This thesis develops the first open population model for any shark species worldwide using the Cormack-Jolly-Seber (CJS) model. In conjunction with a tagging study, five auxiliary studies were conducted to investigate stock structure, post-release mortality, tag shedding, and tag-reporting rates. The results from each of the studies were used to correct for any violations of the models assumptions to provide the first unbiased estimates of survival and abundance for the raggedtooth shark (Carcharias taurus) in South Africa. The C. taurus population exhibited complex stock structuring, by size and sex. Competitive shore anglers fished an estimated 37, 820 fishing days.year⁻¹ (95% C.I. = 28, 281 - 47, 359 days.year⁻¹) for sharks, and caught 1764 (95% C.I. = 321 – 3207) C. taurus. Although released alive, post-release mortality ranged from 3.85% for young-of-the-year sharks to 18.46% for adult sharks. Between 1984 and 2004, a total of 3471 C. taurus were tagged. In all, 302-tagged sharks (8.7%) were recaptured. Both juvenile (< 1.8 m TL) and adult sharks (> 1.8 m TL) displayed philopatric behaviour for specific parts of their ranges, including gestating and parturition areas. Significant differences were observed in the percentage of recaptures between the different tag types, tagging programs, individual taggers and capture methods used to tag sharks. The annual tag retention rate for juvenile sharks, 94.19% (95% C.I. = 80.68% - 100.00%) was significantly higher than for adult sharks, estimated at 29.00% (95% C.I. = 6.76% - 64.39%). Tag reporting rates, from fishermen varied both spatially and temporally from 0.28 (95% C.I. = 0.00 – 0.63) to 0.77 (95% C.I. = 0.56 – 0.97). Associated tag wound damage and biofouling growth indicated that B-type tags were a suitable tag type for use on C. taurus, whereas C-type tags were not. The CJS bias-adjusted estimate for juvenile survival was 0.456 (95% C.I. = 0.367 – 0.516) and for adult sharks, 0.865 (95% C.I. = 0.795 – 0.915). From 1984 to 2004 the mean bias-adjusted population size for juvenile sharks was estimated at 3506 (95% C.I. = 2433 – 4350) and for adult sharks, 5899 (95% C.I. = 7216 – 11904). Trends in abundance over the 20-year study period indicated a stable, healthy population.

The blacknose shark (Carcharhinus acronotus) is a common small coastal shark species found in nearshore waters along the southeast coast of the United States, from North Carolina into the Gulf of Mexico and extending further south into the Bahamas. There has been some debate in recent years over the reproductive periodicity of C. acronotus in waters off the U.S. coast. Earlier studies have suggested that Gulf C. acronotus reproduce on an annual basis whereas the Atlantic populations of this species may reproduce biennially. Additionally, there have been no known studies on the diet of C. acronotus. The goal of the present study was to re-evaluate the reproductive biology of the Atlantic populations of C. acronotus with the intent on clarifying discrepancies in reproduction as well as provide information on dietary trends. This was accomplished by examining male and female reproductive tracts and gut contents in animals caught throughout the Atlantic range of C. acronotus. Based on these data, spermatogenesis occurs between late May to early July with peak sperm production occurring in June and July. In females, follicular development is complete by late June-early July with ovulation occurring shortly afterwards. Mating occurs between mid-June and early July based on the presence of fresh mating scars on females captured during this time. Current data suggests that gestation begins late July with parturition occurring late May to early June the following year. As observed in earlier studies, reproductive periodicity appears to be largely biennial. However, evidence for concurrent follicular development and pregnancy was observed in several females, suggesting that at least a portion of the Atlantic population may reproduce on an annual basis. Dietary data shows a dominance of teleost prey items in the diets of C. acronotus with scianids making up the majority of the identifiable teleosts.

[Truncated abstract. Formulae and special characters in this field can only be approximated. See PDF version for accurate reproduction.] Solar salt producers use solar energy to evaporate seawater as it flows through a series of ponds. The Shark Bay Salt solar ponds, at Useless Inlet in Western Australia, vary in salinity from that of seawater to four times seawater, over the pond sequence. Water column photosynthesis and biomass decreased markedly with increasing salinity along the pond sequence, while benthic productivity increased as cyanobacterial mats developed. Correspondingly, net productivity shifted from autotrophy to heterotrophy in the water column and from heterotrophy to autotrophy in the benthos. Both shifts occurred at intermediate salinity in the pond sequence, where there was low production in both the water column and benthos. Within individual ponds, productivity, algal biomass and physico-chemical conditions were relatively constant over the year of study. Transitions between benthic and planktonic production along the pond sequence were driven mostly by direct responses to salinity stress, as well as the formation of a gypsum crust on the pond floors at higher salinity (>120 g kg-1). This transition is similar to that which occurs in saline lakes undergoing anthropogenic salinisation and identifies critical salinities for the restoration of these lakes.

Cette thèse porte sur deux espèces de grands requins, le requin bouledogue Carcharhinus leucas et le requin tigre Galeocerdo cuvier. Les objectifs sont d'étudier la structure génétique de leurs populations, la taille efficace des populations identifiées et les modes de reproduction de ces deux espèces. Une différenciation génétique importante a été identifiée entre les populations de requin bouledogue de l'Ouest de l'océan Indien et de l'Ouest du Pacifique, reflétant soit une absence de flux de gènes contemporains, soit des flux de gènes uniquement assurés par les mâles. À l'inverse, les populations de requin tigre de ces deux régions sont homogènes génétiquement. Une plus faible diversité génétique a été identifiée chez le requin tigre que chez le requin bouledogue, peut-être liée à une diminution forte des effectifs datant de moins de 3 000 ans. Autour de La Réunion, les populations des requins bouledogue et tigre suivent des dynamiques différentes, liées à leurs modes de reproduction. Chez le requin bouledogue, les individus semblent fidèles à des zones côtières particulières (philopatrie) pour s'accoupler et/ou mettre bas, et les portées sont fréquemment issues de plusieurs pères (polyandrie). À l'inverse, les zones d'accouplement et de mise bas du requin tigre restent mal connues, et cette espèce semble exclusivement monoandre, caractéristiques liées à sa nature semi-océanique. Ces travaux montrent les capacités de dispersion importantes de ces deux espèces. Leurs populations présentent des dynamiques différentes induisant une vulnérabilité différente aux pressions anthropiques. / This PhD thesis focuses on two large shark species, the bull shark Carcharhinus leucas and the tiger shark Galeocerdo cuvier. The aims are to study the genetic structuring of their populations, the effective population size of the delimited populations and the reproductive modes of both species. A strong genetic differentiation was highlighted between bull shark populations from the Western Indian Ocean and the Western Pacific, due to either an absence of contemporary gene flow or to an absence of female gene flow only. On the opposite, tiger shark populations seem genetically homogenous, with important genetic connectivity between both regions. Within each region, no genetic differentiation among localities was highlighted for both species. A weaker genetic diversity was identified for the tiger shark, probably linked to the occurrence of a recent bottleneck occurring less than 3,000 years ago. Around Reunion Island, bull and tiger shark populations present different dynamics, linked to their reproductive modes. Bull shark individuals from both sexes seem to exhibit some fidelity to specific coastal sites (philopatry) to mate and/or deliver embryos, and litters are frequently issued from several fathers (polyandry). On the opposite, mating and pupping areas of the tiger shark remain poorly known, and this species seems exclusively monoandrous, probably linked to its semi-oceanic nature.This work highlights the high dispersal abilities of both species. Their populations present different dynamics, leading to different sensitivities to anthropogenic pressures. These results point out the need to adopt management plans specific to each species

Chapter 1 DNA barcoding based on the mitochondrial cytochrome c oxidase subunit I (COI) gene sequence is emerging as a useful tool for identifying unknown, whole or partial organisms to species level. However, the application of only a single mitochondrial marker for robust species identification has also come under some criticism due to the possibility of erroneous identifications resulting from species hybridizations and/or the potential presence of nuclear-mitochondrial psuedogenes. The addition of a complementary nuclear DNA barcode has therefore been widely recommended to overcome these potential COI gene limitations, especially in wildlife law enforcement applications where greater confidence in the identifications is essential. In this study, we examined the comparative nucleotide sequence divergence and utility of the mitochondrial COI gene (N=182 animals) and nuclear ribosomal internal transcribed spacer 2 (ITS2) locus (N=190 animals) in the 8 known and 1 proposed cryptic species of globally widespread, hammerhead sharks (family Sphyrnidae). Since hammerhead sharks are under intense fishing pressure for their valuable fins with some species potentially set to receive CITES listing, tools for monitoring their fishery landings and tracking trade in their body parts is necessary to achieve effective management and conservation outcomes. Our results demonstrate that both COI and ITS2 loci function robustly as stand-alone barcodes for hammerhead shark species identification. Phylogenetic analyses of both loci independently and together accurately place each hammerhead species together in reciprocally monophyletic groups with strong bootstrap support. The two barcodes differed notably in levels of intraspecific divergence, with average intraspecific K2P distance an order of magnitude lower in the ITS2 (0.297% for COI and 0.0967% for ITS2). The COI barcode also showed phylogeographic separation in Sphyrna zygaena, S. lewini and S. tiburo, potentially providing a useful option for assigning unknown specimens (e.g. market fins) to a broad geographic origin. We suggest that COI supplemented by ITS2 DNA barcoding can be used in an integrated and robust approach for species assignment of unknown hammerhead sharks and their body parts in fisheries and international trade. Chapter 2 The gray reef shark (Carcharhinus amblyrhynchos) is an Indo-Pacific, coral reef associated species that likely plays an important role as apex predator in maintaining the integrity of coral reef ecosystems. Populations of this shark have declined substantially in some parts of its range due to over-fishing, with recent estimates suggesting a 17% decline per year on the Great Barrier Reef (GBR). Currently, there is no information on the population structure or genetic status of gray reef sharks to aid in their management and conservation. We assessed the genetic population structure and genetic diversity of this species by using complete mitochondrial control region sequences and 15 nuclear microsatellite markers. Gray reef shark samples (n=305) were obtained from 10 locations across the species’ known longitudinal Indo-Pacific range: western Indian Ocean (Madagascar), eastern Indian Ocean (Cocos [Keeling] Islands, Andaman Sea, Indonesia, and western Australia), central Pacific (Hawaii, Palmyra Atoll, and Fanning Atoll), and southwestern Pacific (eastern Australia – Great Barrier Reef). The mitochondrial and nuclear marker data were concordant in most cases with population-based analysis showing significant overall structure (FST = 0.27906 (pST = 0.071 ± 0.02), and significant pairwise genetic differentiation between nearly all of the putative populations sampled (i.e., 9 of the 10 for mitochondrial and 8 of the 10 for nuclear markers). Individual-based analysis of microsatellite genotypes identified at least 5 populations. The concordant mitochondrial and nuclear marker results are consistent with a scenario of very low to no appreciable connectivity (gene flow) among most of the sampled locations, suggesting that natural repopulation of overfished regions by sharks from distant reefs is unlikely. The results also indicate that conservation of genetic diversity in gray reef sharks will require management measures on relatively local scales. Our findings of extensive genetic structuring suggests that a high level of genetic isolation is also likely to be the case in unsampled populations of this species.

Longline fishing is the most common elasmobranch capture method in the world, both for commercial fishing, and to a lesser extent for scientific surveys. The capture of an animal on a longline initiates a series of physiological responses designed to promote survivorship in the short term, but if unchecked, can cause reduced individual fitness and/or mortality in the long term. Given widespread declines in shark populations, an improved understanding of the physiological costs of longline capture is needed. The aim of this thesis was to investigate the physiological response of sharks to capture and restraint, to assess novel, non-invasive alternatives to scientific longline surveys, and to generate scientific insight into poorly understood elasmobranch populations in The Bahamas. The results presented herein suggest that some species of shark are able to recover from the physiological stress of capture despite the presence of persistent negative stimuli. Tonic immobility was assessed as a means of generating baseline blood chemistry data, but was found to be inappropriate given that it increases the magnitude of physiological perturbation in the short term. To avoid the stress of capture altogether, Baited Remote Underwater Video Surveys (BRUVS) were considered as a non-invasive alternative to capture based surveys, however, it was concluded that they lack the resolution necessary to answer fine scale demographic questions. For the Caribbean reef shark, longline surveys yielded high resolution data allowing the identification of fine scale spatiotemporal shifts in demographic population structure with minimal cost (mortality). Nevertheless, the ethics of using capture based surveys on sensitive species are questionable when alternative techniques are available. Deep water sharks caught on longline surveys exhibited high mortality rates, however, for these very poorly understood species moribund specimens have great scientific value which in some cases can offset the high ecological costs of the surveys. The results presented in this thesis highlight the on-going need for improved biological and ecological research into the majority of elasmobranch populations, particularly with regards to anthropogenic interactions such as capture. Given the tenuous conservation status of many species, the acquisition of applied, management focused data should remain the priority of elasmobranch scientists.

i Charles University Faculty of Social Sciences Institute of Economic Studies MASTER'S THESIS Are Sharks Worth More Alive Than Dead? A Stated Preference Study on Shark Ecotourism in Costa Rica. Author: Bc. Alicia Maria Berrios Supervisor: Mgr. Milan Ščasný PhD. Academic Year: 2016/2017 ii Declaration of Authorship The author hereby declares that he compiled this thesis independently; using only the listed resources and literature, and the thesis has not been used to obtain a different or the same degree. The author grants to Charles University permission to reproduce and to distribute copies of this thesis document in whole or in part. Prague, January 01st , 2017 Signature iii Acknowledgments With boundless appreciation, I would like to extend my gratitude to Mgr. Milan Ščasný PhD., for his incredible support in writing this research. He spent a countless number of hours on this thesis work, and ultimately, this research wouldn't have been possible without him. I would also like to express my gratitude to Carlos Avila, for his generosity in helping me conduct the in-person interviews. I would also like to express my gratitude to Prof. Melville Saayman, who helped tremendously in the experimental design of this work. Thank you to Mgr. Martin Kryl for programming the survey instrument. Lastly, I would like to...

Anecdotal evidence suggested that immature lemon sharks (Negaprion brevirostris) occur at the Chandeleur Islands in southeastern Louisiana. From May 2009 to August 2011, the Nekton Research Laboratory at the University of New Orleans regularly sampled habitats at the Chandeleur Islands to confirm the presence of immature individuals of this species. During these efforts, 147 immature lemon sharks (neonates, young-of-the-year, and juveniles) were collected. Each shark was PIT tagged and a tissue sample was taken for genetic analyses. Sizes ranged from 56 – 177 cm total length. Sharks showed a preference for sandy substrate and smaller individuals showed significant preference for shallow waters. Collection data for N. brevirostris were obtained from various locations around the Gulf of Mexico for comparison. Based on a review of current literature, collection data, and microsatellite analysis it was possible to classify the Chandeleur Islands as an elasmobranch nursery ground under the definition presented by Huepel et al. (2007). Current literature and high densities of N. brevirostris suggests that the Chandeleur Islands are the only area in the northern Gulf of Mexico where neonatal and YOY lemon sharks have been recorded. Results from a combination of SPOT 5 satellite tags, PIT tags, and FLOY tags show that immature N. brevirostris at the Chandeleur Islands remain in the vicinity of the islands for several months. The abundance of juvenile sharks across years provides evidence of continuous use of these islands as a pupping area. Genetic analysis supports this information with 7 of 15 mothers returning across years. The combination of this information indicates that the Chandeleur Islands are the northern- and western-most documented nursery ground for this species. Special care should be given to this habitat as CPUE for N. brevirostris decreased significantly during this research following the 2010 Deepwater Horizon disaster and subsequent oil prevention measures. Genetic research indicates a high level of inbreeding and genetic separation between the Chandeleur Islands population and other known populations in Florida, Belize, and the Bahamas.

No description available.

The genus Isistius Gill, 1864, which belongs to the family Dalatiidae, currently has three valid species: Isistius brasiliensis Quoy & Gaimard, 1824, I. plutodus Garrick & Springer, 1964 and I. labialis Meng, Zhu & Li, 1985. The most common species, I. brasiliensis, has a wide geographic distribution, and can be found in subtemperate and tropical seas; a comparative analysis of specimens from different localities has never been done. This study has thoroughly analyzed the morphological variation of this species along its distribution, elucidating that it represents only one species, and I. labialis becomes a junior synonym. The other species, I. plutodus, is known from only few specimens, raising doubts about their validity since I. brasiliensis is widely distributed. A detailed comparative analysis of these individuals was undertaken to test the validity of this species. The representatives of all the nominal species within Isistius were studied, identifying them morphologically and re-describing them through more precise characters. Therefore, this study analyzed minutely the external morphology, such as coloration, dentition, dermal denticles, body proportions, and internal morphology, such as the skeleton and musculature, of the known species, also covering morphometric and meristic aspects, to better define the genus and provide relevant morphological subsidies that may integrate future phylogenetic analysis of genera within the family / O gênero Isistius Gill, 1864, pertencente à família Dalatiidae, atualmente apresenta três espécies válidas: Isistius brasiliensis Quoy & Gaimard, 1824, I. plutodus Garrick & Springer, 1964 e I. labialis, Meng, Zhu & Li, 1985. A espécie mais comum, I. brasiliensis, tem uma ampla distribuição geográfica e pode ser encontrada em mares subtemperados e tropicais; uma análise comparativa detalhada de exemplares provenientes de diferentes localidades nunca foi feita. Este estudo examinou detalhadamente a variação morfológica desta espécie ao longo de sua distribuição, elucidando que ela representa apenas uma espécie, além de I. labialis ter se tornado um sinônimo júnior. A outra espécie, I. plutodus, é conhecida apenas por alguns exemplares, levantando dúvidas acerca de sua validade, dado que I. brasiliensis é amplamente distribuído. Foi feita uma análise comparativa detalhada destes indivíduos a fim de testar a validade da espécie. Estudaram-se representantes de todas as espécies nominais de Isistius, identificando-os morfologicamente e os redescrevendo através de caracteres mais precisos. Assim, este estudo analisou detalhadamente a morfologia externa, como coloração, dentição, dentículos dérmicos, proporções corporais, e interna, como esqueleto e musculatura, das espécies conhecidas além de examinar aspectos morfométricos e merísticos que auxiliaram na melhor definição do gênero e forneceram subsídios morfológicos relevantes que podem integrar futuras análises filogenéticas dentro da família