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Spatangoids are probably the least resolved group within echinoids, with known topological incongruencies between phylogenies derived from molecular (very scarce) and morphological data. The present work, based on the analysis of 270 specimens of Spatangidae (Echinoidea, Spatangoida) trawled in the Sardinian seas (Western Mediterranean), allowed us to verify the constancy of some characters that we consider to be diagnostic at the genus level —such as the path of the subanal fasciole and the relationship between labrum and adjacent ambulacral plates —and to distinguish two distinct forms within the studied material. Based on morphological characters, morphometrics, and molecular analyses (sequencing of two mitochondrial markers: cytochrome c oxidase subunit1 (COI) and 16S), most of the individuals were classified as morphotype A and attributed to the species Spatangus purpureus, the most common spatangoid in the Mediterranean Sea, while a few corresponded to a different morphotype (B), genetically close to the species Spatangus raschi. Preliminary morphological analyses seemed to indicate that morphotype B specimens from Sardinia are slightly different from S. raschi and from Spatangus subinermis individuals, the second species of the family known to occur in the Mediterranean Sea. On the basis of morpho-structural observations and molecular analyses, comparing Mediterranean living forms with species from other areas (Central Eastern Atlantic, North Sea and neighboring basins, South African Sea, Philippines and Indonesian Archipelago, New Zealand, and Hawaiian Islands), the clear distinction of S. purpureus from several other species classified as Spatangus was confirmed. Based on the morphological and genetic differences, we propose to maintain the genus Spatangus including in it only the type species S. purpureus among the living species and to establish the new genus Propespatagus nov. gen. to include several other species previously classified as Spatangus. The clear distinction among different genera was also detected in fossil forms of Spatangus, Propespatagus nov. gen., and Sardospatangus (†) from the European Oligo-Miocene sedimentary rocks of Germany; the Miocene of Ukraine, Italy, and North Africa; the Plio-Pleistocene of Italy; and the Mio-Pliocene of Florida (USA). The new data can help in addressing taxonomic ambiguities within echinoids, as well as in improving species identification, and hence biodiversity assessments in the Mediterranean region.

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.

The present study focused on the three species of electric rays known to occur in the Mediterranean Sea: Torpedo torpedo, Torpedo marmorata and Tetronarce nobiliana. Correct identification of specimens is needed to properly assess the impact of fisheries on populations and species. Unfortunately, torpedoes share high morphological similarities, boosting episodes of field misidentification. In this context, genetic data was used (1) to identify specimens caught during fishing operations, (2) to measure the diversity among and within these species, and (3) to shed light on the possible occurrence of additional hidden species in the investigated area. New and already published sequences of COI and NADH2 mitochondrial genes were analyzed, both at a small scale along the Sardinian coasts (Western Mediterranean) and at a large scale in the whole Mediterranean Sea. High levels of genetic diversity were found in Sardinian populations, being significantly different from other areas of the Eastern Mediterranean Sea due to the biotic and abiotic factors here discussed. Sardinian torpedoes can hence be indicated as priority populations/areas to be protected within the Mediterranean Sea. Moreover, sequence data confirmed that only the three species occur in the investigated area. The application of several ‘species-delimitation’ methods found evidence of cryptic species in the three species outside the Mediterranean Sea, as well as in other genera/families, suggesting the urgent need for future studies and a comprehensive revision of the order Torpediniformes for its effective conservation.

Restoration is considered an effective strategy to accelerate the recovery of biological communities at local scale. However, the effects of restoration actions in the marine ecosystems are still unpredictable. We performed a global analysis of published literature to identify the factors increasing the probability of restoration success in coastal and marine systems. Our results confirm that the majority of active restoration initiatives are still concentrated in the northern hemisphere and that most of information gathered from restoration efforts derives from a relatively small subset of species. The analysis also indicates that many studies are still experimental in nature, covering small spatial and temporal scales. Despite the limits of assessing restoration effectiveness in absence of a standardized definition of success, the context (degree of human impact, ecosystem type, habitat) of where the restoration activity is undertaken is of greater relevance to a successful outcome than how (method) the restoration is carried out. Contrary to expectations, we found that restoration is not necessarily more successful closer to protected areas (PA) and in areas of moderate human impact. This result can be motivated by the limits in assessing the success of interventions and by the tendency of selecting areas in more obvious need of restoration, where the potential of actively restoring a degraded site is more evident. Restoration sites prioritization considering human uses and conservation status present in the region is of vital importance to obtain the intended outcomes and galvanize further actions.

In 1990s, the European spiny lobster Palinurus elephas, one of the most commercially important species in the Mediterranean, exhibited a population decline. For this reason, fully protected areas (FPAs) appeared effective in re-establishing natural populations and supporting fishery-management objectives. Here, the reproductive parameters of P. elephas populations in two different FPAs (Su Pallosu and Buggerru, central-western Mediterranean), where a restocking programme was carried out, and in their surrounding commercial zones, were investigated from quantitative and qualitative perspectives. The comparison of fecundity between females collected inside and outside FPAs did not show statistical differences as well as the vitellogenin concentration, which did not vary among eggs of different size classes of females caught inside and outside the FPAs, indicating the same reproductive potential. The study demonstrated a benefit of overexploited populations in terms of enhancement of egg production overtime (15 years for Su Pallosu and 6 years for Buggerru) with a mean egg production 4.25–5.5 times higher at the end of the study than that observed at the beginning of the study. The main driver of eggs production appeared to be size, with larger lobsters more present inside the FPAs than outside. Given these results, the dominant contribution of the two studied FPAs to the regional lobster reproduction is remarkable.

Molecular identifications based on two mitochondrial markers (cytochrome c oxidase subunit I -COI- and 16S ribosomal RNA gene -16S-) have been implemented to confirm the morphological identification of eight specimens collected in the Central western Mediterranean. Molecular data show they belonged to a recently resurrected species of the genus Ommastrephes, i.e., O. caroli, known to be distributed in the Atlantic Ocean and Mediterranean Sea. Despite this, molecular analyses of COI sequences evidenced the presence of potential genetic differentiation between Mediterranean and Atlantic samples, highlighting the need for further studies, with more individuals to investigate the connectivity between individuals living in the two areas. Furthermore, morphological, biometric and reproductive features here reported, could be useful in evaluating possible distinctive biological features between the Mediterranean and Atlantic individuals. Female mature size was larger than the male. The relationships obtained between the beak measurements and body sizes (DML; TW) were better described by a power model. Asynchronous oocytes development with relatively small oocytes (0.05–1.10 mm) and a protracted intermittent spawning with active feeding were observed. This study also reported for the specie O. caroli the first data on the potential fecundity estimated (840061 oocytes), the oviducal load (90000 ripe oocytes) as well as the number of seminal receptacles and the size and morphology of the spermatangia found in the buccal mass of all mated females. Even if on a low sample size, beaks and eye lenses were used for the first time in O. caroli for age estimation. The statistically significant relationship found between increments counted in eye lenses and beaks highlighted the reliability of the lenses to estimate age in O. caroli, even if further studies will be needed for its validation. Assuming a daily increment for both structures, a mean life span of about 12–13 months was estimated for both sexes, which is consistent with the sexual maturity condition observed in all the samples and the semelparity known for cephalopods coleoids.

Marine animal forests are key mesophotic ecosystems that are under threat from increasing natural and human pressures. Despite the fact that various international agreements strive to preserve these fragile ecosystems, the environmental status of the majority of these animal-structured environments is unknown. Assessing their environmental status is the first step needed to monitor these essential habitats’ health over time and include them within conservation and protection frameworks, such as the Marine Strategy Framework Directive. Based on Multibeam data and ROV footage, we characterized the geomorphological setting and evaluated the environmental status of seven black coral forests in the centre of the Western Mediterranean Sea, using the Mesophotic Assemblages Conservation Status (MACS) Index. The presence of two antipatharians, Antipathella subpinnata and Leiopathes glaberrima, characterized the seven investigated sites, dwelling on rocky substrate characterized by different environmental drivers (i.e., depth, slope of the substrate, terrain ruggedness, topographic positioning index, and aspect). From the combined evaluation of the associated benthic community status and the anthropogenic impacts affecting it, a “high” and “good” environmental status was assessed for five out of the seven studied black forests, with only two forests classified as having a “moderate” and “poor” status, respectively. Overall, our study showed a site-specific variability of mesophotic black coral forest status, explained by different biological community structures and environmental conditions mainly associated with morphological and anthropogenic factors.

Summary: Whole-genome sequencing data were produced from a single flathead grey mullet female and assembled into a draft genome sequence, whereas publicly available sequence data were used to obtain a male draft sequence. Two pools, each consisting of 60 unrelated individuals, respectively, of male and female fish were analyzed using Pool-Sequencing. Mapping and analysis of Pool-Seq data against the draft genome(s) revealed >30 loci potentially associated with sex, the most promising locus of which, encoding the follicle-stimulating hormone receptor (fshr) and harboring two missense variants, was genotyped on 245 fish from four Mediterranean populations. Genotype data showed that fshr represents a previously unknown sex-determining locus, although the incomplete association pattern between fshr genotype and sex-phenotype, the variability of such pattern across different populations, and the presence of other candidate loci reveal that a greater complexity underlies sex determination in the flathead grey mullet.

Mediterranean red coral Corallium rubrum is considered the most precious coral worldwide. Harvesting activities are performed by licensed scuba divers and managed through the recent pan-Mediterranean management plan issued by General Fisheries Commission for the Mediterranean (GFCM) along with measures locally enacted, imposing limits on licenses, harvesting season, minimum depth of dive, and size. The use of Remotely Operated Vehicles (ROVs) is prohibited, with the only exception being for scientific purposes. Despite measures already in force, the implementation of additional management tools has been recently recommended. This article reports results from the first monitoring campaign on C. rubrum harvesting based on ROVs for seabed exploration and Onboard Scientific Observers (OSOs), carried out from 2012 to 2015 along the coast of Sardinia (Mediterranean Sea—Western basin). More than 450 dives were monitored, confirming how ROV’s support eases the scouting of exploitable banks, leading to increases in catches. OSOs reported the collection of colonies below the minimum reference size and catches/dive above limits. Onboard observers collected data also on colony diameter, which is crucial for the estimation of population size structure and exploitation status. OSOs proved to be valid tools in providing additional and reliable information on red coral harvesting, thus deserving to be included among mandatory measures for the sustainable exploitation of red coral in the Mediterranean Sea.

Corallium rubrum and Eunicella cavolini are two octocorals, reported as co-occurring species in the deep rocky habitats of the Mediterranean Sea with a high hydrodynamic and moderate eutrophication. Their spatial distribution and demography in the deep sea are mainly affected by temperature and direct and indirect anthropogenic activities; however, knowledge of the factors that potentially influence their co-existence is scarce. This paper provides novel data on the distribution and demography of these two species, at depths between 50 and 290 m in the Western Mediterranean Sea, providing insights on their co-occurrence. Both species exhibited the highest population density at deeper sites (>150 m), showing an inverse size–density relation. Density values ranged from 0.03 colonies m−2 to 32 and 80 col. m−2 for yellow gorgonian and red coral, respectively. The two species co-occurred in 13% of the total frames examined, mostly dwelling between 120 and 160 m depth. Distance-based linear modeling (DistLM) emphasized that when co-occurring the variability of the two species’ densities were significantly driven by the density—rather than the morphology (i.e., height)—of the other species. We stress the need for further studies to elucidate the possible mutual effects of suspension feeders and to test the role of different environmental factors potentially influencing inter-specific relationships.

An integrative approach based on morphological and genetic analyses was undertaken for the first time to confirm the species identification of Mediterranean samples belonging to the genus Tremoctopus. Sequences of two mtDNA genes (cytochrome c oxidase subunit (COI) and 16S) were generated for the first time from Mediterranean samples. Both the similarity-based identifications and tree-based methods indicated that three females can be identified as Tremoctopus violaceus sensu stricto in agreement with their morphological classifications. All Mediterranean sequences clustered with the sequences of Tremoctopus violaceus from the Gulf of Mexico and were clearly differentiated from the sequences attributed to T. gracilis and T. robsoni. The chromatic pattern of the web and some features of gill filaments, arms formula, stylets, radulae, beaks, and stomach contents were given for all the samples; 105,758, 20,140, and 11,237 oocytes were estimated in the mature, immature, and developing samples, respectively. The presence of four spermatangia inside the cavity of the maturing female suggested the ability of this species to mate before reaching full maturity with more partners. Age investigation using beaks, performed for the first time in T. violaceus and within the genus gave results consistent with the different sizes and maturity conditions of the samples.

Marine environmental monitoring has tended to focus on site-specific methods of investigation. These traditional methods have low spatial and temporal resolution and are relatively labour intensive per unit area/time that they cover. To implement the Marine Strategy Framework Directive (MSFD), European Member States are required to improve marine monitoring and design monitoring networks. This can be achieved by developing and testing innovative and cost-effective monitoring systems, as well as indicators of environmental status. Here, we present several recently developed methodologies and technologies to improve marine biodiversity indicators and monitoring methods. The innovative tools are discussed concerning the technologies presently utilized as well as the advantages and disadvantages of their use in routine monitoring. In particular, the present analysis focuses on: (i) molecular approaches, including microarray, Real Time quantitative PCR (qPCR), and metagenetic (metabarcoding) tools; (ii) optical (remote) sensing and acoustic methods; and (iii) in situ monitoring instruments. We also discuss their applications in marine monitoring within the MSFD through the analysis of case studies in order to evaluate their potential utilization in future routine marine monitoring. We show that these recently-developed technologies can present clear advantages in accuracy, efficiency and cost.

The Marine Strategy Framework Directive requires the environmental status of European marine waters to be assessed using biodiversity as one out of 11 descriptors, but the complexity of marine biodiversity and its large span across latitudinal and salinity gradients have been a challenge to the scientific community aiming to produce approaches for integrating information from a broad range of indicators. The Nested Environmental status Assessment Tool (NEAT), developed for the integrated assessment of the status of marine waters, was applied to ten marine ecosystems to test its applicability and compare biodiversity assessments across the four European regional seas. We evaluate the assessment results as well as the assessment designs of the ten cases, and how the assessment design, particularly the choices made regarding the area and indicator selection, affected the results. The results show that only 2 out of the 10 case study areas show more than 50 % probability of being in good status in respect of biodiversity. No strong pattern among the ecosystem components across the case study areas could be detected, but marine mammals, birds, and benthic vegetation indicators tended to indicate poor status while zooplankton indicators indicated good status when included into the assessment. The analysis shows that the assessment design, including the selection of indicators, their target values, geographical resolution and habitats to be assessed, has potentially a high impact on the result, and the assessment structure needs to be understood in order to make an informed assessment. Moreover, recommendations are provided for the best practice of using NEAT for marine status assessments.

Nematodes inhabiting benthic deep-sea ecosystems account for >90% of the total metazoan abundances and they have been hypothesised to be hyper-diverse, but their biodiversity is still largely unknown. Metabarcoding could facilitate the census of biodiversity, especially for those tiny metazoans for which morphological identification is difficult. We compared, for the first time, different DNA extraction procedures based on the use of two commercial kits and a previously published laboratory protocol and tested their suitability for sequencing analyses of 18S rDNA of marine nematodes. We also investigated the reliability of Roche 454 sequencing analyses for assessing the biodiversity of deep-sea nematode assemblages previously morphologically identified. Finally, intra-genomic variation in 18S rRNA gene repeats was investigated by Illumina MiSeq in different deep-sea nematode morphospecies to assess the influence of polymorphisms on nematode biodiversity estimates. Our results indicate that the two commercial kits should be preferred for the molecular analysis of biodiversity of deep-sea nematodes since they consistently provide amplifiable DNA suitable for sequencing. We report that the morphological identification of deep-sea nematodes matches the results obtained by metabarcoding analysis only at the order-family level and that a large portion of Operational Clustered Taxonomic Units (OCTUs) was not assigned. We also show that independently from the cut-off criteria and bioinformatic pipelines used, the number of OCTUs largely exceeds the number of individuals and that 18S rRNA gene of different morpho-species of nematodes displayed intra-genomic polymorphisms. Our results indicate that metabarcoding is an important tool to explore the diversity of deep-sea nematodes, but still fails in identifying most of the species due to limited number of sequences deposited in the public databases, and in providing quantitative data on the species encountered. These aspects should be carefully taken into account before using metabarcoding in quantitative ecological research and monitoring programmes of marine biodiversity.