Rozprawy doktorskie: „Phylogenetic position”

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Bales, Ashley. "The phylogenetic position of Proconsul and catarrhine ancestral morphotypes". Thesis, New York University, 2017. http://pqdtopen.proquest.com/#viewpdf?dispub=10192021.

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There continues to be a lack of agreement concerning the precise phylogenetic placement of Proconsul despite the wealth of fossil material and the extensiveness of its study. The difficulty in resolving the phylogenetic status of this important and well represented Miocene catarrhine is a consequence of its apparent basal position relative to crown catarrhines. This position complicates the inference of character polarities. This dissertation tests three previously proposed hypotheses concerning the phylogenetic position of Proconsul: (1) Proconsul is a stem catarrhine; (2) Proconsul is a stem hominoid; and (3) Proconsul is a basal hominid, most closely related to extant great apes and humans. A phylogenetic analysis based on 719 characters drawn from the skull, forelimb, pelvis and foot, and sampling a diversity of extant anthropoid taxa, offers no compelling support for a hominoid clade that includes Proconsul. The radiation of crown catarrhines involved rapid evolutionary changes from the ancestral catarrhine morphotype, resulting in stem catarrhines appearing much more similar to each other, even where there are key synapomorphies linking them with crown clades. As a result, systematic analyses alone are insufficient to confidently support a single optimal phylogenetic hypothesis. Further exploration of the data, by combining inferred ancestral morphotypes with phenetic visualizations of character evolution, demonstrated that inclusion of Proconsul among Hominoidea or Hominidae pushed the ancestral catarrhine morphotype closer to these clades, respectively. Given a more comprehensive analysis of character evolution under each hypothesis, this dissertation supports the hypothesis that Proconsul is a stem catarrhine. In addition to helping clarify the long-running debate about the phylogenetic status of Proconsul, the results offer fresh insights into the early stages of hominoid evolution and demonstrate the importance of comprehensive phylogenetic analyses in helping to resolve the relationships of problematic stem taxa.

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Bleidorn, Christoph, Lars Podsiadlowski, Min Zhong, Igor Eeckhaut, Stefanie Hartmann, Kenneth M. Halanych i Ralph Tiedemann. "On the phylogenetic position of Myzostomida : can 77 genes get it wrong?" Universität Potsdam, 2009. http://opus.kobv.de/ubp/volltexte/2010/4489/.

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Background: Phylogenomic analyses recently became popular to address questions about deep metazoan phylogeny. Ribosomal proteins (RP) dominate many of these analyses or are, in some cases, the only genes included. Despite initial hopes, hylogenomic analyses including tens to hundreds of genes still fail to robustly place many bilaterian taxa. Results: Using the phylogenetic position of myzostomids as an example, we show that phylogenies derived from RP genes and mitochondrial genes produce incongruent results. Whereas the former support a position within a clade of platyzoan taxa, mitochondrial data recovers an annelid affinity, which is strongly supported by the gene order data and is congruent with morphology. Using hypothesis testing, our RP data significantly rejects the annelids affinity, whereas a platyzoan relationship is significantly rejected by the mitochondrial data. Conclusion: We conclude (i) that reliance of a set of markers belonging to a single class of macromolecular complexes might bias the analysis, and (ii) that concatenation of all available data might introduce conflicting signal into phylogenetic analyses. We therefore strongly recommend testing for data incongruence in phylogenomic analyses. Furthermore, judging all available data, we consider the annelid affinity hypothesis more plausible than a possible platyzoan affinity for myzostomids, and suspect long branch attraction is influencing the RP data. However, this hypothesis needs further confirmation by future analyses.

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Eitel, Michael Sebastian [Verfasser]. "Phylogenetic position, biodiversity, phylogeography and biology of the Placozoa / Michael Sebastian Eitel". Hannover : Technische Informationsbibliothek und Universitätsbibliothek Hannover (TIB), 2010. http://d-nb.info/1036525228/34.

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Lehmann, Jörg. "Relative Timing of Intron Gain and a New Marker for Phylogenetic Analyses". Doctoral thesis, Universitätsbibliothek Leipzig, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-144067.

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Despite decades of effort by molecular systematists, the trees of life of eukaryotic organisms still remain partly unresolved or in conflict with each other. An ever increasing number of fully-sequenced genomes of various eukaryotes allows to consider gene and species phylogenies at genome-scale. However, such phylogenomics-based approaches also revealed that more taxa and more and more gene sequences are not the ultimate solution to fully resolve these conflicts, and that there is a need for sequence-independent phylogenetic meta-characters that are derived from genome sequences. Spliceosomal introns are characteristic features of eukaryotic nuclear genomes. The relatively rare changes of spliceosomal intron positions have already been used as genome-level markers, both for the estimation of intron evolution and phylogenies, however with variable success. In this thesis, a specific subset of these changes is introduced and established as a novel phylogenetic marker, termed near intron pair (NIP). These characters are inferred from homologous genes that contain mutually-exclusive intron presences at pairs of coding sequence (CDS) positions in close proximity. The idea that NIPs are powerful characters is based on the assumption that both very small exons and multiple intron gains at the same position are rare. To obtain sufficient numbers of NIP character data from genomic and alignment data sets in a consistent and flexible way, the implementation of a computational pipeline was a main goal of this work. Starting from orthologous (or more general: homologous) gene datasets comprising genomic sequences and corresponding CDS transcript annotations, the multiple alignment generation is an integral part of this pipeline. The alignment can be calculated at the amino acid level utilizing external tools (e.g. transAlign) and results in a codon alignment via back-translation. Guided by the multiple alignment, the positionally homologous intron positions should become apparent when mapped individually for each transcript. The pipeline proceeds at this stage to output portions of the intron-annotated alignment that contain at least one candidate of a NIP character. In a subsequent pipeline script, these collected so-called NIP region files are finally converted to binary state characters representing valid NIPs in dependence of quality filter constraints concerning, e.g., the amino acid alignment conservation around intron loci and splice sites, to name a few. The computational pipeline tools provide the researcher to elaborate on NIP character matrices that can be used for tree inference, e.g., using the maximum parsimony approach. In a first NIP-based application, the phylogenetic position of major orders of holometabolic insects (more specifically: the Coleoptera-Hymenoptera-Mecopterida trifurcation) was evaluated in a cladistic sense. As already suggested during a study on the eIF2gamma gene based on two NIP cases (Krauss et al. 2005), the genome-scale evaluation supported Hymenoptera as sister group to an assemblage of Coleoptera and Mecopterida, in agreement with other studies, but contradicting the previously established view. As part of the genome paper describing a new species of twisted-wing parasites (Strepsiptera), the NIP method was employed to help to resolve the phylogenetic position of them within (holometabolic) insects. Together with analyses of sequence patterns and a further meta-character, it revealed twisted-wing parasites as being the closest relatives of the mega-diverse beetles. NIP-based reconstructions of the metazoan tree covering a broad selection of representative animal species also identified some weaknesses of the NIP approach that may suffer e.g. from alignment/ortholog prediction artifacts (depending on the depth of range of taxa) and systematic biases (long branch attraction artifacts, due to unequal evolutionary rates of intron gain/loss and the use of the maximum parsimony method). In a further study, the identification of NIPs within the recently diverged genus Drosophila could be utilized to characterize recent intron gain events that apparently involved several cases of intron sliding and tandem exon duplication, albeit the mechanisms of gain for the majority of cases could not be elucidated. Finally, the NIP marker could be established as a novel phylogenetic marker, in particular dedicated to complementarily explore the wealth of genome data for phylogenetic purposes and to address open questions of intron evolution.

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Starr, Julian Richard. "The origin and phylogenetic position of Carex section Phyllostachys in the genus Carex, Cyperaceae". Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp04/mq23510.pdf.

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Ozdemir, Degirmenci Funda. "Molecular Phylogenetic Position Of Turkish Abies(pinaceae)based On Noncoding Trn Regions Of Chloroplast Genome". Master's thesis, METU, 2011. http://etd.lib.metu.edu.tr/upload/12613590/index.pdf.

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Abies is the second largest genus of family Pinaceae (after Pinus), consisting of about 51 species, all native to the Northern Hemisphere. There are six native taxa belonging to this genus growing in pure and mixed stands in Turkey. Abies cilicica subsp. isaurica, Abies nordmanniana subsp. bornmü
lleriana, Abies nordmanniana subsp. equi-trojani, Abies x olcayana are endemic and considered as lower risk (LR) species. To determine the genetic relationships in Turkish firs, 18 populations of different subspecies of Abies were collected from different regions of Turkey and non-coding trn regions of chloroplast DNA were sequenced to assess the genetic structure of the studied species. trnL, trnF and trnV region were examined. All the trn regions of Abies species in the world (aproximately 300 species that found in the IPNI (The International Plant Names Index) were investigated in the database of NCBI. The available trn sequences of 23 Abies species worldwide included into the analyses. All analyses to estimate molecular diversity parameters were carried out with the MEGA software. The constructed phylogenetic tree with the trn sequences revealed that Turkish firs formed a monophyletic group with almost no sequence divergence. v Since sequence data for all three sectors of trn were not available from the NCBI data base, the phylogentic analysis with the sequence data of trnL regions were compartively analyzed in all firs. The results showed that Turkish- European species formed a single clade, which clearly differentiated them from the others, such as Japanese species, A. veitchii. Similarly, according to the sequence data of trnF, Turkish fir species were grouped together and distinctly separated from Asian-American Fir species. The results suggest that all Turkish firs may have evolved from single ancestral fir species, most likely from Abies nordmanniana.

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Villavicencio, José Eduardo Serrano. "Taxonomy of the genus Brachyteles Spix, 1823 and its phylogenetic position within the subfamily Atelinae Gray, 1825". Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/38/38131/tde-16112016-150803/.

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Muriquis, genus Brachyteles Spix, 1823, are the largest of the extant New World primates, and they are one of the three extant genera of the subfamily Atelinae along with Ateles (spider monkeys) and Lagothrix (wooly monkeys). The taxonomy of Brachyteles has constantly changed since its first description in the 19th century. First treated as a monotypic genus, and after several modifications in the number of species, Brachyteles currently contains two species, B. arachnoides (Southern muriqui) and B. hypoxanthus (Northern muriqui). The morphological evidence for this taxonomic arrangement relies on two diagnostic characters: the occurrence of a black-pigmented face and the absence of the first digit (thumb) in Southern muriqui populations vs. mottled face and fully-developed thumb in Northern muriqui populations. In addition, the phylogenetic relationship between atelines is disputed: on the one hand, the molecular evidence suggests an (Ateles (Brachyteles + Lagothrix)) clade and, on the other, most morphological evidence supports a clade (Lagothrix (Ateles + Brachyteles)) based on the high degree of postcranial and locomotory resemblances between Ateles and Brachyteles. My aims here are: 1) to verify how many taxa at the species level group there are in Brachyteles, and 2) to estimate the phylogenetic relationships among Atelinae using morphological characters. To achieve these goals, I have performed a qualitative analysis of external morphological characters as the presence or absence of the thumb, pelage coloration, and face pigmentation to test sexual dimorphism or dichromatism and intrapopulational variation. I also performed linear and geometric morphometrics analyses to test sexual dimorphism and geographical variation in both size and shape of the skull. Finally, I carried out a morphological phylogeny using 74 discrete morphological characters, two ecological and one karyological. This analysis includes 11 species of extant and fossil atelids and the outgroup was composed of Sapajus nigritus and Callicebus personatus. The analysis of the pelage coloration reveals that there is no sexual dimorphism or dichromatism in Brachyteles; besides, the pelage presents a high degree of individual variation. The development of the thumb and the facial pigmentation do not exhibit uniformity; thus, they have no taxonomic meaning. Linear and geometric morphometrics failed on to discriminate between sexes and populations based on the size and shape of the skull. For these reasons, I consider Brachyteles as a monotypic genus with no subspecies. Lastly, the morphologic phylogenetic analysis shows that Brachyteles is more closely related to Lagothrix than to Ateles, suggesting that the postcranial similarities between muriquis and spider monkeys could be a plesiomorphic condition in Atelidae, and the arboreal quadrupedalism of Alouatta and Lagothrix evolved convergently in alouattines and atelines.
Os muriquis ou monos-carvoeiros, gênero Brachyteles Spix, 1823, são os maiores primatas existentes do Novo Mundo, fazendo parte da subfamília Atelinae, juntamente com os gêneros Ateles (macaco-aranha) e Lagothrix (macaco-barrigudo). A taxonomia de Brachyteles tem sofrido constantes alterações desde sua primeira descrição no século XIX. Inicialmente foi tratado como um gênero monotípico, entretanto, após diversas alterações no número de espécies, atualmente considera-se composto por duas espécies, B. arachnoides (muriqui-do-sul) and B. hypoxanthus (muriqui-do-norte). O suporte para este arranjo taxonômico baseia-se em dois caracteres diagnósticos: a ocorrência de face com coloração preta e a ausência do primeiro dígito (polegar) nos muriquis-do-sul vs. face com manchas e polegar totalmente desenvolvido em populações de muriquis-do-norte. Adicionalmente, as relações filogenéticas entre os atelinos é contestada: por um lado, a evidência molecular sugere o clado formado por (Ateles (Brachyteles + Lagothrix)), por outro, a evidência morfológica suporta o clado (Lagothrix (Ateles + Brachyteles)), baseando-se na grande similaridade pós-craniana e locomotora. Desta forma, o meus objetivos neste trabalho são: 1) verificar quantos taxa do grupo da espécie existem em Brachyteles, e 2) estabelecer as relações filogenéticas entre os Atelinae utilizando caracteres morfológicos. Para isso, analisei qualitativamente os caracteres morfológicos externos, como a presença ou ausência de polegar, a coloração da pelagem, e a pigmentação facial, a fim de testar a ocorrência de dimorfismo sexual ou dicromatismo e a variação intraespecífica. Além disso, realizei análises morfométricas lineares e geométricas para testar o dimorfismo sexual e a variação geográfica do tamanho e forma do crânio. Por fim, realizei uma filogenia morfológica utilizando 74 caracteres morfológicos, dois ecológicos e um cariotípico. Estas análises incluíram 11 espécies de atelídeos viventes e fósseis e um grupo-externo composto por Sapajus nigritus e Callicebus personatus. A análise da coloração da pelagem revela que não há dimorfismo sexual ou dicromatismo em Brachyteles; além disso, a pelagem apresenta um alto grau de variação individual. O desenvolvimento do polegar e a pigmentação facial não apresentam uniformidade, assim, não tem relevância taxonômica. A morfometria linear e geométrica falharam em discriminar entre os sexos e as populações com base no tamanho e forma do crânio. Finalmente, as análises filogenéticas mostraram que Brachyteles está mais estreitamente relacionado com Lagothrix do que com Ateles, sugerindo que a similaridade pós-craninana entre os muriquis e os macacos-aranha poderia ser uma condição plesiomórfico dos atelídeos, e o quadrupedalismo arborícola de Alouatta e Lagothrix teria evoluído convergentemente em alouatíneos e atelíneos.

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Müller, Johannes. "A revision of Askeptosaurus italicus and other thalattosaurs from the European Triassic, the interrelationships of thalattosaurs, and their phylogenetic position within diapsid reptiles (Amniota, Eureptilia)". [S.l. : s.n.], 2002. http://ArchiMeD.uni-mainz.de/pub/2002/0127/diss.pdf.

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Gontang, Erin Ann. "Phylogenetic diversity of gram-positive bacteria and their secondary metabolite genes". Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2008. http://wwwlib.umi.com/cr/ucsd/fullcit?p3324374.

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Thesis (Ph. D.)--University of California, San Diego, 2008.
Title from first page of PDF file (viewed October 3, 2008). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references.

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Fujimoto, Masaki Stanley. "The OGCleaner: Detecting False-Positive Sequence Homology". BYU ScholarsArchive, 2017. https://scholarsarchive.byu.edu/etd/6410.

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Within bioinformatics, phylogenetics is the study of the evolutionary relationships between different species and organisms. The genetic revolution has caused an explosion in the amount of raw genomic information that is available to scientists for study. While there has been an explosion in available data, analysis methods have lagged behind. A key task in phylogenetics is identifying homology clusters. Current methods rely on using heuristics based on pairwise sequence comparison to identify homology clusters. We propose the Orthology Group Cleaner (the OGCleaner) as a method to evaluate cluster level verification of putative homology clusters in order to create higher quality phylogenetic tree reconstruction.

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McMahon, Michelle Mary 1965. "Taxon sampling in phylogenetic analysis: An evalution of the basally positioned taxon". Thesis, The University of Arizona, 1996. http://hdl.handle.net/10150/291658.

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Taxon sampling is explicitly examined using simulations and probability analyses. The simulations focus on the ability of two different sampling strategies to correctly reconstruct relationships among subgroups of taxa. One sampling strategy chooses taxa randomly, the other strategy chooses taxa to increase the phylogenetic dispersal of the taxa. Also considered is whether the inclusion of a single basal taxon will increase the frequency of correctly reconstructing the relationships among subgroups. Inclusion of the basal taxon is found to decrease success (correct subgroup relationships). The strategies are found to differ, primarily due to differing tendencies to include the basal taxon (the random strategy includes the basal taxon less frequently and outperforms the dispersed strategy). The inclusion of a basal taxon is also found to decrease the probability of correctly reconstructing ancestral character states. The probability of randomly choosing a single taxon from one side of the root is developed.

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Wakeling, Julia. "Phylogenetic positions of Nahan's Francolin Francolinus nahani and the stone partridge Ptilopachus petrosus : enigmatic African gamebirds". Master's thesis, University of Cape Town, 2004. http://hdl.handle.net/11427/26057.

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Erixon, Per. "Phylogenetic Support and Chloroplast Genome Evolution in Sileneae (Caryophyllaceae)". Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Universitetsbiblioteket [distributör], 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7166.

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Cooke, Catherine A. "The Feeding, Ranging, and Positional Behavior of Cercocebus torquatus (the red-capped mangabey) in Sette Cama, Gabon: A Phylogenetic Perspective". The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1354500922.

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Suvorov, Anton. "Molecular Evolution of Odonata Opsins, Odonata Phylogenomics and Detection of False Positive Sequence Homology Using Machine Learning". BYU ScholarsArchive, 2018. https://scholarsarchive.byu.edu/etd/7320.

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My dissertation comprises three related topics of evolutionary and computational biology, which correspond to the three Chapters. Chapter 1 focuses on tempo and mode of evolution in visual genes, namely opsins, via duplication events and subsequent molecular adaptation in Odonata (dragonflies and damselflies). Gene duplication plays a central role in adaptation to novel environments by providing new genetic material for functional divergence and evolution of biological complexity. Odonata have the largest opsin repertoire of any insect currently known. In particular our results suggest that both the blue sensitive (BS) and long-wave sensitive (LWS) opsin classes were subjected to strong positive selection that greatly weakens after multiple duplication events, a pattern that is consistent with the permanent heterozygote model. Due to the immense interspecific variation and duplicability potential of opsin genes among odonates, they represent a unique model system to test hypotheses regarding opsin gene duplication and diversification at the molecular level. Chapter 2 primarily focuses on reconstruction of the phylogenetic backbone of Odonata using RNA-seq data. In order to reconstruct the evolutionary history of Odonata, we performed comprehensive phylotranscriptomic analyses of 83 species covering 75% of all extant odonate families. Using maximum likelihood, Bayesian, coalescent-based and alignment free tree inference frameworks we were able to test, refine and resolve previously controversial relationships within the order. In particular, we confirmed the monophyly of Zygoptera, recovered Gomphidae and Petaluridae as sister groups with high confidence and identified Calopterygoidea as monophyletic. Fossil calibration coupled with diversification analyses provided insight into key events that influenced the evolution of Odonata. Specifically, we determined that there was a possible mass extinction of ancient odonate diversity during the P-Tr crisis and a single odonate lineage persisted following this extinction event. Lastly, Chapter 3 focuses on identification of erroneously assigned sequence homology using the intelligent agents of machine learning techniques. Accurate detection of homologous relationships of biological sequences (DNA or amino acid) amongst organisms is an important and often difficult task that is essential to various evolutionary studies, ranging from building phylogenies to predicting functional gene annotations. We developed biologically informative features that can be extracted from multiple sequence alignments of putative homologous genes (orthologs and paralogs) and further utilized in context of guided experimentation to verify false positive outcomes.

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Peat, Scott M. "Utilization of Phylogenetic Systematics, Molecular Evolution, and Comparative Transcriptomics to Address Aspects of Nematode and Bacterial Evolution". BYU ScholarsArchive, 2010. https://scholarsarchive.byu.edu/etd/2535.

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Both insect parasitic/entomopathogenic nematodes and plant parasitic nematodes are of great economic importance. Insect parasitic/entomopathogenic nematodes provide an environmentally safe and effective method to control numerous insect pests worldwide. Alternatively, plant parasitic nematodes cause billions of dollars in crop loss worldwide. Because of these impacts, it is important to understand how these nematodes evolve, and, in the case of entomopathogenic nematodes, how their bacterial symbionts evolve. This dissertation contains six chapters. Chapter one is a review of DNA markers and their use in the phylogenetic systematics of entomopathogenic and insect-parasitic nematodes as well as a review of phylogenetic, co-phylogenetic, and population genetic methodologies. Chapter two characterizes positive destabilizing selection on the luxA gene of bioluminescent bacteria. Our data suggests that bacterial ecology and environmental osmolarity are likely driving the evolution of the luxA gene in bioluminescent bacteria. Chapter 3 examines relationships among bacteria within the genus Photorhabdus. Our analyses produced the most robust phylogenetic hypothesis to date for the genus Photorhabdus. Additionally, we show that glnA is particularly useful in resolving specific and intra-specific relationships poorly resolved in other studies. We conclude that P. asymbiotica is the sister group to P. luminescens and that the new strains HIT and JUN should be given a new group designation within P. asymbiotica. Chapter 4 characterizes the morphology of the head and feeding apparatus of fungal feeding and insect infective female morphs of the nematode Deladenus siricidicola using scanning electron microscopy. Results showed dramatic differences in head, face, and stylet morphology between the two D. siricidicola female morphs that were not detected in previous studies using only light microscopy. Chapter five utilizes comparative transciptomics to identify putative plant and insect parasitism genes in the nematode Deladenus siricidicola. Results from this study provide the first transcriptomic characterization for the nematode Deladenus siricidicola and for an insect parasitic member of the nematode infraorder Tylenchomorpha. Additionally, numerous plant parasitism gene homologues were discovered in both D. siricidicola libraries suggesting that this nematode has co-opted these plant parasitism genes for other functions. Chapter six utilizes a phylogenomic approach to estimate the phylogeny of the nematode infraorder Tylenchomorpha.

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Mayberry, Jason Robert. "Through the eyes of bat flies| Behavioral, phylogenetic, and histological analyses of compound eye reduction in bat flies (Streblidae) provide evidence for positive selection". Thesis, State University of New York at Buffalo, 2015. http://pqdtopen.proquest.com/#viewpdf?dispub=3714642.

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It is often presumed that evolutionary reduction is tantamount to deconstruction, or even destruction, because relaxed selective forces have been insufficient to maintain the organ in its original state. However, studies on reduction are often limited by a lack of diversity, both of related species exhibiting reduction and of the reduced form itself. There have also been very few studies on the reduction of compound eyes, despite the fact that their near ubiquity among arthropods alone makes them perhaps the most common type of eye. Bat flies (Streblidae and Nycteribiidae) are a group of dipterans that exhibit variable degrees of compound eye reduction, and therefore provide the opportunity to study reduction of this organ in a phylogenetic context. The first chapter of this work reports on behavioral experiments demonstrating that the eyes of one bat fly species, Trichobius frequens, are functional, and that they neither exhibit phototaxis typical of other dipteran species, nor move toward a light source. The second chapter uses molecular phylogenetics to identify a correlation between eye and wing morphology. The results also suggest that secondary to their eye reduction, bat flies (at least in the case of New World specie, including Trichobius spp.) have secondarily experienced a shift in the structure of their facets that is convergent with other insects whose eyes have been selected for increased sensitivity. In the final chapter, histological and optical analyses of T. frequens eyes are used to reveal significant structural changes to the microstructure of its ommatidia that increase sensitivity at the expense of acuity. Many of these changes are also convergent with similar adaptations that have been demonstrated to increase sensitivity in organisms that function in reduced light environments. The results of these analyses suggest that reduction in T. frequens eyes may have been part of an active remodeling process resulting from a shift in the relative importance of sensitivity and acuity. As this is a process of reduction not generally considered, the findings here turn our attention to alternative hypotheses that should be considered when studying evolutionary reduction of any organ.

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Antonishyn, Nick A. "The inference of phylogenetic relationships among the main lineages of terrestrial plants, with emphasis on the positions of the major bryophyte groups, using small-subunit ribosomal RNA gene sequences". Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp01/MQ30437.pdf.

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Afrache, Hassnae. "Prédiction de la fonction des butyrophilines par l'étude de leur évolution et de leur variabilité génétique". Thesis, Aix-Marseille, 2014. http://www.theses.fr/2014AIXM5032.

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Dans le cadre de cette thèse nous nous sommes intéressés à l'étude de l'évolution et de la variabilité génétique de la famille des butyrophilines (BTN), des récepteurs de la superfamille des immunoglobulines impliqués dans la régulation de la réponse immunitaire. Par une étude phylogénétique approfondie nous avons caractérisé chez les mammifères 14 groupes phylogénétiques résultant d'une série de duplications à partir de huit gènes ancestraux à la base des thériens. Par la suite, nous avons étudié l'évolution des BTN de la région CMH chez les primates et leur variabilité génétique dans les populations humaines par une analyse minutieuse des données de séquençage générées du projet 1000 Genomes pour plus de 1600 individus à travers le monde. Nous avons montré que l'évolution du gène BTNL2 est marquée par une pression de sélection positive diversifiante chez les mammifères qui est accompagnée chez les hominoïdes d'un niveau de polymorphisme élevé induisant la formation de variants tronqués de BTNL2. Chez l'homme, quatre lignages d'allèles ont été identifiés. Ils ont été maintenus à des fréquences intermédiaires par une forte sélection balancée. D'autre part, l'analyse phylogénétique détaillée du groupe BTN3 (BTN3A1, 3A2 et 3A3) a montré la présence d'une évolution concertée, caractérisée par une homogénéisation forte et récurrente de la région codant pour le peptide signale et le domaine IgV chez les hominoïdes, au cours de laquelle les séquences de 3A1 et 3A3 sont remplacées par la séquence de 3A2. Chez l'homme, ces gènes sont polymorphismes important avec plus de 46 allèles chacun, mais avec la présence d'une homogénéisation extrême des séquences du domaine IgV
In this thesis we were interested in studying the evolution and the genetic variability of the butyrophilin family (BTN), a family of immune receptors belonging to the immunoglobulin superfamily implicated in the regulation of immune response. Through a thorough phylogenetic study of the family we characterized 14 phylogenetic groups in mammals resulting from a series of duplications from eight ancestral genes at the base of therian. Thereafter, we studied the evolution of the BTN of the MHC region and their genetic variability in human populations by a careful analysis of sequencing data generated by the consortium 1000 Genomes for more than 1,600 individuals representing 26 populations worldwide. We have shown that the evolution of BTNL2 gene is marked by a positive diversifying selection in placental mammals. This selection pressure is accompanied in hominoids of a high level of polymorphism inducing the formation of truncated BTNL2 variants. In humans this high level of polymorphism results in the presence of four ancient allele lineages that are maintained at intermediate frequencies by a strong balancing selection. On the other hand, a detailed phylogenetic analysis of BTN3 group (BTN3A1, 3A2 and 3A3) showed that these genes evolve in hominoids in a concerted manner characterized by a strong and recurrent homogenization of the regions encoding for the peptide signal and the IgV domain in which the 3A1 and 3A3 sequences are replaced by the 3A2 sequence. In humans these genes are polymorphic with over 46 alleles each, but with the presence of extreme homogenization of IgV domain sequences

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Sousa, Fábio Alberto Vieira de. "Biogeography and phylogenetic position of a Sahara-Sahel mountain endemic, Felovia vae (Ctenodactylidae)". Master's thesis, 2015. https://repositorio-aberto.up.pt/handle/10216/88698.

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Sousa, Fábio Alberto Vieira de. "Biogeography and phylogenetic position of a Sahara-Sahel mountain endemic, Felovia vae (Ctenodactylidae)". Dissertação, 2015. https://repositorio-aberto.up.pt/handle/10216/88698.

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Meyer, Achim [Verfasser]. "Molecular phylogenetic inferences on the position of the Mollusca within the Lophotrochozoa / Achim Meyer". 2009. http://d-nb.info/1000743713/34.

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Lehmann, Jörg. "Relative Timing of Intron Gain and a New Marker for Phylogenetic Analyses". Doctoral thesis, 2013. https://ul.qucosa.de/id/qucosa%3A12477.

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Despite decades of effort by molecular systematists, the trees of life of eukaryotic organisms still remain partly unresolved or in conflict with each other. An ever increasing number of fully-sequenced genomes of various eukaryotes allows to consider gene and species phylogenies at genome-scale. However, such phylogenomics-based approaches also revealed that more taxa and more and more gene sequences are not the ultimate solution to fully resolve these conflicts, and that there is a need for sequence-independent phylogenetic meta-characters that are derived from genome sequences. Spliceosomal introns are characteristic features of eukaryotic nuclear genomes. The relatively rare changes of spliceosomal intron positions have already been used as genome-level markers, both for the estimation of intron evolution and phylogenies, however with variable success. In this thesis, a specific subset of these changes is introduced and established as a novel phylogenetic marker, termed near intron pair (NIP). These characters are inferred from homologous genes that contain mutually-exclusive intron presences at pairs of coding sequence (CDS) positions in close proximity. The idea that NIPs are powerful characters is based on the assumption that both very small exons and multiple intron gains at the same position are rare. To obtain sufficient numbers of NIP character data from genomic and alignment data sets in a consistent and flexible way, the implementation of a computational pipeline was a main goal of this work. Starting from orthologous (or more general: homologous) gene datasets comprising genomic sequences and corresponding CDS transcript annotations, the multiple alignment generation is an integral part of this pipeline. The alignment can be calculated at the amino acid level utilizing external tools (e.g. transAlign) and results in a codon alignment via back-translation. Guided by the multiple alignment, the positionally homologous intron positions should become apparent when mapped individually for each transcript. The pipeline proceeds at this stage to output portions of the intron-annotated alignment that contain at least one candidate of a NIP character. In a subsequent pipeline script, these collected so-called NIP region files are finally converted to binary state characters representing valid NIPs in dependence of quality filter constraints concerning, e.g., the amino acid alignment conservation around intron loci and splice sites, to name a few. The computational pipeline tools provide the researcher to elaborate on NIP character matrices that can be used for tree inference, e.g., using the maximum parsimony approach. In a first NIP-based application, the phylogenetic position of major orders of holometabolic insects (more specifically: the Coleoptera-Hymenoptera-Mecopterida trifurcation) was evaluated in a cladistic sense. As already suggested during a study on the eIF2gamma gene based on two NIP cases (Krauss et al. 2005), the genome-scale evaluation supported Hymenoptera as sister group to an assemblage of Coleoptera and Mecopterida, in agreement with other studies, but contradicting the previously established view. As part of the genome paper describing a new species of twisted-wing parasites (Strepsiptera), the NIP method was employed to help to resolve the phylogenetic position of them within (holometabolic) insects. Together with analyses of sequence patterns and a further meta-character, it revealed twisted-wing parasites as being the closest relatives of the mega-diverse beetles. NIP-based reconstructions of the metazoan tree covering a broad selection of representative animal species also identified some weaknesses of the NIP approach that may suffer e.g. from alignment/ortholog prediction artifacts (depending on the depth of range of taxa) and systematic biases (long branch attraction artifacts, due to unequal evolutionary rates of intron gain/loss and the use of the maximum parsimony method). In a further study, the identification of NIPs within the recently diverged genus Drosophila could be utilized to characterize recent intron gain events that apparently involved several cases of intron sliding and tandem exon duplication, albeit the mechanisms of gain for the majority of cases could not be elucidated. Finally, the NIP marker could be established as a novel phylogenetic marker, in particular dedicated to complementarily explore the wealth of genome data for phylogenetic purposes and to address open questions of intron evolution.

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Jana, Ananya. "Diversity from the Gut to Species: Phylogeny, Population genetics and Microbiome of the Antilope cervicapra". Thesis, 2020. https://etd.iisc.ac.in/handle/2005/5033.

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Evolutionary relationships between members of the Antilopina taxon have been much debated in recent years. The ‘true antelope’ clade is currently comprised of 4 genera viz., Gazella, Nanger, Eudorcas and the monotypic genus Antilope, that includes A. cervicapra. Most studies have focused on the mitochondrial genome or morphological data to study their relationships. However, signals from mitochondrial data can often be misleading when compared with nuclear markers, as has been shown in multiple taxonomic groups. In this study, we revisit the phylogenetic relationships among members of Antilopina, particularly the phylogenetic position of A. cervicapra, using 12 nuclear markers and compare it with the mitochondrial tree. Furthermore, we explore the implications of the results of this study on the taxonomy and biogeography of Indian antelopes. The nuclear phylogenetic trees built using multiple coalescent and concatenated methods all supported a paraphyletic genus Gazella. Antilope was nested within Gazella as opposed to being sister to it, which was suggested by previous studies and our results based on mitochondrial markers. Our fossil-calibrated larger bovid phylogeny, based on nuclear markers, suggested that the Antilope lineage diverged from its sister species more recently in the Pleistocene, rather than in late Miocene as per previous studies. Our biogeographic analyses suggest that the lineage leading to genus Antilope dispersed into India from the Saharo-Arabian realm around 2 mya, post the expansion of grasslands. We speculate that the adaptations of this savanna-grassland specialist did not allow them to extend their range beyond the Indian subcontinent. Whereas, the only other true antelope in India, G. bennetti, extended its range into India more recently, probably after the establishment of the Thar desert in northwest India.

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Müller, Johannes [Verfasser]. "A revision of Askeptosaurus italicus and other thalattosaurs from the European Triassic, the interrelationships of thalattosaurs, and their phylogenetic position within diapsid reptiles (Amniota, Eureptilia) / Johannes Müller". 2002. http://d-nb.info/965496198/34.

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Du, Toit Nicole. "Molecular phylogenetics of Cyclopia Vent.and its position within Podalyrieae (Fabaceae)". Thesis, 2008. http://hdl.handle.net/10210/236.

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The tribe Podalyrieae is a diverse and interesting group with most of its species found in the Cape Floristic Region (120 out of 128 species), the smallest floral kingdom and the subject of intense conservation interest. DNA sequence data from nuclear ribosomal internal transcribed spacer, including the 5.8s coding region, were used to reconstruct the phylogeny of this Cape Floral Clade. Results support a transfer of Cadia (Sophoreae) to Podalyrieae. Cyclopia is well imbedded in a paraphyletic Podalyriinae and not sister to the tribe as previously suggested. A broader concept of Podalyrieae, which include Podalyriinae, Xiphothecinae and Cadia is suggested. Dating the nodes of the phylogenetic tree using non-parametric rate smoothing with a fossil calibration point indicates that the root node of Podalyrieae (+ Cadia) is 34.35MYA.
Dr. M. van der Bank

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Sauer, Tilman. "Evaluierung des phylogenetischen Footprintings und dessen Anwendung zur verbesserten Vorhersage von Transkriptionsfaktor-Bindestellen". Doctoral thesis, 2006. http://hdl.handle.net/11858/00-1735-0000-0006-B383-8.

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Lin, Heng-Ching, i 林恒慶. "Diagnosis and Phylogenetic Analysis of Mycobacterial Infection and Mycobacterium bovis from Intradermal Tuberulolin Test-Positive Herbivore". Thesis, 2011. http://ndltd.ncl.edu.tw/handle/95596970579206998538.

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碩士
國立嘉義大學
獸醫學系研究所
99
Tuberculosis (TB) is a zoonotic disease affecting mammal worldwide. Herbivore’s TB is determined by Mycobacterium bovis and other nontuberculous mycobacteria (NTM). NTM may interfere with the result of intradermal tuberculin test (ITT), and cause fake-positive. According to law, the diagnosis and euthanasia of TB is using ITT in Taiwan. The aim of this study was to understand the pathogenicity, distribution of pathogens detection, and analyze of diagnosis method of ITT positive animal. We sampled from ITT positive animal (cattle and deer) for mycobacterial isolation, pathological examination, acid-fast stain, molecular diagnosis and antibody ELISA. ITT-positive sample included 145 dairy cattle and 12 deer with, and 166 dairy cattle serum and 94 deer serum in this study. Mycobacterium spp. could be isolated from 47 animal (47 / 144, included cattle 132 and deer 12; 32.64 %), 31 out of 144 (21.53%) were identified as Mycobacterium bovis. Gross lesion (gross lesion and histopathology, acid-fast stain and culture) was 56.69 % (89 / 157) positive rate. Most of gross lesions were retropharynx lymph node and mediastinal lymph nodes. The PCR detection rate was higher at hilar lymph nodes, mediastinal lymph nodes and retropharynx lymph node. Those organs could suggest being the sample to diagnosis TB using. Analyze detection rate of Mb-ELISA, Mb-Rp-ELISA and PCR for ITT positive cattle. The result were 4.76 % (4 / 84), 4.76 % (4 / 84) and 86.9 % (73 / 84), respectively. We found that Mb-ELISA or Mb-Rp-ELISA was high specificity but low sensitivity. To detect the mycobacterial infection humoral immunity response did not produce antibody. On the other hand, the sensitivity and specificity of PCR was better than others, and could be an aid for TB diagnosis when compared to ITT result. The sequence of M. bovis was no different significantly between ITT positive animals. Same genotype may infect cattle among different farms. Conclusion of this study, most of ITT positive animals were infected by M. bovis. Retropharynx lymph node, hilar lymph nodes and mediastinal lymph nodes were most lesions found in cattle. The lesions in contrast of deer were found in retropharynx lymph node and lung. Ante mortem diagnosis for TB was primarily relied on ITT test. Other diagnosis method could be an aid for. The DNA sequences variation of M. bovis isolated from deer and cattle were no different significantly, M. bovis infection shared similar phylogenetic relationship.

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Ho, Shao-Wei, i 何紹瑋. "Phylogenetic signal in eco-physiological traits and signature of positive selection in biosynthetic genes in stone oaks (Lithocarpus, Fagaceae)". Thesis, 2016. http://ndltd.ncl.edu.tw/handle/64258185756539404407.

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博士
國立臺灣師範大學
生命科學系
104
The epicuticular waxes are synthesized and transported by wax-related genes in plants. The wax crystals serve as defensive traits and are considered as a trade-off between physical and chemical traits e.g. phenolic acids. Besides, the leaf epicuticular wax may be related to photosynthetic efficiency. I select stone oaks (Lithocarpus, Fagaceae) as our research materials and obtain genetic and physiological data to investigate whether the presence/absences of leaf epicuticular wax is an adaptive trait in stone oaks. The phylogenetic relationship of stone oaks reconstructed by six reference genes showed that trait shifts at least three times from non-crystalized waxy into crystalized waxy epidermis since 140 Mya to 80Mya. I sequenced and tested positive selection signals in four wax-related genes, CER1, CER3, CER5, and CER7, which are categorized as two, backbone synthetic genes, one regulatory, and one transporter genes, respectively. Signature of positive selection on CER1 at three trait transitional events of non-crystalized wax to crystalized wax imply the adaptive feature of presence of leaf epicutucular wax in Lithocarpus. The eco-physiologic analysis showed that contents of phenolic acids and photosynthetic indices are not correlated with leaf epicuticular wax, but certain photosynthetic indices, Y(II), and δ15N showed significant phylogenetic signals associated with the CER1 gene tree. These results suggest the intraspecific differences of photosynthetic efficiency are response to the evolution of backbone gene. In conclusion, the trait shift events of leaf epicuticular wax in stone oaks that are inferred during the period of dramatic climate change during the Middle Miocene to Early Pliocene may be related to the positive selection of wax synthetic genes and associated with difference of photosynthetic efficiency between species.

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Baloyi, Tlangelani. "Drug resistance genotyping and phylogenetic analysis of HIV in chronically infected antiretroviral naive patients". Diss., 2018. http://hdl.handle.net/11602/1342.

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MSc (Microbiology)
Department of Microbiology
Background: Antiretroviral treatment (ART) has grown to be one of the most effective tool in the fight to control HIV/AIDS morbidity and mortality worldwide. However, due to the emergence of drug resistant HIV, ART efficacy can be jeopardized. Drug resistant HIV strain has a potential of becoming a major public threat, as its limit treatment options on people living with HIV. With several findings worldwide reporting drug resistant HIV to be currently being transmitted to ART-naïve persons, measures have been taken to genotype drug resistant HIV prior to treatment initiation. However, in resource limited countries such measures are not executed especially in public sectors due to the costs associated with the required assays for genotyping. Objective: The objectives of the study was to establish a deep sequencing protocol (Next Generation Sequencing-NGS) using an Illumina MiniSeq Platform and subsequently apply it to genotype HIV in chronically infected drug naïve persons for resistance mutations and viral genotypes Methods: HIV positive Individuals without any exposure to ART (Treatment-naive) were recruited. Partial pol fragment (complete protease and ~1104bp reverse transcriptase) were amplified and purified. Libraries were prepared using Nextera XT library preparation kit, fragmented, tagmented, pooled and denatured then sequenced with Illumina MiniSeq instrument. Consensus sequences were derived, aligned and phylogenetically analysed. The Stanford HIV Drug Resistance Algorithm was used to infer the presence of drug resistant mutants, at the viral minority and majority population levels. Results and discussion: An NGS protocol to generate nucleotide sequences for drug resistance inference was established. No major drug resistance mutations were detected against protease, reverse transcriptase inhibitors in the study subjects investigated. Nevertheless, V179D change was observed in one patient (8.3%). V179D has been shown to impact a low-level resistance to NNRTI. On the other hand, several secondary and unusual mutations at known drug sites were detected even at minority threshold level of <20%. Conclusion: No major drug resistance mutations was detected in the drug naïve study population. This finding suggests that there is no risk of treatment failure to the investigated subjects, however it is important to assess the potential phenotypic v | P a g e significance of the identified secondary resistance mutations in the context of HIV-1 subtype C. The established NGS protocol should be applied in subsequent HIV drug resistance studies.
NRF

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Xiao, Dawn Dong-yi. "Phylogeny and Molecular Evolution of the Voltage-gated Sodium Channel Gene scn4aa in the Electric Fish Genus Gymnotus". Thesis, 2014. http://hdl.handle.net/1807/44073.

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Analyses of the evolution and function of voltage-gated sodium channel proteins (Navs) have largely been limited to mutations from individual people with diagnosed neuromuscular disease. This project investigates the carboxyl-terminus of the Nav paralog (locus scn4aa 3’) that is preferentially expressed in electric organs of Neotropical weakly-electric fishes (Order Gymnotiformes). As a model system, I used the genus Gymnotus, a diverse clade of fishes that produce species-specific electric organ discharges (EODs). I clarified evolutionary relationships among Gymnotus species using mitochondrial (cytochrome b, and 16S ribosome) and nuclear (rag2, and scn4aa) gene sequences (3739 nucleotide positions from 28 Gymnotus species). I analyzed the molecular evolution of scn4aa 3’, and detected evidence for positive selection at eight amino acid sites in seven Gymnotus lineages. These eight amino acid sites are located in motifs that may be important for modulation of EOD frequencies.

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