September 15, 2012

Genetic structure of Italian population

I don't see much that is new here, although it is still great to see a new study with a large population size. I'll only comment on the following line:
When compared to other European populations, Sardinia was confirmed to be a genetic “outlier”, whereas the Northern Italian population was genetically close to the French population, and the Southern Italians had some similarities with other Mediterranean populations such as those from Middle East. Unfortunately, lack of data from other relevant reference populations from the South-East Europe, e.g. from the Balkan peninsula, made it impossible to fully analyze the extent of the Eastern contribution in Italian populations.
There are data on the Balkan peninsula on both POPRES (which is not available to me), as well as other recent studies. I maintain a list of data sources at the bottom left of the Dodecad blog. It is hard to get very excited about a study that does not compare Italians against populations from the Balkans and Anatolia.

PLoS ONE 7(9): e43759. doi:10.1371/journal.pone.0043759

An Overview of the Genetic Structure within the Italian Population from Genome-Wide Data

Cornelia Di Gaetano et al.

In spite of the common belief of Europe as reasonably homogeneous at genetic level, advances in high-throughput genotyping technology have resolved several gradients which define different geographical areas with good precision. When Northern and Southern European groups were considered separately, there were clear genetic distinctions. Intra-country genetic differences were also evident, especially in Finland and, to a lesser extent, within other European populations. Here, we present the first analysis using the 125,799 genome-wide Single Nucleotide Polymorphisms (SNPs) data of 1,014 Italians with wide geographical coverage. We showed by using Principal Component analysis and model-based individual ancestry analysis, that the current population of Sardinia can be clearly differentiated genetically from mainland Italy and Sicily, and that a certain degree of genetic differentiation is detectable within the current Italian peninsula population. Pair-wise FST statistics Northern and Southern Italy amounts approximately to 0.001 between, and around 0.002 between Northern Italy and Utah residents with Northern and Western European ancestry (CEU). The Italian population also revealed a fine genetic substructure underscoring by the genomic inflation (Sardinia vs. Northern Italy = 3.040 and Northern Italy vs. CEU = 1.427), warning against confounding effects of hidden relatedness and population substructure in association studies.



mooreisbetter said...

I agree. Pretty darn close to worthless.

1. As you noted, they do not use extant Balkan data, which could have been highly informative.

2. They don't distinguish between micro-regions within Italy, which exist because of the mountainous terrain. (Although this would be asking a lot, I suppose). Still, Molise and Cosenza have very different genetics than Lazio and Reggio Calabria, for example.

3. They note southern affinities to certain Near Eastern populations, but they don't speculate as to why. Southern Italians made up the bulk of Roman legionnaires from c. 200 BC to c. 200 AD. Was it historic gene flow from Southern Italy to those locales? Or was it prehistoric gene flow from the first farmers TO Italy?

Ah, maybe next time.

Rokus said...

"I don't see much that is new here"

To you this should be new. Ötzi reduced the South European component to near inexistence. Italy, instead of being "South European", it is actually 56% North European in the north and close to 50% NE in the south, while the West Asian component is a lot lower. Even Sardinia is nowadays 14% NE.
I think you should remove "Mediterranean" from your component list altogether and put Ötzi instead. Then, behold how the Indo european world looks like.
Kurganists and Neolithic Orientalists are all wrong, the true genetic relation of IE is with Mesolithic northern Europe, that started to expand about 4400 BC.

Dienekes said...

I have no idea what you're talking about.

Rokus said...

Di Gaetano:
'The HapMap CEU individuals showed an average Northern Europe (NE) ancestry (light green) of 83%. A similar pattern is observed in French, Northern Italian and Central Italian populations with a NE ancestry of 70%, 56% and 52% respectively (Figure 3). According to the PCA plot, also in the ADMIXTURE analysis there are relatively small differences in ancestry between Northern Italians and Central Italians while Southern Italians showed a lower average admixture NE proportion (43,6%) than Northern and Central Italy, and a higher Middle East ancestry (light blue) of 28%.'
'The average admixture proportions for Northern European ancestry within current Sardinian population is 14.3%'

I think these proportions are pretty new and very distinct from the general picture so far. The conclusions are all mine.

Dienekes said...

I think these proportions are pretty new and very distinct from the general picture so far.

An ADMIXTURE analysis with 10 populations? I see little added value in it. There are now 100s of population samples publicly available.

Unknown said...

The finding that central Italy is closer to the north is probably just an artifact of the big number of Tuscans included. From what I've read here, Tuscans are closest to north Italians, but the Central_Italian_D sample from Dodecad, which doesn't include Tuscans, seems rather bipartite: About one third clusters with Tuscans/the north, whereas the other two thirds are closer to southern Italy, Sicily in particular, and in international comparison to Greece. I suppose the former rather include people from northern Latium or other regions bordering Tuscany, while the latter are presumably more from the other side of the apennine, where y-haplogroup J2 plays a more important role.

I found it interesting, though, that Emilia-Romagna clusters rather with central Italy than with the north, with one individual close to a Marche individual.