Genomic Diversity in Italy

Angela

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Sazzini et al
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-020-00778-4

"[h=3]Background[/h]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.
[h=3]Results[/h]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.
[h=3]Conclusions[/h]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.
 
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
 
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.
 
" 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
 
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.

jagadeesha-article-fig-1.jpg


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.

chartoftheday_6348_nearly_1_in_6_european_adults_is_considered_obese_n.jpg


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

jagadeesha-article-fig-1.jpg


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.

chartoftheday_6348_nearly_1_in_6_european_adults_i  s_considered_obese_n.jpg


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.



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^^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:

F68fKST.png


At any rate, this isn't a sociology thread, so lets get back on topic.
 
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).
 
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?



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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?
 
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.
 
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
 
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.
 
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.
 
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?
 
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.
 
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.
 
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?



9o8izRI.png

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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