Differential genomics and disease susceptibility along the Italian peninsula

Angela

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See: Sazzini et al:
http://www.nature.com/articles/srep32513

"Complex interplay between neutral and adaptive evolution shaped differential genomic background and disease susceptibility along the Italian peninsula"


"The Italian peninsula has long represented a natural hub for human migrations across the Mediterranean area, being involved in several prehistoric and historical population movements. Coupled with a patchy environmental landscape entailing different ecological/cultural selective pressures, this might have produced peculiar patterns of population structure and local adaptations responsible for heterogeneous genomic background of present-day Italians. To disentangle this complex scenario, genome-wide data from 780 Italian individuals were generated and set into the context of European/Mediterranean genomic diversity by comparison with genotypes from 50 populations. To maximize possibility of pinpointing functional genomic regions that have played adaptive roles during Italian natural history, our survey included also ~250,000 exomic markers and ~20,000 coding/regulatory variants with well-established clinical relevance. This enabled fine-grained dissection of Italian population structure through the identification of clusters of genetically homogeneous provinces and of genomic regions underlying their local adaptations. Description of such patterns disclosed crucial implications for understanding differential susceptibility to some inflammatory/autoimmune disorders, coronary artery disease and type 2 diabetes of diverse Italian subpopulations, suggesting the evolutionary causes that made some of them particularly exposed to the metabolic and immune challenges imposed by dietary and lifestyle shifts that involved western societies in the last centuries."


Given the large amounts of migration from south to north in Italy starting in the late 19th century and massively accelerating in the 1950s, I certainly hope that the authors did as the authors of the Greek study did, and insured that the samples had ancestry dating back to before these migrations.

Honestly, sometimes I despair of Italian researchers. They didn't insure that, or if they did they don't mention it in the methodology. Well, I guess for medical purposes what matters is who lives there now, but for understanding the underlying genetics of the Italian cline it's problematical, so, that has to be considered in analyzing the study.
 
Given the large amounts of migration from south to north in Italy starting in the late 19th century and massively accelerating in the 1950s, I certainly hope that the authors did as the authors of the Greek study did, and insured that the samples had ancestry dating back to before these migrations.

Honestly, sometimes I despair of Italian researchers. They didn't insure that, or if they did they don't mention it in the methodology. Well, I guess for medical purposes what matters is who lives there now, but for understanding the underlying genetics of the Italian cline it's problematical, so, that has to be considered in analyzing the study.
They used the same people as Boattini 2013 for their research, so:
Sample collection

A total of 884 unrelated individuals from continental Italy, Sicily
and Sardinia were collected according to the following sampling
strategy. Firstly, based on the results of a precedent reconstruction
of the surname structure of Italy [24], we defined lists of
monophyletic surnames for each of the 96 Italian provinces.
Secondly, monophyletic surnames frequencies were used to define
eight clusters of homogeneous Italian provinces (sampling macro-
areas, Figure S1). Within each sampling macro-area, we selected a
set of provinces (sampling points) from a minimum of one to a
maximum of three, depending on the geographical extension of
the macro-area as well as their historical background. This was
done in order to depict a sampling grid able to capture as much
genetic variability as possible (given the number of planned
samples/sampling points). Within each sampling point, individuals
were finally sampled according to the standard ‘grandparents’
criterion, thus considering as eligible for our study only those
individuals whose four grandparents were born in the same
sampling macro-area.
It is important to underline that individuals
within sampling points were not selected by surnames. That way 1)
our data are consistent with those from other similar studies; 2) we
avoid to introduce a bias between Y-chromosome and mtDNA
results.
DNA was extracted from fresh blood by a Salting Out modified
protocol [25].
From these they selected their sub-sample. I expect that they were at least before WWII.
 
They used the same people as Boattini 2013 for their research, so:

From these they selected their sub-sample. I expect that they were at least before WWII.

I certainly hope so. Ever since I read that study based on hospital records where the people just had to say they were from that province, I've been a little skeptical of Italian produced papers! At least here they went to greater lengths.

If they tested university students, as is the case with a lot of genetic studies, the grandparents might be post war. That's at least something. Given the migratory changes that went on since the beginning of industrialization at the end of the 19th century, however, it would have been much better if, as in the paper on the Peloponnesus, they had tested elderly rural people whose grandparents were born in the 1860s and 1870s.

Maybe in fact they did. I just don't know.

Anyway, I want to go over the paper thoroughly.
 
If they tested university students, as is the case with a lot of genetic studies, the grandparents might be post war. That's at least something.
There are indeed two promising test subjects - students and elderly patients, who agree to anything the doc proposes, just in case he wouldn't do his best otherwise ... Consent achieved easily. This surname thingie lets me assume that it's easier to cover all the postulations, if they mine the blood labs of the hospitals, which would bias toward the 50+ people. That would come close to the Peloponnese data. I'm optimist ...
 
The samples are surely the ones with 4/4 grandparents with one specific region.
 
Sazzini et alia (2016)...New Italian Popuation Study

This recent study of 737 subjects from 20 locations in 15 Italian regions shows some fresh samples and emphasises the clinal nature of the Italian population, north, centre and south, with Sardinians as outliers.

Source: http://www.nature.com/articles/srep32513
 
These two maps are interestings









The S1 shows perfectly the genetic clinal of Italy. Abruzzo is confirmed to be mostly a southern Italian region genetically and historically, since they were the northern part of the kingdom of Sicily (and then of Naples after 1282). Benevento has central Italian influenced, i also guess it's due to Longobard (there is an high Germanic paternal lineages there) and Celto-Ligurian deportation in Roman era. While samples from Cosenza overlap with Sicilians, Lucanians and Salentini, while the ones from Reggio of Fiorito appeared slightly more "southern". Genetic cline in Calabria, Angela?
 
These two maps are interestings









The S1 shows perfectly the genetic clinal of Italy. Abruzzo is confirmed to be mostly a southern Italian region genetically and historically, since they were the northern part of the kingdom of Sicily (and then of Naples after 1282). Benevento has central Italian influenced, i also guess it's due to Longobard (there is an high Germanic paternal lineages there) and Celto-Ligurian deportation in Roman era. While samples from Cosenza overlap with Sicilians, Lucanians and Salentini, while the ones from Reggio of Fiorito appeared slightly more "southern". Genetic cline in Calabria, Angela?

I don't know. I think the other Calabrian sample is from the Ionian coast of Reggio Calabria somewhere, yes? I couldn't get a precise answer from the researchers. Does anyone have more information?

Even if there is a slight cline, I think what this group of researchers and many others have shown is that southern Italy, including Sicily, is, at a certain level of analysis homogeneous, far more homogeneous than Central Italy, certainly.

Of course, as the POBI analysis of Britain showed, if you drill down deep enough and look at smaller and smaller differences, you can tease out some internal "clusters".
 
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I don't know. I think the other Calabrian sample is from the Ionian coast of Reggio Calabria somewhere, yes? I couldn't get a precise answer from the researchers. Does anyone have more information?

The Calabrian samples in this study are from Cosenza (29 individuals), Catanzaro (10) and Reggio Calabria (26), but not clear what sample have been used in Fig. S2. All of them?

Fig. S2 is "Individual posterior membership probabilities to belong to population clusters suggested by PCA and Procrustes analyses calculated via DAPC and averaged per sampling location.".

Even if there is a slight cline, I think what this group of researchers and many others have shown is that southern Italy, including Sicily is, at a certain level of analysis homogeneous, far more homogeneous than Central Italy, certainly.

Yes, but if Central Italy in the analysis includes also sample from Abruzzo and Molise as reported in the paper, that are southern Italian regions genetically and historically, isn't really rappresentative. L'Aquila is a sample from Abruzzo and is included in the C_ITA (Central Italy) despite it clustered instead with the bulk of Southern Italian samples.

"as well as most from L’Aquila (C_ITA), actually clustered within the bulk of southern samples. "

"Intersection between samples from diverse macro-areas was limited to a subset of individuals from Bologna (C_ITA), which showed close affinity to those from northern provinces, such as Savona, Padova and Vicenza, while some subjects from Ancona (C_ITA), as well as most from L’Aquila (C_ITA), actually clustered within the bulk of southern samples. "


Benevento has central Italian influenced, i also guess it's due to Longobard (there is an high Germanic paternal lineages there) and Celto-Ligurian deportation in Roman era.

I totally agree.


Genetic cline in Calabria, Angela?

I think so.
 
Pax Augusta;504056]The Calabrian samples in this study are from Cosenza (29 individuals), Catanzaro (10) and Reggio Calabria (26), but not clear what sample have been used in Fig. S2. All of them?

I have no idea. As in the recent Greek paper, they leave a lot of things unclear, or at least unclearly labeled. If it's a mixed sample then it probably gives a good idea of "average" Calabrian genetics, yes? It would be more informative than the other Calabrian sample.



Yes, but if Central Italy in the analysis includes also sample from Abruzzo and Molise as reported in the paper, that are southern Italian regions genetically and historically, isn't really rappresentative. L'Aquila is a sample from Abruzzo and is included in the C_ITA (Central Italy) despite clustered instead with the bulk of Southern Italian samples.

"as well as most from L’Aquila (C_ITA), actually clustered within the bulk of southern samples.
"[/QUOTE]

They've made a mess of the Central Italian category, that's for sure, and if other researchers have used the same samples for "Central Italy", their conclusions also now are in question.

Why anyone, in particular Italians, would ever consider the Abruzzi and Molise "Central Italy" genetically is beyond me. Have they never been there? Have they never read any of the pertinent history? I'm guessing these researchers are pretty young, which makes me concerned about the state of the Italian education system in the last two decades or so.
 
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They've made a mess of the Central Italian category, that's for sure, and if other researchers have used the same samples for "Central Italy", their conclusions also now are in question.

Why anyone, in particular Italians, would ever consider the Abruzzi and Molise "Central Italy" genetically is beyond me. Have they never been there? Have they never read any of the pertinent history? I'm guessing these researchers are pretty young, which makes me concerned about the state of the Italian education system in the last two decades or so.

Indeed, I completely agree with you.
 
Indeed, I completely agree with you.

I'd forgotten what a mess they made of this by dividing the data by their idea of "geographic areas" in Italy rather than by "genetic areas".

How absurd can it get? They're surprised that Bologna turns out to be "Northern" Italian and L'Aquila "Southern" Italian.

It occurs to me, though, that researchers could use this collection of Southern Italian samples instead of whatever weirdly drifted sample was used in the Lazaridis Mycenaean paper.
 

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