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The sand goby Pomatoschistus minutus is a major component of marine shelf and estuarine food webs and an important study organism in behavioural research. Yet, despite the sand goby’s significance, its past and present patterns of migration and gene flow are poorly understood. Here we use the mtDNA control region and parts of the flanking tRNA genes of 63 fish from six localities in the Adriatic (Eastern Mediterranean), Western Mediterranean, Atlantic, and North Sea to investigate the phylogeography of this gobiid. Phylogenetic analyses and population genetics statistics reveal the existence of an Evolutionarily Significant Unit, sensu Moritz (1994), in the Adriatic and another in the Western Mediterranean, Atlantic, and North Sea. A possible biogeographical scenario for the separation of the ancestral population is that sand gobies in the Adriatic and Western Mediterranean split between 10,000 and 5000 years ago when due to the rise in sea temperature they migrated northwards and were bisected by the Italian peninsula. A testable prediction of this scenario is that sand gobies from the Western Mediterranean, Adriatic, and Aegean form three reciprocally monophyletic groups which are the descendants of a three-way diversification event. [Copyright &y& Elsevier]

Transitional environments have great ecological value and high productivity, and many species can benefit from their sheltered conditions and food resources. In this study, we performed for the first time a fish-targeted eDNA metabarcoding of the 12S rRNA gene at 16 sites broadly covering the different water bodies of the Marano and Grado Lagoon (northern Adriatic Sea) in two seasons. The eDNA was collected at the same time as the beach seine net, allowing a direct comparison of the two approaches. With eDNA we detected 34 species, covering all the functional guilds occurring in the lagoon. Species of regional interest, that uses the area as a nursery and feeding ground, and diadromous species, highlighting the ecological connectivity between freshwater and marine habitats, were found. While some species were constantly present (e.g. Atherina boyeri, Sparus aurata), others (Squalius cephalus, Platichthys flesus) were influenced by salinity (higher in Grado and lower in Marano), which was confirmed as the main ecological driver in this environment. The comparison with traditional methods, which identified 18 species (11 of which were detected with both approaches), showed that eDNA is very sensitive in detecting most of the biodiversity in the lagoon with a limited sampling effort. Few relevant species (Chelon saliens , Knipowitschia panizzae) lacked reference sequences, which need to be implemented in the databases. Our study represents a significant advance in the understanding of lagoon fish biodiversity and ecological dynamics and contributes to the improvement of management strategies in these ecologically sensitive habitats. • eDNA detected a great richness of fish species, across different functional groups • The molecular approach (eDNA) was more sensitive than the traditional one (seine net) • Reference databases still lack sequences of relevant lagoon fish species [ABSTRACT FROM AUTHOR]