Дисертації з теми "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.
Повний текст джерелаThere 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.
Bleidorn, Christoph, Lars Podsiadlowski, Min Zhong, Igor Eeckhaut, Stefanie Hartmann, Kenneth M. Halanych, and 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/.
Повний текст джерелаEitel, 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.
Повний текст джерелаLehmann, 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.
Повний текст джерелаStarr, 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.
Повний текст джерелаOzdemir, 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.
Повний текст джерелаlleriana, 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.
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/.
Повний текст джерелаOs 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.
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.
Повний текст джерелаGontang, 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.
Повний текст джерелаTitle from first page of PDF file (viewed October 3, 2008). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references.
Fujimoto, Masaki Stanley. "The OGCleaner: Detecting False-Positive Sequence Homology." BYU ScholarsArchive, 2017. https://scholarsarchive.byu.edu/etd/6410.
Повний текст джерелаMcMahon, 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.
Повний текст джерелаWakeling, 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.
Повний текст джерелаErixon, 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.
Повний текст джерелаCooke, 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.
Повний текст джерелаSuvorov, 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.
Повний текст джерелаPeat, 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.
Повний текст джерелаMayberry, 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.
Повний текст джерелаIt 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.
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.
Повний текст джерелаAfrache, 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.
Повний текст джерелаIn 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
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.
Повний текст джерелаSousa, 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.
Повний текст джерелаMeyer, Achim [Verfasser]. "Molecular phylogenetic inferences on the position of the Mollusca within the Lophotrochozoa / Achim Meyer." 2009. http://d-nb.info/1000743713/34.
Повний текст джерелаLehmann, Jörg. "Relative Timing of Intron Gain and a New Marker for Phylogenetic Analyses." Doctoral thesis, 2013. https://ul.qucosa.de/id/qucosa%3A12477.
Повний текст джерелаJana, 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.
Повний текст джерелаMüller, 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.
Повний текст джерелаDu, Toit Nicole. "Molecular phylogenetics of Cyclopia Vent.and its position within Podalyrieae (Fabaceae)." Thesis, 2008. http://hdl.handle.net/10210/236.
Повний текст джерелаDr. M. van der Bank
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.
Повний текст джерелаLin, Heng-Ching, and 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.
Повний текст джерела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.
Ho, Shao-Wei, and 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.
Повний текст джерела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.
Baloyi, Tlangelani. "Drug resistance genotyping and phylogenetic analysis of HIV in chronically infected antiretroviral naive patients." Diss., 2018. http://hdl.handle.net/11602/1342.
Повний текст джерелаDepartment 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
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.
Повний текст джерела