Antimicrobial resistance (AMR) is a worldwide public health concern. While it is evident that the use of antibiotics creates selection pressure for the evolution of antibiotic resistance genes, there are still considerable knowledge gaps relating to the status quo of antibiotic use, emergence of resistant pathogens in different livestock production systems and spread within human and animal communities. This thesis includes a survey of antibiotic use in the dairy sector within a specific area of Zambia and analysis of AMR and virulence factors in E. coli isolated from dairy cattle and diarrhoea human patients with the following objectives. 1. To investigate the usage of antibiotics in the dairy sector and the drivers for use. 2. To determine the prevalence and patterns of antimicrobial resistance in E. coli isolated from faecal samples of dairy cattle. 3. To use whole genome sequencing (WGS) to investigate the molecular epidemiology of resistance determinants in E. coli strains isolated from both dairy cattle and humans. 4. To assess the zoonotic potential of isolated E. coli focusing on Shiga toxin-producing E. coli (STEC) and relationship to STEC associated with clinical disease in the UK. In view of these objectives, the first part of the work was carried out in Zambia and involved a questionnaire, a field survey, isolation of E. coli from dairy cattle faecal samples and phenotypic testing for AMR. In addition, E. coli isolates were obtained from another study that was focused on human patients presenting with diarrhoea at the University Teaching Hospital in Lusaka. The second part involved whole genome sequencing and molecular analyses of E. coli for resistance and virulence genotypes at the Roslin Institute (UK). For the field study, a stratified random sample of 104 farms was studied, representing approximately 20% of all dairy farms in the region. On each farm, faecal samples were collected from a random sample of animals and a standardised questionnaire on the usage of antibiotics was completed. An E. coli isolate was obtained from 98.67% (371/376) of the sampled animals and tested for resistance against the six types of antibiotics (tetracycline, ampicillin, sulfamethoxazole/trimethoprim, cefpodoxime, gentamicin and ciprofloxacin). These E. coli were then analysed together with those from humans for genotypes in the laboratory and from Illumina short read whole genome sequences using bioinformatics tools. Tetracylines and penicillin were the commonly used antibiotics in dairy herds. This finding was in line with the resistance phenotypes detected in E. coli isolated from the dairy cattle. The most prevalent AMR was to tetracycline (10.61; 95%CI: 7.40-13.82), followed by ampicillin (6.02; 95%CI: 3.31-8.73), sulfamethoxazole/ trimethoprim (4.49; 95%CI: 2.42-6.56), cefpodoxime (1.91; 95%CI: 0.46-3.36), gentamicin (0.89; 95%CI: 0.06-1.84) and ciprofloxacin (0%). The risk analysis indicated that AMR was associated with livestock diseases (lumpy skin disease and foot rot), exotic breeds (Jersey and Friesian), location, farm size and certain management practices. Analysis of whole genome sequences showed that isolates from humans had both higher levels and a greater diversity of resistance alleles than the cattle isolates. Common genotypes in both populations were: tetA (16%), tetB (10%), tetC (2%) for cattle isolates with tetA (32%), tetB (22%) and tetD (1%) in human isolates. Other common genotypes were blaTEM (56%), sul1 (29%), sul2 (66%), strA4 (57%) and strB1 (64%) in isolates of human origin while blaTEM (15%), sul1 (3%), sul2 (17%), strA4 (13%) and strB1 (19%) were in the cattle isolates. Whilst the E. coli isolates from cattle encoded resistance to common antibiotics of limited significance to human clinical medicine, isolates from humans had additional extended spectrum beta-lactamases (blaOXA, blaCMY, blaNDM, and blaDHA, blaOKP and blaCTX-M) that encode for resistance to essential antibiotics such as third generation cephalosporins and carbapenems. This was an evidence that AMR is an ongoing public health subject in Zambia but the exclusivity of certain resistances in the human population points to limited or no exchange of genotypes between E. coli of human origin and those from cattle. AMR in humans was probably independently selected by the use of antibiotics of clinical importance such as cephalosporin and fluoroquinolones. The virulence analysis focused on STEC, 11% (41/371) of E. coli isolates from cattle contained Shiga toxin genes (stx) while none (0/73) of the human isolates were positive. Phylogenetic analysis showed a random distribution of bovine STEC, with no indication of clonal spread. Although 89% (16/18) of the STEC tested had a cytotoxic effect on Vero cells, indicative of Shiga toxin production, only three (O45, O111, O157) belonged to one of the seven serogroups (O26, O157, O111, O103, O121, O145 and O45) associated with life-threatening enterohaemorrhagic E. coli (EHEC) infections in humans. In line with this, only the O157 serotype encoded a type 3 secretion system. This shows that, while Stx-encoding strains are common in these dairy herds of Zambia, they are not strain backgrounds known to pose an immediate threat to human health as they lack colonisation factors that are found in typical human EHEC. However, we must remain vigilant as emergence of EHEC strains in these animals remains an ever-present threat.

Este trabalho faz uma descrição detalhada da morfologia de Ceraeochrysa, mapas de distribuição, listas de ocorrência de espécies em cultivos agrícolas para o Brasil e um estudo das relações filogenéticas entre as espécies do gênero. A análise filogenética incluiu 62 espécies de Ceraeochrysa, quatro espécies de grupos externos ao gênero em vários níveis e 50 caracteres morfológicos. Um total de 11 espécies para as quais havia pouca informação sobre machos foram inseridas na matriz uma a uma em análises separadas, de modo a diminuir o efeito de informação ausente. Foi obtida uma única árvore mais parcimoniosa, que corrobora a hipótese de monofilia do gênero. Das características consideradas sinapomórficas para Ceraeochrysapresença de espermateca alongada e de gonapse, a primeira é plesiomórfica para C. placita e C. intacta (que têm a espermateca no formato pill-box), recuperadas como irmãs do restante de Ceraeochrysa, já a segunda característica está presente também nas espécies de Cryptochrysa. O estudo da morfologia gerou uma quantidade importante de caracteres que poderão ser utilizados em novas análises filogenéticas de Chrysopidae. A maioria das espécies brasileiras de Ceraeochrysa é de distribuição conhecida da Amazônia, da Mata Atlântica e do Cerrado, mas não há informação suficiente para um estudo biogeográfico do gênero. Entre as espécies brasileiras, C. cincta, C. cubana e C. claveri são as que têm maior distribuição geográfica e ocorrem em grande diversidade de plantações agrícolas. / This work has a detailed study of the morphology of Ceraeochrysa, distribution maps for the species of the genus, lists of occurrences in crops of the Brazilian species and a phylogenetic analysis of the relationships between the species of the genus. The phylogenetic study included 62 species of Ceraeochrysa, with four outgroup species and 50 morphological characters. A total of 11 species for which there is missing data for males were included in the matrix one by one and analysed independently, so negative effect of missing data in the analysis could be reduced. The monophyly of the genus was recovered, but no uniquely derived characters were found. Of the features often considered synapomorphies of Ceraeochrysathe presence of an elongated spermatheca and the presence of a gonapsisthe former of spermatheca is plesiomorphic for C. placita and C. intacta (which have pill-box format), recovered as sister species for the remaining of the genus, while a gonapsis was seen to also occur in Criptochrysa. The detailed morphological study resulted in a lot of information that can be used in robust phylogenetic studies of the Chrysopidae. Most of the Brazilian species of Ceraeochrysa are known from the Amazon, the Atlantic Forest and the Cerrado, but there is not information enough for a biogeographic study of the genus. Among the Brazilian species, C. cincta, C. cubana, and C. claveri are those that have most widely distributed and occur in great variety of agricultural crops.

Submitted by (lucia.rodrigues@ufrpe.br) on 2017-02-17T15:25:38Z No. of bitstreams: 1 Cleia Santos Cabral.pdf: 1106804 bytes, checksum: 14447df94770ff469bfc234136893b59 (MD5) / Made available in DSpace on 2017-02-17T15:25:38Z (GMT). No. of bitstreams: 1 Cleia Santos Cabral.pdf: 1106804 bytes, checksum: 14447df94770ff469bfc234136893b59 (MD5) Previous issue date: 2012-02-17 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Fusarium wilt, caused by Fusarium oxysporum f. sp. lactucae (FOLac), is an important disease of lettuce in the world. This disease was reported in Brazil, recently. From 2008 to 2011 the laboratories of Plant Pathology of Embrapa Hortaliças (Embrapa Vegetable Crops), Sakata Seeds Sudamerica and Instituto Capixaba de Pesquisa, Assistência Técnica e Extensão Rural (INCAPER) collected some FOLac isolates in states from the Southern and the Southeastern regions of Brazil. The isolates were identified as F. oxysporum by the morphological characteristics of conidia and conidiophores. Isolates were inoculated on lettuce plants, cultivars Elisa, Vera, and Red Salad Bowl, conditions in a greenhouse. Isolates were also inoculated on plants of others Asteraceae species (Cichorium endivia, Cichorium intybus, Sonchus oleraceus, Emilia sonchifolia, Bidens pilosa e Tagetes erecta) and others botanical families as (Solanum lycopersicum, Capsicum annuum, Nicotiana tabacum, Gossypium hirsutum, Phaseolus vulgaris e Ocimum basilicum). Lettuce cultivars Elisa and Vera were suscetible to all isolates while the cultivar Red Salad Bowl was resistant. All isolates were reisolated from diseased plants fulfilling the Koch‟s postulates. Others plant species were not susceptible to any isolate, proving that isolates belong to the species F. oxysporum f. sp. lactucae. The isolates were also inoculated in a differential set of cultivars comprising: „Patriot‟ (Susceptible to all races), „Costa Rica No. 4‟ (resistant to race 1) and „Banchu Red Fire‟ (resistant to race 2). Cultivars „Patriot‟ and „Banchu Red Fire‟ were susceptible while „Costa Rica No. 4‟ was resistant, confirming that all the isolates were race 1. Molecular analysis using a primer specific to race 1 isolates was performed using F. oxysporum f. sp. lycopersici (FOL) raça 3 and a non-pathogenic isolate as negative controls. DNAs of FOLac isolates were amplified by PCR and those of the negative controls were not, confirming the specificity of the primers and the presence of only the race 1 of FOLac in Brazil. In addition, it was used the Translation elongation factor 1-α region (tef-1α) for phylogenetic analysis between FOLac isolates races 1 and 2 and isolates of F. oxysporum. Comparison of the sequences obtained with the tef-1α confirmed the polyphyletic origin of the forma specialis lactucae and also showed a greater genetic variability among Brazilian isolates of FOLac race 1compared with isolates of the same race available in GenBank. After the isolates characterization, it was made a screening of 102 accessions for resistance to the isolate Fus-173 and it was selected 47 as highly resistant. After this, the selected genotypes were evaluated for the stability of resistance in three additional assays, using different FOLac race 1 isolates. In all three assays it was used a highly susceptible cultivar (Regina) as susceptible control. In the first assay, carried out in October 2011, it were used the isolates Fus-202 and Fus-205. In the second assay, carried out in November 2011, it were used the isolates Fus-219 and Fus-222. In the third assay, carried out in December 2011, it were used the isolates (Fus-207, Fus-209 e Fus-220). Inoculation was performed on 25 days old seedlings on greenhouse conditions. Seedlings were inoculated by cutting their roots and emerging them in spore suspension of pathogen. Evaluation was carries out 30 days after inoculation, using a grade scale varying from 0 (heath plants) to 4 (dead plants). Data were transformed in Disease Index (DI) submitted to a variance analysis and the media were compared by the Tukey‟s test (5%). Thirty two accessions were identified as having broad spectrum of resistance to different pathogen isolates in the four inoculation seasons. / A murcha de fusário, causada pelo fungo Fusarium oxysporum f. sp. lactucae (FOLac) é uma das doenças mais importantes da alface. Esta doença foi relatada recentemente no Brasil. Nos anos de 2008 a 2011 foram coletados isolados de FOLac nos Laboratórios de Fitopatologia da Embrapa Hortaliças, Sakata Seed Sudamerica Ltda e do Instituto Capixaba de Pesquisa, Assistência Técnica e Extensão Rural (Incaper). Estes eram provenientes de todos os estados das Regiões Sul e Sudeste do Brasil. A identificação foi feita observando-se as características morfológicas de conídios e conidióforos. Os isolados foram inoculados em plantas das cultivares Elisa, Vera e Red Salad Bowl, em condições de casa de vegetação. Os mesmos também foram inoculados em plantas de outras espécies de Asteraceae (Cichorium endivia, Cichorium intybus, Sonchus oleraceus, Emilia sonchifolia, Bidens pilosa e Tagetes erecta) e de outras famílias (Solanum lycopersicum, Capsicum annuum, Nicotiana tabacum, Gossypium hirsutum, Phaseolus vulgaris e Ocimum basilicum). Os isolados foram identificados como Fusarium oxysporum. As cultivares Elisa e Vera foram suscetíveis a todos os isolados e a Red Salad Bowl foi resistente. Efetuou-se o re-isolamento do patógeno, completando-se assim os Postulados de Koch. Nenhuma outra espécie de planta foi suscetível ao patógeno, confirmando a identificação como F. oxysporum f. sp. lactucae. Em seguida, os isolados foram avaliados quanto a sua virulência numa série de cultivares diferenciadoras de raças: Patriot (suscetível), Costa Rica No. 4 (resistente à raça 1) e Banchu Red Fire (resistente à raça 2). As cultivares Patriot e Banchu Red Fire comportaram-se como suscetíveis a todos os isolados, enquanto a cultivar Costa Rica No. 4 comportou-se como resistente. Concluiu-se que os isolados avaliados são da raça 1 de FOLac. Adicionalmente, foi feito um teste com primers específicos para a raça 1 de FOLac, utilizando como controles um isolado de F. oxysporum f. sp. lycopersici (FOL) raça 3 e um isolado não patogênico de F. oxysporum. O fragmento de DNA foi amplificado por PCR para os isolados de FOLac e não foi amplificado para o isolado de FOL e nem para o isolado não patogênico de F. oxysporum. Este resultado confirma a especificidade desse par de primers e a presença apenas da raça 1 de FOLac no Brasil. Além disso, foi utilizada a região do fator de elongação da tradução (tef-1α) para análise filogenética entre os isolados FOLac raças 1 e 2 e isolados de F. oxysporum. Comparação das seqüências obtidas com o tef-1α confirmou a origem polifilética da forma specialis lactucae e também observou-se uma maior variabilidade genética entre os isolados brasileiros de FOLac raça 1 comparados com isolados da mesma raça disponíveis no GenbanK. Posteriormente, 102 acessos (cultivares comerciais ou linhagens) foram avaliados, visando identificar fontes de resistência a FOLac e analisar a estabilidade da resistência de acessos promissores a diferentes isolados do patógeno. Inicialmente foi feita uma seleção preliminar, utilizando um isolado do patógeno (Fus-173). Em seguida, quarenta e sete acessos altamente resistentes mais uma testemunha suscetível (Regina), identificados na seleção preliminar, foram reavaliados para estabilidade da resistência ao FOLac raça 1, utilizando os isolados (Fus-202 e Fus-205) no mês de Outubro de 2011; isolados (Fus-219 e Fus-222) no mês de Novembro de 2011 e isolados (Fus-207, Fus-209 e Fus-220) no mês de Dezembro de 2011. A inoculação foi realizada em condições de casa de vegetação, pelo método de corte das raízes e imersão na suspensão de conídios do patógeno. A avaliação foi realizada após 30 dias, com auxílio de escala de notas variando de 0 (planta sadia) a 4 (planta morta). Os dados obtidos foram transformados em índice de doença (ID) e submetidos a uma análise de variância e comparação de médias pelo teste de Tukey (5%). Foram identificados trinta e dois acessos apresentando amplo espectro de resistência aos diferentes isolados do patógeno nas quatro épocas de inoculação.

Until 2014, scientific knowledge on the diversity of Chilean Ixodoidea summarized 19 species and only agents of Borrelia and Rickettsia genera had been detected. The objectives of this study were to evaluate the occurrence of further agents of Anaplasma, Borrelia, Coxiella, Ehrlichia, Rickettsia and Hepatozoon by means of molecular tools. Obtained sequences were inserted into a phylogenetic context in order to evaluate their relatedness to microorganisms of know pathogenic roles. As agents of Coxiella genus resulted to be related to endosymbiotic bacteria, data on these organisms was used to perform a taxonomic study with ticks of the Ornithodoors capensis sensu lato complex. The results confirm that Chilean ticks harbor at least three new borrelial, one new rickettsial, and three new Hepatozoon species for science. Moreover, Rickettsia amblyommatis, Rickettsia hoogstraalii and Rickettsia lusitaniae are added to the list of Chilean rickettsiae. Although ticks were positive to Anaplasmataceae PCRs, an accurate study including longer fragments of the 16S RNA targeted gene must be performed in order to confirm their specific identity. Coxiella-like endosymbionts are specific of every of the four O. capensis s. l. species analyzed in this study, and therefore constitute a useful tool in order to confirm the identities and define genetic boundaries of ticks of this group in South America. Finally, the results of this study add at least five new species of Argasidae family into Chilean fauna of ticks, and point the occurrence of several forms that need further assessment in order to accurately confirm their identities. / Até 2014, o conhecimento científico sobre a diversidade de Ixodoidea no Chile estava representado por 19 espécies e apenas agentes infecciosos dos gêneros Borrelia e Rickettsia haviam sido descritos. O objetivo deste estudo foi o de avaliar a ocorrência de outros patógenos transmitidos por carrapatos por meio de técnicas moleculares orientadas para a deteção de Anaplasma, Borrelia, Coxiella, Ehrlichia, Rickettsia e Hepatozoon. As sequências obtidas foram analisadas filogeneticamente, identificando-se suas posições em comparação à de organismos de papeis patogénicos já conhecidos. Como os agentes do gênero Coxiella apresentaram proximidade filogenética em relação a bactérias congenêricas endosimbiontes, os dados sobre estas foram utilizados para realizar um estudo taxonômico em carrapatos do complexo Ornithodoros capensis sensu lato. Em geral, os resultados confirmam a presença de pelo menos três novas espécies de Borrelia, uma nova Rickettsia, e três novas espécies de Hepatozoon para a ciência. Rickettsia amblyommatis, Rickettsia hoogstraalii e Rickettsia lusitaniae foram inseridas como novos agentes associados a carrapatos no Chile. Embora alguns carrapatos fossem positivos para a presença de bactérias da família Anaplasmataceae, futuros estudos devem ser desenvolvidos para confirmar a sua condição especifica, especialmente através da obtenção de maiores fragmentos do gene codificante para RNA 16S. Os organismos tipo Coxiella são específicos para cada uma das quatro espécies de carrapatos do grupo O. capensis analisados neste estudo. Portanto, constituem uma ferramenta de valor taxonômico para confirmar as identidades e limites genéticos destes. Finalmente, os resultados deste estudo adicionam pelo menos cinco novas espécies de carrapatos para a família Argasidae no Chile e apontam a ocorrência de várias morfotipos de condição incerta que precisam de maiores análises para esclarecer a com certeza a sua posição taxonômica.

O vírus da imunodeficiência felina (FIV) é um lentivirus que infecta gatos domésticos (Felis catus), causando uma imunodeficiência progressiva análoga a AIDS (Síndrome da Imunodeficiência Adquirida Humana). A ampla heterogeneidade molecular do FIV e a alta capacidade de promover mutações sob pressões imunológicas, farmacológicas ou ambientais são características inerentes aos lentivirus. A identificação do subtipo de vírus e o conhecimento da diversidade genética das cepas circulantes são fundamentais para o desenvolvimento estratégico de vacinas capazes de resultar na imunização do hospedeiro e no estabelecimento de testes diagnósticos. Objetivando isolar o material genético e realizar a caracterização molecular do vírus da imunodeficiência felina foram coletadas e analisadas amostras de sangue periférico de felinos portadores do FIV, co-habitantes de um abrigo aberto de felinos, em São Paulo, SP, em quatro momentos distintos, T0 (zero), no momento inicial da avaliação e seis, dez e quinze meses após a coleta inicial, correspondendo aos momentos T1, T2 e T3, respectivamente. Foram realizados testes hematológicos e bioquímicos nas quatro coletas com a finalidade de avaliar a evolução clínica da infecção. Adicionalmente foi realizado um estudo de variabilidade genética do FIV, com base no sequenciamento dos produtos amplificados dos gene env obtidos no estudo. Os envelopes clonados foram utilizados para transfectar células resultando na expressão das proteínas do envelope que possibilitaram estudos com os receptores celulares utilizados pelos isolados brasileiros. As análises das seqüências virais mostraram que todas as amostras, do abrigo, pertencem ao subtipo B. Foi observado um baixo percentual de mudança, da região estudada do vírus entre as quatro coletas. O fenômeno de "quasispecies" virais, bastante estudado no HIV, pode ser documentado em nossas amostras. Nos exames hematológicos e bioquímicos; hematócrito, hemoglobina, contagem total de leucócitos, proteína total e gamaglobulinas; dos animais infectados pelo FIV observou-se mudanças entre a primeira e quarta coleta demonstrando assim a importância dos testes utilizados no acompanhamento da infecção pelo FIV. Com relação aos dados com os receptores do FIV, os resultados apontam uma menor complexidade na interação entre os envelopes dos isolados do estudo com o receptor CD134 para proceder a infecção quando comparados com cepas virulentas do FIV. / FIV is an important viral pathogen that infects the domestic cat and causes a slow progressive degeneration of the immune system which eventually leads to a disease comparable to acquired immune deficiency syndrome (AIDS) in humans. Similar to all retroviruses, FIV has a relatively high evolutionary rate and genomic heterogeneity. The determination of subtype and the knowledge of genetic diversity of the current strains are very important to developing a protective vaccine and for the routine diagnosis of infection. The aim of this study was to isolate and characterize samples of feline immunodeficiency virus from cats from an open shelter in Sao Paulo, Brazil. All cats infected with FIV from this shelter were sampled on August 26th, 2007 (T0) and also six (T1), ten (T2) and fifteen (T3) months after the basal sampling (T0). In each sample, blood was analyzed for the following: complete hematology, clinical chemistry and serum protein electrophoresis. Hematological and clinical chemistry parameters were analyzed to determine laboratory parameters characteristic of disease progression which allow a better description of the chronic phase of the infection. Furthermore, analyses of the variants from each sample were performed in order to estimate the degree of divergence following infection with Brazilian strains. The FIV envelope glycoprotein gene from Brazilian FIV isolates cloned were transfected to investigate the receptor usage. The sequences of all virus of the study belong to subtype B. Little sequence variation was observed in circulating viruses between the samples from each infected cat. Quasispecies of FIV have been detected in this study. The following hematological and clinical chemistry parameters were changed in the FIV-infected cats between the first blood sampling and last blood sampling: packed cell volume (PCV), hemoglobin, total white blood cells (WBC), total protein and gamma globulin fractions. Monitoring of hematological and clinical chemistry parameters may prove useful for the evaluation of disease progress. Regarding receptors, our data are consistent with isolates of the study requiring a less complex interaction with CD134 for infection to proceed compared to the virulent FIV isolates.

Until 2014, scientific knowledge on the diversity of Chilean Ixodoidea summarized 19 species and only agents of Borrelia and Rickettsia genera had been detected. The objectives of this study were to evaluate the occurrence of further agents of Anaplasma, Borrelia, Coxiella, Ehrlichia, Rickettsia and Hepatozoon by means of molecular tools. Obtained sequences were inserted into a phylogenetic context in order to evaluate their relatedness to microorganisms of know pathogenic roles. As agents of Coxiella genus resulted to be related to endosymbiotic bacteria, data on these organisms was used to perform a taxonomic study with ticks of the Ornithodoors capensis sensu lato complex. The results confirm that Chilean ticks harbor at least three new borrelial, one new rickettsial, and three new Hepatozoon species for science. Moreover, Rickettsia amblyommatis, Rickettsia hoogstraalii and Rickettsia lusitaniae are added to the list of Chilean rickettsiae. Although ticks were positive to Anaplasmataceae PCRs, an accurate study including longer fragments of the 16S RNA targeted gene must be performed in order to confirm their specific identity. Coxiella-like endosymbionts are specific of every of the four O. capensis s. l. species analyzed in this study, and therefore constitute a useful tool in order to confirm the identities and define genetic boundaries of ticks of this group in South America. Finally, the results of this study add at least five new species of Argasidae family into Chilean fauna of ticks, and point the occurrence of several forms that need further assessment in order to accurately confirm their identities. / Até 2014, o conhecimento científico sobre a diversidade de Ixodoidea no Chile estava representado por 19 espécies e apenas agentes infecciosos dos gêneros Borrelia e Rickettsia haviam sido descritos. O objetivo deste estudo foi o de avaliar a ocorrência de outros patógenos transmitidos por carrapatos por meio de técnicas moleculares orientadas para a deteção de Anaplasma, Borrelia, Coxiella, Ehrlichia, Rickettsia e Hepatozoon. As sequências obtidas foram analisadas filogeneticamente, identificando-se suas posições em comparação à de organismos de papeis patogénicos já conhecidos. Como os agentes do gênero Coxiella apresentaram proximidade filogenética em relação a bactérias congenêricas endosimbiontes, os dados sobre estas foram utilizados para realizar um estudo taxonômico em carrapatos do complexo Ornithodoros capensis sensu lato. Em geral, os resultados confirmam a presença de pelo menos três novas espécies de Borrelia, uma nova Rickettsia, e três novas espécies de Hepatozoon para a ciência. Rickettsia amblyommatis, Rickettsia hoogstraalii e Rickettsia lusitaniae foram inseridas como novos agentes associados a carrapatos no Chile. Embora alguns carrapatos fossem positivos para a presença de bactérias da família Anaplasmataceae, futuros estudos devem ser desenvolvidos para confirmar a sua condição especifica, especialmente através da obtenção de maiores fragmentos do gene codificante para RNA 16S. Os organismos tipo Coxiella são específicos para cada uma das quatro espécies de carrapatos do grupo O. capensis analisados neste estudo. Portanto, constituem uma ferramenta de valor taxonômico para confirmar as identidades e limites genéticos destes. Finalmente, os resultados deste estudo adicionam pelo menos cinco novas espécies de carrapatos para a família Argasidae no Chile e apontam a ocorrência de várias morfotipos de condição incerta que precisam de maiores análises para esclarecer a com certeza a sua posição taxonômica.

L’anatomie interne des crânes des stégocéphales Stanocephalosaurus (Temnospondyli), Laosuchus (Chroniosuchia) et Diplocaulus (Lepospondyli) a pu être révélée par l’utilisation de la tomographie à rayons X et a permis de mieux comprendre leur paléobiologie : 1) l’oreille moyenne de Stanocephalosaurus serait adaptée à la perception de sons dans le milieu subaquatique ; 2) des canaux sensoriels intra-osseux ont été identifiés chez Laosuchus. La morphologie endocrânienne a ensuite été utilisée dans une analyse phylogénétique portant sur les relations de parentés controversées entre stégocéphales et lissamphibiens. Cette analyse montre que la monophylie des lissamphibiens serait due à un phénomène d’attraction des longues branches, résultant de l’optimisation de la simplification crânienne, identifiée comme une convergence. Les morphologies de la boite crânienne, du stapes et du palais favorisent une origine diphylétique des lissamphibiens parmi les temnospondyles. / The intracranial anatomy of the stegocephals Stanocephalosaurus (Temnospondyli), Laosuchus (Chroniosuchia) and Diplocaulus (Lepospondyli) has been revealed by X-rays tomography and allowed to better understand their paleobiology: 1) the middle ear of Stanocephalosaurus would be an underwater adapted hearing system; 2) intraosseous sensorial canals have been identified in Laosuchus. The endocranial morphology have been included in a phylogenetic analysis on the debated relationships between stegocephals and lissamphibians. This analysis shows that the monophyly of Lissamphibia may result from a long-branch attraction, due to the optimisation of the cranial simplification, here as identified convergent. The morphologies of braincase, stapes and palate favour a biphyletic origin of lissamphibians among temnospondyls.

The principal aim of the study which was conducted between May 1995 and May 1997 was to collect and analyze information that would be considered vital to any future management actions that may be applied to the deer living in the wild in the Bali Barat National Park ecosystem in Indonesia. The systems approach used sought to analyze the complex interactions between the soil, plant, animal and human activity subsystems. In particular, interaction between Rusa deer and Muntjac deer was compared where possible, although the principal focus of the study was on the population of Muntjac deer. The soils in habitats frequented by deer in Bali Barat National Park were found to be of relatively low fertility status. Chemical analysis of the soil revealed that all of the mineral element contents considered in this study were in the lowest range for soils, in general. During this study the population of Muntjac deer in the Bali Barat National Park was submitted to phylogenetic analysis to determine whether the Bali population is distinct. Preliminary results indicate that these deer are apart of a diverse, but monophyletic group of Muntiacus Muntjac. The potential unique status of Muntjac deer in Bali Barat National Park, and the need to preserve them as part of the natural resource base that constitutes the Indonesian archipelago increased the importance of this study of the ecosystem and social system surrounding Bali Barat National Park. / Doctor of Philosophy (PhD)

Elucidation of mechanisms that generate and maintain population-level phenotypic variability provides insight into processes that influence within-species genetic divergence. Historically, color pattern polymorphisms were used to infer population-level genetic variability, but recent approaches directly capture genetic variability using molecular markers. Here, I clarify the relationship between genetic variability and color pattern polymorphism within and among populations using the Australian common froglet, Crinia signifera. To illustrate genetic variability in C. signifera, I used phylogenetic analysis of mitochondrial DNA and uncovered three ancient geographically restricted lineages whose distributions are consistent with other southeastern Australian species. Additional phylogeographic structure was identified within the three ancient lineages and was consistent with geographic variation in male advertisement calls. Natural selection imposed by predators has been hypothesized to act on black-and-white ventral polymorphisms in C. signifera, specifically through mimicry of another Australian frog, Pseudophryne. I used clay replicas of C. signifera to test whether predators avoid black-and-white coloration. In fact, black-and-white replicas were preferentially avoided by predators in some habitats, but not in others, indicating that differential selection among habitats plays a role in maintaining color pattern polymorphism. When black-and-white color patterns in a sample of C. signifera populations were compared with those in sympatric Pseudophryne, several color pattern characteristics were correlated between the species. Furthermore, where C. signifera and Pseudophryne are sympatric, color patterns are more similar compared to those in allopatry. Extensive phylogenetic variability suggests that phylogenetic history and genetic drift may also influence C. signifera color pattern. Fine-scale phylogenetic analysis uncovered additional genetic diversity within lineages and low levels of introgression among previously identified clades. Measures of color pattern displayed low levels of phylogenetic signal, indicating that relationships among individuals only slightly influence color patterns. Finally, simulations of trait evolution under Brownian motion illustrated that the phylogeny alone cannot generate the pattern of variation observed in C. signifera color pattern. Therefore, this indicates a minimal role for genetic drift, but instead supports either the role of stabilizing selection due to mimicry, or diversifying selection due to habitat differences, in color pattern variation in C. signifera. / text

This thesis attempts to broaden what is known about bacterial symbionts within amoebae by the use of a number of different molecular methods. Initially a number of different amoeba strains were screened for bacterial symbionts by 16S rRNA gene PCR, then the symbionts were identified by comparative sequence analysis and phylogenetic analysis. The amoeba strains containing bacterial symbionts were characterised by cell morphology, 18S rRNA gene sequencing, internal transcribed spacer sequencing and allozyme electrophoresis. Amoebae belonging to the genera Acanthamoeba, Naegleria, Ripidomyxa and Saccamoeba were identified as containing symbionts that belonged to a wide range of different bacterial genera. Relationships between bacterial symbionts and their host amoebae were analysed by the use of transmission electron microscopy and fluorescent in situ hybridisation using symbiont specific probes. Also described are attempts that were made to isolate and grow the bacterial symbionts outside of their host amoebae as well as experiments to try to transfer bacterial symbionts from one amoeba strain to another. Lastly the results from this study are discussed as a whole to put into perspective how they contribute to the body of knowledge of symbionts within protozoa.