Relevant bibliographies by topics / Phylogeny

Academic literature on the topic 'Phylogeny'

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Published: 4 June 2021
Last updated: 29 July 2024

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Journal articles on the topic "Phylogeny"

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McKinney, Michael L. "Extinction in Phylogeny, or Phylogeny in Extinction?" Ecology 74, no. 6 (September 1993): 1906–7. http://dx.doi.org/10.2307/1939951.

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SMITH, A. B. "Fossils in Phylogeny: Phylogeny Reconstruction in Paleontology." Science 235, no. 4789 (February 6, 1987): 696. http://dx.doi.org/10.1126/science.235.4789.696.

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SAARMA, U., I. JÕGISALU, E. MOKS, A. VARCASIA, A. LAVIKAINEN, A. OKSANEN, S. SIMSEK, et al. "A novel phylogeny for the genus Echinococcus, based on nuclear data, challenges relationships based on mitochondrial evidence." Parasitology 136, no. 3 (January 21, 2009): 317–28. http://dx.doi.org/10.1017/s0031182008005453.

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SUMMARYThe taxonomic status of Echinococcus, an important zoonotic cestode genus, has remained controversial, despite numerous attempts to revise it. Although mitochondrial DNA (mtDNA) has been the source of markers of choice for reconstructing the phylogeny of the genus, results derived from mtDNA have led to significant inconsistencies with earlier species classifications based on phenotypic analysis. Here, we used nuclear DNA markers to test the phylogenic relationships of members of the genus Echinococcus. The analysis of sequence data for 5 nuclear genes revealed a significantly different phylogeny for Echinococcus from that proposed on the basis of mitochondrial DNA sequence data, but was in agreement with earlier species classifications. The most notable results from the nuclear phylogeny were (1) E. multilocularis was placed as basal taxon, (2) all genotypes of Echinococcus granulosus grouped as a monophyletic entity, and (3) genotypes G8 and G10 clustered together. We conclude that the analysis of nuclear DNA data provides a more reliable means of inferring phylogenetic relationships within Echinococcus than mtDNA and suggest that mtDNA should not be used as the sole source of markers in future studies where the goal is to reconstruct a phylogeny that does not only reflect a maternal lineage, but aims to describe the evolutionary history at species level or higher.
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Hubu, Herlin S., Stenly Wullur, Veibe Warouw, Elvy L. Ginting, Robert A. Bara, and Adnan S. Wantasen. "FILOGENI MOLEKULER BAKTERI DARI MEDIA PEMELIHARAAN ROTIFER YANG DIBERI OLAHAN LIMBAH IKAN SEBAGAI SUMBER NUTRISI." JURNAL PESISIR DAN LAUT TROPIS 9, no. 1 (March 29, 2021): 38. http://dx.doi.org/10.35800/jplt.9.1.2021.33574.

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This study aims to identify and construct molecular phylogeny of an isolate bacteria from culture media of rotifer Brachionus rotudiforis supplied with processed fishery waste feed as nutritional source. The use of fish waste-based food for rotifer showed positive effects on growth and nutrient content of the rotifers. Genomic DNA of the isolate bacteria BRLI- 01 was extracted and the 16S rRNA gene was amplified using primers (8F and 1492F) and further sequenced using Sanger sequence technique. The 16S rRNA gene was analysed using SeqScanner® and MEGA® followed with BLAST (Basic Local Alignment Search Tool) analyses in the NCBI (National Centre for Biotechnology Information). Amplification result of 16S rRNA gene bacteria s NCBI site as a reference for identification and phylogeny of bacterial species. BRLI-01 was successfully cultured on rotifer rearing media. The results of the 16S rRNA gene amplification of the isolate bacteria showed a DNA band with a length of 1400 bp. The BLAST result on the NCBI showed that the isolate bacteria BRLI-01 had a percent identity (98.46%) and is in the same phylogony branching position with Vibrio rotiferianus Keywords: Rotifers, Bacteria, Fish waste, 16S rRNA Genes, Phylogeny identification
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López, J. Andrés, Wei-Jen Chen, and Guillermo Ortí. "Esociform Phylogeny." Copeia 2004, no. 3 (August 2004): 449–64. http://dx.doi.org/10.1643/cg-03-087r1.

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Burgess, George H., and Shigeru Shirai. "Squalean Phylogeny." Copeia 1993, no. 4 (December 28, 1993): 1203. http://dx.doi.org/10.2307/1447121.

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Rougler, Guillermo W., John R. Wible, and Michael J. Novacek. "Multituberculate phylogeny." Nature 379, no. 6564 (February 1996): 406. http://dx.doi.org/10.1038/379406a0.

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Sereno, Paul C., and Malcolm C. McKenna. "Multituberculate phylogeny." Nature 379, no. 6564 (February 1996): 406–7. http://dx.doi.org/10.1038/379406b0.

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Meng, Jin, and Andre R. Wyss. "Multituberculate phylogeny." Nature 379, no. 6564 (February 1996): 407. http://dx.doi.org/10.1038/379407a0.

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Telles, Guilherme P., Nalvo F. Almeida, Rosane Minghim, and Maria Emilia M. T. Walter. "Live Phylogeny." Journal of Computational Biology 20, no. 1 (January 2013): 30–37. http://dx.doi.org/10.1089/cmb.2012.0219.

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Dissertations / Theses on the topic "Phylogeny"

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Bernt, Matthias. "Gene order rearrangement methods for the reconstruction of phylogeny." Doctoral thesis, Universitätsbibliothek Leipzig, 2010. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-38666.

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The study of phylogeny, i.e. the evolutionary history of species, is a central problem in biology and a key for understanding characteristics of contemporary species. Many problems in this area can be formulated as combinatorial optimisation problems which makes it particularly interesting for computer scientists. The reconstruction of the phylogeny of species can be based on various kinds of data, e.g. morphological properties or characteristics of the genetic information of the species. Maximum parsimony is a popular and widely used method for phylogenetic reconstruction aiming for an explanation of the observed data requiring the least evolutionary changes. A certain property of the genetic information gained much interest for the reconstruction of phylogeny in recent time: the organisation of the genomes of species, i.e. the arrangement of the genes on the chromosomes. But the idea to reconstruct phylogenetic information from gene arrangements has a long history. In Dobzhansky and Sturtevant (1938) it was already pointed out that “a comparison of the different gene arrangements in the same chromosome may, in certain cases, throw light on the historical relationships of these structures, and consequently on the history of the species as a whole”. This kind of data is promising for the study of deep evolutionary relationships because gene arrangements are believed to evolve slowly (Rokas and Holland, 2000). This seems to be the case especially for mitochondrial genomes which are available for a wide range of species (Boore, 1999). The development of methods for the reconstruction of phylogeny from gene arrangement data has made considerable progress during the last years. Prominent examples are the computation of parsimonious evolutionary scenarios, i.e. a shortest sequence of rearrangements transforming one arrangement of genes into another or the length of such a minimal scenario (Hannenhalli and Pevzner, 1995b; Sankoff, 1992; Watterson et al., 1982); the reconstruction of parsimonious phylogenetic trees from gene arrangement data (Bader et al., 2008; Bernt et al., 2007b; Bourque and Pevzner, 2002; Moret et al., 2002a); or the computation of the similarities of gene arrangements (Bergeron et al., 2008a; Heber et al., 2009). 1 1 Introduction The central theme of this work is to provide efficient algorithms for modified versions of fundamental genome rearrangement problems using more plausible rearrangement models. Two types of modified rearrangement models are explored. The first type is to restrict the set of allowed rearrangements as follows. It can be observed that certain groups of genes are preserved during evolution. This may be caused by functional constraints which prevented the destruction (Lathe et al., 2000; Sémon and Duret, 2006; Xie et al., 2003), certain properties of the rearrangements which shaped the gene orders (Eisen et al., 2000; Sankoff, 2002; Tillier and Collins, 2000), or just because no destructive rearrangement happened since the speciation of the gene orders. It can be assumed that gene groups, found in all studied gene orders, are not acquired independently. Accordingly, these gene groups should be preserved in plausible reconstructions of the course of evolution, in particular the gene groups should be present in the reconstructed putative ancestral gene orders. This can be achieved by restricting the set of rearrangements, which are allowed for the reconstruction, to those which preserve the gene groups of the given gene orders. Since it is difficult to determine functionally what a gene group is, it has been proposed to consider common combinatorial structures of the gene orders as gene groups (Marcotte et al., 1999; Overbeek et al., 1999). The second considered modification of the rearrangement model is extending the set of allowed rearrangement types. Different types of rearrangement operations have shuffled the gene orders during evolution. It should be attempted to use the same set of rearrangement operations for the reconstruction otherwise distorted or even wrong phylogenetic conclusions may be obtained in the worst case. Both possibilities have been considered for certain rearrangement problems before. Restricted sets of allowed rearrangements have been used successfully for the computation of parsimonious rearrangement scenarios consisting of inversions only where the gene groups are identified as common intervals (Bérard et al., 2007; Figeac and Varré, 2004). Extending the set of allowed rearrangement operations is a delicate task. On the one hand it is unknown which rearrangements have to be regarded because this is part of the phylogeny to be discovered. On the other hand, efficient exact rearrangement methods including several operations are still rare, in particular when transpositions should be included. For example, the problem to compute shortest rearrangement scenarios including transpositions is still of unknown computational complexity. Currently, only efficient approximation algorithms are known (e.g. Bader and Ohlebusch, 2007; Elias and Hartman, 2006). Two problems have been studied with respect to one or even both of these possibilities in the scope of this work. The first one is the inversion median problem. Given the gene orders of some taxa, this problem asks for potential ancestral gene orders such that the corresponding inversion scenario is parsimonious, i.e. has a minimum length. Solving this problem is an essential component 2 of algorithms for computing phylogenetic trees from gene arrangements (Bourque and Pevzner, 2002; Moret et al., 2002a, 2001). The unconstrained inversion median problem is NP-hard (Caprara, 2003). In Chapter 3 the inversion median problem is studied under the additional constraint to preserve gene groups of the input gene orders. Common intervals, i.e. sets of genes that appear consecutively in the gene orders, are used for modelling gene groups. The problem of finding such ancestral gene orders is called the preserving inversion median problem. Already the problem of finding a shortest inversion scenario for two gene orders is NP-hard (Figeac and Varré, 2004). Mitochondrial gene orders are a rich source for phylogenetic investigations because they are known for more than 1 000 species. Four rearrangement operations are reported at least in the literature to be relevant for the study of mitochondrial gene order evolution (Boore, 1999): That is inversions, transpositions, inverse transpositions, and tandem duplication random loss (TDRL). Efficient methods for a plausible reconstruction of genome rearrangements for mitochondrial gene orders using all four operations are presented in Chapter 4. An important rearrangement operation, in particular for the study of mitochondrial gene orders, is the tandem duplication random loss operation (e.g. Boore, 2000; Mauro et al., 2006). This rearrangement duplicates a part of a gene order followed by the random loss of one of the redundant copies of each gene. The gene order is rearranged depending on which copy is lost. This rearrangement should be regarded for reconstructing phylogeny from gene order data. But the properties of this rearrangement operation have rarely been studied (Bouvel and Rossin, 2009; Chaudhuri et al., 2006). The combinatorial properties of the TDRL operation are studied in Chapter 5. The enumeration and counting of sorting TDRLs, that is TDRL operations reducing the distance, is studied in particular. Closed formulas for computing the number of sorting TDRLs and methods for the enumeration are presented. Furthermore, TDRLs are one of the operations considered in Chapter 4. An interesting property of this rearrangement, distinguishing it from other rearrangements, is its asymmetry. That is the effects of a single TDRL can (in the most cases) not be reversed with a single TDRL. The use of this property for phylogeny reconstruction is studied in Section 4.3. This thesis is structured as follows. The existing approaches obeying similar types of modified rearrangement models as well as important concepts and computational methods to related problems are reviewed in Chapter 2. The combinatorial structures of gene orders that have been proposed for identifying gene groups, in particular common intervals, as well as the computational approaches for their computation are reviewed in Section 2.2. Approaches for computing parsimonious pairwise rearrangement scenarios are outlined in Section 2.3. Methods for the computation genome rearrangement scenarios obeying biologically motivated constraints, as introduced above, are detailed in Section 2.4. The approaches for the inversion median problem are covered in Section 2.5. Methods for the reconstruction of phylogenetic trees from gene arrangement data are briefly outlined in Section 2.6.3 1 Introduction Chapter 3 introduces the new algorithms CIP, ECIP, and TCIP for solving the preserving inversion median problem. The efficiency of the algorithm is empirically studied for simulated as well as mitochondrial data. The description of algorithms CIP and ECIP is based on Bernt et al. (2006b). TCIP has been described in Bernt et al. (2007a, 2008b). But the theoretical foundation of TCIP is extended significantly within this work in order to allow for more than three input permutations. Gene order rearrangement methods that have been developed for the reconstruction of the phylogeny of mitochondrial gene orders are presented in the fourth chapter. The presented algorithm CREx computes rearrangement scenarios for pairs of gene orders. CREx regards the four types of rearrangement operations which are important for mitochondrial gene orders. Based on CREx the algorithm TreeREx for assigning rearrangement events to a given tree is developed. The quality of the CREx reconstructions is analysed in a large empirical study for simulated gene orders. The results of TreeREx are analysed for several mitochondrial data sets. Algorithms CREx and TreeREx have been published in Bernt et al. (2008a, 2007c). The analysis of the mitochondrial gene orders of Echinodermata was included in Perseke et al. (2008). Additionally, a new and simple method is presented to explore the potential of the CREx method. The new method is applied to the complete mitochondrial data set. The problem of enumerating and counting sorting TDRLs is studied in Chapter 5. The theoretical results are covered to a large extent by Bernt et al. (2009b). The missing combinatorial explanation for some of the presented formulas is given here for the first time. Therefor, a new method for the enumeration and counting of sorting TDRLs has been developed (Bernt et al., 2009a).
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Varón, González Ceferino. "Shape and phylogeny." Thesis, University of Manchester, 2014. https://www.research.manchester.ac.uk/portal/en/theses/shape-and-phylogeny(f432d494-9755-41f9-b067-431023ad3248).html.

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Geometric morphometrics, the science about the study of shape, has developed much in the last twenty years. In this thesis I first study the reliability of the phylogenies built using geometric morphometrics. The effect of different evolutionary models, branch-length combinations, dimensionality and degrees of integration is explored using computer simulations. Unfortunately in the most common situations (presence of stabilizing selection, short distance between internal nodes and presence of integration) the reliability of the phylogenies is very low. Different empirical studies are analysed to estimate the degree of evolutionary integration usually found in nature. This gives an idea about how powerful the effect of integration is over the reliability of the phylogenies in empirical studies. Evolutionary integration is studied looking at the decrease of variance in the principal components of the tangent shape space using the independent contrasts of shape. The results suggest that empirical data usually show strong degrees of integration in most of the organisms and structures analysed. These are bad news, since strong degree of integration has devastating effects over the phylogenetic reliability, as suggested by our simulations. However, we also propose the existence of other theoretical situations in which strong integration may not translate into convergence between species, like perpendicular orientation of the integration patterns or big total variance relative to the distance between species in the shape space. Finally, geometric morphometrics is applied to the study of the evolution of shape in proteins. There are reasons to think that, because of their modular nature and huge dimensionality, proteins may show different patterns of evolutionary integration. Unfortunately, proteins also show strong functional demands, which influence their evolution and that cause strong integration patterns. Integration is then confirmed as a widespread property in the evolution of shape, which causes poor phylogenetic estimates.
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Poe, Stephen Joseph. "Phylogeny of anoles /." Full text (PDF) from UMI/Dissertation Abstracts International, 2000. http://wwwlib.umi.com/cr/utexas/fullcit?p3004359.

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Jacobson, Herbert R. "Generic revision, phylogenic classification, and phylogeny of the termitophilous tribe corotocini(Coleoptera; staphylinidae)." Doctoral thesis, Universite Libre de Bruxelles, 1985. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/213647.

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Garcia, Marcelo. "A mitochondrial metazoan phylogeny." Laboratório Nacional de Computação Científica, 2007. http://www.lncc.br/tdmc/tde_busca/arquivo.php?codArquivo=136.

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Discernir as relações evolutivas entre os grandes grupos animais tem representado um formidável desafio para a Ciência. Os filos animais possuem arquiteturas corporais bastante distintas e por isso difíceis de serem comparadas. Ao mesmo tempo, seu registro fóssil converge aproximadamente para um mesmo intervalo na escala geológica, dificultando uma reconstrução filogenética com caracteres morfológicos. A disponibilidade de dados moleculares sobre os organismos abriu, contudo, novas possibilidades na filogenia animal. Esta dissertação buscou explorar essas possibilidades inferindo uma filogenia com métodos de distância e máxima verossimilhança, a partir de todos os genomas mitocondriais, completamente seqüenciados até o momento. No entanto, apenas alguns grandes agrupamentos como Diploblastica, Bilateria, Deuterostomia e Protostomia foram recuperados com forte suporte estatístico, além de pequenos agrupamentos de animais de mesma ordem ou família, indicando que os efeitos da rápida radiação no Cambriano se estenderam também ao registro molecular. Os resultados também indicam a necessidade de buscar modelos de evolução mais aderentes a este cenário. Deuterostomia, por exemplo, só foi recuperado monofileticamente assumindo-se a distribuição gama para variabilidade entre-sítios, ao custo, entretanto, da perda de definição nos ramos menores. Nematóides e Platelmintos, por sua vez, revelam um possível viés no skew (desvio) do conteúdo GC e AT de seus genes mitocondriais, que não é adequadamente mapeado por modelos de substituição reversíveis. Os indícios são de que a resolução da filogenia animal depende ainda de uma melhor compreensão da evolução molecular em escala genômica.
Inferring the evolutive relations between the animal phyla has been a formidable challenge to Science. The animal phyla represent quite distinct baupläne (body architectures) and are, therefore, difficult to compare. At the same time, their fossil record converges mostly to the same period on the geological scale. The recent availability of molecular data has, however, inaugurated a new front in animal phylogeny. The present work explores this opportunity by inferring a phylogeny with distance and maximum likelihood methods, employing all animal mitochondrial genomes ever sequenced. The results present only a few bigger groups with strong statistical support, like Diploblastica, Bilasteria, Protostomia and Deutorostomia, and many smaller groups of animals belonging to the same order or family. These results seems to confirm that the phyla radiated in such a short time interval that the phylogenetic signal did not hold out to produce a satisfactory resolution of the animal tree to date. Some limits may have yet to be tested, through models of evolution more fit to this scenario. For example was only recovered with the use of gamma distances for site-to-site substitution rate variability, at the expense of compressing the smaller branches throughout the tree. Nematodes and Platyhelminthes reveal a bias in GC and AT skew that cannot be adequately mapped by any reversible substitution pattern. Nevertheless, even if corrections are found for these issues, it is well possible that the hope of a better resolution in the animal tree will lie further on, by a better understanding of the evolutive process in a genomic scale.
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Boussau, Bastien. "Early evolution and phylogeny." Lyon 1, 2008. http://tel.archives-ouvertes.fr/docs/00/34/57/43/PDF/These_03122008.pdf.

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Durant cette thèse je me suis intéressé à l'évolution profonde du vivant, depuis le dernier ancêtre commun universel (LUCA) jusqu'aux ancêtres des trois grands royaumes, les Archées, les Bactéries et les Eucaryotes. J'ai notamment cherché à placer quelques organismes dans l'arbre de la vie, tels que la bactérie Aquifex aeolicus et l'archée Cenarchaeum symbiosum, et j'ai également étudié l'évolution des températures de croissance il y a plusieurs milliards d'années. Pour ce faire, j'ai développé des algorithmes a n de reconstruire l'évolution de séquences géniques, puis j'ai utilisé ces séquences pour prédire les températures optimales de croissances d'organismes aujourd'hui éteints. Mes collègues et moi-même estimons que LUCA ne vivait pas à très haute température, mais que ses directs descendants les ancêtres des Bactéries et du groupe comprenant les Archées et les Eucaryotes vivaient dans des environnements plus chauds. Cela signi e que les deux lignées venant de LUCA ont subi le même type d'évolution en parallèle, qui pourrait avoir été causée par une seule et même pression de sélection. Cette pression pourrait être le résultat d'un intense bombardement météoritique il y a 3. 8 milliards d'années, et avoir été accompagnée d'un changement depuis un génome à ARN pour LUCA vers des génomes à ADN pour ses descendants. Ensuite, dans la lignée des Bactéries, les températures optimales de croissance ont chuté, ce qui pourrait correspondre à l'évolution de la température des océans au cours des 3. 5 derniers milliards d'années
During this thesis, I studied the early evolution of life, from the Last Universal Common Ancestor (LUCA) to the ancestors of the three kingdoms, Archaea, Bacteria and Eukarya. Notably, I have attempted to place a few organisms in the tree of life, namely the bacteria Aquifex aeolicus and the archaea Cenarchaeum symbiosum, and I also studied the evolution of optimal growth temperatures over the last four billion years. To this end, I developed algorithms to reconstruct ancestral gene sequences, and used these sequences to predict the optimal growth temperatures of now-extinct organisms. My colleagues and I estimate that LUCA did not live in a very hot environment, but that its descendants the ancestors of Bacteria and of the group containing Archaea and Eukarya both lived at higher temperatures. This implies that the two lineages descending from LUCA underwent the same kind of evolution in parallel, perhaps caused by the same unique selection pressure. This pressure may have resulted from an intense meteoritic bombardment 3. 8 billion years ago, and have been accompanied by the transition from an RNA genome in LUCA to DNA genomes in its descendants. Subsequently in the bacterial lineage, optimal growth temperature dropped, which may correspond to the evolution of oceanic temperatures in the last 3. 5 billion years
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Ranghoo, Vijayanti Mala. "Phylogeny of freshwater ascomycetes." Thesis, Hong Kong : University of Hong Kong, 1998. http://sunzi.lib.hku.hk/hkuto/record.jsp?B20793042.

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Kolaczkowski, Bryan. "Deconstructing phylogenetic reconstruction : effects of assumption violations on evolutionary inference /." view abstract or download file of text, 2006. http://proquest.umi.com/pqdweb?did=1280150641&sid=1&Fmt=2&clientId=11238&RQT=309&VName=PQD.

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Thesis (Ph. D.)--University of Oregon, 2006.
Typescript. Includes vita and abstract. Includes bibliographical references (leaves 137-144). Also available for download via the World Wide Web; free to University of Oregon users.
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Schulze, Anja. "Phylogeny of vestimentiferan tube worms." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape2/PQDD_0009/NQ52771.pdf.

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Jones, Martin. "Multigene datasets for deep phylogeny." Thesis, University of Edinburgh, 2007. http://hdl.handle.net/1842/2575.

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Though molecular phylogenetics has been very successful in reconstructing the evolutionary history of species, some phylogenies, particularly those involving ancient events, have proven difficult to resolve. One approach to improving the resolution of deep phylogenies is to increase the amount of data by including multiple genes assembled from public sequence databases. Using modern phylogenetic methods and abundant computing power, the vast amount of sequence data available in public databases can be brought to bear on difficult phylogenetic problems. In this thesis I outline the motivation for assembling large multigene datasets and lay out the obstacles associated with doing so. I discuss the various methods by which these obstacles can be overcome and describe a bioinformatics solution, TaxMan, that can be used to rapidly assemble very large datasets of aligned genes in a largely automated fashion. I also explain the design and features of TaxMan from a biological standpoint and present the results of benchmarking studies. I illustrate the use of TaxMan to assemble large multigene datasets for two groups of taxa – the subphylum Chelicerata and the superphylum Lophotrochozoa. Chelicerata is a diverse group of arthropods with an uncertain phylogeny. When a set of mitochondrial genes is used to analyse the relationships between the chelicerate orders, the conclusions are highly dependent upon the evolutionary model used and are affected by the presence of systematic compsitional bias in mitochondrial genomes. Lophotrochozoa is a recently-proposed group of protostome phyla. A number of distinct phylogenetic hypotheses concerning the relationships between lophotrochozoan phyla have been proposed. I compare the phylogenetic conclusions given by analysis of nuclear and mitochondrial protein-coding and rRNA genes to evaluate support for some of these hypotheses.
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Books on the topic "Phylogeny"

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Steel, Mike. Phylogeny. Philadelphia, PA: Society for Industrial and Applied Mathematics, 2016. http://dx.doi.org/10.1137/1.9781611974485.

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Szalay, Frederick S., Michael J. Novacek, and Malcolm C. McKenna, eds. Mammal Phylogeny. New York, NY: Springer New York, 1993. http://dx.doi.org/10.1007/978-1-4615-7381-4.

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Szalay, Frederick S., Michael J. Novacek, and Malcolm C. McKenna, eds. Mammal Phylogeny. New York, NY: Springer New York, 1993. http://dx.doi.org/10.1007/978-1-4613-9246-0.

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Szalay, Frederick S., Michael J. Novacek, and Malcolm C. McKenna, eds. Mammal Phylogeny. New York, NY: Springer New York, 1993. http://dx.doi.org/10.1007/978-1-4613-9249-1.

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S, Szalay Frederick, Novacek Michael J, McKenna Malcolm C, and North Atlantic Treaty Organization, eds. Mammal phylogeny. New York: Springer-Verlag, 1993.

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J, Novacek Michael, and Wheeler Quentin 1954-, eds. Extinction and phylogeny. New York: Columbia University Press, 1992.

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Gould, Stephen Jay. Ontogeny and phylogeny. Cambridge, MA: Harvard University Press, 1985.

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1967-, Purvis Andy, Gittleman John L, and Brooks Thomas, eds. Phylogeny and conservation. Cambridge: Cambridge University Press, 2005.

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Forey, Peter L., and Norman MacLeod. Morphology, shape and phylogeny. London: Taylor & Francis, 2002.

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Flanagan, Kathryn M., and Jason A. Lillegraven, eds. Vertebrates, Phylogeny, and Philosophy. Laramie, WY: University of Wyoming, 1986. http://dx.doi.org/10.2113/gsrocky.24.special_paper_3.1.

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Book chapters on the topic "Phylogeny"

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Frank, J. Howard, J. Howard Frank, Michael C. Thomas, Allan A. Yousten, F. William Howard, Robin M. Giblin-davis, John B. Heppner, et al. "Phylogeny." In Encyclopedia of Entomology, 2868. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-6359-6_2936.

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Moreira, David. "Phylogeny." In Encyclopedia of Astrobiology, 1252–54. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-11274-4_1209.

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Kovář, I. "Phylogeny." In Ecology of Coccinellidae, 19–31. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-017-1349-8_2.

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Prado, José Luis, and María Teresa Alberdi. "Phylogeny." In The Latin American Studies Book Series, 73–84. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-55877-6_4.

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Lichtwardt, Robert W. "Phylogeny." In The Trichomycetes, 274–87. New York, NY: Springer New York, 1986. http://dx.doi.org/10.1007/978-1-4612-4890-3_12.

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Moreira, David. "Phylogeny." In Encyclopedia of Astrobiology, 1887–90. Berlin, Heidelberg: Springer Berlin Heidelberg, 2015. http://dx.doi.org/10.1007/978-3-662-44185-5_1209.

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Mackenstedt, Ute. "Phylogeny." In Encyclopedia of Parasitology, 2146–52. Berlin, Heidelberg: Springer Berlin Heidelberg, 2016. http://dx.doi.org/10.1007/978-3-662-43978-4_2423.

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Saitou, Naruya. "Phylogeny." In Introduction to Evolutionary Genomics, 69–108. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-92642-1_4.

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Saitou, Naruya. "Phylogeny." In Introduction to Evolutionary Genomics, 55–87. London: Springer London, 2013. http://dx.doi.org/10.1007/978-1-4471-5304-7_3.

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Neelabh. "Phylogeny." In Encyclopedia of Animal Cognition and Behavior, 1–4. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-319-47829-6_129-1.

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Conference papers on the topic "Phylogeny"

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Gusfield, Dan. "Persistent phylogeny." In BCB '15: ACM International Conference on Bioinformatics, Computational Biology and Biomedicine. New York, NY, USA: ACM, 2015. http://dx.doi.org/10.1145/2808719.2808765.

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Bonizzoni, Paola, Simone Ciccolella, Gianluca Della Vedova, and Mauricio Soto. "Beyond Perfect Phylogeny." In BCB '17: 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. New York, NY, USA: ACM, 2017. http://dx.doi.org/10.1145/3107411.3107441.

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Rogers, John, and DeAngelo Wilson. "Comparing phylogeny by compression to phylogeny by NJp and Bayesian Inference." In 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2020. http://dx.doi.org/10.1109/bibm49941.2020.9313237.

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Araújo, Graziela S., Guilherme P. Telles, Maria Emília M. T. Walter, and Nalvo F. Almeida. "Distance-based Live Phylogeny." In 8th International Conference on Bioinformatics Models, Methods and Algorithms. SCITEPRESS - Science and Technology Publications, 2017. http://dx.doi.org/10.5220/0006224501960201.

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Gusfield, Dan. "Haplotyping as perfect phylogeny." In the sixth annual international conference. New York, New York, USA: ACM Press, 2002. http://dx.doi.org/10.1145/565196.565218.

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Jones, Jeff A., and Katherine A. Yelick. "Parallelizing the phylogeny problem." In the 1995 ACM/IEEE conference. New York, New York, USA: ACM Press, 1995. http://dx.doi.org/10.1145/224170.224224.

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Narayan, Kartik, Harsh Agarwal, Kartik Thakral, Surbhi Mittal, Mayank Vatsa, and Richa Singh. "DeePhy: On Deepfake Phylogeny." In 2022 IEEE International Joint Conference on Biometrics (IJCB). IEEE, 2022. http://dx.doi.org/10.1109/ijcb54206.2022.10007968.

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Sampaio, Alberto. "Software Phenetics, Phylogeny and Evolution." In Third International IEEE Workshop on Software Evolvability 2007. IEEE, 2007. http://dx.doi.org/10.1109/software-evolvability.2007.13.

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Baca, Stephen M. "Phylogeny and classification of Noteridae." In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.94124.

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Sampaio, Alberto. "Software Phenetics, Phylogeny and Evolution." In Third International IEEE Workshop on Software Evolvability 2007. IEEE, 2007. http://dx.doi.org/10.1109/se.2007.12.

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Reports on the topic "Phylogeny"

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Tiffani L. Williams. High-Performance Phylogeny Reconstruction. Office of Scientific and Technical Information (OSTI), November 2004. http://dx.doi.org/10.2172/834325.

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Moret, Bernard M., and Tandy Warnow. Advances in Phylogeny Reconstruction from Gene Order and Content Data. Fort Belvoir, VA: Defense Technical Information Center, October 2004. http://dx.doi.org/10.21236/ada482523.

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Стригунов, Володимир Іванович, Іван Сергійович Митяй, and Олександр Володимирович Мацюра. Egg shape in the taxonomy and phylogeny of birds of prey. МДПУ імені Богдана Хмельницького, 2016. http://dx.doi.org/10.31812/0564/1510.

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Swinstrom, Kirsten, Roy Caldwell, H. Matthew Fourcade, and Jeffrey L. Boore. The First Complete Mitochondrial Genome Sequences for Stomatopod Crustaceans: Implications for Phylogeny. Office of Scientific and Technical Information (OSTI), September 2005. http://dx.doi.org/10.2172/960399.

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Foster, Michael S. Support for a Symposium on Molecular Approaches to Phylogeny, Evolution and Biogeography. Fort Belvoir, VA: Defense Technical Information Center, December 1992. http://dx.doi.org/10.21236/ada262112.

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Kalgutkar, R. M., and A. R. Sweet. Morphology, taxonomy and phylogeny of the fossil fungal genus Pesavis from northwestern Canada. Natural Resources Canada/ESS/Scientific and Technical Publishing Services, 1988. http://dx.doi.org/10.4095/126976.

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Ksepka, Daniel, and Kristin Lamm. Systematics and Biodiversity Conservation. American Museum of Natural History, 2012. http://dx.doi.org/10.5531/cbc.ncep.0024.

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Abstract:
This exercise uses a fictional group of turtles to demonstrate how to implement cladistic methodology. Using a step-by-step guide, students work to find the most parsimonious cladogram for these fictional turtles. Part I involves delineating characters and building a most parsimonious cladogram based on the distribution of character states, while Part II presents additional challenges by introducing homoplasy. This exercise is designed to familiarize students with the concepts of phylogeny and cladistics, expand their skills of phylogenetic analysis, and use phylogenetic information to determine conservation priority.
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Pandya, Gagan A., Michael H. Holmes, Jeannine M. Petersen, Sonal Pradhan, Svetlana A. Karamycheva, Mark J. Wolcott, Claudia Molins, et al. Whole-Genome Single Nucleotide Polymorphism Based Phylogeny of Francisella tularensis and Its Application to the Development of a Strain Typing Assay. Fort Belvoir, VA: Defense Technical Information Center, October 2009. http://dx.doi.org/10.21236/ada513240.

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Eiserhardt, Wolf. Molekularbiologische Untersuchungen zur Phylogenie der cheilanthoiden Farne (Pteridaceae-Cheilanthoideae) des südlichen Afrika. BEE-Press, December 2007. http://dx.doi.org/10.7809/thesis.examen.001.

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Levisohn, Sharon, Maricarmen Garcia, David Yogev, and Stanley Kleven. Targeted Molecular Typing of Pathogenic Avian Mycoplasmas. United States Department of Agriculture, January 2006. http://dx.doi.org/10.32747/2006.7695853.bard.

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Intraspecies identification (DNA "fingerprinting") of pathogenic avian mycoplasmas is a powerful tool for epidemiological studies and monitoring strain identity. However the only widely method available for Mycoplasma gallisepticum (MG) and M. synoviae (MS)wasrandom amplified polymorphic DNA (RAPD). This project aimed to develop alternative and supplementary typing methods that will overcome the major constraints of RAPD, such as the need for isolation of the organism in pure culture and the lack of reproducibility intrinsic in the method. Our strategy focussed on recognition of molecular markers enabling identification of MG and MS vaccine strains and, by extension, pathogenic potential of field isolates. Our first aim was to develop PCR-based systems which will allow amplification of specific targeted genes directly from clinical material. For this purpose we evaluated the degree of intraspecies heterogeneity in genes encoding variable surface antigens uniquely found in MG all of which are putative pathogenicity factors. Phylogenic analysis of targeted sequences of selected genes (pvpA, gapA, mgc2, and lp) was employed to determine the relationship among MG strains.. This method, designated gene targeted sequencing (GTS), was successfully employed to identify strains and to establish epidemiologically-linked strain clusters. Diagnostic PCR tests were designed and validated for each of the target genes, allowing amplification of specific nucleotide sequences from clinical samples. An mgc2-PCR-RFLP test was designed for rapid differential diagnosis of MG vaccine strains in Israel. Addressing other project goals, we used transposon mutagenesis and in vivo and in vitro models for pathogenicity to correlated specific changes in target genes with biological properties that may impact the course of infection. An innovative method for specific detection and typing of MS strains was based on the hemagglutinin-encoding gene vlhA, uniquely found in this species. In parallel, we evaluated the application of amplified fragment length polymorphism (AFLP) in avian mycoplasmas. AFLP is a highly discriminatory method that scans the entire genome using infrequent restriction site PCR. As a first step the method was found to be highly correlated with other DNA typing methods for MG species and strain differentiation. The method is highly reproducible and relatively rapid, although it is necessary to isolate the strain to be tested. Both AFLP and GTS are readily to amenable to computer-assisted analysis of similarity and construction of a data-base resource. The availability of improved and diverse tools will help realize the full potential of molecular typing of avian mycoplasmas as an integral and essential part of mycoplasma control programs.
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