Thèses : « Phylogenesi »

1

Höhna, Sebastian. « Bayesian Phylogenetic Inference : Estimating Diversification Rates from Reconstructed Phylogenies ». Doctoral thesis, Stockholms universitet, Matematiska institutionen, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-95361.

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Phylogenetics is the study of the evolutionary relationship between species. Inference of phylogeny relies heavily on statistical models that have been extended and refined tremendously over the past years into very complex hierarchical models. Paper I introduces probabilistic graphical models to statistical phylogenetics and elaborates on the potential advantages a unified graphical model representation could have for the community, e.g., by facilitating communication and improving reproducibility of statistical analyses of phylogeny and evolution. Once the phylogeny is reconstructed it is possible to infer the rates of diversification (speciation and extinction). In this thesis I extend the birth-death process model, so that it can be applied to incompletely sampled phylogenies, that is, phylogenies of only a subsample of the presently living species from one group. Previous work only considered the case when every species had the same probability to be included and here I examine two alternative sampling schemes: diversified taxon sampling and cluster sampling. Paper II introduces these sampling schemes under a constant rate birth-death process and gives the probability density for reconstructed phylogenies. These models are extended in Paper IV to time-dependent diversification rates, again, under different sampling schemes and applied to empirical phylogenies. Paper III focuses on fast and unbiased simulations of reconstructed phylogenies. The efficiency is achieved by deriving the analytical distribution and density function of the speciation times in the reconstructed phylogeny.

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Manuscript. Paper 4: Accepted.

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2

Ross, Edith. « Inferring tumour evolution from single-cell and multi-sample data ». Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/274604.

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Tumour development has long been recognised as an evolutionary process during which cells accumulate mutations and evolve into a mix of genetically distinct cell subpopulations. The resulting genetic intra-tumour heterogeneity poses a major challenge to cancer therapy, as it increases the chance of drug resistance. To study tumour evolution in more detail, reliable approaches to infer the life histories of tumours are needed. This dissertation focuses on computational methods for inferring trees of tumour evolution from single-cell and multi-sample sequencing data. Recent advances in single-cell sequencing technologies have promised to reveal tumour heterogeneity at a much higher resolution, but single-cell sequencing data is inherently noisy, making it unsuitable for analysis with classic phylogenetic methods. The first part of the dissertation describes OncoNEM, a novel probabilistic method to infer clonal lineage trees from noisy single nucleotide variants of single cells. Simulation studies are used to validate the method and to compare its performance to that of other methods. Finally, OncoNEM is applied in two case studies. In the second part of the dissertation, a comprehensive collection of existing multi-sample approaches is used to infer the phylogenies of metastatic breast cancers from ten patients. In particular, shallow whole-genome, whole exome and targeted deep sequencing data are analysed. The inference methods comprise copy number and point mutation based approaches, as well as a method that utilises a combination of the two. To improve the copy number based inference, a novel allele-specific multi-sample segmentation algorithm is presented. The results are compared across methods and data types to assess the reliability of the different methods. In summary, this thesis presents substantial methodological advances to understand tumour evolution from genomic profiles of single cells or related bulk samples.

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Hamberg, Erlend Heggheim. « Inferring Phylogenies Using Evolutionary Algorithms : A maximum likelihood approach for constructing phylogenetic trees from molecular data ». Thesis, Norges teknisk-naturvitenskapelige universitet, Institutt for datateknikk og informasjonsvitenskap, 2011. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-13687.

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This thesis has evaluated the use of the computationally expensivemaximum-likelihood (ML) method coupled with an evolutionaryalgorithm (EA) for the problem of inferring evolutionaryrelationships among species (phylogenies) from molecular data. MLmethods allow using all the information from molecular data, suchas DNA sequences, and have several beneficial properties compared toother methods. Evolutionary algorithms is a class of optimizationalgorithms that often perform well in complex fitness landscapes.EAs are also proclaimed to be easy to parallelize, an aspect thatis increasingly more important.A parallel EA system has been implemented and tested on a clusterfor the task of phylogeny inference. The system shows promisingresults and is able to utilize processors of a massively parallelsystem in a transparent manner.

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4

Roeser-Mueller, Kerstin [Verfasser], Erhard [Akademischer Betreuer] Strohm et Christoph [Akademischer Betreuer] Oberprieler. « Phylogenies and pheromones - Defensive symbionts, phylogenetic affiliations and olfactory communication in beewolves (Philanthini, Hymenoptera, Crabronidae) / Kerstin Roeser-Mueller. Betreuer : Erhard Strohm ; Christoph Oberprieler ». Regensburg : Universitätsbibliothek Regensburg, 2012. http://d-nb.info/1033688363/34.

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5

Marchiselli, Simone. « Molecular phylogenesis of Mediterranean Octocorals ». Master's thesis, Alma Mater Studiorum - Università di Bologna, 2013. http://amslaurea.unibo.it/4905/.

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In order to support the conservation of the Mediterranean octocorals improvements on information regarding their taxonomic units and phylogenetic relationships are strongly needed. In the present thesis work, phylogenetic analyses based on the mitochondrial mtMSH and 16S genes were performed including 15 Mediterranean octocorals species on the 56 recognized to date. Moreover, an extended datasets with Atlanto/Pacific congeners Octocorallia species was implemented to clarify their phylogenetic relationships and estimate the divergence times of the Mediterranean species. Results indicated that: 1) there are similarity and differences among molecular and morphological traits depending on the taxonomical level considered; 2) the molecular phylogeny of the Mediterranean octocorals retrace the previous relationships based on wide octocorals analyses; and 3) the divergence time among Mediterranean and Atlanto/Pacific species varies depending on analysed taxa. At higher taxonomic level, the Mediterranean trees supported the division of the Mediterranean Octocorallia into one major clade (Alcyoniina-Holaxonia) plus two unresolved branch including the single species available of Scleraxonia and Stolonifera respectively. This topology was better supported including the Atlanto/Pacific congeners species. The molecular evidence suggested that Alcyonium palmatum and Corallium rubrum species are the youngest with a divergence time estimated around 4 MYA. Particularly, C. rubrum results were in agreement with the hypothesis that recent orogenesis process of the Mediterranean Sea promoted the allopatric speciation of this specie. Increasing the sample design and implementing the emerging next-generation genomic-sequencing technologies, further studies would be able to improve the understanding of the Mediterranean octocorals phylogenetic relationships and evolution.

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6

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 framework leverages a clade's shared evolutionary history to pull species estimates closer towards phylogenetic conserved values and farther away from species specific biases. We propose a new Bayesian model of phylogenetic niche implemented in R. Under our model, species SDM parameters are transformed into biologically interpretable continuous parameters of environmental niche optimum, breadth, and tolerance evolving under multivariate Brownian motion random walk. Through simulation analyses, we demonstrated model accuracy and precision that improved as phylogeny size increased. We also demonstrated our model on a clade of eastern United States Plethodontid salamanders by accurately estimating species niche, even when no occurrence data is present. Our model demonstrates a novel framework where niche changes can be studied forwards and backwards through time to understand ancestral ranges, patterns of environmental specialization, and niche in data deficient species.
Master of Science
As many species face increasing pressure in a changing climate, it is crucial to understand the set of environmental conditions that shape species' ranges--known as the environmental niche--to guide conservation and land management practices. Species distribution models (SDMs) are common tools that are used to model species' environmental niche. These models treat a species' probability of occurrence as a function of environmental conditions. SDM niche estimates can predict a species' range given climate data, paleoclimate, or projections of future climate change to estimate species range shifts from the past to the future. However, SDM estimates are often biased by non-environmental factors shaping a species' range including competitive divergence or dispersal barriers. Biased SDM estimates can result in range predictions that get worse as we extrapolate beyond the observed climatic conditions. One way to overcome these biases is by leveraging the shared evolutionary history amongst related species to "fill in the gaps". Species that are more closely phylogenetically related often have more similar or "conserved" environmental niches. By estimating environmental niche over all species in a clade jointly, we can leverage niche conservatism to produce more biologically realistic estimates of niche. However, currently a methodological gap exists between SDMs estimates and macroevolutionary models, prohibiting them from being estimated jointly. We propose a novel model of evolutionary niche called PhyNE (Phylogenetic Niche Evolution), where biologically realistic environmental niches are fit across a set of species with occurrence data, while simultaneously fitting and leveraging a model of evolution across a portion of the tree of life. We evaluated model accuracy, bias, and precision through simulation analyses. Accuracy and precision increased with larger phylogeny size and effectively estimated model parameters. We then applied PhyNE to Plethodontid salamanders from Eastern North America. This ecologically-important and diverse group of lungless salamanders require cold and wet conditions and have distributions that are strongly affected by climatic conditions. Species within the family vary greatly in distribution, with some species being wide ranging generalists, while others are hyper-endemics that inhabit specific mountains in the Southern Appalachians with restricted thermal and hydric conditions. We fit PhyNE to occurrence data for these species and their associated average annual precipitation and temperature data. We identified no correlations between species environmental preference and specialization. Pattern of preference and specialization varied among Plethodontid species groups, with more aquatic species possessing a broader environmental niche, likely due to the aquatic microclimate facilitating occurrence in a wider range of conditions. We demonstrated the effectiveness of PhyNE's evolutionarily-informed estimates of environmental niche, even when species' occurrence data is limited or even absent. PhyNE establishes a proof-of-concept framework for a new class of approaches for studying niche evolution, including improved methods for estimating niche for data-deficient species, historical reconstructions, future predictions under climate change, and evaluation of niche evolutionary processes across the tree of life. Our approach establishes a framework for leveraging the rapidly growing availability of biodiversity data and molecular phylogenies to make robust eco-evolutionary predictions and assessments of species' niche and distributions in a rapidly changing world.

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8

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 is necessary as researchers analyze tree of life size data sets.

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9

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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In phylogenetic analysis one study the relationship between different species. By comparing DNA from two different species it is possible to get a numerical value representing the difference between the species. For a set of species, all pair-wise comparisons result in a dissimilarity matrix d.

In this thesis I present a few methods for constructing a phylogenetic tree from d. The common denominator for these methods is that they do not generate a tree, but instead give a connected graph. The resulting graph will be a tree, in areas where the data perfectly matches a tree. When d does not perfectly match a tree, the resulting graph will instead show the different possible topologies, and how strong support they have from the data.

Finally I have tested the methods both on real measured data and constructed test cases.

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10

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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11

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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12

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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13

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 and Sullivant’s toric ideals of phylogenetic invariants. Furthermore, I want to look at the statistical properties of polynomial invariants to get a better understanding of how they behave when used with real, “noisy” data.

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14

Möller, Anke. « Die Phylogenese der Sprache und ihre Echos ». [S.l. : s.n.], 2001. http://deposit.ddb.de/cgi-bin/dokserv?idn=965487768.

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Arvestad, Isaac, et 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.
Vi undersöker om programspråksbiblioteket Phylogenetic Likelihood Library (PLL) kan användas för bayesiansk inferens av phylogenetiska träd med en sekventiell Monte Carlo-metod (SMC). Genom att implementera algoritmen med två olika delar av PLL:s programmeringsgränssnitt visar vi att det går att använda PLL för att implementera SMC-algoritmen men att det är oklart om det huvudsakliga programmeringsgränssnittet är lämpligt.

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16

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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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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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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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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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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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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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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Anderson, Cajsa Lisa. « Dating Divergence Times in Phylogenies ». Doctoral thesis, Uppsala University, Department of Evolution, Genomics and Systematics, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8155.

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This thesis concerns different aspects of dating divergence times in phylogenetic trees, using molecular data and multiple fossil age constraints.

Datings of phylogenetically basal eudicots, monocots and modern birds (Neoaves) are presented. Large phylograms and multiple fossil constraints were used in all these studies. Eudicots and monocots are suggested to be part of a rapid divergence of angiosperms in the Early Cretaceous, with most families present at the Cretaceous/Tertiary boundary. Stem lineages of Neoaves were present in the Late Cretaceous, but the main divergence of extant families took place around the Cre-taceous/Tertiary boundary.

A novel method and computer software for dating large phylogenetic trees, PATHd8, is presented. PATHd8 is a nonparametric smoothing method that smoothes one pair of sister groups at a time, by taking the mean of the added branch lengths from a terminal taxon to a node. Because of the local smoothing, the algorithm is simple, hence providing stable and very fast analyses, allowing for thousands of taxa and an arbitrary number of age constraints.

The importance of fossil constraints and their placement are discussed, and concluded to be the most important factor for obtaining reasonable age estimates.

Different dating methods are compared, and it is concluded that differences in age estimates are obtained from penalized likelihood, PATHd8, and the Bayesian autocorrelation method implemented in the multidivtime program. In the Bayesian method, prior assumptions about evolutionary rate at the root, rate variance and the level of rate smoothing between internal edges, are suggested to influence the results.

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24

Collins, Joshua Stewart. « Rekernelisation Algorithms in Hybrid Phylogenies ». Thesis, University of Canterbury. Mathematics and Statistics, 2009. http://hdl.handle.net/10092/2852.

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It has become well known that an evolutionary tree is inadequate to represent fully the history of life. Two possible ways of dealing with this are the rooted subtree prune and regraft distance between a pair of trees, which measures how different they are, and the slightly more biologically sound hybridisation number of a set of trees that attempts to determine the minimum number of hybrid events that must have occurred for a given set of evolutionary trees. When characterised via agreement forests both problems are, although NP hard, fixed parameter tractable---meaning the problem can be converted to a similar problem with a smaller input size. This thesis investigates ways of improving existing algorithms for calculating the minimum rooted subtree prune and regraft distance and hybridisation number for a pair or, in the latter case, set of trees. In both cases a technique is used that allows the problem to be rekernelised during the run of the program. Another, less effective method, is also looked at which finds the rooted subtree prune and regraft distance or hybridisation number solely on what cannot be contained within any agreement forest. Additionally the characterisation of the minimum rooted subtree prune and regraft distance via maximum agreement forests is extended to non-binary trees and the hybridisation number of a set of phylogenetic trees is extended to unrooted trees.

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

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Rydin, Catarina. « The Gnetales : fossils and phylogenies / ». Stockholm : Department of Botany, Stockholm University, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-488.

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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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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 rates over sites and lineages, and to predict model violations. Third, we show how techniques for spline interpolation and function approximation can be applied to estimate functions defined on a tree. We also present an example of the usage of interpolations on phylogenetic trees, by analyzing continuous traits on a phylogenetic tree through fossil data sets.

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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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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 encode this large and important class of proteins are characterized by a mosaic of sequence fragments that encode structural or functional modules, called domains. Multidomain families evolve via domain shuffling, a process that includes insertion, internal duplication, and deletion of domains. This versatile evolutionary mechanism played a transformative role in major evolutionary transitions, including the emergence of multicellular animals and the vertebrate immune system. Multidomain families are ill-suited to current methods for phylogeny reconstruction due to their mosaic composition. Different regions of the same protein may have different evolutionary histories. Moreover, a protein may contain domains that also occur in otherwise unrelated proteins. These attributes pose substantial obstacles for phylogenetic methods that require a multiple sequence alignment as input. In addition, current methods do not incorporate a model of domain shuffling and hence, cannot infer the events that occurred in the history of the family. I address this problem by treating a multidomain family as a set of co-evolving domains, each with its own history. If the family is evolving by vertical descent from a conserved set of ancestral domains, then all constituent domains will have the same phylogenetic history. Disagreement between domain tree topologies is evidence that the family evolved through processes other than speciation and gene duplication. My algorithms exploit this information to reconstruct the history of domain shuffling in the family, as well as the timing of these events and the ancestral domain composition. I have implemented these algorithms in software that outputs the most parsimonious history of events for each domain family. The software also reconstructs a composite family history, including duplications, insertions and losses of all constituent domains and ancestral domain composition. My approach is capable of more detailed and accurate reconstructions than the widely used domain architecture model, which ignores sequence variation between domain instances. In contrast, my approach is based on an explicit model of events and captures sequence variation between domain instances. I demonstrate the utility of this method through case studies of notch-related proteins, protein tyrosine kinases, and membrane-associated guanylate kinases. I further present a largescale analysis of domain shuffling processes through comparison of all pairs of domain families that co-occur in a protein in the human genome. These analyses suggest that (1) a remarkably greater amount of domain shuffling may have occurred than previously thought and (2) that it is not uncommon for the same domain architecture to arise more than once through independent events. This stands in contrast to earlier reports that convergent evolution of domain architecture is rare and suggests that incorporating sequence variation in evolutionary analyses of multidomain families is a crucial requirement for accurate inference.

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Goodall-Copestake, William Paul. « Framework phylogenies for the begoniaceae ». Thesis, University of Glasgow, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.439253.

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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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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 us to determine whether a given set of subsplits will realize a tree and, if so, what the tree looks like.

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Hawarden-Lord, Andrew Sinclair. « Organisational phylogenesis : developing and evaluating a memetic methodology ». Thesis, Sheffield Hallam University, 2004. http://shura.shu.ac.uk/19772/.

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This research evaluates the unorthodox proposition that organisational development proceeds through the Darwinian processes of variation, selection and inheritance acting upon a non-genetic replicating code. This new replicator represents the fundamental unit of cultural transmission and was termed by evolutionist, Richard Dawkins, as the meme. The memetic position re-introduces many often neglected, sometimes shunned, evolutionary arguments into social and organisational debate by providing a naturalistic and plausible hereditary element upon which socio-cultural adaptation operates. The popularity of the neologism 'meme' initially grew through rather ad-hoc non-scientific usage on the Internet. For some time, this geekish tendency has tarnished the idea of memetics and impeded serious academic investigation into the subject. A more rigorous philosophical treatment has been provided by Daniel Dennett who has argued that, while a science of memetic cladistics may be both desirable and feasible, it remains unlikely. On the other hand one of Dawkins' most famous critics, Mary Midgley, heralds dark forebodings that one-day memes may be given actual credence. The present study necessitated the adaptation of conventional genealogical and taxonomic methods, for novel application in confirming congruence between actual organisational phylogeny and hereditary traits. One specific requirement was to develop a means of identifying, capturing and codifying such traits as meme strips for phenetic analysis. In order to handle the computational complexity inherent in the phenetic reconstruction algorithms, proprietary software had to be produced. This was extensively tested upon meme strips generated through simulated evolution. Western Christian denominational families provided a source of empirical evidence and demonstrated that the methods could be successfully applied to real organisational forms. A theological phylogeny was reliably reconstructed thereby upholding the hypothesis of cultural descent with modification based on a memetic replication. Further support for the claim was made in conjunction with the rendering of a facilities management market landscape. More importantly however, the results coming from this research suggest that the potential for formulating a science of memetics may be significantly greater than in Dennett original consideration.

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Soccol, Vanete Thomaz. « Les Leishmania du Nouveau monde : analyse enzymatique, démarche progressive phénétique-cladistique, relations phylogénétiques avec les Leishmania de l'Ancien monde ». Montpellier 1, 1993. http://www.theses.fr/1993MON1T002.

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Rossetti, Yves. « Variations annuelles des donnees psychopathologiques et physiologiques humaines : description phylogenetique et mecanismes de regulation ». Lyon 1, 1990. http://www.theses.fr/1990LYO1M099.

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De, Franceschi Dario. « Phylogénie des Ebénales : analyse de l'ordre et origine biogéographique des espèces indiennes / ». Pondichéry : Institut français de Pondichéry, 1993. http://catalogue.bnf.fr/ark:/12148/cb357117417.

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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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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 natural generalisation of phylogenetic trees, phylogenetic networks are used in biology to rep- resent evolutionary histories that contain reticulate, or non-treelike events such as recombination, hybridisation and horizontal gene trans- fer. The reconstruction of explicit phylogenetic networks from biolog- ical data is currently an active area of phylogenetics research. Here we consider the problem of constructing such networks from trinets, that is, phylogenetic networks on three leaves. More speci�cally, we present the SeqTrinet and TriLoNet methods, which form a supernet- work based approach to constructing level-1 phylogenetic networks directly from multiple sequence alignments.

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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 either the assumed model or the applied method, sometimes an inaccurate tree reconstruction is simply due to insufficient data. This is particularly problematic when a rapid divergence event occurred in the distant past. We analyze an idealized form of this problem and determine a tight lower bound on the growth rate for the sequence length required to resolve the tree (independent of any particular branch length). Finally, we investigate the problem of intermediates in the fossil record. The extent of ‘gaps’ (missing transitional stages) has been used to argue against gradual evolution from a common ancestor. We take an analytical approach and demonstrate why, under certain sampling conditions, we may not expect intermediates to be found.

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

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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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Mooers, Arnie Ã˜yvind. « Patterns of diversification revealed by phylogenies ». Thesis, University of Oxford, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.386648.

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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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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 explored to tackle the problems lying between the two fields, including how to delimit species with genetic information and how ecological traits affect species genetic properties. First, a method of species delimitation based on single locus gene tree, called the generalized mixed Yule coalescent method (GMYC method), is evaluated. Its statistical properties are assessed on both simulated and real data, and the method is extended to relax some simplifying assumptions and to give a robust confidence measure. The simulation studies showed that the reliability of the delimitation depends on population parameters and patterns of diversification processes. Assessment of the performance on a dataset of 5196 water beetle mitochondrial DNA sequences sampled from across Europe showed that the method accurately delimited half of the studied species. The accuracy was affected by several factors, notably the presence of pseudogenes and potential undersampling of species range. Then, the water beetle data and the GMYC method are used to test the effects of species ecological traits on genetic properties, focusing on species habitat type. Habitat type had significant effects on genetic variation and substitution rate via effects on range size and latitudinal distribution of species. However, direct effects of habitat type on genetic properties were not observed.

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Domingues, Kümmel Tria Fernando [Verfasser]. « Rooting phylogenies / Fernando Domingues Kümmel Tria ». Kiel : Universitätsbibliothek Kiel, 2019. http://d-nb.info/1187732745/34.

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Yu, Junjie, et 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 nodes such that the total Hamming distance between adjacent nodes in the tree is minimized. However, these algorithms oversimplify the evolutionary process by considering only the number of protein insertions/deletions (Hamming distance) between two species and by assuming the evolutionary history of each protein is independent. Since the function of a protein may depend on the existence of other proteins, the evolutionary history of these functionally dependent proteins should be similar, i.e. functionally dependent proteins should usually be present (or absent) in a species at the same time. Thus, in addition to the Hamming distance, the protein linkage distance for some pairs/sets of proteins: whole block linkage distance, partial block linkage distance, pairwise linkage distance is introduced. It is proved that the phylogenetic tree reconstruction problem to find the binary strings for the internal nodes of a phylogenetic tree that minimizes the sum of the Hamming distance and the linkage distance is NP-hard. In this thesis, a general algorithm to solve the phylogenetic tree reconstruction with protein linkage problem which runs in O(4^m⋅n) time for whole/partial block linkage distance and O(4^m⋅⋅ (m+n)) time for pairwise linkage distance (compared to the straight-forward O(4^m⋅ m⋅ n) or O(4^m⋅ m^2⋅⋅ n) time algorithm) is introduced where n is the number of species and m is the length of the binary string (number of proteins). It is further shown, by experiments, that our algorithm using linkage information can construct more accurate trees (better matches with the trees constructed by biologists) than the algorithms using only Hamming distance.
published_or_final_version
Computer Science
Master
Master of Philosophy

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Thèses sur le sujet « Phylogenesi »

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