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Illegal, Unreported and Unregulated fishing has had a major role in the overexploitation of global fish populations. In response, international regulations have been imposed and many fisheries have been 'eco-certified' by consumer organizations, but methods for independent control of catch certificates and eco-labels are urgently needed. Here we show that, by using gene-associated single nucleotide polymorphisms, individual marine fish can be assigned back to population of origin with unprecedented high levels of precision. By applying high differentiation single nucleotide polymorphism assays, in four commercial marine fish, on a pan-European scale, we find 93-100% of individuals could be correctly assigned to origin in policy-driven case studies. We show how case-targeted single nucleotide polymorphism assays can be created and forensically validated, using a centrally maintained and publicly available database. Our results demonstrate how application of gene-associated markers will likely revolutionize origin assignment and become highly valuable tools for fighting illegal fishing and mislabelling worldwide.

4 pages; International audience; This article documents the addition of 220 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Allanblackia floribunda, Amblyraja radiata, Bactrocera cucurbitae, Brachycaudus helichrysi, Calopogonium mucunoides, Dissodactylus primitivus, Elodea canadensis, Ephydatia fluviatilis, Galapaganus howdenae howdenae, Hoplostethus atlanticus, Ischnura elegans, Larimichthys polyactis, Opheodrys vernalis, Pelteobagrus fulvidraco, Phragmidium violaceum, Pistacia vera, and Thunnus thynnus. These loci were cross-tested on the following species: Allanblackia gabonensis, Allanblackia stanerana, Neoceratitis cyanescens, Dacus ciliatus, Dacus demmerezi, Bactrocera zonata, Ceratitis capitata, Ceratitis rosa, Ceratits catoirii, Dacus punctatifrons, Ephydatia mülleri, Spongilla lacustris, Geodia cydonium, Axinella sp., Ischnura graellsii, Ischnura ramburii, Ischnura pumilio, Pistacia integerrima and Pistacia terebinthus.

Conservation and long-term management plans of marine species need to be based upon the universally recognized key-feature of species identity. This important assignment is particularly challenging in skates (Rajiformes) in which the phenotypic similarity between some taxa and the individual variability in others, hampers accurate species identification. Here, 432 individual skate samples collected from four major ocean areas of the Atlantic were barcoded and taxonomically analysed. A BOLD project ELASMO ATL was implemented with the aim of establishing a new fully available and well curated barcode library containing both biological and molecular information. The evolutionary histories of the 38 skate taxa were estimated with two concatenated mitochondrial markers (COI and NADH2) through Maximum Likelihood and Bayesian inference. New evolutionary lineages within the genus Raja were discovered off Angola, where paleogeographic history coupled with oceanographic discontinuities could have contributed to the establishment of isolated refugia, playing a fundamental role among skates’ speciation events. These data successfully resolved many taxonomic ambiguities, identified cryptic diversity within valid species and demonstrated a highly cohesive monophyletic clustering among the order, laying the background for further inference of evolutionary patterns suitable for addressing management and conservation issues.

There is a growing interest in the characterization of mining residues, both for environmental assessments and critical raw materials recovery. The lack of sufficient in situ samples hampers an effective geostatistical modelling of material concentrations variability. This paper proposes a method to characterize the aluminum spatial variability in a mine residue from remote sensing data and imprecise information from daily dumping procedures. The method is proposed for the mapping of aluminum within a Greek bauxite residue, using Sentinel-2 imagery. The spatial correlation between metal concentrations and remote sensing indicators (e.g., spectral band ratios) is the premise for mapping aluminum varieties. The proposed method is based on Conditional Gaussian Co-Simulation, where Sentinel-2 images can be used as auxiliary variables. Simulation results are compared with the Co-kriging estimation method. To perform the Co-kriging estimation, the same conditions as simulation are used (same inputs, models, and neighborhoods). Simulation results quantified the metals variability in mining residues, presenting the metal concentration of piled materials in two time periods. For results validation and selecting the best map, fourteen validation samples were used. For the best representative maps of aluminum concentration, a correlation coefficient of about 0.7 between the validation data and obtained aluminum concentration map was obtained.

International audience; Skates are characterised by conservative body morphology which hampers identification and leads to frequent taxonomic confusion and market mislabelling. Accurate specimen classification is crucial for reliable stock assessments and effective conservation plans, otherwise the risk of extinction could be unnoticed. The misclassification issue is evident for the genus Dipturus, distributed worldwide, from the continental shelf and slope to the deep sea. In this study, barcode cytochrome oxidase I gene (COI) sequences were used along with species delimitation and specimen assignment methods to improve taxonomy and zoogeography of species of conservation interest inhabiting the Atlantic Ocean and Mediterranean Sea. In this study, we provided new evidence of the occurence of D. nidarosiensis in the Central-Western Mediterranean Sea and the lack of Atlantic-Mediterranean genetic divergence. The Atlantic endangered species D. laevis and D. batis clustered together under the same molecular operational taxonomic unit (MOTU) with any delimitation methods used, while the assignment approach correctly discriminated specimens into the two species. These results provided evidence that the presence of the barcode gap is not an essential predictor of identification success, but the use of different approaches is crucially needed for specimen classification, especially when threshold-or tree-based methods result less powerful. The analyses also showed how different putative, vulnerable, species dwelling across SouthWestern Atlantic and SouthEastern Pacific are frequently misidentified in public sequence repositories. Our study emphasised the limits associated to public databases, highlighting the urgency to verify and implement the information deposited therein in order to guarantee accurate species identification and thus effective conservation measures for deep-sea skates.

The Mediterranean Large Elasmobranchs Monitoring (MEDLEM) database contains more than 3,000 records (with more than 4,000 individuals) of large elasmobranch species from 21 different countries around the Mediterranean and Black seas, observed from 1666 to 2017. The principal species included in the archive are the devil ray (1,868 individuals), the basking shark (935 individuals), the blue shark (622 individuals), and the great white shark (342 individuals). In the last decades, other species such as the thresher shark (187 individuals), the shortfin mako (180 individuals), and the spiny butterfly ray (138) were reported with increasing frequency. This was possibly due to increased public awareness on the conservation status of sharks, and the consequent development of new monitoring programs. MEDLEM does not have homogeneous reporting coverage throughout the Mediterranean and Black seas and it should be considered as a database of observed species presence. Scientific monitoring efforts in the south-eastern Mediterranean and Black seas are generally lower than in the northern sectors and the absence of some species in our database does not imply their actual absence in these regions. However,the available data allowed us to analyse the frequency and spatial distribution of records, the size frequencies for a few selected species, the overall area coverage, and which species are involved as bycatch by different fishing gears., Sí

How the size of female yellowfin tuna (Thunnus albacares) affects their spawning capability and fecundity is still an open and unresolved question due to the difficulties in investigating these complex effects in highly migratory pelagic marine fish species. However, this information is key to understanding the reproductive potential and resilience of the stock. We investigate how energetic resources are allocated for reproduction by female yellowfin tuna according to their size in the Gulf of Guinea (central-eastern Atlantic Ocean). Our results reveal that larger females have not only larger ovaries by virtue of their greater abdominal cavity, but also different fatty acid profiles in the gonads compared to smaller females, with potential effects on their spawning and recruitment patterns. This study contributes to the knowledge of size-dependent variation in female yellowfin tuna and paves the way for future studies on size-dependent effects on reproductive parameters in this species.

Shallow geothermal energy is of great interest for HVAC (heating, ventilation and air conditioning) designers. While increasingly popular in the residential and commercial sectors, shallow applications are still little used in the industrial sector and unfamiliar to policy makers, designers and stakeholders [1]. Despite this, geothermal applications are feasible for industrial plant for several reasons: operating at high load factors and supplying energy to a single location, geothermal systems would cut energy costs, a large slice of overall industrial production costs. This paper presents the results of a feasibility study carried out for an industrial shallow geothermal project, where the required preheating to the innovative Expanding-Gas-Power-Transformation (EGPT) process was supplied through a Hybrid Geothermal-Air Transcritical Heat Pump. Focus was given to modeling the geothermal component to comply with the heat pump working temperature requirements, integrating this with geostatistics and numerical simulation of heat/water flows.

The genetic structure and population connectivity of the Mediterranean endemic speckled skate Raja polystigma were investigated in 10 population samples (N = 232) at seven exon-primed nuclear microsatellites and at three mitochondrial DNA sequence markers. The phylogeographical and population genetic analyses revealed that R. polystigma in Western and Central Mediterranean represents a near-panmictic population, with a subtle but significant mitochondrial divergence of the Adriatic deme. Nuclear genotypes revealed that 2.5% of the total individuals exhibited an admixed ancestry with the sibling species R. montagui (spotted ray). Individuals with admixed ancestry were detected along with purebred individuals in the Algerian, Southern Tyrrhenian, Sicilian and Adriatic R. polystigma population samples, but they were absent or rare in Sardinian and Northern Tyrrhenian ones. Since the two species co-occurs in the South-Western Mediterranean, we suggested that this area may act as a secondary hybrid zone.

This paper deals with the analysis of overbreak in tunnels excavated with the drill-and-blast method. The overbreak phenomenon has many negative impacts on tunnelling organisation and economy and its precise assessment plays a fundamental role in the process of construction optimisation. The study proposes an operative methodology to estimate overbreak volumes and to distinguish so-called technical overbreak, mainly related to drill-and-blast design and execution, from geological overbreak, typically influenced by rock-mass characteristics. The approach was developed and implemented during the excavation of the Brenner Base Tunnel (BBT) and was based on the interpretation of tunnel laser scanning surveys and high-resolution images of the excavated surfaces. The analysis of more than 1,800 m of excavation from three different tunnels of the BBT system allowed to identify the main factors influencing the technical and the geological overbreak. An empirical model for overbreak prediction, based on the Rock Mass Rating index and the length of blast holes, is subsequently presented and validated in the last part of the paper.

Morphological analysis, molecular characterization, and information on distribution and density of Anadara kagoshimensis (Tokunaga, 1906) specimens collected in the Adriatic Sea were here carried out as based on various material and data from five surveys conducted from 2010 to 2014, for a total of 329 bottom trawl hauls. The morphological and molecular analyses allowed to clarify the confused taxonomy regarding the biggest ark clam alien species invading the Italian waters and the Mediterranean Sea. The analysis on distribution and density revealed that A. kagoshimensis mostly occurs along the Italian coast at depths from 8 to 50 m, with a catch frequency of more than 98% in all hauls performed on silty-clay sediment at 8-30 m depth. The hotspot map clearly shows a reduction of its distribution area from 2010 to 2012.

Yellowfin tuna (Thunnus albacares; YFT) is an apex marine predator inhabiting tropical and sub-tropical pelagic waters. It supports the second largest tuna fishery in the world. Here, we review the available literature on YFT to provide a detailed overview of the current knowledge of its biology, ecology, fisheries status, stock structure and management, at global scale. YFT are characterized by several peculiar anatomical and physiological traits that allow them to survive in the oligotrophic waters of the pelagic realm. They are opportunistic feeders, which allows fast growth and high reproductive outputs. Globally, YFT fisheries have expanded over the last century, progressively moving from coastal areas into the majority of sub-tropical and tropical waters. This expansion has led to a rapid increase in global commercial landings, which are predominantly harvested by industrial longline and purse seine fleets. For management purposes, YFT is divided into four stocks, each of which is currently managed by a separate tuna Regional Fisheries Management Organization. Our current understanding of YFT stock structure is, however, still uncertain, with conflicting evidence arising from genetic and tagging studies. There is, moreover, little information about their complex life-history traits or the interactions of YFT populations with spatio-temporally variable oceanographic conditions currently considered in stock assessments. What information is available, is often conflicting at the global scale. Finally, we suggest future research directions to manage this valuable resource with more biological realism and more sustainable procedures.

Cartilaginous fish are particularly vulnerable to anthropogenic stressors and environmental change because of their K-selected reproductive strategy. Accurate data from scientific surveys and landings are essential to assess conservation status and to develop robust protection and management plans. Currently available data are often incomplete or incorrect as a result of inaccurate species identifications, due to a high level of morphological stasis, especially among closely related taxa. Moreover, several diagnostic characters clearly visible in adult specimens are less evident in juveniles. Here we present results generated by the ELASMOMED Consortium, a regional network aiming to sample and DNA-barcode the Mediterranean Chondrichthyans with the ultimate goal to provide a comprehensive DNA barcode reference library. This library will support and improve the molecular taxonomy of this group and the effectiveness of management and conservation measures. We successfully barcoded 882 individuals belonging to 42 species (17 sharks, 24 batoids and one chimaera), including four endemic and several threatened ones. Morphological misidentifications were found across most orders, further confirming the need for a comprehensive DNA barcoding library as a valuable tool for the reliable identification of specimens in support of taxonomist who are reviewing current identification keys. Despite low intraspecific variation among their barcode sequences and reduced samples size, five species showed preliminary evidence of phylogeographic structure. Overall, the ELASMOMED initiative further emphasizes the key role accurate DNA barcoding libraries play in establishing reliable diagnostic species specific features in otherwise taxonomically problematic groups for biodiversity management and conservation actions., peer-reviewed

Growing demands for marine fish products is leading to increased pressure on already depleted wild populations and a rise in the aquaculture production. Consequently, more captive bred fish are released into the wild through accidental escape or deliberate restocking, stock enhancement and sea ranching programs. The increased mixing of captive bred fish with wild conspecifics may affect the ecological and/or genetic integrity of wild fish populations. From a fisheries management perspective unambiguous identification tools for captive bred fish will be highly valuable to manage risks. Additionally there is great potential to use these tools in wildlife forensics (i.e. tracing back escapees to their origin and determining mislabelling of seafood products). Using SNP data from captive bred and wild populations of Atlantic cod (Gadus morhua L.) and sole (Solea solea L.), we explored the efficiency of population and parentage assignment techniques for the identification and tracing of captive bred fish. Simulated and empirical data were used to correct for stochastic genetic effects. Overall, parentage assignment performed well when a large effective population size characterizes the broodstock and escapees originate from early generations of captive breeding. Consequently, parentage assignments are particularly useful from a fisheries management perspective to monitor the effects of deliberate releases of captive bred fish on wild populations. Population assignment proved to be more efficient after several generations of captive breeding, which makes it a useful method in forensic applications for well-established aquaculture species. We suggest the implementation of a case by case strategy when choosing the best method.

Background: International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection. Methodology/Principal Findings: This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S), cytochrome b (cyt b), and cytochrome oxidase subunit I (COI) for the identification of 50 European marine fish species by combining techniques of "DNA barcoding" and microarrays. In a DNA barcoding approach, neighbour Joining (NJ) phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the "position of label" effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridization experiments (, SCOPUS: ar.j, info:eu-repo/semantics/published

Maggio, T., Lo Brutto, S., Garoia, F., Tinti, F., and Arculeo, M. 2009. Microsatellite analysis of red mullet Mullus barbatus (Perciformes, Mullidae) reveals the isolation of the Adriatic Basin in the Mediterranean Sea. – ICES Journal of Marine Science, 66: 1883–1891. The red mullet Mullus barbatus is commercially one of the most important demersal fish resources in the Mediterranean. Molecular data on its genetic population structure throughout the Mediterranean are reported. Six microsatellite loci displayed a high degree of expected heterozygosity and a high allele number per locus. The Hardy–Weinberg equilibrium test revealed an overall tendency towards heterozygote deficiency, probably caused by the admixture of various demes. Population differentiation was assessed by analysis of molecular variance (AMOVA) and Bayesian analysis. AMOVA showed that most of the variation was within the population, but the mean value of FST was significant, indicating genetic differentiation among the samples analysed. This differentiation is primarily attributable to the isolation of the Adriatic samples and partly to a weaker substructuring of the populations in the Gulf of Lions, Tyrrhenian Sea, Strait of Sicily, and Ionian Sea. Bayesian analysis also revealed genetic differentiation among the samples analysed, identifying two genetic clusters. The restricted gene flow from and to the Adriatic, also recorded for other fish species, most likely reflects the environmental separation of the Adriatic and suggests that management protocols for the red mullet in the Mediterranean should be revisited.

Atlantic bluefin tuna (Thunnus thynnus; BFT) abundance was depleted in the late 20th and early 21st century due to overfishing. Historical catch records further indicate that the abundance of BFT in the Mediterranean has been fluctuating since at least the 16th century. Here we build upon previous work on ancient DNA of BFT in the Mediterranean by comparing contemporary (2009-2012) specimens with archival (1911-1926) and archaeological (2nd century BCE-15th century CE) specimens that represent population states prior to these two major periods of exploitation, respectively. We successfully genotyped and analysed 259 contemporary and 123 historical (91 archival and 32 archaeological) specimens at 92 SNP loci that were selected for their ability to differentiate contemporary populations or their association with core biological functions. We found no evidence of genetic bottlenecks, inbreeding or population restructuring between temporal sample groups that might explain what has driven catch fluctuations since the 16th century. We also detected a putative adaptive response, involving the cytoskeletal protein synemin which may be related to muscle stress. However, these results require further investigation with more extensive genome-wide data to rule out demographic changes due to overfishing, and other natural and anthropogenic factors, in addition to elucidating the adaptive drivers related to these., We thank two anonymous reviewers whose comments improved the quality of the manuscript. This work was carried out under the provision of the FARB Project (University of Bologna), the ICCAT Atlantic Wide Research Programme for Bluefin Tuna (GBYP) Data Recovery Plan, the International Governance Strategy of Fisheries and Oceans Canada (F5211-180183 and F5211-160166), and the MARES Joint Doctorate programme selected under Erasmus Mundus and coordinated by Ghent University (Grant Number: FPA 2011-0016). This work is also a contribution to the MSCA SeaChanges ITN and was part-funded by EU Horizon 2020 (Grant Number: 813383).