A classe Chondrichthyes compreende cerca de 1100 espécies divididas em duas subordens, Holocephali (quimeras) e Elasmobranchii (tubarões e raias). O monofiletismo da classe é sustentado pela calcificação prismática do esqueleto, presença de clásper pélvico, substituição periódica das fileiras dentárias. Porém, as interrelações em Elasmobranchii não estão claras. Duas hipóteses estão em discussão atualmente. A primeira delas, baseada em dados morfológicos, apresenta dois grandes grupos de tubarões, Galeomorphii e Squalomorphii, sendo que as raias (Batoidea) aparecem como espécies derivadas no segundo grupo. A segunda hipótese, baseada em dados moleculares, sugere que Galeomorphii e Squalomorphii forme um clado monofilético e que seja grupo-irmão de Batoidea. Portanto, a dúvida sobre o monofiletismo dos tubarões ainda persiste. Para tentar elucidar esta questão, este trabalho abordou a anatomia comparada dos músculos dos arcos maxilar e hióide de 98 espécies, pertencentes a 37 famílias, de tubarões, raias e quimeras. A musculatura de todas as espécies foi descrita, servindo de base para comparações entre as famílias. No total 35 caracteres são propostos, a partir de informações revisadas da bibliografia e das muitas observações, e devem ser testados em uma matriz de dados já existente. Os caracteres foram discutidos de acordo com questões filogenéticas dentro da subclasse Elasmobranchii, abordando problemas como a relação entre Orectolobiformes e Heterodontiformes, a relação entre Chlamydoselachus e Hexanchidae, o monofiletismo em Squaliformes, as discussões sobre o grupo Hypnosqualea e as relações entre Potamotrygonidae e as demais raias / The class Chondrichthyes comprises about 1110 species in two subclasses, Holocephali (chimaeras) and Elasmobranchii (sharks and rays). The monophyly of this class is supported by prismatic calcification of the skeleton, presence of pelvic claspers, substitution of teeth in dental rows. However, interrelationships within Elasmobranchii are not clear, with two principal hypotheses discussed. The first one, based on morphological data, presents two groups of sharks, Galeomorphii and Squalomorphii, and rays (Batoidea) are considered to have derived within the second group. The second hypotheses, based on molecular data, suggest Galeomorphii and Squalomorphii as a monophyletic clade, sister-group to Batoidea. Therefore, the question about the monophyly of sharks persists. To try to elucidate this issue, the present work examined the comparative anatomy of muscles of jaws and hyoid arches of 97 species, belonging to 37 families of sharks, rays and chimaeras. The musculature of all species was described, serving as a basis for comparisons among the families. A summary of 35 myological characters are proposed, based on information acquired from the literature and on personal observations, and should be tested in the context of a character matrix analyzed in a phylogenetic parsimony analysis. The characters described were discussed addressing the main phylogenetic questions within the subclass Elasmobranchii, regarding, for example, the relationship between Heterodontiformes and Orectolobiformes, the relationship between Chlamydoselachus and Hexanchidae, the monophyly of Squaliformes, the monophyly of Hypnosqualea, and the intrarelationships of potamotrygonid stingrays

Orientador: Fábio Porto Foresti / Resumo: As raias são elasmobrânquios que apresentam o corpo achatado dorso-ventralmente, além de cinco a sete pares de fendas branquiais que se encontram na região ventral do corpo e nadadeiras peitorais desenvolvidas e fundidas à cabeça. No Brasil, existem 29 espécies de raias em perigo de extinção de acordo com a Lista Vermelha da IUCN. As espécies de raias comercializadas muitas vezes são de difícil identificação devido à descaracterização, o que pode ser solucionado com o uso da técnica DNA Barcode, a qual é um sistema de identificação molecular baseado em uma sequência de DNA mitocondrial Citocromo Oxidase subunidade I (COI), atuando como código de barras de DNA de cada espécie. Esse sistema tem sido utilizado com êxito para identificar amostras que são comercializadas descaracterizadas e de forma ilegal. Desta forma, a técnica de DNA Barcode foi utilizada para a identificação de amostras de raias comercializadas em peixarias no estado de São Paulo e na CEAGESP, com o intuito de identificar quais são as espécies utilizadas no comércio e se atualmente ocorre a venda de espécies ameaçadas de extinção, assim como validar a técnica como ferramenta de rotina para controle de qualidade relacionado ao mercado de raias. Foram coletados 239 amostras, das quais 82 foram identificadas como espécies de raias, sendo elas Paratrygon aiereba (40,24%), Gymnura altavela (14,63%), Potamotrygon motoro (13,41%), Hypanus dipterurus (10,98%), Atlantoraja castelnaui (9,76%), Hypanus americanus (4,88%)... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Skates and stingrays are elasmobranch fish that display the body dormant ventrally, as well as five to seven pairs of branchial staves that separate into the ventral region of the body and pectoral fins that are fused to the head. There are currently 29 endangered species of skates and stingrays in Brazil according to the IUCN Red List. The marketed species of the group are often difficult to identify due to decharacterization, which can be solved using the DNA Barcode analysis, a molecular identification system based on a mitochondrial Cytochrome Oxidase subunit I (COI) DNA sequence that acts as a barcode of the DNA of each species. This system has been successfully used to identify illegally uncharacterised types of products. Thus, the DNA Barcode technique was used to identify species of stingrays and skates that are traded in fishmongers in the state of São Paulo and CEAGESP, in order to identify which species are marketed and if the sale of endangered species currently occurs, as well as validate a technique as a routine tool for quality control related to the group species. 239 specimens were collected, of which 82 were identified as species of stingrays and rays, which were Paratrygon aiereba (40,24%), Gymnura altavela (14,63%), Potamotrygon motoro (13,41%), Hypanus dipterurus (10,98%), Atlantoraja castelnaui (9,76%), Hypanus americanus (4,88%), Atlantoraja platana (2,44%) and Bathytoshia centroura (2,44%), of which B. centroura and P. aiereba, G altavela and A. castel... (Complete abstract click electronic access below) / Mestre

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The ability to raise an immune response is essential for all life. Despite this, the evolution of immune systems is poorly understood, as immune genes confound many bioinformatic analyses. This is driven by the rapid rates at which immune genes evolve due to the incessant arms race between host and pathogen often causing standard phylogenetic approaches to fail to accurately model the evolutionary history of immune gene families. Many phylogenetic lessons have been learned since the dawn of the phylogenomics era however, and genome sequences of non-model organisms have now been assembled, permitting improved immune gene detection and hence taxon sampling. In this thesis, I have paired sophisticated phylogenomic tools, including outgroup-free rooting methods, and substitution models that account for structural and functional constraints on protein evolution, with new genome and transcriptome sequence data from taxa that allow inference of the ancestral immune state in vertebrates and animals. Using this approach, I have managed to identify the origins of several key immune genes and families. My results support ancestral complexity in the genes that regulate the functioning of vertebrate adaptive immune systems. My findings also support the presence of a complement system, a front-line innate immune defence, in the ancestor of all animals. I show that this system later underwent a period of major remodelling early in vertebrate evolution, generating novel complement systems in at least three major vertebrate taxa. It is clear from my findings that combining sophisticated phylogenetic models with enriched taxon sampling represents a powerful approach with which to gain understanding of the evolutionary history of the immune system, even in the face of gene loss and the inherent complexity of immune gene evolution.

The taxonomy of gnathiids is solely based on the morphology of the adult males since they are more frequently encountered than the other life stages, therefore female and larval gnathiid descriptions are sometimes absent from species descriptions. Thirty-eight of the almost 180 known gnathiid species are described from Australian waters, with 12 of these collected from the Great Barrier Reef. The only described species parasitising elasmobranchs is Gnathia pantherina Smit and Basson, 2002, a species found on South African sharks and rays. Scientists have examined the relationships between host size and abundance of parasitic larval gnathiid isopods on Heron Island. This is an indication that gnathiids do feed on elasmobranchs but the lack of sampling plays a big role. The objectives of this study are therefore to identify three gnathiid species found on various elasmobranchs from Australia. A phylogenetic analysis will be conducted to confirm whether these species belong to the genus Gnathia Leach, 1814, to determine the relationship between Australian and South African gnathiids species and to see whether there is a correlation between phylogeny and geographic distribution of members of this genus. The statistical analysis using Primer version 5 will be used to provide the specific characteristics responsible for these species groupings seen in the cladograms. Gnathiids were collected from 1996 to 1998 and during March 2002 from various elasmobranchs from Australia. The eight shark and ray species collected from Lizard Island, Heron Island (Shark Bay), and Moreton Bay were; Carcharinus amblyrhynchos Bleeker, 1856, Triaenodon obesus Rüppell, 1837, Rhynchobatus djiddensis Forsskål, 1775, Rhinobatos typus Bennett, 1830, Himantura fai Jordan & Seale, 1906, Taeniura lymma Forsskål, 1775, Urogymnus asperrimus Bloch & Schneider, 1801 and Pastinachus sephen Forsskål, 1775. Larval gnathiid isopods were found attached to the gill filaments and septum of all sharks collected, their numbers and attachment positions were also recorded. After removal from hosts, larvae were kept in fresh sea water until they moulted into adult stages. The males did not conform to descriptions of any known gnathiid species, and were considered to be new to science. The descriptions were based on light and scanning electron microscopy observations. Summary 9 A phylogenetic analysis was conducted to determine where these new species fit into the genus Gnathia and where the new genus Tenerognathia Tanaka, 2005 fits into the family Gnathiidae. The species Caecognathia cryptopais Barnard, 1925 was also included in this study to verify whether this species belongs to the genus Caecognathia Dollfus, 1901. Primer version 5 was used to determine the characteristics responsible for the specific groupings identified by the phylogenetic analysis. The results showed that these three species belong to the genus Gnathia and are only found on Australian elasmobranchs. The findings also contributed to new host records for gnathiids. According to the phylogenetic analysis these new species grouped with the only known elasmobranch gnathiid from southern Africa, G. pantherina. These species made a separate grouping within the Gnathia genus indicating that they have specific characteristics that set them apart from other gnathiids. These characteristics were identified using Primer version 5. It appears that elasmobranch gnathiids are to some extent bigger than teleost gnathiids, have a longer pleotelson and their pylopod’s 2nd article is not circular or conical. However, G. pantherina‘s (from southern Africa) 2nd pylopod article is circular as well as gnathiids from teleosts from the rest of South Africa and Australia. This signifies that this characteristic is host and location specific. The genus Tenerognathia grouped within the genus Gnathia. This might be due to incomplete characteristics information that makes up the data-matrix. The species Caecognathia cryptopais grouped within the genus Caecognathia, confirming that its classification was correct. In conclusion these species are newly described gnathiid species found for the first time on Australian elasmobranchs. This brings the number of known gnathiid species found on elasmobranchs to four. All three life stages were described for Gnathia trimaculata sp. n. and Gnathia australis sp. n and only the male and larvae for Gnathia nigrograndilaris sp. n. The phylogenetic analysis confirmed that there is a correlation between Australian and South African elasmobranch gnathiids, elasmobranchs gnathiids and between phylogeny and geographical distribution. / Dr. N.J. Smit

Cartilaginous fish are the most ancient lineage to possess an adaptive immune system however nothing is known about the processes involved in the development, maintenance or proliferation of B cells in this group. In this thesis studies were undertaken to explore whether transcription factors, cytokines and cell surface markers that are involved in B cell immune responses in mammals are also present in cartilaginous fish. Through sequence database mining forty-one genes involved in B cell immune biology were found; of these twelve were B cell transcription factors. The presence of important B cell transcription factors, such as EBF1, pax5, E2A, Blimp1, PU.1 and Bcl6 suggests that B cells in cartilaginous fish probably undergo a similar developmental pathway as those in mammals. Eight cytokines, eleven cytokine receptors and four B cell surface markers were also identified, including CD40L, BAFF and CD79α that were further studied in this thesis. I cloned CD40L and BAFF from cartilaginous fish, both members of the tumour necrosis factor family and found cartilaginous fish BAFF genes have an extra exon that forms a unique α-helix insertion, and which may impact on receptor binding. The importance of all three molecules for the adaptive immune response was indicated by relatively high expression in shark immune tissue, such as spleen, gut-associated lymphoid tissue, gill and the Leydig organ, and the fact that their expression could be induced by immunostimulants, such as pokeweed mitogen. The finding that CD79α expression significantly correlates with those of immunoglobulin heavy-chains and the co-expression of CD79α and IgM on the B cell surface indicate that as in mammals CD79α in cartilaginous fish is expressed by B cells and associates with surface-bound immunoglobulin to form the active B cell receptor. Thus CD79α may serve as a pan B cell marker in future immunological studies in cartilaginous fish.

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.

The electrosensory and visual adaptations of elasmobranchs to the environment have been more studied than most other senses, however, work on these senses is mostly limited to descriptive analyses of sensitivity, morphology, and behavior. The goal of this work was to explore electrosensory and visual capabilities in a more ecological context. To gain an understanding of the content of bioelectric signals, the magnitude and frequency of these stimuli were recorded from a broad survey of elasmobranch prey items... Color vision adaptations also correlated to the photic environment of each species; cownose rays inhabit turbid, green-dominated waters and had two cone visual pigments that maximize contrast of objects against the green background... Yellow stingrays were trichromatic and likely possess the ability to discriminate colors in their clear, reef and seagrass habitats, which are spectrally rich. Both species showed evidence of ultraviolet sensitivity, which may aid in predator and conspecific detection as an enhanced communication channel. Future studies should investigate the integration of sensory input and sensory involvement in intraspecific communication to gain more insight into ecological adaptations. / by Christine N. Bedore. / Thesis (Ph.D.)--Florida Atlantic University, 2013. / Includes bibliography. / Mode of access: World Wide Web. / System requirements: Adobe Reader.

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.