Scottish Oceans Institute
https://hdl.handle.net/10023/792
2024-03-28T16:16:08ZQuantifying costs and rewards in optimal foraging models of the marine environment. Using bulk feeding mysticete whales as an example
https://hdl.handle.net/10023/29197
Animals feed to maintain body condition and maximise fitness. Feeding is a multi-stage behaviour that encapsulates aspects of an animals' sensory and foraging ecology, and that can be divided into the following broad functional categories; prey detection, capture, and handling (assimilation of acquired energy stores). The evolutionary consequences of foraging have the potential to shape predator-prey dynamics, influence community and ecosystem structure; and to drive the evolution of physiological and morphological adaptations that minimise energetic costs and maximise energy uptake. Excess energy can be converted to fat (lipids) and stored to enhance reproductive potential or to protect against temporary (voluntary) starvation associated often with long distance migration or changes in prey distribution. Understanding how an animal balances these conflicting forces, and makes key foraging decisions is an important aspect to understanding their ecology. Simple questions such as how, when, where, why and what an animal chooses to feed on are difficult to answer without the development and application of new technologies. The development of new tools and analytical approaches is particularly important in the marine environment where these key life history decisions occur offshore and or at depth. Bulk feeding rorqual whales are amongst the largest species to have lived on Earth, and are major consumers of schooling krill and forage fish. Because of their size and ability to consume significant quantities of fish and krill they have an important role in structuring ecological communities. Lunge feeding is an energetically costly bulk feeding behaviour that is practised by all members of this super-family. To understand how energy fluxes pass through the consumer to be expressed as body condition it is first necessary to have reliable proxies of the energetic costs and gains associated with feeding. In this thesis methods for estimating these energy fluxes were explored using data from summer feeding (Balaenoptera physalus) and humpback whales (Megaptera novaeangliae) in Canada, and winter feeding humpback whales in northern Norway. Calibrated speed measurements were used as a proxy for the energetic costs associated with bulk feeding (lunge) and transport in baleen whales (chapter 2). Speed measurements were used to develop a lunge detector (chapter 3). Lunge speed and other kinematic variables associated with bulk feeding were used to identify species-specific signatures in feeding behaviour as a potential method for identifying prey type, and thus their caloric value as a proxy for energy uptake (chapter 4)). The feasibility of using new sensors, (i) sonar to measure prey density and dynamics from the perspective of the feeding whale (chapter 5), and (ii) an ultrasound to measure blubber depth in wild marine mammals as a proxy of body condition (chapter 6) were tested.
2021-06-30T00:00:00ZSwift, René JamesAnimals feed to maintain body condition and maximise fitness. Feeding is a multi-stage behaviour that encapsulates aspects of an animals' sensory and foraging ecology, and that can be divided into the following broad functional categories; prey detection, capture, and handling (assimilation of acquired energy stores). The evolutionary consequences of foraging have the potential to shape predator-prey dynamics, influence community and ecosystem structure; and to drive the evolution of physiological and morphological adaptations that minimise energetic costs and maximise energy uptake. Excess energy can be converted to fat (lipids) and stored to enhance reproductive potential or to protect against temporary (voluntary) starvation associated often with long distance migration or changes in prey distribution. Understanding how an animal balances these conflicting forces, and makes key foraging decisions is an important aspect to understanding their ecology. Simple questions such as how, when, where, why and what an animal chooses to feed on are difficult to answer without the development and application of new technologies. The development of new tools and analytical approaches is particularly important in the marine environment where these key life history decisions occur offshore and or at depth. Bulk feeding rorqual whales are amongst the largest species to have lived on Earth, and are major consumers of schooling krill and forage fish. Because of their size and ability to consume significant quantities of fish and krill they have an important role in structuring ecological communities. Lunge feeding is an energetically costly bulk feeding behaviour that is practised by all members of this super-family. To understand how energy fluxes pass through the consumer to be expressed as body condition it is first necessary to have reliable proxies of the energetic costs and gains associated with feeding. In this thesis methods for estimating these energy fluxes were explored using data from summer feeding (Balaenoptera physalus) and humpback whales (Megaptera novaeangliae) in Canada, and winter feeding humpback whales in northern Norway. Calibrated speed measurements were used as a proxy for the energetic costs associated with bulk feeding (lunge) and transport in baleen whales (chapter 2). Speed measurements were used to develop a lunge detector (chapter 3). Lunge speed and other kinematic variables associated with bulk feeding were used to identify species-specific signatures in feeding behaviour as a potential method for identifying prey type, and thus their caloric value as a proxy for energy uptake (chapter 4)). The feasibility of using new sensors, (i) sonar to measure prey density and dynamics from the perspective of the feeding whale (chapter 5), and (ii) an ultrasound to measure blubber depth in wild marine mammals as a proxy of body condition (chapter 6) were tested.Unravelling the complex reproductive tactics of male humpback whales : an integrative analysis of paternity, age, testosterone, and genetic diversity
https://hdl.handle.net/10023/29070
How the underlying forces of sexual selection impact reproductive tactics including elaborate acoustic displays in cetaceans remains poorly understood. Here, I combined 26 years (1995-2020) of photo-identification, behavioural, (epi)genetic, and endocrine data from an endangered population of humpback whales (New Caledonia), to explore male reproductive success, age, physiology, and population dynamics over almost a third of the lifespan of a humpback whale. First, I conducted a paternity analysis on 177 known mother-offspring pairs and confirmed previous findings of low variation in reproductive success in male humpback whales. Second, epigenetic age estimates of 485 males revealed a left-skewed population age structure in the first half of the study period that became more balanced in the second half. Further, older males (> 23 years) more often engaged in certain reproductive tactics (singing and escorting) and were more successful in siring offspring once the population age structure stabilised, suggesting reproductive tactics and reproductive success in male humpback whales may be age-dependent. Third, using enzyme immunoassays on 457 blubber samples, I observed a seasonal decline in male testosterone in the population over the breeding season. Testosterone levels appeared highest during puberty, then decreased and levelled off at the onset of maturity, yet were highly variable at any point during the breeding season and across males of all ages. Lastly, I investigated the influence of genetic diversity at the major histocompatibility complex (MHC) class I and class IIa (DQB and DRB-a) on patterns of male reproductive success in humpback whales. Mating pairs shared fewer alleles than expected under random mating at MHC class I and IIa, thus, providing evidence of an MHC-mediated female mate choice in humpback whales. This thesis provides novel, critical insights into the evolutionary consequences of commercial whaling on the demography, patterns of reproduction and sexual selection of exploited populations of baleen whales.
2024-06-12T00:00:00ZEichenberger, FrancaHow the underlying forces of sexual selection impact reproductive tactics including elaborate acoustic displays in cetaceans remains poorly understood. Here, I combined 26 years (1995-2020) of photo-identification, behavioural, (epi)genetic, and endocrine data from an endangered population of humpback whales (New Caledonia), to explore male reproductive success, age, physiology, and population dynamics over almost a third of the lifespan of a humpback whale. First, I conducted a paternity analysis on 177 known mother-offspring pairs and confirmed previous findings of low variation in reproductive success in male humpback whales. Second, epigenetic age estimates of 485 males revealed a left-skewed population age structure in the first half of the study period that became more balanced in the second half. Further, older males (> 23 years) more often engaged in certain reproductive tactics (singing and escorting) and were more successful in siring offspring once the population age structure stabilised, suggesting reproductive tactics and reproductive success in male humpback whales may be age-dependent. Third, using enzyme immunoassays on 457 blubber samples, I observed a seasonal decline in male testosterone in the population over the breeding season. Testosterone levels appeared highest during puberty, then decreased and levelled off at the onset of maturity, yet were highly variable at any point during the breeding season and across males of all ages. Lastly, I investigated the influence of genetic diversity at the major histocompatibility complex (MHC) class I and class IIa (DQB and DRB-a) on patterns of male reproductive success in humpback whales. Mating pairs shared fewer alleles than expected under random mating at MHC class I and IIa, thus, providing evidence of an MHC-mediated female mate choice in humpback whales. This thesis provides novel, critical insights into the evolutionary consequences of commercial whaling on the demography, patterns of reproduction and sexual selection of exploited populations of baleen whales.Sounds beneath the surface : a multiple-approach study of bottlenose dolphin acoustic communication
https://hdl.handle.net/10023/28429
Bottlenose dolphins (Tursiops truncatus) live in complex individualized societies that combine stable social units with fluid groups, and they largely rely on sound to interact with one another. This thesis applies a suite of approaches to study their acoustic communication. I studied the wild population of Sarasota, which offers long-term behavioural data and opportunities to deploy sound-and-movement recording tags. Bottlenose dolphins display a wide call repertoire, including graded sounds challenging to classify. I use dolphin social interactions to present a novel tag-based approach for studying communicative roles of call parameters changes. Applying continuously-sampled parameters, this approach examines how individuals change movements as a function of signal features. I focus then on signature whistles, sounds encoding identity information that in Sarasota are documented for most individuals. Signature whistles function as individually-distinctive contact calls, for instance between closely-bonded animals during separation, but their function between groups is poorly documented. Analysing Dtag data from instances of group encounters, I show that dolphins did not regularly produce signature whistles upon detecting another group, nor systematically before joining; instead, signatures appeared to be used strategically depending on the encountered individuals. Dolphins sometimes imitate the signature whistle of others, which is thought to function for addressing known individuals. Performing first-ever playbacks of natural signature whistle copies, I show that free-ranging subjects turned more frequently towards the playback upon hearing copies of their signature vs signature whistles of others, supporting the addressing function of copies. Signature whistle copies are often produced right after the subject’s signature, in so-called vocal matching interactions. Using playbacks with temporarily-captured subjects, I test whether signature whistle matching, or vocal matching per se, has an addressing signalling role. Subjects turned more times and produced their signature more frequently in response to signature whistle matching vs matching of other calls, supporting the former hypothesis.
2023-11-28T00:00:00ZCasoli, MarcoBottlenose dolphins (Tursiops truncatus) live in complex individualized societies that combine stable social units with fluid groups, and they largely rely on sound to interact with one another. This thesis applies a suite of approaches to study their acoustic communication. I studied the wild population of Sarasota, which offers long-term behavioural data and opportunities to deploy sound-and-movement recording tags. Bottlenose dolphins display a wide call repertoire, including graded sounds challenging to classify. I use dolphin social interactions to present a novel tag-based approach for studying communicative roles of call parameters changes. Applying continuously-sampled parameters, this approach examines how individuals change movements as a function of signal features. I focus then on signature whistles, sounds encoding identity information that in Sarasota are documented for most individuals. Signature whistles function as individually-distinctive contact calls, for instance between closely-bonded animals during separation, but their function between groups is poorly documented. Analysing Dtag data from instances of group encounters, I show that dolphins did not regularly produce signature whistles upon detecting another group, nor systematically before joining; instead, signatures appeared to be used strategically depending on the encountered individuals. Dolphins sometimes imitate the signature whistle of others, which is thought to function for addressing known individuals. Performing first-ever playbacks of natural signature whistle copies, I show that free-ranging subjects turned more frequently towards the playback upon hearing copies of their signature vs signature whistles of others, supporting the addressing function of copies. Signature whistle copies are often produced right after the subject’s signature, in so-called vocal matching interactions. Using playbacks with temporarily-captured subjects, I test whether signature whistle matching, or vocal matching per se, has an addressing signalling role. Subjects turned more times and produced their signature more frequently in response to signature whistle matching vs matching of other calls, supporting the former hypothesis.Humpback whales in Brazil : distribution, abundance and human impacts
https://hdl.handle.net/10023/18932
The humpback whale population breeding in Brazilian waters has greatly increased, after near extinction due to whaling in the twentieth century. Today, these animals are under pressure from human activities in the area. In this thesis, habitat use, distribution, abundance, population status and potential threat from oil spills were investigated to improve knowledge of the population’s ecology and provide useful information for conservation and management. Distribution and habitat use were investigated through spatial models applied to line transect data and to tracking data. Line transect data were also used to estimate abundance. Distribution maps from both data types were used with a simulation of oil dispersion to evaluate risk of impact from oil spills. The new abundance estimates, together with information on population increase from another study, were used to update a Bayesian population dynamics model to re-assess population status. Modelling of line transect data indicated whale density to be higher in slower currents, at shorter distances to both the coastline and shelf edge, and at sea surface temperatures between 24 and 25°C, and to be related to shelter. A higher concentration of animals was predicted in the southern portion of Abrolhos bank, an enlargement of the continental shelf. Modelling of tracking data agreed with those findings, despite differences in the nature of the data and analytical methods. Risk maps of oil spill impact indicated that areas in the south of the breeding range present highest risks to the animals. Abundance estimates (14,264, CV = 0.084, in 2008; 20,389, CV = 0.071, in 2012) provide further evidence that the population is increasing, and contributed to improved precision in the population status assessment. New information provided here will inform conservation of the humpback whale population breeding in Brazilian waters and the need for, and implementation of, any necessary management action.
2019-12-03T00:00:00ZBortolotto, Guilherme AugustoThe humpback whale population breeding in Brazilian waters has greatly increased, after near extinction due to whaling in the twentieth century. Today, these animals are under pressure from human activities in the area. In this thesis, habitat use, distribution, abundance, population status and potential threat from oil spills were investigated to improve knowledge of the population’s ecology and provide useful information for conservation and management. Distribution and habitat use were investigated through spatial models applied to line transect data and to tracking data. Line transect data were also used to estimate abundance. Distribution maps from both data types were used with a simulation of oil dispersion to evaluate risk of impact from oil spills. The new abundance estimates, together with information on population increase from another study, were used to update a Bayesian population dynamics model to re-assess population status. Modelling of line transect data indicated whale density to be higher in slower currents, at shorter distances to both the coastline and shelf edge, and at sea surface temperatures between 24 and 25°C, and to be related to shelter. A higher concentration of animals was predicted in the southern portion of Abrolhos bank, an enlargement of the continental shelf. Modelling of tracking data agreed with those findings, despite differences in the nature of the data and analytical methods. Risk maps of oil spill impact indicated that areas in the south of the breeding range present highest risks to the animals. Abundance estimates (14,264, CV = 0.084, in 2008; 20,389, CV = 0.071, in 2012) provide further evidence that the population is increasing, and contributed to improved precision in the population status assessment. New information provided here will inform conservation of the humpback whale population breeding in Brazilian waters and the need for, and implementation of, any necessary management action.Not just fat : investigating novel physiological state biomarkers in cetacean blubber
https://hdl.handle.net/10023/17977
Despite its importance as a predictor of fitness, no consensus has been reached about how to
assess the nutritive body condition of free-ranging cetaceans. Standard indices of condition
used in terrestrial ecology were assessed in cetaceans using data and samples from stranded
animals. The most appropriate morphometric indices were identified as mass/length2 and
girth/length (where mass data were unavailable). Blubber thickness, and blubber lipid content
were poor indicators of condition. Variation in lipid content suggested that there may be tradeoffs
occurring between different blubber functions involved in energy storage, controlling
buoyancy, and preserving thermoregulatory properties in species with different life-history
strategies.
Novel blubber biomarkers of physiological state were investigated as objective and widely
applicable tools for estimating body condition. Blubber cortisol concentrations were negatively
correlated with morphometric indices of condition in stranded animals from two cetacean
families. Blubber cortisol concentrations were thus identified as a candidate biomarker. When
applied to a 13-year dataset of biopsy samples from female humpback whales (Megaptera
novaeangliae), cortisol concentrations showed significant inter-annual variation.
Concentrations were weakly correlated with annual pregnancy rates. High individual
variability in blubber cortisol concentrations was likely a result of the multi-functional nature
of cortisol. Cortisol concentrations thus probably provide a ‘snap shot’ of the metabolic state
of the tissue when sampled.
A proteomic approach was developed to extract and identify proteins in blubber. A range of
proteins involved in numerous metabolic processes and pathways were identified. These
proteins likely capture the range of physiological processes experienced by individuals at the
time of sampling. This new proteomic approach will help to assign novel functions to marine
mammal blubber in keeping with current understanding of the multi-functional role of adipose
tissue as an endocrine organ in mammals. It will also allow the future development of protein
biomarkers of health and physiological state.
2019-06-26T00:00:00ZKershaw, JoannaDespite its importance as a predictor of fitness, no consensus has been reached about how to
assess the nutritive body condition of free-ranging cetaceans. Standard indices of condition
used in terrestrial ecology were assessed in cetaceans using data and samples from stranded
animals. The most appropriate morphometric indices were identified as mass/length2 and
girth/length (where mass data were unavailable). Blubber thickness, and blubber lipid content
were poor indicators of condition. Variation in lipid content suggested that there may be tradeoffs
occurring between different blubber functions involved in energy storage, controlling
buoyancy, and preserving thermoregulatory properties in species with different life-history
strategies.
Novel blubber biomarkers of physiological state were investigated as objective and widely
applicable tools for estimating body condition. Blubber cortisol concentrations were negatively
correlated with morphometric indices of condition in stranded animals from two cetacean
families. Blubber cortisol concentrations were thus identified as a candidate biomarker. When
applied to a 13-year dataset of biopsy samples from female humpback whales (Megaptera
novaeangliae), cortisol concentrations showed significant inter-annual variation.
Concentrations were weakly correlated with annual pregnancy rates. High individual
variability in blubber cortisol concentrations was likely a result of the multi-functional nature
of cortisol. Cortisol concentrations thus probably provide a ‘snap shot’ of the metabolic state
of the tissue when sampled.
A proteomic approach was developed to extract and identify proteins in blubber. A range of
proteins involved in numerous metabolic processes and pathways were identified. These
proteins likely capture the range of physiological processes experienced by individuals at the
time of sampling. This new proteomic approach will help to assign novel functions to marine
mammal blubber in keeping with current understanding of the multi-functional role of adipose
tissue as an endocrine organ in mammals. It will also allow the future development of protein
biomarkers of health and physiological state.Title redacted
https://hdl.handle.net/10023/17149
2016-06-22T00:00:00ZHope, Julie AnneThe impact of multiple stressors on coastal biodiversity and associated ecosystem services
https://hdl.handle.net/10023/16817
Marine and coastal ecosystems are subject to diverse and increasingly intensive anthropogenic
activities, making understanding cumulative effects critically important. However, accurately
accounting for the cumulative effects of human impacts can be difficult, with the possibility of multiple
stressors interacting and having greater impacts than expected, compounding direct and indirect
effects on individuals, populations, communities and ecosystems. Assessment of multiple stressors
therefore requires extensive scientific research that directly tests how single or multiple ecological
components are affected by stressors, both singly and when combined, and as a consequence,
cumulative effects assessments are now increasingly included in environmental assessments.
Currently, there is a need to assess these at larger spatial scales, with additional research also urgently
needed on the responses of ecological components, processes and functions to single and cumulative
stressors. As cumulative environmental impacts could be better addressed by regional stressor effects
assessments that combine methods for predicting multiple pressures on ecosystem recovery
alongside degradation, this study used several separate approaches that can be used in parallel to give
support for local management measures. I tested four completely different methods – a range of
multi-metric indices, a food web model (Ecopath), a predictive model (Ecosim) and a Bayesian Belief
Network model. Each approach was tested and compared in two shallow water estuarine systems, in
Scotland and England, initially concerning the impact of nutrient enrichment and subsequent recovery
and was followed by an investigation of how the addition of multiple stressors (nutrient levels,
temperature and river-flow rates) would impact the future state of each system. The response to
stressors was highly context dependent, varying between and within geographic locations. Overall,
each of the four different approaches complemented each other and gave strong support for the need
to make big reductions in the pressures and to consider trade-offs between impacting pressures. The
models and tools also indicate that in order to reach an improved overall environmental state of each
ecosystem, a focus on nutrient reductions are likely to be the most effective of the controls on
stressors explored and that cumulative effects of the management of nutrient inputs and increased
water temperatures and river-flow are likely to exist.
2017-06-21T00:00:00ZWatson, Stephen C. L.Marine and coastal ecosystems are subject to diverse and increasingly intensive anthropogenic
activities, making understanding cumulative effects critically important. However, accurately
accounting for the cumulative effects of human impacts can be difficult, with the possibility of multiple
stressors interacting and having greater impacts than expected, compounding direct and indirect
effects on individuals, populations, communities and ecosystems. Assessment of multiple stressors
therefore requires extensive scientific research that directly tests how single or multiple ecological
components are affected by stressors, both singly and when combined, and as a consequence,
cumulative effects assessments are now increasingly included in environmental assessments.
Currently, there is a need to assess these at larger spatial scales, with additional research also urgently
needed on the responses of ecological components, processes and functions to single and cumulative
stressors. As cumulative environmental impacts could be better addressed by regional stressor effects
assessments that combine methods for predicting multiple pressures on ecosystem recovery
alongside degradation, this study used several separate approaches that can be used in parallel to give
support for local management measures. I tested four completely different methods – a range of
multi-metric indices, a food web model (Ecopath), a predictive model (Ecosim) and a Bayesian Belief
Network model. Each approach was tested and compared in two shallow water estuarine systems, in
Scotland and England, initially concerning the impact of nutrient enrichment and subsequent recovery
and was followed by an investigation of how the addition of multiple stressors (nutrient levels,
temperature and river-flow rates) would impact the future state of each system. The response to
stressors was highly context dependent, varying between and within geographic locations. Overall,
each of the four different approaches complemented each other and gave strong support for the need
to make big reductions in the pressures and to consider trade-offs between impacting pressures. The
models and tools also indicate that in order to reach an improved overall environmental state of each
ecosystem, a focus on nutrient reductions are likely to be the most effective of the controls on
stressors explored and that cumulative effects of the management of nutrient inputs and increased
water temperatures and river-flow are likely to exist.BayesPiles : visualisation support for Bayesian network structure learning
https://hdl.handle.net/10023/16636
We address the problem of exploring, combining, and comparing large collections of scored, directed networks for understanding inferred Bayesian networks used in biology. In this field, heuristic algorithms explore the space of possible network solutions, sampling this space based on algorithm parameters and a network score that encodes the statistical fit to the data. The goal of the analyst is to guide the heuristic search and decide how to determine a final consensus network structure, usually by selecting the top-scoring network or constructing the consensus network from a collection of high-scoring networks. BayesPiles, our visualisation tool, helps with understanding the structure of the solution space and supporting the construction of a final consensus network that is representative of the underlying dataset. BayesPiles builds upon and extends MultiPiles to meet our domain requirements. We developed BayesPiles in conjunction with computational biologists who have used this tool on datasets used in their research. The biologists found our solution provides them with new insights and helps them achieve results that are representative of the underlying data.
2018-11-01T00:00:00ZVogogias, AthanasiosKennedy, JessieArchambault, DanielBach, BenjaminSmith, V AnneCurrant, HannahWe address the problem of exploring, combining, and comparing large collections of scored, directed networks for understanding inferred Bayesian networks used in biology. In this field, heuristic algorithms explore the space of possible network solutions, sampling this space based on algorithm parameters and a network score that encodes the statistical fit to the data. The goal of the analyst is to guide the heuristic search and decide how to determine a final consensus network structure, usually by selecting the top-scoring network or constructing the consensus network from a collection of high-scoring networks. BayesPiles, our visualisation tool, helps with understanding the structure of the solution space and supporting the construction of a final consensus network that is representative of the underlying dataset. BayesPiles builds upon and extends MultiPiles to meet our domain requirements. We developed BayesPiles in conjunction with computational biologists who have used this tool on datasets used in their research. The biologists found our solution provides them with new insights and helps them achieve results that are representative of the underlying data.Surveying abundance and stand type associations of Formica aquilonia and F. lugubris (Hymenoptera: Formicidae) nest mounds over an extensive area : Trialing a novel method
https://hdl.handle.net/10023/16260
Red wood ants are ecologically important members of woodland communities, and some species are of conservation concern. They occur commonly only in certain habitats in Britain, but there is limited knowledge of their numbers and distribution. This study provided baseline information at a key locality (Abernethy Forest, 37 km2) in the central Highlands of Scotland and trialed a new method of surveying red wood ant density and stand type associations: a distance sampling line transect survey of nests. This method is efficient because it allows an observer to quickly survey a large area either side of transect lines, without having to assume that all nests are detected. Instead, data collected on the distance of nests from the line are used to estimate probability of detection and the effective transect width, using the free software "Distance". Surveys took place in August and September 2003 along a total of 71.2 km of parallel, equally-spaced transects. One hundred and forty-four red wood ant nests were located, comprising 89 F. aquilonia (Yarrow, 1955) and 55 F. lugubris (Zetterstedt, 1838) nests. Estimated densities were 1.13 nests per hectare (95% CI 0.74-1.73) for F. aquilonia and 0.83 nests per hectare (95% CI 0.32-2.17) for F. lugubris. These translated to total estimated nest numbers of 4,200 (95% CI 2,700-6,400) and 3,100 (95% CI 1,200-8,100), respectively, for the whole forest. Indices of stand selection indicated that F. aquilonia had some positive association with old-growth and F. lugubris with younger stands (stem exclusion stage). No nests were found in areas that had been clear-felled, and ploughed and planted in the 1970s-1990s. The pattern of stand type association and hence distribution of F. aquilonia and F. lugubris may be due to the differing ability to disperse (F. lugubris is the faster disperser) and compete (F. aquilonia is competitively superior). We recommend using line transect sampling for extensive surveys of ants that construct nest mounds to estimate abundance and stand type association.
2012-01-03T00:00:00ZBorkin, KerrySummers, RonThomas, LenRed wood ants are ecologically important members of woodland communities, and some species are of conservation concern. They occur commonly only in certain habitats in Britain, but there is limited knowledge of their numbers and distribution. This study provided baseline information at a key locality (Abernethy Forest, 37 km2) in the central Highlands of Scotland and trialed a new method of surveying red wood ant density and stand type associations: a distance sampling line transect survey of nests. This method is efficient because it allows an observer to quickly survey a large area either side of transect lines, without having to assume that all nests are detected. Instead, data collected on the distance of nests from the line are used to estimate probability of detection and the effective transect width, using the free software "Distance". Surveys took place in August and September 2003 along a total of 71.2 km of parallel, equally-spaced transects. One hundred and forty-four red wood ant nests were located, comprising 89 F. aquilonia (Yarrow, 1955) and 55 F. lugubris (Zetterstedt, 1838) nests. Estimated densities were 1.13 nests per hectare (95% CI 0.74-1.73) for F. aquilonia and 0.83 nests per hectare (95% CI 0.32-2.17) for F. lugubris. These translated to total estimated nest numbers of 4,200 (95% CI 2,700-6,400) and 3,100 (95% CI 1,200-8,100), respectively, for the whole forest. Indices of stand selection indicated that F. aquilonia had some positive association with old-growth and F. lugubris with younger stands (stem exclusion stage). No nests were found in areas that had been clear-felled, and ploughed and planted in the 1970s-1990s. The pattern of stand type association and hence distribution of F. aquilonia and F. lugubris may be due to the differing ability to disperse (F. lugubris is the faster disperser) and compete (F. aquilonia is competitively superior). We recommend using line transect sampling for extensive surveys of ants that construct nest mounds to estimate abundance and stand type association.Assessing the utility and limitations of accelerometers and machine learning approaches in classifying behaviour during lactation in a phocid seal
https://hdl.handle.net/10023/16253
Background: Classifying behaviour with animal-borne accelerometers is quickly becoming a popular tool for remotely observing behavioural states in a variety of species. Most accelerometry work in pinnipeds has focused on classifying behaviour at sea often quantifying behavioural trade-offs associated with foraging and diving in income breeders. Very little work to date has been done to resolve behaviour during the critical period of lactation in a capital breeder. Capital breeding phocids possess finite reserves that they must allocate appropriately to maintain themselves and their new offspring during their brief nursing period. Within this short time, fine-scale behavioural trade-offs can have significant fitness consequences for mother and offspring and must be carefully managed. Here, we present a case study in extracting and classifying lactation behaviours in a wild, breeding pinniped, the grey seal (Halichoerus grypus). Results: Using random forest models, we were able to resolve 4 behavioural states that constitute the majority of a female grey seals’ activity budget during lactation. Resting, alert, nursing, and a form of pup interaction were extracted and classified reliably. For the first time, we quantified the potential confounding variance associated with individual differences in a wild context as well as differences due to sampling location in a largely inactive model species. Conclusions: At this stage, the majority of a female grey seal’s activity budget was classified well using accelerometers, but some rare and context-dependent behaviours were not well captured. While we did find significant variation between individuals in behavioural mechanics, individuals did not differ significantly within themselves; inter-individual variability should be an important consideration in future efforts. These methods can be extended to other efforts to study grey seals and other pinnipeds who exhibit a capital breeding system. Using accelerometers to classify behaviour during lactation allows for fine-scale assessments of time and energy trade-offs for species with fixed stores.
Funding for this work was provided by the Durham Doctoral Studentship scheme at Durham University and supported by Natural Environment Research Council’s core funding to the Sea Mammal Research Unit at the University of St. Andrews.
2018-10-16T00:00:00ZSchuert, CourtneyPomeroy, PatrickTwiss, SeanBackground: Classifying behaviour with animal-borne accelerometers is quickly becoming a popular tool for remotely observing behavioural states in a variety of species. Most accelerometry work in pinnipeds has focused on classifying behaviour at sea often quantifying behavioural trade-offs associated with foraging and diving in income breeders. Very little work to date has been done to resolve behaviour during the critical period of lactation in a capital breeder. Capital breeding phocids possess finite reserves that they must allocate appropriately to maintain themselves and their new offspring during their brief nursing period. Within this short time, fine-scale behavioural trade-offs can have significant fitness consequences for mother and offspring and must be carefully managed. Here, we present a case study in extracting and classifying lactation behaviours in a wild, breeding pinniped, the grey seal (Halichoerus grypus). Results: Using random forest models, we were able to resolve 4 behavioural states that constitute the majority of a female grey seals’ activity budget during lactation. Resting, alert, nursing, and a form of pup interaction were extracted and classified reliably. For the first time, we quantified the potential confounding variance associated with individual differences in a wild context as well as differences due to sampling location in a largely inactive model species. Conclusions: At this stage, the majority of a female grey seal’s activity budget was classified well using accelerometers, but some rare and context-dependent behaviours were not well captured. While we did find significant variation between individuals in behavioural mechanics, individuals did not differ significantly within themselves; inter-individual variability should be an important consideration in future efforts. These methods can be extended to other efforts to study grey seals and other pinnipeds who exhibit a capital breeding system. Using accelerometers to classify behaviour during lactation allows for fine-scale assessments of time and energy trade-offs for species with fixed stores.Evolution of muscle regulatory genes in chordates
https://hdl.handle.net/10023/16136
2016-11-30T00:00:00ZColl-Lladó, ClaraThe potential for Assemblage thinking in population geography : assembling population, space and place
https://hdl.handle.net/10023/12645
This study explores ‘Assemblage’ thinking as an approach for population geography research. The paper highlights the recent prominence of Assemblage thinking in human geography, before exploring the potential opportunities for engagement by population geographers. In particular we focus on the production of place as co-constituted by the material (space) and the discursive (knowledge, process and practice). Considering the Assemblage practice of ‘Rendering Technical’, we reflect on the role that population geography plays in authorising knowledge and supporting policy. This is investigated through a critical taxonomic analysis of recent Scottish demographic data. It is argued on the one hand that this captures key economic and population characteristics of ‘place’, while on the other hand it offers a limited technical knowledge. We conclude that a reflexive approach to research using Assemblage thinking may challenge the intimate relationship between population geographers and the state.
This paper is output from an Economic and Social Research Council Award (Reference 1506438) funded in partnership with Marine Scotland, The Scottish Government.
2018-04-10T00:00:00ZDuffy, PaulaStojanovic, TimThis study explores ‘Assemblage’ thinking as an approach for population geography research. The paper highlights the recent prominence of Assemblage thinking in human geography, before exploring the potential opportunities for engagement by population geographers. In particular we focus on the production of place as co-constituted by the material (space) and the discursive (knowledge, process and practice). Considering the Assemblage practice of ‘Rendering Technical’, we reflect on the role that population geography plays in authorising knowledge and supporting policy. This is investigated through a critical taxonomic analysis of recent Scottish demographic data. It is argued on the one hand that this captures key economic and population characteristics of ‘place’, while on the other hand it offers a limited technical knowledge. We conclude that a reflexive approach to research using Assemblage thinking may challenge the intimate relationship between population geographers and the state.Sex-related differences in the postmolt distribution of Weddell seals (Leptonychotes weddellii) in the southern Weddell Sea
https://hdl.handle.net/10023/12266
The population of Weddell seals (Leptonychotes weddellii) in the southern Weddell Sea is in a unique position on the continental shelf edge, with vast shelf waters to the south, and deep Southern Ocean to the north. We describe sex-related differences in the winter distribution of this population, from data collected by 20 conductivity-temperature-depth satellite relay data loggers deployed in February 2011 at the end of the annual molt. The regional daily speed was calculated, and a state-space model was used to estimate behavioral states to positions along individuals’ tracks. GLMMs estimated that males and smaller individuals, diving in shallower water, traveled less far per day of deployment (males 14.6 ± 2.26 km/d, females 18.9 ± 2.42 km/d), and males were estimated to dive in shallower water (males 604 ± 382 m, females 1,875 ± 1,458 m). Males and smaller individuals were also estimated to be more resident; males spent an average 83.4% ± 7.7% of their time in a resident behavioral state, compared to females at 74.1% ± 7.1%. This evidence that male and female Weddell seals in the southern Weddell Sea are adopting different strategies has not been shown elsewhere along their circumpolar distribution.
Funding: NERC grants NE/G014833/1 (MF) and NE/G014086/1 (KWN).
2018-04-01T00:00:00ZLangley, IzzyFedak, MikeNicholls, KeithBoehme, LarsThe population of Weddell seals (Leptonychotes weddellii) in the southern Weddell Sea is in a unique position on the continental shelf edge, with vast shelf waters to the south, and deep Southern Ocean to the north. We describe sex-related differences in the winter distribution of this population, from data collected by 20 conductivity-temperature-depth satellite relay data loggers deployed in February 2011 at the end of the annual molt. The regional daily speed was calculated, and a state-space model was used to estimate behavioral states to positions along individuals’ tracks. GLMMs estimated that males and smaller individuals, diving in shallower water, traveled less far per day of deployment (males 14.6 ± 2.26 km/d, females 18.9 ± 2.42 km/d), and males were estimated to dive in shallower water (males 604 ± 382 m, females 1,875 ± 1,458 m). Males and smaller individuals were also estimated to be more resident; males spent an average 83.4% ± 7.7% of their time in a resident behavioral state, compared to females at 74.1% ± 7.1%. This evidence that male and female Weddell seals in the southern Weddell Sea are adopting different strategies has not been shown elsewhere along their circumpolar distribution.Learning from loss : eroding coastal heritage in Scotland
https://hdl.handle.net/10023/12042
Heritage sites are constantly changing due to natural processes, and this change can happen fastest at the coast. Much legislation has been enacted to protect sites of historic interest, but these do not protect sites from natural processes. Change is already happening, and climate change predictions suggest that the pace will accelerate in the future. Instead of seeing the potential destruction of heritage sites as a disaster, we should embrace the opportunity that they can provide for us to learn about the past and to plan for the future. Heritage laws often enshrine a policy of preservation in situ, meaning that our most spectacular sites are preserved in a state of equilibrium, with a default position of no permitted intervention. However, the options for threatened coastal sites mirror those of shoreline management plans, which usually recommend either the construction of a coastal defence or, more likely, a strategy of managed retreat, where erosion is allowed to take its course after appropriate mitigations strategies have been enacted. Managed retreat can lead to a range of research projects, some of which would not normally be possible at similar, unthreatened and legally protected monuments. Such research also has the potential to involve members of the public, who can help in the discovery process, and cascade what they have learned through their communities. Information shared can be about the heritage site itself, including how communities in the past coped at times of climatic stress; and also about the processes that are now threatening the monument, thus helping teach about present day climate change.
2017-11-09T00:00:00ZGraham Allsop, Elinor LouiseDawson, Thomas ChristopherHambly, JoannaHeritage sites are constantly changing due to natural processes, and this change can happen fastest at the coast. Much legislation has been enacted to protect sites of historic interest, but these do not protect sites from natural processes. Change is already happening, and climate change predictions suggest that the pace will accelerate in the future. Instead of seeing the potential destruction of heritage sites as a disaster, we should embrace the opportunity that they can provide for us to learn about the past and to plan for the future. Heritage laws often enshrine a policy of preservation in situ, meaning that our most spectacular sites are preserved in a state of equilibrium, with a default position of no permitted intervention. However, the options for threatened coastal sites mirror those of shoreline management plans, which usually recommend either the construction of a coastal defence or, more likely, a strategy of managed retreat, where erosion is allowed to take its course after appropriate mitigations strategies have been enacted. Managed retreat can lead to a range of research projects, some of which would not normally be possible at similar, unthreatened and legally protected monuments. Such research also has the potential to involve members of the public, who can help in the discovery process, and cascade what they have learned through their communities. Information shared can be about the heritage site itself, including how communities in the past coped at times of climatic stress; and also about the processes that are now threatening the monument, thus helping teach about present day climate change.The development of molecular tools and resources for selective breeding in aquaculture
https://hdl.handle.net/10023/11843
Human population growth is predicted to continue well into the 21st century, and beyond. The provision of selectively bred organisms will be an essential part of global food security. While the selective breeding of terrestrial animals has been essential to the human success story, the breeding of aquatic organisms has only recently received serious attention. Aquaculture research urgently needs both specific genetic resources for existing aquatic species, and generalised workflows and pipelines for the generation of resources for newly cultivated species. This study presents a stochastic simulation of a selective program for the gilthead seabream (Sparus aurata L.). The simulation models the change of a non-selective breeding program to a scheme improving growth rate by mass selection. The effect of selection on growth rate, inbreeding and projected profits are modelled explicitly. The simulation predicts a profitable and sound breeding scheme for gilthead seabream and can also be easily adapted for new traits and species. A workflow for the filtration of an optimal number genetic variants for molecular parentage assignment was also developed and validated in Atlantic salmon (Salmo salar L.). A discovery dataset of 102 Atlantic salmon from three distinct aquaculture strains were subject to restriction site associated DNA marker sequencing. The resultant single nucleotide polymorphisms were filtered according to quality, property and suitability for probe-based high-throughput genotyping technology. The final SNP panel consisted of 94 mass genotyping assays that gave 100% accurate parentage in independent samples of known pedigree. Finally, a set of standardised trait descriptors were designed for bivalve molluscs to accompany next generation sequencing submissions. These standards are needed to provide consistent trait measurements between investigators for quality control and to enable interoperability of phenotypic and genotypic data in future meta analyses.
2017-06-21T00:00:00ZHolman, Luke EarlHuman population growth is predicted to continue well into the 21st century, and beyond. The provision of selectively bred organisms will be an essential part of global food security. While the selective breeding of terrestrial animals has been essential to the human success story, the breeding of aquatic organisms has only recently received serious attention. Aquaculture research urgently needs both specific genetic resources for existing aquatic species, and generalised workflows and pipelines for the generation of resources for newly cultivated species. This study presents a stochastic simulation of a selective program for the gilthead seabream (Sparus aurata L.). The simulation models the change of a non-selective breeding program to a scheme improving growth rate by mass selection. The effect of selection on growth rate, inbreeding and projected profits are modelled explicitly. The simulation predicts a profitable and sound breeding scheme for gilthead seabream and can also be easily adapted for new traits and species. A workflow for the filtration of an optimal number genetic variants for molecular parentage assignment was also developed and validated in Atlantic salmon (Salmo salar L.). A discovery dataset of 102 Atlantic salmon from three distinct aquaculture strains were subject to restriction site associated DNA marker sequencing. The resultant single nucleotide polymorphisms were filtered according to quality, property and suitability for probe-based high-throughput genotyping technology. The final SNP panel consisted of 94 mass genotyping assays that gave 100% accurate parentage in independent samples of known pedigree. Finally, a set of standardised trait descriptors were designed for bivalve molluscs to accompany next generation sequencing submissions. These standards are needed to provide consistent trait measurements between investigators for quality control and to enable interoperability of phenotypic and genotypic data in future meta analyses.The evolution and regulation of the chordate ParaHox cluster
https://hdl.handle.net/10023/11788
The ParaHox cluster is the evolutionary sister of the Hox cluster. Like the Hox cluster, the ParaHox cluster is subject to complex regulatory phenomena such as collinearity. Despite the breakup of the ParaHox cluster within many animals, intact and collinear clusters have now been discovered within the chordate phyla in amphioxus and the vertebrates, and more recently within the hemichordates and echinoderms. The archetypal ParaHox cluster of amphioxus places it in a unique position in which to examine the regulatory mechanisms controlling ParaHox gene expression within the last common ancestor of chordates, and perhaps even the wider Deuterostomia. In this thesis, the genomic and regulatory landscape of the amphioxus ParaHox cluster is characterised in detail. New genomic and transcriptomic resources are used to better characterise the B.floridae ParaHox cluster and surrounding genomic region, and conserved non-coding regions and regulatory motifs are identified across the ParaHox cluster of three species of amphioxus. In conjunction with this, the impact of retrotransposition upon the ParaHox cluster is examined and analyses of transposable elements and the AmphiSCP1 retrogene reveal that the ParaHox cluster may be more insulated from outside influence than previously thought. Finally, the detailed analyses of a regulatory element upstream of AmphiGsx reveals conserved mechanisms regulating Gsx CNS expression within the chordates, and TCF/Lef is likely a direct regulator of AmphiGsx within the CNS. The work in this thesis makes use of new genomic and transcriptomic resources available for amphioxus to better characterise the genomic and regulatory landscape of the amphioxus ParaHox cluster, serving as a basis for the improved identification and characterisation of functional regulatory elements and conserved regulatory mechanisms. This work also highlights the potential of Ciona intestinalis as a ‘living test tube’ to allow the detailed characterisation of amphioxus ParaHox regulatory elements.
2016-06-22T00:00:00ZGarstang, Myles GrantThe ParaHox cluster is the evolutionary sister of the Hox cluster. Like the Hox cluster, the ParaHox cluster is subject to complex regulatory phenomena such as collinearity. Despite the breakup of the ParaHox cluster within many animals, intact and collinear clusters have now been discovered within the chordate phyla in amphioxus and the vertebrates, and more recently within the hemichordates and echinoderms. The archetypal ParaHox cluster of amphioxus places it in a unique position in which to examine the regulatory mechanisms controlling ParaHox gene expression within the last common ancestor of chordates, and perhaps even the wider Deuterostomia. In this thesis, the genomic and regulatory landscape of the amphioxus ParaHox cluster is characterised in detail. New genomic and transcriptomic resources are used to better characterise the B.floridae ParaHox cluster and surrounding genomic region, and conserved non-coding regions and regulatory motifs are identified across the ParaHox cluster of three species of amphioxus. In conjunction with this, the impact of retrotransposition upon the ParaHox cluster is examined and analyses of transposable elements and the AmphiSCP1 retrogene reveal that the ParaHox cluster may be more insulated from outside influence than previously thought. Finally, the detailed analyses of a regulatory element upstream of AmphiGsx reveals conserved mechanisms regulating Gsx CNS expression within the chordates, and TCF/Lef is likely a direct regulator of AmphiGsx within the CNS. The work in this thesis makes use of new genomic and transcriptomic resources available for amphioxus to better characterise the genomic and regulatory landscape of the amphioxus ParaHox cluster, serving as a basis for the improved identification and characterisation of functional regulatory elements and conserved regulatory mechanisms. This work also highlights the potential of Ciona intestinalis as a ‘living test tube’ to allow the detailed characterisation of amphioxus ParaHox regulatory elements.Inter- and intra-year variation in foraging areas of breeding kittiwakes (Rissa tridactyla)
https://hdl.handle.net/10023/10775
While seabird conservation efforts have largely focused on protection from threats at the colony (e.g. reducing disturbance and predation), attention is increasingly being given to implementing protection measures for foraging areas at sea. For this to be effective, important foraging areas must be identified. Although numerous studies have examined seabird foraging behaviour, information is still lacking on the variability in area utilisation within and among breeding seasons. GPS devices were attached to adult black-legged kittiwakes breeding at an expanding North Sea colony (55°20′N, 1°32′W) during both incubation and chick-rearing in 2012 and during chick-rearing in 2011, to determine whether foraging areas remained consistent and to identify the oceanographic characteristics of areas used for foraging. The type and size of prey items consumed at different stages of the breeding cycle was also examined. During incubation (April-May 2012), kittiwakes foraged substantially further from the colony and fed on larger sandeels than when feeding chicks, and there was significant inter-annual variation in foraging areas used during the chick-rearing period (June-July 2011 and 2012). Foraging areas were characterised by cooler sea surface temperatures and areas of high chlorophyll a concentration, although association with specific oceanographic features changed within the breeding season and between years. These results emphasise the importance of considering how foraging areas and reliance on specific oceanographic conditions change over time when seeking to identify important marine areas for seabirds.
This work was supported by the National Environment Research Council (award number NE/I528369/1) and the Royal Society for the Protection of Birds through a CASE studentship to the University of Glasgow.
2014-09-01T00:00:00ZRobertson, G. S.Bolton, M.Grecian, W. J.Monaghan, P.While seabird conservation efforts have largely focused on protection from threats at the colony (e.g. reducing disturbance and predation), attention is increasingly being given to implementing protection measures for foraging areas at sea. For this to be effective, important foraging areas must be identified. Although numerous studies have examined seabird foraging behaviour, information is still lacking on the variability in area utilisation within and among breeding seasons. GPS devices were attached to adult black-legged kittiwakes breeding at an expanding North Sea colony (55°20′N, 1°32′W) during both incubation and chick-rearing in 2012 and during chick-rearing in 2011, to determine whether foraging areas remained consistent and to identify the oceanographic characteristics of areas used for foraging. The type and size of prey items consumed at different stages of the breeding cycle was also examined. During incubation (April-May 2012), kittiwakes foraged substantially further from the colony and fed on larger sandeels than when feeding chicks, and there was significant inter-annual variation in foraging areas used during the chick-rearing period (June-July 2011 and 2012). Foraging areas were characterised by cooler sea surface temperatures and areas of high chlorophyll a concentration, although association with specific oceanographic features changed within the breeding season and between years. These results emphasise the importance of considering how foraging areas and reliance on specific oceanographic conditions change over time when seeking to identify important marine areas for seabirds.Contrasting migratory responses of two closely-related seabirds to long-term climate change
https://hdl.handle.net/10023/10726
Many marine predators migrate between breeding and non-breeding areas to target resources that are seasonal but spatio-temporally predictable, and so are vulnerable to climate-induced changes in prey phenology and abundance. In the Southern Ocean, small petrels are major consumers, but perturbations in the ecosystem through ocean warming are altering food-web structure and have been linked to poleward shifts in the distribution of their cold-water zooplankton prey. In this study, we focused on 2 small congeneric petrels: the broad-billed prion Pachyptila vittata and the Antarctic prion P. desolata. Both are planktivorous, but the broad-billed prion specialises in feeding on large copepods. We investigated historical trends in non-breeding distribution by analysing feather stable isotope ratios from a time-series dating back to 1926, and examined contemporary non-breeding distributions of broad-billed prions tracked using miniaturised geolocation-immersion loggers. After controlling temporally for the Suess effect, we found that the δ13C signatures of Antarctic prions, but not broad-billed prions, declined during the study period. This suggests a southward shift in Antarctic prion non-breeding distribution over the last century. Both species exhibited significant declines in δ15N during the same period, indicative of long-term decreases in marine productivity in their moulting areas, or changes in the trophic structure of prey communities. Tracked broad-billed prions migrated ca. 1000 km to an area east of the breeding colony where the Louisville seamount chain bisects the subtropical front. Topographically driven upwellings are stable and predictable features and may be crucial in aggregating plankton. Targeting seamounts could therefore mitigate the impact of climate-induced prey shifts by providing refugia for the broad-billed prion.
2016-11-09T00:00:00ZGrecian, W. JamesTaylor, Graeme A.Loh, GraemeMcGill, Rona A. R.Miskelly, Colin M.Phillips, Richard A.Thompson, David R.Furness, Robert W.Many marine predators migrate between breeding and non-breeding areas to target resources that are seasonal but spatio-temporally predictable, and so are vulnerable to climate-induced changes in prey phenology and abundance. In the Southern Ocean, small petrels are major consumers, but perturbations in the ecosystem through ocean warming are altering food-web structure and have been linked to poleward shifts in the distribution of their cold-water zooplankton prey. In this study, we focused on 2 small congeneric petrels: the broad-billed prion Pachyptila vittata and the Antarctic prion P. desolata. Both are planktivorous, but the broad-billed prion specialises in feeding on large copepods. We investigated historical trends in non-breeding distribution by analysing feather stable isotope ratios from a time-series dating back to 1926, and examined contemporary non-breeding distributions of broad-billed prions tracked using miniaturised geolocation-immersion loggers. After controlling temporally for the Suess effect, we found that the δ13C signatures of Antarctic prions, but not broad-billed prions, declined during the study period. This suggests a southward shift in Antarctic prion non-breeding distribution over the last century. Both species exhibited significant declines in δ15N during the same period, indicative of long-term decreases in marine productivity in their moulting areas, or changes in the trophic structure of prey communities. Tracked broad-billed prions migrated ca. 1000 km to an area east of the breeding colony where the Louisville seamount chain bisects the subtropical front. Topographically driven upwellings are stable and predictable features and may be crucial in aggregating plankton. Targeting seamounts could therefore mitigate the impact of climate-induced prey shifts by providing refugia for the broad-billed prion.Comparative estuarine dynamics : trophic linkages and ecosystem function
https://hdl.handle.net/10023/8240
Estuarine systems are of crucial importance to the provision of goods and services on a global scale. High human population densities in coastal systems have caused an increasing input of pollutants, of which nutrient pollution is of major concern. Increasingly, these areas are also impacted by physical disturbance, which can originate from anthropogenic sources (e.g. bait digging, shipping) or climate change causing increasingly frequent and intense storms. The individual impacts of such stressors on ecosystems have been investigated however their combined impacts have received less attention. Cumulative impacts of multiple stressors are unpredictable and will likely result in non-additive effects. Further, the effect of local environmental context on multiple stressors is a relatively understudied topic.
Work in this thesis compared the combined impact of nutrient enrichment and physical disturbance in Scotland and Australia, using a series of manipulative field experiments. Results demonstrate that response to stressors is highly context dependent, varying between and within geographic locations. While the background levels of stress may vary, by comparing these two locations it is possible to comment on the adaptations and response that communities within different parts of the world display when subjected to additional stress. This study demonstrates that environmental context must be considered when implementing future management practices.
Further work demonstrated that the impact of multiple stressors varies depending on how the stress is applied –whether stressors are applied simultaneously or whether there is a delay between two stressors. This study was among the first of its kind, assessing the implications of how multiple stressors react with each other given the order and intensity in which stressors were applied. Results demonstrated that systems can become sensitised to stress making them increasingly vulnerable to additional stress. Future research should be focussed on incorporating ecologically relevant scenarios of how stressors will impact estuaries while considering how environmental context will mediate impacts.
2016-02-01T00:00:00ZKenworthy, JosephEstuarine systems are of crucial importance to the provision of goods and services on a global scale. High human population densities in coastal systems have caused an increasing input of pollutants, of which nutrient pollution is of major concern. Increasingly, these areas are also impacted by physical disturbance, which can originate from anthropogenic sources (e.g. bait digging, shipping) or climate change causing increasingly frequent and intense storms. The individual impacts of such stressors on ecosystems have been investigated however their combined impacts have received less attention. Cumulative impacts of multiple stressors are unpredictable and will likely result in non-additive effects. Further, the effect of local environmental context on multiple stressors is a relatively understudied topic.
Work in this thesis compared the combined impact of nutrient enrichment and physical disturbance in Scotland and Australia, using a series of manipulative field experiments. Results demonstrate that response to stressors is highly context dependent, varying between and within geographic locations. While the background levels of stress may vary, by comparing these two locations it is possible to comment on the adaptations and response that communities within different parts of the world display when subjected to additional stress. This study demonstrates that environmental context must be considered when implementing future management practices.
Further work demonstrated that the impact of multiple stressors varies depending on how the stress is applied –whether stressors are applied simultaneously or whether there is a delay between two stressors. This study was among the first of its kind, assessing the implications of how multiple stressors react with each other given the order and intensity in which stressors were applied. Results demonstrated that systems can become sensitised to stress making them increasingly vulnerable to additional stress. Future research should be focussed on incorporating ecologically relevant scenarios of how stressors will impact estuaries while considering how environmental context will mediate impacts.Occurrence, distribution and abundance of cetaceans in Onslow Bay, North Carolina, USA
https://hdl.handle.net/10023/7772
In this paper the occurrence, distribution and abundance of cetaceans in offshore waters of Onslow Bay, North Carolina, USA is described. Between June 2007 and June 2010 monthly aerial and shipboard line-transect surveys were conducted along ten 74km transects placed perpendicular to the shelf break. In total 42,676km of aerial trackline (218 sightings) and 5,209km of vessel trackline (100 sightings) were observed. Seven species of cetaceans were observed, but the fauna was dominated strongly by common bottlenose and Atlantic spotted dolphins. Both species were present year-round in the study area. Using photo-identification techniques, five bottlenose dolphins and one spotted dolphin were resighted during the three-year period. In general, the abundance of cetaceans in Onslow Bay was low and too few sightings were made to estimate monthly abundances for species other than bottlenose and spotted dolphins. Maximum monthly abundances of bottlenose and spotted dolphins were 4,100 (95% CI: 1,300–9,400) in May 2010 and 6,000 (95% CI: 2,500–17,400) in March 2009, respectively. Bottlenose dolphins were found throughout the study area, although they were encountered most frequently just off the shelf break. In contrast, spotted dolphins exhibited a strong preference for waters over the continental shelf and were not encountered beyond the shelf break.
2014-01-01T00:00:00ZRead, Andrew, J.Barco, S.Bell, J.Borchers, David LouisBurt, M LouiseCummings, E.W.Dunn, J.Fougeres, J.Hazen, L.Williams-Hodge, L.E.Laura, A-M.McAlarney, R.J.Nilsson, P.Pabst, D.A.Paxton, Charles G. M.Schneider, S.Z.Urian, KimWaples, D.M.McLellan, W.A.In this paper the occurrence, distribution and abundance of cetaceans in offshore waters of Onslow Bay, North Carolina, USA is described. Between June 2007 and June 2010 monthly aerial and shipboard line-transect surveys were conducted along ten 74km transects placed perpendicular to the shelf break. In total 42,676km of aerial trackline (218 sightings) and 5,209km of vessel trackline (100 sightings) were observed. Seven species of cetaceans were observed, but the fauna was dominated strongly by common bottlenose and Atlantic spotted dolphins. Both species were present year-round in the study area. Using photo-identification techniques, five bottlenose dolphins and one spotted dolphin were resighted during the three-year period. In general, the abundance of cetaceans in Onslow Bay was low and too few sightings were made to estimate monthly abundances for species other than bottlenose and spotted dolphins. Maximum monthly abundances of bottlenose and spotted dolphins were 4,100 (95% CI: 1,300–9,400) in May 2010 and 6,000 (95% CI: 2,500–17,400) in March 2009, respectively. Bottlenose dolphins were found throughout the study area, although they were encountered most frequently just off the shelf break. In contrast, spotted dolphins exhibited a strong preference for waters over the continental shelf and were not encountered beyond the shelf break.Predicting future European breeding distributions of British seabird species under climate change and unlimited/no dispersal scenarios
https://hdl.handle.net/10023/7735
Understanding which traits make species vulnerable to climatic change and predicting future distributions permits conservation efforts to be focused on the most vulnerable species and the most appropriate sites. Here, we combine climate envelope models with predicted bioclimatic data from two emission scenarios leading up to 2100, to predict European breeding distributions of 23 seabird species that currently breed in the British Isles. Assuming unlimited dispersal, some species would be “winners” (increase the size of their range), but over 65% would lose range, some by up to 80%. These “losers” have a high vulnerability to low prey availability, and a northerly distribution meaning they would lack space to move into. Under the worst-case scenario of no dispersal, species are predicted to lose between 25% and 100% of their range, so dispersal ability is a key constraint on future range sizes. More globally, the results indicate, based on foraging ecology, which seabird species are likely to be most affected by climatic change. Neither of the emissions scenarios used in this study is extreme, yet they generate very different predictions for some species, illustrating that even small decreases in emissions could yield large benefits for conservation.
We thank the European Bird Census Council for their data on European seabird distributions. DJFR was supported by NERC UKPopNet.
2015-11-02T00:00:00ZRussell, Deborah Jill FraserWanless, SarahCollingham, Yvonne C.Huntley, BrianHamer, Keith C.Understanding which traits make species vulnerable to climatic change and predicting future distributions permits conservation efforts to be focused on the most vulnerable species and the most appropriate sites. Here, we combine climate envelope models with predicted bioclimatic data from two emission scenarios leading up to 2100, to predict European breeding distributions of 23 seabird species that currently breed in the British Isles. Assuming unlimited dispersal, some species would be “winners” (increase the size of their range), but over 65% would lose range, some by up to 80%. These “losers” have a high vulnerability to low prey availability, and a northerly distribution meaning they would lack space to move into. Under the worst-case scenario of no dispersal, species are predicted to lose between 25% and 100% of their range, so dispersal ability is a key constraint on future range sizes. More globally, the results indicate, based on foraging ecology, which seabird species are likely to be most affected by climatic change. Neither of the emissions scenarios used in this study is extreme, yet they generate very different predictions for some species, illustrating that even small decreases in emissions could yield large benefits for conservation.Images as proximity sensors : the incidence of conspecific foraging in Antarctic fur seals
https://hdl.handle.net/10023/7581
Background: Although there have been recent advances in the development of animal-attached ‘proximity’ tags to remotely record the interactions of multiple individuals, the efficacy of these devices depends on the instrumentation of sufficient animals that subsequently have spatial interactions. Among densely colonial mammals such as fur seals, this remains logistically difficult, and interactions between animals during foraging have not previously been recorded. Results: We collected data on conspecific interactions during diving at sea using still image and video cameras deployed on 23 Antarctic fur seals. Animals carried cameras for a total of 152 days, collecting 38,098 images and 369 movies (total time 7.35 h). Other fur seals were detected in 74% of deployments, with a maximum of five seals seen at one time (n = 122 images, 28 videos). No predators other than conspecifics were observed. Detection was primarily limited by light conditions, since conspecifics were usually further from each other than the 1-m range illuminated by camera flash under low light levels. Other seals were recorded at a range of depths (average 27 ± 14.3 m, max 66 m). In terms of bouts of dives, still images of other seals were recorded in 5 single dives (of 330) and 28 bouts of dives <2 min apart (of 187). Linear mixed models suggested a relationship between conspecific observations per dive and the number of krill images recorded per dive. Using light conditions as a proxy for detectability, other seals were more likely to be observed at the bottom of dives than during descent or ascent. Seals were also more likely to be closer to each other and oriented perpendicular to each other at the bottom of dives, and in the same direction as each other during ascent. Conclusions: These results are contrary to animal-attached camera observations of penguin foraging, suggesting differing group-foraging tactics for these marine predators. Group foraging could have consequences for models linking predator behaviour to prey field densities since this relationship may be affected by the presence of multiple predators at the same patch.
2015-09-29T00:00:00ZHooker, Sascha KateBarychka, TatsianaJessopp, Mark JStaniland, Iain JBackground: Although there have been recent advances in the development of animal-attached ‘proximity’ tags to remotely record the interactions of multiple individuals, the efficacy of these devices depends on the instrumentation of sufficient animals that subsequently have spatial interactions. Among densely colonial mammals such as fur seals, this remains logistically difficult, and interactions between animals during foraging have not previously been recorded. Results: We collected data on conspecific interactions during diving at sea using still image and video cameras deployed on 23 Antarctic fur seals. Animals carried cameras for a total of 152 days, collecting 38,098 images and 369 movies (total time 7.35 h). Other fur seals were detected in 74% of deployments, with a maximum of five seals seen at one time (n = 122 images, 28 videos). No predators other than conspecifics were observed. Detection was primarily limited by light conditions, since conspecifics were usually further from each other than the 1-m range illuminated by camera flash under low light levels. Other seals were recorded at a range of depths (average 27 ± 14.3 m, max 66 m). In terms of bouts of dives, still images of other seals were recorded in 5 single dives (of 330) and 28 bouts of dives <2 min apart (of 187). Linear mixed models suggested a relationship between conspecific observations per dive and the number of krill images recorded per dive. Using light conditions as a proxy for detectability, other seals were more likely to be observed at the bottom of dives than during descent or ascent. Seals were also more likely to be closer to each other and oriented perpendicular to each other at the bottom of dives, and in the same direction as each other during ascent. Conclusions: These results are contrary to animal-attached camera observations of penguin foraging, suggesting differing group-foraging tactics for these marine predators. Group foraging could have consequences for models linking predator behaviour to prey field densities since this relationship may be affected by the presence of multiple predators at the same patch.Abundance and distribution of delphinids in the Red Sea (Egypt)
https://hdl.handle.net/10023/6802
Knowledge about cetaceans in the Red Sea is limited with only a handful of sporadic or
spatially-limited studies carried out to date. Funded by the Italian Cooperation through
a Debt-for-Nature Swap programme and carried out in collaboration with the Egyptian
NGO HEPCA, this thesis presents the results from the first ever systematic vessel-based
surveys conducted in the southern Egyptian Red Sea from 2010 to 2013 using linetransect
methodology. The main aims of the thesis were (a) to estimate cetacean
abundance, (b) to determine distribution patterns and habitat use of the cetacean
species, (c) to investigate movement patterns for species for which individual
recognition techniques were suitable and (d) to identify areas of conservation concern
for cetaceans with a particular focus on existing protected areas. Eight species were
identified, of which five were commonly encountered (Stenella longirostris, S.
attenuata, Tursiops truncatus, T. aduncus, and Grampus griseus) and three were rare
(Pseudorca crassidens, Sousa plumbea, Balaenoptera edeni). Estimates of abundance
using design-based line transect sampling techniques were obtained for five species: S.
attenuata 10,268 (CV=0.26); S. longirostris 6,961 (CV=0.26); T. aduncus 659 (CV=0.69);
T. truncatus 509 (CV=0.33), and G. griseus 367 (CV=0.37). Habitat modelling revealed
that the two Stenella species were widely distributed across the study area. In
contrast, T. truncatus was concentrated in waters around Ras Banas peninsula (in
particular Satayah offshore reef), and T. aduncus was mainly found along the coast
with possibly separate sub-populations in the northern and southern study area. G.
griseus was only encountered in the southern part. The information provided in this
study will allow the development of a conservation strategy for the protected areas
and will serve as baseline information to carry out future survey work in the Red Sea.
2015-06-24T00:00:00ZCosta, MarinaKnowledge about cetaceans in the Red Sea is limited with only a handful of sporadic or
spatially-limited studies carried out to date. Funded by the Italian Cooperation through
a Debt-for-Nature Swap programme and carried out in collaboration with the Egyptian
NGO HEPCA, this thesis presents the results from the first ever systematic vessel-based
surveys conducted in the southern Egyptian Red Sea from 2010 to 2013 using linetransect
methodology. The main aims of the thesis were (a) to estimate cetacean
abundance, (b) to determine distribution patterns and habitat use of the cetacean
species, (c) to investigate movement patterns for species for which individual
recognition techniques were suitable and (d) to identify areas of conservation concern
for cetaceans with a particular focus on existing protected areas. Eight species were
identified, of which five were commonly encountered (Stenella longirostris, S.
attenuata, Tursiops truncatus, T. aduncus, and Grampus griseus) and three were rare
(Pseudorca crassidens, Sousa plumbea, Balaenoptera edeni). Estimates of abundance
using design-based line transect sampling techniques were obtained for five species: S.
attenuata 10,268 (CV=0.26); S. longirostris 6,961 (CV=0.26); T. aduncus 659 (CV=0.69);
T. truncatus 509 (CV=0.33), and G. griseus 367 (CV=0.37). Habitat modelling revealed
that the two Stenella species were widely distributed across the study area. In
contrast, T. truncatus was concentrated in waters around Ras Banas peninsula (in
particular Satayah offshore reef), and T. aduncus was mainly found along the coast
with possibly separate sub-populations in the northern and southern study area. G.
griseus was only encountered in the southern part. The information provided in this
study will allow the development of a conservation strategy for the protected areas
and will serve as baseline information to carry out future survey work in the Red Sea.Examining fish quality : the evaluation of the use of lipids as a measure of condition in wild Atlantic salmon
https://hdl.handle.net/10023/6728
Considering the response of organisms to their environment is difficult; it is made more so if population numbers cannot be closely monitored. In such cases different methods of population assessment are required. This thesis uses lipids as a measure of Atlantic salmon (Salmo salar L.) quality and investigates its usefulness in indicating fish condition.
The first study examines the relationship between fish total lipid content and W[sub]R condition factor; this study clearly demonstrates that there is a significant positive relationship between the condition factor of a fish and its total lipid content. In the following study the lipid storage between the different tissues of the Atlantic salmon is considered. This indicates that the red muscle and the adipose tissues hold higher concentrations of lipid than the white muscle. However, the white muscle makes up the majority of lipid tissue mass in the Atlantic salmon so contains the bulk of stored lipid in a fish, at low concentration.
The next study investigates the effect of spawning on Atlantic salmon condition. Salmon can be seen preferentially conserving lipid in their musculature and drawing down the lipid stored in their adipose tissues. The following study looked at one key lipid group, triacylglycerides, in salmon. Triacylglycerides are energetically important in fish and this study found that the spawning process depleted triacylglyceride reserves, but that the red muscle conserves triacylglycerides even after spawning.
The final study considers the relationship between maternal quality and egg quality, identifying that longer Atlantic salmon produce eggs with more lipid after spawning migration. Egg lipid concentrations were comparably maintained between fish. Monitoring quality in this way is a useful tool to determine population wellbeing and help indicate where populations are compromised.
2015-06-24T00:00:00ZHowe, Alexandra JaneConsidering the response of organisms to their environment is difficult; it is made more so if population numbers cannot be closely monitored. In such cases different methods of population assessment are required. This thesis uses lipids as a measure of Atlantic salmon (Salmo salar L.) quality and investigates its usefulness in indicating fish condition.
The first study examines the relationship between fish total lipid content and W[sub]R condition factor; this study clearly demonstrates that there is a significant positive relationship between the condition factor of a fish and its total lipid content. In the following study the lipid storage between the different tissues of the Atlantic salmon is considered. This indicates that the red muscle and the adipose tissues hold higher concentrations of lipid than the white muscle. However, the white muscle makes up the majority of lipid tissue mass in the Atlantic salmon so contains the bulk of stored lipid in a fish, at low concentration.
The next study investigates the effect of spawning on Atlantic salmon condition. Salmon can be seen preferentially conserving lipid in their musculature and drawing down the lipid stored in their adipose tissues. The following study looked at one key lipid group, triacylglycerides, in salmon. Triacylglycerides are energetically important in fish and this study found that the spawning process depleted triacylglyceride reserves, but that the red muscle conserves triacylglycerides even after spawning.
The final study considers the relationship between maternal quality and egg quality, identifying that longer Atlantic salmon produce eggs with more lipid after spawning migration. Egg lipid concentrations were comparably maintained between fish. Monitoring quality in this way is a useful tool to determine population wellbeing and help indicate where populations are compromised.Vortical control of forced two-dimensional turbulence
https://hdl.handle.net/10023/5236
A new numerical technique for the simulation of forced two-dimensional turbulence[D. Dritschel and J. Fontane, “The combined Lagrangian advection method,” J. Comput. Phys.229, 5408–5417 (Year: 2010)10.1016/j.jcp.2010.03.048] is used to examine the validity of Kraichnan-Batchelor scaling laws at higher Reynolds number than previously accessible with classical pseudo-spectral methods, making use of large simulation ensembles to allow a detailed consideration of the inverse cascade in a quasi-steady state. Our results support the recent finding of Scott [R. Scott, “Nonrobustness of the two-dimensional turbulent inverse cascade,” Phys. Rev. E75, 046301 (Year: 2007)10.1103/PhysRevE.75.046301], namely that when a direct enstrophy cascading range is well-represented numerically, a steeper energy spectrum proportional to k−2 is obtained in place of the classical k −5/3 prediction. It is further shown that this steep spectrum is associated with a faster growth of energy at large scales, scaling like t −1 rather than Kraichnan's prediction of t −3/2. The deviation from Kraichnan's theory is related to the emergence of a population of vortices that dominate the distribution of energy across scales, and whose number density and vorticity distribution with respect to vortex area are related to the shape of the enstrophy spectrum. An analytical model is proposed which closely matches the numerical spectra between the large scales and the forcing scale.
Jérôme Fontane is supported by the European Community in the framework of the CONVECT project under Grant No. PIEF-GA-2008-221003.
2013-01-14T00:00:00ZFontane, Jerome Jacob LouisDritschel, David GerardScott, Richard KirknessA new numerical technique for the simulation of forced two-dimensional turbulence[D. Dritschel and J. Fontane, “The combined Lagrangian advection method,” J. Comput. Phys.229, 5408–5417 (Year: 2010)10.1016/j.jcp.2010.03.048] is used to examine the validity of Kraichnan-Batchelor scaling laws at higher Reynolds number than previously accessible with classical pseudo-spectral methods, making use of large simulation ensembles to allow a detailed consideration of the inverse cascade in a quasi-steady state. Our results support the recent finding of Scott [R. Scott, “Nonrobustness of the two-dimensional turbulent inverse cascade,” Phys. Rev. E75, 046301 (Year: 2007)10.1103/PhysRevE.75.046301], namely that when a direct enstrophy cascading range is well-represented numerically, a steeper energy spectrum proportional to k−2 is obtained in place of the classical k −5/3 prediction. It is further shown that this steep spectrum is associated with a faster growth of energy at large scales, scaling like t −1 rather than Kraichnan's prediction of t −3/2. The deviation from Kraichnan's theory is related to the emergence of a population of vortices that dominate the distribution of energy across scales, and whose number density and vorticity distribution with respect to vortex area are related to the shape of the enstrophy spectrum. An analytical model is proposed which closely matches the numerical spectra between the large scales and the forcing scale.The effect of slip length on vortex rebound from a rigid boundary
https://hdl.handle.net/10023/5232
The problem of a dipole incident normally on a rigid boundary, for moderate to large Reynolds numbers, has recently been treated numerically using a volume penalisation method by Nguyen van yen, Farge, and Schneider [Phys. Rev. Lett.106, 184502 (2011)]. Their results indicate that energy dissipating structures persist in the inviscid limit. They found that the use of penalisation methods intrinsically introduces some slip at the boundary wall, where the slip approaches zero as the Reynolds number goes to infinity, so reducing to the no-slip case in this limit. We study the same problem, for both no-slip and partial slip cases, using compact differences on a Chebyshev grid in the direction normal to the wall and Fourier methods in the direction along the wall. We find that for the no-slip case there is no indication of the persistence of energy dissipating structures in the limit as viscosity approaches zero and that this also holds for any fixed slip length. However, when the slip length is taken to vary inversely with Reynolds number then the results of Nguyen van yen et al. are regained. It therefore appears that the prediction that energy dissipating structures persist in the inviscid limit follows from the two limits of wall slip length going to zero, and viscosity going to zero, not being treated independently in their use of the volume penalisation method.
2013-09-23T00:00:00ZSutherland, D.Macaskill, C.Dritschel, D.G.The problem of a dipole incident normally on a rigid boundary, for moderate to large Reynolds numbers, has recently been treated numerically using a volume penalisation method by Nguyen van yen, Farge, and Schneider [Phys. Rev. Lett.106, 184502 (2011)]. Their results indicate that energy dissipating structures persist in the inviscid limit. They found that the use of penalisation methods intrinsically introduces some slip at the boundary wall, where the slip approaches zero as the Reynolds number goes to infinity, so reducing to the no-slip case in this limit. We study the same problem, for both no-slip and partial slip cases, using compact differences on a Chebyshev grid in the direction normal to the wall and Fourier methods in the direction along the wall. We find that for the no-slip case there is no indication of the persistence of energy dissipating structures in the limit as viscosity approaches zero and that this also holds for any fixed slip length. However, when the slip length is taken to vary inversely with Reynolds number then the results of Nguyen van yen et al. are regained. It therefore appears that the prediction that energy dissipating structures persist in the inviscid limit follows from the two limits of wall slip length going to zero, and viscosity going to zero, not being treated independently in their use of the volume penalisation method.Shallow-water vortex equilibria and their stability
https://hdl.handle.net/10023/4762
We first describe the equilibrium form and stability of steadily-rotating simply-connected vortex patches in the single-layer quasi-geostrophic model of geophysical fluid dynamics. This model, valid for rotating shallow-water flow in the limit of small Rossby and Froude numbers, has an intrinsic length scale L called the "Rossby deformation length" relating the strength of stratification to that of the background rotation rate. Specifically, L = c/f where c = √gH is a characteristic gravity-wave speed, g is gravity (or "reduced" gravity in a two-layer context where one layer is infinitely deep), H is the mean active layer depth, and f is the Coriolis frequency (here constant). We next introduce ageostrophic effects by using the full shallow-water model to generate what we call "quasi-equilibria". These equilibria are not strictly steady, but radiate such weak gravity waves that they are steady for all practical purposes. Through an artificial ramping procedure, we ramp up the potential vorticity anomaly of the fluid particles in our quasi-geostrophic equilibria to obtain shallow-water quasi-equilibria at finite Rossby number. We show a few examples of these states in this paper.
2011-01-01T00:00:00ZPłotka, H.Dritschel, D.G.We first describe the equilibrium form and stability of steadily-rotating simply-connected vortex patches in the single-layer quasi-geostrophic model of geophysical fluid dynamics. This model, valid for rotating shallow-water flow in the limit of small Rossby and Froude numbers, has an intrinsic length scale L called the "Rossby deformation length" relating the strength of stratification to that of the background rotation rate. Specifically, L = c/f where c = √gH is a characteristic gravity-wave speed, g is gravity (or "reduced" gravity in a two-layer context where one layer is infinitely deep), H is the mean active layer depth, and f is the Coriolis frequency (here constant). We next introduce ageostrophic effects by using the full shallow-water model to generate what we call "quasi-equilibria". These equilibria are not strictly steady, but radiate such weak gravity waves that they are steady for all practical purposes. Through an artificial ramping procedure, we ramp up the potential vorticity anomaly of the fluid particles in our quasi-geostrophic equilibria to obtain shallow-water quasi-equilibria at finite Rossby number. We show a few examples of these states in this paper.The effects of physical, biological and anthropogenic noise on the occurrence of dolphins in the Pacific region of the Panama Canal
https://hdl.handle.net/10023/4484
The main aim of this thesis was to investigate the occurrence of dolphins in Pacific waters adjacent to the Panama Canal in the context of biological, temporal and spatial factors. Acoustic data were collected at 101 sites at a range of distances and depths from the shipping region. Data were collected between March 2010 and April 2011 in a diurnal cycle over a total of 114 recording days. Received sound levels were split into 1/3 Octave bandwidths to study variation in sound pressure levels and then converted to spectrum density levels to show the sound components of the background noise in this region. Generalised Linear Models were used to relate dolphin whistle detections to temporal, spatial, environmental and acoustic variables.
The major sources of background noise were biological noise from soniferous fish and snapping shrimp and anthropogenic noise from vessels characterised by mid to high frequencies produced by artisanal fishing boats. There was monthly and diurnal variation with some locations characterised by loud sounds in the mid to high frequencies at night.
Whistle characteristics analysis revealed that the frequencies and range of the whistles were different to those previously reported under similar conditions. Whistles varied diurnally and in the presence of fish chorus and fishing boats. The study highlights a strong correlation between fish choruses and whistle detection.
Temporal and spatial models showed that whistle detections varied monthly and in relation to fish noise and small vessel engine noise. Dolphins were distributed throughout most of the study area; however, whistle detections varied with distance from the coast.
The results provide new knowledge about background noise composition in this region and provide the first information on the ecology of dolphin whistles in relation to this background noise, especially to fish chorus.
2014-06-01T00:00:00ZCampbell Castillo, InezThe main aim of this thesis was to investigate the occurrence of dolphins in Pacific waters adjacent to the Panama Canal in the context of biological, temporal and spatial factors. Acoustic data were collected at 101 sites at a range of distances and depths from the shipping region. Data were collected between March 2010 and April 2011 in a diurnal cycle over a total of 114 recording days. Received sound levels were split into 1/3 Octave bandwidths to study variation in sound pressure levels and then converted to spectrum density levels to show the sound components of the background noise in this region. Generalised Linear Models were used to relate dolphin whistle detections to temporal, spatial, environmental and acoustic variables.
The major sources of background noise were biological noise from soniferous fish and snapping shrimp and anthropogenic noise from vessels characterised by mid to high frequencies produced by artisanal fishing boats. There was monthly and diurnal variation with some locations characterised by loud sounds in the mid to high frequencies at night.
Whistle characteristics analysis revealed that the frequencies and range of the whistles were different to those previously reported under similar conditions. Whistles varied diurnally and in the presence of fish chorus and fishing boats. The study highlights a strong correlation between fish choruses and whistle detection.
Temporal and spatial models showed that whistle detections varied monthly and in relation to fish noise and small vessel engine noise. Dolphins were distributed throughout most of the study area; however, whistle detections varied with distance from the coast.
The results provide new knowledge about background noise composition in this region and provide the first information on the ecology of dolphin whistles in relation to this background noise, especially to fish chorus.Boundary layer flow beneath an internal solitary wave of elevation
https://hdl.handle.net/10023/4331
The wave-induced flow over a fixed bottom boundary beneath an internal solitary wave of elevation propagating in an unsheared, two-layer, stably stratified fluid is investigated experimentally. Measurements of the velocity field close to the bottom boundary are presented to illustrate that in the lower layer the fluid velocity near the bottom reverses direction as the wave decelerates while higher in the water column the fluid velocity is in the same direction as the wave propagation. The observation is similar in nature to that for wave-induced flow beneath a surface solitary wave. Contrary to theoretical predictions for internal solitary waves, no evidence for either boundary layer separation or vortex formation is found beneath the front half of the wave in the adverse pressure gradient region of the flow.
2010-02-01T00:00:00ZCarr, MagdaDavies, P AThe wave-induced flow over a fixed bottom boundary beneath an internal solitary wave of elevation propagating in an unsheared, two-layer, stably stratified fluid is investigated experimentally. Measurements of the velocity field close to the bottom boundary are presented to illustrate that in the lower layer the fluid velocity near the bottom reverses direction as the wave decelerates while higher in the water column the fluid velocity is in the same direction as the wave propagation. The observation is similar in nature to that for wave-induced flow beneath a surface solitary wave. Contrary to theoretical predictions for internal solitary waves, no evidence for either boundary layer separation or vortex formation is found beneath the front half of the wave in the adverse pressure gradient region of the flow.Investigating annual diving behaviour by Hooded seals (Cystophora cristata) within the Northwest Atlantic Ocean
https://hdl.handle.net/10023/4228
With the exception of relatively brief periods when they reproduce and moult, hooded seals, Cystophora cristata, spend most of the year in the open ocean where they undergo feeding migrations to either recover or prepare for the next fasting period. Valuable insights into habitat use and diving behaviour during these periods have been obtained by attaching Satellite Relay Data Loggers (SRDLs) to 51 Northwest (NW) Atlantic hooded seals (33 females and 18 males) during ice-bound fasting periods (2004−2008). Using General Additive Models (GAMs) we describe habitat use in terms of First Passage Time (FPT) and analyse how bathymetry, seasonality and FPT influence the hooded seals’ diving behaviour described by maximum dive depth, dive duration and surface duration. Adult NW Atlantic hooded seals exhibit a change in diving activity in areas where they spend >20 h by increasing maximum dive depth, dive duration and surface duration, indicating a restricted search behaviour. We found that male and female hooded seals are spatially segregated and that diving behaviour varies between sexes in relation to habitat properties and seasonality. Migration periods are described by increased dive duration for both sexes with a peak in May, October and January. Males demonstrated an increase in dive depth and dive duration towards May (post-breeding/pre-moult) and August–October (post-moult/pre-breeding) but did not show any pronounced increase in surface duration. Females dived deepest and had the highest surface duration between December and January (post-moult/pre-breeding). Our results suggest that the smaller females may have a greater need to recover from dives than that of the larger males. Horizontal segregation could have evolved as a result of a resource partitioning strategy to avoid sexual competition or that the energy requirements of males and females are different due to different energy expenditure during fasting periods.
This work was funded through the Atlantic Seal Research Programme, International Governance Programme (DFO), the Greenland Institute of Natural Resources, and a CFI grant to YFW. The authors also acknowledge the support of the Marine Alliance for Science and Technology for Scotland (MASTS) pooling initiative in the completion of this study. MASTS is funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
2013-11-25T00:00:00ZAndersen, Julie MarieSkern-Mauritzen, MetteBoehme, LarsWiersma, Yolanda F.Rosvig-Asvid, AqqaluHammill, MikeStenson, GarryWith the exception of relatively brief periods when they reproduce and moult, hooded seals, Cystophora cristata, spend most of the year in the open ocean where they undergo feeding migrations to either recover or prepare for the next fasting period. Valuable insights into habitat use and diving behaviour during these periods have been obtained by attaching Satellite Relay Data Loggers (SRDLs) to 51 Northwest (NW) Atlantic hooded seals (33 females and 18 males) during ice-bound fasting periods (2004−2008). Using General Additive Models (GAMs) we describe habitat use in terms of First Passage Time (FPT) and analyse how bathymetry, seasonality and FPT influence the hooded seals’ diving behaviour described by maximum dive depth, dive duration and surface duration. Adult NW Atlantic hooded seals exhibit a change in diving activity in areas where they spend >20 h by increasing maximum dive depth, dive duration and surface duration, indicating a restricted search behaviour. We found that male and female hooded seals are spatially segregated and that diving behaviour varies between sexes in relation to habitat properties and seasonality. Migration periods are described by increased dive duration for both sexes with a peak in May, October and January. Males demonstrated an increase in dive depth and dive duration towards May (post-breeding/pre-moult) and August–October (post-moult/pre-breeding) but did not show any pronounced increase in surface duration. Females dived deepest and had the highest surface duration between December and January (post-moult/pre-breeding). Our results suggest that the smaller females may have a greater need to recover from dives than that of the larger males. Horizontal segregation could have evolved as a result of a resource partitioning strategy to avoid sexual competition or that the energy requirements of males and females are different due to different energy expenditure during fasting periods.Exploring heritage through time and space : Supporting community reflection on the highland clearances
https://hdl.handle.net/10023/4192
On the two hundredth anniversary of the Kildonan clearances, when people were forcibly removed from their homes, the Timespan Heritage centre has created a program of community centred work aimed at challenging pre conceptions and encouraging reflection on this important historical process. This paper explores the innovative ways in which virtual world technology has facilitated community engagement, enhanced visualisation and encouraged reflection as part of this program. An installation where users navigate through a reconstruction of pre clearance Caen township is controlled through natural gestures and presented on a 300 inch six megapixel screen. This environment allows users to experience the past in new ways. The platform has value as an effective way for an educator, artist or hobbyist to create large scale virtual environments using off the shelf hardware and open source software. The result is an exhibit that also serves as a platform for experimentation into innovative ways of community co-creation and co-curation.
2013-10-01T00:00:00ZMcCaffery, John PhilipMiller, Alan Henry DavidKennedy, Sarah ElizabethDawson, TomVermehren, AnnaLefley, CStrickland, KOn the two hundredth anniversary of the Kildonan clearances, when people were forcibly removed from their homes, the Timespan Heritage centre has created a program of community centred work aimed at challenging pre conceptions and encouraging reflection on this important historical process. This paper explores the innovative ways in which virtual world technology has facilitated community engagement, enhanced visualisation and encouraged reflection as part of this program. An installation where users navigate through a reconstruction of pre clearance Caen township is controlled through natural gestures and presented on a 300 inch six megapixel screen. This environment allows users to experience the past in new ways. The platform has value as an effective way for an educator, artist or hobbyist to create large scale virtual environments using off the shelf hardware and open source software. The result is an exhibit that also serves as a platform for experimentation into innovative ways of community co-creation and co-curation.Ecology of the Guiana dolphin (Sotalia guianensis) in the Southern area of the Gulf of Morrosquillo, Colombia : implications for conservation
https://hdl.handle.net/10023/4153
Sotalia guianensis is listed as “Data Deficient” by the IUCN and as “Vulnerable” in Colombia. This study aimed to advance understanding of the ecology of this species and its habitats, and to provide information to conservation management in the southern Gulf of Morrosquillo, Colombia. Systematic boat-based surveys were conducted during 395 days in 2002-2006 and 2009-2010, following established routes. Total survey effort was 15,199 km in an area covering ~ 310km². Fine scale habitat use and behavioural modelling, photo-identification and mark-recapture techniques were used to analyze the ecological patterns for this species. The most recent abundance estimate of dolphins using the study area during dry and rainy seasons, varied from 225 (CV = 0.34; 95% CI: 118-426) to 232 (CV = 0.32; 95% CI: 127-246). Annual survival rate is estimated at 0.948 (95% CI = 0.876-0.980). Overall density was 0.74/km². Dolphins were present year-round in the whole study area. Results indicate that they do not use the study area uniformly and that the use of particular zones is related to eco-geographic variables. Dolphins showed a preference for waters greater than 3m in depth with a slightly increased preference for waters about 5m and 15-25m deep. The average group size was nine individuals. Some individuals show long-term high site fidelity to some zones within the study site boundaries. Even though the site fidelity to feeding areas varied individually, all the individuals focused primarily on one specific area. Foraging was among one of the most predominant behaviours observed. The individual movements show that some dolphins use both bay and gulf waters. Dolphins show a range of surface cooperative foraging and feeding strategies. These cooperative behaviours were influenced by zone, group size and prey type. Based on these results an area of special management for the species will be created in Colombia.
2013-11-29T00:00:00ZDussán-Duque, Beatriz SaloméSotalia guianensis is listed as “Data Deficient” by the IUCN and as “Vulnerable” in Colombia. This study aimed to advance understanding of the ecology of this species and its habitats, and to provide information to conservation management in the southern Gulf of Morrosquillo, Colombia. Systematic boat-based surveys were conducted during 395 days in 2002-2006 and 2009-2010, following established routes. Total survey effort was 15,199 km in an area covering ~ 310km². Fine scale habitat use and behavioural modelling, photo-identification and mark-recapture techniques were used to analyze the ecological patterns for this species. The most recent abundance estimate of dolphins using the study area during dry and rainy seasons, varied from 225 (CV = 0.34; 95% CI: 118-426) to 232 (CV = 0.32; 95% CI: 127-246). Annual survival rate is estimated at 0.948 (95% CI = 0.876-0.980). Overall density was 0.74/km². Dolphins were present year-round in the whole study area. Results indicate that they do not use the study area uniformly and that the use of particular zones is related to eco-geographic variables. Dolphins showed a preference for waters greater than 3m in depth with a slightly increased preference for waters about 5m and 15-25m deep. The average group size was nine individuals. Some individuals show long-term high site fidelity to some zones within the study site boundaries. Even though the site fidelity to feeding areas varied individually, all the individuals focused primarily on one specific area. Foraging was among one of the most predominant behaviours observed. The individual movements show that some dolphins use both bay and gulf waters. Dolphins show a range of surface cooperative foraging and feeding strategies. These cooperative behaviours were influenced by zone, group size and prey type. Based on these results an area of special management for the species will be created in Colombia.Female rose bitterling prefer MHC-dissimilar males : experimental evidence
https://hdl.handle.net/10023/4143
The role of genetic benefits in female mate choice remains a controversial aspect of sexual selection theory. In contrast to “good allele” models of sexual selection, “compatible allele” models of mate choice predict that females prefer mates with alleles complementary to their own rather than conferring additive effects. While correlative results suggest complementary genetic effects to be plausible, direct experimental evidence is scarce. A previous study on the Chinese rose bitterling (Rhodeus ocellatus) demonstrated a positive correlation between female mate choice, offspring growth and survival, and the functional dissimilarity between the Major Histocompatibility Complex (MHC) alleles of males and females. Here we directly tested whether females used cues associated with MHC genes to select genetically compatible males in an experimental framework. By sequentially pairing females with MHC similar and dissimilar males, based on a priori known MHC profiles, we showed that females discriminated between similar and dissimilar males and deposited significantly more eggs with MHC dissimilar males. Notably, the degree of dissimilarity was an important factor for female decision to mate, possibly indicating a potential threshold value of dissimilarity for decision making, or of an indirect effect of the MHC.
2012-07-18T00:00:00ZReichard, MartinSpence, Rowena Grace AlisonBryjova, AnnaBryja, PepaSmith, CarlThe role of genetic benefits in female mate choice remains a controversial aspect of sexual selection theory. In contrast to “good allele” models of sexual selection, “compatible allele” models of mate choice predict that females prefer mates with alleles complementary to their own rather than conferring additive effects. While correlative results suggest complementary genetic effects to be plausible, direct experimental evidence is scarce. A previous study on the Chinese rose bitterling (Rhodeus ocellatus) demonstrated a positive correlation between female mate choice, offspring growth and survival, and the functional dissimilarity between the Major Histocompatibility Complex (MHC) alleles of males and females. Here we directly tested whether females used cues associated with MHC genes to select genetically compatible males in an experimental framework. By sequentially pairing females with MHC similar and dissimilar males, based on a priori known MHC profiles, we showed that females discriminated between similar and dissimilar males and deposited significantly more eggs with MHC dissimilar males. Notably, the degree of dissimilarity was an important factor for female decision to mate, possibly indicating a potential threshold value of dissimilarity for decision making, or of an indirect effect of the MHC.Maximum likelihood estimation of mark-recapture-recovery models in the presence of continuous covariates
https://hdl.handle.net/10023/4073
We consider mark-recapture-recovery (MRR) data of animals where the model parameters are a function of individual time-varying continuous covariates. For such covariates, the covariate value is unobserved if the corresponding individual is unobserved, in which case the survival probability cannot be evaluated. For continuous-valued covariates, the corresponding likelihood can only be expressed in the form of an integral that is analytically intractable, and, to date, no maximum likelihood approach that uses all the information in the data has been developed. Assuming a first-order Markov process for the covariate values, we accomplish this task by formulating the MRR setting in a state-space framework and considering an approximate likelihood approach which essentially discretizes the range of covariate values, reducing the integral to a summation. The likelihood can then be efficiently calculated and maximized using standard techniques for hidden Markov models. We initially assess the approach using simulated data before applying to real data relating to Soay sheep, specifying the survival probability as a function of body mass. Models that have previously been suggested for the corresponding covariate process are typically of the form of di.usive random walks. We consider an alternative non-di.usive AR(1)-type model which appears to provide a significantly better fit to the Soay sheep data.
Supplementary material: R code for model fitting. Sample R code for simulating MRR data and fitting the corresponding model using the HMM-based approach (with MRR model as described in Section 3). Digital Object Identifier: doi:10.1214/13-AOAS644SUPP
2013-01-01T00:00:00ZLangrock, RolandKing, RuthWe consider mark-recapture-recovery (MRR) data of animals where the model parameters are a function of individual time-varying continuous covariates. For such covariates, the covariate value is unobserved if the corresponding individual is unobserved, in which case the survival probability cannot be evaluated. For continuous-valued covariates, the corresponding likelihood can only be expressed in the form of an integral that is analytically intractable, and, to date, no maximum likelihood approach that uses all the information in the data has been developed. Assuming a first-order Markov process for the covariate values, we accomplish this task by formulating the MRR setting in a state-space framework and considering an approximate likelihood approach which essentially discretizes the range of covariate values, reducing the integral to a summation. The likelihood can then be efficiently calculated and maximized using standard techniques for hidden Markov models. We initially assess the approach using simulated data before applying to real data relating to Soay sheep, specifying the survival probability as a function of body mass. Models that have previously been suggested for the corresponding covariate process are typically of the form of di.usive random walks. We consider an alternative non-di.usive AR(1)-type model which appears to provide a significantly better fit to the Soay sheep data.Time is of the essence for ParaHox homeobox gene clustering.
https://hdl.handle.net/10023/3997
ParaHox genes, and their evolutionary sisters the Hox genes, are integral to patterning the anterior-posterior axis of most animals. Like the Hox genes, ParaHox genes can be clustered and exhibit the phenomenon of colinearity - gene order within the cluster matching gene activation. Two new instances of ParaHox clustering provide the first examples of intact clusters outside chordates, with gene expression lending weight to the argument that temporal colinearity is the key to understanding clustering.
2013-06-01T00:00:00ZGarstang, Myles GrantFerrier, David Ellard KeithParaHox genes, and their evolutionary sisters the Hox genes, are integral to patterning the anterior-posterior axis of most animals. Like the Hox genes, ParaHox genes can be clustered and exhibit the phenomenon of colinearity - gene order within the cluster matching gene activation. Two new instances of ParaHox clustering provide the first examples of intact clusters outside chordates, with gene expression lending weight to the argument that temporal colinearity is the key to understanding clustering.Wintertime water mass modification near an Antarctic Ice Shelf front
https://hdl.handle.net/10023/3903
Under ice measurements by seals carrying a miniaturized conductivity–temperature–depth (CTD) instrument fill an important gap in existing observations. Here we present data from an instrumented Weddell seal that spent 8 consecutive months (February–September) for aging in close proximity to Filchner Ice Shelf, thus providing detailed information about the evolution of mixed layer hydrography during the austral autumn and winter. The resultant time series of hydrography shows strong seasonal water mass modification, dominated by an upper–ocean (0–300 m) salinity increase of 0.31, corresponding to 3.1 m sea ice growth, and the development of a 500 m thick winter mixed layer. Observations furthermore highlight a gradual salinity increase in a slow (3–5 cms−1 ) southward flow on the continental shelf, to wards the site, and suggest that the inferred ice production is better considered as a regional average rather than being purely local. No clear seasonality is observed in the properties of the underlying Ice Shelf Water.
2013-02-01T00:00:00ZArthun, MariusNicholls, KeithBoehme, LarsUnder ice measurements by seals carrying a miniaturized conductivity–temperature–depth (CTD) instrument fill an important gap in existing observations. Here we present data from an instrumented Weddell seal that spent 8 consecutive months (February–September) for aging in close proximity to Filchner Ice Shelf, thus providing detailed information about the evolution of mixed layer hydrography during the austral autumn and winter. The resultant time series of hydrography shows strong seasonal water mass modification, dominated by an upper–ocean (0–300 m) salinity increase of 0.31, corresponding to 3.1 m sea ice growth, and the development of a 500 m thick winter mixed layer. Observations furthermore highlight a gradual salinity increase in a slow (3–5 cms−1 ) southward flow on the continental shelf, to wards the site, and suggest that the inferred ice production is better considered as a regional average rather than being purely local. No clear seasonality is observed in the properties of the underlying Ice Shelf Water.Two-dimensional magnetohydrodynamic turbulence in the small magnetic Prandtl number limit
https://hdl.handle.net/10023/3698
In this paper we introduce a new method for computations of two-dimensional magnetohydrodynamic (MHD) turbulence at low magnetic Prandtl number $\Pra=\nu/\eta$. When $\Pra \ll 1$, the magnetic field dissipates at a scale much larger than the velocity field. The method we utilise is a novel hybrid contour--spectral method, the ``Combined Lagrangian Advection Method'', formally to integrate the equations with zero viscous dissipation. The method is compared with a standard pseudo-spectral method for decreasing $\Pra$ for the problem of decaying two-dimensional MHD turbulence. The method is shown to agree well for a wide range of imposed magnetic field strengths. Examples of problems for which such a method may prove invaluable are also given.
2012-07-01T00:00:00ZDritschel, David GerardTobias, SteveIn this paper we introduce a new method for computations of two-dimensional magnetohydrodynamic (MHD) turbulence at low magnetic Prandtl number $\Pra=\nu/\eta$. When $\Pra \ll 1$, the magnetic field dissipates at a scale much larger than the velocity field. The method we utilise is a novel hybrid contour--spectral method, the ``Combined Lagrangian Advection Method'', formally to integrate the equations with zero viscous dissipation. The method is compared with a standard pseudo-spectral method for decreasing $\Pra$ for the problem of decaying two-dimensional MHD turbulence. The method is shown to agree well for a wide range of imposed magnetic field strengths. Examples of problems for which such a method may prove invaluable are also given.Biodiversity assessment of freshwater fishes : Thailand as a case study
https://hdl.handle.net/10023/3559
A key challenge in biodiversity is: How many species are there on earth? This issue is especially acute in poorly surveyed regions with high diversity, particularly Southeast Asia that also experiences many limitations such as lack of funds, documents and experts. To help meet this challenge, I have developed a five-tiered approach for diversity measurement of freshwater fish for use in Thailand. This is: (1) the creation of a newly updated species inventory that uses existing data; (2) exploration of the patterns of species richness, endemism, and uniqueness; (3) estimation of the total species richness; (4) investigation of patterns of rarity; and (5) integration of this knowledge into conservation practice. The system should be applicable to other regions and other taxa where a similar challenge exists.
My work shows that eight hundred and seventy-two species in 17 orders, 55 families and 255 genera of freshwater fishes, accounting for roughly 10% of the world’s freshwater fish diversity, have been reported for Thailand to date. This number was derived from information in the museum collections, literature and all other available sources, including reports written in Thai as well as in English. During this work I uncovered many gaps in biodiversity information, in terms of taxonomic and spatial records, though some families and basins are better represented than others. Taxonomic uncertainty also continues to be a challenge for taxonomists and users.
The high diversity of freshwater fishes in Thailand is the result of both high alpha (α) diversity (diversity within a particular locality) and beta (β) diversity (diversity differences between localities). I concluded that the substantial beta diversity I detected is associated with the geographical separation of the six river basins in Thailand. For example, the species composition of freshwater fishes in the Salween Basin dramatically differs from all other basins of Thailand. In contrast, the Chao Phraya Basin and the Mekong Basin contain the greatest number of shared species. Approximately 55% of species have a wide distribution range (being reported from more than two basins), whereas 45% are highly restricted within a single basin.
Analyses using species richness estimators suggest that the figure of 872 species is an underestimate and that there may be between 1000 and 1300 fish species in Thailand, in other words an increase of between 14.7% and 49.1% over the list I compiled (which is itself an increase of 52.2% over the last report in 1997). Freshwater fish have become increasingly vulnerable to anthropogenic activities. Of the 872 Thai fish species, 6.8% and 15.1% are globally and nationally threatened, respectively. Nonetheless, a striking feature of the database is that the conservation status of the vast majority of species has not so far been assessed, either globally or nationally. Scientists and policy makers will find these results useful in appreciating the magnitude of the tasks involved in surveying, describing and conserving the country’s freshwater fish biota. My work highlights localities and taxa where conservation is a priority and is thus an important resource for policy makers and conservation planners concerned with the management of freshwater fish in Thailand.
2012-11-29T00:00:00ZKhachonpisitsak, SalineeA key challenge in biodiversity is: How many species are there on earth? This issue is especially acute in poorly surveyed regions with high diversity, particularly Southeast Asia that also experiences many limitations such as lack of funds, documents and experts. To help meet this challenge, I have developed a five-tiered approach for diversity measurement of freshwater fish for use in Thailand. This is: (1) the creation of a newly updated species inventory that uses existing data; (2) exploration of the patterns of species richness, endemism, and uniqueness; (3) estimation of the total species richness; (4) investigation of patterns of rarity; and (5) integration of this knowledge into conservation practice. The system should be applicable to other regions and other taxa where a similar challenge exists.
My work shows that eight hundred and seventy-two species in 17 orders, 55 families and 255 genera of freshwater fishes, accounting for roughly 10% of the world’s freshwater fish diversity, have been reported for Thailand to date. This number was derived from information in the museum collections, literature and all other available sources, including reports written in Thai as well as in English. During this work I uncovered many gaps in biodiversity information, in terms of taxonomic and spatial records, though some families and basins are better represented than others. Taxonomic uncertainty also continues to be a challenge for taxonomists and users.
The high diversity of freshwater fishes in Thailand is the result of both high alpha (α) diversity (diversity within a particular locality) and beta (β) diversity (diversity differences between localities). I concluded that the substantial beta diversity I detected is associated with the geographical separation of the six river basins in Thailand. For example, the species composition of freshwater fishes in the Salween Basin dramatically differs from all other basins of Thailand. In contrast, the Chao Phraya Basin and the Mekong Basin contain the greatest number of shared species. Approximately 55% of species have a wide distribution range (being reported from more than two basins), whereas 45% are highly restricted within a single basin.
Analyses using species richness estimators suggest that the figure of 872 species is an underestimate and that there may be between 1000 and 1300 fish species in Thailand, in other words an increase of between 14.7% and 49.1% over the list I compiled (which is itself an increase of 52.2% over the last report in 1997). Freshwater fish have become increasingly vulnerable to anthropogenic activities. Of the 872 Thai fish species, 6.8% and 15.1% are globally and nationally threatened, respectively. Nonetheless, a striking feature of the database is that the conservation status of the vast majority of species has not so far been assessed, either globally or nationally. Scientists and policy makers will find these results useful in appreciating the magnitude of the tasks involved in surveying, describing and conserving the country’s freshwater fish biota. My work highlights localities and taxa where conservation is a priority and is thus an important resource for policy makers and conservation planners concerned with the management of freshwater fish in Thailand.Estimating whale abundance using sparse hydrophone arrays
https://hdl.handle.net/10023/3463
Passive acoustic monitoring has been used to investigate many aspects of marine mammal ecology, although methods to estimate absolute abundance and density using acoustic data have only been developed in recent years. The instrument configuration in an acoustic survey determines which abundance estimation methods can be used. Sparsely distributed arrays of instruments are useful because wide geographic areas can be covered. However, instrument spacing in sparse arrays is such that the same vocalisation will not be detected on multiple instruments, excluding the use of some abundance estimation methods. The aim of this thesis was to explore cetacean abundance and density estimation using novel sparse array datasets, applying existing methods where possible, or developing new approaches.
The wealth of data collected by sparse arrays was demonstrated by analysing a 10-year dataset collected by the U.S. Navy’s Sound Surveillance System in the north-east Atlantic. Spatial and temporal patterns of blue (Balaenoptera musculus) and fin whale (Balaenoptera physalus) vocal activity were investigated using generalised additive models.
Distance sampling-based methods were applied to fin whale calls recorded by an array of Ocean Bottom Seismometers in the north-east Atlantic. Estimated call density was 993 calls/1000 km².hr⁻¹ (CV: 0.39). Animal density could not be estimated because the call rate was unknown. Further development of the call localisation method is required so the current density estimate may be biased. Furthermore, analysing a single day of data resulted in a high variance estimate.
Finally, a new simulation-based method developed to estimate density from single hydrophones was applied to blue whale calls recorded in the northern Indian Ocean. Estimated call density was 3 calls/1000 km².hr⁻¹ (CV: 0.17). Again, density of whales could not be estimated as the vocalisation rate was unknown. Lack of biological knowledge poses the greatest limitation to abundance and density estimation using acoustic data.
2012-06-20T00:00:00ZHarris, Danielle VeronicaPassive acoustic monitoring has been used to investigate many aspects of marine mammal ecology, although methods to estimate absolute abundance and density using acoustic data have only been developed in recent years. The instrument configuration in an acoustic survey determines which abundance estimation methods can be used. Sparsely distributed arrays of instruments are useful because wide geographic areas can be covered. However, instrument spacing in sparse arrays is such that the same vocalisation will not be detected on multiple instruments, excluding the use of some abundance estimation methods. The aim of this thesis was to explore cetacean abundance and density estimation using novel sparse array datasets, applying existing methods where possible, or developing new approaches.
The wealth of data collected by sparse arrays was demonstrated by analysing a 10-year dataset collected by the U.S. Navy’s Sound Surveillance System in the north-east Atlantic. Spatial and temporal patterns of blue (Balaenoptera musculus) and fin whale (Balaenoptera physalus) vocal activity were investigated using generalised additive models.
Distance sampling-based methods were applied to fin whale calls recorded by an array of Ocean Bottom Seismometers in the north-east Atlantic. Estimated call density was 993 calls/1000 km².hr⁻¹ (CV: 0.39). Animal density could not be estimated because the call rate was unknown. Further development of the call localisation method is required so the current density estimate may be biased. Furthermore, analysing a single day of data resulted in a high variance estimate.
Finally, a new simulation-based method developed to estimate density from single hydrophones was applied to blue whale calls recorded in the northern Indian Ocean. Estimated call density was 3 calls/1000 km².hr⁻¹ (CV: 0.17). Again, density of whales could not be estimated as the vocalisation rate was unknown. Lack of biological knowledge poses the greatest limitation to abundance and density estimation using acoustic data.Male mating tactics in the rose bitterling (Rhodeus ocellatus) and European bitterling (Rhodeus amarus)
https://hdl.handle.net/10023/3447
The aim of this study was to investigate the basis to male mating decisions in two related species of bitterling: Rhodeus ocellatus and R. amarus. Bitterling have a resource-based mating system; females lay eggs in the gills of live freshwater mussels and males fertilize the eggs by releasing sperm into the inhalant syphon of the mussel. Male bitterling perform courtship behaviour and aggressively defend mussels in a territory from which they exclude other males. Using laboratory and field experiments it was shown that male aggressive behaviour is inherited through additive maternal genes. Male aggression is also influenced by the number of conspecific males encountered in competition for a mussel, and by the degree of clustering of mussels. Limited availability of mussels results in stronger selection on traits males use in mating context: hence they are more aggressive, larger and more colourful. The differences in mating behaviours in different environments may indicate a conflict between male dominance and female choice, but have not led to reproductive isolation. Resource availability during ontogenesis and male density during embryogenesis, however, do not exert an effect on male aggressive behaviour. Red carotenoid-based nuptial coloration functions as an inter- and intra-sexual signal and undergoes rapid variation in response to changes in mating context. Male bitterling do not modulate their courtship and aggressive behaviour in response to variation in female size, and their choice of mussel species is influenced by, and consistent with, female oviposition choice.
2013-06-26T00:00:00ZCasalini, MaraThe aim of this study was to investigate the basis to male mating decisions in two related species of bitterling: Rhodeus ocellatus and R. amarus. Bitterling have a resource-based mating system; females lay eggs in the gills of live freshwater mussels and males fertilize the eggs by releasing sperm into the inhalant syphon of the mussel. Male bitterling perform courtship behaviour and aggressively defend mussels in a territory from which they exclude other males. Using laboratory and field experiments it was shown that male aggressive behaviour is inherited through additive maternal genes. Male aggression is also influenced by the number of conspecific males encountered in competition for a mussel, and by the degree of clustering of mussels. Limited availability of mussels results in stronger selection on traits males use in mating context: hence they are more aggressive, larger and more colourful. The differences in mating behaviours in different environments may indicate a conflict between male dominance and female choice, but have not led to reproductive isolation. Resource availability during ontogenesis and male density during embryogenesis, however, do not exert an effect on male aggressive behaviour. Red carotenoid-based nuptial coloration functions as an inter- and intra-sexual signal and undergoes rapid variation in response to changes in mating context. Male bitterling do not modulate their courtship and aggressive behaviour in response to variation in female size, and their choice of mussel species is influenced by, and consistent with, female oviposition choice.Instability in internal solitary waves with trapped cores
https://hdl.handle.net/10023/3397
A numerical method that employs a combination of contour advection and pseudo-spectral techniques is used to investigate instability in internal solitary waves with trapped cores. A three-layer configuration for the background stratification in which the top two layers are linearly stratified and the lower layer is homogeneous is considered throughout. The strength of the stratification in the very top layer is chosen to be sufficient so that waves of depression with trapped cores can be generated. The flow is assumed to satisfy the Dubriel-Jacotin-Long equation both inside and outside of the core region. The Brunt-Vaisala frequency is modelled such that it varies from a constant value outside of the core to zero inside the core over a sharp but continuous transition length. This results in a stagnant core in which the vorticity is zero and the density is homogeneous and approximately equal to that at the core boundary. The time dependent simulations show that instability occurs on the boundary of the core. The instability takes the form of Kelvin-Helmholtz billows. If the instability in the vorticity field is energetic enough, disturbance in the buoyancy field is also seen and fluid exchange takes place across the core boundary. Occurrence of the Kelvin-Helmholtz billows is attributed to the sharp change in the vorticity field at the boundary between the core and the pycnocline. The numerical scheme is not limited by small Richardson number unlike the other alternatives currently available in the literature which appear to be.
2012-01-01T00:00:00ZCarr, MagdaKing, Stuart EdwardDritschel, David GerardA numerical method that employs a combination of contour advection and pseudo-spectral techniques is used to investigate instability in internal solitary waves with trapped cores. A three-layer configuration for the background stratification in which the top two layers are linearly stratified and the lower layer is homogeneous is considered throughout. The strength of the stratification in the very top layer is chosen to be sufficient so that waves of depression with trapped cores can be generated. The flow is assumed to satisfy the Dubriel-Jacotin-Long equation both inside and outside of the core region. The Brunt-Vaisala frequency is modelled such that it varies from a constant value outside of the core to zero inside the core over a sharp but continuous transition length. This results in a stagnant core in which the vorticity is zero and the density is homogeneous and approximately equal to that at the core boundary. The time dependent simulations show that instability occurs on the boundary of the core. The instability takes the form of Kelvin-Helmholtz billows. If the instability in the vorticity field is energetic enough, disturbance in the buoyancy field is also seen and fluid exchange takes place across the core boundary. Occurrence of the Kelvin-Helmholtz billows is attributed to the sharp change in the vorticity field at the boundary between the core and the pycnocline. The numerical scheme is not limited by small Richardson number unlike the other alternatives currently available in the literature which appear to be.Tunicates push the limits of animal evo-devo
https://hdl.handle.net/10023/3250
The phylum to which humans belong, Chordata, takes its name from one of the major shared derived features of the group, the notochord. All chordates have a notochord, at least during embryogenesis, and there is little doubt about notochord homology at the morphological level. A study in BMC Evolutionary Biology now shows that there is greater variability in the molecular genetics underlying notochord development than previously appreciated.
2011-01-20T00:00:00ZFerrier, David Ellard KeithThe phylum to which humans belong, Chordata, takes its name from one of the major shared derived features of the group, the notochord. All chordates have a notochord, at least during embryogenesis, and there is little doubt about notochord homology at the morphological level. A study in BMC Evolutionary Biology now shows that there is greater variability in the molecular genetics underlying notochord development than previously appreciated.The influence of mid-ocean ridges on euphausiid and pelagic ecology
https://hdl.handle.net/10023/3229
Chapters 1 & 2. Euphausiids comprise a major component of ecosystems in the pelagic realm, the
world’s largest habitat, but basin scale drivers of euphausiids diversity and abundance
are poorly understood. Mid-Ocean Ridges are the largest topographical feature in the
pelagic realm and their benthic and pelagic fauna have only just recently become the
focus of research. This thesis present new analyses on the drivers of euphausiids species
richness in the Atlantic and the Pacific, giving specific attention to the influence of Mid-Ocean Ridges. New information is given on the biogeography of euphausiids and
pelagic food-web trophology of the Mid-Atlantic Ridge, and on the biogeography of
pelagic decapods on the South-West Indian Ocean ridge.
3. A Generalized Additive Model framework was used to explore spatial patterns of
variability in euphausiid species richness (from recognized areas of occurrence) and in
numerical abundance (from the Continuous Plankton Recorder survey) in conjunction
with variability in a suite of biological, physical and environmental parameters on, and
at either side of, the Mid-Atlantic Ridge. Euphausiid species richness peaked in mid-latitudes
and was significantly higher on the ridge than in adjacent waters, but the ridge
did not influence numerical abundance in the top 10 m significantly. Sea surface
temperature (SST) was the most important single factor influencing both euphausiid
numerical abundance (-76.7%) and species richness (34.44%). Dissolved silicate
concentration, a proxy for diatom abundance, significantly increased species richness
(29.46%). Increases in sea surface height variance, a proxy for mixing, increased the
numerical abundance of euphausiids. GAM predictions of variability in species richness
as a function of SST and depth of the mixed layer were consistent with present theories,
which suggest that pelagic niche-availability is related to the thermal structure of the
near surface water.
4. Using a Generalized Additive Model in the Pacific, the main drivers of species
richness, in order of decreasing importance, were found to be sea surface temperature
(explaining 29.53% in species variability), salinity (20.29%), longitude (-15.01%,
species richness decreased from West to East), distance to coast (10.99%), and
dissolved silicate concentration (9.03%). An additional linear model poorly predicted
numerical abundance. The practical differences in drivers of species richness in the
Atlantic and Pacific Ocean were compared. Predictions of future species richness
changes in the Pacific and Atlantic were made using projected environmental change
from the IPCC A1B climate scenario, suggesting an increase in species richness in
temperature latitudes (30° to 60° N and S) and little to no change in low latitudes (20° N
to 20° S).
5. New baseline information is presented on biogeography, abundance and vertical
distribution of euphausiids along the Mid-Atlantic Ridge (40° to 62° N). 18 species
were recorded, with Euphausia krohni and Thysanoessa longicaudata being most
abundant. Eight species had not been recorded in the area previously. The Subpolar
Front is a northern boundary to some southern species, but not a southern boundary to
northern ubiquitous species that show submergence. Four major species assemblages
were identified and characterised in terms of spatial distribution and species
composition. Numerical abundance was highly variable but decreased by orders of
magnitude with depth. The Mid-Atlantic Ridge showed only a marginal effect on
euphausiid distribution and abundance patterns.
6. Zooplankton and micronektic invertebrate epi- and mesopelagic (0-200 and 200-800 m) vertical distribution (e.g. Euphausiacea, Decapoda, Amphipoda, Thecosomata,
Lophogastrida) on either side of the Subpolar Front of the Mid-Atlantic Ridge is
described. Dietary relationships are explored, using stable isotope ratios and fatty acid
trophic marker (FATM) composition. An increase in trophic level with size was
observed. Individuals from southern stations were higher in dinoflagellate Fatty Acid
Trophic Markers (FATM) (22:6(n-3)) and individuals from northern stations were
higher in Calanus spp and storage FATMs (20:1(n-9) and 22:1(n-9)) reflecting primary
production patterns in the two survey sectors. Observations on the geographical and
vertical variability in trophodynamics are discussed.
7. New baseline information is presented on the biogeography, abundance, and vertical
distribution of mesopelagic (200-1000 m), crustacean micronekton on- and offseamounts
of the South-West Indian Ocean Ridge (26° to 42° S). Species richness and
numerical abundance were typically higher near seamounts and lower over the abyssal
plains, with several species being caught uniquely on seamounts. Observations suggest
that the ‘oasis effect’ of seamounts conventionally associated with higher trophic levels
is also applicable to pelagic micronektic crustaceans at lower trophic levels. Biophysical
coupling of micronekton to seamounts may be an important factor controlling
benthopelagic coupling in seamount food-webs.
8. Euphausiid and pelagic diversity is driven primarily by geographical variability in
temperature, by longitudinal patterns in upwellings, and by variability in nutrient
concentration. Mid-Ocean Ridges modify pelagic ecology, by raising the seafloor and
by bringing in proximity true pelagic and bathypelagic predators associated with the
seabed. The increase in specialized fauna and biomass associated with ridges and
seamounts serves to deplete zooplankton in the near bottom layer (0-200 m) and affect
systems in and above the benthic boundary layer (<200 m from the seafloor), and the
benthopelagic faunal layer. Mid-Ocean Ridges may serve to structure pelagic faunal
distribution, and increase the overall diversity of the world ocean. The influence of
ridges in the ocean basin may be comparable to that of hedges in a farmland; whilst
delimiting the extent of crops (or zooplankton assemblages), hedges serve as local
hotspots of mammal and avian diversity.
2012-06-19T00:00:00ZLetessier, Tom BechChapters 1 & 2. Euphausiids comprise a major component of ecosystems in the pelagic realm, the
world’s largest habitat, but basin scale drivers of euphausiids diversity and abundance
are poorly understood. Mid-Ocean Ridges are the largest topographical feature in the
pelagic realm and their benthic and pelagic fauna have only just recently become the
focus of research. This thesis present new analyses on the drivers of euphausiids species
richness in the Atlantic and the Pacific, giving specific attention to the influence of Mid-Ocean Ridges. New information is given on the biogeography of euphausiids and
pelagic food-web trophology of the Mid-Atlantic Ridge, and on the biogeography of
pelagic decapods on the South-West Indian Ocean ridge.
3. A Generalized Additive Model framework was used to explore spatial patterns of
variability in euphausiid species richness (from recognized areas of occurrence) and in
numerical abundance (from the Continuous Plankton Recorder survey) in conjunction
with variability in a suite of biological, physical and environmental parameters on, and
at either side of, the Mid-Atlantic Ridge. Euphausiid species richness peaked in mid-latitudes
and was significantly higher on the ridge than in adjacent waters, but the ridge
did not influence numerical abundance in the top 10 m significantly. Sea surface
temperature (SST) was the most important single factor influencing both euphausiid
numerical abundance (-76.7%) and species richness (34.44%). Dissolved silicate
concentration, a proxy for diatom abundance, significantly increased species richness
(29.46%). Increases in sea surface height variance, a proxy for mixing, increased the
numerical abundance of euphausiids. GAM predictions of variability in species richness
as a function of SST and depth of the mixed layer were consistent with present theories,
which suggest that pelagic niche-availability is related to the thermal structure of the
near surface water.
4. Using a Generalized Additive Model in the Pacific, the main drivers of species
richness, in order of decreasing importance, were found to be sea surface temperature
(explaining 29.53% in species variability), salinity (20.29%), longitude (-15.01%,
species richness decreased from West to East), distance to coast (10.99%), and
dissolved silicate concentration (9.03%). An additional linear model poorly predicted
numerical abundance. The practical differences in drivers of species richness in the
Atlantic and Pacific Ocean were compared. Predictions of future species richness
changes in the Pacific and Atlantic were made using projected environmental change
from the IPCC A1B climate scenario, suggesting an increase in species richness in
temperature latitudes (30° to 60° N and S) and little to no change in low latitudes (20° N
to 20° S).
5. New baseline information is presented on biogeography, abundance and vertical
distribution of euphausiids along the Mid-Atlantic Ridge (40° to 62° N). 18 species
were recorded, with Euphausia krohni and Thysanoessa longicaudata being most
abundant. Eight species had not been recorded in the area previously. The Subpolar
Front is a northern boundary to some southern species, but not a southern boundary to
northern ubiquitous species that show submergence. Four major species assemblages
were identified and characterised in terms of spatial distribution and species
composition. Numerical abundance was highly variable but decreased by orders of
magnitude with depth. The Mid-Atlantic Ridge showed only a marginal effect on
euphausiid distribution and abundance patterns.
6. Zooplankton and micronektic invertebrate epi- and mesopelagic (0-200 and 200-800 m) vertical distribution (e.g. Euphausiacea, Decapoda, Amphipoda, Thecosomata,
Lophogastrida) on either side of the Subpolar Front of the Mid-Atlantic Ridge is
described. Dietary relationships are explored, using stable isotope ratios and fatty acid
trophic marker (FATM) composition. An increase in trophic level with size was
observed. Individuals from southern stations were higher in dinoflagellate Fatty Acid
Trophic Markers (FATM) (22:6(n-3)) and individuals from northern stations were
higher in Calanus spp and storage FATMs (20:1(n-9) and 22:1(n-9)) reflecting primary
production patterns in the two survey sectors. Observations on the geographical and
vertical variability in trophodynamics are discussed.
7. New baseline information is presented on the biogeography, abundance, and vertical
distribution of mesopelagic (200-1000 m), crustacean micronekton on- and offseamounts
of the South-West Indian Ocean Ridge (26° to 42° S). Species richness and
numerical abundance were typically higher near seamounts and lower over the abyssal
plains, with several species being caught uniquely on seamounts. Observations suggest
that the ‘oasis effect’ of seamounts conventionally associated with higher trophic levels
is also applicable to pelagic micronektic crustaceans at lower trophic levels. Biophysical
coupling of micronekton to seamounts may be an important factor controlling
benthopelagic coupling in seamount food-webs.
8. Euphausiid and pelagic diversity is driven primarily by geographical variability in
temperature, by longitudinal patterns in upwellings, and by variability in nutrient
concentration. Mid-Ocean Ridges modify pelagic ecology, by raising the seafloor and
by bringing in proximity true pelagic and bathypelagic predators associated with the
seabed. The increase in specialized fauna and biomass associated with ridges and
seamounts serves to deplete zooplankton in the near bottom layer (0-200 m) and affect
systems in and above the benthic boundary layer (<200 m from the seafloor), and the
benthopelagic faunal layer. Mid-Ocean Ridges may serve to structure pelagic faunal
distribution, and increase the overall diversity of the world ocean. The influence of
ridges in the ocean basin may be comparable to that of hedges in a farmland; whilst
delimiting the extent of crops (or zooplankton assemblages), hedges serve as local
hotspots of mammal and avian diversity.Examining the response of top marine predators to ecological change using stable isotope proxies
https://hdl.handle.net/10023/3221
Monitoring the response of upper trophic level animals to ecological change is important
to understanding the state and stability of ecosystems. Marine predators
integrate information over large geographical scales and are relatively long-lived; furthermore,
many of these organisms are restricted to terrestrial or freshwater habitats
at certain times during their life history and are accessible to researchers. This thesis
investigated the response of marine predators to ecological change at a variety
of spatial and temporal scales using stable isotope ratio methods with the aims of
developing meaningful proxies, or indices, of variability in marine ecosystems.
The first study explored the intrinsic (i.e. ontogenetic) and extrinsic (i.e. environmental)
factors important to modulating variation in the stable isotope ratios of
C and N in tooth dentin of male Antarctic fur seals (Arctocephalus gazella) in the
Southern Ocean. In the second study, long-term records of variation in δ¹⁵N and δ¹³C values of Atlantic salmon (Salmo salar) scales and grey seal (Halichoerus grypus)
tooth dentin provided evidence for large-scale climate forcing across the eastern
North Atlantic. In the following study, a more detailed examination of intra- and
inter-individual stable isotope variation in Atlantic salmon within a single year was
undertaken in an attempt to better understand recent declines in somatic condition
of these fish.
The last two studies were concerned with the development of high resolution sampling
of fish otoliths using secondary mass spectrometry (SIMS) and the application
of this technique to reconstructing the thermal and metabolic histories of individual
Atlantic salmon from intra-otolith δ¹³C and δ¹⁸O values.
Stable isotope proxies can be used to document shifts in trophic dynamics and
animal movement that may be associated with ecological change. Using multiple
tissues, elements and species, such studies provide unique monitoring tools at a
range of spatial and temporal scales.
2012-11-30T00:00:00ZHanson, Nora NellMonitoring the response of upper trophic level animals to ecological change is important
to understanding the state and stability of ecosystems. Marine predators
integrate information over large geographical scales and are relatively long-lived; furthermore,
many of these organisms are restricted to terrestrial or freshwater habitats
at certain times during their life history and are accessible to researchers. This thesis
investigated the response of marine predators to ecological change at a variety
of spatial and temporal scales using stable isotope ratio methods with the aims of
developing meaningful proxies, or indices, of variability in marine ecosystems.
The first study explored the intrinsic (i.e. ontogenetic) and extrinsic (i.e. environmental)
factors important to modulating variation in the stable isotope ratios of
C and N in tooth dentin of male Antarctic fur seals (Arctocephalus gazella) in the
Southern Ocean. In the second study, long-term records of variation in δ¹⁵N and δ¹³C values of Atlantic salmon (Salmo salar) scales and grey seal (Halichoerus grypus)
tooth dentin provided evidence for large-scale climate forcing across the eastern
North Atlantic. In the following study, a more detailed examination of intra- and
inter-individual stable isotope variation in Atlantic salmon within a single year was
undertaken in an attempt to better understand recent declines in somatic condition
of these fish.
The last two studies were concerned with the development of high resolution sampling
of fish otoliths using secondary mass spectrometry (SIMS) and the application
of this technique to reconstructing the thermal and metabolic histories of individual
Atlantic salmon from intra-otolith δ¹³C and δ¹⁸O values.
Stable isotope proxies can be used to document shifts in trophic dynamics and
animal movement that may be associated with ecological change. Using multiple
tissues, elements and species, such studies provide unique monitoring tools at a
range of spatial and temporal scales.Statistical developments for understanding anthropogenic impacts on marine ecosystems
https://hdl.handle.net/10023/3172
Over the past decades technological developments have both changed and increased
human influence on the marine environment. We now have greater potential than ever before to introduce disturbance and deplete marine resources. Two of the issues currently under public scrutiny are the exploitation of fish stocks worldwide and
levels of anthropogenic noise in the marine environment. The aim of this thesis is to investigate and develop novel analyses and simulations to provide additional insight into some of the challenges facing the marine ecosystem today. These methodologies
will improve the management of these risks to marine ecosystems. This thesis first addresses the issue of competition between humans and grey seals
(Halichoerus grypus) for marine resources, providing compelling evidence that a substantial proportion of the sandeels consumed by grey seals in the North Sea are in fact H. lanceolatus, which is not commercially exploited, rather than the commercially important A. marinus. In addition, we present quantitative results regarding sources of bias when estimating the total biomass of sandeels consumed by grey seals. Secondly, we investigate spatially adaptive 2-dimensional smoothing to improve the prediction of both the presence and density of marine species, information that is often key in the management of marine ecosystems. Particularly, we demonstrate the benefits of
such methods in the prediction of sandeel occurrence. Lastly this thesis provides a
quantitative assessment of the protocols for real-time monitoring of marine mammal presence, which require that acoustic operations cease when an animal is detected
within a certain distance (i.e. the "monitoring zone") of the sound source. We assess monitoring zones of different sizes with regards to their effectiveness in reducing the risks of temporary and permanent damage to the animals' hearing, and demonstrate that a monitoring zone of 2 km is generally recommendable.
2012-06-20T00:00:00ZMarshall, LauraOver the past decades technological developments have both changed and increased
human influence on the marine environment. We now have greater potential than ever before to introduce disturbance and deplete marine resources. Two of the issues currently under public scrutiny are the exploitation of fish stocks worldwide and
levels of anthropogenic noise in the marine environment. The aim of this thesis is to investigate and develop novel analyses and simulations to provide additional insight into some of the challenges facing the marine ecosystem today. These methodologies
will improve the management of these risks to marine ecosystems. This thesis first addresses the issue of competition between humans and grey seals
(Halichoerus grypus) for marine resources, providing compelling evidence that a substantial proportion of the sandeels consumed by grey seals in the North Sea are in fact H. lanceolatus, which is not commercially exploited, rather than the commercially important A. marinus. In addition, we present quantitative results regarding sources of bias when estimating the total biomass of sandeels consumed by grey seals. Secondly, we investigate spatially adaptive 2-dimensional smoothing to improve the prediction of both the presence and density of marine species, information that is often key in the management of marine ecosystems. Particularly, we demonstrate the benefits of
such methods in the prediction of sandeel occurrence. Lastly this thesis provides a
quantitative assessment of the protocols for real-time monitoring of marine mammal presence, which require that acoustic operations cease when an animal is detected
within a certain distance (i.e. the "monitoring zone") of the sound source. We assess monitoring zones of different sizes with regards to their effectiveness in reducing the risks of temporary and permanent damage to the animals' hearing, and demonstrate that a monitoring zone of 2 km is generally recommendable.Impact of environmental change on primary production in model marine coastal ecosystems
https://hdl.handle.net/10023/3143
Coastal ecosystems, including estuaries, provide a range of services to humans,
mediated by the species within these ecosystems. Microphytobenthos (MPB) play a
vital role in many key processes within estuarine ecosystems, and provide a food
source for higher trophic levels. Anthropogenic activity is already causing changes to
ecosystems, through pollution, overexploitation and, more recently, climate change.
Increasing temperature and carbon dioxide levels, and altered biodiversity, are likely
to affect species, and their interactions, within these ecosystems. Much ecological
research has focused on the effects of a single stressor on specific species or
ecosystems, with relatively little work examining the effects of multiple stressors.
The research in this thesis investigates the effects of altered environmental variables
(light, tidal regime, temperature and carbon dioxide) and different macrofaunal
diversity on primary production (MPB biomass) through a series of manipulative lab-based mesocosm experiments. This work also examines the temporal variability of
environmental stressors on species across two trophic levels. Results demonstrate how
multiple environmental stressors interact in a complex and non-additive way to
determine an ecosystem response (MPB biomass, nutrient concentration), and the
effects of altered biodiversity were underpinned by strong species effects. Temporal
variation of stressors had a strong effect on ecosystem response. In marine coastal
ecosystems, environmental changes through ocean acidification will have economic
and social repercussions, directly impacting the human services and livelihoods that
these systems provide. As such, future research should be focused on identifying and
mitigating the inevitable multiple effects that future global change may have on
coastal ecosystems.
2011-01-01T00:00:00ZHicks, NatalieCoastal ecosystems, including estuaries, provide a range of services to humans,
mediated by the species within these ecosystems. Microphytobenthos (MPB) play a
vital role in many key processes within estuarine ecosystems, and provide a food
source for higher trophic levels. Anthropogenic activity is already causing changes to
ecosystems, through pollution, overexploitation and, more recently, climate change.
Increasing temperature and carbon dioxide levels, and altered biodiversity, are likely
to affect species, and their interactions, within these ecosystems. Much ecological
research has focused on the effects of a single stressor on specific species or
ecosystems, with relatively little work examining the effects of multiple stressors.
The research in this thesis investigates the effects of altered environmental variables
(light, tidal regime, temperature and carbon dioxide) and different macrofaunal
diversity on primary production (MPB biomass) through a series of manipulative lab-based mesocosm experiments. This work also examines the temporal variability of
environmental stressors on species across two trophic levels. Results demonstrate how
multiple environmental stressors interact in a complex and non-additive way to
determine an ecosystem response (MPB biomass, nutrient concentration), and the
effects of altered biodiversity were underpinned by strong species effects. Temporal
variation of stressors had a strong effect on ecosystem response. In marine coastal
ecosystems, environmental changes through ocean acidification will have economic
and social repercussions, directly impacting the human services and livelihoods that
these systems provide. As such, future research should be focused on identifying and
mitigating the inevitable multiple effects that future global change may have on
coastal ecosystems.The genetic basis of flesh quality traits in farmed Atlantic salmon
https://hdl.handle.net/10023/3107
The aim was to develop new methods for measuring texture of Atlantic salmon (Salmo salar L.) fillets and investigate the genetic basis of flesh quality traits.
Firstly, a new tensile strength method was developed to quantify the force required to tear a standardized block of salmon muscle with the aim of identifying those samples more prone to factory downgrading as a result of gaping. The repeatability, sensitivity and predictability of the new technique was evaluated against other common instrumental texture measurement methods. Data from the new method were shown to have the strongest correlations with gaping severity r=-0.514, P<0.001) and the highest level of repeatability of data when analysing cold-smoked samples. The Warner Bratzler shear method gave the most repeatable data from fresh samples and had the highest correlations between fresh and smoked product from the same fish (r=0.811, P<0.001). It is therefore recommended that the new method be adopted for measuring gaping potential and the Warner Bratzler method become the standard for firmness assessment.
Genes associated with post mortem softening in mammals were characterised in Atlantic salmon. A previously unknown ancient paralogue of calpastatin (here named CAST2) was identified. Evidence was provided for the existence of highly homologous recent paralogues of CAST2 and CTSD1. Evidence for the ancestral history of these paralogues was provided by phylogenetic analysis. Recent gene duplicates of 6 further genes were identified. In all cases, homology between recent paralogues was greater than 94%. Analysis of synonymous vs non-synonymous nucleotide substitution between the observed paralogue pairs shows a significant purifying selection in most cases. The CTSD1 gene shows significant purifying selection in a pairwise analysis between 12 teleost species (all cases P<0.0001) but a similar analysis of CTSD2 revealed no significant occurrence of purifying selection. The present study provides further support for the idea of asymmetrical selective pressure on paralogues.
Genetic markers were developed that can distinguish individuals with above average fillet yield and texture. A database of firmness, tensile strength and fillet yield was made from 254 individuals from 5 batches of farmed salmon and these fish were genotyped at 7 novel SNP loci. Individuals with the combined favourable genotype at CAPN1a and MYOD1b were associated with an average increase in fillet yield of 2.7% above batch average. A combined genotype of CAPN1a, MYOD1b and MYF5 was significantly associated with an average increase in tensile strength of 9.8% above batch average (P=0.015). In both cases individuals with the combined favourable genotype occurred with a frequency of c. 6% across all batches. The favourable genotypes had no unfavourable effects on other traits.
Highly polymorphic microsatellite loci were used to perform tests of assignment, which revealed an overall correct assignment rate of 92.7% to batch of origin and a minimum reference sample number of 25 was empirically determined. A phylogenetic analysis supported the results of the assignment tests. Given that 7 microsatellites is a relatively small number for a study of this nature, these results suggest that reliable assignment of unknown fish to the true batch of origin is potentially rapid and cost effective.
Overall, the thesis presents molecular markers for broodstock selection, new genes of relevance to flesh quality, a new method of texture analysis and a proposal for an escapee traceability project.
2011-11-30T00:00:00ZAshton, Thomas JamesThe aim was to develop new methods for measuring texture of Atlantic salmon (Salmo salar L.) fillets and investigate the genetic basis of flesh quality traits.
Firstly, a new tensile strength method was developed to quantify the force required to tear a standardized block of salmon muscle with the aim of identifying those samples more prone to factory downgrading as a result of gaping. The repeatability, sensitivity and predictability of the new technique was evaluated against other common instrumental texture measurement methods. Data from the new method were shown to have the strongest correlations with gaping severity r=-0.514, P<0.001) and the highest level of repeatability of data when analysing cold-smoked samples. The Warner Bratzler shear method gave the most repeatable data from fresh samples and had the highest correlations between fresh and smoked product from the same fish (r=0.811, P<0.001). It is therefore recommended that the new method be adopted for measuring gaping potential and the Warner Bratzler method become the standard for firmness assessment.
Genes associated with post mortem softening in mammals were characterised in Atlantic salmon. A previously unknown ancient paralogue of calpastatin (here named CAST2) was identified. Evidence was provided for the existence of highly homologous recent paralogues of CAST2 and CTSD1. Evidence for the ancestral history of these paralogues was provided by phylogenetic analysis. Recent gene duplicates of 6 further genes were identified. In all cases, homology between recent paralogues was greater than 94%. Analysis of synonymous vs non-synonymous nucleotide substitution between the observed paralogue pairs shows a significant purifying selection in most cases. The CTSD1 gene shows significant purifying selection in a pairwise analysis between 12 teleost species (all cases P<0.0001) but a similar analysis of CTSD2 revealed no significant occurrence of purifying selection. The present study provides further support for the idea of asymmetrical selective pressure on paralogues.
Genetic markers were developed that can distinguish individuals with above average fillet yield and texture. A database of firmness, tensile strength and fillet yield was made from 254 individuals from 5 batches of farmed salmon and these fish were genotyped at 7 novel SNP loci. Individuals with the combined favourable genotype at CAPN1a and MYOD1b were associated with an average increase in fillet yield of 2.7% above batch average. A combined genotype of CAPN1a, MYOD1b and MYF5 was significantly associated with an average increase in tensile strength of 9.8% above batch average (P=0.015). In both cases individuals with the combined favourable genotype occurred with a frequency of c. 6% across all batches. The favourable genotypes had no unfavourable effects on other traits.
Highly polymorphic microsatellite loci were used to perform tests of assignment, which revealed an overall correct assignment rate of 92.7% to batch of origin and a minimum reference sample number of 25 was empirically determined. A phylogenetic analysis supported the results of the assignment tests. Given that 7 microsatellites is a relatively small number for a study of this nature, these results suggest that reliable assignment of unknown fish to the true batch of origin is potentially rapid and cost effective.
Overall, the thesis presents molecular markers for broodstock selection, new genes of relevance to flesh quality, a new method of texture analysis and a proposal for an escapee traceability project.Conservation ecology and phylogenetics of the Indus River dolphin (Platanista gangetica minor)
https://hdl.handle.net/10023/3036
The historical range of the Indus River dolphin has declined by 80% since the 19th
century and has been fragmented into 17 river sections by construction of irrigation
barrages. Dolphin sighting and interview surveys showed that river dolphins persist in
six river sections, have been extirpated from ten, and are of unknown status in the
remaining section. Logistic regression and survival modelling showed that low dry
season river discharge was the primary factor responsible for the Indus dolphins range decline.
Abundance of the three largest Indus dolphin subpopulations was estimated using tandem vessel-based direct counts, corrected for missed animals using conditional likelihood
capture-recapture models. The entire subspecies was estimated to number between 1550-1750 in 2006. Dolphin encounter rates within the Guddu-Sukkur subpopulation (10.35/km) were the highest reported for any river dolphin and direct counts suggest that this subpopulation may have been increasing in abundance since the 1970s when hunting was banned.
The dry season habitat selection of Indus dolphins was explored using Generalised
Linear Models of dolphin distribution and abundance in relation to river geomorphology,
and channel geometry in cross-section. Channel cross-sectional area was shown to be
the most important factor determining dolphin presence. Indus dolphins avoided
channels with small cross-sectional area <700m2, presumably due to the risk of
entrapment and reduced foraging opportunities.
The phylogenetics of Indus and Ganges River dolphins was explored using Mitochondrial control region sequences. Genetic diversity was low, and all 20 Indus River dolphin samples were identical. There were no haplotypes shared by Indus and Ganges River dolphins, phylogenetic trees demonstrated reciprocal monophyletic separation and Bayesian modelling suggested that the two dolphin populations diverged approximately 0.66 million years ago.
Declining river flows threaten Indus dolphins especially at the upstream end of their range, and it is important to determine how much water is required to sustain a dolphin population through the dry season. Fisheries interactions are an increasing problem that will be best addressed through localised, community-based conservation activities.
2012-06-20T00:00:00ZBraulik, Gillian T.The historical range of the Indus River dolphin has declined by 80% since the 19th
century and has been fragmented into 17 river sections by construction of irrigation
barrages. Dolphin sighting and interview surveys showed that river dolphins persist in
six river sections, have been extirpated from ten, and are of unknown status in the
remaining section. Logistic regression and survival modelling showed that low dry
season river discharge was the primary factor responsible for the Indus dolphins range decline.
Abundance of the three largest Indus dolphin subpopulations was estimated using tandem vessel-based direct counts, corrected for missed animals using conditional likelihood
capture-recapture models. The entire subspecies was estimated to number between 1550-1750 in 2006. Dolphin encounter rates within the Guddu-Sukkur subpopulation (10.35/km) were the highest reported for any river dolphin and direct counts suggest that this subpopulation may have been increasing in abundance since the 1970s when hunting was banned.
The dry season habitat selection of Indus dolphins was explored using Generalised
Linear Models of dolphin distribution and abundance in relation to river geomorphology,
and channel geometry in cross-section. Channel cross-sectional area was shown to be
the most important factor determining dolphin presence. Indus dolphins avoided
channels with small cross-sectional area <700m2, presumably due to the risk of
entrapment and reduced foraging opportunities.
The phylogenetics of Indus and Ganges River dolphins was explored using Mitochondrial control region sequences. Genetic diversity was low, and all 20 Indus River dolphin samples were identical. There were no haplotypes shared by Indus and Ganges River dolphins, phylogenetic trees demonstrated reciprocal monophyletic separation and Bayesian modelling suggested that the two dolphin populations diverged approximately 0.66 million years ago.
Declining river flows threaten Indus dolphins especially at the upstream end of their range, and it is important to determine how much water is required to sustain a dolphin population through the dry season. Fisheries interactions are an increasing problem that will be best addressed through localised, community-based conservation activities.Evolution of signal multiplexing by 14-3-3-binding 2R-ohnologue protein families in the vertebrates
https://hdl.handle.net/10023/3022
14-3-3 proteins regulate cellular responses to stimuli by docking onto pairs of phosphorylated residues on target proteins. The present study shows that the human 14-3-3-binding phosphoproteome is highly enriched in 2R-ohnologues, which are proteins in families of two to four members that were generated by two rounds of whole genome duplication at the origin of the vertebrates. We identify 2R-ohnologue families whose members share a ‘lynchpin’, defined as a 14-3-3-binding phosphosite that is conserved across members of a given family, and aligns with a Ser/Thr residue in pro-orthologues from the invertebrate chordates. For example, the human receptor expression enhancing protein (REEP) 1–4 family has the commonest type of lynchpin motif in current datasets, with a phosphorylatable serine in the –2 position relative to the 14-3-3-binding phosphosite. In contrast, the second 14-3-3-binding sites of REEPs 1–4 differ and are phosphorylated by different kinases, and hence the REEPs display different affinities for 14-3-3 dimers. We suggest a conceptual model for intracellular regulation involving protein families whose evolution into signal multiplexing systems was facilitated by 14-3-3 dimer binding to lynchpins, which gave freedom for other regulatory sites to evolve. While increased signalling complexity was needed for vertebrate life, these systems also generate vulnerability to genetic disorders.
This work was supported by the UK Medical Research Council via a Developmental Pathway Funding Scheme award and a Research Councils UK fellowship in marine biology.
2012-07-01T00:00:00ZTinti, MicheleJohnson, CatherineToth, RachelFerrier, David Ellard KeithMacKintosh, Carol14-3-3 proteins regulate cellular responses to stimuli by docking onto pairs of phosphorylated residues on target proteins. The present study shows that the human 14-3-3-binding phosphoproteome is highly enriched in 2R-ohnologues, which are proteins in families of two to four members that were generated by two rounds of whole genome duplication at the origin of the vertebrates. We identify 2R-ohnologue families whose members share a ‘lynchpin’, defined as a 14-3-3-binding phosphosite that is conserved across members of a given family, and aligns with a Ser/Thr residue in pro-orthologues from the invertebrate chordates. For example, the human receptor expression enhancing protein (REEP) 1–4 family has the commonest type of lynchpin motif in current datasets, with a phosphorylatable serine in the –2 position relative to the 14-3-3-binding phosphosite. In contrast, the second 14-3-3-binding sites of REEPs 1–4 differ and are phosphorylated by different kinases, and hence the REEPs display different affinities for 14-3-3 dimers. We suggest a conceptual model for intracellular regulation involving protein families whose evolution into signal multiplexing systems was facilitated by 14-3-3 dimer binding to lynchpins, which gave freedom for other regulatory sites to evolve. While increased signalling complexity was needed for vertebrate life, these systems also generate vulnerability to genetic disorders.The use of active sonar to study cetaceans
https://hdl.handle.net/10023/2580
Cetacean species face serious challenges worldwide due to the increasing noise pollution brought to their environment by human activities such as seismic exploration. Regulation of these activities is vaguely defined and uncoordinated. Visual observations and passive listening devices, aimed at preventing conflicts between human wealth and cetaceans’ health have some fundamental limitations and may consequently fail their mitigation purposes. Active sonar technology could be the optimal solution to implement mitigation of such human activities. In my thesis, the proper sonar unit was used to test the feasibility to detect cetaceans in situ. Omnidirectional sonars could be the optimal solution to monitor the presence of cetaceans in the proximity of potential danger areas. To use this class of sonar in a quantitative manner, the first step was to develop a calibration method. This thesis links in situ measurements of target strength (TS) with variation trends linked to the behavior, morphology and physiology of cetacean. The butterfly effect of a cetacean’s body was described for a fin whale insonified from different angles. A relationship between whale respiration and TS energy peaks was tested through a simple prediction model which seems very promising for further implementation. The effect of lung compression on cetacean TS due to increasing depth was tested through a basic mathematical model. The model fit the in situ TS measurements. TS measurements at depth of a humpback whale, when post-processed, correspond to TS measurements recorded at the surface. Sonar technology is clearly capable of detecting whale foot prints around an operating vessel. Sonar frequency response shows that frequencies between 18 and 38 kHz should be employed. This work has established a baseline and raised new questions so that active sonar can be developed and employed in the best interest for the whales involved in potentially harmful conflicts with man.
2012-06-01T00:00:00ZBernasconi, MatteoCetacean species face serious challenges worldwide due to the increasing noise pollution brought to their environment by human activities such as seismic exploration. Regulation of these activities is vaguely defined and uncoordinated. Visual observations and passive listening devices, aimed at preventing conflicts between human wealth and cetaceans’ health have some fundamental limitations and may consequently fail their mitigation purposes. Active sonar technology could be the optimal solution to implement mitigation of such human activities. In my thesis, the proper sonar unit was used to test the feasibility to detect cetaceans in situ. Omnidirectional sonars could be the optimal solution to monitor the presence of cetaceans in the proximity of potential danger areas. To use this class of sonar in a quantitative manner, the first step was to develop a calibration method. This thesis links in situ measurements of target strength (TS) with variation trends linked to the behavior, morphology and physiology of cetacean. The butterfly effect of a cetacean’s body was described for a fin whale insonified from different angles. A relationship between whale respiration and TS energy peaks was tested through a simple prediction model which seems very promising for further implementation. The effect of lung compression on cetacean TS due to increasing depth was tested through a basic mathematical model. The model fit the in situ TS measurements. TS measurements at depth of a humpback whale, when post-processed, correspond to TS measurements recorded at the surface. Sonar technology is clearly capable of detecting whale foot prints around an operating vessel. Sonar frequency response shows that frequencies between 18 and 38 kHz should be employed. This work has established a baseline and raised new questions so that active sonar can be developed and employed in the best interest for the whales involved in potentially harmful conflicts with man.A first survey of the global population size and distribution of the Scottish Crossbill Loxia scotica
https://hdl.handle.net/10023/1957
A survey of Scottish Crossbills Loxia scotica was carried out in 3,506 km2 of conifer woodland in northern Scotland during January to April 2008 to provide the first estimate of the global population size for this endemic bird. Population estimates were also made for Common Crossbills L. curvirostra and Parrot Crossbills L. pytyopsittacus within this range. Crossbills were lured to systematically selected survey points for counting, sexing and recording their calls for later call-type (species) identification from sonograms. Crossbills were located at 451 of the 852 survey points, and adequate tape-recordings made at 387 of these. The Scottish Crossbill had a disjunct distribution, occurring largely within the eastern part of the study area, but also in the northwest. Common Crossbills had a mainly westerly distribution. The population size of postjuvenile Scottish Crossbills was estimated as 13,600 (95%C.I. 8,130–22,700), which will approximate to 6,800 (4,065–11,350) pairs. Common Crossbills were more abundant within this range (27,100, 95% C.I. 14,700–38,400) and Parrot Crossbills rare (about 100). The sex ratio was not significantly different from parity for Scottish Crossbills. The modal number at survey points was two but numbers were larger in January than later in the survey. The numbers and distribution of all crossbill species are likely to vary between years, depending upon the size of the cone crops of the different conifers: all were coning in 2008. Common Crossbill and Parrot Crossbill numbers will also be affected by irruptions from continental Europe. A monitoring scheme is required to detect any population trend, and further work on their habitat requirement (e.g. conifer selection at different seasons) is needed to inform habitat management of native and planted conifer forests to ensure a secure future for this endemic bird.
"The survey was part-financed by Scottish Natural Heritage"
2011-06-01T00:00:00ZSummers, Ron WBuckland, Stephen TerrenceA survey of Scottish Crossbills Loxia scotica was carried out in 3,506 km2 of conifer woodland in northern Scotland during January to April 2008 to provide the first estimate of the global population size for this endemic bird. Population estimates were also made for Common Crossbills L. curvirostra and Parrot Crossbills L. pytyopsittacus within this range. Crossbills were lured to systematically selected survey points for counting, sexing and recording their calls for later call-type (species) identification from sonograms. Crossbills were located at 451 of the 852 survey points, and adequate tape-recordings made at 387 of these. The Scottish Crossbill had a disjunct distribution, occurring largely within the eastern part of the study area, but also in the northwest. Common Crossbills had a mainly westerly distribution. The population size of postjuvenile Scottish Crossbills was estimated as 13,600 (95%C.I. 8,130–22,700), which will approximate to 6,800 (4,065–11,350) pairs. Common Crossbills were more abundant within this range (27,100, 95% C.I. 14,700–38,400) and Parrot Crossbills rare (about 100). The sex ratio was not significantly different from parity for Scottish Crossbills. The modal number at survey points was two but numbers were larger in January than later in the survey. The numbers and distribution of all crossbill species are likely to vary between years, depending upon the size of the cone crops of the different conifers: all were coning in 2008. Common Crossbill and Parrot Crossbill numbers will also be affected by irruptions from continental Europe. A monitoring scheme is required to detect any population trend, and further work on their habitat requirement (e.g. conifer selection at different seasons) is needed to inform habitat management of native and planted conifer forests to ensure a secure future for this endemic bird.Variation in habitat preference and distribution of harbour porpoises west of Scotland
https://hdl.handle.net/10023/1701
The waters off the west coast of Scotland have one of the highest densities of harbour porpoise
(Phocoena phocoena) in Europe. Harbour porpoise are listed under Annex II of the EU Habitats
Directive, requiring the designation of Special Areas of Conservation (SACs) for the species’
protection and conservation.
The main aim of this thesis is to identify habitat preferences for harbour porpoise, and key
regions that embody these preferences, which could therefore be suitable as SACs; and to
determine how harbour porpoise use these regions over time and space. Designed visual and
acoustic line-transect surveys were conducted between 2003 and 2008. Generalised Estimating
Equations (GEEs) were used to determine relationships between the relative density of harbour
porpoise and temporally and spatially variable oceanographic covariates.
Predictive models showed that depth, slope, distance to land and spring tidal range were all
important in explaining porpoise distribution. There were also significant temporal variations in
habitat use. However, whilst some variation was observed among years and months, consistent
preferences for water depths between 50 and 150 m and highly sloped regions were observed
across the temporal models. Predicted surfaces revealed a consistent inshore distribution for the
species throughout the west coast of Scotland. Regional models revealed similar habitat
preferences to the full-extent models, and indicated that the Small Isles and Sound of Jura were
the most consistently important regions for harbour porpoise, and that these regions could be
suitable as SACs.
The impacts of seal scarers on distribution and habitat use were also investigated, and there
were indications that these devices have the potential to displace harbour porpoise.
These results should be considered in the assessment of sites for SAC designation, and in
implementing appropriate conservation measures for harbour porpoise.
2010-11-30T00:00:00ZBooth, Cormac GThe waters off the west coast of Scotland have one of the highest densities of harbour porpoise
(Phocoena phocoena) in Europe. Harbour porpoise are listed under Annex II of the EU Habitats
Directive, requiring the designation of Special Areas of Conservation (SACs) for the species’
protection and conservation.
The main aim of this thesis is to identify habitat preferences for harbour porpoise, and key
regions that embody these preferences, which could therefore be suitable as SACs; and to
determine how harbour porpoise use these regions over time and space. Designed visual and
acoustic line-transect surveys were conducted between 2003 and 2008. Generalised Estimating
Equations (GEEs) were used to determine relationships between the relative density of harbour
porpoise and temporally and spatially variable oceanographic covariates.
Predictive models showed that depth, slope, distance to land and spring tidal range were all
important in explaining porpoise distribution. There were also significant temporal variations in
habitat use. However, whilst some variation was observed among years and months, consistent
preferences for water depths between 50 and 150 m and highly sloped regions were observed
across the temporal models. Predicted surfaces revealed a consistent inshore distribution for the
species throughout the west coast of Scotland. Regional models revealed similar habitat
preferences to the full-extent models, and indicated that the Small Isles and Sound of Jura were
the most consistently important regions for harbour porpoise, and that these regions could be
suitable as SACs.
The impacts of seal scarers on distribution and habitat use were also investigated, and there
were indications that these devices have the potential to displace harbour porpoise.
These results should be considered in the assessment of sites for SAC designation, and in
implementing appropriate conservation measures for harbour porpoise.Assessing the effectiveness of conservation measures : resolving the "wicked" problem of the Steller sea lion
https://hdl.handle.net/10023/1034
“Wicked” problems are those that are complex and that change when solutions are applied. Many conflicts in conservation fall in to this category. The study approached the problem of how to constrain the apparent wickedness of a problem in the conservation management of a species by using simple empirical indicators to carry out iterative assessment of the risk to a population and to document how this risk evolves in relation to the addition of new data and the implementation of management actions. Effects of high levels of uncertainty within data and also concerning population structure were examined through stochastic simulation and by exploration of scenarios. Historical trends in the example used, the Steller sea lion, showed rapid declines in abundance in some regions during the 1980s. The current total population is 130,000-150,000 Steller sea lions through Alaska and British Columbia and this number has been stable since about 1990 in spite of regional differences in population dynamics. Regional differences in the sequence of changes in the number of pups and non-pups, suggested that an internal re-distribution of juveniles could have happened between 1980 and 1990. Current productivity also appears close to the long term mean. Stochastic population projection using various scenarios showed that, based upon this history, the risk of extinction for the population has declined and is below reasonable thresholds for considering the population to be endangered.
2010-07-01T00:00:00ZBoyd, Ian Lamont“Wicked” problems are those that are complex and that change when solutions are applied. Many conflicts in conservation fall in to this category. The study approached the problem of how to constrain the apparent wickedness of a problem in the conservation management of a species by using simple empirical indicators to carry out iterative assessment of the risk to a population and to document how this risk evolves in relation to the addition of new data and the implementation of management actions. Effects of high levels of uncertainty within data and also concerning population structure were examined through stochastic simulation and by exploration of scenarios. Historical trends in the example used, the Steller sea lion, showed rapid declines in abundance in some regions during the 1980s. The current total population is 130,000-150,000 Steller sea lions through Alaska and British Columbia and this number has been stable since about 1990 in spite of regional differences in population dynamics. Regional differences in the sequence of changes in the number of pups and non-pups, suggested that an internal re-distribution of juveniles could have happened between 1980 and 1990. Current productivity also appears close to the long term mean. Stochastic population projection using various scenarios showed that, based upon this history, the risk of extinction for the population has declined and is below reasonable thresholds for considering the population to be endangered.Cellular and molecular studies of postembryonic muscle fibre recruitment in zebrafish (Danio rerio L.)
https://hdl.handle.net/10023/901
Cellular and molecular mechanisms of postembryonic muscle fibre recruitment were investigated in zebrafish (Danio rerio L.), a standard animal model for developmental and genetic studies.
Distinct cellular mechanisms of postembryonic muscle fibre recruitment in fast and slow myotomal muscles were found. In slow muscle, three overlapping waves of stratified hyperplasia (SH) from distinct germinal zones sequentially contributed to a slow and steady increase in fibre number (FN) through the life span. In fast muscle, SH only contributed to an initial increase of FN in early larvae. Strikingly, mosaic hyperplasia (MH) appeared in late larvae and early juveniles and remained active until early adult stages, accounting for >70% of the final fibre number (FFN).
The molecular regulation of postembryonic muscle fibre recruitment was then studied by characterising myospryn and cee, two strong candidate genes previously identified from a large scale screen for genes differentially expressed during the transition from hyperplastic to hypertrophic muscle phenotypes. Zebrafish myospryn contained very similar functional domains to its mammalian orthologues, which function to bind to other proteins known to regulate muscle dystrophy. Zebrafish myospryn also shared a highly conserved syntenic genomic neighbourhood with other vertebrate orthologues. As in mammals, zebrafish myospryn were specifically expressed in striated muscles. Zebrafish cee was a single-copy gene, highly conserved among metazoans, ubiquitously expressed across tissues, and did not form part of any wider gene family. Its protein encompassed a single conserved domain (DUF410) of unknown function although knock-down of cee in C. elegans and yeast have suggested a role in regulating growth patterns. Both myospyrn and cee transcripts were up-regulated concomitant with the cessation of postembryonic muscle fibre recruitment in zebrafish, indicating a potential role in regulating muscle growth. Furthermore, a genome-wide screen of genes involved in the regulation of postembryonic muscle fibre recruitment was performed using microarray. 85 genes were found to be consistently and differentially expressed between growth stages where muscle hyperplasia was active or inactive, including genes associated with muscle contraction, metabolism, and immunity. Further bioinformatic annotation indicated these genes comprised a complex transcriptional network with molecular functions, including catalytic activity and protein binding as well as pathways associated with metabolism, tight junctions, and human diseases.
Finally, developmental plasticity of postembryonic muscle fibre recruitment to embryonic temperature was characterised. It involved transient effects including the relative timing and contribution of SH and MH, plus the rate and duration of fibre production, as well as a persistent alteration to FFN. Further investigation of FFN of fish over a broader range of embryonic temperature treatments (22, 26, 28, 31, 35°C) indicated that 26°C produced the highest FFN that was approximately 17% greater than at other temperatures. This finding implies the existence of an optimal embryonic temperature range for maximising FFN across a reaction norm. Additionally, a small but significant effect of parental temperature on FFN (up to 6% greater at 24 and 26°C than at 31°C) was evident, suggesting some parental mechanisms can affect muscle fibre recruitment patterns of progeny.
This work provides a comprehensive investigation of mechanisms underlying postembryonic muscle fibre recruitment and demonstrates the power of zebrafish as an ideal teleost model for addressing mechanistic and practical aspects of postembryonic muscle recruitment, especially the presence of all major phases of muscle fibre production in larger commercially important teleost species.
2010-06-23T00:00:00ZLee, Hung-TaiCellular and molecular mechanisms of postembryonic muscle fibre recruitment were investigated in zebrafish (Danio rerio L.), a standard animal model for developmental and genetic studies.
Distinct cellular mechanisms of postembryonic muscle fibre recruitment in fast and slow myotomal muscles were found. In slow muscle, three overlapping waves of stratified hyperplasia (SH) from distinct germinal zones sequentially contributed to a slow and steady increase in fibre number (FN) through the life span. In fast muscle, SH only contributed to an initial increase of FN in early larvae. Strikingly, mosaic hyperplasia (MH) appeared in late larvae and early juveniles and remained active until early adult stages, accounting for >70% of the final fibre number (FFN).
The molecular regulation of postembryonic muscle fibre recruitment was then studied by characterising myospryn and cee, two strong candidate genes previously identified from a large scale screen for genes differentially expressed during the transition from hyperplastic to hypertrophic muscle phenotypes. Zebrafish myospryn contained very similar functional domains to its mammalian orthologues, which function to bind to other proteins known to regulate muscle dystrophy. Zebrafish myospryn also shared a highly conserved syntenic genomic neighbourhood with other vertebrate orthologues. As in mammals, zebrafish myospryn were specifically expressed in striated muscles. Zebrafish cee was a single-copy gene, highly conserved among metazoans, ubiquitously expressed across tissues, and did not form part of any wider gene family. Its protein encompassed a single conserved domain (DUF410) of unknown function although knock-down of cee in C. elegans and yeast have suggested a role in regulating growth patterns. Both myospyrn and cee transcripts were up-regulated concomitant with the cessation of postembryonic muscle fibre recruitment in zebrafish, indicating a potential role in regulating muscle growth. Furthermore, a genome-wide screen of genes involved in the regulation of postembryonic muscle fibre recruitment was performed using microarray. 85 genes were found to be consistently and differentially expressed between growth stages where muscle hyperplasia was active or inactive, including genes associated with muscle contraction, metabolism, and immunity. Further bioinformatic annotation indicated these genes comprised a complex transcriptional network with molecular functions, including catalytic activity and protein binding as well as pathways associated with metabolism, tight junctions, and human diseases.
Finally, developmental plasticity of postembryonic muscle fibre recruitment to embryonic temperature was characterised. It involved transient effects including the relative timing and contribution of SH and MH, plus the rate and duration of fibre production, as well as a persistent alteration to FFN. Further investigation of FFN of fish over a broader range of embryonic temperature treatments (22, 26, 28, 31, 35°C) indicated that 26°C produced the highest FFN that was approximately 17% greater than at other temperatures. This finding implies the existence of an optimal embryonic temperature range for maximising FFN across a reaction norm. Additionally, a small but significant effect of parental temperature on FFN (up to 6% greater at 24 and 26°C than at 31°C) was evident, suggesting some parental mechanisms can affect muscle fibre recruitment patterns of progeny.
This work provides a comprehensive investigation of mechanisms underlying postembryonic muscle fibre recruitment and demonstrates the power of zebrafish as an ideal teleost model for addressing mechanistic and practical aspects of postembryonic muscle recruitment, especially the presence of all major phases of muscle fibre production in larger commercially important teleost species.