• Monitoring and surveys of marine biodiversity in Portuguese waters
This information is crucial to identify impacts of phenomena as diverse as global warming, overexploitation of resources and degradation of habitats. For historical reasons, we have collected medium-term data series on the ecology of intertidal and subtidal rocky shore fish, that in some cases extend for more than ten years. We are engaged in the implementation of a national network on marine biodiversity, with colleagues of CIMAR and CESAM. This project is now being extended to the Azores’ University, through its department of oceanography and fisheries. The network aims to achieve the testing and implementation of simple repeatable protocols that can be applied on the entire Portuguese shore. The information resulting from the program of regular surveys will be integrated in a data base, which will also include meteorological and oceanographic information. To achieve these goals, the network on marine biodiversity will also have a strong molecular genetics component. Our aims are to identify distinct stocks and evolutionary significant Units, to access effective population sizes and to evaluate the connectivity among populations for species with different behaviour and life history.

• Biogeography of the Northeastern Atlantic and Mediterranean
A medium term aim of the Unit is to compile a data base as comprehensive as possible, including both distribution and phylogeographic information on inshore fishes of the northeastern Atlantic and Mediterranean. The aim is to identify the glacial refugia and the colonization routes that established the present day ichthyofauna of Europe and Atlantic Islands.

• Freshwater fish biogeography in the Iberian Peninsula
Another medium term program involves the use of primary freshwater fish as models together with geological information, to study the paleobiogeographic history of Iberian freshwaters.
freshwater fish are excellent models to study problems of biogeography and phylogeography, due to their confinement to specific drainages. In cooperation with colleagues of other institutions, namely the Museu Nacional de Ciencias Naturales de Madrid, we are investigating a number of phylogenetic and phylogeographical problems of the Iberian freshwater fish fauna. This cooperation between Portuguese and Spanish colleagues is considered essential because many freshwater fish species are endemic in the two countries. In this area, hybridization is a critical issue because it plays an important role in the evolution of fishes. Because of this, work linking behaviour and mate selection in situations in which hybridizing species co-occur, is one of our current interests. Most fresh water fishes in the Iberian Peninsula are seriously threatened. We are aware that one of our main efforts in the near future must be dedicated to applying the knowledge on the behaviour of fishes in programs directed to their conservation.

• Larval biology of inshore fish
This study aims to study the planktonic phase of inshore fish, and the role of larval behaviour in controlling larval distribution and recruitments.

• Ex-situ reproduction of critically endangered freshwater fish
We are involved in a multi-institution scheme to preserve and developing mass culture of critically endangered freshwater fish, while habitats are not yet restored.

• Fish bioacoustics
The role of sounds in fish behaviour, including territoriality, agonistic interactions and species specific recognition and courtship, are moving from the mainly descriptive phase of the previous triennium, to strongly experimental investigation based on play-back of specific sounds.

• Genetic and physiological control of alternative life histories in lampreys
As very closed related species of lamprey can show strikingly different life histories (parasitic migratory adult versus non feeding short living adults), the two ontogenetic pathways will be investigate, both genetically and by experimental manipulation of the factors that control metamorphosis and sexual maturation.

• Ecology of Sea birds
The movement and activities of sea-birds will be studied with geolocators data loggers to record temperature, light and pressure.

• Monitoring and research on the population of resident bottlenose dolphins in
the Sado estuary
This includes the study of its social and demographic structure, of its genetic structure and relations (Project DolphTox, submitted to FCT), of the contaminant loads in the dolphins, their prey and their environment (Project DolphTox, submitted to FCT), of dolphin movements using remote acoustic detection devices (T-PODs) and GIS, of dolphin feeding hotspots and core areas using a ROV.