An exhaustive phylogeny of the combtooth blenny genus Salaria (Pisces, Blenniidae) shows introgressive hybridization and lack of reciprocal mtDNA monophyly between the marine species Salaria basilisca and Salaria pavo.

A comprehensive phylogeny of the genus Salaria based on mitochondrial and nuclear markers grouped the extant species of the genus in well-characterised marine and freshwater clades, thus rejecting the hypothesis of a polytypic origin of the freshwater Salaria populations and supporting the occurrence of a single invasion event of the inland waters by the genus. Based on both mitochondrial and nuclear DNA datasets, the Salaria species of the freshwater clade proved to be vicariant taxa originating from a common ancestor which could possibly spread throughout the circum-Mediterranean inland waters during the late Miocene Messinian salinity crisis, then experiencing a process of allopatric differentiation after the re-flooding of the Mediterranean basin. Within the marine clade, although the nuDNA datasets showed the existence of well-supported subclades in accordance to the morphological identification of the studied specimens, one of the two subclades obtained in the phylogenetic tree based on the mtDNA dataset included both S. basilisca and S. pavo specimens, thus failing to find the two species as reciprocally monophyletic. Such a mito-nuclear discordance is here ascribed to multiple mtDNA unidirectional introgression events from S. basilisca to S. pavo, and the molecular diversity pattern of the marine Salaria species is here ascribed to a Pleistocene speciation event nowadays partly concealed by the occurrence of introgressive hybridization phenomena between the two taxa. Our results urge for prudence when implementing DNA barcoding approaches since, in the presence of mito-nuclear discordance phenomena, single-marker mtDNA-only analyses might lead to significant misidentifications.