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Landi M.,University of Minho | Dimech M.,Malta Center for Fisheries science | Dimech M.,Food and Agriculture Organisation of the United Nations | Arculeo M.,University of Palermo | And 6 more authors.
PLoS ONE | Year: 2014

Background: DNA barcoding enhances the prospects for species-level identifications globally using a standardized and authenticated DNA-based approach. Reference libraries comprising validated DNA barcodes (COI) constitute robust datasets for testing query sequences, providing considerable utility to identify marine fish and other organisms. Here we test the feasibility of using DNA barcoding to assign species to tissue samples from fish collected in the central Mediterranean Sea, a major contributor to the European marine ichthyofaunal diversity. Methodology/Principal Findings: A dataset of 1278 DNA barcodes, representing 218 marine fish species, was used to test the utility of DNA barcodes to assign species from query sequences. We tested query sequences against 1) a reference library of ranked DNA barcodes from the neighbouring North East Atlantic, and 2) the public databases BOLD and GenBank. In the first case, a reference library comprising DNA barcodes with reliability grades for 146 fish species was used as diagnostic dataset to screen 486 query DNA sequences from fish specimens collected in the central basin of the Mediterranean Sea. Of all query sequences suitable for comparisons 98% were unambiguously confirmed through complete match with reference DNA barcodes. In the second case, it was possible to assign species to 83% (BOLD-IDS) and 72% (GenBank) of the sequences from the Mediterranean. Relatively high intraspecific genetic distances were found in 7 species (2.2%-18.74%), most of them of high commercial relevance, suggesting possible cryptic species. Conclusion/Significance: We emphasize the discriminatory power of COI barcodes and their application to cases requiring species level resolution starting from query sequences. Results highlight the value of public reference libraries of reliability grade-annotated DNA barcodes, to identify species from different geographical origins. The ability to assign species with high precision from DNA samples of disparate quality and origin has major utility in several fields, from fisheries and conservation programs to control of fish products authenticity. © 2014 Landi et al. Source


Ragonese S.,CNR Institute for Coastal Marine Environment | Vitale S.,CNR Institute for Coastal Marine Environment | Dimech M.,Malta Center for Fisheries science | De Santi A.,CNR Institute for Coastal Marine Environment
Marine Ecology | Year: 2012

The deep-water giant red shrimp, Aristaeomorpha foliacea (Risso, 1827) (Decapoda, Aristeidae), represents a highly valuable resource for bottom trawling in the Mediterranean Sea. Recent assessments have described both a worsening of the status of the traditionally exploited stocks and low levels of annual-based instantaneous natural mortality (M 0.4-0.7year -1) in the unexploited stocks. The mortality (M) figures, however, are in contrast with the longevity (T max) of 3-4-year males and 4-5-year females, estimated from classical length frequency distribution analysis. Reduced growth (after the onset of sexual maturity) and pile-up of older individuals in the larger size classes have been considered to be reasonable explanations for the contrast between M and T max. We propose that a discontinuity of the growth models could address this contrast. Because a clear discontinuity in sexual maturity is evident only in males, length frequency distribution data for different sets of males collected from the South of Sicily and the Maltese Islands deep bottoms (400-800m) were fitted with both the classic (c) and double-phased (d) von Bertalanffy growth formula (VBGF). According to the dVBGF, adult males sharply reduce their growth rate after reaching an age between 1.2 and 1.5year, which corresponds to the estimates of age at sexual maturity (t m between 1 and 1.5years). The reduction in growth determines a higher T max (7.3-9.5year) and lower M (0.4-0.6year -1) than previously derived on the basis of cVBGF estimates (T max 3-4years and M 1.2year -1). The dVBGF results suggest that sexual dimorphism and length-sex segregation in giant red shrimps reflect an alternative life history strategy that is based mainly on growth reduction in adult males and it might be adopted for implementing more conservative assessments. © 2011 Blackwell Verlag GmbH. Source


Dimech M.,Bangor University | Dimech M.,Malta Center for Fisheries science | Dimech M.,University of Malta | Kaiser M.J.,Bangor University | And 2 more authors.
Marine Ecology Progress Series | Year: 2012

Fishing with demersal towed gears can have dramatic effects on the structure and functioning of marine ecosystems. We studied the ecosystem effects of the deep-sea red shrimp Aristaeomorpha foliacea trawl fishery (500 to 800 m) in the Strait of Sicily, at the population and community level by sampling in trawled and non-trawled sites as determined by vessel monitoring system (VMS) fishing effort data. The study was conducted within the Maltese 25 nautical mile Fisheries Management Zone as part of the ongoing MEDITS trawl survey. Samples were collected using an experimental otter trawl net with a cod-end stretched mesh size of 20 mm, from 7 stations located in trawled sites (mean depth 616 ± 26 m) and from 7 stations in non-trawled sites (mean depth 556 ± 40 m). Population and community indicators were compared across the trawled and non-trawled sites. Populations of A. foliacea and Etmopterus spinax did not show any differences in biomass between the trawled and non-trawled sites, whereas the biomass of Plesionika martia, Nephrops norvegicus, Helicolenus dactylopterus dactylopterus and Galeus melastomus was 4 times, 16 times, 6 times and 2 times higher, respectively, at the non-trawled sites. Changes in length structure were also detected for all species except for E. spinax. At the community level, higher biomass, density and diversity indices were recorded at the non-trawled sites. Despite the clear evidence of ecosystem changes due to fishing, the main target species, A. foliacea and P. martia, had a high resilience to trawling activities. Setting up trawling lanes as a management option would likely minimise negative impacts on species with slow growth rates and low resilience. © 2012 Inter-Research. Source


Pousis C.,University of Bari | De Giorgi C.,University of Bari | Mylonas C.C.,Hellenic Center for Marine Research | Bridges C.R.,Heinrich Heine University Dusseldorf | And 6 more authors.
Animal Reproduction Science | Year: 2011

The sequence of vitellogenin A (VgA) and vitellogenin B (VgB) cDNAs in Atlantic bluefin tuna (Thunnus thynnus L.) were determined, and vitellogenin expression levels in the liver and oocyte yolk accumulation were compared in wild and captive-reared individuals. Liver and ovary samples were taken from 31 individuals reared experimentally in three commercial Atlantic bluefin tuna fattening sites in the Mediterranean Sea and from 33 wild individuals caught by commercial traps during the fish's migration towards their Mediterranean spawning grounds. The total length of VgA cDNA was 5585 nucleotides and that of VgB was 5267 nucleotides. The identity and similarity between deduced amino acid sequences of VgA and VgB were 60% and 78%, respectively. The Atlantic bluefin tuna VgA and VgB amino acid sequences have high similarities with those of other teleost fishes. Relative levels of VgA and VgB mRNAs were low in April, increased significantly during the reproductive period in May and June, and declined in July. There was a trend towards higher relative levels of VgA and VgB mRNAs in captive fish compared to wild individuals during the reproductive period. The surface occupied by eosinophilic yolk granules in fully vitellogenic oocytes, as well as the frequency of oocytes in late vitellogenesis, was significantly higher in captive compared to wild individuals. The study suggests that the experimental conditions under which Atlantic bluefin tuna individuals were reared allowed the occurrence of normal vitellogenesis, based on gene expression of VgA and VgB in the liver and yolk accumulation in the oocytes. The higher yolk accumulation and frequency of vitellogenic oocytes observed in the ovaries of captive fish suggest that improvements in feeding practices may result in an improved vitellogenic process. © 2010 Elsevier B.V. Source


Fortibuoni T.,Istituto Superiore per la Protezione e Ricerca Ambientale | Bahri T.,Food and Agriculture Organization of the United Nations | Camilleri M.,Malta Center for Fisheries science | Garofalo G.,CNR Institute for Coastal Marine Environment | And 2 more authors.
Journal of Crustacean Biology | Year: 2010

The identification of nursery and spawning areas of coastal fish and shellfish populations represents fundamental information for stock assessment essential for giving advice for managers within the framework of Ecosystem Approach to Fisheries. This study investigates the bathymetric and spatial distribution of young-of-the-year and mature females of the deep-water rose shrimp, Parapenaeus longirostris, in the Strait of Sicily (Central Mediterranean Sea) in order to describe the species nursery and spawning areas. Data were obtained from trawl surveys carried out yearly in spring and autumn from 1994 to 2004, and nursery and spawning areas were inferred by means of GIS techniques. Species maximum abundance occurred between 100 and 300 m. We found that young-of-the-year concentrated on the outer shelf while mature females occurred mostly between the outer shelf and the upper slope. We detected four large areas of aggregation of young-of-the-year, and three areas of aggregation of mature females. High concentrations of young-of-the-year and mature females persistently occupied some of these areas, representing stable nursery and spawning areas. Young-of-the-year and mature females aggregate where retention and enrichment processes occur, linked to the semi-permanent patterns resulting from the meanders of the Atlantic Ionian Stream. We highlight the importance of studying the spatial distribution pattern of commercial species to identify habitats essential to those species' life cycle. We detected deep-water rose shrimp nursery and spawning areas in the Strait of Sicily and discuss their spatial pattern in relation to the hydrological characteristics of the area. © 2010 The Crustacean Society. Source

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