Dissertations / Theses: 'DNA barcoding'

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Zimmermann, Jonas [Verfasser]. "DNA barcoding and eDNA barcoding in diatoms / Jonas Zimmermann." Gießen : Universitätsbibliothek, 2015. http://d-nb.info/106887502X/34.

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Kalianková, Kateřina. "Znakově-orientované metody DNA barcodingu." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2016. http://www.nusl.cz/ntk/nusl-220729.

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This work deals with character-based DNA barcoding. DNA barcoding and character-based DNA barcoding methods are described in the introduction. Another part contains information of method CAOS (Characteristic Attributes Organization) and method BLOG (Barcoding with LOGic). Programs are described in the practical part. The end contains results.

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Pena, Michelle Mendonça [UNESP]. "DNA Barcoding em Utricularia (Lentibulariaceae)." Universidade Estadual Paulista (UNESP), 2015. http://hdl.handle.net/11449/136705.

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A família Lentibulariaceae Rich. é considerada o maior grupo de plantas carnívoras dentre as angiospermas. Utricularia é o gênero de maior riqueza, com aproximadamente 250 espécies. Diversos estudos de identificação baseados em morfologia foram realizados para a família Lentibulariaceae, porém eles se mostram limitados para determinados grupos de espécies. Com base nisso a aplicação do DNA Barcoding pode ser uma importante alternativa. No presente estudo foram utilizadas sequências de DNA dos espaçadores intergênicos cloroplastidiais trnS-trnG e trnL-trnF e também do gene mitocondrial coxI com o objetivo de testá-las com a abordagem DNA Barcoding na diferenciação intraespecífica, interespecífica e entre as seções do gênero Utricularia. Com base nas matrizes de distâncias, a distância intraespecífica média foi de 0,004 para ambos os marcadores cloroplastidiais e de 0,006 para o gene coxI, a distância interespecífica média foi de 0,260 para trnS-trnG, 0,190 para trnL-trnF, 0,043 para coxI e a distância média entre as seções foi de 0,036, 0,029 e 0,025 para trnS-trnG, trnL-trnF e coxI, respectivamente. A análise baseada na árvore de Neighbor-Joining indicou que a maioria das espécies se agruparam em seções de acordo com o proposto para a filogenia do gênero, formando grupos monofiléticos. A eficácia de discriminação interespecífica foi 82% para trnS-trnG e 61% trnL-trnF, a discriminação intraespecífica foi de 36% para trnS-trnG e 23% para trnL-trnF. O gene mitocondrial coxI apresentou 24% de discriminação inter e intraespecífica, com resolução baixa de espécies na árvores de Neighbor-Joining. Esses resultados demonstram que as regiões cloroplastidiais apresentam informações satisfatórias para separação das espécies em clados que corroboram com a filogenia do grupo e que portanto trnS-trnG e trnL-trnF podem ser considerados bons barcodes para o...
The family Lentibulariaceae Rich. is considered the largest group of carnivorous plants among the angiosperms. Utricularia is the richest genus with approximately 250 species. Several studies based on morphological identification have been published for the family Lentibulariaceae, but they are limited regarding some groups of species. Hence, DNA Barcoding may be an important alternative. The present study used DNA sequences of chloroplast intergenic spacers trnS-trnG and trnL-trnF and also the mitochondrial gene coxI in order to test them with the DNA Barcoding approach to intraspecific, interspecific and between sections differentiation in the Utricularia genus. Based on the distance analyses, the average intraspecific distance was 0.004 for both chloroplast markers and 0.006 for the coxI gene, the average interspecific distance was 0.260 to trnS-trnG, 0.190 to trnL-trnF, 0.043 to coxI and the average distance between sections was 0.036, 0.029 and 0.025 to trnS-trnG, trnL-trnF and coxI, respectively. The analysis based on Neighbor-Joining tree indicated that most species were grouped into sections according to the proposed for the phylogeny of the genus, forming monophyletic groups. The efficacy of interspecies discrimination was 82% to trnS-trnG and 61% to trnL-trnF, intraspecific discrimination was 36% to trnS-trnG and 23% to trnL-trnF. The mitochondrial gene coxI showed 24% of inter and intraspecific discrimination, with low resolution of species on trees Neighbor-Joining. These results demonstrate that the chloroplast regions have satisfactory information to separate species in clades that corroborate the phylogeny of the group and therefore trnS-trnG and trnL-trnF can be considered good barcodes for the Utricularia genus

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Pena, Michelle Mendonça. "DNA "Barcoding" em Utricularia (Lentibulariaceae) /." Jaboticabal, 2015. http://hdl.handle.net/11449/136705.

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Orientador: Vitor Fernandes Oliveira de Miranda
Coorientador: Alessandro de Mello Varani
Banca: Marcos Tulio de Oliveira
Banca: Yoannis Domínguez Rodríguez
Resumo: A família Lentibulariaceae Rich. é considerada o maior grupo de plantas carnívoras dentre as angiospermas. Utricularia é o gênero de maior riqueza, com aproximadamente 250 espécies. Diversos estudos de identificação baseados em morfologia foram realizados para a família Lentibulariaceae, porém eles se mostram limitados para determinados grupos de espécies. Com base nisso a aplicação do DNA "Barcoding" pode ser uma importante alternativa. No presente estudo foram utilizadas sequências de DNA dos espaçadores intergênicos cloroplastidiais trnS-trnG e trnL-trnF e também do gene mitocondrial coxI com o objetivo de testá-las com a abordagem DNA "Barcoding" na diferenciação intraespecífica, interespecífica e entre as seções do gênero Utricularia. Com base nas matrizes de distâncias, a distância intraespecífica média foi de 0,004 para ambos os marcadores cloroplastidiais e de 0,006 para o gene coxI, a distância interespecífica média foi de 0,260 para trnS-trnG, 0,190 para trnL-trnF, 0,043 para coxI e a distância média entre as seções foi de 0,036, 0,029 e 0,025 para trnS-trnG, trnL-trnF e coxI, respectivamente. A análise baseada na árvore de "Neighbor-Joining" indicou que a maioria das espécies se agruparam em seções de acordo com o proposto para a filogenia do gênero, formando grupos monofiléticos. A eficácia de discriminação interespecífica foi 82% para trnS-trnG e 61% trnL-trnF, a discriminação intraespecífica foi de 36% para trnS-trnG e 23% para trnL-trnF. O gene mitocondrial coxI apresentou 24% de discriminação inter e intraespecífica, com resolução baixa de espécies na árvores de "Neighbor-Joining". Esses resultados demonstram que as regiões cloroplastidiais apresentam informações satisfatórias para separação das espécies em clados que corroboram com a filogenia do grupo e que portanto trnS-trnG e trnL-trnF podem ser considerados bons "barcodes" para o...
Abstract: The family Lentibulariaceae Rich. is considered the largest group of carnivorous plants among the angiosperms. Utricularia is the richest genus with approximately 250 species. Several studies based on morphological identification have been published for the family Lentibulariaceae, but they are limited regarding some groups of species. Hence, DNA Barcoding may be an important alternative. The present study used DNA sequences of chloroplast intergenic spacers trnS-trnG and trnL-trnF and also the mitochondrial gene coxI in order to test them with the DNA Barcoding approach to intraspecific, interspecific and between sections differentiation in the Utricularia genus. Based on the distance analyses, the average intraspecific distance was 0.004 for both chloroplast markers and 0.006 for the coxI gene, the average interspecific distance was 0.260 to trnS-trnG, 0.190 to trnL-trnF, 0.043 to coxI and the average distance between sections was 0.036, 0.029 and 0.025 to trnS-trnG, trnL-trnF and coxI, respectively. The analysis based on Neighbor-Joining tree indicated that most species were grouped into sections according to the proposed for the phylogeny of the genus, forming monophyletic groups. The efficacy of interspecies discrimination was 82% to trnS-trnG and 61% to trnL-trnF, intraspecific discrimination was 36% to trnS-trnG and 23% to trnL-trnF. The mitochondrial gene coxI showed 24% of inter and intraspecific discrimination, with low resolution of species on trees Neighbor-Joining. These results demonstrate that the chloroplast regions have satisfactory information to separate species in clades that corroborate the phylogeny of the group and therefore trnS-trnG and trnL-trnF can be considered good barcodes for the Utricularia genus
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Stockinger, Herbert. "DNA barcoding of arbuscular mycorrhizal fungi." Diss., lmu, 2010. http://nbn-resolving.de/urn:nbn:de:bvb:19-114870.

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deWaard, Jeremy Ryan. "Forest biomonitoring, biosecurity and DNA barcoding." Thesis, University of British Columbia, 2010. http://hdl.handle.net/2429/30496.

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The economic, social and biological value of our forests makes their sustainability essential to our well-being. To ensure their long-term health, it is critical to regularly and effectively monitor their inhabitants, as well as to detect non-indigenous species early and accurately. These programs rely on the precise diagnosis of species, which can be complicated for terrestrial arthropods by sizeable trap samples, damaged specimens, immature life stages and incomplete taxonomy. The recent advent of DNA barcoding, a technique that differentiates species using sequence variation in a standard gene region, shows tremendous promise for circumventing these obstacles. This dissertation evaluates the integration of barcoding into forest arthropod biomonitoring and biosurveillance programs with several investigations of nocturnal moths (Lepidoptera) in British Columbia, Canada. Barcode reference libraries are constructed for looper moths (Geometridae) and Lymantria (Erebidae) tussock moths, and are determined to successfully discriminate species in over 93% and 97% of cases, respectively. The libraries demonstrate how barcoding might enhance biosurveillance programs by flagging two new records for geometrid moths, and by successfully diagnosing 32 intercepted tussock moth specimens. These two libraries, and a multi-gene phylogeny constructed for Geometridae, are used to conduct faunal inventories in modified forest systems, and investigate the influence of disturbance on three levels of moth diversity—species, genetic, and phylogenetic. A first level inventory of Stanley Park, Vancouver, produces a preliminary list of 190 species, the detection of four new exotic species, and the discovery of two potentially cryptic species. Surveys conducted across several harvest treatments at two silvicultural research forests display no evidence of increased diversity at intermediate disturbance levels, but do reveal a correlation between species and genetic diversity. And lastly, three levels of moth diversity are estimated in ponderosa pine systems that differ widely in attack by Dendroctonus bark beetles, and demonstrate a negative association between species diversity and tree mortality. In combination, all projects suggest that DNA barcoding provides several advantages over traditional biosurveillance and biomonitoring, including the ability to rapidly sort specimens, a reduction in specialist time, the detection of species at low density, and the ability to appraise multiple levels of diversity.

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Claro, Felippe Lourenço. "Estudos do DNA repetitivo no gênero Eigenmannia." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/41/41131/tde-24032014-105922/.

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O DNA repetitivo constitui uma fração considerável do genoma de muitos organismos eucarióticos. Composto tanto por sequências funcionais, como os genes ribossômicos, quanto não codificantes, como é o caso dos elementos transponíveis, mini/microssatélites e o DNA satélite, essa porção do genoma tem sido amplamente utilizada como objeto de estudo, uma vez que sequências repetitivas podem estar associadas, por exemplo, a processos de diferenciação sexual. Esses estudos têm auxiliado tanto na melhor compreensão da dinâmica dessas regiões cromossômicas, como salientado a importância, a conservação e a evolução da porção repetitiva no genoma. O gênero Eigenmannia (Gymnotiformes, Sternopygidae) compreende espécies crípticas do ponto de vista morfológico que exibem variação no número cromossômico e podem apresentar sistemas sexuais XY ou ZW nos quais os elementos do par sexual diferem pela presença de blocos heterocromáticos maiores do que os encontrados em cromossomos autossomos, ou sistemas múltiplos envolvendo translocação Y-autossomo. O presente trabalho tem por objetivos o estudo sobre do gene Citocromo Oxidase I (COI), de forma a verificar a capacidade discriminatória desse gene mitocondrial e sugerir possíveis espécies dos então cariomorfos do gênero Eigenmannia no estado de São Paulo, continuidade do estudo do DNA repetitivo no gênero Eigenmannia, tanto de regiões funcionais do genoma, no caso o gene ribossômico 5S, bem como de elementos transponíveis, permitindo assim uma melhor compreensão sobre a distribuição, conservação nos cariomorfos e verificar sua eventual participação no processo de diferenciação não só de cromossomos sexuais, mas também na evolução cariotípica do grupo. Os resultados obtidos com o gene COI, assim como aqueles obtidos pelo gene ribossômico 5S evidenciam distâncias genéticas consistentes com a hipótese de que os cinco cariomorfos possam ser considerados como espécies distintas. Além disso, a hibridação in situ do gene ribossômico 5S forneceu uma nova evidência para a fusão cromossômica que deu origem ao cromossomo sexual Y, já descrita na literatura, enquanto que a hibridação de sequências teloméricas não forneceu evidências de processos de fusão recentes envolvendo os cariomorfos. Com relação aos elementos transponíveis foi possível verificar padrões distintos nos elementos TC1 e Rex1 no que diz respeito às sequências, uma vez que o elemento TC1 delimitou dois grandes grupos o que pode indicar uma invasão simultânea nos grupos e no retrotransposon Rex1 a invasão tenha ocorrido em um ancestral comum a todos os cariomorfos
The repetitive DNA constitutes a considerable fraction of the genome of many eukaryotic organisms. Compound by both functional sequences, such as ribosomal genes, and non-coding, such as transposable elements, mini / microsatellite DNA and the satellite, this portion of the genome has been widely used as a study object, since the repetitive sequences may be associated with, for example, the processes of sexual differentiation. These studies helped to understand the dynamics of these chromosomal regions, pointing the importance, conservation and evolution of the repetitive portion of the genome. The genus Eigenmannia (Gymnotiformes, Sternopygidae) comprises a morphological cryptic species that exhibit variation in chromosome number and may have sexual XY or ZW systems in which the elements of sexual pair differ by the presence of heterochromatic blocks larger than those found in chromosomes autosomes, or systems involving multiple Y-autosome translocation. The present work aims to study the gene Cytochrome Oxidase I (COI) to verify the discriminatory capacity of this mitochondrial gene and suggest possible species of the so called karyomorphs of the genus Eigenmannia in the state of São Paulo. The study of repetitive DNA in Eigenmannia genus, includes 5S ribosomal gene and transposable elements, thus allowing a better understanding of the distribution, conservation in karyomorphs and verify their possible participation in the process of differentiation not only of sex chromosomes, karyotypic evolution but also in the group. The results obtained with the COI gene, as well as those obtained by the 5S ribosomal gene demonstrate genetic distances consistent with the hypothesis that the five karyomorphs can be regarded as separate species. In addition, in situ hybridization of ribosomal 5S gene provided new evidence for chromosomal fusion which led to the Y sex chromosome, as described in the literature, whereas hybridization of telomeric sequences did not provide evidence of recent fusion events involving the karyomorphs. Regarding transposable elements, it could be verified distinct sequence patterns between TC1 and Rex1 elements, since the TC1 element delimited two groups which may indicate a simultaneously invasion in those groups and retrotransposon Rex1 invasion has occurred in a common ancestor to all karyomorphs

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Brabencová, Klára. "Analýza mitochondriálních genů živočichů pro DNA barcoding." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2014. http://www.nusl.cz/ntk/nusl-220849.

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The aim of this work is a literature review on the topic of the mitochondrial genome and DNA barcoding, building a dataset of mitochondrial sequences from GenBank database and creatione of a software function for extraction of individual genes that are present in the mitochondrial genome. This function was developed in Matlab. DNA barcoding is a method that uses short DNA sequence of mitochondrial genome for identification of species. There is no comprehensive work examining the appropriateness of different mitochondrial genes. This aim investigates the potential of other mitochondrial genes and evaluate their effectiveness for DNA barcoding and calculation of intra-and interspecific variability.

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Kruger, Åsa. "DNA-Barcoding Identification of Medicinal Roots from Morocco." Thesis, Uppsala universitet, Systematisk biologi, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-141818.

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Fogelström, Anna. "DNA barcoding of freshwater fishes in Matang, Malaysia." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-255333.

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Ibrahimovic, Ida. "DNA Barcoding på Växter : Hur kan man använda genetisk barcoding i olika biologiska fält och i den gymnasiala undervisningen?" Thesis, Linköpings universitet, Institutionen för fysik, kemi och biologi, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-154300.

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Syftet med litteraturstudien är att sammanfatta vilken gensekvens som används vid genetisk barcoding av växter och hur väl metoden i fråga tillämpas i tre biologiska yrkesområden: dietanalyser i ekologin, analys av pollensporer i forensisk biologi samt analys av uråldrigt DNA (ancient DNA) i paleontologin. Vidare var det även av intresse att se hur genetisk barcoding kan användas i den gymnasiala undervisningen och hur väl den passar in med de svenska styrdokumenten för skolan. Hur elever har gynnats av den valda metoden samt vilka begränsningar som har uppstått har också berörts. Litteraturstudien baseras på vetenskapliga artiklar som har sökts fram med de nedan listade nyckelorden. Resultaten visar att en kombination av gensekvenser, däribland rbcL, matK, trnH-psbA och ITS, fungerar bäst vid identifiering av växter. I dagsläget är genetisk barcoding fortfarande i utvecklingsfasen, där metoden begränsas av antalet referenssekvenser i databaserna, vilket gör det svårt att utesluta morfologiska identifieringsmetoder i de tre yrkesområdena. Vid användning av barcoding i den gymnasiala undervisningen visar det sig att det stämmer väl överens med de svenska styrdokumenten och ökar elevers intresse för de naturvetenskapliga ämnena, då de kan bidra med värdefull forskning genom tillägg av referenssekvenser i databaserna. De största begränsningarna är att det blir ett stort arbetslass för läraren, att läraren i fråga måste vara bekväm med de olika laboratiska momenten och att skolan ska ha tillgång till nödvändig apparatur.
The purpose of the literature study is to conclude which gene sequences are being used in DNA barcoding on plants and how the method in question is being used in three different biological occupations: diet analysis in ecology, analysis of pollen in forensics and analysis of ancient DNA (aDNA) in paleontology. Further it was also of interest to study how DNA barcoding can be used in high school settings and how the method correlates with the Swedish curriculum. How pupils have benefited from the chosen method and what limitations have arisen have also been touched upon. This literature study is based on scientific articles that have been sought with the keywords listed below. The results show that a combination of gene sequences, including rbcL, matK, trnH-psbA and ITS, works best in plant identification. At present, genetic barcoding is still in the developmental phase, where the method is limited by the number of reference sequences in the databases, which makes it difficult to exclude morphological-based methods in the three occupational fields. When using barcoding in upper secondary education it turns out that it’s in good agreement with the Swedish curriculum and increases the students' interest in the scientific subjects, since they can contribute with genuine research when adding reference sequences in the databases. The main limitations are the workload for the teacher, the teacher in question must be comfortable with the different laboratory steps and that the school must have access to necessary equipment.

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GALIMBERTI, ANDREA. "DNA barcoding: a link between basic and applied science." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2011. http://hdl.handle.net/10281/18920.

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DNA barcoding is a recent and widely used molecular-based identification system that aims to identify biological specimens, and to assign them to a given species. However, DNA barcoding is even more than this, and besides many practical uses, it can be considered the core of an integrated taxonomic system, where bioinformatics plays a key role. Quite soon since its development (in 2003) it became clear that DNA barcoding was suitable for two different purposes: (i) the molecular identification of already described species and (ii) the discovery of undescribed species (the so called ‘DNA taxonomy’). However, such a method has generated a vast debate in the scientific community, which has been from the beginning, deeply divided into pros and cons. The main objective of this research project was to investigate the strength of coherence reached in combining a standardized molecular methodology with classical biological information (e.g. morphology, ecology, host specificity), toward the synthesis of an integrated approach to taxonomy. In order to satisfy this requirement, nine case studies encompassing a wide panel of taxa (i.e. animal, plant and environmental samples) subjected to different taxonomic uncertainties or potentially dealing with economical, conservation or health implications (e.g. food traceability, parasites infectiveness, etc.) have been investigated. More than 500 hundreds biological samples were collected directly in the field or retrieved from museum, herbariums or other institutional collections, allowing to create a synergic network among different disciplines and research fields. Standardization in the collection and processing of biological samples, as well as in the bioinformatic approaches used to manage and analyse molecular data has been a fundamental point in the experimental workflow we adopted. The results obtained with our analyses clearly showed that DNA barcoding represents a powerful tool for taxonomy and it can act as an effective supporting tool for the traceability of food products, for the diagnosis of endoparasites and for the characterization of environmental biodiversity. Although some limitations arise from the incomplete coverage of the existing diversity, the inherent characteristics of the molecular markers adopted as barcodes and other factors, the method showed to be more flexible than expected.

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Rivera, Karol Geraldina. "Taxonomy, systematics and DNA barcoding of selected Penicillium groups." Thesis, University of Ottawa (Canada), 2009. http://hdl.handle.net/10393/28200.

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Cytochrome c oxidase subunit 1 (Cox 1) is the barcode for many animal groups, protists, and macroalgae. Previously in fungi, the efficiency of Cox 1 as a genetic marker was only analysed in Penicillium subgenus Penicillium and Leohumicola spp. In this thesis, two species isolated from the intestinal tracts of caterpillars from Costa Rica, and two potential species complexes, P. sclerotiorum and P. oxalicum belonging to Penicillium subgenus Aspergilloides and Furcatum, were studied using the Genealogical Concordance Concept (Gee) recognition criterion and barcoding methods. Analyses with beta-tubulin (BenA), the nuclear internal transcriber spacer (ITS) region, Cox 1, translation elongation factor 1-alpha (TEF1-alpha), and calmodulin (CaM) revealed that the Penicillium species isolated from Costa Rica are undescribed, and that P. sclerotiorum is a complex of seven phylogenetic species (including the Costa Rican species) that fit the prevailing morphological concept of P. sclerotiorum. The phylogenetic species were compared and newly discovered diagnostic morphological characters were used to create a taxonomic key to the species of the complex. The new species are formally described as P. guanacastense, P. mallochii, P. krugii, P. cainii, P. jacksonii and P. ciebiessum. Analyses of multiple strains of P. oxalicum revealed that it is a single phylogenetic species, despite having a world wide distribution, an unusually high degree of morphological variation, and a diversity of ecological roles. Cox1 proved to be a good barcode for identifying the selected Penicillium groups, and provided a species level resolution of 83.3%. ITS provided the same resolving ability. BenA (91.7%), TEF1-alpha (100%) and CaM (100%) provided a higher species level resolution than Cox1, but BenA, TEF1-alpha, and CaM were difficult to amplify or sequence for some Penicillium groups. A secondary barcode marker is suggested in addition to Cox1 for Penicillium.

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Manton, Erin Rebecca. "DNA barcoding the vascular plant flora of southern British Columbia." Thesis, University of British Columbia, 2016. http://hdl.handle.net/2429/60195.

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DNA barcoding is a tool for rapidly identifying species based on short, standardized sequences of DNA, for example in situations where this may be difficult using morphology alone. I assembled a core DNA barcode reference library for southern British Columbia, home to ~54% of the vascular plant species in Canada, using the core plastid barcode loci rbcL and matK, and assessed its utility for identifying species in this region. The library comprises 4,812 sequences obtained from field-collected and herbarium tissue samples, supplemented with sequences downloaded from BOLD and GenBank, with at least one sequence for 75.4% of the vascular plant species occurring below 50°N in British Columbia. Sequence recoverability was significantly higher for rbcL than for matK (93.5% and 80.2%, respectively), and only marginally lower for both markers when using herbarium specimens (90.5% for rbcL and 77.8% for matK), which demonstrates the future feasibility of using museum specimens for completing a southern BC barcode reference library. As a proxy for assessing marker effectiveness, I scored resolution at the level of species and genus using tests of monophyly for Neighbour Joining trees, and performed sequence similarity searches with BLASTn analyses, both for each locus separately and for a dual-locus marker system (rbcL+matK; scored as a cumulative percentage in the BLAST analyses). Ignoring species represented by singleton sequences, the highest overall level of discrimination (66.9% of species and 91.6% of genera) was achieved for BLASTn analysis of rbcL+matK together. This work represents a significant contribution to a nation-wide barcode database, and provides a preliminary platform for ecological and other applications requiring species identification, where traditional methods are not feasible.
Science, Faculty of
Botany, Department of
Graduate

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Cooke, Tenielle Monique. "DNA barcoding of forensically important flies in the Western Cape." Master's thesis, University of Cape Town, 2016. http://hdl.handle.net/11427/20768.

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One of the central applications of forensic entomology is the determination of the post mortem interval (PMI) from arthropod evidence associated with a corpse. Estimations of the PMI are based on succession and developmental patterns of specific species that visit the body. As first colonisers, Calliphoridae (blow flies) are often used by forensic entomologists to determine the PMI however, developmental rates of visiting fauna differ substantially which makes correct species identification vital. Traditional methods of identification which assign species based on keys that capitalise on morphological differences are insufficient for closely related species, especially during immature stages of the lifecycle or when the specimen is damaged. Molecular identification such as DNA barcoding has therefore become a popular method of identifying species. DNA barcoding characterises species by sequencing and analysing specific regions in the genome. This technique has been used to characterise species in various countries including parts of South Africa. Its application has also been demonstrated in a forensic setting but data for the Western Cape is minimal. This study therefore aimed to assess the utility of DNA barcoding for species level determination of four blow fly species common to the Western Cape of South Africa (Chrysomya chloropyga, Chrysomya albiceps, Chrysomya marginalis, and Lucilia sericata) as well as its ability to identify immature specimens. Ten adult specimens from each species were morphologically and molecularly identified using microscopy and DNA barcoding respectively. The standard DNA barcode, cytochrome c oxidase subunit I (COI) and a secondary marker, the second internal transcribed spacer (ITS2) were analysed. Phylogenetic analyses for both barcodes showed high interspecific divergence values which are desirable for species level differentiation by DNA barcoding. COI sequences from adult flies were also submitted and searched against BOLD for identification and only genus level identity could be achieved, indicating that, COI alone may be insufficient to discriminate between closely related species. DNA sequences from the adult specimens were then used as reference sequences for identification of seven unknown immature specimen using DNA barcoding of both COI and ITS2. Sequence similarity was assessed and identity was assigned based on >98% similarity scores, and all immatures were successfully identified. The use of more than one DNA marker to complement morphological data ensures higher confidence of species level identification. This method provides a reliable and consistent tool for entomologists to use for species identification which results in higher levels of accuracy in PMI estimations.

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Jaafar, Tun Nurul Aimi Mat. "DNA barcoding and population genetic structure of Malaysian marine fishes." Thesis, Bangor University, 2014. https://research.bangor.ac.uk/portal/en/theses/dna-barcoding-and-population-genetic-structure-of-malaysian-marine-fishes(79b4a0eb-48cf-46a1-b44f-8b09d5eed6c4).html.

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The development of a widely available global database of DNA barcodes has been proposed as a species-identification tool for large taxonomic assemblages of animals. The approach has particular value in revealing cryptic species, which typically have high incidence in marine environments. Despite the wealth of DNA barcode data for fish from many temperate regions, there are relatively few such data available for SE Asian waters. In Chapter 2, an initial reference DNA barcode library was produced for the marine fish Family Carangidae, one of the most commercially-important families from the Indo-Malay Archipelago (IMA). Thirty-species of Family Carangidae were collected from the IMA to examine the accuracy of DNA barcoding concepts and protocols, such as ease of amplification of the barcode gene cytochrome c oxidase I (CO/), and implementation of the 'barcoding gap' concept for species delimitation. All described species formed monophyletic clusters in Neighbour-joining phylogenetic tree, although three species representing complexes of six potential cryptic species were detected. Within 723 individuals, three described species (Atule mate, Selar crumenophthalmus and Seriolina nigrofasciata) exhibited conspecific divergences up to ten times greater (4.32-4.82%) than mean estimates (0.24-0.39%) indicating a discrepancy with assigned morphological taxonomic identification, and the existence of cryptic species within the IMA. Additional conspecifics sequences available from other geographical regions revealed the existence of several more complexes of potentially cryptic species outside the IMA. However, to explain the hypothesis of species richness in the IMA, it is necessary to sample the whole family across their broad geographic range. Such information will contribute to the development of an integrated taxonomic framework, thus informing management strategies for subsequent conservation and management of Carangidae. Additionally, the results will provide greater understanding of recruitment, and processes driving species diversification in the IMA.

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Abdullah, Mansour Taleb. "Conserving the biodiversity of Kuwait through DNA barcoding the flora." Thesis, University of Edinburgh, 2017. http://hdl.handle.net/1842/28786.

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Biodiversity across the globe is threatened. Rapid surveying and monitoring techniques are required to understand the origin of the threats to biodiversity and to enable conservation actions to be undertaken. Kuwait is an arid desert country with a small flora of only 402 species. This flora is endangered by environmental factors, overgrazing, and human activities. DNA barcoding the flora and using Next Generation Sequencing (NGS) technologies allowed us to identify plants to species level, conduct a molecular taxonomic revision, and distinguish plant diversity found in soil environmental DNA samples. After investigating the discriminatory power of five commonly used DNA markers from plastid (matK, rbcL, trnH-psbA, trnL) and a nuclear genome (ITS2) on four largest genera of the flora using phylogenetics reconstruction tree based methods, two barcoding markers (rbcL and ITS2) were assigned to build a DNA reference library of the flora. Furthermore, the DNA reference library was tested to identify the plant diversity found below-ground level and comparing it with that above-ground, using environmental soil samples collected from both species rich and poor habitats in Kuwait by applying high-throughput sequencing methods. The DNA database provided in this study could be used as a reference library for the identification process and contribute towards the future of molecular taxonomy, biodiversity and ecological research in Kuwait.

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Deon, Geize Aparecida. "CITOGENÉTICA COMPARATIVA E DIFERENCIAÇÃO GENÉTICA EM Neoplecostomus (SILURIFORMES: LORICARIIDAE) EM AFLUENTES DO RIO PARANÁ." Universidade Estadual de Ponta Grossa, 2017. http://tede2.uepg.br/jspui/handle/prefix/2385.

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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
Loricariidae é uma das maiores famílias de peixes de água doce com 931 espécies válidas distribuídas em 100 gêneros. As espécies pertencentes a essa família são popularmente conhecidas como cascudos que possuem um corpo achatado, coberto por placas ósseas, e boca ventral em forma de ventosa. Pertencente à família Loricariidae e a subfamília Neoplecostominae, o gênero Neoplecostomus compreende espécies de tamanho pequeno que habitam riachos da região sul e sudeste do Brasil. O gênero apresenta interesse em estudos genéticos, visto que é composto por espécies vágeis e que, por raramente migrarem, podem acumular diferenças genéticas entre populações. Das dezesseis espécies válidas descritas até o momento para este gênero, oito foram descritas para a bacia do rio Paraná e há evidências da ocorrência de novas espécies para esta bacia. Sendo assim, este estudo teve como objetivo estudar a diferenciação cariotípica e a diversificação genética no gênero Neoplecostomus das bacias hidrográficas dos rios Iguaçu, Itararé, Cinzas e Tibagi com vistas ao entendimento da evolução cariotípica e descrição da biodiversidade. Para isso, foram realizas coletas em quatro localidades: rio Pinhão (Neoplecostomus sp. 1), rio Samambaias (Neoplecostomus cf. botucatu), rio das Pedras (Neoplecostomus sp. 2) e rio São João (Neoplecostomus yapo). Os dados citogenéticos revelaram um número diploide de 54 cromossomos para as quatro populações, poucas regiões heterocromáticas e sítios cromossomo independentes para os genes ribossomais 5 e 18S. Os resultados citogenéticos evidenciam uma alta estabilidade cariotípica, observado também na subfamília Neoplecostominae. Foram realizadas análises moleculares envolvendo o gene mitocondrial citocromo c oxidase subunidade 1 (COI) e todas as distâncias genéticas foram superiores a 4,7 %. Além disso, contrários à estabilidade cromossômica, os dados de distância genética evidenciaram ausência de fluxo gênico e estruturação populacional, além de sugerir uma provável espécie de Neoplecostomus não descrita para o rio Pinhão, bacia do rio Iguaçu.
The Loricariidae family is one of the largest families of freshwater fishes, with 931 species distributed in 100 genera. Loricariidae members are popularly known as armored catfishes and characterized by a depressed body, covered by bony plates and a ventral sucker mouth. Inside the subfamily Neoplecostominae, the genus Neoplecostomus comprises small species that inhabit streams of south and southeast regions of Brazil. This genus is interested in genetic studies because they rarely migrate and can accumulate genetic differences between populations. Of the sixteen valid species described so far for this genus, eight were described for the Paraná river basin and there is evidence of new species occurring in this basin. Therefore, the objective of this study was to analyze the karyotype differentiation and genetic diversification in the genus Neoplecostomus from Iguaçu, Itararé, Cinzas and Tibagi river basins, with the goal of understand the karyotype evolution and biodiversity. The specimens were captured at four localities: Pinhão river (Neoplecostomus sp. 1), Samambaias river (Neoplecostomus cf. botucatu), Pedras river (Neoplecostomus sp. 2) and São João river (Neoplecostomus yapo). Cytogenetic data revealed a diploid number of 54 chromosomes to the four populations, few heterochromatic regions and independent chromosome sites for 5S and 18S ribosomal genes. The cytogenetic results revealed a high karyotypic stability, which is also observed for the subfamily Neoplecostominae. Also, were performed molecular analyzes by mitochondrial cytochrome c oxidase subunit 1 gene (COI) amplification, where all genetic distances were higher than 4.7%. In addition, contrary to chromosome stability, genetic distance data also showed absence of gene flow, population structure and suggested a probable Neoplecostomus species not described yet for Pinhão river at Iguaçu basin.

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Capelli, Lisa. "DNA barcoding taxonomy and diversity of the Mediterranean sharks and rays." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2012. http://amslaurea.unibo.it/3214/.

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Elasmobranchs are an important by-catch of commercial fisheries targeting bony fishes. Fisheries targeting sharks are rare, but usually almost all specimen bycatched are marketed. They risk extinction if current fishing pressure continues (Ferretti et al., 2008). Accurate species identification is critical for the design of sustainable fisheries and appropriate management plans, especially since not all species are equally sensitive to fishing pressure (Walker & Hislop 1998). The identification of species constitutes the first basic step for biodiversity monitoring and conservation (Dayrat B et al., 2005). More recently, mtDNA sequencing has also been used for species identification and its use has become widespread under the DNA Barcode initiative (e.g. Hebert et al. 2003a, 2003b; Ward et al. 2005, 2008a; Moura et al 2008; Steinke et al. 2009). The aims of this work were: 1) identify sharks and skates species using DNA barcode; 2) compare species of different provenance; 3) use DNA barcode for misidentified species. Using DNA barcode 15 species of sharks (Alopias vulpinus, Centrophorus granulosus, Cetorhinus maximus, Dalatias licha, Etmopterus spinax, Galeorhinus galeus, Galeus melastomus, Heptranchias perlo, Hexanchus griseus, Mustelus mustelus, Mustelus punctulatus, Oxynotus centrina, Scyliorhinus canicula Squalus acanthias, Squalus blainville), 1 species of chimaera (Chimaera monstrosa) and 21 species of rays/skayes (Dasyatis centroura, Dasyatis pastinaca, Dasyatis sp., Dipturus nidarosiensis, Dipturus oxyrinchus, Leucoraja circularis, Leucoraja melitensis, Myliobatis aquila, Pteromylaeus bovinus, Pteroplatytrygon violacea, Raja asterias, Raja brachyura, Raja clavata, Raja miraletus, Raja montagui, Raja radula, Raja polystigma, Raja undulata, Rostroraja alba, Torpedo marmorata, Torpedo nobiliana, Torpedo torpedo) was identified.

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20

Safina, Melania. "DNA barcoding of Pleuronectiformes: in silico analysis and development of markers." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2016. http://amslaurea.unibo.it/12259/.

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DNA barcoding is a method used for the identification and discovery of animal species. It usually involved a 648 base pair fragment of the mitochondrial cytochrome c oxidase subunit I, known as COI. This work is focused on the study of the genetic identification in the families belonging to the order Pleuronectiformes, commonly known as flatfish, and the accuracy of the genetic marker most used for the study of their DNA barcodes. The results indicate possible existence of taxonomical mistakes because several families do not show a gap between maximum intraspecific distance - which is the maximum distance within a specie - and the minimum interspecific distance - which is the minimum distance between a species and its nearest neighbor (NN), meaning that the marker in use cannot reliably distinguish among those species. This study uses a bioinformatic approach to design new Pleuronectiformes barcodes and compares their coverage and resolving power with that of existing barcodes. The new primers, proposed by the program EcoPrimer, are based on two indices that estimate the resolution capacity of the barcodes and the taxonomic coverage of them, for the amplification. The performances of both barcoding regions already in use (COI and 16 rDNA genes), and the new primer pairs designed, were performed through a ‘in silico PCR’. The results show that the new primer pairs, located in a different regions of 16S rDNA gene compared to the universal barcode region used in fishes, present best resolution capacity and taxonomic coverage than the others already in use. This is an essential complement for future barcoding studies.

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SILVA, Patrícia Corrêa da. "Integração dos estudos cromossômicos e DNA barcoding em Rhamphichthys (Pisces: Gymnotiformes)." Universidade Federal do Pará, 2016. http://repositorio.ufpa.br/jspui/handle/2011/9053.

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CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
CNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico
FAPESPA - Fundação Amazônia de Amparo a Estudos e Pesquisas
A Ordem Gymnotiformes é composta por 219 espécies válidas, que estão distribuídas em cinco famílias. Os gêneros mais investigados são Eigenmannia e Gymnotus. Nosso trabalho concentrou-se na família Rhamphichthyidae, gênero Rhamphichthys que, assim como os demais Gymnotiformes, apresentam maior abundância e diversidade na região Amazônica. Foram realizadas coletas nos municípios de Abaetetuba, Barcarena e Belém (Pará) e em Tefé, Reserva Ecológica de Mamirauá (Amazonas), com objetivo de melhor definir as espécies, através da integração de dados citogenéticos clássicos, citogenômicos (através das sondas de sequências repetitivas de DNA) e do DNA Barcoding e assim compreender a evolução deste gênero de peixes na Amazônia. Foram identificados um novo citótipo para o gênero R. rostratus com a presença de cromossomos B e fórmula cariotípica FC=48m/sm+2st/a+(5-10)B, um novo citótipo da região do Amazonas, Rhamphichthys sp. FC = 44m/sm +6st/a, e também de R. marmoratus, FC = 46+4st/a no estado do Pará. A análise das sequências repetitivas nos novos citótipos demonstrou que as sondas de 18S são coincidentes com as regiões de constrição secundárias que são marcadas com nitrato de prata na técnica de coloração clássica da NOR. As sondas de DNA 5S marcam sítios múltiplos, deixando evidente que a evolução da família de genes ribossomais ocorre de maneira independente, pelo menos no gênero Rhamphichthys. Os retroelementos REX1 e REX3 marcaram de forma dispersa pelo genoma, como já foi descrito na literatura para outros peixes. O elemento REX1 marca ainda a região de constrição secundária em R. rostratus, o que também já foi descrito em outras espécies de peixes que habitam ambientes poluídos, expostos a estresses ambientais e também em indivíduos híbridos. A análise de DNA barcoding permitiu a construção de uma árvore bayesiana, que está de acordo com os dados de citogenética. Assim, as populações de R. rostratus com e sem cromossomos B constituem taxa distintos. Por sua vez, a amostra de Mamirauá, aqui denominada Rhamphichthys sp. por não haver sido descrita formalmente, é mais similar tanto nos dados cariotípicos como na análise de barcoding a R. hanni do Sudeste brasileiro. Nossos dados apontam para um número subestimado de espécies em Rhamphichthys, o que reforça a necessidade de uma revisão taxonômica para o gênero.
The Order Gymnotiformes is composed by 219 valid species, which are distributed in five families. The most investigated genera are Eigenmannia and Gymnotus. Our work focused on family Rhamphichthyidae, genus Rhamphichthys that, like other Gymnotiformes, present greater abundance and diversity in the Amazon region. Sampling was carried out in the municipalities of Abaetetuba, Barcarena and Belém (Pará) and Tefé, Ecological Reserve Mamirauá (Amazonas), in order to better define the species, through the integration of classical cytogenetic data, cytogenomic analysis (probes for repetitive DNA sequences) and DNA Barcoding and thus understand the evolution of this fish in the Amazon. A new karyotype was identified for R. rostratus with the presence of B chromosomes and karyotype formula FC = 48m / sm + 2st / a + (5-10) B, as well as a new cytotype from the Amazon region, in Rhamphichthys sp. FC = 44m / sm + 6st / a, and also in R. marmoratus, FC = 46 + 4st / a in the state of Pará. The analysis of repetitive sequences in the new cytotypes demonstrated that probes 18S coincided with the regions of constriction secondary that are marked with silver nitrate in the classical NOR staining technique. The DNA probes 5S mark multiple sites, letting clear that the evolution of the ribosomal gene family is independent, at least in the genus Rhamphichthys. Retroelements REX1 and REX3 marked in a dispersed fashion throughout the genome, as already described in literature for other fishes. The REX1 element also marks the secondary constriction in R. rostratus, which has also been described in other species of fishes that inhabit polluted environments, exposed to environmental stresses and also in hybrid individuals. The barcoding DNA analysis allowed the construction of a Bayesian tree, which is in agreement with the cytogenetic data. Thus, populations of R. rostratus with and without B chromosomes are separate taxa. In turn, the sample from Mamirauá, herein called Rhamphichthys sp., since it was not been formally described, it is more similar in both karyotypic data as the barcoding analysis with R. hanni from southeastern Brazil. Our data let clear that the number of species in Rhamphichthys is underestimated, which reinforces the need for a taxonomic revision of the genus.

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Pappalardo, Anna Maria. "DNA barcoding e biodiversità molecolare: casi di studio nel settore ittico." Doctoral thesis, Università di Catania, 2012. http://hdl.handle.net/10761/1171.

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A fronte della globalizzazione degli scambi commerciali, dei cambiamenti climatici e degli appelli a tutela della biodiversità, la rapida identificazione delle specie costituisce, a livello mondiale, una necessità. L utilizzo di una breve sequenza di DNA per standardizzare l identificazione degli organismi ha recentemente conosciuto gli allori della cronaca sotto l intrigante termine di DNA barcoding . Un segmento di circa 650bp del gene della citocromo ossidasi I mitocondriale (COI) è stato proposto come miglior potenziale barcode, almeno per il regno animale, dove si è potuta verificarne l efficacia in diversi taxa, e gran parte delle specie studiate (>94%) possiede barcode ben differenziati, con bassa variabilità intraspecifica ed alta divergenza tra taxa strettamente imparentati. L innovativa metodologia proposta potrebbe rivelarsi utile in numerosi settori scientifici, quali la biologia evoluzionistica, l ecologia, la filogeografia e la biologia della conservazione, ed avere numerosi riscontri applicativi, soprattutto nell ambito della sicurezza alimentare. In particolare nel settore ittico, la frequente sostituzione di tranci o filetti di specie ittiche pregiate con carni di esemplari di minor valore o l utilizzo di nomi generici usati per etichettare i prodotti della pesca ha messo in luce la necessità di sviluppare sistemi di tracciabilità molecolare. L impossibilità di ricorrere al riconoscimento morfologico quando il pesce è sottoposto a toelettatura richiede lo sviluppo di nuovi approcci analitici, basati sullo studio del DNA e il DNA barcoding si è rivelato un promettente strumento diagnostico alternativo ai tradizionali metodi di indagine e a quelli basati sull analisi delle proteine. L obiettivo principale di questo studio è stato quello di testare l efficacia e l applicabilità del gene della COI come DNA barcode per l identificazione molecolare di specie nel settore ittico sia in campo applicativo (tracciabilità molecolare), sia nella ricerca di base (tassonomia, identificazione di stock ittici). A tal scopo la prima fase della ricerca ha previsto la compilazione di una biblioteca di riferimento di sequenze di DNA barcode, partendo da esemplari la cui identità fosse già stabilita e un successivo screening su diverse specie ittiche di interesse commerciale, anche come prodotti trasformati, tra le più soggette a rischio di frode (es. pesce spada, pesci piatti). Le sequenze della COI e quelle del dominio ipervariabile della regione di controllo mitocondriale, 5 -dloop, (marker popolazione specifico comunemente utilizzato) di esemplari di Xiphias gladius (pesce spada) provenienti da diverse aree geografiche, sono state analizzate e i dati ottenuti hanno mostrato che il gene della COI non solo è un efficiente marker specie-specifico, ma è anche in grado, relativamente alla specie X. gladius di discriminare diversi stock ittici (per es. lo stock del Mediterraneo da quelli dei bacini oceanici). Il DNA barcoding è stato anche applicato per l identificazione di specie mesopelagiche della famiglia Myctophidae a partire da stadi larvali, fornendo un utile contributo all identificazione tassonomica, soprattutto nei casi in cui il tradizionale approccio morfologico è risultato difficile e ambiguo. Infine, un preliminare contributo allo studio della strutturazione genetica della specie Engraulis encrasicolus (acciuga) è stato fornito attraverso l analisi del 5 dloop di esemplari di larve campionati nell area Mediterraneo, per i quali è stato possibile definire quattro diverse aree di riproduzione. Dai dati ottenuti si evince chiaramente l efficienza del DNA barcoding come strumento di analisi complementare alla tassonomia tradizionale grazie al suo potere diagnostico come marcatore genetico specie-specifico e in qualche caso stock-specifico e la sua utilità per la tracciabilità genetico-molecolare applicata ai prodotti alimentari del settore ittico.

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Nicolè, S. "BIODIVERSITY ANALYSIS TROUGH DNA BARCODING Applications in agrifood and seafood products." Doctoral thesis, Università degli studi di Padova, 2010. http://hdl.handle.net/11577/3426881.

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The research activity, the results of which are the subject of doctoral dissertation, focused on the potentials of DNA barcoding, a genomic approach that exploits a short DNA sequence, a barcode, from a standardized region of the plastid genome, mitochondrial and chloroplast, as a universal and unique identification marker for animal and plant species. The main goal was to test a new accurate and automatable method for the genetic traceability of agri-food products, both of animal (fish, crustaceans and molluscs) and plant origin (bean and grapevine). First of all, we chose the specimens for the analysis: we selected pure lines of bean (Phaseolus vulgaris L.), clones of grapevine (Vitis vinifera L.) and samples of fish, crustaceans and molluscs purchased in famous GDO or local market in Chioggia e Sottomarina. Regarding the selection of seafood samples to analyze, we proceeded with the collection of the marine species most commonly involved in fraudulent substitutions. The experimental procedure adopted were the genomic DNA isolation from 37 specimens followed by the amplification of three target regions, cox1 (cytochrome oxydase subunit I), cob (apo-cytochrome b) and 16S-rDNA (ribosomal RNA small subunit) genes. Once obtained these data, we proceeded with a sequence similarity search using BOLD and GenBank as reference databases and each of the sequences as query. Overall, the phenetic approach proved to be an efficient tool to ensure the correct detection of seafood composition and thus to control the label information. In fact, for most of the samples it was possible to confirm the origin of the meat declared on the label, except in five situations where it was impossible to establish with no doubt the origin of the samples flagging them as likely falsification cases, voluntary or by accident. Cox1 gene proved to be a valid target for traceability aims, except in three genera, Thunnus, Macruronus and Gadus, where the identification was more problematic. Finally, even if GenBank database still remains the best web tool for forensic purposes, BOLD database proved to be enough rich to allow the correct recognition of almost all the specimens. Regarding plant DNA barcoding, the goal was to test DNA barcoding strategy as a tool to assess the distinctiveness of species and varieties of pure lines and clones. In the case of bean, we selected 54 pure lines of Phaseolus vulgaris species, 24 Italian pure lines, 18 Mesoamerican landraces and 12 Andean landraces, along with a few P. coccineus, P. lunatus and Vigna unguiculata accessions adopted as reference standards and out-types. These samples were characterized by means of the amplification of 7 chloroplast and two nuclear regions followed by the application of a phenetic approach. The procedure confirmed to be a powerful technique to correctly separate different species, whereas at the varietal level it revealed to be scarcely informative to discriminate gene pools and to identify varieties within P. vulgaris. Thus a second approach, the character-based system, was tested and it allowed to detect within P. vulgaris species a total of 16 haplotypes corresponding to as many subgroups, each one made up by Mesoamerican or Andean accessions along with Italian accessions that clustered with one or the other gene pool. Finally, a third case study is represented by V. vinifera and the potentials of DNA barcoding approach to distinguish grapevine cultivars used in the production of wines. We proceeded with the selection of 123 grapevine cultivars along with other 5 species of Vitis (V. rupestris, V. riparia, V. labrusca, V. cinerea e V. berlandieri) adopted as reference standards and out-types. After a preliminary analysis of the chloroplast DNA that resulted to be monomorphic, we decided to shift to the nuclear genome amplifying four ESTs and the GAI1 (gibberellins insensitive-like) gene. The analysis is still ongoing, but the preliminary results lead to think that a few haplotypes exist within V. vinifera and they could be use to resolve frequent cases of synonymies and homonymies in grapevine. Furthermore, an economically valuable application may be the exploitation of these haplotypes cultivar-specific for the genetic traceability of wines to avoid cases of falsification.
L’attività di ricerca, i cui risultati sono oggetto della dissertazione di dottorato, ha riguardato lo studio delle potenzialità applicative del DNA barcoding, una tecnica molecolare volta all’identificazione degli organismi sulla base dei polimorfismi di specifiche sequenze nucleotidiche localizzate nei genomi plastidiale, mitocondriale e cloroplastico. Il progetto di ricerca ha previsto l’impiego di questo approccio per il riconoscimento di specie ai fini della tracciabilità genetico-molecolare di prodotti agro-alimentari, sia di origine animale (pesci, molluschi e crostacei) che vegetale (fagiolo e vite). Inizialmente si è proceduto all’individuazione degli organismi su cui condurre l’analisi: si sono collezionate linee pure di fagiolo (Phaseolus vulgaris L.), cloni di vite (Vitis vinifera L.) e campioni di pesci, crostacei e molluschi acquistati presso famose GDO o ai mercati locali di Chioggia e Sottomarina. In particolare, per quanto concerne la scelta delle specie ittiche su cui condurre l’analisi, si è svolta un’estesa indagine di mercato con l’intento di individuare le specie maggiormente coinvolte in falsificazioni alimentari, cioè sostituzione di specie pregiate con altre di valore inferiore. Si è successivamente proceduto alla purificazione di 37 campioni di DNA genomico e alla loro caratterizzazione dal punto di vista molecolare mediante amplificazione e sequenziamento di specifici geni mitocondriali, quali cox1 (Cytochrome oxydase subunit I), 16S-rDNA (16S small ribosomal subunit RNA) e cob (cytochrome b). Una volta acquisiti questi dati, l’interrogazione di due banche dati disponibili on line, BOLD per il gene cox1 e GenBank per tutti e tre i geni, ha consentito di identificare l’origine dei campioni confermando nella maggioranza dei casi quanto dichiarato nell’etichetta di accompagnamento del prodotto alimentare. In cinque situazioni non è stato possibile stabilire con certezza l’origine del campione e questo potrebbe indicare possibili casi di sostituzione, fraudolenta o accidentale. Il DNA barcoding pertanto è risultato utile ai fini dell’identificazione di specie in tutti e tre i taxa studiati, pesci, molluschi e crostacei, e il gene cox1 si è dimostrato un ottimo target per questi scopi eccetto che in tre casi particolari, i generi Thunnus, Macruronus e Gadus. Inoltre è risultato evidente che nonostante GenBank persista come la banca dati più ricca in termini di numero di sequenze depositate, il BOLD sta rapidamente incrementando la quantità di informazioni contenute al suo interno lasciando presupporre che in breve tempo diventerà la banca dati di riferimento per studi di genetica forense e di tracciabilità genetica. Per quanto riguarda le specie vegetali, l’obiettivo era l’identificazione univoca di specie, e soprattutto delle loro varietà quando fondate su un solo genotipo (linee pure, ibridi e cloni). Nel caso di fagiolo, si sono isolati i DNA genomici da 54 varietà di Phaseolus vulgaris, 18 provenienti dal Centro America, 12 dal Sud America e 24 line pure coltivate e commercializzate in Italia, insieme con alti 6 campioni usati come fuori gruppo (Phaseolus coccineus, Phaseolus lunatus e Vigna unguiculata). Sono risultate indispensabili indagini preliminari di polimorfismi di singoli geni al fine di determinare la variabilità genetica tra le varietà e la tracciabilità genetica di singole varietà. La caratterizzazione, tramite l’amplificazione di 7 differenti regioni cloroplastiche e due nucleari seguita da un approccio fenetico, ha confermato le potenzialità della tecnica come strumento efficace per la distinzione delle specie, mentre è risultata scarsamente informativa per il riconoscimento di singole varietà. Da qui si è rivelata necessaria l’adozione di un approccio alternativo, basato sulla determinazione della composizione nucleotidica e del polimorfismo a carico di ciascun gene esaminato, che ha permesso di definire 16 aplotipi corrispondenti ad altrettanti sottogruppi varietali, ciascuno costituito da accessioni Mesoamericane o Andine insieme con le varietà Italiane. Infine l’applicazione del DNA barcoding per la distinzione di cultivar di vite ha richiesto l’abbandono dello studio del genoma cloroplastico, troppo poco variabile, a favore di quello nucleare. Si sono isolati i DNA genomici da 123 cultivar di Vitis vinifera e da altre 5 specie (V. rupestris, V. riparia, V. labrusca, V. cinerea e V. berlandieri) e si sono amplificati 4 EST ed il gene GAI1 (gibberellins insensitive-like). L’analisi bioinformatica è ancora in corso, ma risultati preliminari fanno ipotizzare l’esistenza di aplotipi cultivar-specifici che potrebbero venir impiegati in futuro per risolvere i frequenti casi di sinonimie ed omonimie diffusi all’interno di questa specie. Infine un’altra interessante applicazione da un punto di vista economico potrebbe essere l’impiego di questi aplotipi cultivar-specifici per la tracciabilità genetica dei vini e la tutela delle denominazioni controllate da casi di falsificazione e concorrenza sleale.

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Bergmann, Tjard [Verfasser], and Bernd [Akademischer Betreuer] Schierwater. "Character-based barcoding, a symbiosis and potential successor of traditional taxonomy and modern DNA barcoding / Tjard Bergmann ; Betreuer: Bernd Schierwater." Hannover : Gottfried Wilhelm Leibniz Universität Hannover, 2019. http://d-nb.info/1181324130/34.

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Ywamoto, Eric Venturini. "Revisão taxonômica e biogeografia de Atlantirivulus santensis Köhler, 1906 (Rivulidae, Cyprinodontiformes)." Botucatu, 2019. http://hdl.handle.net/11449/181900.

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Orientador: Claudio de Oliveira
Resumo: Atlantirivulus santensis é amplamente distribuída ao longo das drenagens costeiras de São Paulo, Brasil. Algumas evidências de variação morfológica dentro dessa espécie sugerem que possam existir espécies novas que ainda não tenham sido descritas. Nesse sentido, o objetivo do presente estudo é verificar se existem diferentes linhagens de A. santesis utilizando a ferramenta do DNA Barcoding, realizar a revisão taxonômica de A. santesis através de caracteres morfológicos e estabelecer os limites de distribuição desta espécie com o intuito de contribuir para futuros estudos de sistemática dos rivulídeos. Foram analisadas 68 sequências parciais da região Citocromo c Oxidase I do DNA mitocondrial (com aproximadamente 550 pares de bases) de espécimes de A. santensis (Ubatuba, Maresias, Bertioga, São Paulo, Santos, Mongaguá, Pedro de Toledo, Itanhaém e Peruíbe), além de Atlantirivulus simplicis encontrada no limite norte (Paraty-RJ) da distribuição de A. santensis e Atlantirivulus ribeirensis, limite sul, para fins comparativos, como grupos externos. Os dados obtidos foram analisados com os softwares Geneious v.4.8.5, BioEdit v5.0.9 e Mega 7.0. Os resultados foram graficamente representados em dendrogramas de Neighbour-Joining (NJ), Automatic Barcode Gap Definition (ABGD) e PTP. As análises geraram três clusters (mais os dois grupos externos) dentro de A. santensis. O primeiro grupo é composto por espécimes de Peruíbe, Pedro de Toledo e Itanhaém, o segundo por Santos, Mongaguá e São... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: Atlantirivulus santensis is widely distributed along the coastal drains of São Paulo, Brazil. Some evidence of morphological variation within this species suggests that there may be new species that have not yet been described. In this sense, the objective of the present study is to verify if there are different strains of A. santesis using the tool of the DNA Barcoding, to carry out the taxonomic revision of A. santesis through morphological characters and to establish the distribution limits of this species with the intention to contribute for future studies of rivulide systematics. We analyzed 68 partial sequences of the cytochrome c Oxidase I region of the mitochondrial DNA (approximately 550 base pairs) of A. santensis specimens (Ubatuba, Maresias, Bertioga, São Paulo, Santos, Mongaguá, Pedro de Toledo, Itanhaém and Peruíbe), in addition to Atlantirivulus simplicis found in the northern boundary (Paraty-RJ) of the distribution of A. santensis and Atlantirivulus ribeirensis(Juquiá-SP), southern limit, for comparative purposes, as external groups. The data obtained were analyzed with the software Geneious v.4.8.5, BioEdit v5.0.9 and Mega 7.0. The results were graphically represented in NeighborJoining (NJ), Automatic Barcode Gap Definition (ABGD) and PTP dendrograms. The analyzes generated three clusters (plus the two external groups) within A. santensis. The first group consists of specimens from Peruíbe, Pedro de Toledo and Itanhaém, the second from Santos, Mongaguá and ... (Complete abstract click electronic access below)
Mestre

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Ribeiro, Emanuell Duarte. "Diversidade molecular dos Ancistrini (Loricariidae: Siluriformes) reofílicos da ecorregião Xingu-Tapajós." Instituto Nacional de Pesquisas da Amazônia, 2013. http://bdtd.inpa.gov.br/handle/tede/2191.

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Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq
With more than 5,700 species described, Neotropical ichthyofauna is considered the most diverse vertebrate fauna of the world. Neotropical fishes represent 20% of all fish species in the world. Therefore any attempt to understand evolution of vertebrates must rely on the understanding of the diversification of fishes in the Amazon basin and adjacent regions. Among the drainages that comprise the Amazon basin, the Xingu and Tapajós are particularly notable for the large number of rapids and waterfalls, which occur in the transition area between the Brazilian Shield and the Amazonian plain. The environment of the rapids is characterized by a set of extreme environmental features, requiring morphophysiological and behavioral specializations of the associated ichthyofauna. With approximately 250 valid species, the tribe Ancistrini has strong association with rapidly moving waters, and are an important component of the rheophilic fish fauna of the Xingu- Tapajós aquatic ecoregion. The Xingu and Tapajós Rivers are considered historically under-sampled, and the high number of species that have been described in recent years is indicative of the need to expand the taxonomic studies in this ecoregion. The recent infrastructure investments by the federal government into the construction oof hydroelectric developments raises to the state of urgency the need to increase the number of studies aimed to describe and elucidate the processes that generated these communities. For these reasons, the present study aimed to characterize the molecular diversity and phylogenetic structure of ancistrine communities of the Xingu-Tapajós aquatic ecoregion with the goal of clarifying the historical and ecological processes responsible for the current pattern of species co-occurrence. Analyses of DNA barcodes revealed the existence of 46 species of Ancistrini in the ecoregion, that are distributed in 16 genera, one of them probably being a new genus. The high concordance between morphologically and molecularly identified species indicates the reliability of the methodology of DNA barcoding for the identification/delimitation of species, making it a useful tool for the necessary acceleration of the description of new species of Neotropical ichthyofauna. The importance of biotic interactions suggested by analysis of phylogenetic community structure meets the theories proposed for the formation of communities of fish in lotic environments. However some evidence suggests that this difference may be the result of bias related to the taxonomic and geographical scales of the current study.
Com mais de 5.700 espécies descritas a ictiofauna neotropical é considerada a mais diversa fauna de vertebrados. Os peixes neotropicais representam 20% de todas as espécies de peixes do mundo. Deste modo qualquer tentativa de se entender a completa evolução dos vertebrados deve incluir a diversificação dos peixes na bacia amazônica e regiões adjacentes. Dentre as drenagens que compõem a bacia amazônica, os rios Xingu e Tapajós se destacam pelo grande número de corredeiras e cachoeiras, que ocorrem na área de transição entre o escudo brasileiro e a planície amazônica. Os ambientes de corredeira apresentam um conjunto de características extremas à ictiofauna, requerendo dessa especializações morfofisiológicas e comportamentais. Com aproximadamente 250 espécies válidas, a tribo Ancistrini apresenta forte relação aos ambientes de águas correntosas e são um importante componente da ictiofauna reofílica da ecorregião aquática Xingu-Tapajós. O Xingu e Tapajós são considerados rios historicamente pouco amostrados, e o elevado número de espécies que vem sendo descritas nos últimos anos é um indicativo da necessidade de ampliação de estudos taxonômicos nessa ecorregião. Os recentes investimentos do governo federal na construção de empreendimentos hidroelétricos eleva a um estado de urgência a necessidade do aumento de estudos que visem descrever e elucidar os processos que geraram essas comunidades. Por esses motivos, o presente estudo teve como objetivo caracterizar a diversidade molecular e estrutura filogenética das comunidades de Ancistrini da ecorregião aquática Xingu- Tapajós a fim de esclarecer os processos ecológicos e históricos responsáveis pelo atual padrão de co-ocorrência de espécies. As análises de DNA barcodes revelaram a existência de 46 espécies de Ancistrini na ecorregião, essas estão distribuídas por 16 gêneros, sendo um deles um provável gênero novo. A elevada concordância do banco de dados molecular e as espécies morfologicamente identificadas, indica a confiabilidade da metodologia de DNA barcoding na identificação/delimitação de espécies, sendo assim uma ferramenta útil ao necessário aceleramento da descrição de novas espécies da ictiofauna neotropical. A importância das interações bióticas sugerida pelas análises de estruturação filogenética de comunidades vai de encontro às teorias propostas para formação de comunidades de peixes em ambientes lóticos. Entretanto algumas evidências apontam que essa diferença pode ser resultado de viés relacionados às escalas taxonômicas e geográficas utilizadas nesse estudo.

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Mercier, Celine. "Développements méthodologiques autour de l'analyse des données de metabarcoding ADN." Thesis, Université Grenoble Alpes (ComUE), 2015. http://www.theses.fr/2015GREAV060/document.

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Cette thèse s'inscrit dans le cadre du traitement des données issues de séquençage haut débit, et en particulier des données produites en metabarcoding ADN. Le metabarcoding ADN consiste à identifier des taxons ou des groupes taxinomiques à partir de l'ADN présent dans des échantillons environnementaux (eau, sol, fèces...). Après extraction de l'ADN, de courtes séquences utilisées comme marqueurs taxinomiques sont amplifiées par PCR puis séquencées en utilisant les nouvelles techniques de séquençage haut débit. De très importants volumes de données sont ainsi générés, le plus souvent, de plusieurs milliers à plusieurs centaines de milliers de séquences par échantillon. L'objectif principal de cette thèse était le développement de méthodes d'analyse de ces séquences. Les méthodes de classification permettent de traiter de nombreuses problématiques en metabarcoding ADN. La classification supervisée est utilisée pour assigner les séquences à des taxons en les comparant aux séquences de bases de données de référence. Les méthodes de classification non supervisée permettent de créer des groupes taxinomiques (MOTU) à partir des séquences, afin de faire des estimations de biodiversité. Ces méthodes sont aussi employées pour identifier les séquences erronées produites par la PCR et le séquençage notamment, où les séquences erronées dérivent souvent des vraies séquences et leur sont très similaires. Les méthodes de classification demandent une méthode de comparaison des séquences qui soit idéalement à la fois très rapide et exacte. Une telle méthode a été développée, en utilisant un algorithme d'alignement global de type Needleman-Wunsch calculant la longueur de la plus longue sous-séquence commune entre les séquences à aligner, associé à un filtre sans perte permettant d'éviter l'alignement de certaines paires de séquences n'ayant aucune chance de présenter une similarité supérieure à un seuil choisi. L'utilisation d'instructions Single Instruction, Multiple Data, de même que le multithreading optionnel des calculs, permettent d'associer rapidité et exactitude. Cette méthode de comparaison est implantée dans SUMATRA, un programme calculant toutes les similarités deux à deux d'un jeu de données ou entre deux jeux de données, avec possibilité de fixer un seuil de similarité en dessous duquel les similarités ne sont pas rapportées. Elle est aussi utilisée dans SUMACLUST. SUMACLUST est un programme regroupant les séquences en utilisant un algorithme de clustering en étoile, où chaque groupe possède une séquence représentative. Il peut être utilisé pour créer des MOTU, ou pour détecter les séquences erronées dérivant de vraies séquences. Plus spécialisé, le programme SUMACLEAN a été développé pour détecter les séquences contenant des erreurs ponctuelles de PCR. Pour cela, des graphes orientés acycliques sont générés, dont la topologie correspond parfaitement aux cascades d'erreurs générées par les erreurs ponctuelles de PCR. Par ailleurs, une réflexion a été menée pour le développement d'une nouvelle approche de classification supervisée pour l'assignation taxinomique des séquences. Aujourd'hui, la plupart des approches d'assignation utilisent des méthodes mal adaptées au polymorphisme important des marqueurs, et ne considèrent pas suffisamment l'incomplétude et les erreurs inhérentes aux bases de données de référence. Une nouvelle approche a été testée, basée sur l'idée d'un départ depuis la racine de l'arbre taxinomique, suivi d'une descente jusqu'à un arrêt possible lorsque descendre à un niveau taxinomique plus précis semble irraisonnable. Cela permettrait en théorie de mieux gérer les problèmes inhérents aux bases de données de référence, mais pose le problème de la représentation des séquences aux différents niveaux de l'arbre, et du modèle de choix du chemin à prendre, pour lesquels aucune solution complètement satisfaisante n'a été trouvée à ce jour
This thesis positions itself in the context of the processing of high-throughput sequencing data, and specifically DNA metabarcoding data. DNA metabarcoding consists of the identification of taxa or taxonomic groups from DNA extracted from environmental samples (water, soil, animal feces). After extraction of the DNA, short sequences used as taxonomic markers are amplified by PCR, then sequenced using high-throughput sequencing technologies. Important volumes of data are produced that way, usually from several thousands to several hundreds of thousands sequences per sample. This thesis aimed for the development of methods for the analysis of these sequences. Classification methods allow the treatment of numerous problems in DNA metabarcoding. Supervised classification is used for the taxonomic assignment of sequences to taxa, by comparing them to the sequences of a reference database. Unsupervised classification methods are used to create taxonomic groups (MOTUs) from the sequences, in order to estimate biodiversity. They are also used to identify the erroneous sequences generated during the PCR and sequencing steps in particular, where erroneous sequences often derive from true sequences and remain very close to them. Classification approaches used in the context of DNA metabarcoding necessitate a sequence comparison method that should be both fast and exact. Such a method was developed, using a Needleman-Wunsch type global alignment algorithm computing the length of the longest common subsequence between the two sequences being aligned, associated with a lossless filter allowing to avoid the alignment of some pairs of sequences that have no chance to present a similarity superior to a chosen threshold. The use of Single Instruction, Multiple Data instructions, as well as the availability of multithreading speed up the calculations. This comparison method is implanted in SUMATRA, a program computing all the pairwise similarities of a dataset or between two datasets, with the possibility to set a threshold under which similarities are ignored. It is also used in SUMACLUST, a program grouping sequences using a star clustering algorithm, where each cluster possesses a representative sequence. This algorithm can be used to generate MOTUs, or to identify erroneous sequences deriving from true sequences, by using the fact that true sequences tend to end up as the representative sequences of their cluster. More specialized, the SUMACLEAN program was developed to identify sequences containing ponctual PCR errors. To that end, directed acyclic graphs are created, whose topology matches perfectly the successions of errors generated by ponctual errors during PCR. A new approach for the taxonomic assignment of sequences with a supervised classification method was also studied. Nowadays, most taxononomic assignment approaches use methods that are badly suited for the important polymorphism of markers, and don't take in account enough the incompleteness and errors inherent to reference databases. A new approach was tested, based on the idea of a start from the root of the taxonomic tree, and a descent in it with a possible stop before reaching a leaf, if descending to a more precise taxonomic level seems unreasonable. This approach would theoretically allow for a better handling of the problems inherent to reference databases, but poses a few issues, such as the representation of sequences at intermediate tree levels, and the model used to make choices regarding the path to take in the tree, for which no satisfying solutions have been found yet

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Bravo, Mayra. "Genetisk kartläggning av mygg : Artbestämning av mygg genom barcoding." Thesis, Umeå universitet, Biomedicinsk laboratorievetenskap, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-58621.

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Rydberg, Anders. "DNA Barcoding as a Tool for the Identification of Unknown Plant Material." Thesis, Uppsala universitet, Systematisk biologi, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-141813.

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Bolson, Mônica. "Aplicação de DNA Barcoding em espécies vegetais arbóreas da floresta ombrófila mista." reponame:Repositório Institucional da UFPR, 2012. http://hdl.handle.net/1884/28066.

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Silva, Fabio Nauer da. "Filogenia molecular e diversidade do gênero Hypnea (Gigartinales, Rhodophyta) na costa brasileira." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/41/41132/tde-25032014-180135/.

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O presente trabalho utiliza marcadores moleculares para auxiliar na caracterização e filogenia das espécies de macroalgas vermelhas do gênero Hypnea na costa do Brasil. O gênero Hypnea Lamouroux (1813) apresenta cerca de 67 espécies descritas e possui distribuição geográfica em águas quentes ao redor do mundo. Além disso, o gênero possui grande importância econômica e ecológica, como fonte de alimento e produção industrial de carragenana. Porém, a identificação das espécies de Hypnea com base exclusivamente em dados morfológicos é dificultada em virtude da plasticidade fenotípica presente no grupo, de sua morfologia relativamente simples e da ampla distribuição geográfica de suas espécies. Em vista disso, utilizamos a técnica de \"DNA barcoding\" que permite a análise de um grande número de amostras. Neste trabalho foram utilizados dois \"DNA barcodes\" (a região 5\' do gene mitocondrial cox1 e o \"universal plastid amplicon\" UPA), e para as análises filogenéticas foi utilizado o gene plastidial rbcL. Além disso, estudos morfológicos foram feitos a fim de delimitar o real valor dos caracteres morfo-anatômicos citados na literatura para a separação de espécies do gênero Hypnea. Ao todo, foram obtidas 230 amostras brasileiras de Hypnea, provenientes de 11 estados brasileiros, e 10 amostras de outros países. Um total de 367 sequências de marcadores moleculares foi obtido neste trabalho. Confirmamos a ocorrência de nove espécies para o gênero: H. cervicornis, \"H. flexicaulis\", \"H. musciformis\", H. spinella, \"H. stellulifera\", Hypnea sp. 1, Hypnea sp. 2, Hypnea sp. 3 e Hypnea sp. 4. As amostras coletadas e previamente identificadas em campo como H. cornuta revelaram-se, pelos estudos da biologia molecular, serem \"H. stellulifera\". As espécies H. musciformis, H. nigrescens, H. valentiae foram consideradas variações morfológicas de uma mesma espécie, denominada de \"H. musciformis\". A identificação das espécies com base apenas em características morfológicas mostrou-se insatisfatória, devido principalmente a plasticidade fenotípica presente no grupo, além da existência de espécies com morfologias convergentes. A técnica de \"DNA barcode\", principalmente com relação ao marcador cox1, mostrou-se essencial na identificação e delimitação das espécies, revelando cenários que passariam despercebidos com o uso apenas da morfologia
This study uses molecular markers to aid in the characterization and phylogeny of species of the genus Hypnea, a red macroalgae, on the coast of Brazil. The genus Hypnea Lamouroux (1813) presents about 67 described species and has geographical distribution in warm waters around the world. Furthermore, the genus has great economic and ecological importance as a source of food and industrial production of carrageenan. However, the identification of the species of Hypnea based solely on morphological data is difficult due to phenotypic plasticity present in this group, its relatively simple morphology and broad geographical distribution of its species. In view of this, we use the technique of \"DNA barcoding\" that allows the analysis of a large number of samples. In this work we used two \"DNA barcodes\" (the 5 \'region of the mitochondrial gene cox1 and universal plastid amplicon UPA), and for phylogenetic analysis the plastid gene rbcL was used. In addition, morphological studies were made in order to delimit the actual value of morpho-anatomical caracters cited in the literature for the separation of species of Hypnea. Altogether, 230 Hypnea samples were obtained from 11 Brazilian states, and 10 samples from other countries. A total of 367 sequences of molecular markers were obtained in this study. We confirm the occurrence of nine species of the genus: H. cervicornis, \"H. flexicaulis\", \"H. musciformis\", \"H. spinella, \"H. stellulifera\", Hypnea sp. 1, Hypnea sp. 2, Hypnea sp. 3 and Hypnea sp. 4. Samples collected in the field and previously identified as H. cornuta based on molecular data, proved to be \"H. stellulifera\". The species H. musciformis, H. nigrescens and H. valentiae were considered morphological variations of the same species, named \"H. musciformis\". The identification of species based on morphological characteristics proved unsatisfactory, mainly due to phenotypic plasticity in this group and the existence of species with convergent morphologies. The technique of \"DNA barcode\", especially with respect to cox1 marker, was essential for the identification and definition of species, revealing scenarios that would go unnoticed by using only morphology

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Guimarães, Natália Rodrigues. "Diversidade do gênero Hypnea (Gigartinales, Rhodophyta) do estado de São Paulo baseada em marcadores moleculares e morfologia." Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/41/41132/tde-19012012-151152/.

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O gênero Hypnea J.V. Lamouroux (1813) (Cystocloniaceae, Gigartinales), com cerca de 67 espécies descritas, apresenta ampla distribuição geográfica pelas costas marinhas de águas quentes ao redor do mundo. Algumas espécies de Hypnea são usadas para a produção de carragenanas, hidrocolóides de grande importância na indústria atual. A taxonomia do gênero é bastante problemática e a identificação das espécies é complicada devido a uma morfologia relativamente simples que muitas vezes é influenciada pelas condições do habitat onde se encontram. Apesar das revisões regionais já realizadas, o número certo de espécies e o status de algumas delas permanece em dúvida. Estudos moleculares já foram realizados com o gênero Hypnea principalmente para região da Ásia. A técnica do \"DNA barcoding\" tem sido testada em Rhodophyta com sucesso para identificação rápida de espécies, utilizando a região 5´ do gene mitocondrial da citocromo c oxidase subunidade I, o marcador cox1. Outro marcador recentemente testado como \"DNA barcode\" é o domínio V do gene plastidial 23S, o marcador UPA. Além destes, o marcador plastidial rbcL tem sido utilizado como ferramenta para estudos filogenéticos do gênero Hypnea. No presente trabalho, foram sequenciadas para o marcador cox1, 49 amostras provenientes do no litoral do estado de São Paulo, uma amostra proveniente do estado do Rio de Janeiro e cinco amostras mantidas em cultura provenientes dos litorais dos estados de São Paulo e Espírito Santo. Foram identificados seis grupos taxonômicos diferentes segundo o marcador cox1. Representantes de cada um desses grupos foram sequenciados para os marcadores UPA e rbcL. A divergência interespecífica encontrada entre as amostras sequenciadas neste estudo para o marcador cox1 foi 62 - 100 pb (10,1 - 16,3%); para o marcador UPA foi 9 - 16 pb (2,5-4,4%) e para o marcador rbcL foi 42 - 88 pb (3,2 - 6,7%). As divergências intraespecíficas das amostras obtidas neste estudo foram, 0 - 5 pb (0 - 0,9 %) para o marcador cox1, 0 - 1pb (0 - 0,3%) para o marcador UPA e 0 - 6 pb (0 - 0,5%) para o marcador rbcL. As divergências observadas corroboram a existência de seis entidades taxonômicas diferentes. Após análise da morfologia e comparação com sequências disponíveis no GenBank as espécies do gênero Hypnea foram nomeadas como: H. cervicornis, H.flexicaulis, H. musciformis, H. spinella, Hypnea sp.1 e Hypnea sp.2. Sendo a espécie Hypnea flexicaulis a primeira citação para o Oceano Atlântico. Baseado nos estudos moleculares e morfológicos, concluímos que a espécie H. nigrescens, anteriormente citada para o Estado de São Paulo, é na verdade uma variação morfológica de H. musciformis. Ainda, concluímos que as espécies de H. cervicornis e H. spinella não devem ser colocadas em sinonímia uma vez que suas características morfológicas e as diferenças nas sequências obtidas através dos três marcadores utilizados mostram que são duas espécies distintas
The genus J.V. Lamouroux (1813) (Cystocloniaceae, Gigartinales), comprises 67 described species, has a wide geographical distribution on the tropical shores around the world. Some species of Hypnea are used for the production of carrageenan, hydrocolloids of great importance in today´s industry. The taxonomy of the genus is very problematic and Hypnea species identification is complicated by a relatively simple morphology that is often influenced by the conditions of the habitat. Although some regional reviews have been carried out, the right number of species and the status of some species remain in doubt. Molecular studies have been carried out mainly dealing with species from Asia. The technique of \"DNA barcoding\" has been successfully tested in Rhodophyta for rapid identification of species using the 5 \'region of the mitochondrial gene cytochrome c oxidase subunit I, the marker cox1. Recently, another marker tested as \"DNA barcode\" is the domain V of the plastidial 23S gene, the marker UPA. In addition, the plastidial marker rbcL has been used as a tool for phylogenetic studies of the genus Hypnea. In this study, were sequenced for the marker cox1, 49 samples from the coast of São Paulo State, a sample from the State of Rio de Janeiro and five samples maintained in culture from the coastal states from the States of São Paulo and Espirito Santo. We identified six different taxonomic groups according to the marker cox1. Representatives of each of these groups were sequenced for the UPA and rbcL markers. The divergence found among the cox1 sequences in this study was from 62 to 100 bp (10.1 - 16.3%), for the UPA marker was from 9 to 16 bp (2.5 to 4.4%), and for the rbcL marker was 42 to 88 bp (3.2 - 6.7%). The intraspecific divergences for the samples sequenced in this study were 0-5 bp (0 -0.9%) for the cox1, 0-1 bp (0 - 0.3%) for the UPA and 0-6 bp (0 - 0.5%) for the rbcL. The observed divergences for the three molecular markers confirm the existence of six different taxonomic entities. After analysis of the morphology and comparison with sequences available in GenBank for the genus Hypnea these taxonomic entities were named as: H. cervicornis, H. flexicaulis, H. musciformis, H. spinella, Hypnea sp. 1 and sp2. As the species Hypnea flexicaulis this is the first citation to the Atlantic Ocean. Based on morphological and molecular studies, we conclude that the species H.nigrescens, quoted earlier for the State of São Paulo, is actually a morphological variation of H. musciformis. Still, we conclude that the species H. cervicornis and H.spinella should not be placed in synonymy since its morphological characteristics and differences in the sequences obtained from the three molecular markers show that they are two distinct species

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Gomes, Gleison Robson Desidério. "Smicridea McLachlan, 1871 (Trichoptera: Hydropsychidae: Smicrideinae) do Brasil: Associação de larvas e adultos usando sequências de DNA mitocondrial e metamorfótipo." Instituto Nacional de Pesquisas da Amazônia, 2016. http://bdtd.inpa.gov.br/handle/tede/2211.

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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.

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Cerqueira, Najila Nolie Catarine Dantas. "Análise comparativa da composição genética de exemplares da fauna de peixes marinho-estuarinos encontrados na costa do Brasil." Botucatu, 2018. http://hdl.handle.net/11449/153566.

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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)
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Oliveira, Raul Barrera Camacho. "Genética molecular na identificação de espécies de raias exploradas comercialmente no estado de São Paulo." Botucatu, 2020. http://hdl.handle.net/11449/192937.

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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)
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Yusseff, Sohath Zamira. "Distribution, Dna Barcoding And Phylogenetics Of Caribbean Calliphoridae Flies: Tools For Forensic Studies." ScholarWorks @ UVM, 2018. https://scholarworks.uvm.edu/graddis/847.

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Blow flies (Diptera: Calliphoridae) are among the most dominant and conspicuous insects in the decomposition process. They are important in forensic entomology to determine time of death and, in certain situations, cause of death or relocation of a body. Insects are now included as standard operating procedures in crime scene investigations in many countries, however, this is not standard procedure in the Caribbean area due to lack of knowledge of insects involved in cadaveric decomposition. Successful application of forensic entomology depends on solid underlying data. Our main goal is to advance the knowledge of Calliphoridae in the Caribbean to enable forensic entomology studies. We performed a mega-transect across the Caribbean and extensively collected flies attracted to rotten meat baits during five years from 2011 to 2015. Overall we collected 61,332 flies of which 34,650 were Calliphoridae. We sampled 16 of the 18 species of forensically important Caribbean Calliphoridae and three continental species. We determine the diversity and distribution of Calliphoridae in the Caribbean. We also present a thorough DNA barcode dataset, covering the geographic range of most species in the region. Finally we established phylogenetic relationships among Calliphoridae species and test biogeographical hypotheses, and patterns of diversification and endemism in the Caribbean. In sum, this is the most comprehensive study of the family Calliphoridae from the Caribbean that will open the door for future research on forensic entomology in the region.

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Schilcher, Felix Maximilian Verfasser], Elmar [Akademischer Betreuer] Weinhold, and Dominik [Akademischer Betreuer] [Wöll. "Barcoding von genomischer DNA und Anwendung im Bereich des DNA-Mappings / Felix Maximilian Schilcher ; Elmar Weinhold, Dominik Wöll." Aachen : Universitätsbibliothek der RWTH Aachen, 2021. http://d-nb.info/1240765525/34.

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Freitas, Thaís Kaus de. "EVOLUÇÃO DO GENE MITOCONDRIAL COI EM AEGLIDAE (CRUSTACEA, ANOMURA) E IMPLICAÇÕES PARA DNA BARCODING." Universidade Federal de Santa Maria, 2014. http://repositorio.ufsm.br/handle/1/5326.

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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
The mitochondrial gene COI is widely used as a molecular marker, and the region used for DNA barcoding is getting more and more popular to species delimitation and identification. However, the evolution patterns can vary along the genes depending on factors as the gene position in genome and taxonomic group, among others. Using one unique delimited region for all groups may not be suitable to a certain targeted taxon, or to answer its evolutionary questions. We examined the patterns of COI intra- and interspecific nucleotide divergence for aeglid crustaceans and we found highly variable divergence profiles along the COI gene; a possible evolutionary pattern for the Jerry-Pat region; lacking of evolutionary pressures by concentrated divergence; intra- and interspecific divergence levels overlap, but no overlapping in substitution profiles along the gene; a putative new COI region to access the total COI diversity in aeglids. We conclude that the barcoding region does not accurately reflect the evolution of the gene COI in aeglids.
O gene mitocondrial COI é amplamente utilizado como marcador molecular, sendo a região de DNA barcoding cada vez mais popular para delimitação e identificação de espécies. No entanto, os padrões de evolução variam ao longo dos genes dependendo de fatores como posição do gene no genoma, grupo taxonômico, entre outros. O uso de uma única região delimitada para qualquer grupo pode não ser adequado para o táxon de interesse ou para responder suas questões evolutivas. Nós examinamos os padrões de divergência nucleotídica intra e interespecíficas no gene COI de crustáceos eglídeos e obtivemos: perfis de divergência altamente variáveis ao longo de todo COI; possível padrão de evolução na região de Jerry-Pat; ausência de pressões evolutivas por divergência concentrada; sobreposição de níveis de divergência intraespecífica e com interespecífica, mas sem sobreposição dos perfis de substituição ao longo do gene; sugestão de nova região para acessar a diversidade total de COI em eglídeos. Concluímos que a região de barcoding não reflete acuradamente a evolução do gene mitocondrial COI em eglídeos.

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LIMA, JÚNIOR Nelson Correia de. "Delimitação de espécies em Hymenochaetaceae Donk (Basidiomycota, Fungi) a partir de dados morfológicos e DNA barcoding." Universidade Federal de Pernambuco, 2016. https://repositorio.ufpe.br/handle/123456789/25954.

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Hymenochaetaceae Donk (Basidiomycota, Fungi) caracteriza-se por apresentar basidiomas ressupinados a pileados, reação xantocróica positiva, presença de setas himeniais (na maioria) e de hifas generativas sem grampos de conexão, além de reunir fungos causadoras de podridão branca. A circunscrição dos gêneros e espécies em Hymenochaetaceae é imprecisa, principalmente no âmbito da taxonomia tradicional, o que torna dúbia a identificação de espécies quando são utilizados exclusivamente dados morfológicos. Nessa perspectiva, estudos baseados em sequências de DNA das regiões ITS e LSU (rDNA) estão sendo responsáveis por significativos progressos na taxonomia do grupo, porém estudos com táxons neotropicais são escassos. No presente estudo foram utilizados espécimes de Hymenochaetaceae coletados em diferentes biomas brasileiros para extração de DNA genômico, amplificação das regiões ITS e LSU por meio de PCR e posterior sequenciamento. Foi observado o delineamento morfológico e/ou molecular de duas espécies de Fomitiporia, duas de Fulvifomes, quatro de Fuscoporia, seis de Hymenochaete, duas de Phellinotus, uma de Phellinus e uma de Tropicoporus. Dentre essas, são propostas: uma nova espécie de Fuscoporia; uma sinonimização em Phellinus, uma em Tropicoporus, uma em Hymenochaete e uma possível sinonimização em Fomitiporia; além da confirmação de combinação Fulvifomes rhytiphloeus a partir de evidências moleculares. São registradas ainda uma nova ocorrência de Fomitiporia e de Hymenochaete para o Brasil. De modo geral, observou-se que as sequências da região ITS e/ou LSU foram úteis no delineamento das espécies em estudo, principalmente em espécies morfologicamente semelhantes e próximas do ponto de vista evolutivo.
Hymenochaetaceae Donk (Basidiomycota, Fungi) is characterized by sessile or pileate basidiomes, positive xanthochroic reaction, occurrence of hymenial setae (frequent) and absence of clamps. Besides, species of this group are also known for producing white rot. The circumscription of genera and species within Hymenochaetaceae is inaccurate, especially under the traditional taxonomy, which makes dubious species identification when used exclusively morphological data. From this perspective, studies based on DNA sequences of the regions ITS and LSU (rDNA) are accounting for significant progress in the taxonomy of the group, but studies with Neotropical taxa are scarce. In this study, Hymenochaetaceae specimens were collected in different Brazilian biomes for DNA extraction, amplification of the regions ITS and LSU by PCR and subsequent sequencing. We observed the morphological and/or molecular delimitation of two species of Fomitiporia, two of Fulvifomes, four of Fuscoporia, seven of Hymenochaete, two of Phellinotus, one of Phellinus and one of Tropicoporus. Among these it is proposed: a new species of Fuscoporia; one synonymization in Phellinus, one in Tropicoporus, one in Hymenochaete and a possible synonymization in Fomitiporia; and a confirmation of the combination in Fulvifomes rhytiphloeus upon molecular data. We also report a new record of Fomitiporia and another of Hymenochaete from Brazil. In general, it was observed that sequences of ITS and/or LSU region are useful for species delimitation, particularly for those which are morphologically similar and evolutionarily close related.

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FRIGERIO, JESSICA. "Towards food traceability: discovering biomolecular technologies for complex food products." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2021. http://hdl.handle.net/10281/309984.

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Nel settore agroalimentare, le frodi alimentari aumentano ogni anno e i consumatori richiedono prodotti più controllati. Un sistema di identificazione e tracciabilità biomolecolare potrebbe essere utilizzato per valutare la qualità delle materie prime e dei prodotti alimentari finiti. Il test del DNA è una metodologia molto utilizzata nel campo alimentare, in particolare la metodologia del DNA barcoding. Tuttavia, il DNA barcoding ha alcuni limiti nell'analisi dei prodotti alimentari complessi. I trattamenti industriali potrebbero alterare la qualità del DNA della materia prima e questa analisi potrebbe essere difficile da applicare. Inoltre, il DNA barcoding non può essere applicato per prodotti multispecie. Infine, il DNA barcoding è un’analisi lunga e costosa. Partendo da questi limiti, l'obiettivo principale di questo progetto di dottorato è stato quello di identificare e testare analisi biomolecolari innovative per la valutazione dell'identità delle materie prime e dei prodotti alimentari trasformati. In particolare, sono state sviluppate tre linee di ricerca. Nella prima linea di ricerca è stato valutato se il DNA barcoding può essere applicato per tracciare la componente vegetale negli integratori alimentari, a partire dalla materia prima di partenza fino ai prodotti lavorati finiti. Abbiamo selezionato un pannello di 64 fitoestratti e intermedi di produzione ottenuti attraverso tre diversi metodi di estrazione con diversi solventi. Abbiamo sequenziato sia regioni del DNA barcoding che del DNA mini-barcoding. I fitoestratti ottenuti attraverso il trattamento idroalcolico, con la percentuale più bassa di etanolo e con solventi acquosi hanno avuto un tasso di identificazione maggiore. Questo studio dimostra che il DNA barcoding è uno strumento utile per tracciare alcune tipologie di integratori alimentari. Un secondo limite che si verifica nel mercato alimentare è relativo ai prodotti multispecie, perché il DNA barcoding non consente di analizzarli. Nella seconda linea di ricerca abbiamo voluto testare il DNA-metabarcoding per caratterizzare ingredienti dell’etichetta vegetali o contaminanti in 5 categorie di prodotti commerciali a base di insetti. Lo stesso approccio è stato utilizzato per valutare la sua sensibilità ai casi di contaminazione e contraffazione nella farina di insetti con farine vegetali a basso costo (e potenzialmente allergeniche) come il grano e la soia. Inoltre, è stato valutato anche il profilo batterico. L'analisi del DNA-metabarcoding ha rivelato un'elevata efficacia come metodo di screening per identificare sia gli ingredienti vegetali che i possibili eventi di adulterazione. Per quanto riguarda il profilo batterico, i dati hanno rivelato che alcuni batteri formano un "core microbioma" che caratterizza i prodotti a seconda dell'insetto, suggerendo la presenza un microbiota conservato. Al fine di valutare l'applicazione del DNA-metabarcoding anche per la tracciabilità delle tisane, abbiamo analizzato 15 tisane commerciali per identificare tutte le specie presenti nei prodotti e verificare la corrispondenza con l'etichetta. Abbiamo testato due diversi marker. I risultati hanno mostrato che non tutte le specie dichiarate sull'etichetta sono state trovate ma sono stati rilevati alcuni contaminanti. I due marcatori sono stati in grado di rilevare specie diverse: alcune specie sono state rilevate solo da un marcatore, alcune solo dall'altro. Per analisi future sarebbe necessario utilizzare entrambi i marker per ottenere migliori risultati di tracciabilità. In questa ricerca abbiamo definito che il DNA-metabarcoding è un metodo prezioso per la tracciabilità della catena di approvvigionamento alimentare. La terza linea di ricerca mirava a creare un mock-up per l'identificazione del tartufo utilizzando la LAMP, una tecnica di amplificazione isotermica degli acidi nucleici. Questo kit a basso costo permette l'identificazione del tartufo bianco T.magnatum in un totale di 90 minuti
In the agri-food sector, food frauds are increasing every year and there is a demand from the consumer to better understand food products. A suitable bio-molecular identification and traceability system could be used to assess the quality of raw materials up to the finished food products to guarantee the consumer on the identity of the products purchased. DNA testing is a methodology frequently used in the food field, especially DNA barcoding methodology. However, DNA barcoding technique has some limits in the complex food products analysis. Industrial treatments could alter DNA quality of raw material, therefore this analysis could be challenging to apply. Furthermore, DNA barcoding cannot be applied for multispecies products because is feasible only for monospecies products. Finally, DNA barcoding is time-consuming and expensive. Starting from these limits, the main objective of this PhD project was to identify and test innovative biomolecular analyses for the identity assessment of raw materials and processed food products. Three lines of research have been developed in this PhD thesis. In the first line of research was evaluated whether DNA barcoding can be applied to trace the plant component in food supplements from the starting raw material to the finished processed products. We selected a panel of 64 phytoextracts and intermediate of production obtained through three different extraction methods with different solvents. We sequenced and analysed the sequence variability at DNA barcoding and mini-barcoding marker regions. Phytoextracts obtained through hydroalcoholic treatment, with the lower percentage of ethanol and aqueous processing had a major rate of identification. This study proves that DNA barcoding is a useful tool for some typology of food supplement traceability. A second limit that occurs in the food market is related to multispecies products, because DNA barcoding does not allow to analyse them. In the second line of research we wanted to test DNA metabarcoding to characterize plant declared ingredients or contaminants in five categories of commercial insect-based products. The same approach has been used to assess its sensitivity to cases of contamination and counterfeits in insect flour with low cost (and potentially allergenic) vegetable flours like wheat and soybean. Moreover, also the bacteria profile was evaluated. The DNA metabarcoding analysis revealed a high efficacy as a screening method to identify both plant ingredients and possible adulteration events. Concerning the bacteria profile, our data revealed that some bacteria formed a “core microbiome” characterizing the products depending on the insect, suggesting that a resident microbiota is conserved. In order to evaluate the application of DNA metabarcoding also for herbal teas traceability, we analysed fifteen commercial herbal teas to identify all the species in the products and verify the correspondence with the label. Furthermore, to verify the quantitative ability of DNA-metabarcoding, we created six mocks mixture with different percentages of five species of different matrices both starting from raw material and genomic DNA. For all the samples we tested two different markers. Results showed that not all the species declared on the label was found and we were able to detect some contaminants. The two markers were able to detect different species: some species were detected only by one marker, others only by the other. For future analyses it would be necessary to use both the markers to obtain better results in traceability. In conclusion in this line of research we defined that DNA metabarcoding is a valuable method for food supply chain traceability. The third line of research aimed to create a mock-up for truffle identification using the LAMP technique, an isothermal nucleic acid amplification technique. This low-cost kit allows the identification of the white truffles T.magnatum in a total of 90 minutes.

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FIALHO, V. L. S. "DISCRIMINAÇÃO GENÉTICA DE ESPÉCIES DE PFAFFIA SPP. (GINSENG BRASILEIRO) USANDO CÓDIGO DE BARRAS DE DNA." Universidade Federal do Espírito Santo, 2017. http://repositorio.ufes.br/handle/10/7092.

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Plantas das espécies Pfaffia spp. são amplamente utilizadas em território nacional e são popularmente conhecidas como Ginseng-brasileiro. As espécies mais conhecidas são a Pfaffia glomeratae a Pfaffia paniculata. Há indicações de uso como tônico e revigorante geral, no tratamento de fadiga física, esgotamento mental, falta de memória, como auxiliar no tratamento de distúrbios circulatórios, dentre outros. Embora as duas espécies sejam utilizadas com os mesmos propósitos, deve-se considerar que a diferença química entre elas pode interferir nos espectros de ações farmacológicas e toxicológicas. A identificação morfológica das raízes é tarefa difícil sobretudo devido a sua forma de comercialização. Por isso, faz-se necessário o desenvolvimento de novas metodologias de identificação das espécies comercializadas. O objetivo principal deste trabalho foi identificar, em nível de espécie, amostras de Ginseng-brasileiro vendidos no mercado brasileiro, utilizando, para isso, o código de barras de DNA (DNA barcode). O DNA de 60 amostras comerciais foi extraído e os genes matK e rbcL foram amplificados por PCR e sequenciados. Além disso, amostras referência, morfologicamente identificadas, das duas espécies foram utilizadas para comparação e submetidas ao mesmo protocolo. Posteriormente, as amostras foram confrontadas com amostras referências e com o banco de dados BOLD (Barcode of Life Data Systems). Dentre as amostras referências, 90% amplificaram, tanto para matK quanto para rbcL. As amostras comerciais obtiveram taxa de amplificação de 95% para ambos os genes. Todas amostras foram sequenciadas. Encontrou-se uma diferença interespecífica entre P. glomerata e P. paniculata de 1,92% para matK e 1,90% para rbcL. Não foi encontrada variação intraespecífica. Das 58 amostras avaliadas, 67,24% foram identificadas, sendo 61,54% P. glomerata e 38,46% P. paniculata. O restante, 32,76% não foram identificadas conforme o rótulo, caracterizando adulteração. Desses, 22,41% não foram identificadas e 10,34% apresentaram substituição de espécies. O método de identificação por DNA bacode possibilitou a identificação, em nível de espécie, das amostras comercializadas como Ginseng brasileiro obtidas do mercado brasileiro, como P. glomerata e P. paniculata.

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Crobe, Valentina. "DNA barcoding of atlantic skates (Chondrichthyes, Rajiformes): taxonomic and phylogeographic inferences and conservation impacts." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2018.

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Anthropogenic impacts are responsible for alarming declines in the abundance and distribution of several marine species. Their future conservation and long-term management plans need to be conceived upon a universally recognised key-feature: species identity. In the past, this important assignment resulted particularly arduous among skates (Rajiformes), in which the phenotypic similarity between some taxa and the individual variability in others, entangled accurate species identification. This research project aimed to confirm the power of DNA barcoding for the discrimination between skate species across the Atlantic Ocean and for its use as effective tool to minimize the risk of species misidentification. In this perspective, this work aimed to compile a new and fully available barcode library, the ELASMO-ATL project, which gathered biological and molecular information of Atlantic rajid fauna. In addition, considering the vast geographical distribution of six species, this study investigated whether the mitochondrial gene Cytochrome Oxidase subunit I (COI) can preliminarily identify potential geographical populations. DNA barcodes were obtained from 398 individuals collected during past scientific surveys across four main FAO divisions (FAO 27, FAO 34, FAO 41 and FAO 47), obtained data successfully resolved many taxonomic ambiguities and demonstrated a highly cohesive monophyletic clustering within the order, as well as a high number of concordant Barcode Index Number (BINs). Further inference of evolutionary patterns suitable for addressing management and conservation issues should be undertaken considering the six species selected for the phylogeographic analysis. In conclusion, a well-curated barcode library was established and this novel resource provides samples, specimens information and corresponding reference sequences of the group in question for future studies.

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Domènech, Andreu Marc. "Reconciling standardised inventories and DNA barcoding to infer diversity patterns in Iberian spider communities." Doctoral thesis, Universitat de Barcelona, 2021. http://hdl.handle.net/10803/673877.

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Unveiling the patterns and identifying the factors that drive community assembly are key questions in ecology and evolution, especially in the current state of climate change and biodiversity loss. Because of its particular location, its geological and climatic history, and its complex relief, the Iberian provides an excellent arena for the study of past and present patterns of biodiversity and its drivers. In this thesis, we aim at revealing patterns of taxonomic, functional and phylogenetic diversity and the determinants of community assembly in spiders from white-oak forests across the Iberian Peninsula. We generated more than 3,200 DNA barcodes from 371 species, which greatly increased the DNA barcode reference library of Iberian spiders for future studies. We also combined morphological and molecular species delimitation methods to identify instances of overlooked diversity, which allowed us to discover and describe a new species and to detect an instance of introgression between closely related species. We also revealed that certain functional traits of spiders are related to high levels of population structure, which can help us to characterise those groups that might be more vulnerable to local extinctions. We investigated the impact of adding information of juvenile spiders, which are usually discarded because they are not morphologically identifiable to species level, on diversity estimates by means of metabarcoding approaches. We found that they contribute a large proportion of extra diversity, and that they can change our interpretations of the differences among communities based on species composition. We further determined that metabarcoding approaches, if properly corrected, may also contribute abundance information to diversity estimates. Estimating the phylogenetic diversity of a community requires building a robust tree for the species of interest. We decided to investigate some of the variables that may influence the estimation of phylogenetic diversity. We found that combining at least one mitochondrial and one nuclear genes of the species of interest and including a backbone with additional species and genes had the greatest impact in phylogenetic inference, followed by the incorporation of time information and by enforcing a topological. We assessed the alpha taxonomic, functional and phylogenetic diversity of Iberian spider communities, and we found that they provide different yet complementary information, which is fundamental for designing effective conservation strategies. We uncovered the importance of past climatic conditions to explain the levels of phylogenetic diversity of the communities but not those of functional diversity. Differences in environmental variables among communities, on the other hand, did not explain the variation observed in functional and phylogenetic diversity, most likely because of both the high habitat type similarity and the relatively narrow geographic scope of the study.
Revelar els patrons i identificar els factors que determinen l’assemblatge de comunitats són qüestions claus en ecologia i evolució, especialment en l’actual situació de canvi climàtic i pèrdua de biodiversitat. A causa de la seva localització particular, de la seva dinàmica història geològica i climàtica, i del seu relleu complex, la Península Ibèrica proporciona un context excel·lent per a l’estudi dels patrons de biodiversitat presents i passats i dels seus desencadenants. En aquesta tesi, busquem revelar els patrons de diversitat taxonòmica, funcional i filogenètica i els determinants de l’assemblatge de comunitats en aranyes de rouredes de la Península Ibèrica. Hem generat més de 3.200 codis de barres de l’ADN corresponents a 371 espècies, els quals amplien la llibreria de referència de codis de barres d’ADN d’aranyes ibèriques per a futurs estudis. També hem combinat mètodes de delimitació d’espècies morfològics i moleculars per identificar casos de diversitat críptica, la qual cosa ens va permetre descobrir i descriure una nova espècie i detectar un cas d’introgressió entre espècies properes. A més, hem revelat que cert trets funcional de les aranyes estan relacionats amb nivells alts d’estructura poblacional, la qual cosa ens pot ajudar a caracteritzar els grups que podrien ser més vulnerables a extincions locals. Hem investigat l’impacte d’afegir la informació de les aranyes juvenils, les quals solen descartar-se perquè no són morfològicament identificables a nivell d’espècie, en les estimes de diversitat mitjançant tècniques de metabarcoding. Hem trobat que aporten una gran proporció de diversitat extra, i que poden canviar les nostres interpretacions sobre les diferències entre comunitats basades en la composició d’espècies. A més, hem determinat que les tècniques de metabarcoding, amb els factors de correcció correctes, també poden aporta informació d’abundància a les estimes de diversitat. Estimar la diversitat filogenètica d’una comunitat requereix construir un arbre robust per les espècies d’interès. Nosaltres vam decidir investigar algunes de les variables que poden influenciar les estimes de diversitat filogenètica. Vam trobar que combinar com a mínim un gen mitocondrial i un de nuclear de les espècies d’interès i incloure una base d’espècies i gens addicionals tenia l’impacte més gran en la inferència filogenètica, seguit de la incorporació d’informació temporal i del fet de forçar una certa restricció topològica. Vam estimar la diversitat alfa taxonòmica, funcional i filogenètica de les comunitats ibèriques d’aranyes, vam trobar que les tres proporcionen informació diferent i complementaria, la qual cosa és fonamental per dissenyar estratègies de conservació efectives. Vam revelar la importància de les condicions climàtiques passades a l’hora d’explicar els nivells de diversitat filogenètica entre comunitats però no els de diversitat funcional. Les diferències en les variables ambientals entre comunitats, però, no explicaven la variació observada en la diversitat funcional i filogenètica, probablement a causa de l’alta semblança en el tipus d’hàbitat i l’escala relativament petita de l’estudi.

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Meierotto, Sarah. "DNA BARCODING AS A TOOL FOR SPECIES DISCOVERY AND DOCUMENTATION IN THE SUPERFAMILY ICHNEUMONOIDEA." UKnowledge, 2018. https://uknowledge.uky.edu/entomology_etds/47.

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Changes to traditional taxonomic methods to incorporate new technologies and methods have already improved the quality of species hypotheses, but more work can be done to improve the speed of new species documentation. The mitochondrial COI DNA barcode has been successfully used to identify species with high accuracy since the early 2000s, and has been used in conjunction with morphological examinations and other DNA markers to discover and delimit new species. This thesis explores the application of DNA barcodes as the primary data for delimitation and diagnosis of new species of ichneumonoids. The genera Zelomorpha and Hemichoma are revised and 18 new species from the Área de Conservación Guanacaste in Costa Rica are diagnosed based on COI barcodes. Two additional species are described based on morphology. An illustrated morphological key and morphological diagnoses for each species are also included.

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Zapata, Sonia. "Contribution à l'étude des Psychodopygina d'Equateur (Diptera, Psychodidae, Phlebotominae) : Biologie et systématique." Thesis, Reims, 2012. http://www.theses.fr/2012REIMS031/document.

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Des prospections réalisées en Equateur (Amazonie et côte pacifique) ont permis la collecte d'un matériel entomologique abondant et diversifié, notamment chez les Psychodopygina. Nos travaux ont permis de réaliser plusieurs travaux de systématique, essentiellement moléculaire. Afin de tester les hypothèses phylogénétiques développées par Galati (2010), nous avons conduit une étude de phylogénie moléculaire chez les Psychodopygina. Basée sur les séquences des domaines D1, C2 et D2 de l'ADNr 28S et sur celles d'une partie du cytochrome b de l'ADNmt, elle inclut 49 espèces représentant les sept genres de la sous tribu et la majorité des sous-genres et séries. Les marqueurs ribosomiques sont mieux adaptés à la problématique que le marqueur mitochondrial. Le genre Psychodopygus est monophylétique. En raison du positionnement de Ny. richardwardi parmi les Trichophoromyia, nous concluons à la paraphylie des genres Nyssomyia et Trichophoromyia. Le genre Psathyromyia est également paraphylétique, tout comme le genre Martinsmyia. Le genre Bichromomyia serait le groupe frère du genre Psychodopygus et la validité du genre Vianniamyia, inclus dans le genre Psathyromyia doit être discutée. Des phylogénies moléculaires plus terminales ont été réalisées par comparaison de séquences de l'ITS2, de l'EF-1α et du cytochrome b.Chez les Psychodopygus de la série Guyanensis, une étude moléculaire couplée à une étude morphologique et morphométrique de morphotypes différents chez Ps. geniculatus, en sympatrie avec Ps. corossoniensis et Ps. luisleoni nous a conduit à décrire une espèce nouvelle pour la science : Ps. francoisleponti.Chez Pa. aragaoi, notre étude pilote basée sur l'analyse de morphotypes différents allopatriques et sympatriques renforce l'hypothèse de l'existence probable d'un complexe d'espèces chez ce taxon. Chez Ny. trapidoi, les analyses moléculaires et enzymatiques conduites sur des exemplaires clairs et foncés ne supportent pas la mise en évidence de deux populations comme cela avait été auparavant démontré. Nos approches épidémiologiques ont permis de mettre en évidence l'ADN d'Endotrypanum monterogeii chez plusieurs exemplaires de Ny. trapidoi. Si aucun phlebovirus n'a été détecté dans les échantillons étudiés, nous rapportons la présence d'un flavivirus chez Pa. abonnenci. Mots-clés: Psychodopygina, Equateur, ADN ribosomique, ADN mitochondrial, phylogénie, Endotrypanum
Most Ecuadorian sand flies studied so far belong to Psychodopygina sub tribe and the present research uses morphometric and modern molecular techniques to answer many some questions regarding this taxon in Ecuador. We present phenetic and phylogenetic analyses based on the sequences of the domains D1, C2 and D2 of the 28S rDNA and cytochrome b mtDNA were used to test the classification of Psychodopygina sub tribe proposed by Galati (2010). Our study includes 49 species representing the seven genera included in the sub tribe and its main subgenera and series. The results support the monophyly of the genus Psychodopygus. The genera Psathyromyia, Nyssomyia and Trichophoromyia are paraphyletic. Bichromomyia is the sister group of Psychodopygus and the validity of the genus Viannamyia is doubtful because it is included inside the Psathyromyia genus. Our data strongly suggest the presence of two populations within Ps. geniculatus and the lack of intermediate forms between these two morphotypes incited us to describe a new sympatric species, Psychodopygus francoisleponti.We also carried out a pilot study based on the analysis of different allopatric and sympatric morphotypes of Pa. aragaoi which suggested the existence of a possible complex of species in this taxa.Finally, we analyzed of mitochondrial gene sequences and isoenzymes from Ny. trapidoi collecte from Ecuador and our result did not support the existence of two sibling species within as previously reported in the literature. From an epidemiological point of view, we emphasize the probable vectorial role of Nyssomyia trapidoi for Endotrypanum monterogeii. Moreover, no phlebovirus was detected in the processed sand flies whereas a flavivirus has been found in a pool of Psathyromyia. abonnenci females.Key words: Psychodopygina, Ecuador, ribosomal DNA, mitochondrial DNA, phylogeny, Endotrypanum

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Helmersson, Erik. "Molecular identification of mosquito species : Evaluation of a rapid DNA extraction method together with DNA barcoding as a tool for identification of species." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-208957.

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The current method to determine a mosquito specimen to a certain species is by morphological keys basically following the taxonomy developed by Carl Linnaeus in the 1700. Since Watson and Crick presented their model of the double-helix DNA in 1953, a new era of molecular based taxonomic studies have revolutionized the field. The revolution is not in terms of how the classification of species is done but how the biological diversity is seen. However, morphological, ecological and behavioral characteristics are still important and are used together with the information a gene or whole genome can give. DNA barcoding is one of the promising methods for molecular identification. A small segment of a gene, approximately 400-1000 base pairs (bp), are examined by a Polymerase chain reaction (PCR) and sequencing. Like the barcodes in the grocery store these sequences work like unique ID: s for every species. This thesis shows how a fast DNA extraction method could be combined with DNA barcoding to get a 658-bp segment of the mitochondrial gene cytochrome c oxidase subunit 1 (COI) from different species of the mosquito family Culicidae. A total of 15 thoraxes or wings, from individual specimen of mosquitoes, were examined and 11 different barcode sequences could be retrieved. Six correspond to already published COI sequences and could therefore be determined to the species level, including a sequence from a new species for Sweden, Aedes (Ochlerotatus) nigrinus. All mosquitoes were collected during the national inventory of species in summer of 2012 in Sweden, ”Myggjakten”, and have been morphological examined by experts at the National Veterinary Institute (SVA) prior to molecular determination. This thesis also highlights the importance of building a reference library of barcode sequences, so DNA barcoding could become an effective diagnostic tool. Inventory projects like “Myggjakten” may, if repeated, provide excellent material for such a library collection of barcode data.
När en stickmyggsart skall artbestämmas är den vanligaste metoden att använda morfologiska nycklar. I princip görs det här efter den taxonomi som Carl von Linne utvecklade på 1700-talet. Men sedan Watson och Crick presenterade sin DNA modell 1953 så har dock en ny era av molykylärt baserade metoder revolutionerat taxonomin. Förändringen består egentligen inte i hur vi klassificerar och använder taxonomin utan mer hur vi ser på den biologiska mångfalden. Morfologiska och ekologiska studier, samt studier av arters beteende, är fortfarande viktiga och komplementerar den molekylära informationen från ett genom eller från en enstaka gen. DNA barcoding är en av de lovande nya molekylära metoderna för artbestämning. Ett litet segment av en gen, på ungefär 400-1000 baspar (bp), undersöks med hjälp av polymeras-kedjereaktion (PCR) och sekvensering. Likt streckkoder i livsmedelsbutiken ger metoden ett unikt ID för varje art. Den här studien visar hur en snabb DNA-extraktionsmetod kan kombineras med DNA barcoding, för att ge en 658-bp lång DNA-sekvens, från den mitokondriella genen cytokrom c oxidas subunit 1 (COI) från olika arter av myggfamiljen Culicidae. I undersökningen ingick 15 mellankroppar eller vingar från individuella stickmyggor och av dessa kunde 11 olika barcode sekvenser utläsas. Sex av dessa stämde överrens med redan publicerade COI-sekvenser och kunde bestämmas till artnivå, varav en av sekvenserna kommer från den nyligen i Sverige funna morfologiskt artbestämda Aedes (Ochlerotatus) nigrinus. Stickmyggorna i detta arbete insamlades av privatpersoner på olika ställen i Sverige under sommaren 2012 i det nationella mygginsamlingsprojektet ”Myggjakten”. Dessa artbestämdes morfologiskt av personal på Statens veterinärmedicinska anstalt (SVA) innan de artbestämdes molekylärt. Det här arbetet belyser även vikten av att bygga upp ett referensbibliotek av barcode sekvenser för att DNA-barcoding ska kunna bli ett effektivt diagnostiskt verktyg vid studier av vektorburna zoonoser. Nationella projekt som Myggjakten kan vara mycket användbara för insamling av sådana data.

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Lundin, Sverker. "Methods to Prepare DNA for Efficient Massive Sequencing." Doctoral thesis, KTH, Genteknologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-105116.

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Massive sequencing has transformed the field of genome biology due to the continuous introduction and evolution of new methods. In recent years, the technologies available to read through genomes have undergone an unprecedented rate of development in terms of cost-reduction. Generating sequence data has essentially ceased to be a bottleneck for analyzing genomes instead to be replaced by limitations in sample preparation and data analysis. In this work, new strategies are presented to increase both the throughput of library generation prior to sequencing, and the informational content of libraries to aid post-sequencing data processing. The protocols developed aim to enable new possibilities for genome research concerning project scale and sequence complexity. The first two papers that underpin this thesis deal with scaling library production by means of automation. Automated library preparation is first described for the 454 sequencing system based on a generic solid-phase polyethylene-glycol precipitation protocol for automated DNA handling. This was one of the first descriptions of automated sample handling for producing next generation sequencing libraries, and substantially improved sample throughput. Building on these results, the use of a double precipitation strategy to replace the manual agarose gel excision step for Illumina sequencing is presented. This protocol considerably improved the scalability of library construction for Illumina sequencing. The third and fourth papers present advanced strategies for library tagging in order to multiplex the information available in each library. First, a dual tagging strategy for massive sequencing is described in which two sets of tags are added to a library to trace back the origins of up to 4992 amplicons using 122 tags. The tagging strategy takes advantage of the previously automated pipeline and was used for the simultaneous sequencing of 3700 amplicons. Following that, an enzymatic protocol was developed to degrade long range PCR-amplicons and forming triple-tagged libraries containing information of sample origin, clonal origin and local positioning for the short-read sequences. Through tagging, this protocol makes it possible to analyze a longer continuous sequence region than would be possible based on the read length of the sequencing system alone. The fifth study investigates commonly used enzymes for constructing libraries for massive sequencing. We analyze restriction enzymes capable of digesting unknown sequences located some distance from their recognition sequence. Some of these enzymes have previously been extensively used for massive nucleic acid analysis. In this first high throughput study of such enzymes, we investigated their restriction specificity in terms of the distance from the recognition site and their sequence dependence. The phenomenon of slippage is characterized and shown to vary significantly between enzymes. The results obtained should favor future protocol development and enzymatic understanding. Through these papers, this work aspire to aid the development of methods for massive sequencing in terms of scale, quality and knowledge; thereby contributing to the general applicability of the new paradigm of sequencing instruments.

QC 20121126

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Valenzuela, Rodriguez Gian Pier. "DNA barcoding y delimitación de especies de la Familia Anostomidae en la cuenca amazónica peruana." Bachelor's thesis, Universidad Nacional Mayor de San Marcos, 2022. https://hdl.handle.net/20.500.12672/17868.

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La familia Anostomidae, que comprende especies comúnmente reconocidas como “lisas”, es considerada una de las más importantes dentro del orden Characiformes, siendo la segunda familia con mayor riqueza (sólo superada por Characidae), actualmente agrupa a 151 especies, de las cuales 90 son reportadas para la cuenca amazónica y 25 para Perú. En el presente trabajo, se utiliza metodologías moleculares, como los códigos de barras de ADN, que ayuda en la rápida y correcta identificación de especies y en el descubrimiento de posibles especies crípticas. Se obtuvo 169 secuencias del gen COI (subunidad I de la Citocromo Oxidasa) de 20 especies nominales, las cuales fueron identificadas taxonómicamente y los vouchers preservados para futuros estudios taxonómicos. Las especies pertenecen a diferentes cuencas principales en Perú: Ucayali, Marañón, Huallaga, Amazonas, Madre de Dios. De acuerdo al análisis de delimitación de especies (GMYC, PTP y bPTP) se logro identificar diversidad críptica dentro de la familia Anostomidae en Perú, discriminando 22 diferentes MOTUs (Unidades Taxonómicas Operacionales Moleculares), separando a las especies Leporinus pearsoni y Leporinus cf. parae en 2 MOTUs cada una, correspondiendo cada MOTU a una cuenca diferente (Alto Amazonas y Alto Madeira). Leporinus cf. parae, junto a Leporinus trimaculatus y Leporinus subniger pertenecen a un complejo, que suele ser identificado erróneamente como Leporinus friderici. El resultado obtenido sienta una base para realizar estudios taxonómicos integrativos en función a cada MOTU obtenida en este estudio. La técnica de ADN Barcoding y la de delimitación de Especies hicieron posible separar y reconocer especies dentro de la familia Anostomidae
Perú. Universidad Nacional Mayor de San Marcos. Fondo Nacional de Desarrollo Científico, Tecnológico y de Innovación Tecnológica (FONDECYT). Incertezas taxonómicas de especies de la familia Anostomidae con distribución en la Amazonia Peruana. Contrato 431-2019

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Ramos, Maíce Giovanini. "DNA Barcoding na identificação de espécies de tubarões exploradas comercialmente no litoral de São Paulo." Botucatu, 2016. http://hdl.handle.net/11449/150114.

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Orientador: Fábio Porto Foresti
Resumo: Atualmente estamos em uma corrida entre a descrição da biodiversidade da Terra e sua extinção. Estima-se que a maior parte dessa biodiversidade está sendo extinta antes mesmo de ser descrita. Dentre essa grande diversidade, os peixes são os vertebrados de maior sucesso evolutivo, caracterizando uma diversidade impressionante. Os tubarões, por exemplo, caracterizam em predadores do topo de cadeia alimentar, sendo descritas atualmente aproximadamente 500 espécies, e cada vez mais novas descobertas são feitas com relação a novas espécies. Porém as populações de tubarões estão em declínio devido ao consumo desenfreado de suas nadadeiras pelo mercado e comércio asiático. Soma-se a isso a grande dificuldade na identificação morfológica que é associada à prática de remoção da cabeça e de partes do corpo. A descaracterização pode dificultar, ou no caso de algumas espécies, até mesmo impossibilitar sua identificação. Portanto a necessidade de identificar as espécies de forma mais rápida e eficiente levou ao desenvolvimento de marcadores moleculares, que pudessem servir de respaldo para o monitoramento e controle do comércio desses animais. Uma dessas ferramentas é o DNA Barcode, o qual foi utilizado nesse trabalho para a identificação de nadadeiras coletadas no mercado de peixe de algumas cidades como Santos, Ubatuba e Cananéia do estado de São Paulo. O sequenciamento do gene mitocondrial Citocromo Oxidase subunidade I foi realizado. Posteriormente foram analisadas as sequências no si... (Resumo completo, clicar acesso eletrônico abaixo)
Mestre

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Brown, Carly. "Applications of DNA-barcoding in the identification and understanding of grass invasions in Southern Africa." Thesis, University of the Western Cape, 2014. http://hdl.handle.net/11394/4650.

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Magister Scientiae (Biodiversity and Conservation Biology)
The spread of invasive species is one of the greatest threats to global biodiversity. Alien plant invasions also have serious economic impact in terms of the delivery of ecosystem goods and services. Studies of biological invasions in southern Africa have tended to overlook grasses (family Poaceae), although there are many naturalised species in the region. Only a few of these, all perennials, have been officially categorised as invasive in South Africa, but in the winter rainfall region of the Western Cape, grass invasion especially by Mediterranean European annuals have also been noted. These grasses can be difficult to identify. DNA barcoding has been suggested as an alternative method of identifying grasses in the hope of facilitating identification of existing invaders and preventing future invasions. In this study a list of all known naturalised grasses in South Africa was compiled, and a DNA barcoding reference database was assembled for these naturalised grass species as well as for native southern African grass species. The two official markers for plant DNA barcoding (rbcLa + matK) were used in barcoding and phylogenetic analyses, both individually and in combination. The barcoding data was assessed for identification efficacy using three distance-based metrics and one tree-based metric in the R package SPIDER, both including and excluding singleton data. This study lists 128 naturalised grass species and subspecies found in South Africa. In the DNA barcoding analyses, matK was found to perform better as a single barcode than rbcLa, with identification success rates of up to 84% for matK and 76% for rbcLa, using the most successful metric which was the Nearest Neighbour criterion for both of these markers in the data sets without singletons. The combined rbcLa + matK data set performed better than either of the two individual markers, with identification success rates of up to 91% in the data without singletons, with the most successful metric again being the Nearest Neighbour criterion. The combined rbcLa + matK data would therefore be the recommended DNA barcode for southern African grasses of the three data sets tested, based on the results of this study. Phylogenetic trees were constructed with the DNA barcoding data using Bayesian Inference (BI) and Maximum Parsimony (MP) to assess the usefulness of the data in phylogenetic studies and to confirm the efficacy of this grass DNA barcoding data when using tree-based methods of identification. Both the matK and combined datasets resolved all of the grass tribes represented in this study as monophyletic, but the rbcLa data did not.

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