Dissertations / Theses on the topic 'Phylogenetic analyses'
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Fujisawa, Tomochika. "Statistical analyses of genealogical-phylogenetic data." Thesis, Imperial College London, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.556548.
Full textBandoni, Susan Marie. "Phylogenetic analyses of the Amphilinidea and Gyrocotylidea : (Cercomeria: Brooks, 1982)." Thesis, University of British Columbia, 1985. http://hdl.handle.net/2429/24472.
Full textScience, Faculty of
Zoology, Department of
Graduate
Thomas, Gavin Huw. "Sexual conflict, ecology and breeding systems in shorebirds : phylogenetic analyses." Thesis, University of Bath, 2004. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.413066.
Full textDonati, Beatrice. "Graph models and algorithms in (co-)evolutionary contexts." Thesis, Lyon 1, 2014. http://www.theses.fr/2014LYO10235/document.
Full textIn the results presented in the present manuscripts, graph theory and combinatorial optimizationtecniques, have been used to model and solve biological problems. The manuscript is divided in twoparts, each one containing the mathematical and biological background of a given application and ouroriginal contributions to it.Part I groups a set of results designed for phylogenetics analysis, and in particular for reconstructingthe co-evolution of two groups of organisms (the so called co-phylogeny reconstruction problem).Although the addressed problem was treated in the available there was no method that solved suchproblem in a complete and efficient way. We thus developed and implemented a new one, calledEucalypt, with this purpose in mind. This not only provides a novel and usable software for cophylogenyreconstruction but also allows to investigate how the event-based model performs inpractice in terms of thenumber and quality of the solutions obtained. We compared our method to the available software. Bylooking at the results obtained, some interesting considerations about the advantages anddisadvantages of the commonly accepted mathematical model could be drawn. Finally, we introduceda new version of the problem where the host-switches are distance bounded: the k-bounded-All-MPRproblem. Eucalypt solves both problems in polynomial delay. These results have been accepted forpublication by the jounal Algorithms for Molecular Biology. The relative software is publicyavailable.Our studies show that the 'most parsimonious scenario' approach presents some limitationsthat cannot be ignored. To deal with these problems, we developed a second algorithm, called Coala,based on an approximate Bayesian computation approach for estimating the frequency of the events.The benefits of this method are twofold: it provides more confidence in the set of costs to be used in areconciliation, and it allows to estimate the frequency of the events in the cases where a reconciliationmethod cannot be applied. These results are currently under review by the jounal Systematic Biology.The relative software is publicy available.In Part 2 another set of studies is presented. Our original model for the contig scaffolding problem,and our algorithm MeDuSa, are presented and tested. Unlike traditional software, it does not rely eitheron paired-end information of sequencing reads or on a phylogenetic distance of the microorganismsused in the analysis. This drastically increases the usability of our software and, at the same time,reduces the computational time required for genome scaffolding. We show that the algorithmimplemented in MeDuSa, in most cases, is capable of producing less and longer scaffolds incomparison to commonly used scaffolders, while maintaining high accuracy and correctness of thepredicted joins. These results are currently under revision by the journal Bioinformatics.Finally, during the development of this method we encountered some pure theoretical open problemsand we decided to dedicate part of our job to their analysis. The last chapter is then dedicated to a setof problems, all related to the Implicit Hitting set enumeration problem. After some formal definitions,an original NP-completeness result is presented and the future directions of our work are described
Milton, Joseph J. "Phylogenetic analyses and taxonomic studies of Senecioninae : southern African Senecio section Senecio." Thesis, St Andrews, 2009. http://hdl.handle.net/10023/701.
Full textStaron, Anna. "Phylogenetic and functional analyses of stress-responsive bacterial transmembrane signal transducing systems." Diss., lmu, 2012. http://nbn-resolving.de/urn:nbn:de:bvb:19-149558.
Full textBorner, Janus [Verfasser], and Thorsten [Akademischer Betreuer] Burmester. "Molecular phylogenetic analyses of Ecdysozoa and Haemosporida / Janus Borner ; Betreuer: Thorsten Burmester." Hamburg : Staats- und Universitätsbibliothek Hamburg, 2017. http://d-nb.info/1140166573/34.
Full textLehmann, Jörg. "Relative Timing of Intron Gain and a New Marker for Phylogenetic Analyses." Doctoral thesis, Universitätsbibliothek Leipzig, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-144067.
Full textGarcia-Pena, Gabriel Ernesto. "Phylogenetic comparative analyses of breeding systems and life-history strategies in shorebirds." Thesis, University of Bath, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.527144.
Full textLong, Peter. "Ecological and life-history basis of wetland bird conservation : phylogenetic and spatial analyses." Thesis, University of Bath, 2008. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.512313.
Full textFrancis, Ore. "Bioinformatics, phylogenetic and biochemical analyses of the proteins of the muskelin/RanBP9/CTLH complex." Thesis, University of Bristol, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.665153.
Full textSouza, Dennis Góss de. "Comparative analyses of microbial phylogenetic and functional processes following long-term land-use change." Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/91/91131/tde-05012016-152905/.
Full textNos últimos anos, ecologistas microbianos aumentaram drasticamente seus esforços para elucidar a \"caixa preta\" dos padrões e processos que modulam a diversidade e funcionalidade dos microrganismos do solo, examinando sua diversidade genética (e.g. através de metagenômica) e medindo suas características funcionais. O objetivo dessa tese foi avaliar a interação dos processos ecológicos de dispersão, diversificação, seleção e deriva gênica, sobre (1) as comunidades microbianas do solo, após a conversão da floresta em pastagem ou plantio direto, em longo período e (2) sobre as comunidades microbianas da rizosfera de soja, em sistema de plantio direto, em longo período. O cultivo de pastagens em longo período levou a uma seleção homogeneizante das comunidades microbianas, reduzindo a beta-diversidade, com conseguinte alteração em funções no solo relacionadas ao estresse. O plantio direto em longo período levou a uma menor alteração da diversidade, com manutenção das funções encontradas na floresta. A planta de soja demonstrou poder de seleção homogeneizante, e este aumentou com o tempo. Contudo, as funções selecionadas na rizosfera foram mantidas, indicando resiliência funcional.
Oliver, Jeffrey Catlin. "Population, Phylogenetic, and Coalescent Analyses of Character Evolution in Gossamer-Winged Butterflies (Lepidoptera: Lycaenidae)." Diss., The University of Arizona, 2007. http://hdl.handle.net/10150/194227.
Full textNürk, Nicolai M. [Verfasser]. "Phylogenetic analyses in St. John’s wort (Hypericum) : inferring character evolution and historical biogeography / Nicolai M. Nürk." Berlin : Freie Universität Berlin, 2011. http://d-nb.info/102635868X/34.
Full textMapaya, Ruvimbo Jessy. "Molecular and morphological phylogenetic analyses of Euphorbia L. (Euphorbiaceae) with an emphasis on Southern African representatives." Master's thesis, University of Cape Town, 2003. http://hdl.handle.net/11427/6131.
Full textThe genus Euphorbia is morphologically diverse and nearly cosmopolitan. Both succulent and non-succulent species are found within the genus. Succulent species are found in most arid and semi-arid areas of the world, but show their greatest concentration and diversity of form in Southern Africa especially the Cape Floristic Region. The monophyly and phylogenetic relationships of the genus Euphorbia were investigated based on morphology and on sequences of the nuclear ribosomal internal transcribed spacer (ITS) and chloroplast psbA-trnH intergenic spacer. Fifty-one species of Euphorbia and four outgroups from Monadenium and Ciutia were sampled. Matrices were analysed using parsimony and maximum likelihood methods. Separate analyses of data partitions resulted in largely non-conflicting topologies; therefore the data sets were combined. The results showed that the genus Euphorbia is paraphyletic and four monophyletic groups with a number of putative synapomorphies defining each clade were strongly supported in most analyses. The Cape succulents fall into two well-supported clades. The results thus provided evidence for Cape radiations. Most analyses indicated that one of the Cape groups is sister to a group consisting of species mostly from Southern Africa (excludingthe Cape Region). Increased taxon sampling is however needed to clarify relationships within the monophyletic groups. Morphological characters recovered broad groups within Euphorbia. Due to inadequate sampling in some sections, modifications in the present classification of Euphorbia are not suggested. The total evidence tree was used to explore morphological character evolution through character state optimisations. The presence of root tubers was homoplasious and this character state is hypothesized to have arisen at least five times under current sampling. Cylindrical stems, conspicuous leaves and absence of leaf spines were some of the pleisiomorphic states observed in some sampled members of the genus Euphorbia. Although the results obtained in the CUlTent study are preliminary, they have created further challenges for future studies of phylogenetic relationships and morphological character evolution in the genus Euphorbia.
Achigan-Dako, Enoch G. "Phylogenetic and genetic variation analyses in cucurbit species (Cucurbitaceae) from West Africa : definition of conservation strategies /." Göttingen : Cuvillier, 2008. http://d-nb.info/991005759/04.
Full textRybalka, Nataliya [Verfasser]. "Assessing phylogenetic delineations of taxa of filamentous Xanthophyceae (Stramenopiles) using DNA sequence analyses and morphology / Nataliya Rybalka." Kiel : Universitätsbibliothek Kiel, 2016. http://d-nb.info/1100397507/34.
Full textBhatnagar, Srijak. "Identification of Factors That Drive Taxonomic, Phylogenetic, and Functional Composition of Microbial Communities Using DNA Sequence Analyses." Thesis, University of California, Davis, 2017. http://pqdtopen.proquest.com/#viewpdf?dispub=10623208.
Full textMicrobial life represents the majority of the diversity of life on planet earth. Microbes are found in all ecosystems. The microbial community of an ecosystem can be an indicator of its health and the foundation of the ecosystem function. Thus, an understanding of the microbial community of an ecosystem is vital to understanding the ecosystem itself. To fully grasp the microbial community structure, it is essential to understand the factors that shape the community composition and diversity of the ecosystem. This works focusses on the primary drivers of microbial composition in three ecosystems: an estuary, the gut of Drosophila melanogaster, and walnut grove soil.
In the benthic estuarine environment of Trunk River, physical perturbations in the water column above decaying seagrass altered the composition of the microbial community causing a visible microbial bloom. To understand the microbial community progression in the bloom, we simulated perturbed sites in the river and studied four different depths in the water column for two weeks. We found the bloom was largely made up of Prosthecochloris vibrioformis, a phototrophic sulfur oxidizer. The bloom appears to be driven by pH, salinity, and sulfide gradients, forming at a depth of ≈ 25cm beneath the surface of the water.
For the third chapter, we explored the effect of host diet on its gut microbial community. We created a controlled experiment in Drosophila melanogaster, a model organism. A population of D. melanogaster preconditioned on a balanced lab diet was split into two treatment diets, a high-sugar diet and a high-yeast diet. The microbial communities in the fecal matter of the flies were sampled for 4 days to understand their compositional changes. We found that a shift in the diet of D. melanogaster changed the phylogenetic, taxonomic, and functional compositions of the microbial communities. Each dietary change led to a distinct taxonomic, phylogenetic, and functional composition by the end of the experiment. The functional diversity of both treatment groups decreased, indicating a shift away from a diverse set of metabolic capabilities when subjected to a more comprehensive nutrition to a more specific set of metabolic capabilities adapted for the main nutrient, either sucrose or yeast extract.
In the fourth chapter, Pesticide-treated orchard soils were used to understand the effects of deliberate intervention (external factors) on microbial ecosystems. We also studied the potential of pathogens to colonize soil that had been exposed to such external factors. In a controlled experiment, soil was subjected to different fumigation treatments with and without subsequent amendment. It was then inoculated and incubated with Agrobacterium tumefaciens. The results indicate a fumigant-specific shift in the phylogenetic, taxonomic, genic, and functional composition of the soil. The low diversity fumigated soil was also better colonized by the A. tumefaciens. However, post-fumigation amendment with vermicompost increased the diversity, shifting the compositions towards non-fumigated vermicompost and suppressing A. tumefaciens colonization.
With this work, we have been able to implicate some of the important factors at play in the determination of microbial composition in various ecosystems. Additionally, we showed that the influence of these factors on microbial community is measurable on different metrics of composition.
Staroń, Anna [Verfasser], and Thorsten [Akademischer Betreuer] Mascher. "Phylogenetic and functional analyses of stress-responsive bacterial transmembrane signal transducing systems / Anna Staron. Betreuer: Thorsten Mascher." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2012. http://d-nb.info/1027669476/34.
Full textDiallo, Abdoulaye. "Inference of insertion and deletion scenarios for ancestral genome reconstruction and phylogenetic analyses: algorithms and biological applications." Thesis, McGill University, 2009. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=40771.
Full textCette thèse traite d'algorithmes pour la reconstruction de génomes ancestraux et l'analyse phylogénétique. Elle étudie particulièrement les scénarios d'insertion et délétion (indels) dans les séquences génomiques, leur utilité (1) pour l'étude des familles d'espèces, (2) pour l'évaluation des alignements multiples de séquences et la reconstruction phylogénétique, (3) et pour l'annotation de séquences génomiques fonctionnelles. Dans cette thèse, le problème de la reconstruction du scénario d'indels est étudié en utilisant le critère de maximum de vraisemblance. Ce problème peut être défini de la manière suivante: étant donné un alignement multiple de séquences orthologues et un arbre phylogénétique traduisant l'histoire évolutive de ces séquences, reconstruire le scénario d'indels le plus vraisemblable capable d'expliquer les brèches présentes dans l'alignement. Ce problème, dénommé ''Indel Maximum Likelihood Problem (IMLP)'', est une importante étape de la reconstruction de séquences ancestrales. Il est également important pour l'étude des processus évolutifs, des fonctions des gènes, de l'adaptation et de la convergence.Dans une première étape de cette thèse, nous montrons que l'IMLP peut être résolu en utilisant un nouveau type de données combinant un arbre phylogénétique et un modèle de Markov caché. Les états de ce modèle de Markov caché correspondent à un scénario évolutif d'une colonne de l'alignement. Ses transitions modélisent la dépendance entre les colonnes voisines de l'alignement.Les algorithmes standard de Viterbi et de Forward-Backward ont été optimisés pour produire le scénario ancestral le plus vraisemblable et pour calculer le niveau de confiance associé aux prédictions. Dans cette thèse, Nous présentons également une heuristique qui permet d'adapter la méthode à des données de grandes tailles. En second, nous montrons l'utilité du score d'indel dans l'évaluatio
Maß, Janina [Verfasser], Martin [Gutachter] Lercher, and Andreas P. M. [Gutachter] Weber. "Phylogenetic Analyses on the Evolution of C4 Photosynthesis / Janina Maß ; Gutachter: Martin Lercher, Andreas P. M. Weber." Düsseldorf : Universitäts- und Landesbibliothek der Heinrich-Heine-Universität Düsseldorf, 2020. http://d-nb.info/1223705374/34.
Full textFijridiyanto, Izu Andry. "Phylogenetic analyses of Malesian Litsea Lam.(Lauraceae) and related genera based on the chloroplast and nuclear genomes." 京都大学 (Kyoto University), 2009. http://hdl.handle.net/2433/124461.
Full textGao, Yu. "Isolation, expression, purification and characterisation of a novel acetyl xylan esterase from streptomyces species ORS10." Thesis, University of the Western Cape, 2012. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_7860_1339756096.
Full textLignocellulosic biomass represents an important renewable resource for biofuels production. Lignocellulosic biomass is comprised of cellulose, hemicellulose and lignin. Lignocellulosics are highly recalcitrant to enzymatic degradation and due to its complex nature a range of enzymes are required to synergistically hydrolyse biomass. Many microorganisms are capable of producing these enzymes as part of their hemicellulolytic hydrolysis system(s). The aim of this study was the characterisation of a thermophilic actinobacterial isolate (ORS10), capable of producing hemicellulosic enzymes, and the cloning and characterization of a hemicellulosic enzyme produced by the isolate. Phylogenetic analyses clustered ORS10 with species of the genus Streptomyces. BLAST analysis revealed that ORS10 was most closely related to Streptomyces achromogenes (99% identity). A small-insert genomic library was constructed and a putative acetylxylan esterase (AXEase) gene, axe10, was identified. The enzyme, Axe10, has moderate similarity to &alpha
/&beta
hydrolase proteins, and contains an esterase/lipase superfamily conserved domain and a typical AXEase catalytic triad. The axe10 gene was sub-cloned into an expression vector [pET21a(+)] and a 28.7 kDa protein with demonstrated AXE activity was purified from E. coli Rosetta (DE3) pLysS. Axe10 displayed optimum activity at 37oC and pH 7.0. Despite being derived from a thermophilic Streptomyces species Axe10 was not thermostable. However, given the relative novelty of Axe10, further characterisation and assessment of this enzyme is warranted.
Juswara, Lina S. "Phylogenetic Analyses of subtribe Goodyerinae and Revision of Goodyera section Goodyera (Orchidaceae) from Indonesia, and Fungal Association of Goodyera section Goodyera." The Ohio State University, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=osu1275490522.
Full textRobinson, Stacie Joy. "Landscape genetics of black bears (Ursus americanus) on the Kenai Peninsula, Alaska : phylogenetic, population genetic and spatial analyses /." PURL, 2007. http://www.arlis.org/docs/vol1/166237019.pdf.
Full textTakishita, Kiyotaka. "Molecular phylogenetic analyses of nuclear- and plastid- encoded genes from dinoflagellates: Implication for origin of the dinoflagellate plastid." Kyoto University, 2000. http://hdl.handle.net/2433/151594.
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新制・課程博士
博士(農学)
甲第8563号
農博第1146号
新制||農||809(附属図書館)
学位論文||H12||N3442(農学部図書室)
UT51-2000-M27
京都大学大学院農学研究科応用生物科学専攻
(主査)教授 内田 有恆, 教授 中原 紘之, 教授 大山 莞爾
学位規則第4条第1項該当
Nakano, Takafumi. "Systematic Revision of the Monotypic Family Orobdellidae (Hirudinida: Arhynchobdellida: Erpobdelliformes), with Molecular Phylogenetic Analyses of the Known Orobdellid Species." 京都大学 (Kyoto University), 2013. http://hdl.handle.net/2433/180531.
Full textLien, Yi-Tiang. "Molecular phylogenetic and ecological analyses of algal endosymbionts (zooxanthellae) in the scleractinian corals in the temperate region of Japan." Kyoto University, 2013. http://hdl.handle.net/2433/175072.
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新制・課程博士
博士(農学)
甲第17643号
農博第2005号
新制||農||1012(附属図書館)
学位論文||H25||N4764(農学部図書室)
30409
京都大学大学院農学研究科応用生物科学専攻
(主査)教授 山下 洋, 教授 左子 芳彦, 教授 朝倉 彰
学位規則第4条第1項該当
Knapp, Sonja. "Plant biodiversity in urbanized areas analyses of plant functional traits in space and time, plant rarity and phylogenetic diversity." Wiesbaden Vieweg + Teubner, 2009. http://d-nb.info/995192685/04.
Full textKahloul, Senda. "Analyse structurale et fonctionnelle de la sous-unité SKP1 du complexe SCF (Skp1-Cullin-Fbox) chez le riz (Oryza sativa)." Thesis, Clermont-Ferrand 2, 2012. http://www.theses.fr/2012CLF22326/document.
Full textIn eukaryotes, the ubiquitin Ub/26S proteasome pathway is responsible for the selective degradation of most intracellular proteins. This cellular process is initiated by protein polyubiquitination mediated by a three-step cascade involving: an ubiquitin-activating enzyme (E1), an ubiquitin-conjugating enzyme (E2) and an ubiquitin-protein ligase (E3). The E3 ubiquitin ligases contain several classes, among which the best-known are Skp1-Cullin-F-box (SCF) complexes. The SKP1 protein binds both Cullin and F-box which recognizes specifically the target proteins. Whereas protists, fungi and some vertebrates have a single functional SKP1 gene, many animal and plant species possess multiple SKP1 homologues. Twenty one and thirty-two SKP1-related genes have been described respectively in the Arabidopsis and Oryza sativa genome. Despite the importance of the SCF complex, there have been a few reports of systematic surveys of interactions between the dozens of SKP1-like proteins and the hundreds of F-box proteins in rice. In a first step, we retrieved and analyzed 288 SKP1-like genes belonging to 17 species including the moss Physcomitrella patens, five monocots and 11 eudicots. Structural and phylogenetic analysis of rice OSK genes and other plant SKP1-like genes have indicated that the different members of the plant SKP1 can be split into different subfamily. Our analyses indicated that OSK1 and OSK20 belong to a class of SKP1 genes that contain one intron at a conserved position. In a second step, we studied expression profiles of the rice Skp1-like genes. Our EST survey indicated that OSK1 and OSK20 are the most widely represented genes in public EST databases. Meta-analysis of the expression of rice SKP1-like genes indicated that OSK genes exhibit an expression profile that was heterogeneous in terms of tissues, conditions and overall intensity. Yeast two-hybrid results revealed that OSK proteins display a differing ability to interact with F-box proteins. However, OSK1 and OSK20 seemed to interact with most F-box proteins tested. Subcellular localization studies indicated that OSK1 and OSK20 are nuclear and cytosolic proteins. Based on the results obtained in this study, we can suggest that rice OSK1 and OSK20 are likely to have similar functions as do the Arabidopsis ASK1 and ASK2 genes. Similarly, we suggest a list of functional equivalent in the other sequenced plant genomes
Ohsako, Takanori. "Classification and phylogenetic analyses of the genus Fagopyrum (Polygonaceae) including two new species based on morphological and nucleotide sequence data." Kyoto University, 2000. http://hdl.handle.net/2433/181042.
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新制・課程博士
博士(農学)
甲第8413号
農博第1097号
新制||農||798(附属図書館)
学位論文||H12||N3370(農学部図書室)
UT51-2000-F317
京都大学大学院農学研究科応用生物科学専攻
(主査)教授 大西 近江, 教授 遠藤 隆, 教授 津田 盛也
学位規則第4条第1項該当
Page, Timothy J., and n/a. "An Evolutionary History of the Freshwater Shrimp Family Atyidae in Australia." Griffith University. Australian School of Environmental Studies, 2007. http://www4.gu.edu.au:8080/adt-root/public/adt-QGU20070725.120145.
Full textPage, Timothy J. "An Evolutionary History of the Freshwater Shrimp Family Atyidae in Australia." Thesis, Griffith University, 2007. http://hdl.handle.net/10072/367826.
Full textThesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Australian School of Environmental Studies
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Schneider, Ulrike Julia [Verfasser], M. [Akademischer Betreuer] Röser, M. E. [Akademischer Betreuer] Barkworth, and F. R. [Akademischer Betreuer] Blattner. "Molecular phylogenetic analyses and classification of the Pooideae (Poaceae) : [kumulative Dissertation] / Ulrike Julia Schneider. Betreuer: M. Röser ; M. E. Barkworth ; F. R. Blattner." Halle, Saale : Universitäts- und Landesbibliothek Sachsen-Anhalt, 2013. http://d-nb.info/1047097060/34.
Full textCarvajal, Campos Amaranta. "Characterization of Aspergillus section Flavi : molecular markers as tools to unmask cryptic species." Thesis, Toulouse 3, 2018. http://www.theses.fr/2018TOU30036/document.
Full textSome fungi, mostly Ascomycota, are able to synthesize secondary metabolites that are toxic to humans and vertebrates, called mycotoxins. Since the presence of these fungi in staples represents a potential risk to human and livestock health, staples are eliminated when they are contaminated. The section Flavi is one most important group of fungi from an economic and public health point of view because it comprises several mycotoxin producer species. Amongst the mycotoxins produced by this group are aflatoxins (AFs), considered a main concern because of their deleterious effects on humans and vertebrates. Species from section Flavi grow mainly in tropical and subtropical regions where environmental conditions are optimal, and harvest and storage conditions are not always appropriate to avoid production of mycotoxins, which enhance their growth. In temperate regions, these species are less frequent; however, climate changes can favor their colonization. Species identification in Aspergillus section Flavi is challenging because of inter- and intra- variability of traits. Therefore, the use of one identification method (morphological, molecular or secondary metabolite profile characterization) is futile. Conversely, the development of molecular tools has facilitated the task. The aim of this study was to screen the species relationships in Aspergillus section Flavi based on different molecular markers (ITS, benA, cmdA, amdS, preA, preB, ppgA, aflP, Mat1 genes), and subsequently identify which ones allow a fine species classification in the section Flavi by phylogenetic inference. The use of phylogenetic inference in the present study showed that it is a robust approach to identify Aspergillus section Flavi species. The use of this technique confirmed some of the hypotheses proposed in the Flavi section, since more genetic information was added, thus strengthening the placement of the species in the Flavi section. In addition, we described a new cryptic species in this section Aspergillus korhogoensis that is nested in A. flavus clade as the sister taxon of A. parvisclerotigenus. Likewise, the molecular markers (benA, cmdA, mcm7, rpb1, preB, preA or ppgA) were good candidates for studying other sections in Aspergillus. The use of phylogenetic inference is a good method for fine-scale species identification; however, it should be used carefully, and the morphological approach and characterization of secondary metabolites should also be carried out. Based on our results, concatenated matrices are recommended to perform phylogenetic inference in this section, and the best combination includes benA, cmdA, and the inclusion of at least one another gene (preB, mcm7, rpb1, preA or ppgA). Conversely, the use of ITS in Aspergillus may lead to an underestimation of the diversity because the gene is highly conserved. Studying mating type MAT1 loci in the section is helpful to increase the knowledge of sexual reproduction in ascomycetes. In addition, several functions of fungal biological machinery are linked to Mat1 loci genes. Secondary metabolic profile characterization of Aspergillus section Flavi strains should be performed, not only as an identification tool, but also to discriminate toxinogenic and atoxinogenic strains. Section Flavi encloses species able to produce a mixture of mycotoxins and beneficial compounds. Amongst mycotoxins that should be screened are AFs, cyclopiazonic acid, A and B versicolorin, sterigmatocystin, tenuazonic acid. An exhaustive study of the secondary metabolism can also be useful to investigate novel beneficial products
Chennakrishnaiah, Shilpa. "Analysis of Y-chromosome Diversity in Lingayat and Vokkaliga Populations of Southern India." FIU Digital Commons, 2011. http://digitalcommons.fiu.edu/etd/423.
Full textMayberry, Jason Robert. "Through the eyes of bat flies| Behavioral, phylogenetic, and histological analyses of compound eye reduction in bat flies (Streblidae) provide evidence for positive selection." Thesis, State University of New York at Buffalo, 2015. http://pqdtopen.proquest.com/#viewpdf?dispub=3714642.
Full textIt is often presumed that evolutionary reduction is tantamount to deconstruction, or even destruction, because relaxed selective forces have been insufficient to maintain the organ in its original state. However, studies on reduction are often limited by a lack of diversity, both of related species exhibiting reduction and of the reduced form itself. There have also been very few studies on the reduction of compound eyes, despite the fact that their near ubiquity among arthropods alone makes them perhaps the most common type of eye. Bat flies (Streblidae and Nycteribiidae) are a group of dipterans that exhibit variable degrees of compound eye reduction, and therefore provide the opportunity to study reduction of this organ in a phylogenetic context. The first chapter of this work reports on behavioral experiments demonstrating that the eyes of one bat fly species, Trichobius frequens, are functional, and that they neither exhibit phototaxis typical of other dipteran species, nor move toward a light source. The second chapter uses molecular phylogenetics to identify a correlation between eye and wing morphology. The results also suggest that secondary to their eye reduction, bat flies (at least in the case of New World specie, including Trichobius spp.) have secondarily experienced a shift in the structure of their facets that is convergent with other insects whose eyes have been selected for increased sensitivity. In the final chapter, histological and optical analyses of T. frequens eyes are used to reveal significant structural changes to the microstructure of its ommatidia that increase sensitivity at the expense of acuity. Many of these changes are also convergent with similar adaptations that have been demonstrated to increase sensitivity in organisms that function in reduced light environments. The results of these analyses suggest that reduction in T. frequens eyes may have been part of an active remodeling process resulting from a shift in the relative importance of sensitivity and acuity. As this is a process of reduction not generally considered, the findings here turn our attention to alternative hypotheses that should be considered when studying evolutionary reduction of any organ.
Lehmann, Jörg [Verfasser], Peter F. [Akademischer Betreuer] Stadler, Peter F. [Gutachter] Stadler, and Burkhard [Gutachter] Morgenstern. "Relative Timing of Intron Gain and a New Marker for Phylogenetic Analyses / Jörg Lehmann ; Gutachter: Peter F. Stadler, Burkhard Morgenstern ; Betreuer: Peter F. Stadler." Leipzig : Universitätsbibliothek Leipzig, 2014. http://d-nb.info/1238602053/34.
Full textFabillo, Melodina. "Leaf and inflorescence structure and phylogenetics of Tripogon and affiliated genera (Poaceae: Chloridoideae)." Thesis, Queensland University of Technology, 2015. https://eprints.qut.edu.au/83726/1/Melodina_Fabillo_Thesis.pdf.
Full textMilinkovitch, Michel. "Phylogenetic analyses of molecular data in vertebrates with special emphasis on the implications of mitochondrial DNA sequences for reevaluating morphological and behavioral evolution in cetaceans." Doctoral thesis, Universite Libre de Bruxelles, 1994. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/212689.
Full textKaleme, Prince K. "Habitat fragmentation, patterns of diversity and phylogeography of small mammal species in the Albertine rift." Thesis, Stellenbosch : Stellenbosch University, 2011. http://hdl.handle.net/10019.1/18110.
Full textENGLISH ABSTRACT: The Albertine Rift is characterized by a heterogeneous landscape which may, at least in part, drive the exceptional biodiversity found across all taxonomic levels. Notwithstanding the biodiversity and beauty of the region, large areas are poorly understood because of political instability with the inaccessibility of most of the region as a contributing factor. The majority of studies in the Albertine Rift have focussed on charismatic mega fauna, with other taxa receiving less attention. One of the taxonomically and numerically more abundant small mammal genera is the genus Praomys, an African endemic with a wide distribution range spanning most of west, central and east Africa. Four species are typically recognized from the Albertine Rift namely P. degraaffi, P. jacksoni, P. misonnei and P. verschureni. In this study I used a combination of DNA sequence data (mitochondrial control region, mitochondrial cytochrome b and 7th intron of the nuclear ß-fibrinogen gene) as well as morphometric data (traditional and geometric) to investigate the systematics of the Praomys taxa occurring in the Albertine Rift. To allow meaningful DNA assessments and in an attempt to identify potential drivers of diversifications, other Praomys species were also included from public sequence data bases for comparisons. The main focus was on P. jacksoni (the numerically most abundant taxon; also, up to 2005, all Praomys in the Albertine Rift were mostly collected as “jacksoni”) and P. degraaffi (an Albertine Rift endemic). A surprising finding was the presence of P. mutoni; this represents a range extension for this species into the Albertine Rift. Distinct evolutionary lineages were found in both P. jacksoni (confirmed by sequence data as well as morphometrics) as well as P. degraaffi (based only on sequence data; insufficient samples precluded a full morphometric investigation). These lineages (in both P. jacksoni as well as P. degraaffi) appear to be separated along a north – south gradient; however, further investigations should confirm this. To further investigate the genetic patterns at local scales across the Albertine Rift, as well as introgression between species as revealed by sequence data, a species-specific microsatellite library was developed for P. jacksoni. Twelve polymorphic markers were identified of which nine also amplified in P. degraaffi. Introgression was confirmed between the two focal species with almost 20% of the individuals analysed being jacksoni-degraaffi hybrids. This is perhaps not so surprising given that there is considerable overlap in their ranges (between ~ 1500 m a.s.l. to 2450 m a.s.l.) as well as the relative ages of the species (the divergence time between these two species were estimated at 3.8 Mya). The presence of distinct lineages within each of these species was confirmed by microsatellite analyses (these lineages diverged approcimately at same time at ca. 3.4 Mya). As suggested by sequence and morphometric data, these lineages had a largely north – south distribution but with considerable overlap in the central Albertine Rift in the vicinity of Lake Kivu. The phylogeographic patterns obtained for both focal species were not consistent with the physical barriers such as the rivers, lakes or mountains, nor were they exclusively associated with Pleistocene phenomena such as the change of the course of the rivers or uplift; rather, the lineages predate the Pleistocene and fall firmly in the Pliocene (>3 Mya). Biogeographically, the north - south location of lineages with a centrally - located contact zone could be a result of parapatric speciation due to habitat fragmentation or past climate change, followed by secondary contact. Barcoding using genetic information provides a useful tool to identify unknown taxa, cryptic diversity or where different life stages are difficult to identify. From an invasion biology perspective, it allows for the rapid identification of problem taxa against a known data base. By adopting such a barcoding approach (senso lato), the presence of three invasive rodents was confirmed in the Democratic Republic of the Congo (DRC); these are Rattus rattus (black rat), R. norvegicus (Norway rat) and Mus musculus domesticus (house mouse). A comparison with global data available for these species revealed two possible introduction pathways namely via the shipping port at Kinshasa/Matadi (with strong links to Europe) and via the slave trade routes in the east (strong links to the Arab world and the east). Of these three taxa, only R. rattus is currently documented from the DRC although the others have received mention in the gray literature. These findings draw attention to the lack of any official policy regarding biosecurity in the DRC, and argue for the development of strict control measures to prevent further introductions.
AFRIKAANSE OPSOMMING: Die Albertine Rift word gekenmerk deur 'n heterogene landskap wat kan, ten minste gedeeltelik, die uitsonderlike biodiversiteit wat oor al die taksonomiese vlakke gevind word teweeg bring. Nieteenstaande die biodiversiteit en die skoonheid van die streek, is groot gebiede onbekend as gevolg van politieke onstabiliteit met die ontoeganklikheid van meeste van die streek as 'n bydraende faktor. Die meerderheid van studies in die Albertine Rift het gefokus op die charismatiese mega fauna, met ander taxa wat minder aandag ontvang. Een van die taksonomies en numeries meer volop klein soogdier genera is die genus Praomys, 'n Afrika endemiese groep met 'n wye verspreiding wat strek oor die grootste deel van van wes-, sentraal en oos-Afrika. Vier spesies word tipies erken van die Albertine Rift naamlik P. degraaffi, P. jacksoni, P. misonnei en P. verschureni. In hierdie studie het ek 'n kombinasie van DNA volgorde data (mitochondriale beheer streek, mitochondriale sitochroom b en 7de intron van die kern ß-fibrinogeen geen) sowel as morfometriese data (tradisioneel en meetkundig) gebruik om die sistematiek van die Praomys taxa te ondersoek. Om betekenisvolle DNA aanslae toe te laat en in 'n poging om potensiële aandrywers van diversiteit te identifiseer, is ander Praomys spesies van openbare volgorde data basisse vir vergelykings ingesluit. Die hooffokus is op P. jacksoni (die numeries volopste takson, ook, tot en met 2005 is alle Praomys in die Albertine Rift meestal as "jacksoni" versamel) en P. degraaffi ('n Albertine Rift endemiese spesie). 'n Verrassende bevinding was die teenwoordigheid van P. mutoni, dit verteenwoordig' n verspreidingsuitbreiding vir hierdie spesie in die Albertine Rift. Bepaalde evolusionêre ontwikkelingslyne was in beide P. jacksoni (bevestig deur die volgorde data sowel as morfometrie) sowel as P. degraaffi (wat slegs gebaseer is op die volgorde data, onvoldoende monsters verhinder 'n volledige morfometriese ondersoek). Hierdie lyne (in beide P. jacksoni sowel as P. degraaffi) word geskei langs 'n noord - suid gradiënt, maar verdere ondersoeke moet dit bevestig. Om die genetiese patrone op plaaslike skaal oor die Albertina Rift verder te ondersoek, sowel as introgressie tussen spesies soos geopenbaar deur die volgorde data, is 'n spesie-spesifieke mikrosatelliet biblioteek ontwikkel vir P. jacksoni. Twaalf polimorfiese merkers is geïdentifiseer waarvan nege ook amplifiseer in P. degraaffi. Introgressie is bevestig tussen die twee brandpunt spesies met byna 20% van die individue wat ontleed is as jacksoni-degraaffi basters. Dit is miskien nie so verbasend gegee dat daar aansienlike oorvleueling is in hul gebiede (tussen ~ 1500 m bo seespieel tot 2450 m bo seespieel), sowel as die relatiewe ouderdomme van die spesies (die divergensie tussen hierdie twee spesies is geskat op 3,8 Mya). Die teenwoordigheid van verskillende lyne in elk van hierdie spesies is bevestig deur mikrosatelliet ontleding (hierdie lyne het gedivergeer ongeveer 3,4 Mya). Soos voorgestel deur die DNA volgorde en morfometriese data, het hierdie lyne 'n grootliks noorde – suid verspreiding, maar met 'n aansienlike oorvleueling in die sentrale Albertine Rift in die omgewing van die Kivumeer. Die filogeografiese patrone wat vir beide die brandpunt spesies gevind is nie in ooreenstemming met die fisiese struikelblokke soos die riviere, mere of berge nie, en hou ook nie uitsluitlik verband met die Pleistoseen verskynsels soos die verandering van die loop van die riviere nie; die afstammelinge is eerder veel ouer as die Pleistoseen en val binne die Plioseen (> 3 Mya). Biogeografies, die noorde – suid plasing van die lyne met 'n sentraal geleë kontak sone kan die gevolg wees van parapatriese spesiasie te danke aan habitatfragmentasie as gevolg van verandering in die klimaat, gevolg deur 'n sekondêre kontak. Strepieskodering met behulp van genetiese inligting verskaf 'n nuttige instrument om onbekend taxa, kriptiese diversiteit of waar verskillende lewensfases moeilik is om te identifiseer, te identifiseer. Vanuit 'n indringerbiologie perspektief, maak hierdie benadering dit moontlik om vinnige identifikasies van die probleem taksa teen' n bekende data basis te bekom. Deur gebruik te maak van so 'n strepieskoderingsbenadering (senso lato), is die teenwoordigheid van drie indringende knaagdiere bevestig in die Demokratiese Republiek van die Kongo (DRK), naamlik Rattus rattus (swart rot), R. norvegicus (Noorweë rot) en Mus musculus domesticus (huis muis). 'n Vergelyking met die globale data wat beskikbaar is vir hierdie spesies het aan die lig gebring dat twee moontlike betree-roetes bestaan, naamlik via die skeepshawe by Kinshasa / Matadi (met sterk skakels na Europa), en via die slawehandel roetes in die ooste (sterk skakels na die Arabiese wêreld en die ooste) . Van hierdie drie taxa, is tans slegs R. rattus van die Demokratiese Republiek van die Kongo gedokumenteer, hoewel die ander melding ontvang in die grys literatuur. Hierdie bevindinge vestig die aandag op die gebrek aan enige amptelike beleid ten opsigte van biosekuriteit in die Demokratiese Republiek van die Kongo, en argumenteer vir die ontwikkeling van streng beheermaatreëls om verdere indringerspesies te voorkom.
Kaspari-Marghussian, Armineh. "Reassessing the prehistoric ceramics of the Late Neolithic and Transitional Chalcolithic periods in the Central Plateau of Iran : archaeometric characterisation, typological classification and stylistic phylogenetic analyses." Thesis, Durham University, 2017. http://etheses.dur.ac.uk/12355/.
Full textZen, Siqueira Joao Paulo. "Clinical and environmental Aspergillus: morphological and molecular characterization, phylogeny, and antifungal susceptibility profile." Doctoral thesis, Universitat Rovira i Virgili, 2017. http://hdl.handle.net/10803/456300.
Full textAspergillus es uno de los géneros de Ascomycetes más comunes y ubicuos, habitando una gran diversidad de sustratos. El objetivo principal de esta tesis fue contribuir al mejor conocimiento de este género, explorando la diversidad de especies en muestras clínicas y ambientales. En esta tesis se estudió un total de 433 aislamientos obtenidos de diferentes fuentes (muestras clínicas, suelo, estiércol de animales herbívoros, y restos vegetales). La identificación de los aislamientos se llevó a cabo mediante análisis filogenéticos de múltiples marcadores, incluyendo secuencias de ITS, β-tubulina, calmodulina, y RPB2, y por caracterización fenotípica. Cuando se consideró relevante, los aislamientos clínicos fueron sometidos a pruebas de susceptibilidad antifúngica frente a los principales fármacos disponibles. En resumen, se identificaron 98 especies de Aspergillus, 49 de muestras clínicas (248 aislamientos), 48 de suelo (92 aislamientos), 48 de estiércol (82 aislamientos) y 10 de restos vegetales (10 aislamientos). Considerando las secciones poco estudiadas de Aspergillus en el contexto clínico, las secciones más frecuentes fueron Nidulantes (incluyendo la antigua sección Versicolores), con 84 aislamientos y 14 especies; Circumdati, con 35 aislamientos y siete especies; Aspergillus, con 25 aislamientos y cinco especies; y Usti, con 19 aislamientos y dos especies. Ocho especies fueron aisladas de muestras clínicas por primera vez y tres fueron propuestas como nuevas especies. Los antifúngicos, en general, mostraron buena actividad frente a los aislados ensayados, con la excepción de la actividad reducida de anfotericina B contra miembros de la sección Circumdati. En cuanto a los aislamientos ambientales, se propusieron 14 nuevas especies basadas en caracteres fenotípicos y moleculares; cinco pertenecientes a la sección Terrei (tres de estiércol y dos de tierra); cuatro a la sección Candidi (todos de estiércol); dos a la sección Nidulantes (ambos de suelo); y una de cada una de las secciones Flavipedes, Cremei, y Usti (todos de estiércol).
Aspergillus is one of the most common and ubiquitous genus of Ascomycetes, inhabiting a great diversity of environmental substrates. The main objective of this thesis was to contribute to the better knowledge of this genus, exploring the species diversity in clinic and environmental substrates. A total of 433 isolates were studied in this thesis, which were obtained from different sources (clinical samples, soil, dung, plant debris). The identification of the isolates was carried out by multilocus phylogenetic analyses including sequences of four markers (ITS, β-tubulin, calmodulin, and RPBII) and phenotypic characterization. When relevant, clinical isolates were submitted to antifungal susceptibility testing against the main drugs available. In summary, 98 species of Aspergillus were identified, 49 from clinical samples (248 isolates), 48 from soil (92 isolates), 48 from herbivore dung (82 isolates), and 10 from plant debris (10 isolates). Considering the poorly studied sections of Aspergillus in the clinical setting, the most frequent sections were Nidulantes (including the former Versicolores section), 84 isolates and 14 species; Circumdati, 35 isolates and seven species; Aspergillus, 25 isolates and five species; and Usti, 19 isolates and two species. Eight species were isolated from clinical samples for the first time and three were proposed as new. The antifungal drugs, in general, showed good activity against the isolates tested, with exception of the reduced activity of amphotericin B against members of section Circumdati. Regarding the environmental isolates, 14 new species were proposed based on phenotypic and molecular data; five belonging to the section Terrei (three from herbivore dung and two from soil); four to the section Candidi (all from dung); two to the section Nidulantes (both from soil); and one in each of the sections Flavipedes, Cremei, and Usti (all from dung).
Powell, Robyn Faye. "Systematics, diversification and ecology of the Conophytum-clade (Ruschieae; Aizoaceae)." University of the Western Cape, 2016. http://hdl.handle.net/11394/5453.
Full textThe Ruschieae is the most diverse and speciose tribe within the large subfamily Ruschioideae (Aizoaceae), with approximately 71 genera and a distribution centred in the arid parts of the Greater Cape Floristic Region (GCFR) of South Africa. Recent phylogenetic analyses provided the first insights into generic relationships within the tribe, with a number of novel generic relationships discovered. The tribal phylogeny recovered 12 large clades, of which the Conophytum-clade was one the most morphologically diverse based on leaf and capsule characters. The Conophytum-clade is an early-diverging lineage of the Ruschieae and includes the following 10 genera: Cheiridopsis N.E.Br., Conophytum N.E.Br., Enarganthe N.E.Br., Ihlenfeldtia H.E.K.Hartmann, Jensenobotrya A.G.J.Herre, Namaquanthus L.Bolus, Octopoma N.E.Br., Odontophorus N.E.Br., Ruschianthus L.Bolus and Schlechteranthus Schwantes. The present study presents an expanded phylogenetic analysis of the Conophytum-clade, with the sampling of the majority of species in the genera and a representative sampling (56% of species) of the speciose genus Conophytum. Phylogenetic data for up to nine plastid gene regions (atpB–rbcL, matK, psbJ–petA, rpl16, rps16, trnD– trnT, trnL–F, trnQᶷᶷᶢ–rps16, trnS–trnG) were produced for each of the sampled species. The produced plastid data was analyses using maximum parsimony, maximum likelihood and Bayesian inference. The combined plastid phylogenetic analyses were used in combination with morphological, anatomical and palynological data to assess generic and subgeneric circumscriptions within the clade. Upon assessment of generic circumscriptions in the Conophytum-clade, the number of recognised genera in the clade decreased from ten to seven. Arenifera A.G.J.Herre, which had not been sampled in any phylogeny of the Ruschieae, and Octopoma were recovered as polyphyletic, with species placed in the Conophytum-clade, while the type species was placed in the xeromorphic clade of the tribal phylogeny. The species of Arenifera and Octopoma placed in the Conophytum-clade were subsequently included in Schlechteranthus upon assessment of generic circumscriptions between the taxa. Two morphological groupings were recognised within Schlechteranthus, one including the species of Schlechteranthus and the other including species previously recognised as Arenifera and Octopoma. These two morphological groupings were treated as subgenera, with the erection of the new subgenus Microphyllus R.F.Powell. A detailed taxonomic revision of subgenus Microphyllus is presented with a key to species, descriptions of the species (including a new species: S. parvus R.F.Powell & Klak), known geographical distributions and illustrations of the species. In addition to the changes mentioned above, the expanded sampling and phylogenetic analyses of the Conophytum-clade recovered Ihlenfeldtia and Odontophorus embedded in Cheiridopsis. The species of Ihlenfeldtia were recovered with species of heiridopsis subgenus Aequifoliae H.E.K.Hartmann, while the species of Odontophorus were recovered as polyphyletic within the Cheiridopsis subgenus Odontophoroides H.E.K.Hartmann clade. Cheiridopsis was subsequently expanded to include the species of Ihlenfeldtia and Odontophorus, with these species accommodated in the subgenera of Cheiridopsis. The phylogenetic placement and relationship of these species was supported by the shared capsule morphology. The expanded sampling of the clade did not resolve the phylogenetic relationship of the monotypic genera Enarganthe, Jensenobotrya, Namaquanthus and Ruschianthus, with these genera unresolved in the Conophytum-clade. These genera however, exhibit a unique combination of morphological characters, such as a glabrous leaf epidermis and variation in pollen exine and colpi structure, in contrast to the other genera of the clade. The assessment of the generic circumscription of these genera, based on the molecular, morphological, anatomical and palynological data suggested that the generic statuses of these monotypic genera should be maintained. The expanded phylogenetic sampling of the morphologically diverse and speciose genus Conophytum recovered the genus as monophyletic. This monophyly was supported by the unique floral type in Conophytum, with the fused petaloid staminodes forming a tube. None of the sectional classifications were recovered as monophyletic but the phylogenetic analyses did recover a few clades which more or less corresponded to the current sectional classification of the genus. A number of clades were also recovered which included species from a range of different sections. Diverse leaf and floral traits were shown to have evolved numerous times across the genus. This was particularly interesting with regards to the selected floral traits, as the phylogeny indicated a number of switches in floral morphologies across the genus. The floral diversity was assessed in complex species communities of Conophytum across the GCFR, where up to 11 species of Conophytum are found occurring sympatrically, and floral traits were shown to be different across the species within the communities. Pollination competition and adaptation were suggested as possible drivers of floral diversity in the genus, with differences in phenology, anthesis and floral morphology within the species complex communities. The unique floral type of Conophytum has enabled the species to develop a diverse range of specialised flowers, with a variety of structures, scents and colours, resulting in the diverse floral morphologies found across the genus. The complex Conophytum species communities included both closely as well as distantly related species, suggesting the soft papery capsules of Conophytum are wind dispersed. This adaptation to long distance seed dispersal resulted in a significantly higher phylogenetic diversity in Conophytum when compared to its sister genus, Cheiridopsis. A population genetics study of Conophytum also suggested that the capsules may be wind dispersed, with an indication of genetic connectivity between the geographically isolated populations of C. marginatum Lavis across the Bushmanland Inselberg Region. Although the capsules are dispersed by wind, the seeds are released from the hygrochastic capsules by runoff during rainfall events. The relationship between seed dispersal and runoff is evident from the genetic structure of populations of C. maughanii N.E.Br. and C. ratum S.A.Hammer that occur on the tops and the surrounding bases of the inselbergs, as the drainage pattern was found to directly influence population structure in these species. In addition, the AFLP analyses provided insight into the conservation of the flagship species C. ratum. The summit populations of this species were shown to sustain the populations at the base of the Gamsberg. This finding is especially important, as the distribution of the species is restricted to the Gamsberg inselberg, where mining has already commenced as of this year.
National Research Foundation (NRF)
Kariyawasam, Haputhanthri Kankanamge Tharanga Niroshini. "Taxonomy, distribution and pest status of Plutella species (Lepidoptera: Plutellidae) in Australia and New Zealand." Thesis, Queensland University of Technology, 2018. https://eprints.qut.edu.au/116545/1/Tharanga%20Niroshini_Kariyawasam%20Haputhanthri%20Kankanamge_Thesis.pdf.
Full textMolinier, Virginie. "Diversité génétique et aromatique de la truffe de Bourgogne." Thesis, Dijon, 2013. http://www.theses.fr/2013DIJOS021/document.
Full textTruffles are ectomycorrhizal Ascomycota fungi belonging to the Tuberaceae family and more specifically to the Tuber genus. More than thirty Tuber species are currently described in Europe. In this thesis, we specifically focused on the Tuber aestivum-uncinatum model. This truffle is commonly called "Burgundy Truffle" and has a gastronomic and cultural interest.The first part of this thesis focused on the taxonomic status of the Burgundy truffle (Tuber uncinatum). For this, we used a multi-marker approach combining several genetic markers commonly used at the interspecific scale. Our analyses showed that the two taxa, Tuber aestivum (summer truffle) and Tuber uncinatum are conspecific.In the second part, we addressed the genetic diversity of Tuber aestivum. To do this, we firstly developed specific microsatellite markers by "direct shotgun pyrosequencing". This method has allowed the development of 15 polymorphic microsatellite markers. Then, we used those markers to genotype individuals from different European locations. We have identified four differentiated subpopulations that not correspond, for the majority, to a geographical distribution. However, one cluster differs from the others by its location (south of France) and its genetic characteristics (presence of rare alleles). These preliminary results may indicate the existence of a particular ecotype attached to a southern ecology: Tuber aestivum sensu stricto.We were then interested, in the third part of this thesis, to the aromatic diversity of Tuber aestivum at a local scale. Our results highlight the existence of a moderate differentiation between individuals from a natural truffle orchard and individuals from planted orchard. From one season to another, genotypic stability was observed. Only C8 volatile organic compounds seem to be related to the genotypes.In the last part, we analyzed harvesting data, over more than thirty years, from an hazelnut truffle orchard initially inoculated by Tuber melanosporum. Through simple statistical analyzes, we noted changes in both quantity and weight of truffles harvested according to the seasons and hazelnut trees. It appears that Tuber aestivum rapidly replaced Tuber melanosporum (in three years). The disappearance of Tuber melanosporum can probably be explained by the canopy closure; Tuber melanosporum not appreciating excessive shading
Kaya, Galip. "Phylogenetic analyses of five sheep infective Eimeria species (E. ovinoidalis, E. crandallis, E. weybridgensis, E. ahsata, E. faurei) : development of novel total nucleic acid extraction method from small numbers of Eimeria oocysts." Thesis, University of Bristol, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.263922.
Full textBauer, Jennifer E. "A Phylogenetic and Paleobiogeographic Analysis of the Ordovician Brachiopod Eochonetes." Ohio University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1397486053.
Full textKrig, Kåre. "Methods for phylogenetic analysis." Thesis, Linköping University, Department of Mathematics, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-56814.
Full textIn phylogenetic analysis one study the relationship between different species. By comparing DNA from two different species it is possible to get a numerical value representing the difference between the species. For a set of species, all pair-wise comparisons result in a dissimilarity matrix d.
In this thesis I present a few methods for constructing a phylogenetic tree from d. The common denominator for these methods is that they do not generate a tree, but instead give a connected graph. The resulting graph will be a tree, in areas where the data perfectly matches a tree. When d does not perfectly match a tree, the resulting graph will instead show the different possible topologies, and how strong support they have from the data.
Finally I have tested the methods both on real measured data and constructed test cases.
Lusa, Makeli Garibotti 1982. "Morfoanatomia e fitoquímica de espécies da subtribo Lychnophorinae (Asteraceae: Vernonieae) como subsídios para as análises filogenéticas do grupo = Morphoanatomy and phytochemistry of species of Lychnophorinae subtribe (Asteraceae: Vernonieae) as subsidies for the phylogenetic analyses of group." [s.n.], 2014. http://repositorio.unicamp.br/jspui/handle/REPOSIP/314879.
Full textTese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: Asteraceae é uma das maiores famílias entre as angiospermas, possuindo de 24.000 a 30.000 espécies, o que representa, aproximadamente, 10% da flora mundial. Atualmente são reconhecidas 21 subtribos pertencentes à Vernonieae. Entre elas, Lychnophorinae tem uma distribuição quase restrita ao Brasil, ocorrendo nos campos rupestres e cerrados do Planalto Central. A subtribo apresenta 18 gêneros e 104 espécies, distribuídos entre os mais variados hábitos: ervas perenes, arbustos, subarbustos, arvoretas, árvores e caulirosuletum. Estudos filogenéticos recentes indicam que a subtribo é monofilética. As linhagens mais basais e mais derivadas são bem sustentadas, contudo, as relações entre os demais clados persistem apenas parcialmente resolvidas. Por esse motivo, nesse estudo são investigadas espécies da subtribo em relação à morfoanatomia e à química dos principais metabólitos de caules aéreos e folhas, buscando-se novos caracteres que possam ser úteis para um melhor entendimento evolutivo do grupo, inclusive possíveis sinapomorfias. Para tanto, foram eleitas espécies chaves dentro de Lychnophorinae, representantes das principais linhagens. Para as análises estruturais e histoquímicas, amostras de caules e de folhas foram processadas de acordo com as técnicas usuais em anatomia vegetal. Para as análises fitoquímicas, os extratos foram analisados por cromatografia liquida e espectrometria de massas. As reconstruções dos estados ancestrais dos caracteres foram efetuadas em uma filogenia baseada em dados morfológicos e moleculares. Em Lychnophorinae, os principais locais de síntese dos metabólitos secundários são: tricomas glandulares, idioblastos epidérmicos e tecidos parenquimáticos das folhas e dos caules. As análises fitoquímicas evidenciaram a presença de flavonoides, derivados do ácido trans-cinâmico, lactonas sesquiterpênicas e poliacetilenos. A reconstrução dos estados ancestrais dessas substâncias na filogenia da subtribo indicam possíveis sinapomorfias químicas. No decorrer das análises morfoanatômicas foram observadas duas importantes novidades em Lychnophorinae. A primeira relata a ocorrência de fitomelanina em caules aéreos e folhas de Lychnophorinae. As reconstruções dos estados ancestrais dos caracteres sugerem que o ancestral comum mais recente das Lychnophorinae já apresentava fitomelanina no caule espessado. A segunda novidade morfoanatômica diz respeito a um modo não usual de retenção de água sobre ápices caulinares, onde uma substância hialina é resultado da degradação parietal de tricomas não glandulares, tendo natureza hidrofílica. Essa substância possivelmente apresenta a função de proteger os órgãos jovens contra dessecação. Durante as investigações anatômicas de caules e folhas de Lychnophorinae, nós observamos características peculiares, frequentemente relatadas como xéricas, e procuramos entender se tais características mostravam algum padrão que agrupava as espécies. Nós realizamos análises multivariadas levando em consideração tais características. Os resultados indicaram quatro grupos funcionais em Lychnophorinae e sinalizaram que as espécies agrupadas, ocupavam os mesmos nichos, os quais refletiam condições específicas nos diferentes ambientes. Finalmente, após a conclusão das análises anatômicas, as características foram mapeadas na filogenia de Lychnophorinae e geraram importantes informações, como a identificação de oito possíveis sinapomorfias. As informações geradas nesse estudo sugerem que a evolução da diversidade morfológica e anatômica em Lychnophorinae pode ter sido direcionada por pressões adaptativas, derivadas de fatores ecofisiológicos dos ambientes restritos em que habitam a maioria das espécies
Abstract: Asteraceae is one of the largest flowering plants families, with 24,000-30,000 species, representing approximately 10% of the world's flora. Currently, 21 subtribes are recognized in Vernonieae. Among them, Lychnophorinae is nearly endemic to Brazil, occurring in campos rupestres areas and savannas of Central Plateau. The subtribe has 18 genera and 104 species distributed among the various habits: perennial herbs, shrubs, subshrubs, treelets, trees and caulirosuletum. Recent phylogenetic studies show that the subtribe is monophyletic. The most "basal" and more "derived" strains are well supported, however, relationships between the remaining clades persist partially unresolved. Therefore, in this study, species of the subtribe are investigated in relation to morphoanatomy and chemistry of the main metabolites of aerial stems and leaves, searching for new characters that might be useful for a better understanding of the group evolution, including possible synapomorphies. To this aim, key species were chosen in Lychnophorinae, representing the principal lineages. For structural and histochemical analyzes, samples of leaves and stems were processed according to usual plant anatomy techniques. For phytochemical analysis, the extracts were analyzed by liquid chromatography and mass spectrometry. Reconstructions of ancestral states of the characters was performed using parsimony in a phylogeny based on morphological and molecular data. In Lychnophorinae, the major sites of synthesis of secondary metabolites are: glandular trichomes, epidermal idioblasts and parenchyma of the leaves and stems. The phytochemical analysis revealed the presence of flavonoids, derivatives of trans-cinnamic acid, sesquiterpene lactones and polyacetylenes. The reconstruction of ancestral states of these substances in the phylogeny of the subtribe indicate possible chemical synapomorphies. During the morphoanatomic analyzes two important events in Lychnophorinae were observed. The first reports the occurrence of phytomelanin aerial stems and leaves of Lychnophorinae. Reconstructions of ancestral states of the characters suggest that the most recent common ancestral of Lychnophorinae presented phytomelanin in thickened stem. The second morphoanatomical novelty relates to a method of unusual water retention of apexes, where a substance hyaline is a result of parietal degradation of non glandular trichomes, and it has hydrophilic nature. This substance probably has the function to protect young organs from desiccation. During the anatomical investigations of stems and leaves of Lychnophorinae, we observed frequently reported as xeric peculiar characteristics, and seek to understand whether these characteristics showed some pattern that grouped species. We performed multivariate analysis taking into account the peculiar characteristics. The results indicated four functional groups Lychnophorinae and signaled that grouped species occupy the same niche, which reflect specific conditions in different environments. Finally, after completing the anatomical analyzes, the features were mapped on the phylogeny of Lychnophorinae and generated important information such as the identification of eight possible synapomorphies. The information generated in this study suggest that the evolution of morphological and anatomical diversity in Lychnophorinae may have been driven by adaptive pressures, derived from ecophysiological factors of restricted environments in which most species inhabit
Doutorado
Biologia Vegetal
Doutora em Biologia Vegetal