Marine fish assemblage typologies for the portuguese coast in the context of the European Marine Strategy Directives

Tese de mestrado em Ecologia e Gestão Ambiental, apresentada à Universidade de Lisboa, através da Faculdade de Ciências, 2007The 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 200 m 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 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 assessmentResumo alargado em português disponível no document

From plates to baits: using a remote video foraging system to study the impact of foraging on fouling non-indigenous species

Marinas are a gateway for the introduction and establishment of non-indigenous species (NIS). In these habitats, competition and predation are crucial determinants for NIS establishment and invasiveness. However, fish trophic preferences and biotic effects inside marinas are poorly known. This study proposes a novel method that combines the deployment of settlement plates to recruit different assemblages, followed by their use as bait in remote underwater video systems. This combined approach, addressed as a remote video foraging system (RVFS), can record fish foraging behaviour, including feeding choices and their impacts on fouling assemblage composition. An experimental RVFS trial carried out in a marina of Madeira Island, Portugal (NE Atlantic), identified the Mediterranean parrotfish, Sparisoma cretense, as the most important fouling grazer in the area. S. cretense behaved as a generalist and increased the heterogeneity of fouling assemblages, which can hamper NIS dominance of the fouling and reduce the pressure of propagules from the marina to the natural environment. The RVFS tool was useful to understand the trophic links between foragers and fouling and has the potential to provide relevant information for the management of NIS introductions, establishment and spread.info:eu-repo/semantics/publishedVersio

Citizen science and expert judgement: A cost-efficient combination to monitor and assess the invasiveness of non-indigenous fish escapees

Mapping the distribution and evaluating the impacts of marine non-indigenous species (NIS) are two fundamental tasks for management purposes, yet they are often time consuming and expensive. This case study focuses on the NIS gilthead seabream Sparus aurata escaped from offshore farms in Madeira Island in order to test an innovative, cost-efficient combined approach to risk assessment and georeferenced dispersal data collection. Species invasiveness was screened using the Aquatic Species Invasiveness Screening Kit (AS-ISK), and revealed a high invasion risk. Occurrences of S. aurata were assessed involving citizens in GIS participatory mapping and data from recreational fishing contests. A probability map showed that S. aurata is well dispersed around Madeira Island. This assessment proved to be a cost-efficient early warning method for detecting NIS dispersal, highlighting the urgent need for additional surveys that should search for sexually mature individuals and assess the direct and indirect impacts in the native ecosystemFundação para a Ciência e Tecnologia - FCTinfo:eu-repo/semantics/publishedVersio

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

Tese de doutoramento, Biologia (Biologia Marinha e Aquacultura), Universidade de Lisboa, Faculdade de Ciências, 2013The 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.O nível crescente de pressão humana sobre os ecossistemas marinhos levou a uma maior sensibilização para a necessidade de compreender a interconexão de efeitos directos e indirectos sobre comunidades e populações. Assim, na avaliação de associações de peixes marinhos, assiste-se a uma transição da monitorização do efeito da pesca em populações exploradas para a análise do efeito de várias fontes de impacto sobre comunidades. Esta tese contribui para as novas exigências metodológicas da avaliação de integridade funcional em associações de peixes marinhos, utilizando a costa portuguesa como área de estudo. O primeiro estudo pretende analisar a distribuição e caracterização das associações de peixes em recifes rochosos e áreas de substrato móvel, baseando-se apenas em dados publicados. Embora seja possível uma caracterização geral, vários aspectos negativos dessas abordagens foram identificados e demonstrados, como as lacunas de informação, a questionável comparabilidade dos dados e a falta de detalhe sobre variação a pequena escala. Os dois estudos que se seguem destinam-se a compreender a variabilidade em recifes temperados. O primeiro centra-se na quantificação da complexidade topográfica, através da proposta de um novo índice que reflecte a resposta das comunidades de peixes a características topográficas; o segundo analisa a influência dessa complexidade no poder estatístico para detectar alterações em métricas de estrutura e função, com algumas orientações sobre o esforço amostral. Os dois estudos finais propõem um quadro metodológico para a definição de tipos de associações de peixes funcionalmente homogéneos, tendo em conta a variabilidade externa. No primeiro estudo, associações de peixes de recife são classificadas em tipos que persistem face à variabilidade entre transectos, enquanto que no segundo estudo, associações de substrato móvel da plataforma continental são classificadas em áreas que conservam a sua homogeneidade face à variação inter-anual contida em 5 anos de dados de monitorização.Fundação para a Ciência e a Tecnologia (FCT, SFRH/BD/46639/2008 e projeto proPEst-OE/MAR/UI0199/2011

Effect of underwater visual survey methodology on bias and precision of fish counts: a simulation approach

Bias in underwater visual census has always been elusive. In fact, the choice of sampling method and the behavioural traits of fish are two of the most important factors affecting bias, but they are still treated separately, which leads to arbitrarily chosen sampling methods. FishCensus, a two-dimensional agent-based model with realistic fish movement, was used to simulate problematic behavioural traits in SCUBA diving visual census methods and understand how sampling methodology affects the precision and bias of counts. Using a fixed true density of 0.3 fish/m2 and a fixed visibility of 6 m, 10 counts were simulated for several combinations of parameters for transects (length, width, speed) and point counts (radius, rotation speed, time), generating trait-specific heatmaps for bias and precision. In general, point counts had higher bias and were less precise than transects. Fish attracted to divers led to the highest bias, while cryptic fish had the most accurate counts. For point counts, increasing survey time increased bias and variability, increasing radius reduced bias for most traits but increased bias in the case of fish that avoid divers. Rotation speed did not have a significant effect in general, but it increased bias for fish that avoid divers. Wider and longer transects and a faster swim speed are beneficial when sampling mobile species, but a narrower, shorter transect with a slow swim is beneficial for cryptic fish.info:eu-repo/semantics/publishedVersio

Fish behaviour effects on the accuracy and precision of underwater visual census surveys. A virtual ecologist approach using an individual-based model

Underwater visual census (UVC) methods are used worldwide to monitor shallow marine and freshwater habitats and support management and conservation decisions. However, several sources of bias still undermine the ability of these methods to accurately estimate abundances of some species. The present study introduces FishCensus, a spatially-explicit individual-based model that simulates underwater visual census of fish populations. The model features small temporal and spatial scales and uses a movement algorithm which can be shaped to reflect complex behaviours and effects of diver presence. Four different types of fish were used in the model, featuring typically problematic behavioural traits, namely schooling behaviour, cryptic habits, shyness and boldness. Corresponding control types were also modelled, lacking only the key behavioural traits. Sampling was conducted by a virtual diver using four true fish densities and employing two distinct methods: strip transects and stationary point counts. Comparisons with control fish have shown that schooling and bold behaviours induce positive bias and reduce precision, while cryptic and shy behaviours induce negative bias and increase precision, although shy behaviour did not have a significant effect on precision in transects. By looking at deviations from true density, however, schooling, shy and bold fish densities were strongly overestimated by both methods, while cryptic fish were slightly underestimated. Schooling and bold fish had the lowest precision overall, followed by shy fish. Fish rarity decreased precision, but had no effect on bias. Stationary points had less precision than transects for all fish types, and led to much higher counts, resulting in greater overestimation of density overall. By modelling complex behaviour, it was possible to separate the contributions of detectability and non-instantaneous sampling on bias, and gain a deeper understanding of the effect of behavioural traits on UVC estimates. The model can be used as a tool for planning and optimization of monitoring programs or to calculate conversion factors for past or ongoing surveys, assuming behavioural patterns are well replicated.info:eu-repo/semantics/publishedVersio

From a local observation to a European-wide phenomenon: Amphibian deformities at Serra da Estrela Natural Park, Portugal

In the last decades increasing records of morphological abnormalities in many amphibian populations have become subject of scientific interest. Once considered a mere curiosity, this worldwide phenomenon has been highlighted as a potential local conservation issue, for it appears to be yet another threat to amphibian diversity. Our study reports the first cases of amphibian deformities for North-Central Portugal, which are put in context with a review comprising European records since the 18th century. Amphibian populations (Lissotriton boscai, Triturus marmoratus and Pelophylax perezi) were sampled for four sampling years at Serra da Estrela Natural Park. With approximately 1400 post-metamorphic individuals examined, we found 12 cases of deformity including anophtalmy, brachydactyly, ectrodactyly, ectomely, polydactyly and polyphalangy. Deformity prevalence varied between years and species, rarely exceeding 2%. Our results are in accordance with European trends, since the majority of the recorded cases were found in limbs of urodeles. The presence of deformities in three different species points toward environmental causes, with predation as the most parsimonious explanation. Although not alarming, we reinforce the need for continuous monitoring of amphibian communities, from an interdisciplinary perspective, since even protected and pristine areas are not immune to new emerging threats that can act in synergy.info:eu-repo/semantics/publishedVersio

A framework for the assessment of MPA effectiveness based on life history of fishes

Changes in ecosystems structure and function due to the high impacts human pressures on oceans have led to the increasing numbers of Marine Protected Areas (MPA), since MPA are widely accepted as adequate tools to protect, maintain, and restore ocean ecosystems. Increases in density, size and biomass of organisms within protected areas have often been found. However, their worldwide effectiveness is compromised by the interaction of several factors, such as inadequate conduction of processes (e.g. due to political reasons) and the common lack of appropriate scientific datasets to support planning and management decisions. This study proposes a framework for assessing the potential effectiveness of an already implemented MPA and identifying major gaps. The framework is based on three components: species–habitat association, species' life history and functional groups and pressures affecting the MPA. The potential of the MPA to support the lifecycle of fish species was assessed in order to identify effective management actions. The theoretical framework was applied to Arrábida MPA (Portugal) in order to exemplify its practical results. Arrábida MPA showed potential to support the lifecycle of most species, although some key life phases (spawning and nursery) are not efficiently protected by the actual limits/level of protection of the MPA, namely for some of the most important fisheries’ target species. This framework is particularly useful as an alternative or a complementary support to early decisions for MPA management and the identification of priority actions needed to ensure the accomplishment of initial objectives or the suitability of their adaptation. This approach can be implemented in MPA worldwide, although the accuracy of results will be closely related with the quality of input data. The present framework can contribute to improve the effectiveness of global MPA networks and to fulfill international conservation targets, such as OSPAR, Convention for Biological Diversity and European Natura 2000 network.info:eu-repo/semantics/publishedVersio

Designing Unmanned Aerial Survey Monitoring Program to Assess Floating Litter Contamination

Monitoring marine contamination by floating litter can be particularly challenging since debris are continuously moving over a large spatial extent pushed by currents, waves, and winds. Floating litter contamination have mostly relied on opportunistic surveys from vessels, modeling and, more recently, remote sensing with spectral analysis. This study explores how a low-cost commercial unmanned aircraft system equipped with a high-resolution RGB camera can be used as an alternative to conduct floating litter surveys in coastal waters or from vessels. The study compares different processing and analytical strategies and discusses operational constraints. Collected UAS images were analyzed using three different approaches: (i) manual counting (MC), using visual inspection and image annotation with object counts as a baseline; (ii) pixel-based detection, an automated color analysis process to assess overall contamination; and (iii) machine learning (ML), automated object detection and identification using state-of-the-art convolutional neural network (CNNs). Our findings illustrate that MC still remains the most precise method for classifying different floating objects. ML still has a heterogeneous performance in correctly identifying different classes of floating litter; however, it demonstrates promising results in detecting floating items, which can be leveraged to scale up monitoring efforts and be used in automated analysis of large sets of imagery to assess relative floating litter contamination