Thesis (Ph. D.)--University of Washington, 2005. / Vita. Includes bibliographical references (p. 97-102).

Thesis (Ph. D.)--University of Texas at Austin, 2004. / Supervisor: Tandy Warnow. Vita. Includes bibliographical references.

Orientador: Augusto Shinya Abe / Banca: Sergio Furtado dos Reis / Banca: Francisco Luis Franco / Resumo: O gênero Rhinocerophis pertence à família Viperidae e subfamília Crotalinae. Esta subfamília é composta por 31 gêneros e cerca de 170 espécies distribuídas pelas Américas e Ásia. Historicamente este gênero era considerado como um dos grupos pertencentes ao gênero Bothrops, no entanto diversos estudos baseados em evidências morfológicas e moleculares sugeriam a existência de grupos monofiléticos, o que levou à subdivisão em grupos menores e mais homogêneos, tanto na morfologia quanto em aspectos ecológicos. Assim, Bothrops (senso lato) foi subdividido em Rhinocerophis, Bothropoides e o gênero nominal. A monofilia de Rhinocerophis tem sido sugerida em diversos trabalhos, entretanto as relações filogenéticas entre as espécies que o compõe não são satisfatoriamente compreendidas. Neste trabalho foi corroborada a hipótese de monofilia do gênero e proposta a hipótese de relacionamento filogenético entre suas espécies. A análise filogenética de parcimônia foi baseada em caracteres da morfologia externa, anatomia hemipeniana e osteologia craniana. Para tal, foram incluídas nesta análise, além de Rhinocerophis, espécies pertencentes a Bothropoides, Bothriopsis, Bothrops e Bothrocophias hyoprora, representantes do grupo-externo, totalizando dezessete espécies. Bothrocophias hyoprora foi a espécie escolhida para enraizar o cladograma por ser evidentemente externa aos demais táxons. Foram examinados 538 espécimes, 42 hemipênes e 44 crânios, que originou uma matriz com 99 caracteres. A análise desta matriz resultou em uma única árvore mais parcimoniosa com 195.784 passos, índice de consistência igual a 0,67 e índice de retenção igual a 0,79. A monofilia de Rhinocerophis foi sustentada por dez sinapomorfias e as relações entre os táxons obtidas foram as seguintes: (((R. ammodytoides - R. itapetiningae) ((R. alternatus - R. jonathani)... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The genus Rhinocerophis belongs to the family Viperidae and subfamily Crotalinae. This subfamily is composed of 31 genera and about 170 species distributed throughout the Americas and Asia. Historically, this genus was regarded as one of the groups belonging to the genus Bothrops,however several studies based on morphological and molecular evidence suggesting the existence of monophyletic groups, which led to the subdivision into smaller groups and more homogeneous, both in morphology and in ecological aspects.Thus, Bothrops (sensu lato) was subdivided into Rhinocerophis, Bothropoides and the nominal. The monophyly of Rhinocerophis has been suggested in several studies, however the phylogenetic relationships among species that comprise it are not sufficiently understood.This work was supported the hypothesis of monophyly of the genus and proposed the hypothesis of phylogenetic relationships between its species. The phylogenetic parsimony analysis was based on characters of external morphology, hemipenial anatomy and cranial osteology. To this end, included in this analysis, beyond Rhinocerophis, species belonging to Bothropoides, Bothriopsis, Bothrops and Bothrocophias hyoprora, representatives of outgroups, totaling seventeen species. Bothrocophias hyoprora species was chosen to root the cladogram to be obviously foreign to the other taxa. We examined 538 specimens, 42 hemipenes and 44 skulls, which led to a matrix with 99 characters. The analysis of this matrix resulted in a single most parsimonious tree of 195.784 steps, consistency index equal to 0,67 and retention index 0,79. Monophyly of Rhinocerophis was supported by ten synapomorphies and the relationships among the taxa revealed the following: (((R. ammodytoides - R. itapetiningae) ((R. alternatus - R. jonathani) (R. cotiara - R. fonsecai) )). Topology of the cladogram also confirms the position of Rhinocerophis basal to a clade... (Complete abstract click electronic access below) / Mestre

Tropical forests have been studied by community ecologists since the earliest days of the field because of their diversity and complexity and much of the theory behind community assembly has been developed in the tropics. However, the processes that act to assemble species in tropical forest across a very fine scale are still poorly understood. This study investigates community structure in 20ha area of hyper diverse tropical rainforest in Sabah, Malaysia. In order to examine community phylogenetic structure, I reconstructed a molecular phylogeny for all species in the study site using DNA barcoding loci. From this, I calculated phylogenetic diversity metrics for each community and then used a null model to compare observed phylogenetic diversity with that which would be expected if communities were randomly assembled with respect to phylogeny. The analyses showed that communities are more closely related than predicted by the null model. I also collected species functional trait data and showed that species assemblages and community weighted mean trait values correlate with environmental gradients on the plot. I also compared functional diversity to data simulated from null models. This showed that communities are on average more functionally similar than predicted at random. Finally, I performed a multivariate analysis with environmental, spatial, phylogenetic and trait data from communities across the plot. The analyses recovered an elevational and soil gradient that correlated strongly with community composition. Species occupying different ranges along this gradient had differing trait values and were phylogenetically distinct. These analyses demonstrate that even fine scale environmental variation is influential in assembling communities over a small area of forest. A soil nutrient gradient is consistently recovered that correlates with topography, suggesting that soil nutrient distribution is mediated by the downslope movement of water leaching soils on ridge tops and leading to accumulation of nutrients in valleys. This gradient is associated with species compositional variation and also with community weighted mean functional traits, indicating that the environment is influencing species distributions even over very small areas. Communities were both functionally and phylogenetically clustered, adding further support to this conclusion.

The Grey-bellied Pygmy Mouse (Mus triton) has been for a long time considered as a single species, although validity of the single species status was questioned. In order to revise current taxonomy of M. triton, I analyzed sequences of one mitochondrial (cytochrome b) and two nuclear genes (IRBP and Intron 7 of the fibrinogen) from specimens collected across the most of its known distributional range. Four well-supported phylogroups at species level, differentiated during the Plio-Pleistocene, were evidenced. Divergence dating suggests that the diversification of "triton" species complex was likely caused by Plio-Pleistocene climatic oscillations together with highly diverse topography of Eastern Africa

Morphology and phylogeny for 36 heterocytous cyanobacterial strains are studied. Discussion with morphological, ecological, and phylogenetically related taxa is given for each strain. Potentially new genera and species are found, one of them being proposed as a novel genus.

Rhinocricus Karsch, 1881 possui atualmente 207 espécies descritas e distribuídas principalmente pelo continente americano, das quais 65 são descritas para o Brasil. A descrição do gênero foi baseada na presença de escobinas (depressões na porção distal dos prozonitos). O presente estudo avaliou a monofilia de três grupos de espécies previamente propostos em Rhinocricus. A matriz de dados foi composta por 39 caracteres morfológicos e 30 espécies terminais, sendo 21 como grupo interno e nove do grupo externo. Nós realizamos uma analise de parcimônia com pesos implicitos usando o software TNT e obtivemos a melhor árvore com a mesma topologia para três melhores valores de K (5.992, 7.309, 9.105). Nenhum dos três grupos de espécies de Rhinocricus foi recuperado monofilético. Rhinocricus (Erythocricus) sanguineostriatus foi recuperado irmão de todas as outras espécies, e Argentocricus Verhoeff, 1941 resultou parafilético. Os caracteres diagnósticos tradicionalmente utilizados para separar grupos de espécies, subgênero e gênero não foram recuperados como sinapomorfias. Ainda durante o exame do material quatro novas espécies de Rhinocricus foram descobertas e são aqui descritas. Futuras investigações incluindo amostras mais amplas de espécies são necessárias, para estabelecer hipóteses de relacionamento robustas entre R. (Erythocricus), Argentocricus, e o restante das espécies de Rhinocricus, deste modo identificando grupos monofiléticos no gênero e suas sinapomorfias. / Rhinocricus Karsch, 1881 currently has 207 species described and distributed mainly by the American continent, of which 65 are described for Brazil. The genus was based on the presence of scobinae (depressions in distal portion of prozonit). The present study evaluated the monophyly of three groups of species previously proposed in Rhinocricus. The data matrix was composed for 39 morphological characters and 30 species as terminal taxa, being 21 the ingroup, and nine the outgroup. We performed a parsimony analysis with implied weights using TNT software, obtaining the same best topology with three optimal K-values (5.992, 7.309, 9.105). None of the three previously proposed species groups of Rhinocricus was recovered monophyletic. Rhinocricus (Erythocricus) was recovered sister to all other species, and Argentocricus Verhoeff, 1941 resulted paraphyletic. The diagnostic characters traditionally used to separate species groups, subgenera, and genera were not recovered as synapomorphies. Still during the examination of the material four new species of Rhinocricus were discovered and here described. Further investigation including a broader species sample is needed attempting to establish robust relationship hypotheses between R. (Erythocricus), Argentocricus, and the remainder species of Rhinocricus, thus identifying the monophyletic groups in the genus and their synapomorphies.

Population structure and phylogenetic relationships were studied in coccidia parasitizing the rodent families Muridae and Arvicolidae, in 40 localities in 14 European countries. Sequences of mitochondrial gene for cytochrome c oxidase subunit I (COI) and nuclear 18S rRNA gene (SSU) were used for phylogenetic analyses and for reconstruction of evolutionary relationships among coccidian species.

Abstract In order to examine the prevalence of Cryptosporidium in wild Arvicolinae in the Czech Republic and understand the role that wild rodents play in the transmission of this parasite to humans and livestock, 152 faecal samples from 129 common voles (Microtus arvalis) and 23 bank voles (Clethrionomys glareolus) were collected on 9 localities in 2012. All samples were examined for presence of Cryptosporidium sp. using both the aniline-carbol-methyl violet staining method and molecular tools. The age, sex and faecal consistency were noted at the time of sampling. Microscopical examination revealed the presence Cryptosporidium sp. oocysts in 2 samples originated from common voles and 2 samples from bank voles. Genotyping was done through PCR amplification and characterization of the SSU rRNA and actin loci. Cryptosporidium specific DNA was detected in 10 samples (4 from common voles and 6 from bank voles) including those microscopically positive. Cryptosporidium infection was not linked to diarrhoea. Sequence and following phylogeny analyses revealed two new Cryptosporidium genotypes originated from bank voles and two new genotype from common vole, phylogeneticaly distinct from known species and genotypes. The host specificity needs to be verified by experimental infection in the future.

Made available in DSpace on 2016-01-13T13:28:01Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-04-24. Added 1 bitstream(s) on 2016-01-13T13:33:34Z : No. of bitstreams: 1 000855644.pdf: 12006624 bytes, checksum: ebdef53dd60214df61e00ed63cee2be3 (MD5) / Crocodilomorfos são o grupo de vertebrados fósseis mais expressivo do Grupo Bauru, contando com 25 espécies formalmente descritas, distribuídas entre quatro principais agrupamentos: Notosuchia, Baurusuchidae, Peirosauridae e Trematochampsidae. À luz dos novos morfótipos descritos se faz necessária uma análise filogenética, a fim de testar possíveis relações com os táxons estabelecidos. Adicionalmente nenhum trabalho traz uma abordagem metodológica a respeito da paleobiogeografia destes grupos. Deste modo, os objetivos desse trabalho foram realizar uma análise filogenética e utilizar seus resultados pela primeira vez em uma análise de Parcimônia de Brooks. O resultado da análise levou a 3 árvores de 2259 passos cada uma, gerando uma árvore de consenso também com 2270 passos. Mesoeucrocodylia foi recuperado, sendo composto por dois clados mais inclusivos: Neosuchia e Gondwanasuchia. Este último formado Sebecia e Notosuchia. Sebecia inclui um grupo monofilético formado por Trematochampsidae, Peirosauridae e Itasuchidae, um clado que inclui Caririsuchus, Itasuchus, Barreirosuchus, Pepesuchus e MCT-1723-R. Este último táxon apresenta semelhanças morfológicas profundas com Pepesuchus e foi classificado como Pepesuchus sp. As relações dentro desse clado sempre formam politomias, foram resgatadas todas resolvidas. Notosuchia inclui um grupo de formas mais avançadas composto por dois clados. Um deles é Baurusuchia, que resgatas as subfamílias Pissarrachampsinae e Baurusuchinae, mas não encontra Baurusuchus pachecoi e Baurusuchus salgadoensis como táxons irmãos. O outro clado dentro de Notosuchia é formado por Notosuchidae como grupo irmão de um clado formado por Morrinhosuchus e Sphagesauridae, com Labidiosuchus e Adamantinasuchus no âmbito desta família. Mariliasuchus robustus compartilha diversas similaridades morfológicas com Mariliasuchus amarali, enquanto que as diferenças entre ambos os táxons... / Crocodylomorphs are the most expressive group of vertebrate fossils from the Bauru Group, counting 25 formally described species, distributed among four main groups: Notosuchia, Baurusuchidae, Peirosauridae, Trematochampsidae. Facing the new morphotypes described it is necessary a phylogenetic analysis to test possible relationships with established taxa. Besides, none work brings a methodology regarding a biogeographic approach to these goups, thus the objectives of this study were to perform a phylogenetic analysis and use the results to a Brooks Parsimony analysis. The result of the analysis took to 3 trees of 2259 steps each, generating a consensus tree of 2270 steps. Mesoeucrocodylia was recovered, consisting of two more inclusive clades: Neosuchia and Gondwanasuchia. The latter is composed by Sebecia and Notosuchia, Sebecia includes a monophyletic group composed by Trematochampsidae, Peirosauridae, and Itasuchidae, a clade comprising Caririsuchus, Itasuchus, Barreirosuchus, Pepesuchus, and MCT-1723-R. This last taxon showing large morphologic similarities with Pepesuchus and was classified like Pepesuchus sp. The relationships inside this clade always return polytomies, and they were recovered all solved. Notosuchia included a group of advanced forms comprising two clades, one of this is Baurusuchia, recovering the subfamilies Pissarrachampsinae and Baurusuchinae, but not finding Baurusuchus pachecoi and Baurusuchus salgadoensis like sister-taxa. The other clade inside Notosuchia is formed by Notosuchidae with a sister-group of a clade comprising by Morrinhosuchus and Sphagesauridae, with Labidiosuchus and Adamantinasuchus inside that family. Mariliasuchus robustus sharing several morphological similarities with Marliasuchus amarali,while the differences between both the taxa are resultants of sexual dimorphism. Therefore, M. robustus is a junior synonym of M. amarali. The results of Brooks Parsimony analysis is a General Area ...