Browsing by Author "Costa, Maria H."
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- A Ranking system for reference libraries of DNA Barcodes: application to marine fish species from PortugalPublication . Costa, Filipe O.; Landi, Monica; Martins, Rogelia; Costa, Maria H.; Lima Costa, Maria Emília; Carneiro, Miguel; Alves, Maria J.; Steinke, Dirk; Carvalho, Gary R.Background: The increasing availability of reference libraries of DNA barcodes (RLDB) offers the opportunity to the screen the level of consistency in DNA barcode data among libraries, in order to detect possible disagreements generated from taxonomic uncertainty or operational shortcomings. We propose a ranking system to attribute a confidence level to species identifications associated with DNA barcode records from a RLDB. Here we apply the proposed ranking system to a newly generated RLDB for marine fish of Portugal. Methodology/Principal Findings: Specimens (n = 659) representing 102 marine fish species were collected along the continental shelf of Portugal, morphologically identified and archived in a museum collection. Samples were sequenced at the barcode region of the cytochrome oxidase subunit I gene (COI-5P). Resultant DNA barcodes had average intra-specific and inter-specific Kimura-2-parameter distances (0.32% and 8.84%, respectively) within the range usually observed for marine fishes. All specimens were ranked in five different levels (A-E), according to the reliability of the match between their species identification and the respective diagnostic DNA barcodes. Grades A to E were attributed upon submission of individual specimen sequences to BOLD-IDS and inspection of the clustering pattern in the NJ tree generated. Overall, our study resulted in 73.5% of unambiguous species IDs (grade A), 7.8% taxonomically congruent barcode clusters within our dataset, but awaiting external confirmation (grade B), and 18.7% of species identifications with lower levels of reliability (grades C/E). Conclusion/Significance: We highlight the importance of implementing a system to rank barcode records in RLDB, in order to flag taxa in need of taxonomic revision, or reduce ambiguities of discordant data. With increasing DNA barcode records publicly available, this cross-validation system would provide a metric of relative accuracy of barcodes, while enabling the continuous revision and annotation required in taxonomic work.
- Benthic biotope index for classifying estuarine habitatsPublication . Caeiro, S.; Costa, Maria H.; Goovaerts, Pierre; Martins, Flávio Augusto Bastos da CruzAn integration of sediment physical, chemical, biological, and toxicity data is necessary for a meaningful interpretation of the complex sediment conditions in the marine environment. Assessment of benthic community is a vital component for that interpretation, yet their evaluation is complex and requires a large expenditure of time and funds. Thus, there is a need for new tools that are less expensive and more understandable for managers. This paper presents a benthic biotope index to predict from physical and chemical variables the occurrence of macrobenthic habitats, applied to Sado Estuary, as a case of study.
- Hypocholesterolaemic pharmaceutical simvastatin disrupts reproduction and population growth of the amphipod Gammarus locusta at the ng/L rangePublication . Neuparth, Teresa; Martins, Carla; de los Santos, Carmen B.; Costa, Maria H.; Martins, Irene; Costa, Pedro M.; Santos, Miguel M.Simvastatin (SIM), a hypocholesterolaemic drug, is among the most widely used pharmaceuticals worldwide and is therefore of emerging environmental concern. Despite the ubiquitous nature of SIM in the aquatic ecosystems, significant uncertainties exist about sublethal effects of the drug in aquatic organisms. Therefore, here we aimed at investigating a multi-level biological response in the model amphipod Gammarus locusta, following chronic exposures to low levels of SIM (64 ng/L to 8 mg/L). The work integrated a battery of key endpoints at individual-level (survival, growth and reproduction) with histopathological biomarkers in hepatopancreas and gonads. Additionally, an individual-based population modelling was used to project the ecological costs associated with long-term exposure to SIM at the population level. SIM severely impacted growth, reproduction and gonad maturation of G. locusta, concomitantly to changes at the histological level. Among all analysed endpoints, reproduction was particularly sensitive to SIM with significant impact at 320 ng/L. These findings have important implications for environmental risk assessment and disclose new concerns about the effects of SIM in aquatic ecosystems.
- Integration of numerical models in geographic databases: the case of Sado estuary managementPublication . Painho, M.; Sena, R.; Caeiro, S.; Martins, Flávio Augusto Bastos da Cruz; Costa, Maria H.; Neves, R.Geographic information systems (GIS) are now widely applied in coastal resource management. Their ability to organise and interface information from a large range of public and private data sources, and their ability to combine this information, using management criteria, to develop a comprehensive picture of the system explains the success of GIS in this area. The use of numerical models as a tool to improve coastal management is also widespread. Less usual is a GIS-based management to ol implementing a comprehensive management model and integrating a numerical modelling system into itself. In this paper such a methodology is proposed. A GIS-based management tool based on the DPSIR model is presented. An overview of the MOHID numerical modelling system is given and the method of integrating this model in the management tool is described. This system is applied to the Sado Estuary (Portugal). Some preliminary results of the integration are presented, demonstrating the capabilities of the management system.
- Metodologia de gestão dinâmica do estuário do SadoPublication . Caeiro, S.; Martins, Flávio Augusto Bastos da Cruz; Costa, Maria H.; Painho, M.; Neves, R.O estuário do Sado é um sistema litoral onde existem conflitos de gestão ambiental, uma vez que por um lado, localiza-se junto da zona industrial da Península de Setúbal e por outro lado, uma grande parte da sua área está classificada como Reserva Natural. Sendo uma área de especial sensibilidade, torna-se necessário implementar modelos de gestão, que passam pela elaboração de metodologias que avaliem o estado de qualidade da zona costeira. O objectivo deste trabalho é apresentar uma metodologia conceptual de gestão do estuário do Sado, ligado a um modelo dinâmico e ecológico suportado por uma infraestrutura de informação do tipo DPSIR e com base num sistema SIG (Sistema de Informação Geográfica). Desta forma pretende-se integrar a avaliação da qualidade do ecossistema, com base em indicadores da qualidade ambiental previamente seleccionados, com informação socio-económica. Nesta metodologia as propostas de intervenção e a avaliação do seu impacte no estuário são baseadas nos dados ambientais recolhidos e nas previsões dos efeitos dessas acções. Pretende-se que a modelação dinâmica e ecológica do sistema desempenhe um papel fundamental tanto na caracterização do estuário como nas propostas de intervenção. A simulação permite a caracterização do sistema, a comparação de cenários alternativos e a quantificação do impacte de acções de intervenção. Os dados de campo e os resultados da modelação são integrados numa plataforma comum que facilite o relacionamento e o cruzamento de toda a informação. Esta metodologia permitirá assim a elaboração de uma interface de suporte à gestão/decisão do Estuário do Sado para entidades com poder de decisão sobre este ecossistema.
- Optimization of an estuarine monitoring program: selecting the best spatial distributionPublication . Caeiro, S.; Nunes, L.; Goovaerts, Pierre; Ribeiro, Luís; Painho, M.; Costa, Maria H.Monitoring estuarine programs are fundamental to evaluate the status and trends of pollution abatement actions, fulfillment of environmental quality standards and compliance with permit conditions. Their sampling designs should provide statistically unbiased estimates of the status and trends with quantitative confidence limits on both spatial and temporal scales. Variance reduction techniques have proved to be good methodologies for choosing better spatial and temporal designs. The aim of this work is to select a subset of monitoring sampling stations based on locations from an extensive estuarine sediment campaign. In this campaign 153 sites were sampled in the Sado estuary (southern Portugal). In each location three sediment parameters were determined with the objective of defining spatially homogenous environmental areas. The new monitoring program is based on fewer and on the most representative monitoring stations inside each homogeneous environmental area for their future contaminant assessment. Simulated annealing was used to iteratively improve on the mean square error of estimation, by removing one station at a time and estimating it by indicator kriging using the remaining stations in the sub-set, within a controlled non-exhaustive looping scheme. Different sub-set cardinalities were tested in order to determine the optimal cost-benefit relationship between the number of stations and monitoring costs. The model results indicate 60 station design to be optimal, but 17 additional stations with expertise criteria of proximity to point sources and characterization of all homogenous areas were added.
- Section 2: Monitoring programmes: the fundamental component of estuaries management. How to design one?Publication . Nunes, L.; Caeiro, S.; Ramos, Tomás Barros; Cunha, Maria da Conceição; Ribeiro, Luís; Costa, Maria H.This article focuses on the design of a conceptual framework to design and assess environmental estuarine monitoring programmes, including the networks, to detect quality status changes in coastal areas within environmental management programmes. Monitoring is a fundamental component in any management system, and in particular in sensitive areas under strong human pressures, like estuaries. These pressures will be reflected in impacts in the ecosystem and also in responses from it. A monitoring program including the network and the indicators measured, should be designed to be able to identify the i) pressures, ii) the state and effects, and iii) the responses of human action in the estuary according to casualty chains, also the monitoring performance should be measured to assess the effectiveness of the monitoring program itself. Answers to these needs are studied in this article, namely in what concerns the selection and location of the monitoring stations. To evaluate the “best” monitoring design one should first clearly identify the objectives of the network and which indicators (in the sense of important variables that reflect environmental attributes) are most appropriate for the particular situation. In this work two methods for monitoring network design will be evaluated, namely i) variance-reduction based, and ii) space-filling. These two are examples of a statistically-based method, and of a random-allocation-based method. The most appropriate objective functions are used to reflect the objectives of the monitoring. In all cases the objective function models are solved with the simulated annealing meta-heuristic algorithm, implemented by the team to solve monitoring optimisation problems. Due to the amount and quality of the information available, the Sado estuary is used as a case-study to demonstrate the results of the methods and helping in the comparative analysis.
- Spatial and temporal assessment of sediment contamination in Sado estuary: a methodological approachPublication . Nunes, L.; Caeiro, S.; Costa, Maria H.; Caetano, M.; Martins, Flávio Augusto Bastos da Cruz; Castro, O.; Vale, C.For better management of estuarine ecosystems their contamination assessment should be easily communicated to local managers and decision makers. The problem is the lack of available data and the search of methodologies to enable that assessment using only few data. The Sado estuary in Portugal is as good example of a site where human pressures and ecological values collide with each other and where the degree of metal and organic contamination has not been subject to an overall assessment, either in terms of spatial or temporal variability, in a way that managers can understand.