Dissertations / Theses on the topic 'Chondrichtyan'

Chondrichthyans (sharks, rays, skates, and chimaeras) are a diverse taxonomic clade inhabiting bodies of water all over the world. As a lineage, chondrichthyans split from the other jawed vertebrates 450 million years ago, the most basal split in the gnathostome vertebrate tree. Although they have been studied for centuries, knowledge about these animals lags behind that of many other vertebrate groups. This work uses Computed Tomography (CT) to explore morphological variation across phylogenetically diverse species of chondrichthyans. CT imaging is a nondestructive method for viewing internal structures of extant and fossilized specimens. After CT scan data acquisition, reconstruction software was used to manually segment the skeletal anatomical into constituent structures, creating 3-Dimensional representations of the structures. In most groups of vertebrate organisms, skeletal structures are made of calcified bone which has high radiopacity, leading to greater contrast between the skeleton and soft tissues. Chondrichthyans, by comparison, have skeletons composed of cartilage which is much less radiopaque than bone, resulting in lower contrast with surrounding tissues. Variations in the skeletal structures are discussed along with notes on calcification within the chondrichthyan orders. This work is presented as a summary of the variation observed in the skeletal anatomy, building upon previous works in chondrichthyan anatomy, expanding the current state of knowledge of the diversity in chondrichthyan fish skeletons. This project is part of a collaborative effort to develop a phylogenetic tree of life for modern chondrichthyans.

Nearly half of the known species of sharks in the world live in the deep sea, yet little is known of the biology or life history of these important predators of the deep. Fishing effort for deep-water sharks, both targeted and incidental, has been increasing worldwide over the last few decades. However, in most cases the impact of this harvest is unknown due to the paucity in landings data and the lack of stock assessments for these species. This research was conducted to provide some of the basic life history information needed to improve the understanding and properly manage deep-water sharks. Specifically, information is presented herein on age determination using dorsal fin spines; the potential for radiometric age validation using dorsal fin spines; the age, growth, and reproductive biology of Squalus mitsukurii from Hawaiian waters; and the reproductive biology and embryonic development of Centrophorus cf. niaukang and Etmopterus princeps.;Dorsal fin spines offer an alternate structure for age determination in phalacanthous chondrichthyans. In this study, I sought to identify optimal methods of age determination using dorsal fin spines of 14 species of squaliform sharks and two species of holocephalans. Growth bands can be found in three zones of the fin spine: on the enamel cap (if present), at the base of the whole spine, or in the inner dentine layer. Each of these three methods was applied to fin spines from these 16 species. Results of each method are compared and discussed, with an optimal aging method suggested for each species.;Radiometric methods have been used to validate age estimates from teleost otoliths, shark vertebrae, and coral skeletons. The radioisotopes 210Pb and 226Ra were ineffective for age determination of dorsal fin spines, possibly due to a violation of the assumption of constant isotopic uptake, or conversely the spine may not act as a closed system.;A study of age, growth and reproductive biology of Squalus mitsukurii was conducted near Oahu, Hawaii. Age estimates ranged from 3 to 26 years for females and 6 to 23 years for males. Growth parameters estimated with multiple growth models indicated that this a K-selected species, characterized by high longevity, late maturity, and slow growth. Observed fecundity also indicated that reproductive output is low for this species.;A study of embryonic development in Centrophorus cf. niaukang and Etmopterus princeps indicated that the process of embryogenesis results in a range in organic matter depletion from the time of fertilization to parturition. Centrophorus cf. niaukang embryos showed a reduction of 19.5% in organic matter, while E. princeps embryos showed a reduction of 7.8% in organic matter over the course of embryonic development. These results indicate that at least one of these species may be matrotrophic. Observed fecundity and maturity ogives are also presented for each species.;This study on age determination, growth, and reproductive biology of several species of deep-water sharks and holocephalans indicated that these are K-selected species. Future harvest of these species should proceed with caution, as they are prone to overexploitation and localized depletion.

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.

The Late Permian mass extinction occurring at 252.6 ± 0.2 Ma is the most severe Phanerozoic extinction event and was preceded and followed by additional disturbances. Patterns and processes of extinction and recovery of marine vertebrates have been little studied compared to marine invertebrates. This project focuses on Chondrichthyes, which, together with other marine fish, appeared to have been relatively unaffected by the extinction, while most of their supporting ecosystem collapsed. This study explores the authenticity of extinction among chondrichthyans and possible explanations for the observed patterns, because extinction severities on the taxonomic and ecological levels may be decoupled or the quality of the fossil record may be variable. The presented analyses are based on a newly compiled database that supercedes older compilations. It is supplemented by material obtained from numerous localities globally, which includes newly described taxa. Hence, this study attempts to be the most up-to-date and comprehensive analysis of patterns and trends in chondrichthyan diversity and distribution that is currently available. The data demonstrate that, despite some variability in the Permian–Triassic chondrichthyan fossil record, the Lopingian record is shown to be of adequate completeness and, furthermore, range-through genus diversity is not significantly correlated with the number of taxonomic occurrences. Genus diversity declined from the mid-Guadalupian following an increasing extinction rate, which intensified throughout the Lopingian and thus supports a combined overall extinction as a result of the end-Guadalupian and Late Permian events. Furthermore, global distribution of chondrichthyan diversity shifted away from tropical regions and particularly the Boreal Sea gained in diversity, tracking extinction and recovery in marine benthic invertebrates in both time and space. No significant dependence of extinction on taxonomic structure or palaeoecological traits exists, which suggests proportional losses, except during the end-Smithian crisis. Also, a significant size decrease is absent among Permian/Triassic boundary-crossing taxa, suggesting selective loss of large-sized chondrichthyans rather than adaptive size decrease. Ultimately, the Hybodontiformes, Neoselachii, Xenacanthiformes and Holocephali are identified as the survivors, which possessed a varying combination of characteristics such as moderate body-size, adaptation to brackish/freshwater environments, benthic or generalist littoral (clutching) feeding behaviour, and a wide palaeogeographic range.

Worldwide, numerous shark populations are in rapid decline due to chronic overfishing. Their slow reproductive capacity make them susceptible to extinction. To monitor the status of chondrichthyan species, the method or combination of methods used should be non-selective, applicable in a variety of habitats and under most environmental conditions. Baited Remote Underwater Video (BRUV) surveys have shown major benefits over traditional capture-based survey methods in multiple areas. They have been shown to be non-extractive, causing no major disturbance to the substrata and its epibenthos. Large, mobile animals that avoid divers and active fishing surveys are detected. The recorded video removes the need for specialist observers to conduct all the fieldwork. The video allows impartial and repeatable measurements and standardizes data collection and training in association with remote taxonomists. The method is also cheaper than alternatives. Ninety-five sites were sampled with 60 minute video recordings across the whole of False Bay during the period of June-July 2012. Fifteen species of chondrichthyans were recorded, of which Haploblepharus edwardsii was the most abundant, being observed at 83 of 95 sites. One hour was sufficient to capture all the chondrichthyans within the observed area as the average time of arrival was about half an hour into the recording. The distribution of the chondrichthyan population was remarkably uniform across the bay. Depth, habitat and substrate type were significant predictors of species composition (P = 0.004, 0.025 and 0.001 respectively). Opportunistic encounters (one individual observed) included Carcharodon carcharias, Squalus megalops, Rhinobatos annulatus and Myliobatis aquila.

The fishing operations of a reference fleet of French commercial deep-water bottom trawlers from Lorient operating to the west of the British Isles have been described between 1999 and 2001, and their subsequent impact on several species of deep-water chondrichthyans from the area were assessed. Landings from a three-year market sampling programme showed that the deep-water fishery is highly seasonal in nature operating at greater depths in the summer months. The depth fished by vessels is primarily related to the targeted species of the fishery. Biological data from research cruises and discard observer trips have indicated that most chondrichthyan species in this study exhibit strict baythymetric distributions. The quantity and species of chondrichthyans caught as bycatch or discarded from the fishery are therefore dependent on which targeted species is caught and at what depth, and these factors can vary considerably over a limited depth range. Data collected on the reproductive biology of these species have shown that, in most instances, deep-water chondrichthyans have extremely low reproductive rates with low fecundities, slow growth and that they mature at large sizes, suggesting that they are susceptible to overfishing. A limited analysis conducted in ICES Divison VIa between pre- and post-fishery research cruises showed a decrease in catch rates for Centroscymnus coelolepis, Centrophorus squamosus and Chimaera monstrosa by decade and gear type, suggesting that these species may be some of the most vulnerable deep-water chondrichthyans when faced with intensive commercial fishing. Nevertheless data used in multivariate models were fragmentary and unbalanced in nature, and therefore results should be treated with caution. More species-specific fisheries and biological data are required in the northeast Atlantic to provide accurate management programs for deepwater chondrichthyans.

Since the discoveries of vertebrate bioapatite’s ability to record oxygen isotopecomposition of ambient seawater were made (Kolodny, 1983), oxygen isotopes have beenwidely used as a climatic and oceanographic proxy. The δ18OP aquatic vertebrate apatite isa function of the δ18Ow value of the ambient water, yet “vital effects” on the δ18OP compositionhave been reported previously (Venneman et al., 2013). I have analysed δ18O compositionin the teeth of six extant shark and ray (chondrichthyan) species from the tropical ocean tankof the Blackpool Sea Life Center, UK. The teeth were naturally shed and collected from thetank substrate.Preparation of samples was performed in the Laboratory of Isotope Geology at the NaturalHistory Museum of Stockholm (Sweden), and the δ18O was measured at the NordSIM facility,using secondary ionization mass spectrometry (SIMS) by a high precision and high spatialresolutionCAMECA IMS 1280 ion microprobe.Data treatment was followed by statistical analysis. Results show significant δ18O differencesat inter-tissue level. I could also illustrate the impact of organics-pretreatment on the finalδ18O values, with the outcome of one more favourable pretreatment for SIMS analysis. Intertaxonvariability was observed, without much statistical confidence, but I hypothesize that itmay be due to the difference in tissue crystallization and organic quantity between species.

La gestion et la conservation des pêcheries sont problématiques pour la plupart des chondrichthiens; cela tient principalement au manque de données scientifiques causé par les défis logistiques impliqués par les prélèvements par grandes profondeurs. De plus, plusieurs les techniques analytiques, à l’exemple du contenu stomacal et des mesures morphologiques, demandent des quantités d’échantillons importantes difficilement obtenues. De nouvelles techniques exigent moins d'échantillons, en particulier celles mettant en oeuvre la biochimie qui sont de plus en plus utilisées pour résoudre des questions écologiques et biologiques complexes au niveau individuel et démographique des populations. Cette thèse a testé plusieurs techniques biochimiques (analyses de lipide, mercure, et isotope de carbone et azote) pour mieux comprendre les aspects de la reproduction, de l'écologie trophique, de l'amplification du mercure et de la physiologie de chondrichthiens des profondeurs. La plupart des espèces font partie de l'Ordre des Squaliformes. D'autres espèces appartiennent à différentes Familles: Chimaeridae, Rhinochimaeridae, Scyliorhinidae et Hexanchidae. Tous les échantillons ont été capturés dans les filets de pêcheurs dans les eaux du plateau continental et des marges du sud-est de l'Australie. L’analyse de la composition en lipides de différents tissus révèlent que le foie des chondrichthiens est riche en lipides (38 à 70% de la masse des tissus humides), en majeure partie des lipides neutres et des acides gras mono-saturés. Le foie est un tissu multifonctionnel, qui joue un rôle essentiel dans la distribution de la biosynthèse lipidique, le stockage de l’énergie et la régulation de la flottaison. A l’inverse, le tissu musculaire est un organe structurel, à faible concentration en lipide (<2 %) qui se compose essentiellement de lipides polaires. La composition des lipides rénaux et pancréatiques montre que leur fonctionnement métabolique est complexe. L'analyse des lipides des organes reproducteurs a révélé que l’énergie utile à la gestation chez les adultes chondrichthiens en pré-ovulation nécessite un pourcentage important de lipide (follicule ovarien 18 à 34 %). Les variations de triacylglycérols (8 à 48 %), des éthers diacylglycéryls (0,2 à 28 %) et des cires (0,5 à 20 %) ont été observées dans tous les échantillons. Ces variations impliquent l'utilisation de classes lipidiques multiples pour favoriser le développement embryonnaire. Les réserves maternelles sont différentes entre espèces ovipares et vivipares et entre les élasmobranches et les holocéphales. L’allocation la plus important de lipides est trouvée chez les requins vivant dans les environnements les plus profonds. Cette observation suggère que leur fécondité est plus faible et que leur vulnérabilité face à la pêche est plus importante. Le régime alimentaire des requins a été déterminé par des techniques complémentaires: traceurs lipidiques et analyses du contenu stomacal. 41 taxons de proie ont été identifiés. Ils étaient surtout composés de poissons et de céphalopodes du domaine demersal. En utilisant les profils des acides gras, la variabilité de la composition de nourriture a été établie pour chaque espèce en associant la signature de ces profils dans les tissus des chondrichthiens aux profils de plusieurs proies. Les deux techniques ont montré que les chondrichthiens sont des prédateurs opportunistes qui consomment une large gamme de proie. Les concentrations en mercure et sa distribution des tissus ont été examinés pour accéder à sa bioamplification dans ce type d’organisme et de déterminer des niveaux de contamination pour la consommation publique. Le mercure total (THg : toutes formes chimiques confondues) et le méthylmercure (MeHg : la forme la plus toxique et bioaccumulable) ont été dosées. Pour la plupart des espèces, les niveaux de THg étaient supérieurs au seuil maximal recommandé par les législations en vigueur dans plusieurs pays dont l’Australie (>0,1 mg kg-1 pois humide, ph) et une concentration aussi forte que 6,6 mg kg-1 (ph) a été enregistrée. L'
Analyse de spéciation a montré que le mercure est présent à plus de 91 % sous forme de MeHg, et même avec des taux supérieurs à 95 % chez les espèces des environnements les plus profonds. Les concentrations maximales en THg ont été trouvés dans les tissus musculaires (59 à 82 % de charge corporelle). Les reins et le foie possèdent aussi des taux élevés, respectivement de 0,3 à 4,2 et 0,5 à 1,5 mg kg-1 (ph), tandis que la peau enregistre les concentrations les plus faibles (> 0,3 mg kg-1, ph). Cette étude de l’organotropisme permet de conclure que les reins et le foie sont associés au métabolisme du métal, à l'élimination et au stockage à court terme, alors que le muscle est le sites le plus important du stockage du mercure à long terme. Les isotopes stables de carbone et d’azote ont été utilisés pour évaluer l'influence de la position trophique (d15N) et de la source de carbone (d13C) sur l'accumulation du THg chez les chondrichthiens. Le d15N varie entre 12,4 à 16,6 ‰ démontrant la large gamme de positions trophiques occupées par ces espèces. La variation interspécifique du d13C est quant à elle minimale (–18,7 à –17,1 ‰). Les concentrations en mercure notées chez la plupart des requins augmentent en fonction de la taille, de la position trophique (d15N) et du stade de maturité de l’animal. Dans la communauté des chondrichthiens des profondeurs on observe des taux modérés de bioamplification du mercure, ceci est révélé par la faible pente de la relation, log (THg mg kg-1 ww) = 0,2 (d15N) – 2,4 (R2 = 0,35 ; P <0,05). Le THg et les acides gras de 61 espèces appartenant aux niveaux trophiques intermédiaires ont été analysés dans le but d’étudier les régimes alimentaires des proies et la bioaccumulation de ce métal à travers la chaîne alimentaire démersale. L'utilisation intégrée de ces techniques biochimiques a fourni des données fondamentales sur la reproduction, l'accumulation en mercure et l'écologie trophique des chondrichthiens des profondeurs. La compréhension de ces fonctions est impérative non seulement pour la mise en place d’une gestion durable des pêcheries, mais aussi pour la protection des habitats des chondrichthiens et leurs écosystèmes associés
For most deepwater chondrichthyans, fisheries and conservation management is problematic, largely due to the lack of scientific data resulting from inherent logistical challenges working within deep-sea environments. Furthermore, many conventional analytical techniques (stomach content analysis and morphometrics) require large sample sizes and are often quantitatively inadequate. Thus, new and more robust methods requiring fewer specimens are needed. Biochemical ‘tracer’ techniques are increasingly being used to resolve complex ecological and biological questions at individual species and population levels. This research explored the integrated use of multiple biochemical techniques (lipid and fatty acid profiling, stable nitrogen and carbon isotope and mercury analysis) to understand aspects of the reproduction, feeding ecology, metal accumulation and physiology of deepwater chondrichthyans. Most were from the Order Squaliformes. Other species include those from the Families: Chimaeridae, Rhinochimaeridae, Scyliorhinidae and Hexanchidae. All specimens were caught as fisheries bycatch from the continental slope waters off southeast Australia. The examination of lipid composition and partitioning revealed that deepwater chondrichthyans have large, lipid rich (38–70 % wet weight, ww) livers high in neutral lipids and monounsaturated fatty acids. Liver is a multifunctional tissue, playing a vital role in lipid distribution and biosynthesis, buoyancy regulation and storage. In contrast, muscle is a structural organ, low in lipid (<2 %) and consisting primarily of polar lipids. Lipid composition of kidney and pancreas show that they, too, have complex roles in lipid metabolism and storage. Lipid analysis of reproductive tissues revealed high maternal investment in deepwater chondrichthyans as indicated by high lipid content in mature pre-ovulated ovarian follicles (18–34 %). Variable levels of triacylglycerols (8–48 %), diacylglyceryl ethers (0.2–28 %) and wax esters (0.5–20 %) were observed in all specimens, demonstrating the use of multiple lipid classes to fuel embryonic development. The maternal provisions differed between oviparous and viviparous species and between elasmobranchs and holocephalans. Greater lipid investment was displayed by sharks living in deeper environments, suggesting lower fecundity and increased vulnerability to fishing. Diet was examined by complementary lipid biomarker and traditional stomach content techniques. A total of 41 prey taxa were identified using stomach content analysis and consisted mainly of bathyal-demersal fish and cephalopods. Using multidimensional scaling analysis, the extent of variability in composition within each species was determined by grouping the signature fatty acid profiles of shark tissues with profiles for demersal fish, squid and crustaceans. Both techniques showed that deepwater chondrichthyans are opportunistic predators, and that there is some degree of specialisation and overlap between them. Total (THg) and inorganic (monomethyl, MeHg) mercury concentrations and tissue distribution were examined to determine the extent of biomagnification and evaluate levels for human consumption. Mean THg levels for most species were above the regulatory threshold (>0.1 mg kg-1 ww) and levels as high as 6.6 mg kg-1 ww were recorded. Speciation analysis demonstrated that 91% mercury was bound as MeHg with higher percentages (>95%) observed in species occupying deeper environments. Higher levels of THg were stored in muscle which accounted for between 59–82% of the total body burden of mercury. High levels were also found in kidney (0.3–4.2 mg kg-1 ww) and liver (0.5–1.5) with lower levels observed in skin (>0.3). Both the kidney and liver are likely to be associated in metal metabolism, short term storage and elimination procedures, while the muscle is the major site for long term storage. Stable isotopes were used as natural dietary tracers, to further evaluate dietary relationships and to assess the influence of trophic position (d15N) and carbon sources (d13C) on THg accumu
lation. Isotopic nitrogen (d15N) values ranged from 12.4 to 16.6 ‰ demonstrating a broad range of trophic positions. Minor variation in carbon (d13C) enrichment was observed between species (–18.7 to –17.1‰). In most shark species, mercury concentrations increased with size, trophic position (d15N), and maturity stage, but not between location or collection period. As a community, deepwater sharks demonstrated moderate rates of THg biomagnification, as indicated by the regression slope (log (THg) = 0.2 d15N – 2.4, R2 = 0·35, P < 0·05). THg and fatty acid analyses of 61 mid-trophic species were measured for their usage in studies of diet in high-order predators and mercury bioaccumulation in the extended demersal food chain. The integrated use of these biochemical techniques has provided fundamental data on the reproduction, metal accumulation and trophic ecology of deepwater chondrichthyans. Understanding these parameters is imperative not only for the implementation of sustainable management but for habitat protection of deepwater chondrichthyans and their associated ecosystems

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.

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.

Includes abstract.
Includes bibliographical references.
Commercial fishing in False Bay, South Africa, began in the 1600s. Today chondrichthyans are regularly taken in multiple fisheries throughout the Bay. Using time series data and life history information I assessed the vulnerability of chondrichthyans to exploitation in False Bay. Extensive time series from five fishing methods, between 1897 and 2011, enabled catch trend analyses for chondrichthyans as a whole as well as for specific species. Commercial linefish, beach seine, and recreational angling provided the best source of data because they cover the range of habitats found in the Bay and are the least selective methods.

Includes abstract.
Includes bibliographical references.
Commercial fishing in False Bay, South Africa, began in the 1600s. Today chondrichthyans are regularly taken in multiple fisheries throughout the Bay. Using time series data and life history information I assessed the vulnerability of chondrichthyans to exploitation in False Bay. Extensive time series from five fishing methods, between 1897 and 2011, enabled catch trend analyses for chondrichthyans as a whole as well as for specific species. Commercial linefish, beach seine, and recreational angling provided the best source of data because they cover the range of habitats found in the Bay and are the least selective methods.

Trawl fisheries have been operating in South African waters for roughly 110 years. In contrast to other trawl fisheries, the South African fishery was opened by government-funded scientific trawl surveys beginning in 1898. Detailed records of survey trawls undertaken immediately prior to and during the beginning of commercial trawling activity provided a rare opportunity to examine longterm changes in fish abundance. This dissertation focuses on the chondrichthyans, which are believed to be the group of fishes most at risk from intense exploitation. Despite some problems associated with changes in taxonomy and the efficiency of gear, this analysis was able to compare two distinct periods at three taxonomic levels: The periods were taken to represent baseline values prior to the opening of trawl fisheries and contemporary data, separated by roughly 80 years of intense, trawling activity. Three historically important trawl grounds were identified as having sufficient samples from each period. Between the surveys, trawl velocity did not deviate much from contemporary trawl velocities, although all surveys were found to have a significantly different velocity. In respect to the catch composition, significant changes were found in the relative abundance of the total catch composition, as a general shift from large, long-lived species towards smaller species was found. This applied both for teleosts as well as chondrichthyans, with the entire chondrichthyan catch composition showing a decrease, with the exception of Callorhinchus capensis, which increased significantly. Changes in chondrichthyan swept-area density were found to follow those trends found in the relative abundance: An increase was found in Callorhinchus capensis, whereas all other species decreased. All chondrichthyans were classed in low productivity categories and were assigned a high risk factor to overfishing. Reasons for the declines in the chondrichthyan assemblage were low fecundity, slow maturation and the inability due to these factors to adapt to an environment altered by trawling. Only in the case of Callorhinchus capensis were secondary effects of trawling such as the removal of competitor species likely to have caused the increase in relative abundance and swept area density as well as Callorhinchus capensis having a relatively high fecundity among chondrichthyans. In general, chondrichthyan decreases exceeded those of teleosts, and this work provides broad empirical support for the hypothesis that the low fecundity and slow growth of chondrichthyan species places this group at higher risk than teleosts.

Les chondrichthyens sont caractérisés par des particularités anatomiques uniques, ce qui, combiné à leur position phylogénétique, en fait un groupe particulièrement attrayant en biologie de l’évolution. Compte tenu de leur squelette cartilagineux, leur registre fossile est principalement constitué de dents isolées, dont la microstructure des tissus est utilisée depuis longtemps dans un contexte taxonomique. Celle-ci permet en effet de différencier les chondrichthyens modernes (néosélaciens) des groupes éteints dans le registre fossile. La microstructure dentaire de nombreux d’entre eux demeure toutefois peu connue, notamment celle des batoïdes, pourtant le groupe de chondrichthyen le plus diversifié à l’heure actuelle.La première partie de ce travail porte sur une description approfondie de la microstructure dentaire des batoïdes, basée sur un large échantillonnage de formes fossiles et actuelles. Ces observations ont permis de décrire une diversité microstructurale importante et inattendue compte tenu de la stabilité évolutive de ces tissus chez les requins. Cette variation est ensuite abordée à travers une approche histologique et transcriptionelle du développement dentaire de formes actuelles. Les résultats obtenus suggèrent la convergence de ces tissus avec l’émailloïde présent chez certains ostéichthyens. La troisième partie de ce travail porte sur la calcification du squelette cartilagineux au cours du développement embryonnaire, dans un contexte morphologique et moléculaire. Les modalités de calcification des pièces squelettiques apparaissent ainsi beaucoup plus versatiles chez les chondrichthyens que chez les ostéichthyens
Chondrichthyans exhibit a number of interesting features which make them valuable organisms to investigate from an evo-devo perspective. However, due to their cartilaginous skeleton, isolated teeth are usually the only available fossil material to reconstruct their evolutionary history. Their teeth are covered by enameloid, a hypermineralized tissue whose microstructure has proven a useful taxonomic tool to differentiate between modern forms (neoselachians) and their extinct relatives. However it is poorly known in several groups, thus casting doubts on the validity of such characters.In this work, I first describe the enameloid microstructure of batoids based on an extensive sampling of both their extant and extinct diversity. I highlight unexpected diversity in the microstructural organization of enameloid which was thought to be very stable in neoselachians. The developmental basis for this diversity was then investigated in two extant chondrichthyan models through classic histological techniques and in situ hybridization. The results highlight differences in their enameloid organic matrix, as well as important differences with enameloid formation in osteichthyans, casting doubts on the homology of the two tissues. Finally I investigate skeletogenesis in the lesser spotted catshark from both a morphological and molecular perspective. Using X-Ray microtomography and in situ hybridization, I highlight both the mineralization sequence of the cartilaginous skeleton and the molecular context in which it calcifies over the course of embryonic development. I find that skeletal calcification in chondrichthyans appears to be much more versatile than in osteichthyans

Afin de determiner l'interet du revetement cutane dans la systematique et la phylogenie des raies, 239 especes appartenant aux taxons des pristiformes (poissons-scies) et rajiformes (raies s. S. ) ont ete etudiees. L'analyse de la morphologie et de l'arrangement des denticules et tubercules cutanes a permis d'apporte des renseignements complementaires sur la taxonomie des pristiformes, des rhinobatoides et des rajoides. Plusieurs caracteres morphologiques d'interet majeur ont ete nouvellement decrits. Neuf caracteres lies au revetement cutane ont ete utilises dans une matrice cladistique inspiree des travaux de nishida (1990). L'analyse obtenue a partir du logiciel paup 3. 0 precise les relations phylogenetiques des rhinobatidae, des platyrhinidae et met en evidence de nouveaux regroupements systematiques. Les resultats morphologiques, systematiques et phylogenetiques precisent les variations du revetement cutane avec les conditions de vie de batoides.

L’objectif de cette étude était de contribuer à une meilleure compréhension des poissons cartilagineux dans les eaux côtières libanaises du bassin oriental de la Méditerranée. Dans ce contexte, les différents aspects relatifs à la distribution, la diversité, la biologie et l’écologie de ces espèces ont été développés. Au total, 315 spécimens de poissons cartilagineux ont été échantillonnés appartenant à 25 espèces, dont 11 espèces de requins et 14 espèces de batoïdes. Aucune chimère n’a été enregistrée. Les données ont été collectées à partir (a) de captures expérimentales dans le cadre du projet "CIHEAM PESCA-Libano" et (b) d’observations périodiques des poissons dans les poissonneries et capturés par les pêcheurs. A partir des données de captures expérimentales, la distribution spatio-temporelle a été évaluée à travers lecalcul de ‘la capture par unité d'effort’. Cette dernière a été estimée à la fois à partir des données des scientifiques et commerciales, en prenant en considération le nombre total d’espèces. Différentes relations longueur-poids ont été établies pour 3 requins et 5 batoïdes, et cela pour les espèces présentant un nombre d’individus supérieur à 10. Finalement, la biologie et l’écologie de deux espèces commerciales bien exploitées dans les eaux côtières libanaises ont été présentées
The aim of this study is to contribute to a better knowledge of cartilaginous fish in the Lebanese coastal waters, Eastern Mediterranean. Emphasis was placed on various aspects of the distribution, diversity, biology and ecology of these species. In this study, a total of 314 specimens of cartilaginous fish were sampled. These specimens constituted of 25 cartilaginousfish species, 11 shark species and 14 batoid species. No chimaeras were recorded. The data was collected from two sources: (a) an experimental survey in the framework of the CIHEAM PESCA-Libano project and (b) periodic observation of fisheries and catches of hired fishermen. Spatiotemporal distribution was evaluated using the Catch Per Unit Effort of the experimental survey data. Spatiotemporal diversity was also estimated taking into account the total number of species caught in the survey and fisheries/fishermen data. Length-weight relationships for three sharks and five batoids were also presented for species of the combined data sources having more than 10 individuals. Finally, the biology and ecology of two commercially significant and exploited species were also presented as a first step in their fishery management andconservation

Telomeres, the protective caps at the ends of all vertebrate chromosomes, naturally undergo changes in length. These changes in telomere lengths may be a “molecular clock” by providing a counting mechanism of DNA replication events. In populations of jawed vertebrates (gnathostomes), telomere length has been shown to change with age; and thus measurements of telomere lengths may provide a novel means of determining the ages of free-living animals. Determinations of the age structure of populations of aquatic vertebrates (teleosts, chondrichthyans and marine mammals) are vital for sustainable management and conservation efforts. Yet, the commonly applied increment based ageing techniques are limited by the subjectivity of increment patterning and destructive sampling. I aimed to assess the application of telomere length as an age determinate for populations of aquatic vertebrates and to evaluate the biological implications and evolutionary origins of this trait amongst the gnathostomes. Telomere length change with age was investigated in an exemplar chondrichthyan, teleost and marine mammal species, to determine whether aquatic gnathostomes share the general pattern of declining telomeres with age, as found in terrestrial mammals. Chapter Two provides the first assessment of telomere length change with age in a chondrichthyan species, the Port Jackson shark. Four types of tissues from Port Jackson sharks, ranging in age from 0 to 17 years, were sampled and telomere length were estimated using three measurement methods: (i) relative quantitative PCR (qPCR); (ii) absolute qPCR; and (iii) the terminal restriction fragment (TRF) analysis. No relationship between telomere length and age was found for any of the tissues, using any method. In Chapter Three, telomere length was measured in specimens of the common carp from two tissues using the absolute qPCR method. Telomere length measurements were then correlated with ages estimated from otolith increment counts and length-at-age calculations. Measurements of telomere length were highly variable in both muscle biopsies and fin clips; however, telomeres from muscle biopsies significantly increased in length – in contrast to the more generalised pattern of telomere length attrition and marking the second reported case of an increase in telomere length with age in vertebrates. In terrestrial mammals telomere shortening is negatively correlated with donor age. In Chapter Four, I tested whether this pattern of declining telomere lengths was found in a pinniped species, the Australian sea lion. Telomere lengths were measured in flipper clips from specimens by absolute qPCR and compared between three age classes: pups, juveniles, and adults. Mean telomere lengths of the adults were significantly smaller than the juvenile and pup classes confirming that the Australian sea lion shares the general mammalian pattern of telomere length attrition. Relationships between the rate of telomere length change with age and species longevity have been observed in birds and mammals, suggesting that the rate of telomere length change is an informative measure of ageing. In Chapter Five, using a data set of 20 teleost and chondrichthyan species, I tested whether fishes showed a similar pattern. I found that the rate of telomere length change with age is significantly different between species of fishes and that these rates of change are inversely correlated with longevity. The findings of Chapters Two, Three & Four indicated that telomeres do not provide a suitable means of determining the ages of individuals and at best are limited to assigning broad age classes. This is largely due to the high degree of variability of telomere lengths between individuals within all age classes. In addition, these Chapters (2, 3 & 4) also highlight that patterns of telomere length change with age are highly variable within the gnathostomes; and thus, telomere length change cannot be characterised by a single pattern for all lineages. In fact, three patterns of telomere length change with age in the gnathostomes were found: (i) declining telomere lengths; (ii) increasing telomere lengths; and (iii) no significant change in telomere length with age. However, identifying the selective factors responsible for the assignment of patterns of telomere length change is hampered by a lack of the understanding of the evolutionary origins of these patterns. Therefore, in Chapter Six I sought to outline the phylogenetic distribution of patterns of telomere length change with age in the gnathostomes to determine the evolutionary origin(s) of this trait. Two alternative hypotheses for the evolution of telomere length change were tested by ancestral state reconstruction in a set of 40 gnathostomes, for which I have significantly expanded the sampling of chondrichthyans and teleosts. The most likely/parsimonious pattern of telomere length change in the common gnathostome ancestor suggested that telomere length change with age was not present ancestrally and has since evolved independently. I was also able to elucidate the evolutionary history of transitions to and between the three patterns of telomere length change within the available gnathostome lineages, with the birds and teleosts displaying the highest rates of evolutionary lability of patterns of telomere length change with age. The macro-evolutionary analysis (Chapter 6) identified relatively rapid evolutionary patterns of telomere length change with age in two gnathostome clades. However, as highlighted by the variability of telomere lengths among individuals within all age classes, furthering an interpretation of the causes and consequences of variable patterns of telomere length change will require a focus at the species level and a shift to following individuals through out their lifetime.
Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2010

A revision of the species of Eudactylina (Eudactylinidae : Siphonostomatoida) and Kroyeria (Kroyeriidae : Siphonostomatoida) was conducted, based on type and other specimens of parasitic copepods from museums and personal collections. A description of the external morphology of each genus is included. Taxonomic, phyloge netic, and functional significance of the morphology of the general habitus, first and second antennae, oral and thoracic appendages are discussed. The taxonomic account of the above genera recognized all nominal species in the literature. Illustrations and phylogenetic analyses, however, were necessarily restricted to only the material examined in an attempt to standardize the abstractions and interpretations associated with character observation. Detailed redescriptions are given of E. acuta, E. aspera, E. chilensis, E. corrugata, E. indivisa, E. insolens, E. Iongispina, E. myliobatidos, E. oliveri, E papillosa, E. peruensis, E. pollex, E. pusilla, E. similis, E. spinifera, E. squamosa, E tuberifera, E. turgipes, and new descriptions (all in press) are given of, E. aphiloxenous, E. dactylocerca, E. diabolophila, E. epakto Iampte’ E. hornbosteli, E. nykterimyzon, E. pristiophori, E. urolo phi, and E. vaquetillae followed by the detailed reclescriptions of K. carchariaeglauci, K. caseyi, K. dispat K. elongata, K. gemursa, K. lineata, K. longicauda, K. papillipes, K. spatulata, K. sphyr nae, K. triakos and new descriptions (all in press) of K. branchioecetes, Kcresseyi, K. decepta, K. procerobscena, and K. rhophemophaga. In an attempt to unravel evolutionary relationships of their elasmobranch hosts and themselves a phylogenetic analysis of each genus is presented. In the heuristic analysis of Eudactyilna, 75 morphological characters resulted in a single tree with a consisitency index of 0.77 and a retention index of 0.88, indicating a high degree of character congruence. An exact search of nine species of Eudactylina with 55 charac ters resulted in a single tree with a consistency index of 0.88 and a retention index of 0.88. The Eudactylina-derived host cladograms posit monophyly of the shark-like squaloids , squatinids, pristiophorids, and batoids. This suggests that shark-like squaloids, angelsharks, and sawsharks are more closely related to rays than to other galeomorph sharks, whereas the pristiophorids represent the sister taxon to batoids. The eudactylinid dade found on the rhinopterids and mobulids appears to represent a colonization event followed by tight cospeciation. Eudactylina-derived carcharhinid relationships approximate conventional or currently accepted hypotheses. Eudactylina derived phyogenetic relationships of a subset of species from Squatina and Myliobatis indicate speciation patterns consistent with major vicariant events associated with the breakup of Pangaea during the Jurassic period approximately 160 MY. The phylogenetic analysis of Kroyeria, using 44 morphological characters result ed in a single tree with a consistency index of 0.75 and a retention index of 0.75. The Kroyeria-derived and Kroyeria-Kroeyerina-derived host cladograms posit an unconven tional placement for Galeocerdo. Galeocerdo diverges at the bottom of the tree before the Triakidae. A sphyrnid dade follows, functioning as the sister taxon to remaining members of the Carcharhinidae. The genus Carcharhinus appears paraphyletic with Negaprion and Prionace imbedded within this dade, corroborating similarly held views by other systematists. Congruent host and parasite cladogram topologies from both holocephalan and elasmobranch hosts suggest the existence of well-established and specific host-para site associations as early as the late Devonian, approximately 400 MY.

Chondrichthyans—sharks, rays, skates, and chimaeras—influence top down control of food webs and connect disparate ecosystems, yet populations of many species around the world have experienced sharp declines in abundance. Marine protected areas (MPAs) have a long history of conserving marine biodiversity, but their effectiveness to protect representative and critical habitat for threatened species on a global scale is controversial and hindered by a lack of biological and ecological data for the majority of chondrichthyan species. In this thesis, I use non-invasive baited remote underwater video (BRUV) and citizen science diver data to explore diverse chondrichthyan communities in two countries, South Africa and Costa Rica, with data-poor chondrichthyan fisheries and limit conservation funding, and the relationships of these chondrichthyans to biotic and abiotic factors in their habitats in and around MPAs. First, through a literature review, I find substantial taxonomic and geographic biases in understanding of reef shark biology, ecology, and conservation, which impair ability to implement effective conservation measures for these species. After identifying these research gaps, I used BRUVs to explore the diversity of a chondrichthyan hotspot in South Africa, finding many poorly understood endemic chondrichthyans. I discovered strong associations of the chondricthyan community to different habitat types (sand versus reef and kelp habitat), which resulted in poor diversity within one of the region’s larger MPAs—a whale sanctuary whose focus on large charismatic whales left mostly poorer quality sand habitat protected. However, a high occurrence of chondrichthyans within a neighbouring MPA suggested even small MPAs can conserve a high abundance of smaller species, especially if residency can be demonstrated. I then used the BRUV data to examine the relationships amongst these chondrichthyans and the community of other marine animals within the region, finding strong co-occurrence patterns that suggest chondrichthyans, particularly the endemic catsharks, could serve as effective ‘umbrella’ species for conservation in this region where little other information is available for conservation planning and monitoring. Finally, at Cocos Island, an MPA off Costa Rica, I discovered similarly strong, species-specific associations to another aspect of habitat: temperature. I found significant and species-specific responses to the El Niño–Southern Oscillation (ENSO). For example, the scalloped hammerhead Sphryna lewini counts declined by 224.7% during strong El Niño conditions and by 14.7% with just a 1°C rise in SST, while the benthic whitetip reef shark Triaenodon obesus had a weaker response, dropping by only 7.9% and 4.4%, respectively. In general, strong El Niño events reduced sightings within the MPA, providing some of the first indications of how a rising frequency and intensity of these events will impact the spatial distribution of both chondrichthyans and their habitat in the Eastern Tropical Pacific. Overall, this thesis provides insight into the factors influencing chondrichthyan abundance and diversity, demonstrating the importance of considering both biotic and abiotic factors during MPA design and the need to study these factors across diverse taxonomic groups and ecosystems.
Graduate
2021-05-08

As fisheries move into deeper waters the ability of deepwater chondrichthyans to sustain fishing is relatively unknown, although the limited information to date suggests most are inherently vulnerable to exploitation. Knowledge of deepwater chondrichthyans life history traits is required to enable effective management of deepwater chondrichthyans, as life history traits are important indicators of the productivity of species and consequently, species abilities to tolerate fishing pressure. This dissertation aimed to further knowledge of the life histories of deepwater chondrichthyans by assessing patterns in their traits and studying the life history of species taken as bycatch in a deepwater trawl fishery within the Great Barrier Reef Marine Park. It also addressed the issue of the inability to age many deepwater chondrichthyans through investigation of a novel approach to ageing, that is, by using near infrared spectroscopy. The association of chondrichthyan life history traits and habitat was examined among the three main marine habitats of shelf, pelagic and deepwater, and also within the deepwater habitat. Life history traits were obtained from 226 populations of chondrichthyans across the three habitats. These traits were analysed for patterns using a linear mixed effects model that controlled for the correlation among species due to their common evolutionary history. Life history differences were identified between chondrichthyans from shelf, pelagic and deepwater habitats, and within the deep habitat down the continental slope. Deepwater species as a group, had lower growth rates, later age at maturity and higher longevity than both shelf and pelagic groups of species. In the deep habitat, with increasing depth, most species matured later, lived longer, had smaller litters and bred less frequently. The group of deepwater species also had a smaller body size than the groups of shelf and pelagic species, which indicates body size is not appropriate as a predictor of vulnerability in most deepwater chondrichthyans. The visual interaction hypothesis offers a potential explanation for these findings, and it is apparent habitat influences the trade-offs in allocation of energy for survival and reproduction. In general, deepwater chondrichthyans are more vulnerable to exploitation than shelf and pelagic species and this vulnerability markedly increases with increasing depth. The life history traits of the deepwater chondrichthyans as a group are unique from the shelf and pelagic groups of species, and reflect adaptations driven by both mortality and resource limitations of their habitat. The chondrichthyan bycatch from the deepwater eastern king prawn fishery at the Swain Reefs, in the southern Great Barrier Reef Marine Park, was sampled onboard two commercial prawn trawlers. In all, 1533 individuals were collected from 11 deepwater chondrichthyan species, with a skate, Dipturus polyommata, most dominant by number at 50% of the bycatch. A dogfish, Squalus megalops and a catshark, Asymbolus pallidus were the other dominant species accounting for 28% and 15% of the bycatch, respectively. They were followed by a gummy shark, Mustelus walkeri which accounted for 3% of the bycatch. The remainder of the species were captured infrequently, and included an angelshark (Squatinidae), stingarees (Urolophidae) and a shortnose chimaerid (Chimaeridae). Preliminary biological data was obtained from all these infrequently caught species. Dipturus polyommata, S. megalops and M. walkeri all had reliable ageing structures and were taken in sufficient numbers to enable detailed life history studies. A fourth deepwater species (a dogfish, Squalus montalbani) that occurs in the Great Barrier Reef Marine Park but which was collected from New South Wales, was provided to this study and was also investigated for age, growth and reproduction life history information. Dipturus polyommata was a small skate that was the shortest lived of the four species, with an observed maximum longevity of 10 years. It also had the fastest growth, with a von Bertalanffy growth completion parameter of k = 0.208 year⁻¹ for combined sexes, and it matured at the earliest age, with males reaching maturity at 4.0 years and females at 5.1 years. Mustelus walkeri was a moderately sized shark that lived longer than D. polyommata, with the oldest male 9 years and oldest female 16 years. It also grew more slowly with a combined sexes k = 0.033 year⁻¹ , and matured later with males estimated to mature at 7–10 years and females at 10– 14 years. The two dogfish species, S. megalops and S. montalbani were small and moderately sized dogfish, respectively. They had the slowest growth rates of all four species; with S. megalops combined sexes k = 0.003 year⁻¹ and S. montalbani combined sexes k = 0.007 year⁻¹. These dogfish were also longer lived than D. polyommata and M. walkeri with maximum observed ages for males and females of 18 and 25 years for S. megalops, and 28 and 27 years for S. montalbani. Further, they were the oldest at maturity with S. megalops males mature at 12.6 years and females at 19.1 years. Squalus montalbani males were mature at 21.8 years and females at 26 years. All viviparous species had low fecundity with litter sizes of 5–7 for M. walkeri, 2–3 for S. megalops and 9–16 for S. montalbani. The oviparous D. polyommata had an average ovarian fecundity of 8 follicles which was low compared to other small–medium sized Dipturus species. The age, growth and reproduction of these four species corroborated the life history pattern analyses. Assuming that fishing mortality was the same among species, it is likely that the shallowest dwelling D. polyommata was the most productive, followed by the slightly deeper occurring M. walkeri and then the two deeper dwelling dogfish. Squalus megalops was likely more productive than the deepest occurring S. montalbani. Reliable age information is essential to accurately predict the ability of chondrichthyan species to sustain exploitation, yet many deepwater chondrichthyans cannot be aged as they do not have reliable age structures. A novel approach to ageing, that is, using near infrared spectroscopy for ageing (NIRS), was first trialled on two coastal species, Sphyrna mokarran and Carcharhinus sorrah, both of which been previously age validated. NIRS successfully predicted their ages up to 10 years of age for both species, with the correlations between the known ages of the vertebrae and their near infrared spectra strong at R² values of 0.89 and 0.84 for S. mokarran and C. sorrah, respectively. The NIRS approach was then applied to three species of deepwater sharks using their dorsal fin spines, vertebrae and fin clips. Ages were successfully estimated for the two dogfish, S. megalops and S. montalbani, and NIRS spectra were correlated with body size in the catshark, Asymbolus pallidus. Correlations between estimated-ages of the dogfish dorsal fin spines and their NIRS spectra were good, with S. megalops R² = 0.82 and S. montalbani R² = 0.73. NIRS spectra from S. megalops vertebrae and fin clips that have no visible growth bands were correlated with estimated-ages, with R² = 0.89 and 0.76, respectively. This study demonstrated that the NIRS approach to ageing was feasible for age estimation of sharks. The NIRS ageing approach is rapid, which is a major advantage of the method, and could enable large numbers of sharks to be aged quickly. This offers the fisheries management benefit of improving the reliability of age information for stock and risk assessments. NIRS also has the capacity to non-lethally estimate ages from fin spines and fin clips, and thus could significantly reduce the numbers of sharks that need to be lethally sampled for ageing studies. This NIRS approach is the first chemical assay approach investigated in shark ageing that is simple, rapid and cost-effective. The detection of ageing materials by NIRS in poorly calcified deepwater shark vertebrae that have no visible bands, could potentially enable ageing of this group of sharks that are vulnerable to exploitation. This ageing and life history research has improved the understanding of deepwater chondrichthyans. This group of chondrichthyans have a unique suite of life history traits that render them more vulnerable to fishing pressure than their counterparts in shelf and pelagic waters, with their vulnerability increasing with depth. This knowledge is vitally important to fisheries management because the deeper the fishing, the less capacity the chondrichthyans have to recover. The findings of this dissertation can be used to facilitate more effective management and conservation strategies needed to ensure this group of chondrichthyans are sustainably fished and not placed at risk of extinction.

archives@tulane.edu
In this dissertation, I characterize the origins, phylogenetic distribution, and function of Follicle Cell Processes (FCP) in Class Chondrichthyes. FCP are actin associated tubes that have been detected in the intercellular space between a developing oocyte and the surrounding follicle cells in chondrichthyan fishes. Using light microscopy, I describe the presence FCP in Hydrolagus colliei, a species of Subclass Holocephali, a divergent lineage at the base of the chondrichthyan phylogeny. FCP were also detected in species representing six of nine studied orders of Subclass Elasmobranchii, the sister group of holocephalans, but absent in three examined batoid orders. To establish the role FCP play in vitellogenesis - the process of providing yolk to developing oocytes - I performed fluorescent microscopy, staining specifically for myosin, an actin-associated transport protein previously identified in vitellogenic oocytes. The detection of myosin in oocytes during vitellogenesis and its association with actin in FCP are inconclusive. I performed RNA sequencing on follicles and ovarian tissues from Mustelus sinusmexicanis, using Illumina Hi-Seq 4000 profiling with the specific aim of identifying the types of myosins and actins involved in yolk transport. Three (MYH9, MYH10, and MYO5A) of particular interest and one actin (ACTG1L) were differentially expressed in the tissues. MYO5A is a class V myosin that has been associated with cytoplasmic vesicle transport, though it is most abundant in melanocytes and nerve cells. MYH9 and MYH10 are membrane associated non-muscle class II myosin paralogs, and MYH9 was upregulated in the ovarian tissues; MYH10 was upregulated in the corresponding follicle tissues. ACTG1L, the only actin transcript differentially expressed codes for a gamma actin isoform involved in internal cell mobility.
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Lydia Crawford

Magister Scientiae (Biodiversity and Conservation Biology)
The oligonchoinean monogenean family Hexabothriidae Price, 1942 currently consists of approximately 60 valid species, representing 15 genera. Hexabothriids are gill parasites of chondrichthyan fishes (sharks, rays and chimaeras). Some hexabothriid species have been reported as problematic in public aquaria, directly responsible for host pathology and subsequent host mortalities. However, without information on specific hexabothriid species and their host associations, accurate captive management of hexabothriids in public aquaria is hindered. Hexabothriid taxonomy is in a state of confusion. The historic taxonomic restoration of the priority of Hexabothrium sees the beginning of the taxonomic uncertainty of the hexabothriids, and is continued into the present literature particularly among lower-level taxa in Hexabothriidae. In addition, there is currently no consensus for a single accepted morphometric protocol for the discrimination of hexabothriid taxa, which leads to unnecessary ambiguity of character variable nomenclature, measurement and interpretation. A call for stability in the nomenclature and morphometric discrimination of species is therefore proposed. A novel morphometric protocol is tested for the sclerotised haptoral armature, supported by the proteolytic digestion of structures for optimal representation. Character variables, subjected to univariate and multivariate analyses were systematically accepted or rejected based on their potential to discriminating species of Callorhynchocotyle Suriano and Incorvaia, 1986. The hexabothriid genera Callorhynchocotyle and Branchotenthes, represented by South African taxa, are reviewed, using these variables. Four Callorhynchocotyle species and 2 Branchotenthes species are redescribed with the inclusion of some new voucher specimens.

Chondrichthyans are cartilaginous fishes that include the extant chimaeras, sharks, and batoids, and their extinct relatives. In this dissertation, I examined the growth, development, and relationships of extinct and extant chondrichthyans. I reexamined the skeleton of fossil and fetal specimens of the angel sharks (Squatiniformes) and reanalyzed the current morphologically based hypothesis of chondrichthyan evolution, which conflicts with the current molecular based hypothesis. I did this by including extinct taxa and new characters based on dentition, and the ethmoid, occipital, pectoral, and vertebral skeleton. My results supported the pre-existing morphological hypothesis that angel sharks, saw sharks, and batoids form a clade. However, some of my new characters, particularly those based on the vertebral morphology, indicate that fetal and juvenile angel sharks do not share as many apomorphies with batoids as previously hypothesized from the examination of adults. I also examine the relationships of major groups within batoids, beginning with the construction of a hypothesis of the evolutionary history of electric rays (Torpediniformes). My results are consistent with previous rank-based classifications. However, they deviate from previous classifications depending on the criteria used to generate the hypothesis and on which taxon, or combination of taxa, were used to root the ingroup phylogeny. Because pectoral and vertebral morphology are so critical to morphological hypotheses, I also examined the growth and development of the synarcual cartilage in batoid fishes, with particular emphasis on the synarcual of skates (Rajiformes). My results demonstrate that calcification and chondrification do not proceed in the same order, temporally and spatially. Finally, I redescribe the extinct batoid †Cyclobatis, known only from the Cretaceous, and evaluate its phylogenetic position. My results indicate that †Cyclobatis, the oldest known rajid, is also the sister taxon to a clade of all known extant members of Rajidae. Furthermore, the inclusion of new characters, mainly derived from the synarcual, help to resolve the interrelationships of Rajidae.
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