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1
Scholfield, Claire Ingrid. "Molecular Taxonomy of the Rhodophyta." Thesis, Cardiff University, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.310158.
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Muthumeenakshi, Sreenivasaprasad. "Molecular taxonomy of the genus Trichoderma." Thesis, Queen's University Belfast, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.264087.
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Dhanasekaran, Vijaykrishna. "Freshwater fungi biodiversity, origins and molecular taxonomy /." Thesis, Click to view the E-thesis via HKUTO, 2005. http://sunzi.lib.hku.hk/hkuto/record/B32017583.
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Hodgetts, Jennfier. "The taxonomy of phytoplasmas : a molecular approach." Thesis, University of Nottingham, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.508216.
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Silva, Bruna Demari e. "Estudos taxonômicos de espécies do gênero Culex (Diptera: Culicidae) da região neotropical, utilizando a subunidade I do gene mitocondrial citocromo oxidase." Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/6/6132/tde-28012010-105230/.
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Diversas espécies de mosquitos do gênero Culex Linnaeus são vetores de nematóides que causam filariose linfática (Wuchereria bancrofti) e de vários arbovírus, incluindo o Vírus do Nilo Ocidental (VNO) que causa encefelites em animais e humanos. Embora seja o maior gênero da família Culicidae, com 763 espécies conhecidas, pouco se sabe sobre a taxonomia e as relações filogenéticas do grupo. Considerando-se a grande diversidade de espécies do gênero Culex, as dificuldades para a identificação morfológica, devidas principalmente ao fato das fêmeas serem morfologicamente muito similares, o presente trabalho teve como objetivos: (1) Solucionar problemas relacionados à nomenclatura; (2) Estimar as relações filogenéticas entre espécies de diferentes subgêneros; (3) Examinar o monofiletismo de subgêneros da Região Neotropical; (4) Estimar as relações evolutivas entre subgêneros neotropicais; (5) Estimar a posição filogenética do gênero Lutzia em relação à Culex; (6) Discutir sobre a utilização do gene citocromo c oxidase da subunidade I (COI) para o gênero Culex. Foram analisadas sequências correspondentes a um fragmento de 478 pares de bases do gene COI de 36 indivíduos pertencentes a 16 espécies do gênero Culex. Foram avaliadas espécies de quatro subgêneros, Culex, Phenacomyia, Melanoconion e Microculex e uma espécie do gênero Lutzia. As sequências do gene COI foram comparadas através das análises de Máxima Parcimônia, Máxima Verossimilhança e Bayesiana. Os resultados das análises das sequências de COI, utilizando ao modelo de Kimura 2-parâmetros, de Culex dolosus, Culex mollis e Culex imitator, demonstram a presença de divergências intraespecíficas altas (3,1%, 2,3% e 3,5%, respectivamente). Os valores do modelo Kimura 2-parâmetros indicam que esses taxa podem representar complexos de espécies. As topologias de MV, MP e Bayesiana mostraram que tanto o gênero Culex como o subgênero Culex são parafiléticos, pois o primeiro não inclui o gênero Lutzia e o segundo exclui o Phenacomyia. Os resultados indicam que Lutzia é subgênero de Culex e Phenacomyia um grupo monofilético do subgênero Culex. O marcador molecular COI foi de fácil utilização e análise, provando ser ferramenta útil para estudos filogenéticos e para a taxonomia molecular de CulexSpecies of the genus Culex Linnaeus mosquitoes have been pointed out as the main vectors of lymphatic filariases. Furthermore, they are important vectors of encephalitis across the world, including the West Nile Virus. Although being the major genus in Culicidae family, with 763 valid species, Culex, in a taxonomic and phylogenetic sense, is one of the least known. Considering the great diversity of species of mosquitoes in this genus, and the fact that females of several species are vary similar morphologically, the present study aimed to: (1) Solve problems related to nomenclature (2) estimate the phylogenetic relationships of species used in the work; (3) examine the monophyly of subgenera of the Neotropical Region; (4) estimate the evolutionary relationships between neotropical subgenera; (5) estimate the phylogenetic position of the genus Lutzia in the Culex, (6) discuss the use of the gene cytochrome c oxidase subunit I (COI) to the genus Culex. We analyzed sequences corresponding to a fragment of 478 base pairs of the COI gene of 36 individuals belonging to 16 species of the genus Culex. Species were evaluated in four subgenera, Culex, Phenacomyia, Melanoconion and Microculex and one species of the genus Lutzia. The COI gene sequences were compared using analysis of Maximum Parsimony, Maximum Likelihood and Bayesian. The results of the analysis of the COI sequences, used the model of Kimura 2-parameters of Culex dolosus, Culex mollis and Culex imitator, demonstrate the presence of high intraspecific divergence (3.1%, 2.3% and 3.5% respectively). These values indicate that these taxa may represent complexes of species. The topologies of ML, MP and Bayesian showed that both genus Culex as subgenus Culex are paraphyletic because the first does not include the genus Lutzia and the second excludes the Phenacomyia subgenus. The results indicate that Lutzia is a subgenus of Culex and Phenacomyia is a monophyletic group of subgenus Culex. The molecular marker COI was easy to use and analyzing, proving to be useful tool for phylogenetic studies and the molecular taxonomy of Culex
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Cao, Wenguang. "Wheat taxonomy and cultivar identification using molecular markers." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/nq24007.pdf.
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Krüger, Manuela. "Molecular phylogeny, taxonomy and evolution of arbuscular mycorrhizal fungi." Diss., lmu, 2011. http://nbn-resolving.de/urn:nbn:de:bvb:19-140769.
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Jeewon, Rajesh. "Pestalotiopsis taxonomy : molecular phylogenetics, species nomenclature and teleomorph relationships /." Thesis, Hong Kong : University of Hong Kong, 2001. http://sunzi.lib.hku.hk/hkuto/record.jsp?B24367394.
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Cai, Junpeng. "Molecular phylogenetic analysis on some ascomycetous spoilage yeasts." Thesis, University of Reading, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.297332.
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Lee, Chung-Kun. "Phylogeny and Taxonomy of Commelinaceae (Commelinales)." Doctoral thesis, Kyoto University, 2021. http://hdl.handle.net/2433/263508.
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Blomster, Leena Jaanika. "Molecular and morphological approaches to the taxonomy of Enteromorpha (Chlorophyta)." Thesis, Queen's University Belfast, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.324827.
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Rinkel, Barbara Elizabeth. "A molecular and morphological taxonomy of epi-/endophytes (Ulvophyceae, Chlorophyta)." Thesis, University of Bristol, 2007. http://hdl.handle.net/1983/e737a534-1eed-4d51-a7f7-954abcaeada8.
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Stoch, Fabio. "Molecular taxonomy, phylogeny and biogeography of European niphargids (Crustacea, Amphipoda)." Doctoral thesis, Universite Libre de Bruxelles, 2021. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/326119.
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Les écosystèmes des eaux souterraines sont de plus en plus reconnus pour leur faune endémique, phylogénétiquement ancienne et écologiquement spécialisée. Avec plus de 425 espèces décrites, les amphipodes niphargidés constituent la famille des eaux souterraines la plus riche en espèces au monde et un système modèle intéressant pour la biologie de l'évolution. Cependant, les scientifiques doivent faire face à des données incomplètes et biaisées en raison de trois déficits majeurs: le déficit Linnéen pour la taxonomie, le déficit Darwinien pour la phylogénie, et le déficit Wallacien pour la biogéographie. La présente thèse vise à évaluer l'importance de ces déficits chez les niphargidés, ouvrant ainsi la voie pour y remédier. Le premier chapitre est une évaluation des effets de la découverte d'espèces cryptiques (une des causes du déficit Linnéen) sur notre compréhension des modèles de distribution à grande échelle de la diversité des niphargidés. Contrairement à ce que l'on attendait, les espèces cryptiques putatives sont réparties de manière homogène le long des gradients environnementaux, et leur découverte ne modifie donc pas notre compréhension des modèles de distribution. Le deuxième chapitre analyse l'importance de l'application des techniques moléculaires à la taxonomie des niphargidés. En étudiant le genre Microniphargus, la morphologie seule s'est avérée peu informative en raison de la pédomorphose et de l'homoplasie. L'utilisation de marqueurs ADN a permis d'attribuer le genre à une famille différente (Pseudoniphargidae), venant éclaircir les relations phylogénétiques au sein des Niphargidae (et contribuant ainsi à remédier au déficit Darwinien). Le troisième chapitre traite du rôle des régressions et transgressions marines sur la distribution des niphargidés en utilisant la biogéographie moléculaire et une modélisation biogéographique innovante (afin de remédier au déficit Wallacien). Les résultats soutiennent l'idée que la dispersion a joué un rôle essentiel dans la biogéographie historique des niphargidés, en montrant que leurs voies de dispersion sont corrélées à des événements paléogéographiques anciens. Enfin, le quatrième chapitre traite de la taxonomie, de la phylogénie et de la biogéographie d'un clade de niphargidés distribué dans la région des Alpes et des Carpates, et illustre un cas de discordance mitonucléaire dans la délimitation d'espèces vivant dans des zones affectées par les glaciations quaternaires. Une histoire complexe de divergence de lignées évolutives et de contacts secondaires pendant les fluctuations climatiques du Pléistocène explique la plus grande variabilité de l'ADN mitochondrial par rapport aux marqueurs nucléaires. Dans une telle situation, la description formelle d'espèces cryptiques basée sur le seul barcodage de l'ADN mitochondrial, comme dans certains articles récents sur les niphargidés, n'est pas recommandée. Cette thèse ouvre plusieurs perspectives pour des recherches futures basées sur la taxonomie intégrative et la modélisation biogéographique, permettant aux niphargidés très diversifiés de jouer un rôle majeur dans la surveillance des écosystèmes des eaux souterraines.Doctorat en Sciences
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Ranasinghe, Subhani Wathsala. "Molecular species delimitation, taxonomy and biogeography of Sri Lankan Gesneriaceae." Thesis, University of Edinburgh, 2017. http://hdl.handle.net/1842/28889.
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The plant family Gesneriaceae is represented in Sri Lanka by six genera: Aeschynanthus, Epithema, Championia, Henckelia, Rhynchoglossum and Rhynchotechum, with 13 species (plus one subspecies/variety) of which ten are endemic including the monotypic genus Championia, according to the last revision in 1981. They are exclusively distributed in undisturbed habitats, and some have high ornamental value. The species are morphologically diverse, but face a problem of taxonomic delineation, which is further complicated by the presence of putative hybrids. Sri Lanka and Indian Peninsula, represent the Deccan plate of the ancient Gondwanan supercontinent. The presence of a relict flora may indicate the significance of the geological history of the Deccan plate for the evolution of angiosperms. The high degree of endemism here, along with their affinities to the global angiosperm flora paints a complex picture, but its biogeographic history is still unclear. The pantropical family Gesneriaceae distributed in Sri Lanka and South India is therefore an appropriate study group in this context. Besides, the family itself has a complex but largely unresolved biogeographical history especially concerning the origin and diversification of Old World Gesneriaceae. Modern approaches for the taxonomic studies were applied, integrating morphological and molecular data. Multiple samples were collected for each species across their geographical distribution. Nuclear ITS and chloroplast trnL-F sequences for the taxa from Sri Lanka were used to generate regional genus phylogenies of all six genera, using maximum parsimony. The rate of evolution of the nuclear ITS region versus chloroplast trnL-F was varied greatly across the six genera studied. Molecular delimitations were mostly congruent with the classical taxonomy. Over 65 taxonomic characters were studied in detail to recognize synapomorphies for clades and taxa. A complete taxonomic revision of Gesneriaceae in Sri Lanka, including lectotypification, was conducted based on both, the molecular and morphological data. This resulted in the recognition of 14 species in the six genera, including one newly described species H. wijesundarae Ranasinghe and Mich. Möller. Henckelia communis and H. angusta were not supported molecularly as two separate entities but are recognized as two species because of consistent morphological differences between them. Henckelia humboldtiana is proposed to represent a species complex due to its highly variable and inconsistent molecular and morphological diversity and overlap with H. incana and H. floccosa; more research is needed here. National conservation assessments were conducted, and all 14 species were recognized as threatened. Biogeographic affinities of Sri Lankan Gesneriaceae were elucidated, generating a dated phylogeny using an existing matrix of four plastid gene regions; trnL-F, matK, rps16 and ndhF, amended by sequences generated in this study. The final combined matrix included 175 taxa including newly generated sequences for the 13 Sri Lankan taxa. Phylogenetic trees were generated using parsimony, maximum likelihood and Bayesian inference. Molecular dating was carried out using BEAST and ancestral area reconstruction using BioGeoBears. These analyses indicated that the six genera of Gesneriaceae arrived in Sri Lanka separately and sometimes different time periods. One lineage dated back to the early diversification of the subfamily Didymocarpoideae (generally regarded as the Old World Gesneriaceae), which occurred around the KT boundary, before the Deccan plate was connected to Asia.
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Longo, Dânae. "Delimitação taxonômica do complexo Petúnia integrifolia : uma abordagem molecular." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2005. http://hdl.handle.net/10183/13702.
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Os chamados ‘complexos de espécies’ são definidos como grupos de organismos que compartilham características morfológicas muito semelhantes. Os complexos de espécies representam um problema para os sistemas de classificação baseados apenas em caracteres morfológicos, uma vez que os critérios para delimitação de espécies são subjetivos e, por isso, variam de acordo com cada taxonomista. O complexo integrifolia, que reúne diversos taxa com características florais muito semelhantes à espécie Petunia integrifolia (Hook.) Schinz & Thell, é um exemplo dessa problemática taxonômica. A determinação de espécies dentro desse complexo, baseada apenas em caracteres morfométricos, é até hoje ainda muito controversa. Nesse trabalho, os espaçadores internos transcritos do DNA nuclear ribossomal (ITS1 e ITS2) e dois espaçadores intergênicos (trnS-trnG e psbA-trnH) do DNA plastidial (cpDNA) foram seqüenciados em 69 indivíduos pertencentes a cinco entidades taxonômicas do complexo integrifolia na tentativa de entender sua história evolutiva e melhor contribuir para a correta delimitação das espécies. Análises populacionais e filogeográficas dos três marcadores do cpDNA mostraram que apenas a entidade taxonômica descrita como Petunia interior pode ser considerada uma espécie distinta de Petunia integrifolia. As outras quatro entidades taxonômicas estão divididas em duas linhagens genéticas independentes e alopátricas, que surgiram mais ou menos na mesma época após um evento de diminuição populacional seguido de rápida expansão. Uma dessas linhagens está localizada na planície costeira do Rio Grande do Sul e Santa Catarina, enquanto a outra linhagem se distribui na porção continental do RS ao oeste da Lagoa dos Patos. Análises morfométricas mais detalhadas mostram que essas duas linhagens genéticas podem ser distinguidas taxonomicamente e, portanto, são definidas como duas subespécies de Petunia integrifolia. Há indícios de que um processo de especiação por adaptação a dois ambientes distintos (alta salinidade na planície costeira e baixa salinidade na porção continental) esteja envolvido na divergência dessas duas linhagens. No entanto, para confirmar essa hipótese, são necessários estudos adicionais.“Species complex” are usually defined as group of species that are morphologically very similar and consequently are very difficult to distinguish. Species complexes, therefore, represent a serious problem to the classification systems based only in morphological characters, the criteria used to delimit species being subjective. The integrifolia complex, that congregates taxa with floral characteristics very similar to Petunia integrifolia (Hook.) Schinz & Thell, it is an example of this taxonomic challenge. The determination of the species inside of this complex, based only in morphometric characters, it is still very controversial. In this work, the internal transcribed spacers of the ribosomal nuclear DNA (ITS1 and ITS2) and two intergenic spacers (trnS-trnG and psbAtrnH) of the plastidial DNA (cpDNA) had been sequenced in 69 individuals pertaining to five taxonomic entities of the integrifolia complex, in the attempt to understand its evolutionary history and contribute to the better delimitation of the species. Populational and phylogeographic analyses of the three markers and of cpDNA had shown that only the taxonomic entity described as Petunia interior can be considered a distinct species of Petunia integrifolia. The four other taxonomic entities are divided in two independent and allopatric lineages, that diversified almost simultaneously after an event of population bottleneck followed by a fast expansion. One of these lineages is located in the coastal plain of the Rio Grande do Sul and Santa Catarina states, while to other lineage it’s distributed in the continental region of the Rio Grande do Sul to the west of the Lagoa dos Patos. Detailed morphometric analyses shown that these two lineages can be taxonomically distinguished and therefore, they may be considered as two subspecies of Petunia integrifolia. Some findings suggest that a process of adaptation to these two distinct environments (high salinity in the coastal plain and low salinity in the continental region) may be involved in the divergence of the two lineages. Additional studies are required to test this hypothesis.
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Trader, Brian Wayne. "Molecular and Morphological Investigation of Astilbe." Diss., Virginia Tech, 2006. http://hdl.handle.net/10919/28145.
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Astilbe (Saxifragaceae) is a genus of herbaceous perennials widely cultivated for their ornamental value. The genus is considered taxonomically complex because of its geographic distribution, variation within species, and the lack of adequate morphological characters to delineate taxa. To date, an inclusive investigation of the genus has not been conducted. This study was undertaken to (a) develop a well-resolved phylogeny of the genus Astilbe using an expanded morphological data set and sequences from the plastid gene matK, (b) use single nucleotide polymorphisms to determine the lineages of cultivated varieties, and (c) successfully culture Astilbe in vitro and evaluate potential somaclonal variation of resulting Astilbe microshoots.
Phylogenetic trees generated from a morphological character matrix of 28 character states divided Astilbe into three distinct clades. Relationships were well resolved among the taxa, though only a few branches had greater than 50% bootstrap support. There is evidence from the phylogeny that some described species may actually represent variation within populations of species. From our analysis I propose an Astilbe genus with 13 to 15 species and offer a key for distinguishing species and varieties.
There was little matK sequence variation among taxa of Astilbe. Phylogeny of Astilbe generated from the maximum parsimony and maximum likelihood analysis of matK sequences resulted in a polytomy of seven Astilbe species, with relationships within the genus poorly resolved. A second phylogeny of 21 taxa of Astilbe was more informative, aligning cultivated varieties near species from which they were derived. The matK sequence variation for Astilbe taxa was aligned to reveal DNA polymorphisms. Closely related taxa retained polymorphisms at the same sites within the gene sequence. These polymorphic sites could potentially be utilized to confirm the lineage of popular cultivated Astilbe varieties.
Propagation of Astilbe seedlings in tissue culture gave rise to various numbers of microshoots from each of 15 seedlings. Multivariate and cluster analysis of morphological characters from 138 plants derived from 15 seedlings revealed potential somaclonal variants. These variants were characterized by one or more of the following traits: dwarf habit, dark green leaves (high chlorophyll content), increased flowering, or larger plant size. Somaclonal variants with desirable phenotypes may be valuable for cultivar development.Ph. D.
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Gimenes, Kethely Fernandes Brasil. "Delimitação de espécies em Cubozoa : morfologia e molecular do gênero Tamoya /." Assis, 2017. http://hdl.handle.net/11449/151448.
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Orientador: Sérgio Nascimento StamparResumo: Existe uma considerável abundância de espécies de cnidários no litoral do Brasil e uma das espécies mais intrigantes e pouco conhecidas é a Tamoya haplonema, a qual dentre suas características mais interessantes se destaca a presença de um padrão de bandas nos tentáculos, o que não é comum nos cubozoários, classe à qual pertence. Essa espécie é conhecida desde meados do século XIX, sendo uma das poucas espécies no Atlântico Sul capaz de causar acidentes graves em humanos. Em 2011 alguns registros de espécimes do mesmo gênero para o Mar do Caribe resultaram na descrição de uma nova espécie, Tamoya ohboya. Essa espécie foi delimitada, principalmente, por dados moleculares e devido à disponibilidade de poucos indivíduos a definição é dúbia em vários trechos. Já foi constatado que o cenário taxonômico do gênero Tamoya no Atlântico Ocidental não é consistente. Desta maneira, o principal objetivo deste estudo foi a comparação taxonômica do gênero Tamoya no Atlântico Sul e Mar do Caribe.Para tal, indivíduos do gênero Tamoya do Atlântico Sul foram analisados e comparados com T.ohboya, utilizando dados morfológicos/morfométricos e moleculares, incluindo o estudo da composição dos nematocistos através das medidas e análises comparativas. Os resultados morfológicos, bem como a análise do cnidoma e os resultados moleculares deixam claro que T.haplonema e T.ohboya são na realidade a mesma espécie.
Abstract: There is a considerable abundance of cnidarian species along the Brazilian coast and one of the most intriguing and little known species is the medusa Tamoya haplonema, which among its most interesting characteristics stands out the presence of a pattern of bands in the tentacles, which is not common in the Cubozoa, the class to which it belongs. This species has been known since the mid-nineteenth century, being one of the few species in the Southern Atlantic capable of causing serious stings to humans. In 2011 specimens of the same genus the Caribbean Sea resulting in the description of a new species, Tamoya ohboya. This species was delimited, mainly, by molecular data and due to the availability of few individuals the definition is dubious in several parts. It has already been verified that the taxonomic scenario of the genus Tamoya in the Western Atlantic is not consistent. Thus, the main objective of this study was the taxonomic comparison of the genus Tamoya in the South Atlantic and the Caribbean Sea. Thus individuals of the genus from the South Atlantic were analyzed and compared with T.ohboya, using morphological / morphometric and molecular data, including the study of the nematocysts composition through measurements and comparative analyzes. The morphological results as well as the analysis of the cnidome and molecular results make it clear that T.haplonema and T.ohboya are actually the same species.
Mestre
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Sparmann, Sarah Franziska. "Contributions to the molecular phylogeny, phylogeography, and taxonomy of scyphozoan jellyfish." Thesis, University of British Columbia, 2012. http://hdl.handle.net/2429/43461.
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Scyphozoan jellyfish are a major group of large, bloom-forming marine animals that can disrupt ecological stability and interfere with marine-oriented industries. The widespread geographical distributions and high degrees of morphological plasticity within many species make understanding the overall diversity of scyphozoans difficult. Molecular phylogenetic approaches have the potential to offer powerful insights into many aspects of scyphozoan biology, such as species identification, evolutionary history, and phylogeography that will improve our ability to monitor and manage the roles these animals play in marine ecosystems. We established datasets of 16S rDNA and cytochrome c oxidase subunit I (COI) sequences of several different species of scyphozoans in order to better understand phylogenetic, phylogeographical, and taxonomic patterns within the group. Phylogenetic analysis of 16S rDNA sequences resolved closely related taxa but was too variable to resolve deeper relationships with robust statistical support. Combining this marker with a more conserved dataset of nuclear 18S rDNA sequences resulted in a phylogenetic tree with clades that had higher statistical support than in trees inferred from each marker alone. 16S rDNA sequences also showed phylogeographical patterns in Cyanea, distinguishing clearly between a Northeastern Pacific (NEP) clade and a Northwestern Atlantic clade (NWA) (9.71 - 9.93% mean genetic difference MGD), as well as two Atlantic subclades (NWA1, NWA2) (1.79% MGD). Distances within clades ranged from 0.05 - 0.2%. Therefore, 16S rDNA sequences were able to delimit different (putative) species that reflected distinct geographical distributions. In addition, comparative analyses of morphological features and COI sequences from Northeast Pacific isolates of Cyanea demonstrated that C. ferrugenia is a valid lion’s mane species found in the Northeast Pacific Ocean.
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Lea, Vincent John. "Molecular analysis of genetic diversity and taxonomy of tea, Camellia sinensis." Thesis, University of Cambridge, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.624949.
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Bueno, Verônica Mantovani. "Delimitação de espécies em Rhinebothroides Mayes, Brooks & Thorson, 1981 (Cestoda: Tetraphyllidea) com ênfase no complexo Rhinebothroides freitasi (Rego, 1979)." Universidade de São Paulo, 2010. http://www.teses.usp.br/teses/disponiveis/41/41133/tde-17082010-133238/.
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Membros do gênero Rhinebothroides são parasitas exclusivos de potamotrigonídeos, elasmobrânquios de água doce endêmicos da região Neotropical. Atualmente, seis espécies são reconhecidas para este gênero dentre as oito espécies nominais disponíveis. A taxonomia de Rhinebothroides é convoluta, pois a maioria de suas espécies são diagnosticadas por caracteres morfométricos e merísticos definidos por estudos que desconsideram a variabilidade intraespecífica destas linhagens. A ampla distribuição de algumas espécies, bem como seus padrões generalistas de especificidade padrão este discrepante em relação à tetrafilídeos marinhos sugere a existência de complexos de espécies que requerem melhor refinamento taxonômico. Este estudo visa refinar a taxonomia de um destes complexos Rhinebothroides freitasi, no qual estão inseridas outras 3 especies nominais (R. campbelli, R. circularisi, R. venezuelensis) cujas circunscrições são ambíguas. Neste estudo, partiuse da premissa de que a conjunção de dados moleculares e morfológicos pode elucidar a taxonomia deste complexo. Com este objetivo, dados moleculares para os genes 28S, ITS1 e COI foram compilados para 57 haplótipos de Rhinebothroides representando todas as espécies válidas para o gênero e a ampla distribuição biogeográfica no gênero nas bacias hidrográficas brasileiras. A otimização direta das sequências nucleotídicas destes haplótipos concatenadas com outros 26 terminais que incluem linhagens de tetrafilídeos marinhos e de água doce, resultou em cinco clados de Rhinebothroides que possuem morfologia congruente com a série tipo de cinco espécies nominais. Desta forma, este estudo reconhece cinco espécies de Rhinebothroides como válidas: R. glandularis, R. freitasi, R. moralarai, R. scorzai e R. venezuelensis. Dentre as espécies do complexo R. freitasi, os dados morfológicos compilados para ~ 400 indivíduos permitiu delimitar os níveis de variabilidade morfológica de R. freitasi e R. venezuelensis. A representatividade biogeográfica e de hospedeiros contemplada neste estudo revela que, ao contrário das linhagens de tetrafilídeos marinhos, membros de Rhinebothroides possuem baixa especificidade aos seus hospedeiros.Members of Rhinebothroides are parasites of the Neotropical freshwater stingrays of the family Potamotrygonidae. To date, six species are recognized for the genus within which there are eight nominal species available. The taxonomy of Rhinebothroides is confusing, since most of its species are currently diagnosed by morphometric and meristic characters that have been defined by studies that disregarded the intraspecific variability of its lineages. The widespread distribution of some species, as well as their relaxed host specificity pattern which differs from what has been documented for marine tetraphyllideans suggests the existence of species complexes that require taxonomic refinement. This study aims at refining the taxonomy of one of these complexes Rhinebothroides freitasi, in which are included other three nominal species (R. campbelli, R. circularisi, R. venezuelensis) circumscribed ambiguously. In this study, it has been assumed that the combination of molecular and morphological data can shed some light on the taxonomic status of this complex. Within this framework, molecular data were compiled for 28S, ITS1, and COI for 57 haplotypes of Rhinebothroides representing all currently valid species within the genus and their biogeographical distribution along the major Brazilian river basins. The direct optimization of nucleotide sequences from these haplotypes, simultaneously analised with 26 terminals which included marine and freshwater lineages of tetraphyllideans, generated a phylogenetic hypothesis that recognized five major clades within Rhinebothroides. Each of these clades are morphologically congruent with the type series of five nominal species. Therefore, this study recognizes five valid species within Rhinebothroides: R. glandularis, R. freitasi, R. moralarai, R. scorzai, and R. venezuelensis. Within the R. freitasi complex, the compiled morphological data for ~ 400 specimens provided a robust assessment of intraspecific variability for R. freitasi and R. venezuelensis. The biogeographic and host extensive sampling available for this study reveals that members of Rhinebothroides show low host specificity, as opposed to the marine tetraphyllidean lineages.
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Rodríguez, Andrade Ernesto. "Caracterización fenotípica y filogenia molecular de hongos extremófilos." Doctoral thesis, Universitat Rovira i Virgili, 2020. http://hdl.handle.net/10803/670209.
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Els fons extremòfils són capaços de sobreviure sota condicions ambientals que impedeixen la proliferació de la gran majoria d'organismes. Actualment, aquests han estat blanc d'estudis, per la seva potencial biotecnològic per la producció de metabòlits implicats en la resistència en aquests ambients. en el present estudi es van caracteritzar, morfològica i molecularment, 192 aïllats de diferents fonts (mels, vins escumosos, taps de suro, sóls, superfíciesamb biopel·lícules microbianes i origen clínic) amb finalitat d'aclarir la seva taxonomia i posició filogenètica. Els resultats obtinguts van mostrar una gran biodiversitat fúngica obtinguda d'aquests substrats, la majoria amb característiques extremòfils, aquests pertanyents principalment a la divisió Asscomycota, però també amb representants de les divisions Basidiomycota i Mucoromycota, això va permetre la descripció i publicació d'un gran nombre de tàxons nous per a la ciència, els que van ser distribuïts en diverses famílies, gèneres i espècies (més de 30 espècies noves).
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Rando, G. "Taxonomy of SERM activity in vivo." Doctoral thesis, Università degli Studi di Milano, 2008. http://hdl.handle.net/2434/57961.
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The limited success, in terms of prevention of diseases associated to menopause, of hormone replacement therapies imposes further research aimed at better defining the risks and real advantages. SERMs (Selective Estrogen Receptor Modulators) are a class of estrogen mimetics prescribed for the treatment of the menopause. SERMs do not fall into distinct categories of agonists and antagonists, since their action is regulated by tissue-specific expression of a number of auxiliary proteins called coactivators or corepressors. This complexity limits the systemic analysis of their activities, and SERMs development may fail in the late stages of drug development as a result of unforeseen toxicity. The recent description of reporter mice (ERE-luc) for in vivo analysis of hormone receptor activity opens new horizons for drug discovery. The aim of the present thesis was to obtain a taxonomy of drug activity in vivo by developing a method to profile the interaction of SERMs on the transcriptional activity of the ER in ovarectomized ERE-luc female mice as a model of menopause. These novel animal models, in association with in vivo imaging technologies, provided a global view of the target tissues allowing to discover specific signatures of SERM action following acute and repeated drug treatment. This new knowledge lead to propose a new ontology for hormone replacement therapy regimens based on their closeness with the physiological ER activity picture observed in intact cycling females.
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PEREIRA, Bárbara Natieli Silva. "Caracterização molecular de dípteros imaturos com interesse forense." Universidade Federal de Pernambuco, 2016. https://repositorio.ufpe.br/handle/123456789/17915.
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CNPq
A Entomologia Forense é a aplicação de insetos, ácaros e outros artrópodes em investigações criminais. Na Medicina Legal, sua principal aplicação é na elucidação de crimes violentos. Para tanto, faz-se necessária a correta identificação das espécies, o que, por muitas vezes é uma tarefa difícil, principalmente na fase larval por apresentarem poucas diferenças morfológicas. Tendo em vista esta dificuldade para identificação, o presente trabalho objetivou identificar através de técnicas de biologia molecular espécimes imaturos de dípteros com interesse forense. Foram coletados dípteros imaturos em dez cadáveres decompostos recém-admitidos aos Serviços de Medicina Legal dos estados da Paraíba e Pernambuco. O DNA foi isolado a partir da técnica de extração orgânica. Em seguida, foram realizadas reações de amplificação e sequenciamento de um segmento do gene citocromo B. As sequências foram identificadas através da busca por homologia contra sequências depositadas no GenBank a partir do BLASTn; os grupos monofiléticos foram agrupados através do modelo K2P, conduzidos no programa MEGA e a diversidade genética estimada no DNAsp. Por meio das análises foi possível identificar seis espécies pertencentes a três famílias, estando a espécie Chrysomya albiceps presente em seis cadáveres decompostos; as análises de diversidade genética para C. albiceps revelaram baixo polimorfismo, propondo ausência de barreiras genéticas entre as populações. Conclui-se que o marcador é eficiente para a identificação de espécies, no entanto para diversidade genética faz-se necessária a utilização de marcadores alternativos.
Forensic Entomology is the application of insects, mites and other arthropods in criminal investigations. In Legal Medicine, its main application is in the elucidation of violent crimes. Therefore, the correct identification of the species is needed, which in is often a difficult task, especially in the larval stage when they have little morphological differences. In view of this difficulty in identification, this study aimed to identify, by molecular biology techniques, immature specimens of Diptera with forensic interest. Were collected immature Diptera in ten decomposing corpses newly admitted to the Legal Medicine Services of the states of Paraiba and Pernambuco. DNA was isolated from the organic extraction method with phenol-chloroform. Then, were performed amplification and sequencing reactions in a segment of the cytochrome B gene. The sequences were identified by homology search against sequences deposited in GenBank throught BLASTn; the monophyletic groups were grouped by the K2P model, conducted in the MEGA program and the genetic diversity estimated in DNAsp. Through the analysis was possible to identify six species belonging to three families, being the kind Chrysomya albiceps present in six decomposing corpses; the analysis of genetic diversity for C. albiceps showed low polymorphism, suggesting the absence of genetic barriers between populations. It concludes that the marker is effective for identifying species, however for genetic diversity is necessary the use of alternative markers.
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Zanotto, Paolo Marinho de Andrade. "Aspects of the molecular evolution of baculoviruses and flaviviruses." Thesis, University of Oxford, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.318444.
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Bryan, G. T. "The Gaeumannomyces-Phialophora complex : molecular taxonomy and characterisation of avenacinase-like proteins." Thesis, University of East Anglia, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.296807.
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Rea, Alexander. "Classical and molecular taxonomy, pathogenicity testing and genetic analysis of Phytophthora species." Thesis, Rea, Alexander (2011) Classical and molecular taxonomy, pathogenicity testing and genetic analysis of Phytophthora species. PhD thesis, Murdoch University, 2011. https://researchrepository.murdoch.edu.au/id/eprint/32395/.
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When this study commenced in April 2007, a recent molecular re-evaluation of a number of historical isolates of Phytophthora kept by the Vegetation Health Service (VHS) at the Department of Environment and Conservation (DEC) of Western Australia (WA) had indicated the presence of at least nine undescribed taxa. This study has described three of these as novel pathogenic species of Phytophthora and expands our knowledge of the number and diversity of species occurring within this vast landscape and the role they play in the ecology of the ecosystems in which they occur. Together with the description of P. multivora and five ITS clade 6 species a total of nine species have now been described following their isolation from natural (and disturbed) ecosystems in WA.
Phytophthora elongata, a pathogen predominantly isolated in association with diseased Eucalyptus marginata, was the first species to be described as part of this study. Phytophthora elongata shares many morphological similarities with P. citricola to which it had traditionally been mistakenly classified. It serves as an excellent example of the utility of molecular taxonomic approaches to delineate morphologically cryptic species. In agreement with previous studies the results of sequencing both the ITS rDNA and coxl gene of this species in this study revealed no genetic variation at these loci suggesting that this population is clonal and likely to have been recently introduced to the jarrah forest. The discovery of P. bisheria, the closest described phylogenetic relative of P. elongata, in undisturbed native forest in Taiwan suggests a possible Asian origin for P. elongata. However, the occurrence of the closest known phylogenetic taxon of P. elongata, P. taxon elongata-like, in the southern jarrah forest is noteworthy.
The other species described in this study, P. constricta and P. arenaria, occur in the sandy heath-land vegetation referred to in WA as kwongan and both appear to be well adapted physiologically to the ecosystems in which they occur. However, these two species differ considerably in morphology and are distant phylogenetically. Like P. elongata, the use of a molecular phylogenetic approach clearly elucidates these taxa as species distinct from morphologically similar species. Indeed in the case of P. constricta (ITS clade 9) and P. arenaria (ITS clade 4), the most morphologically similar species, P. megasperma (clade 6) and P. cactorum (clade 1), respectively, belong to distant ITS clades. The study of both P. constricta and P. arenaria also illustrates the importance of fully characterising species to gain insights into their biology and physiology, that explain how these species survive in the ecosystems in which they occur. For example, the high oospore-wall index and the relationship between temperature and growth for P. arenaria are indicative of adaptation to survival in the kwongan vegetation of the northern sandplains. This, coupled with the ITS rDNA and coxl sequence diversity observed for the isolates examined in this study suggests that this species may be endemic to WA. Similarly, the sequence diversity observed for the coxl gene for P. constricta suggest that it too may be endemic, whilst its slightly lower optimal temperature for growth and oospore wall index make it well adapted to the cooler southern kwongan from which it has predominantly been isolated. Thus, although species identification using traditional morphological methods is being increasingly overlooked in favour of molecular diagnostic tools, these studies illustrate the importance of insights gained by characterising all aspects of the biology of an organism. This may be particularly relevant in the context of plant biosecurity, when one is interested in the invasive potential of a pathogen or its suitability to persist in a given situation. In addition to confirming the pathogenic ability of the three described species on hosts they have been isolated from natural ecosystems, the results of this study have also demonstrated that P. elongata is a pathogen of Banksia attenuata, a potential host that is widespread throughout the south-west botanical province.
The diversity observed within the coxl locus lead to the hypothesis that P. multivora may be endemic to WA. In the present study DNA sequence variation at four nuclear and three mitochondrial loci was assessed for a putative worldwide collection of P. multivora isolates and subjected to coalescent-based genealogical and population genetic analysis. Overall the results clearly show that the isolates from the Republic of South Africa (RSA), taken as a population, have greater values for all measures of genetic diversity, including a greater number of multi-locus nuclear and mitochondrial genotypes than those from WA. It therefore appears likely that P. multivora has been introduced to WA, possibly from RSA.
This study also analysed the genetic diversity within P. plurivora and closely related taxa from Phytophthora ITS clade 2a. The loci assessed in this study were the same as those used in the study of P. multivora. Compared to P. multivora, markedly lower levels of genetic diversity were observed amongst the assessed isolates of P. plurivora. Interestingly, the genealogical analysis of the predominantly European P. plurivora isolates revealed two clonal lineages, consistent with P. plurivora being introduced to Europe on at least two occasions. Furthermore, this study revealed two undescribed taxa closely related to P. citricola sensu stricto amongst isolates obtained from the Royal Horticultural Society gardens in Surrey, England, and the first recorded isolation of P. plurivora in Australia.
In addition to describing three novel pathogenic species of Phytophthora and examining the genetic diversity and evolutionary history of P. multivora, P. plurivora and closely related taxa, the present study emphasises the role played by the movement of plants across international borders in spreading plant pathogens around the globe, highlighting the potential risk that this trade poses to biosecurity.
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Reignoux, Sabrina N. A. "Molecular taxonomy and population genetics of Lophodermium on Pinus sylvestris in Scotland." Thesis, University of Edinburgh, 2010. http://hdl.handle.net/1842/27254.
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Endophytes are organism s w hich infect plants asym ptom atically for at least part of their life cycle. The vast m ajority of endophytes are ascom ycete fungi. They show high species diversity and are often closely related to econom ically im portant pathogens. There is some evidence that endophytes protect their host from pathogen and herbivores. Little is know n about the evolutionary relationship betw een potentially m utualistic endophytes and related pathogens and how these tw o groups differ in population biology and genetics. The Lophoderm ium /Pinus sylvestris endophyte/host system is ideal for investigating these questions since native pine forests harbour closely related Lophoderm ium species w hich range from endophytic (L. pinastri, L. conigenum) to parasitic (L. seditiosum). C urrent taxonom y recognises only one species, L. pinastri, fruiting on senescent needles. H ow ever there are recent indications that this taxon includes cryptic species. In this thesis m olecular approaches w ere used to clarify the taxonom y of Lophodermium on Scots pine. Genealogical Concordance Phylogenetic Species Recognition based on ACTIN and ITS sequences revealed three cryptic species w ithin L. pinastri two of w hich w ere w idely distributed. The existence of these taxa w as supported by AFLP genetic m arker analysis and differences in culture grow th rate. A nalysis of Inter-SSR m arkers revealed that L. seditiosum and L. conigenum are both out-crossing species and that unlike one of the cryptic L. pinastri species, their populations are genetically differentiated. Im plication of the discovery of cryptic L. pinastri species and opportunities offered by the clarification of the taxonom y of Lophodermiumon Scots pine are discussed.
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Ribeiro, Felipe Bezerra. "Taxonomia e relações filogenéticas dos lagostins de água doce do gênero Parastacus Huxley, 1879 (Crustacea, Decapoda, Parastacidae)." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2017. http://hdl.handle.net/10183/163676.
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Os lagostins de água doce sulamericanos (Família Parastacidae) são representados por três gêneros: Parastacus Huxley, 1879, Samastacus Riek, 1971 and Virilastacus Hobbs, 1991. Esse grupo é distribuído no Sul do Brasil (Rio Grande do Sul and Santa Catarina), Uruguai, Argentina e Chile. Os objetivos dessa tese foram revisar a taxonomia do gênero Parastacus e investigar a sua monofilia e relações filogenéticas entre suas espécies e entre os outros gêneros sulamericanos. Para esse propósito, várias coleções e museus ao redor do mundo foram analisados (Brasil, Argentina, Uruguai, Chile, Estados Unidos, Alemanha, Holanda, Inglaterra e França) em adição a coletas realizadas entre Março de 2013 a Setembro de 2016. Os espécimes foram analisados em estereomicroscópio e os desenhos foram preparados com auxílio de camara lucida. Para as análises genéticas, uma abordagem multigênica foi utilizada com dois marcadores mitocondriais (Cox1 e 16S) e um nuclear (28S). A análise filogenética foi realizada por Inferência Bayesiana e a distância genética p também foi calculada. Adicionalmente, o risco de extinção foi assessado para algumas espécies de acordo com o sub-critério B1 da IUCN que leva em consideração a estimativa da Área de Extenção de Ocorrência. Oito espécies foram redescritas: Parastacus brasiliensis (von Martens, 1869), P. defossus Faxon, 1898, P. laevigatus Buckup & Rossi, 1980, P. pilimanus (Von Martens, 1869), P. pugnax (Poepigg, 1835), P. promatensis Fontoura & Conter, 2008 e P. varicosus Faxon, 1898. Um novo gênero foi proposto para alocar a espécie P. nicoleti (Philippi, 1882) que também foi redescrita. Treze novas espécies foram descritas. Assim como, chaves de identificação, descrições, diagnoses, sinonímias e mapas de distribuição foram providos. As árvores filogenéticas resultantes corroboraram com a monofilia de Parastacus e do clado sulamericano, além de dar suporte para o estabelecimento de um novo gênero e novas espécies. Com essa tese, o aumento da riqueza específica para Parastacus é de mais de 150% e as novas informações sobre habitat e distribuição trarão suporte para futuros estudos de conservação e manejo.South American freshwater crayfish (Family Parastacidae) are represented by three genera: Parastacus Huxley, 1879, Samastacus Riek, 1971 and Virilastacus Hobbs, 1991. This group is distributed in Southern Brazil (Rio Grande do Sul and Santa Catarina), Uruguay, Argentina and Chile. The goals of this thesis is to review the taxonomy of the genus Parastacus and to investigate the monophyly and phylogenetic relationships within Parastacus and among South American crayfish genera. For this purpose, several collections and museums around the world were analyzed (Brazil, Argentina, Uruguay, Chile, United States of America, Germany, Netherlands, England, and France) in addition to collectings carried out from March 2013 to September 2016. Specimens were analyzed under a stereomicroscope and drawings were prepared with the aid of a camara lucida. For genetic analysis, a multigenic approach was used with two mitochondrial (Cox1 and 16S) and one nuclear (28S) markers. Phylogenetic analysis were performed with Bayesian Inference and genetic p-distances were also calculated. In addition, the extinction risk was assessed according to the sub-criterion B1 of IUCN that estimates the Extent of Occurrence (EOO) for some species. Eight species are redescribed: Parastacus brasiliensis (von Martens, 1869), P. defossus Faxon, 1898, P. laevigatus Buckup & Rossi, 1980, P. pilimanus (Von Martens, 1869), P. pugnax (Poepigg, 1835), P. promatensis Fontoura & Conter, 2008 and P. varicosus Faxon, 1898. A new genus is proposed to encompass the species P. nicoleti (Philippi, 1882) and this species is also redescribed. In addition, 13 new species are described. Identification keys, descriptions, diagnoses, synonymies and distribution maps of the genera and species are provided. Phylogenetic trees corroborated the monophyly of Parastacus and the South American crayfish clade, and give support for the establishment of a new genus and new species. With this thesis, the increase in specific richness for Parastacus is more than 150% and new information about habitat and distribution will bring support for future conservation and management studies.
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Scatigna, André Vito 1989. "Molecular phylogeny and conservation genetics of Philcoxia P.Taylor & V.C.Souza (Plantaginaceae) = Filogenia molecular e genética da conservação de Philcoxia P.Taylor & V.C.Souza (Plantaginaceae)." [s.n.], 2014. http://repositorio.unicamp.br/jspui/handle/REPOSIP/314829.
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Orientador: André Olmos SimõesDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: Philcoxia é um gênero recentemente descrito, composto por quatro espécies reconhecidas e uma nova espécie, endêmicas das formações arenosas do Cerrado e Caatinga. Por conta de sua raridade e da vulnerabilidade de seu habitat, o gênero pode ser considerado criticamente ameaçado de extinção. Recentes evidências filogenéticas sustentam a inclusão do gênero na tribo Gratioleae (Plantaginaceae). Entretanto, as relações de Philcoxia dentro da tribo continuam controversas desde sua descrição. Apresentamos, aqui, estudos filogenéticos de Gratioleae, focados no teste do monofiletismo de Philcoxia, suas relações interespecíficas e seu posicionamento. As análises filogenéticas foram feitas pelos métodos de Máxima Parcimônia e inferência Bayesiana. Sequências dos íntrons rpl16, rps16 e trnL e do espaçador trnL-trnF, todas do DNA cloroplastidial, foram analisadas, incluindo 31 amostras, entre as quais quatro espécies de Philcoxia, 23 outras espécies de Gratioleae e mais quatro táxons (grupo externo) de Plantaginaceae. As espécies de Philcoxia formam um clado fortemente sustentado, irmão de Stemodia stellata. Philcoxia minensis é mais próxima de P. rhizomatosa e P. bahiensis é mais próxima de P. tuberosa. O clado que inlcui Philcoxia e S. stellata é relacionado aos clados formados por Achetaria, Scoparia e alguns representantes de Stemodia. Realizamos, também, o desenvolvimento e caracterização de marcadores microssatélites inéditos para estudos em genética de populações voltados para conservação de P. minensis. Pares de iniciadores foram desenhados para 27 locos de microssatélites e testados em 30 indivíduos de uma população de P. minensis e em quatro indivíduos de P. bahiensis. Dezessete locos foram amplificados com sucesso, doze dos quais se mostraram polimórficos. Os 12 marcadores polimórficos serão usados em futuros estudos relacionados ao sistema de reprodução e à diversidade genética de P. minensis e são potenciais ferramentas para esses estudos com P. bahiensis. Além disso, a nova espécie Philcoxia rhizomatosa é descrita e ilustrada. Ela apresenta folhas maiores que outras espécies do gênero e também possui um rizoma bastante conspícuo e ramificado. Esta nova espécie é aparentemente endêmica de um areal em Botumirim, Minas Gerais, em vegetação de transição entre Cerrado e Caatinga. Testes de carnivoria positivos sugerem que P. rhizomatosa é uma planta carnívora
Abstract: Philcoxia is a recently described genus, composed of four currently recognized species and one additional new species, endemic to the Brazilian sandy formations of the Cerrado and Caatinga. Due to its rarity and the vulnerability of the formation where it occurs, this genus could be treated as critically endangered. Recent evidences from molecular phylogenetics support the inclusion of the genus within the tribe Gratioleae (Plantaginaceae). The affinities of Philcoxia within the tribe, however, have been controversial since it was first described. Here, we present a phylogenetic analysis of Gratioleae, focusing on the test of the monophyly of Philcoxia, its interspecific relationships and its placement. Phylogenetic analyses were conducted using Maximum Parsimony and Bayesian approaches. Sequence data from rpl16, rps16 and trnL introns and trnL-trnF intergenic spacer were analysed, including 31 samples representing four species of Philcoxia, 23 additional Gratioleae species and four outgroup taxa from Plantaginaceae. Philcoxia species form a strongly supported clade, sister of Stemodia stellata. Philcoxia minensis is closely related to P. rhizomatosa and P. bahiensis is closer to P. tuberosa. The clade Philcoxia plus S. stellata is related to clades formed by Achetaria, Scoparia and Stemodia representatives. We also developed and characterized new microsatellite markers as tools for further studies in population genetics aiming the conservation of P. minensis. Primer pairs were developed for 27 microsatellite loci and validated in 30 individuals of P. minensis from a natural population and tested in four idivividuals from a natural population of P. bahiensis. Seventeen loci successfully amplified, twelve of which were polymorphic. The 12 polymorphic markers are suitable for studies concerning mating system and genetic diversity of P. minensis and also may be usefull tools to study similar issues regarding its related species, P. bahiensis. In addition, the new species Philcoxia rhizomatosa is described and illustrated. It has bigger leaves than other species in the genus and presents a conspicuous and branched rhizome. This new taxa is possibly endemic to a sand patch in the transition vegetation between the Cerrado and the Caatinga in Botumirim, Minas Gerais, Brazil. Tests for carnivory were performed and showed activity of phosphatase, suggesting that P. rhizomatosa is a carnivorous plant
Mestrado
Biologia Vegetal
Mestre em Biologia Vegetal
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Talavera, Edwin Rafael Villanueva. "Métodos Bayesianos aplicados em taxonomia molecular." Universidade de São Paulo, 2007. http://www.teses.usp.br/teses/disponiveis/18/18152/tde-03102007-105125/.
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Neste trabalho são apresentados dois métodos de agrupamento de dados visados para aplicações em taxonomia molecular. Estes métodos estão baseados em modelos probabilísticos, o que permite superar alguns problemas apresentados nos métodos não probabilísticos existentes, como a dificuldade na escolha da métrica de distância e a falta de tratamento e aproveitamento do conhecimento a priori disponível. Os métodos apresentados combinam por meio do teorema de Bayes a informação extraída dos dados com o conhecimento a priori que se dispõe, razão pela qual são denominados métodos Bayesianos. O primeiro método, método de agrupamento hierárquico Bayesiano, está baseado no algoritmo HBC (Hierarchical Bayesian Clustering). Este método constrói uma hierarquia de partições (dendrograma) baseado no critério da máxima probabilidade a posteriori de cada partição. O segundo método é baseado em um tipo de modelo gráfico probabilístico conhecido como redes Gaussianas condicionais, o qual foi adaptado para problemas de agrupamento. Ambos métodos foram avaliados em três bancos de dados donde se conhece a rótulo da classe. Os métodos foram usados também em um problema de aplicação real: a taxonomia de uma coleção brasileira de estirpes de bactérias do gênero Bradyrhizobium (conhecidas por sua capacidade de fixar o \'N IND.2\' do ar no solo). Este banco de dados é composto por dados genotípicos resultantes da análise do RNA ribossômico. Os resultados mostraram que o método hierárquico Bayesiano gera dendrogramas de boa qualidade, em alguns casos superior que o melhor dos algoritmos hierárquicos analisados. O método baseado em redes gaussianas condicionais também apresentou resultados aceitáveis, mostrando um adequado aproveitamento do conhecimento a priori sobre as classes tanto na determinação do número ótimo de grupos, quanto no melhoramento da qualidade dos agrupamentos.In this work are presented two clustering methods thought to be applied in molecular taxonomy. These methods are based in probabilistic models which overcome some problems observed in traditional clustering methods such as the difficulty to know which distance metric must be used or the lack of treatment of available prior information. The proposed methods use the Bayes theorem to combine the information of the data with the available prior information, reason why they are called Bayesian methods. The first method implemented in this work was the hierarchical Bayesian clustering, which is an agglomerative hierarchical method that constructs a hierarchy of partitions (dendogram) guided by the criterion of maximum Bayesian posterior probability of the partition. The second method is based in a type of probabilistic graphical model knows as conditional Gaussian network, which was adapted for data clustering. Both methods were validated in 3 datasets where the labels are known. The methods were used too in a real problem: the clustering of a brazilian collection of bacterial strains belonging to the genus Bradyrhizobium, known by their capacity to transform the nitrogen (\'N IND.2\') of the atmosphere into nitrogen compounds useful for the host plants. This dataset is formed by genetic data resulting of the analysis of the ribosomal RNA. The results shown that the hierarchical Bayesian clustering method built dendrograms with good quality, in some cases, better than the other hierarchical methods. In the method based in conditional Gaussian network was observed acceptable results, showing an adequate utilization of the prior information (about the clusters) to determine the optimal number of clusters and to improve the quality of the groups.
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Schmidt, Chris Alan. "Molecular Phylogenetics and Taxonomic Revision of Ponerine Ants (Hymenoptera: Formicidae: Ponerinae)." Diss., The University of Arizona, 2009. http://hdl.handle.net/10150/194663.
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I report the results of the first detailed phylogenetic study of the ant subfamily Ponerinae, a diverse lineage whose properties make it an attractive model system for investigating social and ecological evolution in ants. Molecular sequence data were obtained from seven nuclear genes for 86 ponerine taxa, representing all three ponerine tribes, 22 of the 28 currently recognized genera, and 14 of the 18 informal subgenera of Pachycondyla, a genus strongly suspected to be non-monophyletic. Divergence dates, historical biogeography, and the origin of reproduction by gamergate workers were estimated on the inferred phylogeny. The most important results of this study include: (1) the monophyly of Ponerinae; (2) the paraphyly of Ponerini; (3) the extensive non-monophyly of Pachycondyla; (4) a rapid basal radiation in Ponerini; (5) resolution of many deeper relationships within Ponerini; (6) a rapid and rich basal radiation in the Odontomachus group; (7) an origin for Ponerinae in the upper Cretaceous, with a major burst of diversification near the K/T boundary; (8) a history of rich and continual ponerine diversification during the Cenozoic; (9) a history of regionalized radiations and frequent faunal exchange between major biogeographic provinces; and (10) support for multiple origins of gamergates in Ponerinae. Ponerine taxonomic classification is revised to reflect both these phylogenetic results and a reappraisal of ponerine morphological diversity. The monogeneric tribe Thaumatomyrmecini is newly synonymized under Ponerini, and the diverse genus Pachycondyla is fragmented into 15 genera, largely along the lines of its junior synonyms, though two new genera are erected: Buniapone (gen. nov.) and Mayaponera (gen. nov.). Some junior synonyms of Pachycondyla are transferred to junior synonym status under other genera: Wadeura as a junior synonym of Cryptopone (syn. nov.), Xiphopelta as a junior synonym of Pseudoponera (syn. nov.), and both Termitopone and Syntermitopone as junior synonyms of Neoponera (syn. nov.). Molecular and morphological justifications for these taxonomic changes are given alongside discussions of phylogenetic relationships. Keys to the world genera of Ponerinae are provided, and morphological diagnoses and species lists are given for each genus. Finally, the available information on ponerine ecology and behavior is reviewed and synthesized.
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El, Semary Nermin Adel Hussein. "Anabaena and associated bacteria : molecular approaches to studying microbial community structure and taxonomy." Thesis, University of Bristol, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.420889.
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Brownell, Lindsay Kirlin. "One fish, two fish, lungfish, youfish : embracing traditional taxonomy in a molecular world." Thesis, Massachusetts Institute of Technology, 2014. http://hdl.handle.net/1721.1/92629.
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Thesis: S.M. in Science Writing, Massachusetts Institute of Technology, Department of Humanities, Graduate Program in Science Writing, 2014.Cataloged from PDF version of thesis.
Includes bibliographical references (pages 23-24).
In today's increasingly digitized, data-driven world, the "old ways" of doing things, especially science, are quickly abandoned in favor of newer, ostensibly better methods. One such discipline is the ancient study of taxonomy, the discovery and organization of life on Earth. New techniques like DNA sequencing are allowing taxonomists to gain insight into the tangled web of relationships between species (among the Acanthomorph fish, for example). But is the newest, shiniest toy always the best? Are we in danger of losing vital information about the world if we abandon the thousands of years of cumulative human knowledge to gather dust in basements? This thesis explores the current crossroads at which taxonomy finds itself, and offers a solution to preserve the past while diving headlong into the future.
by Lindsay Kirlin Brownell.
S.M. in Science Writing
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Sherry, Minu. "Cytology, ploidy and molecular taxonomy of Prosopis juliflora DC and Prosopis pallida HBK." Thesis, Coventry University, 2012. http://curve.coventry.ac.uk/open/items/c467c5bc-b765-483d-b0f5-f7e1d59d84b0/1.
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Prosopis juliflora (Sw.) DC. and P. pallida (H.&.B. ex Willd.) H.B.K. occur naturally in the Americas and they are morphologically similar species. They are multipurpose trees and their ability to grow in poor soil conditions has encouraged their introduction throughout the arid regions of the tropics and semi tropics. The taxonomy of the genus Prosopis Linnaeus emend. Burkart is unclear and a revision of the genus is suggested by several studies. Due to their similarity, the differentiation of P. juliflora and P. pallida is difficult. Although there has been some success in differentiating the species using ploidy, leaf morphology and molecular markers, further approaches are required. This study looked for suitable cytological characters and molecular markers that would differentiate the two tropical species. The cytological character analysis allowed for the development of a dichotomous key for their identification based on leaf stomatal characters. Stomatal length and epidermal cell density are the two characters on which the keys were developed. Correct identification of the species will allow for genetic improvement programmes and conservation efforts in the native regions. Multivariate statistical analysis showed that P. juliflora and P. pallida were separable into two groups. This could help in the classification of unknown herbarium specimens or previously misidentified samples. The phylogenetic relationship of the two species is also disputed and previous RAPD studies show close genetic similarity between the two species, suggesting a reconsideration of the series within section Algarobia. There are also disputes regarding the geographical distribution of both species and naming of new species. In this study, similarity index analysis and cluster analysis on the RAPD data revealed P. juliflora to be more closely related to North American Prosopis spp. than to P. pallida.
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Zhigila, Daniel Andrawus. "Molecular phylogenetics, taxonomy and niche-based conservation risk assessment of Thesium L. (Santalaceae)." Doctoral thesis, Faculty of Science, 2020. http://hdl.handle.net/11427/33064.
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Thesium L. (Santalales: Santalaceae) is a large (360 species) genus of hemiparasitic perennial or annual species with a mainly Old-World distribution and a greatest concentration in southern Africa (ca. 186 species). Although Thesium is a major component of southern African flora, it often goes unnoticed and is poorly studied. The last revision of the entire genus was done by De Candolle in 1857. South African Thesium was last revised by Hill almost a century ago. Since Hill's revision, the number of collections have grown, and 49 new species have been described. Currently, no comprehensive Thesium taxonomic key exists, and species delimitation remains difficult due to a high variation in character states, rendering the genus in need of major revision. Within southern Africa, ca. 103 species occur in the Greater Cape Floristic Region (GCFR), of which about 72 are regional endemics. The GCFR Thesium, including ecologicalspecialists and generalists, offers an appropriate system for evaluating both the correlates of range extent, specialisation and the relative extinction risks associated with both ecological strategies. Here, it is predicted that a combination of edaphic, elevation and climate variables influence the geographic range of Thesium in the GCFR. Recent phylogenetic hypotheses revealed that Thesium is paraphyletic with respect to Austroamericium, Chrysothesium, Kunkeliella and Thesidium, suggesting the need for generic realignment. In addition, existing subgeneric and sectional classifications of this large genus lack a phylogenetic basis, thus compromising their predictive value. Using an expanded taxon sampling and a combination of nuclear (ITS) and chloroplast (matK, rpl32- trnL and trnL-F) DNA sequence data, chapter two re-assesses the phylogenetic relationships of Thesium and uses these as the basis of a new subgeneric classification of the genus. The phylogeny obtained confirms the need to place the four segregate genera into synonymy, resulting in a monophyletic Thesium. In addition, it resolves five, well-supported major clades within Thesiumwhich I recognize as subgenera. The South African endemic subgenus Hagnothesium is sister to the Eurasian subgenus Thesium (including Thesium, Kunkeliella and Mauritanica). The subgenus Psilothesium, occurring in tropical South America (formerly genus Austroamericium) and tropical Africa, is sister to the rest of the subgenera, which are all confined to South Africa. Within the latter, the subgenus Discothesium consists of subtropical and temperate species, whereas subgenus Frisea, comprising previously recognized sections Annulata, Barbata Frisea, Imberbia and Penicillata, is restricted to the GCFR. To facilitate identification of subgenera, I present identification keys, assigned species, provide brief diagnoses, identified ancestral morphological characters and, supply distribution and ecological data. Thesium subgenus Hagnothesium is endemic to the GCFR. In the past, there has been a propensity in revisionarywork ofthe subgenus Hagnothesium to split taxa into distinctspecies or vice-versa. Consequently, 15 different names exist although only six are accepted formally. Following recent molecular phylogenetic studies, the monophyly of the subgenus Hagnothesium is now well-established, but the circumscription of species within the section remains problematic given the complicated nomenclatural history which has added further confusion. Chapter three presents a revision of subgenus Hagnothesium using a total evidence approach to propose a modern taxonomy. I studied both herbarium collections and plants in their natural populations to circumscribe species boundaries, geographical ranges and estimates of their conservation status. Species of the subgenus Hagnothesium are dioecious, generally having four- merous, campanulate flowers, spikes borne in bract axils and arranged along the length of branchlets, with valvate perianth lobes and a short to absent hypanthial tube. The following eight species were recognized, of which one is here described as new: T. fragile L.f., T. fruticulosum (A.W.Hill) J.C.Manning & F.Forest, T. hirtum (Sond.) Zhigila, Verboom & Muasya comb. nov., T. leptostachyum A.DC., T. longicaule Zhigila, Verboom & Muasya nom. nov., T. microcarpum A.DC., T. minus (A.W.Hill)J.C.Manning & F.Forest and T. quartzicolum Zhigila, Verboom & Muasya sp. nov. I provide updated taxonomic keys, species descriptions, illustrations, distribution maps, new combinations, synonyms, and notes on the red list status for each species. In addition, six new species of Thesium endemic to the GCFR (but not included in subgenus Hagnothesium) are described and illustrated in chapter four. These are: Thesium aspermontanum Zhigila, Verboom & Muasya sp. nov., T. dmmagiae Zhigila, Verboom & Muasya sp. nov., T. neoprostratum Zhigila, Verboom & Muasya sp. nov., T. nigroperianthum Zhigila, Verboom & Muasya sp. nov., T. rhizomatum Zhigila, Verboom & Muasya sp. nov., and T. stirtonii sp. nov. Also, Thesium assimile var. pallidum is elevated to species rank as T. sawae Zhigila, Verboom & Muasya stat. nov. Morphological and ecological differences between species, along with their putative affinities, preliminary conservation status, phenology, etymology and distributional maps are presented. Narrow-ranged species are expected to be more at greater risk of extinction than generalists due to climate change. Such risk is greatest in biodiversity hotspots such as the GCFR, which house both ecological specialists and generalists. It was hypothesized that range size, ecological specialization and consequent climatically-modulated extinction-risk are all phylogenetic structured, such that climate change will precipitate a disproportionate loss of phylogenetic diversity. Past and future species distribution ranges were developed using MaxEnt models based on present-day occurrences and environmental conditions. There was a strong positive correlation between the ecological niche breadth of species, as determined by large-scale environmental variables, and their range extents. One hundred and one Thesium species were modelled, of which 71 species (83%) were predicted to have had broad range sizes during the Last Glacial Maxima, and 27 species (17%) recorded range contractions historically to the present. Similarly, 45 species (44%) will potentially expand their ranges, while 51 species (50%) are predicted to reduce their ranges in the future. Of the 65 species currently ranked as Least Concern or Data Deficient in the South African Red list, 24 species will likely shift into higher extinction risk categories. Interestingly, five ecological specialists (5%), although having experienced a range reduction from the LGM to the present, are predicted to persist in the face of future climate change. However, the range extent, ecological specialisation and extinction risk are phylogenetically random and therefore should have a negligible impact on the phylogenetic diversity of the GCFR Thesium. Overall, this study confirms the monophyly of the genus Thesium and sets its infrageneric classification scheme in place. The context of this classification framework allows the systematic revision of the genus, one clade at a time. Towards this goal, I revised the Hagnothesium clade and additionally described six new species from other clades. The climate, elevation and soil variables influence the distribution range and specialism of GCFR Thesium clades. However, ecological specialism of species and extinction risks were predicted to be phylogenetically random.
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Robinson, Julian. "Molecular taxonomy of the genus Acacia (Miller) and related species in the Mimosoideae." Thesis, University of St Andrews, 1997. http://hdl.handle.net/10023/14197.
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The construction of a chloropast DNA restriction enzyme site based phylogeny for the genus Acacia and several related genera was completed. This investigation was initiated due to a perceived need for an independent viewpoint on the phylogeny of the genus. The results of this analysis challenge several previous attempts at classification of the genus using morphological characters. The cpDNA data suggest that subgenus Acacia and subgenus Aculeiferum are closely related. The third subgenus of Acacia, subgenus Phyilodineae, is probably unrelated to either of the other two subgenera. Instead it appears to be closely related to taxa in the Ingeae, a sister tribe to the Acacieae. This analysis also suggests that Faidherbia albida is basal to the Ingeae. The interspecific relationships of taxa within each of the subgenera of Acacia were also partly resolved. Within subgenus Acacia the African accessions studied could not be resolved due to a lack of variation. The American accessions of subgenus Acacia were resolved, and appear to confirm groupings within these taxa suggested by morphological analyses. Within subgenus Aculeiferum the interspecific relationships were less clear, and little support was given to the sections proposed by Vassal (1972), with the exception of section Filicinae, which appears to be monophyletic, the relationships of taxa within subgenus Aculeiferum in regard to their geographical origin suggest that subgenus Aculeiferum was quite well differentiated when Gondwanaland fragmented. The results of an investigation into the putative hybrid A.laeta appear to confirm earlier suggestions that it is a hybrid between A.Senegal and A.mellifera. The appearance of non-additive hybrid phenotypes in the ribosomal nuclear DNA studied prevented an unequivocal determination of the parents of A.laeta. On the basis of the cpDNA characters it appears that A.mellifera is always the maternal parent. The relationships of the subspecies of A.tortilis using RAPD techniques, revealed an interesting divide between North African and South African accessions. The taxa studied appeared to be grouped primarily according to their geographical location, the subspecific designation appearing to be of secondary importance. The divide between the accessions appears to be the boundary of one of the phytogeographical regions of Wickens (1976), corresponding approximately to the Kenyan-Tanzanian border. The physical or biological basis for this boundary is unknown. The investigation also proved the utility of the RAPD technique for investigations of this nature.
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Bayes, Michelle. "A molecular phylogenetic study of the galagos, strepsirrhine primates and archontan mammals." Thesis, Oxford Brookes University, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.266454.
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Stothard, John Russell. "Application of molecular probes to assess genetic variation within freshwater snails of the genus #Bulinus'." Thesis, Imperial College London, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.297300.
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Ames, Cheryl L. "Taxonomy, morphology, and RNA-Seq transcriptomics of the cubozoan Alatina alata, an emerging model cnidarian." Thesis, University of Maryland, College Park, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10159153.
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Cnidarians are often considered simple animals, but the more than 13,000 estimated species (e.g., corals, hydroids and jellyfish) of the early diverging phylum exhibit a broad diversity of forms, functions and behaviors, some of which are demonstrably complex. In particular, cubozoans (box jellyfish) are cnidarians that have evolved a number of distinguishing features. Some cubozoan species possess complex mating behaviors or particularly potent stings, and all possess well-developed light sensation involving image-forming eyes. Like all cnidarians, cubozoans have specialized subcellular structures called nematocysts that are used in prey capture and defense. The objective of this study is to contribute to the development of the box jellyfish Alatina alata as a model cnidarian. This cubozoan species offers numerous advantages for investigating morphological and molecular traits underlying complex processes and coordinated behavior in free-living medusozoans (i.e., jellyfish), and more broadly throughout Metazoa. First, I provide an overview of Cnidaria with an emphasis on the current understanding of genes and proteins implicated in complex biological processes in a few select cnidarians. Second, to further develop resources for A. alata, I provide a formal redescription of this cubozoan and establish a neotype specimen voucher, which serve to stabilize the taxonomy of the species. Third, I generate the first functionally annotated transcriptome of adult and larval A. alata tissue and apply preliminary differential expression analyses to identify candidate genes implicated broadly in biological processes related to prey capture and defense, vision and the phototransduction pathway and sexual reproduction and gametogenesis. Fourth, to better understand venom diversity and mechanisms controlling venom synthesis in A. alata, I use bioinformatics to investigate gene candidates with dual roles in venom and digestion, and review the biology of prey capture and digestion in cubozoans. The morphological and molecular resources presented herein contribute to understanding the evolution of cubozoan characteristics and serve to facilitate further research on this emerging cubozoan model.
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Heras, Mena Sandra. "Els límits i les relacions entre els peixos acanthopterygii: filogènia molecular de mugilomorpha i atherinomorpha." Doctoral thesis, Universitat de Girona, 2010. http://hdl.handle.net/10803/7921.
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Sovint, la sistemàtica, basada principalment en caràcters morfològics, no es correspon amb els processos evolutius relacionats amb l'aparició dels grups d'organismes. En l'actualitat, la utilització de les dades moleculars es fa indispensable per a una revisió i millora de la classificació biològica de diversos organismes, com els peixos Acanthopterygii. A la sèrie Mugilomorpha la incongruència entre la taxonomia i la filogènia sorgeix de l'elevada semblança morfològica trobada per part dels seus membres. Pel que fa referència a la sèrie Atherinomorpha, la problemàtica principal resideix en determinar la seva proximitat evolutiva respecte a la sèrie anterior i en establir les relacions filogenètiques dins de la mateixa. Per tant, s'hi ha volgut estimar tant la divergència genètica dins de cada sèrie com inferir les relacions filogenètiques entre ambdues mitjançant la seqüenciació directa del DNA de les regions mitocondrials corresponents al tRNA-Phe, 12S rRNA, COI, cytb, tRNA-Thr, tRNA-Pro i regió control.Often, systematics, based mainly on morphologic characters, does not correspond with the evolutionary processes related to the emergence of the groups of organisms. Nowadays, the utilization of molecular data turns indispensable to a revise and improve the biological classification of several organisms, such as Acanthopterygii fishes. In series Mugilomorpha, the incongruence between taxonomy and phylogeny arises from the high morphological similarity found between its members. Concerning series Atherinomorpha, the main problem lies in determining its evolutionary proximity in relation to series Mugilimorpha and in establishing the phylogenetical relationships inside itself. Therefore, both genetic divergence within each series and phylogenetical relationships between them have been wanted to estimate. For this reason, the direct sequencing of the mitochondrial regions corresponding to tRNA-Phe, 12S rRNA, COI, cytb, tRNA-Thr, tRNA-Pro and control region was achieved.
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Carvalho, Fabricio Lopes de. "Sistemática do gênero Palaemon Weber, 1795 (Decapoda, Palaemonidae): uma abordagem molecular e morfológica de padrões filogeográficos, evolução de características ecológicas e status taxonômico das espécies do Brasil." Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/59/59139/tde-13022015-111713/.
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Os camarões do gênero Palaemon Weber, 1795 possuem ampla variedade morfológica, ecológica e reprodutiva. Estudos baseados em dados moleculares indicam que o gênero pode não ser monofilético. Por outro lado, análises cladísticas baseadas em dados morfológicos recuperam Palaemon como um grupo natural. Além de questões em nível genérico, a validade de algumas espécies com ocorrência no Brasil também é questionada. Nesse contexto, foi utilizada uma abordagem molecular (genes COI, 16S, H3 e 18S) e morfológica com ampla amostragem taxonômica para 1) avaliar a hipótese de monofilia do gênero Palaemon; 2) avalia a hipótese de que padrões biogeográficos, de ocupação de hábitat, reprodutivos e morfológicos acompanham as relações filogenéticas entre as espécies de Palaemon; 3) avaliar o status taxonômico das espécies com ocorrência no Brasil. A filogenia recuperada indica que as espécies de Palaemon estão distribuídas em três linhagens distintas e caracteres morfológicos permitem a identificação de pelo menos quatro grupos monofiléticos. Os resultados indicam a necessidade de criação de dois novos gêneros e revalidação de Alaocaris Holthuis, 1949. A provável colonização da América e Europa ocorreu em mais de um momento em cada região e o ancestral comum mais recente da maioria das espécies de Palaemon, Macrobrachium Spence Bate, 1868 e gêneros próximos provavelmente foi uma linhagem anfídroma. A análise conjunta de dados moleculares e morfológicos demonstram a existência de nove espécies de Palaemon no Brasil, oito previamente descritas (P. argentinus, P. carteri, P. ivonicus, P. mercedae, P. northropi, P. octaviae, P. paivai, P. pandaliformis) e uma espécie nova (P. yuna).Shrimps of the genus Palaemon Weber, 1795 have wide morphological, ecological and reproductive variability. Studies based on molecular data indicate that the genus might not be monophyletic. On the other hand, cladistics analyses based on morphological data recover Palaemon as a natural group. Besides generic level issues, the validity of some species from Brazil is questioned. In that context, we used a molecular (COI, 16S, H3 and 18S genes) and morphological approach with broad taxonomic sampling in order to 1) evaluate the hypothesis of monophyly of the genus Palaemon; 2) evaluate the hypothesis that biogeographical, habitat occupation, reproductive and morphological patterns follow the phylogenetic relationships among the species of Palaemon; 3) evaluate the taxonomic status of the species of Palaemon from Brazil. The recovered phylogeny indicates that the species of Palaemon are distributed into three distinct lineages. Morphological characters allow the identification of at least four monophyletic groups. The results indicate that the erection of two new genera and re-erection of Alaocaris Holthuis, 1949 is needed. The colonization of America and Europe probably took place more than once in each continent. The more recent common ancestor of the majority of the species of Palaemon, Macrobrachium Spence Bate, 1868 and closely related genera probably was an amphidromous lineage. The molecular and morphological approach indicates that there are nine species of Palaemon in Brazil, eight of them previously described (P. argentinus, P. carteri, P. ivonicus, P. mercedae, P. northropi, P. octaviae, P. paivai, P. pandaliformis) and one new species (P. yuna).
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Mengual, Sanchis Ximo. "Molecular phylogeny and evolution of predatory Syrphidae (Insecta: Diptera)." Doctoral thesis, Universidad de Alicante, 2008. http://hdl.handle.net/10045/14536.
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Viola, Laerte Bento. "Diversidade morfológica e molecular e filogenia de isolados brasileiros de tripanossomas de cobras, jacarés e lagartos." Universidade de São Paulo, 2008. http://www.teses.usp.br/teses/disponiveis/42/42135/tde-03102008-153958/.
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Tripanossomas de répteis há muito são descritos em lagartos, tartarugas, crocodilos e cobras de todos os continentes. A classificação destes tripanossomas tem sido feita de acordo com a morfologia de formas sanguíneas e hospedeiro de origem. No entanto, estes critérios tradicionais não são suficientes para descrição de espécies, gerando varias sinonímias. Vinte e sete isolados foram mantidos em culturas contínuas. Estas são as primeiras culturas de tripanossomas de lagartos da América do Sul, e as unicas culturas de tripanossomas de jacarés e cobras disponíveis no mundo. As analises filogenéticas de tripanossomas de répteis realizadas usando seqüências dos genes SSUrRNA e gGAPDH corroboram a polifília de tripanossomas de répteis. O clado que inclui isolados provenientes de cobras e lagartos sugere uma associação com hospedeiros Squamata, sugerindo que flebotomíneos tenham um papel importante na transmissão destes tripanossomas. Os dados morfológicos e moleculares resultantes deste estudo permitiram a descrição de 7 novas espécies de tripanossomas.Reptile trypanosomes have been described in lizards, tortoises, crocodiles and snakes of all continents. Reliable classification of reptile trypanosomes requires analysis based on traditional parameters and molecular phylogeny. However, these criteria are not enough for species description, generating synonymies Twenty-seven isolates were established in continuous cultures: 9 from lizards, 8 from snakes and 10 from caimans. Cultures of these isolates displayed distinct morphology and growth behavior, representing the first cultures of lizard trypanosomes from S. America and the only available cultures from caimans and snakes. The phylogenetic analysis of the reptile trypanosome using SSU rRNA and gGAPDH gene sequences corroborated the polyphyly of reptile trypanosomes. The clade harboring snake and lizard trypanosomes suggested an association with Squamata hosts, with evidence that sand flies play an important role in the transmission of these trypanosomes. Morphological and molecular data from this study permitted the description of 7 new trypanosome species.
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Weis, Andrea. "Integrative taxonomy of antarctic and subantarctic sea spiders (Pycnogonida) using morphological and molecular methods." Diss., Ludwig-Maximilians-Universität München, 2013. http://nbn-resolving.de/urn:nbn:de:bvb:19-164778.
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Oda, Takashi. "Molecular phylogeny of the genus Amanita, and its application to taxonomy, biogeography and evolution." Kyoto University, 2005. http://hdl.handle.net/2433/145448.
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Kyoto University (京都大学)0048
新制・課程博士
博士(農学)
甲第11238号
農博第1453号
新制||農||902(附属図書館)
学位論文||H17||N3983(農学部図書室)
22847
UT51-2004-U443
京都大学大学院農学研究科地域環境科学専攻
(主査)教授 二井 一禎, 教授 高藤 晃雄, 教授 武田 博清
学位規則第4条第1項該当
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Scott, Euan Andrew. "Molecular systematics of the galliformes, with particular reference to the endemic Vietnamese Gallopheasants (Lophura) and the Green Peafowl (Pavo muticus)." Thesis, Manchester Metropolitan University, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.284864.
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OLIVEIRA-CARVALHO, Maria de Fátima de. "Taxonomia, distribuição geográfica e filogenia do gênero Codium Stackhouse (Bryopsidales-Chlorophyta) no litoral brasileiro." Universidade Federal Rural de Pernambuco, 2008. http://www.tede2.ufrpe.br:8080/tede2/handle/tede2/4905.
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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES
Codium Stackhouse is a genus exclusively marine which is represented by 125 taxa and it is distributed in the seas of almost the whole world, except for the polar regions. The highest infrageneric diversity is found in the temperate and subtropical zone seas. In Brazil, there are few informations about the genus, and the majority of the studies deals with floristic surveys from many localities, with just few publications. The aim of this work is to present the survey of this genus with emphasis to its taxonomy and the distribution of its representatives. The morphological studies were based in material collected from many Brazilian states (PB, PE, BA, ES, RJ, SP, SC and RS), in the intertidal region, during the low tides, with the help of spatulas and when necessary through diving in the reef ponds. The specimens were preserved with formalin (4%). For a better comprehension of the phenotypical variations and aiming to contemplate a number of samples as high as possible in the Brazilian states, the material of Codium was studied in the following indexed national herbaria: JPB, PEUFR, ALCB, HUEFS, RB, R, HB, RFA, SP, SPF and FLOR. They were also analyzed the exsiccates of the specimens collected by the Almirante Saldanha, Canopus and Recife Commission oceanographic expeditions. Besides, wereanalyzed as exsiccates of Codium from Brazil deposited in the Herbarium of the University of California, Berkeley (UC). All the exsiccates were carefully analyzed and confirmed and/or corrected as for the identifications. The identification of the taxa was based in morphological characters (habit, ramification pattern and the dimensions of the stalks), anatomical (diameter of the medular filaments, morphology and dimensions of the utricula and disposition of the hairs or scars) and reproductive (morphology, dimentions and insertions of the gametangia). In the Brazilian coast, it was registered the occurrence of seven infrageneric taxa, distributed in the following sections: Adhaerentia (C. Intertextum), Spongiosa (C. spongiosum), Tomentosa (C. isthmocladum, C. repens and Codium sp.) and Elongata (C. decorticatum and C. taylorii). From this work, C. tomentosum is considered as a doubtful species to the Brazilian littoral and C. profundum as “nome nudum” and because of this, cited as Codium sp. As for the great morphological plasticity the species C. decorticatum, C. isthmocladum and C. taylorii were those which showed the greatest difficulties in the taxonomical identification. Three species of straight habit as C. isthmocladum, C.decorticatum and C. taylorii and prostrate habit C. intertextum were those which presented the highest distribution in the Brazilian coast. Through the present study,some species had their geographical distribution increased to the Brazilian coast, as C. decorticatum (Ceará, Paraíba and Alagoas); C. intertextum (Alagoas), C. isthmocladum (Alagoas, Sergipe and Paraná) and C. taylorii (Ceará, Paraíba, Alagoas and Paraná). Besides the taxonomy based in morphological and reproductive characters the DNA sequencing was performed aiming the comprehension of the polymorphism found in some species. In the moment, the DNA sequencing is the most powerful technique to detecting the polymorphism in the genotype and it has been very used in comparing the different taxonomical levels. Sequences of the first exon of the large subunity RUBISCO (rbcL) has been used in the molecular delimitation and phylogeny of the species. To the present study, samplings were obtained from Codium in many localities of Brazil (PB, PE, BA, RJ, SP and SC), besides Fernando de Noronha Islands. The extraction process, amplification, sequencing and analysis of data were performed in the University of São Paulo (USP) in the laboratory of Marine Algae Edson J. de Paula (LAM). In this study, the sequences for the exon 1 of the gene rbcL were obtained from 24samplings of six species found in the Brazilian coast: C. decorticatum, C. intertextum, C. isthmocladum, C. spongiosum, C. taylorii and C. repens. The exon 1 of the rbcL showed 788 pairs of the base for all samplings. From the 24 sequenced samplings, ten unique sequences were obtained, which were phylogenetically analyzed with other sequences from GenBank, using different methods of inferences. The resulting trees were similar and they showed three principal monophyletic groupings. The grouping A, composed by non-ramificated prostrated habit species and in the majority with grouped and small utricules; the grouping B, consisting in the great majority, species with erect habit, cylindrical stalk, with individual utricules with intermidiary sizes. The Brazilian species group with similar from other geographical localities and they are between the main monophyletic groupings. These results indicate that the colonization of the South American Atlantic occurred many times possibly of species which came from Indo-Pacific.
Codium Stackhouse é um gênero exclusivamente marinho, engloba 125 táxons e encontra-se distribuído nos mares de quase todo o mundo, com exceção para as regiões polares. A maior diversidade infragenérica encontra-se nos mares da zona temperada e subtropical. No Brasil, são poucas as informações sobre o gênero, sendo que a maioria dos estudos refere-se a levantamentos florísticos de diversas localidades, se restringindo a um pequeno número de publicações. O objetivo deste trabalho é apresentar o levantamento do referido gênero no litoral brasileiro com ênfase na taxonomia e distribuição de seus representantes. Os estudos morfo-anatômicos foram baseados em material coletado em diversos estados brasileiros (PB, PE, BA, ES, RJ, SP, SC e RS), na região entre-marés, durante as baixas marés, com auxílio de espátulas, e quando necessário, através de mergulhos livres nas poças recifais. Os exemplares foram conservados em solução de formaldeído a 4%. Para uma melhor compreensão das variações fenotípicas e visando contemplar um maior número possível de amostras nos estados brasileiros, foi consultado o material de Codium depositado nos seguintes herbários nacionais indexados: JPB, PEUFR, ALCB, HUEFS, RB, R, HB, RFA, SP, SPF e FLOR. Também foram analisadas as exsicatas dos exemplares coletados pelas expedições oceanográficasAlmirante Saldanha, Akaroa, Canopus e Comissão Recife. Além disso, foram analisadas as exsicatas de Codium procedentes do Brasil depositadas no Herbário da Universidade da Califórnia, Berkeley (UC). Todas as exsicatas foram cuidadosamente analisadas, se procedendo à confirmação e/ou correção das identificações. A identificação dos táxons foi baseada em caracteres morfológicos (hábito, padrão de ramificação e dimensões dos ramos), anatômicos (diâmetro dos filamentos medulares, morfologia e dimensões dos utrículos e disposição de pêlos ou cicatrizes) e reprodutivos (morfologia, dimensões e inserção dos gametângios). Na costa brasileira, foi registrada a ocorrência de sete táxons infragenéricos, distribuídos nas seguintes seções: Adhaerentia (C. intertextum), Spongiosa (C. spongiosum), Tomentosa (C. isthmocladum, C. repens e Codium sp.) e Elongata (C. decorticatum e C. taylorii). C. tomentosum está sendo considerada como espécie duvidosa para o litoral brasileiro e C. profundum como “nome nudum” e, por isto, citada como Codium sp. Devido à marcada plasticidade morfológica, as espécies C. decorticatum, C. isthmocladum e C. taylorii foram as que apresentaram maioresdificuldades na identificação taxonômica. Três espécies de hábito ereto como C. isthmocladum, C. decorticatum e C. taylorii e a de hábito prostrado C. intertextumforam as que apresentaram maior distribuição na costa brasileira. Algumas espécies tiveram sua distribuição geográfica ampliada para a costa brasileira, como C. decorticatum (Ceará, Paraíba e Alagoas); C. intertextum (Alagoas), C. isthmocladum (Alagoas, Sergipe e Paraná) e C. taylorii (Ceará, Paraíba, Alagoas e Paraná). Além da taxonomia baseada em caracteres morfológicos e reprodutivos foi feito o sequenciamento de DNA visando entender melhor o polimorfismo encontrado em algumas espécies. No momento, o sequenciamento de DNA é a técnica mais poderosa para detectar polimorfismo no genótipo e tem sido bastante utilizada na comparação de diferentes níveis taxonômicos. Seqüências do primeiro éxon da grande subunidade RUBISCO (rbcL) têm sido usadas na delimitação molecular e filogenia de espécies. Para o presente estudo, foram obtidas amostras de Codium em diversas localidades do Brasil (PB, PE, BA, RJ, SP e SC), além do Arquipélago de Fernando de Noronha. As amostras foram preservadas em álcool a 70% e sílica gel. O processo de extração, amplificação, sequenciamento e análise dos dados foram realizados na Universidade de São Paulo (USP) no laboratório de AlgasMarinhas Edson J. de Paula (LAM). Neste estudo, as seqüências para o éxon 1 do gene rbcL foram obtidas de 24 amostras de seis espécies ocorrentes na costa brasileira: C. decorticatum, C. intertextum, C. isthmocladum, C. spongiosum, C. taylorii e C. repens. O éxon 1 do rbcL apresentou 788 pares de base para todas as amostras. Das 24 amostras seqüenciadas, dez seqüências únicas foram obtidas, as quais foram filogeneticamente analisadas com outras seqüências do GenBank, usando diferentes métodos de inferências. As árvores resultantes foram similares, apresentando três principais agrupamentos monofiléticos. O agrupamento a, composto por espécies de hábito prostrado, não ramificado e na maioria com utrículos agrupados e pequenos; o agrupamento b, consistindo na sua maioria, espécies de hábito ereto, ramo cilíndrico, com utrículos grandes individuais e finalmente o agrupamento c composto por espécies de hábito ereto, ramo cilíndrico a levemente achatado, utrículos individuais, com tamanhos intermediários. As espécies brasileiras agruparam com similares de outras localidades geográficas e aparecem entre os principais agrupamentos monofiléticos. Estes resultados indicamque a colonização do Atlântico sul americano ocorreu muitas vezes, possivelmente de espécies provenientes do Indo-Pacífico.
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Fortuna-Perez, Ana Paula. "O genero Zornia J. F. Gmel. (Leguminosae, Papilionoideae, Dalbergieae) : revisão taxonomica das especies ocorrentes no Brasil e filogenia." [s.n.], 2009. http://repositorio.unicamp.br/jspui/handle/REPOSIP/314807.
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Orientador: Ana Maria Goulart de Azevedo TozziTese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: Zornia J.F. Gmel. possui distribuição pantropical e contém 75 espécies, das quais 36 ocorrem no Brasil. Para o gênero, têm sido reconhecidos dois subgêneros: Zornia subg. Myriadena (Desv.) Mohlenbr. e Zornia subg. Zornia; o último está dividido em três seções: Zornia sect. Zornia, Zornia sect. Isophylla Mohlenbr. e Zornia sect. Anisophylla Mohlenbr. Há problemas nesta classificação infragenérica, pois muito dos caracteres diagnósticos utilizados são subjetivos e nem sempre se mostram descontínuos. Zornia, que está incluído no clado Adesmia, junto com mais cinco gêneros ocorrentes na América do Sul, Adesmia DC., Poiretia Vent., Amicia Kunth, Chaetocalyx DC. e Nissolia Jacq., é caracterizado principalmente pelas flores dispostas em inflorescências espiciformes com bractéolas peltadas, aos pares, protegendo cada flor. Considerando a expressiva diversidade de táxons de Zornia existente no Brasil, a pouca descontinuidade entre os caracteres diagnósticos infragenéricos e a escassez de revisões taxonômicas recentes deste gênero, este estudo teve por objetivos: a) realizar a revisão taxonômica das espécies de Zornia ocorrentes no Brasil; b) estudar a filogenia de Zornia no intuito de verificar as relações infragenéricas e determinar padrões de evolução morfológica; c) determinar tempo de diversificação e padrões biogeográficos do gênero. A revisão taxonômica foi realizada através de análise morfológica de exsicatas e observações de populações em campo. As matrizes dos estudos moleculares foram analisadas sobs os critério de parcimônia e de bayesiana. Foram reconhecidas e descritas até o momento 36 espécies de Zornia para o Brasil, incluindo duas novas. Descrições com comentários sobre relações taxonômicas e morfológicas e distribuição geográfica para as espécies são fornecidas. Os estudos filogenéticos morfológicos e moleculares feitos neste estudo sugerem que Zornia seja monofilético, ao mesmo tempo em que revela que os subgêneros e seções atualmente reconhecidos para o gênero mostraram-se para ou polifiléticos. A datação molecular mostrou que ocorreu um único evento migratório de Zornia da América para África ou Austrália há 4,61 milhões de anos, e esta disjunção se deve provavelmente à dispersão a longa distância.
Abstract: Zornia J.F. Gmel. has a pantropical distribution and consists of 75 species. Thirty six of theses species occur in Brazil. For this genus, two subgenera have been recognized: Zornia subg. Myriadena (Desv.) Mohlenbr. and Zornia subg. Zornia; the latter is divided into three sections: Zornia sect. Zornia, Zornia sect. Isophylla Mohlenbr. and Zornia sect. Anisophylla Mohlenbr. This infrageneric classification is problematic, because most of the diagnostic characters used are subjective and they are not always discontinuous. Zornia is included in the Adesmia clade together with five more genera that occur in South America (Adesmia DC., Poiretia Vent., Amicia Kunth, Chaetocalyx DC. and Nissolia Jacq.). The genus Zornia is characterized mainly by flowers arranged in spiciform inflorescences, with paired peltade bracteoles protecting each flowers. Considering the expressive diversity of Zornia taxons in Brazil, the little morphological discontinuity between the infrageneric diagnostic characters, and the lack of recent taxonomic revisions of this genus, this study aimed at: a) carrying out a taxonomic revision of Zornia species that occur in Brazil; b) studying Zornia phylogeny in order to verify the infrageneric relationships; c) determining divergence time and biogeography patterns for the genus. The taxonomic revision was done by morphological analysis of herbarium materials and by observing field populations. The matrices of molecular studies were analyzed by Parsimony and Bayesian analyses. So far thirty six species of Zornia have been described for Brazil, including two new species. Descriptions with comments on taxonomic and morphological relationships, and on geographic distribution of the species have been provided. The phylogenetic studies in this work suggest that Zornia is monophyletic. At the same time this study shows that the subgenera and the sections currently acknowledged for the genus are paraphyletic or polyphyletic. The molecular dating shows that only one migratory event of Zornia occurred 4.61 Ma ago from America to Africa or Australia, and this disjunction is probably due to long distance dispersal.
Universidade Estadual de Campi
Biologia Vegetal
Doutor em Biologia Vegetal
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BRAYNER, Suellen Gomes. "Taxonomia e distribuição dos representantes da ordem Nemaliales na Costa do Nordeste brasileiro." Universidade Federal Rural de Pernambuco, 2011. http://www.tede2.ufrpe.br:8080/tede2/handle/tede2/4944.
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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES
The Order is represented by Nemaliales cylindrical or slightly flattened, branched, and multiaxial organization. These organisms are distributed mainly between the Tropics of Cancer and Capricorn (Atlantic, Indian and Pacific Oceans). The highest number for species the Brazilian coast is located in the Northeast (19 species), followed by the Southeast (16 species) and southern (3 species). Aiming to validate the species included in this order, this study focused on the morphological characters combined with molecular biology. The material was collected in the intertidal area during daytime low tides, from October 2007 to December 2009. The collections were supplemented by examination of herbarium collections of national, assisting in the understanding of morphological variability and phytogeographical distribution of species on the coast of northeastern Brazil. Were identified 12 species of the order Nemaliales to the coast of northeastern Brazil: Ganonema farinosum (J.V. Lamour.) K.C. Fan & Yung C. Wang, Liagora ceranoides J.V. Lamour., Nemalion helminthoides (Velley) Batters, Titanophycus validus (Harvey) Huisman, G.W. Saunders & R.A. Sherwood and Trichogloea requienii (Dub.) Kütz. (Liagoraceae); Dichotomaria marginata (J. Ellis & Sol.) J.V. Lamour, D. obtusata (J. Ellis & Sol.) J.V. Lamour, Galaxaura rugosa (J. Ellis & Sol.) J.V. Lamour, Tricleocarpa cylindrica (J. Ellis & Sol) Huisman & Borow., T. fragilis (L.) Huisman & A. R. Townsed. and Galaxaura sp. (Galaxauraceae) and S. furcellata (Turner) J. Agardh (Scinaiaceae). Of these 12 species, DNA extractions were performed for 40 samples, however it was possible to obtain PCR product to 27. We generated sequences of plastid Universal Amplicon (UPA) for 27 samples and the gene that encodes the large subunit (rbcL) of the enzyme ribulose - 1,5 - bisphosphate carboxylase-oxygenase (Rubisco) for 11 samples. Among the samples selected for amplification of rbcL, just for the taxon Galaxaura sp. collected on the beach of Beef, Pernambuco, it was not possible to amplify. For the other samples amplified and sequenced the size of the UPA and rbcL gene, including the PCR primers was 411 nucleotides and 1362, respectively. From the morphology combined with molecular biology, this study suggests three new species, besides the delimitation of the others.
A Ordem Nemaliales possui representantes com talos cilíndricos ou ligeiramente achatados, ramificados, e com organização multiaxial. Esses organismos estão distribuídos, principalmente, entre os trópicos de Câncer e Capricórnio (Oceanos Atlântico, Índico e Pacífico). O maior registro para o litoral brasileiro encontra-se no Nordeste (19 espécies), seguido pelo Sudeste (16 espécies) e sul (3 espécies). Com o objetivo de validar as espécies incluídas nesta ordem, o presente estudo enfocou os caracteres morfológicos aliados à biologia molecular. O material foi coletado na região entre-marés, durante as marés baixas diurnas, no período de outubro de 2007 a dezembro de 2009. As coletas foram complementadas com exame de exsicatas de herbários nacionais, auxiliando na compreensão da variabilidade morfológica e distribuição fitogeográfica das espécies no litoral do nordeste brasileiro. Foram identificadas 12 espécies da ordem Nemaliales para a costa do nordeste brasileiro: Ganonema farinosum (J.V. Lamour.) K.C. Fan & Yung C. Wang, Liagora ceranoides J.V. Lamour., Nemalion helminthoides (Velley) Batters, Titanophycus validus (Harvey) Huisman, G.W. Saunders & A.R. Sherwood e Trichogloea requienii (Mont.) Kütz. (Liagoraceae); Dichotomaria marginata (J. Ellis & Sol.) J.V. Lamour , D. obtusata (J. Ellis & Sol.) J.V. Lamour, Galaxaura rugosa (J. Ellis & Sol.) Lamour, Tricleocarpa cylindrica (J. Ellis & Sol.) Huisman & Borow., T. fragilis (L.) Huisman & R.A. Townsed. e Galaxaura sp. (Galaxauraceae) e S. furcellata (Turner) J. Agardh (Scinaiaceae). Destas 12 espécies, foram feitas extrações de DNA para 40 amostras, entretanto foi possível obter produto de PCR para 27. Foram geradas sequências de Universal Plastid Amplicon (UPA) para 27 amostras e do gene que codifica a subunidade grande (rbcL) da enzima ribulose - 1,5 - bifosfato carboxilase-oxigenase (rubisco) para 11 amostras. Dentre as amostras selecionadas para amplificação do rbcL, apenas para o táxon Galaxaura sp. coletado na Praia de Carne de Vaca, Pernambuco, não foi possível amplificar. Para as demais amostras amplificadas e seqüenciadas o tamanho do gene UPA e rbcL, incluindo os primers de PCR foi de 411 nucleotídeos e 1.362, respectivamente. A partir da morfologia aliada a biologia molecular, o presente estudo sugere três novas espécies, além da correta delimitação das demais.
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Zen, Siqueira Joao Paulo. "Clinical and environmental Aspergillus: morphological and molecular characterization, phylogeny, and antifungal susceptibility profile." Doctoral thesis, Universitat Rovira i Virgili, 2017. http://hdl.handle.net/10803/456300.
Full textAbstract:
Aspergillus és un dels gèneres de Ascomycetes més comuns i ubics, habitant una gran diversitat de substrats. L'objectiu principal d'aquesta tesi va ser contribuir al millor coneixement d'aquest gènere, explorant la diversitat d'espècies en mostres clíniques i ambientals. En aquesta tesi es va estudiar un total de 433 aïllaments obtinguts de diferents fonts (mostres clíniques, terra, fems d'animals herbívors, restes vegetals). La identificació dels aïllaments es va dur a terme per anàlisi filogenètics de múltiples marcadors, incloent seqüències d'ITS, β-tubulina, calmodulina, i RPB2, i caracterització fenotípica. Quan es va considerar rellevant, els aïllaments clínics van ser sotmesos a proves de susceptibilitat antifúngica contra els principals fàrmacs disponibles. En resum, es van identificar 98 espècies d'Aspergillus, 49 de mostres clíniques (248 aïllaments), 48 de terra (92 aïllaments), 48 de fem (82 aïllaments) i 10 de restes vegetals (10 aïllaments). Considerant les seccions poc estudiades d'Aspergillus en el context clínic, les seccions més freqüents van ser Nidulantes (incloent l'antiga secció Versicolores), 84 aïllaments i 14 espècies; Circumdati, 35 aïllaments i set espècies; Aspergillus, 25 aïllaments i cinc espècies; i Usti, 19 aïllaments i dues espècies. Vuit espècies van ser aïllades de mostres clíniques per primera vegada i tres van ser propostes com a noves espècies. Els antifúngics, en general, van mostrar bona activitat enfront dels aïllats assajats, amb l'excepció de l'activitat reduïda de amfotericina B contra membres de la secció Circumdati. Quant als aïllaments ambientals, es van proposar 14 noves espècies basades en caràcters fenotípics i moleculars; cinc pertanyents a la secció Terrei (tres de fem i dues de terra); quatre a la secció Candidi (tots de fem); dues a la secció Nidulantes (tots dos de terra); i una de cada una de les seccions Flavipedes, Cremei, i Usti (tots de fem).Aspergillus es uno de los géneros de Ascomycetes más comunes y ubicuos, habitando una gran diversidad de sustratos. El objetivo principal de esta tesis fue contribuir al mejor conocimiento de este género, explorando la diversidad de especies en muestras clínicas y ambientales. En esta tesis se estudió un total de 433 aislamientos obtenidos de diferentes fuentes (muestras clínicas, suelo, estiércol de animales herbívoros, y restos vegetales). La identificación de los aislamientos se llevó a cabo mediante análisis filogenéticos de múltiples marcadores, incluyendo secuencias de ITS, β-tubulina, calmodulina, y RPB2, y por caracterización fenotípica. Cuando se consideró relevante, los aislamientos clínicos fueron sometidos a pruebas de susceptibilidad antifúngica frente a los principales fármacos disponibles. En resumen, se identificaron 98 especies de Aspergillus, 49 de muestras clínicas (248 aislamientos), 48 de suelo (92 aislamientos), 48 de estiércol (82 aislamientos) y 10 de restos vegetales (10 aislamientos). Considerando las secciones poco estudiadas de Aspergillus en el contexto clínico, las secciones más frecuentes fueron Nidulantes (incluyendo la antigua sección Versicolores), con 84 aislamientos y 14 especies; Circumdati, con 35 aislamientos y siete especies; Aspergillus, con 25 aislamientos y cinco especies; y Usti, con 19 aislamientos y dos especies. Ocho especies fueron aisladas de muestras clínicas por primera vez y tres fueron propuestas como nuevas especies. Los antifúngicos, en general, mostraron buena actividad frente a los aislados ensayados, con la excepción de la actividad reducida de anfotericina B contra miembros de la sección Circumdati. En cuanto a los aislamientos ambientales, se propusieron 14 nuevas especies basadas en caracteres fenotípicos y moleculares; cinco pertenecientes a la sección Terrei (tres de estiércol y dos de tierra); cuatro a la sección Candidi (todos de estiércol); dos a la sección Nidulantes (ambos de suelo); y una de cada una de las secciones Flavipedes, Cremei, y Usti (todos de estiércol).
Aspergillus is one of the most common and ubiquitous genus of Ascomycetes, inhabiting a great diversity of environmental substrates. The main objective of this thesis was to contribute to the better knowledge of this genus, exploring the species diversity in clinic and environmental substrates. A total of 433 isolates were studied in this thesis, which were obtained from different sources (clinical samples, soil, dung, plant debris). The identification of the isolates was carried out by multilocus phylogenetic analyses including sequences of four markers (ITS, β-tubulin, calmodulin, and RPBII) and phenotypic characterization. When relevant, clinical isolates were submitted to antifungal susceptibility testing against the main drugs available. In summary, 98 species of Aspergillus were identified, 49 from clinical samples (248 isolates), 48 from soil (92 isolates), 48 from herbivore dung (82 isolates), and 10 from plant debris (10 isolates). Considering the poorly studied sections of Aspergillus in the clinical setting, the most frequent sections were Nidulantes (including the former Versicolores section), 84 isolates and 14 species; Circumdati, 35 isolates and seven species; Aspergillus, 25 isolates and five species; and Usti, 19 isolates and two species. Eight species were isolated from clinical samples for the first time and three were proposed as new. The antifungal drugs, in general, showed good activity against the isolates tested, with exception of the reduced activity of amphotericin B against members of section Circumdati. Regarding the environmental isolates, 14 new species were proposed based on phenotypic and molecular data; five belonging to the section Terrei (three from herbivore dung and two from soil); four to the section Candidi (all from dung); two to the section Nidulantes (both from soil); and one in each of the sections Flavipedes, Cremei, and Usti (all from dung).