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. 2020 Feb 24;11(1):939.
doi: 10.1038/s41467-020-14523-6.

Genetic History From the Middle Neolithic to Present on the Mediterranean Island of Sardinia

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Free PMC article

Genetic History From the Middle Neolithic to Present on the Mediterranean Island of Sardinia

Joseph H Marcus et al. Nat Commun. .
Free PMC article

Abstract

The island of Sardinia has been of particular interest to geneticists for decades. The current model for Sardinia's genetic history describes the island as harboring a founder population that was established largely from the Neolithic peoples of southern Europe and remained isolated from later Bronze Age expansions on the mainland. To evaluate this model, we generate genome-wide ancient DNA data for 70 individuals from 21 Sardinian archaeological sites spanning the Middle Neolithic through the Medieval period. The earliest individuals show a strong affinity to western Mediterranean Neolithic populations, followed by an extended period of genetic continuity on the island through the Nuragic period (second millennium BCE). Beginning with individuals from Phoenician/Punic sites (first millennium BCE), we observe spatially-varying signals of admixture with sources principally from the eastern and northern Mediterranean. Overall, our analysis sheds light on the genetic history of Sardinia, revealing how relationships to mainland populations shifted over time.

Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1. Number of SNPs covered, sampling locations and ages of ancient individuals.
a The number of SNPs covered at least once and age (mean of 2σ radiocarbon age estimates) for the 70 ancient Sardinian individuals. b The sampling locations of ancient Sardinian individuals and a reference dataset of 961 ancient individuals from across western Eurasia and North Africa (with “jitter” added to prevent overplotting; see Supp Data 1E for exact locations).
Fig. 2
Fig. 2. Principal components analysis based on the Human Origins dataset.
a Projection of ancient individuals’ genotypes onto principal component axes defined by modern Western Eurasians and North Africans (gray labels, see panel (c) for legend for all abbreviations but ‘Can', for Canary Islands). b Zoom into the region most relevant for Sardinia. Each projected ancient individual is displayed as a transparent colored point in panel (a) and (b), with the color determined by the age of each sample (see panel (d) for legend). In panel (b), median PC1 and PC2 values for each population are represented by three-letter abbreviations, with black or gray font for moderns and a color-coded font based on the mean age for ancient populations. Ancient Sardinian individuals are plotted as circles with edges, color-coded by age, and with the first three letters of their sample ID (which typically indicates the archeological site). Modern individuals from the Sidore et al. sample of Sardinia are represented with gray circles and modern individuals from the reference panel with gray squares. See Fig. 5 for a zoomed in representation with detailed province labels for Sardinian individuals. The full set of labels and abbreviations are described in Supp. Data 1E, F. c Geographic legend of present-day individuals from the Human Origins and our Sardinian reference dataset. d Timeline of selected ancient groups. Note: The same geographic abbreviation can appear multiple times with different colors to represent groups with different median ages.
Fig. 3
Fig. 3. Genetic similarity matrices.
We calculated FST (upper panel) and outgroup-f3 (lower panel) of ancient Sardinian (Middle/Late Neolithic to Nuragic periods) and modern Sardinian individuals (grouped into within and outside the Ogliastra region) with each other (left), various ancient (middle), and modern populations (right) of interest. The full sharing matrices can be found in Supp. Figs. 10/11, where we also include post-Nuragic sites. For ancient groups, sample sizes and time-spans are provided in Fig 1d. The full set of labels and abbreviations are described in Supp. Data 1E, F.
Fig. 4
Fig. 4. Admixture coefficients estimated by ADMIXTURE (K = 6).
Each stacked bar represents one individual and color fractions depict the fraction of the given individual's ancestry coming from a given “cluster”. For K = 6 (depicted here), Sardinian individuals up until the Nuragic share similar admixture proportions as other western European Neolithic individuals. Present-day as well as most post-Nuragic ancient Sardinian individuals have elevated Steppe-like ancestry (blue), and an additional ancestry component prevalent in Near Eastern/Levant populations (orange). An ancient North-African component (green) appears at low fraction in many present-day Mediterranean populations, and somewhat stronger in samples from the Sardinian Punic site Villamar. ADMIXTURE results for all K = 2, … , 11 are depicted in the supplement (Supp. Fig. 19).
Fig. 5
Fig. 5. Present-day genetic structure in Sardinia reanalyzed with aDNA.
a Scatter plot of the first two principal components from Fig. 2a with a zoom-in on present-day Sardinia diversity in our sample. Median PC values for each Sardinian region are depicted as large circles. b PCA results based on present-day Sardinian individuals, subsampling Cagliari and Ogliastra to 100 individuals to avoid effects of unbalanced sampling. In both panels, each individual is labeled with an abbreviation that denotes the source location if at least three grandparents were born in the same geographical location (“small” three-letter abbreviations) or if grand-parental ancestry is missing with question mark. We also projected each ancient Sardinian individual on to the top two PCs (points color-coded by age, see Fig. 1 for the color scale).

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