Genetic analysis of two Portuguese populations of <Emphasis Type="Italic">Ruditapes decussatus</Emphasis> by RAPD profiling

The clam Ruditapes decussatus is commercially important in the south of Portugal. The random amplified polymorphic DNA (RAPD) technique was applied to assess the genetic diversity and population structure of two Portuguese populations occurring in the Ria Formosa (Faro) and the Ria de Alvor, respectively. Twenty-five individuals of each population were investigated by RAPD profiles. Genetic diversity within populations, measured by the percentage of polymorphic loci (%P), varied between 68.57% (Alvor) and 73.88% (Faro). Shannon’s information index (H) and Nei’s gene diversity (h) were 0.281 and 0.176, respectively, for the Alvor population and 0.356 and 0.234 for the Faro population. Overall, genetic variation within R. decussatus populations was high. The total genetic diversity (H _T) was explained by a low variation between populations (G _ST = 0.145), which is consistent with high gene flow (N _m = 2.9). The analysis of molecular variance (AMOVA) showed that 65% of variability is within populations and 35% between populations (Φ_PT = 0.345; P ≥ 0.001). The value of Nei’s genetic distance was 0.0881, showing a low degree of population genetic distance, despite the different geographic origin. This is the first study on the population genetics of R. decussatus by RAPD technique. The results may be useful for restocking programs and aquaculture.     

Isolation and characterization of ten microsatellite loci for Senegal sole (Solea senegalensis Kaup)

Senegal sole (Solea senegalensis Kaup) is a high‐value marine flatfish exploited in both fisheries and aquaculture. Here we describe the isolation of seven tetranucleotide and three dinucleotide polymorphic microsatellite loci. Characteristics of a captive broodstock and a wild population are described. Three loci displayed a significant departure from Hardy–Weinberg expectations in both populations, suggesting a substantial frequency of null alleles. The remaining seven loci were found to be in equilibrium in the wild population, whereas only four of them were in the cultured population. Cross‐species amplification was successful for three loci in other five flatfishes.     

Seahorse (Hippocampinae) population fluctuations in the Ria Formosa Lagoon,south Portugal

Comparisons of three sets of surveys in the Ria Formosa Lagoon, Portugal, over a 13 year period (2001–2002, 2008–2009 and 2010–2013) revealed significant population fluctuations in at least one of the two seahorse (Hippocampinae) species living there, and that those fluctuations were potentially associated with habitat changes in the lagoon. After a significant decline between the first two survey periods (2001–2002 v. 2008–2009), long‐snouted seahorse Hippocampus guttulatus populations increased significantly between 2008–2009 surveys and new 2010–2013 surveys. There were no significant differences in H. guttulatus populations between the 2001–2002 and 2010–2013 surveys. In contrast, there were no significant differences in short‐snouted seahorse Hippocampus hippocampus densities among the 16 sites surveyed throughout the three sampling periods, although the ability to detect any change was hampered by the low densities of this species in all time periods. Fluctuations in H. guttulatus densities were positively correlated with the percentage of holdfast coverage, but with none of the other environmental variables tested. These results highlight the importance of holdfast availability in maintaining stable seahorse populations. While population fluctuations are certainly more promising than a consistent downward decline, such extreme fluctuations observed for seahorses in the Ria Formosa Lagoon could still leave these two species vulnerable to any additional stressors, particularly during low density periods.     

The distribution of seagrass (Zostera noltii) in the Ria Formosa lagoon system and the implications of clam farming on its conservation

Ria Formosa lagoon in southern Portugal has an important population of seagrasses that includes Zostera noltii in the intertidal area. The area is classified as a Natural Park and supports a major economic activity – clam farming. This activity has a direct influence on Z. noltii populations by removal of seagrass beds and altering habitat. Geographic Information Systems and spatial analysis were used to produce the first distribution map of Z. noltii in the Ria Formosa and to analyse interactions between clam farming and the level of seagrass protection according to the Natural Park of Ria Formosa. Stakeholder analyses, using interviews, questionnaires and participant observation, were conducted to gain a better understanding of clam farming's influence on seagrass populations. Seagrass covers 45% of the intertidal area while clam farming covers 14%. An additional 75% of the total area of Z. noltii can be potentially converted into clam cultures. The current management of clam farming is largely ineffective, representing a significant obstacle to seagrass conservation.     

A tool for tracking genetic contributions of wild Penaeus (Melicertus) plebejus broodstock to hatchery populations

Stock enhancement, restocking and sea ranching are being increasingly applied in both fisheries and conservation. The contribution of hatchery stock to fishery harvest and the maintenance of the genetic structure of stocked populations are both important considerations when releasing captive‐bred organisms into natural systems. Use of wild‐caught broodstock generally overcomes some of the genetic problems associated with domesticated hatchery populations, but there is still a need to ensure that a sufficient proportion of the natural population contribute to production of the stocked cohort to realise the genetic benefits of using wild‐caught broodstock. Releases of Penaeus (Melicertus) plebejus are under investigation as a means of increasing prawn production in recruitment‐limited areas. We used the highly variable mitochondrial control region (mtCR) to assign post‐larvae to maternal lineages in the hatchery and also to investigate the reproductive performance of female broodstock in terms of contribution to the production of the cohorts of post‐larvae in the hatchery. Our data showed that mtCR can be a useful tool for tracking lineages and provided genetic evidence that unequal contribution and underproducing females can occur even in wild‐caught broodstock. This work therefore highlights the importance of monitoring the genetic composition of pre‐release hatchery stocks.     

Feasibility of a project for active restocking of the sea adjacent the salt pans of Tarquinia (Italy)

The depletion of fish stocks in the Mediterranean suggests that restocking may be a useful approach for restoring fisheries. In this paper we consider the potential for using derelict salt pans at Tarquinia (50 miles north of Rome) to rear fish for restocking in adjacent coastal areas. We discuss candidate species for stock enhancement, ways of minimizing stress in the capture of broodstock, genetic monitoring of wild catches, various aspects of operational restocking (release stage of larvae or juveniles, etc) and suggest approaches for evaluating results. Finally, we provide an economic and financial analysis of investment costs and likely benefits for different scenarios, and guidelines for a restocking policy that may be implemented by public authorities.     

Environmental modulation of androgen levels and secondary sex characters in two populations of the peacock blenny Salaria pavo

Morphology and endocrinology were studied in two populations of the peacock blenny Salaria pavo, with different regimes of sexual selection imposed by differences in nest site availability. The peacock blenny is a small, sexually dimorphic benthic fish that presents exclusive paternal care of the clutch and inhabits rocky shores of the Mediterranean and adjacent Atlantic areas. In a population from the Gulf of Trieste (Northern Adriatic sea) inhabiting rocky shores where nest sites are abundant, male-male competition for nests is low, males court females and a low frequency of alternative reproductive tactics (small, parasitic female-mimicking sneaker males that change tactic into nest holders in subsequent breeding seasons) occurs. Conversely at Ria Formosa, a coastal lagoon in Southern Portugal, where nest sites are scarce and highly aggregated, male-male competition for nests is very high, there is sex-role reversal with female courtship and a high frequency of alternative reproductive tactics is observed. Concomitantly, at Ria Formosa nest holder males are larger and present more developed secondary sex characters and higher levels of 11KT than at the Gulf of Trieste. However, the gonads of nest holders and parasitic males were larger in the Gulf of Trieste population. Competition for nests at Ria Formosa seems to promote more developed secondary sex characters in nest site scarcity conditions, while competition for females at the Gulf of Trieste seems to be spurring sperm competition among males in populations where nest sites are more abundant. 11KT was thus associated with the development and expression of secondary sex characters in contrasting environments. These results exemplify how the modulation of behavioral plasticity and secondary sex characters by the social environment can be mediated by androgens.     

Comparison of population genetic estimates amongst wild,F1 and F2 cultured abalone (Haliotis midae)

Haliotis midae is South Africa's most important aquaculture species. The reproduction cycle is currently not closed as many farms rely on wild‐caught broodstock for seed production. However, there is an increasing interest in genetic improvement in commercial stocks, with a growing number of producers implementing selective breeding strategies. High throughput commercial production and mass spawning make it difficult to maintain breeding records; therefore, mostly mass selection is practised. The high fecundity and unequal parental contributions also often lead to increased levels of inbreeding. This study therefore aimed to assess the genetic effects of such breeding practices on commercial populations of H. midae. Using microsatellite loci, the genetic properties of a wild, an F1 and an F2 population were estimated and compared. Although there was no significant loss of genetic diversity amongst the cultured populations in comparison with the wild progenitor population, there was low‐to‐moderate genetic differentiation between populations. Relatedness amongst the F2 population was significant, and the rate of inbreeding was high. The effective population size for the F2 (±50) was also comparatively small with respect to the wild (∞) and F1 (±470) populations. These results suggest that farms need to give caution to breeding practices beyond the first (F1) generation and aim to increase effective population sizes and minimise inbreeding to ensure long‐term genetic gain and productivity. This study also confirms the usefulness of population genetic analyses for commercial breeding and stock management in the absence of extensive pedigree records.     

Interpopulational variation of the mating system in the peacock blenny Salaria pavo

The ecology and mating system of two populations of the peacock blenny Salaria pavo that have been reported to differ in sexual behaviour were studied. In the Gulf of Trieste, a northern Adriatic Sea population lives in rocky shores, whilst in the Ria Formosa, an Atlantic population inhabits a coastal lagoon with sandy barrier islands. In the Gulf of Trieste, nest availability was found to be higher and nest aggregation lower than in Ria Formosa. Nesting males courted females more and in higher proportion, and inversely, females directed less courtship displays towards nest holders in the Gulf of Trieste than in Ria Formosa. The relative frequency of small female-like males that reproduce by parasitically fertilizing eggs in the larger males’ nests was lower in the Gulf of Trieste population. This variation in the sexual behaviour of nesting males and females is likely to reflect a plastic behavioural response to the varying ecological conditions. The difference between populations in the relative frequency of parasitic males suggests that the male alternative reproductive tactics are condition-dependent.     

Identification and characterization of microsatellites for striped bass from repeat-enriched libraries

Striped bass (Morone saxatilis) is economically important in the US due to its value as an aquaculture species and in supporting commercial and recreational fisheries, especially those off the Atlantic coast and in the Gulf of Mexico. Modern strategies for managing fishery populations and aquaculture broodstocks employ the use of molecular genetic markers to identify individuals, assign parentage, and characterize population genetic structure and levels of inbreeding and migration. As part of a collaborative effort to utilize molecular genetic technologies in striped bass breeding programs we generated microsatellite markers for use in population genetic studies, broodstock selection and management strategies, and the construction of a genetic map. We developed 345 new microsatellite markers for striped bass, a subset (n=71) of which was characterized by genotyping samples from two striped bass broodstock populations to evaluate marker polymorphism, percent heterozygosity, Hardy–Weinberg equilibrium (HWE), linkage disequilibrium (LD) and utility for population genetic studies.     

Weight‐length relationships for five fish species from a temperate coastal lagoon of southern Europe

The weight‐length relationships (WLR) were estimated for five fish species of Ria Formosa, a coastal lagoon in southern Portugal. WLRs for Gobius couchi, Pomatoschistus microps and Parablennius pilicornis were determined for the first time ever and for Gobius cruentatus for the first time for the southern European Atlantic coast.     

Genetic structure and management of the Neotropical migratory fish Megaleporinus obtusidens on a highly impacted river basin

Habitat fragmentation caused by hydroelectric dams has depleted fish populations worldwide. Restocking actions are usually adopted to recover those populations, but hatchery management protocols rarely guarantee the maintenance of genetic diversity and a balanced contribution among captive breeders each generation. Here, a set of 10 microsatellite markers was used to assess the genetic diversity (average allelic richness A_R?=?10.87 and expected heterozygosity H_E?=?0.742, respectively) and structuring of Megaleporinus obtusidens, a migratory freshwater fish inhabiting over 2500 km of the São Francisco River in Brazil. Three main genetic clusters were identified in this species across the river basin that could be related to the sharply different climatic and hydrologic regimes from the Upper to the Lower course. A significant reduction (> 50%) in genetic diversity was observed in the broodstock when compared to their wild conspecifics, especially in the allelic richness. The information here presented will aid for management of genetic resources of this species in the São Francisco River taking as reference the genetic clusters identified. Furthermore, the results indicated that restocking is not necessary unless signals of population depletion occurs and, if so, hatchery reproductive protocols should rely on artificial fertilization rather than mass spawning.

     

Partitioning kin groups of broodstock in the critically endangered Chinese sturgeon,Acipenser sinensis Gray 1835

Pedigrees of broodstock with unknown relationship of the critically endangered Chinese sturgeon, Acipenser sinensis, was evaluated using microsatellite markers to facilitate genetic management in restocking programs with small broodstock size. We characterized the distributions of relatedness values to reconstruct kin groups in four hatchery families with known pedigrees using microsatellites. The distributions of relatedness values for kin classes were used for partitioning full sibling groups of wild A. sinensis broodstock kept in two hatcheries, resulted in 13 full sibling clusters, four of which containing 62% of all the wild individuals. This indicates high probability of choosing close related breeder pairs in random mating, thus selective breeding is necessary to minimize inbreeding and maintain genetic diversity. This study provides a useful tool for genetic management in conservation programs of A. sinensis in aim of preserving self‐sustained wild populations.     

Strategies for the retention of high genetic variability in European flat oyster (<Emphasis Type="Italic">Ostrea edulis</Emphasis>) restoration programmes

The native European flat oyster Ostrea edulis is listed in the OSPAR Convention for the Protection of the Marine Environment of the North-East Atlantic (species and habitat protection) and in the UK Biodiversity Action Plan. Once extremely abundant in the nineteenth century, European stocks of O. edulis have declined during the twentieth century to rare, small, localised populations due to overexploitation, habitat degradation and, most recently, the parasitic disease bonamiosis. Selective breeding programmes for resistance to bonamiosis have been initiated in France and Ireland. High genetic diversity and bonamiosis-resistance would be important features of any sustainable restoration programmes for O. edulis. Oysters were sampled across Europe from four hatchery sources, four pond-cultured sources and four wild, but managed fisheries and were genotyped at five microsatellite loci. Hatchery-produced populations from small numbers of broodstock showed a significant loss of genetic diversity relative to wild populations and pedigree reconstruction revealed that they were each composed of a single large full-sib family and several small full-sib families. This extremely low effective population size highlights the variance in reproductive success among the potential breeders. Pond-cultured oysters were intermediate in genetic diversity and effective population size between hatchery and wild populations. Controlled hatchery production allows the development of bonamiosis-resistant strains, but at the expense of genetic diversity. Large scale pond culture on the other hand can provide a good level of genetic diversity. A mixture of these two approaches is required to ensure a healthy and sustainable restoration programme for O. edulis in Europe.     

Otolith mass marking techniques for aquaculture and restocking: benefits and limitations

The use of farmed and restocked fish to supplement the worldwide human consumption of fish, recreational fishing stocks, and conservation efforts, is growing at a rapid rate. Yet, monitoring the benefits of using hatchery-raised fish for supplementation is lacking, often due to hatcheries not marking or tagging all fish prior to release, despite a range of easy to apply, cost effective and accurate mass-marking methods being available to mark farmed and restocked fish en masse. Here we review otolith marking techniques that have the capability of mass marking millions of hatchery-reared fish that are, or could be, used for monitoring and compliance purposes. The otolith mass marking methods consist of otolith thermal marking and a range of otolith chemical marking methods (tetracyclines, alizarin compounds, calcein, strontium chloride, stable isotopes of Ba and Sr, and rare earth elements). We assessed and compared marking technique in terms of (1) ease of application, (2) cost of application, (3) mark retention and detectability, and (4) fish welfare. In addition, we determine the suitability of different otolith marking techniques for mass marking entire hatchery populations whether it be for restocking purposes, or for identifying and tracing escapees from aquaculture facilities. We conclude that although some techniques have restricted use due to regulations, the majority of otolith mass marking techniques are simple, easy to apply, cost effective and highly suitable for long term monitoring of hatchery produced fish.     

Temperature tolerance and survival of intertidal populations of the seagrass <Emphasis Type="Italic">Zostera noltii</Emphasis> (Hornemann) in Southern Europe (Ria Formosa,Portugal)

The dwarf seagrass Zostera noltii is an important primary producer in Atlantic coastal ecosystems from Mauritania to southern Norway and the Mediterranean Sea. Sessile intertidal organisms existing at the interface between marine and terrestrial environments may be particularly vulnerable to environmental change. In this study, we asked how near to thermal tolerance limits natural populations of Z. noltii are in the Ria Formosa coastal lagoon system in southern Portugal. We recorded the maximum temperatures in the Ria Formosa during the 2007 summer, and conducted experiments to determine the sub-lethal temperature of Z. noltii shoots sampled at two sites located at different tidal heights. Mortality rates and photosynthetic performance were recorded within a range of heat shock temperatures between 35 and 41°C. Survival was recorded ≤37°C, while higher temperatures led to a sudden drop in photosynthetic capacity followed by mortality (shoot loss) that occurred more rapidly with increasing temperatures. At 39°C and above, the rate of shoot mortality in both sites was close to 100%, occurring between 5 and 13 days after the heat shock. Survival was ca. 95 and 90% at 35 and 37°C, respectively. From these results for Z. noltii populations in the Ria Formosa we estimated sub-lethal temperature to be approximately 38°C for Z. noltii, close to the maximum of 36°C recorded in the summer 2007. Considering predicted trajectories in the coming decades, these results raise concern as to the future viability of intertidal Z. noltii populations near the southernmost edge of their distribution. Handling editor: S. M. Thomaz     

DNA Polymorphism of Percidae population structure in the Kuibyshev water reservoir of Russia

The depletion of fish stocks in the Mediterranean suggests that restocking may be a useful approach for restoring fisheries. In this paper we consider the potential for using derelict salt pans at Tarquinia (50 miles north of Rome) to rear fish for restocking in adjacent coastal areas. We discuss candidate species for stock enhancement, ways of minimizing stress in the capture of broodstock, genetic monitoring of wild catches, various aspects of operational restocking (release stage of larvae or juveniles, etc ) and suggest approaches for evaluating results. Finally, we provide an economic and financial analysis of investment costs and likely benefits for different scenarios, and guidelines for a restocking policy that may be implemented by public authorities.     

Isolation and characterization of microsatellite DNA loci in sea bass,Lates calcarifer Bloch

Polymerase chain reaction (PCR)‐based isolation of microsatellite arrays (PIMA) technique was used to isolate seven polymorphic microsatellite loci in sea bass, Lates calcarifer Bloch. A total of 62 samples of wild and cultivated sea bass collected from a few populations within Peninsular Malaysia were used in the study. For seven polymorphic loci, the number of alleles ranged from four to nine and locus heterozygosities ranged from 0.710 to 1.000. The loci will be useful for studying population structure, genetic variability of wild and hatchery stocks of L. calcarifer and broodstock management purposes.     

Nutrient fluxes in intertidal communities of a South European lagoon (Ria Formosa) – similarities and differences with a northern Wadden Sea bay (Sylt-Rømø Bay)

During an annual cycle, flux rates of oxygen, nitrate, nitrite, ammonium, phosphate and silicate were measured in light and dark bell jars at three sites in Ria Formosa (Algarve, Portugal) enclosing either a natural macrophytic community (macroalgae on sand or mud, a seagrass bed of Zostera noltii) or bare sediments. The results are compared with a preceeding study in which the same bell jar technique has been applied in the Sylt-Rømø Bay of the northern Wadden Sea. Nitrate flux was mainly directed from the water column to the benthic communities in Ria Formosa, as well as in the Sylt-Rømø Bay. However, nitrate uptake was higher in the northern, more eutrophic study area. In Ria Formosa, nutrient concentrations were lower than in the Sylt-Rømø Bay possibly due to strong water exchange with Atlantic waters. High temperatures and strong insolation had a greater impact on nitrate fluxes in Ria Formosa than in the Sylt-Rømø Bay. Bioturbating macrofauna increased ammonium efflux in the Sylt- Rømø Bay while this effect was not as pronounced in the Ria Formosa study sites. Benthic phosphate uptake dominated in the Ria Formosa and was correlated to initial phosphate concentrations in incoming waters. At both study sites, oxygen and nutrient fluxes were correlated with temperature. Additionally, flux rates were strongly influenced by biotic components and levels of eutrophication. A literature survey showed that mainly in temperate regions, material fluxes increase with temperature, whereas in warmer areas, ammonium and phosphate fluxes between sediment and water were generally lower.     

Marine plant harvest in Portugal

This work brings together the scattered information on marine plant harvests and the colloid extraction industry in Portugal, as an initial contribution to the improvement of resource management. The first phase of exploitation of marine plant resources started prior to the 14th century, with the gathering and sale of storm-tossed seaweeds for fertilizer. The harvest of seagrasses and algae at Ria de Aveiro was of great economic importance. The second phase of resource exploitation began with the wider scale harvest of agarophyte species for colloid extraction. Portugal is at present the third largest harvester of the agarophytes Gelidium and Pterocladia (2500 t annually), and it is the fifth largest agar producer (350 t annually). Other colloid-producing species, including Chondrus crispus and Mastocarpus stellatus, are also harvested for export. The total agarophyte landings, agar production and income from agar exports is far below the maximum levels attained in the early 1970s. The status of stocks in each different harvest zone on the continental coast and the Azores is examined. Although there is an effective management structure for the Portuguese marine plant resource, research is needed to provide a sound biological basis for management. author for correspondence