MSc Thesis*

"Marine fish assemblage typologies for the Portuguese coast in the context of the European Marine Strategy Directive"



The proposed European Marine Strategy Directive (MSD) enforces the need for protection and conservation of the marine environment, having as the main objective the achievement of ‘good environmental status’ of the marine waters under jurisdiction of the Member States by 2021. In the MSD, fish are included as a biological element, thus constituting a new requirement for the assessment of marine waters that needs to be evaluated on the initial assessment to be presented by the fourth year after entry into force. These requirements urge the definition of marine fish assemblage typologies in order to permit the establishment of type-specific reference values that characterise a ‘good’ marine fish assemblage.
With the aim of establishing and characterising marine fish assemblages for the Portuguese continental shelf, from intertidal areas down to the 200m isobath, a large variety of available data from studies conducted in Portuguese waters was collected and species were assigned into ecological guilds of several categories. Using guild and species data independently, a detrended correspondence analysis identified depth and bottom type as the factors underlying the main distribution gradient and led to the establishment of six assemblage typologies.
A non-metric analysis of similarities (ANOSIM) tested the consistency of the defined typologies and a similarity percentage analysis (SIMPER) routine identified the species and guilds that characterise each typology. Furthermore, the effects of latitude and seasonality were tested using ANOSIM and SIMPER within each typology, revealing that the first mainly affects soft substrate assemblages 20 to 100 m deep and the latter is noticed only on deeper assemblages, within the same substrate.

The established typologies revealed distinct structural and functional characteristics, thus requiring the establishment of different reference values for quality assessment.

PhD Thesis

"Dealing with uncertainty and heterogeneity in the assessment of structural and functional integrity in marine fish assemblages"



The increasing level of human pressure on marine ecosystems has led to higher awareness towards the need to understasnd the inter-connection of direct and indirect effects on communities and populations. Therefore, in the assessment of marine fish assemblages, there is an ongoing shift from monitoring the effect of fishing in exploited populations to analysing the effect of several impact sources on communities.

This thesis contributes to the new methodological requirements of functional integrity assessments in marine fish assemblages, using the Portuguese coast as a study area. The first study attempts to analyse the distribution and characterisation of fish assemblages in rocky reefs and soft substrate areas by relying only on published data. Although a rough characterisation is achieved, several negative aspects of these approaches were pinpointed and demostrated, namely information gaps, questionable data comparability and the lack of detail on fine-scale variation. The two studies that follow are aimed at understanding variability in temperate reefs. The first one focuses on quantifying topographic complexity, through the proposal of a new index that reflects the response of fish communities to topographic features, and the second one analyses the influence of this complexity on the power to detect changes in structural and functional fish-based metrics, with some guidelines regarding sampling efforts. The two final studies propose a framework for the definition of functionally homogeneous fish assemblage types, while taking into account background variability. In the first study, reef fish assemblages are classified into types that persist in the face of fine-scale among-transect variability, while in the second study, soft substrate fish assemblages of the continental shelf are classified into areas that retain their homogeneity in the face of inter-annual variation, as described by 5 years of monitoring data.

* 5 years later I would publish a paper using a very similar analysis, but pinpointing the problems of relying only on published data to define management units for environmental quality assessment. I suggest reading that paper instead of my MSc thesis, since it better reflects my current views on this subject.