Sarno et al 2014 study on Sicilian y-dna and mtdna: key information.

[Sikeliot]

This study is 3 years old but was never discussed in depth, so I am breaking it down here.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0096074

On Greek input:

"When Sicilian and Southern Italian populations were contextualized within the Euro-Mediterranean genetic space, we observed different historical dynamics for maternal and paternal inheritances. Y-chromosome results highlight a significant genetic differentiation between the North-Western and South-Eastern part of the Mediterranean, the Italian Peninsula occupying an intermediate position therein. In particular, Sicily and Southern Italy reveal a shared paternal genetic background with the Balkan Peninsula and the time estimates of main Y-chromosome lineages signal paternal genetic traces of Neolithic and post-Neolithic migration events. "



Paternal DNA:

More precisely, the first sPC (Figure 1a) separates the Iberian, Central-European and North-Western Italian populations on one hand (black squares), from the Balkans and the Levant on the other hand (white squares). Sicily and Southern Italy particularly revealed to be well set in the genetic context of the Central and South-Eastern Mediterranean group, the only exception being Catania (CT), which instead shows a stronger affinity to the North-Western cluster (Iberian Peninsula, Germany and Northern Italy).

Interestingly, the second sPC (Figure 1b), despite being much less representative compared to the first one in terms of both variance and spatial autocorrelation, identifies a subdivision between the two Mediterranean coastlines, which seems to involve the Eastern and Western parts of Sicily. The first group (black squares) is indeed represented by populations from the South-Eastern Mediterranean shore (Levant and North-Africa), including also the most western Sicilian provinces (Trapani and Agrigento) and the Iberian populations. Conversely, the second cluster (white squares) is mainly a North-Eastern Mediterranean centred group, encompassing the Balkans, South-Italy and East-Sicily, together with the other central European populations.

http://i68.tinypic.com/2di3sex.jpg


Maternal DNA:

As previously emerged for Y-chromosome, sPC1 plot reveals a North-West/South-East (NW-SE) distribution of mtDNA genetic variation (Figure 3a). Nearly all of the Mediterranean populations (with some exceptions, i.e. AG, TV, BUR) appear indeed distributed along a longitudinal transect running from North African and Near Eastern countries (large white squares) to the Iberian Peninsula (large black squares), with the bulk of the South-Eastern European populations (including Balkans and Italy) roughly occupying an intermediate position therein (see also Figure S2b). Among them, Sicily and Southern-Italy appear linked to the South-Eastern Mediterranean coast. When the reliability of this sPC1-identified structure has been tested by means of AMOVA, the proportion of genetic variation between groups (FCT) results lower than in the case of Y-chromosome (2.45%) but still significant (P-value<0.001).

http://i68.tinypic.com/33adul3.jpg


On Levantine and North African input: The Levantine input is mostly on the maternal side, while the paternal side shows the high Balkan (likely Greek) input.

From a Y-chromosome point of view, SSI form a fairly coherent group with the Levantine and the Balkan populations (cluster 2), despite showing some minor contribution (black component) also from the North-Western Mediterranean group (cluster 3). From a mtDNA point of view, our results show the differentiation between European and non-European Mediterranean populations, with North Africa and the Levant clustering in separate and different groups (1 and 2). However – and differently from the other European populations – SSI shows a noteworthy contribution (grey component) from the Levantine cluster. Both genetic systems reveal a negligible contribution from North Africa (white component).


http://i67.tinypic.com/2rg2bn7.jpg


Y-chromosome admixture proportions to the current SSI genetic pool indeed confirm an high paternal contribution from the South-Eastern Mediterranean populations, and particularly from the Balkan Peninsula (∼60%), whereas about 25% of SSI Y-chromosomes can be traced back to North-Western European group. Analogously, although the present-day SSI mtDNA genetic pool is largely shared with the other South-Eastern European populations of the Mediterranean Basin (respectively Balkan and Italian Peninsulas), a remarkable proportion of maternal ancestry (especially if compared with its paternal counterpart) derives from the Levant.

[Tacitus]

Nice to see this study get some attention but you forget that samples were taken from Calabria, Puglia, and Basilicata too so it's not just restricted to Sicily.

https://s3-eu-west-1.amazonaws.com/ppreviews-plos-725668748/1477905/preview.jpg

Also, you omitted two important points of analysis:

1) Time of most recent common ancestor (TMRCA) for southern Italian Y-DNA and mtDNA (N.B. YBP=1950 CE):

As for TMRCA estimates, STR variation within the most frequent haplogroups of SSI suggests that most of them (with the exception of haplogroup G2a-P15: 9339±3302 YBP) date back to relatively recent times (Table 1), in some cases falling into time periods compatible with specific documented historical events occurred in SSI. Despite the fact that these time estimates must be taken with caution, as they might be affected by the choice of both STRs markers and their mutation rates, overall our results agree in suggesting that most of the Y-chromosomal diversity in modern day Southern Italians originated during late Neolithic and Post-Neolithic times (∼2,300 YBP for E-V13; from ∼3,200 to ∼3,700 YBP for J sub-lineages; ∼4,300 YBP for R-M17 and R-P312; and ∼2,000 YBP for R-U106 and R-U152).
...
Differently from Y-chromosome results, TMRCA estimates for the most frequent mtDNA haplogroups of Sicily and Southern Italy (Table 1) date back to pre-Neolithic times and could be mainly classified in lineages pre-dating the Last Glacial Maximum - LGM (∼32,200 YBP for HV; ∼31,100 YBP for J2; ∼28,900 and ∼28,600 YBP for T1 and T2; ∼27,300 for U5; and ∼25,000 YBP for J1) or dating immediately after it (∼16,700 YBP for H5 and ∼15,700 YBP for H1).

https://s3.postimg.org/kjfijz8nn/journal_pone_0096074.png

2) Haplogroup distribution throughout southern Italy and Sicily:

In contrast with previous investigations on the distribution pattern of genetic variation in Sicily [7]–[8], our results point to a substantially homogeneous composition of maternal and paternal genetic pools both within Sicily (East vs. West) as well as between Sicily and Southern Italy (Table S4). The absence of significant differences in the distribution of HG frequencies along the east-west axis of the island, as observed not only among our Sicilian populations, but also when including the samples from Di Gaetano et al. (2009) [8], provides further support to these conclusions. The comparison of the whole SSI dataset with a subset based on founder surnames, moreover suggests that the observed homogeneity in Y-chromosome composition is not the result of recent events (e.g. increased population mobility related to the social and economic changes of the 19th and 20th centuries); on the contrary it has been preserved at least since the initial founding and spreading of surnames in Italy. In addition, and consistently with the complex history of migration pathways and cultural exchanges characterizing the peopling history of the area, high levels of Y-chromosome and mtDNA genetic variability at both SNP and haplotype (STRs or sequence) data, have been observed in all the SSI populations here examined (Table S5).

[Sikeliot]

Nice to see this study get some attention but you forget that samples were taken from Calabria, Puglia, and Basilicata too so it's not just restricted to Sicily.

https://s3-eu-west-1.amazonaws.com/ppreviews-plos-725668748/1477905/preview.jpg


So the study found evidence of Greek influences on the y-dna side, and some Levantine on the maternal. Does this mean this is the case for EVERY region sampled, since the study found the distribution of haplogroups to be homogenous?

[Tacitus]

So the study found evidence of Greek influences on the y-dna side, and some Levantine on the maternal. Does this mean this is the case for EVERY region sampled, since the study found the distribution of haplogroups to be homogenous?

As of right now? Probably, yeah, the only southern regions they didn't look at were Campania, Abruzzo and Molise, and I don't think they'd be that different from the other regions studied.

[Sikeliot]

As of right now? Probably, yeah, the only southern regions they didn't look at were Campania, Abruzzo and Molise, and I don't think they'd be that different from the other regions studied.

But what I mean is, does this mean people everywhere from Trapani to Enna to Matera all have roughly the same amount of Greek input on the y-dna and Levantine on the mtdna?

I think more variation would be found in small towns. I still don't discount the possibility of some town in the middle of Sicily or Calabria with elevated Levantine affinity, but who knows. The study does say the Levantine input is in excess of other Europeans, so this might translate into autosomal and be why studies like Lazaridis et al found them to be, with Maltese and Ashkenazim, in their own cluster separate from whichever Greek population was sampled and the Tuscans.

[Tacitus]

But what I mean is, does this mean people everywhere from Trapani to Enna to Matera all have roughly the same amount of Greek input on the y-dna and Levantine on the mtdna?

What they mean is that the haplogroup distribution is fairly uniform throughout, so it's not as though Trapani will have exactly the same amount of, for example, E-V13 or H5 as Enna or Matera, etc.

Additionally, we need to designate what exactly is "Greek" and "Levantine" here. They don't specifically mention Greece in the paper (edit: they do at the end when discussing E-V13) but the Balkans in general, and the Levantine mtDNA goes all the way back to the Last Glacial Maximum and expanded into Europe (haplogroup H originated in the Middle East but it's the most common mtDNA haplogroup in Europe). E-V13 is possibly Greek going by TMRCA. Some of the J lineages cold be linked to Greece, but probably came to Italy via the Balkans during the Bronze Age (and ultimately originating the Caucasus).


I think more variation would be found in small towns. I still don't discount the possibility of some town in the middle of Sicily or Calabria with elevated Levantine affinity, but who knows.
They still followed the classic "grandparent method" though:

The genetic structure of Sicily and Southern Italy (SSI) was investigated by means of a high resolution analysis of 326 Y-chromosomes and 313 mtDNAs representing eight different SSI provinces (Figure S1). Five of these (Agrigento, Catania, Ragusa-Siracusa, Matera, Lecce) were previously published in Boattini et al. (2013) [12], whereas the remaining three (Trapani, Enna, Cosenza) were typed and analysed here for the first time. Individual samples were collected according to the standard ‘grandparents criterion’ (i.e. three generations of ancestry in the sampled province). In addition, a subsample of 129 Y-chromosomes has been selected on the basis of surnames, thanks to the availability of Italian-province-specific lists of founder surnames [13]. Due to their link with Y-chromosomes, the selection of males bearing surnames which unequivocally belong to specific places can be used to select autochthonous participants in regional population genetic studies and to obtain an “older” picture of Y-chromosomal diversity [14]. That way, we were able to simulate a putative Late-Middle-Ages sample, that is the period during which surnames spread in Italy, thus allowing to verify the effects of very recent admixture events on population genetic structure.[/B]

[Sikeliot]

Additionally, we need to designate what exactly is "Greek" and "Levantine" here. They don't specifically mention Greece in the paper (edit: they do at the end when discussing E-V13) but the Balkans in general, and the Levantine mtDNA goes all the way back to the Last Glacial Maximum and expanded into Europe (haplogroup H originated in the Middle East but it's the most common mtDNA haplogroup in Europe). E-V13 is possibly Greek going by TMRCA. Some of the J lineages cold be linked to Greece, but probably came to Italy via the Balkans during the Bronze Age (and ultimately originating the Caucasus).

I would not discount some of haplogroup J having been there with the Sicanians and other native southern Italian peoples. I think southern Italy and Greece have different subclades of J, with those of southern Italy being older.

[Sikeliot]

What they mean is that the haplogroup distribution is fairly uniform throughout, so it's not as though Trapani will have exactly the same amount of, for example, E-V13 or H5 as Enna or Matera, etc.

Then this study does not suggest western Sicilians are less Levantine than easterners. In fact in one plot they diverge, with west Sicily going toward the Levant and southern Mediterranean, and east Sicily and southern Italy toward the Balkan cluster.