Dissertations / Theses on the topic 'Seabird conservation'

Seabirds are considered one of the most threatened groups of birds in the world. They face additional mortality both on their breeding islands from introduced predators and at sea by fishing fleets, as fisheries bycatch, as well as other human impacts. Seabird bycatch has negatively affected many seabird populations worldwide, with trawl, gillnet and longline fisheries considered the most destructive to seabird populations. Seabird bycatch from trawl and gillnet fisheries has been significantly reduced in recent years, but large numbers of seabirds are still killed annually by longline fisheries. Of the two types of longline fisheries (demersal and pelagic), pelagic longlining is considered the most harmful to seabirds as lines remain closer to the surface for longer periods than demersal longlining, and it is harder to weight lines to ensure rapid sinking beyond the depth they are accessible to birds. Seabirds are killed when they swallow baited hooks and consequently drown. Despite the large number of studies investigating seabird bycatch from pelagic longline fisheries, there remain gaps in our understanding of seabird bycatch from pelagic longline fisheries. This thesis addresses some of these knowledge gaps and makes recommendations as to how seabird bycatch from pelagic longliners can be reduced at both a local and global scale. Chapters 2 and 3 investigate the factors affecting seabird bycatch from pelagic longliners off South Africa, provide a summary of seabird bycatch from the fishery for the period 2006–2013 and quantify the structure of seabird assemblages associated with pelagic longline vessels off South Africa. This was achieved by analysing seabird bycatch data collected by fisheries observers as well as data from sea trials onboard pelagic longliners. Seabird bycatch by pelagic longliners off South Africa over the 8-year study period has been significantly reduced from the 8-year period (1998–2005), mainly driven by a significant reduction in seabird bycatch rates from foreign-flagged vessels, which are responsible for c. 80% of fishing effort off South Africa. Seabird bycatch rates from South African vessels still remain high, four times higher than the interim national target of < 0.05 birds per 1000 hooks. The species composition of seabird bycatch off South Africa is best explained by an understanding of the structure of the seabird assemblage associated with longline vessels. For most species, bycatch and attendance ratios were similar, but for some species such as shy-type and black-browed albatrosses there were large mismatches, likely caused by differences in foraging behaviour and foraging dominance hierarchies. In Chapters 4 and 5 the foraging ecology of the most commonly recorded bycatch species off South Africa, the white-chinned petrel (Procellaria aequinoctialis), is investigated. An understanding of the foraging ecology of commonly recorded bycatch species enhances our understanding of seabird bycatch and helps to improve the design of current and future mitigation measures. The year-round movements of white-chinned petrels from Marion Island were investigated with Global Location Sensors (GLS loggers) and GPS loggers. Adult white-chinned petrels undertake only limited east-west movements of, with all birds remaining between southern Africa and Antarctica. These results strengthen the theory that there is limited spatial overlap year-round between white-chinned petrel populations from South Georgia, the southern Indian Ocean islands and New Zealand sub-Antarctic islands, suggesting that these populations can be managed as separate stocks. The diving behaviour of white-chinned and grey petrels (P. cinerea), another common bycatch species in Southern Ocean longline fleets, were examined with the use of temperature-depth recorders (TDRs), deployed on birds from Marion Island and Gough Island. My study was the first to analyse TDR dive data from any Procellaria petrel, and recorded them reaching maximum dive depths of 16 and 22 m, respectively. Current best practise suggests that baited hooks be protected to a depth of 5 m by bird-scaring lines, but my results suggest this depth should be increased to at least 10 m. Although line weighting is a proven mitigation measure to reduce seabird bycatch from pelagic longliners, fishers have concerns that it will compromise fish catches, crew safety and operational efficiency. In Chapter 6 I analyse line weighting data from trials onboard three pelagic longline vessels, to address the concerns of fishermen. My results show that sliding leads can be incorporated into pelagic longline fisheries without compromising fish catch, crew safety or operational efficiency. I thus recommend that sliding leads be used on pelagic longline vessels fishing off South Africa. By incorporating studies investigating the factors affecting seabird bycatch, seabird foraging ecology and the efficacy of seabird bycatch mitigation measures, my thesis has broadened our understating of seabird bycatch from pelagic longliners and makes meaningful recommendations to further reduce bycatch, both locally and globally. Although seabird bycatch rates have declined off South Africa, through the use of a number different mitigation measures, they still remain higher than the South African national target and thus more work is needed to achieve this target. To reduce seabird bycatch from pelagic longliners to acceptable levels, studies from the world's various longline fleets needs to be considered and improved upon, with seabird conservationists and fishermen working together to achieve this goal.

Their high energetic demands make seabirds sensitive to changes in prey availability, which is often reflected in their diet and energetic expenditure during breeding. Populations of the three seabirds endemic to southern Africa's Benguela upwelling ecosystem that rely on small pelagic fish have decreased dramatically over the last decade. In contrast, the population of the greater crested tern Thalasseus bergii has increased. To understand these conflicting trends, I investigated the foraging ecology and energy requirements of greater crested tern breeding in the Western Cape, South Africa. Diet was assessed by a novel non-invasive methodology developed in this study, using digital photography. More than 24,000 prey items from at least 51 different prey taxa were identified, with 34 new prey species recorded, revealing a high degree of foraging plasticity for this seabird. Greater crested terns rely mainly on anchovy Engraulis encrasicolus (65%), which averaged 84 mm long. Prey composition differed significantly between breeding stages, with anchovy especially dominant at the onset of the breeding period and the diet becoming more variable as the season progressed. Time-energy models for breeding terns were built based on activity budgets collected from non-invasive video-recordings and focal observations. Foraging trips were significantly longer during incubation than the chick provisioning stages, and feeding rates doubled from early to late chick provisioning. This study illustrated a steady increase in energy needs of adults throughout the breeding season, due to their increased foraging effort to meet chick energy needs. In comparison to other Benguela endemic seabirds that also rely on small pelagic fish, terns displayed substantially lower energy requirements at both individual and population levels. I also explored the benefits underlying interactions within mixed-species aggregations by investigating the costs induced by kleptoparasitism between mixed colonies of greater crested terns and Hartlaub's gulls Chroicocephalus hartlaubii and colonies with greater crested terns alone. Video-recordings coupled with focal observations showed that terns suffer direct costs to chick provisioning rates and indirect costs through energy expenditure in a mixed-species colony, suggesting that these breeding assemblages may be a form of parasitism rather than a mutualistic association. Despite the detrimental effects of interspecific kleptoparasitism, the marked foraging plasticity and low energetic requirements of greater crested terns, described in this study, coupled with specific life history traits such as low fidelity to breeding sites and extended post-fledging care, are key factors that allow this species to cope with changes in the availability and abundance of their main prey. Understanding species-specific behavioural responses to ecosystem variations in the Benguela upwelling system is vital for assessing the impact of commercial fisheries on seabird populations and fish stocks. Finally, the implementation of the method developed in this study, in long-term monitoring programmes, may provide crucial knowledge for conservation plans and key input to realising an ecosystem approach to fisheries management.

Firstly, I am very grateful to Birdlife International for the MSc scholarship. I am also very grateful to Professor Peter Ryan of the FitzPatrick Institute of African Ornithology, University of Cape Town, for agreeing to supervise this project and for his guidance, insights and comments on the write-up. I am grateful to Sarah Saldanha, for all the support during this MSc. Many thanks also to Dr Ross Wanless, Dr Rima Jabado and Ruben Rocha for all support, guidance and advice. I want to thank a lot Andy Angel for their accommodation and all support in South Africa. I am grateful to all the UCT staff and BirdLife Senegal Staff for all the support during this study. Many thanks to my family for all the encouragement and support. I want to thank to all the Cabo Verde fishers for their willingness to share their knowledge and experience. Finally, many thanks to the Conservation Biology class of 2019, for all their support.

Includes bibliographical references.
Molecular techniques have a broad, and growing, application in the field of wildlife conservation, ranging from the systematic identification and classification of taxa, through studying genetic connectivity between populations, to parentage and individual barcoding. While they are applied to a wide range of spatial- and temporal-scales, molecular approaches complement traditional methods used to classify, investigate and understand the natural world. This study uses multiple lines of evidence, at various scales, to investigate how seabird biology influences population-level responses to changing environments. The focal area is the Agulhas-Benguela Ecosystem (ABE) along the south-western coast of Africa. Globally, biodiversity loss due to environmental change in marine ecosystems is significantly affecting the phenology, distribution, dispersal patterns, and demographic rates of organisms across trophic-levels. Broad-scale changes are occurring that have consequences for both commercial fisheries and threatened marine top-predators. Seabirds are valuable indicators of the state of marine ecosystems, and changes in their distribution and dispersal patterns may reflect those of species in lower trophic-levels. This is the case in the ABE, where some endemic seabird species are better at responding to changes in their environment than others. Twentieth century shifts in the distribution of key pelagic prey species in the ABE have had serious consequences for endemic seabirds. The African Penguin Spheniscus demersus, Cape _ Gannet Moms capensis and Cape Cormorant Phalacrocorax capensis rely on these pelagic fish, and all three species are threatened and in decline. In this study population genetic and phylogeographic methods are used to: (i) quantify levels of genetic diversity, and determine regional-scale structure within all three focal species; (ii) explore fine-scale population structure in African Penguin; and (iii) compare wild and captive populations of African Penguins. The conservation of genetic diversity is essential for the long-term persistence of species. Population genetics can help us to understand the evolutionary processes that have shaped patterns of genetic diversity in the focal species, and predict how they might respond to further environmental changes. Comparative phylogeography, combined with capture-mark- recapture models based on ringing data and annual census counts, provide the most complete picture of the micro-evolutionary forces at play in this unique ecosystem, and highlight seabird life-history characteristics may facilitate adaptation and survival under novel conditions. This is the first conservation genetic study of endemic seabirds in the ABE. Although the three focal species differ in a number of aspects of their breeding and foraging ecology, and in some life-history characteristics, they have evolved under similar selective pressures across their shared range, and represent natural replicates that allow us to determine the dominant drivers of population genetic change. Flexibility in foraging behaviour and the degree of breeding site fidelity exhibited by each of the three focal species affect the rate and effectiveness of their demographic responses to changes in their environment. Understanding connectivity among seabird populations is crucial for their long-term conservation, and has been investigated in numerous studies of seabird species from around the world. Similar to many of these, this study found very low levels of genetic structure among populations of all three focal species based on DNA sequence data, suggesting long-term gene-flow among them, despite potential physical and non-physical barriers. Overall, the patterns observed suggest that high connectivity characterises their breeding regions, and most breeding colonies, buffering the respective populations against environmental variability. These results were supported by fine-scale analyses of the African Penguin using microsatellite markers that also suggested high levels of gene-flow, which may have masked genetic signatures of the regional- and colony-level bottlenecks experienced by this species. Microsatellite-based genetic diversity and fine-scale structure were also compared among wild and captive populations of African Penguins to assess the genetic consequences of a planned conservation breeding program. The genetic composition of birds in captivity largely reflects that found in wild populations. The success of reintroduction in terms of decreasing extinction risk in the wild is uncertain, and should be implemented as part of a broader management plan that addresses the primary threats to wild populations. Further research is required to improve our understanding of many aspects of endemic southern African marine avifauna and better inform our ability to ensure their continued persistence in this system.

Includes bibliographical references.
Seabird bycatch in commercial fisheries is one of the major factors causing decreases in many seabird populations. In trawl fisheries, high mortalities have been recorded as a result of seabirds being struck by trawl warps (the cables used to tow the trawl net). Tori (bird-scaring) lines have been used to decrease seabird mortality in some trawl fisheries by up to 90%. However, tori lines are not effective at reducing the number of birds that drift towards the trawl warps while feeding on factory discards alongside the vessel. The Albatross Task Force (ATF) helped to develop and test a new device, the Rory Line (RL), to be used in conjunction with tori lines, and designed to reduce warp strikes by placing a physical barrier between the scupper (where factory discards are released) and the danger zone (where the trawl warps enter the water) at the stern of the vessel. This study tests the efficacy of the RL at reducing the number of birds drifting into the danger zone and the number of birds being struck by the trawl warps.

This thesis includes several research works on population dynamics and conservation of seabirds in two small islands of the western Mediterranean: the Columbretes Islands (Castellón) and the island of Benidorm (Alicante). Most of the works included in the thesis report have been already published in scientific journals. This thesis includes both works discussing the role of certain biological factors (Section I) on seabird population dynamics and assessing the effects of human activities (Section II) on population numbers. Each section is preceded by an introductory chapter dealing, in a more informal manner, with the topic approached by that section. Section I approaches specifically the influence of immigration and environmental stochasticity on the population dynamics of shags Phalacrocorax aristotelis (Chapter 1), the role of philopatry and conspecific atraction in breeding site selection in Audouin's gull Larus audouinii (Chapter 2), the determinants of colony-site dynamics in Audouin's gull (Chapter 3), the movements of yellow-legged gulls Larus michahellis from the Mediterranean to the Atlantic (Chapter 4), the presence of immigrant Cory's shearwaters Calonectris diomedea from Atlantic colonies in Mediterranean colonies (Chapter 5). Section II includes works discussing the role of landfills in disease dispersal among yellow-legged gulls (Chapter 6), the role of discards of the trawling fishing fleet as a food source during the summer for gulls (Chapter 7), the role of fishing discards on the dynamics of a colony of Audouin's gull facing local extinction (Chapter 8) and the impact of tourism on a small colony of the Eleonora's falcon Falco eleonorae (Chapter 9). A number of conclusions are listed. Basically we found that adult survival is the demographic parameter with the largest impact on the growth rate of colonies, although transfer processes play a very important role as well since seabirds are structured in subpopulations (patches) separated in space. Human activities can affect all demographic parameters (fecundity/mortality and immigration/emigration) and must be taken into account to understand seabird dynamics, specially fishing activities which may even produce the local extinction of colonies. Past is also a factor to be taken into account since present-day dynamics result from the interplay between local, regional and historical factors. Most of the seabird colonies in the Mediterranean are small sized and hence prone to genetic erosion and stochasticity besides being composed by species and subspecies with a high degree of endemism. Colonies not occupied at present must also be included in conservation plans since seabirds have high dispersal capabilities. Finally, the tremendous importance of the social factor in seabird colonies can be used as an effective conservation tool.

Seabirds are wide-ranging apex-predators and useful bio-indicators of marine systems. Nevertheless, changes are occurring in the marine environment, and seabirds require protection from the deleterious effects of climate change, fisheries, pollution, offshore development, introduced predators and invasive species. The UK supports internationally important populations of seabirds but also has vast wind and wave resources, therefore understanding how seabirds use the marine environment is vital in order to quantify the potential consequences of further exploiting these resources. In this thesis I first describe the range of wave energy converting devices operational or in development in the UK, and review the potential threats and benefits these developments may have for marine birds. I then synthesise data from colony-based surveys with detailed information on population dynamics, foraging ecology and near-colony behaviour, to develop a projection model that identifies important at-sea areas for breeding seabirds. These models show a positive spatial correlation with one of the most intensive at-sea seabird survey datasets, and provide qualitatively similar findings to existing tracking data. This approach has the potential to identify overlap with offshore energy developments, and could be developed to suit a range of species or whole communities and provide a theoretical framework for the study of factors such as colony size regulation. The non-breeding period is a key element of the annual cycle of seabirds and conditions experienced during one season may carry-over to influence the next. Understanding behaviour throughout the annual cycle has implications for both ecological theory and conservation. Bio-logging can provide detailed information on movements away from breeding colonies, and the analysis of stable isotope ratios in body tissues can provide information on foraging during the non-breeding period. I combine these two approaches to describe the migration strategies of northern gannets Morus bassanus breeding at two colonies in the north-west Atlantic, revealing a high degree of both winter site fidelity and dietary consistency between years. These migratory strategies also have carry-over effects with consequences for both body condition and timing of arrival on the breeding grounds. Finally, I investigate the threats posed to seabirds and other marine predators during the non-breeding period by collating information on the distributions of five different species of apex predator wintering in the Northwest African upwelling region. I describe the threat of over-fishing and fisheries bycatch to marine vertebrates in this region, and highlight the need for pelagic marine protected areas to adequately protect migratory animals throughout the annual cycle. In summary, the combination of colony-based studies, bio-logging, stable isotope analysis and modelling techniques can provide a comprehensive understanding of the interactions between individuals and the marine environment over multiple spatial and temporal scales.

The ability to move and forage efficiently plays a major role in determining the fate of individuals, and has important implications for population dynamics and ecosystem functioning. Migration is a particular type of movement strategy, whereby animals may travel remarkable distances in order to take advantage of seasonality in resource availability or to avoid arduous winter conditions; however, this can be at a cost in terms of increased mortality. Indeed, anthropogenic threats in non-breeding areas are a major cause of population declines and a better understanding of non-breeding spatial ecology is required in order to advance both ecological theory and conservation management. The recent development of animal tracking technologies, in particular light-based geolocation, has made it possible to track large-scale and long-term movements; however, there are still gaps in our knowledge, such as the links between migratory and reproductive performance, connectivity among populations and the ontogeny of migration strategies. In this thesis, I utilise multi-species and longitudinal datasets from albatrosses and petrels, some of the most mobile species on Earth, to explore the drivers of variation in movements, habitat use and foraging behaviour, and the implications for life history and conservation. In Chapter 1, I provide an overview of the key topics of this thesis. In Chapter 2, I provide quantitative recommendations of minimum sample sizes needed to track pelagic seabird migrations, using data from 10 species. In Chapter 3, I examine between- and within-population differences in the habitat preferences and distributions of albatrosses, including the relative roles of habitat specialization and intra-specific competition. In Chapter 4, I investigate the year-round movement and foraging strategies of petrels living in nutrient-poor environments. In Chapter 5, I examine potential links between foraging behaviour during the non-breeding season and reproductive senescence. In Chapter 6, I explore the ontogeny of foraging behaviour and foraging site fidelity in young albatrosses, shedding light on their “lost years” at sea. Finally, I conclude with a general discussion summarizing main findings and suggesting future work. Overall, my results highlight the complex relationships among individual traits, the environment, movements and foraging behaviour, and population dynamics across the lifespan of individuals, with implications for the conservation of this highly threatened group of species.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
A região da Bacia de Campos está exposta a diversas atividades antrópicas, que interferem diretamente no funcionamento do ecossistêmico marinho. O estudo da fauna marinha na costa centro-norte fluminense mostra grande relevância, diversas aves marinhas residem ou passam grande parte de seu período migratório ao longo da Bacia de Campos, entre elas está Sula leucogaster (Boddaert, 1783). Embora essas aves sejam altamente móveis, suas populações apresentam uma estrutura populacional genética robusta. Com o intuito de verificar a estruturação e as relações evolutivas da população de Sula leucogaster na Bacia de Campos foram recolhidas 91 amostras de encalhe e os dados gerados para esta região foram comparados com dados já publicados de outras bacias oceânicas. A partir da região controle do DNA mitocondrial foram gerados 26 haplótipos, todos exclusivos da Bacia de Campos, muitos raros e apenas oito possuíram frequência comum. As análises mostraram que a população da Bacia de Campos é um estoque genético de Sula leucogaster. Tal fato pode ser atribuído ao comportamento filopátrico e ao hábito costeiro dessa espécie que impede o fluxo gênico entre populações. Além disso, a população da Bacia de Campos detém baixa variabilidade genética e possivelmente está sofrendo efeito gargalo ou seleção purificadora, corroborados por valores do teste Fu, o que é comum para espécies que se dividem em subpopulações. Os dados filogenéticos demonstram um contato recente entre as populações da Bacia de Campos e da ilha de Ascensão. As condições oceanográficas também têm influência na estruturação de populações de Sula leucogaster, visto que a ausência de barreiras e a proximidade geográfica poderiam favorecer contato secundário com o Mar do Caribe, fato não evidenciado nas análises. Sendo assim, a divergência de populações nessa espécie e a baixa variabilidade genética são fatores preocupantes para a manutenção da população de atobás marrons em uma área de grande impacto ambiental
The region of Campos Basin is exposed to various anthropogenic activities that affect directly the behavior of marine ecosystem. The study of marine fauna in North-Central coast of Rio de Janeiro is of great importance, several marine and coastal birds live or spend most of their migratory period along the Campos Basin, between them is Sula leucogaster (Boddaert, 1783). Although these birds are highly mobile, their populations have a robust genetic population structure. In order to check the structure and evolutionary relationships of the population of Sula leucogaster in the Campos Basin, 91 stranding samples were collected, and the data of this region were compared with the published data. From the control region of mitochondrial DNA, 26 haplotypes were identified, all of them being unique to the Campos Basin. Most of these haplotypes were rare, only eight have common frequencies. The analyses show that the population of the Campos Basin is a genetic stock of Sula leucogaster. This fact can be attributed to the filopatric behavior and coastal habit of this species that prevents the gene flow between populations. Moreover, the population of the Campos Basin has low genetic variability and is possibly suffering a bottleneck effect or purifying selection, supported by Fu test values, which is common for species divided into subpopulations. The phylogenetic data demonstrates a recent contact between the populations of the Campos Basin and Ascensão island. The oceanographic conditions also influence the structuring of populations of Sula leucogaster populations, as the absence of barriers and geographical proximity could favor secondary contact with the Caribbean Sea, which was not evident in the analyzes. Thus, the low amount of gene flow and the low genetic variability are worrying factors for the maintenance of the population of brown boobies in this area of high environmental impact

The approach is based on four criterias; 1) elasticity of adult and juvenile survival on population growth rate, 2) redlist status and 3) local abundances and 4) flight properties. I also investigated whether the different criteria differed based on geographic maps of the vulnerability in coastal areas in Norway, and the method presented in this study was compared to another framework for vulnerability assessment, developed by Garthe and Hüppop (2004). The present study contributes to a refined framework of vulnerability assessment, which to a larger extent consider the population dynamics of seabirds, compared to other methods based on multiple factor indexes. The study also contributes to the discussion of the methodological aspects of vulnerability assessments of seabirds.

The background to this thesis is Australia’s Oceans Policy, which aims to develop an integrated and ecosystem-based approach to planning and management. An important part of this approach is the identification of natural regions in regional marine planning, for example by establishing marine protected areas for biodiversity conservation. These natural regions will need to be identified on a range of scales for different planning and management actions. The scale of the investigation reported in this thesis is applicable to spatial management at 1 km to 10 km scale and monitoring impacts at the 10s of m to 1 km biotope scale. Seabed biotopes represent a combination of seabed physical attributes and related organisms. To map seabed biotopes in deep water, remote sensing using a combination of acoustic, optical and physical sensors is investigated. The hypothesis tested in this thesis is that acoustic bathymetry and backscatter data from a Simrad EM1002 multi-beam sonar (MBS) can be used to infer (act as a surrogate of) seabed biotopes. To establish a link between the acoustic data and seabed biotopes the acoustic metrics are compared to the physical attributes of the seabed in terms of its substrate and geomorphology at the 10s m to 1 km scale using optical and physical sensors. At this scale the relationship between the dominant faunal functional groups and both the physical attributes of the seabed and the acoustic data is also tested. These tests use data collected from 14 regions and 2 biomes to the south of Australia during a voyage in 2000. Based on 62 reference sites of acoustic, video and physical samples, a significant relationship between ecological seabed terrain types and acoustic backscatter and bathymetry was observed.These ecological terrain types of soft-smooth, soft-rough, hard-smooth and hard-rough were chosen as they were the most relevant to the biota in their ability to attach on or burrow into the seabed. A seabed scattering model supported this empirical relationship and the overall shape of backscatter to incidence angle relationship for soft and hard seabed types. The correlation between acoustic data (backscatter mean and standard deviation) and the visual and physical samples was most consistent between soft-smooth and hard-rough terrain types for a large range of incidence angles (16o to 70o). Using phenomenological backscatter features segmented into 10 common incidence angle bins from -70o to 70o the length resolution of the data decreased to 0.55 times depth. The decreased resolution was offset by improved near normal incidence (0o to 30o) seabed type discrimination with cross validation error reducing from 32% to 4%. A significant relationship was also established between the acoustic data and the dominant functional groups of fauna. Faunal functional groups were based on the ecological function, feeding mode and substrate preference, with 8 out of the 10 groups predicted with 70% correctness by the four acoustically derived ecological terrain types. Restricting the terrain classification to simple soft and hard using the acoustic backscatter data improved the prediction of three faunal functional groups to greater than 80%. Combining the acoustic bathymetry and backscatter data an example region, Everard Canyon, was interpreted at a range of spatial scales and the ability to predict the preferred habitat of a stalked crinoid demonstrated.Seabed terrain of soft and hard was predicted from the acoustic backscatter data referenced to a common seabed incidence angle of 40o. This method of analysis was selected due to its combined properties of high spatial resolution, consistent between terrain discrimination at the widest range of incidence angles and consistent data quality checking at varying ranges. Based in part on the research reported in this thesis a mid-depth Simrad EM300 multibeam sonar was purchased for use in Australian waters. A sampling strategy is outlined to map all offshore waters with priority within the 100 m to 1500 m depths.

The background to this thesis is Australia’s Oceans Policy, which aims to develop an integrated and ecosystem-based approach to planning and management. An important part of this approach is the identification of natural regions in regional marine planning, for example by establishing marine protected areas for biodiversity conservation. These natural regions will need to be identified on a range of scales for different planning and management actions. The scale of the investigation reported in this thesis is applicable to spatial management at 1 km to 10 km scale and monitoring impacts at the 10s of m to 1 km biotope scale. Seabed biotopes represent a combination of seabed physical attributes and related organisms. To map seabed biotopes in deep water, remote sensing using a combination of acoustic, optical and physical sensors is investigated. The hypothesis tested in this thesis is that acoustic bathymetry and backscatter data from a Simrad EM1002 multi-beam sonar (MBS) can be used to infer (act as a surrogate of) seabed biotopes. To establish a link between the acoustic data and seabed biotopes the acoustic metrics are compared to the physical attributes of the seabed in terms of its substrate and geomorphology at the 10s m to 1 km scale using optical and physical sensors. At this scale the relationship between the dominant faunal functional groups and both the physical attributes of the seabed and the acoustic data is also tested. These tests use data collected from 14 regions and 2 biomes to the south of Australia during a voyage in 2000. Based on 62 reference sites of acoustic, video and physical samples, a significant relationship between ecological seabed terrain types and acoustic backscatter and bathymetry was observed.
These ecological terrain types of soft-smooth, soft-rough, hard-smooth and hard-rough were chosen as they were the most relevant to the biota in their ability to attach on or burrow into the seabed. A seabed scattering model supported this empirical relationship and the overall shape of backscatter to incidence angle relationship for soft and hard seabed types. The correlation between acoustic data (backscatter mean and standard deviation) and the visual and physical samples was most consistent between soft-smooth and hard-rough terrain types for a large range of incidence angles (16o to 70o). Using phenomenological backscatter features segmented into 10 common incidence angle bins from -70o to 70o the length resolution of the data decreased to 0.55 times depth. The decreased resolution was offset by improved near normal incidence (0o to 30o) seabed type discrimination with cross validation error reducing from 32% to 4%. A significant relationship was also established between the acoustic data and the dominant functional groups of fauna. Faunal functional groups were based on the ecological function, feeding mode and substrate preference, with 8 out of the 10 groups predicted with 70% correctness by the four acoustically derived ecological terrain types. Restricting the terrain classification to simple soft and hard using the acoustic backscatter data improved the prediction of three faunal functional groups to greater than 80%. Combining the acoustic bathymetry and backscatter data an example region, Everard Canyon, was interpreted at a range of spatial scales and the ability to predict the preferred habitat of a stalked crinoid demonstrated.
Seabed terrain of soft and hard was predicted from the acoustic backscatter data referenced to a common seabed incidence angle of 40o. This method of analysis was selected due to its combined properties of high spatial resolution, consistent between terrain discrimination at the widest range of incidence angles and consistent data quality checking at varying ranges. Based in part on the research reported in this thesis a mid-depth Simrad EM300 multibeam sonar was purchased for use in Australian waters. A sampling strategy is outlined to map all offshore waters with priority within the 100 m to 1500 m depths.

Seabirds feeding ecology was studied at sea to assess the significance of two commercial fisheries, trawlers (demersal fishery with diurnal activity) and purse seiners (pelagic fishery with nocturnal activity), in the NW Mediterranean. Trawlers offered high amounts of discards (mostly fish of small size) on a predictable basis, and consequently attracted large numbers of seabirds. At the Ebro Delta, discards provided in average 65% of the energy requirements of the seabird breeding community, being most important for large gulls and of little significance for terns. Purse seiners produced few discards, on an irregular basis, and attracted lower numbers of seabirds during discarding (after dawn). During the fishing operation, at night, only Audouin's Gulls Larus audouinii attended these vessels, capturing live fish concentrated near the sea surface, attracted by powerful lamps. During the breeding season, Audouin's Gulls preferentially attended trawlers in spite of potential competition with the more aggressive and opportunistic Yellow-legged Gulls Larus cachinnans, since the former showed to be more efficient at capturing discards and reduced competition by showing a wider range of feeding techniques. Only during trawler closures, Audouin's Gulls occurred in important numbers at purse seiners (thus acting as a secondary food resource for most individuals). During the non-breeding season Audouin's Gulls shifted to preferentially attend purse seiners, presumably because competition at trawlers strengthened at this period. The rare and threatened Balearic Shearwater Puffinus mauretanicus also made significant use of discards, which represented more than 40% of the energy requirements of the whole population during the breeding season. Seabirds feeding upon discards showed higher levels of mercury, as discards make accessible to them demersal fish that is more polluted than epipelagic fish (natural prey for most seabirds). Thus, the risks of toxicity by this metal are higher for those species capturing discards. Given the significance of commercial fisheries for seabirds in the NW Mediterranean, and considering the increasing ecosystem-based approach to fisheries management, fisheries managers should regard these birds when designing fishing policies.

Movement is a widespread characteristic in the animal kingdom —occurring at many spatiotemporal scales— with consequences at an individual, population, species, and even ecosystem level. It is a very diverse character, with many different drivers that stem from the way in which individuals interact with their environment. Of these, one of the most important is the distribution of resources, particularly for migratory and foraging movements. In migration, the search for an optimal environment involves movement at large spatiotemporal scales, following seasonal changes in resource distribution. In foraging movements, the search for resources happens at small spatiotemporal scales, and involves different strategies to optimise the search and capture of food, including the ability to obtain foraging cues from conspecifics. In seabirds, movement —at large and local scales— has deep repercussions in their life-history traits, evolutionary history, morphology, physiology and behaviour, which makes them a very valuable study group to understand the role, the causes and consequences of migratory and foraging movements in the ecology of marine top- predators. The study of migratory and foraging movements has been revolutionised by the development of smaller, cheaper and better tracking devices, promoting multi-colony, population and even species approaches to the study of animal movement, but which also come with a set of methodological challenges that have to be addressed in order to make unbiased inferences of space and habitat use at population or species level from individual movement data. In this thesis, we develop methods to test the possible biases introduced by the use of individual tracking data to infer distribution at a population or species level. we then apply these tools to a multi-colony dataset of non-breeding locations of Cory’s (Calonectris borealis), Scopoli’s (C. diomedea) and Cape Verde (C. edwardsii) shearwaters, to study their migratory connectivity and non-breeding habitat segregation at the colony, population and species level. Lastly, we apply state-of-the-art spatial models to study foraging distributions of three neighbouring colonies of Cory’s shearwaters, detect the segregation among them and unravel the environmental and behavioural drivers of this segregation. I developed several functions in the R environment aimed at the detection of the effects of individual site fidelity and temporal variability in the inference of spatial use at a colony or population level, and to calculate the degree in which the movements of a single population can be representative of those of the entire species. These tools are applicable to individual movement data regardless of the species or tracking device. we also used these tools to demonstrate the spatial and ecological segregation between the non-breeding distributions of three taxa of Calonectris shearwaters studied, as well as detecting a stronger degree of migratory connectivity at a population than at a colony level, indicating that individuals of different colonies within a population mix in the non-breeding areas, but birds from different populations do not, which has important implications for their population dynamics and for their conservation and management. Lastly, we demonstrated segregation among the foraging distributions of three neighbouring colonies of Cory’s shearwaters, both in the waters surrounding the colony and in distant, foraging grounds, finding evidences of both environmental and behavioural drivers behind this segregation, and suggesting a mechanism through which transfer of information between individuals can be shaping the distributions of foraging seabirds. The results of this thesis provide relevant tools for the field of movement ecology, as they can be used for analysing movements of mobile species, regardless of species, tracking device or spatiotemporal scale. In addition, they are relevant for the field of seabird ecology as they provide insights into the causes of space and habitat use in long-ranging pelagic seabirds.
El moviment és una característica omnipresent en el regne animal, a les més diverses escales espacio-temporals i amb conseqüències a diferents nivells (individual,. poblacional, específic i fins i tot ecosistèmic). La força impulsora del moviment més predominant i generalitzada és distribució dels recursos en el medi, important tant a gran escala (moviments migratoris) com en els moviments diaris de recerca d’aliment a escala petita. En les aus marines en particular, el moviment té repercussions profundes en les seves característiques morfològiques i de comportament, en la seva història de vida, i la seva història evolutiva. El desenvolupament de dispositius de seguiment més petits, barats i precisos ha promocionat la proliferació d’estudis del moviment animal des d’un punt de vista multi- colònia, de població i fins i tot d’espècie. En aquesta tesi, desenvolupo diferents funcions per testar els biaixos introduïts en l’estudi del moviment, a través de dades de seguiment individual, a nivell de població o espècie. Posteriorment, utilitzo aquestes eines per a analitzar la connectivitat migratòria i la segregació dels hàbitats d’hivernada, des d’un punt de vista multi-colònia, de les baldrigues cendroses de l’Atlàntic (Calonectris borealis), del Mediterrani (C. diomedea), i de Cap Verd (C. edwardsii). Per últim, aplico un mètode innovador de modelatge espacial per a estudiar les distribucions d’alimentació de baldrigues cendroses de l’Atlàntic criant en tres colònies veïnes, per detectar-ne la segregació i descobrir-ne les causes, tant ambientals com comportamentals, incloent com els diferents mecanismes de transferència d’informació entre individus poden afectar a aquestes distribucions. Els resultats d’aquesta tesi tenen rellevància per a la ecologia del moviment en general, ja que són aplicables a dades de moviment individual de qualsevol espècie, independentment de l’aparell de seguiment utilitzat, i en el camp de l’ecologia de les aus marines, ja que proporciona nous coneixements sobre els diferents factors afectant la distribució i l’ús de l’espai, tant durant la cria com durant la hivernada, en aus pelàgiques.

Sea turtles, marine mammals and sea birds are vulnerable to higher mortality rates as a direct function of incidental capture (bycatch) in marine fisheries. Their migratory behavior exposes them to multiple fishing gear types and fishing practices and efforts to understand the rates of interaction between these taxa and fishing necessarily entails analysis of data over large spatial areas (ocean-basin) and multiple types of fishing activities. The acquisition the requisite data, however, requires considerable resources and many regions in the world are data-poor with respect to bycatch, including the Wider Caribbean Region (WCR) in the west central Atlantic Ocean basin. This dissertation presents the results of multiple strategies used to assess sea turtle, marine mammal and seabird bycatch in the WCR, with a particular focus on sea turtle bycatch. The research incorporated a synthetic review of the literature, expert consultation, statistical techniques, and geospatial analyses to assess the bycatch seascape for the region. I conclude that sea turtle bycatch in the WRC is significantly linked to turtle rookeries, especially those on the continental land mass and in the southern section of the Caribbean basin, in large part because of the near shore artisanal nature of the fisheries and the importance of these habitats for foraging and reproduction. The limited information on marine mammal bycatch does not permit robust inferences, but it clearly identifies threats to at least one vulnerable marine mammal species, the tucuxi (Sotalia fluviatilis). Information on seabird bycatch was even more limited; the most vulnerable seabird populations occur in the higher latitudes (temperate zones) while the seabird populations in the WCR face significant threats from habitat loss and over-exploitation. This dissertation proposes specific recommendations for improving and advancing the information base for a regional, ecosystem-level management and mitigation of bycatch.

Dissertation

Characterizing the population genetic structure of a species can provide insight into isolating effects of local adaptation and genetic drift, and homogenizing effects of gene flow. The relative interplay between gene flow and genetic drift can indicate whether multiple conservation units are needed to preserve biodiversity. Baja California, Mexico is a biodiversity hotspot where many individuals are genetically differentiated from conspecific individuals breeding elsewhere. Cassin’s auklet (Ptychoramphus aleuticus), a zooplanktivorous seabird, breeds in colonies along the Pacific coast of North America. One subspecies, P. a. australe, is described from Baja California and another, P. a. aleuticus, is described from the rest of its range to the Aleutian Islands, Alaska. Many of the colonies throughout its range have been declining in numbers likely as a result of decreases in food availability in cold-water upwellings along the coast. The mitochondrial control region and eleven nuclear microsatellites were analyzed using programs based on coalescent and Bayesian theory to determine how the southern subspecies compares genetically to the main subspecies. First, population genetic structure was characterized throughout Cassin’s auklet’s breeding range using pairwise genetic differentiation indices, hierarchical analysis of variance, statistical parsimony and Bayesian clustering methods. The two subspecies were genetically differentiated but individuals breeding in the Channel Islands were more genetically similar to P. a. australe individuals. Population genetic differentiation was not evident within the two genetic groups. Second, gene flow between the two genetic groups was estimated using coalescent and Bayesian methods. Significant gene flow was estimated from the northern group (Aleutian Islands to Southeast Farallon Islands) into the southern group (Channel Islands to San Benito Island) but not from the southern group into the northern group since the time of divergence, possibly as a result of the non-breeding distribution. Results show that the two genetic populations diverged recently and the populations have experienced a recent population change in size. Restrictions in home range and foraging range may cause population genetic differentiation, resulting in two distinct management units. Genetic differentiation of the southern population provides support for Baja California and southern California being a biodiversity hotspot.
Thesis (Master, Biology) -- Queen's University, 2012-09-28 14:02:24.007

Following catastrophic exploitation throughout the North Atlantic, breeding seabird populations have begun to recover thanks to regulatory protection and restoration and management efforts. As bird populations increase, new challenges emerge, including overgrowth of vegetation that limits the open nesting habitat favored by most tern species. Though managers have used a variety of measures to reduce vegetation cover, these techniques have rarely been quantified or compared experimentally. During the summers of 2009 and 2010, I applied two different techniques, controlled burning and artificial weed barriers (muslin fabric and artificial turf) to experimental plots on Eastern Egg Rock and Outer Green Island, near-shore seabird nesting islands in mid-coastal Maine. I then monitored vegetation regrowth and use by nesting terns to assess the effectiveness of these techniques for opening and maintaining Common Tern nesting habitat during a full breeding season, comparing treated plots to vegetated control plots and existing tern nesting habitat. Burned areas did not remain open for the full nesting season, but regrew shortly after laying, leading to near-complete nest failure in these plots. Tern nest and fledging success was similar in weed barrier (1.37 chicks/pair) and untreated tern nesting habitat (1.38 chicks/pair) plots. Replacement of existing vegetation, tested at a limited scale on Outer Green Island, did not succeed. These three techniques represent only a small fraction of vegetation management techniques used throughout the North Atlantic region. Through literature review and consultation with North Atlantic colony managers, I collected information on vegetation management on 34 tern nesting islands between 33 and 55° N latitude and developed a summary of different vegetation control techniques used. I identified 14 technique types suitable for use in nesting colonies: i.e., that can be applied before and after (but not during) the nesting period of May-July, that do not cause destructive impacts to the surrounding ecosystem, and that involve materials and labor that can be transported to inaccessible offshore islands. Of these techniques, 8 created usable tern nesting habitat for a full breeding season, and the most successful techniques required constructing habitat over existing vegetation. The success of different methods depended heavily on the plant communities and soil types involved. In general, vegetation management options were more limited and less successful for elevated, rocky islands than for low, sandy islands. Often, techniques that successfully removed one species or group of species (i.e., perennial grasses) failed due to rapid colonization by other species (i.e., herbaceous annuals). This review of past and ongoing vegetation management techniques used on seabird nesting islands, including their costs, methods for application, and effectiveness, provides seabird managers a reference when evaluating current and future vegetation management programs.

During 2008 – 2009, we quantified foraging behavior of adult Atlantic puffins (Fratercula arctica) by deploying time-depth recorders (TDRs) on 18 adults and collected morphological measurements from 40 adults nesting on Petit Manan Island, Maine. Dive data were successfully retrieved from 5 birds foraging for 14 days in 2008, and 8 birds foraging for 18 days in 2009. Pooling across all birds, a total of 8,097 dives were recorded, with peaks in activity during 0400-0800 and 1600-2000, and no diving between 2100 and 0400. Mean (± SD) dives/bird/day was 276.4 (± 84.7), with dives grouped into bouts lasting 17.8 (± 31.5) minutes, consisting of 8.9 (± 3.4) dives. Dive depth was less than 15 m for 86% of the dives. Mean maximum dive depth across birds was 9.7 (± 1.7) m, with the deepest dive being 40.7 m. Females made fewer deep dives (27-41 m), had more midday dives (1000 - 1559), and their dives were spread across a greater number of bouts per day than males. Given a mean foraging trip length of 60.1 (± 38.3) minutes for 26 birds observed in 2009, we estimate that adult puffins foraged, on average, within 31 km of the colony. Morphological measures were recorded by a single observer and included body mass, wing chord, bill depth, bill length, culmen, and head-bill length, and represented 19 males and 21 females, based on blood sample analysis. Data were analyzed using classification trees, and our final tree used culmen length and bill depth to correctly classify 34 of 40 (85%) birds (kappa = 0.695, P < 0.01). Use of our model can greatly improve the ability of biologists to identify sex of puffins in the field at this colony site, but variability in morphological data we collected at addition colonies indicates that future work is needed to determine its applicability throughout the Gulf of Maine. During 2009, we measured burrow characteristics of alcids and empty burrows. Breeding success and burrow characteristics were measured for nests of 104 puffins, 58 guillemots and 4 razorbills, with burrow characteristics measured for an additional 12 guillemot and 56 empty burrows. Mean diameter of burrow openings of puffins, guillemots, razorbills and empty burrows were significantly different, and artificial puffin burrows had significantly smaller openings than natural while artificial and natural guillemot burrows had similar opening diameters. Hatch, chick, and nest success of puffins was similar among burrow types, but guillemots had higher hatch and nest success in artificial burrows. The variables we used to create models for predicting hatch and nest success for puffins and guillemots had inadequate discriminatory power to predict success.

Changes in the marine ecosystem can affect the distribution, survival, and reproductive success of seabirds. Therefore, a better understanding of factors influencing the marine distribution and abundance of seabirds can provide insight into ecological hypotheses and have important conservation implications. Yet at-sea habitat selection by seabirds has received far less attention than have investigations of their breeding biology. I studied the patterns and processes of marine habitat selection by seabirds in nearshore waters of Pacific Rim National Park Reserve, Vancouver Island, British Columbia. The study focused on comparative analyses among five sympatric species: marbled murrelet (Brachyramphus marmoratus), common murre (Uria aalge), rhinoceros auklet (Cerorhinca monocerata), pigeon guillemot (Cepphus columba) and pelagic cormorant (Phalacrocorax pelagicus). I used a multi-scaled and multi-disciplined approach combining shore-based telescope observations, vessel-based surveys, and developed new techniques for mapping nearshore seabird distributions. Patterns of habitat selection were examined through vessel-based surveys and species-habitat modeling. Vessel-based transects are fundamental to studies of seabird ecology, yet standardized protocols often fail to account for detectability biases. Distance-sampling methods were used to quantify seabird detectability along transects and showed extensive variability (20-80% of birds detected) depending on species, year, and observer. Corrected estimates of bird densities were used in habitat selection modeling, which demonstrated inter-specific and inter-annual differences in species-habitat associations. Most species showed distinct partitioning in habitats, particularly with respect to substrate and along gradients of depth and sea-surface temperature/salinity. Thus, environmental variability is a key factor structuring habitat use and coexistence in this community of piscivorous seabirds. Processes of habitat selection were studied through observations of foraging behaviour, estimates of prey availability, and spatial-statistical analysis of seabird distributions. Marbled murrelets increased foraging effort in years and seasons with scarce prey and poor oceanographic conditions and decreased foraging effort at sites with high prey availability. Despite their flexible activity budgets, increased foraging effort was inadequate to buffer reproductive success in a poor prey year, suggesting that prey availability is a limiting factor in habitat use and population growth for murrelets. Theodolite-based mapping studies examined the fine-scale distribution patterns of murrelets and murres. Nearest neighbour spatial statistics tested for competition over foraging space and showed avoidance of murres by murrelets. The results of these studies have implications for the management and conservation of the imperiled marbled murrelet in British Columbia and elsewhere in their range. I demonstrate a clear link between prey availability and consequences for reproductive success. Habitat selection models provide a step towards identifying critical marine habitats which must be protected under the Species at Risk Act. Murrelets show high forage site fidelity and associations with spatially fixed habitat components (beaches), suggesting that marine protected areas may have an important role to play in the conservation, management and recovery of murrelet populations.

Seabird species are increasingly threatened around the world due to a range of anthropogenic impacts affecting at-sea and breeding habitat. One such species is the Ancient Murrelet, an Alcid species nesting on the Pacific Coast of Canada. Ancient Murrelets are an important species in Canadian waters as approximately 50 % of the world’s breeding population nest in a small region of the British Columbia coast. Ancient Murrelets are listed as a species of Special Concern, due to threats in their breeding colonies; threats to their at-sea habitat, such as disturbance from shipping traffic, oil pollution, and fisheries bycatch, are currently poorly- documented due to the challenges associated with studying seabirds in their offshore environments. Conservation efforts to protect this species require information on movements and habitat use at sea. Therefore, there exists a critical need for research that provides new knowledge on where murrelets are travelling and the habitats in which they are foraging. The objective of this thesis research is to investigate movement behaviour and at-sea habitat of Ancient Murrelets during breeding season foraging trips. Movement modelling using hidden Markov models differentiated the tracks into behaviour states, and identified foraging locations at sea. Foraging locations were used in regression modelling to investigate the degree to which variability in Ancient Murrelet foraging locations could be explained by seafloor depth, slope and tidal current, and spatial measures such as distance from the breeding colony. From characteristics of movement paths, hidden Markov models identified three movement behaviour states, which were interpreted as transit, resting, and foraging behaviours. Logistic regression models suggested that depth, seafloor slope, tidal speed, and distance from the colony exhibited a negative influence on locations where birds chose to forage. Nevertheless, of the locations where foraging took place, foraging intensity was found to be higher in deeper areas suggesting Ancient Murrelets may be focusing efforts in areas of higher prey abundance. The combination of individual movement analysis and habitat analysis provides an important first step in gaining a greater understanding of Ancient Murrelet behaviour and foraging habitat at sea. These findings can inform marine management planning in this region and conservation of this vulnerable species.
Graduate
2021-04-17