<p>Taksonomija&nbsp; i&nbsp; sistematika&nbsp; su&nbsp; okosnica&nbsp; nauke&nbsp; o biodiverzitetu,&nbsp; obzirom&nbsp; da&nbsp; su&nbsp; osnova&nbsp; za identifikaciju&nbsp; i&nbsp; razdvajanje&nbsp; jedinstvenih filogenetskih&nbsp; entiteta&nbsp; (vrsta),&nbsp; ali&nbsp; i&nbsp; vi&scaron;ih taksonomskih&nbsp; kategorija.&nbsp; Rod&nbsp;<em> Merodon&nbsp;</em> Meigen,1803&nbsp; pripada&nbsp; familiji&nbsp; Syrphidae,&nbsp; podfamiliji Eristalinae,&nbsp; tribusu&nbsp; Merodontini.&nbsp; Vodeći&nbsp; je&nbsp; rod osolikih muva po bogatstvu vrstama u Evropi (124 vrsta).&nbsp; Sirfide&nbsp; predstavljaju&nbsp; veoma&nbsp; važnu&nbsp; grupu<br />organizama&nbsp; i&nbsp; njihov&nbsp; značaj&nbsp; u&nbsp; prirodi&nbsp; je&nbsp; vi&scaron;estruk (polinacija,&nbsp; regulatori&nbsp; brojnosti&nbsp; &scaron;tetnih&nbsp; insekata bioindikatori&nbsp; stani&scaron;ta,&nbsp; razlagači&nbsp; materija&nbsp; u raspadanju&nbsp; itd).&nbsp; Iako&nbsp; su&nbsp; se&nbsp; istraživanjima&nbsp; roda Merodon&nbsp; bavili&nbsp; brojni&nbsp; autori,&nbsp; dosada&scaron;nje filogenetske&nbsp; analize&nbsp; nisu&nbsp; u&nbsp; potpunosti&nbsp; rasvetlile njegovu sistematsku poziciju, kao i položaj taksona na&nbsp; filogenetskom&nbsp; stablu.&nbsp; U&nbsp; cilju&nbsp; &scaron;to&nbsp; boljeg razumevanja sistematike i filogenije roda&nbsp; <em>Merodon</em>, neophodno&nbsp; je&nbsp; analizirati&nbsp; genske&nbsp; regione&nbsp; koji evoluiraju različitim mutacionim stopama, kao i &scaron;to veći&nbsp; broj&nbsp; filogenetski&nbsp; informativnih&nbsp; morfolo&scaron;kih karaktera. U&nbsp; ovom&nbsp; radu&nbsp; su&nbsp; u&nbsp; cilju&nbsp; istraživanja sistematike&nbsp; roda&nbsp; <em>Merodon&nbsp; </em>analizirani&nbsp; molekularni (mtDNK, 18S rRNK, 28S rRNK) i 250 morfolo&scaron;kih<br />karaktera&nbsp; (pomoću&nbsp; binokularne&nbsp; lupe&nbsp; i&nbsp; Skening elektronskog&nbsp; mikroskopa),&nbsp; pojedinačno&nbsp; i kombinovano&nbsp; a&nbsp; upotrebom&nbsp; metoda&nbsp; za&nbsp; filogenetsku analizu-&nbsp; <em>maximum&nbsp; parsimony</em>&nbsp; (MP)&nbsp; i&nbsp;<em> maximumlikelihood (</em>ML). Analizirano je ukupno 329 jedinki. Pokazalo&nbsp; se&nbsp; da&nbsp; je&nbsp; u&nbsp; ovakvom&nbsp; tipu&nbsp; istraživanja neophodan&nbsp; integrativni&nbsp; pristup,&nbsp; odnosno kombinacija&nbsp; &scaron;to&nbsp; vi&scaron;e&nbsp; karaktera&nbsp; poreklom&nbsp; iz različitih&nbsp; izvora.&nbsp; Na&nbsp; osnovu&nbsp; ML&nbsp; stabla&nbsp; svih&nbsp; gena tribus&nbsp; Merodontini&nbsp; je&nbsp; monofiletski&nbsp; gde&nbsp; se&nbsp; vrsta<br /><em>Nausigaster&nbsp; meridionalis</em>&nbsp; pojavljuje&nbsp; kao&nbsp; sestrinska ostalim rodovima tribusa (<em>Azpeytia, Platynochaetus, Megatrigon,&nbsp; Eumerus&nbsp;&nbsp; tricolor&nbsp;</em> kladi&nbsp; i&nbsp; ostalim vrstama&nbsp; roda&nbsp;<em> Eumerus</em>).&nbsp; Rod&nbsp; <em>Eumerus&nbsp;</em> je parafiletski&nbsp; i&nbsp; sastoji&nbsp; se&nbsp; iz&nbsp; dve&nbsp; monofiletske&nbsp; linije: <em>Eumerus&nbsp; tricolor&nbsp;</em> klade&nbsp; (potencijalnog&nbsp; roda)&nbsp; i ostalih&nbsp; vrsta&nbsp; roda&nbsp; Eumerus.&nbsp; Rod&nbsp; Merodon&nbsp; je monofiletski&nbsp; prema&nbsp; analizama&nbsp; kombinovane matrice&nbsp;&nbsp; molekularnih&nbsp; i&nbsp; morfolo&scaron;kih&nbsp; podataka,&nbsp; 5&#39; kraja&nbsp; mtDNK&nbsp; COI&nbsp; i&nbsp; analize&nbsp; matrice&nbsp; morfolo&scaron;kih karaktera.&nbsp; U&nbsp; okviru&nbsp; roda&nbsp; <em>Merodon</em>&nbsp; detektovano&nbsp; je ukupno&nbsp; pet&nbsp; klada&nbsp; (<em>aureus,&nbsp; albifrons,&nbsp; desuturinus, natans&nbsp; i&nbsp; avidus</em>),&nbsp; odnosno&nbsp; četiri&nbsp; glavne&nbsp; evolutivne linije,&nbsp; potencijalna&nbsp; podroda:&nbsp; aureus,&nbsp; albifrons&nbsp; + desuturinus,&nbsp; natans&nbsp; i&nbsp; avidus.&nbsp; Mitohondrijalni&nbsp; geni pokazali su se veoma informativnim u sagledavanju<br />filogenetskih odnosa i izdvajanja većine klada, kao i grupa&nbsp; vrsta,&nbsp; &scaron;to&nbsp; ukazuje&nbsp; na&nbsp; veću&nbsp; varijabilnost sekvenci&nbsp; COI&nbsp; gena&nbsp; u&nbsp; odnosu&nbsp; na&nbsp; nuklearne&nbsp; gene. Nuklearni&nbsp; geni&nbsp; samostalno&nbsp; nisu&nbsp; doprineli rasvetljavanju&nbsp; filogenetskih&nbsp; odnosa&nbsp; između&nbsp; klada<br />(28S&nbsp; rRNK&nbsp; izdvaja&nbsp; samo&nbsp; natans&nbsp; kladu)&nbsp; u&nbsp; okviru roda&nbsp;<em> Merodon</em>,&nbsp; ali&nbsp; su&nbsp; izdvojili&nbsp; tribus<em>&nbsp; Merodontini,</em>kao&nbsp; i&nbsp;<em> Eumerus&nbsp; tricolor&nbsp; </em>liniju.&nbsp; Nuklearni&nbsp; geni&nbsp; su izdvojili&nbsp; i&nbsp; pojedine&nbsp; grupe&nbsp; vrsta&nbsp; u&nbsp; okviru&nbsp; roda <em>Merodon</em>,&nbsp; &scaron;to&nbsp; govori&nbsp; u&nbsp; prilog&nbsp; tome&nbsp; da&nbsp; nuklearni geni mogu biti informativni kako na vi&scaron;im, tako i na nižim&nbsp; taksonomskim&nbsp; nivoima.&nbsp; Mala&nbsp; varijabilnost nuklearnog&nbsp; gena&nbsp; u&nbsp; okviru&nbsp; roda&nbsp; Merodon,&nbsp; naročito<br />slučaju&nbsp; 18S&nbsp; rRNK,&nbsp; govori&nbsp; o&nbsp; njegovoj konzervativnosti.&nbsp; Utvrđeno&nbsp; je&nbsp; da&nbsp; morfolo&scaron;ki<br />karakteri genitalija mužjaka nose važan filogenetski signal&nbsp; za&nbsp; izdvajanje&nbsp; klada&nbsp; i&nbsp; grupa&nbsp; vrsta&nbsp; te&nbsp; upravo kombinacija&nbsp; različitih&nbsp; morfolo&scaron;kih&nbsp; struktura&nbsp; i njihova uloga sa različitim stepenom selekcije koja deluje&nbsp; na&nbsp; njih,&nbsp; uslovljava&nbsp; i&nbsp; njihovu&nbsp; evolucionu diverzifikaciju.&nbsp; Ipak,&nbsp; analize&nbsp; molekularnog&nbsp; i morfolo&scaron;kog&nbsp; seta&nbsp; karaktera&nbsp; pojedinačno&nbsp; nisu&nbsp; u potpunosti&nbsp; rasvetlili&nbsp; filogenetske&nbsp; odnose&nbsp; u&nbsp; okviru<br />roda&nbsp;<em> Merodon</em>,&nbsp; &scaron;to&nbsp; opravdava&nbsp; potrebu&nbsp; za kombinovanom analizom.&nbsp;</p> / <p>Taxonomy&nbsp; and&nbsp; systematics&nbsp; provide&nbsp; the&nbsp; framework&nbsp; for&nbsp; biodiversity&nbsp; research, since&nbsp; they represent a foundation for identification&nbsp; and&nbsp; delimitation&nbsp; of&nbsp; phylogenetic&nbsp; units&nbsp; (species), as well as higher taxonomic ranks. Genus<em>&nbsp; Merodon&nbsp; </em>Meigen,&nbsp; 1803&nbsp; belongs&nbsp; to family&nbsp; Syrphidae,&nbsp; subfamily&nbsp; Eristalinae, tribus&nbsp; Merodontini.&nbsp; Hoverflies&nbsp; play&nbsp; crucial&nbsp; ecological&nbsp; roles&nbsp; (pollination,&nbsp; decomposition&nbsp; and&nbsp; recycling&nbsp; of&nbsp; a&nbsp; vast&nbsp; range&nbsp; of&nbsp; materials, bioindicators&nbsp; etc).&nbsp; Despite&nbsp; the&nbsp; fact&nbsp; that genus<em>&nbsp; Merodon</em>&nbsp; is&nbsp; the&nbsp; species&nbsp; richest hoverfly&nbsp; genus&nbsp; in&nbsp; Europe&nbsp; (124&nbsp; described&nbsp; species so far), only few authors have dealt with&nbsp; its&nbsp; systematics&nbsp; and&nbsp; phylogenetic&nbsp; relationships&nbsp; of&nbsp; this&nbsp; large&nbsp; phytophagous genus. In order to understand the systematics and&nbsp; phylogeny&nbsp; of&nbsp; genus&nbsp; Merodon,&nbsp; it&nbsp; is&nbsp; necessary to analyze comprehensive number of&nbsp; gene&nbsp; regions&nbsp; known&nbsp; to&nbsp; evolve&nbsp; with various&nbsp; mutational&nbsp; rates,&nbsp; and&nbsp; as&nbsp; many&nbsp; feasible,&nbsp; phylogenetically&nbsp; important&nbsp; morphological&nbsp; characters.&nbsp; In&nbsp; this&nbsp; thesis, molecular (mtDNA, 18S rRNA, 28S rRNA)and&nbsp; 250&nbsp; morphological&nbsp; characters&nbsp; (with&nbsp; the aid&nbsp; of&nbsp; binocular&nbsp; and&nbsp; scanning&nbsp; electron microscope)&nbsp; were&nbsp; analyzed,&nbsp; separately&nbsp; and combined,&nbsp; with&nbsp; phylogenetic&nbsp; methods <em>maximum&nbsp; parsimony&nbsp; </em>(MP)&nbsp; and&nbsp; <em>maximum likelihood</em>&nbsp; (ML).&nbsp; In&nbsp; total&nbsp; 329&nbsp; specimens were&nbsp; analyzed.&nbsp; It&nbsp; has&nbsp; been&nbsp; proven&nbsp; that&nbsp; in these types of research integrative approach is crucial, as it considers a large&nbsp; amount of data from various sources. In ML analysis of all&nbsp; genes&nbsp; tribus&nbsp; Merodontini&nbsp; is monophyletic,&nbsp; with&nbsp; Nausigaster meridionalis&nbsp; grouping&nbsp; as&nbsp; a&nbsp; sister&nbsp; to&nbsp; the remaining&nbsp; Merodontini&nbsp; (<em>Azpeytia, Platynochaetus,&nbsp; Megatrigon,&nbsp; Eumerus&nbsp; </em>and <em>Eumerus&nbsp; tricolor&nbsp;</em> lineage). Genus&nbsp;<em> Eumerus </em>is&nbsp; paraphyletic,&nbsp; and&nbsp; within&nbsp; this&nbsp; genus&nbsp; two main&nbsp; monophyletic&nbsp; lineages&nbsp; can&nbsp; be identified:&nbsp;<em> Eumerus&nbsp; tricolor&nbsp; </em>clade&nbsp; (putative genera)&nbsp; and&nbsp; the&nbsp; remaining&nbsp; taxa&nbsp; of&nbsp; genus Eumerus.&nbsp; Genus&nbsp; <em>Merodon</em>&nbsp; monophyly&nbsp; is confirmed,&nbsp; based&nbsp; on&nbsp; all&nbsp; data&nbsp; analysis&nbsp; 5&#39; mtDNA&nbsp; COI&nbsp; and&nbsp; morphological&nbsp; dataset. Within&nbsp; genus&nbsp; <em>Merodon</em>&nbsp; five&nbsp; monophyletic clades&nbsp; can&nbsp; be&nbsp; identified&nbsp; (<em>aureus,&nbsp; albifrons, desuturinus,&nbsp; natans&nbsp; and&nbsp; avidus</em>),&nbsp; or&nbsp; four evolutionary&nbsp; lineages,&nbsp; putative&nbsp; subgenera: aureus,&nbsp; albifrons&nbsp; +&nbsp; desuturinus,&nbsp; natans&nbsp; and avidus.&nbsp; Mitochondrial DNA is proved to be very&nbsp; informative&nbsp; in&nbsp; resolving&nbsp; systematic position&nbsp; of&nbsp; clades,&nbsp; species&nbsp; groups&nbsp; and&nbsp; taxa, which confirms the higher variability of COI mtDNA&nbsp; sequences&nbsp; compared&nbsp; to&nbsp; nuclear genes. Nuclear genes alone didn&#39;t resolve the systematic&nbsp; position&nbsp; and&nbsp; phylogenetic relationships&nbsp; between&nbsp; most&nbsp; clades&nbsp; (28S rRNA&nbsp; identified&nbsp; only&nbsp; natans&nbsp; clade)&nbsp; within genus&nbsp; <em>Merodon,</em>&nbsp; but&nbsp; these&nbsp; genes&nbsp; confirmed the&nbsp; monophyly&nbsp; of&nbsp; tribus&nbsp; Merodontini&nbsp; and putative&nbsp; genera&nbsp; <em>Eumerus&nbsp; tricolo</em>r.&nbsp; Nuclear genes&nbsp; were&nbsp; also&nbsp; informative&nbsp; for&nbsp; some species&nbsp; groups,&nbsp; which&nbsp; implies&nbsp; that&nbsp; nuclear genes&nbsp; could&nbsp; be&nbsp; beneficial&nbsp; in&nbsp;&nbsp; resolving systematic position of both lower and higher taxonomic ranks. Low&nbsp; variability of nuclear genes within genus <em>Merodon</em>, especially 18SrRNA,&nbsp; proves&nbsp; the&nbsp; fact&nbsp; that&nbsp; they&nbsp; are&nbsp; conservative&nbsp; genes.&nbsp; Morphological&nbsp; characters&nbsp; of&nbsp; male&nbsp; genitalia&nbsp; carry&nbsp; the strongest&nbsp; phylogenetic&nbsp; signal,&nbsp; since&nbsp; they show a great evolutionary divergence in the shape&nbsp; and&nbsp; structural&nbsp; complexity,&nbsp; as&nbsp; a&nbsp; result of&nbsp; sexual&nbsp; selection.&nbsp; As&nbsp; molecular&nbsp; nor morphological&nbsp; characters&nbsp; alone&nbsp; couldn&#39;t fully&nbsp; resolve&nbsp; the&nbsp; phylogenetic&nbsp; relationships&nbsp; within genus&nbsp; <em>Merodon</em>,&nbsp; all data&nbsp; approach is proven&nbsp; to&nbsp; be&nbsp; necessary&nbsp; in&nbsp; this&nbsp; type&nbsp; of&nbsp; research.<br />&nbsp;</p>

Biologists use ontologies as a method to organize and publish their acquired knowledge. Computer scientists have shown the value of ontologies as a means for knowledge discovery. This dissertation makes a number of contributions to enable systematic biologists to better leverage their ontologies in their research. Systematic biology, or phylogenetics, is the study of evolution. “Assembling a Tree of Life” (AToL) is an NSF grand challenge to describe all life on Earth and estimate its evolutionary history. AToL projects commonly include a study a taxon (organism) to create an ontology to capture its anatomy. Such anatomy ontologies are manually curated based on the data from morphology-based phylogenetic studies. Annotated digital imagery, morphological characters and phylogenetic (evolutionary) trees are the key components of morphological studies. Given the scale of AToL, building an anatomy ontology for each taxon manually is infeasible. The primary contribution of this dissertation is automatic inference and concomitant formalization required to compute anatomy ontologies. New anatomy ontologies are formed by applying transformations on an existing anatomy ontology for a model organism. The conditions for the transformations are derived from observational data recorded as morphological characters. We automatically created the Cypriniformes Gill and Hyoid Arches Ontology using the morphological character data provided by the Cypriniformes Tree of Life (CTOL) project. The method is based on representing all components of a phylogenetic study as an ontology using a domain meta-model. For this purpose we developed Morphster, a domain-specific knowledge acquisition tool for biologists. Digital images often serve as proxies for natural specimens and are the basis of many observations. A key problem for Morphster is the treatment of images in conjunction with ontologies. We contributed a formal system for integrating images with ontologies where images either capture observations of nature or scientific hypotheses. Our framework for image-ontology integration provides opportunities for building workflows that allow biologists to synthesize and align ontologies. Biologists building ontologies often had to choose between two ontology systems: Open Biomedical Ontologies (OBO) or the Semantic Web. It was critical to bridge the gap between the two systems to leverage biological ontologies for inference. We created a methodology and a lossless round-trip mapping for OBO ontologies to the Semantic Web. Using the Semantic Web as a guide to organize OBO, we developed a mapping system which is now a community standard. / text

A criação de seções em Eumaeini contribuiu significativamente para a classificação de uma tribo ainda com tantos problemas taxonômicos. No entanto, estudos ainda devem ser realizados no intuito de esclarecer relações filogenéticas entre gêneros e espécies das seções, além de reconstruir a história evolutiva de caracteres biologicamente relevantes (p. ex. órgãos sexuais secundários), fornecendo assim subsídios para a compreensão dos processos de especiação que contribuem para a diversidade do grupo. Dessa forma, o principal objetivo do presente trabalho é estabelecer uma classificação mais estável para seção Atlides, inferindo relações filogenéticas entre os gêneros e espécies da seção. Como desdobramentos desse objetivo, pode-se: testar o monofiletismo do gênero Theritas Hübner, com base em caracteres morfológicos; propor grupos monofiléticos dentro de Theritas, para posterior revisão das espécies; descrever nova espécie listada como sp. #128 na checklist do Atlas of Neotropical Lepidoptera; e fornecer subsídios pra o entendimento da evolução dos caracteres sexuais secundários encontrados na seção Atlides. Foram levantados 82 caracteres morfológicos: dois de cabeça, 65 de asas, dois de tórax, um de abdômen (externo), oito de genitália masculina e quatro de genitália feminina. As relações filogenéticas foram estudadas de acordo com o método cladístico. Testes assumindo pesos iguais e diferentes dos caracteres foram realizados. A pesagem dos caracteres seguiu o método de pesagem implícita com constante de concavidade (k) com valores iguais a 3, 4, 5, 6, 7, 8, 10, 25, 50, 250 e 1000. Foram resultadas três árvores mais parcimoniosas no estudo com pesagem uniforme de caracteres (L=296, Ci= 50, Ri= 78). Como resultado do estudo cladístico tem-se que a seção Atlides não constitui um grupo monofilético da forma como havia sido proposta; o gênero Theritas Hübner não constitui um grupo monofilético, sendo desmembrado em três gêneros: Theritas Hübner, 1818 (sensu stricto), Denivia Johnson, 1992, revalidado e Margaritheclus Bálint, 2002, revalidado. A espécie listada como sp. #128 pertence à Denivia Johnson e foi descrita como Denivia silma Martins & Robbins, espécie nova. São propostas três novas combinações, uma em Margaritheclus Bálint e duas em Denivia Johnson, além de um sinônimo novo em Theritas Hübner. Os órgãos sexuais secundários mostraram-se homoplásticos, tendo a regulação gênica como uma explicação plausível para o padrão evolutivo apresentado. / The establishment of sections in Eumaeini contributed significantly to the classification of this tribe, which still has many taxonomic problems. However, many studies have yet to be performed, aiming to understand phylogenetic relationships of genera and species, and to reconstruct the evolutionary history of biologically relevant characters (ex. secondary sexual organs), providing supports for understanding speciation processes that contribute to the diversity of the group. Thus, the main objective of the present study is to establish a more stable classification for the Atlides section. As consequences of this objective, it was possible to test the monophyly of the genus Theritas Hübner, based on morphological characters; proposing monophyletic groups within Theritas, for further review of the species; describing a new species listed as sp. # 128 in checklist of the Atlas of Neotropical Lepidoptera; and providing guide lines for understanding the evolution of secondary sexual characters found in the Atlides section. A total of 82 morphological characters were collected: two from head, 65 from wings, two from thorax, one from external abdomen, eight from male genitalia and four from female genitalia. Phylogenetic relationships were studied according to the cladistic method. Tests assuming equal and different characters\' weights were performed. The characters\' weights were established using the implicit weighting method with values of 3, 4, 5, 6, 7, 8, 10, 25, 50, 250 and 1000 for the constant of concavity (k). Three most parsimonious trees were obtained with equal characters weights analyses (L=296, Ci= 50, Ri= 78). Cladistics results showed that Atlides section does not constitute a monophyletic group as it had been proposed; Theritas Hübner, 1818 does not constitute a monophyletic group and it has being dismembered into three genera: Theritas Hübner, 1818 (sensu stricto), Denivia Johnson, 1992, revalidated and Margaritheclus Bálint, 2002, revalidated. The new species listed as sp. # 128 belongs to Denivia Johnson and it was described as Denivia silma Martins & Robbins, new species. It was proposed three new combinations, one in Margaritheclus Bálint and two in Denivia Johnson, and one new synonym in Theritas Hübner. The secondary sexual organs proved to be homoplastic, with gene regulation as a plausible explanation for the evolutionary pattern presented.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Cultivation of Walnut-pecan (Carya illinoinensis [Wangenh.] K. Koch) has intensified in recent years in the state of Rio Grande do Sul. However, the research related to plant pathology has not developed to the same degree, so producing pecan nuts have faced many unknown diseases in the state. The main objective of this study was: a) identify and characterize causal agents of new diseases on Walnut-pecan in Rio Grande do Sul, and as specific objectives: b) to collect and to identify pathogens in different locations in Rio Grande do Sul, c) evaluate the pathogenicity of isolates collected in plantations of Walnut-pecan from different locations in Rio Grande do Sul, d) perform the isolates morphological characterization collected from diseased plants of Walnut-pecan, and e) to identify the isolates species. For this purpose, samples were taken in seven cities in the state for isolating potentially pathogenic fungi which were also collected and analyzed soil samples to characterize the area and georeferencing. Pathogens, Fusarium spp. and Pestalotiopsis spp. which were not yet reported were tested for their pathogenicity. The first genus was tested by inoculation on substrate, and the second by leaf inoculation with spore suspension. The pathogenic isolates were characterized by mycelial growth, sporulation, conidial dimensions, colony pigmentation and formation of specific structures to each genus. The same isolates were also identified by molecular sequencing of the ITS and TEF-1α genes for Fusarium spp. and ITS and β-tubulin genes for Pestalotiopsis spp. Twelve pathogenic isolates of Fusarium spp. and eleven of Pestalotiopsis spp. were identified. The variables used on morphological characterization were able to differentiate the isolates, especially the width of conidia for Fusarium spp. and diameter of the colonies for Pestalotiopsis spp. The sequencing of the ITS regions and TEF-1α to Fusarium spp. confirmed the separation of isolates through morphological characteristics and identified five species: F. chlamydosporum, F. oxysporum, F. equiseti, Giberella fujikuroi species complex and F. graminearum species complex and for Pestalotiopsis spp. sequencing of the ITS regions and β-tubulin could identify some species, such as P. clavisora and P. cocculi, and other isolates remained without precise identification of the species, since the phylogeny of the genus is still poorly known. / O cultivo da nogueira-pecan (Carya illinoinensis [Wangenh.] K. Koch) tem se intensificado nos últimos anos no estado do Rio Grande do Sul. Entretanto, as pesquisas relacionadas aos problemas fitossanitários da espécie não se desenvolveram na mesma intensidade, de modo que muitos produtores do estado têm enfrentado enfermidades desconhecidas. Diante disto, o objetivo geral do presente trabalho foi identificar e caracterizar os agentes causais de novas doenças que atacam a nogueira-pecan no Rio Grande do Sul. Como objetivos específicos estabeleceram-se: a) coletar e identificar agentes patogênicos em diferentes localidades no Rio Grande do Sul; b) avaliar a patogenicidade de isolados coletados em plantios de nogueira-pecan de diferentes localidades no Rio Grande do Sul; c) caracterizar morfofisiologicamente os isolados coletados de plantas doentes de nogueira-pecan; e d) identificar, em nível de espécie, os isolados provenientes de plantas doentes de nogueira-pecan. Para tanto, foram realizadas coletas em sete municípios do estado, para isolamento de fungos potencialmente patogênicos. Também foram coletadas e analisadas amostras de solo para caracterização da área e georreferenciamento dos pontos. Os patógenos, ainda não relatados, Fusarium spp. e Pestalotiopsis spp., foram testados quanto a sua patogenicidade. O primeiro foi testado com inoculação em substrato, e o segundo com inoculação foliar por suspensão de esporos. Os isolados patogênicos foram caracterizados morfofisiologicamente através das variáveis crescimento micelial, esporulação, dimensões de conídios, pigmentação das colônias e formação de estruturas específicas de cada gênero. Os mesmos isolados também foram identificados molecularmente através de sequenciamento dos genes ITS e TEF-1α, para Fusarium spp., e ITS e β-tubulina, para Pestalotiopsis spp. Foram identificados doze isolados patogênicos de Fusarium spp. e onze de Pestalotiopsis spp. As variáveis utilizadas na caracterização morfofisiológica foram suficientes na diferenciação dos isolados, especialmente a largura dos conídios, para Fusarium spp. e o diâmetro das colônias, para Pestalotiopsis spp. O sequenciamento das regiões ITS e TEF-1α, para Fusarium spp., confirmou a separação dos isolados por meio das características morfofisiológicas e identificou cinco espécies, sendo elas F. chlamydosporum, F. oxysporum, F. equiseti, Giberella fujikuroi species complex e F. graminearum species complex. Para Pestalotiopsis spp., o sequenciamento das regiões ITS e β-tubulina permitiu que se identificassem algumas espécies, como é o caso de P. clavisora e P. cocculi. Outros isolados permaneceram sem identificação precisa da espécie, já que a filogenia do gênero ainda é pouco conhecida.

Made available in DSpace on 2014-08-20T13:32:45Z (GMT). No. of bitstreams: 1 tese_daiane_de_pinho_benemann.pdf: 2735667 bytes, checksum: 56ce2e3c78770a1745bd363c525c5392 (MD5) Previous issue date: 2012-05-24 / Gerbera is one of the most important plants in the global ornamental market. Due to fierce competition in this market, obtaining different genotypes is necessary. Therefore, information on the genetic variability of this species may help breeding programs in order to select new promising genotypes. This study aimed to develop EST-SSR markers for gerbera, and to check the genetic variability among accessions by multivariate analysis using morphological (qualitative and quantitative), and molecular markers. Also to analyze the correlation between morphological and molecular markers to elucidate the genetic variability of Gerbera spp.. As a result, 17 EST-SSR markers were developed for use in studies of molecular characterization. These were highly polymorphic and allowed the differentiate of all gerbera accessions. The analysis of morphological (quantitative and qualitative) characters, by means of multivariate analysis and principal components enabled the delection of a wide genetic variability among accessions of gerbera. The correlation analysis between morphological characters show that there is some influence on other characters. The analysis of molecular and morphological data, using the sum of the dissimilarity matrices, it was possible to obtain a better grouping of the accessions studied. The results of this study may assist gerbera breeding programs in the selection of parental genotypes for controlled crossings. / A gérbera é uma das plantas mais importantes no mercado mundial de ornamentais. Dada a grande concorrência nesse mercado, a obtenção de genótipos diferenciados é uma necessidade constante, sendo assim, informações sobre a variabilidade genética desta espécie podem auxiliar programas de melhoramento, visando a seleção de novos genótipos promissores. No presente estudo buscou-se desenvolver marcadores EST-SSR para gérbera, com os objetivos de caracterizar molecularmente esta espécie, verificar a variabilidade genética entre acessos, por meio da análise multivariada utilizando caracteres morfológicos (qualitativos e quantitativos), analisar a correlação entre os caracteres morfológicos e moleculares para uma melhor elucidação da variabilidade genética de Gerbera spp.. Como resultados, 17 marcadores EST-SSRs foram desenvolvidos para uso em estudos de caracterização molecular. Estes foram altamente polimórficos e capazes de diferenciar todos os acessos de gérbera. A análise dos caracteres morfológicos (quantitativos e qualitativos), por meio de análise multivariada e componentes principais, possibilitou verificar a existência de ampla variabilidade genética entre os acessos de gérbera. Através da correlação entre os caracteres morfológicos, constatou-se que existe influência de alguns caracteres sobre outros. Na análise conjunta dos dados moleculares e morfológicos, por meio da soma das matrizes de dissimilaridade, foi possível obter um melhor agrupamento entre os acessos estudados. Os resultados obtidos neste estudo poderão auxiliar programas de melhoramento genético de gérbera na seleção de progênies promissoras para cruzamentos controlados.

The genus Tsuga is comprised of eight extant species found in North America and East Asia and four species represented by fossils from Europe and Japan. This study presents the first phylogenetic analysis based on structural, biochemical, and molecular sequence data. Characters obtained from published and unpublished literature were combined with new morphological characters from seeds, seedlings, and leaf cuticle material. Results from parsimony analyses of these characters differed from the published molecular based phylogeny. The non-molecular based phylogeny resolves two separate clades, a North American and an Asian, but did not group the western North American species, as in the molecular based analysis. Character states were traced on the trees to interpret character evolution. The combined analysis resulted in a phylogeny that differed from the previously published molecular tree by resolving a clade between T. caroliniana and T. diversifolia and placing T. dumosa outside of the Asian clade.

De nos jours, l’identification automatique des espèces de plantes par l’analyse d’images, devient incontournable pour faire perdurer, standardiser voire approfondir les connaissances relatives à la communauté végétale. Cette thèse aborde le problème d’identification automatique des espèces de plantes en utilisant les images de feuilles. Elle s’attaque à deux principaux challenges: Le premier challenge est le grand nombre et la large variabilité de la morphologie foliaire des espèces et le deuxième challenge est la variabilité intra-espèces qui se manifeste localement au niveau de régions particulières des feuilles. Pour pallier à ces deux problèmes, un retour à la botanique et notamment aux concepts botaniques foliaires a été établi pour définir une structuration automatique des feuilles à deux niveaux: Le premier niveau concerne un schéma de catégorisation selon les deux concepts botaniques “arrangement” et “lobation”. Le deuxième niveau consiste à définir les parties sémantiques qui composent la feuille. L’approche de la thèse s’articule autour de deux principaux volets: Dans le premier volet, nous nous intéressons à mettre en place cette structuration guidée par la sémantique botanique en définissant des propriétés géométriques simples corrélées avec les définitions et les observations botaniques. Dans le deuxième volet, nous étudions la faisabilité et la pertinence d’intégrer cette structuration dans la chaîne d’identification. Particulièrement, nous établissons des recherches ciblées dans les catégories et nous définissons des modèles de parties à significations botaniques. Nous établissons notre évaluation sur les deux bases d’images de Scans de feuilles ImageCLEF 2011 et ImageCLEF 2012. Nous comparons notre approche par rapport à un schéma d’identification de référence, appliqué sur la totalité de la base et en utilisant l’image entière, et par rapport à plusieurs méthodes référencées dans la littérature. / Nowadays, automatic identification of plant species, by image analysis, has become crucial to maintain, standardize or deepen knowledge about the plant community. This thesis focus on the problem of automatic identification of plant species using leaf images. It addresses two main challenges: The first challenge is the large number and the high variability in foliar morphology across species. The second challenge is the intra-species variability which occurs locally at particular regions of leaves. To overcome these two problems, a return to botany and especially to leaf botanical concepts is established in order to define an automatic structuring of leaves at two levels: The first level concerns a categorisation scheme according to the botanical concepts “arrangement” and “lobation". The second level consists in decomposing leaves into semantic parts. The approach of the thesis is based on two key parts: In the first part, we focus on establishing this botanical-based structuring process by defining simple geometric properties correlated with botanical definitions and observations. In the second part, we investigate the feasibility and opportunities to integrate this structuring process in the identification scheme. Particularly, we make targeted researches in categories and we define specific part-based models.Experiments are conducted using the ImageCLEF 2011 and 2012 Scan images leaf databases. We compare our approach with respect to the reference identification scheme, applied on the whole databaseand using the entire images, and with respect to several methods referenced in the literature.

Els treballs realitzats en aquesta tesi tenen com objectius l'aplicació de la sistemàtica molecular i la filogeografia per resoldre relacions filogenètiques, clarificar la taxonomia i descriure la història de les poblacions de les espècies incloses dins de dos grups de mamífers d'elevat interés conservacionista: els mustélids (família Mustelidae) i els macacs (génere Macaca).L'ús de diferents marcadors genétics mitocondrials (el gen citocrom b i la regió control) i un de nuclear (les seqüencies flanquejants d'una regió repetitiva) ha permés reconstruir les relacions filogenètiques entre 33 espècies de mustelids; delimitar quatre grups filogeogràfics en el teixò euroasiàtic (Meles meles); detectar la venta de productes derivats d'aquesta espècie en països on està protegida; i estudiar el procès d'especiació del macac japonès (Macaca fuscata). A partir dels resultats obtinguts també s'han proposat canvis en la taxonomia d'aquests grups. Al final de la tesi es fan reflexions sobre el paper que desenvolupen els marcadors moleculars en la sistemàtica, sobre com classificar aquelles espècies que no ha finalitzat els seus processos d'especiació i sobre les aplicacions de la sistemàtica, la biologia evolutiva i la genètica en la conservació de la biodiversitat. / The objectives of this thesis were the application of molecular systematics and phylogeography to resolve phylogeny, to clarify taxonomy and to study the population history of species included within two groups of mammals of high conservation interest: the mustelids (Family Mustelidae) and the macaques (Genus Macaca).Using different mitochondrial (cytochrome b gene and control region) and nuclear (flanking sequences of a repetitive region) markers, we have been able to reconstruct the phylogeny of 33 mustelid species; to delimit four phylogeographic groups in the Eurasian badger (Meles meles); to detect the trade of Eurasian badger products in countries where this species is protected; and to study the speciation process of the Japanese macaque (Macaca fuscata). According to our results we have also proposed taxonomic changes in these groups.At the end of the thesis, there are also some reflections about the role of genetic markers in systematics; about how to classify the species that have not finished their speciation process; and about the application of systematics, evolutionary biology and genetics in conservation biology.

Conselho Nacional de Desenvolvimento Científico e Tecnológico / Considering the expansion of grown of common bean for large mechanized areas and the need of biofortication of basic foods consumed by the Brazilian population, to minimize minerals deficiencies, obtaining common bean lines with high agronomic performance and higher minerals concentration in the grains represents technological advances for the culture. The objectives of this study were: (1) to estimate the genetic parameters for morphological, phenological, grain yield and nutritional characters in four biofortified populations of common bean in F6:8 generation; (2) assess the effectiveness of different selection strategies, direct selection and selection indexes, with the adoption of economic weights equivalent to coefficient of genetic variation (CVg) and proportional to a gain of 10% in average for each character, without restriction and also restriction to gains in only one of the mineral; and (3) to select common beans lines of high agronomic performance, as erect architecture and grain yield, and biofortified for potassium, phosphorus, zinc and copper concentrations in grains. Thus, a total of 169 common beans lines in F6:8 generation were evaluated in two experiments in a simple lattice design in the rainy season 2012/2013 and dry season 2013, in Santa Maria/RS. The following traits: note lodging, general adaptation note, insertion height of the first and last pod, cycle, number of pods and grains per plant, weight of 100 grains, grain yield and potassium, phosphorus, zinc and copper concentrations in grains were evaluated and the genetic parameters were estimated in each biofortification population. For simultaneous selection were tested selection indexes: direct selection, classical index, base index, parameters and weights-free index, based on desired gains index, multiplicative index and the "ranks" sum index. Significant line x environment interaction was observed for most of the characters, except for potassium, phosphorus and copper concentrations in grains. Genetic variability has not been obtained only for the copper concentration in grains. The weight of 100 grains and grain yield show high heritability in F6:8 generation in all populations studied. The characters of note lodging, height of the first pod, cycle, number of pods per plant and number of grains per plant were from moderate to high heritability. The others characters have from low to high heritability, except for the potassium and zinc concentrations in grains that exhibit from low to moderate heritability. The direct selection enabled high gain selection for individual characters, but caused undesirable changes in other characters under selection. The multiplicative index is the best strategy for simultaneous selection for the identification of common beans lines for erect architecture, high grain yield and high potassium, phosphorus and zinc concentration in grains. The L92, L 97, L 137 and L 146 lines are promising and remain under evaluation by the breeding program. / Considerando a expansão do cultivo de feijão para as grandes áreas mecanizadas e a necessidade de bioforticação de alimentos básicos consumidos pela população brasileira, para minimizar as deficiências minerais, a obtenção de linhagens de feijão com alto desempenho agronômico e com maior concentração de minerais nos grãos representam avanços tecnológicos para a cultura. Assim, os objetivos deste estudo foram: (1) obter estimativas de parâmetros genéticos para os caracteres morfológicos, fenológicos, da produção e nutricionais em quatro populações biofortificadas de feijão em geração F6:8; (2) verificar a eficiência de diferentes estratégias de seleção, seleção direta e índices de seleção, com a adoção de pesos econômicos equivalentes ao coeficiente de variação genético (CVg) e proporcionais a um ganho de 10% na média para cada caractere, sem restrição, e também com restrição para obter ganhos em apenas um dos minerais; e (3) selecionar linhagens de feijão de alto desempenho agronômico, quanto a arquitetura ereta e à produtividade de grãos, e biofortificadas quanto as concentrações de potássio, de fósforo, zinco e cobre nos grãos. Para tanto, um total de 160 linhagens de feijão em geração F6:8 e nove genitores foram avaliados em dois experimentos conduzidos em delineamento látice simples nos cultivos de safra 2012/2013 e de safrinha 2013, em Santa Maria/RS. Os caracteres nota de acamamento, altura de inserção da primeira e da última vagem, ciclo, número de vagens e de grãos por planta, massa de 100 grãos, produtividade de grãos e concentração de potássio, fósforo, zinco e cobre nos grãos foram avaliados e os parâmetros genéticos foram estimados em cada uma das quatro populações biofortificadas. Para a seleção simultânea, as estratégias testadas foram: seleção direta, índice clássico, índice base, índice livre de pesos e parâmetros, índice baseado nos ganhos desejados, índice multiplicativo e índice baseado na soma de ranks . Interação linhagem x ambiente significativa foi observada para a maioria dos caracteres, com exceção da concentração de potássio, fósforo e cobre nos grãos. Variabilidade genética não foi obtida apenas para a concentração de cobre nos grãos. Os caracteres massa de 100 grãos e produtividade de grãos apresentam alta herdabilidade em geração F6:8 em todas as populações avaliadas. Os caracteres nota de acamamento, altura de inserção da primeira vagem, ciclo, número de vagens por planta e número de grãos por planta foram de moderada a alta herdabilidade. Os demais caracteres apresentam herdabilidade de baixa a alta magnitude, a exceção da concentração de potássio e de zinco nos grãos que exibem de baixa a moderada herdabilidade. A seleção direta possibilitou alto ganho de seleção para caracteres individuais, mas provocou alterações indesejáveis nos demais caracteres sob seleção. O índice multiplicativo é a melhor estratégia de seleção simultânea para identificar linhagens de feijão de arquitetura ereta, alta produtividade de grãos e alta concentração de potássio, fósforo e zinco nos grãos. As linhagens L 72, L97, L 137 e L 146 são promissoras e continuarão em avaliação pelo programa de melhoramento.

The objectives of this study were to evaluate whether advanced common bean lines differ in phenological, morphological, grain yield and cooking quality characters; to study the linear correlations between these characters; and to select superior lines for these characters for use in breeding programs. For this purpose, 14 common bean lines of trial Use and Cultivation South -Brazilian Bean (VCU - SB) were growing in normal rainy 2012/2013 and in dry season 2013 in Santa Maria, Rio Grande do Sul, Brazil. Data were subjected to analysis of individual and joint variance, using the F test at 5 % probability. If the effect of line and control was significant, the stratification of averages was performed by the Scott-Knott test at 5 % probability. Interaction line x growing season significant was observed for the characters: number of days from emergence to flowering, reproductive period, cycle, lodging, stay green, number of lateral branches, number of pods per plant, number of grains per plant, number of grains per pod, weight of 100 grains, grain yield, grain length and width. The line and control evaluated differed significantly among the characters: number of days from emergence to flowering, cycle, number of nodes on main stem, width and thickness of grains, grain brightness and time of cooking, allowing you to select improved lines for these characters. Positive linear correlation of high magnitude was observed between grain yield and number of pods per plant (r = 0.632) and weight of 100 grains (r = 0.942), while the grain yield and the number of days from emergence to flowering (r = -0.857) and the cycle (r = -0.677) had high negative linear correlation. The LP 09-40 line and BRS Valente control have the lower note of lodging in the two growing seasons, allowing the use of these blocks of crosses to obtain lines with erect architecture. The CNFP 10794 and DF 06-17 lines may be used as parents in hybrid combinations for presenting high yield and reduced cooking time and high yield and early cycle, respectively. / Os objetivos deste trabalho foram avaliar se as linhagens avançadas de feijão diferem quanto aos caracteres fenológicos, morfológicos, de produção e de qualidade de cozimento; estudar as correlações lineares entre esses caracteres; e selecionar linhagens superiores para esses caracteres para uso em programas de melhoramento. Para tanto, foram avaliadas 14 linhagens de feijão do Ensaio de Valor Cultivo e Uso Sul-brasileiro de Feijão (VCU-SB) em cultivo de safra 2012/2013 e de safrinha 2013 em Santa Maria, Rio Grande do Sul, Brasil. Os dados obtidos foram submetidos à análise de variância individual e conjunta, usando o teste F a 5% de probabilidade. Sendo o efeito de linhagens significativo, a estratificação das médias obtidas foi realizada pelo teste de Scott-Knott a 5% de probabilidade. Interação linhagem x época de cultivo significativa foi observada para os caracteres: número de dias da emergência a floração, período reprodutivo, ciclo, acamamento, stay green, número de ramos laterais, número de vagens por planta, número de grãos por planta, número de grãos por vagem, massa de 100 grãos, produtividade de grãos, comprimento e largura de grãos. As linhagens e as testemunhas avaliadas diferiram significativamente para os caracteres: número de dias da emergência a floração, ciclo, número de nós no ramo principal, largura e espessura dos grãos, luminosidade dos grãos e tempo de cozimento dos grãos, possibilitando a seleção de linhagens superiores para esses caracteres. Correlação linear positiva de alta magnitude foi observada entre a produtividade de grãos e o número de vagens por planta (r = 0,632) e a massa de 100 grãos (r = 0,942), enquanto que a produtividade de grãos e o número de dias da emergência a floração (r = -0,857) e o ciclo (r = -0,677), apresentaram alta correlação linear negativa. A linhagem LP 09-40 e a testemunha BRS Valente apresentam as menores notas de acamamento nas duas épocas de cultivo, o que possibilita o uso dessas em blocos de cruzamentos para a obtenção de linhagens com porte ereto. As linhagens CNFP 10794 e DF 06-17 poderão ser utilizadas como genitores em combinações híbridas por apresentarem alta produtividade de grãos e reduzido tempo de cozimento e alta produtividade de grãos e ciclo reduzido, respectivamente.