Synthetic marine habitats such as artificial reefs (ARs) are deployed to offset marine habitat losses and aid conservation of marine communities, including species at risk. Though environmental benefit is often assumed, AR’s ability to support northern temperate marine fish communities has rarely been tested. The structural orientation and location of a reef can strongly influence biodiversity and productivity of faunal communities inhabiting it. For ARs, understanding how reef characteristics affect species and community composition are key in optimizing their use in conservation initiatives. I used ROV and sonar to survey threatened rockfish (Sebastes spp.) and other groundfish species associated with 18 ARs and natural reefs (NRs) along the northeast Pacific coastal shelf, along the coast of BC, Canada. In my second chapter, I investigate how ARs compare to NRs in achieving conservation objectives as measured by fish abundance and species richness. I found that community composition significantly differed between NRs and ARs. ARs had high variability in rockfish abundance, while NRs consistently supported intermediate rockfish abundances. Groundfish diversity was markedly greater on NRs. Depth and relief significantly explained variability in abundance and species richness. Interestingly, rockfish abundance was negatively associated with proximity to nearest rockfish conservation area. In my third chapter, I assess variation between AR fish communities on six reefs to better understand efficacy of meeting conservation objectives. I quantified structural characteristics of each reef using high-definition sonar data to create three-dimensional models and calculate measurements of reef structure. I also examined the effects of surrounding habitat associated with reef locations. I found that depth, conservation status, rugosity, and reef age significantly explained rockfish abundance. Groundfish species richness was significantly associated with conservation status, relief, reef size, and an interaction between depth and reef age. This research is a first step in proposing underlying mechanisms for differences between fish communities on ARs in BC, and which reef attributes facilitate successful contributions to conservation. Though ARs show promise in the conservation of some threatened species, the maintenance of diverse fish communities may depend on protection of heterogeneous natural reef communities. Given that a critical component of AR success is structure, using three-dimensional technologies can be used as a tool to understand species-habitat association on existing reefs and help predict the success of future reefs. / Graduate

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.

The goal of this research was to develop statistically robust ecosystem-based approaches, while optimizing data acquisition on relatively unexploited fish species in South Florida reefs, i.e., parrotfishes, Family Scaridae, in Biscayne Bay (with seasonal roller frame beam trawl surveys, 1996-2000) and Florida Keys (with annual Reef Fish Visual Censuses, 1997-2001), by following these steps: (I) analysis of information gaps for the stocks, including systematics, biogeography, population dynamics, reproductive ecology, trophodynamics, habitat use, and fisheries dynamics of Western Atlantic parrotfishes; (II) determination of primary research objectives from prioritization in Step I; (III) determination of essential fish habitats, ontogenetic shifts, migrations, and reef-seagrass habitat, from integration of stratified sampling design for fisheries-independent surveys, habitat selection theory-based analyses, and length-based analyses; (IV) estimation of population dynamics and fisheries-specific parameters encompassing life history demographics from empirical data or comparisons to theoretical expectations adapted to local conditions; (V) simulation modeling of a realistic range of fishing scenarios and demographic characteristics to evaluate the efficacy of potential traditional fisheries and spatial management strategies; and (VI) application of sampling optimization procedures and fisheries ecology approaches. Four scarid species had an estimated combined abundance of ca. 36.8 x 106 individuals in the Florida Keys. Connectivity among seagrass beds, coral reefs and deep waters had three major patterns: seagrass dwellers, reef dwellers, with inshore-to-offshore ontogenetic , and a seagrass-reef connection, using Biscayne Bay as an important recruitment ground. Marine protected areas of the Florida Keys National Marine Sanctuary did not show effects on abundance, size composition or spatial distribution of any parrotfish studied. Simulations suggested relatively short longevities (5-10 years), moderate body growth curvature, high instantaneous natural mortality rates (0.3-0.6 y super minus one), and low annual survival rates (27-54%). Simulated estimates of fishing mortalities ranged from 0.3 to 0.6 y super minus one, indicating low levels of exploitation, but low Spawning Potential Ratios (SPR = 23.5-26%). Proposed potential exploitation based on a legal minimum size equal to their size at first maturity and fishing rates equal or below to their natural mortality should secure SPR values at 45-48%.

Although flow deflectors are routinely placed in streams to create fish pool habitat, there is dissent in the literature as to what constitutes for them an appropriate design height to ensure their success. Our objectives were to (1) examine the temporal evolution of bed topography around submerged deflectors in a laboratory flume, for different deflector heights and discharge; and (2) quantify the flow dynamics in their vicinity. Results indicate that, all else being equal, higher deflectors (characterized by less overtopping) produce a greater volume of fish pools. In contrast, over a fixed deflector design, a higher discharge (synonymous with greater overtopping) results in larger pools, because flow velocities are then faster. We also observed differences in the temporal behaviour of scour: that next to high and medium height deflectors is self-similar, but not that for the shorter model. Our results challenge the notion that low deflectors are ineffective, provide information on the development of scour next to submerged structures, and reveal key differences between the geometry of the scour holes engendered by the different deflector height models.

A three-dimensional numerical model (PHOENICS) was used to investigate the role of stream deflector angle and length on the flow field in a rectangular laboratory flume. Subsequent bed topography surveys were performed to examine the role of obstruction angle on scour hole development over time. The model was capable of predicting laboratory velocity and turbulent kinetic energy measurements, performing better for flow over a flat stable bed than over a deformed sand bed. A new method of incorporating complex bed topography into a structured Cartesian mesh was developed in the process. Flow field properties such as dynamic pressure, velocity amplification, separation zone length and width, and downwelling extent and magnitude were found to be strongly dependent on deflector geometry. Equilibrium scour hole depths and geometry are also angle-dependent. A predictive equation was produced explaining the rate at which scour holes reach equilibrium, and compared well with existing literature. Finally, a method was developed whereby characteristics of the flow field over a flat, stable bed could be used to predict equilibrium scour hole geometry.

Thesis (Ph. D.)--University of Washington, 1998. / Vita. Includes bibliographical references (leaves [157]-174).

In the marine realm, there has been considerable habitat degradation caused by multiple human disturbances that often act synergistically, strongly affecting fish and invertebrate populations and, consequently, one of the major stakeholders of these resources, fishers. However, the mechanisms underlying how marine habitats support fisheries remain understudied. In this dissertation I examined the importance of fish habitat at global, regional and local scales in two distinct systems (mangrove habitats in the tropics and rockfish habitats in inshore waters of Vancouver Island) combining a suite of different approaches. First, I explored the mangrove-fishery linkage relationship by conducting a global meta-analysis. I found strong evidence supporting the importance of mangrove area to enhance fisheries. This relationship, however, varied across countries, likely based on regional geomorphological settings and fishery management policies. Subsequently, I determined the use of mangrove and adjacent habitats by fish in a tropical lagoon system in the continental Caribbean (Colombia), systems often overlooked in the Caribbean when analyzing mangroves as fish habitat. I collected fish with gillnets at different distances from mangroves and at different sites within the same lagoon system. While fish used mangroves, fish abundance was not higher in these habitats compared to adjacent ones, as predicted. However, diversity tended to be higher in mangroves. Nevertheless, the major driver affecting abundance, diversity and biomass was salinity. That is, diversity and abundance decreased as salinity increased. Next, I used a Local Ecological Knowledge approach to explore the mangrove-fishery linkage relationship because fishers are seldom incorporated into such relationships. By conducting semi-structured interviews I found that fishers fish close to their village and to mangroves, that in addition to fishing they use mangroves for firewood and as construction material. Fishers also agreed that mangroves are important for their fishing activity, as these habitats are critical for fish and crustaceans caught in the system. Finally, I examined the importance of derived benthic parameters for rockfish abundance and distribution at large spatial scales (100s km) in inshore waters of Vancouver Island. I established that higher complexity better explains presence and higher abundance of rockfish. Furthermore, the results provided valuable information for fishery and spatial management and habitat conservation to help recover rockfish populations. All together, these findings highlight the urgency to preserve coastal marine habitats for both juvenile and adult marine organisms to sustain small-scale fisheries as a food source and for traditional purposes. While conserving habitats is a key component of a broader and more complex ecosystem approach that includes overfishing and other anthropogenic pressures, in the absence of a holistic approach the chances of success are minimal. / Graduate / 2019-04-18

Some shallow (<7m, water depth) nearshore hardbottom areas of Southeast Florida have been reported to function as important juvenile habitat. I characterized the nearshore fish communities along a 30km stretch of coastline of Broward County, Florida from visual census data. Two-hundred transect-counts, 100 point-counts and 98 rover-diver counts were completed by myself and others during June-August, 2001. The abundance of all fish species and their sizes were recorded. The transects (30m long, 2m wide, 1m high) were laid perpendicular (compass heading 90°) to the innermost edge of hardbottom. Transects were placed every 152m of coastline. Altemately, a point-count or 20 min rover-diver count was also performed over the hard bottom just north of the 30m transect. All counts occurred between approximately 2m and 6m water depth. One hundred-sixty nine species and over 72,000 fish were recorded. Recently settled juveniles (≤ 5cm) were the dominant component (>80%) of the inshore fish community, consisting primarily (>90%) of grunts (Haemulidae).

Despite the increases in the intensity and frequency of disturbances on coral reefs in the Red Sea over the past decade, patterns of variability in fish communities are still poorly understood. This study aims to contribute to a better understanding of how fish communities vary along multiple spatial scales (10-100’ of kilometers) and to provide a baseline for future comparisons, fundamental to assess responses to climate change and other disturbances. Coral reefs along the Saudi Arabian Red Sea coast were surveyed from 2017 to 2019. The reefs ranged from 28° N to 18 °N and were categorized according their geographical location and grouped within three regions, namely north (24-28.5°N; 12 reefs), central (20.4-22.3°N; 11 reefs), and south (18.5-21.2°N; 30 reefs). The quantification of spatial patterns was conducted based on both taxonomic- and trait-based approaches. Considering the dependence of fish communities on the benthic habitat the relationship between different attributes of the fish assemblages and coral cover was also investigated. A consistent pattern of separation between assemblages of the northern and central region from the ones in the south was observed in nearshore reefs but was not evident for offshore reefs. The southern region supported higher densities, biomass, and species richness than the other two regions. The analysis showed that transect and reef scales contributed to the greatest variation in fish communities, suggesting higher levels of variability within small spatial scales. Several parameters of the fish community (total species, total density, total biomass, total functional entities, functional richness, functional redundancy) were positively correlated to coral cover, particularly in the northern region. Responses were not consistent across the Red Sea basin, suggesting that management plans should be regionally based. This study can be helpful to design management strategies as it provides a current baseline from both taxonomic and trait perspectives for Red Sea reefs that can be used to evaluate future changes due to natural and human-based disturbances.

In-stream concrete structures were studied through model tests and river tests. The model studies indicated that four designs provided good habitat in the model stream. These structures were the inverted weir, the "V" structure, the slab with legs and the cylinder. Through the river studies it was determined that these structures did not influence enough of the total river area to be effective in providing good fish habitat. Also an appreciable amount of yearly maintenance would be required to free the structures from silting in, debris, and vandalism. The slab with legs was the only promising structure.