Dissertations / Theses on the topic 'Fish habitat assessment'

In recent times, habitat models at the meso-scale are becoming increasingly accepted techniques to quantify the impact of hydro-morphological pressures on rivers, to help guide water resource planning through the design of environmental flows, or renaturalization of rivers through restoration. Despite their potential, broader applicability of meso-scale habitat models is limited by the difficulty to conduct field-based mesohabitat mapping in large streams or at high flows, at which wadeability decreases. Furthermore, construction of reliable habitat-streamflow rating curves can be a highly time consuming process, as it requires mapping over a wide range of streamflow values. An important gap in the use of habitat models for ecological river management is also represented by the poor understanding of biological communities' response to habitat improvement. The present PhD thesis aims to address some of these fundamental gaps in habitat modeling and its links with biological communities' response through an integrative set of different modeling tools. The scene is set by a non specialist preface (Chapter 1), followed by a detailed analysis of the scientific state-of-art that highlights the fundamental research questions of the thesis (Chapter 2). Chapter 3 and 4 address some of the key challenges in the integration of 2D hydraulic modeling and habitat modeling at the meso-scale, namely the reproduction of an accurate description of the meso-scale distributions of water depth and velocities in gravel bed-rivers, and the spatial mapping of hydro-morphological units (HMUs). Two study cases were selected in the North-East Italian alpine region, in the province of South Tyrol, which were chosen for their contrasting characteristics, in terms of channel size, hydro-morphology and river type. The study reach in the Mareta River was recently restored to a braided morphology, while in the Aurino reach a meander bend was restored to improve fish habitats. In Chapter 3, three different commonly used approaches were compared in terms of their ability to accurately describe the meso-scale hydraulics of a river reach of the Mareta River, and of their effects on the description of meso-habitat suitabilities for two fish species, the marble trout (Salmo marmoratus) and the European bullhead (Cottus gobio). Two approaches were based on 2D hydraulic modeling, which were constructed on computational meshes with varying resolution and quality: (1) high resolution meshes derived from topographical data obtained from Airborne LiDAR Bathymetry; and (2) a mesh extrapolated from topographical cross-sectional profiles. The third approach used for the comparison was based on in-stream surveys. Results from the comparison suggest that decreasing resolutions and mesh quality negatively affects the accuracy of the results, with the largest residual differences found for the cross-sectional based modeling and the surveys. Amongst the analyzed HMU types, the highest sensitivities to the choice of approach were recorded for backwaters, followed by morphologically complex units such as pools, steps and rapids. The least sensitive units were riffles and glides. While similar effects were also observed for the estimated habitat suitabilities, errors in suitability estimates were minimized when deriving habitat-streamflow rating curves at the reach scale. In Chapter 4, a novel approach for the delineation of habitats at the meso-scale, based on the outputs of two-dimensional hydraulic modeling was developed. The approach uses a four-step strategy: 1) hydraulic data at the micro-scale is classified into groups by means of an unsupervised clustering algorithm (k-means); 2) homogeneous flow patches are identified and polygonized in the channel; 3) a region growing process ensures that all hydraulic patches reach a scale that is equivalent to the river meso-scale; and 4) an optimal segmentation is selected by minimizing a Global Score. Applications of the model were tested on the two case studies of the Mareta and Aurino rivers, and habitat suitability was assessed for three fish species: marble trout; grayling (Thymallus thymallus); European bullhead. A high level of agreement was found when comparing model- and survey-based habitat suitability estimates. Compared to existing approaches, the developed methodology is unsupervised, and does not require a river- and site-specific calibration. While habitat models are largely used in the context of river rehabilitation, in recent times the assumption that optimizing habitat quality and quantity also improves ecological health of rivers has been questioned. A need for predictive process-based modeling has been recognized, which is able to quantitatively assess how spatial and temporal habitat dynamics affects ecologically relevant measures, such as recruitment and population potential. Within this context, a tool in the form of an age-structured population model was developed (Chapter 5), that is based on the quantification of the suitable habitat area in a river reach, and can be used for the assessment and comparison of river restoration scenarios. The model uses a Bayesian approach, which was parameterized for the common Barbel (Barbus barbus), a cyprinid litophilic fish, and was used to study the effects of habitat limitations on the population dynamics. By testing various scenarios of habitat availabilities for the common Barbel, it was hypothesized that improvements in the fish stock can be reached only when a well specified ratio of spawning habitat to fry habitat exists, and even substantial improvements of only either spawning or juvenile habitats will result in little or no increase of abundance. A synthesis of the key findings of the thesis is finally presented in Chapter 6, together with their broader ecohydraulic and management implications.

In recent times, habitat models at the meso-scale are becoming increasingly accepted techniques to quantify the impact of hydro-morphological pressures on rivers, to help guide water resource planning through the design of environmental flows, or renaturalization of rivers through restoration. Despite their potential, broader applicability of meso-scale habitat models is limited by the difficulty to conduct field-based mesohabitat mapping in large streams or at high flows, at which wadeability decreases. Furthermore, construction of reliable habitat-streamflow rating curves can be a highly time consuming process, as it requires mapping over a wide range of streamflow values. An important gap in the use of habitat models for ecological river management is also represented by the poor understanding of biological communities' response to habitat improvement. The present PhD thesis aims to address some of these fundamental gaps in habitat modeling and its links with biological communities' response through an integrative set of different modeling tools. The scene is set by a non specialist preface (Chapter 1), followed by a detailed analysis of the scientific state-of-art that highlights the fundamental research questions of the thesis (Chapter 2). Chapter 3 and 4 address some of the key challenges in the integration of 2D hydraulic modeling and habitat modeling at the meso-scale, namely the reproduction of an accurate description of the meso-scale distributions of water depth and velocities in gravel bed-rivers, and the spatial mapping of hydro-morphological units (HMUs). Two study cases were selected in the North-East Italian alpine region, in the province of South Tyrol, which were chosen for their contrasting characteristics, in terms of channel size, hydro-morphology and river type. The study reach in the Mareta River was recently restored to a braided morphology, while in the Aurino reach a meander bend was restored to improve fish habitats. In Chapter 3, three different commonly used approaches were compared in terms of their ability to accurately describe the meso-scale hydraulics of a river reach of the Mareta River, and of their effects on the description of meso-habitat suitabilities for two fish species, the marble trout (Salmo marmoratus) and the European bullhead (Cottus gobio). Two approaches were based on 2D hydraulic modeling, which were constructed on computational meshes with varying resolution and quality: (1) high resolution meshes derived from topographical data obtained from Airborne LiDAR Bathymetry; and (2) a mesh extrapolated from topographical cross-sectional profiles. The third approach used for the comparison was based on in-stream surveys. Results from the comparison suggest that decreasing resolutions and mesh quality negatively affects the accuracy of the results, with the largest residual differences found for the cross-sectional based modeling and the surveys. Amongst the analyzed HMU types, the highest sensitivities to the choice of approach were recorded for backwaters, followed by morphologically complex units such as pools, steps and rapids. The least sensitive units were riffles and glides. While similar effects were also observed for the estimated habitat suitabilities, errors in suitability estimates were minimized when deriving habitat-streamflow rating curves at the reach scale. In Chapter 4, a novel approach for the delineation of habitats at the meso-scale, based on the outputs of two-dimensional hydraulic modeling was developed. The approach uses a four-step strategy: 1) hydraulic data at the micro-scale is classified into groups by means of an unsupervised clustering algorithm (k-means); 2) homogeneous flow patches are identified and polygonized in the channel; 3) a region growing process ensures that all hydraulic patches reach a scale that is equivalent to the river meso-scale; and 4) an optimal segmentation is selected by minimizing a Global Score. Applications of the model were tested on the two case studies of the Mareta and Aurino rivers, and habitat suitability was assessed for three fish species: marble trout; grayling (Thymallus thymallus); European bullhead. A high level of agreement was found when comparing model- and survey-based habitat suitability estimates. Compared to existing approaches, the developed methodology is unsupervised, and does not require a river- and site-specific calibration. While habitat models are largely used in the context of river rehabilitation, in recent times the assumption that optimizing habitat quality and quantity also improves ecological health of rivers has been questioned. A need for predictive process-based modeling has been recognized, which is able to quantitatively assess how spatial and temporal habitat dynamics affects ecologically relevant measures, such as recruitment and population potential. Within this context, a tool in the form of an age-structured population model was developed (Chapter 5), that is based on the quantification of the suitable habitat area in a river reach, and can be used for the assessment and comparison of river restoration scenarios. The model uses a Bayesian approach, which was parameterized for the common Barbel (Barbus barbus), a cyprinid litophilic fish, and was used to study the effects of habitat limitations on the population dynamics. By testing various scenarios of habitat availabilities for the common Barbel, it was hypothesized that improvements in the fish stock can be reached only when a well specified ratio of spawning habitat to fry habitat exists, and even substantial improvements of only either spawning or juvenile habitats will result in little or no increase of abundance. A synthesis of the key findings of the thesis is finally presented in Chapter 6, together with their broader ecohydraulic and management implications.

Many aspects concerning the association of riverine fish with in-channel habitat remain poorly understood, greatly hindering the ability of researchers and managers to address declines in fish assemblages. Recent insights gained from landscape ecology suggest that small, uni-scalar approaches are unlikely to effectively determine those factors that influence riverine structure and function and mediate fish-habitat associations. There appears to be merit in using multiple-scale designs built upon a geomorphologically-derived hierarchy to bridge small, intermediate and large spatial scales in large rivers. This thesis employs a hierarchical design encompassing functional process zones (referred to hereafter as zones), reaches and mesohabitats to investigate fish-habitat associations as well as explore patterns of in-channel habitat structure in one of Australia's largest dryland river systems; the Barwon-Darling River. In this thesis, empirical evidence is presented showing that large dryland rivers are inherently complex in structure and different facets of existing conceptual models of landscape ecology must be refined when applied to these systems. In-channel habitat and fish exist within a hierarchical arrangement of spatial scales in the riverscape, displaying properties of discontinuities, longitudinal patterns and patch mosaics. During low flows that predominate for the majority of time in the Barwon-Darling River there is a significant difference in fish assemblage composition among mesohabitats. There is a strong association between large wood and golden perch, Murray cod and carp, but only a weak association with bony herring. Golden perch and Murray cod are large wood specialists, whereas carp are more general in there use of mesohabitats. Bony herring are strongly associated with smooth and irregular banks but are ubiquitous in most mesohabitats. Open water (mid-channel and deep pool) mesohabitats are characterised by relatively low abundances of all species and a particularly weak association with golden perch, Murray cod and carp. Murray cod are weakly associated with matted bank, whereas carp and bony herring associate with this mesohabitat patch in low abundance. Nocturnal sampling provided useful information on size-related use of habitat that was not evident from day sampling. Both bony herring and carp exhibited a variety of habitat use patterns throughout the die1 period and throughout their lifetime, with temporal partitioning of habitat use by juvenile bony herring and carp evident. Much of the strong association between bony herring and smooth and irregular banks was due to the abundance of juveniles (&lt100mm in length) in these mesohabitats. Adult bony herring (&gt100mm length) occupied large wood more than smooth and irregular banks. At night, juvenile bony herring were not captured, suggesting the use of deeper water habitats. Adult bony herring were captured at night and occupjed large wood, smooth bank and irregular bank. Juvenile carp (&lt200mm length) were more abundant at night and aggregated in smooth and irregular banks more than any other mesohabitat patch. Adult carp (&gt200mm length) occupied large wood during both day and night. There is a downstream pattern of change in the fish assemblage among river zones, with reaches in Zone 2 containing a larger proportion of introduced species (carp and goldfish) because of a significantly lower abundance of native species (bony herring, golden perch and Murray cod) than all other zones. In comparison, the fish assemblage of Zone 3 was characterised by a comparatively higher abundance of the native species bony herring, golden perch and Murray cod. A significant proportion of the amongreach variability in fish assemblage composition was explained at the zone scale, suggesting that geomorphological influences may impose some degree of top-down constraint over fish assemblage distribution. Although mesohabitat composition among reaches in the Barwon-Darling River also changed throughout the study area, this pattern explained very little of the large-scale distribution of the fish assemblage, with most of the variability in assemblage distribution remaining unexplained. Therefore, although mesohabitat patches strongly influence the distribution of species within reaches, they explain very little of assemblage composition at intermediate zone and larger river scales. These findings suggest that small scale mesohabitat rehabilitation projects within reaches are unlikely to produce measurable benefits for the fish assemblage over intermediate and large spatial scales in the Barwon-Darling River. This indicates the importance taking a holistic approach to river rehabilitation that correctly identifies and targets limiting processes at the correct scales. The variable nature of flow-pulse dynamics in the Barwon-Darling River creates a shifting habitat mosaic that serves to maintain an ever-changing arrangement of habitat patches. The inundation dynamics of large wood habitat described in this thesis highlights the fragmented nature of mesohabitat patches, with the largest proportion of total in-channel large wood remaining unavailable to fish for the majority of the time. At low flows there is a mosaic of large wood habitat and with increasing discharge more potential large wood habitat becomes available and does so in a complex spatial manner. What results in this dryland river is a dynamic pattern of spatio-temporal patchiness in large wood habitat availability that is seen both longitudinally among different river zones and vertically among different heights in the river channel. Water resource development impacts on this shifting habitat mosaic. Projects undertaking both fish habitat assessment and rehabilitation need to carefully consider spatial scale since the drivers of fish assemblage structure can occur at scales well beyond that of the reach. Fish-habitat associations occurring at small spatial scales can become decoupled by process occurring across large spatial scales, making responses in the fish assemblage hard to predict. As rivers become increasingly channelised, there is an urgent need to apply research such as that conducted in this thesis to better understand the role that in-channel habitats play in supporting fish and other ecosystem processes. Habitat rehabilitation projects need to be refined to consider the appropriate scales at which fish assemblages associate with habitat. Failure to do so risks wasting resources and forgoes valuable opportunities for addressing declines in native fish populations. Adopting multi-scalar approaches to understanding ecological processes in aquatic ecosystems, as developed in this thesis, should be a priority of research and management. To do so will enable more effective determination of those factors that influence riverine structure and function at the approariate scale.

Enneacanthus chaetodon, the blackbanded sunfish, has become increasingly rare throughout its distribution in the Eastern United States. In Virginia, E. chaetodon maintains an endangered status and individuals persist in six populations. Mitochondrial DNA (mtDNA) and microsatellite data were assessed to determine the genetic characters and gene diversity of the Virginia populations. The results of these analyses were then compared to five additional populations; four from New Jersey and one from North Carolina that were known to have relatively good fitness and were not impacted severely by habitat alteration. The results of this study are relevant to selection of proper management techniques and strategies for this species. Mitochondrial DNA analyses detected no variation in the Virginia populations but significant (P F > 0.2) of inbreeding. The New Jersey and North Carolina populations demonstrated lower amounts of inbreeding than populations in Virginia. New Jersey displayed a significant (P < 0.05) amount of subdivision among populations compared to Virginia. Hypothesis testing supported the contention that the regions are significantly different from one another and that Virginia populations may have gone through one or more population bottlenecks in the past, explaining the low levels of diversity observed and significantly high inbreeding coefficients. Captive breeding programs could be implemented as a management measure to increase population numbers and restore fish into areas where they have been known to inhabit in the recent past. From a proper management perspective, habitat protection and maintenance are more important than supplementation to population survival. Success of either approach with Virginia populations would provide a useful model for managing small populations of blackbanded sunfish in other regions.This project was supported by a grant from the Virginia Department of Game and Inland Fisheries (VDGIF), grant #ED0817BB.

The overexploitation of marine living resources challenges the scientific community for developing new analytical approaches providing effective tools for marine management, ensuring long-term conservation of the harvested and threatened species. Currently, the scientific efforts are mainly focused on the development of techniques and concepts to improve the assessment and management of these populations from a holistic point of view within the framework of the Ecosystem Based Management (EBM). While the principles and objectives of EBM have been accepted by the scientific community and those responsible for the management of the fisheries and conservation, there is not a consensus about how it should be implemented. One of the decisive reasons hindering its implementation is the complexity related to the modeling of complex socio-ecological systems, which covers from environmentally driven effects to social aspects in the management. Focusing on key processes of ecosystems such as the relationships between species ecological processes and essential habitats offers a path to advance towards the implementation of EBM without having to reach the development of excessively complex end-to-end models of an ecosystem. The research developed along this PhD has two main objectives. 1) the application of new concepts and techniques to improve the characterization of essential habitats of two top predator species, the dusky grouper (Epinephelus marginatus, Lowe 1834) and the Atlantic bluefin tuna (Thunnus thynnus, Linnaeus 1758). 2) To propose new methodologies based on habitat information to improve current assessment and management approaches of those species. Conservation of dusky grouper and Atlantic bluefin tuna exploited populations is tackled today from different technical approaches due to differences in their ecological characteristics. Dusky grouper is a highly resident species that inhabits rocky bottoms in coastal Mediterranean ecosystems, where conservation of exploited populations through the establishment of marine protected areas has provided positive results. Atlantic bluefin tuna is a highly migratory pelagic species with a wide geographical distribution along the Atlantic waters, and performs long migrations during spring to reach the spawning areas, among of which the Balearic Sea is one of the main ones. Management of Atlantic Bluefin tuna is approached mainly by technical measures such as minimum weight regulation and limitations in the total allowable catches, established as a function of the status of the adult stock populations calculated from virtual population analysis. In recent years the application of traditional landscape ecology techniques to characterize habitat in the coastal environment has promoted the beginning of the seascape ecology discipline. These techniques have been applied here to improve the definition of dusky grouper essential habitats and to identify changes in habitat use along ontogenetic development. The definition of dusky grouper habitats at different developmental stages provided insights about the species ecology and provided criteria for designing more efficient Marine Protected Areas (MPAs). Findings from the study of dusky grouper essential habitat and the improvement on habitat definition by using seascape metrics provide the basis for developing new methods for MPA design within the framework of Rapid Assessment Programs. Therefore, in this PhD a method is proposed for rapid multidisciplinary environmental assessment of coastal areas for the design and management of MPAs. This method provide tools for the selection, design and management of coastal MPAs when time, budget or potential human pressures, either alone or in combination, create an urgent need for prioritization. The conceptual scheme applied to link littoral species with essential habitats and the transference to management has been adapted to the pelagic environment. Transferring ideas and techniques of seascape ecology to the pelagic realm was not straightforward. New pelagic seascape metrics have been proposed and tested to study the Atlantic Bluefin tuna spawning habitats around the Balearic Sea, advancing in the knowledge of species ecology. The developed pelagic seascape metrics have been applied to the development of a spawning habitat forecasting model to assist managers. This methodology is entirely based on oceanographic data obtained from operational data sources. Finally, monitoring and modeling Atlantic bluefin tuna pelagic essential habitats at larval stages allowed developing new larval indices, providing information on Atlantic bluefin tuna adult eastern stock population.<br>L’estat actual dels recursos vius i dels ecosistemes marins suposa un desafiament constant per a la comunitat científica, que obliga a un progrés continu que asseguri, a llarg termini, la seva explotació sostenible i la seva conservació. Avui en dia els esforços en la investigació se centren, en gran mesura, en el desenvolupament de tècniques i conceptes per millorar l’avaluació i la gestió d’aquestes poblacions des d’un punt de vista holístic en el marc de la gestió basada en l’ecosistema (EBM per les seves sigles en anglès). Mentre que els principis i objectius de l’EBM han estat acceptats per la comunitat científica i pels responsables de la gestió de la pesca i de la conservació, no existeix un consens sobre com s’ha d’aplicar. Un dels motius determinants que obstaculitzen la seva implantació és la complexitat associada a la modelització de sistemes socio-ecològics complexos, que abasta des dels efectes ambientals fins a aspectes socials en la gestió dels recursos. La identificació de processos clau en un ecosistema, com puguin ser les relacions entre l’ecologia de determinades espècies amb els seus hàbitats essencials, ofereix una possibilitat per avançar cap a l’aplicació de la EBM sense haver d’assolir el desenvolupament de models super-complexos que abordin tots els processos que ocorren en un ecosistema. Els diferents estudis desenvolupats al llarg d’aquesta tesi doctoral tenen dos objectius principals. En primer terme s’ aborda l’aplicació de noves tècniques i conceptes per tal de millorar la caracterització dels hàbitats essencials de dues espècies marines localitzades en els estatges superiors de la cadena tròfica, com són l’anfós (Epinephelus marginatus, Lowe 1834) i la tonyina vermella (Thunnus thynnus, Linnaeus 1758). En segon terme, el desenvolupament de metodologies basades en la informació obtinguda sobre els seus hàbitats essencials, la qual cosa permetrà millorar l’avaluació i gestió de les poblacions d’aquestes espècies. Avui dia, la conservació de les poblacions explotades de l’anfós i la tonyina vermella s’aborden des d’enfocaments ben diferenciats, sobre la base de les seves característiques ecològiques. L’anfós és una espècie altament resident que habita fons rocosos dels ecosistemes costaners de l’oceà Atlàntic, l’oceà Índic i el mar Mediterrani. La conservació de les seves poblacions explotades es basa principalment en l’establiment d’àrees marines protegides. Per la seva banda, la tonyina vermella és una espècie pelàgica amb una àmplia distribució geogràfica al llarg de l’Atlàntic, que realitza llargues migracions durant la primavera per arribar a les àrees de reproducció, entre les quals s’hi troba el Mar Balear. La gestió d’aquesta espècie es basa, principalment, en l’establiment de quotes de pesca a partir de l’avaluació de l’estat de les poblacions mitjançant l’aplicació de models monoespecífics. En els darrers anys l’aplicació de tècniques procedents de l’ecologia del paisatge terrestre (landscape ecology) en estudis d’ecologia del medi costaner ha donat lloc a l’inici de la “ecologia del paisatge marí” (seascape ecology). En els estudis desenvolupats en el marc d’aquest doctorat s’han aplicat aquestes tècniques per millorar la definició dels hàbitats essencials de l’anfós i per identificar canvis en l’ús de l’hàbitat al llarg del seu desenvolupament ontogènic. La millora en la identificació dels hàbitats essencials de l’anfós a diferents etapes del seu desenvolupament ha proporcionat informació rellevant sobre la seva ecologia i criteris per al disseny d’àrees marines protegides més eficients quant a la conservació d’aquesta espècie. Els resultats obtinguts durant l’estudi dels hàbitats essencials de l’anfós i la millora en la caracterització de l’estructura dels hàbitats a través de l’aplicació de mesures de paisatge submarí han proporcionat la base per al desenvolupament d’una metodologia de disseny d’àrees marines protegides en el marc dels programes d’avaluació ràpida (RAPs per les seves sigles en anglès). En aquesta tesi doctoral es proposa un mètode per a l’avaluació ràpida d’àrees costaneres des d’un enfocament multidisciplinari. Aquest mètode proporciona eines per a la selecció, disseny i gestió d’àrees marines protegides costaneres quan el factor temps, el pressupost o l’acció humana, ja sigui individualment o combinats, crea una necessitat urgent de priorització. L’esquema conceptual aplicat en l’anàlisi de les relacions entre l’ecologia de l’anfós i els seus hàbitats essencials i la transferència d’aquesta informació a la millora en l’avaluació i gestió de l’espècie s’ha adaptat a l’ambient pelàgic. La transferència d’idees i tècniques de l’ecologia del paisatge marí a l’ambient pelàgic ha suposat un repte al llarg d’aquest doctorat. S’han proposat noves mètriques de paisatge marí pelàgic, que s’han aplicat en l’estudi dels hàbitats de reproducció de la tonyina vermella en el Mar Balear, la qual cosa ha permès avançar en el coneixement de l’ecologia d’aquesta espècie i d’altres de túnids. Aquests avanços han permès el desenvolupament d’un model de predicció de la localització de les zones de reproducció de la tonyina a les Balears, basats completament en l’aplicació de dades procedents de l’oceanografia operacional (teledetecció i models hidrodinàmics). Finalment, la monitorització dels estadis larvaris de la tonyina vermella i l’anàlisi dels seus hàbitats essencials han permès desenvolupar índexs d’abundància larvària, i demostrar que la informació sobre l’hàbitat millora significativament l’avaluació d’aquest índexs. Aquests índexs larvaris estàn permetent analitzar l’evolució de la fracció adulta de la població oriental de tonyina vermella de l’Atlàntic, que es reprodueix al Mediterrani.<br>El estado actual de los recursos vivos y de los ecosistemas marinos supone un desafío constante para la comunidad científica, obligando a un progreso continuo que asegure, a largo plazo, su explotación sostenible y su conservación. Hoy en día los esfuerzos en la investigación se centran, en gran medida, en el desarrollo de técnicas y conceptos para mejorar la evaluación y gestión de estas poblaciones desde un punto de vista holístico en el marco de la gestión basada en el ecosistema (EBM por sus siglas en inglés). Mientras que los principios y objetivos de la EBM han sido aceptados por la comunidad científica y los responsables de la gestión de la pesca y la conservación, no existe un consenso sobre cómo debe aplicarse. Una de las razones determinantes que obstaculizan su implementación es la complejidad asociada a la modelización de sistemas socio-ecológicos complejos, que abarca desde los efectos ambientales hasta aspectos sociales en la gestión de los recursos. La identificación de procesos clave en un ecosistema, tales como las relaciones entre la ecología de determinadas especies con sus hábitats esenciales, ofrece una posibilidad para avanzar hacia la aplicación de la EBM sin tener que alcanzar el desarrollo de modelos super-complejos que aborden todos los procesos que ocurren en un ecosistema. Los diferentes estudios desarrollados a lo largo de esta tesis doctoral tienen dos objetivos principales. En primer lugar, la aplicación de nuevas técnicas y conceptos para la mejora de la caracterización de los hábitats esenciales de dos especies marinas localizadas en los estados superiores de la cadena trófica, el mero (Epinephelus marginatus, Lowe 1834) y el atún rojo del Atlántico (Thunnus thynnus, Linnaeus 1758). En segundo lugar, el desarrollo de nuevas metodologías, basadas en la información obtenida sobre hábitats esenciales, que permitan mejorar la evaluación y la gestión de las poblaciones de estas especies. Hoy en día, la conservación de las poblaciones explotadas del mero y el atún rojo se abordan desde enfoques técnicos bien diferenciados, en base a sus características ecológicas. El mero es una especie altamente residente que habita en fondos rocosos de los ecosistemas costeros del Mediterráneo. La conservación de sus poblaciones explotadas mediante el establecimiento de reservas marinas ha dado buen resultado. El atún rojo del Atlántico es una especie pelágica con una amplia distribución geográfica a lo largo de las aguas del Atlántico, que realiza largas migraciones durante la primavera para llegar a las áreas de reproducción, entre las que se encuentra el Mar Balear. La gestión de esta especie se basa, principalmente, en el establecimiento de tallas mínimas de captura y de cuotas de pesca a partir de la evaluación del estado de las poblaciones mediante la aplicación de modelos uni-específicos. En los últimos años la aplicación de técnicas procedentes de la ecología del paisaje terrestre (landscape ecology), en estudios de ecología en el medio costero ha dado lugar al inicio de la “ecología del paisaje marino”(seascape ecology). En los estudios desarrollados en el marco de este doctorado se han aplicado estas técnicas para mejorar la definición de los hábitats esenciales del mero y para identificar cambios en el uso del hábitat a lo largo de su desarrollo ontogénico. La mejora en la identificación de los hábitats esenciales del mero en diferentes etapas de desarrollo ha proporcionado información relevante sobre la ecología de esta especie y criterios para el diseño de áreas marinas protegidas más eficientes en cuanto a su conservación. Los resultados obtenidos durante el estudio de los hábitats esencial de mero, y la mejora en la caracterización de la estructura de los hábitats mediante la aplicación de medidas de paisaje marino, han proporcionado la base para el desarrollo de una metodología de diseño de áreas marinas protegidas en el marco de los programas de evaluación rápida (RAPs por sus siglas en ingles). En esta tesis doctoral se propone un método para la evaluación rápida de aéreas costeras desde un enfoque multidisciplinar. Este método proporciona herramientas para la selección, diseño y gestión de áreas marinas protegidas costeras cuando el factor tiempo, el presupuesto o la acción humana, ya sea solos o en combinación, crea una necesidad urgente de priorización. El esquema conceptual aplicado en el análisis de las relaciones entre la ecología del mero y sus hábitats esenciales y la transferencia de esta información a la mejora en la evaluación y gestión de esta especie, se ha adaptado al ambiente pelágico. La transferencia de ideas y técnicas de la ecología de paisaje marino al ambiente pelágico ha supuesto un reto a lo largo de este doctorado. Se han propuesto nuevas métricas de paisaje marino pelágico, que se han aplicado en el estudio de los habitats de reproducción del Atún rojo en aguas del Mar Balear, lo que ha permitido avanzar en el conocimiento de la ecología de esta especie y otras especies de túnidos. Estos avances han permitido el desarrollo de un modelo de predicción de la localización de las zonas de reproducción del atún rojo en Baleares, basados enteramente en la aplicación de datos procedentes de la oceanografía operacional (teledetección y modelos hidrodinámicos). Finalmente, la monitorización de los estadios larvarios del atún rojo y el análisis de sus hábitats esenciales han permitido desarrollar índices de abundancia larvaria, y demostrar que la información sobre hábitat mejora significativamente la evaluación de estos índices. Estos índices larvarios están permitiendo analizar la evolución de la población adulta de la población oriental del atún rojo del Atlántico, que se reproduce en el Mediterráneo.

In 2000 the European Union introduced the Water Framework Directive, new legislation that regulates the use of surface waters within the European Community. The goal of this legislation is to protect, enhance and restore all surface waters within the Community to Good Surface Water Status. Good-Status is described as having low levels of anthropogenic distortion in its hydro-morphological and physiochemical components as well as possessing biota that would normally be associated with the type-specific aquatic ecosystem. The assessment of ecosystem status is to be defined by comparisons with intact representative reference sites, by using modelling techniques that define reference conditions, a combination of the two, or expert judgement. As undisturbed aquatic ecosystems are rare or non-existent in Europe the base-line data will have to be defined using the latter methodologies. The aim of this project is to help define reference conditions for lotic systems in Europe based on the physical instream habitat parameters of a resident species. Brown trout (Salmo trutta), a ubiquitous and well studies species endemic to Europe, was used as the target organism to develop the assessment protocol. The project focused on the requirements this species has of aspects of its physical habitat; specifically, its usage of depth, velocity, and substrate. An extensive survey of the scientific literature was used to define the requirements trout has for the three physical parameters at four life stages. These are the spawning, nursery, juvenile and adult-resident life stages. These requirements were expressed as tolerance profiles, which defined suitable, usable and not-suitable habitat. The methodology was demonstrated by evaluating the physical habitat available at six reaches in three small streams, March, Burnhouse and Bin Burns, which drain into the Carron Valley Reservoir in central Scotland. From the perspective of water depth, these streams seem best suited as nursery areas, are less well suited as juvenile habitat, and do not appear to be well matched for adult residents. The assessment of both velocity and substrate indicated that the portion of the study reaches available for use by resident brown trout increased with trout size. The assessment of all three physical habitat parameters at all study reaches found variable portions of the streams suitable for use by spawning trout. When the habitat variables are integrated all stream segments streams seem best suited as nursery and spawning areas. To a lesser extent juvenile trout can use these burns and very little habitat is available for use by adult resident trout. The tolerance profiles that were created in this study are standardized assessment criteria that when compared with stream survey data can produce an appraisal of habitat availability in any fluvial freshwater system that supports populations of brown trout (Salmo trutta). The assessment method can be combined to produce an integrated habitat assessment, using both an index and by the calculation of Froude number, which is a more realistic approach than the assessment of individual habitat parameters as salmonids choose their microhabitat based on multiple factors. This approach allows an investigator to determine the amount and relative portion of useable habitat and to determine the quality of that habitat. Finally, by examining the physical habitat variable that most strongly correlates with the final integrated habitat distribution the individual habitat parameter that is most important to the distribution of physical habitat at a site can be determined. While this technique would certainly benefit from further development it does show potential to aid in physical habitat assessment of trout streams.

In the past century, hydropower development in Sweden has been facilitated by the lack of appropriate environmental legislation. This exploitation has resulted in the current poor ecological status of most Swedish water bodies affected by hydropower, and in the need for new policies that reflect the 2000 European Water Framework Directive. Thus, the Swedish Agency for Marine and Water management (SwAM), the Swedish Energy Agency (SEA) and Svenska Kraftnät have elaborated a new national plan for the revision of almost all hydropower licenses in the next 20 years, and Vattenkraftens Miljöfond has carried out a pilot project on Ljungan river, to test different working methods for regional collaboration, and to find effective solutions for achieving the greatest possible benefit for the aquatic environment, while ensuring an efficient national hydropower supply. This thesis focuses on the fish habitat rehabilitation of a portion of Ljungan river highly affected by hydropower practices. By combining a 1D/2D hydraulic model, calibrated and validated, with a habitat model that defines the hydraulic preferences of the target fish species, it was possible to run different simulations and to quantify the optimal habitat obtainable in each scenario, following the PHABSIM methodology. The outputs of this analysis were produced in the form of Composite Suitability Index (CSI) maps and Weighted Usable Area (WUA)­discharge curves. The former resulted to be a very useful tool for analyzing the spatial distribution of suitable habitats for certain ecological processes, and for planning in­stream habitat improvement measures, while the latter have been efficiently used to identify and quantify the maximum habitat improvement achievable with the different mitigation scenarios. This approach helped to firstly assess the habitat improvement that would result from removing the weirs located along the river, leading to the conclusion that the removal would be effective only if combined with other morphological changes of the river channel. Additionally, the coupled eco­hydraulic model has been useful for the design of ecological flow scenarios able to achieve different levels of habitat improvement, including scenarios aimed at minimizing energy production losses. The use of the PHABSIM methodology resulted to be very suitable for the scale and scope of the project. However, it also required to limit the iii ecological drivers considered in the analysis and to make some simplistic assumptions about target species behavior, which must always be underlined and acknowledged when using the results in decision­making processes.<br>Under det senaste århundradet har vattenkraftsutbyggnaden i Sverige underlättats av bristen på lämplig miljölagstiftning. Detta utnyttjande har lett till att de flesta svenska vattenförekomster har en dålig ekologisk status och att det behövs en ny politik som återspeglar det europeiska ramdirektivet för vatten från 2000. Således har Havs­ och vattenmyndigheten, Energimyndigheten och Svenska Kraftnät utarbetat en ny nationell plan för översyn av nästan alla vattenkraftslicenser under de kommande 20 åren, och Vattenkraftens Miljöfond har genomfört ett pilotprojekt i Ljungan älv för att testa olika arbetsmetoder för regionalt samarbete och hitta effektiva lösningar för att uppnå största möjliga nytta för vattenmiljön samtidigt som man säkerställer en effektiv nationell vattenkraftförsörjning. Denna avhandling fokuserar på återställandet av fiskhabitatet i en del av Ljungan älven som är starkt påverkad av vattenkraftsutövning. Genom att kombinera en 1D/2D hydraulisk modell, kalibrerad och validerad, med en habitatmodell som definierar målfiskarternas hydrauliska preferenser var det möjligt att göra olika simuleringar och kvantifiera den optimala livsmiljö som kan erhållas i varje scenario, enligt PHABSIM­metodiken. Detta tillvägagångssätt har använts för att först och främst bedöma den förbättring av livsmiljön som skulle bli resultatet av att ta bort de dammar som finns längs älvsträckan, vilket ledde till slutsatsen att avlägsnandet skulle vara effektivt endast om det kombineras med andra morfologiska förändringar av flodfåran. Dessutom har den kopplade ekohydrauliska modellen varit användbar för att utform ekologiska flödesscenarier som kan uppnå olika nivåer av habitatförbättring, inklusive scenarier som syftar till att minimera förlusterna i energiproduktionen.

Subsistence fishing is a vital component of Alaska’s North Slope borough economy and culture that is being threatened by human disturbance. These threats mean the fish must be protected, but the size of the region makes conservation planning difficult. Fortunately, advances in species distribution models (SDMs), environmental DNA (eDNA), and remote sensing technologies provide potential to better understand species’ needs and guide management. The objectives of my study were to: (1) map the current habitat suitability for twelve fish species, occurring in Alaska’s North Slope,(2) determine if SDMs based on eDNA data performed similarly to, or improved, models based on traditional sampling data, and (3) predict how species distributions will shift in the future in response to climate change. I was able to produce robust models for 8 of 12 species that relate environmental characteristics to a species’ presence or absence and identify stream reaches where species are likely to occur. Unfortunately, the use of eDNA data did not produce useful models in Northern Alaskan rivers. However, I was able to generate predictions of species distributions into the future that should help inform management for years to come.

Chrysoblephus puniceus is an over-exploited linefish species, endemic to the coastlines off southern Mozambique and eastern South Africa. Over-exploitation and habitat loss are two of the biggest threats to the sustainability of fisheries globally. Assessing the genetic stock structure (a prerequisite for effective management) and predicting climate related range changes will provide a better understanding of these threats to C. puniceus which can be used to improve the sustainability of the fishery. Two hundred and eighty four genetic samples were collected from eight sampling sites between Ponta da Barra in Mozambique and Coffee Bay in South Africa. The mitochondrial control region and ten microsatellite loci were amplified to analyse the stock structure of C. puniceus. The majority of microsatellite and mtDNA pairwise population comparisons were not significant (P > 0.05) although Xai Xai and Inhaca populations had some significant population comparisons for mtDNA (P < 0.05). AMOVA did not explain any significant variation at the between groups hierarchical level for any pre-defined groupings except for a mtDNA grouping which separated out Xai Xai and Inhaca from other sampling sites. SAMOVA, isolation by distance tests, structure analysis, principle component analysis and spatial autocorrelation analysis all indicated a single population of C. puniceus as being most likely. The migrate-n analysis provided evidence of current driven larval transport, with net migration rates influenced by current dynamics.Two hundred and thirty six unique presence points of C. puniceus were correlated with seasonal maximum and minimum temperature data and bathymetry to model the current distribution and predict future distribution changes of the species up until 2030. Eight individual species distribution models were developed and combined into a mean ensemble model using the Biomod2 package. Winter minimum temperature was the most important variable in determining models outputs. Overall the ensemble model was accurate with a true skills statistic score of 0.962. Binary transformed mean ensemble models predicted a northern and southern range contraction of C. puniceus' distribution of 15 percent; by 2030. The mean ensemble probability of occurrence models indicated that C. puniceus' abundance is likely to decrease off the southern Mozambique coastline but remain high off KwaZulu-Natal. The results of the genetic analysis support the theory of external recruitment sustaining the KwaZulu Natal fishery for C. puniceus. While the high genetic diversity and connectivity may make C. puniceus more resilient to disturbances, the loss of 15 percent; distribution and 11 percent; genetic diversity by 2030 will increase the species vulnerability. The decrease in abundance of C. puniceus off southern Mozambique together with current widespread exploitation levels could result in the collapse of the fishery. A single transboundary stock of C. puniceus highlights the need for co-management of the species. A combined stock assessment between South Africa and Mozambique and the development of further Marine Protected Areas off southern Mozambique are suggested as management options to minimise the vulnerability of this species.

This study examined the effects of the January 2010 cold spell on mangrove utilizing coral reef fishes off the southeast coast of Florida, USA, in the vicinity of Biscayne National Park (BNP). An ongoing, fishery-independent mangrove visual survey documenting fish assemblages in BNP provided data from the years 1998 to 2014 for examination. Of particular interest were the presence, abundance, and size structure for five mangrove utilizing coral reef fishes: sergeant major (Abudefduf saxatilis), yellowfin mojarra (Gerres cinereus), schoolmaster snapper (Lutjanus apodus), gray snapper (Lutjanus griseus), and great barracuda (Sphyraena barracuda). These species were selected for analysis due to their economic and ecologic importance, their potential as environmental indicators, their connectedness to multiple habitats, and their abundance within the available data set. Data were collected using a modified visual ‘belt transect’ method, consisting of 60 m2 transects running parallel to the mangrove shorelines. Data for average length of fish were reconstructed to form standard normal distributions and the resulting lengths were assigned to various age-classes to create species-specific length-frequency distributions. Variations in presence and abundance were examined across three time periods (1998-2009; 2010-2011; 2012-2014), as well as comparisons of length-frequency distributions. Following the January 2010 cold spell, the presence and abundance values for the two years immediately following the event were significantly decreased compared to the years prior to the cold spell for most of the five species at either mainland (ML) or leeward key (LK) locations. Additionally, the presence and abundance estimates typically remained statistically decreased when compared against the remaining years in the available data set. The size structures for the majority of the five species at either location, however, were not consistently significantly different between the three time periods, as was hypothesized. Instead, the analyses showed mixed results, with the size structure typically shifting towards smaller individuals immediately following the event. These findings suggest that drops in water temperature resulting from cold spells are capable of directly impacting mangrove utilizing reef fish species, albeit to varying degrees depending on various factors, such as physiological tolerances, ecological life history strategies, and habitat requirements.

Fisheries sustainability is inherently linked to an understanding of the population-level effects of fishing. With an accurate characterization of historical fish and fishery dynamics, management agencies are more equipped to create regulations that sustain fishery resources over the long term. The overarching goal of this dissertation is to contribute to the advancement of fisheries stock assessment and promote resource sustainability. My research focused on highly migratory species (HMS), particularly fishes that reside in the open ocean. These species constitute some of the highest valued global fisheries; however, numerous factors compromise HMS stock assessment and management. These challenges are fully described in Chapter 1, which also includes corresponding research and management recommendations. A key limitation in HMS assessments underlying my research is the lack of independent scientific monitoring programs. In the absence of research surveys, HMS stock assessments must rely on fishery catch and effort data. Therefore, special care is required to infer population dynamics from entities that were not established to monitor populations. In particular, the habitat in which fishing occurs largely dictates the amount and composition of fishes captured. Unfortunately, habitat effects on fishery-dependent data are not commonly accounted for in HMS assessments. Chapter 2 presents the results of a performance evaluation of methods used for estimating HMS abundance trends, including traditional generalized linear models (GLMs), an existing method that considers habitat (statHBS), and a proposed method that hybridizes traditional and habitat-based approaches (HabGLM). I demonstrate that HabGLM was most accurate of those evaluated, while exhibiting minimal sensitivity to errors in input data. I recommend the use of HabGLM in future HMS stock assessments; however, despite being most accurate, there were scenarios where HabGLM still did not sufficiently capture the true abundance pattern. In Chapter 3, the HabGLM was applied to 35 HMS in the Atlantic Ocean using fisher logbook data from the US pelagic longline fishery. This comprehensive analysis portrays an HMS community in the Atlantic as generally depleted, with current abundances of 76% of the species at less than half of their 25-year observed maxima. However, despite these depletions, 26% of the species exhibited population growth, suggesting recent fishing intensities may be adequate for sustaining or rebuilding certain populations. While interpretations of abundance trends can be informative, fisheries management is more often guided by the output of stock assessments. Thus, in Chapter 4, I present the results of a study that evaluated the effects of abundance index quality on the performance of a stock assessment model (Stock Synthesis), with a focus on Atlantic blue marlin (Makaira nigricans). In general, assessment model performance was superior when based on abundance indices estimated using HabGLM; however, the management quantities derived from this best case scenario were still overly optimistic, and when the fisheries were regulated accordingly, population biomass was projected to be well below the management target level. Overall, my research emphasizes that (1) habitat should be directly incorporated into HMS stock assessments, and (2) independent stock monitoring programs are essential for effective fisheries management.

Small pelagic fish are species that live in the water column and have little relationship with the sea bottom. During the day they may form schools with feeding, defence or energetic efficiency purposes and disperse during the night. The importance of small pelagic fishes within the marine ecosystem rely in the proportion of biomass they represent and the clue function they develop as intermediate links in the energy transfer between lower and upper levels of the trophic chain. Their populations are particularly sensitive to environmental fluctuations (Cole and McGlade, 1998; Lloret et al., 2004) and frequently highly exploited by commercial fisheries. These may occasionally collapse the stocks affecting both the marine ecosystem and the fisheries they sustain. In the Mediterranean, almost 50% of the total annual landings are attributable to small pelagic fishes (Lleonart and Maynou, 2003). In the Western Mediterranean Sea, sardine (Sardina pilchardus) and anchovy (Engraulis encrasicolus) are the two most important species in terms of landed biomass and commercial interest (Lleonart and Maynou, 2003). Despite their importance little is known about the spatial distribution of these stocks or about the relationship between the spatial distribution and environmental variables. Since the ‘90s acoustic surveys are annually performed in the Spanish Mediterranean continental shelf in late autumn (Abad et al., 1998 a,b) coinciding with anchovy’s recruitment and the beginning of the spawning season for sardine (Abad and Giráldez, 1993; Giráldez and Abad, 1995). Although the main goal of these surveys is to estimate abundance and biomass of sardine and anchovy, data about the whole pelagic community has also been gathered. Furthermore, in the last decade it was detected an increasing appearance of other small and medium-sized pelagic species and the application of a multi-species approach to Mediterranean fisheries assessment was advised (Lleonart and Maynou, 2003). The present work is structured in two sections. The first section of the work will analyse the spatial distribution (1D and 2D) of sardine and anchovy by means of geostatistical techniques, both transitive and intrinsic methods (Matheron, 1969). Special attention will be paid to the estimation of the uncertainty associated to abundance estimations and, concretely, the uncertainty caused by sampling scheme which is thought to be one of the main contributors to random error (ICES, 1998). The second section will explore the environmental factors that drive the presence or absence of anchovy and sardine in late autumn. Satellite environmental data as sea surface temperature, salinity, chlorophyll-a, photosintethic active radiation, sea level anomalies or bottom depth will be related to the presence-absence of sardine and anchovy stocks through Generalised Additive Models (GAM) to try to depict the relationships that may be found between both (Bellido et al., 2008; Giannoulaki et al., 2008). The spawning area of sardine will also be studied in order to model the presence-absence of sardine eggs and try to understand the evolution of their stocks.<br>Los pequeños peces pelágicos son especies que viven en la columna de agua y que tienen poca relación con el fondo marino. Durante el día forman bancos de peces con el objetivo de alimentarse, defenderse de potenciales depredadores o por motivos de eficiencia energética, dispersándose durante la noche. La importancia de los pequeños pelágicos en el ecosistema marino radica en la proporción de biomasa que representan y en la función clave que desempeñan como eslabones intermedios, transfiriendo energía entre los niveles tróficos inferiores y superiores de la cadena trófica. Sus poblaciones son particularmente sensibles a las fluctuaciones ambientales (Cole and McGlade, 1998; Lloret et al., 2004) y frecuentemente se encuentran en un régimen de explotación elevado por parte de las pesquerías comerciales. Esto puede comportar de manera ocasional el colapso de sus poblaciones explotables, afectando al ecosistema marino y a las pesquerías que las mantinen. Casi el 50% del total de la biomssa anual desembarcada en los puertos del Mediterráneo provienen de los pequeños peces pelágicos (Lleonart and Maynou, 2003). En el Mediterráneo Occidental, la sardina (Sardina pilchardus) y el boquerón (Engraulis encrasicolus) son las dos especies más importantes, tanto en términos de biomasa como capturada como por su interés comercial (Lleonart and Maynou, 2003). A pesar de su importancia, la distribución espacial de las poblaciones explotables es poco conocida así como también lo es la relación de la distribución espacial con los parámetros ambientales. Desde principios de los años 90, se llevan a cabo campañas acústica en la plataforma continental española del Mediterráneo a finales de otoño (Abad et al., 1998 a,b), coincidiendo con el reclutamiento de la anchoa y la época de puesta de la sardina (Abad and Giráldez, 1993; Giráldez and Abad, 1995). A pesar de que el principal objetivo de estas campañas es la estimación de la abundancia y de la biomas de la sardina y el boquerón, datos de la comunidad pelágica en conjunto también se recogen periódicamente. Además, a lo largo de la última década se ha detectado una aparición incremental de otras especies de pequeños y medianos pelágicos y por tanto, se aconsejó la aplicación de un enfoque multiespecífo en la evaluación de pesquerías del Mediterráneo (Lleonart and Maynou, 2003). El presente trabajo se estructura en dos seciones. La primera sección del trabajo analizará la distribución espacial (1D y 2D) de la sardina y el boquerón por medio de técnicas geoestadísticas, tanto transitivas como intrínsecas (Matheron, 1969). Se prestará especial atención a la incertidumbre asociasda a las estimaciones de abundancia y, concretamente, a la incertidumbre asociada al diseño de muestro que se considera uno de los factores que contribuyen con mayor intensidad al error aleatorio (ICES, 1998). La segunda sección explorará los factores ambientales que condicioinan la presencia o ausencia de sardina y boquerón a finales de otoño. Datos ambientales obtenidos de satélite, como la temperatura superficial del mar, la salinidad, clorofila, radiación fotosintéticamente activa, anomalía del nivel del mar y la profundidad del fondo marino se relacionarán con la presencia-ausencia de las poblaciones explotables de sardina y boquerón mediante modelos aditivos generalizados (GAM, del acrónimo inglés) para determinar las relaciones existentes (Bellido et al., 2008; Giannoulaki et al., 2008). El hábitat de la puesta de sardina será igualmente estudiada para modelar la presencia-ausencia de huevos de sardina e intentar entender la evolución de las especies explotables.<br>Els petits peixos pelàgics són espècies de peixos que viuen a la columna d’aigua i que tenen poca relació amb el fons marí. Durant el dia formen bancs de peixos amb l’objectiu alimentar-se, defensar-se en front potencial depredadors o per eficiència energètica, dispersant-se durant la nit. La importància dels petits pelàgics a l’ecosistema marí radica en la proporció de biomassa que representen i en la funció clau que exerceixen com esglaons intermedis, transferint energia entre les nivells inferiors i superiors de la cadena tròfica. Les seves poblacions són particularment sensibles a les fluctuacions ambientals (Cole and McGlade, 1998; Lloret et al., 2004) i freqüentment es troben baix un règim d’explotació elevat per part de les pesqueres comercials. Això pot comportar de manera ocasional el col·lapse de les seves poblacions explotables, afectant a l’ecosistema marí i a les pesqueries que sostenen. Gairebé el 50% del total de la biomassa anual desembarcada als ports del Mediterrani prové dels petits peixos pelàgics (Lleonart and Maynou, 2003). Al Mediterrani Occidental, la sardina (Sardina pilchardus) i l’aladroc (Engraulis encrasicolus) són les dues espècies més importants, tant en termes de biomassa capturada com pel seu interès comercial (Lleonart and Maynou, 2003). Malgrat la seva importància, la distribució espaial de les poblacions explotables és poca coneguda així com també ho és la relació d’aquesta distribució espaial amb variables ambientals. D’ençà de principis dels anys 90, es duen a terme campanyes acústiques a la plataforma continental del Mediterrani espanyol a finals de la tardor (Abad et al., 1998 a,b), coincidint amb el reclutament de l’aladroc i amb l’època de posta de la sardina (Abad and Giráldez, 1993; Giráldez and Abad, 1995). Tot i que el principal objectiu d’aquestes campanyes és l’estimació de l’abundància i de la biomassa de la sardina i l’aladroc, dades del conjunt de la comunitat pelágica també es recolleixen. A més a més, al llarg de la darrera dècada s’ha detectat una aparició incremental d’altres espècies de petits i mitjans pelàgics i per tant, es va aconsellar l’aplicació d’un enfoc multiespecífic a l’avaluació de les pesqueres del Mediterrani (Lleonart and Maynou, 2003). El present treball s’estructura en dues seccions principals. La primera secció del treball analitzarà la distribució espaial (1D i 2D) de la sardina i l’aladroc per mitjà de tècniques geoestadístiques, tant transitives com intrínseques (Matheron, 1969). Es prestarà especial atenció a la incerteza associada a les estimacions d’abundància i, concretament, a la incertesa originada pel disseny de mostreig que és considerat un dels factors que contribueixen amb més intensitat a l’error aleatori (ICES, 1998). La segona secció explorarà els factors ambientals que condicionen la presència o absència de sardina i aladroc a finals de tardor. Dades ambientals obtingudes de satèl·lit, com la temperatura superficial de la mar, la salinitat, clorofil·la, radiació fotosintèticament activa, anomalies del nivell de la mar i la profunditat del fons marí es relacionaran amb la presència-absència de les poblacions explotables de sardina i aladroc mitjançant models additius generalitzats (GAM, de l’acrònim anglès) per determinar les relacions existents (Bellido et al., 2008; Giannoulaki et al., 2008). L’hàbitat de la posta de la sardina serà igualment estudiada per tal de modelar la presència-absència d’ous de sardina i intentar entendre l’evolució de les seves poblacions explotables.

碩士<br>國立臺灣大學<br>土木工程學研究所<br>94<br>In general, the principles of stream ecological engineering are usually determined by traditional engineer’s experience. After studying relavant literature we found “wing deflectors” were used in Japan. They help streams to meander during normal discharge and do not obstruct the entire cross section of the river during flooding. In Taiwan, we found similar stream ecological engineering in Nei Gou Stream although with a slightly different design. In this study we test the change of hydraulic condition effects fish habitat in different design distance. A flume experiment and a 2-D numerical model, TABS-2, were employed to simulate the hydraulic characteristics in fixed-bed condition. In addition, by selecting Gobioidi, Cyprinidae and Homalopteridae as the indicator species, the change of fish habitat and the habitat diversity for two different Froude number conditions were discussed. In low Froude number (Fr=0.42) condition, the “wing deflector” design will decrease fish habitat area but will increase the habitat diversity. In high Froude number (Fr=0.61) condition, the “wing deflector” design will decrease Cyprinidae habitat area but will increase Gobioidi and Homalopteridae habitat area and also increase the habitat diversity. Results of the simulation show that with a wider design distance, both the fish habitat area and the habitat diversity will increase.

Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2007.<br>Source: Dissertation Abstracts International, Volume: 68-11, Section: B, page: 7582. Adviser: Edwin E. Herricks. Includes supplementary digital materials. Includes bibliographical references (leaves 244-264) Available on microfilm from Pro Quest Information and Learning.

My research in coastal Ecuador and the northern Gulf of Mexico (GOM) elucidated differences in value of shallow estuarine habitats for fishes and invertebrates. I focused on mangrove and tidal river habitats in Ecuador, and oyster reef, vegetated marsh edge, and nonvegetated bottom habitats in the GOM. Coastal Ecuador has lost 20-30% of mangrove wetlands over the past 30 years. Such habitat loss can impair the ecological functions of wetlands. In this study I identified the fish community of the remaining mangrove wetland in Rio Palmar, Ecuador. For comparison, an adjacent tidal river without mangroves, Rio Javita, was also sampled. I found that although Rios Palmar and Javita are characterized by relatively low fish-species richness compared to other tropical estuarine systems, they appear to provide important habitat for several economically- and ecologically-valued species. In the GOM, I examined the fish and invertebrate communities of adjacent oyster reef (oyster), vegetated marsh edge (VME), and nonvegetated bottom (NVB) habitats. Three main relationships emerged: 1) Oyster and VME provide habitat for significantly more species (as a measure of richness) relative to NVB; 2) Oyster and VME provide habitat for uncommon and rare species; and 3) Many of the species collected in multiple habitats occurred at higher abundances in oyster or VME habitat. Contrary to the current low value ranking of oyster habitat relative to other estuarine and salt marsh habitats, oyster provides high quality habitat for many species. Understanding how key species utilize estuarine habitats is critical for future conservation and management efforts. My research indicated that VME habitat may provide better foraging options for juvenile pinfish (Lagodon rhomboides), and together with corroborating evidence from other studies, suggest that VME provides a critical nursery function for juvenile pinfish, especially in estuaries where seagrass habitat is sparse or nonexistent. Additionally, I documented that juvenile white shrimp (Litopenaeus setiferus) select for oyster habitat because of higher food availability and not because of refuge needs from predation by blue crabs. Oyster habitat appears to provide a nursery function for juvenile white shrimp. Overall, my research demonstrated that structurally complex habitats, such as mangroves, VME, and oyster provide essential habitat at the community, population, and individual levels.

There is a need to define a more efficient and accurate approach to aquatic habitat mapping. Traditional approaches have focused on intense biological/non-biological sampling and observation analysis within specific and restrained scales. Therefore, an underwater video mapping system (UVMS) has been developed in efforts to identify federally protected aquatic species’ habitats within the Obed Wild and Scenic River (OBRI). The UVMS kayak apparatus provides georeferenced video footage correlated with GPS (global positioning systems) for GIS (geographic information systems) mapping applications. Based on its fluvial and geomorphological trends, OBRI was dissected quantitatively and integrated into databases for species-specific GIS habitat queries. Substrate type, depth, above water river characteristics (pool/riffle/run), and substrate embeddedness were extracted to access specific habitats. To better pinpoint optimal microhabitat locations, a physical habitat suitability model was developed to rank preferred habitat locales. Rankings were sequentially broken into five categories: optimal, sub-optimal, marginal, sub-marginal, and poor habitat criteria. Habitat suitability findings for the interested species habitats varied tremendously, favoring fish species. Spotfin chub, Erimonax monacha, optimal habitat was found to cover 22.14 km of river length within OBRI (30 % of OBRI’s spatial extent). The blackside dace, Phoxinus cumberlandensis, (38.9 km) and the duskytail darter, Etheostoma percnurum, (50.9 km) met optimal habitat conditions that yielded 51% and 69% of OBRI’s spatial extent, respectively. In general, optimal habitats for the six mussels were sporadically distributed and had low occurrences. Primarily, these mussel species prefer highly embedded areas with very specific depths and pool/riffle/run conditions. Cumberland elktoe, Alasmidonta atropurea, optimal habitat ranges spanned across 4.32 km (6% of OBRI’s spatial extent) with most of the habitat characteristics in OBRI being marginal. The purple bean, Villosa perpurpurea, optimal habitat was identified within 2.61 km of OBRI (3.5% of OBRI’s spatial extent). Most of the physical conditions of OBRI supplied poor to sub-marginal habitat for the purple bean, at least from a thalweg perspective. Only 385 m coincided with optimal habitat for the cumberland bean, Villosa trabalis, (0.5% of OBRI’s spatial extent) with most habitats in long sub-marginal reaches. Optimal habitats for the cumberlandian combshell, Epioblasma brevidens, the tan riffleshell, Epioblasma florentina walkeri, and the littlewing pearlymussel, Pegias fibula, were deficient, only occurring in 484 m, 276 m, and 252 m of OBRI, respectively (0.7%, 0.4%, and 0.3% of OBRI’s spatial extent). Marginal to sub-marginal habitats dominated the park for these three mussel species.

In this study Bradford’s (2008) approach for setting ecological flow and water level targets is tested and refined through application within the Lake Simcoe Region Conservation Authority’s (LSRCA) subwatershed of Lover’s Creek. A method for defining subwatershed objectives and identifying habitat specialists through expert input is proposed and tested. The natural regime of each streamflow and wetland site is characterized along with the hydrological alteration at each site. Potential ecological responses to the hydrologic alterations are then hypothesized for the different types of changes calculated at each site. Methods for setting overall ecosystem health and specific ecological objective flow targets are proposed and tested. These targets are integrated into a flow regime for each site and a process for using this information for decision making is suggested. Flow magnitude quantification is attempted using hydraulic modelling and sediment transport equations, however the data used were found to be inadequate for this application. The accuracy of the targets developed using the method presented in this paper is mainly limited by the accuracy of the hydrological model and quantified flow magnitudes. Recommendations for improving these components of the assessment are made. The unique approach and recommendations presented in this paper provide explicit steps for developing flow targets for subwatersheds within the LSRCA. This research contributes toward the advancement of EFA within the LSRCA, which provides opportunity for enhanced protection and restoration of ecosystem health across the watershed.<br>Lake Simcoe Region Conservation Authority