Browsing by Author "Rufino, Marta M."
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- Assessing the morphological variability of unio delphinus spengler, 1783 (Bivalvia: Unionidae) using geometric morphometryPublication . Morais, Pedro; Rufino, Marta M.; Reis, Joaquim; Dias, Ester; Sousa, RonaldoThe morphological variability of freshwater bivalve species, observed between and within river basins, may hamper their correct identification, even by experienced researchers. Classic morphometric measurements, i.e. shell length, height and thickness, or their ratios, are generally insufficient to distinguish populations and/or species. These issues may be overcome using a geometric morphometric method, which allows analysis of the overall shape of the individual, independently of its size. Thus, we aimed to test the usefulness of two geometric morphometric tools, landmarks and sliding semilandmarks, to evaluate the morphological variability of Unio delphinus Spengler, 1783 in three habitats of the Guadiana Basin (SW Iberian Peninsula, Europe): estuary, river and stream. We used 13 landmarks located on the shell interior (at the teeth, muscle scars and pallial line) and 35 sliding semilandmarks for the shell contour. These morphometric analyses showed that the shell shape of U. delphinus differs significantly among different habitats. Estuarine and stream shells are the most disparate (James index = 649.114, permutation P-value <0.001) and variability is not related to variations in shell size. The main differences in shell morphology are the following: (1) estuarine shells are more elongate, while riverine shells are more subovate; (2) the anterior curvature at the umbo is steeper in estuarine and riverine shells; (3) estuarine shells have an arched curvature at the ventral part of the shell, which is absent in specimens from the other habitats. Our data suggest that the morphology of U. delphinus shells might be influenced by the water flow characteristics of each habitat, since shells exhibited characteristics that are typically observed in freshwater mussels from lotic and lentic habitats.
- Designing a coastal monitoring marine biodiversity survey, using trammel nets and gillnets in PortugalPublication . Rufino, Marta M.; Maia, Catarina; Dinis, David; Farias, Inês; Moura, Teresa; Gomes, Pedro; Quaresma, Ivania; Martins, Rogélia; Figueiredo, Ivone; Serra-Pereira, Bárbara; Gaspar, Miguel; Moreno, AnaAlthough coastal areas are of great importance, they often lack long term monitoring surveys, which are essential for effective management, fisheries sustainability, and marine spatial planning. To address this, we conducted two experimental surveys aimed at assessing communities and their biodiversity, with the objective of designing a monitoring program for marine coastal biodiversity, based on gear type, depth, sampling arrangement, total net length, and panel position within the haul. Depth was found to be the most important factor shaping biodiversity, while gear type had the greatest impact on assessing species richness. Overall, both number of species and diversity increased with depth, though significant differences were only found between hauls deployed at 10 m and deeper (30-50 m). Trammel nets caught a larger number of species compared to gillnets, and there was evidence of an interaction between depth and gear, in terms of abundance and at the community level; samples taken deeper than 10 m showed more gear-related differences. We found that neither the panel position within the haul nor the number of nets had any impact on species diversity or abundance. Similarly, there was no evidence for an effect related to the arrangement of nets, as results were consistent whether using separated or continuous net panels. However, the number of nets used as a sampling unit significantly influenced the results, as the variation in species abundance and diversity with depth and gear type was similar, when 20 or 30 nets were used, but became more variable when only 10 nets were used, even with increased replication. We concluded that both trammel nets and gillnets should be included in a coastal biodiversity monitoring program, as each catches a different set of species, including both demersal and pelagic taxa. Further, we recommend using a minimum of 20 nets (ideally 30+) per station, with replication. The evaluated monitoring system has a minimal impact on the ecosystem, can be easily deployed using commercial vessels and effectively captures a large number of species, being thus, highly recommended to be used in coastal monitoring surveys.
- Estimating fishing effort in small-scale fisheries using high-resolution spatio-temporal tracking data (an implementation framework illustrated with case studies from Portugal)Publication . Rufino, Marta M.; Mendo, Tania; Samarão, João; Gaspar, MiguelSmall-scale fisheries (SSF, boats < 12 m) represent 90% of this sector at a worldwide scale and 84% of the EU fleet. Mapping the areas and intensity where the fishing operations occur is essential for spatial planning, safety, fisheries sustainability and biodiversity conservation. The EU is currently regulating position tracking of SSF fishing vessels requiring precision resolved geo-positional data (sec to min resolution).Here we developed a series of procedures aimed at categorizing fishing boats behaviour using high resolution data. Our integrated approach involve novel routines aimed at (i) produce an expert validated data set, (ii) pre-processing of positional data, (iii) establishing minimal required temporal resolution, and (iv) final assessment of an optimized classification model. Objective (iv) was implemented by using statistical and machine learning (ML) routines, using novel combinations of fixed thresholds estimates using regression trees and classification methods based on anti-mode, Gaussian Mixture Models (GMM), Expectation Maximisation (EM) algorithms, Hidden Markov Models (HMM) and Random Forest (RF). Of relevance, the final evaluation framework in-corporates both error quantification and fishing effort indicators. We tested the method by running through four SSF fisheries from Portugal recorded every 30 sec, with 183 boat trips validated, and concluded that the more robust time interval for data acquisition in these metiers should be <2 min and that mode and random forest methods with pre-data treatment gave the best results. A special effort was concentrated in a visual support provided by the results produced by this new method, making its interpretation easier, thus facilitating trans-ference and translation into other fishery levels. After the current validation in the Portuguese SSF fleet, we posit that our novel procedure has the potential to serve as an integrated quantitative approach to the EU SSF management.
- Habitat structure shaping megabenthic communities inhabiting subtidal soft bottoms along the Algarve coast (Portugal)Publication . Rufino, Marta M.; Pereira, Alexandre M.; Pereira, Fabio; Moura, Paula; Vasconcelos, Paulo; Gaspar, MiguelThe present study analysed the megabenthic diversity in subtidal soft bottoms and assessed the main environmental drivers of megabenthic community organisation along the Algarve coast (southern Portugal). We tested the hypothesis that megabenthic communities respond to the same environmental drivers than macrofauna. We found that similar to macrofauna, megafaunal communities were organised in relation to the depth of closure, light reaching the bottom, and the hydrodynamic conditions related with exposure within the shallower areas. The influence of the main river outflow prevailed over other drivers, but only up to 9 m depth. We found that seven different spatial units should be considered, each characterised by different indicator species. Additionally, among a total of 412 taxa collected between 4 and 50 m depth, we provide the characteristics of the 64 commonest species in terms of occurrence, frequency, distribution, abundance, bathymetric and sedimentary preferences, which constitutes most valuable information for ecosystem modelling. Megabenthic alpha diversity decreased with depth, contrary to evenness and was higher in the proximity of the river Guadiana and in highly exposed shores. We conclude that the megafauna, which is significantly quicker to collect and analyse, can provide an accurate alternative to macrofauna sampling, as their communities are shaped by the same drivers.
- Influence of wind, rainfall, temperature, and primary productivity, on the biomass of the bivalves Spisula solida, Donax trunculus, Chamelea gallina and Ensis siliquaPublication . Bento De Almeida, Joana Maria; Gaspar, Miguel; Castro, Margarida; Rufino, Marta M.Coastal bivalve populations are characterized by large temporal fluctuations, driven by recruitment success dependent on environmental conditions. The present study evaluated the relationship of rainfall, chlorophyll-α, sea surface temperature (SST) and wind, with the biomass of four commercial bivalve species (Spisula solida, Donax trunculus, Chamelea gallina and Ensis siliqua) that occur both along the Barlavento (western region), and the Sotavento (eastern region), along the South coast of Portugal, between 1999 and 2011. Multiple regression models were used to test two hypotheses: a) the association between environmental conditions three months prior to the spawning period and the biomass in the following year (response variable) and b) the association between environmental conditions during the spawning season plus one month and the biomass in the following year. Wind was not included in the model to test a). The environmental variables considered were not important for E. siliqua. In the period prior to spawning, temperature was significant for S. solida (both study areas), rain for D. trunculus and C. gallina (western area) and chlorophyll-α for C. gallina (western area). All the correlations were positive. During the spawning period, rain was significant for all three species but with different trends. The correlation with rain in months early in the spawning season was positive for S. solida (both areas) and D. trunculus (western area). The correlation with the rain in months towards the end of the spawning period was negative for D. trunculus, and C. gallina (western area). Chlorophyll-α in months at later stages of spawning was significant and positive for D. trunculus (both areas) and C. gallina (western area). The wind, expressed as an index developed to indicate the overall occurrence of winds blowing parallel to the coast (assumes to favour the retention of larvae in appropriate environments), was negatively correlated with biomass for mid to late spawning season for S. solida (eastern area) and D. trunculus (western area). For C. gallina there was a positive correlation with wind early in the spawning season. The SST was not an important variable during the spawning period with the exception of D. trunculus where the temperature at mid spawning season was significant with a negative correlation in the western coast and positive in the eastern coast. This study highlighted the annual spatial distribution of four commercially important bivalves and how environmental factors are likely to play an important role on both biomass and location of the fishing beds. Monitoring of the environmental variables could provide information to predict biomasses of bivalve species, an important tool for its management, as well as predict trends and plan strategies in response to global environmental changes.
- Ocean kinetic energy and photosynthetic biomass are important drivers of planktonic foraminifera diversity in the Atlantic OceanPublication . Rufino, Marta M.; Salgueiro, Emilia; H L Voelker, Antje; Polito, Paulo S.; Cermeño, Pedro A.; Abrantes, FatimaTo assess the anthropogenic effect on biodiversity, it is essential to understand the global diversity distribution of the major groups at the base of the food chain, ideally before global warming initiation (1850 Common Era CE). Since organisms in the plankton are highly interconnected and carbonate synthesizing species have a good preservation state in the Atlantic Ocean, the diversity distribution pattern of planktonic foraminifera from 1741 core-top surface sediment samples (expanded ForCenS database) provides a case study to comprehend centennial to decadal time-averaged diversity patterns at pre-1970 CE times, the tempo of the substantial increase in tropospheric warming. In this work, it is hypothesized and tested for the first time, that the large-scale diversity patterns of foraminifera communities are determined by sea surface temperature (SST, representing energy), Chl-a (a surrogate for photosynthetic biomass), and ocean kinetic energy (as EKE). Alpha diversity was estimated using species richness (S), Shannon Wiener index (H), and Simpson evenness (E), and mapped using geostatistical approaches. The three indices are significantly related to SST, Chl-a, and EKE (71-88% of the deviance in the generalized additive mixed model, including a spatial component). Beta diversity was studied through species turnover using gradient forest analysis (59% of the variation). The primary community thresholds of foraminifera species turnover were associated with 5-10 degrees C and 22-28 degrees C SST, 0.05-0.15 mg m-(3) Chl-a, and 1.2-2.0 cm(2) s-(2) log10 EKE energy, respectively. Six of the most important foraminifera species identified for the environmental thresholds of beta diversity are also fundamental in transfer functions, further reinforcing the approaches used. The geographic location of the transition between the four main biogeographic zones was redefined based on the results of beta diversity analysis and incorporating the new datasets, identifying the major marine latitudinal gradients, the most important upwelling areas (Benguela Current, Canary Current), the Equatorial divergence, and the subtropical fronts (Gulf Stream-North Atlantic Drift path in the north, and the South Atlantic current in the south). In conclusion, we provide statistical proof that energy (SST), food supply (Chl-a), and currents (EKE) are the main environmental drivers shaping planktonic foraminifera diversity in the Atlantic ocean and define the associated thresholds for species change on those variables.
- Seasonality in coastal macrobenthic biomass and its implications for estimating secondary production using empirical modelsPublication . Saulnier, Erwan; Brind'Amour, Anik; Tableau, Adrien; Rufino, Marta M.; Dauvin, Jean‐Claude; Luczak, Christophe; Le Bris, HervéMacrobenthic secondary production is widely used to assess the trophic capacity, health, and functioning of marine and freshwater ecosystems. Annual production estimates are often calculated using empirical models and based on data collected during a single period of the year. Yet, many ecosystems show seasonal variations. Although ignoring seasonality may lead to biased and inaccurate estimates of annual secondary production, it has never been tested at the community level. Using time series of macrobenthic data collected seasonally at three temperate marine coastal soft-bottom sites, we assessed seasonal variations in biomass of macrobenthic invertebrates at both population and community levels. We then investigated how these seasonal variations affect the accuracy of annual benthic production when assessed using an empirical model and data from a single sampling event. Significant and consistent seasonal variations in biomass at the three study sites were highlighted. Macrobenthic biomass was significantly lower in late winter and higher in summer/early fall for 18 of the 30 populations analyzed and for all three communities studied. Seasonality led to inaccurate and often biased estimates of annual secondary production at the community level when based on data from a single sampling event. Bias varied by site and sampling period, but reached similar to 50% if biomass was sampled at its annual minimum or maximum. Since monthly sampling is rarely possible, we suggest that ecologists account for uncertainty in annual production estimates caused by seasonality.