Dissertations / Theses on the topic 'Molecular phylogeny'
To see the other types of publications on this topic, follow the link: Molecular phylogeny.
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the top 50 dissertations / theses for your research on the topic 'Molecular phylogeny.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Browse dissertations / theses on a wide variety of disciplines and organise your bibliography correctly.
1
Hide, Elizabeth Anne. "A molecular approach to sponge phylogeny." Thesis, University of Cambridge, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.360785.
Full text
2
Campbell, Jinx. "Molecular phylogeny of the Halosphaeriaceae, Ascomycota." Thesis, University of Portsmouth, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.327000.
Full text
3
Macdonald, Kenneth S. "Molecular Phylogeny of Lake Baikal Amphipods." W&M ScholarWorks, 1999. https://scholarworks.wm.edu/etd/1539617748.
Full text
4
Simon, Sabrina [Verfasser]. "Deep molecular phylogeny of the Pterygota / Sabrina Simon." Hannover : Technische Informationsbibliothek und Universitätsbibliothek Hannover, 2010. http://d-nb.info/1009413708/34.
Full text
5
Darbyshire, Stephen James. "Molecular phylogeny of North American Festuca Linnaeus (Poaceae)." Thesis, University of Ottawa (Canada), 1992. http://hdl.handle.net/10393/7575.
Full textAbstract:
Current hypotheses of the phyletic relationships in the genus Festuca and generic segregates, as expressed in classification systems, were tested using molecular data (DNA restriction endonuclease site variation of the chloroplast and nuclear genomes). Taxa native or introduced to North America were used as exemplars for seven subgenera: Drymanthele, Subulatae, Subuliflorae, Obtusae, Schedonorus, Leucopoa sensu lato (sections Leucopoa and Breviaristatae) and Festuca; and four generic segregates: Leucopoa sensu stricto (section Leucopoa), Argillochloa, Vulpia and Lolium. Cladistic analysis of 67 shared, polymorphic chloroplast DNA restriction sites (11 endonucleases) indicated that Festuca and subgeneric taxa, as circumscribed in morphologically based classifications, are polyphyletic. Phenetic analysis of 108 polymorphic chloroplast DNA restriction sites (11 endonucleases) and nuclear ribosomal DNA restriction fragment patterns (12 endonucleases) supported the results of the cladistic analysis. Two main evolutionary lines were indicated within the genus Festuca as presently constructed. One contained the vast majority of the genus Festuca exemplars, including the subgenera Drymanthele, Subulatae, Subuliflorae, Obtusae and Festuca, as well as Vulpia, Argillochloa and subgenus Leucopoa section Breviaristatae. The other lineage included subgenus Schedonorus, subgenus Leucopoa section Leucopoa and the genus Lolium. Analyses support the recognition of four related genera in the two lineages, Vulpia and Festuca (including subgenus Leucopoa section Breviaristatae, and the subgenera Drymanthele, Subulatae, Subuliflorae, Obtusae, and Festuca) in one and Leucopoa sensu stricto (including only section Leucopoa) and Lolium (including Festuca subgenus Schedonorus) in the other, respectively. The recognition of the monotypic generic segregate Argillochloa (= Festuca dasyclada) is not supported by the analyses.
6
Zhang, Ying, and 张英. "Revision of Pleosporales : morpho-molecular phylogeny and typification." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2010. http://hdl.handle.net/10722/196082.
Full text
7
Li, Jun, and 李俊. "Molecular evolution and phylogeny of methanogenic archael genomes." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2014. http://hdl.handle.net/10722/208152.
Full textAbstract:
Methane (CH4) is the major chemical component of natural gas, as well as a particularly potent greenhouse gas. Methanogens are the archaeal organisms that produce methane and play a key role in biological methanogenesis. A total of six taxonomic orders of archaeal methanogens have been discovered and almost all previous phylogenetics studies have confirmed that these methanogens are genetically diversified and do not belong to a phylogenetically monophyletic group. To date, the relationships between methanogens and closely related non-methanogen species at the taxonomic order level remain unresolved and different studies have often produced contradictory results based on different gene markers. These studies suggest the complicated and distinct evolutionary histories between different genes in these genomes.
In this thesis, 74 fully sequenced archaeal genomes, including 41 methanogens, were collected and used in a comprehensive comparative genomics and evolutionary analysis. First, numerous phylogenomic trees were reconstructed based on various datasets using several methods and the results show that Methanopyrales is close to Methanobacteriales (or Methanopyrales) in the statistically best species tree. In addition, Methnocellales and Methanosarcinales, and as well as Methanomicrobiales and Halobacteriales are sister clades in the best species tree, but the confidence level is low. Further incongruence tests among the phylogenetic forest, which is composed of 3,694 ortholog gene families, reveal that the archaeal core genes have much stronger consistent vertical evolutionary signals than other genes, but these core genes are not topologically fully congruent with each other.
Secondly, a series of weighted network analyses were implemented to decompose the hierarchical structure and to reveal the co-evolved gene modules, global and local features in the archaeal methanogen phylogenetic forest. The results show that this co-evolution network contains 7 statistical robust modules, and the module with the highest average node strength includes the majority of the core genes located in the central position of the network. Further in-depth evolutionary analysis reveals that the modularized evolution in the archaeal phylogenetic forest is closely related to the time of origin, HGT rate and ubiquitous vertical inheritance in gene families.
Lastly, to investigate the causes for and factors related to the pervasive topology incongruence in the phylogenetic forest, in-depth clanistics analysis and HGT detection were carried out. These results show that (1) about 63% of gene families experienced at least 1 HGT event in their whole history; (2) core genes are not immune to HGT but they do have much lower HGT rates than other genes; (3) methanogens have distinct trends of HGTs from non-methanogen species; and (4) highly frequent inter-order HGTs, even for core genes, in methanogen genomes lead to their scrambled phylogenetic relationships. Further clanistics analysis screened out 119 candidate genes related to methanogenic pathways adaptation and most of these gene families have experienced at least one HGT.
In conclusion, a complex evolutionary scenario for methanogenic archaeal species was described in this thesis as a combination of complicated vertical and non-vertical evolutionary processes in a modularized phylogenetic forest.published_or_final_version
Biological Sciences
Doctoral
Doctor of Philosophy
8
Barker, Nigel Paul. "A molecular phylogeny of the subfamily Arundinoideae (Poaceae)." Doctoral thesis, University of Cape Town, 1995. http://hdl.handle.net/11427/17509.
Full textAbstract:
Includes bibliography.The subfamily Arundinoideae has long been considered to be an unnatural assemblage of genera, the relationships of which are obscure or unknown. Because morphological and anatomical data have, to date, been unable to elucidate relationships among these genera, sequence data from two chloroplast genes are used to elucidate relationships among 33 arundinoid genera. Sequence data from the variable, grass-specific insert in the rpoC2 gene is used to determine the relationships among 73 grass species from all currently recognised subfamilies. Phylogenetic analysis of this sequence data required the development of specialised alignment techniques based on testing assumptions of positional homology. Results of the analyses based on these alignments suggest that the Arundinoideae is divisible into four lineages, corresponding approximately to the tribes Danthonieae, Arundineae, Aristideae and Thysanolaeneae. Several arundinoid representatives are placed in other subfamilies. The rpoC2 sequence data was too variable to elucidate relationships at the tribal and subfamilial level. For this purpose, sequence data of the highly conserved rbcL gene was obtained from 22 taxa selected from the lineages identified by the rpoC2 study. Phylogenetic analysis of a total of 36 sequences resolved some of the relationships of the major clades, but other relationships were poorly supported. In an attempt to improve the resolution of these major clades, the rpoC2 and rbcL data sets were combined with restriction site data. These three data sets were analysed in a variety of combinations using both data combination and tree consensus methods to assess support of the phylogenetic relationships. Despite this, the resolution of the relationships among the Arundineae, Danthonieae, Aristideae and Chloridoideae was not resolved with any finality, although a (Arundineae (Danthonieae (Aristideae, Chloridoideae))) relationship is proposed as being most likely. The molecular phylogeny implies that eight grass subfamilies should be recognised. Two of these, the Danthonioideae and Aristidoideae, are new and the Arundinoideae is redelimited. Furthermore, new tribes in the subfamilies Centothecoideae (Thysanolaeneae) and Chloridoideae (Centropodieae) are proposed to accommodate lineages and taxa misplaced in the subfamily Arudinoideae as previously delimited.
9
Liu, Lihong. "Molecular phylogeny, classification, evolution and detection of pestiviruses /." Uppsala : Dept. of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, 2009. http://epsilon.slu.se/20098.pdf.
Full text
10
Orrell, Thomas M. "A molecular phylogeny of the Sparidae (Perciformes: Percoidei)." W&M ScholarWorks, 2000. http://web.vims.edu/library/Theses/Orrell2000.pdf.
Full text
11
Jones, Martin. "Multigene datasets for deep phylogeny." Thesis, University of Edinburgh, 2007. http://hdl.handle.net/1842/2575.
Full textAbstract:
Though molecular phylogenetics has been very successful in reconstructing the evolutionary history of species, some phylogenies, particularly those involving ancient events, have proven difficult to resolve. One approach to improving the resolution of deep phylogenies is to increase the amount of data by including multiple genes assembled from public sequence databases. Using modern phylogenetic methods and abundant computing power, the vast amount of sequence data available in public databases can be brought to bear on difficult phylogenetic problems. In this thesis I outline the motivation for assembling large multigene datasets and lay out the obstacles associated with doing so. I discuss the various methods by which these obstacles can be overcome and describe a bioinformatics solution, TaxMan, that can be used to rapidly assemble very large datasets of aligned genes in a largely automated fashion. I also explain the design and features of TaxMan from a biological standpoint and present the results of benchmarking studies. I illustrate the use of TaxMan to assemble large multigene datasets for two groups of taxa – the subphylum Chelicerata and the superphylum Lophotrochozoa. Chelicerata is a diverse group of arthropods with an uncertain phylogeny. When a set of mitochondrial genes is used to analyse the relationships between the chelicerate orders, the conclusions are highly dependent upon the evolutionary model used and are affected by the presence of systematic compsitional bias in mitochondrial genomes. Lophotrochozoa is a recently-proposed group of protostome phyla. A number of distinct phylogenetic hypotheses concerning the relationships between lophotrochozoan phyla have been proposed. I compare the phylogenetic conclusions given by analysis of nuclear and mitochondrial protein-coding and rRNA genes to evaluate support for some of these hypotheses.
12
Mengual, Sanchis Ximo. "Molecular phylogeny and evolution of predatory Syrphidae (Insecta: Diptera)." Doctoral thesis, Universidad de Alicante, 2008. http://hdl.handle.net/10045/14536.
Full text
13
Willows-Munro, Sandi. "The molecular evolution of the spiral-horned antelope (Mammalia: Tragelaphini)." Thesis, Stellenbosch : Stellenbosch University, 2003. http://hdl.handle.net/10019.1/53659.
Full textAbstract:
Thesis (MSc)--Stellenbosch University, 2003.ENGLISH ABSTRACT: The evolutionary history of the African tribe Tragelaphini (spiral-horn antelope) is controversial. Past phylogenetic relationships among species were based on morphology or limited fossil evidence and are in conflict with mitochondrial DNA sequencing studies that have been conducted more recently. Although the group is distinguished from other African ungulates by the presence of spirally-twisted horns, the nine recognized extant species differ considerably in morphology, feeding habits and their habitat preference. The present study aims to resolve the phylogenetic uncertainties of the Tragelaphini using nuclear DNA sequence data derived from four independent DNA loci (MGF, PRKCl, SPTBN and THY). These data were combined with all previously published DNA sequences to produce a molecular supermatrix comprising approximately 6000 characters. Both parsimony and model based phylogenetic analyses of the nuclear DNA support the associations resulting from the analysis of mitochondrial genes. These findings suggest that the morphological characters previously used to delimit species within the group are subject to convergent evolution. The molecular phylogeny presented herein suggests that early members of Tragelaphini diverged from the other bovids during the mid-Miocene approximately 15.7 million years before present (MYBP). The common nyala (Tragelaphus enqest; and lesser kudu (Tragelaphus imberbis) representing the most basal species, separated from the other tragelaphids approximately 7.1 MYBP. This was subsequently followed by the radiation of those species adapted to a more tropical environment and they include the mountain nyala (Tragelaphus buxtom), bongo (Tragelaphus euryceros), sitatunga (Tragelaphus spekel) and bushbuck (Tragelaphus scriptus), and the arid adapted clade comprising the giant eland (Taurotragus derbianus), common eland (Taurotragus oryx) and greater kudu (Tragelaphus strepsiceros). It is thought that this split occurred at the Miocene-Pliocene boundary approximately 5.4 MYBP. The timing of evolutionary events within the tribe suggests climatic oscillations and subsequent biotic shifts as the major driving forces underpinning speciation in the tribe Tragalaphini.
AFRIKAANSE OPSOMMING; Die evolusionêre geskiedenis van die ras Tragelaphini (spiraalhoringwildsbokke) is kontroversieël. Vorige filogenetiese verwantskappe tussen die spesies is gebaseer op morfologie of beperkte fossiel bewyse. Meer onlangse studies, gebaseer op mitochondriale ONS nukleotieddata, is in teenstryding met baie van die evolusionêre hypotese afkomstig van morfologiese studies. Alhoewel die groep van die ander hoefdiere uitgeken kan word deur die aanwesigheid van spiraalvormige horings, verskil die nege hedendaagse spesies grootliks ten opsigte van morfologie, voedingswyse en habitat. Die hoof doelwit van hierdie studie was om die filogenetise verwantskappe tussen die Tragelaphini spesies te ontleed deur gebruik te maak van nukluêre ONS nukleotieddata afkomstig van vier onafhanklike ONS merkers (MGF, PRKCl, SPTBN en THY). Die data verkry is saamgevoeg by vorige gepubliseerde ONS nukleotidedata om 'n "supermatris" van sowat 6000 karakters te produseer. Parsimonie en modelgebaseerde filogenetise analise van die nukluêre ONS nukleotieddata het ooreengestem met die resultate van vorige mitochondriale studies. Hierdie bevindings dui daarop dat die morfologiese karakters wat voorheen gebruik is om die evolusionêre verwantskappe tussen die Tragelaphini spesies te ontleed onderhewig is aan konvergente evolusie. Die molekulêre filogenie wat hierin beskryf word stel voor dat die ras Tragelaphini gedurende die mid- Miocene, omtrent 15.7 miljoen jaar (MJ) gelede van die ander lede van die subfamilie Bovinae geskei het. Tragelaphus angasi en Tragelaphus imberbis, die mees basale spesies in die filogenie, het omtrent 7.1 MJ gelede van die ander lede van die Tragelaphini geskei. Hierdie skeiding is gevolg deur 'n split tussen die spesies aangepas vir 'n meer tropiese habitat (Tragelaphus buxtoni, Tragelaphus euryceros, Tragelaphus spekei en Tragelaphus scriptus) en die spesies aangepas vir 'n droë habitat (Taurotragus derbianus, Taurotragus oryx en Tragelaphus strepsiceros) Hierdie finale skeiding het gedurende die Miocene-Pliocene oorgang plaasgevind. Die tydsberekening van die evolusionêre gebeurtenisse wat binne die Tragelaphini ras plaasgevind het, gekoppel aan paleoklimaatdata, dui aan dat veranderinge in klimaat en die geassosieerde habitatveranderinge verantwoordelik was vir die spesiasie patroon wat ons vandag in die Tragelaphini ras waarneem.
14
Krüger, Manuela. "Molecular phylogeny, taxonomy and evolution of arbuscular mycorrhizal fungi." Diss., lmu, 2011. http://nbn-resolving.de/urn:nbn:de:bvb:19-140769.
Full text
15
Wang, Yean. "Molecular polymorphisms for phylogeny, pedigree and population structure studies." University of Sydney, 2007. http://hdl.handle.net/2123/1541.
Full textAbstract:
Doctor of PhilosophyA number of types of molecular polymorphisms can be used for studying genetic relationship and evolutionary history. Microsatellites are hypervariable and can be very useful tools to determine population structure, distinguish sibling species, as well as verifying parental relationships and pedigrees. However, while microsatellite polymorphisms are useful for solving relationships between populations within a species, relations among species or genera will probably be obscured due to a high degree of homoplasy —identity arising from evolutionary convergence not by descent. For long range evolutionary history, such as phylogeny from old world monkey to human, mtDNA markers may be better candidates. The aim of this thesis is to assess molecular polymorphisms of different types and their optimal use in different situations. Two widely separated taxa were used for testing –the green monkey Chlorocebus sabaeus, and the sibling dipteran flies Bactrocera tryoni and B. neohumeralis, known collectively as the Queensland fruit fly. In the present study a complete 16,550 bp mtDNA sequence of the green monkey Chlorocebus sabaeus is reported for the fist time and has been annotated (Chapter 2). Knowledge of the mtDNA genome contributes not only to identification of large scale single nucleotide polymorphisms (SNPs) (Chapter 4) or other mtDNA polymorphisms development, but also to primate phylogenetic and evolutionary study (Chapter 3). Microsatellites used for the green monkey paternity and pedigree studies were developed by cross-amplification using human primers (Chapter 5). For studies of population structure and species discrimination in Queensland fruit fly (Chapter 7), microsatellites were isolated from a genomic library of Bactrocera tryoni (Chapter 6) The total length of 16550 bp of complete mtDNA of the green monkey C. sabaeus, which has been sequenced and annotated here, adds a new node to the primate phylogenetic tree, and creates great opportunity for SNP marker development. The heteroplasmic region was cloned and five different sequences from a single individual were obtained; the implication of this are discussed. The phylogenetic tree reconstructed using the complete mtDNA sequence of C. sabaeus and other primates was used to solve controversial taxonomic status of C. sabaeus. Phylogenies of primate evolution using different genes from mtDNA are discussed. Primate evolutionary trees using different substitution types are compared and the phylogenetic trees constructed using transversions for the complete mtDNA were found close to preconceived expectations than those with transversions + transitions. The sequence of C. sabaeus 12SrRNA reported here agrees with the one published by ven der Kuyl et al. (1996), but additional SNPs were identified. SNPs for other regions of mtDNA were explored using dHPLC. Twenty two PCR segments for 96 individuals were tested by dHPLC. Fifty five SNPs were found and 10 haplogroups were established. Microsatellite markers were used to construct a genealogy for a colony of green monkeys (C. sabaeus) in the UCLA Vervet Monkey Research Colony. Sixteen microsatellites cross-amplified from human primers were used to conduct paternity analysis and pedigree construction. Seventy-eight out of 417 offspring were assigned paternity successfully. The low success rate is attributed to a certain proportion of mismatches between mothers and offspring; the fact that not all candidate fathers were sampled, the limitations of microsatellite polymorphisms; and weakness of the exclusion method for paternity assessment. Due to the low success rate, the pedigree is split into a few small ones. In a complicated pedigree composed of 75 animals and up to four generations with multiple links a power male mated with 8 females and contributed 10 offspring to the pedigree. Close inbreeding was avoided. Population structure within two species of Queensland fruit fly Bactrocera tryoni and Bactrocera neohumeralis (Tephritidae: Diptera) is examined using microsatellite polymorphisms. Queensland fruit flies B. tryoni and B. neohumeralis are sympatric sibling species that have similar morphological and ecological features. They even share polymorphism at the molecular level. Mating time difference is the main mechanism by which they maintain separate species. In the present study, 22 polymorphic and scorable microsatellites were isolated from B. tryoni and tested in the two species sampled from sympatric distribution areas. Pairwise genetic distance analysis showed explicit differentiation in allele frequencies between the two species, but very weak differences between conspecific populations. Gene flow is higher within B. tryoni than within B. neohumeralis, and gene exchange between the two species exists. An averaging linkage clustering tree constructed by UPGMA showed two major clusters distinguishing the two species, and it appears that population structure is highly correlated with geographic distance. The relationship between molecular markers, evolution, and selection are discussed using comparative studies within two large taxa: primate and insect. The degree of conservation and polymorphism in microsatellites varies between taxa, over evolutionary time.
16
Massoni, Julien. "Phylogeny, molecular dating and floral evolution of Magnoliidae (Angiospermae)." Phd thesis, Université Paris Sud - Paris XI, 2014. http://tel.archives-ouvertes.fr/tel-01044699.
Full textAbstract:
Deep phylogenetic relationships in the angiosperms had long been uncertain. However, by the end of the 1990s, large-scale studies contributed to the current well resolved picture of the tree of flowering plants, in which eudicots, monocots, and magnoliids are the three largest clades. Whereas monocots and eudicots have been recognized since the very first phylogenetic analyses, the monophyly of magnoliids (Canellales, Laurales, Magnoliales, and Piperales) is a more recent result. Magnoliidae, as now circumscribed, consist of 20 families and ca. 10,000 species mostly distributed in the tropics. Before the present thesis, several parts of the magnoliid tree had been well studied, but little was known about the evolutionary history of Magnoliidae as a whole. The first chapter of this thesis is a phylogenetic study conducted to clarify the relationships among families and orders of Magnoliidae. To do so, I sampled 199 species of Magnoliidae and 12 molecular markers from the three genomes and conducted phylogenetic analyses using parsimony, maximum likelihood, and Bayesian methods. The results confirm, with a greater level of support, two clades in Magnoliidae: Canellale + Piperales, and Laurales + Magnoliales. In addition, the relationships among the 20 families are generally well supported, and Lactoridaceae and Hydnoraceae are nested within Aristolochiaceae (Piperales). In the second chapter, the ages and phylogenetic positions of 10 fossils attributed to Magnoliidae were reviewed in detail. The goal of this study was to provide new reliable calibration points in order to conduct molecular dating analyses. These fossils were selected from the rich fossil record of the group because of their previous inclusion in phylogenetic analyses with extant taxa. The resulting calibration scheme provides six solid, internal minimum age constraints. The third chapter includes molecular dating analyses using the present calibration scheme and the same molecular dataset of Chapter 1. This study tends to push back in time the ages of the crown nodes of Magnoliidae (127.1-198.9 Ma), and of the four orders, Canellales (126.3-141.0 Ma), Piperales (88.2-157.7 Ma), Laurales (111.8-165.6 Ma), and Magnoliales (115.0-164.2 Ma). In the same chapter, I investigated the mode of diversification in the group. The strongly imbalanced distribution of species appears to be best explained by models of diversification with 6 to 14 diversification rate shifts. Finally, in the last chapter, I traced the evolution of 26 floral characters to reconstruct the ancestral flowers in key nodes of Magnoliidae. I used the phylogeny of Chapter 1 and an exemplar approach. Our results show that the most recent common ancestor of all Magnoliidae was a tree bearing actinomorphic, bisexual flowers with a differentiated perianth of two alternate, trimerous whorls of free perianth parts (outer and inner tepals) and probably three free stamens. This work provides key results on the evolution of Magnoliidae and raises several new questions such as the impact of geological crises on diversification of the group or the influence of pollinators and the environment on the evolution of floral morphology.
17
Valiadi, Martha. "Bioluminescence in dinoflagellates : diversity, molecular phylogeny and field ecology." Thesis, University of Southampton, 2011. https://eprints.soton.ac.uk/209735/.
Full textAbstract:
Marine dinoflagellates are an ecologically important group of protists within the plankton, performing key process such as photosynthesis, heterotrophy and toxin production. Some dinoflagellates are also capable of producing bioluminescence and they are the most abundant protists that produce light in the surface waters of the oceans. This study employed molecular tools to investigate the identity of bioluminescent species, the genetic basis, diversity and functional regulation of bioluminescence, and the distribution of marine bioluminescent dinoflagellate populations. Using “universal” and taxon specific PCR primers designed to amplify the luciferase gene (lcf), the distribution of this gene within dinoflagellates was found to be taxon specific and the first lcf sequences obtained from four genetically distant genera revealed a previously unknown high diversity of this gene. The luciferin binding protein gene (lbp) was detected for the first time in three genera of ecologically important gonyaulacoid dinoflagellates, showing that this understudied gene is common in dinoflagellate bioluminescence systems. Phylogenetic analyses of both lcf and lbp provided new insight on species divergence within the toxic genus Alexandrium and pointed out important pitfalls in using protein coding genes for phylogenetic studies. The lcf PCR primers were employed in the first field study using a molecular approach to detect natural populations of bioluminescent dinoflagellates, showing that this approach outperforms optical bioluminescence measurements and that their distribution and composition is intimately tied to hydrographic patterns that create distinct environmental zones. The lcf PCR primers were also employed to study the regional variation in bioluminescence of Noctiluca scintillans, showing for the first time that the environment maintains or eliminates bioluminescence, by finding that a hydrographically isolated non bioluminescent variety in the west coast of the USA has “switched off” its bioluminescence system while diverging to possibly become a different species. Also, a novel lbp was discovered in N. scintillans which improved the current model for the evolution of bioluminescence genes in dinoflagellates. This thesis is the first study to employ molecular tools in a comprehensive and multifaceted investigation of dinoflagellate bioluminescence and has contributed significantly to building a fundamental understanding of this remarkable phenomenon.
18
Wang, Yean. "Molecular polymorphisms for phylogeny, pedigree and population structure studies." Thesis, The University of Sydney, 2006. http://hdl.handle.net/2123/1541.
Full textAbstract:
A number of types of molecular polymorphisms can be used for studying genetic relationship and evolutionary history. Microsatellites are hypervariable and can be very useful tools to determine population structure, distinguish sibling species, as well as verifying parental relationships and pedigrees. However, while microsatellite polymorphisms are useful for solving relationships between populations within a species, relations among species or genera will probably be obscured due to a high degree of homoplasy —identity arising from evolutionary convergence not by descent. For long range evolutionary history, such as phylogeny from old world monkey to human, mtDNA markers may be better candidates. The aim of this thesis is to assess molecular polymorphisms of different types and their optimal use in different situations. Two widely separated taxa were used for testing –the green monkey Chlorocebus sabaeus, and the sibling dipteran flies Bactrocera tryoni and B. neohumeralis, known collectively as the Queensland fruit fly. In the present study a complete 16,550 bp mtDNA sequence of the green monkey Chlorocebus sabaeus is reported for the fist time and has been annotated (Chapter 2). Knowledge of the mtDNA genome contributes not only to identification of large scale single nucleotide polymorphisms (SNPs) (Chapter 4) or other mtDNA polymorphisms development, but also to primate phylogenetic and evolutionary study (Chapter 3). Microsatellites used for the green monkey paternity and pedigree studies were developed by cross-amplification using human primers (Chapter 5). For studies of population structure and species discrimination in Queensland fruit fly (Chapter 7), microsatellites were isolated from a genomic library of Bactrocera tryoni (Chapter 6) The total length of 16550 bp of complete mtDNA of the green monkey C. sabaeus, which has been sequenced and annotated here, adds a new node to the primate phylogenetic tree, and creates great opportunity for SNP marker development. The heteroplasmic region was cloned and five different sequences from a single individual were obtained; the implication of this are discussed. The phylogenetic tree reconstructed using the complete mtDNA sequence of C. sabaeus and other primates was used to solve controversial taxonomic status of C. sabaeus. Phylogenies of primate evolution using different genes from mtDNA are discussed. Primate evolutionary trees using different substitution types are compared and the phylogenetic trees constructed using transversions for the complete mtDNA were found close to preconceived expectations than those with transversions + transitions. The sequence of C. sabaeus 12SrRNA reported here agrees with the one published by ven der Kuyl et al. (1996), but additional SNPs were identified. SNPs for other regions of mtDNA were explored using dHPLC. Twenty two PCR segments for 96 individuals were tested by dHPLC. Fifty five SNPs were found and 10 haplogroups were established. Microsatellite markers were used to construct a genealogy for a colony of green monkeys (C. sabaeus) in the UCLA Vervet Monkey Research Colony. Sixteen microsatellites cross-amplified from human primers were used to conduct paternity analysis and pedigree construction. Seventy-eight out of 417 offspring were assigned paternity successfully. The low success rate is attributed to a certain proportion of mismatches between mothers and offspring; the fact that not all candidate fathers were sampled, the limitations of microsatellite polymorphisms; and weakness of the exclusion method for paternity assessment. Due to the low success rate, the pedigree is split into a few small ones. In a complicated pedigree composed of 75 animals and up to four generations with multiple links a power male mated with 8 females and contributed 10 offspring to the pedigree. Close inbreeding was avoided. Population structure within two species of Queensland fruit fly Bactrocera tryoni and Bactrocera neohumeralis (Tephritidae: Diptera) is examined using microsatellite polymorphisms. Queensland fruit flies B. tryoni and B. neohumeralis are sympatric sibling species that have similar morphological and ecological features. They even share polymorphism at the molecular level. Mating time difference is the main mechanism by which they maintain separate species. In the present study, 22 polymorphic and scorable microsatellites were isolated from B. tryoni and tested in the two species sampled from sympatric distribution areas. Pairwise genetic distance analysis showed explicit differentiation in allele frequencies between the two species, but very weak differences between conspecific populations. Gene flow is higher within B. tryoni than within B. neohumeralis, and gene exchange between the two species exists. An averaging linkage clustering tree constructed by UPGMA showed two major clusters distinguishing the two species, and it appears that population structure is highly correlated with geographic distance. The relationship between molecular markers, evolution, and selection are discussed using comparative studies within two large taxa: primate and insect. The degree of conservation and polymorphism in microsatellites varies between taxa, over evolutionary time.
19
Lee, Chung-Kun. "Phylogeny and Taxonomy of Commelinaceae (Commelinales)." Doctoral thesis, Kyoto University, 2021. http://hdl.handle.net/2433/263508.
Full text
20
Hu, Hongli, and 胡红莉. "Morphological and molecular studies of selected dothideomycetes." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2010. http://hub.hku.hk/bib/B43905936.
Full text
21
Rebholz, Wilhelmus Ewald Reinaard. "Molecular phylogenetics and conservation aspects of antelopes." Doctoral thesis, University of Cape Town, 1996. http://hdl.handle.net/11427/26971.
Full textAbstract:
This thesis concerns the molecular phylogenetics of three tribes of the family Bovidae, the Antilopini, Neotragini, and Tragelaphini. None of these tribes have been studied extensively with molecular techniques. The tribe Antilopini is one of the most speciose tribes (it includes 6 genera with 20 species) and the classification of several species of the genus Gazella is not clear. The tribe Neotragini is thought to be paraphyletic. Mitochondrial sequences of the cytochrome c oxidase ill and cytochrome b genes totalling 1083 base pairs have been determined for 52 taxa and used to determine phylogenetic relationships using cladistic and distance methods. Karyological analysis identified polymorphisms in several species (especially in Gazella saudiya and G. subgutturosa). Karyotypes of G. dorcas pelzelni and an XXY karyotype of a G. dorcas individual are shown for the first time. The main conclusions are that the Antilopini and the Tragelaphini are monophyletic and that the tribe Neotragini is paraphyletic. There is a lack of phylogenetic resolution between tribes which is probably due to the rapid radiation of the different tribes about 20 million years ago. The genus Taurotragus in the tribe Tragelaphini is shown to be paraphyletic and it would be appropriate to incorporate these taxa in the genus Tragelaphus. The genus Gazella could be paraphyletic, due to the position of Antilope cervicapra, in which case the genus needs to be split into two genera or renamed as Antilope. It is also argued that the use of the subgenus Trachelocele should be discontinued and that its only species, G. subgutturosa should be included in the subgenus Gazella. G. rufifrons and G. thomsonii may be more appropriately considered as conspecific. Cytogenetic and sequence data reveal that the herd of G. saudiya in Al Areen Wildlife Park is hybridised with G. bennettii and it is argued that it is important to identify unhybridised G. saudiya in other collections, since this species is on the brink of extinction. This case study demonstrates the need to genetically screen individuals which are part of a captive breeding program, especially if they are intended for reintroduction into the wild.
22
Barnes, Ian. "The molecular identification of goose species in archaeozoological assemblages." Thesis, University of York, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.298376.
Full text
23
Suzuki, Hiroshi. "Evolutionary Divergence in Floral Scents and Molecular Phylogeny of Magnoliaceae." 京都大学 (Kyoto University), 1999. http://hdl.handle.net/2433/181993.
Full text
24
Cassens, Insa. "Molecular evolutionary biology of cetaceans :phylogeny, phylogeography and conservation genetics." Doctoral thesis, Universite Libre de Bruxelles, 2004. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/211152.
Full text
25
Wang, Yean. "Phylogeny, pedigree, and population structure studies application of molecular polymorphisms." Saarbrücken VDM Verlag Dr. Müller, 2007. http://d-nb.info/98875634X/04.
Full text
26
Söhner, Sylvia. "Molecular diversity and phylogeny of the Calcareous Dinophytes (Thoracosphaeraceae, Peridiniales." Diss., Ludwig-Maximilians-Universität München, 2013. http://nbn-resolving.de/urn:nbn:de:bvb:19-164593.
Full text
27
Sheridan, Grainne E. C. "Molecular studies of watercress phylogeny and the crook-root pathogen." Thesis, University of Bath, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.338381.
Full text
28
James, Celia M. "The phylogeny and molecular biology of the genus Pelargonium (Geraniaceae)." Thesis, University of Cambridge, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.362869.
Full text
29
Phiri, Ethel Emmarantia. "Molecular phylogeny and biogeography of the Afrotropical freshwater crab fauna." Thesis, Stellenbosch : Stellenbosch University, 2014. http://hdl.handle.net/10019.1/86312.
Full textAbstract:
Thesis (PhD)--Stellenbosch University, 2014.ENGLISH ABSTRACT: Freshwater organisms, such as crabs (Crustacea: Decapoda: Brachyura), are useful in studies examining inland historical biogeographic patterns and speciation because they are isolated to specific drainage systems, which often serve as barriers to gene flow. The Afrotropical freshwater crab fauna (Potamonautidae) present ideal organisms for investigating hypothesis relating to evolutionary histories because they occur on continental Africa (sub-Sahara) and islands. However, there is a great deal of undiscovered freshwater crab diversity, especially with the prevalence of undiscovered cryptic lineages, which are poorly studied among freshwater crabs, leading to uncertain regional diversity. In this research, multiple genetic (mt- and nuDNA) markers were used to infer the phylogenetic relationships and the biogeographical histories of the Afrotropical freshwater crab superfamily, Potamonautidae. Divergence time estimations were used to infer biogeographic histories, to ascertain whether speciation could be linked to past geologic and / or climatic events. Two widely distributed Potamonautes species complexes were targeted for the investigation of regional cryptic species diversity. In Chapter 2, the intraspecific phylogenetic variability within Potamonautes perlatus sensu lato occurring on the Cape Fold Mountain range (South Africa) was examined, with sampling localities occurring in western- and southern flowing drainages. Previous research suggested possible cryptic speciation within this species complex; however, no tangible inferences could be made because of analytical constraints. Two major clades were recovered: one corresponding to western flowing drainages and another to southern flowing drainages. Moreover, three cryptic lineages were recovered: P. perlatus sensu stricto, restricted to western flowing drainages, and two geographically discrete novel cryptic lineages from the southern flowing drainages, described as P. barbarai sp. nov and P. barnardi sp. nov., with divergence (±2.61 Mya) linked to Pleistocene climatic events. Subsequent to the recovery of the two novel lineages from the Cape Fold Mountain range, the Pleistocene climatic events. Subsequent to the recovery of the two novel lineages from the Cape Fold Mountain range, the revision of the P. clarus / P. depressus species complex from the Tugela and uMkomazi drainages (Drakensberg Mountain range, South Africa) was conducted. This species complex was previously found to comprise at least five cryptic lineages (Chapter 3). A coalescent multilocus (three mt- and three nuDNA) Bayesian species delimitation method was used, and an additional three cryptic lineages were recovered, bringing the total to eight species (two already described as P. clarus and P. depressus), with divergence having occurred approximately 10.3 Mya. Following the recent discovery of novel freshwater crab lineages in the mountainous areas of Mozambique and Malawi, a sampling trip to the Zimbabwean Highlands was undertaken, where a novel freshwater crab species was discovered and described as P. mutareensis, highlighting the need to sample high-lying regions (Chapter 4). Furthermore, two additional novel lineages from Mozambique (P. bellarussus sp. nov.) and the Mpumalanga Province in South Africa (P. flavusjo sp. nov) were described (Chapter 5). In Chapter 6, increased taxon sampling, with additional specimens acquired from various museums and personal collections was used to obtain a better resolution of the phylogeny of the Afrotropical Potamonautidae and to infer the ancestral affinities of the two sub-families, Deckeniinae and Potamonautinae. The Potamonautidae were found to have speciated eastward from West Africa, with a late Cretaceous divergence (±107 – 96.04 Mya). The Potamonautinae originated in West Africa (three genera), while the paraphyletic Potamonautes and Platythelphusa had East African affinities. Potamonautes was not monophyletic, comprising several fragmented geographic clades, which may suggest that this genus requires revision. Nevertheless, the overall speciation within the Potamonautidae reflects past geological and climatic events, such as rifting and uplift episodes and the contraction of forests, which occurred from the Tertiary onwards.
30
Ntsohi, Refiloe. "Molecular phylogeny of Tribolium (Danthonioideae: Poaceae) and its taxonomic implications." Bachelor's thesis, University of Cape Town, 2003. http://hdl.handle.net/11427/25689.
Full textAbstract:
Molecular sequence data from two noncoding regions of DNA (ITS AND TRNL-F) were used to produce a phylogeny for the genus Tribolium and its African and Australasian allies. Topological comparisons of the combined molecular data with the appended existing morphological tree were made. A significant incongruence was revealed. Molecular data indicate that Tribolium is paraphyletic. The formally defined sections: Uniolae, Acutiflorae and Tribolium have been retrieved by the molecular data. The analysis retrieved Karroochloa as polyphyletic. Monophyly of Schismus is strongly supported. The Australasian species form a monophyletic clade. Data support early divergence of the Merxmuellera species and Pseudopentameris macrantha.
31
Stoch, Fabio. "Molecular taxonomy, phylogeny and biogeography of European niphargids (Crustacea, Amphipoda)." Doctoral thesis, Universite Libre de Bruxelles, 2021. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/326119.
Full textAbstract:
Les écosystèmes des eaux souterraines sont de plus en plus reconnus pour leur faune endémique, phylogénétiquement ancienne et écologiquement spécialisée. Avec plus de 425 espèces décrites, les amphipodes niphargidés constituent la famille des eaux souterraines la plus riche en espèces au monde et un système modèle intéressant pour la biologie de l'évolution. Cependant, les scientifiques doivent faire face à des données incomplètes et biaisées en raison de trois déficits majeurs: le déficit Linnéen pour la taxonomie, le déficit Darwinien pour la phylogénie, et le déficit Wallacien pour la biogéographie. La présente thèse vise à évaluer l'importance de ces déficits chez les niphargidés, ouvrant ainsi la voie pour y remédier. Le premier chapitre est une évaluation des effets de la découverte d'espèces cryptiques (une des causes du déficit Linnéen) sur notre compréhension des modèles de distribution à grande échelle de la diversité des niphargidés. Contrairement à ce que l'on attendait, les espèces cryptiques putatives sont réparties de manière homogène le long des gradients environnementaux, et leur découverte ne modifie donc pas notre compréhension des modèles de distribution. Le deuxième chapitre analyse l'importance de l'application des techniques moléculaires à la taxonomie des niphargidés. En étudiant le genre Microniphargus, la morphologie seule s'est avérée peu informative en raison de la pédomorphose et de l'homoplasie. L'utilisation de marqueurs ADN a permis d'attribuer le genre à une famille différente (Pseudoniphargidae), venant éclaircir les relations phylogénétiques au sein des Niphargidae (et contribuant ainsi à remédier au déficit Darwinien). Le troisième chapitre traite du rôle des régressions et transgressions marines sur la distribution des niphargidés en utilisant la biogéographie moléculaire et une modélisation biogéographique innovante (afin de remédier au déficit Wallacien). Les résultats soutiennent l'idée que la dispersion a joué un rôle essentiel dans la biogéographie historique des niphargidés, en montrant que leurs voies de dispersion sont corrélées à des événements paléogéographiques anciens. Enfin, le quatrième chapitre traite de la taxonomie, de la phylogénie et de la biogéographie d'un clade de niphargidés distribué dans la région des Alpes et des Carpates, et illustre un cas de discordance mitonucléaire dans la délimitation d'espèces vivant dans des zones affectées par les glaciations quaternaires. Une histoire complexe de divergence de lignées évolutives et de contacts secondaires pendant les fluctuations climatiques du Pléistocène explique la plus grande variabilité de l'ADN mitochondrial par rapport aux marqueurs nucléaires. Dans une telle situation, la description formelle d'espèces cryptiques basée sur le seul barcodage de l'ADN mitochondrial, comme dans certains articles récents sur les niphargidés, n'est pas recommandée. Cette thèse ouvre plusieurs perspectives pour des recherches futures basées sur la taxonomie intégrative et la modélisation biogéographique, permettant aux niphargidés très diversifiés de jouer un rôle majeur dans la surveillance des écosystèmes des eaux souterraines.Doctorat en Sciences
info:eu-repo/semantics/nonPublished
32
Unwin, Matthew M. "Molecular Systematics of the Eriocaulaceae Martinov." View electronic version of this work, 2004. http://www.ohiolink.edu/etd/send-pdf.cgi?miami1082582823.
Full text
33
Temponi, Livia Godinho. "Sistemática de Anthurium sect. Urospadix (Araceae)." Universidade de São Paulo, 2007. http://www.teses.usp.br/teses/disponiveis/41/41132/tde-21082007-143011/.
Full textAbstract:
Este estudo consta da análise filogenética de Anthurium seção Urospadix e grupos correlatos. O gênero tem sido considerado complexo taxonomicamente e tem sido considerado com pouca resolução interna. Nós realizamos análises de parcimônia com os dados morfológicos e moleculares e com os conjuntos de dados combinados. Caracteres anatômicos têm sido empregados em clássicos tratamentos para Araceae e a anatomia foliar pode prover vários caracteres para esclarecer as relações filogenéticas dentro de Anthurium. Com o intuito de averiguar os caracteres já descritos em um número maior de espécies de Anthurium, além de buscar novos caracteres, nós realizamos estudos anatômicos da folha de 77 espécies de Anthurium, sendo 35 da seção Urospadix. Especificamente, os dados foram obtidos de dissociações epidérmicas e secções transversais da porção mediana da nervura principal, limbo e pecíolo. Nós observamos 17 caracteres, nove dos quais são potencialmente informativos para a filogenia de Anthurium. Estudos palinológicos de 34 espécies de Anthurium também foram realizados e revelaram pólen 3-4-porado em todas as espécies. Grãos de pólen de todas as espécies examinadas são altamente similares quanto à forma e dimensões. Entretanto, o tipo de abertura e a ornamentação da exina exibem variações e podem ser úteis em estudos sistemáticos do grupo. Os três caracteres apresentados aqui aparecem como sinapomorfias para o gênero ou grupos dentro de Anthurium. Os resultados de 64 caracteres morfológicos (anatomia, morfologia externa e palinologia) e 177 caracteres moleculares (regiões trnC-ycf6, trnG e trnH-psbA do cloroplasto), ofereceram um arcabouço filogenético para avaliar os caracteres utilizados na sistemática destes grupos, bem como discutir questões da sistemática do grupo e os padrões evolutivos e biogeográficos envolvidos. Baseado nos conceitos tradicionais, a seção Urospadix contém 74 espécies e apresenta uma distribuição disjunta, com dois centros de diversidade: a América Central e Oeste da América do Sul e o leste do Brasil. Entretanto, baseado na nova circunscrição que aceitamos aqui, Anthurium seção Urospadix Engl., contém um menor número de espécies e, como tratado aqui, o grupo é restrito à Costa Atlântica Brasileira.We present a phylogenetic analysis of Anthurium sect. Urospadix and related groups (Araceae). The genus has traditionally been considered taxonomically difficult and there has been little resolution of relationship within it. We performed parsimony analyses on morphological and molecular, and combined data sets. Anatomical characters have been used in classic taxonomic treatments of Araceae and it appears that leaf anatomy may provide several characters for addressing phylogenetic relationships within Anthurium. To verify these characters in a larger number of species and to examine new ones, we investigated the leaf anatomy of 77 Anthurium species, including 35 of section Urospadix. Specifically, we investigated the anatomy of the epidermis and traverse sections of the mid rib, leaf lamina, and petiole. We identified 17 characters, nine of which are potentially informative with respect to the Anthurium phylogeny. The palynological studies of 34 Anthurium species indicate that pollen is 3-4 porate in all species. Pollen grains from all examined species are highly similar in form and dimensions. However, the aperture type and the exine sculpturing are variable and may be useful for systematic studies of the group. The three characters presented here appear to provide synapomorphies for the genera or groups within Anthurium. The results of analyses on morphological (external morphology, palynology, and leaf anatomy; 64 characters), molecular (trnCycf6, trnG, and trnH-psbA regions of the chloroplast; 177 varied characters), and combined data sets, provide a phylogenetic framework for evaluating the characters used in systematic studies of the group, as well as for discussing evolutionary and biogeographic patterns. Based on the traditional concept sect. Urospadix contains 74 species and it had a disjunct distribution, with centers of diversity in Central Americawestern South America and in eastern Brazil. However, based on the new circumscription that we consider here, Anthurium sect. Urospadix Engl. contains a smaller number of species and, as treated here, the group is restricted to Atlantic Coast of Brazil.
34
Heestand, Esprit Noel. "Phylogeny and Evolution of Anthopleura (Cnidaria: Anthozoa: Actiniaria)." The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1250600903.
Full text
35
Grazziotin, Felipe Gobbi [UNESP]. "Filogenia molecular da família Dipsadidae (serpentes : Colubroidea)." Universidade Estadual Paulista (UNESP), 2011. http://hdl.handle.net/11449/106595.
Full textAbstract:
Made available in DSpace on 2014-06-11T19:35:44Z (GMT). No. of bitstreams: 0
Previous issue date: 2011-12-21Bitstream added on 2014-06-13T21:08:02Z : No. of bitstreams: 1
grazziotin_fg_dr_rcla.pdf: 876560 bytes, checksum: 3e4c47b55167b94d86962842d103f78a (MD5)A relação filogenética entre os caenofídeos (serpentes avançadas) tem sido matéria de debate durante décadas. As principais questões para a sistemática eram representadas pela condição monofilética da família Colubridae, e a composição de sua subfamílias. Mais recentemente, novos métodos para inferir filogenias baseadas em critérios objetivos, bem como a utilização da biologia molecular, lançaram alguma luz sobre estas questões tradicionais. Aqui, são apresentados os resultados de duas análises filogenéticas moleculares das serpentes cenofídeas, focando principalmente nas serpentes neotropicais (subfamílias Xenodontinae e Dipsadinae). Otimização direta com base na máxima parcimônia, e homologia estática (alinhamento múltiplo), utilizando máxima parcimônia e máxima verossimilhança foram aplicados em uma matriz expandida de dados molecular. Os principais resultados de ambas as análises são: posicionamento de Acrochordus, Xenodermatideos e Pareatideos como grupos irmãos sucessivos de todos os caenofídeos restantes; viperídeos e homalopsideos são clados irmãos sucessivos de todos as demias serpentes, foram recuperados os seguintes clados monofiléticos dentro do crown-group Caenophidia: psammofídeos Afro-Asiaticos (incluindo Mimophis de Madagascar), Elapidae, Pseudoxyrhophiinae, Colubrinae, Natricinae, Dipsadinae e Xenodontinae. Homoroselaps está associada com os atractaspidídeos. Dois grupos taxonômicos superiores dentro de Caenophidia e uma nova subfamília dentro Dipsadidae foram nomeados. As análises filogenéticas sugerem mudanças taxonômicas dentro dos xenodontíneos; cinco novas tribos, oito novos gêneros foram criados e dois gêneros foram ressuscitados. Os gêneros Xenoxybelis e Pseudablabes foram sinonimizados com Philodryas; Liophis e Umbrivaga com Erythrolamprus e Lystrophis e Waglerophis com Xenodon
The phylogenetic relationship among the caenophidian (advanced) snakes has been a matter of debate for decades. The principal issues for the systematic were represented by the monophyletic condition of the large family Colubridae, and the composition of its subfamilies. More recently, new methods for infering phylogenies based on objective criteria, and the use of molecular biology, shed some light on these traditional issues. Here, two molecular phylogenetic analyses of caenophidian snakes focusing principally in the Neotropical snakes (subfamilies Xenodontinae and Dipsadinae) are presented. Direct optimization based on maximum parsimony, and static homology (multiple alignment) using maximum parsimony and maximum likelihood were applied on a expanded molecular data matrix. The major results of both analyses are: placement of Acrochordus, Xenodermatids, and Pareatids as successive outgroups to all remaining caenophidians; viperids and homalopsids are sucessive sister clades to all remaining snakes; the following monophyletic clades within crown group caenophidians: Afro- Asian psammophiids (including Mimophis from Madagascar), Elapidae, Pseudoxyrhophiinae, Colubrinae, Natricinae, Dipsadinae, and Xenodontinae. Homoroselaps is associated with atractaspidids. Two higher taxonomic clades within Caenophidia one new subfamily within Dipsadidae were nomed. The phylogenetic analyses suggest taxonomic changes within xenodontines, five new tribes, eight new genera were created and two genera were resurrected. The genera Xenoxybelis and Pseudablabes were synonymize with Philodryas; Liophis and Umbrivaga with Erythrolamprus; and Lystrophis and Waglerophis with Xenodon
36
Xue, Bine, and 薛彬娥. "Molecular phylogenetics of Polyalthia (Annonaceae): identifying clades and morphological synapomorphies in alarge polyphyletic genus." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2013. http://hub.hku.hk/bib/B49799319.
Full textAbstract:
The genus Polyalthiais one of the largest genera in the early-divergent angiosperm family Annonaceae, with ca. 155 currently accepted species. The genus has long been recognised as a morphologically heterogeneous assemblage lacking conspicuous synapomorphies, and is one of the most significant impediments to revisionary and floristic taxonomic research in the family. The polyphyletic status of the genus has been confirmed in several molecular phylogenetic studies, with several other genera (Enicosanthum, Fenerivia, Haplostichanthus, Marsypopetalum, Monoon, Trivalvariaand Woodiellantha)either closely related to or with species formally assigned to Polyalthia.
This thesis presents the most comprehensive molecular phylogenetic study of Polyalthiato date, including 44Polyalthiaspecies and 16 species from putatively related genera. The phylogeny was reconstructed using maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI)methods, based on three chloroplast DNA regions (matK, rbcLand trnL-F). The Polyalthia species are shown to segregate into four clades: (I) a clade sister to Miliusa; (II) a clade that includes four Polyalthia species and also Marsypopetalum pallidum, sister to Trivalvaria; (III) a clade that also includes all Enicosanthum and Woodiellantha species sampled, sister to Neo-uvaria; and (IV) a clade that also includes all Haplostichanthus species sampled, sister to Popowia. All four identified Polyalthia clades are located in the tribe Miliuseae.
In order to assess the relationships among different Polyalthia clades as well as the relationships among all the genera in Miliuseae, a pilot study on the phylogenetic utility of a wide range of markers was carried out. Based on the result, eight chloroplast markers (matK, rbcL, trnL-F, psbA-trnH, ndhF, ndhF-rpl32, rpl32-trnLand ycf1) were selected and further sequenced for the clade representatives. Although unsuccessful in resolving the Miliuseae, the recognition of three of the four Polyalthia clades as monophyletic genera was confirmed.
Diagnostic morphological and anatomical characters were evaluated for clades II–IV, with the emphasis on putative synapomorphies. The morphology of the species not sampled for molecular study was examined in detail and compared against diagnostic characters to determine correct taxonomic placement. Based on the results, five Polyalthia species are transferred to Marsypopetalum. The generic name Monoon is resurrected for the clade that includes Enicosanthum and Woodiellantha, with the transfer of 37 species from Polyalthia s.l., 18 species from Enicosanthum and one Woodiellantha species. The generic name Haplostichanthus is synonymised with Polyalthias.str., with the 11 Haplostichanthus species transferred to Polyalthias.str..
The eight Polyalthia species reported from Fiji were further sampled in a phylogenetic reconstruction based on three markers (matK, rbcLand trnL-F). Three groups were identified, allied with Goniothalamus, Polyalthia Clade I and Meiogyne respectively.
The flower of Fenerivia capuronii (Cavaco & Keraudren) R.M.K. Saunders was selected for anatomical studies to examine whether the flange represents a reduced calyx as suggested for F. heteropetala and thus to test a possible homoetic mutation in F. capuronii. The results show that there is no vascular supply in the flange of F. capuronii, and that the putative homeotic change within Feneriviais therefore likely to only occur in F. heteropetala.published_or_final_version
Biological Sciences
Doctoral
Doctor of Philosophy
37
Jakes, Kathryn Anne. "Morphology and molecular phylogeny of selected haemoprotozoan parasites of Australian wildlife /." St. Lucia, Qld, 2004. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe17828.pdf.
Full text
38
Langrell, Stephen Richard Henry. "Molecular phylogeny, detection and epidemiology of Nectria canker (Nectria Galligena Bres.)." Thesis, Imperial College London, 2000. http://hdl.handle.net/10044/1/8140.
Full text
39
Haddrath, Oliver. "Ratite molecular evolution, phylogeny and biogeography inferred from complete mitochondrial genomes." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape2/PQDD_0033/MQ63250.pdf.
Full text
40
Sparmann, Sarah Franziska. "Contributions to the molecular phylogeny, phylogeography, and taxonomy of scyphozoan jellyfish." Thesis, University of British Columbia, 2012. http://hdl.handle.net/2429/43461.
Full textAbstract:
Scyphozoan jellyfish are a major group of large, bloom-forming marine animals that can disrupt ecological stability and interfere with marine-oriented industries. The widespread geographical distributions and high degrees of morphological plasticity within many species make understanding the overall diversity of scyphozoans difficult. Molecular phylogenetic approaches have the potential to offer powerful insights into many aspects of scyphozoan biology, such as species identification, evolutionary history, and phylogeography that will improve our ability to monitor and manage the roles these animals play in marine ecosystems. We established datasets of 16S rDNA and cytochrome c oxidase subunit I (COI) sequences of several different species of scyphozoans in order to better understand phylogenetic, phylogeographical, and taxonomic patterns within the group. Phylogenetic analysis of 16S rDNA sequences resolved closely related taxa but was too variable to resolve deeper relationships with robust statistical support. Combining this marker with a more conserved dataset of nuclear 18S rDNA sequences resulted in a phylogenetic tree with clades that had higher statistical support than in trees inferred from each marker alone. 16S rDNA sequences also showed phylogeographical patterns in Cyanea, distinguishing clearly between a Northeastern Pacific (NEP) clade and a Northwestern Atlantic clade (NWA) (9.71 - 9.93% mean genetic difference MGD), as well as two Atlantic subclades (NWA1, NWA2) (1.79% MGD). Distances within clades ranged from 0.05 - 0.2%. Therefore, 16S rDNA sequences were able to delimit different (putative) species that reflected distinct geographical distributions. In addition, comparative analyses of morphological features and COI sequences from Northeast Pacific isolates of Cyanea demonstrated that C. ferrugenia is a valid lion’s mane species found in the Northeast Pacific Ocean.
41
Zaldivar-Riveron, Alejandro. "Molecular and morphological phylogeny of the cyclostome braconid wasps (Hymenoptera : Ichneumonoidea)." Thesis, Imperial College London, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.420956.
Full text
42
Hassan, Ruhana. "Phylogeny within the Choanaflagellida using morphological and ultrastructural and molecular approaches." Thesis, University of Birmingham, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.414963.
Full text
43
Amaral, Zettler Linda Angela. "A molecular approach to questions in the phylogeny of planktonic sarcodines." Thesis, Massachusetts Institute of Technology, 1996. http://hdl.handle.net/1721.1/38838.
Full text
44
Planz, John Valentine. "Molecular Phylogeny and Evolution of the American Woodrats, Genus Neotoma (Muridae)." Thesis, University of North Texas, 1992. https://digital.library.unt.edu/ark:/67531/metadc278829/.
Full textAbstract:
The evolutionary relationships of woodrats (Neotoma) were elulcidated through phylogenetic analyses of mitochondrial DNA restriction site and allozyme data. DNA samples from eleven nominal species from the genus Neotoma and two outgroup taxa, Ototylomys phyttotis and Xenomys nelsoni, were cleaved using a suite of 17 Type II restriction endonucleases. Mitochondrial DNA restriction profiles were visualized following electrophoresis of restriction digests via methods of Southern transfer and hybridization with 32P- and digoxigenin-labeled mtDNA probes. Restriction mapping resulted in the identification of 37 unique mtDNA haplotypes among the woodrat taxa examined. Proteins representing 24 presumptive structural gene loci were examined through starch gel electrophoresis. Binary-coded allozyme data and allozyme frequency data were analyzed using PAUP and FREQPARS, respectively. Phylogenetic analyses of the mtDNA restriction site data incorporated three different character type assumptions: unordered binary characters, Dollo characters, and differentially weighted unordered characters employing the STEPMATRIX option of PAUP. Proposed phylogenies for Neotoma are based on majority-rule consensus trees produced using bootstrap procedures. Phylogenetic analyses of the woodrat data sets revealed a distinct dichotomy among populations of white-throated woodrats (N. albigula) suggesting the presence of cryptic species within that taxon. MtDNA and allozyme data support the specific status of N. devia as distinct from N. lepida, and additionally reveal the presence of a third cryptic species referable to N. intermedia among the desert woodrats. Phylogenetic analyses of the genetic data also suggest subgeneric status for the desert woodrats, which is in agreement with evidence from morphology. The genetic data revealed a sister group relationship between N. stephensi and samples of N. mexicana, suggesting the placement of N. stephensi into the N. mexicana species-group. Neotoma fuscipes and N. cinerea formed a monophyletic lineage basal to the remaining members of the subgenus Neotoma which supports the assignment of N. fuscipes to the subgenus Teonoma with N. cinerea. Although stringent, Dollo parsimony methods produced the best supported phylogenies among the species of Neotoma. The STEPMATRIX approach was unable to resolve species relationships within species-groups but clearly delineated the higher taxonomic levels between species-groups and subgenera.
45
Crema, Silvia <1976>. "Molecular diversity of Primula apennina and phylogeny of Primula Subsection Euauricula." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2009. http://amsdottorato.unibo.it/1833/1/crema_silvia_tesi.pdf.
Full textAbstract:
Primula apennina Widmer is endemic to the North Apennines (Italy). ISSR were used to detect the genetic diversity within and among six populations representative of the species distribution range. High levels of genetic diversity were revealed both at population (PPB = 75.92%, HS = 0.204, Hpop = 0.319) and at species level (PPB = 96.95%, HT = 0.242, Hsp = 0.381). Nei gene diversity statistics (15.7%), Shannon diversity index (16.3%) and AMOVA (14%) detected a moderate level of interpopulation diversity. Principal coordinate and bayesian analyses clustered the populations in three major groups along a geographic gradient. The correlation between genetic and geographic distances was positive (Mantel test, r = 0.232). All together, these analyses revealed a weak but significant spatial genetic structure in P. apennina, with gene flow acting as a homogenizing force that prevents a stronger differentiation of populations. Conservation measures are suggested based on the observed pattern of genetic variability.
P. apennina belongs to Primula subsect. Euauricula which includes 15 species distributed on the whole Alps and Apennines. A phylogenetic analysis was carried out using AFLP markers in order both to clarify the relationships among the species of subsection Euauricula that remained unresolved in previous works and to make some hypoteses on their evolutive dynamics. NJ, PCO and BAPS analyses strongly confirmed the monophyly of P. subsect. Euauricula and all the species form strongly supported clades. NJ tree topology suggested a simultaneous fragmentations of ancestral species in a large number of isolated populations that survived in refugia along the unglaciated margins of the Alps in response to the Pleistocene climatic oscillations.
46
Crema, Silvia <1976>. "Molecular diversity of Primula apennina and phylogeny of Primula Subsection Euauricula." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2009. http://amsdottorato.unibo.it/1833/.
Full textAbstract:
Primula apennina Widmer is endemic to the North Apennines (Italy). ISSR were used to detect the genetic diversity within and among six populations representative of the species distribution range. High levels of genetic diversity were revealed both at population (PPB = 75.92%, HS = 0.204, Hpop = 0.319) and at species level (PPB = 96.95%, HT = 0.242, Hsp = 0.381). Nei gene diversity statistics (15.7%), Shannon diversity index (16.3%) and AMOVA (14%) detected a moderate level of interpopulation diversity. Principal coordinate and bayesian analyses clustered the populations in three major groups along a geographic gradient. The correlation between genetic and geographic distances was positive (Mantel test, r = 0.232). All together, these analyses revealed a weak but significant spatial genetic structure in P. apennina, with gene flow acting as a homogenizing force that prevents a stronger differentiation of populations. Conservation measures are suggested based on the observed pattern of genetic variability.
P. apennina belongs to Primula subsect. Euauricula which includes 15 species distributed on the whole Alps and Apennines. A phylogenetic analysis was carried out using AFLP markers in order both to clarify the relationships among the species of subsection Euauricula that remained unresolved in previous works and to make some hypoteses on their evolutive dynamics. NJ, PCO and BAPS analyses strongly confirmed the monophyly of P. subsect. Euauricula and all the species form strongly supported clades. NJ tree topology suggested a simultaneous fragmentations of ancestral species in a large number of isolated populations that survived in refugia along the unglaciated margins of the Alps in response to the Pleistocene climatic oscillations.
47
Saltamachia, Stephen J. "New Observations and Phylogeny of the Entomopathogenic Fungus Desmidiospora myrmecophila." Thesis, University of Louisiana at Lafayette, 2019. http://pqdtopen.proquest.com/#viewpdf?dispub=10844649.
Full textAbstract:
The genus Ophiocordyceps contains the most diverse assemblage of fungi attacking ants worldwide and are remarkably well adapted to the specific ecologies of their hosts. Desmidiospora myrmecophila is closely related to ant-pathogenic species within Ophiocordyceps, possibly specific to queens, but the sheer infrequency of encounters and previously unsuccessful attempts to culture this fungus has precluded any meaningful assessment until now. A new record of Desmidiospora myrmecophila from Louisiana was found infecting a foundress Camponotus pennsylvanicus queen, the same host species favored by the more common and ubiquitous ant-pathogenic Ophiocordyceps unilateralis found in the same geographic locality. To evaluate a long-held assumption that these fungi represent synanamorphs of a single species, we sampled our Desmidiospora specimen along with the local O. unilateralis population for molecular comparison. We are able to present for the first time the in vitro characteristics and morphology of Desmidiospora myrmecophila as well as a phylogenetic context for this fungus based on combined molecular analysis of representative members of the Ophiocordycipitaceae. Our results place the Desmidiospora myrmecophila lineage within the genus Ophiocordyceps but with a basal affiliation to the ant-pathogen clade. These results further implicate Desmidiospora myrmecophila as an important and quintessential example of cryptic diversity among an already taxonomically diverse and ecologically important group of fungi.
48
Surveswaran, Siddharthan. "Molecular phylogenetics and medicinal plants of Asclepiadoideae from India." Thesis, Click to view the E-thesis via HKUTO, 2007. http://sunzi.lib.hku.hk/HKUTO/record/B39559002.
Full text
49
Heiss, Aaron Andrew. "Molecular phylogeny of the oxymonads." Thesis, 2006. http://hdl.handle.net/2429/17972.
Full textAbstract:
The oxymonads are a group of structurally complex anaerobic flagellates about which we
know very little. They are found in association with complex microbial communities in
the guts of animals. There are five recognized families of oxymonads; molecular data
have been acquired for four of these. Here, I describe the first molecular data from the
last remaining group, represented by Saccinobaculus, an organism that is found
exclusively in the hindgut of the wood-eating cockroach Cryptocercus. I sequenced
small subunit ribosomal RNA (SSU rRNA) from total gut DNA to describe
Saccinobaculus SSU rRNA diversity. I also sequenced SSU rRNA from manually
isolated cells of the two most abundant and readily identifiable species: the type species
S. ambloaxostylus and the taxonomically contentious S. doroaxostylus. I inferred
phylogenetic trees including all five known oxymonad subgroups in order to elucidate the
internal phylogeny of this poorly-studied group, to resolve some outstanding issues of the
taxonomy and identification of certain Saccinobaculus species, and to investigate the
evolution of character states within it. My analysis recovered strong support for the
existence of the five subgroups of oxymonads, and consistently grouped the subgroups
containing Monocercomonoides and Streblomastix, but was unable to resolve any further
higher-order branching patterns. Additionally, I sequenced alpha-tubulin from S.
ambloaxostylus, which in conjunction with environmentally obtained tubulin sequences
established the use of an alternate genetic code by organisms related to
Monocercomonoides and not by Saccinobaculus. This same alternate code is also used
by Streblomastix, further cementing the relationship between that organism and the group
including Monocercomonoides.Science, Faculty of
Botany, Department of
Graduate
50
Kolisko, Martin. "Molecular Phylogeny of Amitochondriate Excavates." 2011. http://hdl.handle.net/10222/14303.
Full textAbstract:
Resolving the phylogenetic tree of eukaryotes is an ongoing challenge for evolutionary biologists. One of the most intriguing questions is the phylogenetic status of Excavata, a group that is well supported by morphological evidence, yet usually not recovered as a clade in molecular phylogenies. The most problematic group of excavates are diplomonads (e.g., Giardia), which tend to have very highly divergent gene sequences, making any phylogenetic analyses that include these protists very susceptible to long branch attraction artifact.
This thesis first explores which organisms are most closely related to diplomonads. Phylogenies of three marker genes demonstrate that enteromonads, formerly considered a possible sister group to diplomonads, are a polyphyletic group within diplomonads, suggesting complex evolution of cell morphology in this lineage. However, a large diversity of Carpediemonas-like organisms (CLOs) was discovered from marine/saline samples. Most of the major clades of CLOs had not been detected by previous environmental PCR studies. SSU rRNA gene phylogenies show that CLOs form a series of relatively short branches at the base of diplomonads. Phylogenomic analysis of eukaryotes (161 genes), incorporating EST data from 5 excavates, including 3 CLOs, shows that the non-monophyly of Excavata in phylogenomic studies is likely caused by long branch attraction artifact, since most of the methods used to suppress long branch attraction significantly weaken support for this topology. Furthermore, the shorter-branching CLOs represent valuable replacements for the long branching diplomonads; we recovered a robustly supported monophyletic Excavata, when long branches, including diplomonads (and parabasalids), were removed from the analysis. Subsequently, comparative analysis of the putative proteomes of three CLO isolates, the retortamonad Chilomastix, diplomonads and parabasalids was performed. Several putative evolutionary steps leading to the extremely reduced mitochondrial organelle of diplomonads were derived through the comparative analysis of predicted organellar proteomes.
This thesis shows the importance of taxon sampling for inferring deep eukaryotic evolution. The more robust understanding of the phylogeny of Excavata, especially diplomonads and parabasalids, and the new availability of a number of deep branching relatives of diplomonads, provide a framework for comparative analyses exploring the evolution of anaerobic organelles or parasitism.