F_st values (in bold) and genomic control inflation factor (λ_GC) (<i>in italics</i>) between Sardinian linguistic macro-areas.

<p>F_st values (in bold) and genomic control inflation factor (λ_GC) (<i>in italics</i>) between Sardinian linguistic macro-areas.</p

SNP-Based Principal Component Analysis of 1,077 individuals from Sardinia.

<p><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091237#pone-0091237-g002" target="_blank">Figure 2</a> A) division accounting linguistic macro-areas. Key of the colors: red: <i>Campidanese</i>; green: <i>Alghero</i>; deep blue: <i>Gallurese</i>; light blue: <i>Logudorese</i>; yellow: <i>Sassarese</i>; purple: <i>Nuorese</i>. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0091237#pone-0091237-g002" target="_blank">Figure 2</a> B) division accounting geographical areas. Key of the colors: green: <i>Southern Sardinia</i>; grey: <i>Central Sardinia</i>; yellow: <i>Northern Sardinia</i>.</p

Nine genomic regions showing signals of positive selection in the Sardinian's genome ordered by |iHS|.

<p>Column headers: Position on NCBI36/hg18 of region showing evidence for selection; Size in Kb of the genomic region; nSNP |iHS|>4 indicates the number of SNPs with an absolute |iHS| higher than 4 in each region; nSNP is the number of SNPs in each region; Max iHS is the highest value of each region; Max iHS SNP is the polymorphism with the highest value for each region; P-values: nominal p-values; Empirical p-values: after permutation-based multiple testing corrections; Genes: the genes within the region. When, in the genomic region, there are more than 4 genes, only the first 4 are indicated.</p

Mean inbreeding coefficients.

<p>Mean inbreeding coefficients, standard errors (SE) and T test <i>p-Values</i> of Sardinia macro-areas and peninsular Italy.</p

Map of Mediterranean basin showing the localization of Sardinia and Sardinian linguistic domains.

<p>A) Map of the Mediterranean basin showing the geographic position of Sardinia. B) The Sardinian linguistic domains: 1 = <i>Gallurese</i> (77 individuals); 2 = <i>Nuorese</i> (88); 3 = <i>Logudorese</i> (385); 4 = <i>Sassarese</i> (342); 5 = <i>Alghero</i> (87); 6 = <i>Campidanese</i> (98).</p

Mean genomic inbreeding coefficients (F_RoH %) using 0.5 and 5 Mb minimum RoH thresholds and mean sum of RoH.

<p>* <i>p-value</i> smaller than 0.05 when comparing each linguistic macro-area to peninsular Italy.</p

ADMIXTURE software results for K = 2–4.

<p>Ancestry for each individual inferred using ADMIXTURE software.</p

Identity-by-state (IBS) sharing between and within populations.

<p>Density estimates for empirical distributions of genome-wide mean proportions of alleles sharing identity-by-state between subjects from different population or within the same populations, are shown for A) Northern Europe (CEU and French), B) Middle East (Bedouin, Palestinian and Druze), C) Northern Africa (Mozambite), D) within Italian populations. Color code as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043759#pone-0043759-g001" target="_blank">Figures 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043759#pone-0043759-g002" target="_blank">2</a>.</p

Datasets and individuals number from each population.

<p>Individuals included were filtered for individual call rate >98% and Identity By State (IBS) >0.05. Individuals included belong to Northern Italian (N-IT), Central Italian (C-IT), Southern Italian (S-IT), Sardinian (SAR), CEU HapMap (CEU), French (FRE), Palestinian (PAL), Bedouin (BED), Druze (DRU), and Mozabite (MOZ).</p

Clustering of the European, Northern African and Middle Eastern individuals by the Structure software.

<p>Model-based ancestry analysis based on a subset of HGDP-CEPH and HapMap CEU data using the merged data of 126K autosomal SNPs. Ancestry for each individual was inferred using ADMIXTURE <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043759#pone.0043759-Alexander1" target="_blank">[50]</a> at K = 4. Abbreviations as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043759#pone-0043759-g001" target="_blank">Figure 1</a>.</p