Assessment of the “health” of an ecosystem is often of great interest to those interested in monitoring and conservation of ecosystems. Traditionally, scientists have quantified the health of an ecosystem using multimetric indices that are semi-qualitative. Recently, a statistical-based index called the Latent Health Factor Index (LHFI) was devised to address many inadequacies of the conventional indices. Relying on standard modelling procedures, unlike the conventional indices, accords the LHFI many advantages: the LHFI is less arbitrary, and it allows for straightforward model inference and for formal statistical prediction of health for a new site (using only supplementary environmental covariates). In contrast, with conventional indices, formal statistical prediction does not exist, meaning that proper estimation of health for a new site requires benthic data which are expensive and time-consuming to gather. As the LHFI modelling methodology is a relatively new concept, it has so far only been demonstrated (and validated) on freshwater ecosystems. The goal of this thesis is to apply the LHFI modelling methodology to estuarine ecosystems, particularly to the previously unassessed system in Richibucto, New Brunswick. Specifically, the aims of this thesis are threefold: firstly, to investigate whether the LHFI is even applicable to estuarine systems since estuarine and freshwater metrics, or indicators of health, are quite different; secondly, to determine the appropriate form that the LHFI model if the technique is applicable; and thirdly, to assess the health of the Richibucto system. Note that the second objective includes determining which covariates may have a significant impact on estuarine health. As scientists have previously used the AZTI Marine Biotic Index (AMBI) and the Infaunal Trophic Index (ITI) as measurements of estuarine ecosystem health, this thesis investigates LHFI models using metrics from these two indices simultaneously. Two sets of models were considered in a Bayesian framework and implemented using Markov chain Monte Carlo techniques, the first using only metrics from AMBI, and the second using metrics from both AMBI and ITI. Both sets of LHFI models were successful in that they were able to make distinctions between health levels at different sites.

Assessment of the “health” of an ecosystem is often of great interest to those interested in monitoring and conservation of ecosystems. Traditionally, scientists have quantified the health of an ecosystem using multimetric indices that are semi-qualitative. Recently, a statistical-based index called the Latent Health Factor Index (LHFI) was devised to address many inadequacies of the conventional indices. Relying on standard modelling procedures, unlike the conventional indices, accords the LHFI many advantages: the LHFI is less arbitrary, and it allows for straightforward model inference and for formal statistical prediction of health for a new site (using only supplementary environmental covariates). In contrast, with conventional indices, formal statistical prediction does not exist, meaning that proper estimation of health for a new site requires benthic data which are expensive and time-consuming to gather. As the LHFI modelling methodology is a relatively new concept, it has so far only been demonstrated (and validated) on freshwater ecosystems. The goal of this thesis is to apply the LHFI modelling methodology to estuarine ecosystems, particularly to the previously unassessed system in Richibucto, New Brunswick. Specifically, the aims of this thesis are threefold: firstly, to investigate whether the LHFI is even applicable to estuarine systems since estuarine and freshwater metrics, or indicators of health, are quite different; secondly, to determine the appropriate form that the LHFI model if the technique is applicable; and thirdly, to assess the health of the Richibucto system. Note that the second objective includes determining which covariates may have a significant impact on estuarine health. As scientists have previously used the AZTI Marine Biotic Index (AMBI) and the Infaunal Trophic Index (ITI) as measurements of estuarine ecosystem health, this thesis investigates LHFI models using metrics from these two indices simultaneously. Two sets of models were considered in a Bayesian framework and implemented using Markov chain Monte Carlo techniques, the first using only metrics from AMBI, and the second using metrics from both AMBI and ITI. Both sets of LHFI models were successful in that they were able to make distinctions between health levels at different sites.

Depuis de nombreuses années, les évaluations de la faune circulante au sein de l’estuaire de la Gironde s’appuient sur plusieurs dispositifs de suivis ichtyologiques, chroniques de pêches scientifiques et professionnelles. Cependant, ces approches conventionnelles nécessitent souvent un échantillonnage conséquent, restent ponctuelles dans le temps, spatialement limitées et destructrices. Tester la mise en œuvre d’un suivi acoustique prend ainsi toute son sens et son intérêt. Plus largement appliqué en milieux marin et lacustre, cette approche reste encore rarement utilisée en estuaires. En raison de l’extrême variabilité intrinsèque de ce type d’écosystème, la mise en œuvre de cet outil est un réel défi. En s’appuyant sur la connaissance préalablement acquise, une réflexion méthodologique approfondie a été menée pour définir des stratégies d’échantillonnage acoustiques afin d’optimiser la récolte de ce type de données. Plusieurs stratégies acoustiques ont d’abord été testées en tenant compte de la complexité et de la taille importante de l’écosystème étudié. La pertinence de ces données recueillies a ensuite été confrontée aux données des pêches scientifiques. Enfin, l’hydroacoustique a été mis à profit pour répondre à des questions sur la dynamique ichtyologique à des échelles spatiales et temporelles plus fines notamment pour étudier les influences tidales et nycthémérales. Ce travail démontre qu’il est possible de mettre en place un suivi acoustique des peuplements ichtyologiques pour un estuaire comme la Gironde. Comme outil complémentaire aux approches traditionnelles, l’hydroacoustique ouvre un large champ de possibilités pour appréhender la biocénose piscicole pour les milieux estuariens. / For many years, assessments of fish densities within the Gironde estuary have been based on a number of different fish monitoring techniques, as well as professional and scientific surveys. However, these approaches are often destructive. They require substantial sampling, and are limited from the points of view of both time and space. With this in mind, the benefits of non-invasive acoustic monitoring are clear. While such methods are often used in lakes and other marine environments, they have yet to be widely applied to shallow-water areas, in particular estuaries. Applying an acoustic approach to this kind of intrinsically changeable environment represents a real challenge. In this research project, an in-depth methodological study was carried out to determine the optimum way of applying acoustic sampling. Several acoustic monitoring strategies were then tested, keeping in mind the size and complexity of the ecosystem under investigation. The results of these tests were then checked for relevance against data from scientific fisheries. Finally, hydroacoustics was used to examine fish dynamics at finer spatial and temporal scales, notably in the study of diurnal and tidal influences. The results of this study show that it is possible to use acoustic monitoring to complement traditional methods of estimating fish populations in estuarine areas, and that the use of such a combination opens up a broad range of new possibilities.

Η οικολογία και η δυναμική της εγκατάστασης εξετάστηκαν για τέσσερα μεσογειακά παράκτια είδη: Diplodus vulgaris, Diplodus sargus, Oblada melanura και Diplodus annularis. Η διερεύνηση τους έγινε με υποδιαίρεση της βενθικής ιχθυονυμφικής τους φάσης σε έξι οντογενετικά στάδια βάσει χρωματικών πρότυπων που εμφάνιζαν διαδοχή και ήταν χαρακτηριστικά για κάθε είδος. Η συλλογή δεδομένων έγινε για κάθε οντογενετικό στάδιο με στρωματοποιημένη δειγματοληψία, με τις στρώσεις να αποτελούν συνδυασμό τύπου υποστρώματος και βάθους στην παράκτια περιοχή ανατολικά των εκβολών του Αχελώου, από βάθος 0 έως 5m. Τα δεδομένα συλλέχθηκαν με απ’ ευθείας παρατηρήσεις με χρήση καταδυτικής συσκευής. Υπολογίστηκαν οι πυκνότητες κάθε οντογενετικού σταδίου στους διάφορους τύπους υποστρώματος και βάθη μέσα στο έτος. Η κατανομή των πυκνοτήτων αυτών έδωσε στοιχεία για τις οικολογικές προτιμήσεις των βενθικών ιχθυονυμφών και των νεαρών, καθώς και για τους ρυθμούς μεταμόρφωσης κάθε είδους. Επίσης ελέγχθηκε το πρότυπο συμπεριφοράς των ιχθυονυμφών του μελανουριού κατά την εγκατάσταση τους, μ’ επινόηση ειδικής μεθοδολογίας κι ενός δείκτη που απέδωσε ποσοτικά τις διάφορες εκφάνσεις της συμπεριφοράς. Σύμφωνα με τ’ αποτελέσματα της εργασίας, φάνηκε ότι ο σαργόπαπας και ο σαργός εγκαθίστανται την κρύα περίοδο του έτους, ενώ το μελανούρι και ο σπάρος τη θερμή. Όλα τα είδη εμφάνισαν γρηγορότερο ρυθμό μεταμόρφωσης κατά τα πρώτα στάδια, ενώ τα είδη που εγκαταστάθηκαν το καλοκαίρι είχαν συνολικά γρηγορότερους ρυθμούς μεταμόρφωσης από τα χειμερινά. Τα είδη εμφάνισαν διαφοροποίηση στη χρονική και χωρική κατανομή τους ώστε να ελαττώνονται οι ανταγωνιστικές δράσεις. Το είδος με τη μακρύτερη χρονική παρουσία ήταν ο σαργόπαπας (10 μήνες), ο οποίος εμφάνισε ευρύτητα ως προς τις οικολογικές του απαιτήσεις διασπειρόμενος σ’ όλο το εύρος βάθους και τύπους υποστρώματος, εκτός του αμμώδους. Στον αντίποδα, το μελανούρι είχε τη μικρότερη συνολική παρουσία (4 μήνες) και απόλυτη εξάρτηση από σκληρό υπόστρωμα. Ο σαργός κι ο σπάρος έδειξαν ενδιάμεσες οικολογικές απαιτήσεις με προτίμηση στα σκληρά υποστρώματα και στα φανερόγαμα αντίστοιχα. Κανένα είδος δεν έδειξε προτίμηση σε αμμώδεις βυθούς. Ιδιαίτερο οικολογικό ρόλο εμφάνισε το ρηχότερο τμήμα της παράκτιας ζώνης και οι μεταβατικές ζώνες διαφορετικών υποστρωμάτων. Οι βενθικές ιχθυονύμφες του μελανουριού επέδειξαν τάση παραμονής για μέρες με μικρές ομάδες σε σημεία του υποστρώματος. Στα επόμενα στάδια σχημάτισαν μεγάλες ομάδες με μικρότερη εξάρτηση από το υπόστρωμα. / The ecology and dynamics of settlement process were studied for four sparids (Diplodus vulgaris, D. sargus. D. annularis and Oblada melanura), in a coastal littoral in western Hellas. The benthic larval phase of each species was divided in six ontogenetic stages, according to specific patterns in appearance that followed a sequence. Preliminary observations showed non homogeneous distribution of the larvae in the area, so stratified sampling was applied. Strata represented the different substratum types accounted in each of the three depth zones of 0-1m, 1-2m and 2-5m. Data concerned abundances of each ontogenetic stage in each stratum during a 15 month interval and they were collected by visual census. Moreover, data on site-attachment ontogenetically depended behavior of benthic larvae of O. melanura were also collected. The later behavior was studied via an index devised for quantifying different expressions of residence behavior. Two of the studied species (D. vulgaris and D. sargus), settled during the cold period of the year while the other two settled during summer. Metamorphosis rates were faster at the first ontogenetic stages for all species, while they were faster in total for the summer species. Temporal and spatial distribution of the species was arranged in order to minimize competition. D. vulgaris and D. sargus settled in the same substratum types in different periods and O. melanura and D. annularis settled during the same period in different substrata. D. vulgaris remained in the nursery area the longest period, exhibiting the broadest ecological requirements, being distributed in different substrata and depths. O. melanura remained half as long in the nursery area, exhibiting the narrowest ecological requirements, staying always over hard substratum in shallow waters. The other two species exhibited intermediate conditions, with D. sargus preferring hard substratum and D. annularis, seagrass beds. None of the studied species preferred soft substratum. The shallowest part of the littoral appeared to be very important for three species (D. vulgaris, D. sargus, O. melanura) and the transition zones (between two different substrata), for all four of them. Benthic larvae of Oblada melanura commenced settlement in small shoals that resided for varying number of days in specific sites over stones or rocky substratum. Gradually as metamorphosis proceeded they became more kinetic forming larger shoals that expanded their home range.