November 11, 2015

Genetic structure of 1,272 Italians

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).
European Journal of Human Genetics advance online publication 11 November 2015; doi: 10.1038/ejhg.2015.233

The Italian genome reflects the history of Europe and the Mediterranean basin

Giovanni Fiorito et al.

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.

Link

13 comments:

Onur said...

There is a mistake in the title of this blog post. This study tests 1,272 individuals from all over Europe, the Middle East and North Africa. The number of Italians tested is little more than 300.

andrew said...

Italy has only been a unified country since about 1870 CE, so this isn't terribly surprising.

mooreisbetter said...

I have profound respect for some of the authors involved in this paper, but some of their techniques left me scratching my head in amazement. Not the positive kind.

1. They attempt to draw broad inferences about Calabrians by a sample of 12 individuals from the most cosmopolitan southern city in Calabria? Calabria is 150 miles long and 15,0000 square kilometers. It's full of inpenetrable valleys and peaks, which any fool can tell are genetically quite disparate. I question the value of this data. It would be like ignoring the inland (barbagia) of Sardinia and taking samples from some seaside resort. That doesn't quite work.

2. Where are the samples from rural places, for that matter? Nothing from Abruzzo? Really? Nothing from Molise? These are some of the most unspoiled, un-invaded, un-admixed parts of Italy. Why not use them as a baseline? Why not compare them to the neighboring regions to see if the hypotheses actually applies?

3. For that matter, nothing from Campania? Really? I would think that rural Campania would be a good baseline, because of its Central Italian location, to compare the validity of the other Central Italian data. I would suspect the old Greek settlements in Campania near Naples would be a good place to check the southern Italian data. Strange that this huge and significant region was left out.

4. Perhaps it is the low sample sizes and the other obvious defects in the methodology, but I'm assuming that is why the people from Val D'Aosta resemble so closely some of the southern Italians according to this study? That just doesn't pass the smell test.

eurologist said...

Not sure about this paper. It's a tour-de-force that could have been. Nice, basic work - but nothing I can see we did not know already.

And the same old criticisms when using quantitative analyses: only cast your (genetic) net wide for wide inferences, cast it narrow for regional information.

How about an analysis that includes the SE of France, Switzerland, SW and S Germany, Austria, the W Balkans, Greece, the W Levant and Anatolian coast, (and N Africa - but only in a second run)?

mooreisbetter said...

When there are 4 comments, and 3 express the same concern: "Houston, we have a problem."

First an aside to comment 2, by Andrew: Educate yourself, young man. That "Italy has only been a country" saying applies to everyone (France, Germany, Poland, to name a few.)

And, with respect to Italy, it's just not true.

Italy first got its name c. 1000 BC, based on the name of an eponymous tribe living in what is now Calabria.

It became a unified, cohesive political unit in the days after Julius Caesar (i.e. 44 BC) and the power consolidation of Augustus shortly thereafter.

As Sir Ronald Syme wrote, the poet Horace said only tongue in cheek that Augustus's campaign slogan was "Tota Italia" (all of Italy).

At that time, Italians in the precise geographic area we call Italy were unified politically.

First, only Italians were Roman citizens during that period.

Second, as the Empire was composed of nation-states welded together, the Empire recognized each nation-state as a province with borders. Not too different from the modern EU.

Italy's borders were the same as today:

https://en.wikipedia.org/wiki/Roman_Italy

This situation stayed the same for roughly 500 years, and this was a long time ago.

So pull your head out of Metternich's behind, please.

Anyway, as for the paper: the sample size was TINY. It conflicts with several other papers. It didn't sample key regions like Provence, Huesca, Catalonia, and too many to name within Italy.

It is not informative at all.

aaa said...

Thank you all for your ‘constructive’ comments.
This message is just to point out that the major criticisms you posed are discussed as limitations of the study, and of course some of your suggestions will be take into account in the next future.
Any other constructive suggestion is welcome, in order to produce results appropriate for a sophisticated audience.
Giovanni Fiorito

truth said...

When a study with Corsicans ?

Roma Sabinus said...

@ aaa {Giovanni Fiorito)

That political unity does not equal ethnic (genetic) unity is well established concerning Italians (Ralph and Coop 2013 and virtually every study featuring Italian groups); In fact your recent study is little more than a repetitive paper of your colleague C. Di Gaetano (et al 2012!);

Thus my criticism:
Use your future fund money in a more productive way;
How about sequencing aDNA? 3 Remedello folks have been recently sequenced in Altentoft et al (2015), so why not in the future additionally sequence more Remedello as well as Rinaldone, Gaudo and Bonnanaro folks? Or >finally< some Y-chr. haplogroups from actual Etruscans?

Or what about obtaining data from these archaeological sites,
http://www.pia-journal.co.uk/articles/10.5334/pia.462/
in order to find out whether an Indo-European presence already existed in Italy before the Urnfield migrations (beg. ~1200BC);

New aDNA data is more important than info that is already known i.e. that Sardininas are isolated and North Italians and South Italians are genetically not related;

Roma Sabinus said...

@ aaa {Giovanni Fiorito)

That political unity does not equal ethnic (genetic) unity is well established concerning Italians (Ralph and Coop 2013 and virtually every study featuring Italian groups); In fact your recent study is little more than a repetitive paper of your colleague C. Di Gaetano (et al 2012!);

Thus my criticism:
Use your future fund money in a more productive way;
How about sequencing aDNA? 3 Remedello folks have been recently sequenced in Altentoft et al (2015), so why not in the future additionally sequence more Remedello as well as Rinaldone, Gaudo and Bonnanaro folks? Or >finally< some Y-chr. haplogroups from actual Etruscans?

Or what about obtaining data from these archaeological sites,
http://www.pia-journal.co.uk/articles/10.5334/pia.462/
in order to find out whether an Indo-European presence already existed in Italy before the Urnfield migrations (beg. ~1200BC);

New aDNA data is more important than info that is already known i.e. that Sardininas are isolated and North Italians and South Italians are genetically not related;

Alessandro said...

@aaa
In my opinion Siena and Arezzo are not the best places to have an average for Tuscans (The biggest Tuscan population density is in the northern half at the end), especially for more northern ones like Pistoiesi, Lucchesi, and rural areas of Pisa and Florence. I assume these to be closer to Emilians and Liguarians than Senesi are. At the end you have chosen Ferrara that is at border with Veneto and Lombardy, and Savona, which is in the riviera di Ponente, while for Tuscany two cities in the center of the region.

filemone said...

@ aaa {Giovanni Fiorito)

In my opinion, no scientific work, especially of this nature, should ever be adddressed to a restricted (or "sophisticated", as you say) audience.
Science should be clear, understandable and relevant for society, when are the taxpayers who pay for it.

aaa said...

“sophisticated” is used to be sarcastic, and is referred to the people that have defined the paper unuseful. I just want to add that, as you probably know, there is a lot of work of a lot of people behind a scientific paper. Qualified people have positively judged the paper suitable for publication before you.
The work is probably unuseful for your point of view, that I suppose to be an anthropological point of view. I agree that for anthropologist ancient DNA would be more informative. But actually, anthropology is not the only field of sciences. This paper had other aims.
I will not go over the discussion because I actually don’t know who I’m talking with. To my knowledge, you can even be my 15 years old nephew.
If you want to discuss the usefulness of the paper please write me in private. You know my name and surname.
Best,
Giovanni Fiorito

aaa said...

why don't you publish my comment?
Can I have at least an explanation?
Then, I will definitely leave this blog if I'm not the welcome
Giovanni Fiorito