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Thread: Genomic Diversity in Italy

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    6 members found this post helpful.

    Genomic Diversity in Italy

    See:

    Sazzini et al
    https://bmcbiol.biomedcentral.com/ar...15-020-00778-4

    "Background

    The cline of human genetic diversity observable across Europe is recapitulated at a micro-geographic scale by variation within the Italian population. Besides resulting from extensive gene flow, this might be ascribable also to local adaptations to diverse ecological contexts evolved by people who anciently spread along the Italian Peninsula. Dissecting the evolutionary history of the ancestors of present-day Italians may thus improve the understanding of demographic and biological processes that contributed to shape the gene pool of European populations. However, previous SNP array-based studies failed to investigate the full spectrum of Italian variation, generally neglecting low-frequency genetic variants and examining a limited set of small effect size alleles, which may represent important determinants of population structure and complex adaptive traits. To overcome these issues, we analyzed 38 high-coverage whole-genome sequences representative of population clusters at the opposite ends of the cline of Italian variation, along with a large panel of modern and ancient Euro-Mediterranean genomes.
    Results

    We provided evidence for the early divergence of Italian groups dating back to the Late Glacial and for Neolithic and distinct Bronze Age migrations having further differentiated their gene pools. We inferred adaptive evolution at insulin-related loci in people from Italian regions with a temperate climate, while possible adaptations to pathogens and ultraviolet radiation were observed in Mediterranean Italians. Some of these adaptive events may also have secondarily modulated population disease or longevity predisposition.
    Conclusions

    We disentangled the contribution of multiple migratory and adaptive events in shaping the heterogeneous Italian genomic background, which exemplify population dynamics and gene-environment interactions that played significant roles also in the formation of the Continental and Southern European genomic landscapes.


    So far so good. As I always proposed, a good part of the longevity of Italians can be attributed to genes. Good habits certainly also play a factor, especially food and low alcohol intake.

    I have one major problem with it already, however. Most Italians aren't "at" the extremes of the genetic variation. They're isn't a wall just south of Rome, even if it is a "break". Variation in Italy is still clinal.


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    Is it just me, or is there a big problem with assuming that variants more associated with continental Europe actually represent continued ancestry from the Upper Paleolithic versus those variants being re-introduced to Italy during subsequent migrations from the north?

    Did they check the Neolithic inhabitants of Northern Italy to see if they have those variants? Wouldn't that be the only way of knowing?
    Do

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    Quote Originally Posted by Angela View Post
    Is it just me, or is there a big problem with assuming that variants more associated with continental Europe actually represent continued ancestry from the Upper Paleolithic versus those variants being re-introduced to Italy during subsequent migrations from the north?

    Did they check the Neolithic inhabitants of Northern Italy to see if they have those variants? Wouldn't that be the only way of knowing?
    Do
    Sazzini once again proves that he is not a very capable population geneticist.

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    " However, the appreciable frequency of some maternal strains, especially in southern Italy, suggested a link with the populations of the Caucasus and the Levant, which predates the Neolithic and may support the role of this area as a refugee during the Last Glacial Maximum (LGM)"

    Perhaps this explains why part of the Italian population goes more towards the eastern Mediterranean - different from the Sardinians. Not that this is anything new, but I was generally in doubt whether this difference was before or after the EEF colonization of Europe.

    I don't know if there is another country in Europe with as much internal diversity as Italy, but France also seems to be quite diverse if you compare Brittany with Occitania or Provence. Anyway, I believe that diversity is good and each region has its own customs, traditions and why not; genetic variability

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    I think perhaps they should have applied some more critical thinking to some of these associations. I can see that there might, in fact undoubtedly are, pigmentation genes in Southern Italy, leaching into the center, which promote rapid and dark tanning. I used to occasionally visit an expat site where Americans living in Southern Italy would exclaim over how much "lighter" the locals were in the winter than the summer.

    Likewise, perhaps there is something to the claim that southern Italians have immune systems more aggressive toward pathogen infection. Hot climates equal more pathogens, so it makes sense. It might even have a bit to do with lower Covid 19 rates there. Who knows?

    The finding about obesity and diabetes, by which I assume they mean Type 2 Diabetes, needs further investigation. (I'll have to check that when I go through everything more carefully, including the Supplement.)

    Just generally, diabetes doesn't have much to do with meat and fat consumption, except in so far as it adds to the total calories. From what I've seen the first thing that specialists advise is to cut out too processed carbohydrates.

    Here is a diabetes incidence map. Unfortunately, I couldn't find one which broke out Type 1 diabetes from the total; however, it seems Type 1 only represents 1-3% at the most.



    Furthermore, the obesity figures don't bear this out. They are extremely high in Great Britain, high in the east and northeast etc. areas which have quite a bit more WHG/EHG ancestry. The U.S., predominantly northwestern European as far as "white" people are concerned, are if not the most obese people in the world, one of the most obese. You should try walking around the Walmarts in Alabama/Mississippi or Michigan etc. As one more example, Spain has more WHG than even Northern Italy, but obesity figures are higher.



    Really, before publishing I think they should have done some more research.

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    Quote Originally Posted by Angela View Post
    I think perhaps they should have applied some more critical thinking to some of these associations. I can see that there might, in fact undoubtedly are, pigmentation genes in Southern Italy, leaching into the center, which promote rapid and dark tanning. I used to occasionally visit an expat site where Americans living in Southern Italy would exclaim over how much "lighter" the locals were in the winter than the summer.

    Likewise, perhaps there is something to the claim that southern Italians have immune systems more aggressive toward pathogen infection. Hot climates equal more pathogens, so it makes sense. It might even have a bit to do with lower Covid 19 rates there. Who knows?

    The finding about obesity and diabetes, by which I assume they mean Type 2 Diabetes, needs further investigation. (I'll have to check that when I go through everything more carefully, including the Supplement.)

    Just generally, diabetes doesn't have much to do with meat and fat consumption, except in so far as it adds to the total calories. From what I've seen the first thing that specialists advise is to cut out too processed carbohydrates.

    Here is a diabetes incidence map. Unfortunately, I couldn't find one which broke out Type 1 diabetes from the total; however, it seems Type 1 only represents 1-3% at the most.



    Furthermore, the obesity figures don't bear this out. They are extremely high in Great Britain, high in the east and northeast etc. areas which have quite a bit more WHG/EHG ancestry. The U.S., predominantly northwestern European as far as "white" people are concerned, are if not the most obese people in the world, one of the most obese. You should try walking around the Walmarts in Alabama/Mississippi or Michigan etc. As one more example, Spain has more WHG than even Northern Italy, but obesity figures are higher.



    Really, before publishing I think they should have done some more research.
    I haven't finished reading it all yet, but the article claims to be the broadest ever done in Italian populations. I think the issue of pigmentation is the most irrelevant in genomic terms - generally pigmentation genes represent a miniscule / negligible amount of the total genome of a person or population.






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    In fact: there is a Sicilian rap clip that I love and people are very tanned - even rap discusses discrimination with Southern Italians. I believe that most southern Italians are happy to be from the south.






    [COLOR=rgba(0, 0, 0, 0.54)]
    [/COLOR][COLOR=rgba(0, 0, 0, 0.54)]
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    2 members found this post helpful.
    ^^That sentiment seems to exist in Portugal as well, when I was in the airport in Porto, the buffoon airport officer asked us where we had stayed. We told him we were in Lisbon, and he felt the need to express how much he disliked people from that region, because of "different culture". To an outsider, the culture seemed fairly the same to me.

    The guy in Porto sort of looked like that Sicilian guy in that video, actually.

    In terms of phenotype, Sardinians are darkest people in Italy. Perhaps the high amount of EEF in both Sardinians and Iberians can partly explain why they look as dark, or are darker than some Southern Italians. Despite being genetically "North" of Northern Italians:



    At any rate, this isn't a sociology thread, so lets get back on topic.
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    2 members found this post helpful.
    Quote Originally Posted by Ack View Post




    Sicilian rapper Ensi untanned.





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    Pax: Glad you posted it, Ensi looks like someone who tans in the summer and winter months gets fair. So freaking what? Ack most not understand the term "Terrone" it has a link back to people who were and are economically tied to agriculture, small family farmers or working for large land owners in Olive and Grape industry. For the record, I don't know who Ensi is as I don't folllow American rap much less Sicilian rap music. However, I have noticed on lots of the Italian shows on Mhz, there is lots of this music on the police shows like Inspector Coliandro, which I like, and the Roberto Saviano's Gommorah (hmm not so much).

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    Quote Originally Posted by Pax Augusta View Post
    Sazzini once again proves that he is not a very capable population geneticist.

    was this what annoyed you about marco Sazzini from Uni of Bologna ?

    https://www.youtube.com/watch?v=dDvqAkyc4sw

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    Quote Originally Posted by torzio View Post
    was this what annoyed you about marco Sazzini from Uni of Bologna ?

    https://www.youtube.com/watch?v=dDvqAkyc4sw

    Sazzini's papers are all mouth and no trousers. Tanto fumo e niente arrosto.

    This is from his last 2020 study. Does that make sense to you?




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    Quote Originally Posted by Pax Augusta View Post
    Sazzini's papers are all mouth and no trousers. Tanto fumo e poco arrosto.

    This is from his last 2020 study. Does that make sense to you?



    reminds me of Laz and his ....north italy = bulgaria-Bergamo-south france- basque theory

    did you click on the supplementary addition at bottom of the paper?

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    Quote Originally Posted by torzio View Post
    reminds me of Laz and his ....north italy = bulgaria-Bergamo-south france- basque theory

    It is certainly not his theory, but the most banal observation of any PCA. Throwing in Bulgaria with the south of France and the Basques is amateurish stuff in 2020 though.

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    Quote Originally Posted by Pax Augusta View Post
    It is certainly not his theory, but the most banal observation of any PCA. Throwing in Bulgaria with the south of France and the Basques is amateurish stuff in 2020 though.
    was it Miles , some say Laz, I doubt it was haak...............we can blame Laz on that ..............then again as some say here and other threads, papers more than 2 years old are useless ...............Laz, Haak ( 2015 ) etc ............it is not my thoughts

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    Quote Originally Posted by torzio View Post
    we can blame Laz on that ..............then again as some say here and other threads, papers more than 2 years old are useless ...............Laz, Haak ( 2015 ) etc ............it is not my thoughts

    There's a difference between paper and paper. Haak 2015 is based on the comparison between acient DNA and modern samples, other papers, like Sazzini's, are the usual speculations based on modern samples only.

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    Quote Originally Posted by Pax Augusta View Post
    It is certainly not his theory, but the most banal observation of any PCA. Throwing in Bulgaria with the south of France and the Basques is amateurish stuff in 2020 though.
    You run any kind of 4 participant Oracle will give you strange combinations because they are trying to best fit your ethnicity. Some of the combinations make sense from what we know of history and archaeology, others not so much.

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    3 members found this post helpful.
    The admixture stuff is amateurish indeed, embarrassing, really, given it's 2020.

    I think Sazzini worked with Hellenthal last time, and he's using the same programs Hellenthal used. You know, the one which found Armenian input in Poles in the Medieval Era. Oy veh!

    I thought after the Moots/Stanford paper it would have been clear that those tools don't date admixture properly. They just show you the most recent admixture, and even then not very accurately. Remember Hellenthal said there was a big admixture event of "Southeastern/Near Eastern" types with the more northwestern locals in AFTER the fall of Rome, i.e. the Byzantine Era, and proposed a migration at that time into Italy.

    The absurdity of that was made clear by ancient dna. Aegean/coastal Anatolian ancestry was already in Italy in 600 BC. In 350 BC? we have a Cretan like member of a Latin tribe. There was no mass migration from Byzantine areas to Italy. There was Langobard entry into parts of a very Mediterranean local population, but it was only the latest in a string of migrations via Central Europe, just as any "Southeastern" ancestry was just the latest string in migrations from the southeast, which began at least by the beginning of the Bronze Age.

    My goodness, didn't Sazzini and company realize that ancient dna completely nullified those findings they came to by working with Hellenthal?

    Honestly, as I said, as an Italian it's embarrassing to see them put out stuff like this.

    Another more general issue I have with the paper and the prior one, and Hellenthal et al: At what point does ancestry from Anatolia/northern Syria start becoming "Near Eastern"? Same question for Iran Neo/CHG ancestry. Words are my business, and definitions, and this kind of analysis is the absolute worst in terms of clarity of terms. Is the 45-50% EEF in the English and the Germans "Near Eastern" Is the Iran Neo/CHG in the Slavs "Near Eastern"?

    According to this paper, apparently not. So, when does it become Near Eastern? Late Bronze Age? Iron Age? Classical Era? Why does it suddenly become alien?

    As I've said before, to me it's just same old, same old. Same components in different percentages, coming from the same part of the world, using the same routes. The only difference is the time period, and additional Iran Neo. Big whoops.

    Also, given how all standard analyses show the similarity between Southern Italians and Greeks, especially Peloponnese and Island Greeks, and Northern Italians and Albanians, Bulgarians, etc. how come these groups are modeled so differently? Didn't that question ever occur to them? It invalidates the approach.

    God, don't they teach critical thinking any more?

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    Quote Originally Posted by Ack View Post
    I haven't finished reading it all yet, but the article claims to be the broadest ever done in Italian populations. I think the issue of pigmentation is the most irrelevant in genomic terms - generally pigmentation genes represent a miniscule / negligible amount of the total genome of a person or population.


    quite possible for me that, after the findings of Mathiesen, SL24A5 and those FZD genes are the only really important factors for pigmentation in westeurasia. SL24A5 gives the base while the darker populations are just tanning way faster maybe because of those FZD genes and never have long enough sunless periods to turn lighter.

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    Oh yeah, the tanning. My stepfather is 7/8 Italian (all southern) and even though I tan much better than my mother (who is 99.4% Northwest European, predominantly English), he makes me look like a Swede in the summer.

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    Quote Originally Posted by Pax Augusta View Post
    Sazzini's papers are all mouth and no trousers. Tanto fumo e niente arrosto.

    This is from his last 2020 study. Does that make sense to you?



    Any paper that only includes the Near-East ( Anatolia , Asia Minor ) for Italy and not the Caucasus is basically wrong ........the populace of Italy also included the people around the black sea , which was smaller in size and not linked to the med ................they also ignore Ghirotto 2013 paper that etruscans have been in Italy since 3000BC , so this Anatolian/near-east only for Italy is garbage

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    Quote Originally Posted by Jovialis View Post
    ^^That sentiment seems to exist in Portugal as well, when I was in the airport in Porto, the buffoon airport officer asked us where we had stayed. We told him we were in Lisbon, and he felt the need to express how much he disliked people from that region, because of "different culture". To an outsider, the culture seemed fairly the same to me.

    The guy in Porto sort of looked like that Sicilian guy in that video, actually.

    In terms of phenotype, Sardinians are darkest people in Italy. Perhaps the high amount of EEF in both Sardinians and Iberians can partly explain why they look as dark, or are darker than some Southern Italians. Despite being genetically "North" of Northern Italians:



    At any rate, this isn't a sociology thread, so lets get back on topic.
    At no time did I assume that tanning was in any way specific to Sicilians - I even mentioned that pigment alleles are a small part of the genome. Regardless of the total genome, whether more or less south, the tanning capacity seems to exist throughout southern Europe - it would risk including all western Europe. The purpose was not to imply that Sicilians are darker - on the contrary, I reaffirmed that the issue of pigmentation is a minority in the genotype. I have been to Iberia, France, Bergamo and other Western countries and in all of them I have seen white and tanned people. I believe that the phenotypic difference between north and south of Italy is more related to the color of eyes and hair, but in terms of tanning response all south / west of Europe - I think outside the British - have. There is absolutely no demerit in that. I don't understand why some people are sensitive to the topic.


    It makes no evolutionary sense to expect southern Europeans to be as pale as northern ones - regardless of whether they are in Iberia, Italy, Greece or any other southern region

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    Quote Originally Posted by Pax Augusta View Post
    Sicilian rapper Ensi untanned.




    .No surprise. This is called tanning and is common throughout western Europe - regardless of whether it is in Sicily, Lombardy, France or Iberia. I think the difference between north and south of Italy is not in the color of the skin or the ability to tan, but in the color of the eyes and hair. Maybe I have been misunderstood, but there is no need to chase photos where he is not tanned to 'prove' something because at no time did I want to imply anything negative about it.
    The ability to tan is useful in Western Europe and there is no reason to react sensitively to the topic. Tanning is a useful skill, not a demerit.

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    Another fact: Sardinians may have less alleles for light eyes and hair than Sicilians, but the western appearance is not limited to pigmentation and the facial features of Sardinians are very Western - unlike many Sicilians and even people from the Lazio region - Which is obviously not a demerit for Sicilians or for any population more related to the Middle East - including some Iberians who also have more 'Semitic' traits, although the EEF predominance in Iberia is much greater. Although Sicilians and other southern Italians group together with Ashkenazi Jews in autosomes, the perception of pigmentation of Ashkenazi Jews is different - many are red, blond and have an 'east' pigmentation, although the autosomal issue is different. The autosomal issue does not always effectively predict the phenotype. For this reason, it is complicated to generalize any European population based on autosomes. Probably many Sicilians have 'western' characteristics while others do not. Fortunately, diversity exists in the overwhelming majority of populations and this should never be understood as a demerit.

  24. #24
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    2 members found this post helpful.
    Quote Originally Posted by Ack View Post
    These are the participants of the Portuguese big brother. Nothing particularly light or dark by Southern European standards. Lighter or darker people than usual can be brought in anywhere in Europe, but some stereotypes are suitable for some people's personal fantasies.



    I cannot say that this is the case, but some northern Italians are unable to overcome the fact that they are not genetically north of the Iberians despite centuries of Moorish political domination in Iberia. Somehow they try to compensate for the discomfort by feeding stereotypes about pigmentation as much as the Iberians and the Italians are within the usual for southern Europe and really significant changes in phenotype are from Paris upwards. Iberians, northern Italians and French have more in common than differences. The intrigue is completely meaningless.

    Unfortunately, some northern Italians are known to have this type of complex even with their closest countrymen from central or southern Italy. But I still believe that most do not have this type of complex and they know that they are not Austrians - and even if they were: it would not be any kind of pride or demerit to the point of reacting badly to any association with everything that is from the south.
    I have no idea what you're carrying on about. The only one posting off topic after off topic post about pigmentation is you. There's also no one here now who is comparing the pigmentation of various Southern European communities except you. Cut it out. There are sites where people do that. This isn't one of them.

    As for Sardinians, you can hunt for pictures of exceptionally light ones all you want. Clearly you have never been there. They are noticeably darker not only in hair and eyes but in skin pigmentation, which is borne out by the results of snp analysis. Some of them in the interior also have a very "unique" look definitely not found in the mainland or elsewhere in Europe.

    Likewise you've obviously never spent decades surrounded by Askenazim as I have. They do not, minus some exceptions, look like eastern Europeans. That's why it was so difficult for them to hide during the 30s and 40s. All I see here is the nonsense you've read on racialist sites, which is completely ungrounded in reality and scientific data.

    There will be no more off topic posts on this thread by anyone.

  25. #25
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    Quote Originally Posted by Angela View Post
    I have no idea what you're carrying on about. The only one posting off topic after off topic post about pigmentation is you. There's also no one here now who is comparing the pigmentation of various Southern European communities except you. Cut it out. There are sites where people do that. This isn't one of them.

    As for Sardinians, you can hunt for pictures of exceptionally light ones all you want. Clearly you have never been there. They are noticeably darker not only in hair and eyes but in skin pigmentation, which is borne out by the results of snp analysis. Some of them in the interior also have a very "unique" look definitely not found in the mainland or elsewhere in Europe.

    Likewise you've obviously never spent decades surrounded by Askenazim as I have. They do not, minus some exceptions, look like eastern Europeans. That's why it was so difficult for them to hide during the 30s and 40s. All I see here is the nonsense you've read on racialist sites, which is completely ungrounded in reality and scientific data.

    There will be no more off topic posts on this thread by anyone.
    Just deleted it because it was off topic. I should have read the last sentence, sorry Angela.

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