Submitted by Gizele Lima (gizele.lima@inpa.gov.br) on 2017-02-13T20:16:06Z No. of bitstreams: 2 Dissertação Smicridea Gleison.pdf: 9709188 bytes, checksum: cb071ce30f7f53d2718bbb3372b41707 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2017-02-13T20:16:06Z (GMT). No. of bitstreams: 2 Dissertação Smicridea Gleison.pdf: 9709188 bytes, checksum: cb071ce30f7f53d2718bbb3372b41707 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2016-05-25 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Smicridea McLachlan, 1871 is the single genus of Smicrideinae in the New World. Its species are quite diverse in the Neotropics and are clustered into two subgenera, Smicridea and Rhyacophylax. However, the larvae of a big part of this diversity remain unknown, especially in Brazil, where among the 50 species recorded only seven has the larvae known. This fact compromises its applicability as biomarkers in biomonitoring programs of the quality of aquatic environments. Therefore, to be illustrated and morphologically described at the species level, larvae need to be associated with identified adults. In this sense, were carried associations between larvae and adult Smicridea of Brazil through metamorphotypes and sequence comparison of mitochondrial gene Cytochrome Oxidase subunit I (COI). From the analysis of material from various locations in Brazil, when metamorphotypes were not found or not available, mitochondrial DNA of the specimens was extracted for subsequent amplification, purification and sequencing of the COI gene fragment. The sequences obtained, together with some of the downloaded DNA barcode database (BOLD) were edited and aligned, resulting in a fragment of 620 bp. Based on sequences, intra- and interspecific genetic distances were calculated using evolutionary model Kimura 2-parameters and from these distances were built filogramas using the neighbor-joining method (NJ) with branches of support inferred by bootstrapping with 1.000 replications. In this study, associations between larvae and adults were performed for 11 species of Smicridea, four by metamorphotypes and seven through COI gene sequences, based on the philogram groupings generated by NJ and according to association’s criteria. Of associated species, seven belong to S. (Rhyacophylax) and four to S. (Smicridea), three of which are new to science. Larvae conspecific to adult of known species with adult males of the new species are described, illustrated and their extended distribution. In addition, an illustrated taxonomic identification key is provided for the 17 species of Smicridea with known larval stage that occurs Brazil. / Smicridea McLachlan, 1871 é o único gênero de Smicrideinae presente no Novo Mundo. Suas espécies são bastante diversas na região Neotropical e estão agrupadas em dois subgêneros, Smicridea e Rhyacophylax. Porém, as larvas de grande parte dessa diversidade permanecem desconhecidas, principalmente no Brasil, onde das 50 espécies registradas apenas sete têm larvas conhecidas. Este fato compromete sua aplicabilidade como bioindicadores em programas de biomonitoramento da qualidade de ambientes aquáticos. Portanto, para serem ilustradas e descritas morfologicamente em nível de espécie, larvas precisam ser associadas com adultos identificados. Nesse sentido, realizou-se associações entre larvas e adultos de Smicridea do Brasil através de metamorfótipos e comparação de sequências do gene mitocondrial Citocromo Oxidase subunidade I (COI). A partir da análise de material proveniente de diversas localidades do Brasil, quando metamorfótipos não foram encontrados ou disponíveis, foi extraído DNA mitocondrial dos espécimes para posterior amplificação, purificação e sequenciamento do fragmento do gene COI. As sequências obtidas, juntamente com algumas obtidas no banco de dados do DNA barcode (BOLD), foram editadas e alinhadas, resultando em um fragmento de 620 bp. Baseado nas sequências, distâncias genéticas intra e interespecífica foram calculadas usando modelo evolutivo Kimura 2-Parâmetros e a partir dessas distâncias foram construídos filogramas usando o método de Neighbor-Joining (NJ) com suporte dos ramos inferido por bootstrap com 1.000 replicações. Neste estudo, associações entre larvas e adultos foram realizadas para 11 espécies de Smicridea, quatro por meio de metamorfótipos e sete através de sequências do gene COI, com base nos agrupamentos do filograma gerado por NJ e de acordo com critérios de associação. Das espécies associadas, sete pertencem a S. (Rhyacophylax) e quatro a S. (Smicridea), das quais três são novas para a ciência. Larvas coespecíficas a adultos de espécies conhecidas juntamente com adultos machos das novas espécies são descritas, ilustradas e suas distribuições estendidas. Além disso, uma chave ilustrada de identificação taxonômica é fornecida para as 17 espécies de Smicridea com estágio larval conhecido que ocorrem no Brasil.

DNA barcoding has illuminated genetically distinct lineages within what appears to be one morphological species. For example, a large-scale DNA barcode analysis of Lepidoptera in the Área de Conservación Guanacaste has revealed that 8% of the morphospecies show more than one DNA barcode lineage. To assess the evolutionary significance of five of these lineages I conducted further molecular analyses by sequencing mitochondrial cytochrome b, nuclear Elongation Factor 1α and ribosomal Internal Transcribed Spacer 2, and compare their gene phylogenies with the provisional species tree hypothesized by DNA barcode genetic distances. Both mitochondrial and nuclear markers support the existence of three cryptic species in one of the five cases. Morphological and ecological correlates are still lacking to understand the origin of this divergence. The lack of corroboration between markers in the four remaining species either suggests that the chosen nuclear markers have not diverged since speciation, or there has been recent hybridization between lineages. In one case, hybridization is strongly suggested. / Natural Sciences and Engineering Research Council of Canada, Genome Canada through the Ontario Genomics Institute

Orientador: Claudio de Oliveira / Resumo: A elevada biodiversidade da ictiofauna marinha no oceano Atlântico do litoral do Brasil resulta num desafio para os estudos de especiação. As barreiras biogeográficas influenciam grandemente o isolamento genético de algumas espécies marinhas, porém a eficácia da transposição dessas barreiras, por alguns peixes podem ocorrer, fazendo com que não haja alterações no fluxo gênico das espécies. No entanto, poucos são os estudos realizados com a ictiofauna marinha em relação aos padrões zoogeógrafos e a rica biodiversidade íctica que se encontra no litoral do Brasil. Considerando o exposto, em nosso trabalho de pesquisa, utilizamos a ferramenta DNA barcoding com objetivo de testar a hipótese da existência de barreiras entre as 10 espécies de peixes que apresenta diferentes hábitos de vida, em áreas geográficas com condições ambientais distintas na costa do Brasil que gerem um isolamento a nível populacional ou especifico e contribuir na formação de um banco de tecido de espécies de peixes marinho-estuarinos. Os fragmentos de DNA barcode com cerca de 600 pares de bases do Citocromo Oxidase C subunidade 1 (COI), foram amplificados por PCR e sequenciados para 145 indivíduos. A análise de divergência genética observada nos espécimes Chaetodipterus faber, Hemicaranx amblyrhynchus, Selene vomer e Nebris microps apresentaram valores intraespecífico menor que 2%, sugerindo que estas espécies adotam uma única unidade evolutiva (U.E) Provavelmente essas espécies não apresentaram diferenciaçã... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The high biodiversity of the marine ichthyofauna in the Atlantic Ocean of the Brazilian coast results in a challenge for the studies of speciation. Biogeographic barriers greatly influence the genetic isolation of some marine species, but the effectiveness of transposition of these barriers by some fish may occur so that there is no change in the gene flow of the species. However, few studies have been carried out with the marine ichthyofauna in relation to the zoogeograph standards and the rich fish biodiversity that is found in the Brazilian coast. Considering the above, in our research work, we used the DNA barcode tool to study 10 species of fish that presents different habits of life, in geographic areas with distinct environmental conditions in the Brazilian coast that generate isolation at the population or specific level and contribute to the formation of a tissue bank of marine-estuarine fish species. In addition to comparing the sequences generated for different areas of the coast of Brazil. DNA barcode fragments with about 600 base pairs of the Cytochrome Oxidase C subunit 1 (COI) were amplified by PCR and sequenced to 145 individuals. The Neighbor-Joining analysis revealed that four species presented a single evolutionary unit in the studied area: Chaetodipterus faber, Hemicaranx amblyrhynchus, Selene vomer, and Nebris microps, presenting genetic distance inferior to 2%. Probably these species do not present genetic differentiation due to their ability to cross th... (Complete abstract click electronic access below) / Mestre

Orientador: Fábio Porto Foresti / Resumo: As raias são elasmobrânquios que apresentam o corpo achatado dorso-ventralmente, além de cinco a sete pares de fendas branquiais que se encontram na região ventral do corpo e nadadeiras peitorais desenvolvidas e fundidas à cabeça. No Brasil, existem 29 espécies de raias em perigo de extinção de acordo com a Lista Vermelha da IUCN. As espécies de raias comercializadas muitas vezes são de difícil identificação devido à descaracterização, o que pode ser solucionado com o uso da técnica DNA Barcode, a qual é um sistema de identificação molecular baseado em uma sequência de DNA mitocondrial Citocromo Oxidase subunidade I (COI), atuando como código de barras de DNA de cada espécie. Esse sistema tem sido utilizado com êxito para identificar amostras que são comercializadas descaracterizadas e de forma ilegal. Desta forma, a técnica de DNA Barcode foi utilizada para a identificação de amostras de raias comercializadas em peixarias no estado de São Paulo e na CEAGESP, com o intuito de identificar quais são as espécies utilizadas no comércio e se atualmente ocorre a venda de espécies ameaçadas de extinção, assim como validar a técnica como ferramenta de rotina para controle de qualidade relacionado ao mercado de raias. Foram coletados 239 amostras, das quais 82 foram identificadas como espécies de raias, sendo elas Paratrygon aiereba (40,24%), Gymnura altavela (14,63%), Potamotrygon motoro (13,41%), Hypanus dipterurus (10,98%), Atlantoraja castelnaui (9,76%), Hypanus americanus (4,88%)... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Skates and stingrays are elasmobranch fish that display the body dormant ventrally, as well as five to seven pairs of branchial staves that separate into the ventral region of the body and pectoral fins that are fused to the head. There are currently 29 endangered species of skates and stingrays in Brazil according to the IUCN Red List. The marketed species of the group are often difficult to identify due to decharacterization, which can be solved using the DNA Barcode analysis, a molecular identification system based on a mitochondrial Cytochrome Oxidase subunit I (COI) DNA sequence that acts as a barcode of the DNA of each species. This system has been successfully used to identify illegally uncharacterised types of products. Thus, the DNA Barcode technique was used to identify species of stingrays and skates that are traded in fishmongers in the state of São Paulo and CEAGESP, in order to identify which species are marketed and if the sale of endangered species currently occurs, as well as validate a technique as a routine tool for quality control related to the group species. 239 specimens were collected, of which 82 were identified as species of stingrays and rays, which were Paratrygon aiereba (40,24%), Gymnura altavela (14,63%), Potamotrygon motoro (13,41%), Hypanus dipterurus (10,98%), Atlantoraja castelnaui (9,76%), Hypanus americanus (4,88%), Atlantoraja platana (2,44%) and Bathytoshia centroura (2,44%), of which B. centroura and P. aiereba, G altavela and A. castel... (Complete abstract click electronic access below) / Mestre

A short sequence of ca. 658-bp of the mitochondrial gene COI was used to investigate its utility as a DNA barcode in the medically important Simuliidae or black flies. Sixty-five species and species complexes were tested. Results indicate that the barcoding gene discriminated among morphologically distinct species with nearly 100% of efficacy and proved useful for revealing cryptic diversity. The DNA barcoding gene was also tested for revealing phylogeographic patterns in the western cordilleran Prosimulium travisi and the Prosimulium neomacropyga species-group. Phylogeographic analyses on these species revealed areas that acted as glacial refugia, postglacial history, cryptic speciation episodes and timing of the events that lead to their present-day distribution. The results obtained concur with other phylogeographic studies on similarly-distributed cordilleran organisms. In conclusion, the barcoding gene not only resulted useful for species discrimination in black flies but also for studies at the population level, providing value-added to this molecular marker.

A short sequence of ca. 658-bp of the mitochondrial gene COI was used to investigate its utility as a DNA barcode in the medically important Simuliidae or black flies. Sixty-five species and species complexes were tested. Results indicate that the barcoding gene discriminated among morphologically distinct species with nearly 100% of efficacy and proved useful for revealing cryptic diversity. The DNA barcoding gene was also tested for revealing phylogeographic patterns in the western cordilleran Prosimulium travisi and the Prosimulium neomacropyga species-group. Phylogeographic analyses on these species revealed areas that acted as glacial refugia, postglacial history, cryptic speciation episodes and timing of the events that lead to their present-day distribution. The results obtained concur with other phylogeographic studies on similarly-distributed cordilleran organisms. In conclusion, the barcoding gene not only resulted useful for species discrimination in black flies but also for studies at the population level, providing value-added to this molecular marker.

The morphological phenotypic characters involving sexual selection but with highly individual variability are likely to challenge the prezygotic isolating mechanism driven by differentiation of mechanical structures. This kind of characters may also puzzle species identification and taxonomy. Therefore clarifying the correlation between the phenotypic variability and biological/non-biological factors becomes necessary in order to understand the role of this phenomenon under natural selection and sexual selection. The Syntomini represents one of the few lepidopterous groups that exhibit highly individual variability in both wing pattern and reproductive structures. The evolutionary and taxonomic significance of this phenomenon, however, has never been studied using modern methods although it has been documented for long. In order to test several hypotheses relevant to phenotypic variability, the present study focuses the phylogenetic relationship of Amata wilemani Rothschild, 1914, a subalpine moth species with extremely high variability in wing coloration and genitalia. The phylogenetic relationship between the three color morphs of A. wilemani and 38 Syntomini species plus 2 Lithosiinae outgroups was reconstructed using fragments of COI, EF1a and 28S. All color morphs of A. wilemani were recovered to form a monophyletic group under all data partitioning strategies with Amata formosensis (Wileman, 1928) or its closely related species in China as the potential sister group. The result of gene network analysis suggests low divergence between haplotypes of A. wilemani. Because no correlation between color morphs, phenology, geographical distribution, altitudinal gradient, and genitalic morphlogy was detected, it is concluded that A. wilemani should be regarded as a single species with high phenotypic variability, and this may suggest existence of intraspecific competition. The present study also found that Amata karapinensis (Strand, 1915), which was synonymized with A. wilemani by previous authors, should be revived. The incongruence between the phylogenetic relationships based on morphological and molecular characters shows a need of a comprehensive phylogenetic study of this highly diverse group.

A species threshold was used to assign unidentified Hymenoptera into DNA barcode Operational Taxa (DbOT) for both an assessment of species richness in rose gall communities and as part of a broad scale survey of genome size diversity. The species threshold of 2.2% was calculated from minimum interspecific divergence of DNA barcode (COI, mtDNA) and internal transcribed spacer region 1 (ITS1, rDNA) sequences from both identified and unidentified Hymenoptera associated with rose galls induced by Diplolepis (Cynipidae). Analysis of both DNA barcodes and ITS1 sequences suggested that several described species of Diplolepis (Cynipidae), Periclistus (Cynipidae), and Torymus (Torymidae) require re-examination to define species boundaries. It was also determined that the total number of DbOTs is higher than previous estimates of species richness of Hymenoptera associated with rose galls induced by Diplolepis. Additionally, genome size estimations were determined for 51 DbOTs from all eight families of Hymenoptera associated with rose galls induced by Diplolepis, five of which did not have any previous genome size estimates. A subsequent large-scale survey of Hymenoptera enabled by the use of the DbOT approach produced genome size estimations for 309 DbOTs from 36 families in 13 superfamilies. It was shown that Hymenoptera do not have smaller genome sizes than other holometabolous orders, and that a parasitoid lifestyle does not appear to constrain genome size. The suggested positive relationship between genome size and development time was investigated by comparing mean genome size of taxa with known or apparent differences in development rate. It was concluded that statistical comparisons between taxa that are grouped in broad categories would be unlikely to detect significant differences in mean genome size because the range of biological features within such categories is highly variable. However, comparisons between interacting groups with narrowly defined development strategies determined that mean genome size was statistically smaller in taxa that obtained resources within a narrow window of opportunity. This result suggests that rapid development in relation to competitors may be important in species of Hymenoptera with higher mortality risk.

I aimed to expand our understanding of community assembly and species co-existence by examining the implications of phylogenetic robustness on metrics describing phylogenetic community structure, as well as the phylogenetic patterns of co-occurring insect species in Churchill, MB. Using a variety of tree reconstruction methods, I found that cytochrome c oxidase subunit I (COI) was able to accurately estimate phylogenetic community structure metrics calculated from a multi-gene phylogeny when using more biologically realistic approaches. This included incorporating known phylogenetic relationships among families, and methods that employ best-fit models of molecular evolution (i.e. Bayesian inference). My second study examined the phylogenetic community patterns of freshwater insects. Overall communities were phylogenetically clustered suggesting environmental filtering, but community structure varied with time, habitat, taxonomic group, and water chemistry (particularly pH and turbidity). My thesis has suggested more robust techniques for calculating phylogenetic community structure, and described patterns of phylogenetic community composition in subarctic freshwater insects. / Natural Sciences and Engineering Research Council of Canada (NSERC), International Barcode of Life (iBOL), Genome Canada, Ontario Genomics Institute, Canadian Foundation for Innovation, Ontario Ministry of Research and Innovation, Churchill Northern Studies Centre, and Aboriginal Affairs and Northern Development Canada.

Accurate identification of pathogens and vectors is essential in epidemiological studies of mosquito-borne pathogens. However, the members of the communis and punctor complexes are difficult to distinguish because they are highly cryptic species, with little to no species-specific morphological characters. The objective of this thesis is to develop molecular tools, including RFLP and DNA barcoding using cytochrome oxidase I (COI), internal transcribed spacer 2 (ITS2) and the intron of ribosomal protein S12 (RPS12) to facilitate identification of the members of these two complexes in Manitoba. A distinct interspecific distance for COI was found between the members of the communis complex included here, and diagnostic RFLP profiles were developed for Oc. communis and Oc. churchillensis. Relatively low average interspecific genetic distances using COI, ITS2 and RPS12 were observed between the members of the punctor complex, indicates no discernable boundaries between these species based on DNA barcoding.