DSpace Collection:

Estimating whale abundance using sparse hydrophone arrays

Harris, Danielle V. — Wed, 20 Jun 2012 00:00:00 GMT

Abstract: Passive acoustic monitoring has been used to investigate many aspects of marine mammal ecology, although methods to estimate absolute abundance and density using acoustic data have only been developed in recent years. The instrument configuration in an acoustic survey determines which abundance estimation methods can be used. Sparsely distributed arrays of instruments are useful because wide geographic areas can be covered. However, instrument spacing in sparse arrays is such that the same vocalisation will not be detected on multiple instruments, excluding the use of some abundance estimation methods. The aim of this thesis was to explore cetacean abundance and density estimation using novel sparse array datasets, applying existing methods where possible, or developing new approaches. The wealth of data collected by sparse arrays was demonstrated by analysing a 10-year dataset collected by the U.S. Navy’s Sound Surveillance System in the north-east Atlantic. Spatial and temporal patterns of blue (Balaenoptera musculus) and fin whale (Balaenoptera physalus) vocal activity were investigated using generalised additive models. Distance sampling-based methods were applied to fin whale calls recorded by an array of Ocean Bottom Seismometers in the north-east Atlantic. Estimated call density was 993 calls/1000 km².hr⁻¹ (CV: 0.39). Animal density could not be estimated because the call rate was unknown. Further development of the call localisation method is required so the current density estimate may be biased. Furthermore, analysing a single day of data resulted in a high variance estimate. Finally, a new simulation-based method developed to estimate density from single hydrophones was applied to blue whale calls recorded in the northern Indian Ocean. Estimated call density was 3 calls/1000 km².hr⁻¹ (CV: 0.17). Again, density of whales could not be estimated as the vocalisation rate was unknown. Lack of biological knowledge poses the greatest limitation to abundance and density estimation using acoustic data.

Male mating tactics in the rose bitterling (Rhodeus ocellatus) and European bitterling (Rhodeus amarus)

Casalini, Mara — Wed, 26 Jun 2013 00:00:00 GMT

Abstract: The aim of this study was to investigate the basis to male mating decisions in two related species of bitterling: Rhodeus ocellatus and R. amarus. Bitterling have a resource-based mating system; females lay eggs in the gills of live freshwater mussels and males fertilize the eggs by releasing sperm into the inhalant syphon of the mussel. Male bitterling perform courtship behaviour and aggressively defend mussels in a territory from which they exclude other males. Using laboratory and field experiments it was shown that male aggressive behaviour is inherited through additive maternal genes. Male aggression is also influenced by the number of conspecific males encountered in competition for a mussel, and by the degree of clustering of mussels. Limited availability of mussels results in stronger selection on traits males use in mating context: hence they are more aggressive, larger and more colourful. The differences in mating behaviours in different environments may indicate a conflict between male dominance and female choice, but have not led to reproductive isolation. Resource availability during ontogenesis and male density during embryogenesis, however, do not exert an effect on male aggressive behaviour. Red carotenoid-based nuptial coloration functions as an inter- and intra-sexual signal and undergoes rapid variation in response to changes in mating context. Male bitterling do not modulate their courtship and aggressive behaviour in response to variation in female size, and their choice of mussel species is influenced by, and consistent with, female oviposition choice.

The influence of mid-ocean ridges on euphausiid and pelagic ecology

Letessier, Tom Bech — Tue, 19 Jun 2012 00:00:00 GMT

Abstract: 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 midlatitudes 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- 800m) vertical distribution (e.g. Euphausiacea, Decapoda, Amphipoda, Thecosomata, Lophogastrida) on either side of the Subpolar Front of the Mid-Atlantic Ridge is described. Dietary relationships are explored, using stable isotope ratios and fatty acid trophic marker (FATM) composition. An increase in trophic level with size was observed. Individuals from southern stations were higher in dinoflagellate Fatty Acid Trophic Markers (FATM) (22:6(n-3)) and individuals from northern stations were higher in Calanus spp and storage FATMs (20:1(n-9) and 22:1(n-9)) reflecting primary production patterns in the two survey sectors. Observations on the geographical and vertical variability in trophodynamics are discussed. 7. New baseline information is presented on the biogeography, abundance, and vertical distribution of mesopelagic (200-1000 m), crustacean micronekton on- and offseamounts of the South-West Indian Ocean Ridge (26° to 42° S). Species richness and numerical abundance were typically higher near seamounts and lower over the abyssal plains, with several species being caught uniquely on seamounts. Observations suggest that the ‘oasis effect’ of seamounts conventionally associated with higher trophic levels is also applicable to pelagic micronektic crustaceans at lower trophic levels. Biophysical coupling of micronekton to seamounts may be an important factor controlling benthopelagic coupling in seamount food-webs. 8. Euphausiid and pelagic diversity is driven primarily by geographical variability in temperature, by longitudinal patterns in upwellings, and by variability in nutrient concentration. Mid-Ocean Ridges modify pelagic ecology, by raising the seafloor and by bringing in proximity true pelagic and bathypelagic predators associated with the seabed. The increase in specialized fauna and biomass associated with ridges and seamounts serves to deplete zooplankton in the near bottom layer (0-200 m) and affect systems in and above the benthic boundary layer (<200 m from the seafloor), and the benthopelagic faunal layer. Mid-Ocean Ridges may serve to structure pelagic faunal distribution, and increase the overall diversity of the world ocean. The influence of ridges in the ocean basin may be comparable to that of hedges in a farmland; whilst delimiting the extent of crops (or zooplankton assemblages), hedges serve as local hotspots of mammal and avian diversity.

Examining the response of top marine predators to ecological change using stable isotope proxies

Hanson, Nora N. — Fri, 30 Nov 2012 00:00:00 GMT

Abstract: Monitoring the response of upper trophic level animals to ecological change is important to understanding the state and stability of ecosystems. Marine predators integrate information over large geographical scales and are relatively long-lived; furthermore, many of these organisms are restricted to terrestrial or freshwater habitats at certain times during their life history and are accessible to researchers. This thesis investigated the response of marine predators to ecological change at a variety of spatial and temporal scales using stable isotope ratio methods with the aims of developing meaningful proxies, or indices, of variability in marine ecosystems. The first study explored the intrinsic (i.e. ontogenetic) and extrinsic (i.e. environmental) factors important to modulating variation in the stable isotope ratios of C and N in tooth dentin of male Antarctic fur seals (Arctocephalus gazella) in the Southern Ocean. In the second study, long-term records of variation in δ15N 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.

Impact of environmental change on primary production in model marine coastal ecosystems

Hicks, Natalie — Sat, 01 Jan 2011 00:00:00 GMT

Abstract: Coastal ecosystems, including estuaries, provide a range of services to humans, mediated by the species within these ecosystems. Microphytobenthos (MPB) play a vital role in many key processes within estuarine ecosystems, and provide a food source for higher trophic levels. Anthropogenic activity is already causing changes to ecosystems, through pollution, overexploitation and, more recently, climate change. Increasing temperature and carbon dioxide levels, and altered biodiversity, are likely to affect species, and their interactions, within these ecosystems. Much ecological research has focused on the effects of a single stressor on specific species or ecosystems, with relatively little work examining the effects of multiple stressors. The research in this thesis investigates the effects of altered environmental variables (light, tidal regime, temperature and carbon dioxide) and different macrofaunal diversity on primary production (MPB biomass) through a series of manipulative lab-based mesocosm experiments. This work also examines the temporal variability of environmental stressors on species across two trophic levels. Results demonstrate how multiple environmental stressors interact in a complex and non-additive way to determine an ecosystem response (MPB biomass, nutrient concentration), and the effects of altered biodiversity were underpinned by strong species effects. Temporal variation of stressors had a strong effect on ecosystem response. In marine coastal ecosystems, environmental changes through ocean acidification will have economic and social repercussions, directly impacting the human services and livelihoods that these systems provide. As such, future research should be focused on identifying and mitigating the inevitable multiple effects that future global change may have on coastal ecosystems.

The use of active sonar to study cetaceans

Bernasconi, Matteo — Fri, 01 Jun 2012 00:00:00 GMT

Abstract: Cetacean species face serious challenges worldwide due to the increasing noise pollution brought to their environment by human activities such as seismic exploration. Regulation of these activities is vaguely defined and uncoordinated. Visual observations and passive listening devices, aimed at preventing conflicts between human wealth and cetaceans’ health have some fundamental limitations and may consequently fail their mitigation purposes. Active sonar technology could be the optimal solution to implement mitigation of such human activities. In my thesis, the proper sonar unit was used to test the feasibility to detect cetaceans in situ. Omnidirectional sonars could be the optimal solution to monitor the presence of cetaceans in the proximity of potential danger areas. To use this class of sonar in a quantitative manner, the first step was to develop a calibration method. This thesis links in situ measurements of target strength (TS) with variation trends linked to the behavior, morphology and physiology of cetacean. The butterfly effect of a cetacean’s body was described for a fin whale insonified from different angles. A relationship between whale respiration and TS energy peaks was tested through a simple prediction model which seems very promising for further implementation. The effect of lung compression on cetacean TS due to increasing depth was tested through a basic mathematical model. The model fit the in situ TS measurements. TS measurements at depth of a humpback whale, when post-processed, correspond to TS measurements recorded at the surface. Sonar technology is clearly capable of detecting whale foot prints around an operating vessel. Sonar frequency response shows that frequencies between 18 and 38 kHz should be employed. This work has established a baseline and raised new questions so that active sonar can be developed and employed in the best interest for the whales involved in potentially harmful conflicts with man.

Variation in habitat preference and distribution of harbour porpoises west of Scotland

Booth, Cormac G — Tue, 30 Nov 2010 00:00:00 GMT

Abstract: The waters off the west coast of Scotland have one of the highest densities of harbour porpoise (Phocoena phocoena) in Europe. Harbour porpoise are listed under Annex II of the EU Habitats Directive, requiring the designation of Special Areas of Conservation (SACs) for the species’ protection and conservation. The main aim of this thesis is to identify habitat preferences for harbour porpoise, and key regions that embody these preferences, which could therefore be suitable as SACs; and to determine how harbour porpoise use these regions over time and space. Designed visual and acoustic line-transect surveys were conducted between 2003 and 2008. Generalised Estimating Equations (GEEs) were used to determine relationships between the relative density of harbour porpoise and temporally and spatially variable oceanographic covariates. Predictive models showed that depth, slope, distance to land and spring tidal range were all important in explaining porpoise distribution. There were also significant temporal variations in habitat use. However, whilst some variation was observed among years and months, consistent preferences for water depths between 50 and 150 m and highly sloped regions were observed across the temporal models. Predicted surfaces revealed a consistent inshore distribution for the species throughout the west coast of Scotland. Regional models revealed similar habitat preferences to the full-extent models, and indicated that the Small Isles and Sound of Jura were the most consistently important regions for harbour porpoise, and that these regions could be suitable as SACs. The impacts of seal scarers on distribution and habitat use were also investigated, and there were indications that these devices have the potential to displace harbour porpoise. These results should be considered in the assessment of sites for SAC designation, and in implementing appropriate conservation measures for harbour porpoise.

Cellular and molecular studies of postembryonic muscle fibre recruitment in zebrafish (Danio rerio L.)

Lee, Hung-Tai — Wed, 23 Jun 2010 00:00:00 GMT

Abstract: Cellular and molecular mechanisms of postembryonic muscle fibre recruitment were investigated in zebrafish (Danio rerio L.), a standard animal model for developmental and genetic studies. Distinct cellular mechanisms of postembryonic muscle fibre recruitment in fast and slow myotomal muscles were found. In slow muscle, three overlapping waves of stratified hyperplasia (SH) from distinct germinal zones sequentially contributed to a slow and steady increase in fibre number (FN) through the life span. In fast muscle, SH only contributed to an initial increase of FN in early larvae. Strikingly, mosaic hyperplasia (MH) appeared in late larvae and early juveniles and remained active until early adult stages, accounting for >70% of the final fibre number (FFN). The molecular regulation of postembryonic muscle fibre recruitment was then studied by characterising myospryn and cee, two strong candidate genes previously identified from a large scale screen for genes differentially expressed during the transition from hyperplastic to hypertrophic muscle phenotypes. Zebrafish myospryn contained very similar functional domains to its mammalian orthologues, which function to bind to other proteins known to regulate muscle dystrophy. Zebrafish myospryn also shared a highly conserved syntenic genomic neighbourhood with other vertebrate orthologues. As in mammals, zebrafish myospryn were specifically expressed in striated muscles. Zebrafish cee was a single-copy gene, highly conserved among metazoans, ubiquitously expressed across tissues, and did not form part of any wider gene family. Its protein encompassed a single conserved domain (DUF410) of unknown function although knock-down of cee in C. elegans and yeast have suggested a role in regulating growth patterns. Both myospyrn and cee transcripts were up-regulated concomitant with the cessation of postembryonic muscle fibre recruitment in zebrafish, indicating a potential role in regulating muscle growth. Furthermore, a genome-wide screen of genes involved in the regulation of postembryonic muscle fibre recruitment was performed using microarray. 85 genes were found to be consistently and differentially expressed between growth stages where muscle hyperplasia was active or inactive, including genes associated with muscle contraction, metabolism, and immunity. Further bioinformatic annotation indicated these genes comprised a complex transcriptional network with molecular functions, including catalytic activity and protein binding as well as pathways associated with metabolism, tight junctions, and human diseases. Finally, developmental plasticity of postembryonic muscle fibre recruitment to embryonic temperature was characterised. It involved transient effects including the relative timing and contribution of SH and MH, plus the rate and duration of fibre production, as well as a persistent alteration to FFN. Further investigation of FFN of fish over a broader range of embryonic temperature treatments (22, 26, 28, 31, 35°C) indicated that 26°C produced the highest FFN that was approximately 17% greater than at other temperatures. This finding implies the existence of an optimal embryonic temperature range for maximising FFN across a reaction norm. Additionally, a small but significant effect of parental temperature on FFN (up to 6% greater at 24 and 26°C than at 31°C) was evident, suggesting some parental mechanisms can affect muscle fibre recruitment patterns of progeny. This work provides a comprehensive investigation of mechanisms underlying postembryonic muscle fibre recruitment and demonstrates the power of zebrafish as an ideal teleost model for addressing mechanistic and practical aspects of postembryonic muscle recruitment, especially the presence of all major phases of muscle fibre production in larger commercially important teleost species.