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ACKNOWLEDGEMENTS : This study was partially supported by the European Maritime and Fisheries Fund MAR2020 project “VALOREJET: Valorização de espécies rejeitadas e de baixo valor commercial,” MAR-01.03.01-FEAMP0003, and by Fundação para a Ciência e Tecnologia through research contracts attributed to Vera Sequeira (CEECIND/02705/2017) and Ana Rita Vieira (CEECIND/01528/2017) and strategic project UID/MAR/04292/2019. The depletion and overexploitation of several fish stock demands for a valorisation of non-target and discarded species. Nonetheless, such species are often poorly studied, and information on their biological parameters must be gathered for effective population management. For 1 year, the reproductive strategy of the piper gurnard Trigla lyra and the red gurnard Chelidonichthys cuculus was studied by monthly samples obtained from commercial boats operating on western Portuguese coast. Both species showed a biased sex ratio towards females, especially for larger length classes. Length at first maturity could be estimated only for red gurnard (22.1 and 19.9 cm for females and males, respectively) because all piper gurnard individuals caught were mature. Piper gurnard showed determinate fecundity and a short spawning season, from November to February with a peak in January, whereas red gurnard showed indeterminate fecundity and a wide spawning season, from late December to May. The relative annual fecundity estimated for red gurnard (1893 ± 728 oocytes x g-1 eviscerated weight [EW]) was higher than the one estimated for piper gurnard (1018 ± 250 oocytes x g-1 EW). Although important information for understanding the species dynamics is presented in this study, additional information on other life-history parameters and of species landings is required. info:eu-repo/semantics/publishedVersion

The complexity and spatio–temporal scale of populations’ dynamics influence how populations respond to large‐scale ecological pressures. Detecting and attributing synchrony (i.e. temporally coincident fluctuations in populations’ parameters) is key as synchronous populations can become more vulnerable to stochastic events that can affect the viability of harvest and have profound consequences to community structure. Here, we aimed to estimate the level of synchrony in fish growth within and among species across 1 million km2 and identify the environmental drivers contributing to synchronous population fluctuations. We developed otolith increment‐based growth chronologies for two deep‐sea scorpaenid fishes (Helicolenus dactylopterus and Pontinus kuhlii) from geographically and bathymetrically disjunct populations in the northeast Atlantic (one species in three locations; two species with different depth preferences). We used hierarchical models to partition variation in growth within and between populations attributing it to intrinsic (age, species, population) and extrinsic (environmental variables) drivers. We assessed synchrony in growth variation within and among species and identified common change points in population specific growth patterns. We documented time‐variant synchrony in growth variation of geographically and bathymetrically segregated deep‐sea fish populations, lasting 25 and 18 years, respectively. The observed synchrony was likely driven by shared environmental forcing (Moran effect) as large‐scale climate indices (East Atlantic pattern and North Atlantic Oscillation) were important environmental drivers of overall growth variation while the onset of synchrony in growth variation was likely related to marine regime shifts occurring in a wide area of the northeast Atlantic that affected the entire ecosystem. However, our capacity to extrapolate growth information across species and locations was dependent on the timing and magnitude of environmental change. Developing a better understanding of the mechanisms driving growth synchrony is key to ensure sustainable management of populations in habitats that are fragile and highly sensible to environmental change, such as the deep‐sea.

Climate change and fishing are drastically impacting marine ecosystems. Comprehending the biological consequences of these effects on commercially exploited fish is especially challenging. Here, we developed a 43-year otolith increment width-based growth chronology for one of the most important commercially exploited fish species in the Northeast Atlantic (European hake, Merluccius merluccius). Increasingly complex linear mixed-effects models were used to partition growth variation into intrinsic (age, sex, and age-at-capture) and extrinsic (environmental and biotic variables) factors, allowing age interaction with extrinsic variables to assess age-dependent responses in growth. Our results provided strong evidence that European hake growth is impacted by ocean temperature, namely sea surface temperature and temperature at depth, and species abundance (recruitment), with different responses depending on fish age. We found evidence that increasing ocean temperature could be highly detrimental for species growth especially during the first years of life. We provided insights into the effects of environmental and biotic factors on species growth variation. Such information is key to recognize the sensitivity of European hake growth to climate change, which may contribute to sustainable management policies for this valuable resource.

The boarfish Capros aper is one of the most commonly discarded non-commercial species in the International Council for the Exploration of the Sea (ICES) Subdivision VIII in the Atlantic. An increasing interest in this fishery and an incomplete knowledge on the status of the stock justified the present investigation focused on the determination of fecundity type and its estimation, supported by sex steroid profiles for 17 beta-oestradiol (E2), 11-ketotestosterone and 17,20 beta-dihydroxypregn-4-en-3-one (17,20 beta-P). C. aper was found to have indeterminate fecundity with a mean relative batch fecundity during the spawning peak of 50 oocytes g(-1) eviscerated weight (W-E) and a mean relative annual fecundity of 4020 oocytes g(-1) W-E. E2 variations throughout the year indicated the existence of at least two important spawning events, one in winter (January-February) and the other in summer (June-August), with concentrations in females increasing from those with growing oocytes in the developing phase to those in the spawning capable phase. Higher E2 concentrations were also found from 2000 to 2400 hours and from 0800 to 1200 hours suggesting more intense vitellogenesis activity during the night and in the morning, in contrast to 17,20 beta-P concentrations, which were higher between 1200 and 2000 hours, suggesting a more intense spawning activity during this period. UID/MAR/04292/2019, UID/Multi/04326/2019, CEECIND/02705/2017, CEECIND/01528/2017, SFRH/BPD/108917/2015 info:eu-repo/semantics/publishedVersion

We live in a world of limited biological resources and ecosystems, which are essential to feed people. Consequently, diversifying target species and considering full exploitation are essential for fishery sustainability. The present study focuses on the valorization of three low commercial value fish species (blue jack mackerel, Trachurus picturatus, black seabream, Spondyliosoma cantharus, and piper gurnard, Trigla lyra) and of two unexploited species (comber, Serranus cabrilla and boarfish, Capros aper) through the development of marine-based food products with added value. A preliminary inquiry with 155 consumers from Regi&atilde, o de Lisboa e Vale do Tejo (Center of Portugal) was conducted to assess fish consumption, the applicability of fish product innovation, and the importance of valorizing discarded fish. Five products (black seabream ceviche, smoked blue jack mackerel p&acirc, t&eacute, dehydrated piper gurnard, fried boarfish, and comber pastries) were developed and investigated for their sensory characteristics and consumer liking by hedonic tests to 90 consumers. The most important descriptors were identified for each product (texture, flavor, color, and appearance). Comber pastries had the highest purchase intention (88%), followed by black seabream ceviche (85%) and blue jack mackerel p&acirc, (76%). Sensory evaluations showed a clear tendency of consumers to accept reformulated products, with the introduction of the low-value and unexploited species under study.

Overfishing is increasing over time, and according to FAO (Food and Agriculture Organization), about one third of the world&rsquo, s fish stocks are now overfished. Thus, diversifying the target species is essential for fisheries sustainability contributing to improve resource-efficient processes. Non-target species can be valuable resources for the development of new food products. However, those species are scarcely studied, and it is of high importance to trace their seasonal sensory profile as a first step towards their valorisation. Therefore, in this study, seasonal influence on sensory properties of five low commercial value or unexploited fish species, namely Trachurus picturatus (blue jack mackerel), Spondyliosoma cantharus (black seabream), Trigla lyra (piper gurnard), Serranus cabrilla (comber) and Capros aper (boarfish), was assessed in order to identify the most favourable season for catching each species. Fish samples were assessed by a panel of 16 semi-trained assessors for sensory attributes previously identified. The evaluation takes place every 2 months. Statistical differences were reported between attributes and seasons for all species, except for T. lyra, which did not present any difference in its sensory attributes throughout the year.

© 2020 by the authors., Phylogenetic relatedness is a key diversity measure for the analysis and understanding of how species and communities evolve across time and space. Understanding the nonrandom loss of species with respect to phylogeny is also essential for better-informed conservation decisions. However, several factors are known to influence phylogenetic reconstruction and, ultimately, phylogenetic diversity metrics. In this study, we empirically tested how some of these factors (topological constraint, taxon sampling, genetic markers and calibration) affect phylogenetic resolution and uncertainty. We built a densely sampled, species-level phylogenetic tree for spiders, combining Sanger sequencing of species from local communities of two biogeographical regions (Iberian Peninsula and Macaronesia) with a taxon-rich backbone matrix of Genbank sequences and a topological constraint derived from recent phylogenomic studies. The resulting tree constitutes the most complete spider phylogeny to date, both in terms of terminals and background information, and may serve as a standard reference for the analysis of phylogenetic diversity patterns at the community level. We then used this tree to investigate how partial data affect phylogenetic reconstruction, phylogenetic diversity estimates and their rankings, and, ultimately, the ecological processes inferred for each community. We found that the incorporation of a single slowly evolving marker (28S) to the DNA barcode sequences from local communities, had the highest impact on tree topology, closely followed by the use of a backbone matrix. The increase in missing data resulting from combining partial sequences from local communities only had a moderate impact on the resulting trees, similar to the difference observed when using topological constraints. Our study further revealed substantial differences in both the phylogenetic structure and diversity rankings of the analyzed communities estimated from the different phylogenetic treatments, especially when using non-ultrametric trees (phylograms) instead of time-stamped trees (chronograms). Finally, we provide some recommendations on reconstructing phylogenetic trees to infer phylogenetic diversity within ecological studies., This study was supported by the project BIODIV ISLAND-CONT (Biodiversity drivers on islands and continents–706482) funded by Marie Sklodowska-Curie Individual Fellowships (H2020-MSCA-IF-2015) to the first author N.M.-H. The research was additionally funded by four other projects that provided the material collected: 1. ERA-Net Net-Biome research framework, financed through Portuguese FCT-NETBIOME grant 0003/2011 (P.A.V.B.). 2. ERA-Net Net-Biome financed through Canary Islands Government ACIISI grants SE-12/02, SE-12/03, SE-12/04 (B.C.E.), co-financed by FEDER. 3. FCT MACDIV–FCT-PTDC/BIABIC/0054/2014 (P.A.V.B.,B.C.E., P.C., I.R.A., F.R., O.S.P., A.V.). 4. Organismo Autónomo de Parques Nacionales Spain (OAPN #485/2012) (M.A.A.). Additional support was provided by grant 2017SGR83 from the Catalan Government to M.A.A. M.D. was supported by an APIF PhD fellowship from the University of Barcelona. J.L.-F. was supported by a Juan de la Cierva Fellowship (FJCI-2015-23723). I.R.A. was funded by Portuguese funds through FCT–Fundação para a Ciência e a Tecnologia, I.P., under the Norma Transitória–DL57/2016/CP1375/CT0003. Open access funding provided by University of Helsinki.

Knowledge on population units is critical for understanding population dynamics and providing an adequate fisheries management. Despite its vast distribution and commercial importance, there is no information on black seabream population structure. Different approaches to otolith analysis were used to elucidate on the stock structure of this species. Otoliths from seven areas along the eastern Atlantic: English Channel, Bay of Biscay, Galicia (Spain), Peniche (west coast of Portugal), Algarve (south coast of Portugal), the Canary Islands and Angola were compared through elliptical Fourier analysis and oxygen and carbon stable isotopes ratio. Otolith shape analysis data achieved 80% of correct assigned specimens in discriminant analysis while poor correct assignment levels were achieved with the stable isotopes ratio. However, the PERMANOVA conducted on δ13C and δ18O values revealed significant differences between all areas, with exception of the two Portuguese areas. The results of this study indicate that black seabream spends most of its life in the same area and that the studied populations should probably be considered as different stock units. However, some mixture was detected in the European region pointing for the usefulness of life history parameters and genetic studies to enlighten the stock structure of the species.

Resolution of population structure represents an effective way to define biological stocks and inform efficient fisheries management. In the present study, the phylogeography of the protogynous sparid Spondyliosoma cantharus, in the East Atlantic and Mediterranean Sea, was investigated with nuclear (S7) and mitochondrial (cytochrome b) DNA markers. Significant divergence of four regional genetic groups was observed: North Eastern Atlantic, Mediterranean Sea, Western African Transition (Cape Verde) and Gulf of Guinea (Angola). The two southern populations (Cape Verde and Angola) each comprised reciprocally monophyletic mtDNA lineages, revealed low levels of diversity in Cape Verde and high diversity for Angola despite being represented by only 14 individuals. A complete divergence between North Atlantic and Mediterranean populations was depicted by the mitochondrial marker, but a highly shared nuclear haplotype revealed an incomplete lineage sorting between these regions. Bayesian skyline plots and associated statistics revealed different dynamics among the four regions. Cape Verde showed no expansion and the expansion time estimated for Angola was much older than for the other regions. Mediterranean region seems to have experienced an early population growth but has remained with a stable population size for the last 30000 years while the North Atlantic population has been steadily growing. The lack of genetic structuring within these regions should not be taken as evidence of demographic panmixia in light of potential resolution thresholds and previous evidence of intra-regional phenotypic heterogeneity.

Two hundred and seven individuals (103 females and 104 males) of bluemouth Helicolenus dactylopterus (Scorpaeniformes, Sebastidae), a commercially important deep-water species with an unusual reproductive strategy, from the eastern Atlantic Ocean ranging from 13·9 to 37·5 cm total length (LT ) were analysed from September 2011 to October 2012. The analysis included gonad maturity phases and blood-plasma levels of oestradiol-17β (E2 ), 11-ketotestosterone (11-KT) and 17,20β-dihydroxypregn-4-en-3-one (17,20β-P). Results confirmed the existence of an annual reproductive cycle with asynchrony between females and males and a spawning season from January to May. A pronounced peak in 17,20β-P in October for both sexes was associated with possible mating behaviour and recent copula. Levels of E2 increased preceding the elevation of the gonado-somatic index during ovarian growth and were lower during regression and regeneration. The frequency distribution of oocyte-embryonic stages and variation of hormone levels suggest the existence of daily rhythms. Fertilization was detected between 2000-0000 and 0800-1200 h and spawning took place throughout the day peaking between 2000 and 0000 h. The cyclic pattern of sex steroids and ovarian recruitment provides a new insight into the reproductive strategy of this species.

The capacity of bacterial pathogens to infect their hosts depends on the tight spatiotemporal regulation of virulence genes. The Listeria monocytogenes (Lm) metal efflux pump repressor CadC is highly expressed during late infection stages, modulating lipoprotein processing and host immune response. Here we investigate the potential of CadC as broad repressor of virulence genes. We show that CadC represses the expression of the bile salt hydrolase impairing Lm resistance to bile. During late infection, in absence of CadC-dependent repression, the constitutive bile salt hydrolase expression induces the overexpression of the cholic acid efflux pump MdrT that is unfavorable to Lm virulence. We establish the CadC regulon and show that CadC represses additional virulence factors activated by sB during colonization of the intestinal lumen. CadC is thus a general repressor that promotes Lm virulence by down-regulating, at late infection stages, genes required for survival in the gastrointestinal tract. This demonstrates for the first time how bacterial pathogens can repurpose regulators to spatiotemporally repress virulence genes and optimize their infectious capacity. This work was supported by grants to DC (FEDER - Fundo Europeu de Desenvolvimento Regional funds through the NORTE 2020 - Norte Portugal Regional Operational Programme, Portugal 2020, and by Portuguese funds through FCT - Fundação para a Ciência e a Tecnologia/Ministério da Ciência, Tecnologia e Ensino Superior in the framework of the project NORTE-01-0145-FEDER-030020 PTDC/SAU-INF/30020/2017); to PC (European Research Council - ERC - Advanced Grant BacCellEpi 670823). R.P. and A.C. received an FCT Doctoral Fellowship (SFRH/BD/89542/2012, SFRH/BD/29314/2006) through FCT/MEC co-funded by QREN and POPH (Programa Operacional Potencial Humano). SS was supported by FCT Investigator program (COMPETE, POPH and FCT).

Background Here we present the data obtained from the samples collected as part of a large research project (MACDIV) which aims at understanding the drivers of spider (Araneae) community assembly in Macaronesian islands. To obtain the data, we applied the sampling protocol COBRA (Conservation Oriented Biodiversity Rapid Assessment), in twelve 50 m x 50 m native forest plots and five dry habitat plots on the island of Madeiraand in 5 dry habitat plots on the island of Porto Santo. Through this publication, we contribute to the knowledge of the arachnofauna of the Madeiran archipelago. New information From the samples that we collected, we obtained a total of 14,902 specimens, of which 49% were adults (7,263). We identified these specimens to 87 species and 18 morphospecies (undescribed), belonging to 26 families. Species of the family Linyphiidae dominated the samples, with 24 (morpho)species. Out of the 105 recorded (morpho)species, 34 were endemic, 26 native non-endemic, 22 introduced and 23 species of unknown origin. We report seven new records of possibly recently introduced species in the Madeiran archipelago. We also present 21 new records for Madeira island and 32 for Porto Santo (33 for the whole archipelago)., This research was supported by the project FCT MACDIV financed by Fundação para a Ciência e a Tecnologia – ref. FCT-PTDC/BIABIC/0054/2014, that also supported the Open Access of the manuscript. We are grateful to the Madeira Natural Park for the logistic support as well as permission for the collection of specimens.

This study was partially supported by the European Maritime and Fisheries Fund MAR2020 project ‘VALOREJET: Valorização de espécies rejeitadas e de baixo valor comercial’, MAR-01.03.01-FEAMP-0003 and by Fundação para a Ciência e Tecnologia through research contracts attributed to V.S. (CEECIND/02705/2017) and A.R.V. (CEECIND/01528/2017), and strategic project UID/MAR/ 04292/2019. Reproduction of Trachurus picturatus off the western Portuguese coast was studied over 1 yr. During histological analyses, the presence of Kudoa sp. was detected in advanced vitellogenic oocytes. Kudoa infections are known to cause economic loss through the induction of postmortem liquefaction of fish muscles, but ovarian infection as reported in this study will seriously affect the reproductive potential of the species and thus impact fisheries productivity. Only females showed gonad infection which led to total degradation of advanced vitellogenic oocytes. No macroscopic, somatic or condition indices revealed differences between infected and uninfected females, rendering this infection event a concealed suppression of reproduction. info:eu-repo/semantics/publishedVersion

International audience; Environmental change often combined with selective harvesting has profound and diverse impacts on marine fish populations. Unlocking the biological consequences of these effects on wild fish is notoriously challenging, especially in highly productive but naturally variable systems with uncertain futures such as Eastern Boundary current systems. Here, we developed otolith increment-based growth chronologies covering half a century (53 years) for a small pelagic fish (Atlantic horse mackerel, Trachurus trachurus) in the northern limb of the Canary current upwelling system. We used increasingly complex mixed-effects models to partition individually resolved growth variation among intrinsic (Age and Age-at-capture) and extrinsic (biotic and abiotic factors) sources in four complementary data sets: a general population chronology, and three chronologies derived from age groups that reflect ontogenetic habitat shifts. First, we investigated the timing and scale of growth phase shifts and assessed the effects of extrinsic factors on inter-annual growth variation. Second, we quantified among and within cohort growth variability over time. Our results provided strong evidence for inter-annual SST and primary productivity variation impacting on Atlantic horse mackerel growth. We also identified phase shifts in growth that point to larger ecosystem-wide changes (regime shifts), potentially driven by large-scale climatic indices, such as North Atlantic Oscillation and East Atlantic pattern. Cohort-dependent growth effects likely reflect persistent environmental influences and density dependence. Further, we found evidence for carryover effects in growth whereby a poor start in life tended to persist despite compensatory growth being observed in some individuals. We show how population productivity can be impacted by multiple, interacting environmental and biotic factors leading to potential ecosystem regime shifts. Such information is key to understand recruitment dynamics and population persistence, and will have important implications for fisheries management and to those seeking to understand the effects of large-scale climate change on marine productivity.

We analysed the ovarian dynamics of the anadromous semelparous allis shad Alosa alosa for which our working hypothesis was that mature pre-spawning females would have very low or even exhausted primary growth (PG) oocyte reserves; semelparity has been linked with the depletion of the pool of PG oocytes. To test this hypothesis, the PG oocytes were enumerated, their recruitment pattern to the secondary growth (SG) phase was analysed and their potential replenishment from the pool of oogonia was examined in females caught very close to the Mondego River mouth, in central Portugal and along the river. The development of the SG oocytes was also analysed, the fecundity (batch, total and annual) values were estimated and the intensity of atresia was quantified. Ovarian samples and histological sections were investigated in parallel. A dynamic recruitment pattern of PG oocytes to the SG phase was revealed, where all PG oocytes were recruited and were not replenished by oogonia. Annual fecundity was subject to down-regulation due to atresia prior to spawning and its size was multiple times higher than the size of batch fecundity. Lack of population synchronicity in ovarian development and spawning migration was also observed. This multifaceted analysis of the ovarian dynamics of this species will contribute to management efforts for this critically endangered and economically important fish throughout its geographical distribution. The results reported in this study will also assist in unravelling the complexity of the early processes of oogenesis in fish.

The nearshore ecosystem is an important nursery ground for many fish species. Considering that these areas have a considerable economic value because they support a wide variety of highly valuable species, it is essential to study the structure of their fish communities and the factors that may inlfuence them. The nearshore fish assemblages were studied from March to November of 2015 at 15 sandy beaches, arranged in 6 seaports, along 700 Km in the coast of Portugal. This Atlantic coastline is an important geographical transition area between cold-temperate and warm-temperate regions. Sampling was performed by the beach seine fishery, an artisenal fishery that operates in these areas. The fish assemblage was studied according to its species richness, biogeographical origin, habitat use and resource exploitation, in both biomass and number of individuals. The nearshore fish assemblage was diverse with 70 species belonging to 32 families, though a few species dominated the community: Engraulis encrasicolus, Trachurus trachurus, Sardina pilchardus and Scomber colias. Results indicated that the structure and composition of the fish assemblage from northern and southern seaports are different. Overall, species richness was higher in the southern seaports. Planktivorous species dominated the community in the northernmost seaport, and piscivorous species dominated the community in the remaining seaports. As expected, cold-temperate species presented higher abundance in the northern seaports, and both warm-temperate and sub-tropical species increased in number towards the southern limits. Tropical species were only present in the southernmost area. The main driver for variations in the fish community structure and composition was the water temperature gradient imposed by latitude, highlighting the environmental control in shaping marine biological communities.

Age and growth of Mora moro and Epigonus telescopus were studied using 634 and 232 otoliths, respectively, from specimens caught in the Azores between 1999 and 2009. Otoliths of both species were sectioned through the nucleus, a preparation method that improved the age assignment. Marginal increment analysis showed that, for both species, growth increments (consisting of as single set of translucent and opaque growth increments) were formed annually. M. moro specimens ranged from 22 to 76 cm fork length, were aged from 8 to 59 years, and showed a sexual dimorphism in growth. E. telescopus specimens ranged from 32 to 70 cm fork length which corresponds to ages between 12 and 39 years. No differences in growth between sexes were observed. Growth behaviour of M. moro was better explained by the three parameter von Bertalanffy model. The five parameter model provided a better fit to the E. telescopus data. Under this model a change in growth at 26 years for females and 25 years for males may be related to the onset of sexual reproduction.

The knowledge of the reproductive strategy is essential for the comprehensive understanding of the population dynamics of any fish species. This study intends to define the spawning season, verify the type of fecundity regulation and estimate relative annual fecundity for Serranus atricauda inhabiting the south-west of Portugal seamounts (Gorringe, Ampere and Lion). Monthly samples, between September 2010 and December 2011, were obtained from commercial vessels. This species is synchronously hermaphroditic, and mature individuals were found all year round, with gonadosomatic index peak from February to September. No clear relation between hepatosomatic index and Fulton’s condition factor and gonadal development was found, and therefore, it is probable that reproductive success depends more on environmental conditions and food availability during the spawning season than on body energy reserves. No gap exists between pre-vitellogenic and vitellogenic oocytes and the oocyte size-frequency distribution during the main spawning season show no dominant cohort progressing through time. The number of standing stock of advanced vitellogenic oocytes showed an increase trend along the spawning season decreasing only at its end and the relative intensity of α-atresia was always low throughout this period with an increase towards the end. All these criteria corroborate the indeterminate fecundity type assigned to S. atricauda in previous studies. Mean relative annual fecundity estimated was 5,655 ± 4,321 oocytes per gram of gutted weight.

Several studies on bluemouth age and growth have been published over the last two decades, but they show inconsistent differences in maximum age estimates, suggesting interpretation differences in reading whole or sectioned otoliths. In order to clarify this issue, the present study was carried out to assess bias and precision of age reading between three age readers using three aging procedures (the ventral face of sectioned otoliths, the ventral face of whole otoliths, and the posterior region of whole otoliths) in the same individuals of the same statistical sample covering a wide total body length range (10–44 cm). Good precision between – reader comparisons and aging procedures was detected with coefficients of variation and average percent errors below 6.70% and 4.17%, respectively. The lowest total agreement between readers was obtained for the ventral face of sectioned otoliths (40.00%) and the highest for the posterior region of whole otoliths (64.17%) increasing to 83.48% and 88.33%, respectively, within ±1 year. The percentage of agreement within ±1 year between aging methodologies was above 90%. No systematic disagreement between readers was detected (p > 0.05) as also no significant differences between readers (U, p > 0.82) and aging procedures (U, p overall = 0.92, p by 5 cm length class >0.55). The results of this study indicate that both sectioned and whole otoliths can be used for aging bluemouth across its length range.

The diet and feeding behaviour of the forkbeard Phycis phycis was studied based on 246 stomachs collected between May 2011 and April 2012 from a commercial fleet operating off the central west coast of Portugal. A total of 44 prey items were identified in the stomachs which were merged into major groups to avoid problems with low expected frequencies. The following taxonomic categories were considered: non-decapod Crustacea, Caridea, Anomura, Munida spp., Processa spp., Brachyura, Pisces, Trisopterus luscus. In order to investigate possible diet differences between fish size classes, a cluster analysis was performed using the mean abundance of each prey group by forkbeard 5 cm length class, and three length groups (LG) were obtained: 42.5 cm. Seasonally, Caridea was the main prey group during winter and autumn while Pisces was predominant during the rest of the year. Caridea was the most important prey group for LG1 and LG2 while in LG3 Pisces was the principal one. The forkbeard feeding behaviour may be characterized as presenting a shift pattern from a more generalist diet (small Crustacea, mainly Caridea) in the young adults to a more specialist strategy (teleosts) in the adults.

Age and growth of Pontinus kuhlii were studied using otoliths of 153 males and 148 females, with males having a greater length (and age) than females. A high level of agreement was achieved among readers. Due to gear selectivity, only ages above 7 years (males) and 8 years (females) were estimated in whole otoliths. To estimate length-at-age in younger specimens, backcalculation was also considered but its use in otoliths with ages greater than 22 years was not possible because the growth rings were too close to each other. Von Bertalanffy growth parameters were estimated by sex using each of these methods and also using an approach that combines mean length-at-age obtained from backcalculation and direct reading on the otoliths. The likelihood ratio test showed significant differences between sexes in the three approaches and Akaike’s information criterion suggests that the backcalculation approach was the best one for describing P. kuhlii growth: TL=38.89[1-e (-0.07(t+1.96)) ] and TL=56.50[1-e (–0.04(t+1.87)) ] for females and males, respectively. Natural mortality estimates varied around 0.15 year –1 and 0.07 year –1 for females and males, while the total mortality estimated for 2011 was 0.33 year –1 for females and 0.21 year –1 for males.

In order to investigate the feeding habits of Helicolenus dactylopterus dactylopterus along the continental Portuguese coast, a total of 619 individuals were sampled of which 60% contained food in their stomach and 35% had more than one prey item. Among the 81 prey items that were identified in the stomachs, benthic and benthopelagic prey prevail on this species diet. Acantephyra sp, Pasiphaea sp, mysidacea, and teleostei n.i. were the prey with the higher percent index of relative importance (%IRI) value. Three length groups (5–20 cm, 21–27 cm, and 28–48 cm) were defined through cluster analysis of the mean abundance of prey items. A permutational MANOVA detected significant differences in the diet and stomach fullness index for TLG, season, and maturation stage. Smaller fishes had a generalized diet, feeding mainly on mysidacea changing their diet above 20 cm TL, where a major consumption of natantia was found. The larger individuals, >28 cm TL, present a less generalized diet with pisces as dominant prey group. Seasonally, natantia and pisces were the principal prey groups during spring and winter, respectively, while mysidacea and other crustaceans were predominant during the rest of the year. Mysidacea were also the main prey group for immature individuals while natantia and pisces were the principal prey groups to the other maturity stages. The results of this study indicate that H. d. dactylopterus has a diverse diet focused on small crustaceans such as misyds and as specimens grow shrimps and fishes become more consumed, with larger specimens having a more specialized diet. The different nutritional needs during spawning season also seemed to influence the feeding habits of H. d. dactylopterus.

The bluemouth, Helicolenus dactylopterus dactylopterus (Pisces: Sebastidae), is a zygoparous species with internal fertilization that stores the spermatozoa in crypts within the female ovaries. It spawns gelatinous egg masses that were investigated in this study. Histological analysis confirmed that the ovarian wall and peduncular epithelia play an important role in the production of this gelatinous matrix that contained both oocytes and embryos. Cleavage and blastulae were the most frequent embryonic development stages observed and the tail bud was the latest stage reached. The chemical composition of the matrix was also investigated, revealing that water and proteins are the major components of this substance. This is the first study exclusively dedicated to the investigation of the composition, function and importance of the gelatinous matrix of H. d. dactylopterus in the context of its reproductive strategy.

The understanding of the stock structure of a species is essential to effectively manage fisheries. Otolith shape analysis has been successfully applied in stock identification using the elliptic Fourier analysis. This method was used to assess possible differences in the otolith shape of Helicolenus dactylopterus caught around the Azores, Madeira and mainland Portugal. A total of 294 individuals ranging from 23 to 29 cm in total length, equally distributed by sex and area, were analysed. The multivariate analysis of variance performed on the otolith normalized elliptic Fourier descriptors (NEFDs) revealed significant differences for both area and sex, but no interaction was found between the two factors. In the canonical discriminant analysis an overall classification success of 69.4% and 66.7% was achieved for females and males respectively. These results suggest the usefulness of otolith shape analysis for stock differentiation of bluemouth from Portuguese waters.

Total mercury (THg), cadmium (Cd) and lead (Pb) concentrations were investigated in muscle, liver and gonad tissue of black scabbardfish (Aphanopus carbo) from the southern northeast Atlantic at three Portuguese locations: the mainland and the archipelagos of the Azores and Madeira. Particular emphasis was placed on the comparison of metal levels between geographic locations. Other factors such as size, sex and sexual maturity were also investigated. The median concentrations (mg/kg ww) of THg showed a decreasing trend in the order liver>muscle>gonad. Cadmium levels decreased in the order liver>gonad>muscle and Pb levels decreased in the order gonad>liver>muscle. According to the EU limits, the concentration observed in some specimens, particularly those of THg, raises some food safety concerns. In all the tissues the concentrations of each toxic metal differed between locations. In particular: i) THg concentrations in specimens from Madeira were significantly higher than those from the Azores and the mainland; ii) Cd levels in specimens from the mainland were significantly higher than those from Madeira and the Azores; and iii) for all analysed tissues Pb levels were significantly higher in specimens from the Azores than in those from the mainland. The differences in toxic metal levels between locations were further discussed in relation to aspects of species dynamics and the influence of the main environmental features at each location.

Though whole otoliths are commonly adopted in age assignment of black scabbardfish, this study showed that sectioned otoliths are more appropriate because growth increments are more evident and ageing of larger specimens is easier. Vertebrae are not the most appropriate structure for ageing but, in the absence of otoliths, this structure may be useful in age assignment of this species. To verify possible differences between age and growth among specimens from the southern NE Atlantic, 1075 sectioned otoliths from specimens from mainland Portugal, 436 from Madeira and 107 from the Azores were analysed and the distribution of length-at-age obtained for each sex and region was determined. Significant differences were obtained in the comparison of the distribution of length-at-age between Madeira, the mainland and the Azores. The von Bertalanffy growth model was applied to back-calculated mean length-at-age data from Madeira (Lt = 1586 [1 – e –0.119(t+2.282) ] females; Lt = 1461 [1 – e –0.146(t+1.441) ] males) and mainland (Lt = 1354 [1 – e –0.170(t+2.040) ] females; Lt = 1240 [1 – e –0.208(t+1.654) ] males), and significant differences in the growth equations were obtained. Furthermore, a regression tree model was used to investigate how growth is conditioned by reproduction. The results showed a clear separation between individuals from the two areas, both females and males from the mainland (non-reproductive individuals) being characterised by a lower gonadosomatic index and a lower age.

Black scabbardfish stock structure is still unknown in European waters where, due to the scarcity of biological information, the ICES considers that there is a single stock unit. This study is the final outcome of a scientific project that applies a holistic approach to research on the population structure of the black scabbardfish and aims to define the most appropriate strategy for the conservation of this resource in southern NE Atlantic waters. The factors studied include life history parameters, otolith shape analysis, parasites, landings-and-effort data and contaminants. Sampling was conducted between 2005 and 2007 in three areas of the southern NE Atlantic: mainland Portugal, Madeira and the Azores. The mainland and the Azores have an established commercial fishery, whereas the Azores has only an exploratory fishery. The majority of results indicated the existence of different stocks of black scabbardfish in the study area. Of the 8 parameters, 6 were in agreement with separate stocks between the mainland and Madeira, 5 were in agreement with separate stocks between the mainland and the Azores, and 4 were in agreement with separate stocks between Madeira and the Azores.

Gonads of the NE Atlantic black scabbardfish were examined to give an insight into the reproductive biology of this species. It was concluded that black scabbardfish had determinate fecundity because: (i) a distinct hiatus in oocyte size was observed between pre-vitellogenic and vitellogenic oocytes; (ii) vitellogenic oocytes increased in size during the spawning season; (iii) the number of vitellogenic oocytes did not increase during the spawning season; and (iv) the intensity of atresia was low in pre-spawning and spawning ovaries. Fecundity estimates ranged from 73 to 373 oocytes g-1 female. Comparison of developing ovaries from mainland Portugal and Madeira revealed that those from Madeira were more advanced in development, with more cortical alveoli stage oocytes and a higher gonadosomatic index. Starting in July, the reproductive development of all females from mainland Portugal was interrupted by a generalised atresia of developing oocytes. Completion of gametogenesis and spawning only occurred for fish from Madeira but some fish from this area also failed to complete oocyte development due to mass follicular atresia of vitellogenic oocytes. The percentage of Madeiran fish that failed to spawn due to follicular atresia ranged from 21.2% in 2006 to 37.4% in 2005.

The importance of cephalopods in marine ecosystems is well recognized as they serve as important predators and prey in many food chains. During a 1-year period, cuttlefish were monthly sampled in five areas throughout the Sado estuary, and the stomachs of 445 individuals were examined. Significant changes in the diet according to their life stage were revealed, but similar food habits were presented by males and females. Juvenile individuals (the smaller ones with no visible distinct gonads) preyed mainly upon small crustaceans, while the immature ones (maturity stages I and II) had the most diverse diet with brachyurans as the major prey group. The mature individuals (maturity stages III and IV) showed a clear preference for larger crabs and fishes. Although the cuttlefish are known for their opportunistic feeding behaviour, a preference for some prey according to length and behaviour could be perceived during this study. Seasonal differences in the diet were mostly due to the variation of individuals according to their maturity stage during the year.

Sequeira, V., Neves, A., Vieira, A. R., Figueiredo, I., and Gordo, L. S. 2009. Age and growth of bluemouth, Helicolenus dactylopterus, from the Portuguese continental slope. – ICES Journal of Marine Science, 66: 524–531. In all, 933 bluemouth (Helicolenus dactylopterus) were obtained from bottom-trawl research surveys along the Portuguese continental slope between October 2005 and February 2007 and from commercial landings. Age was determined by reading whole sagittal otoliths, and age estimates were validated by daily growth increment (DGI) analysis. Fish ranged from 5.2 to 44.9 cm, which corresponded to fish between 0 and 30 years old. The mean total length obtained from DGI analysis for age class 1 fish was 8.6 cm, corresponding to otoliths with a mean radius of 1.8 mm. As no statistical differences between sex were observed, the von Bertalanffy growth equation fitted was Lt = 45.50[1 − e−0.05(t+4.01)]. Comparisons with other studies using Hotelling's T2 test and the growth perform index (Ф) are drawn. The growth rates estimated in this study using whole otolith readings were the lowest of all the studies available, and the estimated L∞ is lower then those obtained for Azorean waters and higher than those published for the Mediterranean.

The cultivar of irrigated rice BRSMG Predileta has high grain yield, resistance to the main rice diseases and produces good quality grains for industry and cooking. It was recommended in 2007 by the Genetic Improvement Program for lowland rice in Minas Gerais, developed by EPAMIG in partnership with Embrapa Arroz e Feijao.

Comber is an important bycatch species in the trawl fishery both in the Mediterranean and the Atlantic. Age and growth studies have been restricted to the eastern Mediterranean and no methodologies were ever applied to ensure accuracy and precision. In this study a total of 471 otoliths from specimens ranging from 12 to 26 cm were used. Precision indices showed a high level of agreement between readers and no evidence of systematic disagreement was obtained. To estimate fish growth and due to the absence of individuals smaller than 12 cm, three approaches were used to estimate the von Bertalanffy growth parameters: whole otolith readings, back calculation and a combination of both methodologies. Akaike’s information criterion suggests that the back calculation approach was the best one for describing comber growth: TL = 25.26 [1−e(−0.21(t+1.72)]. Natural mortality estimates varied between M = 0.44 year−1 and M = 0.48 year−1 while estimates of the fishing mortality varied between 0.12 year−1 and 0.16 year−1 and the exploitation rate between 0.20 and 0.27.

Bluemouth, Helicolenus dactylopterus is zygoparous species with internal fertilization spawning multiple batches of early-celled embryos in gelatinous masses. Its unusual reproductive strategy required methodological adjustments to estimate potential annual fecundity. The present study applied an adaptation of the gravimetric method, estimated batch fecundity based on different spawning fraction criteria (gestation, early-celled, and blastula females), and compared these estimates with the number of developing oocytes (NDOR) in the beginning of spawning to clarify the oocyte development pattern. Spawning fraction estimation based on the gestation criterion was considered the most reliable given its low variance and the subjectivity of staging early-celled embryos. On average, 87 batches were spawned with a mean spawning interval estimated at 1.73 days, and a mean relative annual total fecundity of 1,773 embryos g−1 carcass. The inexistence of a clear decreasing trend in the NDOR throughout the spawning season, and the lower NDOR estimates in females in the beginning of spawning comparing with relative annual fecundity (gestation criterion) suggests vitellogenic oocyte recruitment supporting previous results of indeterminate fecundity in Portuguese coast. The method proposed can be considered in fecundity studies of other commercial important species which extrudes gelatinous egg masses.

Samples of boarfish Capros aper, small red scorpionfish Scorpaena notata and comber Serranus cabrilla were collected from monthly by-catch samples on board commercial trawlers off the western coast of Portugal. A histological approach was undertaken to study each species’ reproductive strategy and annual sexual cycle. Temporal variations of the gonadosomatic index and of two condition indices (hepatosomatic and Fulton's K) were also analysed. Results showed that C. aper and S. notata are gonochoristic whilst S. cabrilla is a simultaneous hermaphrodite. Fertilization is external and development of secondary growth follicles is asynchronous in the three species. Mass atresia characterized the end of the spawning season in S. notata and S. cabrilla. In C. aper a high prevalence of atresia was observed throughout the year and was not attributed to regressing or regenerating phases or skip spawning events. The main spawning season of the three species was in the summer and it is suggested that spawning is related to upwelling. During the summer, the spawning interval was 1.09, 1.23 and 1.84 days for S. cabrilla, S. notata and C.aper, respectively. The results of this study indicate potential plasticity and environmental adaptation of sexual strategies.

The knowledge of population structure of a species is essential to effectively assess and manage fisheries. In the present study, genetics, by mitochondrial DNA cytochrome b sequence analysis, and body geometric morphometrics were used to evaluate the existence of distinct populations of the forkbeard (Phycis phycis), an important commercial species in several European countries, especially Portugal and Spain. For geometric morphometric analysis, specimens were collected in the Northeast Atlantic Ocean—Azores, Madeira and mainland Portugal, and for genetic analysis, these samples were complemented with samples collected in the Mediterranean Sea—Spain, Italy and Croatia, in order to cover the entire distribution area of the species. Body shape of the forkbeard from the Northeast Atlantic was found to be highly variable. This variation was probably associated with different environmental factors between the study areas. Despite morphological variation, a low genetic differentiation between samples from different areas was found, most likely due to gene flow that occurred in the past or with the demographic history of the species. Moreover, the presence of unique haplotypes in the Northeast Atlantic and in the Mediterranean suggests that recent gene flow between populations from these areas should be limited. Altogether, a high haplotype diversity, a low nucleotide diversity, a “star-like” network and the results of the mismatch distribution, indicate a possible signature of recent population expansions, which probably started during the end of the Last Glacial Maximum and led to the colonization of the Northeast Atlantic and the Mediterranean.

Background There have been conflicting reports in the literature on association of gene copy number with disease, including CCL3L1 and HIV susceptibility, and β-defensins and Crohn's disease. Quantification of precise gene copy numbers is important in order to define any association of gene copy number with disease. At present, real-time quantitative PCR (QPCR) is the most commonly used method to determine gene copy number, however the Paralogue Ratio Test (PRT) is being used in more and more laboratories. Findings In this study we compare a Pyrosequencing-based Paralogue Ratio Test (PPRT) for determining beta-defensin gene copy number with two currently used methods for gene copy number determination, QPCR and triplex PRT by typing five different cohorts (UK, Danish, Portuguese, Ghanaian and Czech) of DNA from a total of 576 healthy individuals. We found a systematic measurement bias between DNA cohorts revealed by QPCR, but not by the PRT-based methods. Using PRT, copy number ranged from 2 to 9 copies, with a modal copy number of 4 in all populations. Conclusions QPCR is very sensitive to quality of the template DNA, generating systematic biases that could produce false-positive or negative disease associations. Both triplex PRT and PPRT do not show this systematic bias, and type copy number within the correct range, although triplex PRT appears to be a more precise and accurate method to type beta-defensin copy number.

Knowing fish reproductive strategy is essential for understanding population dynamics. This study intends to define the spawning season, length at first maturity, fecundity type, and estimate fecundity of forkbeard, Phycis phycis, from the Portuguese coast. Monthly samples collected from commercial landings between May 2011 and December 2012 were used. Results show that forkbeard is a group-synchronous and batch spawner species. Mature females were found between September and January, mature males were found between August and January, and a significant concomitant increase in gonadosomatic index suggests a spawning season from September to January. Length at first maturity was estimated as 35.9 and 28.5 cm TL for females and males, respectively. Reproductive abnormalities - mosaic intersex, follicular cysts in ovaries, and early mature males - were detected. For fecundity-type definition, a hiatus between primary and secondary growth oocytes was detected. A significant increase in the mean diameter of secondary growth oocytes and a decreasing trend in their number during the spawning season were observed. The intensity of α-atresia was low throughout the spawning season. These four criteria suggest that forkbeard has determinate fecundity. Mean relative annual fecundity estimated was 1833 ± 857 oocytes g⁻¹ gutted weight. Nonreproductive females that skipped a spawning season attained 36.1%.