Feeding habits of European hake (Merluccius merluccius) in the central Mediterranean Sea

European hake (Merluccius merluccius) is an important predator of deeper shelf-upper slope Mediterranean communities. It is a nectobenthic species distributed over a wide depth range (20−1000 m) throughout the Mediterranean Sea and the north east Atlantic region (Fisher et al., 1987). Notwithstanding the ecological and economic importance (Oliver and Massutí, 1995) of hake in the Mediterranean, many aspects of its biology (e.g., recruitment and reproduction), due to multiple spawning (Sarano, 1986) and the current state of exploitation, are poorly understood (Arneri and Morales-Nin, 2000).

Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius)

Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyses and more recently genome-wide studies have challenged such view, suggesting that adaptive divergence might occur even when neutral markers provide genetic homogeneity across populations. Here, 381 SNPs located in transcribed regions were used to assess large- and fine-scale population structure in the European hake (Merluccius merluccius), a widely distributed demersal species of high priority for the European fishery. Analysis of 850 individuals from 19 locations across the entire distribution range showed evidence for several outlier loci, with significantly higher resolving power. While 299 putatively neutral SNPs confirmed the genetic break between basins (F(CT) = 0.016) and weak differentiation within basins, outlier loci revealed a dramatic divergence between Atlantic and Mediterranean populations (F(CT) range 0.275-0.705) and fine-scale significant population structure. Outlier loci separated North Sea and Northern Portugal populations from all other Atlantic samples and revealed a strong differentiation among Western, Central and Eastern Mediterranean geographical samples. Significant correlation of allele frequencies at outlier loci with seawater surface temperature and salinity supported the hypothesis that populations might be adapted to local conditions. Such evidence highlights the importance of integrating information from neutral and adaptive evolutionary patterns towards a better assessment of genetic diversity. Accordingly, the generated outlier SNP data could be used for tackling illegal practices in hake fishing and commercialization as well as to develop explicit spatial models for defining management units and stock boundaries.

Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake

The growing accessibility to genomic resources using next-generation sequencing (NGS) technologies has revolutionized the application of molecular genetic tools to ecology and evolutionary studies in non-model organisms. Here we present the case study of the European hake (Merluccius merluccius), one of the most important demersal resources of European fisheries. Two sequencing platforms, the Roche 454 FLX (454) and the Illumina Genome Analyzer (GAII), were used for Single Nucleotide Polymorphisms (SNPs) discovery in the hake muscle transcriptome. De novo transcriptome assembly into unique contigs, annotation, and in silico SNP detection were carried out in parallel for 454 and GAII sequence data. High-throughput genotyping using the Illumina GoldenGate assay was performed for validating 1,536 putative SNPs. Validation results were analysed to compare the performances of 454 and GAII methods and to evaluate the role of several variables (e.g. sequencing depth, intron-exon structure, sequence quality and annotation). Despite well-known differences in sequence length and throughput, the two approaches showed similar assay conversion rates (approximately 43%) and percentages of polymorphic loci (67.5% and 63.3% for GAII and 454, respectively). Both NGS platforms therefore demonstrated to be suitable for large scale identification of SNPs in transcribed regions of non-model species, although the lack of a reference genome profoundly affects the genotyping success rate. The overall efficiency, however, can be improved using strict quality and filtering criteria for SNP selection (sequence quality, intron-exon structure, target region score).

Novel tools for conservation genetics in marine fish: population structure and evolution of the European hake (Merluccius merluccius) inferred by SNP variation and applications to traceability

The research presented in my PhD thesis is part of a wider European project, FishPopTrace, focused on traceability of fish populations and products. My work was aimed at developing and analyzing novel genetic tools for a widely distributed marine fish species, the European hake (Merluccius merluccius), in order to investigate population genetic structure and explore potential applications to traceability scenarios. A total of 395 SNPs (Single Nucleotide Polymorphisms) were discovered from a massive collection of Expressed Sequence Tags, obtained by high-throughput sequencing, and validated on 19 geographic samples from Atlantic and Mediterranean. Genome-scan approaches were applied to identify polymorphisms on genes potentially under divergent selection (outlier SNPs), showing higher genetic differentiation among populations respect to the average observed across loci. Comparative analysis on population structure were carried out on putative neutral and outlier loci at wide (Atlantic and Mediterranean samples) and regional (samples within each basin) spatial scales, to disentangle the effects of demographic and adaptive evolutionary forces on European hake populations genetic structure. Results demonstrated the potential of outlier loci to unveil fine scale genetic structure, possibly identifying locally adapted populations, despite the weak signal showed from putative neutral SNPs. The application of outlier SNPs within the framework of fishery resources management was also explored. A minimum panel of SNP markers showing maximum discriminatory power was selected and applied to a traceability scenario aiming at identifying the basin (and hence the stock) of origin, Atlantic or Mediterranean, of individual fish. This case study illustrates how molecular analytical technologies have operational potential in real-world contexts, and more specifically, potential to support fisheries control and enforcement and fish and fish product traceability.

Suitability of real-time quantitative PCR to estimate the relative telomere length in European Hake (Merluccius merluccius Linnaeus, 1758)

Telomere length measurement has been proposed as a promising tool to estimate the age of individuals in natural populations. We used real-time quantitative PCR (qPCR) to measure relative telomere length in four tissues (brain, kidney, liver and muscle) of European hake (Merluccius merluccius) in different groups based upon body length an otolith age estimate. We observed a high level of inter-individual differences in the measurements of relative telomere length in hakes of similar age and body length groups. The results of qPCR analysis showed a great variability in all measures and a lack of repeatability and reproducibility with significant statistical differences in the results of the different assays. The paper discusses the technical reasons for the variability in qPCR obtained in this work and by other authors.

Adverse consequences of stock recovery : European hake, a new “choke” species under a discard ban?

Date of Acceptance: 28/01/2014 Funded by Seventh Framework Programme as part of the European research project EcoFishMan. Grant Number: FP7-265401 The Marine Alliance for Science and Technology for Scotland Scottish Funding Council. Grant Number: HR09011

Adverse consequences of stock recovery : European hake, a new “choke” species under a discard ban?

Date of Acceptance: 28/01/2014 Funded by Seventh Framework Programme as part of the European research project EcoFishMan. Grant Number: FP7-265401 The Marine Alliance for Science and Technology for Scotland Scottish Funding Council. Grant Number: HR09011

Gill net selectivity for European hake Merluccius merluccius from southern Portugal: implications for fishery management

A study of European hake Merluccius merluccius gill net selectivity was undertaken off the Algarve (Southern Portugal), between 1999 and 2001. Four nominal mesh sizes (70, 80, 90 and 100 mm) were used in fishing trials and the 'share each length class catch total' (SELECT) method was used to fit gill net selectivity curves. Hake were caught in the same size range by all mesh sizes, between 17 and 65 cm total length. While most fishes were wedged, significant and similar proportions were entangled in all mesh sizes, contributing to the wide size range, and in some cases, bimodal shape of catch size frequency distributions. Insignificant numbers of undersized hake were caught, with most catches consisting of mature female fish. Catch rates decreased sharply with increasing mesh size. The bimodal model gave the best fit for hake that were wedged, with estimated modal lengths of 40.1, 46.7 and 51.0 cm for the 70, 80 and 90 mm nominal mesh sizes, respectively. The high catch per unit effort of the smallest mesh size, with most fish caught being female, together with the fact that the modal length of the fitted selectivity curve is well below the size at maturity for hake in Portuguese waters, suggests that the 80 mm nominal mesh size is more appropriate for ensuring resource sustainability.

A multitracer approach to assess the spatial contamination pattern of hake (Merluccius merluccius) in the French Mediterranean

Chemical contamination levels and stable isotope ratios provide integrated information about contaminant exposure, trophic position and also biological and environmental influences on marine organisms. By combining these approaches with otolith shape analyses, the aim of the present study was to document the spatial variability of Hg and PCB contamination of the European hake (Merluccius merluccius) in the French Mediterranean, hypothesizing that local contaminant sources, environmental conditions and biological specificities lead to site-specific contamination patterns. High Hg concentrations discriminated Corsica (average: 1.36 ± 0.80 μg g− 1 dm) from the Gulf of Lions (average values < 0.5 μg g− 1 dm), where Rhône River input caused high PCB burdens. CB 153 average concentrations ranged between 4.00 ± 0.64 and 18.39 ± 12.38 ng g− 1 dm in the Gulf of Lions, whatever the sex of the individuals, whereas the highest values in Corsica were 6.75 ± 4.22 ng g− 1 dm. Otolith shape discriminated juveniles and adults, due to their different habitats. The use of combined ecotracers was revealed as a powerful tool to discriminate between fish populations at large and small spatial scale, and to enable understanding of the environmental and biological influences on contamination patterns.

Reduction of elasmobranch by-catch in the hake semipelagic near-bottom longline fishery in the Algarve (Southern Portugal)

Elasmobranch fish, particularly deep-sea sharks, are the most important component of the by-catch of the hake semipelagic near-bottom 'pedra-e-bola' longline fishery in the Algarve (South Portugal) and most of these fish are discarded. The effects of the removal of the lower hooks were evaluated, in terms of target and by-catch reductions, by quantifying the catches of each hook relative to the distance from the bottom. The analysis showed that most European hake (Merluccius merluccius), the target species of this fishery, were caught in the middle range of the hooks, with very few individuals caught near the bottom, whereas for sharks the situation was the opposite, with most hooked near the bottom. The removal of the lower three pairs of hooks would result in a small reduction in the catch of the target species, but a much more significant reduction in elasmobranch by-catch. In the specific case of the blackmouth catshark (Galeus melastomus), discard mortality would be further minimized due to the fact that the lower hooks capture significantly smaller animals that are always discarded compared with hooks that are more distant from the bottom.

The hake deepwater semi-pelagic ("pedra-bola") longline fishery in the Algarve (southern Portugal)

A 2-year study of the European hake (Merluccius merluccius) semi-pelagic ("pedra-bola) longline fishery was carried out in the Algarve (southern Portugal). This fishery takes place on the continental slope at 200-700 m depths. using monofilament longlines that are lifted off the bottom at regular intervals by glass balls. Hook selectivity trials were carried out with four hook sizes (SIAPAL brand numbers 10, 9, 7 and 5) from March to August 1997 and May to August 1998. At least 32 species of fish and invertebrates were caught, with hake dominating the catch (41 and 45% of the catch in numbers), followed by Galeus melastomus (23 and 19%), Micromesistius poutassou (10 and 7%), Benthodesmus elongatus (8 and 5%), Etmopterus pusillus (6 and 9%) and Scyliorhinus canicula (5 and 4%). Apart from the hake, and some species of commercial value such as G. melastomus (only the large individuals), Ray's bream (Brama brama, 1.4 and 4%), silver scabbard fish (Lepidopus caudatus. 1 and 2.5%), swordfish (Xiphins gladius, <1%), wreckfish (Polyprion americanus, <1%). conger eel (Conger conger. <1%), and bluemouth rockfish (Helicolenus dactylopterus, <1%)- most of the other species are discarded, used as bait in traps or consumed by the fishermen. Catch rates (number of fish per 100 hooks) for hake and for all species combined decreased significantly with hook size. Hake catch size frequency distributions for the different hook sizes in 1997 and 1998 were highly overlapped, with the four different hooks catching a wide range of sizes. Although catch size frequency distributions for the different sized hooks were not significantly different in 1997, hake caught in 1998 were characterised by smaller sizes and size ranges. (C) 2001 Elsevier Science B.V. All rights reserved.

Caratteristiche merceologiche, nutrizionali, sensoriali e di freschezza di Nasello (Merluccius merluccius), Lanzardo (Scomber japonicus) e Suro (Trachurus trachurus)

Three finfish species frequently caught in the waters of the Gulf of Manfredonia (Apulia, Italy) were studied in order to know how the flesh composition (proximate, fatty acid, macro- and micro- element contents) could be affected by the season effect. The species we examined were European hake (Merluccius merluccius), chub mackerel (Scomber japonicus) and horse mackerel (Trachurus trachurus), which were analysed at the raw state in three catch season and after cooking in two catch season. More precisely, European hake and chub mackerel caught during winter, summer and fall were analysed at the raw state. The composition of the flesh of grilled European hake and chub mackerel was study on fish caught in winter and fall. Horse mackerel of summer and winter catches were analysed both at the raw and grilled state. Furthermore, an overall sensory profile was outlined for each species in two catch season and the relevant spider web diagrams compared. On the whole, two hundred and eighty fish were analysed during this research project in order to obtain a nutritional profile of the three species. One hundred and fifty was the overall number of specimens used to create complete sensory profiles and compare them among the species. The three finfish species proved to be quite interesting for their proximate, fatty acids, macro- and micro-element contents. Nutritional and sensory changes occurred as seasons elapsed for chub and horse mackerel only. A high variability of flesh composition seemed to characterise these two species. European hake confirmed its mild sensory profile and good nutritional characteristics, which were not affected by any season effect.

Autenticazione d’origine, stima della Freshness quality e studio del profilo nutrizionale come elementi fondanti per la valorizzazione dell’alimento ittico

Questa tesi è dedicata alla qualità dell'alimento ittico in tre delle sue possibili accezioni. Dopo aver spiegato il complicato rapporto del consumatore con gli alimenti ittici e come l'Unione Europea abbia cercato di fare chiarezza al riguardo, gli argomenti di discussione saranno: Autenticazione d'origine La polpa di 160 esemplari di spigola (Dicentrachus labrax), suddivisi tra selvatici, allevati intensivamente e allevati estensivamente, provenienti dall'Italia e dall'estero per un totale di 18 fonti indagate, è stati analizzata individualmente per caratterizzarne la componente lipidica, isotopica e minerale e verificare le potenzialità di queste informazioni ai fini della autenticazione di origine in senso lato. Stima della Freshness Quality Numerosi lotti di seppia (Sepia officinalis), nasello (Merluccius merluccius) e triglia di fango (Mullus barbatus) sono stati sottoposti a due possibili modalità di stoccaggio sotto ghiaccio fondente, per indagare come, nell’arco della loro vita commerciale, ne evolvessero importanti connotati chimici (cataboliti dell’ATP e loro rapporti), fisici (proprietà dielettriche dei tessuti) e sensoriali (Quality Index Methods specie-specifici. Studio del profilo nutrizionale La componente lipidica di numerosi lotti di mazzancolla (Penaeus kerathurus), canocchia (Squilla mantis) e seppia (Sepia officinalis) è stata caratterizzata allo stato crudo e dopo cottura secondo tecniche “dedicate” per stabilire il contributo di queste matrici come fonte di acidi grassi polinsaturi della serie omega 3 e per pervenire alla determinazione dei loro coefficienti di ritenzione vera.

Bycatch of crustacean and fish bottom trawl fisheries from southern Portugal (Algarve)

As part of two research projects for analysing bycatch and discards, we quantified catch composition, catch rates, bycatch and discard,, in two important commercial bottom trawl fisheries (crustacean and fish trawls) off the Southern coast of Portugal (Algarve). Stratified sampling by onboard observers took place from February 1999 to March 2001 and data were collected from 165 tows during 52 fishing trips. Commercial tat-get species included crustaceans: blue and red shrimp (Aristeus antennatus), deep-water rose shrimp (Parapenaeus longirostris), Norway lobster (Nepharops norvegicus); and fishes: scabreams (Diplodus spl). and Pagellus Spp.), horse Mackerels (Trachurus spp.) and European hake (Merluccius merluccius). The trawl fisheries are characterised by considerable amounts of bycatch: 59.5% and 80.4% of the overall total catch for crustacean and fish trawlers respectively. A total of 255 species were identified, which belonged to 15 classes of organisms ( 137 vertebrates, 112 invertebrates and algae). Crustacean trawlers had higher bycatch biodiversity. Bony fish (45.6% and 37.8%) followed by crustaceans (14.6% and 11.5%) were the dominant bycatch components of both crustacean and fish trawlers respectively. The influence of a number of factors (e.g. depth, fishing gear, tow duration and season) on bycatch and discards is discussed.

Size selectivity of diamond and square mesh cod ends for four by-catch species in the crustacean fishery off the Portuguese south coast

The effects of an increase in cod end mesh size from 55 to 60 and 70 mm and a change of mesh configuration from 55 mm diamond to 55 turn square mesh on the size selectivity of four by-catch species (the red shrimp Aristeus antennatus, the European hake Merluccius merluccius, the horse mackerel Trachurus trachurus and the blue whiting Micromesistius poutassou) commonly captured in the crustacean fishery off the Portuguese south coast, were evaluated. Selectivity parameters for blue whiting, the most abundant species in the catches, were estimated taking into account between-haul variation, while for the remaining species, captured in much lower quantities, the selectivity estimates were based on pooled data by length class for all hauls within the same cod end. Length at 50% retention, L-50, was found to increase with mesh size and with the change in mesh configuration for all the studied species. For blue whiting trawling depth and cod end catch were found to play a role in between-haul variation by increasing L-50 as well. The results suggest that an increase in the current minimum mesh size of 55-70 mm would be advisable to be compatible with the minimum landing sizes (MLSs) of 29 mm carapace length and 27 cm total length for red shrimp and hake, respectively, while it would greatly reduce the amount of discards, particularly those for blue whiting, that accounted for approximately 50% of the total catch weight. Horse mackerel was the only species for which the use of a larger mesh size would result in a significant escapement of individuals above the MLS of 15 cm. (C) 2002 Elsevier Science B.V. All rights reserved.