscany while the ones from Latium are very close to them. They are from Viterbo who are very close to Tuscany geographically and it was a very Etruscan area.
    Well, they knew enough not to sample from Latina or Frosinone; I think samples from there would have clustered with southern Italians. Choosing where to sample in Lazio is actually a problem, given how much migration there's been to the area from all over the country going back a hundred years in some cases. So, I guess they were stuck with areas closer to Toscana.

    I never bought into that whole thing that the Abruzzi and Lazio were so similar. I just thought they were probably sampling a lot of people who had ancestry from the Abruzzi. There's lots of them in Lazio. It's like people from Liguria going to Torino to work. It's been happening for a hundred years, way before the massive 1950s era migrations.

    Their Tuscan samples are Arezzo and Siena. I think they should really have included one more from the North West so we could see if there was more overlap with Liguria etc.

    I still don't think Ferrara was the best choice for Emilia Romagna.

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    Quote Originally Posted by Angela View Post
    Well, they knew enough not to sample from Latina or Frosinone; I think samples from there would have clustered with southern Italians. Choosing where to sample in Lazio is actually a problem, given how much migration there's been to the area from all over the country going back a hundred years in some cases. So, I guess they were stuck with areas closer to Toscana.

    Their Tuscan samples are Arezzo and Siena. I think they should really have included one more from the North West so we could see if there was more overlap with Liguria etc.

    I still don't think Ferrara was the best choice for Emilia Romagna.
    Yeah it's true. Modern people from Latina is mostly Venetian nowadays, while in Rome basically it lives all Italy. Surely the Tuscans from Lucca or Pisa were much more close to Ligurians.

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    Aostan cluster pretty north but i do not understand if they refer to the French Aostans or Italian ones.

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    Quote Originally Posted by Hauteville View Post
    Yeah it's true. Modern people from Latina is mostly Venetian nowadays, while in Rome basically it lives all Italy. Surely the Tuscans from Lucca or Pisa were much more close to Ligurians.
    Wouldn't it be a mix in Latina? Venetians plus southerners? Wasn't Latina part of the Kingdom of the Two Sicilies until Mussolini? Or am I misremembering?

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    It shouldn't be a surprise to anyone that there's quite a difference genetically between northern and southern Italians, but the fst numbers showed a difference a bit larger than I had been expecting.

    It was noted by Dienekes on his blog post about the paper.

    http://www.dienekes.blogspot.com/201...-italians.html

    "From the paper:
    The distribution of the pairwise Fst distances between all population pairs is shown in Supplementary Table S3. The genetic distance between Southern and Northern Italians (Fst=0.0013) is comparable to that between individuals living in different political units (ie, Iberians-Romanians Fst=0.0011; British-French Fst=0.0007), and, interestingly, in >50% of all the possible pairwise comparisons within Europe (Supplementary Figure S7)."



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    Quote Originally Posted by Angela View Post
    Wouldn't it be a mix in Latina? Venetians plus southerners? Wasn't Latina part of the Kingdom of the Two Sicilies until Mussolini? Or am I misremembering?
    Gaeta yes, but Latina was founded in Fascist period and it was populated with Venetians and some other northern Italians as well.
    l comune di Littoria fu popolato con l'immigrazione massiccia di coloni soprattutto veneti, friulani, emiliani eromagnoli, oggi denominati nell'insieme comunit venetopontine, ai quali furono consegnati i poderi edificati dall'Opera Nazionale Combattenti, similmente a quanto operato nei limitrofi comuni della pianura.
    https://it.wikipedia.org/wiki/Latina#La_fondazione

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    Quote Originally Posted by Hauteville View Post
    Gaeta yes, but Latina was founded in Fascist period and it was populated with Venetians and some other northern Italians as well.

    https://it.wikipedia.org/wiki/Latina#La_fondazione
    Ah, I see. I was thinking of the provincia of Latina, and so including Gaeta and Formia, and just speculating that if you took samples from the two areas you'd probably get very different results. (given there hadn't been any intermarriage, of course)

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    Just to go back to the graphic showing all the Italian samples in relation to one another, it's interesting how there really isn't much of a cline within Northern Italy itself, other than Aosta clusering further north. Lombardia, Piemonte, Liguria and Romagna (it's not Emilia at all since it's all from Ferrara) are all jumbled up together. (You like that technical genetic jargon? :))

    Why didn't they include a couple of samples from the Veneto, I wonder? I think they might occupy the area where Aosta and the rest of the northern Italians meet. Had they sampled Friulani, they might have been listing off to the east toward Slovenia a bit.

    It's supported by the IBD analyses that they did. Lots of IBD sharing among Northern Italians and between Northern and Central Italians and very little between Southern Italians and people from north of Rome. Fwiw, that's borne out by the analyses that 23andme used to do, but won't be doing any longer, apparently. I have yet to get a match at the default level with anyone from southern Italy. They're all northern Italians, specifically northwest Italians, or Tuscans, with a few odd ducks from Sweden and one with British Isles ancestry.

    For those who aren't Italian, they obviously chose people with ancestry only from these specific areas in order to figure out the migrations which have affected Italy. There's going to be a lot of people in modern Italy who have IBD sharing running both north and south, stemming from intermarriages after the large migration from southern Italy to northern Italy during and after the 1950s. It's just that they weren't included in the analysis.

    The Italian Genome-Italian variation.jpg
    Attached Images Attached Images

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    Quote Originally Posted by Eldritch View Post
    Aostan cluster pretty north but i do not understand if they refer to the French Aostans or Italian ones.
    See:
    https://en.wikipedia.org/wiki/Aosta_Valley

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    The Alder analysis is the weakest part of the paper, I think. For what they're worth, here are the three graphics where any number of "admixtures" and "admixture times" are proposed.

    The Italian Genome Paper-Admixture Dates for Northern Italy.jpg

    The Italian Genome Paper-Admixture Dates for Central Italy.jpg

    The Italian Genome Paper-Admixture Dates for Southern Italy.jpg

    Some of the ones for Central Italy make a little more sense...Russians and Druze maybe around 1000 BC? Indo-Europeans arriving around 1800 to 2000 BC but admixture lagging a bit behind?

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    Quote Originally Posted by Angela View Post
    The Alder analysis is the weakest part of the paper, I think. For what they're worth, here are the three graphics where any number of "admixtures" and "admixture times" are proposed.

    The Italian Genome Paper-Admixture Dates for Northern Italy.jpg

    The Italian Genome Paper-Admixture Dates for Central Italy.jpg

    The Italian Genome Paper-Admixture Dates for Southern Italy.jpg

    Some of the ones for Central Italy make a little more sense...Russians and Druze maybe around 1000 BC? Indo-Europeans arriving around 1800 to 2000 BC but admixture lagging a bit behind?

    From my perspective, some of these results are just silly if taken at face value or perhaps if taken literally is a better way to put it. Look at the chart for southern Italians, for example. We know from prior work and this paper as well that there's a minor North African input into southern Italians. We know that there was Saracen rule from about 700-1000 AD (depending on the area). Looking for the ones in that target date, they came up with Basque and Mozabite, Iberian and Egyptian, Lithuanian and Moroccan and Finnish and Druze. Really? Those were the two populations who admixed? Lots of Basques, Lithuanians and Finns running around in Sicily before the North Africans showed up? :) The North Africans were just the last layer of migration.

    For Central Italians it's a bit better. A "Russian" like population and a "Druze" like population might roughly approximate what went on around 1000 BC if the Indo-Europeans didn't arrive there until around 1800 BC and admixture took a little longer?

    For Northern Italians too, Lezghins/Syria 1000 BC might not be too bad? Not good, mind you, just not as bad as most of them.

    Or again, because of repeated layers of migration from the same general areas, the dates just represent the latest layer.
    Last edited by Angela; 12-11-15 at 20:51.

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    No the North African admixture is present only in Sardinia, Calabria and Sicily. Calabrian samples are only from Reggio Calabria, so they are clearly mixed with Sicilians.

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    Quote Originally Posted by Angela View Post

    Their Tuscan samples are Arezzo and Siena. I think they should really have included one more from the North West so we could see if there was more overlap with Liguria etc.

    I still don't think Ferrara was the best choice for Emilia Romagna.
    I agree, Ferrara isn't really Emilia and neither Romagna. Neither Arezzo and Siena are the best choice for the whole Tuscany but just good enough for Southern Tuscany. I agree they should really have included one more from the North West Tuscany, Pistoia and Lucca would be good choices.

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    Why do you think is there such a large genetic distance between northern and southern Italians?

    Also - is there an intermediary population (central Italians?), or a "very sharp" boundary?

    And if there is a sharp genetic boundary, then roughly where is the dividing line?

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    Quote Originally Posted by Angela
    Basically all the tests, IBD, ADMIXTURE, and PCA, say Italian genetic diversity correlates with geography.
    Sorry but if even Iberians are closer genetically to Romanians, than Northern Italians are to Southern Italians, then we can't say it is "just geography". It correlates with geography only as far as different ancestral ethnic groups settled different geographical areas...

    Geographical distance from Iberia to Romania is many times greater, than from Southern Italy to Northern Italy...

    And you also wrote, that there is (or was until ca. 1950) almost no IBD sharing between Southern and Northern Italy - why?

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    Quote Originally Posted by Danelaw View Post
    No the North African admixture is present only in Sardinia, Calabria and Sicily. Calabrian samples are only from Reggio Calabria, so they are clearly mixed with Sicilians.
    We have no way of knowing that. They didn't include Apulia (which usually just looks southern Italian) or Campania, for example.

    From the evidence of 23andme, and Dodecad, it seems that Sicilians and southern Italians, all southern Italians, cluster together generally speaking, and show the same minority ancestry, although I would speculate that the cline is still there so there's probably slightly less North African as you move north, not that there's much to begin with...much less than you can find in Iberia for example, although it doesn't appear that way here because they don't use samples from all over Spain and Portugal. (That's what the results I've seen seem to indicate as well.)

    I know that's not what some Sicilians themselves have tended to believe, but it seems to be a fact. (I should send this to an old professor of mine from university. He always insisted to his students that he was Sicilian, not Italian, not even southern Italian. Of course, culture is what matters the most, so he might not be swayed by these results. :)

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