Rozprawy doktorskie: „Phylogenetic analyses”

1

Fujisawa, Tomochika. "Statistical analyses of genealogical-phylogenetic data". Thesis, Imperial College London, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.556548.

Pełny tekst źródła

Streszczenie:

Thanks to the recent advancement of the sequence technologies, generating large volumes of DNA sequence data is now becoming more feasible. Sequencing several samples across many species from a range of clades enables us to connect the two fields of study previously separated due to the lack of data: population genetics and phylogenetics. The former has focused on detailed genetic processes in a few species, while the latter has studied large-scale evolutionary relationships across many species. In this thesis, methods to utilize the new type of data, genealogical-phylogenetic data, are explored to tackle the problems lying between the two fields, including how to delimit species with genetic information and how ecological traits affect species genetic properties. First, a method of species delimitation based on single locus gene tree, called the generalized mixed Yule coalescent method (GMYC method), is evaluated. Its statistical properties are assessed on both simulated and real data, and the method is extended to relax some simplifying assumptions and to give a robust confidence measure. The simulation studies showed that the reliability of the delimitation depends on population parameters and patterns of diversification processes. Assessment of the performance on a dataset of 5196 water beetle mitochondrial DNA sequences sampled from across Europe showed that the method accurately delimited half of the studied species. The accuracy was affected by several factors, notably the presence of pseudogenes and potential undersampling of species range. Then, the water beetle data and the GMYC method are used to test the effects of species ecological traits on genetic properties, focusing on species habitat type. Habitat type had significant effects on genetic variation and substitution rate via effects on range size and latitudinal distribution of species. However, direct effects of habitat type on genetic properties were not observed.

Style APA, Harvard, Vancouver, ISO itp.

2

Bandoni, Susan Marie. "Phylogenetic analyses of the Amphilinidea and Gyrocotylidea : (Cercomeria: Brooks, 1982)". Thesis, University of British Columbia, 1985. http://hdl.handle.net/2429/24472.

Pełny tekst źródła

Streszczenie:

The amphilinideans and gyrocotylideans are small groups of monozoic platyhelminths parasitizing fishes and occasionally turtles. They have traditionally been placed with the cestodes because they lack a gut. Systematic relationships of the two groups are poorly understood. Eight species of amphilinideans are considered valid. A phylogenetic analysis of 46 character states comprising 34 homologous series produced a single phylogenetic tree with a consistency index value of 89%, indicating a very low degree of homoplasy. The number of genera has been reduced from six to three, in an attempt to construct a classification which reflects the phylogenetic relationships of the group. The phylogenetic relationships exhibit a fairly high degree of congruence (70%) with a currently accepted hypothesis of phylogenetic relationship of the teleosts. This implies that coevolution has occurred, although with many parasite losses and extinctions. An analysis of the biogeographic distribution of the amphilinideans using the methods of vicariance biogeography produced complete or nearly complete congruence of the distribution of amphilinideans with hypotheses of area relationship, indicating that vicariance is the best explanation for the biogeographic distribution of the group. Ten species of gyrocotylideans are recognized, of which seven were examined in this study. A phylogenetic analysis of 24 character states comprising 13 homologous series produced two trees of equal length. The consistency index for each tree is 88%, indicating a very low degree of homoplasy. The phylogenetic analysis of the gyrocotylideans has provided a summary of the current knowledge of the gyrocotylideans which can serve as a framework for further investigations. Slightly more than half of the observed associations between gyrocotylideans and holocephalans can be attributed to coevolution. Remaining associations can be attributed to colonization, but these represent recolonizations of plesiomorphic hosts. The geographic distribution of gyrocotylideans remains enigmatic, as it does not appear to reflect plate movements. It is suggested that their distribution may be pfe-Pangaean in origin. The phylogenetic analyses of the amphilinideans and gyrocotylideans have provided corroboration for a hypothesis of relationship for the Subphylum Cercomeria. Seven new characters have been identified as autapomorphies for the amphilinideans and gyrocotylideans, while an additional seven new characters support the Subclass Cestodaria and the Infrasubclass Cestoidea. Amphilinideans and gyrocotylideans both appear to be relict groups, but of different types. The amphilinideans were probably more widespread and more numerous than they are at present (i.e. they are geographic and numerical relicts). The gyrocotylideans, on the other hand, appear to have never been diverse or widespread, and are therefore phylogenetic relicts.
Science, Faculty of
Zoology, Department of
Graduate

Style APA, Harvard, Vancouver, ISO itp.

3

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.

Pełny tekst źródła

Style APA, Harvard, Vancouver, ISO itp.

4

Donati, Beatrice. "Graph models and algorithms in (co-)evolutionary contexts". Thesis, Lyon 1, 2014. http://www.theses.fr/2014LYO10235/document.

Pełny tekst źródła

Streszczenie:

Cette thèse s'inscrit dans le cadre de la bioinformatique. Les outils mathématiques les plus utilisés dans ce travail relèvent de la théorie des graphes, des statistiques, de la théorie des ensembles et des mathématiques discrètes. Ces mathématiques ont permis de développer des modèles de systèmes biologiques ainsi que des algorithmes efficaces dans l'étude concrète de ces modèles. La nécessité d'analyses de jeux de données de très grande taille a rendu critique dans notre démarche cette notion d'efficacité des algorithmes. Il faut enfin remarquer que le champ biologique qui a servi de support à cette thèse nous a conduit à explorer un domaine particulier au sein de la théorie de la complexité, à savoir le développement et l'analyse des algorithmes d'énumération [etc...]
In 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

Style APA, Harvard, Vancouver, ISO itp.

5

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.

Pełny tekst źródła

Style APA, Harvard, Vancouver, ISO itp.

6

Staron, 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.

Pełny tekst źródła

Style APA, Harvard, Vancouver, ISO itp.

7

Borner, Janus [Verfasser], i 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.

Pełny tekst źródła

Style APA, Harvard, Vancouver, ISO itp.

8

Lehmann, 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.

Pełny tekst źródła

Streszczenie:

Despite decades of effort by molecular systematists, the trees of life of eukaryotic organisms still remain partly unresolved or in conflict with each other. An ever increasing number of fully-sequenced genomes of various eukaryotes allows to consider gene and species phylogenies at genome-scale. However, such phylogenomics-based approaches also revealed that more taxa and more and more gene sequences are not the ultimate solution to fully resolve these conflicts, and that there is a need for sequence-independent phylogenetic meta-characters that are derived from genome sequences. Spliceosomal introns are characteristic features of eukaryotic nuclear genomes. The relatively rare changes of spliceosomal intron positions have already been used as genome-level markers, both for the estimation of intron evolution and phylogenies, however with variable success. In this thesis, a specific subset of these changes is introduced and established as a novel phylogenetic marker, termed near intron pair (NIP). These characters are inferred from homologous genes that contain mutually-exclusive intron presences at pairs of coding sequence (CDS) positions in close proximity. The idea that NIPs are powerful characters is based on the assumption that both very small exons and multiple intron gains at the same position are rare. To obtain sufficient numbers of NIP character data from genomic and alignment data sets in a consistent and flexible way, the implementation of a computational pipeline was a main goal of this work. Starting from orthologous (or more general: homologous) gene datasets comprising genomic sequences and corresponding CDS transcript annotations, the multiple alignment generation is an integral part of this pipeline. The alignment can be calculated at the amino acid level utilizing external tools (e.g. transAlign) and results in a codon alignment via back-translation. Guided by the multiple alignment, the positionally homologous intron positions should become apparent when mapped individually for each transcript. The pipeline proceeds at this stage to output portions of the intron-annotated alignment that contain at least one candidate of a NIP character. In a subsequent pipeline script, these collected so-called NIP region files are finally converted to binary state characters representing valid NIPs in dependence of quality filter constraints concerning, e.g., the amino acid alignment conservation around intron loci and splice sites, to name a few. The computational pipeline tools provide the researcher to elaborate on NIP character matrices that can be used for tree inference, e.g., using the maximum parsimony approach. In a first NIP-based application, the phylogenetic position of major orders of holometabolic insects (more specifically: the Coleoptera-Hymenoptera-Mecopterida trifurcation) was evaluated in a cladistic sense. As already suggested during a study on the eIF2gamma gene based on two NIP cases (Krauss et al. 2005), the genome-scale evaluation supported Hymenoptera as sister group to an assemblage of Coleoptera and Mecopterida, in agreement with other studies, but contradicting the previously established view. As part of the genome paper describing a new species of twisted-wing parasites (Strepsiptera), the NIP method was employed to help to resolve the phylogenetic position of them within (holometabolic) insects. Together with analyses of sequence patterns and a further meta-character, it revealed twisted-wing parasites as being the closest relatives of the mega-diverse beetles. NIP-based reconstructions of the metazoan tree covering a broad selection of representative animal species also identified some weaknesses of the NIP approach that may suffer e.g. from alignment/ortholog prediction artifacts (depending on the depth of range of taxa) and systematic biases (long branch attraction artifacts, due to unequal evolutionary rates of intron gain/loss and the use of the maximum parsimony method). In a further study, the identification of NIPs within the recently diverged genus Drosophila could be utilized to characterize recent intron gain events that apparently involved several cases of intron sliding and tandem exon duplication, albeit the mechanisms of gain for the majority of cases could not be elucidated. Finally, the NIP marker could be established as a novel phylogenetic marker, in particular dedicated to complementarily explore the wealth of genome data for phylogenetic purposes and to address open questions of intron evolution.

Style APA, Harvard, Vancouver, ISO itp.

9

Garcia-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.

Pełny tekst źródła

Style APA, Harvard, Vancouver, ISO itp.

10

Long, 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.

Pełny tekst źródła

Style APA, Harvard, Vancouver, ISO itp.

11

Francis, 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.

Pełny tekst źródła

Streszczenie:

Ubiquitination is an essential post-translational modification that regulates signalling and protein turnover in eukaryotic cells. However, many ubiquitin E3 ligases remain poorly understood. The mammalian muskelin/RanBP9/CTLH complex contains eight proteins, five of which, RanBP9 (RanBPM), TWA1, Maea, Rmnd5a and muskelin, share striking similarities of domain organisation. In Saccharomyces cerevisiae, the related GID complex includes the Rmnd5a homologue GID2 which has E3 ubiquitin ligase activity and down-regulates gluconeogenesis. E3 ubiquitin ligase activity of mammalian Rmnd5a has not been reported. To better understand the large mammalian complex a major goal of this thesis was to analyse its evolution as a multi-protein system. Bioinformatic studies identify that TWA1, Rmnd5 and Maea are conserved throughout five eukaryotic supergroups. RanBPM is absent from excavates and from some lineages within other super-groups, and muskelin is present only in opisthokonts. Phylogenetic analysis based on the shared sequence regions that correspond to the lissencephaly-l homology (LisH) and C-terminal to LisH (CTLH) domains revealed closer relationships between Rmnd5 and MAEA, and TWAl and RanBPM, respectively. In-depth sequence analyses confirmed the greater similarity of the LisH/ CTLH domains of Rmnd5 and MAEA vs. TWAl and RanBPM, respectively, and id~ntified unique signatures of conserved residues within the LisH and CTLH domains of each protein. ~ further goal was to purify and express Rmnd5a and TWAl for laboratory experiments. Bacterially expressed Rmnd5a exhibits E3 ubiquitin ligase activity in Escherichia coli BL21lysates but not as a purified protein. Bacterial expression and purification of TWAl enabled biophysical characterisation of TWAl as an all a-helical, natively-dimerised protein. TWAl crystals were produced. When optimized, crystals diffracted to 3.5A, though a 3D structure was not resolved. Threaded structure predictions of Rmnd5a and TWAl agreed with secondary structure prediction algorithms. These studies advance knowledge of structural! functional relationships of proteins in this poorly-understood complex.

Style APA, Harvard, Vancouver, ISO itp.

12

Souza, 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/.

Pełny tekst źródła

Streszczenie:

In the last years, microbial ecologists have dramatically increased their efforts to elucidate the \"black box\" of patterns and processes that modulate the diversity and functionality of soil microorganisms, examining their genetic diversity (e.g. through metagenomic) and measuring their functional characteristics. The aim of this thesis was to evaluate the interaction of the ecological processes of dispersion, diversification, selection and genetic drift on (1) the soil microbial communities, after conversion of forest to grassland or no-till cropping in long-term and (2) on the microbial communities in the rhizosphere of soybean in long-term no-till system. The cultivation of grassland in long-term led to a homogenizing selection of microbial communities, reducing beta-diversity, with consequent changes in the soil functions related to stress. No-till long-term led to minor changes of diversity, maintaining the functions found in the forest. The soybean plant has shown homogenizing power selection, and this increased with time. However, the functions selected in the rhizosphere were maintained, indicating functional resilience.
Nos 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.

Style APA, Harvard, Vancouver, ISO itp.

13

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.

Pełny tekst źródła

Streszczenie:

To understand the processes responsible for the diversity of life, one must consider evolutionary history. By incorporating a phylogenetic approach to studies of character evolution and species interactions, we may better understand the mechanisms governing this tangled bank. This work addresses fundamental questions regarding morphological and behavioral evolution, using gossamer-winged butterflies (Lepidoptera: Lycaenidae) as model systems.By investigating the pattern of genetic variation in a group of closely related species of copper butterflies (Lycaena), I show morphological divergence occurred in the absence of gene flow between Lycaena xanthoides and L. editha. Additionally, genetic divergence between populations of L. xanthoides has occurred without considerable morphological divergence. These findings highlight the utility of genetic data for inferring species boundaries and identification of cryptic lineages.Inferring evolutionary relationships among closely related species should benefit from multiple sources of information, e.g., unlinked genetic markers. Here I extend a method of reconstructing species relationships based on multiple reconstructed gene trees, using the number of incomplete lineage sorting events ('deep coalescences') as the objective function. This approach provides a more complete understanding of species' histories by accommodating population-level processes which may lead to discordance between gene genealogies and species phylogenies. The approach is evaluated with simulated and empirical data, and I discuss conditions which may result in misleading inferences.Finally, incorporating data from multiple gene trees, I investigate the evolution of association in a lycaenid-ant interaction. Lycaenid butterfly caterpillars are often involved in mutualisms with ant hosts: these larvae use volatile signals and provide carbohydrate rewards from the dorsal nectary organ (DNO) to associated ants to gain protection from natural enemies. However, larvae of some lycaenid species, such as L. xanthoides, do not possess the reward-producing organ, yet are still found in association with ants. Evaluating the relationship in a phylogenetic framework, I show that L. xanthoides likely evolved from a non-ant-associated ancestor. This suggests that L. xanthoides has 'cracked the code' that other, honest-signaling lycaenid larvae use to communicate to ants. Evolution of mutualisms between honest-signaling larvae and ants will likely be affected by the impact of illicit-signaling larvae.

Style APA, Harvard, Vancouver, ISO itp.

14

Nürk, 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.

Pełny tekst źródła

Style APA, Harvard, Vancouver, ISO itp.

15

Mapaya, 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.

Pełny tekst źródła

Streszczenie:

Bibliography: leaves 106-120.
The 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.

Style APA, Harvard, Vancouver, ISO itp.

16

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.

Pełny tekst źródła

Style APA, Harvard, Vancouver, ISO itp.

17

Rybalka, 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.

Pełny tekst źródła

Style APA, Harvard, Vancouver, ISO itp.

18

Bhatnagar, 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.

Pełny tekst źródła

Streszczenie:

Microbial 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.

Style APA, Harvard, Vancouver, ISO itp.

19

Staroń, Anna [Verfasser], i 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.

Pełny tekst źródła

Style APA, Harvard, Vancouver, ISO itp.

20

Diallo, 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.

Pełny tekst źródła

Streszczenie:

This thesis focuses on algorithms related to ancestral genome reconstruction and phylogenetics analyses. Specially, it studies insertion and deletion (indel) in genomic sequences, their utilities for (1) evolutionary studies of species families, (2) multiple alignment and phylogenetic trees reconstruction assessment, and (3) functional DNA sequence annotation. Here, the indel scenarios reconstruction problem is presented, in a likelihood framework, and it can be stated as follows: given a multiple alignment of orthologous sequences and a phylogenetic tree for these sequences, reconstruct the most likely scenario of insertions and deletions capable of explaining the gaps observed in the alignment. This problem, that we called the Indel Maximum Likelihood Problem (IMLP), is an important step toward the reconstruction of ancestral genomic sequences, and is important for studying evolutionary processes, genome function, adaptation and convergence. In this thesis, first, we showed that we can solve the IMLP using a new type of tree hidden Markov model whose states correspond to single-base evolutionary scenarios and where transitions model dependencies between neighboring columns. The standard Viterbi and Forward-backward algorithms are optimized to produce the most likely ancestral reconstruction and to compute the level of confidence associated to specific regions of the reconstruction. A heuristic is presented to make the method practical for large data sets, while retaining an extremely high degree of accuracy. The developed methods have been made available for the community through a web interface. Second we showed the utilities of the defined indel score for assessing the accuracy of multiple sequence alignment and phylogenetic tree reconstruction. Third, the provided method is included into the framework of the ancestral protein reconstruction of phages under a reticulate evolution and the evolutionary studies of the carcinogencity of the Human Papilloma Vir
Cette 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

Style APA, Harvard, Vancouver, ISO itp.

21

Maß, Janina [Verfasser], Martin [Gutachter] Lercher i 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.

Pełny tekst źródła

Style APA, Harvard, Vancouver, ISO itp.

22

Fijridiyanto, 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.

Pełny tekst źródła

Style APA, Harvard, Vancouver, ISO itp.

23

Gao, 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.

Pełny tekst źródła

Streszczenie:

Lignocellulosic 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.

Style APA, Harvard, Vancouver, ISO itp.

24

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.

Pełny tekst źródła

Style APA, Harvard, Vancouver, ISO itp.

25

Robinson, 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.

Pełny tekst źródła

Style APA, Harvard, Vancouver, ISO itp.

26

Takishita, 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.

Pełny tekst źródła

Streszczenie:

Kyoto University (京都大学)
0048
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

Style APA, Harvard, Vancouver, ISO itp.

27

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.

Pełny tekst źródła

Style APA, Harvard, Vancouver, ISO itp.

28

Lien, 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.

Pełny tekst źródła

Streszczenie:

Kyoto University (京都大学)
0048
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

Style APA, Harvard, Vancouver, ISO itp.

29

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.

Pełny tekst źródła

Style APA, Harvard, Vancouver, ISO itp.

30

Kahloul, 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.

Pełny tekst źródła

Streszczenie:

Chez les eucaryotes, la voie de protéolyse Ub/ protéasome 26S est responsable de la dégradation sélective de la plupart des protéines intracellulaires. Cette dégradation par le protéasome 26S est initiée par une polyubiquitination de la protéine réalisée grâce à l’action d’une cascade enzymatique impliquant 3 types d'enzymes nommées « ubiquitin-activating enzyme » (E1), « ubiquitin-conjugating enzyme » (E2) et « ubiquitin-protein ligase » (E3). Il existe différentes classes d’ubiquitines ligases (E3), parmi lesquelles la plus connue est le complexe SCF (Skp1-Cullin-F-box). La protéine SKP1 fixe à la fois la Culline et la F-box qui va reconnaitre spécifiquement la protéine cible. Contrairement aux protistes, les champignons et certains vertébrés qui possèdent un unique gène SKP1 fonctionnel, de nombreux animaux et espèces de plantes présentent plusieurs SKP1 homologues. Vingt et un et trente deux gènes SKP1 ont été décrits respectivement chez Arabidopsis thaliana et Oryza sativa. En dépit de l’importance du complexe SCF, chez le riz, peu de travaux décrivent les interactions entre les dizaines de protéines « SKP1-like » et les centaines de protéines F-box. Dans un premier temps, nous avons collecté et analysé les séquences de 288 gènes « SKP1-like » appartenant à 17 espèces, dont la mousse Physcomitrella patens, cinq monocotylédones et 11 eudicotylédones. Les analyses structurales et phylogénétiques de ces gènes indiquent qu’ils peuvent être divisés en différentes sous-familles. Nos analyses ont montré qu’OSK1 et OSK20 chez le riz constituent une classe de gènes SKP1 à intron unique conservé. Dans un deuxième temps, nous avons étudié le profil d’expression des gènes « SKP1-like » chez le riz. Notre investigation sur le nombre d’EST a montré que les gènes OSK1 et OSK20 sont les plus largement représentés dans les bases de données EST publiques. La méta-analyse de l’expression des gènes « SKP1-like » chez le riz, indique que les gènes OSK présentent des profils d'expression hétérogènes selon les tissus et les conditions physiologiques. Les résultats des intearctions protéine-protéine en double hybride ont révélé que les protéines OSK présentent différentes capacités d’interactions avec les protéines F-box. Cependant, OSK1 et OSK20 semblent interagir avec la plupart des protéines F-box testées. Les études de localisation subcellulaire ont indiqué que OSK1 et OSK20 sont des protéines nucléaires et cytosoliques. En se basant sur les divers résultats obtenus dans ce travail, nous pouvons suggérer que chez le riz, les gènes OSK1 et OSK20 sont fonctionnellement équivalents aux gènes ASK1 et ASK2 chez Arabidopsis thaliana. Nous pouvons également proposer les équivalents de ces gènes chez les autres espèces végétales dont le génome a été séquencé
In 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

Style APA, Harvard, Vancouver, ISO itp.

31

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.

Pełny tekst źródła

Streszczenie:

Kyoto University (京都大学)
0048
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

Style APA, Harvard, Vancouver, ISO itp.

32

Page, Timothy J., i 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.

Pełny tekst źródła

Streszczenie:

The aim of this thesis is to use phylogenetic analyses of mitochondrial DNA to investigate the biogeography and evolutionary relationships within the freshwater shrimp family Atyidae in Australia at a nested series of scales, both geographic and systematic. At the largest scale, the relationships between Australian and Indo-West Pacific species were inferred using the two most common atyid genera in Australia, Caridina and Paratya. Most atyids are hypothesised to have colonised Australia from Southeast Asia, but Paratya may be a Gondwanan relict given its distribution. Australian Paratya all form a strong clade, with a sister relationship to species from Tasman Sea islands. Molecular clock estimates place all of the splits within Paratya after the break-up of Gondwana, with Australia being colonised once 3½-8½ million years ago. This transoceanic dispersal is conjectured to have taken place through oceanic currents because of the amphidromous life cycle of some taxa of Paratya. Caridina has a very different biogeographic history in Australia, as numerous Australian species have close evolutionary relationships with non-Australian taxa from locations throughout the region. This implies many colonisations to or from Australia over a long period, and thus highlights the surprising adeptness of freshwater shrimp in dispersal across ocean barriers and the unity of much of the region's freshwater biota. A number of potential species radiations within Australia were also identified. This agrees with patterns detected for a large number of Australian freshwater taxa, and implies a vicariant explanation due to the development of colder, dryer climates. The systematic relationships of the remaining two Australian surface genera (Caridinides, Australatya) and two subterranean genera (Parisia, Pycnisia) were also investigated. Australatya forms a strong clade with Pacific 'Atya-like' genera, and Caridinides falls within a clade containing Australian Caridina. The hypogean genera, Parisia and Pycnisia, form a strong clade in all analyses, implying an Australian subterranean speciation. The possibility of a relationship between Parisia/Pycnisia and some Australian Caridina species may have implications for the monophyly of the highly disjunct genus Parisia, as it may descend from local Caridina species and represent convergent morphologies. The common and speciose genus Caridina was used as a model taxon for analyses within Australia. At the medium scale, molecular taxonomic techniques were used to uncover cryptic species within a problematic east Australian species complex. At least five species were detected. Phylogeographic and population genetic analyses were carried out on each of these five cryptic species, which diverged from each other in the late Miocene/Pliocene. There were very large differences between the species in the scales of overall geographic distribution, intraspecific divergence and population structure. These were characterised as either: 1) species with large ranges, low intraspecific divergence, limited phylogeographic structuring (Caridina sp. D); 2) species with large ranges, high intraspecific divergence, a high level of phylogeographic structuring (sp. B); 3) species with a limited range, low intraspecific divergence, no phylogeographic structuring (sp. E); or 4) species with limited ranges, high intraspecific divergences, a high level of phylogeographic structuring (sp. A & C). These patterns reflect a combination of large-scale factors, such as landscape structure and climate change, and small-scale factors, such as species-specific tolerances to local conditions and differing dispersal capabilities. Life history variation (egg size) between species may be correlated with different dispersal abilities. Species with the smallest eggs have the least intraspecific divergence and largest distribution, while those with the biggest eggs have the most divergence and smallest distribution, with medium-sized egg species in between. At the smallest phylogeographic scale, C. sp. C from the sand dune islands of Moreton Bay in southeastern Queensland was further analysed. Two different lineages (C1, C2) were found which diverged from each other during the late Miocene/Pliocene and so are older than the current landscape in which they are found. Small-scale phylogeographic analyses within C1, C2 and a sympatric fish identified divergences dating to the Pleistocene (about 100-300 thousand years ago). This implies that ice age sea-level changes may have structured these populations, although there is little observable influence of the last glacial maximum (about 18 thousand years ago). This study has highlighted a number of taxonomic anomalies within the Atyidae. The detection of many cryptic species implies that biodiversity within freshwater invertebrates is higher than currently appreciated. The evolutionary and biogeographic relationships of Australian atyids have proved complex, with many taxa having their own individual histories. At the large Indo-Pacific scale, dispersal is most evident, but within Australia, both vicariance and dispersal have been responsible for structuring all taxa at every scale.

Style APA, Harvard, Vancouver, ISO itp.

33

Page, Timothy J. "An Evolutionary History of the Freshwater Shrimp Family Atyidae in Australia". Thesis, Griffith University, 2007. http://hdl.handle.net/10072/367826.

Pełny tekst źródła

Streszczenie:

The aim of this thesis is to use phylogenetic analyses of mitochondrial DNA to investigate the biogeography and evolutionary relationships within the freshwater shrimp family Atyidae in Australia at a nested series of scales, both geographic and systematic. At the largest scale, the relationships between Australian and Indo-West Pacific species were inferred using the two most common atyid genera in Australia, Caridina and Paratya. Most atyids are hypothesised to have colonised Australia from Southeast Asia, but Paratya may be a Gondwanan relict given its distribution. Australian Paratya all form a strong clade, with a sister relationship to species from Tasman Sea islands. Molecular clock estimates place all of the splits within Paratya after the break-up of Gondwana, with Australia being colonised once 3½-8½ million years ago. This transoceanic dispersal is conjectured to have taken place through oceanic currents because of the amphidromous life cycle of some taxa of Paratya. Caridina has a very different biogeographic history in Australia, as numerous Australian species have close evolutionary relationships with non-Australian taxa from locations throughout the region. This implies many colonisations to or from Australia over a long period, and thus highlights the surprising adeptness of freshwater shrimp in dispersal across ocean barriers and the unity of much of the region's freshwater biota. A number of potential species radiations within Australia were also identified. This agrees with patterns detected for a large number of Australian freshwater taxa, and implies a vicariant explanation due to the development of colder, dryer climates. The systematic relationships of the remaining two Australian surface genera (Caridinides, Australatya) and two subterranean genera (Parisia, Pycnisia) were also investigated. Australatya forms a strong clade with Pacific 'Atya-like' genera, and Caridinides falls within a clade containing Australian Caridina. The hypogean genera, Parisia and Pycnisia, form a strong clade in all analyses, implying an Australian subterranean speciation. The possibility of a relationship between Parisia/Pycnisia and some Australian Caridina species may have implications for the monophyly of the highly disjunct genus Parisia, as it may descend from local Caridina species and represent convergent morphologies. The common and speciose genus Caridina was used as a model taxon for analyses within Australia. At the medium scale, molecular taxonomic techniques were used to uncover cryptic species within a problematic east Australian species complex. At least five species were detected. Phylogeographic and population genetic analyses were carried out on each of these five cryptic species, which diverged from each other in the late Miocene/Pliocene. There were very large differences between the species in the scales of overall geographic distribution, intraspecific divergence and population structure. These were characterised as either: 1) species with large ranges, low intraspecific divergence, limited phylogeographic structuring (Caridina sp. D); 2) species with large ranges, high intraspecific divergence, a high level of phylogeographic structuring (sp. B); 3) species with a limited range, low intraspecific divergence, no phylogeographic structuring (sp. E); or 4) species with limited ranges, high intraspecific divergences, a high level of phylogeographic structuring (sp. A & C). These patterns reflect a combination of large-scale factors, such as landscape structure and climate change, and small-scale factors, such as species-specific tolerances to local conditions and differing dispersal capabilities. Life history variation (egg size) between species may be correlated with different dispersal abilities. Species with the smallest eggs have the least intraspecific divergence and largest distribution, while those with the biggest eggs have the most divergence and smallest distribution, with medium-sized egg species in between. At the smallest phylogeographic scale, C. sp. C from the sand dune islands of Moreton Bay in southeastern Queensland was further analysed. Two different lineages (C1, C2) were found which diverged from each other during the late Miocene/Pliocene and so are older than the current landscape in which they are found. Small-scale phylogeographic analyses within C1, C2 and a sympatric fish identified divergences dating to the Pleistocene (about 100-300 thousand years ago). This implies that ice age sea-level changes may have structured these populations, although there is little observable influence of the last glacial maximum (about 18 thousand years ago). This study has highlighted a number of taxonomic anomalies within the Atyidae. The detection of many cryptic species implies that biodiversity within freshwater invertebrates is higher than currently appreciated. The evolutionary and biogeographic relationships of Australian atyids have proved complex, with many taxa having their own individual histories. At the large Indo-Pacific scale, dispersal is most evident, but within Australia, both vicariance and dispersal have been responsible for structuring all taxa at every scale.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
Australian School of Environmental Studies
Full Text

Style APA, Harvard, Vancouver, ISO itp.

34

Schneider, Ulrike Julia [Verfasser], M. [Akademischer Betreuer] Röser, M. E. [Akademischer Betreuer] Barkworth i 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.

Pełny tekst źródła

Style APA, Harvard, Vancouver, ISO itp.

35

Carvajal, 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.

Pełny tekst źródła

Streszczenie:

Certains champignons, notamment des Ascomycètes, peuvent synthétiser des métabolites secondaires toxiques pour les hommes et les vertébrés, appelés mycotoxines. Étant donné que la présence de ces champignons dans les aliments de base constitue un risque potentiel pour la santé humaine et animale, les aliments de base sont éliminés lorsqu'ils sont contaminés. La section Flavi est un des groupes de champignons les plus importants du point de vue économique et sanitaire car il comprend des espèces productrices de mycotoxines. Parmi les mycotoxines produites par ce groupe se trouvent les aflatoxines (AF), considérées comme une préoccupation majeure en raison de leurs effets délétères chez les vertébrés. Les espèces de la section Flavi se développent principalement dans les régions tropicales et subtropicales car elles bénéficient de conditions environnementales optimales. De plus, les conditions de récolte et de stockage sont souvent inappropriées, favorisant ainsi leur développement. Dans les régions tempérées, ces espèces se rencontrent moins fréquemment. Cependant, le réchauffement climatique pourrait favoriser leur colonisation. L'identification des espèces d'Aspergillus de la section Flavi est un défi, en raison de l'inter- et intra-variabilité des caractères. Par conséquent, l'utilisation d'une seule méthode d'identification (caractérisation morphologique, moléculaire ou du profil des métabolites secondaires) est insuffisante. Inversement, le développement d'outils moléculaires a facilité la tâche. Le but de notre étude était de déterminer les relations entre les espèces d'Aspergillus de la section Flavi à partir de différents marqueurs moléculaires (ITS, benA, cmdA, amdS, préA, perB, ppgA, aflP, gènes Mat1), puis d'identifier ceux qui permettent une classification des espèces par inférence phylogénétique. L'utilisation de l'inférence phylogénétique dans cette étude a montré qu'il s'agit d'une approche robuste pour identifier les espèces d'Aspergillus de la section Flavi, notamment en confirmant certaines hypothèses déjà proposées pour les espèces de la section Flavi. En effet, l'ajout de marqueurs moléculaires a permis de confirmer le placement phylogénétique des espèces dans la section Flavi. De plus, une nouvelle espèce cryptique a pu être décrite : Aspergillus korhogoensis (appartenant au clade A. flavus). Notre étude a également pu mettre en évidence que les marqueurs moléculaires sélectionnés (benA, cmdA, mcm7, rpb1, preB, preA et ppgA) sont de bons candidats pour l'étude d'autres sections d'Aspergillus. L'utilisation de l'inférence phylogénétique est une méthode élégante permettant d'identifier de façon précise les espèces. Sur la base de nos résultats, il est recommandé d'utiliser des matrices concaténées pour effectuer une inférence phylogénétique dans cette section, et la meilleure combinaison inclut les gènes benA, cmdA, et l'inclusion d'un autre gène : mcm7, rpb1, preB, preA ou ppgA. A l'inverse, l'utilisation du gène ITS chez Aspergillus peut conduire à une sous-estimation de la diversité car le gène est très fortement conservé. L'étude des gènes du loci Mat1 dans la section est utile pour accroître les connaissances sur la reproduction sexuée chez les ascomycètes. De plus, plusieurs fonctions de la machinerie biologique fongique sont liées aux gènes du loci Mat1. La caractérisation du profil métabolique secondaire chez les souches d'Aspergillus de la section Flavi doit être utilisée, non seulement comme outil d'identification, mais également pour discriminer les souches toxinogènes et atoxinogènes. La section Flavi renferme des espèces capables de produire à la fois de mycotoxines et de composés bénéfiques. Parmi les mycotoxines qui devraient faire l'objet d'une attention particulière figurent les AF, l'acide cyclopiazonique, les versicolorines a et b, la stérigmatocystine. Une étude plus approfondie du métabolisme secondaire sera également utile pour la recherche de nouveaux composés bénéfiques
Some 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

Style APA, Harvard, Vancouver, ISO itp.

36

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.

Pełny tekst źródła

Streszczenie:

Archaeological and genetic evidence have long supported the notion that the Indian subcontinent played an important role in the dispersal of modern humans out of Africa. In the present study, two Dravidian populations, namely Lingayat (N=101) and Vokkaliga (N=102) were examined using high-resolution analyses of Y-chromosome single nucleotide polymorphism (Y-SNP) and their associated seventeen short tandem repeat (STR) loci. The results revealed a prevalence of the major indigenous Indian Y-haplogroups (H, L, F* and R2), which collectively accounted for three-fourths of the Lingayat and Vokkaliga paternal gene pool. In addition, the presence of ancient lineages such as F*-M213, H*-M69 and C*-M216 suggested that modern humans reached India very early after their migration out of Africa. Finally, high haplotype diversity values at 17 Y-STR loci for Lingayat (0.9981) and Vokkaliga (0.9901) populations as well as the absence of shared haplotypes between them emphasized the importance of independent databases for forensic casework.

Style APA, Harvard, Vancouver, ISO itp.

37

Mayberry, 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.

Pełny tekst źródła

Streszczenie:

It 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.

Style APA, Harvard, Vancouver, ISO itp.

38

Lehmann, Jörg [Verfasser], Peter F. [Akademischer Betreuer] Stadler, Peter F. [Gutachter] Stadler i 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.

Pełny tekst źródła

Style APA, Harvard, Vancouver, ISO itp.

39

Fabillo, 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.

Pełny tekst źródła

Streszczenie:

This thesis provides new knowledge on an understudied group of grasses, some of which are resurrection grasses (i.e. able to withstand extreme drought). The sole Australian species (Tripogon loliiformis) is morphologically diverse and could be more than one species. This study sought to determine how many species of Tripogon occur in Australia, their relationships to other species in the genus and to two other genera of resurrection grasses (Eragrostiella and Oropetium). Results of the research indicate there is not enough evidence, from DNA sequence data, to warrant splitting up T. loliiformis into multiple species. The extensive morphological diversity seems to be influenced by environmental conditions. The three genera are so closely related that they could be grouped into a single genus. This new knowledge opens up pathways for future investigations, including studying genes responsible for desiccation tolerance and the conservation of native grasses that occur in rocky habitats.

Style APA, Harvard, Vancouver, ISO itp.

40

Milinkovitch, 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.

Pełny tekst źródła

Style APA, Harvard, Vancouver, ISO itp.

41

Kaleme, 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.

Pełny tekst źródła

Streszczenie:

Thesis (PhD) - Stellenbosch University, 2011.
ENGLISH 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.

Style APA, Harvard, Vancouver, ISO itp.

42

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/.

Pełny tekst źródła

Streszczenie:

This thesis introduce new approaches into the understanding of chronology and cultural-technological development of the Neolithic and Chalcolithic settlements within the Central Plateau of Iran through the study of the evolution of ceramic craft specialisation between ca. 5700-4800 BC by analysing newly excavated pottery from the different three areas of this region: the Tehran, Qazvin and Kashan plains. Despite having been investigated for almost 90 years, the prehistoric ceramics of the Central Iranian Plateau have mainly been studied in a basic manner, based on the study of colour and decoration of pottery as the criteria to identify, characterise, and compare the various pottery types of the region with little attention to technology and production. In the present thesis a multidisciplinary research method has been adopted by utilising scientific analysis technics such as X-ray Diffraction (XRD), X-ray fluorescence (XRF) and scanning electron microscope (SEM) as well as typological classification and more advanced methods such as phylogenetic analyses in studying and characterisation the pottery. Based on the results of scientific analyses as well as the archaeological data this research will provide valuable information on the course of evolution and the origin of the changes observed in ceramic technology, and will determine the level of specialisation and standardisation in the pottery-making, as well as the mode of production in these prehistoric sites. Through comparison of the pottery characteristics from different sites of the same tradition it will also assess the similarity of sources of raw materials and the techniques of shaping and firing the pottery. Utilising the valuable information gathered by the aforementioned methods this thesis represents a more comprehensive and reliable information concerning the economic and cultural connections and interactions of the prehistoric communities living in this region in the Late Neolithic and the Transitional Chalcolithic periods.

Style APA, Harvard, Vancouver, ISO itp.

43

Zen, 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.

Pełny tekst źródła

Streszczenie:

Aspergillus és un dels gèneres de Ascomycetes més comuns i ubics, habitant una gran diversitat de substrats. L'objectiu principal d'aquesta tesi va ser contribuir al millor coneixement d'aquest gènere, explorant la diversitat d'espècies en mostres clíniques i ambientals. En aquesta tesi es va estudiar un total de 433 aïllaments obtinguts de diferents fonts (mostres clíniques, terra, fems d'animals herbívors, restes vegetals). La identificació dels aïllaments es va dur a terme per anàlisi filogenètics de múltiples marcadors, incloent seqüències d'ITS, β-tubulina, calmodulina, i RPB2, i caracterització fenotípica. Quan es va considerar rellevant, els aïllaments clínics van ser sotmesos a proves de susceptibilitat antifúngica contra els principals fàrmacs disponibles. En resum, es van identificar 98 espècies d'Aspergillus, 49 de mostres clíniques (248 aïllaments), 48 de terra (92 aïllaments), 48 de fem (82 aïllaments) i 10 de restes vegetals (10 aïllaments). Considerant les seccions poc estudiades d'Aspergillus en el context clínic, les seccions més freqüents van ser Nidulantes (incloent l'antiga secció Versicolores), 84 aïllaments i 14 espècies; Circumdati, 35 aïllaments i set espècies; Aspergillus, 25 aïllaments i cinc espècies; i Usti, 19 aïllaments i dues espècies. Vuit espècies van ser aïllades de mostres clíniques per primera vegada i tres van ser propostes com a noves espècies. Els antifúngics, en general, van mostrar bona activitat enfront dels aïllats assajats, amb l'excepció de l'activitat reduïda de amfotericina B contra membres de la secció Circumdati. Quant als aïllaments ambientals, es van proposar 14 noves espècies basades en caràcters fenotípics i moleculars; cinc pertanyents a la secció Terrei (tres de fem i dues de terra); quatre a la secció Candidi (tots de fem); dues a la secció Nidulantes (tots dos de terra); i una de cada una de les seccions Flavipedes, Cremei, i Usti (tots de fem).
Aspergillus 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).

Style APA, Harvard, Vancouver, ISO itp.

44

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.

Pełny tekst źródła

Streszczenie:

Philosophiae Doctor - PhD
The 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)

Style APA, Harvard, Vancouver, ISO itp.

45

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.

Pełny tekst źródła

Streszczenie:

Plutella xylostella L. is a global pest of cruciferous crops. A new, closely-related Australian taxon, P. australiana, was identified in 2013, with significant potential impacts on market access and on introduction of biological control agents in Australia. Cytochrome oxidase 1 'barcode' sequencing and comparison of the genitalia of adults collected from 3 states in Australia (including Tasmania) and New Zealand identified significant morphological similarity between the two taxa, and two features that can be used to differentiate adult females of the two taxa. Larval collections identified two host plants of P. australiana of potential commercial importance.

Style APA, Harvard, Vancouver, ISO itp.

46

Molinier, Virginie. "Diversité génétique et aromatique de la truffe de Bourgogne". Thesis, Dijon, 2013. http://www.theses.fr/2013DIJOS021/document.

Pełny tekst źródła

Streszczenie:

Les Truffes sont des champignons ascomycètes ectomycorhiziens appartenant à la famille des Tuberaceae et plus précisément au genre Tuber. On dénombre à ce jour plus d’une trentaine d’espèces de Tuber en Europe. Lors de ce travail de thèse, nous nous sommes plus précisément focalisés sur le modèle Tuber aestivum-uncinatum. Cette truffe communément appelée « Truffe de Bourgogne » présente un intérêt à la fois gastronomique et culturel.La première partie de ce travail de thèse a porté sur la clarification du statut taxonomique de la truffe de Bourgogne (Tuber uncinatum). Pour cela, nous avons utilisé une approche multi-marqueurs combinant des marqueurs génétiques couramment utilisés à l’échelle interspécifique. Nos analyses ont montré que les deux taxons Tuber aestivum (la truffe d’été) et Tuber uncinatum sont conspécifiques. Durant la deuxième partie, nous nous sommes intéressés à la diversité génétique de Tuber aestivum. Pour cela, nous avons tout d’abord développé des marqueurs microsatellites spécifiques par une approche de « direct shotgun pyrosequencing ». Cette méthode a permis le développement de 15 marqueurs microsatellites polymorphes. Nous les avons ensuite utilisés pour génotyper des individus provenant de différentes localisations en Europe. Nous avons pu identifier quatre sous populations différenciées qui ne correspondent pas, pour la majorité, à une répartition géographique. Cependant, un des clusters se différencie des autres à la fois par sa situation géographique (sud de la France) et ses caractéristiques génétiques (présence d’allèles rares). Ces résultats préliminaires pourraient indiquer l’existence d’un écotype particulier attaché à une écologie méridionale, Tuber aestivum sensu stricto.Nous nous sommes ensuite intéressés, dans la troisième partie de ce travail de thèse à la diversité aromatique de Tuber aestivum à l’échelle locale. Les résultats obtenus permettent de mettre en évidence l’existence d’une différenciation modérée entre les individus issus d’une truffière naturelle et les individus issus d’une truffière plantée. D’une saison de récolte à l’autre, une stabilité génotypique a été observée. Au niveau aromatique, seuls les composés C8 semblent être liés aux génotypes.Dans la dernière partie, nous nous sommes intéressés à l’analyse de données de récolte sur plus de trente ans au sein d’une truffière plantée de noisetiers inoculés initialement par Tuber melanosporum. Grâce à des analyses statistiques simples, nous avons pu noter les fluctuations tant en quantité qu’en poids des truffes récoltées suivant les saisons et les arbres truffiers. Il apparait que le remplacement de Tuber melanosporum par Tuber aestivum s’est fait de manière très rapide (trois ans). La disparition de Tuber melanosporum peut probablement être expliquée par la fermeture de la canopée des noisetiers, Tuber melanosporum n’appréciant pas un ombrage excessif
Truffles 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

Style APA, Harvard, Vancouver, ISO itp.

47

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.

Pełny tekst źródła

Style APA, Harvard, Vancouver, ISO itp.

48

Bauer, 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.

Pełny tekst źródła

Style APA, Harvard, Vancouver, ISO itp.

49

Krig, Kåre. "Methods for phylogenetic analysis". Thesis, Linköping University, Department of Mathematics, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-56814.

Pełny tekst źródła

Streszczenie:

In 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.

Style APA, Harvard, Vancouver, ISO itp.

50

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.

Pełny tekst źródła

Streszczenie:

Orientadores: Beatriz Appezzato da Glória, Fernando Batista da Costa
Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
Made available in DSpace on 2018-08-25T23:31:20Z (GMT). No. of bitstreams: 1 Lusa_MakeliGaribotti_D.pdf: 111212555 bytes, checksum: dcca67728c1e6b3b3529dd3542283773 (MD5) Previous issue date: 2014
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

Style APA, Harvard, Vancouver, ISO itp.

Rozprawy doktorskie na temat „Phylogenetic analyses”

Utwórz poprawne odniesienie w stylach APA, MLA, Chicago, Harvard i wielu innych