Microsatellites are one of the most popular markers in genetic studies but typically they need to be isolated and characterized de novo for each species. In this work, a genomic library enriched for a trinucleotide motif was constructed to identify polymorphic microsatellite loci in Aequipecten opercularis, a scallop species commercially fished in Europe, and to examine the level of genetic variation and genetic differentiation in samples from Spain and Northern Ireland. Sequencing of 83 clones led to the identification of 30 microsatellite-containing sequences which showed often other repeated sequences. Five microsatellite loci were successfully amplified and found polymorphic. The number of alleles and the expected heterozygosity per locus ranged from 9 to 86 and 0.341 to 0.927, respectively, all localities showing similar levels of genetic variation (allelic richness, 13.164–15.487; expected heterozygosity, 0.527–0.638). Discrepancies in genotype proportions from Hardy-Weinberg equilibrium were observed in 11 out of 25 locality-locus combinations, a heterozygote deficiency occurring in all cases probably due to null alleles. Significant genetic differentiation was detected among A. opercularis from Northern Ireland, Fuengirola (southern Spain) and the homogeneous samples from northwest Spain. Isolation by distance was the most likely hypothesis to explain the differentiation detected.

This study assessed the Zanzibar sea cucumber fishery using a multidisciplinary approach. Data was collected by (i) interviewing various groups of actors in the fishery and reviewing management documentation and legislation, (ii) by monitoring catches and (iii) through a visual census of coastal sea cucumber populations in areas open and closed to fishing. The fishery showed clear signs of being unsustainable with high fishing effort, and weak formal and informal management institutions. The fishery operation was characterised by an intricate cross-scale structure with both fishers and sea cucumber products being transported across national borders. The visual census of commercial sea cucumber stocks at three sites open to fishing around Zanzibar showed low densities across the range of sea cucumber value groups including low value species. Furthermore, the diversity of commercial sea cucumber species was lower in fished reefs than on a protected reef. The poor status of the sea cucumber populations was confirmed by the perception of an overfished resource by the interviewed actors active in the fishery. This was also depicted by the paucity of high value species, and high representation of low value and newly commercialised species in fishers catch. We conclude that the current state of Zanzibar’s sea cucumber populations is compromising the fisheries self-replenishment and existence and that the fishery is in urgent need of a complete management reform.

The black-browed (Thalassarche melanophrys) and Atlantic yellow-nosed (Thalassarche chlororhynchos) albatrosses and the white-chinned petrel (Procellaria aequinoctialis) are the seabird species most frequently captured by pelagic longline fisheries in the southwest Atlantic. This study estimates this type of bycatch and describes the spatial-temporal patterns of the incidental capture of these species by the Uruguayan pelagic longline fleet, based on data collected by scientific observers on 47 fishing trips from 2004 to 2007. Three generalized linear models (GLM) models were employed to predict bycatch for each species based on the observed data. We also developed a spatio-temporal species-specific analysis. Captures were recorded in Uruguayan waters, mainly over the slope and depth waters, and in international waters adjacent to Uruguay, the north of Argentina, and the south of Brazil. The highest catch rates for black-browed albatrosses and white-chinned petrels were recorded on the Uruguayan slope from fall to spring, while the highest values for Atlantic yellow-nosed albatrosses were recorded further to the north, in the international waters off Brazil in late winter. The average estimated number of black-browed and Atlantic yellow-nosed albatrosses and white-chinned petrels caught during the study period was 1683, 257 and 239 birds, respectively. Taking into account the total effort of the fleet, these values represent an estimated catch rate of 0.276, 0.042, and 0.039 birds/1000 hooks for these species, respectively. The results of the present study suggest that the annual impact of this fishery is medium to high on the black-browed albatross, low on the Atlantic yellow-nosed albatross and low on the white-chinned petrel. However, the situation of these species in the southwest Atlantic should be viewed with considerable concern, as our understanding of the impact of the bycatch on their populations requires more research. Any effort to reduce seabird mortality in the southern hemisphere should target this geographic region.

The completion of genomic sequences of physiologically important genes frequently reveals non-coding genetic elements such as tandem repeats (micro- and minisatellites) that are often more polymorphic than nearby coding sequences. We obtained the complete genomic sequences of three hormone genes in sea bass Dicentrarchus labrax: growth hormone (dlGH), somatolactin (dlSL) and insulin-like growth factor-1 (dlIGF-1), including 5′- and 3′-untranslated regions. Mini- and microsatellites were discovered in both flanking and intron regions. Some were partially conserved across Perciformes. To assess the usefulness and relevance of these gene-associated markers for understanding population structure, an investigation was made on genetic diversity and differentiation at four of them in (i) five wild populations from the North Sea, the Bay of Biscay and the Western Mediterranean, and (ii) two samples of hatchery-bred individuals from a freshwater-acclimation experiment. Gene and allelic diversities were lower in cultured individuals than in wild ones. Significant genetic differentiation was demonstrated between Bay of Biscay + North Sea and Mediterranean populations (Fst > 0.06, p < 0.001), primarily due to dlGH-associated markers. Significant genetic differentiation was also detected among the Atlantic and North Sea samples, but restricted to the locus associated with dlSL. Significant genetic differentiation was also found among experimental individuals before and after a salinity challenge (Fst ≈ 0.05, p < 0.001), but was due to dlSL and dlIGF-1 loci. Gene-associated markers proved to be more efficient than formerly used anonymous microsatellite markers in providing a clear picture of genetic differentiation.

A method of geometric morphometrics was used to characterize body shape variation in meiotic gynogenetic and triploid sea bass in comparison with diploid controls. A total of 13 coordinate landmark data were recorded on the profile of 34-month-old control (n = 81), gynogenetic (n = 117) and triploid (n = 131) siblings generated from two females (A and B). Three main axes of morphometric variation were consistent, and these accounted for 60.8 and 57.6% of the total variability in females A and B, respectively. There were significant shape deviations of triploid and gynogenetic fish relative to the controls, and differences were particularly evident in the progeny of one female. Overall, triploids displayed a more slender shape than diploids, whereas gynogenetic fish were deeper bodied and had flexed caudal peduncles and cranial features. The results are discussed especially in relation to the characterization of triploid fish for commercial purposes.

The population abundance estimates used in stock assessments or required to establish management measures, depend on the sampling of the entire demographic spectrum of a population resident in a given area. However, for sea turtles, most population estimates are based mainly on nesting beach survey data and only consider a fraction of the population. The Southwest Atlantic Ocean (SWA) is an important foraging and development area for juveniles of the loggerhead sea turtle Caretta caretta where reproductive stocks from various nesting beaches mix. Declines in C. caretta populations have been observed in many parts of the world and bycatch rates of this species in the SWA are among the highest worldwide. This study standardizes the catch rates of loggerheads caught by pelagic longline fisheries in the region, using data collected by observer programs from Brazil and Uruguay. Generalized linear models (GLM) with a delta lognormal approximation were used. The variables used in the model take into account spatial and temporal variations as well as the characteristics of the fleet. In total, 6 272 344 hooks were observed between 1998 and 2007, with minimum effort registered in 2000 (12 010 hooks) and maximum effort in 2005 (1 989 431 hooks). During this period 3778 loggerheads were incidentally captured. The catch rates of loggerheads by the Uruguayan and Brazilian pelagic longline fisheries show oscillations through the years without a clear tendency; however, a low negative trend was observed from 1998 to 2005 with an increase in the last two years (2006 and 2007). The capture per unit of effort (CPUE) values varied between 0.38 to 1.78 ind/1000 hooks in 2005 and 2007, respectively. Distinct zones with differential catch rates were identified, with the higher CPUE values over the continental slope of Uruguay and adjacent waters. The incidental catch rates of this species are influenced, not only by fishing area, but also by year, season, sea surface temperature and gear type. In consequence, these variables and other potential ones should be considered in bycatch estimates by different fisheries because the loggerhead sea turtles are not uniformly distributed. This study intends to contribute not only to the general knowledge of loggerhead sea turtles in the SWA but to a future assessment of their populations at a global scale.

Seagrass meadows support high biodiversity and are important for invertebrate harvesting activities in developing countries. The aim of this study was to estimate the social and ecological effects of invertebrate harvesting, i.e. how this exploitation may affect/has affected seagrass variables (biomass, shoot density and canopy height), macrofaunal community structure, the use and importance of these resources for the livelihood of local people over time. A multi-disciplinary approach was used, including interviews with harvesters, observations of the number/activities of invertebrate harvesters, and a biological field study in Zanzibar, Tanzania. The study showed that women/children harvest invertebrates, and they prefer large seagrass patches, high to medium shoot density, and high seagrass cover. All interviewees said they had noticed a decline in seagrass distribution over the last decade,  >20% considered it a large decline. Interviewees also reported decreased numbers of animals, but no change in the number of animal species over the last decade. The main reasons for the decline of seagrass and animals according to interviewees, are an increase in the number of harvesters, and a change in attitude, i.e. people being less careful about the intertidal zone and seagrasses. Invertebrate harvesting was found important for food security and provision of cash income. The current average catch weight was ca. 2 kg/collection day/person, and 3 kg and 5 kg, 5–10 and 30 years ago respectively according to interviewees. At present, the harvesting women earn ca 60–70% and ca 40% of what they would have if catches were the same sizes as they were 5–10 and 30 years ago respectively, according to our calculations. The field sampling within seagrass beds showed that an inaccessible/remote site had significantly higher invertebrate abundance and species richness/diversity than an exploited site (ANOVA). Multivariate statistics further revealed weak but significant differences for animal abundance and biomass between these sites. By combining findings from both interviews and field sampling this study shows that invertebrate harvesters can influence macrofaunal community structure in seagrass meadows, which in turn results in negative impacts on local harvesters’ economy and livelihood.

Fish tests must be developed for both regulatory and conservation reasons, as such testing forms an indispensable component of integrated toxicity testing strategy for the marine environment. To standardise a fish embryo test, the acute toxicity of metals and polycyclic aromatic hydrocarbons (PAHs) to early life stages (ELS) of turbot (Psetta maxima) was studied. Embryos were exposed to dilutions of cooper, cadmium, mercury, fluoranthene, phenanthrene, pyrene and naphthalene in darkness and under visible light. Hatching success, yolk sac alterations, pericardial edema, skeletal deformities and mortality were observed. The effective concentrations (EC50, EC10,) no observed effect concentration (NOEC) and the lowest observed effect concentration (LOEC) were determined at the end of the bioassays. Exposure to metals and PAHs in ecologically relevant concentrations, either in darkness or under artificial light, caused significant lethal and sublethal effects in turbot, such as alterations in yolk sac, pericardial edema and skeletal abnormalities. According to the 96 h EC50, the ranking of acute toxicity for metals was respectively: 47.4 (46.8–59.2) μg L−1 Cu; 51.5 (20.9–91.7) μg L−1 Cd, and 83.2 (62.3–125) μg L−1 Hg. For PAHs, acute toxicities were 5.2 (4.3–6) μg L−1 pyrene, 12.3 (6.4–12.7) μg L−1 fluoranthene, 52.2 (30.4–82.7) μg L−1 phenanthrene, and 142 (55–228) μg L−1 naphthalene. Pyrene was consistently the most toxic PAH. In addition, light exposures were performed and photo-enhanced toxicity was found only for fluoranthene and pyrene. Turbot embryos were found to be more tolerant to metals and PAHs than were hatched larvae. These results suggest that, considering the short duration of the ELS turbot test and its high sensitivity, it is suitable for use as a standard test for marine fish.

Recirculation aquaculture system (RAS) is the type of land-based aquaculture production that interferes the least with the environment, particularly due to low effluent volume and overall water requirement. Water reuse, sometimes limited by the accumulation of waste products excreted by fish, can be improved by incorporating another biotechnical component in the form of high rate algal pond (RAS+HRAP), thus adding to the economy and self sustainability of the system. Our goal was to evaluate whether rearing fish for 1 year in a RAS or RAS+HRAP led to differences in fish production and health, by assessing: (1) fish growth; (2) impact on the morphological structure of sea bass target tissues (liver, kidney, and spleen); (3) susceptibility to monogenean parasites; (4) resistance to pathogen challenge with Listonella anguillarum; and (5) total blood protein. Over the one-year experimental period, sea bass showed no statistical differences in any parameter evaluated, suggesting that there was a satisfactory purification rate in the RAS+HRAP system.

Variations in fish communities of shallow lakes in the Yangtze basins were investigated from September 2007 to September 2009. Six lakes were chosen for comparative study of species composition and diversity in relation to environmental variations. Lake heterogeneity was described with environmental physico-chemical variables, using principal component analysis. Sixteen families, composed of 75 species of fish were found in the studied lakes, Cyprinidae being the dominant group. Fish species were divided by habitat preference and trophic guild: benthopelagic and herbivorous fish were the most common guilds in all lakes. Species diversity and richness were significantly higher in spring, while the evenness, expressed by equitability of Simpson’s index, was not significantly different among seasons. Species richness and diversity were significantly higher in vegetated lakes (e.g. Liangzihu Lake) than in non-vegetated lakes (e.g. Biandantang Lake), with the largest area (Liangzihu Lake) harbouring the largest species richness and the greatest diversity. The relationship between environmental variables and fish assemblage were analysed using canonical correspondence analysis (CCA). The dominant gradients describing species composition and abundance among the sampling sites were: total phosphorus, total nitrogen, chlorophyll a, transparency and water depth. Our study led to the following conclusions: 1) the water quality was better - i.e. high transparency, low total phosphorus (TP) and total nitrogen (TN) and chlorophyll a- in vegetated lakes than in unvegetated lakes; 2) vegetated lakes had higher fish diversity than unvegetated lakes; 3) fish relative abundance (CPUE: number of fish per fishing pass) was significantly related to water chemical parameters. Consequently, the details of the findings are useful and relevant for developing suitable conservation strategies to sustain the integrity of fish communities in these lakes.

The sea cucumber stocks off the east and northwest coasts of Sri Lanka were estimated by surveying 1307 km2 and 1779 km2 by an underwater visual census (UVC) in June and October 2008 respectively. The presence of twenty-five sea cucumber species belonging to seven genera; Actinopyga, Bohadschia, Holothuria, Pearsonothuria, Stichopus, Thelenota and Acaudina was identified in five hundred sampling sites randomly selected in each area. The overall average density (± SD) of sea cucumbers was higher in the northwest (350 ± 648 ind ha-1) than in the east (90 ± 130 ind ha-1) and low-value species were predominant in both survey areas (79 ± 125 ind ha-1 in the east, 244 ± 488 in the northwest) when compared with medium (10 ± 34 ind ha-1, 105 ± 175 ind ha-1, respectively) and high-value category (<2 ind ha-1). The estimated total biomass in the northwest (13 024 t) was roughly four times greater than the east (3027 t). Holothuria edulis was the most abundant species in numbers while Holothuria atra had the highest stock biomass in both areas. Sea cucumber densities were significantly different among the habitat (p < 0.001) and depth categories. The highest density was reported in rocky habitat associated with seagrass and / or macroalgae. The density of low-value species was significantly high in 1–10 m depth category (p < 0.001) in the northwest while other commercial groups were dominant in 20–30 m depth range in both areas. Temporal banning of the fishery for high and medium-value species would be a better management option to avoid further stock depletion.

The design and evaluation of survey-based management strategies is addressed in this article, using three case-study fisheries: North Sea herring, Bay of Biscay anchovy and North Sea cod, with a brief history and the main management issues with each fishery outlined. A range of operational management procedures for the case study stocks were designed and evaluated using trends that may be derived from survey indices (spawner biomass, year-class strength and total mortality) with an array of simple and more structured observation error regimes simulated. Model-free and model-based indicators of stock status were employed in the management procedures. On the basis of stochastic stock-specific simulations, we identified the following key determinants of successful management procedures: (i) adequate specification of the stock-recruit relationship (model structure, parameter estimates and variability), (ii) knowledge of the magnitude and structure of the variation in the survey indices, and (iii) explication of the particular management objectives, when assessing management performance. More conservative harvesting strategies are required to meet specified targets in the presence of increasing stochasticity, due to both process and observation error. It was seen that survey-based operational management procedures can perform well in the absence of commercial data, and can also inform aspects of survey design with respect to acceptable levels of error or bias in the surveys.

The white shrimp (Fenneropenaeus indicus) is an ecologically and economically important penaeid species, widely distributed in the Indo-Pacific region. To obtain information on the genetic variation and population structure of F. indicus, sequencing analysis was conducted on a fragment of cytochrome oxidase subunit I (COI) of the mitochondrial DNA. Individuals (n = 217) from eight locations covering four main geographic regions along the coastal belt of Sri Lanka were analysed. The sequences, a 602-base pairs (bp) fragment in length, revealed high haplotype and nucleotide diversity that yielded 82 haplotypes. A mismatch analysis produced a unimodal distribution of pairwise differences between haplotypes, consistent with a historic rapid population expansion. Little or no genetic differentiation was observed between most samples, although genetic distances based on pairwise differences between haplotypes started to increase when geographic distances exceeded about 130 km. A population in Bundala (southeast) had lower diversity and was genetically differentiated from the others. This information could be important for the sustainable management and utilization of this resource.

Farfantepenaeus notialis (Crustacea, Decapoda) constitutes about 70% of the total shrimp catch in the Colombian Caribbean. In this study, we examined morphological characteristics of F. notialis to investigate stock differentiation, provided biological data such as size at 50% sexual maturity and discussed the importance of this information to fisheries management. The study was conducted in the Colombian Caribbean Sea from June to December of 2004 in four locations: Uraba gulf, Morrosquillo gulf, Amansaguapos, and La Vela cape. Individual shrimp were measured according to ten body segments and sex determined. We used discriminant function analysis (DFA) of size-adjusted data to generate two-dimensional plots of the morphometric indices to test for geographic variation in morphometry by mean of canonical dimensions. The length-frequency distributions showed statistically significant differences between the measurements of both sexes, males were smaller than female in all measures. In females, size range was 16 to 46 mm cephalothorax length (CL) and size at sexual maturity (CL50%) was 30.6 mm. Size range was 19 to 32 mm (CL) for males. The DFA of morphological differences between individuals (female/male) showed strong overlapping and no clear separation between regions. We did not find morphometric variability between regions, which indicates a single population of F. notialis from the morphometric point of view.

The Rideau Canal in Canada was constructed in the 1800s to enable strategic military and commercial transport in eastern Ontario between Lake Ontario and the Ottawa River. Today, the Rideau Canal is managed by Parks Canada and remains an engineered ecosystem, particularly in the urban Ottawa reach (7 km long) where it is largely channelized and is partially drained during the winter to protect canal infrastructure (i.e., locks) and provide recreational opportunities (i.e., skating). Interestingly, the Ottawa reach of the Rideau Canal supports one of the few wild urban muskellunge (Esox masquinongy) fisheries in North America supported by natural reproduction. However, little is known about the spatial ecology, residency patterns or survival of this apex freshwater predator in urban environments or canal systems. Radio-telemetry was used to study adult (N = 10; total size range of 64 to 122 cm) muskellunge in the Ottawa reach of the Rideau Canal over a multiple year period. The seasonal movements and home range of muskellunge were greatest during spring corresponding with the period when water levels in the canal were raised and muskellunge were presumably seeking out suitable spawning habitats following ice-off. During the summer fish ranged throughout the entire 7 km urban reach of the canal and by early fall muskellunge moved to the deeper parts of the reach and became largely restricted to an embayment known as Dow’s Lake prior to the lowering of the canal where they stayed for the entire winter. The same pattern of seasonal movements persisted across several years. None of the tagged muskellunge were stranded from the fall canal drainage. One fish emigrated from the urban reach of the canal during the study period, moving upstream through a lock to an exurban reach. In addition, a single tagged fish died from a winterkill event. Environmental influences such as seasonality and water depth (associated with canal operations) are believed to be the primary mechanisms contributing to habitat selection and movement patterns of muskellunge in this reach of the Rideau Canal. Data on the spatial ecology of muskellunge in the urban reaches of the Rideau Canal will inform management of this unique population of fish to ensure that the historic and ecological values are balanced to preserve this iconic Canadian natural heritage site and its biota.

The black bullhead, Ameiurus melas of the family Ictaluridae, is a freshwater fish native to North America that was introduced throughout Europe in the late 1800s. Using mitochondrial DNA (mtDNA) as a genetic marker, the present study investigates the genetic structure and historical demography of A. melas in North America. MtDNA-based phylogenetic analyses revealed the existence of two distinct lineages (A and B) of A. melas. While lineage A clustered with the previously reported sequences of A. melas, lineage B emerged as a unique clade like other species of the genus Ameiurus. Individuals belonging to lineage B were mostly from the south central region of the United States, the region that never glaciated during the last Ice Age. Results of a fossil-based molecular clock analysis suggest that lineage A and the paraphyletic lineage B of A. melas diverged from their respective common ancestors approximately 3 (±0.2) and 15.9 (±1.3) million years ago. Lineage B could possibly be a hybrid species, possessing the mtDNA haplotype of its maternal parent, an Ameiurus species that has gone extinct. While lineage A showed evidence of population expansion, lineage B did not show any evidence of population expansion, but rather is comprised of geographically structured populations.

Melicertus kerathurus represents an economically important resource for fisheries and aquaculture. Seven microsatellite loci from 373 specimens of M. kerathurus collected in different parts of the Mediterranean and NE Atlantic were identified. Four of these microsatellites showed a moderate level of polymorphism, with 2 to 14 alleles per locus, whereas three had a monomorphic profile. Observed and expected heterozygosity ranged between 0.28 to0.64 and 0.28 to 0.65, respectively. Three microsatellite loci deviated from Hardy-Weinberg equilibrium in some populations, with a deficit of heterozygosity. Mean Fst values showed significant differentiation among sample sites analysed and indicate that these loci are useful for the study of genetic variation in this species. These results may supply functional information on the population genetic structure of Melicertus kerathurus, valuable for future sustainable management strategies.

The redclaw crayfish (Cherax quadricarinatus) is a freshwater crayfish species endemic to northern Australia and Papua New Guinea that is the focus of a growing culture industry in number of regions around the world. Here we isolated and characterized 15 microsatellite loci from Cherax quadricarinatus and tested variability of the loci in 66 unrelated cultured individuals. Thirteen of 15 microsatellite loci were polymorphic. Number of alleles per locus ranged from two to seven while observed and expected heterozygosities ranged from 0.172 to 0.985 and from 0.373 to 0.778, respectively. Eleven loci conformed to Hardy–Weinberg equilibrium in the sampled population. These microsatellite loci developed here provide an important resource for studying genetic diversity and population structure in redclaw crayfish and potentially in other related species.

During 84 days, the effects of density on juvenile sea bass (Dicentrarchus labrax) (76±16 g) were studied in an experimental tank-based flow through system. Performance, stress response and resistance to virus infection were analysed under five stabilized rearing densities: 10, 20, 40, 70 and 100 kg m-3. Water quality parameters (CO2, total ammonia nitrogen and O2) were measured and maintained close to the recommended values for farmed sea bass by adjusting water renewal exchange. No significant differences were observed between density treatments, neither on stress response (cortisol) nor susceptibility to nodavirus. With regards to biological performances, the daily feed intake and specific growth rate were significantly lower in fish reared at the 100 kg m-3 density. Results on the effects of density in sea bass reared in flow through (present study) and in recirculating aquaculture systems (RAS) (Sammouth et al. 2009) were compared as a contribution to the identification of density not affecting health and welfare in farmed sea bass.