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Southern Europe.
Leiden clustering yields three broad groups of clusters with southern European membership, as follows: one grouping individuals born around the eastern Mediterranean (i.e., Italy, Greece, Turkey, and Cyrpus), the Iberia Peninsula (Spain and Portugal), and finally two outgroup clusters (“Mixed European” and “Malta”).
Most sampled Greek individuals form a single cluster that in the nnls analysis is modeled as a mixture of haplotypes from neighboring southern clusters such as “Italy” and “Turkey,” but as well haplotypes from the north from NE Balkans. We observe a smaller cluster grouped with the “Greece” cluster on the dendrogram (Fig. 2) that contains all sampled Albanian individuals and also projects separately to Greece in PCA; this finding is suggestive of an additional structure that we explore in our IBD-based analyses below. Elsewhere in this branch are the majority of Cypriots, Turkish, and Italian samples grouped into their own three respective clusters. In Italy, our clustering approach does not resolve the north–south clustering previously observed (4).
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Modern Cypriots (especially Greek Cypriots) are genetically intermediate but cluster primarily with the South European (Mediterranean) group in most autosomal analyses. They form a homogeneous domain with Aegean island Greeks (e.g., Crete, Dodecanese), southern Italians (Sicily/Calabria), and Sicilians, as shown in PCA and ADMIXTURE plots from Lazaridis et al. (2017) and Stamatoyannopoulos et al. (2017, Eur J Hum Genet). This reflects dominant Bronze Age Aegean/Anatolian ancestry (~60–70%), pulling them into the "Southern European" cline despite ~20–30% Levantine input.
However, they exhibit a "bridge" position toward West Asia:
In global PCA (e.g., 1000 Genomes/HO), Cypriots plot between southern Europeans and West Asians (Lebanese, western Turks), closer to the former but with overlap into the latter due to shared Neolithic farmer and Phoenician components.
Commercial tests (e.g., 23andMe) often assign them to "West Asian & North African" (WANA) clusters because reference panels emphasize Levantine/West Asian markers, but scientific studies (e.g., Haber et al., 2013) place them in a "Levantine Christian + South European" branch.
They lack significant Slavic/Northern European admixture (~2–3% vs. 10–20% in mainland Greeks), making them more "southern-shifted" than continental Greeks but still distinct from core West Asians (e.g., higher F_ST to Syrians than to Cretans).
In summary, Cypriots are best described as a South European population with West Asian affinities, forming the eastern edge of the Mediterranean genetic continuum. This aligns with their history as a crossroads of Aegean, Levantine, and Anatolian migrations.