Academic literature on the topic 'Fish habitat assessment'

Compensation measures in response to Fisheries and Oceans Canada (DFO) Policy for the Management of Fish Habitat includes provisions for habitat creation and enhancement. Thus, an assessment of nearshore habitat utilization patterns by fishes is needed to put DFO compensation measures in the context of the "no net loss of the productive capacity of fish habitat" directive. Measures of abundance, richness, and diversity of fishes were compared across nine habitat types in a lake using rapid visual underwater assessment. Multivariate analyses separated habitats into three groups and identified two distinct species assemblages. Most species were associated with macrophytes, but a few were primarily associated with rocky substrate. Shallow mud (open) habitats contained significantly fewer species and had lower mean scores and diversity than all other habitat types. Rocky habitats had lower mean scores and diversity than some vegetated habitat types containing similar fish assemblages. Surprisingly, within-site fish assemblage heterogeneity was similar to among-site heterogeneity, and among-habitat heterogeneity was lower than within-habitat heterogeneity, further supporting our inability to distinguish among vegetated habitat types. Our results suggest that habitat heterogeneity is critical in maintaining diverse communities and that compensation measures should account for differences in fish–habitat associations among varied habitats.

Canada's fish habitat management is guided by the principle of "no net loss of the productive capacity of fish habitat" (NNL). Many development proposals are assessed using habitat information alone, rather than fish data. Because fish–habitat linkages are often obscured by uncertainty, uncertainty must be factored into NNL assessments. Using a quantitative framework for assessing NNL and lake habitats as a context, the implications of uncertainty for decision making are examined. The overall behaviour of a net change equation given uncertainty is explored using Monte Carlo simulation. Case studies from Great Lakes development projects are examined using interval analysis. The results indicate that uncertainty, even when large, can be incorporated into assessments. This has important implications for the habitat management based on NNL. First, schemas to specify relative levels of uncertainty using simple habitat classifications can support robust decision making. Second, attaining NNL requires greater emphasis on minimizing habitat loss and creating new areas to compensate for losses elsewhere and less on detailing small incremental changes in modified habitats where the fish response is difficult to demonstrate. Third, the moderate to high levels of uncertainty in fish–habitat linkages require that created compensation is at least twice the losses to reasonably ensure NNL.

The core assumptions of critical habitat designation are a positive relationship between habitat and population size and that a minimum habitat area is required to meet a recovery target. Effects of habitat on population limitation scale from (i) effects on performance of individuals (growth, survival, fecundity) within a life history stage, to (ii) limitation of populations by habitats associated with specific life history stages, and (iii) larger-scale habitat structure required for metapopulation persistence. The minimum subset of habitats required to achieve a recovery target will depend on the extent, quality, and spatial configuration of habitats available to sequential life history stages. Although populations may be limited by available habitat for a single life history stage, altering habitat quality for subsequent stages will also affect individual survival and population size, providing multiple leverage points within a life history for habitat management to achieve recovery targets. When habitat-explicit demographic data are lacking, consequences of uncertainty in critical habitat assessment need to be explicit, and research should focus on identifying habitats most likely to be limiting based on species biology.

A net change equation is derived for assessing no net loss of productivity of fish habitat (NNL). NNL is the guiding principle of the Canadian policy for the management of fish habitat. The equation provides a middle ground between the extremes of no conservation and no development. Projects affecting fish habitat are accountable for the productive capacity in loss areas and the difference between current and future productivities in modified areas. The equation implies quantitative conservation targets overall and loss-offsetting equivalencies in modified habitat areas. Generalization of the net change equation to heterogeneous habitats is illustrated with a development in a coastal wetland on the Great Lakes. The net change framework has implications for linkages between suitable habitat supply and fish population dynamics. Area fish habitat management plans envisioned in the policy and site-level net change assessments are connected. Quantitative ways are proposed for simultaneous assessment of NNL and ``harmful alteration, disruption, or destruction'' of fish habitat, as required in the Canadian Fisheries Act. Defensible methods for applying the net change equation are superior to earlier nonquantitative approaches. If the available science is insufficient, the precautionary principle is recommended. Future development steps for the quantitative net change framework are suggested.

We used a bioenergetic model to determine if cutthroat trout ( Oncorhynchus clarkii bouvieri ) abundance was related to net energy intake rates (NEI) and the proportion of suitable habitat and to evaluate potential changes in habitat quality due to climate change and stream fertilization efforts. We conducted monthly sampling of cutthroat trout, invertebrate drift, and physical habitat features in pool and riffle habitats. Fish in this study selected foraging positions that enabled them to maximize NEI, and most fish were capable of sustaining high growth rates from July to September. Mean NEI and the proportion of suitable habitat at sites were greater in pools relative to riffle habitats and declined from July to October, primarily due to a decline in temperature over the four months. Cutthroat trout biomass was significantly related to NEI and the proportion of suitable habitat at a site. Model simulations indicated that climate change might reduce habitat quality for small-bodied trout, while extending the growing season for larger fish. Increased food abundance provided only marginal changes to model outcomes, whereas reductions in food significantly reduced habitat quality.

A common assumption throughout the marine ecological and fisheries literature is that growth is a valid indicator of habitat quality and can be used as a criterion for designation of essential fish habitat (EFH). In this study, the validity of growth as an index of habitat quality was tested by examining how variability in otolith growth was related to abiotic and biotic environmental conditions and could be biased by previous growth history, density dependence, and selective mortality. The study was conducted with juvenile Atlantic croaker (Micropogonias undulatus) collected in two North Carolina, USA, estuaries during two seasons of two recruitment years. Water temperature, a component of habitat quality, explained nearly 40% of the variability in juvenile otolith growth. There was also evidence that estimates of growth could be biased by density dependence (slower growth at higher conspecific abundance) and by selective mortality (higher mortality of individuals with relatively slower larval and juvenile otolith growth). Studies using growth-based assessment of habitat quality that fail to identify factors underlying growth rate differences among habitats may reach incorrect decisions regarding quality of different habitats and assignment of EFH.

Abstract Stål, J., and Pihl, L. 2007. Quantitative assessment of the area of shallow habitat for fish on the Swedish west coast. – ICES Journal of Marine Science, 64: 446–452. Much effort has been focused recently on juvenile and adult fish habitat use in shallow coastal areas. However, to understand fully the importance of such habitats for fish production it is necessary also to quantify the area of existing habitat types. We inventory and quantify the area of major habitat types in a 1000 km2 area of the Swedish west coast, on a scale appropriate for coastal-zone management. An echosounder and GPS-transmitter mounted on a small boat were used to estimate the distribution of habitat along transects in seven regions of differing coastal morphology. The signal from the echosounder separated major habitat types, and recordings were verified by video documentation and visually. The information was used with GIS-software to estimate the quantitative extent of bottom habitats at depth ranges of 0–3, 3–6, and 6–10 m. Of the major habitat types, soft substrata dominated all except one region, and increased in size with depth in all regions. There were rocky substrata in all regions, but as steep rock walls in the north and more gently sloping substrata with pebbles and boulders in the south. Approximately half the rocky habitat was in the shallowest depth range. Seagrass meadows on soft substrata were mainly in the shallow protected archipelago of the central coast.

To explore the potential of assessments of stream geomorphic condition and habitat quality in evaluating lotic productivity, we investigated concordance of stream biotic productivity (aquatic macroinvertebrates, crayfish, fish, and belted kingfishers ( Ceryle alcyon )) and their physical habitat correlates in 18 streams in the Champlain Valley, Vermont, USA. Pearson correlation analysis indicated significant concordance between macroinvertebrate density and fish biomass (r = 0.76), between the density of macroinvertebrates in the orders Ephemeroptera, Plecoptera, and Trichoptera and fish biomass (r = 0.81), and between fish biomass and kingfisher brood weight (r = 0.54). We used principal component analysis followed by linear regression to investigate relationships between physical habitat condition and biotic productivity and to identify key components of physical habitat condition assessments. Our analysis supported the combined use of geomorphic and habitat assessments as a comprehensive indicator of stream physical habitat condition. We found relationships between habitat assessment scores and productivity measures of all taxa except crayfish, suggesting similar responses to physical condition across trophic levels. Our results encourage the use of additional taxa, in addition to widely used macroinvertebrate metrics, as indicators of the composite effects of physical habitat impairment in stream ecosystems.

When different genotypes choose different habitats to better match their phenotypes, genetic differentiation within a population may be promoted. Mating within those habitats may subsequently contribute to reproductive isolation. In cichlid fish, visual adaptation to alternative visual environments is hypothesized to contribute to speciation. Here, we investigated whether variation in visual sensitivity causes different visual habitat preferences, using two closely related cichlid species that occur at different but overlapping water depths in Lake Victoria and that differ in visual perception ( Pundamilia spp.). In addition to species differences, we explored potential effects of visual plasticity, by rearing fish in two different light conditions: broad-spectrum (mimicking shallow water) and red-shifted (mimicking deeper waters). Contrary to expectations, fish did not prefer the light environment that mimicked their typical natural habitat. Instead, we found an overall preference for the broad-spectrum environment. We also found a transient influence of the rearing condition, indicating that the assessment of microhabitat preference requires repeated testing to control for familiarity effects. Together, our results show that cichlid fish exert visual habitat preference but do not support straightforward visual habitat matching.

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 (<100mm in length) in these mesohabitats. Adult bony herring (>100mm 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 (<200mm length) were more abundant at night and aggregated in smooth and irregular banks more than any other mesohabitat patch. Adult carp (>200mm 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.
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.
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.
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.

AbstractIntroducing the main concepts of ERA Acute, this chapter describes the overall framework and purpose of the methodology. ERA Acute is a recently developed oil spill risk assessment (OSRA) methodology for quantification of oil spill impacts and risk (Environmental Risk Assessment, ERA). It covers four environmental compartments; sea surface (seabirds, turtles, marine mammals), water column (fish eggs/larvae), shoreline and seafloor (species and habitats) using continuous impact functions and introduces the Resource Damage Factor (RDF). The methodology depends on external oil spill modelling and input data related to the presence and vulnerability of Valued Ecosystem Components (VECs). ERA Acute is developed to provide an improvement over the currently used “MIRA” method on the Norwegian Continental Shelf (NCS) and is better suited for risk management, decision-making and analyses from screening studies to full environmental risk assessments.

<em>Abstract.—</em> The quality and quantity of habitats determine ecosystem productivity. Hence, they determine the potential fish productivity that sustains the fish harvests extractable from freshwaters and seas. Efforts to conserve and protect fish habitats are frustrated by key unanswered questions: which habitat types and how much must be protected to ensure natural self-sustaining fish stocks? Minns and Bakelaar presented a prototype method for assessing suitable habitat supply for fish stocks in Lake Erie, an analysis that can be used to address conservation issues. Here, the method is refined and extended, taking the assessment of habitat supply for pike <em>Esox lucius </em> in the Long Point region of Lake Erie as a case study. As with the previous study, much emphasis is placed on “learning by doing.” Because available inventories of habitat features are coarse and incomplete, improved guidelines for estimating habitat supply are expected from these prototype studies. The habitat supply method previously presented by Minns and Bakelaar is elaborated in three ways here: (1) the basic physical habitat assessment is derived from a remote-sensing inventory database; (2) methods of quantifying the thermal regime and integrating it with other habitat elements are examined; (3) habitat supply estimates are used in a pike population model, and pike biomass and production are simulated for the Long Point region of Lake Erie and then compared with available records. The roles of error and uncertainty are examined for all elements in the estimation and application of suitable habitat supply values. There is potential for supply measurement and analysis to guide fish habitat management.

<em>Abstract.—</em> The quality and quantity of habitats determine ecosystem productivity. Hence, they determine the potential fish productivity that sustains the fish harvests extractable from freshwaters and seas. Efforts to conserve and protect fish habitats are frustrated by key unanswered questions: which habitat types and how much must be protected to ensure natural self-sustaining fish stocks? Minns and Bakelaar presented a prototype method for assessing suitable habitat supply for fish stocks in Lake Erie, an analysis that can be used to address conservation issues. Here, the method is refined and extended, taking the assessment of habitat supply for pike <em>Esox lucius </em> in the Long Point region of Lake Erie as a case study. As with the previous study, much emphasis is placed on “learning by doing.” Because available inventories of habitat features are coarse and incomplete, improved guidelines for estimating habitat supply are expected from these prototype studies. The habitat supply method previously presented by Minns and Bakelaar is elaborated in three ways here: (1) the basic physical habitat assessment is derived from a remote-sensing inventory database; (2) methods of quantifying the thermal regime and integrating it with other habitat elements are examined; (3) habitat supply estimates are used in a pike population model, and pike biomass and production are simulated for the Long Point region of Lake Erie and then compared with available records. The roles of error and uncertainty are examined for all elements in the estimation and application of suitable habitat supply values. There is potential for supply measurement and analysis to guide fish habitat management.

<em>Abstract.</em> —The American lobster <em>Homarus americanus </em> is usually associated with rocky substrate that provides or can be modified into shelter and that may be an essential habitat to early benthic-phase juveniles. The dependence on shelter-providing habitat not only makes possible the definition of essential habitat for lobsters but also permits the assessment of abundance based on the areal extent of habitat. Here, we describe such a habitat-based assessment, performed in response to an oil spill on the coast of Rhode Island, USA. Results from a side-scan sonar survey performed after the spill indicated that the amount of lobster habitat affected by the oil was approximately 9.8 km2 along nearly 15 km of coastline. Postspill lobster density ranged from 0.24 lobsters m22 in the impact region to 1.63 lobsters m22 in the control region. Qualitative (map contours of lobster density) and quantitative (statistical tests) approaches suggested a significant effect of the spill had been detected by our sampling. An estimate of the total number of lobsters killed was required to scale restoration efforts. We calculated the total number of lobsters in the area by overlaying contours of lobster density on a habitat map generated by side-scan sonar, then multiplying the density of lobsters in each contour interval by the area of appropriate lobster habitat (cobble and boulder) in the contour interval. To calculate loss, we subtracted postspill abundance from prespill abundance. Prespill density was estimated to be 1.76 m22, which is an adjusted average of airlift samples taken at six Rhode Island sites four months prior to the spill. Calculations of loss based on habitat-specific density estimates were adjusted to reflect undersampling. The loss was estimated to be to be 9.0 × 106 lobsters. Variability associated with this loss estimate is large; 95% confidence intervals estimated that between 6.7 × 106 and 15.6 × 106 lobsters were lost. The calculated loss was very sensitive to changes in prespill density estimates; a change of 0.1 lobsters m22 resulted in a change of 0.75–0.9 × 106 lobsters lost. Habitatbased assessment of lobster population size is possible but requires detailed habitat maps and accurate density estimates. Natural variability and sampling limitations give such assessment a wide range of possible values. Nevertheless, the airlift sampling technique, together with sidescan sonar maps of habitat, could provide a powerful tool for estimating the abundance of inshore lobsters.

<em>Abstract.</em> —The American lobster <em>Homarus americanus </em> is usually associated with rocky substrate that provides or can be modified into shelter and that may be an essential habitat to early benthic-phase juveniles. The dependence on shelter-providing habitat not only makes possible the definition of essential habitat for lobsters but also permits the assessment of abundance based on the areal extent of habitat. Here, we describe such a habitat-based assessment, performed in response to an oil spill on the coast of Rhode Island, USA. Results from a side-scan sonar survey performed after the spill indicated that the amount of lobster habitat affected by the oil was approximately 9.8 km2 along nearly 15 km of coastline. Postspill lobster density ranged from 0.24 lobsters m22 in the impact region to 1.63 lobsters m22 in the control region. Qualitative (map contours of lobster density) and quantitative (statistical tests) approaches suggested a significant effect of the spill had been detected by our sampling. An estimate of the total number of lobsters killed was required to scale restoration efforts. We calculated the total number of lobsters in the area by overlaying contours of lobster density on a habitat map generated by side-scan sonar, then multiplying the density of lobsters in each contour interval by the area of appropriate lobster habitat (cobble and boulder) in the contour interval. To calculate loss, we subtracted postspill abundance from prespill abundance. Prespill density was estimated to be 1.76 m22, which is an adjusted average of airlift samples taken at six Rhode Island sites four months prior to the spill. Calculations of loss based on habitat-specific density estimates were adjusted to reflect undersampling. The loss was estimated to be to be 9.0 × 106 lobsters. Variability associated with this loss estimate is large; 95% confidence intervals estimated that between 6.7 × 106 and 15.6 × 106 lobsters were lost. The calculated loss was very sensitive to changes in prespill density estimates; a change of 0.1 lobsters m22 resulted in a change of 0.75–0.9 × 106 lobsters lost. Habitatbased assessment of lobster population size is possible but requires detailed habitat maps and accurate density estimates. Natural variability and sampling limitations give such assessment a wide range of possible values. Nevertheless, the airlift sampling technique, together with sidescan sonar maps of habitat, could provide a powerful tool for estimating the abundance of inshore lobsters.

<em>Abstract</em>.—Three adjacent tidal creek systems (Page, Kemps, and Broad creeks) on Cape Eleuthera, The Bahamas were studied to quantify the variation in fish community structure and habitat characteristics over small (<5 km) spatial scales. Snorkeling transects were used to census the fish community on a summer new moon during slack high tide and involved the simultaneous assessment of each creek and each zone within the creek (i.e., mouth, middle, and upper) replicated over three consecutive days. The simultaneous assessment (involving large teams) was done to enable direct comparison without spatial sampling being confounded by time. Habitat assessments included measurements of water quality parameters, sediment sampling, and vegetation surveys. Despite their close proximity, creeks differed in both fish community structure and habitat characteristics. Broad Creek had the greatest fish species richness (<em>n </em>= 15), followed by Kemps Creek (<em>n </em>= 14) and Page Creek (<em>n </em>= 10). Mangrove habitats had significantly greater fish species diversity in Broad Creek while sea grass habitats resulted in higher species richness in Page Creek, relative to other habitat types. Mangrove and algal plain habitats had the highest fish species diversity in Kemps Creek. Within creeks, fish abundance was dependent on zonation, with the largest number of fish being found in creek mouths compared to upper sections. Water quality parameters (i.e., temperature, dissolved oxygen, and salinity) differed among the creeks, presumably reflecting creek morphology. Out of the 10 different species of vegetation observed, 60% were found in all tidal creeks. Coarse sand was the predominant particle size for all creeks, with variation in the second most abundant particle size between Page Creek and the others. This study reveals the great heterogeneity of tidal creek fish community and habitat characteristics and illustrates that conservation and management strategies along with monitoring programs must recognize the variation that can occur among and within coastal creeks over relatively small spatial scales.

Since the early 1980’s TransCanada PipeLines Ltd. (TransCanada) has employed a number of stream bank stabilization measures in an effort to minimize the loss of fish habitat and to reduce the risk of long term erosion and sedimentation. Traditional stream crossing stabilization involved the re-contouring of streambanks to a stable slope (generally 2:1) and then lining the banks with rock armour and seeding. TransCanada began using alternate techniques, primarily log-walls in 1981. Since 1981 TransCanada has evolved the use stream bank stabilization techniques to include bio-stabilization techniques such as live log-walls, fascines, live staking, and brush layering in combination with more traditional structures. In 2004, TransCanada initiated a two year project to assess the success of biostabilization techniques used on a number of watercrossing throughout the its’ Alberta System. A total of 22 stream crossings were assessed in 2004 and 24 in 2005. Sites assessed were located the foothills and boreal forest areas of Alberta. In the majority of cases the biostabilization methods utilized were still intact and functioning as planned by providing stable streambanks and fish habitat. Several factors appeared to be influencing the value of the measures employed. Cattle grazing on sites where fencing did not exclude cattle from the crossing site resulted in destruction or reduced value of the measures employed. Uncontrolled All Terrain Vehicle activity resulted in a reduced value of the measure employed. Implementation of biostabilization techniques in the winter months (frozen ground conditions) created challenges in implementation of biostabilization measures resulting in less favorable results compared to other sites constructed in early and late fall. Seeding to control surface erosion also appeared to affect overall success of woody vegetation used as part of the biostabilization techniques. Biostabilization techniques employed by TransCanad have been effective in stabilizing watercrossings and providing fish habitat. In designing biostabilization systems for watercrossings consideration should be given to overall stabilization objectives, stream flow information, fish and fish habitat values, and likelihood of success given the geographic region, timing of construction, and surrounding land-use pressures.

The Fisheries Act legislates Fisheries & Oceans Canada (DFO) to regulate all development activities affecting fish-bearing waters to ensure no net loss in habitat productivity. To meet the increasing regulatory demands of oil and gas development, DFO is developing a Fisheries Risk Assessment Tool (FRAT). The current focus is along the Mackenzie River Valley, Northwest Territories. The FRAT is applied to proposed pipeline stream crossings and evaluates the risk to fisheries resources from geohazards causing sedimentation impacts. Ultimately, the FRAT may be applied across Canada to streamline DFO’s regulatory process for pipeline stream crossings. The FRAT consists of a Geophysical Database that characterizes physical attributes of the river valley and channel in the vicinity of a crossing, plus a Fisheries Database that characterizes the fisheries resources and habitat of the stream. Algorithms have been developed to quantitatively estimate sedimentation hazard likelihood and fisheries sensitivity, which are coupled in a qualitative risk matrix that assigns an overall risk rating to each stream crossing. The overall risk rating then designates the level of regulatory review and authorization process carried out by DFO under the Fisheries Act. Geohazard algorithms are being calibrated and tested using field data and stream crossing construction scenarios are being incorporated into the risk assessment tool. This paper describes the FRAT and its application in the Mackenzie Valley, and presents preliminary results from risk analysis of pipeline stream crossings.

This paper describes a multi-year program to assess pipeline crossings of sensitive watercourses along a major pipeline project. During the Front End Engineering and Design (FEED) phase a sensitive watercourse assessment team (SWAT) was established to provide a biophysical and construction assessment of selected watercourses to be crossed by a proposed pipeline project in western Canada. The SWAT comprised a fisheries biologist, a pipeline watercourse construction specialist and other technical support personnel. The field work included assessing biophysical data, fish habitat values, access to the crossing location, construction issues, site-specific mitigative measures and potential habitat compensation options, as well as providing photo documentation and a conceptual crossing sketch. The advantages of the SWAT assessment at a crossing site were: • It provided an effective and efficient field assessment of the proposed watercourse crossing in the early phase of the project. • It was a multidisciplinary assessment. • It provided a recommendation as to a preferred crossing location at the site. • It provided a recommendation as to preferred crossing method and timing of construction at the site. • The data were site-specific to the preferred crossing location. Three consecutive years of baseline biophysical field data were compiled and site reports generated using a custom designed database. Over 200 sensitive watercourses were identified based on environmental, geotechnical, and constructability factors and were visited by the SWAT team, sometimes more than once, for a total of 271 individual site assessments. Data collected during the FEED phase included site-specific information that can be used for ongoing project discussions, regulatory and community consultations, permitting and Fisheries and Oceans Canada (DFO) authorizations. The SWAT program also provided recommendations for minor or significant shifts in crossing location for 40% of the sites visited, resulting in changes to the pipeline alignment during the route evolution process.

Ocean sequestration of CO2 has been proposed as a possible measure to retard the increasing rate of the atmospheric CO2 concentration. Since some negative impacts on marine animals and ecosystems are likely to ensue, we must carefully investigate biological effects of ocean CO2 sequestration before embarking on this mitigation practice. Considering the expected depths for CO2 ocean sequestration (&gt; 1,000 m), it is desirable to use deep-sea animals for the experimental assessment of CO2 ocean sequestration. In addition, experimental protocols preferably mimic environmental conditions at the releasing site: CO2 concentrations vary due to mixing with surrounding seawater at low temperatures (0–2 °C) and under high pressures. This paper describes our recent experiments to elucidate the effects of high CO2 on marine fishes. A deep-sea fish Careproctus trachysoma (habitat depth 400–800 m) can be captured alive and be used for in vivo CO2 exposure experiments. 100% mortality occurred when the fish was exposed to seawater equilibrated with a gas mixture containing 3% CO2 conditions at 2 °C within 48 h, whereas mortality was never observed when shallow-water fishes (Mustelus manazo, Paralichthys olivaceus and Seriola quinqueradiata) were tested under the same CO2 conditions but at higher temperatures (17–20 °C). It is currently not clear whether this difference in mortality is due to often presumed high susceptibility of deep-sea organisms to environmental perturbations. Subsequent experiments demonstrated that low water temperature accelerates mortality by CO2 exposure. Thus, half lethal time decreased from 105h to only 5 h when water temperature was decreased from 26 °C to 20 °C (CO2 8.5%, Sillago parvisquamis). Therefore, the high CO2 susceptibility of C. trachysoma could be solely due to low water temperature. Temporally varying CO2 conditions resulted in markedly different mortality patterns when compare with mortality recorded under constant CO2 conditions. Step-wise increases in ambient CO2 resulted in much lower mortalities than under one-step increases to the same CO2 levels. Further, a sudden drop of CO2 from 9–10% CO2 to air level (0.038%) killed all the surviving fish within a few minutes.

Construction of the 493 km Corridor Pipeline System commenced in summer 2000, and is scheduled for completion in 2002. The system connects the two major components of the Athabasca Oil Sands Project — the Muskeg River Mine, north of Ft. McMurray and the Upgrader adjacent to Shell Canada Limited’s Scotford Refinery, near Fort Saskatchewan. The pipeline will also link the Upgrader with terminals in the Edmonton Area. The system includes dual pipelines (610 mm and 323.9 mm O.D.) as well as associated pump stations and valve sites. Corridor Pipeline Limited is a wholly-owned subsidiary of BC Gas Inc. Corridor pipeline crosses Hartley Creek near the south boundary of Shell’s lease C-13, north of Ft. McMurray, in the Ft. McKay First Nations traditional lands. An evaluation of the proposed crossing completed for the project application identified the location as highly sensitive to pipeline construction activities because of the high fish habitat quality and historical presence of sport and coarse fish. Although a fish survey completed for the above evaluation identified only coarse fish species, the provincial approval for the project required a trenchless crossing method unless authorized in writing by the Director. After completing detailed geotechnical and fisheries assessments of the crossing site, authorization from the director was subsequently obtained to complete the crossing using an isolation method. Planning and consultation with Ft. McKay First Nations to construct through their traditional lands incorporated aspects of traditional ecological knowledge. As part of the program, Corridor Pipeline committed to completion of a traditional plant survey. The results of the survey identified Hartley Creek as having cultural significance to the band. The riparian zone in this area supports a large concentration of food and medicinal plant species. Specialized mitigative measures were incorporated in order to maintain the density and diversity of the Hartley Creek riparian zone. This paper presents information with regard to the environmental studies and the regulatory process used to obtain approval to complete construction of the Hartley Creek crossing using an isolation method instead of the trenchless method originally required by the provincial government. It also explains the consultation program with the Ft. McKay First Nations and environmental planning used to maintain the density and diversity of riparian vegetation at this culturally significant crossing location.

The macrophyte thicket ecosystems of higher aquatic vegetation in the Neva Bay (NB) and Eastern Gulf of Finland (EGoF) perform many important roles, including acting as the habitats, nesting sites and migration sites for aquatic and semi-aquatic birds, creating the specific conditions necessary for the spawning and growth of many species of fish, and taking part in the self-purification of the aquatic ecosystems. Many anthropogenic disturbances, hydraulic works in particular, have a significant negative impact on these macrophyte thicket ecosystems. In recent years, the active growth of a new type of macrophyte thicket has been observed in the NB. This is due to the aftereffects of the construction of the Saint Petersburg Flood Prevention Facility Complex (FPFC). It is quite likely that the total macrophyte thicket area in these waters is currently increasing. In the future, it will be necessary to assess the environmental impacts of the hydraulic works on the macrophyte thicket of the NB and EGoF, taking into account the background processes of the spatiotemporal dynamics of the reed beds in the waters in question. To do this, it will be necessary to carry out a comprehensive study of these ecosystems and identify patterns in their spatial and temporal dynamics. The program of the study has been developed and is currently being implemented by Eco-Express-Service, a St. Petersburg eco-design company.

The macrophyte thicket ecosystems of higher aquatic vegetation in the Neva Bay (NB) and Eastern Gulf of Finland (EGoF) perform many important roles, including acting as the habitats, nesting sites and migration sites for aquatic and semi-aquatic birds, creating the specific conditions necessary for the spawning and growth of many species of fish, and taking part in the self-purification of the aquatic ecosystems. Many anthropogenic disturbances, hydraulic works in particular, have a significant negative impact on these macrophyte thicket ecosystems. In recent years, the active growth of a new type of macrophyte thicket has been observed in the NB. This is due to the aftereffects of the construction of the Saint Petersburg Flood Prevention Facility Complex (FPFC). It is quite likely that the total macrophyte thicket area in these waters is currently increasing. In the future, it will be necessary to assess the environmental impacts of the hydraulic works on the macrophyte thicket of the NB and EGoF, taking into account the background processes of the spatiotemporal dynamics of the reed beds in the waters in question. To do this, it will be necessary to carry out a comprehensive study of these ecosystems and identify patterns in their spatial and temporal dynamics. The program of the study has been developed and is currently being implemented by Eco-Express-Service, a St. Petersburg eco-design company.