Dissertations / Theses on the topic 'Marine habitat'

Virtually all marine conservation planning and management models in place or proposed have in common the need for improved scientific rigour in identifying and characterising the marine habitats encompassed. An emerging central theme in the last few years has been the concept of representativeness, or representative systems of Marine Protected Areas (MPAs). The habitat classification and mapping needed to incorporate considerations of representativeness into MPA planning must logically be carried out at the same scale at which management occurs. Management of highly protected areas occurs almost exclusively at local scales or finer, independent of the reservation model or philosophy employed. Moreton Bay, on Australia’s east coast, was selected for studies at the local scale to map and classify macrobenthic habitats. In a site scale (1 km) trial for the major habitat classification study, remote underwater videography was used to map and characterise an unusual assemblage of epibenthic invertebrates on soft sediments. The assemblage included congregations of the comatulid crinoid Zygometra cf. Z. microdiscus (Bell) at densities up to 0.88 individuals.m-2, comparable to those found in coral reef habitats. There was no correlation between the distribution of this species and commonly used abiotic surrogates depth (6 – 18 m), sediment composition and residual current. This site scale trial is the first quantitative assessment of crinoid density and distribution in shallow water soft-sediment environments. The high densities found are significant in terms of the generally accepted picture of shallow-water crinoids as essentially reefal fauna. The findings highlight the conservation benefits of an inclusive approach to marine habitat survey and mapping. Assemblages such as the one described, although they may be of scientific and ecological significance, would have been overlooked by common approaches to marine conservation planning which emphasise highly productive or aesthetically appealing habitats. Most habitat mapping studies rely solely or in part on abiotic surrogates for patterns of biodiversity. The utility of abiotic variables in predicting biological distributions at the local scale (10 km) was tested. Habitat classifications of the same set of 41 sites based on 6 abiotic variables and abundances of 89 taxa and bioturbation indicators were compared using correlation, regression and ordination analyses. The concepts of false homogeneity and false heterogeneity were defined to describe types of errors associated with using abiotic surrogates to construct habitat maps. The best prediction by abiotic surrogates explained less than 30% of the pattern of biological similarity. Errors of false homogeneity were between 20 and 62%, depending on the methods of estimation. Predictive capability of abiotic surrogates at the taxon level was poor, with only 6% of taxon / surrogate correlations significant. These results have implications for the widespread use of abiotic surrogates in marine habitat mapping to plan for, or assess, representation in Marine Protected Areas. Abiotic factors did not discriminate sufficiently between different soft bottom communities to be a reliable basis for mapping. Habitat mapping for the design of Marine Protected Areas is critically affected by the scale of the source information. The relationship between biological similarity of macrobenthos and the distance between sites was investigated at both site and local scales, and for separate biotic groups. There was a significant negative correlation between similarity and distance, in that sites further apart were less similar than sites close together. The relationship, although significant, was quite weak at the site scale. Rank correlograms showed that similarity was high at scales of 10 km or less, and declined markedly with increasing distance. There was evidence of patchiness in the distributions of some biotic groups, especially seagrass and anthozoans, at scales less than 16 km. In other biotic groups there was an essentially monotonic decline in similarity with distance. The spatial agglomeration approach to habitat mapping was valid in the study area. Site spacing of less than 10 km was necessary to capture important components of biological similarity. Site spacing of less than 2.5 km did not appear to be warranted. Macrobenthic habitat types were classified and mapped at 78 sites spaced 5 km apart. The area mapped was about 2,400 km2 and extended from estuarine shallow subtidal waters to offshore areas to the 50 m isobath. Nine habitat types were recognised, with only one on hard substrate. The habitat mapping characterised several habitat types not previously described in the area and located deepwater algal and soft coral reefs not previously reported. Seagrass beds were encountered in several locations where their occurrence was either unknown or had not previously been quantified. The representation of the derived habitat types within an existing marine protected area was assessed. Only two habitat types were represented in highly protected zones, with less than 3% of each included The study represents the most spatially comprehensive survey of epibenthos undertaken in Moreton Bay, with over 40,000 m2 surveyed. Derived habitat maps provide a robust basis for inclusion of representative examples of all habitat types in marine protected area planning in and adjacent to Moreton Bay. The utility of video data to conduct a low-cost habitat survey over a comparatively large area was also demonstrated. The method used has potentially wide application for the survey and design of marine protected areas.

Virtually all marine conservation planning and management models in place or proposed have in common the need for improved scientific rigour in identifying and characterising the marine habitats encompassed. An emerging central theme in the last few years has been the concept of representativeness, or representative systems of Marine Protected Areas (MPAs). The habitat classification and mapping needed to incorporate considerations of representativeness into MPA planning must logically be carried out at the same scale at which management occurs. Management of highly protected areas occurs almost exclusively at local scales or finer, independent of the reservation model or philosophy employed. Moreton Bay, on Australia’s east coast, was selected for studies at the local scale to map and classify macrobenthic habitats. In a site scale (1 km) trial for the major habitat classification study, remote underwater videography was used to map and characterise an unusual assemblage of epibenthic invertebrates on soft sediments. The assemblage included congregations of the comatulid crinoid Zygometra cf. Z. microdiscus (Bell) at densities up to 0.88 individuals.m-2, comparable to those found in coral reef habitats. There was no correlation between the distribution of this species and commonly used abiotic surrogates depth (6 – 18 m), sediment composition and residual current. This site scale trial is the first quantitative assessment of crinoid density and distribution in shallow water soft-sediment environments. The high densities found are significant in terms of the generally accepted picture of shallow-water crinoids as essentially reefal fauna. The findings highlight the conservation benefits of an inclusive approach to marine habitat survey and mapping. Assemblages such as the one described, although they may be of scientific and ecological significance, would have been overlooked by common approaches to marine conservation planning which emphasise highly productive or aesthetically appealing habitats. Most habitat mapping studies rely solely or in part on abiotic surrogates for patterns of biodiversity. The utility of abiotic variables in predicting biological distributions at the local scale (10 km) was tested. Habitat classifications of the same set of 41 sites based on 6 abiotic variables and abundances of 89 taxa and bioturbation indicators were compared using correlation, regression and ordination analyses. The concepts of false homogeneity and false heterogeneity were defined to describe types of errors associated with using abiotic surrogates to construct habitat maps. The best prediction by abiotic surrogates explained less than 30% of the pattern of biological similarity. Errors of false homogeneity were between 20 and 62%, depending on the methods of estimation. Predictive capability of abiotic surrogates at the taxon level was poor, with only 6% of taxon / surrogate correlations significant. These results have implications for the widespread use of abiotic surrogates in marine habitat mapping to plan for, or assess, representation in Marine Protected Areas. Abiotic factors did not discriminate sufficiently between different soft bottom communities to be a reliable basis for mapping. Habitat mapping for the design of Marine Protected Areas is critically affected by the scale of the source information. The relationship between biological similarity of macrobenthos and the distance between sites was investigated at both site and local scales, and for separate biotic groups. There was a significant negative correlation between similarity and distance, in that sites further apart were less similar than sites close together. The relationship, although significant, was quite weak at the site scale. Rank correlograms showed that similarity was high at scales of 10 km or less, and declined markedly with increasing distance. There was evidence of patchiness in the distributions of some biotic groups, especially seagrass and anthozoans, at scales less than 16 km. In other biotic groups there was an essentially monotonic decline in similarity with distance. The spatial agglomeration approach to habitat mapping was valid in the study area. Site spacing of less than 10 km was necessary to capture important components of biological similarity. Site spacing of less than 2.5 km did not appear to be warranted. Macrobenthic habitat types were classified and mapped at 78 sites spaced 5 km apart. The area mapped was about 2,400 km2 and extended from estuarine shallow subtidal waters to offshore areas to the 50 m isobath. Nine habitat types were recognised, with only one on hard substrate. The habitat mapping characterised several habitat types not previously described in the area and located deepwater algal and soft coral reefs not previously reported. Seagrass beds were encountered in several locations where their occurrence was either unknown or had not previously been quantified. The representation of the derived habitat types within an existing marine protected area was assessed. Only two habitat types were represented in highly protected zones, with less than 3% of each included The study represents the most spatially comprehensive survey of epibenthos undertaken in Moreton Bay, with over 40,000 m2 surveyed. Derived habitat maps provide a robust basis for inclusion of representative examples of all habitat types in marine protected area planning in and adjacent to Moreton Bay. The utility of video data to conduct a low-cost habitat survey over a comparatively large area was also demonstrated. The method used has potentially wide application for the survey and design of marine protected areas.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Environmental and Applied Science
Full Text

Rates of habitat alteration and degradation are increasing worldwide due to anthropogenic influence. On coral reefs, the loss of live coral reduces structural complexity while facilitating algal increase. In many coastal lagoons seagrass and corals are cleared to make room for cultivated macroalgae. This thesis deals with reef and lagoon habitat structure and how fish assemblage patterns may be related to physical and biological features of the habitat. It further examines assemblage change following habitat disturbance. Four studies on East African coral reefs concluded that both the abundance and species richness of recruit and adult coral reef fish were largely predicted by the presence of live coral cover and structural complexity (Papers I-III, VI). Typically, recruits were more selective than adults, as manifested by limited distributions to degraded sites. Paper VI compared short- and long-term responses of fish assemblages to the 1997-1998 bleaching event. The short-term response to coral mortality included the loss of coral dwelling species in favour of species which feed on algae or associated detrital resources. Counterintuitively, fish abundance and taxonomic richness increased significantly at one of two sites shortly after the bleaching. However, the initial increase was later reversed and six years after the death of the coral, only a limited number of fish remained. The influence of fleshy algae on fish assemblages was studied in algal farms (Paper IV), and examined experimentally (Paper V). The effects of algal farming in Zanzibar were significant. Meanwhile, manually clearing algal-dominated patch reefs in Belize from macroalgae resulted in short-term increases of abundance, biomass and activity of a few species, including major herbivores. The findings of this thesis demonstrate the significance of habitat as a structuring factor for tropical fish assemblages and predicts that coral death, subsequent erosion and algal overgrowth may have substantial deleterious impacts on fish assemblage composition, abundance and taxonomic richness, with recovery being slow and related to the recovery of the reef framework.

Bathymetrical mapping performed using multibeam sonar systems is widely used in marine science and for habitat mapping. The incoherent part of the multibeam data, the backscatter data, is less commonly used. Automatic classification of processed backscatter has a correlates well with three sediment classes, defined as fine-(clay-silt), medium- (sand) and coarse- (gravel–till) grained substrates. This relation is used directly as a theme in a modified habitat classification scheme, while a more detailed substrate classification is incorporated as another theme. This theme requires a manual interpretation and comprehensive knowledge of the substrate. This can partly be obtained by a newly developed technique using the backscatter strength plotted against the grazing angle. These plots make it possible to determine the critical angle and thereby calculate the compressional acoustic speed in seabed sediments. Marching a theoretical modeled backscatter curve to the measured backscatter strength at lower grazing angles provides estimates of four additional geoacoustic parameters.

The following four broad aims were addressed in this study. (1) To ascertain whether the characteristics of the benthic macroinvertebrate assemblages within the different nearshore marine habitat types identified by Valesini et al. (2003) on the lower west coast of Australia differ significantly, and whether the pattern of those spatial differences matches those among the environmental characteristics that were used to distinguish those habitat types; (2) To develop a quantitative approach for classifying nearshore habitats in estuarine waters that employs readily-available data for a range of enduring environmental characteristics, and to use that approach to classify the various habitat types present in nearshore waters of the Swan-Canning Estuary on the lower west coast of Australia; (3) To test the hypothesis that the characteristics of the benthic macroinvertebrate assemblages in the in the Swan-Canning Estuary differ significantly among nearshore habitat types, and that the pattern of those differences matches that among the environmental characteristics used to distinguish those habitat types and (4) To test the hypothesis that, as a result of environmental changes in the Swan-Canning Estuary, the characteristics of the benthic macroinvertebrate assemblages at various habitats in this estuary in 1986/7 differ from those in 2003/4. To address the first aim, benthic macroinvertebrates were sampled seasonally for one year in the subtidal waters and intertidal zone (upper and lower swash zones) at the six nearshore habitat types that were identified by Valesini et al. (2003) on the lower west coast of Australia. The habitat types, which differed mainly in the extent of their exposure to wave activity and whether seagrass and/or nearshore reefs were present, had been distinguished quantitatively using values for a suite of seven statistically-selected enduring environmental characteristics. The faunal samples yielded a total of 121 species representing eight phyla, among which the Polychaeta, Malacostraca and Bivalvia were the most speciose classes and contributed ~ 38, 23 and 10%, respectively, to the total number of individuals. The total number of species and mean density of macroinvertebrates was far greater at the most protected habitat type (1), which also contained dense beds of seagrass, than at any other habitat type, i.e. 70 species and 209.2 individuals 0.1 m-2, compared to 32 species and 36.9 individuals 0.1 m-2 at the most exposed habitat type (6), which had a substrate comprised only of sand. Differences among habitat type influenced the benthic macroinvertebrate species composition to a greater extent than differences among either zones or seasons. Significantly different faunal compositions were detected among those latter two factors only at the most protected habitat type. The faunal assemblage at habitat type 1 was clearly the most distinct from those at the other five habitat types, particularly in the subtidal zone (R-statistics=0.642-0.831, p=0.1%), and was typified by five abundant polychaete species that were adapted to deposit-feeding. In contrast, the fauna at habitat type 6 was typified by four crustacean species and a species of bivalve and polychaete, whose mobility and tough external surface facilitated their survival and feeding in those turbulent waters. The extents of the differences in species composition among the six habitat types was significantly matched with that among the suite of enduring environmental characteristics that distinguished those habitat types, particularly in the case of the subtidal zone (Rho=0.676). Such results indicated that the environmental variables used to distinguish the nearshore habitat types could be used to reliably predict the types of benthic macroinvertebrate species likely to occur at any site along the lower west coast of Australia. The above biological validation of the nearshore marine habitat classification scheme developed by Valesini et al. (2003) provided the justification for the approach to the second broad aim of this study, namely to develop a quantitative scheme for classifying habitat types in the Swan-Canning Estuary. This approach was similar to that employed by Valesini et al. (2003) in that it considers that differences among habitat types are well reflected by differences in a suite of enduring environmental variables. However, it improves on that earlier method by employing a completely objective and quantitative approach. Thus, a large number of environmentally-diverse nearshore sites (102) were initially selected throughout the Swan-Canning Estuary and a suite of 13 enduring environmental variables quantified at each using remotely-sensed images of the estuary in a Geographic Information System. Such variables were chosen to reflect either (i) the type of substrate and submerged vegetation present, (ii) the extent of exposure to wave action or (iii) the location of the site within the estuary with respect to its vicinity to marine and fresh water sources. These data were then subjected to the CLUSTER routine and associated SIMPROF procedure in the PRIMER v6 multivariate statistical package to quantitatively identify those groups of sites that did not differ significantly in their environmental characteristics, and thus represented habitat types. Eighteen habitat types were identified, which were shown to well reflect spatial differences in a suite of non-enduring water quality and sediment characteristics that were measured in situ at a range of estuarine sites during both summer and winter in 2005 (Rho=0.683 and 0.740, respectively, p=0.1%). However, those latter environmental characteristics required far more time in the field and laboratory to quantify than the enduring variables used to identify the habitat types. Benthic macroinvertebrates were sampled during summer and winter in 2005 in the shallow subtidal regions (~1 m depth) at sites representing eight of the habitat types identified in the Swan-Canning Estuary. These samples contained a total of 51 and 36 species during summer and winter, respectively, and, in both seasons, represented nine phyla, namely Annelida, Crustacea, Mollusca, Sipuncula, Nematoda, Platyhelminthes, Cnidaria, Uniramia and Nemertea. The compositions of the benthic macroinvertebrate assemblages differed significantly among habitat types and, to a similar extent, between seasons (Global R-statistic=0.408 and 0.409, respectively, p=0.1%). However, the spatial differences were considerable greater in winter than in summer (Global R-statistic=0.536 vs 0.280, p=0.1%), presumably due to the greater spatial variation in particular non-enduring in situ environmental characteristics, such as redox depth and salinity. While the number of species, overall density and taxonomic distinctness of benthic macroinvertebrates also differed significantly among habitats, those variables differed to a greater extent between seasons, being greater in winter than in summer. While the measures of taxonomic distinctness tended to be greater at habitat types located in the lower to middle reaches, i.e. habitat types 6, 7, 9, 10, 13 and 18, than the upper reaches i.e. habitat types 1 and 3, the number of species and overall density reflected this trend only during winter. During summer, the mean numbers of species at habitat types 1, 3, 6 and 10 (3.4-6.0) were significantly lower than those at habitat types 7, 13, and 18 (8.8-10.9), whereas the overall density of benthic macroinvertebrates was far greater at habitat type 7 (32260 individuals 0.1 m-2)than at any other habitat type in this season (3135-18552 individuals 0.1 m-2). Overall, the greatest differences in assemblage composition occurred between those at habitat types 1 and 18 (R-statistic=0.669, p=0.1%), which were located in the uppermost region of the estuary and the lower reaches of the basin, respectively, and differed to the greatest extent in their enduring environmental characteristics. The assemblage at habitat type 1, and also that at habitat type 3, located just downstream, were relatively distinct from those at all other habitat types, particularly during winter (R-statistics=0.666-0.993, p=0.1%). The fauna at the first of these habitat types was relatively depauperate, containing low numbers of species and densities, and was characterised by the polychaetes Leitoscoloplos normalis and Ceratonereis aequisetis and the bivalve Arthritica semen. The assemblage at habitat type 3 was also characterised by those three species and the amphipod Paracorophium minor and the polychaete Boccardiella limnicola. In contrast, the assemblage at habitat type 18 was characterised by a more diverse assemblage, i.e. the polychaetes Capitella capitata, C. aequisetis, L. normalis and Pseudopolydora kempi, the amphipods, Grandidierella propodentata and Corophium minor and the bivalve Sanguinolaria biradiata. The number of species was among the highest at this habitat type during both seasons, which was also reflected in the high taxonomic diversity, and the overall density was the highest in winter and second highest in summer. Despite the above faunal differences, those between assemblages at habitat types 7 and 9, which were both located in the basin of the Swan-Canning Estuary, were similar in magnitude to those that occurred between pairs of habitat types located in two different regions of the estuary. Although both habitat types 7 and 9 were characterised by a similar suite of species, i.e. Oligochaete spp., C. aequisetis, C. capitata, C. minor, G. propodentata, L. normalis, and S. biradiata, the substantial differences in assemblage composition between these habitat types in both summer and winter (R-statistics=0.570 and 0.725, respectively) was due to marked differences in the relative contributions of each of these species. Significant and strong correlations were shown to exist in both summer and winter between the pattern of differences in the benthic macroinvertebrate assemblages among habitat types and that among the enduring environmental characteristics used to identify those habitat types (Rho=0.625 and 0.825, respectively, p=0.1%). Furthermore, these correlations were greater than those obtained between the benthic macroinvertebrate fauna and any combination of the non-enduring environmental characteristics (i.e. water quality and sediment parameters) recorded in situ at each habitat type (Rho=0.508 and 0.824, in summer and winter, respectively, p=o.1%). This demonstrates the greater capacity of surrogate enduring environmental characteristics to account for differences in the range of variables that may influence the distribution of benthic invertebrate fauna. Thus, the lists of characteristic benthic macroinvertebrate taxa produced for each of the eight habitat types studied in the Swan-Canning Estuary provide a reliable benchmark by which to gauge any future changes in those fauna. Moreover, these results indicate that the above habitat classification scheme can be used to reliably predict the types of benthic macroinvertebrate fauna that are likely to occur at any nearshore site of interest in this estuarine system. The final component of this study showed that the benthic macroinvertebrate assemblages at four sites in the middle reaches of the Swan-Canning Estuary in 2003/4 differed significantly from those recorded at the same sites in 1986/7. Such differences were reflected in (1) changes in the relative densities of a suite of ten species that were responsible for distinguishing the faunas in these two periods, (2) the absence of 22 rare species in 2003/4 (i.e. 42% of the number of species recorded in 1986/7), (3) the presence of 17 new species in 2003/4, including an abundant polychaete that is likely to have been introduced and (4) a far greater extent of seasonal variation in the number of species and densities of benthic macroinvertebrates in 2003/4. Such changes are likely to be related to lower sediment oxygen levels in certain seasons in 2003/4, as well as an altered hydrological regime due to increased temperatures and decreased rainfall in that more recent period. The fact that these changes have occurred within the Swan-Canning Estuary highlights the need for effective management tools, such as the habitat classification scheme and associated faunal survey undertaken in this study. Such data will provide a sound basis by which to examine the ways in which fauna vary spatially within the system, and allow for the establishment of comprehensive benchmarks for detecting future changes.

Thesis (S.M.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2010.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student submitted PDF version of thesis.
Includes bibliographical references (p. 125-127).
In this thesis, I expand a spatially-explicit bioeconomic fishery model to include the negative effects of fishing effort on habitat quality. I consider two forms of effort driven habitat damage: First, fishing effort may directly increase individual mortality rates. Second, fishing effort may increase competition between individuals, thereby increasing density-dependent mortality rates. I then optimize effort distribution and fish stock density according to three management cases: (1) a sole owner, with jurisdiction over the entire fishery, who seeks to maximize profit by optimizing effort distribution; (2) a manager with limited control of effort and stock distributions, who seeks to maximize tax revenue by setting the length of a single, central reserve and a uniform tax per unit effort outside it; and (3) a manager with even more limited enforcement power, who can only set a tax per unit effort everywhere in the habitat space. I demonstrate that the economic efficiency of reserves depends upon model parameterization. In particular, reserves are most likely to increase profit (or tax revenue) when density-dependent fish mortality rates are affected. Interestingly, for large habitats that are sufficiently sensitive to density-dependent fish mortality effects, reserve networks (alternating fished and unshed areas of fixed periodicity) emerge. These results suggest that spatial forms of management which include marine reserves may enable signicant economic gains over nonspatial management strategies, in addition to the well-established conservation benefits provided by closed areas.
by Holly Villacorta Moeller.
S.M.

In this dissertation, I experimentally examine predation-induced mortality upon juvenile queen conch, Strombus gigas, and assess the importance of select habitat predator and conch characteristics affecting predation intensity. Experiments were conducted during the summer and early fall of 1987, 1988, 1990 and 1991 in seagrass beds and adjacent sand flats near Lee Stocking Island, Exuma Cays, Bahamas. These experiments indicate that various factors act interactively to produce habitat-specific mortality rates in queen conch due to predation. These include (1) habitat type, whereby seagrass beds offer some protection; (2) local population dynamics, such that populated seagrass beds appear to enhance conch survival; (3) population density in some seagrass beds, such that mortality is inversely density-dependent; (4) conch size, such that larger conch have higher survival rates, depending on the specific type of habitat; and (5) predation intensity and predator guilds, which likely differ across habitats, producing habitat-specific mortality rates. When integrated with complementary studies of queen conch trophodynamics, these results provide critical information regarding key ecological factors affecting conch survival. In particular, results from the hatchery-reared experiments demonstrate the potential use of hatchery-reared stocks in natural habitats, and hence a valuable option for enhancement of fishery stocks throughout the Caribbean. In general, the integration of results obtained in this dissertation, with complementary studies of queen conch trophodynamics, should provide valuable suggestions of queen conch habitats, densities and scales of patchiness producing highest survivorship and growth rates in nature.

The habitat associations between the caridean shrimp Nauticaris marionis and sessile epibenthic assemblages and substratum types of the Sub-Antarctic Prince Edward Islands were investigated. Twenty five stations, varying in substratum type, depth and location on the shelf and slope around the islands were sampled photographically with a towed benthic camera sled. At each station the substratum type was classified, sessile epibenthic cover was quantified through the use of digital quadrats and shrimp density was estimated. Results add to the broadly described distribution patterns of N. marionis by identifying specifically the habitat characteristics they generally utilize. The distribution of N. marionis was found to be influenced by a combination of substratum and sessile epibenthic assemblages, but not substratum type alone. Shrimp inhabited stations with >50 % biogenic cover on mud and gravel substrata, but were not found at stations with rocky-sand or rocky-mud substrata. Their distribution appears to also be influenced by depth, as shrimp were only found within a depth range of 50 - 160 m in this study. A strong correlation was found between N. marionis density and depth. Shrimp were found both inshore around the islands, and on the relatively shallow saddle between the islands. In comparison with previous studies, N. marionis was found at similar, if not higher, densities in this study, although they occupied a narrower depth range.

La biodiversità marina regola il funzionamento ecosistemico, responsabile della produzione di beni e servizi importanti per la biosfera ed il benessere umano. I cambiamenti climatici globali e le attività umane stanno alterando la biodiversità degli oceani ed il funzionamento ecosistemico. Al momento, partendo dalla consapevolezza che le sole misure di conservazione non sono sufficienti a invertire la degradazione degli ecosistemi, è riconosciuto che il restauro ambientale è una azione di cruciale importanza per far fronte a questa minaccia. Tuttavia, è necessaria una maggiore conoscenza scientifica per rendere efficaci azioni di restauro, specialmente negli ambienti profondi che sono largamente sconosciuti. Tra le maggiori attività che avranno impatti sugli habitat marini vi sono lo sfruttamento di risorse minerarie e la pesca a strascico, le quali, risospendendo particelle polimetalliche e sedimenti, avranno effetti principalmente sulle specie bentoniche. In questa tesi, il Corallium rubrum, specie strutturante di elevata valenza ecologica, è stato esposto a questi due tipi di particolato. Dopo la rimozione della fonte di impatto, questo organismo è in grado di recuperare parzialmente tassi di alimentazione e la sua integrità tissutale. Questo esperimento fornisce utili informazioni non solo per meglio comprendere gli effetti di tali attività su organismi bentonici, ma anche per definire possibili misure di mitigazione attraverso una modulazione appropriata della loro intensità e durata. Allevare in acquario specie di corallo minacciate potrà essere utile per futuri progetti di restauro che prevedono il trapianto di colonie donatrici. Una dieta appropriata da somministrare durante l’allevamento può avere effetti benefici sulla loro crescita ed il loro successo riproduttivo. In questa tesi, è stata studiata la selezione di cibo da parte di alcuni coralli profondi (Desmophyllum pertusum, Madrepora oculata and Dendrophyllia cornigera), i quali hanno mostrato una preferenza per il crostaceo Mysis relicta. I risultati ottenuti dalle analisi condotte sugli isotopi stabili hanno inoltre fornito nuove informazioni sulle nicchie trofiche occupate nel Mar Mediterraneo da queste specie. Una volta ampliate le conoscenze sugli habitat e le specie da restaurare, è necessario valutare l’efficacia delle procedure di rispristino che si vogliono applicare. In questa tesi, sono stati studiati gli effetti di due esperimenti pilota di trapianto della fanerogama Cymodocea nodosa e della gorgonia Eunicella singularis su attributi di funzionamento ecosistemico. I risultati ottenuti indicano che il trapianto di tali organismi, se opportunamente pianificato, non solo garantisce la loro sopravvivenza, ma può anche avere effetti positivi su processi ecosistemici chiave. Tuttavia, sono necessari ulteriori studi per valutare la possibile estensione di queste azioni per affrontare l'attuale scala spaziale di perdita di specie/habitat. Questo lavoro fornisce nuovi elementi per la comprensione dei potenziali benefici ecologici derivanti dal restauro ambientale e delle sue ricadute per la conservazione del capitale naturale.
Marine biodiversity regulates ecosystem functions, which are responsible for the production of goods and services for the biosphere and human well-being. Global changes and human activities are altering ocean biodiversity and ecosystem functioning. At present, stemming from the awareness that conservation and management are often not enough to halt and revert the degradation of threatened ecosystems, it has been recognized that active restoration is crucial to cope with this issue. More knowledge is needed to make restoration actions effective, especially for the largely unknown deep ocean. Two of the main activities that will alter marine habitats are ore exploitation and bottom trawling that, resuspending polymetallic and sediment particles, will affect benthic species. In this thesis, the habitat-forming species Corallium rubrum was exposed to these types of particles. After the removal of the disturbance, its feeding rates and tissue integrity partially recovered. This experiment provides new insights on the consequences of these activities as well as on potential mitigation strategies by properly modulating their intensity and duration. Rearing endangered corals in aquaria can be useful for future projects that aim to restore degraded reefs by transplanting healthy colonies. An appropriate diet may positively impinge on their growth or reproduction success. In this perspective, I studied the food selection of cold-water corals (Desmophyllum pertusum, Madrepora oculata and Dendrophyllia cornigera) was studied and these species showed a preference for the crustacean Mysis relicta. Stable isotope analyses provided also novel information on the trophic niches occupied by these coral species in the Mediterranean Sea. After expanding the knowledge on the habitat or the species to be restored, it is necessary to evaluate the effectiveness of the restoration actions that it might be applied. In this thesis, the effects of two pilot transplantation experiments of the seagrass Cymodocea nodosa and the gorgonian Eunicella singularis on ecosystem functioning of surrounding sediments have been studied. The results showed that transplantation can be effective and that it can have also positive effects on key-ecological processes. However, further studies are needed to assess the potential of scaling-up these actions addressing the present scale of species/habitat loss. This work provides new elements for a better understanding of the potential ecological benefits that can contribute to the conservation of the natural capital.

A wave energy park has been established on the Swedish west coast outside Lysekil and pioneer work about its interactions with the marine environment has been conducted. So far, little is known about the effects of offshore energy installations on the marine environment, and this thesis assists in minimizing environmental risks as well as in enhancing potential positive effects on the marine environment. The Lysekil research site is situated about two kilometres offshore and has been under development since 2005. During this time 26 “environmental devices”, without generators, consisting of a steel buoy attached via a wire to a foundation on 25 m depth have been placed out for ecological studies on macrofauna in surrounding sediments and on colonization of the foundations and the buoys. Sediment samples to examine macrofauna in the seabed have been taken during five seasons. Biomass, abundance and diversity of infauna in the test site were generally low, but higher than in a nearby control site. The species composition was typical for the area and depth. In addition to sediment analysis, the effect of wave power concrete foundations on the marine environment has been investigated by scuba diving. The surface orientation and its effect on colonization by sessile organisms was examined on the first five foundations, placed out in 2005, and observations of habitat use by fish and crustaceans were made. The results show a succession of colonization over time (three years of investigation) with a higher cover by sessile organisms on vertical surfaces. Mobile fauna abundance on and around the foundations was generally low. Three months after the deployment of the 21 new foundations in 2007, assemblages of mobile organisms were examined visually. Also here, mobile species exhibit a low density, but still higher than on surrounding soft bottoms. The edible crab used artificial holes in the foundations frequently. The foundations were placed in two different clusters, north and south, and the degree to which early recruits covered the foundations and the succession of epibenthic communities were documented during two years. Sessile organisms colonized the northern foundations more rapidly, producing a higher diversity which suggests that the placement of wave energy devices affects colonization patterns. Biofouling on buoys was examined and blue mussels, Mytilus edulis, dominated with a cover about 90%. Wave exposed buoys were particularly favoured by M. edulis which there had a higher biomass and larger shells compared to those on sheltered buoys. Biofouling on wave power buoys, independent whether these had a cylindrical or toroidal shape, was insufficient to markedly affect their energy production. Finally, the thesis incorporates a review describing wave power projects in general pointing out the need of future research on for instance no-take zones, marine bioacoustics and electromagnetic fields. The main conclusions are that large-scale renewable wave energy conversion will cause ecological impact primarily by adding new hard substrate to an area but not by harming organisms or decreasing biodiversity within wave power parks.

Previous psychological research has demonstrated the benefits of visiting natural environments, especially coastal areas. However, research within Marine Biology has shown that such visits can harm natural habitats. Consequently, this thesis uses an integrative approach to examine both the risks to the environment and benefits to the human visitors in the context of rocky shores (intertidal areas where solid rock predominates). This was investigated using seven studies that involved a range of methods. Perception-based surveys (Studies 1 & 2) explored the perceived impacts on the visitor, and the potential impacts these visits can have on the rocky shore. Study 3 then examined the impacts on visitors’ well-being & marine awareness directly using a before-after survey on current visitors to two rocky shores. The most prominent habitat threat (leaving rubbish) was then examined in greater detail. Studies 4 and 5 examined the effects of marine litter on individuals’ well-being using two laboratory experimental designs; comparing individuals’ quantitative (Study 4) and qualitative (Study 5) responses to natural and littered shores. The final two studies then focused on an activity that reduces marine litter: Study 6 adopted a pre-post design to examine the benefits of engaging in beach cleans for current volunteers, whilst Study 7 used an experimental design comparing beach cleans with two other coastal activities on a more naïve sample. Overall, these studies provide evidence that experiencing rocky shores are beneficial for well-being and marine awareness. Counteracting such benefits, litter left behind after recreational visits were found to be detrimental to individuals’ well-being. As one potential solution to this issue, beach cleans were found to have the same, and additional beneficial effects on the individual as other coastal activities. Thus, activities which have a relatively positive impact on the environment can also have similar if not additional benefits to the visitor. This programme of research shows the importance of taking a holistic, integrative approach that takes into account both the risks to the environment and benefits to the individual resulting from recreational visits to natural environments.

Complex oyster reefs created by the Eastern oyster, Crassostrea virginica, though once prominent features of the Chesapeake Bay region, have become relatively scarce in comparison to historic descriptions. This decline, caused by a combination of overfishing, disease, habitat destruction and pollution, this decline continues despite substantial restoration efforts that have spanned decades. In response to this decline, the states of Virginia and Maryland considered the intentional introduction of the non-native Suminoe oyster, C. ariakensis. Previous studies questioned the reef-building capability of this Crassostrea species, which may affect its habitat function. Through a combination of field and mesocosm studies, I examined the possibility that this non-native oyster species would provide an ecologically-functional equivalent of the native oyster species if introduced into Chesapeake Bay. Habitat complexity and associated benthic communities of experimental triploid C. virginica and C. ariakensis reefs were investigated at four sites of varying salinity, tidal regime, water depth, predation intensity and disease pressure in the Chesapeake Bay region (Virginia and Maryland). Four experimental treatments were established at each site: C. virginica; C. ariakensis; 50:50 of C. virginica: C. ariakensis; and shell only. Abundance, biomass, species richness, evenness, dominance and diversity of reef-associated fauna were evaluated in relation to habitat location and oyster species over a period of 21 months. Habitat complexity varied spatially, although no differences among complexity indices were associated with oyster species. Increases in vertical reef heights and surface rugosity were observed over time for all experimental reefs, and treatment effects were observed after 19 months of development, when C. ariakensis reefs exceeded the vertical heights of C. virginica reefs, removing any doubt regarding the Suminoe oyster's reef-building capability. Spatial comparisons of reef-associated macrofauna suggested functional equivalency between oyster species with respect to habitat at intertidal locations (where C. ariakensis survival was low), and at subtidal sites of low salinity. at subtidal locations of higher salinities, however, the numbers of organisms associated with C. virginica reefs per unit of oyster biomass were significantly greater than the numbers of organisms associated with C. ariakensis. Multivariate analyses of data from subtidal high salinity sites also revealed unique communities associated with C. virginica treatments, while mixed oyster species assemblages were functionally equivalent to mono-specific C. ariakensis experimental treatments. Temporal comparisons at one mesohaline subtidal site revealed that the observed effects of oyster species on habitat function in higher salinity locations are inconsistent over time and likely overshadowed by seasonal larval recruitment dynamics and local hydrodynamics. Though a common oyster reef trophic cascade between juvenile oysters, C. virginica; mud crabs, Panopeus herbstii; and oyster toadfish, Opsanus tau was successfully replicated during mesocosm trials, specific trophic interactions were not significantly affected by oyster substrate species or habitat complexity (as it was defined within the constraints of the experiment). Together, these experiments represent the first effort to quantify the potential habitat function of C. ariakensis in Chesapeake Bay, and provide evidence of species-specific similarities and differences in reef-associated communities.

Habitat fragmentation leads to small, isolated habitat patches in which ecological processes may differ substantially from those in larger, continuous habitats. Seagrass is a structurally complex but fragmented subtidal habitat that serves as a refuge from predation for juveniles of the blue crab, Callinectes sapidus Rathbun. I compared the effects of eelgrass ( Zostera marina L.) patch size and shoot density on juvenile blue crab survival both before (June) and after (September) shoot defoliation and cownose ray disturbance changed eelgrass habitat, and used artificial seagrass to determine the influence of eelgrass patch size on juvenile blue crab survival in the absence of covarying shoot density. Under natural conditions, eelgrass patch size, eelgrass shoot density and density-dependent cannibalism all influenced juvenile blue crab survival, but crab survival varied temporally. Crab survival was inversely correlated with eelgrass patch size in the absence of covarying shoot density, in contrast to patterns typically observed in fragmented terrestrial landscapes; this was likely due to low predator abundance in small patches. I tested the hypothesis that crab survival is maximized at an intermediate level of seagrass fragmentation due to the inverse relationship between crab survival and patch size by modeling the joint effects of patch size and proportional cover on juvenile blue crab survival. When I assumed predation on crabs to be independent of crab density, maximal crab survival (ca. 34%) occurred at intermediate values of seagrass fragmentation. Approximately 18% of crabs survived irrespective of the proportion of the landscape covered by seagrass when crab survival was assumed to be density-dependent. My findings indicate that (i) effects of habitat fragmentation on survival may differ between seagrass and terrestrial landscapes, (ii) seagrass habitat fragmentation has a significant but not overriding influence on faunal survival, and (iii) seagrass patch size, seagrass complexity, and blue crab density all influence juvenile blue crab survival, but their effects vary temporally. Habitat fragmentation studies should incorporate multiple scales of space and time, as well as potentially confounding environmental variables.

Estuarine habitats serve as important nurseries for many species of juvenile fishes and invertebrates. Due to concerns about declining fishery stocks and habitat degradation, it is critical that the value of different habitats be evaluated, so that areas that are most important can be prioritized for habitat conservation and restoration. This dissertation used Atlantic croaker (Micropogonias undulatus) as a model species to quantitatively examine patterns of early juvenile nursery habitat use, factors influencing growth and mortality, and to test the widely held assumption that ?growth is a valid indicator of habitat quality?. A unique aspect of this study was consideration of how growth and survival of juvenile Atlantic croaker were influenced by the joint effects of individual (larval and juvenile growth) and cohort (density-dependent) characteristics, as well as biotic and abiotic characteristics of the nursery. Late-larval and early juvenile Atlantic croaker were collected weekly, using a 1-m beam trawl in river, upper-estuary, and creek habitats of two estuaries (White Oak River estuary and Newport River estuary, North Carolina, USA), sampled during two seasons (fall and spring) of two recruitment years (2001-2002 and 2002-2003). Subsequent analysis of otolith microstructure was used to provide estimates of growth rates, population age structure, and mortality. Juvenile Atlantic croaker were most abundant in oligohaline river nursery areas (primary nursery area), with the upper-estuary serving as an important ?refuge? habitat following periods of high freshwater outflow that forced fish down-estuary. In addition to management implications (i.e., time and area closures of shrimp trawling), such flood events have important implications for growth-based assessment of habitat quality: A positive covariance between larval and juvenile growth was found only after periods in which croaker were displaced from river nursery areas, when food was apparently in short supply. Atlantic croaker cohorts from both estuaries also exhibited evidence for selective mortality favoring survival of individuals that were faster growing as larvae and early juveniles, as well as evidence for density-dependent growth (i.e., slower average cohort growth rates at higher conspecific density). The results of this study indicate that growth is not a robust indicator of habitat quality. Unless factors such as previous environmental history, density-dependence, and selective mortality are accounted for, growth-based assessment of habitat quality may reach incorrect conclusions regarding the value of different habitats.

The queen conch (Strombus gigas) is a large marine gastropod found throughout the tropical western Atlantic including Florida. Overfishing and habitat loss have led to Caribbean-wide population declines requiring regional protections. On Florida’s east coast, aggregations of conch were previously reported just south of a major shipping port near Ft. Lauderdale, unusually high latitude for the species. This study was designed to investigate the spatial extent and population demographics of the Ft. Lauderdale conch. In summer 2012, broad-scale population surveys were conducted to document benthic cover and conch distribution and size data along 72 random transects stratified across four habitats within 2 km north and south of the inlet. Younger conchs were found throughout the study area, but mostly in the colonized pavement west (CPW) habitat while old conchs were found exclusively at one CPW site south of the inlet. Significantly more conch were found on the CPW south habitat than any other. Benthic cover data suggests that CPW south may have a unique community composition dominated by macroalgae and sand. In summer 2013, the CPW south habitat was surveyed using cross-shelf transects measuring aggregation extent and demographics. Five hundred and twenty five conch were found, at a density of 495 conch per hectare. Confirmed mating sightings, females with eggs, and solitary egg masses were found indicating mating in this nearshore habitat is successful. Future research should include expanded broad-scale surveys to determine if other aggregations exist and monitoring to examine the effects of environmental change on this vulnerable species.

Marine predators such as seabirds, cetaceans, turtles, pinnipeds, sharks and large teleost fish are essential components of healthy, biologically diverse marine ecosystems. However, intense anthropogenic pressure on the global ocean is causing rapid and widespread change, and many predator populations are in decline. Conservation solutions are urgently required, yet only recently have we begun to comprehend how these animals interact with the vast and dynamic oceans that they inhabit. A better understanding of the mechanisms that underlie habitat selection at sea is critical to our knowledge of marine ecosystem functioning, and to ecologically-sensitive marine spatial planning. The collection of studies presented in this thesis aims to elucidate the influence of biophysical coupling at oceanographic fronts – physical interfaces at the transitions between water masses – on habitat selection by marine predators. High-resolution composite front mapping via Earth Observation remote sensing is used to provide oceanographic context to several biologging datasets describing the movements and behaviours of animals at sea. A series of species-habitat models reveal the influence of mesoscale (10s to 100s of kilometres) thermal and chlorophyll-a fronts on habitat selection by taxonomically diverse species inhabiting contrasting ocean regions; northern gannets (Morus bassanus; Celtic Sea), basking sharks (Cetorhinus maximus; north-east Atlantic), loggerhead turtles (Caretta caretta; Canary Current), and grey-headed albatrosses (Thalassarche chrysostoma; Southern Ocean). Original aspects of this work include an exploration of quantitative approaches to understanding habitat selection using remotely-sensed front metrics; and explicit investigation of how the biophysical properties of fronts and species-specific foraging ecology interact to influence associations. Main findings indicate that front metrics, particularly seasonal indices, are useful predictors of habitat preference across taxa. Moreover, frontal persistence and spatiotemporal predictability appear to mediate the use of front-associated foraging habitats, both in shelf seas and in the open oceans. These findings have implications for marine spatial planning and the design of protected area networks, and may prove useful in the development of tools supporting spatially dynamic ocean management.

Habitats of Chesapeake Bay have been altered due to anthropogenic impacts and climate change. Due to these human disturbances, seagrasses have been extirpated from many areas in lower Chesapeake Bay and persisting beds face future losses as water temperatures continue to rise. Further loss of seagrass habitat will negatively impact juvenile blue crabs (Callinectes sapidus) that use seagrass beds as nursery grounds. Habitat degradation allows for more successful introductions of exotic species, and the communities formed from the mixing of native and exotic species are known as emerging ecosystems. Gracilaria vermiculophylla, an exotic macroalga, may be an emerging nursery habitat for juvenile blue crabs in Chesapeake Bay; however the extent to which the alga is present and used as a nursery by juvenile blue crabs are largely unknown. I investigated algal distribution in the shallow littoral areas of the York River, a subestuary of Chesapeake Bay, over two years (2013 – 2014) and found that G. vermiculophylla presence correlated with salinity and that algal presence and biomass increased with seagrass presence, although biomass was generally low. The alga was present in areas where seagrasses have been lost, and is therefore likely providing nursery habitat in these areas of high megalopal recruitment. Benthic epifaunal communities had lower species richness and were less abundant in G. vermiculophylla relative to seagrass, while benthic infaunal communities had lower species richness but similar abundance in the alga relative to seagrass. Juvenile blue crab densities were similar in the alga and seagrass, although seagrass supported about 3 times as many first and second instar crabs than G. vermiculophylla. Young juvenile blue crabs preferred seagrass, which may be due to epifaunal prey preference, and G. vermiculophylla likely represents a secondary nursery habitat. Juvenile blue crab growth rates of crabs 15 – 50 mm carapace width were similar in the alga, native seagrass, and unvegetated habitat, indicating that growth does not drive ontogenetic shifts in habitat use by larger (20 – 30 mm carapace width) juveniles. Similar growth rates also suggest that G. vermiculophylla performs similarly to seagrass as a nursery habitat in terms of providing resources for growth. Simulations of density-dependent migration of young juvenile blue crabs between habitat types suggest that G. vermiculophylla may mediate continued seagrass loss, at least in part. Together, these results increase our understanding of an emerging Chesapeake Bay ecosystem and the impacts that changes to nursery habitats have on the juvenile component of the blue crab population.

Bottlenose dolphins (Tursiops truncatus) exhibit variable distribution patterns, depending upon their geographic location. Habitat utilization patterns in Biscayne Bay, Florida, were examined using the Biscayne Bay Bottlenose Dolphin Photo-ID database obtained from the National Oceanic and Atmospheric Administration (NOAA) Southeast Fisheries Science Center (SEFSC) Miami Laboratory. Habitat coverages in Biscayne Bay were obtained from the Atlas of Marine Resources Version 1.3B CD and the Biscayne Bay National Park CD. Dolphin sightings were overlaid on the habitat coverages using GIS Arcview software. The effects of habitat, season, behavior, zone (sectioned area of Biscayne Bay), and depth on patterns of bottlenose dolphin distribution were examined by analysis of variance to determine the significance of the factors. The total number of dolphins observed during the sightings analyzed was 1,538. The number of dolphins per sighting varied from 1 to 28 dolphins, with a mean of 5.14. The average number of dolphins per survey effort was 10.32. Several significant changes in habitat have occurred between 1991-1992 to 1997. The changes in habitat had some influence on the dolphins’ behavior distribution. The highest proportion of all behavior types was found in moderately dense seagrass beds and dredge bottom areas. Habitat quality (habitat types) of Biscayne Bay influenced dolphin sightings, while habitat quantity (habitat area) influenced dolphin numbers. Analysis of variance statistics supported the strong significant effect of habitat on the variation of sightings and dolphin numbers (P < 0.001). No significant difference in sightings was found between seasons or zones throughout the study period. The fall season had the lowest number of dolphins and sightings. The low number of surveys during the fall season does not account for all the influence on the dolphin numbers. Strong significant differences were observed between behaviors (P < 0.001). The majority of initial behaviors included traveling, feeding, and socializing. Changes in behaviors were apparent as observations continued. It was determined that the proximity of the research vessel and the duration of observation influenced dolphin behavior. Tail slap and chuffing behavior and boat interaction doubled and quadrupled, respectively during sightings. A strong variation in the number of sightings and number of dolphins occurred between different depths (P < 0.001). The majority of dolphins were observed in depths of 2.1 - 3 meters. This coincides with the fact that the majority of Biscayne Bay depths are within that range. A time series analysis was performed to determine if there was a cycle present in the pattern of dolphin distribution, and no significant cycle was found. Future analysis of dolphin composition (resident, migratory, nomadic) may yield cyclic patterns.

This thesis uses data collected between 2007 and 2010 in an intensive, effort-based visual monitoring survey in southwest Cornwall, UK. The survey was carried out from a strategic watchpoint overlooking a regionally unique seabed feature, the Runnelstone Reef, which has previously been identified as key site for all three of the study’s target species: harbour porpoise Phocoena phocoena, basking shark Cetorhinus maximus and Balearic shearwater Puffinus mauretanicus. The location of the survey site is perceived as a productive, coastal marine ‘hotspot’ by local wildlife observers, eco-tour companies, conservation bodies and commercial fishermen. The aim of the study was to use a multidisciplinary approach to investigate the drivers behind the increased abundance and diversity of mega-vertebrates at the site. A wide range of environmental data, from fine-scale bathymetry to remote-sensed oceanographic data, were utilised in an attempt understand the potential interactions between the target species and the environment at a variety of scales. Although the target species have very different ecologies and each represent a different taxonomic Class; they each face significant threats throughout their range due to human impacts and are all listed as species of conservation concern on a number of UK, European and International Directives and Conventions. Therefore, improving our understanding of their distribution and highlighting interactions between the animals and their environment is an important objective, both for science and conservation. Harbour porpoise sightings showed significant fine scale temporal clustering associated with tidal flow, as well as spatial clustering around parts of the survey area with steepest seafloor slopes. The timing and location of highest porpoise densities coincided with tidal-topographically controlled hydrodynamic features identified using fine-scale current profile data (ADCP). The sightings and acoustic monitoring (C-POD) data both showed a high amount of temporal variability at seasonal, daily and hourly scales, highlighting the complex nature of the fine scale animal-environment interactions. Daily patterns in basking shark sightings data were investigated as a function of physical environmental covariates, with particular focus on the effect of meso-scale thermal fronts. In line with previous national scale studies of the species, shark sightings were significantly affected by sea surface temperature (SST) and there was evidence for a change in seasonal abundance compared to the long-term pattern. In addition, the variance of SST over the preceding weeks was identified as being a key predictor of the abundance of sharks in the survey area. Surprisingly, there was not a significant effect of the presence, persistence or thermal gradient strength of fronts on daily shark sightings. The implications of this result are discussed with reference to results of previous studies and the focus of marine protected area policy in the UK. The broad scale spatio-temporal analyses of Balearic shearwater sightings data from the UK, Ireland and France indicate that the birds continue to be recorded in significant numbers throughout areas previously considered to be at the northernmost extent of their range. Record counts of passing birds were recorded off southwest UK in the last two years, along with unprecedented aggregations in bays along the Brittany coast, comprising approximately 20 % of the estimated global population. The data presented provide much-needed quantitative information on the at-sea distribution and behaviour of this Critically Endangered species during the interbreeding period, and support earlier studies suggesting a northwards shift in their migratory distribution.

Understanding the relationship between habitat and fish distribution is a central component in the recent shift towards ecosystem based fisheries management (EBFM). Determining the habitat requirements of commercially and ecologically important species will be essential if spatial management strategies such as marine protected areas (MP As) are to be used successfully to conserve marine resources. A review of demersal fish habitat research highlighted numerous areas lacking in this field of habitat science. These included the propensity for studies to focus on abiotic habitat variables such as depth and sediment over large spatial scales (≥ 100s km²) and the low number of studies analysing biotic habitat variables in general. I conclude that development of sound predictive science in this field is reliant on a change in research focus toward reductions in study scale, or increases in resolution for abiotic habitat variables and more integration of biotic variables into studies. The three field studies included in this thesis analyse the importance of prey resource for the distribution of demersal fishes over spatial scales ranging from hundreds of metres to tens of kilometres. The first study investigates the relationship between prey and predator abundance and prey size and predator mouth gape size for nine demersal fish species around the Balearic Islands in the Mediterranean. The results demonstrate that prey abundance and size are of significance for some demersal fish species feeding primarily on benthos and will help in defining habitat requirements of demersal fish species. Demersal fish feeding ecology is studied in more depth when I investigate the effects of a bottom trawl fishery on an invertebrate benthic community and the subsequent effects this has on two commercially important flatfishes (P. platessa and L. limanda). This chapter closes the gap between the effects of bottom fishing on benthic communities and the reduced condition of some fishes found within these areas. The results of this study suggest that alterations in prey abundances, sizes and availabilities caused by chronic bottom trawling may lead to reduced feeding efficiencies, particularly for species with narrow prey spectrums. This in turn could result in reduced conditions of affected fishes living in chronically disturbed areas. The final data chapter uses detailed habitat maps, based on differences in sediment characteristics between three sites to take a small spatial scale, high resolution approach to describing demersal fish habitat. This investigates changes in the feeding ecology of a demersal fish species, Callionymus lyra, with body length. Although significant differences in prey size and prey taxa selectivity were found, no significant relationships between prey resource and predator distribution were apparent for any of the year classes analysed. The potential ecological and methodological reasons for these findings are discussed in-depth. Finally, a general discussion examines the main findings and suggests areas for future development.

I used 1.75 m&\sp2& drop rings and throw rings to sample communities of nekton at high and low tides in contiguous salt marshes, unvegetated flats, and seagrass beds (Ruppia maritima) of lower Chesapeake Bay. Thirty-two species of nekton were captured between June and October 1995, with a mean overall abundance of 28.6 inds m&\sp{lcub}-2{rcub}& and a mean biomass of 3.8 g m&\sp{lcub}-2{rcub}& (dry weight, dw). Blue crabs, Callinectes sapidus, were the biomass dominants and used seagrass and marsh edge habitats extensively from recruitment to maturity. Palaemonetes shrimp were the most abundant nekton; patterns of allopatry and apparent sympatry were found among the three species present. Menidia menidia used the marsh surface at night. Behavioral patterns for marsh residents Fundulus heteroclitus, F. majalis, Lucania parva, Gobiosoma bosc, and P. intermedius differed from patterns reported elsewhere. This suggests behavioral flexibility in habitat use between regions. Seagrass and marsh edges supported a large biomass of nekton. Secondary production on the marsh surface was estimated at 7.4-8.0 gdw m&\rm\sp{lcub}-2{rcub}150\ d\sp{lcub}-1{rcub}& (28.4-30.7 gww m&\rm\sp{lcub}-2{rcub}150\ d\sp{lcub}-1{rcub}&) between June and October 1995 (150 days). Gut contents of predators were examined, and a mathematical model was constructed to estimate consumption and export by nekton. Predation on invertebrates was highest in marsh edge areas, at 44.2 gdw m&\rm\sp{lcub}-2{rcub}150\ d\sp{lcub}-1{rcub}& removed; predation at the edge by transients (export) was 28.0 gdw m&\rm\sp{lcub}-2{rcub} 150\ d\sp{lcub}-1{rcub}.& The value of marsh edge was clearly linked to both vegetated and unvegetated components as refuge and feeding. Predation in the entire marsh was approximately 13 gdw m&\rm\sp{lcub}-2{rcub} 150\ d\sp{lcub}-1{rcub},& and transient export was 5.6 gdw m&\rm\sp{lcub}-2{rcub} 150\ d\sp{lcub}-1{rcub}.& Most export from marsh interior habitats was via blue crab predation on Uca and Sesarma. Predation in unvegetated areas was 13.3-17.0 gdw m&\rm\sp{lcub}-2{rcub} 150\ d\sp{lcub}-1{rcub};& export was 8.0-11.7 gdw m&\rm\sp{lcub}-2{rcub}150\ d\sp{lcub}-1{rcub}.& The unvegetated intertidal was an important resource for nekton due to lengthy inundation and abundant polychaete prey. The trophic contribution of each habitat was significant. Marsh, unvegetated, and seagrass habitats function together in this area to provide feeding and refuge for intertidal nekton.

Coastal seagrass ecosystems are complex habitats that are increasingly influenced by human perturbations. Disturbances that affect the strength of bottom-up (i.e. resource availability) and top-down (i.e. consumer) controls may also influence biomass distribution between trophic levels, sediment biogeochemistry, and seagrass ecosystem metabolism. Here, I experimentally tested how top-down and bottom-up perturbations interact with community structure (diversity, food chain length of epibenthic consumers) to alter sediment biogeochemistry and ecosystem metabolism in an experimental eelgrass (Zostera marina ) system. My data indicated that resource availability influenced SOM composition and ecosystem metabolism. Light availability tended to be a stronger determinant of SOM composition while nutrient enrichment affected secondary production of invertebrate grazers more strongly than primary producers or SOM. Top-down predator effects on SOM composition and ecosystem flux rates tended to be weak. However, the strength of the trophic cascade may partly be a function of grazer community composition and grazer susceptibility to predation. Finally, my results indicated that grazer species identity and community composition strongly influenced SOM composition. In addition to the main effects of light, nutrients, predators, and grazers there were a variety of interactive effects between resources and food web composition. Consequently, the effects of resource availability and food web composition on seagrass ecosystem functioning should not be considered in isolation.

Dwarf sperm whales, Kogia sima, are among the most commonly stranded yet least known pelagic cetaceans. I assessed seasonal and spatial variation in dwarf sperm whale group size and abundance off Great Abaco Island, the Bahamas. After correcting for survey effort and variation in sighting efficiency among sea states, I found that dwarf sperm whale group size and habitat use varied seasonally. In summer, dwarf sperm whale groups were small (median = 2.5, range = 1-8) and were found only in the two deep habitats within the study area (slope 400-900 m, deep 900-1600 in). In winter, group sizes increased (median = 4, range = 1-12) and sightings were almost six times higher in the slope habitat, where vertical relief is highest, than other habitats. My results suggest that studies of pelagic cetaceans and conservation plans must explicitly account for seasonal variation in group size and habitat use.

Includes bibliographical references.
The aims of this study were to investigate elements of the demographics, fine-scale habitat use and site fidelity of sevengill sharks. The study was conducted at an aggregation hotspot within a Marine Protected Area, near Miller’s Point in False Bay, South Africa.

Top predators serve important roles within their respective ecosystem through top-down and bottom-up effects, yet understanding how these roles vary among individuals within predator populations is still in its early stages. Such individuality can have important implications for the functional roles predators play within their respective ecosystems. Therefore, elucidating the factors that drive persistent individual differences within populations is crucial for understanding how individuals, and in turn populations, will respond to environmental changes and anthropogenic stressors, and the implications of these responses for particular ecological functions. In this dissertation I investigated the movements, residency patterns, and trophic interactions of a juvenile bull shark (Carcharhinus leucas) population in a coastal estuary that serves as a nursery. I found that bull sharks undergo ontogenetic niche shifts in their diets and habitat use, with a gradual shift from using freshwater and estuarine resources to marine resources as sharks grew. This behavioral shift appeared to be driven by age-based differences in tradeoffs between safety from predators and availability of prey. Nested within population-level trends in behavior, there was considerable, and consistent, individual variation in both movements and trophic interactions suggesting individual specialization and divergent behavioral tactics within the population. Different behavioral types likely play different roles in food web connectivity and ecosystem dynamics, thus understanding the drivers and importance of phenotypic variability among species will be crucial for improving management strategies and predicting the responses of species and ecosystems to impending changes in environmental conditions and human impacts.

Seagrasses modify the coastal areas they occupy by trapping sediments and improving water clarity, providing habitat for marine animals, and cycling nutrients. Populations are in decline worldwide, and in the lower Chesapeake Bay, U.S., Zostera marina populations are decreasing due to poor water quality and high summertime temperatures. Ruppia maritima, a seagrass that is smaller, but has a greater tolerance of high temperatures than Z. marina, is replacing Z. marina in some areas. This study examined bed characteristics and microbial community structures of each seagrass species, as well as mixed assemblages, at three sites in the lower Chesapeake Bay where R. maritima has been replacing Z. marina over recent years. The objective of this study was to determine the potential of R. maritima to ameliorate detrimental effects of Z. marina loss. Samples were taken in June and August of 2013. In contrast to expectations that R. maritima would increase in abundance by August, R. maritima biomass and density decreased. Sediment grain size showed interactions between site and habitat type; two sites of the three showed greater mean fine sediments in Z. marina than R. maritima stands. Where sediment erodibility was measured, eroded mass was greater in the Z. marina sediment compared to the R. maritima sediment in June, while eroded mass was greater in R. maritima sediment in August. This suggests that sediment trapping capabilities may differ seasonally between the two species, with Z. marina generally capable of trapping more fine sediments than R. maritima; however this capability may be affected by location and season. Z. marina provided better quality habitat for epifauna in the early summer, but results from late summer were inconsistent as both species died back. Microbial communities, which affect sediment nutrient cycling, were found to be similar among sediments occupied by both species of seagrass, although the effects of site and month were strong. There was also a greater relative abundance of sulfate reducers in the August samples than the June samples. Overall, the results demonstrate that although the quality of some ecosystem services were greater in Z. marina compared to R. maritima, R. maritima still possessed the ability to provide valuable ecosystem services, and could be considered as a restoration option in the Chesapeake Bay, especially in areas where the potential for Z. marina regrowth is low.

Global biodiversity is in decline, with the marine environment experiencing significant and increasing anthropogenic pressures. As a response, very large (105–106 km2) marine protected areas (MPAs) have become the dominant form of environmental protection in the marine environment. At present, however, paucity in scientific sampling makes prioritising which regions of the ocean to protect, especially over such large spatial scales, particularly problematic. One such very large MPA, covering an area of over 1 million Km2, is located at the sub-Antarctic South Georgia and South Sandwich Islands (SGSSI). This study uses the SGSSI MPA as a model system to assess the application of benthic habitat mapping as an evidence-based framework for the spatial prioritisation of marine conservation. This study presents an interdisciplinary methodology to marine landscape mapping, as a top-down, objective statistical approach to hierarchically partition and map the benthic environment into physical habitats types. Ordination analysis demonstrates a statistically significant relationship between environmentally-derived landscape mapping clusters and the composition of benthic species data from the region, thus attributing ecological relevance to the marine landscape map. Furthermore, this study adopts a bottom-up approach to habitat mapping, using an ensemble of habitat suitability models. Potential distributions are modelled for a range of benthic faunal attributes relevant to marine management, based on taxonomic classification, functional traits and vulnerability to disturbance. These modelled distributions are used to describe, for the first time, the bio-physical characteristics of SGSSI’s benthic environment. Synthesising both top-down and bottom-up approaches to habitat mapping, this study assesses the physical landscape clusters and modelled distribution results in relation to the spatial protection currently enforced at SGSSI. This synthesis addresses, (i) whether marine spatial planning in the region is representative in terms of the habitats and fauna it protects; and (ii) whether this interdisciplinary methodology at SGSSI can inform on MPA design and designation more universally, in what is an increasingly exploited, yet still poorly understood marine environment.

I examined small mammal demography and habitat associations in 4 forest cover types on Quantico Marine Corps Base, VA. Study sites included clearcut, shelterwood, mature-riparian, and mature-upland habitats. My primary objective was to determine whether the abundance, species composition and demographic characteristics (density, survival, reproductive effort) of small mammals varied with respect to forest cover type. Secondarily, I was interested in identifying patterns of small mammal habitat selection and the factors that influence those patterns at micro- and macroscales. Small mammals were captured from May 1997-January 1999 on 10 sites (2 clearcut, 4 shelterwood, 2 riparian, and 2 mature) using a combination of Sherman live-traps and pitfall traps. Small mammal abundance and demographic characteristics were examined across forest cover types using a combination of statistical analyses, including Chi-square tests, Kruskal-Wallis tests and repeated measures ANOVA. I surveyed microhabitat features at individual trap stations (n=1000) using variable sized plots and the point quarter method and used these data to determine macrohabitat characteristics for sites (n=10). I examined species-habitat relationships at micro- and macro-spatial scales using Kruskal-Wallis tests, Wilcoxon Rank Sum tests, simple linear regression, stepwise multiple regression and stepwise logistic regression. Fourteen species of small mammals were captured over 7 trapping occasions. Five species including white-footed mice (Peromyscus leucopus), northern short-tailed shrews (Blarina brevicauda), eastern chipmunks (Tamias striatus), meadow voles (Microtus pennsylvanicus), and woodland voles (Microtus pinetorum), accounted for approximately 95% of the total number of individuals captured. Overall relative abundance and species composition of small mammals differed significantly across forest cover types. Catch per unit effort was greatest in shelterwoods followed by riparian, clearcut and mature forest cover types. I found significant differences in the abundances of white-footed mice and eastern chipmunks across forest cover types but not in those of northern short-tailed shrews, meadow voles or woodland voles. Shelterwood stands provided the highest quality habitat for white-footed mice and eastern chipmunks while clearcut stands provided high quality habitat for northern short-tailed shrews. Assessments of habitat quality for other species were based on weak evidence or inconclusive. Microhabitat preferences for the 5 small mammal species with > 100 captures were generally consistent with those previously reported in the literature. White-footed mice, eastern chipmunks and northern short-tailed shrews were associated with woody debris and brushy microsites, while meadow voles were associated with grassy vegetation and woodland voles with the presence of soft mast and woody stem densities. For each of these species, microhabitat was able to predict presence at individual trapping stations at a level better than expected by chance. For white-footed mice and woodland voles, however, habitat selection was found to be dependent upon macrohabitat, suggesting that habitat selection for these species is dynamic. Macrohabitat features were related to the abundance of several small mammal species. In general, the habitat characteristics important to individual species at microscales tended to be important at macroscales as well. The results of this study suggest that current even-aged forest management practices on Quantico Marine Corps Base are compatible with the maintenance of native populations of small mammals. Disturbances created by harvesting, at least temporarily, resulted in favorable microhabitat conditions for a variety of small mammal species. Species such as southern flying squirrels, however, were sensitive to disturbance, although it is likely that successional changes allow rapid recolonization of disturbed sites.
Master of Science

Recent studies have demonstrated that the morphologically similar white marlin (Kajikia albida) and roundscale spearfish (Tetrapturus georgii) co-occur in the western North Atlantic, including the U.S. Mid‐Atlantic Bight. Differences in scale morphology have been proposed as one morphological character to discriminate these species, but a thorough analysis of scale morphology is lacking. Because the validity of the roundscale spearfish was not established until 2006, much of the biological information previously collected for “white marlin” may include data for both white marlin and roundscale spearfish. The objectives of this study were to obtain a better understanding of the movements and habitat utilization of positively identified white marlin that inhabit the U.S. Mid-­‐Atlantic Bight during summer months, and to describe the morphological variation of white marlin and roundscale spearfish scales. Eleven long‐term (6 or 12 month) pop-up satellite archival tags were placed on white marlin that were caught and released in the U.S. recreational fishery. Nine tags reported information on temperature, pressure (depth), and light levels for light‐based geolocation for periods of 8 days to 12 months. Most fish moved out of the Mid-Atlantic Bight in September, and overwintered in areas ranging from east of the Gulf Stream off the Carolinas to the Caribbean, and as far south as northern Brazil. of the seven fish that retained tags for more than 40 days, five spent time in known spawning grounds in waters of the Dominican Republic leading up to the spring spawning season. These data demonstrate a large degree of connectivity among white marlin in the western North Atlantic. as noted in previous studies, individuals spent a large proportion of their time in the surface waters (0-10m; 75% across all white marlin pooled), the vast majority of their time in the top 100 m of the water column (97%), and within eight degrees of sea surface temperature (98%), although definite shifts in habitat utilization were evident as fish departed coastal offshore waters of the Mid‐Atlantic Bight. Diel habitat utilization varied greatly, with white marlin spending 81% of total nighttime in the surface waters (0‐10m), and only 26% of total daytime in surface waters. Past studies have characterized the scales of white marlin and roundscale spearfish as being morphologically distinct, but little effort has been made to describe variation within an individual, among individuals, or between species. to better understand morphological variation of scales and squamation patterns of distinct body regions of these two species, individual scales were collected from 11 specific anatomical regions, and scale patches were collected from 3 specific regions of each white marlin and roundscale spearfish brought into marlin tournament weigh stations in the Mid-Atlantic Bight during 2012 and 2013. Scales were measured and described, and scale patches were cleared and stained to examine the level of imbrication of the scales, as well as the overall squamation patterns. In addition to the scales, denticular plates, ossified formations occurring on the surface layer of the dermis, were measured and described. Although considable morphological variation was observed among scales from different anatomical regions of individuals of both species, white marlin scales generally have pointed anterior ends, fewer posterior points, and are more heavily imbricated than those of roundscale spearfish, which are frequently rounded anteriorly, but often have many posterior points and are farther separated within the skin. Over all areas and individuals, roundscale spearfish scales were significantly wider and had a lower length-­‐to-­‐width aspect ratio than those of white marlin. Detailed scale descriptions allow for a more accurate characterization of the variation within and differences between these two species, and could potentially be a valuable tool for investigating istiophorid systematics.

Anthropogenic sound has profoundly changed the acoustic environment of aquatic habitats, with growing evidence that even a short exposure to man-made sound sources can negatively affect marine organisms. Marine invertebrates have received little attention regarding their responses to anthropogenic sound, despite their pivotal role in marine ecosystems, and preliminary evidence of their sensitivity. In this thesis, I critically review the methods used in studies investigating the effects of anthropogenic noise on marine invertebrates. I identify methodological trends that have developed along the timeline of this topic, and use this information to suggest three research strategies to further the development of research in this field. From this review, current knowledge gaps are identified, and two main routes to address them are taken in this thesis. Firstly, to address the shortage of particle motion data in anthropogenic sound literature, two new low-cost and easily accessible particle motion sensors were developed and tested, one of them at 0.1% of the cost of currently commercially available models. These sensors will allow the measurement and reproduction of the sound fields experienced by marine invertebrates in bioacoustic research, even when research budgets are tight. Particle motion is the main sound component detected by invertebrates, yet neglected in many aquatic bioacoustical studies. Secondly, to expand on the comparably small quantity of research investigating the effects of anthropogenic sound on marine invertebrates, a series of controlled laboratory experiments were conducted. Two commercially and ecologically important model species were chosen, the blue mussel Mytilus edulis, representing sessile benthic invertebrates, and the European lobster Homarus gammarus, representing mobile benthic invertebrates. Experiments on M. edulis were conducted taking a mechanistic, integrative approach to investigate the effects of sound on multiple levels of biological organisation, including biochemistry, physiology, and behaviour. The ultimate aim was to understand the underlying drivers behind, and interactions between, responses. Comet assay analysis of haemocytes and gill cells demonstrated a significant six-fold higher single strand breakage in the DNA of cells of mussels exposed to ship-noise playback, compared to those kept under ambient conditions. Superoxide dismutase analysis did not identify an excess of superoxide ions, and glutathione, and glutathione peroxidase assays showed no increase in either glutathione or glutathione peroxidase. TBAR assays however revealed 68% more thiobarbituric acid reactive substances, indicating lipid peroxidation in the gill epithelia of noise exposed specimens. Algal clearance rates and oxygen-consumption rates of noise-exposed mussels were significantly lower (84% reduction and 12% reduction respectively), than those of control animals, while valve gape was significantly (60%) wider. This seemingly converse reaction indicates a shock response in mussels with the onset of noise exposure. Finally, at the genetic level, heat shock protein 70 expression was investigated, but no change was identified during noise exposure. Investigation into the noise induced behavioural responses of H. gammarus suggests seasonal differences in behaviour, using movement as a metric, in response to anthropogenic noise playbacks. During both summer and winter exposures, lobsters spent most time away from the highest noise area (98% of the observed time in summer and 78% in winter). The observed seasonal differences in the time spent in the highest noise area (2% in summer and 22% in winter) could be linked to the lobsters' requirement for shelter during winter. This requirement seems to have had a stronger influence over the animals' behaviour than any desire to avoid high noise levels. The information generated in this thesis can be used by researchers working in the field of marine sound to develop well rounded studies exploring the effects of sound on not only marine invertebrates but other faunal groups as well. The construction details provided to produce low cost particle motion sensors, will allow bioacoustic researchers to easily include particle motion measurements in all future studies investigating the effects of sound on fish and invertebrates. The results of the conducted mussel and lobster experiments evidence how multiple aspects of invertebrate biology can be affected by noise. The observed impacts on both sessile and mobile life forms highlight that the effects of noise cannot be fully understood before a wide range of species with different biological and ecological traits have been studied. The integrative approach to noise research used here can serve as a model for other species, and the results pooled to inform governments and industry of the effects of anthropogenic noise in the marine environment.

The Pourtalès Terrace is a gently curved, narrow triangular platform that parallels the Florida Keys for 213 km running from southern Key Largo to between Key West and the Marquesas Keys. The main Terrace surface begins in 200 m and dips gently to approximately 450 m, where the Pourtalès Escarpment slopes steeply to the deep floor of the southern Straits of Florida. The Terrace platform exhibits a wide variety of Neogene-age geological features, including high-relief ledges, mounds, sinkholes and deep-water biogenic build-ups called bioherms. Previous research revealed dense and diverse benthic assemblages dominated by stylasterid hydrocorals, octocorals and sponges. Many Terrace features also represent popular, long-term fishing targets. Due to concerns about resource sustainability, (National Oceanic and Atmospheric Administration (NOAA) and the South Atlantic Fishery Management Council (SAFMC) included the Terrace in the Comprehensive Ecosystem-Based Amendment 1 (CE-BA 1, June 2010) that protects deep-water Coral Habitat Areas of Particular Concern (CHAPCs) along the southeastern U.S continental margin by prohibiting use of a variety of potentially damaging bottom fishing gear. NOAA also established the East Hump Marine Protected Area (MPA) as a Type II MPA, permanently closed to fishing for and possession of snapper and grouper species. To develop a more robust database on Terrace habitats and resources, a research cruise (September 2011) used ROV Kraken 2 to survey 14 sites both inside and outside the CHAPC and MPA for biological diversity, density, and distribution, with a focus on deep-sea coral and sponge assemblages. The surveys resulted in 58 h of videotape, 2,866 images, and collected 150 specimens of benthic invertebrates. All dive sites were mapped with multibeam sonar. This project used Coral Point Count with Excel extensions (CPCe)©, PRIMER 6.1.10 beta, JMP© statistical software, and Environmental Systems Research Institute (ESRI) ArcMap 10.3 Geographic Information Systems (GIS) to quantitatively analyze transect images and video from the ROV transects. This information was used to characterize dive sites in terms of benthic invertebrate faunal communities, depth, and topography; and compare results relative to protected versus unprotected sites. Of the 14 sites surveyed 10 were analyzed and split into 42 transects of approximately 30 m2 based on five depth and location bin classes. Each site was initially separated into habitat types based on qualitative geomorphologic features for statistical analysis (i.e., mound slope, mound wall, mound top, deep mound, valley, Lophelia mound, sinkhole), using methods established by Reed et al. (2011; 2014). In initial analysis, depth and location were found to be superior to geomorphology as an indicator of what was driving differences in communities among transects. As a result each transect was placed into one of five depth and location bin classes based on depth (m) of each image and location relating to CHAPC/MPA area borders: West 150-300 m (12 transects), North Central 150-250 m (14), Central 250-300 m (8), South 450-500m (5) and South 500-550 m (3). Distinct differences in communities of each depth and location bin class in relation to percent cover and organism density were apparent. Communities vary strongly among bins with some similarities: e.g., West 150-300, North-Central 150-250, and Central 250-300 all included Stylaster miniatus (Stylasteridae): South 450-500 and South 500-550 included Paramuricea sp. 3 among their most dominant species. Also similar species were found within similar depth ranges. Protection status (within CHAPC, CHAPC/MPA, or No Protection) did not affect differences in communities, suggesting protection regulations have not been implemented long enough to show significant differences between protected and unprotected sites. Several new geologic features were found e.g., the southernmost Lophelia pertusa coral mound in U.S. waters. Some important features were described that lie outside of CHAPC/MPA borders, suggesting new borders should be designated. Results showed a strong relationship between depth and location in forming deep-water communities, and that these factors could be used as proxies for creating habitat maps in unmapped areas. These results will also provide managers and scientists with a valuable baseline for assessing benthic invertebrate communities, their changes over time, and the effectiveness of protected areas on the Pourtalès Terrace.

With an increase in demand on deep-sea resources comes a need for appropriate and effective management of this ecosystem. The establishment of a representative network of deep-sea Marine Protected Areas offers one tool with which to address the conservation needs of the deep sea. While a number of deep-sea habitats have been identified as vulnerable to anthropogenic activities (e.g. cold-water coral reefs and sponge aggregations), poor knowledge of the distribution of these habitats hinders conservation efforts and network planning, and thus we need habitat maps. With improvements in acoustic data resolution acquired from the deep sea, and the ability to cover large areas rapidly, the use of acoustic techniques in mapping biological habitats is growing. Multibeam bathymetry and its derived terrain variables can potentially provide important information that can aid in the delineation and characterisation of biological communities. A necessary prelude to mapping is therefore the definition of biological assemblages for use as mapping units. Two megahabitat features (seamount and submarine canyons) were sampled using acoustic and ground-truthing to characterise and map the distribution of benthic assemblages. Species were identified as distinct morpho-types and catalogued, and still images quantitatively analysed. Standard multivariate community analysis was undertaken to define distinct faunal assemblage that may act as mapping units. Those clusters identified by the SIMPROF routine were taken against a set of criteria to reject/accept as robust assemblages that may be used as mapping units. Twenty two benthic assemblages or biotopes were defined from multivariate analysis of quantitative species data, 11 from the SW Approaches and 11 from Anton Dohrn Seamount, and a further one from video observations (SW Approaches). Taken against current definitions, 11 of these were considered as Vulnerable Marine Ecosystems (VME). Diversity was measured to compliment the comprehensive description of biotopes. The use of multivariate diversity indices proved better for comparing diversity of biotopes as it captures a more than one aspect of diversity of the community. Two biotopes were common to both megahabitat features, cold-water coral reef habitats, and those from Anton Dohrn Seamount were more diverse than from the SW Approaches. Modelling techniques were employed to test the relationship between biotopes and environmental and geophysical parameters, which may be used as surrogates to map VME. Generalised Additive Models of Vulnerable Marine Ecosystems revealed multibeam bathymetry and its derived parameters to be significant surrogate for mapping the distribution of some assemblages, particularly those that appear to be influenced by current regime; whilst not so well for those whose distribution is not so strongly current driven e.g. soft sediment communities. In terms of deep-sea mapping, the use of multibeam can prove a useful mapping tool if the resolution of the data is at an appropriate scale that will identify meso-scale geomorphological features, such as cliff-top mounds, that may act as proxies for occurrence of biotopes, but this relationship is still unclear. Surrogates were used to map VME across the seamount and submarine canyons, and full coverage maps were produced for all biotopes occurring on these megahabitat features.

The rainbow parrotfish Scarus guacamaia is a prominent herbivore in the coastal waters of southeastern Florida whose life history is strongly linked to a dependence on both mangrove and coral reef habitats. Rainbow parrotfish in turn serve in maintaining the health of coral reefs by keeping algal populations in check. This study used NOAA Fisheries data from the Mangrove Visual Census and the Reef Visual Census in Biscayne Bay and Upper Florida Bay. Observations of abiotic factors at individual sites were used to correlate and predict presence and absence of this species. This was done to visualize habitat presence and ontogenetic shifts present in this species between juvenile and adult stages through ArcGIS mapping. Logistic regression analysis was used to predict presence or absence using the environmental variables of temperature, dissolved oxygen, salinity, average depth, distance from channel openings, mangrove presence, temperature Δ, and salinity Δ. Average depth, distance from channel openings, temperature Δ and salinity Δ were significant in predicting the presence of this species, while salinity, temperature, dissolved oxygen, and mangrove presence were not. Conservation efforts for this species, listed as vulnerable under the IUCN, need to be given greater consideration. The health of this and other parrotfish may have a greater impact on coral reef ecosystems across the Caribbean Sea than currently acknowledged and management breadth and priorities should be adjusted to reflect this role.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2016.
Cataloged from PDF version of thesis.
Includes bibliographical references.
Marine populations are increasingly subjected to changing conditions whether through harvest or through broad-scale habitat change. Historically, few models have accounted for such trends over time, and even fewer have been used to study how trends affect optimal harvests. I developed and analyzed several models that explore, first, endogenous change caused by harvest and, second, exogenous change from factors (such as rising ocean temperatures) outside harvesters' control. In these models, I characterized the profit-or yield-maximizing strategy when harvesting damages habitat in a multispecies fishery, when harvest creates a selective pressure on dispersal, and when rising temperatures cause changes in vital rates. I explore this last case in both deterministic and stochastic environments, and also allow the harvester to learn about unknown parameters of the stock recruitment model while harvesting. I also develop an unambiguous definition of and describe a statistical test for a shift in a species' spatial distribution. My results demonstrate that optimal harvesting strategies in a changing environment differ in important ways from optimal strategies in a constant environment.
by Emily Alison Moberg.
Ph. D.

Biology
Ph.D.
Examining how ecological processes are influenced by spatial variation can provide valuable insights into how communities are formed and how they may change in dynamic landscapes. In this thesis I address three objectives surrounding the spatial and temporal variation in species’ recruitment and predation, the influence of habitat isolation on consumer-resource relationships, and the influence of habitat fragmentation on a multi-trophic system. I used marine invertebrates, specifically crustaceans, bivalves, and sessile species as a model system. First, I address the spatial and temporal variation in local and regional processes in a multispecies assemblage of marine sessile invertebrates. Using diverse communities of marine sessile invertebrates as a model system I tested the hypothesis that spatial and temporal variation in recruitment and predation would shape local communities, and that both recruitment and predation would have significant effects on the abundance and structure of adult communities. I found that both recruitment and predation vary through time and space leading to the emergence of regional community divergence. I also address how habitat isolation interacts with top-down and bottom-up processes in seagrass ecosystems. Spatial structure of the habitat may mediate top-down and bottom-up controls of species abundances through decreased habitat connectivity and increased habitat isolation. I manipulated top down and bottom up processes by excluding mesograzers, adding resources, or altering both factors in isolated and contiguous patches of artificial seagrass. I then measured epiphyte recruitment, epiphyte abundances, and macroalgae abundance. I paired this with epiphyte sampling from isolated natural seagrass patches. I found that habitat isolation significantly decreased the abundance of epiphytes settling on seagrass blades due to dispersal limitation for epiphytic invertebrates. I found that consumers had strong effects on epiphyte biomass in continuous habitats, but not isolated habitats. Resource additions increased macroalgae cover and epiphyte biomass only in isolated habitats. The results suggest that isolated habitats may be nutrient limited and that top-down effects are stronger in continuous habitats, while bottom-up effects may dominate in isolated habitats. In my third objective, I address how habitat fragmentation may alter marine food webs. I examined whether predation rates, prey, and predator behavior differed between continuous and fragmented seagrass habitat in a multi-trophic context at two sites in Barnegat Bay, NJ. I hypothesized that blue crab predation rates and foraging would decrease in fragmented seascapes, due to a reduction in adult blue crab densities, increasing survival rates of juvenile blue crabs and hard clams. I expected hard clams to exhibit weaker predator avoidance behavior in fragmented habitats because of decreased predation. I found that species’ responses to fragmentation were different based on trophic level. Clams experienced higher predation and burrowed deeper in continuous habitats at both sites. Densities of blue crabs, the primary predator of hard clams, were higher in continuous habitats at both sites. Predation on juvenile blue crabs was significantly higher in fragmented seagrass at one site. Our results suggest that in fragmented seascapes, the impact of fragmentation on higher trophic level predators may drive predation rates and prey responses across the seascape, which may lead to trophic cascades in fragmented habitats.
Temple University--Theses

Blue marlin Makaira nigricans and white marlin Kajikia albida (formerly Tetrapturus albidus) are overfished in the Atlantic Ocean, with the vast majority of fishing mortality resulting from the pelagic longline fishery that targets tunas (Thunnus spp.) and swordfish Xiphias gladius. Time series of catch-per-unit-effort (CPUE) data have been fundamental to assessments of blue marlin and white marlin stocks, but these time series have been affected by a shift over time in pelagic longline fishing practices from shallow to deeper sets. One method for adjusting CPUE data for changes in fishing practices is a habitat-based standardization that modifies fishing effort in proportion to the vertical distribution of the species of interest and the fishing gear. For these models to be successfully applied to population assessments, the vertical habitat utilized by blue marlin and white marlin must be known. Pop-up satellite archival tags (PSATs) provide a means of collecting high resolution vertical movement and distribution data for billfishes. In my study, 62 blue marlin and 40 white marlin were caught in recreational fisheries off the U.S. mid-Atlantic, Yucatan Peninsula, northern Caribbean, Venezuela, and Brazil, tagged with Microwave Telemetry, Inc. PTT-100 HR PSATs, and released. Data were recovered from PSATs attached to 57 surviving blue marlin and 36 surviving white marlin. PSATs successfully transmitted 18-100% of the data they recorded (mean 72%). The minimum 10-day displacements of both species averaged 242 km (range 9 to 942 km) and varied significantly between tagging locations, but not between species. Blue marlin spent a significantly higher (62%) amount of time in the upper 10 m of water than white marlin (56%). Both species spent greater than 95% of the time in water that was within 8o C of the sea surface temperature. Only 3.1% of white marlin demonstrated diel differences in the maximum depth of dives, while 29% of blue marlin dove into deeper waters during the day. Variables identified as explaining the most variation in dives were total dive duration, bottom time, ascent time, number of wiggles, wiggle depth, interdive interval, skew of ascent and descent, % time ascending, and % time descending. Using these variables, two dive types were identified through cluster analysis: simple dives representing traditional "U" and "V" shapes, and complex dives with multiple descents, plateaus, and wiggles. There were significant differences in dive variables among locations, individuals, diel periods, and dive types. There was significant overlap in range, habitat use, and vertical movement patterns, and therefore no strong evidence of niche partitioning between blue marlin and white marlin. My analyses can be used to further define the physical and physiological factors limiting marlins' vertical movements and therefore improve stock assessments based on longline CPUE data by correcting for changes in fishing practices.

Les changements climatiques affecteront les écosystèmes terrestres et marins mais les conséquences en termes de répartition globale de la biodiversité sont encore mal connues. Les études portant sur la sélection des habitats des prédateurs marins pour leurs recherches alimentaire et leurs évolutions provoquées par le réchauffement climatique sont en plein développement actuellement. Les suivis télémétriques apportent des informations précieuses sur la variabilité spatio-temporelle de la distribution en mer des prédateurs marins. L’ensemble des problématiques étant très importantes, nous avons décidé de nous focaliser sur les oiseaux marins. Le premier objectif de ce projet de thèse est d’étudier, la distribution et la sélection des habitats d’alimentation des oiseaux marins tropicaux pendant leurs phases de reproduction et pendant leurs migrations. Afin de caractériser les habitats d’un point de vue abiotique. Le deuxième objectif de ce projet de thèse est d’utiliser les scénarios d’évolution des habitats océaniques produits par GIEC pour simuler, à l’aide des modèles d’habitats, l’évolution temporelle de la distribution des habitats favorables. Le troisième objectif de ce projet de thèse est d’utiliser les données de suivi disponibles d'identifier les « points chauds » de la biodiversité.Nous nous sommes intéressés, dans un premier temps, aux puffins du Pacifique. Plus particulièrement, nous avons étudié les variations entre les différentes colonies d’une même espèce, du point de vue de la distribution, de l’activité et de la sélection des habitats. Ensuite, nous avons étudié l'impact de l'évolution du changement climatique sur les habitats d'hivernage des Pétrels (Pterodroma baraui) de Barau, une espèce endémique de l'île de la Réunion. Nous avons construit des modèles de sélection des habitats. Ces modèles ont ensuite été utilisés pour prédire l’évolution des habitats d'hivernage à l’horizon 2100, en fonction de différents scénarios du GIEC. Enfin, Nous avons compilé les données de suivi disponibles sur les oiseaux marins, les tortues de mer et les mammifères marins pour étudier la répartition de la mégafaune marine dans l'océan Indien, et d'identifier les points chauds de haute densité et de haute diversité. Afin de mettre en place, à terme, des zones marines protégées. »
Climate change will affect terrestrial and marine ecosystems, but the consequences in terms of global biodiversity distribution are still unclear. Studies about selection of marine habitats and trends caused by global warming are growing. The telemetric monitoring provide valuable information on the spatial and temporal variability on distribution of marine predators. All the issues are very important, we have decided to focus on seabirds. The first objective of this thesis project is to study the distribution and selection of foraging habitat of tropical seabirds during their reproductive phase and during their migrations. To characterize the habitat of an abiotic point of view. The second objective of this thesis project is to use scenarios for ocean habitats produced by IPCC to simulate, using habitat models, the temporal evolution of the distribution of suitable habitat. The third objective of this thesis project is to use the available monitoring data to identify "hotspots" of biodiversity. We looked, at first, the puffins Pacific. More particularly, we studied the variations between the different colonies of the same species, from the viewpoint of the distribution, activity and habitat selection. Then we studied the impact of the evolution of climate change on wintering habitat of Barau’s Petrels (Pterodroma baraui). We built habitat selection models. These models were then used to predict the evolution of wintering habitat in 2100, according to different IPCC scenarios. Finally, we have compiled the available telemetry data on seabirds, sea turtles and marine mammals to study the distribution of marine megafauna in the Indian Ocean, and to identify hotspots of high density and high diversity. To establish, in time, protected marine areas