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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.
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 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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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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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 ecologically viable and that maximize PD. The NP-hardness
of this problem is proved and it is established which special cases of the problem are
computationally easy and which are computationally hard. It is also shown that it is
NP-complete to decide whether the feasible solution obtained by the greedy algorithm is
optimal. We formulate the optimization problem as an integer linear program and find
exact solutions to the largest food web currently in the empirical literature. In addition,
we give a generalization of PD that can be used for example when we do not know the
true evolutionary history. Based on this measure, an optimization problem is formulated.
We discuss the complexity and the approximability properties of this problem.
In the generalized field of bullets model (g-FOB), species are assumed to become
extinct with possibly different probabilities, and extinction events are independent. We
show that under this model the distribution of future phylogenetic diversity converges to
a normal distribution as the number of species grows. When extinction probabilities are
influenced by some binary character on the tree, the state-based field of bullets model
(s-FOB) represents a more realistic picture. We compare the expected loss of PD under
this model to that under the associated g-FOB model and find that the former is always
greater than or equal to the latter. It is natural to further generalize the s-FOB model to
allow more than one binary character to affect the extinction probabilities. The expected
future PD obtained for the resulting trait-dependent field of bullets model (t-FOB) is
compared to that for the associated g-FOB model and our previous result is generalized.
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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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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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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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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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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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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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 - PhDThe 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)
13
Arvestad, Isaac, i 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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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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Högnabba, Filip. "Phylogenetic studies of cyanobacterial lichens /". Helsinki : Yliopistopaino, 2007. http://ethesis.helsinki.fi.
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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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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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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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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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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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Yu, Junjie, i 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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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 Pseudophleum are not closely allied to Alopecurus or each other, and are even further from Phleum. Phleum is a distinct lineage that is not closely allied to any other included Alopecurinae genus. Evidence for revising infrageneric classifications of Alopecurus and Phleum is presented, as is evidence for separating A. magellanicus into two or more subspecies.
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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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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 used by linguists. The output suggests there is a large split between northwest and southeast regions of the Huasteca, and that the northeast villages compose a subregion on their own. One can trace the relationships between communities on the output tree and follow a path backwards towards Central Mexico, suggesting a north-east migration.
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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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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, a number of methods addressing phylogenetic network reconstruction and evaluation have been introduced. One of suchmethods has been proposed byMoret et al. (2004). They defined a phylogenetic network as a directed acyclic graph obtained by positing a set of edges between pairs of the branches of an underlying tree to model reticulation events. Recently, two works by Jin et al. (2006), and Snir and Tuller (2009), respectively, using this definition of phylogenetic network, have appeared. Both works demonstrate the potential of using maximum likelihood estimation for phylogenetic network reconstruction. We propose a Bayesian approach to the estimation of phylogenetic network parameters. We allow for different phylogenies to be inferred at different parts of our DNA alignment in the presence of reticulation events, at the species level, by using the idea that a phylogenetic network can be naturally decomposed into trees. A Markov chainMonte Carlo algorithmis provided for posterior computation of the phylogenetic network parameters. Also a more general algorithm is proposed which allows the data to dictate how many phylogenies are required to explain the data. This can be achieved by using stochastic search variable selection. Both algorithms are tested on simulated data and also demonstrated on the ribosomal protein gene rps11 data from five flowering plants. The proposed approach can be applied to a wide variety of problems which aim at exploring the possibility of reticulation events in the history of a set of taxa.
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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.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 dynamic programming approach that reduces the computational complexity from exponential to linear in the number of taxa. However, with the advent of efficient modern sequencing techniques the size of data sets are rapidly increasing beyond current computational capability. Parallel computing has been used successfully to address many similar problems and is currently receiving attention in the realm of phylogenetic analysis. Work has been done using data decomposition, where the likelihood calculation is parallelised over DNA sequence sites. We propose an alternative way of parallelising the likelihood calculation, which we call segmentation, where the tree is broken down into subtrees and the likelihood of each subtree is calculated concurrently over multiple processes. We introduce our proposed system, which aims to drastically increase the size of trees that can be practically used in phylogenetic analysis. Then, we evaluate the system on large phylogenies which are constructed from both real and synthetic data, to show that a larger decrease of run times are obtained when the system is used.
AFRIKAANSE OPSOMMING:Filogenetiese analise is die studie van evolusionêre verwantskappe tussen organismes. Filogenetiese of evolusionêre bome word aangewend om die evolusionêre verwantskappe, soos herwin vanuit DNS-kettings data, tussen organismes uit te beeld. Die aanneemlikheid van ’n gegewe filogenie word oor die algemeen bereken en aangewend vir menigte doeleindes, insluitende die afleiding van filogenetiese bome, om te monster vanuit ’n versameling van sulke moontlike bome en vir die afleiding van ander belangrike parameters in die evolusionêre proses. Dit word vermag met behulp van Felsenstein se algoritme, ’n alombekende benaderingwyse wat gebruik maak van dinamiese programmering om die berekeningskompleksiteit van eksponensieel na lineêr in die aantal taxa, te herlei. Desnieteenstaande, het die koms van moderne, doeltreffender orderingsmetodes groter datastelle tot gevolg wat vinnig besig is om bestaande berekeningsvermoë te oorskry. Parallelle berekeningsmetodes is reeds suksesvol toegepas om vele soortgelyke probleme op te los, met groot belangstelling tans in die sfeer van filogenetiese analise. Werk is al gedoen wat gebruik maak van data dekomposisie, waar die aanneemlikheidsberekening oor die DNS basisse geparallelliseer word. Ons stel ’n alternatiewe metode voor, wat ons segmentasie noem, om die aanneemlikheidsberekening te parallelliseer, deur die filogenetiese boom op te breek in sub-bome, en die aanneemlikheid van elke sub-boom gelyklopend te bereken oor verskeie verwerkingseenhede. Ons stel ’n stelsel voor wat dit ten doel het om ’n drastiese toename in die grootte van die bome wat gebruik kan word in filogenetiese analise, teweeg te bring. Dan, word ons voorgestelde stelsel op groot filogenetiese bome, wat vanaf werklike en sintetiese data gekonstrueer is, evalueer. Dit toon aan dat ’n groter afname in looptyd verkry word wanneer die stelsel in gebruik is.
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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 previously unsequenced genera (2) and species (61). I then use this phylogeny to test hypotheses regarding heterogeneity in diversification rates and how this shaped overall patterns of snake diversity in Chapter 2. I also used the species-level phylogeny to test the evolution of habitat use in snakes, morphological variation, and whether distantly-related species exhibit morphological convergence in Chapter 3. Finally, in Chapter 4 I investigate how prehensile tails effect striking performance in arboreal snakes.
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Bhattacharya, Deblina Patra, Sebastian Canzler, Stephanie Kehr, Jana Hertel, Ivo Grosse i 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 in much detail. In plants, however, their evolution has attracted comparably little attention. Results: In order to chart the phylogenetic distribution of individual snoRNA families in plants, we applied a sophisticated approach for identifying homologs of known plant snoRNAs across the plant kingdom. In response to the relatively fast evolution of snoRNAs, information on conserved sequence boxes, target sequences, and secondary structure is combined to identify additional snoRNAs. We identified 296 families of snoRNAs in 24 species and traced their evolution throughout the plant kingdom. Many of the plant snoRNA families comprise paralogs. We also found that targets are well-conserved for most snoRNA families. Conclusions: The sequence conservation of snoRNAs is sufficient to establish homologies between phyla. The degree of this conservation tapers off, however, between land plants and algae. Plant snoRNAs are frequently organized in highly conserved spatial clusters. As a resource for further investigations we provide carefully curated and annotated alignments for each snoRNA family under investigation.
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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 TecnolÃgicoPhylogenetic 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, and biological classication are important to the understanding of phylogenies. Phylogenetic information may provide important knowledge to biological research work, such as, organ transplantation from animals, and drug toxicologic tests performed in other species as a precise prediction to its application in human beings. To solve a phylogeny problem implies that a phylogenetic tree must be built from known data about a group of species, according to an optimization criterion. The approach to this problem involves two main steps: the rst refers to the discovery of perfect phylogenies, in the second step, information extracted from perfect phylogenies are used to infer more general ones. The techniques that are used in the second step take advantage of evolutionary hypothesis. The problem becomes NP-hard for a number of interesting hypothesis, what justify the use of inference methods based on heuristics, metaheuristics, and approximative algorithms. The description of an innovative technique based on local search with multiple start over a diversied neighborhood summarizes our contribution to solve the problem. Moreover, we used parallel programming in order to speed up the intensication stage of the search for the optimal solution. More precisely, we developed an efcient algorithm to obtain approximate solutions for a phylogeny problem which infers an optimal phylogenetic tree from characteristics matrices of various species. The designed data structures and the binary data manipulation in some routines accelerate simulation and illustration of the experimentation tests. Well known instances have been used to compare the proposed algorithm results with those previously published. We hope that this work may arise researchers' interest to the topic and contribute to the Bioinformatics area.
Ãrvores filogenÃticas sÃo estruturas que expressam a similaridade, ancestralidade e relacionamentos entre as espÃcies ou grupo de espÃcies. Conhecidas como Ãrvores evolucionÃrias ou simplesmente filogenias, as Ãrvores filogenÃticas possuem folhas que representam as espÃcies (tÃxons) e nÃs internos que correspondem aos seus ancestrais hipotÃticos. Neste trabalho, alÃm das informaÃÃes necessÃrias para o entendimento de toda a sistemÃtica filogenÃtica, sÃo apresentadas tÃcnicas algorÃtmicas para construÃÃo destas Ãrvores. Os conceitos bÃsicos de biologia molecular, evoluÃÃo da vida e classificaÃÃo biolÃgica, aqui descritos, permitem compreender o que à uma Filogenia e qual sua importÃncia para a Biologia. As informaÃÃes filogenÃticas fornecem,por exemplo, subsÃdios importantes para decisÃes relativas aos transplantes de ÃrgÃos ou tecidos de outras espÃcies para o homem e para que testes de reaÃÃo imunolÃgica ou de toxicidade sejam feitos antes em outros sistemas biolÃgicos similares ao ser humano. Resolver um Problema de Filogenia corresponde à construÃÃo de uma Ãrvore filogenÃtica a partir de dados conhecidos sobre as espÃcies em estudo, obedecendo a algum critÃrio de otimizaÃÃo. A abordagem dada a esse problema envolve duas etapas, a primeira, referente aos casos em que as filogenias sÃo perfeitas cujos procedimentos desenvolvidos serÃo utilizados na segunda etapa, quando deve ser criada uma tÃcnica de inferÃncia para a filogenia num caso geral. Essas tÃcnicas consideram de forma peculiar as hipÃteses sobre o processo de evoluÃÃo. Para muitas hipÃteses de interesse o problema se torna NP-DifÃcil, justificando-se o uso de mÃtodos de inferÃncia atravÃs de heurÃsticas, meta-heurÃsticas e algoritmos aproximativos. Nossa contribuiÃÃo neste trabalho consiste em apresentar uma tÃcnica de resoluÃÃo desse problema baseada em buscas locais com partidas mÃltiplas em vizinhanÃas diversificadas. Foi utilizada a programaÃÃo paralela para minimizar o tempo de execuÃÃo no processo de intensificaÃÃo da busca pela soluÃÃo Ãtima do problema. Desta forma, desenvolvemos um algoritmo para obter soluÃÃes aproximadas para um Problema da Filogenia, no caso, para inferir, a partir de matrizes de caracterÃsticas de vÃrias espÃcies, uma Ãrvore filogenÃtica que mais se aproxima da histÃria de sua evoluÃÃo. Uma estrutura de dados escolhida adequadamente aliada à manipulaÃÃo de dados em binÃrio em algumas rotinas facilitaram a simulaÃÃo e ilustraÃÃo dos testes realizados. InstÃncias com resultados conhecidos na literatura foram utilizadas para comprovar a performance do algoritmo. Esperamos com este trabalho despertar o interesse dos pesquisadores da Ãrea de ComputaÃÃo, consolidando, assim, o crescimento da BioinformÃtica.
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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 alignment. We focus on the reconstruction of the topology of phylogenetic trees, which means reconstructing the shape of the tree considering labels at the leaves.To this end, one usually assumes that DNA sequences evolve according to a Markov process ruled by a prescribed model of nucleotide substitutions. These substitution models specify some transition matrices at the edges of the tree and a distribution of nucleotides at the root. Given a tree T and a substitution model, one can compute the distribution of nucleotide patterns at the leaves of T in terms of the model parameters. This joint distribution is represented by a vector whose entries can be expressed as polynomials on the model parameters and satisfy certain algebraic relationships. The study of these relationships and the geometry of the algebraic varieties defined by them (called phylogenetic varieties) have provided successful insight into the problem of phylogenetic reconstruction. However, from a biological perspective we are not interested in the whole variety, but only in the region of points that arise from stochastic parameters (the so-called phylogenetic stochastic region). The description of these regions leads to semi-algebraic constraints which play an important role since they characterize distributions with biological and probabilistic meaning. One of the main motivations for this thesis follows from the following question. Could the use of semi-algebraic tools improve the already existent algebraic tools for phylogenetic reconstruction?To answer this question, we compute the Euclidean distance of data points arising from an alignment of nucleotide to the phylogenetic varieties and their stochastic regions in a some scenarios of special interest in phylogenetics, such as trees with short external branches and/or subject to the long branch attraction phenomenon. In some cases, we compute these distances analytically and we can decide which tree has stochastic region closer to the data point. As a consequence, we can prove that, even if the data point was close to the phylogenetic variety of a given tree, it might be closer to the stochastic region of another tree. In particular, considering the stochastic phylogenetic region seems to be fundamental to cope with the phylogenetic reconstruction problem when dealing with the long branch attraction phenomenon.However, incorporating semi-algebraic tools into phylogenetic reconstruction methods can be extremely difficult and the procedure to do it is not evident at all. In this thesis, we present two phylogenetic reconstruction methods that combine algebraic and semi-algebraic conditions for the general Markov model. The first method we present is SAQ, which stands for Semi-Algebraic Quartet reconstruction method. Next, we introduce a more versatile method, ASAQ (for Algebraic and Semi-Algebraic Quartet reconstruction method}), which combines SAQ with the method Erik+2 (based on certain algebraic constraints). Both are phylogenetic reconstruction methods for DNA alignments on four taxa which have been proven to be statistically consistent.We test the suggested methods on simulated and real data to check their actual performance in several scenarios. Our simulation studies show that both methods SAQ and ASAQ are highly successful, even when applied to short alignments or data that violates their assumptions.La filogenètica és l'estudi de la història evolutiva entre grups d'entitats biològiques (anomenades tàxons). Aquests processos evolutius estan modelitzats per arbres filogenètics els nodes dels quals representen diferents tàxons i les branques corresponen als processos evolutius entre ells. Les fulles normalment representen tàxons actuals i l'arrel és el seu avantpassat comú. Actualment, la reconstrucció filogenètica pretén estimar l'arbre filogenètic que millor explica les relacions evolutives de tàxons actuals utilitzant únicament informació del seu genoma organitzada en un alineament. En aquesta tesi ens centrem en la reconstrucció de la topologia dels arbres filogenètics, és a dir, reconstruir la forma de l'arbre tenint en compte els noms associats a les fulles. Amb aquesta finalitat, assumim que les seqüències d'ADN evolucionen segons un procés de Markov d'acord amb un model de substitució de nucleòtids. Aquests models de substitució assignem matrius de transició a les arestes d’un arbre i una distribució de nucleòtids a l'arrel. Donat un arbre i un model, es pot calcular la distribució de les possibles observacions de nucleòtids a les fulles en termes dels paràmetres del model. Aquesta distribució conjunta s’expressa en forma de vector, les entrades del qual es poden escriure com polinomis en funció dels paràmetres del model i satisfan certes relacions algebraiques. L'estudi d'aquestes relacions i de la geometria de les varietats algebraiques que defineixen (anomenades varietats filogenètiques) han servit per entendre millor el problema de la reconstrucció filogenètica. No obstant això, des d'una perspectiva biològica no estem interessats en tota la varietat, sinó només en la regió de punts que resulten de paràmetres estocàstics (l'anomenada regió estocàstica). La descripció d'aquestes regions condueix a restriccions semi-algebraiques que tenen un paper important ja que caracteritzen les distribucions amb significat biològic. Una de les principals motivacions d'aquesta tesi és la següent: Podria l'ús d'eines semi-algebraiques millorar les eines algebraiques ja existents per a la reconstrucció filogenètica? Per poder respondre, calculem la distància euclidiana entre punts de dades obtinguts a partir d’un alineament i varietats filogenètiques i les seves regions estocàstiques en escenaris d'especial interès en la filogenètica. En alguns casos, podem calcular aquestes distàncies de forma analítica i això ens permet demostrar que, fins i tot si un punt de dades fos proper a la varietat filogenètica d'un arbre donat, podria estar més a prop de la regió estocàstica d'un altre arbre. En particular, considerar la regió estocàstica sembla ser fonamental per fer front al problema de la reconstrucció filogenètica quan tractem amb del fenomen d'atracció de branques llargues. Tot i això, incorporar d'eines semi-algebraiques en els mètodes de reconstrucció filogenètica pot ser extremadament difícil i el procediment per fer-ho no és gens evident. En aquesta tesi, presentem dos mètodes de reconstrucció filogenètica que combinen condicions algebraiques i semi-algebraiques per al model general de Markov. El primer mètode que presentem és el SAQ, que rep el nom de Semi-Algebraic Quartet reconstruction method. A continuació, introduïm un mètode més versàtil, l'ASAQ (Algebraic and Semi-Algebraic Quartet reconstruction method), que combina el SAQ amb el mètode Erik+2 (basat en certes restriccions algebraiques). Tots dos són mètodes de reconstrucció filogenètica per a alineaments d'ADN per quatre tàxons i hem demostrat que tots dos són estadísticament consistents. Finalment, testem els mètodes proposats amb dades simulades i dades reals per comprovar el seu rendiment en diversos escenaris. Les nostres simulacions mostren que ambdós mètodes SAQ i ASAQ obtenen
Matemàtica aplicada
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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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