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Investigating marine species population structure in a multidisciplinary framework can reveal signatures of potential local adaptation and the consequences for management and conservation. In this study we delineate the population structure of common sole (Solea solea) in the Mediterranean Sea using genomic and otolith data, based on single nucleotide polymorphism (SNPs) markers, otolith shape and otolith trace element composition data. We correlated SNPs with environmental and spatial variables to evaluate the impact of the selected features on the actual population structure. Specifically, we used a seascape genetics approach with redundancy (RDA) and genetic-environmental association (GEA) analysis to identify loci potentially involved in local adaptation. Finally, putative functional annotation was investigated to detect genes associated with the detected patterns of neutral and adaptive genetic variation. Results from both genetic and otolith data suggested significant divergence among putative populations of common sole, confirming a clear separation between the Western and Eastern Mediterranean Sea, as well as a distinct genetic cluster corresponding to the Adriatic Sea. Evidence of fine-scale population structure in the Western Mediterranean Sea was observed at outlier loci level and further differentiation in the Adriatic. Longitude and salinity variation accounted for most of the wide and fine spatial structure. The GEA detected significant associated outlier loci potentially involved in local adaptation processes under highly structured differentiation. In the RDA both spatial distribution and environmental features could partially explain the genetic structure. Our study not only indicates that separation among Mediterranean sole population is led primarily by neutral processes because of low connectivity due to spatial segregation and limited dispersal, but it also suggests the presence of local adaptation. These results should be taken into account to support and optimize the assessment of stock units, including a review and possible redefinition of fishery management units.

The present study, based on microsatellite markers, describes a population genetic analysis of the small-spotted catshark Scyliorhinus canicula (Linnaeus, 1758), representing one of the most abundant and commonly caught cartilaginous fishes in the Mediterranean Sea and adjacent areas. The analyses were performed to unravel the genetic features (variability, connectivity, sex-biased dispersal) of their relative geographic populations, both at the small (around the coast of Sardinia, Western Mediterranean Sea) and at a larger spatial scale (pan-Mediterranean level and between the Atlantic Ocean and the Mediterranean Sea). Individual clustering, multivariate and variance analyses rejected the hypothesis of genetic homogeneity, with significant genetic differences mainly within the Mediterranean between the Western and Eastern basins, as well as between the Mediterranean and the NE Atlantic Ocean. In detail, our results seem to confirm that the Strait of Gibraltar could not represent a complete barrier to the exchange of individuals of small-spotted catshark between the Atlantic Ocean and the Mediterranean Sea. In the latter area, a complex genetic structuring for S. canicula was found. Apart from differences among the Western, Eastern and Adriatic sites, within the Western basin the small-spotted catsharks around Sardinian waters are strongly differentiated from all others (both from the eastern Tyrrhenian Sea and southernmost part of the Algerian basin) and are demographically stable. Several possible mechanisms, both biological and abiotic (e.g., migratory behavior, waterfronts, and oceanographic discontinuities), are discussed here to explain their peculiar characteristics. Overall, the genetic data presented, both at the local and regional level, could represent a baseline information, useful for the temporal monitoring of populations, and to assess the effects of present or future fishing/management/conservation measures.

Among the main measures adopted to reduce anthropogenic impacts on elasmobranch communities, understanding the ecology of deep-sea sharks is of paramount importance, especially for potentially vulnerable species highly represented in the bycatch composition of commercial fisheries such as the blackmouth catshark Galeus melastomus. In the present work, we unravelled the first indication of population genetic structure of G. melastomus by using a novel and effective panel of nuclear, and polymorphic DNA markers and compared our results with previous findings supporting high genetic connectivity at large spatial scales. Given the lack of species-specific nuclear markers, a total of 129 microsatellite loci (Simple Sequence Repeats, SSRs) were cross-amplified on blackmouth catshark specimens collected in eight geographically distant areas in the Mediterranean Sea and North-eastern Atlantic Ocean. A total of 13 SSRs were finally selected for genotyping, based on which the species exhibited signs of weak, but tangible genetic structure. The clearcut evidence of genetic differentiation of G. melastomus from Scottish waters from the rest of the population samples was defined, indicating that the species is genetically structured in the Mediterranean Sea and adjacent North-eastern Atlantic. Both individual and frequency-based analyses identified a genetic unit formed by the individuals collected in the Tyrrhenian Sea and the Strait of Sicily, distinguished from the rest of the Mediterranean and Portuguese samples. In addition, Bayesian analyses resolved a certain degree of separation of the easternmost Aegean sample and the admixed nature of the other Mediterranean and the Portuguese samples. Here, our results supported the hypothesis that the interaction between the ecology and biology of the species and abiotic drivers such as water circulations, temperature and bathymetry may affect the dispersion of G. melastomus, adding new information to the current knowledge of the connectivity of this deep-water species and providing powerful tools for estimating its response to anthropogenic impacts.

DNA barcoding is a molecular tool that enables rapid and accurate identification of biological species by sequencing a short, standardized region of the mitochondrial gene cytochrome c oxidase I ( COI) as internal species tag. The aim of the present study was to use DNA barcoding in addition to classical taxonomy in order to obtain a more reliable species-identification of leptocephali, the characteristic larval forms of the superorder Elopomorpha, often difficult to identify and to match with their adult stage. Based on the examination of external morphology, meristics, and pigmentation, 2785 leptocephalus larvae collected in the Adriatic Sea between 2010 and 2012, were ascribed to 7 morphotypes, belonging to Anguilliform order (Ariosoma balearicum, Conger conger, Gnathophis mystax, Nettastoma melanurum, Dalophis imberbis, Chlopsis bicolor, Facciolella sp.) and 69 specimens were sequenced for a 655 bp region of the mitochondrial cytochrome oxidase subunit I gene (COI) to confirm the previous morphological analysis. The highly consistent results obtained revealed a good performance of COI barcoding as a diagnostic method for the identification of these larvae, but the limited number of leptocephali species annotated in the reference databases for barcode (Barcode of Life Data Systems and GenBank) allowed to validate only partially the morphological analysis. Moreover two species, Gnathophis mystax and Facciolella sp., showed unexpected outcomes. The data obtained in this work represent the first results of a wider project aimed at the creation of a new barcode database for the assessment of leptocephali diversity in the Mediterranean Sea (Barcoding of the Adriatic Leptocephali [BAL]), contributing to the knowledge of these unusual larvae and of their adult forms.

European hake (EH), Merluccius merluccius, is a demersal fish distributed from the North Sea and Atlantic to the Levantine Sea in the Mediterranean. EH is an important predator of deep Mediterranean upper shelf slope communities and it is currently characterised by growth overexploitation. EH adults feed mainly on fish and squids whereas the young (