Owing to its peculiar paleogeographic history, Crete island is one of the most interesting biodiversity hotspots within the Aegean area. We here analyze the lineage diversity of Cretan Reticulitermes termites obtained on mitochondrial genes (COII and 16S) and nuclear Inter-SINE loci. The evolutionary pattern here detected shows a high correlation between clade divergence and geological events of the specific geographical area. The new haplotypes identified in Crete converge with those of specimens collected in northern Turkey, Thrace and Macedonia/Calcydia: this allows to suggest a unique genetic lineage for the Aegean area. A taxonomic and phylogenetic re-analysis of the Reticulitermes genus in Mediterranean Europe agrees with the species rank suggested for Reticulitermes balkanensis and Reticulitermes urbis, as well as for Reticulitermes banyulensis and Reticulitermes grassei from France and the Iberian peninsula. A level of divergence compatible with a specific rank of differentiation is scored also among the three Reticulitermes lucifugus subspecies from Italy and Corse, with the Sardo-Corsican entity basal to the other taxa. In the eastern area, the "Aegean" entity, including the Cretan lineages, results the most apical clade while R. urbis, distributed along the East Adriatic shores and Peloponnesus, lays as the most basal one.
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