The resurgence of Texas' snook (Family Centropomidae) recreational fishery is coupled with an uncertainty as to what species occur in State waters, a limited understanding of life history, and habitat needs of its constituents. This study described species composition and early life history aspects of juvenile (< 100 mm SL) centropomids taken in bag seine collections in estuarine and freshwater habitats along the upper, middle, and lower coast of Texas during 2006 to 2010. Centropomus specimens (n = 548) captured from 41 locations across the Texas coast as well as congeners from Mexico (n = 24), Florida (n = 7), and Costa Rica (n = 3) were used in a genetics- and meristic-based determination of species composition, growth rates, range of hatching dates, geographic distribution, and habitat association. Genetic analyses of the mitochondrial DNA 16s ribosomal RNA gene and the mitochondrial control region (D - loop) validated the presence of smallscale fat snook (C. parallelus Poey, 1860, n = 333), common snook (C. undecimalis Bloch 1792, n = 212) and Mexican snook (C. poeyi Chavez, 1961, n = 3) in Texas, with the last of these validations representing the first known record of this species in Texas. AMOVA of 16s and D - loop sequences failed to detect genetic differentiation within Texas for C. parallelus and C. undecimalis. However, AMOVA for 16s and D - loop C. undecimalis sequences did yield significant genetic differences between Texas and Mexico against those from Florida and Costa Rica. Juvenile centropomids (< 100 mm SL) in Texas occupied backwater habitats with dissipated currents similar to those of Florida congeners (tidal sloughs, freshwater habitats, and structured shorelines). Coastal ranges of these species differed with C. parallelus taken from the Rio Grande to West Galveston Bay, whereas C. undecimalis was captured from the Rio Grande northward near Palacios. Three C. poeyi were captured at only two locations (Laguna Vista and Port Aransas). Daily growth rates varied between species and capture years, with these ranging from 0.22 to 0.97 mm d^-1. Analyses of hatch-date distribution suggest centropomids in Texas begin spawning in August and continue it through late September into mid-November.

Invasive species are generally problematic where they occur, especially in terms of ecology, economy and disease. Members of the genus Rattus Fischer, 1803 particularly, are known as one of the most destructive invasive species to date since they cause widespread damage on terrestrial and island ecosystems. Two Rattus species have historically been reported as invasive species in South Africa, Rattus rattus Linnaeus, 1758, which has a widespread distribution throughout the country and Rattus norvegicus Berkenhout, 1769 which is primarily distributed along the coast of South Africa. A third species, Rattus tanezumi Temminck, 1844 (which forms part of the R. rattus species complex), a south-east Asian endemic, was first reported in 2005 to also occur in South Africa (and Africa). As this species is morphologically similar to R. rattus, its identification is reliant on molecular typing approaches. In the current study, molecular, morphological and disease aspects of South African Rattus were assessed. The nature and extent of variation between the three species was investigated using cytochrome b sequences and extensive mitochondrial d-loop database for comparative purposes. D-loop data identified one, four and two haplotypes for R. tanezumi, R. rattus and R. norvegicus, respectively whereas cytochrome b data identified additional haplotypes for R. rattus and R. tanezumi. Pairwise sequence divergence was highest between R. norvegicus and R. tanezumi (12.5% for D-loop and 12.0% for cyt b). Rattus norvegicus was recovered in the central parts of South Africa for the first time and occurred sympatrically with R. tanezumi at one locality, whereas Rattus rattus and R. tanezumi occurred sympatrically at three localities. The external and qualitative cranial morphology of all three species was compared in an attempt to find differences that could be used to morphologically differentiate between these Rattus species. Whereas R. norvegicus can easily be distinguished from R. rattus and R. tanezumi, there are no discernible morphological differences to distinguish R. rattus and R. tanezumi. A taxonomic synthesis and an identification key of the three species of Rattus based on qualitative morphology, molecular and cytogenetic data using genetically-identified individuals is provided. Members of South African Rattus were also found to be carriers of the bacteria Bartonella Strong et al., 1915 and Helicobacter Goodwin et al., 1989 emend. Vandamme et al., 1991. Bartonella elizabethae (Daly et al., 1993) Brenner et al., 1993, occurring in Rattus around the world was for the first time recovered from South African Rattus. This bacterium has been associated with infective endocarditis in humans and may pose a threat to immuno-compromised individuals in rural South African communities where Rattus occurs commensally. Two Helicobacter species, H. rodentium Shen et al., 1997 and H. muridarum Lee et al., 1992, were identified neither of which have known zoonotic potential. Apart from contributing to general small mammal studies in Africa, the present study may have implications in epidemiological, agricultural, biological conservation, and invasion biology research associated with problem rodents in the southern African subregion and beyond. / Dissertation (MSc)--University of Pretoria, 2010. / Zoology and Entomology / unrestricted

The field of conservation genetics, in combination with non-invasive sampling, provides a powerful set of tools for investigating the conservation status and natural history of rare species that are otherwise difficult to study. A systematic literature review demonstrated that this is certainly the case for many forest associated antelope species, which are poorly studied and yet constitute some of the most heavily hunted wildlife in Africa. The aim of the present study was to use non-invasive sampling to investigate genetic patterns in forest antelope populations in the high-biodiversity Udzungwa Mountains, Tanzania, within the context of the conservation of these species and the wider ecosystem. Genetic information was derived from faecal samples collected across the Udzungwa landscape and assigned to five antelope species (N = 618, collected 2006-09). Faecal pellet length was measured for a subset of samples but statistical assignment to species by this method proved unreliable. Phylogenetic analysis using mitochondrial control region sequences unexpectedly revealed that Harvey’s duiker within the Udzungwas are paraphyletic with respect to sequences from a putative sister species from southern Africa. However, there was no corresponding pattern in the microsatellite dataset suggesting that these mitochondrial lineages do not represent contemporary genetic isolation. Instead, Harvey’s duiker nuclear variation is shaped both by isolation by distance, due to positive spatial autocorrelation at short distances, and clustering of distinct genotypes from western outlying forests. These forests also harbour the endangered Abbott’s duiker and therefore require effective conservation management. Despite being detected throughout the Udzungwas, genetic diversity in Abbott’s duiker was very low in comparison to other species. These results suggest several promising research directions but also have significant conservation implications that will be disseminated to the Tanzanian wildlife authorities and the wider conservation community.

The replication of chromosomes can be challenged by endogenous and environmental factors, interfering with the progression of replication forks. Therefore, cells have to coordinate DNA synthesis with mechanisms ensuring the stability and the recovery of halted forks. Homologous recombination (HR) is a universal mechanism that supports DNA repair and the robustness of DNA replication. Nonetheless, mechanisms regulating HR pathways, such as ectopic versus allelic recombination, remain poorly understood. Another essential pathway for genome stability is the wrapping of newly replicated DNA around nucleosomes, leading to the constitution of a chromatin fibre, which allows the structural organization of the genetic material. In Saccharomyces cerevisiae, deficiencies in chromatin assembly pathways lead to replication forks instability and consequent increase in the rate of HR. Histone chaperones play a crucial role during chromatin assembly, thus I decided to focus on the H3-H4 histone chaperone Chromatin Assembly Factor 1 (CAF-1), to study its role in HR processes in Schizosaccharomyces pombe. Indeed, HR includes a DNA synthesis step and little is known about the associated chromatin assembly. My data excluded a role for CAF-1 in allelic recombination and in the maintenance of forks stability. However, CAF-1 was found to play an important role during ectopic recombination, in promoting chromosomal rearrangements induced by halted replication forks. My data support a model according to which CAF-1 allows the stabilization of early recombination intermediates (D-loop), via nucleosome deposition during the elongation of these intermediates. Doing so, CAF-1 counteracts the dissociation of early recombination intermediates by the helicase Rqh1. Therefore, CAF-1 appears to be part of an equilibrium that regulates stability/dissociation of early steps of recombination events. Importantly, I found that the role of CAF-1 in this equilibrium is of particular importance during non-allelic recombination, revealing a novel regulation level of HR mechanisms and outcomes by chromatin assembly.

Orientador: Rogério Caetano da Costa / Resumo: O camarão-rosa Farfantepenaeus paulensis é um dos mais importantes recursos pesqueiros da costa sul-sudeste do Brasil. Os fundos de pesca da espécie incluem dois estoques reprodutivos principais, localizados nas costas dos estados de Santa Catarina e São Paulo. A espécie apresenta ciclo de vida do tipo II, com uma fase reprodutiva no ambiente marinho e recrutamento juvenil em áreas estuarinas e baías. O conhecimento sobre o fluxo gênico entre estoques é a base de todo o ordenamento pesqueiro, uma vez que unidades genéticas podem apresentar características particulares e, normalmente, necessitam de estratégias específicas de manejo. Porém, há poucas informações que podem servir de subsídio para verificar se os diferentes estoques pesqueiros de F. paulensis também representam estoques genéticos distintos. O crescimento desordenado da frota industrial, o incremento da pesca artesanal nas áreas de criadouro, somado à pequena eficácia da legislação pesqueira, associados à ineficiência da fiscalização, levaram a um cenário de colapso da pescaria do camarão rosa no fim dos anos 90. Um melhor entendimento da estruturação genética das populações de F. paulensis é necessário, não somente pelo seu alto valor comercial e ecológico, mas também para permitir a implementação de medidas de manejo mais efetivas. Assim, o presente trabalho buscou avaliar a estruturação genética das populações do camarão rosa F. paulensis ao longo de sua distribuição no Atlântico Sul Ocidental, utilizando como ... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The pink shrimp Farfantepenaeus paulensis is one of the most important fishing resources on the south-southeast coast of Brazil. The fishing zone of the species includes two main reproductive stocks, located on the coasts of Santa Catarina and São Paulo states. The species exhibits the type II life cycle, with an offshore reproductive stage and a juvenile recruitment in bays and estuarine areas. Knowledge on the amount of gene flow between stocks is the basis of all fisheries management, since genetic units may have particular characteristics and usually require specific management strategies. However, there is little information to verify whether F. paulensis's different fish stocks also represent different genetic stocks. The unrestricted growth of the industrial fleet, the increase in artisanal fishing in breeding areas, coupled with the low effectiveness of fisheries legislation and the inefficiency of inspection, led to a collapse of the pink shrimp fishery in the late 1990s. A better understanding of the genetic structuring of the populations of F. paulensis is necessary, not only for its high commercial and ecological value, but also to allow the implementation of more effective management measures. Thus, the present work aimed to assess the genetic structuring of the populations of the pink shrimp F. paulensis throughout its distribution in the Western South Atlantic, using as molecular marker the Control Region (D-loop) of the mitochondrial DNA (Chapter 1). In additi... (Complete abstract click electronic access below) / Doutor

Submitted by Alison Vanceto (alison-vanceto@hotmail.com) on 2016-09-27T12:23:30Z No. of bitstreams: 1 TeseAGN.pdf: 2192797 bytes, checksum: e995724f0c22f92176dd1473070b69a6 (MD5) / Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-09-27T20:09:23Z (GMT) No. of bitstreams: 1 TeseAGN.pdf: 2192797 bytes, checksum: e995724f0c22f92176dd1473070b69a6 (MD5) / Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-09-27T20:09:29Z (GMT) No. of bitstreams: 1 TeseAGN.pdf: 2192797 bytes, checksum: e995724f0c22f92176dd1473070b69a6 (MD5) / Made available in DSpace on 2016-09-27T20:09:35Z (GMT). No. of bitstreams: 1 TeseAGN.pdf: 2192797 bytes, checksum: e995724f0c22f92176dd1473070b69a6 (MD5) Previous issue date: 2015-08-13 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / The Salminus genus is characterized by predatory fish medium to large, migratory and ichthyophagi, very appreciated in fisheries and gastronomy. Among these stands out the Salminus hilarii species, popularly known as tabarana and considered top of the food chain, due to its high degree of selectivity for environments with rich water oxygen which constitutes a good environmental indicator. This species occurs in the São Francisco basins, Paraná basins and Jaguaribe river, and depends on specific hydrological conditions to carry out their reproduction. In this context and because of intense anthropogenic interference that such river systems have suffered, population's study of tabaranas in the upper Paraná basin can contribute to a better understanding of aspects related to its population structure and conservation of their populations. Thus, the aim of this study was to characterize the population genetic structure of S. hilarii at different periods in rivers of the Upper Paraná basin, in order to better understand the population dynamics of fish and effectively contribute to their conservation. It was used for molecular analysis 15 polymorphic microsatellite loci and mtDNA (D-loop). The results revealed the existence of population differentiation among the rivers sampled. Nevertheless, individuals sampled in the Jacaré-pepira river and Cubatão showed no genetic difference, indicating the occurrence of gene flow between populations sufficient to maintain the genetic homogeneity. Moreover, it was possible to identify the temporal structure into the Turvo and Jacaré-pepira river. A high genetic diversity was found in populations of Upper Paraná basin sampled rivers. The D-loop analysis showed no population structure between samples, but indicated the occurrence of a high diversity. The contradictory results may be due to mutational rates of the markers used, since microsatellites have high mutational rate. These results are important for understanding the behavior and biology of these fish, and also to establish fisheries management programs and conservation S. hilarii in the upper Paraná basin. / O gênero Salminus é caracterizado por peixes predadores de médio à grande porte, migradores e ictiófagos, muito apreciados na pesca e na gastronomia. Dentre esses, destaca-se a espécie Salminus hilarii, conhecida popularmente como tabarana e considerada topo de cadeia alimentar, devido ao seu alto grau de seletividade por ambientes com águas ricas em oxigênio o que torna a espécie uma bom indicador ambiental. Essa espécie ocorre nas bacias do São Francisco, alto rio Paraná e do rio Jaguaribe e depende de condições hidrológicas específicas para realizar sua reprodução. Dentro desse contexto e devido à intensa interferência antrópica que tais sistemas hidrográficos vêm sofrendo, estudar populações de tabaranas na bacia do alto Paraná pode contribuir efetivamente para o melhor entendimento de aspectos relacionados à sua estrutura populacional e conservação da espécie. Assim, o objetivo geral deste trabalho foi caracterizar a estrutura genética de populações de S. hilarii em diferentes períodos em rios da bacia do alto Paraná, com o intuito de compreender melhor a dinâmica populacional desse peixe e contribuir efetivamente para sua conservação. Para as análises moleculares utilizou-se 15 locos polimórficos de microssatélites e o mtDNA (D-loop). Os resultados obtidos revelaram a existência de diferenciação populacional entre os rios amostrados. Apesar disso, os indivíduos amostrados no rio Jacaré-pepira e ribeirão do Cubatão não apresentaram diferença genética entre eles, indicando a ocorrência de fluxo gênico entre as populações suficiente para manter a homogeneidade genética. Além disso, foi possível identificar a estruturação temporal dentro do rio Turvo e do rio Jacaré-pepira. Uma alta diversidade genética foi encontrada nas populações dos rios amostrados da bacia do alto Paraná. As análises do D-loop não evidenciaram estruturação populacional entre as amostragens, mas indicou a ocorrência de uma alta diversidade. A contradição dos resultados deve-se as taxas mutacionais dos marcadores utilizados, uma vez que os microssatélites possuem taxas mutacionais elevadas. Esses resultados são importantes para o entendimento do comportamento e biologia desses peixes e, ainda, para estabelecer programas de manejo de pesca e conservação de S. hilarii na bacia do alto Paraná.

Today, DNA-barcoding with the gene COI is regularly used in the identification of fish. However, this is not an adequate way of identifying species of tuna due to COI lacking sufficient interspecies divergence. This is problematic since fraud and mislabeling are a major concern within the fish and tuna industries. Thus, there is a need for a new genetic barcode region when identifying the 15 tuna species within the tribe Thunnini. This study has considered six mitochondrial genetic regions (16S, ATP8, COII, CR, CytB, and ND2) and their potential as barcodes in comparison to COI. To be of practical use, the barcode has to be able to differentiate between all 15 tuna species, as well as contain conserved primer binding sites and be approximately 400 bp, or shorter. Analyses of the regions were made through Multiple Sequence Alignments built using ClustalW in Mega 11.0. The candidates were first evaluated through neighbor-joining trees and plots of inter- and intraspecies variation, and then analyzed further in search of conserved regions for primer binding, flanking a segment of approximately 400 bp (or shorter). This resulted in two possible barcode candidates with corresponding primers from the CR and ND2 genes. As a final step, these two were analyzed for specificity using BLAST, to evaluate their actual utility in differentiating the tuna species. The results show that they both can identify the different tuna species, but that ND2 is superior with 100% identification accuracy. In addition to the theoretical analysis, the ability of the primers was measured through a real PCR amplification. Unfortunately, only the CR barcode could be evaluated, but the results show it to be practically useful. Even though the utility of ND2 in PCR could not be analyzed, it is highly recommended as a region for further investigations. Given the strong theoretical support, it definitely shows promise as a new barcode for species identification of tuna.