Thesis (M. Sc. (Zoology))--University of Pretoria, 2003. / Includes bibliographical references (leaves 140-153).

The sicklefin lemon shark Negaprion acutidens is a large-bodied (> 3m) coastal shark species, widely distributed in tropical and sub-tropical Indo-Pacific waters. Despite its large size and wide distribution, very little is known about its movement behaviour throughout ontogeny. The primary aim of this thesis was to gain an understanding of the movements of sub-adult N. acutidens, in and around the St. Joseph Atoll, Republic of Seychelles, to facilitate the effective conservation of this vulnerable species. A total of 22 sharks (139 – 202 cm TL) were equipped with coded acoustic transmitters and passively monitored using moored acoustic receivers for a period of 20 month from March 2009 to October 2010. The use of passive acoustic telemetry arrays to study behavioural ecology has increased in popularity in recent years and been successfully applied to study a host of teleost and elasmobranch species in a diversity of habitats, ranging from sheltered estuaries to the offshore pelagic environment. However, the practicalities of designing an effective network of receivers to optimally monitor animal movements can be challenging. In this study the receiver array was optimised through a series of incremental steps to achieve an efficient design that allowed for the specific objectives to be addressed. The specific objectives of this study were to i) gain an understanding of the long term space use patterns and site fidelity of sub-adult N. acutidens within degree of use of the St. Joseph Atoll lagoon and surrounding habitats, and ii) investigate their short term behavioural patterns in response to natural rhythmic cycles. The important role the atoll plays in the sub-adult stage of this species was demonstrated by the very low numbers of detections outside the atoll compared to the very large numbers of detections inside the atoll. Over the course of a year the tagged sharks showed a high degree of site fidelity to the atoll, with 79 – 100% of the individuals detected during each month and 50% being detected on a near daily basis. This result provides testimony of the nursery role of the atoll and importance of these habitats in the early life history for this species. Individual area use was generally found to be restricted to the eastern part of the atoll incorporating a portion of the central deep lagoon and a nearby adjacent area of the sand flats. The movements of sub-adult N. acutidens on and off of the shallow flats surrounding the central lagoon (likely for foraging) were found to be strongly influenced by the tidal height and the diel cycle. Tagged sharks were found to utilise the flats more regularly when the tidal height was greater than 90 cm and particularly more so during the night and early morning than during daylight times. The combined results of this study expose the vulnerability of this species to rapid local depletion. Similarly, the effectiveness of spatial management measures, such as no-take marine protected areas is highlighted as an efficient tool for the future conservation of this species. In the St. Joseph Atoll in particular, the use of a multi-levelled protection approach, where the eastern portion on the atoll is completely restricted while the remaining area is utilized for non-consumptive tourism activities, could be highly effective. Future research should investigate changes in area use throughout the ontogeny of this species as well improve the understanding of the breeding site fidelity and population size of reproductive females using the St. Joseph Atoll.

A unique opportunity to study both benthic microbial mats and modern stromatolites from a common niche is presented by the hypersaline environment of Hamelin Pool, Shark Bay, Australia. However, prior to this study, the microbial mat communities have not been well characterised. To investigate the taxonomic and functional diversity of Hamelin Pool pustular and smooth mats, and their similarity to Hamelin Pool stromatolites, culturing, culture-independent, and lipid analysis methods were employed. The cultured isolates obtained included heterotrophic bacteria similar to those obtained from other hypersaline environments, and 19 strains of cyanobacteria including potentially novel species. For the first time archaeal isolates were obtained from the pustular and smooth mats, and further characterisation of two strains indicated they might represent novel species of the genus Haloferax. Total DNA was extracted from the mats and 16S rRNA gene clone libraries were generated targeting the bacteria, cyanobacteria, archaea and eukarya. Both the pustular and smooth mat bacterial clone libraries were highly diverse, with 11 bacterial divisions represented, and Chao1 estimates of total species richness indicating ~3000 ??? 6000 species. Cyanobacterial and archaeal clone libraries revealed unique phylotypes associated with sediments of differing morphology. Statistically significant differences between the mat populations and Hamelin Pool stromatolite communities were identified using !-LIBSHUFF, a program designed to compare two 16S rRNA gene libraries. Signature lipid biomarkers were assessed for the pustular and smooth mats and an intertidal stromatolite from Hamelin Pool. Fatty acids (as methyl esters), wax esters, hydrocarbons, ether-bound lipids, hopanoids and sterols indicated the presence of oxygenic phototrophs, anoxygenic phototrophs, sulfate-reducing bacteria, sulfur-oxidising bacteria, heterotrophic bacteria and archaea in each of the sediment types. Limited contributions from diatoms, bivalves and their dinoflagellate symbionts, and from higher plant aerosols were also detected. Significantly, 2-methyl hopanoids and eight pseudohomologous series of branched alkanes with quaternary carbon centers were identified in the mats and stromatolites. Although differing in lithification status and precise microbial composition, the pustular and smooth mats are excellent analogues for the extant stromatolites of Hamelin Pool, and by corollary, provide a fascinating link to Precambrian microbial communities.

A unique opportunity to study both benthic microbial mats and modern stromatolites from a common niche is presented by the hypersaline environment of Hamelin Pool, Shark Bay, Australia. However, prior to this study, the microbial mat communities have not been well characterised. To investigate the taxonomic and functional diversity of Hamelin Pool pustular and smooth mats, and their similarity to Hamelin Pool stromatolites, culturing, culture-independent, and lipid analysis methods were employed. The cultured isolates obtained included heterotrophic bacteria similar to those obtained from other hypersaline environments, and 19 strains of cyanobacteria including potentially novel species. For the first time archaeal isolates were obtained from the pustular and smooth mats, and further characterisation of two strains indicated they might represent novel species of the genus Haloferax. Total DNA was extracted from the mats and 16S rRNA gene clone libraries were generated targeting the bacteria, cyanobacteria, archaea and eukarya. Both the pustular and smooth mat bacterial clone libraries were highly diverse, with 11 bacterial divisions represented, and Chao1 estimates of total species richness indicating ~3000 ??? 6000 species. Cyanobacterial and archaeal clone libraries revealed unique phylotypes associated with sediments of differing morphology. Statistically significant differences between the mat populations and Hamelin Pool stromatolite communities were identified using !-LIBSHUFF, a program designed to compare two 16S rRNA gene libraries. Signature lipid biomarkers were assessed for the pustular and smooth mats and an intertidal stromatolite from Hamelin Pool. Fatty acids (as methyl esters), wax esters, hydrocarbons, ether-bound lipids, hopanoids and sterols indicated the presence of oxygenic phototrophs, anoxygenic phototrophs, sulfate-reducing bacteria, sulfur-oxidising bacteria, heterotrophic bacteria and archaea in each of the sediment types. Limited contributions from diatoms, bivalves and their dinoflagellate symbionts, and from higher plant aerosols were also detected. Significantly, 2-methyl hopanoids and eight pseudohomologous series of branched alkanes with quaternary carbon centers were identified in the mats and stromatolites. Although differing in lithification status and precise microbial composition, the pustular and smooth mats are excellent analogues for the extant stromatolites of Hamelin Pool, and by corollary, provide a fascinating link to Precambrian microbial communities.

The first aim of this thesis was to test the hypothesis that the spatial and food resources in the nearshore waters of a subtropical embayment in Western Australia (Shark Bay) will be partitioned within and amongst the main elasmobranch species that occur in that large water body. The size and age compositions, growth rates and reproductive biology of females and males of the nervous shark Carcharhinus cautus in Shark Bay were then determined to better understand the mode of life of this abundant species in this embayment. The second aim was to determine the species and size compositions of chondrichthyans landed by fisheries employing different methods in south-eastern Indonesia. The implications of these data for management were next determined and aspects of the reproductive biology of the most abundant of those species were explored, in a very preliminary manner. The nearshore, shallow waters of Shark Bay are used as a nursery area by several shark species and the different habitats in those waters are partitioned, to a certain degree, amongst those species. Ten species of shark (5 families), five species of ray (4 families) and twelve species of teleost (10 families) were caught in those waters. Carcharhinus cautus was the most abundant species, contributing 59.9% to the total number of elasmobranchs and 42.3% to all fish caught. This species and Negaprion acutidens were collected mainly or entirely from unvegetated sites, whereas Rhizoprionodon acutus, Carcharhinus brevipinna and Chiloscyllium punctatum were caught largely or exclusively at the seagrass site. The number of elasmobranch species and number of individuals of elasmobranchs were greatest in the seagrass site and least in the unvegetated site where no vegetation was present nearby, and they were significantly less in the latter site than in the one where dense mangroves were present nearby. These two biotic variables were also significantly greater in summer and autumn than in winter when temperatures were lowest. The species composition of elasmobranchs in each habitat type almost invariably differed significantly from that in each of the other habitat types and there was evidence that the species composition of elasmobranchs varied in a similar seasonal manner at the three unvegetated sites. Carcharhinus cautus, and probably also Hemigaleus microstoma and Chiloscyllium punctatum, were the only species that completed their life cycles in the nearshore, shallow waters of Herald Bight. However, the capture of the juveniles of a further four species with umbilical scars emphasises the importance of these waters as a nursery habitat for shark species. The dietary compositions of one ray species (Rhinobatus typus) and three shark species (Carcharhinus cautus, Negaprion acutidens, Rhizoprionodon acutus) undergo size-related changes and differ among these species, thereby reducing the potential for competition for food within and among these four species. Rhinobatus typus fed almost exclusively on penaeid prawns and portunid crabs, which is reflected in its narrow dietary breadth, whereas different species of teleosts constituted a major component of the diets of each size class of the three shark species. The relative contributions of the different species of teleost to the diets of the three shark species varied. The variations in dietary composition among the four species reflect differences in behaviour, modes of feeding and relative mouth sizes. Carcharhinus cautus copulates in late October–early November, shortly followed by ovulation (and thus conception) and parturition occurs about 11 months later. The reproductive cycle of C. cautus is biennial. Female and male C. cautus reached ca 28 and 32% of their lengths at their maximum observed ages, respectively, at the time of parturition. Females and males of C. cautus attained maximum total lengths of 1330 and 1110 mm, respectively, and maximum ages after parturition of 16 and 12 years, respectively. Maturity was attained at about 1010 mm by females and 910 mm by males and at least 50% of females and males had become mature by the end of their sixth and fourth years of life, respectively. The three-parameter von Bertalanffy growth curves provided reasonably good fits to the lengths at age of females and males of C. cautus during just postnatal life and throughout the whole of pre- and postnatal life. However, the four-parameter Schnute growth curve significantly improved the fit to these data for both females and males from conception and for females from birth. The question of when, from a biological view point, it might be appropriate to switch from using a von Bertalanffy growth curve to the more complex Schnute growth curve are discussed. A total of 139 chondrichthyan species, comprising 77 species of shark representing 17 families, 61 species of ray representing 11 families and a single species of holocephalan, were recorded at the ten landing sites surveyed in south-eastern Indonesia. However, it should be recognised that up to 49 of the 139 chondrichthyan species recorded have apparently not yet been described and thus assigned a species name. The most speciose and commonly recorded families were the Dasyatidae and Carcharhinidae, which collectively contributed 84.8%, respectively, to the total number of individuals of all species. The use of MDS ordination demonstrated that the species compositions at the eight main landing sites reflected to a greater extent the fishing methods used rather than the geographical location of those sites. Data on the reproductive biology of males demonstrated that a number of elasmobranch species were fished prior to the time that they attained maturity. The three most abundant chondrichthyan species that were caught both as juveniles and adults were Dasyatis kuhlii, Dasyatis zugei and Himantura walga. Since the reproductive cycle of each of these species did not follow a seasonal pattern, the timing of conception and parturition and the duration of gestation of these species could not be determined. The fecundity of these three species was very low, i.e. maximum of two but usually only a single embryo. The size at maturity of the three species, using data on the prevalence of mature fish, ranged from minima of 163 mm for females and males of H. walga to maxima of 237 mm for females and 239 mm for males of D. kuhlii. The translucent zones on the vertebral centra of D. kuhlii were apparently deposited annually and were thus used to estimate the ages of the individuals of this species. The maximum estimated ages of female and male D. kuhlii were 15 and 10 years, respectively.

Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, Discipline of Environmental Biology, 2006. / "January 2006" Bibliography: pages 188-209. Also available in print form.

This thesis explores the use of an Autonomous Underwater Vehicle (AUV) to track and pursue a tagged shark through the water. A controller was designed to take bearing and range to the shark tag and then control the AUV to pursue it. First, the ability of a particle filter to provide an accurate estimation of the location of the shark relative to the AUV is explored. Second, the ability of the AUV to follow the shark's path through the water is shown. This ability allows for localized environmental sampling of the shark's preferred path. Third, various path weightings are used to optimize the efficiency of pursuing the shark. This demonstrates that the proposed controller is efficient and effective. Fourth, the benefits of the addition of a second AUV are explored and quantified. The secondary AUV is shown to maintain formation without direct communication from the primary AUV. However, the communication of the AUVs increases the accuracy of all measurements and allows for future expansion in the complexity of the controller. Fifth, the effects of predicting the shark$'$s future movement is explored. Sixth, the effect of noise in the signal from the shark tag is tested and the level of noise at which the AUV can no longer pursue the shark is shown. This investigates the real world ability of the controller to accept noisy inputs and still generate the appropriate response. Finally, the positive results of the previous sections are combined and tested for various noise levels to show the improved controller response even under increased noise levels. To validate the proposed estimator and controller, seven tests were conducted. All tests were conducted on existing shark path data recorded by a stationary acoustic receiver and a boat mounted acoustic receiver. Tests were conducted on data sets from two different species of sharks, (Shovelnose and White) with two very different swimming behaviors. This shows the solution's flexibility in the species of shark tracked.

Research into seed biology and restoration ecology of areas disturbed by mining is crucial to their revegetation. Shark Bay Salt, a solar salt facility in the Shark Bay World Heritage Area in Western Australia has several areas of disturbance as a result of 'soil borrowing'. Soil from these areas termed 'borrow pits' was used to create infrastructure such as the roads and embankments surrounding the evaporation ponds. Many of the pits contain little to no vegetation after >10 years since disturbance ceased, hence research into their restoration is now essential. A vegetation survey at the site established the key species in the undisturbed vegetation, and investigated the vegetation in borrow pits subject to natural migration and topsoil replacement. The vegetation communities in the borrow pits were vastly different to those in the undisturbed vegetation, highlighting the need for research into revegetation. An investigation into the use of 'borrowed' topsoil on a small scale showed that seedling recruitment from 'borrowed' topsoil was generally similar in the donor site (natural vegetation) and the borrow pits. Due to the absence of topsoil for further revegetation, it was necessary to understand seed germination and dormancy characteristics to establish seed pre-treatments prior to seed broadcasting and seedling (greenstock) planting. An investigation into seed germination and dormancy characteristics of 18 common species revealed that most species germinated equally well at 26/13oC and 33/18oC, however seven species had improved performance at 26/13oC. Untreated seeds of seven species exhibited high germination. Seeds of two species had low imbibition, which increased with hot-water treatment, and hence require scarification for germination. Germination of seeds of three species substantially increased with gibberellic acid (GA3), smoke water (SW) and karrikinolide (KAR1, a butenolide isolated from smoke). Seeds of the remaining six species had low germination regardless of treatment. As a result, species were classified as likely to be non-dormant (44%), physiologically dormant (44%) or physically dormant (11%). Physiological dormancy of three species was at least partly alleviated by dry afterripening, whereby moisture content of seeds was adjusted to 13% or 50% equilibrium relative humidity and seeds were stored at 30oC or 45oC for several months. All iv after-ripening conditions increased germination percentage and rate of two species with one only germinating when treated with GA3 or KAR1. The germination of the third species was dependent on after-ripening temperature and seed moisture content.

Thesis (MSc Food Sc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: The aim of this study was to determine the proximate composition of five individual body sites of the Mustelus mustelus shark in order to evaluate the cross carcass variation of the individual proximate components (moisture, protein, lipid, ash) of the meat. This variation was determined in order to find a representative sample of the edible part of the shark (fillet and body flap). Secondly, this sample representing the entire shark fillet was used to investigate the endogenous factors (gender, size and life cycle stage) and their effects on the individual proximate components and other meat components (amino acids, fatty acids, minerals, histamine and mercury contents). Finally, all this data was combined to describe the average chemical composition and nutritional value of M. mustelus meat. None of the proximate components showed any variation between the different fillet positions. This indicated that the fillet is homogenous and samples for chemical analyses can be taken anywhere on the fillet as representative of the entire fillet. It was found that all three main effects (gender, size and life cycle stage) did not have major influences on most of the components of the chemical composition of M. mustelus meat analysed. Higher fatty acid levels (SFA, MUFA and PUFA) were observed in large females than in large males as well as in non-pregnant large females compared to pregnant large females. According to statistical analysis, large males had higher total mercury levels than large females. The only component affected by size variation was the fatty acids, showing a trend to decrease in quantity before maturity was reached. Variation due to life cycle stages was mostly evident in the fatty acid component with some small effects on two mineral components, aluminium and copper, which had slightly higher levels in pregnant large females than in non-pregnant large females. M. mustelus meat has an average proximate composition of 75% moisture, 23% protein, 1.6% lipids and 1.4% ash (weight per wet weight). The protein is, however, an over-estimation of the true protein value as the meat contains significant amounts of non-protein nitrogen (NPN) in the form of urea which contributes to the N concentration. M. mustelus meat is a good source of some essential amino acids, especially lysine and threonine (78% of the daily requirements for an adult in a 100g portion), but low in minerals. The meat has a healthy lipid content with a good ratio (>0.45) of PUFA:SFA (0.83) as well as a healthy (<4) n-6:n-3 fatty acid ratio of 0.39. The histamine content was very low or not detectable but some samples contained total mercury values above the maximum safe limit. Although further research is needed for some meat components, these results are a valuable contribution to the new South African Food Composition Tables being compiled. / AFRIKAANSE OPSOMMING: Die doel van hierdie studie was om die proksimale samestelling van die vleis vanaf vyf afsonderlike posisies op die liggaam van die Mustelus mustelus haai te bepaal. Sodoende is die variasie, met betrekking tot die verskillende proksimale komponente (vog, proteïen, lipiede en as), in terme van die totale karkas, bepaal. Die proksimale variasie is bepaal om vas te stel hoe ʼn verteenwoordigende monster van die totale karkas geneem kan word. Gevolglik is hierdie verteenwoordigende monster gebruik om die effek van geslag, grootte en die verskillende fases van die lewens-siklus op die afsonderlike proksimale komponente asook ander vleis komponente (aminosure, vetsure, minerale, histamien en kwik inhoud) te ondersoek. Laastens is al hierdie inligting gebruik om die algemene samestelling en voedingswaarde van M. mustelus vleis te bespreek. Geen van die proksimale komponente het enige variasie getoon tussen afsonderlike liggaamsposisies nie. Hierdie resultaat dui daarop dat die vleis van ʼn M. mustelus haai homogeen is regoor die karkas en dat ʼn vleis monster vanaf enige posisie op die karkas geneem kan word as ʼn verteenwoordigende monster. Daar is gevind dat geslag, grootte en fase van die lewens-siklus geen merkwaardige invloed het op die vleis se samestelling nie. Hoër vetsuur konsentrasies (versadigde, monoonversadigde en poli-onversadigde vetsure) is gevind in groot vroulike haaie en nie-dragtige vroulike haaie as in groot manlike haaie en dragtige vroulike haaie onderskeidelik. Statisties, het groot manlike haaie hoër vlakke van totale kwik as groot vroulike haaie. Die enigste vleis komponent wat beïnvloed is deur die grootte van die haai, is die vetsure, wat verminder het voor volwassenheid bereik is en dan weer vermeerder soos die haai groter word. Variasie as gevolg van die verskillende fases van die lewens-siklus is meestal gevind in die vetsuursamestelling, en die minimale het ook gevarieer ten opsigte van die elemente aluminium en boor wat effense hoër vlakke getoon het in dragtige haaie as in nie-dragtige haaie. M. mustelus vleis het ʼn gemiddelde proksimale samestelling van 75% vog, 23% proteïen, 1.6% lipiede en 1.4% as (nat massa). Die proteïen waarde is ʼn oorskatting van die ware proteïen waarde as gevolg van hoë nie-proteïen stikstof in die vorm van ureum wat bydra tot die totale stikstof inhoud. M. mustelus vleis blyk ʼn goeie bron van sommige essensiële aminosure soos lisien en treonien (78% van die daaglikse aanbevole dosis), maar laag in mineraal inhoud. Die vleis het ʼn gesonde vet inhoud met ʼn goeie (>0.045) poli-onversadigde:versadigde vetsuur verhouding (0.83) asook ʼn gesonde (<4) omega 6 tot omega 3 vetsuur verhouding van 0.39. Die histamien inhoud van die vleis was baie laag of onder die meetbare limiet, maar sekere monsters het ʼn totale kwik inhoud getoon wat bo die maksimum veilige limiet is. Hoewel verdere navorsing ten opsigte van sekere van die vleis komponente vereis word, lewer hierdie resultate ʼn waardevolle bydrae tot die nuwe Suid-Afrikaanse voedsel samestellings tabelle wat tans opgestel word.

Habitat use of mesophotic coral reefs by sharks is largely unknown. However, it is well established that mesophotic reefs are the site of spawning aggregations for many species of teleost fish. These aggregations represent seasonal concentrations of potential prey biomass that may influence the habitat use of predatory species such as large sharks. I employed acoustic monitoring to examine the movements of three shark species [lemon shark (Negaprion brevirostris), tiger shark (Galeocerdo cuvier), and Caribbean reef shark (Carcharhinus perezi)] to determine 1) the comparative spatiotemporal patterns of mesophotic reef habitat use by the three shark species and 2) the spatiotemporal relationship between these sharks and grouper spawning aggregations at a fish spawning aggregation (FSA) site (Hind Bank and Grammanik Bank) along the southern reef shelf edge off St. Thomas, United States Virgin Islands (USVI). Tiger and lemon sharks were detected across nearly the entire acoustic array, which spanned ~ 1060 km2. When present, Caribbean reef sharks used a much smaller activity space, composed exclusively of mesophotic reef habitat located within FSA sites. Individuals from all three species were typically detected for stretches of several consecutive days, while periods without detections usually lasted less than one week. Lemon sharks were present at the FSA site more often during the grouper spawning season (Dec-May) than the non-spawning season (Jun-Nov), but showed no preference toward specific areas within the FSA site, which varied by location and grouper species composition. In contrast, there was no relationship between the presence of tiger and Caribbean reef sharks at the FSA site and the grouper spawning season. My results suggest that despite different habitat use 5 patterns and varying degrees of fidelity, this mesophotic reef serves as an important habitat to all three shark species.