Scottish Oceans Institute Theseshttps://hdl.handle.net/10023/7932024-03-29T12:13:51Z2024-03-29T12:13:51ZQuantifying costs and rewards in optimal foraging models of the marine environment. Using bulk feeding mysticete whales as an exampleSwift, René Jameshttps://hdl.handle.net/10023/291972024-02-09T11:30:19Z2021-06-30T00:00:00ZAnimals 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 diversityEichenberger, Francahttps://hdl.handle.net/10023/290702024-02-15T03:07:58Z2024-06-12T00:00:00ZHow 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 communicationCasoli, Marcohttps://hdl.handle.net/10023/284292023-09-21T10:43:26Z2023-11-28T00:00:00ZBottlenose 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 impactsBortolotto, Guilherme Augustohttps://hdl.handle.net/10023/189322021-04-12T15:55:01Z2019-12-03T00:00:00ZThe 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 blubberKershaw, Joannahttps://hdl.handle.net/10023/179772021-03-19T12:05:21Z2019-06-26T00:00:00ZDespite 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 redactedHope, Julie Annehttps://hdl.handle.net/10023/171492019-05-28T08:57:11Z2016-06-22T00:00:00Z2016-06-22T00:00:00ZHope, Julie AnneThe impact of multiple stressors on coastal biodiversity and associated ecosystem servicesWatson, Stephen C. L.https://hdl.handle.net/10023/168172019-03-29T10:39:56Z2017-06-21T00:00:00ZMarine 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.Evolution of muscle regulatory genes in chordatesColl-Lladó, Clarahttps://hdl.handle.net/10023/161362018-12-12T11:18:27Z2016-11-30T00:00:00Z2016-11-30T00:00:00ZColl-Lladó, ClaraThe development of molecular tools and resources for selective breeding in aquacultureHolman, Luke Earlhttps://hdl.handle.net/10023/118432019-03-29T10:35:02Z2017-06-21T00:00:00ZHuman 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 clusterGarstang, Myles Granthttps://hdl.handle.net/10023/117882019-07-01T10:16:46Z2016-06-22T00:00:00ZThe 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.Comparative estuarine dynamics : trophic linkages and ecosystem functionKenworthy, Josephhttps://hdl.handle.net/10023/82402023-03-20T14:51:10Z2016-02-01T00:00:00ZEstuarine 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.Abundance and distribution of delphinids in the Red Sea (Egypt)Costa, Marinahttps://hdl.handle.net/10023/68022019-07-01T10:17:53Z2015-06-24T00:00:00ZKnowledge 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 salmonHowe, Alexandra Janehttps://hdl.handle.net/10023/67282019-07-01T10:20:09Z2015-06-24T00:00:00ZConsidering 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.The effects of physical, biological and anthropogenic noise on the occurrence of dolphins in the Pacific region of the Panama CanalCampbell Castillo, Inezhttps://hdl.handle.net/10023/44842019-07-01T10:15:19Z2014-06-01T00:00:00ZThe 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.Ecology of the Guiana dolphin (Sotalia guianensis) in the Southern area of the Gulf of Morrosquillo, Colombia : implications for conservationDussán-Duque, Beatriz Saloméhttps://hdl.handle.net/10023/41532019-03-29T10:41:12Z2013-11-29T00:00:00ZSotalia 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.Biodiversity assessment of freshwater fishes : Thailand as a case studyKhachonpisitsak, Salineehttps://hdl.handle.net/10023/35592017-10-27T16:04:40Z2012-11-29T00:00:00ZA 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 arraysHarris, Danielle Veronicahttps://hdl.handle.net/10023/34632019-07-01T10:12:25Z2012-06-20T00:00:00ZPassive 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)Casalini, Marahttps://hdl.handle.net/10023/34472019-03-29T10:38:49Z2013-06-26T00:00:00ZThe 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.The influence of mid-ocean ridges on euphausiid and pelagic ecologyLetessier, Tom Bechhttps://hdl.handle.net/10023/32292019-03-29T10:41:08Z2012-06-19T00:00:00ZChapters 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 proxiesHanson, Nora Nellhttps://hdl.handle.net/10023/32212019-03-29T10:33:58Z2012-11-30T00:00:00ZMonitoring 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 ecosystemsMarshall, Laurahttps://hdl.handle.net/10023/31722019-07-01T10:08:55Z2012-06-20T00:00:00ZOver 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 ecosystemsHicks, Nataliehttps://hdl.handle.net/10023/31432019-04-01T11:12:31Z2011-01-01T00:00:00ZCoastal 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 salmonAshton, Thomas Jameshttps://hdl.handle.net/10023/31072016-08-09T09:09:45Z2011-11-30T00:00:00ZThe 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)Braulik, Gillian T.https://hdl.handle.net/10023/30362019-07-01T10:16:59Z2012-06-20T00:00:00ZThe 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.The use of active sonar to study cetaceansBernasconi, Matteohttps://hdl.handle.net/10023/25802019-07-01T10:18:44Z2012-06-01T00:00:00ZCetacean 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.Variation in habitat preference and distribution of harbour porpoises west of ScotlandBooth, Cormac Ghttps://hdl.handle.net/10023/17012019-07-01T10:11:34Z2010-11-30T00:00:00ZThe 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.Cellular and molecular studies of postembryonic muscle fibre recruitment in zebrafish (Danio rerio L.)Lee, Hung-Taihttps://hdl.handle.net/10023/9012019-03-29T10:28:31Z2010-06-23T00:00:00ZCellular 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.