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Faller, Beáta. "Combinatorial and probabilistic methods in biodiversity theory". Thesis, University of Canterbury. Mathematics and Statistics, 2010. http://hdl.handle.net/10092/3985.
Pełny tekst źródłaJirásková, Kristýna. "Metody rekonstrukce fylogenetických superstromů". Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2012. http://www.nusl.cz/ntk/nusl-219518.
Pełny tekst źródłaKosíř, Kamil. "Metody rekonstrukce fylogenetických superstromů". Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2014. http://www.nusl.cz/ntk/nusl-220860.
Pełny tekst źródłaTokac, Nihan. "Efficiency of algorithms in phylogenetics". Thesis, Durham University, 2016. http://etheses.dur.ac.uk/11768/.
Pełny tekst źródłaDouady, Christophe Jean Gabriel. "Molecular phylogenetics of the insectivora". Thesis, Queen's University Belfast, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.394635.
Pełny tekst źródłaFletcher, W. A. J. "Computational statistics in molecular phylogenetics". Thesis, University College London (University of London), 2011. http://discovery.ucl.ac.uk/1306705/.
Pełny tekst źródłaKim, Cheol-Min. "Phylogenetics of Trigynaspida (Acari: Mesostigmata) /". The Ohio State University, 2001. http://rave.ohiolink.edu/etdc/view?acc_num=osu1486572165276144.
Pełny tekst źródłaCooke, Patrick Alan. "BioInformatics, Phylogenetics, and Aspartate Transcarbamoylase". Thesis, University of North Texas, 2000. https://digital.library.unt.edu/ark:/67531/metadc2580/.
Pełny tekst źródłaBuckman, Rebecca S. "Phylogenetics of Thysanoptera (Insecta: Paraneoptera)". BYU ScholarsArchive, 2012. https://scholarsarchive.byu.edu/etd/2999.
Pełny tekst źródłaFarid, Arian. "Molecular Phylogenetics of Floridian Boletes". Scholar Commons, 2018. https://scholarcommons.usf.edu/etd/7618.
Pełny tekst źródłaCICCOLELLA, SIMONE. "Practical algorithms for Computational Phylogenetics". Doctoral thesis, Università degli Studi di Milano-Bicocca, 2022. http://hdl.handle.net/10281/364980.
Pełny tekst źródłaIn this manuscript we described the main computational challenges of the cancer phylogenetic field and we proposed different solutions for the three main problems of (i) the progression reconstruction of a tumor sample, (ii) the clustering of SCS data to allow for a cleaner and faster inference and (iii) the evaluation of different phylogenies. Furthermore we combined them into a usable pipeline to allow for a faster analysis.
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 źródłaThe 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)
Kist, Nicolaas Christiaan. "Bayesian phylogenetic approaches to retroviral evolution : recombination, cross-species transmission, and immune escape". Thesis, University of Oxford, 2017. http://ora.ox.ac.uk/objects/uuid:997289db-0a6e-4cd4-b465-9fc962ce40b8.
Pełny tekst źródłaCatanzaro, Daniele. "Models and methods for molecular phylogenetics". Doctoral thesis, Universite Libre de Bruxelles, 2008. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/210453.
Pełny tekst źródłaDoctorat en Sciences
info:eu-repo/semantics/nonPublished
Chang, Ying. "Molecular phylogenetics of mosses and relatives". Thesis, University of British Columbia, 2011. http://hdl.handle.net/2429/37148.
Pełny tekst źródłaSubramanian, Ayshwarya. "Inferring tumor evolution using computational phylogenetics". Research Showcase @ CMU, 2013. http://repository.cmu.edu/dissertations/275.
Pełny tekst źródłaHeibl, Christoph. "R programming in phylogenetics and evolution". Diss., Ludwig-Maximilians-Universität München, 2014. http://nbn-resolving.de/urn:nbn:de:bvb:19-178834.
Pełny tekst źródłaWinney, Bruce Joseph. "Cormorant population genetics and Turaco phylogenetics". Thesis, University of Nottingham, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.285767.
Pełny tekst źródłaKidd, Sarah E. "Molecular Phylogenetics of the Hawaiian Geraniums". Bowling Green State University / OhioLINK, 2005. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1131138585.
Pełny tekst źródłaRobertson, Charles E. "Ecology, phylogenetics, and ultrastructure of Archaea". Connect to online resource, 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3337146.
Pełny tekst źródłaArab, Daej A. Kh A. M. "Australian Nasutitermitinae: Phylogenetics, Evolution, and Biodiversity". Thesis, The University of Sydney, 2015. http://hdl.handle.net/2123/13671.
Pełny tekst źródłaHanson-Smith, Victor 1981. "Error and Uncertainty in Computational Phylogenetics". Thesis, University of Oregon, 2011. http://hdl.handle.net/1794/12151.
Pełny tekst źródłaThe evolutionary history of protein families can be difficult to study because necessary ancestral molecules are often unavailable for direct observation. As an alternative, the field of computational phylogenetics has developed statistical methods to infer the evolutionary relationships among extant molecular sequences and their ancestral sequences. Typically, the methods of computational phylogenetic inference and ancestral sequence reconstruction are combined with other non-computational techniques in a larger analysis pipeline to study the inferred forms and functions of ancient molecules. Two big problems surrounding this analysis pipeline are computational error and statistical uncertainty. In this dissertation, I use simulations and analysis of empirical systems to show that phylogenetic error can be reduced by using an alternative search heuristic. I then use similar methods to reveal the relationship between phylogenetic uncertainty and the accuracy of ancestral sequence reconstruction. Finally, I provide a case-study of a molecular machine in yeast, to demonstrate all stages of the analysis pipeline. This dissertation includes previously published co-authored material.
Committee in charge: John Conery, Chair; Daniel Lowd, Member; Sara Douglas, Member; Joseph W. Thornton, Outside Member
Hou, Chen. "Proteomics and phylogenetics of the Gnetales". Licentiate thesis, Stockholms universitet, Institutionen för ekologi, miljö och botanik, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-102194.
Pełny tekst źródłaHernandez, Rosales Maribel. "The Orthology Road". Doctoral thesis, Universitätsbibliothek Leipzig, 2013. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-127823.
Pełny tekst źródłaSpinks, Phillip Quinton. "Molecular phylogenetics and conservation of freshwater turtles /". For electronic version search Digital dissertations database. Restricted to UC campuses. Access is free to UC campus dissertations, 2004. http://uclibs.org/PID/11984.
Pełny tekst źródłaSilva, Dylan De. "Phylogenetics of the genus Echium L. (Boraginaceae)". Thesis, University of Reading, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.485364.
Pełny tekst źródłaSeears, Heidi. "Biogeography and phylogenetics of the planktonic foraminifera". Thesis, University of Nottingham, 2011. http://eprints.nottingham.ac.uk/11879/.
Pełny tekst źródłaHone, David William Elliott. "The phylogenetics and macroevolution of the Archosauromorpha". Thesis, University of Bristol, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.432067.
Pełny tekst źródłaEales, James Matthew. "Text-mining of experimental methods in phylogenetics". Thesis, University of Manchester, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.529251.
Pełny tekst źródłaMorris, Kirsty Janet. "North Atlantic octocorals : distribution, ecology and phylogenetics". Thesis, University of Southampton, 2011. https://eprints.soton.ac.uk/338892/.
Pełny tekst źródłaRebholz, Wilhelmus Ewald Reinaard. "Molecular phylogenetics and conservation aspects of antelopes". Doctoral thesis, University of Cape Town, 1996. http://hdl.handle.net/11427/26971.
Pełny tekst źródłados, Santos Ferreira Lins Luana. "Molecular phylogenetics, evolution and systematics of isopoda". Thesis, The University of Sydney, 2014. http://hdl.handle.net/2123/12705.
Pełny tekst źródłaCherlin, Svetlana. "Rooting major cellular radiations using statistical phylogenetics". Thesis, University of Newcastle upon Tyne, 2016. http://hdl.handle.net/10443/3492.
Pełny tekst źródłaau, V. Andjic@murdoch edu, i Vera Andjic. "Phylogeny, phylogeography and movement of Kirramyces spp. associated with leaf blight diseases of plantation eucalypts". Murdoch University, 2008. http://wwwlib.murdoch.edu.au/adt/browse/view/adt-MU20080805.133632.
Pełny tekst źródłaBordewich, Magnus. "The complexity of counting and randomised approximation". Thesis, University of Oxford, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.289352.
Pełny tekst źródłaWanke, Stefan, Mendoza Carolina Granados, Julia Naumann, Marie-Stéphanie Samain, Paul Goetghebeur i Smet Yannick De. "A genome-scale mining strategy for recovering novel rapidly-evolving nuclear single-copy genes for addressing shallow-scale phylogenetics in Hydrangea". Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-192196.
Pełny tekst źródłaSvennblad, Bodil. "On Estimating Topology and Divergence Times in Phylogenetics". Doctoral thesis, Uppsala University, Mathematical Statistics, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8441.
Pełny tekst źródłaThis PhD thesis consists of an introduction and five papers, dealing with statistical methods in phylogenetics.
A phylogenetic tree describes the evolutionary relationships among species assuming that they share a common ancestor and that evolution takes place in a tree like manner. Our aim is to reconstruct the evolutionary relationships from aligned DNA sequences.
In the first two papers we investigate two measures of confidence for likelihood based methods, bootstrap frequencies with Maximum Likelihood (ML) and Bayesian posterior probabilities. We show that an earlier claimed approximate equivalence between them holds under certain conditions, but not in the current implementations of the two methods.
In the following two papers the divergence times of the internal nodes are considered. The ML estimate of the divergence time of the root is improved if longer sequences are analyzed or if more taxa are added. We show that the gain in precision is faster with longer sequences than with more taxa. We also show that the algorithm of the software package PATHd8 may give biased estimates if the global molecular clock is violated. A change of the algorithm to obtain unbiased estimates is therefore suggested.
The last paper deals with non-informative priors when using the Bayesian approach in phylogenetics. The term is not uniquely defined in the literature. We adopt the idea of data translated likelihoods and derive the so called Jeffreys' prior for branch lengths using Jukes Cantor model of evolution.
Sebastian, Patrizia. "Phylogenetics and biogeography of two clades of Cucurbitaceae". Diss., lmu, 2012. http://nbn-resolving.de/urn:nbn:de:bvb:19-146298.
Pełny tekst źródłaJewell, Sean William. "Divide and conquer sequential Monte Carlo for phylogenetics". Thesis, University of British Columbia, 2015. http://hdl.handle.net/2429/54514.
Pełny tekst źródłaScience, Faculty of
Statistics, Department of
Graduate
Nylander, Johan A. A. "Bayesian Phylogenetics and the Evolution of Gall Wasps". Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3996.
Pełny tekst źródłaRandall, Ryan Nicole. "Experimental phylogenetics: a benchmark for ancestral sequence reconstruction". Thesis, Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/48998.
Pełny tekst źródłaIdid, Mohammed Rizman. "Phylogenetics and population structure of Lake Malawi cichlids". Thesis, University of Hull, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.418795.
Pełny tekst źródłaCorfe, Ian J. "Competing hypotheses and character conflict in palaeontological phylogenetics". Thesis, University of Bristol, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.496222.
Pełny tekst źródłaGardiner, Laura Maria. "Phylogenetics and conservation of the Genus Vanda (Orchidaceae)". Thesis, University of East Anglia, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.446457.
Pełny tekst źródłaGillett, C. P. D. T. "Molecular phylogenetics of the superfamily Curculionoidea (Insecta: Coleoptera)". Thesis, University of East Anglia, 2014. https://ueaeprints.uea.ac.uk/67069/.
Pełny tekst źródłaBozkus, Nebahat. "Cluster detection by lifting with application to phylogenetics". Thesis, University of Leeds, 2018. http://etheses.whiterose.ac.uk/21300/.
Pełny tekst źródłaPereira, da Conceicoa Lyndall Louise. "Phylogenetics and historical biogeography of the Teloganodidae (Ephemeroptera)". Thesis, Rhodes University, 2016. http://hdl.handle.net/10962/64900.
Pełny tekst źródłaBarnes, Keith N. "The phylogenetics and evolution of Africa's larks (Alaudidae)". Doctoral thesis, University of Cape Town, 2007. http://hdl.handle.net/11427/6228.
Pełny tekst źródłaThe larks are a group of dull coloured birds that are conservative in plumage coloration and pattern due to the requirements for camouflage in open habitats. Because many species inhabit structurally similar habitats the group is also characterised by a great deal of morphological convergence. Variation in plumage and morphology is frequently as great within species as it is between species, leading to many inconsistent and controversial taxonomic treatments and classifications at an intra- and inter-generic level, and when defining specific and sub-specific boundaries. The advent of genetic techniques and success at applying these to species complexes in southern Africa suggested that a molecular phylogeny of the family would elucidate relationships that could not be determined via traditional taxonomic practices. In this study 2009 nucleotides of two mitochondrial DNA genes, cytochrome b and 16S rRNA (Chapter 2), and 2872 nucleotides of the nuclear exon RAG-l (Chapter 3) were used to generate a robust phylogeny of the family Alaudidae. The former analysis included 55 species and the latter 25. These data were also combined to construct a combined evidence phylogeny (Chapter 7). Within the family, several genera recognised by more traditional taxonomies are polyphyletic, including Ammomanes, Eremalauda .and Certhilauda. Two other genera, Calandrella and Mirafra, are best treated as multiple genera (Chapter 2). The sampled Alaudidae can be divided into three main radiations, the ammomanid larks, mirafrid larks and alaudid larks (Chapter 3). Within the ammomanid larks, there is strong support for: (1) a southern African' radiation comprising Chersomanes, the Long-billed Lark complex (Certhilauda) and Ammomanes (Ammomanopsis) grayi ,with Alaemon allied to this radiation; and (2) a .Saharo-Sindian radiation comprising Ramphocoris c1otbey, Ammomanes cinc(urus, and A. deserti sister to the Afro-Sindian sparrowlark Eremopterix clade. The Madagascan endemic Mirafra hova was a surprise basal member of Eremopterix.
Aguiar, Alexandre Pires. "Phylogenetics and systematics of the World Stephanidae (Hymenoptera) /". The Ohio State University, 2000. http://rave.ohiolink.edu/etdc/view?acc_num=osu1488195154356513.
Pełny tekst źródłaLopez-Osorio, Federico. "Phylogenetics And Molecular Evolution Of Highly Eusocial Wasps". ScholarWorks @ UVM, 2016. http://scholarworks.uvm.edu/graddis/569.
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