Catch rates (kg hour−1) of horse mackerel (Trachurus trachurus), blue whiting (Micromesistius poutassou) and hake (Merluccius merluccius) from a series of 22 groundfish surveys conducted off Portugal between 1989 and 1999 were analysed using integrated logistic and gamma Generalized Linear Models (GLM). This methodology deals with the large amount of zeros in survey data matrices by modelling the probability of catch and the amount of positive catch separately, and then integrating the two sub-models into a single catch rate model of abundance. Among the explanatory variables included in the models, the geographic areas occupied by fish assemblages, i.e., groups of persistent co-occurring species, explained most of the variability observed for horse mackerel and blue whiting, while depth was the most important factor for hake. Because of hake's ubiquity on the Portuguese margin, models for this species were less parsimonious and explained a lower proportion of total variability compared with the other species. The abundance of horse mackerel is much higher in the winter and reduces with depth. Blue whiting and horse mackerel exhibited opposite trends in abundance from 1991 to 1994, with the latter species presenting a higher abundance throughout this period. No clear temporal trends of abundance were detected for hake. The effect of trawling hour in models suggested that horse mackerel and blue whiting exhibit vertical migrations, staying close to the bottom by day, when abundance is higher. The current approach proved to cope well with sparse catch data matrices and brought out novel information on the ecology of fish species in the Portuguese continental margin by successfully integrating environmental information into the analysis of fish abundance.

The aggregate backscattering cross-section, σag is the sum of backscattering cross-sections of all fish in a shoal. It is a basic acoustical parameter used for shoal description and biomass estimation. Simulations were undertaken for evaluating the impact of horizontal dimension, density, depth and beam width on measurements of σag for shoals with constant abundance. The important factor determining measurement bias is the ratio of shoal size expressed as along cross-section length relative to along ship beam width at mean shoal depth. The results show that 10 log10(σag) is underestimated by about 8 dB for a 5 m long shoal located at 200 m depth if detected by a 7° beam. A formula for correcting σag estimates for shoal sizes bigger than 1.3 times the beam width is proposed. The negative measurement bias can also be reduced by using transducers with narrower beam widths.

Patterns of spatial and temporal variability of coastal fish assemblages were compared between areas subjected to different levels of protection at two different depths using a visual census technique. A no take reserve was compared with recreational fishing areas around a small Mediterranean island at 5 m and 20 m depth. Univariate and multivariate statistical techniques were used to test the hypothesis that protection could have different effects at different depths. A total of 56 species were identified during the survey. The most represented families were Sparidae and Labridae. Results showed an interaction between depth and levels of protection that was not persistent across the study period. This result was consistent for the whole fish assemblage and for the target species; most species showed higher abundance in protected areas at 20 m depth.

We explored the relationships between diet and morphology in 30 fish species from forested tropical streams of the Bolivian Amazon. These species were first assigned to eight broad trophic guilds based on stomach contents analysis. The relationships between diet and morphology were then examined using Redundancy Analysis, after having checked for potential phylogenetical effects. Results show that, independently of any phylogenetic constraints, some of the trophic guilds could be grossly predicted from few relevant morphological attributes (i.e. relative intestinal length, standard length and mouth orientation) and thus suggest a significant link between diet and morphology. In other words, species having similar diet tend to converge to some extent on some morphological attributes. This link was nevertheless rather weak, suggesting that even if morphology may set limits to patterns of resource use, these limits are broad enough to allow fishes changing their choice of prey resources to respond to local biotic and/or abiotic conditions.

The Cyprinidae is the largest freshwater fish family in Vietnam, with over 220 recognised species, many of which play an important role in aquaculture or are harvested from the wild. Despite numerous studies on the taxonomy of this family based on traditional morphological data, the relationships between major cyprinid groups is poorly understood and the taxonomic validity of a number of these groups is under debate. While an increasing number of molecular studies on cyprinid relationships have been conducted many have used restricted sampling and none have incorporated Vietnamese species. In this study, mitochondrial 16S rRNA, D-loop and cytochrome b gene sequences from 25 species of cyprinids collected from Vietnam were obtained and combined with sequences of cyprinids available in GenBank, in order to investigate the taxonomic validity of subfamilies within Cyprinidae and their phylogenetic relationships. The molecular data supported traditional division of the Cyprinidae into two major lineages: Cyprinines and Leuciscines. The placement of the Danioninae as the sister lineage to this grouping was not supported. Many of the subfamily boundaries were questioned and doubt was raised on some of the generic level classifications. The validity of species designation in Cyprinus, Tor and Cyclocheilichthys was also questioned. This study will need to be extended with greater taxon and gene sampling to further consolidate our understanding of cyprinid relationships and classification.

Live preys commonly used in fish larval rearing seem to be imbalanced in terms of amino acids. Manipulation of their amino acid composition is difficult, but the use of microencapsulated diets allows this manipulation. This study analysed the effect of amino acid supplementation, in order to compensate for dietary amino acid imbalances, on growth and survival of gilthead seabream (Sparus aurata) larvae. Larvae were reared until 32 days after hatching, in a closed recirculating water system (19 °C), using only live food (rotifers and Artemia). Thereafter, larvae were fed Artemia or one of the experimental microencapsulated diets: supplemented with indispensable amino acids (IAAsup diet), or supplemented with dispensable amino acids (DAAsup diet). Experiment lasted for 10 days. Dietary supplementation with indispensable amino acids resulted in A/E ratios [(each indispensable amino acid) × (total indispensable amino acids)−1 × 1000]more similar to the ones of larval seabream and in higher IAA:DAA ratios than in the DAAsup diet. Survival was similar in larvae fed the IAAsup diet (75%) or Artemia (87%), but was significantly lower in larvae fed the DAAsup diet (52%). Larvae from all treatments more than doubled their average dry weight during the experimental period. Final dry weight was similar in larvae fed both microcapsules, but these were lighter than larvae fed with Artemia. Relative growth rate (RGR) and total biomass production tended to be higher in larvae fed the IAAsup (RGR = 9% day−1) than the DAAsup diet (RGR = 7.5% day−1) and only in this last treatment these parameters were significantly lower than in larvae fed with Artemia. Therefore, dietary supplementation with indispensable amino acids resulted in a more balanced dietary amino acid profile, which significantly increased survival. Further studies introducing microdiets earlier in the development seem necessary in order to optimise growth.

Quantifying of sediment reworking processes provides new insights into benthic ecosystem functioning of the Thau lagoon, an important European shellfish farming area. In order to evaluate bioturbation rates of surface sediments, profiles of 7Be (half-life: 53 days) and 234Th (half-life: 24.1 days) were measured in cores collected since December 2001 to December 2006. Several sites were selected to sample the diversity of the Thau lagoon: C4, T10, and T11 in the middle of the lagoon, C5, T7 and T8 nearby oyster farming, T2 and T4 in the western edge, T12 in the eastern part closed to industry. 234Th in excess (234Thxs ; i.e. supplied to sediment by settling particles) and 7Be both show seasonal variations in activities and in penetration within sediment. Taking into account the moderate sedimentation rates of the Thau lagoon, sites (0.1–0.4 cm per year), the penetration of both short-lived radionuclides to variable depths, from 1 up to 8 cm, indicates efficient biological mixing of upper sediments. Bioturbation rates (D b) to the distribution of excess 234Th (234Pb-D b) and of 7Be (7Be-D b) range between 1 and 35 cm2 y−1, depending on site and season. Surface sediment mixing of the Thau lagoon is primarily controlled by the quality of particle input, i.e. the food supply to the benthic fauna, mainly governed by the hydrological and seasonal conditions. But locally shellfish production is a key parameter that influences bioturbation through biodeposition.

Diel, nocturnal and lunar input patterns of pre-settlement coral reef fish were described in Wallis, a typical high-island in the south-central Pacific, with a mid-size lagoon and a 2-m spring tidal range. Crest nets were set on the barrier reef to collect incoming pre-settlement fish. A diel input pattern was observed, with 82 to 99% of the larvae arriving at night. Nocturnal input of pre-settlement fish occurred throughout the night, at different times depending on the lunar phases. In contrast to studies done in other locations, the input was not higher during the first part of the night. The input level was related to moonlight and water level, but independent of tide direction. High input levels were recorded during all lunar phases, except the full moon. This lunar pattern differed from maximum settlement observed during the new moon in other locations. Consequently, a sampling strategy for studying temporal patterns of coral reef fish settlement in typical west Pacific high-islands should include new and quarter of the moon phases and should be extended to the entire night.

The effect of short-time Artemia spp. feeding on growth performance and cumulative survival rate of barbel (Barbus barbus) larvae were studied under controlled aquaria conditions during the 21-day larval period. Three different diets (presenting reduced Artemia feeding) were tested for first exogenous nutrition of larvae (since 13 days post hatch): (1) artificial feed (Asta); (2) Artemia nauplii for 7 days followed by artificial feed; (3) Artemia nauplii for 14 days followed by artificial feed. The longer period of live food statistically improved growth of larvae (W = 174 ± 20 mg and SGR = 14.5 ± 0.5% d−1). The artificial dry food Asta without the addition of Artemia nauplii caused statistically decreased growth (W= 135 ± 22 mg and SGR= 13.1 ± 0.7% d−1). However, the growth of larvae with the short period of Artemia nauplii (W = 153 ± 25 mg and SGR = 13.8 ± 0.7% d−1) did not differ compared to either group. All used feeding diets did not have a significant effect on the cumulative survival rate of larvae ranging from 73 ± 1% to 74 ± 1% at the end of the larval rearing period.

The effects of the rearing environment on growth performance and survival rate of juveniles were tested under intensive controlled conditions in aquaria and troughs for 84 days following the larval period (from 34 to 118 dph). The environment of the troughs caused significantly decreased growth (W = 2079 ± 433 mg and SGR = 3.1 ± 0.05% d−1) of juveniles compared to ones reared in aquaria (W = 3236 ± 264 mg and SGR = 3.6 ± 0.1% d−1) at the end of the juvenile rearing period. Nevertheless, rearing environment did not have a significant influence on the cumulative survival rate of barbels (S C = 90 ± 4% and 81 ± 3% in aquaria and troughs, respectively).

An histology and pathological survey on carpet-shell clam cultured in the south of Galicia (NW Spain) (Ruditapes decussatus) was carried out for a two years period (2000-2001). A temporal distribution of the potentially pathogenic agents were determined by histological analysis. In addition, stocks of molluscs reported to suffer mortalities during the studied period were also analyzed and the pathogenic burden determined. Pathogens do not follow a temporal pattern over studied period and no significant differences were detected nor on the presence nor in prevalence of these pathogens among all the analysed stocks. Therefore, no direct relationship can be established between infection by any pathogen and mortality episodes.

Fin condition was examined in 100–500 g hatchery-reared rainbow trout sampled in a large range of environmental conditions of an experimental farm. A method that is simple to use, requires little training, and does not need costly sophisticated equipment or reference to a model is proposed to assess fin erosion (defined as a decrease in size and profile alteration of fins). A procedure to reliably measure the length of the longest ray present in two selected fins (dorsal and pectoral) is described. Fin general profile is assessed using five levels of erosion based on the precise rank of intact or eroded rays to limit subjective bias. The suitability of the two descriptors of fin erosion under laboratory, farm or field conditions is discussed.

A microcontrolled fish tag which records post-tagging life span, was developed and tested as a prototype. The method of making the tag and the results of tank test trials on chinook salmon (Oncorhynchus tshawytscha) and field trials on chum salmon (Oncorhynchus keta) are presented. This tag was specifically designed to measure survey life (SL) but may have other applications. Survey life is an essential component for area-under-the-curve (AUC) estimation of Pacific salmon (Oncorhynchus spp.) spawning escapements. Accurate escapement estimates are critically important for salmon fisheries management and science. However, AUC spawner estimates must often employ average SL values from historic rather than year-specific studies because direct estimates of SL can require extensive and costly tag-recapture programs. Using assumed SL values can introduce serious bias in population estimates, therefore alternative methods of determining annual SL are important. In this study, the new tag estimated SL by measuring the elapsed time from tagging until the fish came to rest permanently on its lateral or dorsal surface. Details on how to construct the tag are provided so that researchers will be able to make their own.