Spatial Principal Component Analysis (sPCA) based on Y-chromosome haplogroups frequencies.

<p>The first two global components, sPC1 (a) and sPC2 (b), are depicted. Positive values are represented by black squares; negative values are represented by white squares; the size of the square is proportional to the absolute value of sPC scores.</p

An Ancient Mediterranean Melting Pot: Investigating the Uniparental Genetic Structure and Population History of Sicily and Southern Italy

<div><p>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. The main goal was to investigate the structuring of maternal and paternal genetic pools within Sicily and Southern Italy, and to examine their degrees of interaction with other Mediterranean populations. Our findings show high levels of within-population variability, coupled with the lack of significant genetic sub-structures both within Sicily, as well as between Sicily and Southern Italy. 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. On the contrary, despite showing some correspondence with its paternal counterpart, mtDNA reveals a substantially homogeneous genetic landscape, which may reflect older population events or different demographic dynamics between males and females. 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.</p></div

Discriminant Analysis of Principal Components (DAPC) based on Y-chromosome sPC1-identified structure.

<p>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 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096074#pone.0096074.s004" target="_blank">Table S1</a>.</p

Y-STR haplotypes and haplogroups in Partecipanza and S. Giovanni in Persiceto samples

Y-STR haplotypes and haplogroups in Partecipanza and S. Giovanni in Persiceto sample

Admixture-like barplots for Y-chromosome (a) and mtDNA (b).

<p>The barplots represent DAPC-based posterior membership probabilities for each of the considered populations and for each inferred cluster (<i>mclust</i> 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.</p

Presence of major HV lineages in Italy.

<p>(A) presence of haplogroup HV*(xH,V); (B) presence of major lineages HV0, HV1, HV-73(HV2), HV4, HV-16311. Gray dots indicate sampled sites. The size of the square is proportional to the number of HV individuals in each site (see legend).</p

Discriminating power between R-M269 sub-lineages.

<p>Three STR panels are considered: Yfiler (top), RM11 (middle) and Yfiler + RM11 (bottom). Results are represented with admixture-like plots, in which vertical bars represent probabilities for each individual to be affiliated to a given R-M269 sub-lineage (membership probabilities). Mean per-group membership probabilities are reported in horizontal bars at the bottom of each plot.</p

Mutation rates and 95% confidence intervals for the considered Y-STR sets (Yfiler, RM11, RM13) in pedigree-based Datasets (A and B).

<p>Diachronic changes in mutation rates were calculated for three increasing bins of generations (1–10, 11–20, 21–26). NGEN: total number of generations; NMUT: number of observed mutations.</p

Average mutation rates for the considered Y-STR sets (Yfiler, RM11, RM13) in deep rooted pedigrees (Dataset A) and in close relatives (Dataset B).

<p>Dotted vertical lines represent 95% confidence intervals (when available). For comparison, estimates from literature are included^10,8,11.</p

Median Joining network of HV4 lineages.

<p>Mutations weighted proportionally to their frequency in the phylogeny.</p