Submitted by Renata Lopes (renatasil82@gmail.com) on 2017-04-04T17:26:25Z No. of bitstreams: 1 guilhermerossigorni.pdf: 1287469 bytes, checksum: 646f7d2690ba7bbe109e210c664f269b (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2017-04-06T10:42:19Z (GMT) No. of bitstreams: 1 guilhermerossigorni.pdf: 1287469 bytes, checksum: 646f7d2690ba7bbe109e210c664f269b (MD5) / Made available in DSpace on 2017-04-06T10:42:19Z (GMT). No. of bitstreams: 1 guilhermerossigorni.pdf: 1287469 bytes, checksum: 646f7d2690ba7bbe109e210c664f269b (MD5) Previous issue date: 2007-02-23 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Este estudo visa ao levantamento de espécies e um melhor entendimento da distribuição espacial da Classe Oligochaeta em córregos de baixa ordem do Parque Estadual de Campos do Jordão (PECJ) (SP - Brasil). Para isto, foi elaborado um trabalho abordando três aspectos apresentados nesta dissertação em forma de capítulos: 1) levantamento da riqueza de espécies de Oligochaeta; 2) distribuição espacial e temporal das espécies de Oligochaeta; 3) distribuição em meso-escala (mesohabitats) das espécies de Oligochaeta. As amostras da fauna, utilizando-se um amostrador tipo “Surber”, foram realizadas em trechos dos córregos Galharada, Campo do meio e Serrote durante o período de maio de 2005 a maio de 2006. De maneira geral, nossos resultados indicam que: 1) apesar das características peculiares dos córregos de baixa ordem do PECJ, a fauna Oligochaeta apresentou-se bastante rica; 2) a utilização de técnicas refinadas no processamento das amostras resultou em uma cobertura amostral satisfatória, fazendo-se necessária em trabalhos que visam ao levantamento de espécies de Oligochaeta em áreas de preservação ambiental; 3) Os processos hidrológicos dos córregos, juntamente ao aporte alimentar parecem ser os principais fatores de influência na composição da comunidade de Oligochaeta; 4) As espécies de Tubificidae demonstraram maior afinidade por habitats livres de correnteza contendo certa quantidade de detritos orgânicos, enquanto que as espécies de Naididae preferem habitats com certa correnteza onde há retenção de detritos vegetais. Nossos achados remontam à importância da manutenção de áreas preservadas para a conservação da biodiversidade, visto que qualquer tipo de alteração nesses ambientes pode acarretar drásticas perdas na composição das comunidades. / This study aims to survey species and to better understand the spatial distribution of the Class Oligochaeta in low order streams at Campos do Jordão State Park (PECJ) in the state of São Paulo, Brazil. For this purpose, three aspects were examined and presented as chapters in this dissertation: 1) a survey of the variety of Oligochaeta; 2) spatial and temporal distribution of Oligochaeta species; 3) mesoscale distribution (mesohabitats) of Oligochaeta species. Samples of the fauna were collected between May 2005 and May 2006 in stretches of Galharada, Campo do Meio and Serrote streams using a Surber sampler. In general, our results indicate that: 1) despite the peculiar characteristics of PECJ’s low order streams, the Oligochaeta fauna was considered quite rich; 2) the use of fine techniques in sample processing resulted in satisfactory sample coverage, making this use necessary for surveys of Oligochaeta species in environmental conservation areas; 3) apparently, the main factors influencing the Oligochaeta community composition are hydrological processes in the streams and food intake; 4) Tubificidae species showed greater affinity for non-flowing habitats with organic debris, while Naididae species showed greater affinity for flowing habitats where vegetable debris are retained. Our findings point to the importance of maintaining preserved areas for the conservation of biodiversity, as any alteration to these environments may cause drastic losses in the communities’ composition.

Cette thèse s'intéresse à la conception et le développement des techniques de bioinfor- matique qui peuvent faciliter l'utilisation de l'approche metabarcoding pour mesurer la diversité d'espèces. Le metabarcoding peut être utilisé avec le séquencage haut débit pour l'identification d'espèces multiples à partir d'un seul échantillon environnemental. La véritable force du metabarcoding réside dans l'utilisation de barcode marqueurs choisi pour une étude particulière et l'identification d'espèces ou des taxons peut être réalisé avec des marqueurs soigneusement conçu. Avec l'avancement des techniques haut débit de séquençage, une énorme quantité des données de séquences est produit qui contient un nombres substantiel des mutations. Ces mutations posent un grand problème pour les estimations correctes de la biodiversité et pour le d'assignation de taxon. Les trois problèmes majeurs dans le domaine de la bioinformatique que j'ai abordés dans cette thèse sont: i) évaluer la qualité d'une barcode marker , ii) concevoir des nouveaux région barcode et iii) d'analyser les données de séquençage pour traiter les erreurs et éliminer le bruit en séquences. Pour évaluer la qualité d'un barcode marker, on a développé deux mesures quantita- tive,formelle: la couverture (Bc) et la spécificité (Bs). La couverture donne une mesure de universalité d'une pairs de primer pour amplifier un large nombre de taxa, alors que la spécificité donne une mesure de capacité à discriminer entre les différents taxons. Ces mesures sont très utiles pour le classement des barcode marker et pour sélectionner les meilleurs markers. Pour trouver des nouveaux région barcode notamment pour les applications metabarcod- ing, j'ai développé un logiciel, ecoPrimers3. Basé sur ces deux mesures de qualité et de l'information taxinomique intégré, ecoPrimers nous permet de concevoir barcode markers pour n'importe quel niveau taxonomique . En plus, avec un grand nombre de paramètres réglables il nous permet de contrôler les propriétés des amorces. Enfin, grâce a des algorithmes efficaces et programmé en langage C, ecoPrimers est suffisamment efficace pour traiter des grosses bases de données, y compris génomes bactériens entièrement séquencés. Enfin pour traiter des erreurs présentes dans les données de séquencage , nous avons analysé un ensemble simple d'échantillons de PCR obtenus à partir de l'analyse du régime alimentaire de Snow Leopard. En mesurant les corrélations entre les différents paramètres des erreurs, nous avons observé que la plupart des erreurs sont produites pendant l'amplification par PCR. Pour détecter ces erreurs, nous avons développé un algorithme utilisant les graphes, qui peuvent différencier les vrai séquences des erreurs induites par PCR. Les résultats obtenus à partir de cet algorithme a montré que les données de-bruitée a donnent une estimation réaliste de la diversité des espèces étudiées dans les Alpes françaises. / This thesis is concerned with the design and development of bioinformatics techniques that can facilitate the use of metabarcoding approach for measuring species diversity. Metabarcoding coupled with next generation sequencing techniques have a strong po- tential for multiple species identification from a single environmental sample. The real strength of metabarcoding resides in the use of barcode markers chosen for a particular study. The identification at species or higher level taxa can be achieved with carefully designed barcode markers. Moreover with the advent of high throughput sequencing techniques huge amount of sequence data is being produced that contains a substantial level of mutations. These mutations pose a problem for the correct estimates of biodi- versity and for the taxon assignation process. Thus the three major challenges that we addressed in this thesis are: evaluating the quality of a barcode region, designing new barcodes and dealing with errors occurring during different steps of an experiment. To assess the quality of a barcode region we have developed two formal quantitative mea- sures called barcode coverage (Bc) and barcode specificity (Bs). Barcode coverage is concerned with the property of a barcode to amplify a broad range of taxa, whereas barcode specificity deals with its ability to discriminate between different taxa. These measures are extremely useful especially for ranking different barcodes and selecting the best markers. To deal with the challenge of designing new barcodes for metabarcoding applications we have developed an efficient software called ecoPrimers. Based on the above two quality measures and with integrated taxonomic information, ecoPrimers1 enables us to design primers and their corresponding barcode markers for any taxonomic level. Moreover with a large number of tunable parameters it allows us to control the properties of primers. Finally, based on efficient algorithms and implemented in C language, ecoPrimers is efficient enough to deal with large data bases including fully sequenced bacterial genomes. Finally to deal with errors present in DNA sequence data, we have analyzed a simple set of PCR samples obtained from the diet analysis of snow leopard. We grouped closely related sequences and by measuring the correlation between different parameters of mutations, we have shown that most of the errors were introduced during PCR amplification. In order to deal with such errors, we have further developed an algorithm using graphs approach, that can differentiate true sequences from PCR induced errors. The results obtained from this algorithm showed that de-noised data gave a realistic estimate of species diversity studied in French Alpes. This algorithm is implemented in program obiclean.