Alps, Apennines and major islands: a complex network of evolutionary units in the Italian Brown Trout

The evolutionary history of brown trout in the Mediterranean basin has been shaped by the glacial and interglacial phases of the Quaternary, which caused repeated extinction events followed by recolonization. In this context, Mediterranean islands, such as Sardinia, have assumed a crucial role as biodiversity hotspots, due to the prolonged isolation of their populations. A recent phylogenetic study of the genus Salmo based on whole-genome analysis suggested that Sardinian trout could represent a distinct species. To further investigate the genetic structure of these populations, the genomic approach of Genotyping-by-Sequencing (GBS) was used on 130 individuals belonging to nine native populations of the Mediterranean area (five from the Italian peninsula and four from Sardinia). The samples were selected to exclude individuals introgressed with the domestic Atlantic trout, in order to avoid homogenization effects and faithfully represent the genetic diversity attributable to the Italian taxon S. ghigii. Genetic analyses showed a clear hierarchical structure: the Sardinian and peninsular populations were divided into two distinct monophyletic groups, confirming previous studies. The application of different species delimitation methods revealed an even greater genetic complexity, identifying between 7 and 9 Significant Evolutionary Units (ESU), depending on the thresholds used. In Sardinia, three distinct ESUs were detected: one in the eastern sector and two in the south-western sector of the island, in line with data obtained from the mitochondrial DNA control region. In the Italian peninsula, instead, four ESUs were identified: one Alpine, one Adriatic Apennine and two Tyrrhenian Apennine. The genetic distances between the peninsular ESUs were greater than those estimated between two recognized species, S. trutta from northern Europe and S. cettii, both associated with the Atlantic mitochondrial lineage (AT). Finally, it is important to underline that all the populations – with the exception of the two belonging to the Alpine ESU – are significantly differentiated from each other, justifying their classification as Minimum Management Units (MU) for the management and conservation practices of this species, already seriously impacted by incorrect human manipulation.