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Rozprawy doktorskie na temat „Phylogenetic”

Autor: Grafiati

Data publikacji: 4 czerwca 2021

Data aktualizacji: 25 lipca 2025

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1

Jirásková, 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.

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The phylogenetic reconstruction has noted great development in recent decades. The development of computers and device for sequencing biopolymers have been an enormous amount od phylogenetic data from different sources and different types. The scientists are trying to reconstruct a comlet tree of life from these data. The phylogenetic supertree are theoretically this option because a supertree alow a combination of all information gathered so far – in contras to the phylogenetic trees. This thesis present the method of reconstruction supertrees using average konsensus method.

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Kosíř, 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.

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The Phylogenetic reconstruction has seen great development in the last 30 years. Computers have become more powerful and more generally accessible, and computer algorithms more sophisticated. It comes the effort of scientists to reconstruct the entire tree of life from a large amount of phylogenetic data. Just for this purpose are formed phylogenetic supertrees that allow the combination of all information gathered so far. The aim of this work is to find a method to construct supertree that will give correct results.

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3

Mecham, Jesse L. "Jumpstarting phylogenetic searches /." Diss., CLICK HERE for online access, 2006. http://contentdm.lib.byu.edu/ETD/image/etd1403.pdf.

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McHugh, Sean W. "Phylogenetic Niche Modeling." Thesis, Virginia Tech, 2021. http://hdl.handle.net/10919/104893.

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Projecting environmental niche models through time is a common goal when studying species response to climatic change. Species distribution models (SDMs) are commonly used to estimate a species' niche from observed patterns of occurrence and environmental predictors. However, a species niche is also shaped by non-environmental factors--including biotic interactions and dispersal barrier—truncating SDM estimates. Though truncated SDMs may accurately predict present-day species niche, projections through time are often biased by environmental condition change. Modeling niche in a phylogenetic f

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5

Mecham, Jesse Lewis. "Jumpstarting Phylogenetic Searches." BYU ScholarsArchive, 2006. https://scholarsarchive.byu.edu/etd/483.

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Phylogenetic analysis is a central tool in studies of comparative genomics. When a new region of DNA is isolated and sequenced, researchers are often forced to throw away months of computation on an existing phylogeny of homologous sequences in order to incorporate this new sequence. The previously constructed trees are often discarded, and the researcher begins the search again from scratch. The jumpstarting algorithm uses trees from the prior search as a starting point for a new phylogenetic search. This technique drastically decreases search time for large data sets. This kind of analysis i

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6

Faller, Beáta. "Combinatorial and probabilistic methods in biodiversity theory." Thesis, University of Canterbury. Mathematics and Statistics, 2010. http://hdl.handle.net/10092/3985.

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Phylogenetic diversity (PD) is a measure of species biodiversity quantified by how much of an evolutionary tree is spanned by a subset of species. In this thesis, we study optimization problems that aim to find species sets with maximum PD in different scenarios, and examine random extinction models under various assumptions to predict the PD of species that will still be present in the future. Optimizing PD with Dependencies is a combinatorial optimization problem in which species form an ecological network. Here, we are interested in selecting species sets of a given size that are ecological

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7

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

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<p>In phylogenetic analysis one study the relationship between different species. By comparing DNA from two different species it is possible to get a numerical value representing the difference between the species. For a set of species, all pair-wise comparisons result in a dissimilarity matrix <em>d</em>.</p><p>In this thesis I present a few methods for constructing a phylogenetic tree from <em>d</em>. The common denominator for these methods is that they do not generate a tree, but instead give a connected graph. The resulting graph will be a tree, in areas where the data perfectly matches a

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8

Pardi, Fabio. "Algorithms on phylogenetic trees." Thesis, University of Cambridge, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.611685.

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9

Wang, Min-Hui. "Classification using phylogenetic trees /." The Ohio State University, 1999. http://rave.ohiolink.edu/etdc/view?acc_num=osu1488190595939375.

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10

Sundberg, Kenneth A. "Partition Based Phylogenetic Search." BYU ScholarsArchive, 2010. https://scholarsarchive.byu.edu/etd/2583.

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Evolutionary relationships are key to modern understanding of biological systems. Phylogenetic search is the means by which these relationships are inferred. Phylogenetic search is NP-Hard. As such it is necessary to employ heuristic methods. This work proposes new methods based on viewing the relationships between species as sets of partitions. These methods produce more parsimonious phylogenies than current methods.

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11

Hansen, Michael. "Algebra and Phylogenetic Trees." Scholarship @ Claremont, 2007. https://scholarship.claremont.edu/hmc_theses/194.

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One of the restrictions used in all of the works done on phylogenetic invariants for group based models has been that the group be abelian. In my thesis, I aim to generalize the method of invariants for group-based models of DNA sequence evolution to include nonabelian groups. By using a nonabelian group to act one the nucleotides, one could capture the structure of the symmetric model for DNA sequence evolution. If successful, this line of research would unify the two separated strands of active research in the area today: Allman and Rhodes’s invariants for the symmetric model and Strumfels a

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12

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.

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Philosophiae Doctor - PhD<br>The Ruschieae is the most diverse and speciose tribe within the large subfamily Ruschioideae (Aizoaceae), with approximately 71 genera and a distribution centred in the arid parts of the Greater Cape Floristic Region (GCFR) of South Africa. Recent phylogenetic analyses provided the first insights into generic relationships within the tribe, with a number of novel generic relationships discovered. The tribal phylogeny recovered 12 large clades, of which the Conophytum-clade was one the most morphologically diverse based on leaf and capsule characters. The Conophytum

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13

Arvestad, Isaac, and Henrik Lagebrand. "Implementing Bayesian phylogenetic tree inference with Sequential Monte Carlo and the Phylogenetic Likelihood Library." Thesis, KTH, Skolan för elektroteknik och datavetenskap (EECS), 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-229429.

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We investigate the usability of the Phylogenetic Likelihood Library (PLL) in Bayesian phylogenetic tree inference using Sequential Monte Carlo (SMC) algorithms. This is done by implementing two different versions of the same algorithm with two different approaches of the use of PLL. The implementation using the main PLL API encountered performance issues that the lower level implementation did not. We conclude that it is possible to use PLL in SMC methods but it is unclear if the main API is suitable.<br>Vi undersöker om programspråksbiblioteket Phylogenetic Likelihood Library (PLL) kan använd

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14

Fleissner, Roland. "Sequence alignment and phylogenetic inference." Berlin : Logos Verlag, 2004. http://diss.ub.uni-duesseldorf.de/ebib/diss/file?dissid=769.

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15

Rehmsmeier, Marc. "Database searching with phylogenetic trees." [S.l.] : [s.n.], 2001. http://deposit.ddb.de/cgi-bin/dokserv?idn=963977423.

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16

Deepak, Akshay. "SearchTree mining robust phylogenetic trees /." [Ames, Iowa : Iowa State University], 2010. 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:1476290.

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17

Haber, Matthew Horace. "The centrality of phylogenetic thinking /." For electronic version search Digital dissertations database. Restricted to UC campuses. Access is free to UC campus dissertations, 2005. http://uclibs.org/PID/11984.

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18

Schmidt, Heiko A. "Phylogenetic trees from large datasets." [S.l. : s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=968534945.

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19

Fleissner, Roland. "Sequence alignment and phylogenetic inference." [S.l. : s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=971844704.

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20

Gottschling, Marc. "Phylogenetic analysis of selected Boraginales." [S.l. : s.n.], 2003. http://www.diss.fu-berlin.de/2003/30/index.html.

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21

Högnabba, Filip. "Phylogenetic studies of cyanobacterial lichens /." Helsinki : Yliopistopaino, 2007. http://ethesis.helsinki.fi.

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22

Roos, Marinus Cornelis. "Phylogenetic systematics of the Drynarioideae /." Amsterdam [u.a.] : North-Holland, 1985. http://www.gbv.de/dms/bs/toc/013141155.pdf.

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23

Jetté, Migüel. "Reconstructing functions on phylogenetic trees." Thesis, McGill University, 2006. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=99187.

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This thesis introduces three new tools for studying the evolution of different organisms given the evolutionary, or phylogenetic, tree that relates them. First, we show how posterior state probabilities can be used for exploring phylogenetic uncertainty, through posterior entropy of ancestral states. Second, we derive an explicit formula for the expected number of substitutions on a branch in a phylogeny, given the pattern at the leaves. Algorithms were implemented, as part of the ATV software, to calculate these values. They are used, in conjunction with SplitsTree4, to assess variation in ra

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24

Ryder, Robin Jeremy. "Phylogenetic models of language diversification." Thesis, University of Oxford, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.543009.

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25

Stolzer, Maureen. "Phylogenetic Inference for Multidomain Proteins." Research Showcase @ CMU, 2011. http://repository.cmu.edu/dissertations/47.

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In this thesis, I present a model of multidomain evolution with associated algorithms and software for phylogenetic analysis of multidomain families, as well as applications of this novel methodology to case-studies and the human genome. Phylogenetic analysis is of central importance to understanding the origins and evolution of life on earth. In biomedical research, molecular phylogenetics has proved an essential tool for practical applications. Current molecular phylogenetic methods are not equipped, however, to model many of the unique characteristics of multidomain families. Genes that enc

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26

Welbourn, Warren Calvin. "Phylogenetic studies of trombidioid mites /." The Ohio State University, 1985. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487262825074137.

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27

Kashiwada, Akemi. "Constructing Phylogenetic Trees from Subsplits." Scholarship @ Claremont, 2005. https://scholarship.claremont.edu/hmc_theses/171.

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Phylogenetic trees represent theoretical evolutionary relationships among various species. Mathematically they can be described as weighted binary trees and the leaves represent the taxa being compared. One major problem in mathematical biology is the reconstruction of these trees. We already know that trees on the leaf set X can be uniquely constructed from splits, which are bipartitions of X. The question I explore in this thesis is whether reconstruction of a tree is possible from subsplits, or partial split information. The major result of this work is a constructive algorithm which allows

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28

Bauer, Jennifer E. "A Phylogenetic and Paleobiogeographic Analysis of the Ordovician Brachiopod Eochonetes." Ohio University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1397486053.

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29

Porter, Megan L. "Crustacean phylogenetic systematics and opsin evolution." Diss., CLICK HERE for online access, 2005. http://contentdm.lib.byu.edu/ETD/image/etd859.pdf.

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30

Oldman, James. "Constructing phylogenetic networks based on trinets." Thesis, University of East Anglia, 2015. https://ueaeprints.uea.ac.uk/59446/.

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The motivation of phylogenetic analysis is to discover the evolutionary relationships between species, with the broader aim of understanding the origins of life. Our understanding of the molecular character- istics of species through DNA sequencing permanently changed the approach to understanding the evolution of species. Indeed, the ad- vancement of technology has played a major role in the fast sequencing of DNA as well as the use of computers in solving biological problems in general. These evolutionary relationships are often visualised and represented using a phylogenetic tree. As a natu

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31

Fischer, Mareike. "Novel Mathematical Aspects of Phylogenetic Estimation." Thesis, University of Canterbury. Mathematics and Statistics, 2009. http://hdl.handle.net/10092/2331.

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In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. Inferring this underlying tree is challenging. We investigate some curious cases in which different methods like Maximum Parsimony, Maximum Likelihood and distance-based methods lead to different trees. Moreover, we state that in some cases, ancestral sequences can be more reliably reconstructed when some of the leaves of the tree are ignored - even if these leaves are close to the root. While all these findings show problems inherent to eit

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32

Keivany, Yazdan. "Phylogenetic relationships of Gasterosteiformes (Teleostei, Percomorpha)." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp02/NQ59608.pdf.

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33

Habib, Farhat Abbas. "Genotype-phenotype correlation using phylogenetic trees." Columbus, Ohio : Ohio State University, 2007. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1187297400.

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34

Fuentes, Carvajal Andreina. "Phylogenetic relationships within Coleeae (Bignoniaceae juss.)." Click here to access thesis, 2007. http://www.georgiasouthern.edu/etd/archive/fall2007/carvajal_a_fuentes/carvajal_andreina_f_200708_MS.pdf.

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Thesis (M.S.)--Georgia Southern University, 2007.<br>"A thesis submitted to the Graduate Faculty of Georgia Southern University in partial fulfillment of the requirements for the degree Master of Science." In Biology, under the direction of Michelle Zjhra. ETD. Electronic version approved: December 2007. Includes bibliographical references (p. 38-42)

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35

Ababneh, Faisal. "Models and estimation for phylogenetic trees /." Connect to full text, 2006. http://hdl.handle.net/2123/927.

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36

Cho, Anna. "Constructing Phylogenetic Trees Using Maximum Likelihood." Scholarship @ Claremont, 2012. http://scholarship.claremont.edu/scripps_theses/46.

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Maximum likelihood methods are used to estimate the phylogenetic trees for a set of species. The probabilities of DNA base substitutions are modeled by continuous-time Markov chains. We use these probabilities to estimate which DNA bases would produce the data that we observe. The topology of the tree is also determined using base substitution probabilities and conditional likelihoods. Felsenstein [2] introduced this method of finding an estimate for the maximum likelihood phylogenetic tree. We will explore this method in detail in this paper.

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37

Wu, Qiong. "Phylogenetic Networks : New Constructions and Applications." Thesis, University of East Anglia, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.514315.

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38

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

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Thanks to the recent advancement of the sequence technologies, generating large volumes of DNA sequence data is now becoming more feasible. Sequencing several samples across many species from a range of clades enables us to connect the two fields of study previously separated due to the lack of data: population genetics and phylogenetics. The former has focused on detailed genetic processes in a few species, while the latter has studied large-scale evolutionary relationships across many species. In this thesis, methods to utilize the new type of data, genealogical-phylogenetic data, are explor

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39

Yu, Junjie, and 于俊杰. "Phylogenetic tree reconstruction with protein linkage." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2012. http://hub.hku.hk/bib/B49618167.

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Phylogenetic tree reconstruction for a set of species is an important problem for understanding the evolutionary history of the species. Existing algorithms usually represent each species as a binary string with each bit indicating whether a particular gene/protein exists in the species. Given the topology of a phylogenetic tree with each leaf representing a species (a binary string of equal length) and each internal node representing the hypothetical ancestor, the Fitch-Hartigan algorithm and the Sankoff algorithm are two polynomial-time algorithms which assign binary strings to internal nod

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40

Boudko, Ekaterina. "Phylogenetic Analysis of Subtribe Alopecurinae (Poaceae)." Thèse, Université d'Ottawa / University of Ottawa, 2014. http://hdl.handle.net/10393/30696.

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Subtribe Alopecurinae (Poeae, Poaceae) sensu lato‘s seven genera share interesting morphological similarities (dense spicate panicles and one-flowered spikelets) that were widely thought to have a common origin. However, recent molecular evidence for three of the genera has suggested that the subtribe may be polyphyletic. To test this, five DNA regions were sequenced and analyzed using phylogenetic methods. Results confirm that Alopecurinae s.l. as presently treated is polyphyletic and should be dissolved. Additionally, the genus Cornucopiae may be just another Alopecurus. Limnas and Pseudophl

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41

Garcia, John. "Phylogenetic methods in Huasteca Nahuatl dialectology." Thesis, California State University, Long Beach, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=1526912.

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<p> The Nahuatl language spoken by Aztec/Mexica continues to be spoken throughout Central Mexico and in the Huasteca region. Variation within the Huasteca has yet to be fully explored, and this study integrates a questionnaire published by Lastra and interviews I conducted with native speakers representing different communities. The data produced from this were used to find features that distinguish different towns and then were analyzed using cladistics, a phylogenetic method used by biologists to propose a hypothesis of the evolutionary relationships among species, and which has also been us

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42

Dissanayake, Deepthi. "Phylogenetic research of the family Chrysobalanaceae." Thesis, University of Reading, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.390620.

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Williams, Annette Mary. "Phylogenetic analysis of the genus Streptococcus." Thesis, University of Reading, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.333267.

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44

Radice, Rosalba. "A Bayesian approach to phylogenetic networks." Thesis, University of Bath, 2011. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.538163.

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Traditional phylogenetic inference assumes that the history of a set of taxa can be explained by a tree. This assumption is often violated as some biological entities can exchange genetic material giving rise to non-treelike events often called reticulations. Failure to consider these events might result in incorrectly inferred phylogenies, and further consequences, for example stagnant and less targeted drug development. Phylogenetic networks provide a flexible tool which allow us to model the evolutionary history of a set of organisms in the presence of reticulation events. In recent years,

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45

Hayward, Peter. "Parallel likelihood calculations for phylogenetic trees." Thesis, Stellenbosch : Stellenbosch University, 2011. http://hdl.handle.net/10019.1/17919.

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Thesis (MSc)--Stellenbosch University, 2011.<br>ENGLISH ABSTRACT: Phylogenetic analysis is the study of evolutionary relationships among organisms. To this end, phylogenetic trees, or evolutionary trees, are used to depict the evolutionary relationships between organisms as reconstructed from DNA sequence data. The likelihood of a given tree is commonly calculated for many purposes including inferring phylogenies, sampling from the space of likely trees and inferring other parameters governing the evolutionary process. This is done using Felsenstein’s algorithm, a widely implemented dyna

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46

Figueroa, Alex. "Phylogenetic Relationships and Evolution of Snakes." ScholarWorks@UNO, 2016. http://scholarworks.uno.edu/td/2222.

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Snakes represent an impressive evolutionary radiation of over 3,500 widely-distributed species, categorized into 515 genera, encompassing a diverse range of morphologies and ecologies. This diversity is likely attributable to their distinctive morphology, which has allowed them to populate a wide range of habitat types within most major ecosystems. In my first chapter, I provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including

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47

Bhattacharya, Deblina Patra, Sebastian Canzler, Stephanie Kehr, Jana Hertel, Ivo Grosse, and Peter F. Stadler. "Phylogenetic distribution of plant snoRNA families." Universitätsbibliothek Leipzig, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-215736.

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Background: Small nucleolar RNAs (snoRNAs) are one of the most ancient families amongst non-protein-coding RNAs. They are ubiquitous in Archaea and Eukarya but absent in bacteria. Their main function is to target chemical modifications of ribosomal RNAs. They fall into two classes, box C/D snoRNAs and box H/ACA snoRNAs, which are clearly distinguished by conserved sequence motifs and the type of chemical modification that they govern. Similarly to microRNAs, snoRNAs appear in distinct families of homologs that affect homologous targets. In animals, snoRNAs and their evolution have been studied

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48

Viana, Gerardo ValdÃso Rodrigues. "Techniques for construction of phylogenetic trees." Universidade Federal do CearÃ, 2007. http://www.teses.ufc.br/tde_busca/arquivo.php?codArquivo=1353.

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FundaÃÃo Cearense de Apoio ao Desenvolvimento Cientifico e TecnolÃgico<br>Phylogenetic tree structures express similarities, ancestrality, and relationships between species or group of species, and are also known as evolutionary trees or phylogenies. Phylogenetic trees have leaves that represent species (taxons), and internal nodes that correspond to hypothetical ancestors of the species. In this thesis we rst present elements necessary to the comprehension of phylogenetic trees systematics, then efcient algorithms to build them will be described. Molecular biology concepts, life evolution, an

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49

Garrote, López Marina. "Algebraic and semi-algebraic phylogenetic reconstruction." Doctoral thesis, Universitat Politècnica de Catalunya, 2021. http://hdl.handle.net/10803/672316.

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Phylogenetics is the study of the evolutionary history and relationships among groups of biological entities (called taxa). The modeling of those evolutionary processes is done by phylogenetic trees whose nodes represent different taxa and whose branches correspond to the evolutionary processes between them. The leaves usually represent contemporary taxa and the root is their common ancestor. Nowadays, phylogenetic reconstruction aims to estimate the phylogenetic tree that best explains the evolutionary relationships of current taxa using solely information from their genome arranged in an ali

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50

Habib, Farhat. "Genotype-phenotype correlation using phylogenetic trees." The Ohio State University, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=osu1187297400.

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