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Over half a century ago, following the development and integration of the adequate technology, the deep sea transitioned from being the last frontier for exploration on our planet to the subject of industrial-level exploitation. While the main impacts in the deep sea are currently the product of large-scale fisheries and offshore energy production (mainly oil and gas), the expected transition of the global economy towards greener (or, in this case, bluer) solutions will likely include the use of the marine domain as a setting for renewable energy infrastructure (e.g., floating wind farms loosely anchored to the seabed) and seabed mining for rare minerals that are fundamental to the renewable energy technologies. Despite the risks posed by these impacts, the development of robust management guidelines for deep-sea habitats and resources has not kept pace with technological progress and growing economic forces. As a result, this highlights an opportunity to develop standardized methodologies, goals and overall strategies. To achieve this, it is imperative for scientists and managing authorities to reach a high level of consensus in both data acquisition and treatment, as well as in reliable ecological indicators to track both natural and human-induced ecosystem changes. (...)

During recent years, terrestrial and extraterrestrial ocean research have increasingly joined forces to merge expertise and technical solutions in the exploration of marine systems on Earth and in space. This includes solutions for robotic applications, autonomy and sensor integration, as well as data analysis. These synergies in biomimetic design, platform artificial intelligence (AI) and life-tracing sensor packages will be applied to the monitoring and surveillance of environmentally delicate habitats on Earth such as cold-water coral reefs or fishing grounds, as well as decommissioning sites. Thus, marine scientific and industrial offshore infrastructures may provide innovative test-bed services for robotics and sensor development.

3 pages, The occupancy assumption “one burrow system, one animal” (Sardà and Aguzzi, 2012) raises a number of generic research questions concerning the true occupation of burrows in many Nephrops stocks. The burrow system acts as the centre of a strong territorial rhythmic behaviour (Rice and Chapman, 1971; Farmer, 1975) leading the adults’ lobsters to evict subordinates from burrows in a dominance hierarchy framework (Sbragaglia et al., 2017); indeed, two wild adult lobsters are rarely found in the same shelter (Cobb and Wang, 1985). Other studies showed evi-dence that no spatial segregation occurs between juveniles and adults (Maynou and Sardà, 1997) achieving the establishment of adult-juvenile complexes (at least 1 adult and 1 juvenile per bur-row), which become separated as juveniles grow (Tuck et al., 1994). Moreover, Nehprops bur-rows systems could also be inhabited by other benthic crustacean species (e.g. Munida sp.) or may remain empty and intact for an unknown period of time after animals’ death (Sardà and Aguzzi, 2012). These factors still create uncertainties about the true numbers of animals occupy-ing burrow systems, representing an important issue when providing a relative or absolute index for determination of Nephrops’ stock status (i.e. Harvest Rate; Sardà and Aguzzi, 2012). [...]

The presence of the opal chimaera, Chimaera opalescens, is reported for the first time in the deep waters of the Azores, with the capture of four specimens by fishermen and the video recording of an additional five individuals. Species identification was supported by the 646 bp sequenced fragment of the mitochondrial gene cytochrome oxidase subunit I. Because C. opalescens is a recently recognised species that had been recurrently misidentified as rabbitfish, Chimaera monstrosa, the historical data of C. monstrosa in the Azores were reviewed to assess the possible presence of both Chimaera species in the region. Although several authors have reported the occurrence of C. monstrosa in the Azorean waters since the 1800s, the majority of these are based on only three specimens caught during the late 1800s. The investigation performed using literature and examination of the museum specimens still available concluded that the most likely scenario is that C. monstrosa is absent from the Azores and past records of that species in the region are most likely misidentifications of C. opalescens.

Despite 400–450 million years of independent evolution, a strong phenotypic convergence has occurred between two groups of fish: tunas and lamnid sharks. This convergence is characterized by centralization of red muscle, a distinctive swimming style (stiffened body powered through tail movements) and elevated body temperature (endothermy). Furthermore, both groups demonstrate elevated white muscle metabolic capacities. All these traits are unusual in fish and more likely evolved to support their fast-swimming, pelagic, predatory behavior. Here, we tested the hypothesis that their convergent evolution was driven by selection on a set of metabolic genes. We sequenced white muscle transcriptomes of six tuna, one mackerel, and three shark species, and supplemented this data set with previously published RNA-seq data. Using 26 species in total (including 7,032 tuna genes plus 1,719 shark genes), we constructed phylogenetic trees and carried out maximum-likelihood analyses of gene selection. We inferred several genes relating to metabolism to be under selection. We also found that the same one gene, glycogenin-1, evolved under positive selection independently in tunas and lamnid sharks, providing evidence of convergent selective pressures at gene level possibly underlying shared physiology.

The phylogenetic relationships among theNorth Atlantic Gaidropsarus and between the three Gaidropsarinae genera Gaidropsarus, Ciliata and Enchelyopus are reviewed with the hitherto most comprehensive taxonomic sampling of this group. Phylogenetic results (maximum parsimony, maximum likelihood and Bayesian inference) based on nuclear (rhodopsin) and concatenated mitochondrial (12s, 16s and cytb)markers clearly support this subfamily. For the north-eastern Atlantic species of Gaidropsarus, two previously unreported clades were strongly supported, clarifying the relationships within the genus, and revealing fewer distinct taxa in the north Atlantic Gaidropsarus than previously stipulated. The data challenge the specific status of Gaidropsarus mediterraneus and Gaidropsarus guttatus and raise doubts concerning the distinctiveness of other species. A taxonomic revision of the genus is suggested. This study was funded by the Eco-Ethology Research Unit Strategic Plan (PEst-OE/MAR/UI0331/2011) – Fundação para a Ciência e a Tecnologia (FCT; partially FEDER funded). S.M.F.was supported by an FCT grant (SFRH/BPD/84923/2012). IMAR-Univ Azores was funded through the pluriannual and programmatic funding scheme as research unit #531 and associate laboratory LARSyS #9, with financial support from OE and COMPETE, through FCT and DRCTC/GovAzores. S.S. was a researcher contracted by MAR/DOP under the Ciência 2007 recruitment programme funded by FCT and is now a research fellow supported by the Marie Curie grant cofunded by the EU under the FP7-People-2012-COFUND; Co-funding of Regional, National and International Programmes, GA n.600407 and the Bandiera Project RITMARE.

Journal homepage: http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1755-0998 The present investigation provides an efficient diagnostic method based on polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analysis to discriminate between two cryptic species of scabbardfish, Aphanopus carbo and A. intermedius, with commercial relevance in several European fish markets. Two DNA fragments from the mtDNA, including control region and partial cytochrome oxidase subunit I genes of about 1100 bp and 700 bp, respectively, were isolated by PCR amplification. Digestion of the amplicon including the control region with HaeII and the amplicon including the COI gene with Sau3AI restriction enzymes allowed an unequivocal discrimination between the two scabbardfish species. This PCR–RFLP method allowed a clear and rapid discrimination of the trichiurid species studied.

Coryphoblennius galerita is a small intertidal fish with a wide distribution and limited dispersal ability, occurring in the northeastern Atlantic and Mediterranean. In this study, we examined Atlantic and Mediterranean populations of C. galerita to assess levels of genetic divergence across populations and to elucidate historical and contemporary factors underlying the distribution of the genetic variability. We analyse three mitochondrial and one nuclear marker and 18 morphological measurements. The combined dataset clearly supports the existence of two groups of C. galerita : one in the Mediterranean and another in the northeastern Atlantic. The latter group is subdivided in two subgroups: Azores and the remaining northeastern Atlantic locations. Divergence between the Atlantic and the Mediterranean can be the result of historical isolation between the populations of the two basins during the Pleistocene glaciations. Present-day barriers such as the Gibraltar Strait or the ‘Almeria-Oran jet’ are also suggested as responsible for this isolation. Our results show no signs of local extinctions during the Pleistocene glaciations, namely at the Azores, and contrast with the biogeographical pattern that has been observed for Atlantic– Mediterranean warm-water species, in which two groups of populations exist, one including the Mediterranean and the Atlantic coast of western Europe, and another encompassing the western tropical coast of Africa and the Atlantic islands of the Azores, Madeira and Canaries. Species like C. galerita that tolerate cooler waters, may have persisted during the Pleistocene glaciations in moderately affected locations, thus being able to accumulate genetic differences in the more isolated locations such as the Azores and the Mediterranean. This study is one of the first to combine morphological and molecular markers (mitochondrial and nuclear) with variable rates of molecular evolution to the study of the relationships of the Atlantic and Mediterranean populations of a cool-water species.

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Zooplankton plays a pivotal role in marine ecosystems and the characterisation of its biodiversity still represents a challenge for marine ecologists. In this study, mesozooplankton composition from 46 samples collected in summer along the western Adriatic Sea, was retrieved by DNA metabarcoding analysis. For the first time, the highly variable fragments of the mtDNA COI and the V9 region of 18S rRNA genes were used in a combined matrix to compile an inventory of mesozooplankton at basin scale. The number of sequences retrieved after quality filtering were 824,148 and 223,273 for COI and 18S (V9), respectively. The taxonomical assignment against reference sequences, using 95% (for COI) and 97% (for 18S) similarity thresholds, recovered 234 taxa. NMDS plots and cluster analysis divided coastal from offshore samples and the most representative species of these clusters were distributed according to the dominant surface current pattern of the Adriatic for the summer period. For selected sampling sites, mesozooplankton species were also identified under a stereo microscope providing insights on the strength and weakness of the two approaches. In addition, DNA metabarcoding was shown to be helpful for the monitoring of non-indigenous marine metazoans and spawning areas of commercial fish species. We defined pros and cons of applying this approach at basin scale and the benefits of combining the datasets from two genetic markers.

Deep-sea fishes provide a unique opportunity to study the physiology and evolutionary adaptation to extreme environments. We carried out a high throughput sequencing analysis on a 454 GS-FLX titanium plate using unnormalized cDNA libraries from six tissues ofA. carbo. Assemblage and annotations were performed by Newbler and InterPro/Pfam analyses, respectively. The assembly of 544,491 high quality reads provided 8,319 contigs, 55.6% of which retrieved blast hits against the NCBI nonredundant database or were annotated with ESTscan. Comparison of functional genes at both the protein sequences and protein stability levels, associated with adaptations to depth, revealed similarities betweenA. carboand other bathypelagic fishes. A selection of putative genes was standardized to evaluate the correlation between number of contigs and their normalized expression, as determined by qPCR amplification. The screening of the libraries contributed to the identification of new EST simple-sequence repeats (SSRs) and to the design of primer pairs suitable for population genetic studies as well as for tagging and mapping of genes. The characterization of the deep-sea fishA. carbofirst transcriptome is expected to provide abundant resources for genetic, evolutionary, and ecological studies of this species and the basis for further investigation of depth-related adaptation processes in fishes.