Phytoplankton and microbial plankton of the Bay of Biscay and Western Iberian Shelf

The region of the Northeast Atlantic represents a gradient between two oceanographic regimes: (i) the subtropical waters of southern Portugal and southwestern Spain, and (ii) the temperate waters characterizing the northwestern and northern Iberian coasts (Cantabrian Sea) and the rest of the Bay of Biscay along the French coast.

Thesis abstract. Applying species distribution modeling for the conservation of Iberian protected invertebrates

This article outlines the approaches to modeling the distribution of threatened invertebrates using data from atlases, museums and databases. Species Distribution Models (SDMs) are useful for estimating species’ ranges, identifying suitable habitats, and identifying the primary factors affecting species’ distributions. The study tackles the strategies used to obtain SDMs without reliable absence data while exploring their applications for conservation. I examine the conservation status of Copris species and Graellsia isabelae by delimiting their populations and exploring the effectiveness of protected areas. I show that the method of pseudo‐absence selection strongly determines the model obtained, generating different model predictions along the gradient between potential and realized distributions. After assessing the effects of species’ traits and data characteristics on accuracy, I found that species are modeled more accurately when sample sizes are larger, no matter the technique used.

Ecological niche modeling, cytogenetics and phylogeography of the genera Geomalacus and Letourneuxia (Gastropoda, Pulmonata) from the Iberian-Moroccan region

First described more that 150 years ago, the systematics of the genera Geomalacus and Letourneuxia (Arionidae, Gastropoda, Pulmonata) is still challenging. The taxonomic classification of arionid species is based on extremely labile characters such as body size or color that depends both on diet and environment, as well as age. Moreover, there is little information on the genetic diversity and population structure of the Iberian slugs that could provide extra clues to disentangle their problematic classification. The present work uses different analytical tools such as habitat suitability (Ecological Niche Modeling - ENM), cytogenetic analysis and phylogeography to establish the geographical distribution and evolutionary history of these pulmonate slugs. The potential distribution of the four Geomalacus species was modeled using ENM, which allowed the identification of new locations for G. malagensis, including a first report in Portugal. Also, it was predicted a much wider distribution for G. malagensis and G. oliveirae than previously known. Classical cytogenetic analyses were assayed with reproductive and a novel use of somatic tissues (mouth and tentacles) returning the number of chromosomes for the four Geomalacus species and L. numidica (n = 31, 2n = 62) and the respective karyotypes. G. malagensis and L. numidica present similar chromosome morphologies and karyotypic formulae, being more similar to each other than the Geomalacus among themselves. We further reconstructed the phylogeny of the genera Geomalacus and Letourneuxia using partial sequences of the mitochondrial cytochrome oxidase subunit I (COI) and the nuclear ribosomal small subunit (18S rRNA), and applied an independent evolutionary rate method, the indicator vectors correlation, to evaluate the existence of cryptic diversity within species. The five nominal species of Geomalacus and Letourneuxia comprise 14 well-supported cryptic lineages. Letourneuxia numidica was retrieved as a sister group of G. malagensis. G. oliveirae is paraphyletic with respect to G. anguiformis. According to our dating estimates, the most recent common ancestor of Geomalacus dates back to the Middle Miocene (end of the Serravallian stage). The major lineage splitting events within Geomalacus occurred during the dry periods of the Zanclean stage (5.3-3.6 million years) and some lineages were confined to more humid mountain areas of the Iberian Peninsula, which lead to a highly geographically structured mitochondrial genetic diversity. The major findings of this are the following: (1) provides updated species distribution maps for the Iberian Geomalacus expanding the known geographic distribution of the concerned species, (2) unravels the cryptic diversity within the genera Geomalacus and Letourneuxia, (3) Geomalacus oliveirae is paraphyletic with G. anguiformis and (4) Letourneuxia numidica is sister group of G. malagensis.

Ecology of west Iberian kelps: Laminaria ochroleuca and Saccorhiza polyschides living near their distributional limits

Tese de Doutoramento, Ecologia (Ecologia das Populações), Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015

Length-weight relationships of six syngnathid species from Ria Formosa, SW Iberian coast

In this study, the length-weight (LWR) parameters were estimated for six syngnathid species, including 2 seahorses and 4 pipefishes, from Ria Formosa, a temperate lagoon from the south coast of Portugal. A total of 5070 fishes were used to determine the LWR. The estimated b value ranged from 2.95 (Nerophis ophidion) to 3.36 (Syngnathus abaster). To the authors' best knowledge, LWR parameters were estimated for the first time for Nerophis ophidion and Syngnathus typhle for the Atlantic waters. Data here present are essential for management and conservation of these flagship species.

EUNIS habitat's thresholds for the Western coast of the Iberian Peninsula — A Portuguese case study

The European Nature Information System (EUNIS) has been implemented for the establishment of a marine European habitats inventory. Its hierarchical classification is defined and relies on environmental variables which primarily constrain biological communities (e.g. substrate types, sea energy level, depth and light penetration). The EUNIS habitat classification scheme relies on thresholds (e.g. fraction of light and energy) which are based on expert judgment or on the empirical analysis of the above environmental data. The present paper proposes to establish and validate an appropriate threshold for energy classes (high, moderate and low) and for subtidal biological zonation (infralittoral and circalittoral) suitable for EUNIS habitat classification of the Western Iberian coast. Kineticwave-induced energy and the fraction of photosynthetically available light exerted on the marine bottom were respectively assigned to the presence of kelp (Saccorhiza polyschides, Laminaria hyperborea and Laminaria ochroleuca) and seaweed species in general. Both data were statistically described, ordered fromthe largest to the smallest and percentile analyseswere independently performed. The threshold between infralittoral and circalittoral was based on the first quartile while the ‘moderate energy’ class was established between the 12.5 and 87.5 percentiles. To avoid data dependence on sampling locations and assess the confidence interval a bootstrap technique was applied. According to this analysis,more than 75% of seaweeds are present at locations where more than 3.65% of the surface light reaches the sea bottom. The range of energy levels estimated using S. polyschides data, indicate that on the IberianWest coast the ‘moderate energy’ areas are between 0.00303 and 0.04385 N/m2 of wave-induced energy. The lack of agreement between different studies in different regions of Europe suggests the need for more standardization in the future. However, the obtained thresholds in the present study will be very useful in the near future to implement and establish the Iberian EUNIS habitats inventory.

Multi-scale cortical keypoint representation for attention and object detection

Keypoints (junctions) provide important information for focus-of-attention (FoA) and object categorization/recognition. In this paper we analyze the multi-scale keypoint representation, obtained by applying a linear and quasi-continuous scaling to an optimized model of cortical end-stopped cells, in order to study its importance and possibilities for developing a visual, cortical architecture.We show that keypoints, especially those which are stable over larger scale intervals, can provide a hierarchically structured saliency map for FoA and object recognition. In addition, the application of non-classical receptive field inhibition to keypoint detection allows to distinguish contour keypoints from texture (surface) keypoints.

Design of laminated structures using piezoelectric materials

Composite structures incorporating piezoelectric sensors and actuators are increasingly becoming important due to the offer of potential benefits in a wide range of engineering applications such as vibration and noise supression, shape control and precisition positioning. This paper presents a finit element formulation based on classical laminated plate theory for laminated structures with integrated piezoelectric layers or patches, acting as actuators. The finite element model is a single layer triangular nonconforming plate/shell element with 18 degrees of freedom for the generalized displacements, and one electrical potential degree of freedom for each piezsoelectric elementlayer or patch, witch are surface bonded on the laminate. An optimization of the patches position is performed to maximize the piezoelectric actuators efficiency as well as, the electric potential distribuition is search to reach the specified structure transverse displacement distribuition (shape control). A gradient based algorithm is used for this purpose. The model is applied in the optimization of illustrative laminated plate cases, and the results are presented and discussed.

Finit element model for active control of adaptive laminated structures

A finite element formulation for active vibration control of thin plate laminated structures with integrated piezoelectric layers, acting as sensors and actuators in presented. The finite element model is a nonconforming single layer triangular plate/shell element with 18 degrees of freedom for the generalized displacements and one electrical potential degree of freedom for each piezoelectric element layer, and is based on the kirchhoff classical laminated theory. To achieve a mechanism of active control of the structure dynamic response, a feedback control algorithm is used, coupling the sensor and active piezoelectric layers, and Newmark method is used to calculate yhe dynamic response of the laminated structures. The model is applied in the solution of several illustrative cases, and the results are presented and discussed.

Invariant multi-scale object categorisation and recognition

Object recognition requires that templates with canonical views are stored in memory. Such templates must somehow be normalised. In this paper we present a novel method for obtaining 2D translation, rotation and size invariance. Cortical simple, complex and end-stopped cells provide multi-scale maps of lines, edges and keypoints. These maps are combined such that objects are characterised. Dynamic routing in neighbouring neural layers allows feature maps of input objects and stored templates to converge. We illustrate the construction of group templates and the invariance method for object categorisation and recognition in the context of a cortical architecture, which can be applied in computer vision.

Geographic variation in sardine population traits: implications for stock assessment

Tese dout., Ciências e Tecnologias das Pescas, Universidade do Algarve, 2007

Análise estrutural/comportamental da população de cágado mediterrânico, Mauremys leprosa, na ribeira temporária da Asseca

Dissertação de Mestrado, Biologia Marinha, Especialização em Ecologia e Conservação Marinha, Faculdade de Ciências do Mar e Ambiente, Universidade do Algarve, 2009

Biogeography of the fire salamander (Salamandra salamandra, L.) in Portugal

Dissertação de mest., Biologia Marinha, Faculdade de Ciências do Mar e do Ambiente, Universidade do Algarve, 2008

Microplankton composition, production and upwelling dynamics in Sagres (SW Portugal) during summer 2001

Microplankton community, production, and respiration were studied alongside physical and chemical conditions at Sagres (SW Portugal) during the upwelling season, from May to September 2001. The sampling station was 5 km east of the upwelling center off Cabo S. Vicente, and 2 km of an offshore installation for bivalve aquaculture.

Chromatographic analysis and comparison of chemical composition of the samples between olive oils in Europe and some chinese oils

Dissertação de mest., Qualidade em Análises, Faculdade de Ciências e Tecnologia, Univ. do Algarve, 2013