9
Genetic study on Southern Italains and Sicilians
An Ancient Mediterranean Melting Pot: Investigating the Uniparental Genetic Structure and Population History of Sicily and Southern Italy
Published: April 30, 2014
http://journals.plos.org/plosone/art...l.pone.0096074
Due to their strategic geographic location between three different continents, Sicily and Southern Italy have long represented a major Mediterranean crossroad where different peoples and cultures came together over time. However, its multi-layered history of migration pathways and cultural exchanges, has made the reconstruction of its genetic history and population structure extremely controversial and widely debated. To address this debate, we surveyed the genetic variability of 326 accurately selected individuals from 8 different provinces of Sicily and Southern Italy, through a comprehensive evaluation of both Y-chromosome and mtDNA genomes.
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 event
Overall, both uniparental genetic structures and TMRCA estimates confirm the role of Sicily and Southern Italy as an ancient Mediterranean melting pot for genes and cultures.
Results
Y-Chromosome perspective
Haplogroups G-P15 (12.3%), E-V13 and J-M410* (both 9.5%), together with R-M269* (7.4%) represent the most frequent lineages found in Sicily and Southern Italy (SSI). These are followed by five R1-sublineages (R-M17, R-L2, R-P312, R-U152, R-U106), whose frequencies range from 5.2% to 3.7%, and by J-M267 which embraces almost the 5% of total variability. All these paternal lineages reportedly originated in Europe or in the Near East, whereas much lower it seems to be the African paternal contribution, mainly represented by haplogroups belonging to HG-E sub-lineages (E-V12, 2.76%; E-V22, 2.15%; E-M81, 1.53%). Contrary to what previously reported in literature [8], no differential distribution of Y-chromosome lineages has been found in our dataset. Fisher exact tests performed on HG frequencies between Southern Italy and Sicily (P-value: 0.4765), as well as between Eastern and West Sicily (P-value: 0.2998), indeed do not reveal any significant differentiation. No significant percentage of variance among groups of populations (FCT) has been detected by regional AMOVAs (Table S4). In the same way, when our Sicilian populations were grouped with those of Di Gaetano et al. 2009 following their East-West subdivision scheme and by using the same HG resolution level, both AMOVA (variation among groups 0.30%, P-value 0.091) and Fst index (P-value 0.094), failed to reveal any significant difference in Y-chromosome HGs composition, thus pointing out a substantial homogeneous pattern of genetic variation within the island.
Moreover, when the distribution of Y-chromosome lineages in the present-day Sicilian and Southern-Italian population has been compared with the one of the surname-based selected subset, no significant differentiation appeared (P-value: 0.9551).
High levels of within-population variability have been observed for all the 8 populations analysed, as well as for the whole dataset (Table S5), thus suggesting a high genetic heterogeneity at a micro-geographical level among the considered Sicilian and Southern-Italian populations, as confirmed also by the presence of 312 out of 326 unique STRs haplotypes. In addition, all shared haplotypes involve at most two individuals.
In order to more deeply explore the genetic relationships among Mediterranean groups, our samples were then compared with the 29 Euro-Mediterranean, Levantine and North-African populations extracted from the literature (Table S1), by using a common level of Y-HGs resolution.
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. When the reliability of the sPCA-identified structures was tested by means of an AMOVA based on haplogroup frequencies, the proportion of genetic variation between groups (FCT) results however two times higher when grouping according to the sPC1 (8.31%, P-value<0.001) than sPC2 (4.31%, P-value = 0.004). The sPCA-suggested pattern of genetic relationships among the different Mediterranean populations, has been confirmed in the classical PCA plots reported in Figure S2a
The two high-structured Mediterranean clusters identified with sPC1, were further tested by means of DAPC analysis. Membership probabilities, represented with a structure-like plot (Figure 2), highlight the intermediate position of the Italian samples between the two Mediterranean clusters. In this context, Sicily and Southern Italy show clearly their stronger affinity with the populations from the South-Eastern Mediterranean side (with the partial exception of Catania - CT).
The barplot represents DAPC-based posterior membership probabilities for each of the considered populations to belong at each of the two sPC1-identified groups (white = South-Eastern Mediterranean; black = North-Western Mediterranean). Population codes as in Table S1.
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).
Mitochondrial DNA perspective
The observed mtDNA HGs distribution reflects the typical maternal variability pattern documented for Mediterranean Europe. In fact, most of the individuals belong to super-haplogroup H, that on the whole accounts for the 38% of the total mtDNA lineages detected in our dataset. Within H, H1 represents the most frequent sub-lineage (10.9%), followed by H5 (3.2%) and H3 (2.6%). Noteworthy is also haplogroup HV, that has been found at relatively high frequencies (4.8%). Most of the remaining samples belong to haplogroups U5, K1, J1, J2, T1, T2, thus confirming prevalent European and Middle-Eastern genetic ancestries. MtDNA haplotypes of African origin are instead represented by few haplogroups at low frequencies, namely M1 (1.3%), U6a (0.6%) and L3 (0.6%).
Similarly to Y-chromosome, mtDNA does not reveal any kind of population sub-structure both within Sicily (East vs. West Sicily) as well as between Sicily and Southern Italy, neither considering haplogroups nor haplotypes (sequences). AMOVA results show low and non-significant FCT values when population samples were grouped according to geography (Table S4). Analogously, Fisher exact tests reveal no significantly different HG composition in any of the geographic regions considered (South Italy vs, Sicily, P-value: 0.5019; East Sicily vs. West Sicily, P-value: 0.0698). In the same way, both AMOVA (variation among groups 0.52%, P-value 0.082) and Fst (P-value 0.076) based on HG frequencies show the absence of significant genetic differentiation along the east-west axis of Sicily.
The highest eigenvalue obtained is the most positive one (sPC1) associated with the presence of a global structure. 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).
Fisher exact tests were applied to determine if differences in HG frequencies among population groups were statistically significant (Table S6). As expected, haplogroup H is found to be over-represented in Euro-Mediterranean populations and under-represented in North-African ones, while the opposite has been observed for haplogroup L. Haplogroup K is over-represented in Levantine populations, and haplogroup M in North-Africa. However, when the deepest level of HG resolution has been exploited for single pairwise comparisons between SSI and Mediterranean reference populations, we do not found any HG whose frequency is significantly higher than in our dataset. The only exception is a slightly significant (P-value: 0.045) over-representation of H1 haplotypes in the Iberian Peninsula.
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).
Comparative analysis of maternal and paternal genetic pools
Figure 4. Admixture-like barplots for Y-chromosome (a) and mtDNA (b).
The barplots represent DAPC-based posterior membership probabilities for each of the considered populations and for each inferred cluster (mclust algorithm). The affiliation of each population to a given cluster and its corresponding colour code are represented by letters (within coloured squares) on the top of each bar. Labels: NAFR: North-Africa, LEV: Levant, BALK: Balkans, SSI: Sicily and South-Italy, NCI: North-Central Italy, IBE: Iberian Peninsula, GER: Germany.
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).
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.
More --> http://journals.plos.org/plosone/art...l.pone.0096074
Originally Posted by Sikeliot
Bookmarks