Tesi: "Phylogenetic analysis"

1

Krig, Kåre. "Methods for phylogenetic analysis". Thesis, Linköping University, Department of Mathematics, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-56814.

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

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

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

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2

Gottschling, Marc. "Phylogenetic analysis of selected Boraginales". [S.l. : s.n.], 2003. http://www.diss.fu-berlin.de/2003/30/index.html.

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3

Boudko, Ekaterina. "Phylogenetic Analysis of Subtribe Alopecurinae (Poaceae)". Thèse, Université d'Ottawa / University of Ottawa, 2014. http://hdl.handle.net/10393/30696.

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Subtribe Alopecurinae (Poeae, Poaceae) sensu lato‘s seven genera share interesting morphological similarities (dense spicate panicles and one-flowered spikelets) that were widely thought to have a common origin. However, recent molecular evidence for three of the genera has suggested that the subtribe may be polyphyletic. To test this, five DNA regions were sequenced and analyzed using phylogenetic methods. Results confirm that Alopecurinae s.l. as presently treated is polyphyletic and should be dissolved. Additionally, the genus Cornucopiae may be just another Alopecurus. Limnas and Pseudophleum are not closely allied to Alopecurus or each other, and are even further from Phleum. Phleum is a distinct lineage that is not closely allied to any other included Alopecurinae genus. Evidence for revising infrageneric classifications of Alopecurus and Phleum is presented, as is evidence for separating A. magellanicus into two or more subspecies.

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4

Williams, Annette Mary. "Phylogenetic analysis of the genus Streptococcus". Thesis, University of Reading, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.333267.

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5

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

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6

Yu, Junjie, e 于俊杰. "Phylogenetic tree reconstruction with protein linkage". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2012. http://hub.hku.hk/bib/B49618167.

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

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7

Paquette, Lance. "Phylogenetic analysis of the bryozoan Suborder Rhabdomesina". Diss., Connect to online resource - MSU authorized users, 2008.

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8

Park, Hyun Jung. "Large-scale analysis of phylogenetic search behavior". [College Station, Tex. : Texas A&M University, 2007. http://hdl.handle.net/1969.1/ETD-TAMU-1452.

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9

Msimanga, Wela Patrick. "Phylogenetic analysis of HIV-1 in Mpumalanga". Thesis, Stellenbosch : Stellenbosch University, 2013. http://hdl.handle.net/10019.1/80344.

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Thesis (MScMedSc)--Stellenbosch University, 2013.
The diversity of HIV-1 sequences derived from patients in Bushbuckridge, Mpumalanga, was investigated. The gag p24, pol p10 and p66/p51, pol p31 and env gp41 gene fragments from 51 patients were amplified and sequenced. Quality control on the sequences was carried out using the LANL QC online tool. HIV-1 subtype was assigned using the LANL QC (RIP), REGA and jpHMM online tools. Subtype for the pol gene fragment was further designated using the SCUEAL online tool. Most of the sequences, that is 89%, belonged to HIV-1 subtype C. LANL QC (RIP), REGA, jpHMM also detected recombinants in 11% of the sequences. One of the isolates could only have the env gp41 gene fragment amplified and sequenced, which was determined to be HIV-1 subtype B. Phylogenetic analysis using the Neighbor-Joining and Maximum Likelihood methods from MEGA v 5 showed that, except for the env gp41 designated as a subtype B, all sequences in the study clustered with HIV-1 subtype C. Significantly, phylogenetic analysis showed that not only are the Bushbuckridge, Mpumalanga sequences related to HIV-1 subtype C sequences from southern Africa, India, Ethiopia and Brazil, but it is possible there has been multiple introductions of HIV-1 in the province. SDRMs were observed in two samples.

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10

Couto, Diogo Ribeiro do. "A PHYLOGENETIC ANALYSIS OF FASCIOLARIIDAE (GASTROPODA: BUCCINOIDEA)". Universidade de São Paulo, 2017. http://www.teses.usp.br/teses/disponiveis/38/38131/tde-08022017-214445/.

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The neogastropod family Fasciolariidae comprise of important representatives of tropical and subtropical molluscan assemblages, with over 500 species in the subfamilies Fasciolariinae, Fusininae and Peristerniinae. Fasciolariids with many well-known species such as tulip shells, horse-conchs, spindles, among others have a long complicated taxonomical history, with several genus names being used to group heterogeneous contingents of many unrelated species. Recently, however, taxonomical revisions have begun to set straight its taxonomy. The present work aims to resolve the phylogeny of the family Fasciolariidae, through: 1) a morphological phylogenetic parsimony analysis in TnT based on 95 characters and 53 taxa which revealed a monophyletic Fasciolariidae, with the genera Dolicholatirus and Teralatirus representing the first split in the family, followed by three splits that correspond to a fusinine grade, which also include the genus Pseudolatirus (Peristerniinae); a last split groups the peristerniine genera Peristernia and Fusolatirus, while the last group comprises of fasciolariines and the remaining peristerniines. None of these clades correspond to the present-day accepted circumscription of the three recognized subfamilies. 2) Complementing the work of Couto et al. (2016), which used a five-gene molecular dataset to analyze the phylogeny of the family. To this dataset, the previous morphological matrix was added, generating a total evidence dataset that was implemented in POY. This analysis revealed a non-monophyletic family with the genera Dolicholatirus and Teralatirus as non-fasciolariids; the remaining fasciolariids are well-supported, with the first split a monophyletic Fusininae and Pseudolatirus; a second split groups Peristernia and Fusolatirus; while the last, the remaining peristerniines and fasciolariines. Total evidence was congruent with the morphological data with the exception of the Fusininae that appeared as a crown-group and not as a grade; Lamellilatirus lamyi (Peristerniinae) nested within the fasciolariines. Finally, 3) supplement the phylogenetic analysis of Simone (2011), inserting the analyzed taxa from the morphological analysis in the same dataset. This resulted in a monophyletic Buccinoidea superfamily, a monophyletic Fasciolariidae, despite low resolution of relationship for internal taxa; Dolicholatirus nested within Fasciolariidae and the fusinines with Pseudolatirus appeared as a monophyletic crown-group.
A família de neogastrópodes Fasciolariidae é composta por representantes significativos da malacofauna em mares tropicais e subtropicais, com mais de 500 espécies descritas nas subfamílias Fasciolariinae, Fusininae e Peristerniinae. Os fasciolarídeos possuem um longo e confuso histórico taxonômico, com muitas espécies sendo alocados em gêneros claramente heterogêneos, resultando em agrupamentos que não refletem relação de parentesco. O presente estudo tem como objetico gerar hipóteses de filogenia da família Fasciolariidae; dessa maneira, foi realizada: 1) uma análise filogenética através de parcimonia no programa TnT, baseada em 95 caracteres morfológicos e 53 espécies, na qual demostrou a monofilia da família. Em relação aos arranjos internos dos fasciolarídeos, as subfamílias que compõem esse clado não são monofiléticas. Segundo a topologia obtida, observou-se que a primeira divergência separa um grupo com os gêneros Dolicholatirus e Teralatirus; a seguir, três divisões que correspondem a um grado de fusiníneos, que também inclui o gênero Pseudolatirus (Peristerniinae); uma última divisão, na qual se observa uma dicotomia que agrupa os gêneros de peristerníneos Peristernia e Fusolatirus, e os demais peristerníneos e fasciolaríneos. 2) Complementar o trabalho de Couto et al. (2016), que utilizaram dados moleculares de cinco genes para analisar a filogenia da família. A esses dados, foram incluídos também a matriz da análise morfológica, a fim de realizar uma análise de evidência total implementada no programa POY. O resultado dos dados concatenados corrobora com a análise molecular evidenciando a família Fasciolariidae como um clado não monofilético, uma vez que os gêneros Dolicholatirus e Teralatirus não estão incluídos na família; os demais fasciolarídeos formam um clado com uma primeira divisão que separa os fusiníneos e Pseudolatirus dos demais; uma segunda divisão compondo os peristerníneos Peristernia e Fusolatirus e a última agrupa os demais peristerníneos e fasciolaríneos. Dados de evidência total foram congruentes com a análise morfológica, com exceção dos fusiníneos, que apareceram como um grupo monofilético e Lamellilatirus lamyi (Peristerniinae) dentro dos fasciolaríneos. Finalmente, 3) inserir as espécies analisadas na análise morfológica, na matriz de dados de Simone (2011). Esta última análise resultou um uma superfamília Buccinoidea monofilética, a família Fasciolariidae sendo monofilético apesar de com uma topologia com pouca resolução interna para os táxons internos; Dolicholatirus e Teralatirus estão incluídos na família e os fusiníneos mais o gênero Pseudolatirus como um grupo monofilético.

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11

Robson, Brown Katharine Amanda. "A phylogenetic systematic analysis of homonid behaviour". Thesis, University of Cambridge, 1995. https://www.repository.cam.ac.uk/handle/1810/271944.

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12

AL-Saghir, Mohannad Ghazi. "Phylogenetic Analysis of the Genus Pistacia (Anacardiaceae)". Diss., Virginia Tech, 2006. http://hdl.handle.net/10919/28131.

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Pistacia is an economically important genus because it contains the pistachio crop, P. vera, which has edible seeds of considerable commercial importance. The evolutionary history of the genus and the taxonomic relationships among the species are controversial and not well understood. This study that has been conducted on this genus to refine taxonomic and evolutionary relationship utilizing different types of data (including morphology, anatomy and molecular) The studied species were the following: Pistacia aethiopica J. O. Kokwaro, P. atlantica Desf., P. chinensis Bunge, P. eurycarpa Yaltirik, P. falcata Becc. ex Martelli, P. integerrima Stew. ex Brand., P. khinjuk Stocks, P. lentiscus L., P. mexicana HBK, P. mutica Fisch. & Mey., P. palaestina Boiss., P. terebinthus L., P. texana Swingle, P. vera L., and P. weinmannifolia Poiss. ex Franch. Phylogenetic analysis based on morphological data strongly supported the monophyly of Pistacia. The genus divided into two monophyletic groups. One group (Section Pistacia) contains P. atlantica, P. chinensis, P. eurycarpa, P. falcata, P. integerrima, P. khinjuk, P. mutica, P. palaestina, P. terebinthus, and P. vera while the other group (Section Lentiscus) contains P. aethiopica, P. lentiscus, P. mexicana, P. texana, and P. weinmannifolia. In anatomical analysis, all species had anomocytic stomata. In most species, the stomata density was higher on the abaxial surface than the adaxial. The ratio of abaxial to adaxial stomatal density varied from 0.0 to 1.7. Stomatal distribution may provide insights into how Pistacia species evolve in terms of leaf anatomy and respond to different climatic changes. Stomatal distribution changed (losing stomata on either surface) as the genus moved into regions of higher rainfall. This study revealed leaflets of P. vera, which have random orientation, were isobilateral, while leaflets of the other species were dorsiventral and were oriented horizontally. RAPD analysis showed that P. khinjuk and P. vera are very close species. This study provides more insights into understanding the evolution, taxonomy and genetics of this economically important genus.
Ph. D.

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13

Lewis, Louise Ann. "Molecular phylogenetic analysis of Neochloris (Chlorophyceae, Chlorophyta) /". The Ohio State University, 1991. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487688507505424.

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14

Ferguson, Meg Elizabeth. "Statistical Analysis of Species Level Phylogenetic Trees". Bowling Green State University / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1503051433382274.

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15

Jandhyam, Haritha Lakshmi. "Molecular phylogenetic analysis of novel spiroplasma isolates". Click here to access thesis, 2009. http://www.georgiasouthern.edu/etd/archive/spring2009/haritha_l_jandhyam/jandhyam_haritha_l_200901_ms.pdf.

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Thesis (M.S.)--Georgia Southern University, 2009.
"A thesis submitted to the Graduate Faculty of Georgia Southern University in partial fulfillment of the requirements for the degree Master of Science." Directed by Laura B. Regassa. ETD. Includes bibliographical references (p. 64-69) and appendices.

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16

Powell, Robyn Faye. "Systematics, diversification and ecology of the Conophytum-clade (Ruschieae; Aizoaceae)". University of the Western Cape, 2016. http://hdl.handle.net/11394/5453.

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Philosophiae Doctor - PhD
The Ruschieae is the most diverse and speciose tribe within the large subfamily Ruschioideae (Aizoaceae), with approximately 71 genera and a distribution centred in the arid parts of the Greater Cape Floristic Region (GCFR) of South Africa. Recent phylogenetic analyses provided the first insights into generic relationships within the tribe, with a number of novel generic relationships discovered. The tribal phylogeny recovered 12 large clades, of which the Conophytum-clade was one the most morphologically diverse based on leaf and capsule characters. The Conophytum-clade is an early-diverging lineage of the Ruschieae and includes the following 10 genera: Cheiridopsis N.E.Br., Conophytum N.E.Br., Enarganthe N.E.Br., Ihlenfeldtia H.E.K.Hartmann, Jensenobotrya A.G.J.Herre, Namaquanthus L.Bolus, Octopoma N.E.Br., Odontophorus N.E.Br., Ruschianthus L.Bolus and Schlechteranthus Schwantes. The present study presents an expanded phylogenetic analysis of the Conophytum-clade, with the sampling of the majority of species in the genera and a representative sampling (56% of species) of the speciose genus Conophytum. Phylogenetic data for up to nine plastid gene regions (atpB–rbcL, matK, psbJ–petA, rpl16, rps16, trnD– trnT, trnL–F, trnQᶷᶷᶢ–rps16, trnS–trnG) were produced for each of the sampled species. The produced plastid data was analyses using maximum parsimony, maximum likelihood and Bayesian inference. The combined plastid phylogenetic analyses were used in combination with morphological, anatomical and palynological data to assess generic and subgeneric circumscriptions within the clade. Upon assessment of generic circumscriptions in the Conophytum-clade, the number of recognised genera in the clade decreased from ten to seven. Arenifera A.G.J.Herre, which had not been sampled in any phylogeny of the Ruschieae, and Octopoma were recovered as polyphyletic, with species placed in the Conophytum-clade, while the type species was placed in the xeromorphic clade of the tribal phylogeny. The species of Arenifera and Octopoma placed in the Conophytum-clade were subsequently included in Schlechteranthus upon assessment of generic circumscriptions between the taxa. Two morphological groupings were recognised within Schlechteranthus, one including the species of Schlechteranthus and the other including species previously recognised as Arenifera and Octopoma. These two morphological groupings were treated as subgenera, with the erection of the new subgenus Microphyllus R.F.Powell. A detailed taxonomic revision of subgenus Microphyllus is presented with a key to species, descriptions of the species (including a new species: S. parvus R.F.Powell & Klak), known geographical distributions and illustrations of the species. In addition to the changes mentioned above, the expanded sampling and phylogenetic analyses of the Conophytum-clade recovered Ihlenfeldtia and Odontophorus embedded in Cheiridopsis. The species of Ihlenfeldtia were recovered with species of heiridopsis subgenus Aequifoliae H.E.K.Hartmann, while the species of Odontophorus were recovered as polyphyletic within the Cheiridopsis subgenus Odontophoroides H.E.K.Hartmann clade. Cheiridopsis was subsequently expanded to include the species of Ihlenfeldtia and Odontophorus, with these species accommodated in the subgenera of Cheiridopsis. The phylogenetic placement and relationship of these species was supported by the shared capsule morphology. The expanded sampling of the clade did not resolve the phylogenetic relationship of the monotypic genera Enarganthe, Jensenobotrya, Namaquanthus and Ruschianthus, with these genera unresolved in the Conophytum-clade. These genera however, exhibit a unique combination of morphological characters, such as a glabrous leaf epidermis and variation in pollen exine and colpi structure, in contrast to the other genera of the clade. The assessment of the generic circumscription of these genera, based on the molecular, morphological, anatomical and palynological data suggested that the generic statuses of these monotypic genera should be maintained. The expanded phylogenetic sampling of the morphologically diverse and speciose genus Conophytum recovered the genus as monophyletic. This monophyly was supported by the unique floral type in Conophytum, with the fused petaloid staminodes forming a tube. None of the sectional classifications were recovered as monophyletic but the phylogenetic analyses did recover a few clades which more or less corresponded to the current sectional classification of the genus. A number of clades were also recovered which included species from a range of different sections. Diverse leaf and floral traits were shown to have evolved numerous times across the genus. This was particularly interesting with regards to the selected floral traits, as the phylogeny indicated a number of switches in floral morphologies across the genus. The floral diversity was assessed in complex species communities of Conophytum across the GCFR, where up to 11 species of Conophytum are found occurring sympatrically, and floral traits were shown to be different across the species within the communities. Pollination competition and adaptation were suggested as possible drivers of floral diversity in the genus, with differences in phenology, anthesis and floral morphology within the species complex communities. The unique floral type of Conophytum has enabled the species to develop a diverse range of specialised flowers, with a variety of structures, scents and colours, resulting in the diverse floral morphologies found across the genus. The complex Conophytum species communities included both closely as well as distantly related species, suggesting the soft papery capsules of Conophytum are wind dispersed. This adaptation to long distance seed dispersal resulted in a significantly higher phylogenetic diversity in Conophytum when compared to its sister genus, Cheiridopsis. A population genetics study of Conophytum also suggested that the capsules may be wind dispersed, with an indication of genetic connectivity between the geographically isolated populations of C. marginatum Lavis across the Bushmanland Inselberg Region. Although the capsules are dispersed by wind, the seeds are released from the hygrochastic capsules by runoff during rainfall events. The relationship between seed dispersal and runoff is evident from the genetic structure of populations of C. maughanii N.E.Br. and C. ratum S.A.Hammer that occur on the tops and the surrounding bases of the inselbergs, as the drainage pattern was found to directly influence population structure in these species. In addition, the AFLP analyses provided insight into the conservation of the flagship species C. ratum. The summit populations of this species were shown to sustain the populations at the base of the Gamsberg. This finding is especially important, as the distribution of the species is restricted to the Gamsberg inselberg, where mining has already commenced as of this year.
National Research Foundation (NRF)

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17

Bauer, Jennifer E. "A Phylogenetic and Paleobiogeographic Analysis of the Ordovician Brachiopod Eochonetes". Ohio University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1397486053.

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18

Habib, Farhat Abbas. "Genotype-phenotype correlation using phylogenetic trees". Columbus, Ohio : Ohio State University, 2007. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1187297400.

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19

MUNDELL, J. NICOLE. "PHYLOGENETIC ANALYSIS OF KENTUCKY STRAINS OF XYLELLA FASTIDIOSA". UKnowledge, 2005. http://uknowledge.uky.edu/gradschool_theses/406.

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Phytopathogenic bacterium, Xylella fastidiosa, causes a number of economically important diseases, including Pierces disease (PD) of grape and bacterial leaf scorch (BLS) of a number of landscape trees. In Kentucky (KY), BLS affects a number of shade trees including many oak and maple species. In 2001, PD was diagnosed in grapevines in western KY. Xylella fastidiosa is also detected in many asymptomatic landscape plants and grasses. It was the goal of this research to identify hosts of X. fastidiosa around KY and use phylogenetic analysis to compare sequences of the 16S rDNA and gyrase B (gyrB) genes between samples. This research tests the hypothesis that sequence comparison can identify asymptomatic hosts and vectors that serve as a source of inoculum for pathogenic strains of X. fastidiosa. Plant collections were done in urban areas of KY between 2002 and 2004 and samples were tested for the presence of X. fastidiosa by ELISA and PCR. A number of symptomatic and asymptomatic plants were found to be hosts. Primer sets specifically developed for X. fastidiosa were used to amplify part of the 16S rDNA and the gyrB gene from DNA extracted directly from plant tissue. Sequence data from these specifically amplified products were assembled using Phrap, aligned with ClustalW, then phylogenetic analysis was done with Paup 4.0b10 beta. Comparisons with strains outside of Kentucky were also done using X. fastidiosa sequence obtained from NCBI. Maximum parsimony (MP) trees from the 16S rDNA showed a clade of sequence from oak and grass samples that is an outgroup to sequence from NCBI and other samples in this study. According to BLAST, sequences in this outgroup clade seem to be more closely related to the genera Xanthomonas or Stenotrophomonas than Xylella. However, the gyrB gene MP tree showed sequence from three of the samples that were part of this outgroup clade as being closely related to those X. fastidiosa sequences that are part of the ingroup of both 16S rDNA and gyrB trees. The topology difference between the 16S rDNA and gyrB trees suggest there may have been recombination in the genomic region containing one of these genes.

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20

Martinez-Murcia, Antonio J. "Phylogenetic analysis of the genera Leuconostoc and Aeromonas". Thesis, University of Reading, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.336137.

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21

Cai, Junpeng. "Molecular phylogenetic analysis on some ascomycetous spoilage yeasts". Thesis, University of Reading, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.297332.

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22

Sheehy, Robert Rowland. "A phylogenetic analysis of the Accipitridae (class Aves)". Diss., The University of Arizona, 1995. http://hdl.handle.net/10150/187367.

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The avian family Accipitridae is a large, diverse family composed of approximately 230 species divided into 56 genera. The evolutionary relationships among Acciptrid taxa have been examined previously using phenetic and parsimony approaches and a variety of data sets. These studies have resulted in conflicting phylogenies, presumably due to the high level of homoplasy, perhaps, the result of convergence on diet. To develop a firm understanding of the relationships among the major species groups (i.e., morphological types) an analysis of DNA sequence data from the mitochondrial encoded cytochrome-b gene was undertaken. Parsimony, distance and maximum likelihood methods were used to explore the phylogenetic relationships among the Accipitridae. Major findings of the molecular study includes support for the polyphyly of the Kite genera and the sister group relationship of the Osprey (Pandion) with Acciptrid taxa. Evidence based on branch length analysis suggest one or two of periods of rapid morphological diversification. Osteological characters from 44 genera were analyzed alone, and in concert with molecular data. These data yielded phylogenetic trees that were very similar to those trees produced solely by the molecular data. Statistical support for the osteological tree, as demonstrated by bootstrap values, was very weak; supporting, only partially, the clade of old world vultures (Aegypiinae). The phylogenetic signal contained in the osteological data set was estimated using the g1 statistic determined from random tree length distributions. G1 values were found to be dependent on the frequency distribution of character states. Analysis of the g1 statistic from native and shuffled data sets was found to be a less biased method of examining a data set for phylogenetic signal. Divergence times estimated from branch lengths suggest that the Accipitridae diverged from other diurnal raptors approximately 75 million years ago. Clades representing the major morphological diversity among the Accipitridae diverged about 40 million years ago over a period of approximately 7 million years.

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23

Antony, Lucille Marilyn May Kriger d'Amorim. "A phylogenetic analysis of the Rhodacaroidea (Acari: mesostigmata) /". The Ohio State University, 1986. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487268021748041.

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24

Malosso, Elaine. "Effects of plant amendment on microbial community structure and fungal biomass in Antarctic soils". Thesis, University of Newcastle Upon Tyne, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.289240.

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25

Chamberlain, A. T. "A taxonomic review and phylogenetic analysis of Homo habilis". Thesis, University of Liverpool, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.382041.

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26

Zhang, Jiajie [Verfasser]. "Models and algorithms for phylogenetic marker analysis / Jiajie Zhang". Lübeck : Zentrale Hochschulbibliothek Lübeck, 2015. http://d-nb.info/1074176758/34.

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27

Buendia, Patricia. "Phylogenetic analysis of within-host serially-sampled viral data". FIU Digital Commons, 2006. http://digitalcommons.fiu.edu/etd/2019.

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The primary goal of this dissertation is the study of patterns of viral evolution inferred from serially-sampled sequence data, i.e., sequence data obtained from strains isolated at consecutive time points from a single patient or host. RNA viral populations have an extremely high genetic variability, largely due to their astronomical population sizes within host systems, high replication rate, and short generation time. It is this aspect of their evolution that demands special attention and a different approach when studying the evolutionary relationships of serially-sampled sequence data. New methods that analyze serially-sampled data were developed shortly after a groundbreaking HIV-1 study of several patients from which viruses were isolated at recurring intervals over a period of 10 or more years. These methods assume a tree-like evolutionary model, while many RNA viruses have the capacity to exchange genetic material with one another using a process called recombination. A genealogy involving recombination is best described by a network structure. A more general approach was implemented in a new computational tool, Sliding MinPD, one that is mindful of the sampling times of the input sequences and that reconstructs the viral evolutionary relationships in the form of a network structure with implicit representations of recombination events. The underlying network organization reveals unique patterns of viral evolution and could help explain the emergence of disease-associated mutants and drug-resistant strains, with implications for patient prognosis and treatment strategies. In order to comprehensively test the developed methods and to carry out comparison studies with other methods, synthetic data sets are critical. Therefore, appropriate sequence generators were also developed to simulate the evolution of serially-sampled recombinant viruses, new and more through evaluation criteria for recombination detection methods were established, and three major comparison studies were performed. The newly developed tools were also applied to “real” HIV-1 sequence data and it was shown that the results represented within an evolutionary network structure can be interpreted in biologically meaningful ways.

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28

Graham, Sean W. "Phylogenetic analysis of breeding-system evolution in heterostylous monocotyledons". Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/tape16/PQDD_0002/NQ27937.pdf.

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29

Wang, Jeremy R. "Analysis and Visualization of Local Phylogenetic Structure within Species". Thesis, The University of North Carolina at Chapel Hill, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=3562960.

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While it is interesting to examine the evolutionary history and phylogenetic relationship between species, for example, in a sort of "tree of life", there is also a great deal to be learned from examining population structure and relationships within species. A careful description of phylogenetic relationships within species provides insights into causes of phenotypic variation, including disease susceptibility. The better we are able to understand the patterns of genotypic variation within species, the better these populations may be used as models to identify causative variants and possible therapies, for example through targeted genome-wide association studies (GWAS). My thesis describes a model of local phylogenetic structure, how it can be effectively derived under various circumstances, and useful applications and visualizations of this model to aid genetic studies.

I introduce a method for discovering phylogenetic structure among individuals of a population by partitioning the genome into a minimal set of intervals within which there is no evidence of recombination. I describe two extensions of this basic method. The first allows it to be applied to heterozygous, in addition to homozygous, genotypes and the second makes it more robust to errors in the source genotypes.

I demonstrate the predictive power of my local phylogeny model using a novel method for genome-wide genotype imputation. This imputation method achieves very high accuracy—on the order of the accuracy rate in the sequencing technology—by imputing genotypes in regions of shared inheritance based on my local phylogenies.

Comparative genomic analysis within species can be greatly aided by appropriate visualization and analysis tools. I developed a framework for web-based visualization and analysis of multiple individuals within a species, with my model of local phylogeny providing the underlying structure. I will describe the utility of these tools and the applications for which they have found widespread use.

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30

Broad, Gavin Roy. "Phylogenetic analysis of host utilisation patterns in parasitoid hymenoptera". Thesis, Imperial College London, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.368910.

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31

Savva, George Mario. "Towards a liklihood framework for whole genome phylogenetic analysis". Thesis, University of East Anglia, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.426346.

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32

Pisani, Davide. "Comparing and combining trees and data in phylogenetic analysis". Thesis, University of Bristol, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.247894.

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33

Ho, Pangus. "Analysis of word-order universals using Bayesian phylogenetic inference". Thesis, Massachusetts Institute of Technology, 2012. http://hdl.handle.net/1721.1/77015.

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Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2012.
Cataloged from PDF version of thesis.
Includes bibliographical references (p. 65-66).
This thesis examines the novel approach by Dunn et al. (2011) that employs the Bayesian phylogenetic inference to compute the Bayes Factors that determine whether the evolutions of a set of word-order traits in four language families are correlated or independent. In the first part of the thesis, the phylogenetic trees of the Indo-European and Bantu language families are reconstructed using several methods and the differences among the resulting trees are analyzed. In the second part of the thesis, the trees are used to conduct various modifications to the original experiments by Dunn et al. in order to evaluate the accuracy and the utility of the method. We discovered that the Bayes Factors computation using the harmonic mean estimator is very unstable, and that many of the results reported by Dunn et al. are irreproducible. We also found that the computation is very sensitive to the accuracy of the data because a one-digit error can alter the Bayes Factors significantly. Furthermore, through an examination of the source code of BayesTraits, the software package that were used compute the Bayes Factors, we discovered that Dunn et al. supplied invalid inputs to the software, which renders their whole calculations erroneous. We show how the results of the computations would change if the inputs were corrected.
by Pangus Ho.
M.Eng.

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34

Cobbe, Neville Richard. "Phylogenetic and functional analysis of SMC4 in Drosophila melanogaster". Thesis, University of Edinburgh, 2003. http://hdl.handle.net/1842/11994.

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35

Spencer, Marc Richard. "A Phylogenetic Analysis of the Basal Ornithischia (Reptilia, Dinosauria)". Bowling Green State University / OhioLINK, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1185914798.

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36

Clark, Jonathan Bradley. "A molecular phylogenetic analysis of the intracellular bacteria rickettsiae /". The Ohio State University, 1990. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487678444257197.

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37

Mowbray, Alison. "Molecular and phylogenetic analysis of a Bacillus thuringiensis genetic locus". Thesis, University of Cambridge, 1999. https://www.repository.cam.ac.uk/handle/1810/256731.

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The diptericidal $\textit{Bacillus thuringiensis}$ (Bt) ssp. $\textit{fukuokaensis}$ strains 84-I and 17A were investigated for the presence of novel Cry proteins. N-terminal amino acid, immunological and PCR analysis indicated that both strains contain a novel set of $\delta$-endotoxins. N-terminal amino acid sequence analysis indicated that the larger proteins from each strain (90 and 72-kDa of 84-I and 70 and 65-kDa of 17A) were related to the Cry proteins of Bt ssp. $\textit{israelensis}$(Bti). Immunoblotting experiments confirmed that Cry10A-type proteins were present in both strains although subsequent PCR did not give a positive reaction for either strain using $\textit{cry10A}$ specific primers indicating that the Cry10-types were indeed novel. To further investigate the 65-kDa protein of 17A, the gene encoding it was cloned from a size-enriched plasmid DNA library. Unsuccessful attempts were also made to clone the 90-kDa protein of 84-I. Sequence alignments of the deduced protein product of the 17A gene ($\textit{am1}$) showed it to represent the second identification of a natural C-terminal truncate of a Cry4-type protein, the first being Cry10A. The missing C-terminal region of AMl appears to be encoded as a complete Orf ($\textit{am2}$) immediately downstream of the first protein gene. When DNA containing both the $\textit{am1}$ and $\textit{am2}$ genes was subcloned into the pSVP27A expression vector high levels of expression of both proteins were observed in acrystalliferous Bt. The protein was deposited in inclusion bodies which were found to be toxic to $\textit{Dacus oleae}$. Extensive phylogenetic analysis was carried out to determine the relationship between, and possible evolutionary origins of, AMl, the Cry proteins of Bti and two further Cry10A-type $\delta$-endotoxins (Cry19A from Bt ssp. $\textit{jegathesan}$ and Cry20A from 84-I) identified in other laboratories during the course of this project. Based on the amino acid sequence alignment, all seven proteins appear to have evolved from a common ancestor to form three distinct groups which mirror the structural organisation of the genes. Based on these groupings and a previous hypothesis of Dervyn $\textit{et al.}$ (1995), a hypothesis was proposed as to the evolution of the 130-kDa Cry4-type proteins from a 70-kDa Cry2-type ancestor. The above hypothesis is based on the assumption that transfer of $\delta$-endotoxin genes between subspecies has occurred at some point in evolutionary history. Evidence for this transfer was found when the genetic context of the $\textit{am1}$ gene was investigated. Two novel insertion sequences (Tl) and (T2) were identified with sequence similarity to IS$\textit{240A}$ from Bti and an insertion sequence associated with the $\textit{Orf1}$ gene of 84-I. The identification of a further incomplete reading frame with similarity to integrase/recombinase proteins involved in Class II transposition raises the possibility that T1 and T2 form part of a novel Class II transposon. A novel $\alpha$/$\beta$-type small, acid soluble protein (SASP) gene was also discovered. This gene, which may be plasmid encoded, showed considerable sequence similarity to $\alpha$/$\beta$-type SASP from $\textit{Bacillus megaterium}$. The discovery of this gene raises new questions about taxonomic relations between the $\textit{Bacilli}$.

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38

Garnham, Janine B. "Parallelization of the maximum likelihood approach to phylogenetic inference /". Online version of thesis, 2007. http://hdl.handle.net/1850/4778.

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39

Lee, Michael Soon Yoong. "Evolutionary morphology of Pareiasaurs". Thesis, University of Cambridge, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.338262.

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40

Guarido, Milehna. "Identification and phylogenetic analysis of Aedes species (Diptera: Culicidae) and arboviruses associated with them across tropical and temperate regions of South Africa (2015-2018)". Thesis, University of Pretoria, 2020. http://hdl.handle.net/2263/78358.

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Abstract (sommario):

Emerging and re-emerging diseases have increased worldwide in incidence in the past decades. Of these emerging diseases 60.3% are caused by zoonotic pathogens of which 22.8% are arboviruses or arthropod borne viruses. Arboviruses are transmitted by hematophagous insects, especially moquitoes. Multiple factors such as human population growth, climate change and adaptations of certain Aedes mosquito vector species to urban environments and anthropophilic have been attributed to causing this rise in arboviral infections. In Southern Africa, zoonotic arboviruses belonging to the families Flaviviridae (genus Flavivirus), Togaviridae (genus Alphavirus), and those in the order Bunyavirales, family Phenuiviridae: (genus Phlebovirus) and Peribunyaviridae (genus Orthobunyaviruses), have proven, in the past, to be of both medical and veterinary importance. Recent detection of neurological cases in South Africa, most likely, due to flaviviruses, alphaviruses and orthobunyaviruses in the Simbu serogroup, has rekindled interest in these zoonotic diseases. This interest is also warranted because of lack of recent information on arboviral prevalence in mosquito species, distributions, abundance, and ecology, especially of Aedes species, the likely primary vectors of these arboviruses in Southern Africa. To update this lack of information, this study t reports on zoonotic arboviruses circulating in selected areas in the north-eastern provinces of South Africa in mosquitoes with a focus on Aedes. Many Aedes species are morphologically quite difficult to identify especially when they are old, and scales rubbed off in the process of trapping. To aid in the identification of Aedes in this study we provide molecular barcodes for Aedes species occurring in in South Africa and define their phylogenetic relationship with other mainly Afrotropical Aedes mosquitoes based on the cytochrome oxidase I gene sequences. The first Chapter provides a comprehensive review of the literature and describes the importance of arboviruses worldwide and in South Africa, highlighting the role of Aedes mosquitoes as vectors. In Chapter 2, what is known about the broad patterns of Aedes mosquito species diversity, abundance, and distribution in different habitats across selected sites in five different provinces in South Africa is described. The sites selected were chosen because of evidence of neurological cases in humans and animals in recent years likely due to arboviral infections. In total, 61,737 adult mosquitoes were collected from January 2014 to May 2018, using three kinds of carbon dioxide baited trap types About 16% (11,440) were Aedes species, of which, 14 species were recognised or suspected vectors of mosquito-borne diseases because of positive infections, including Aedes mcintoshi which was the most abundant Aedes species captured. The effect of the climatic conditions on the mosquito population dynamics were also investigated. Aedes species were present in the sites following the peak of the rainfall and were mostly captured in temperatures between 18°C and 27°C. Chapter 3 focuses on determining the blood meal source present in engorged Aedes mosquitoes sampled to give an assessment of blood feeding tendencies that would serve useful to determine their vector status. Aedes species were identified feeding on a broad range of livestock, and wildlife, only two specimens were identified as feeding on avian species.Chapter 4 focuses on interpretations of cytochrome oxidase subunit 1 (COI) gene sequences to identify Aedes species in South Africa and to analyse the relationship among the species. A total of 52 COI sequences were aligned representing 21 Aedes species. In several cases these were the first African aedine species uploaded in NCBI GenBank. Neomelaniconion species clustered together, except for Ae. aurovenatus. Finally, the data also suggested that Ae. cumminsii present in South Africa belongs to the subspecies ssp. mediopunctatus. In Chapter 5 results of arboviral infections in Culicidae mosquitoes captured from the selected sites, particularly Aedes species is provided. Arboviral infection or prevalence screening was performed using multiple genus specific polymerase chain reactions (PCR). Alphavirus and Orthobunyavirus were detected in different Culicidae genera, including Aedes, Culex, Anopheles and Mansonia. There were no isolations of pathogenic flaviviruses in mosquitoes. The only alphaviruses detected in mosquitoes were Middelburg, Sindbis and Ndumu viruses during the period of the study. Shuni virus was the only member of Orthobunyavirus genus, detected. Even though, the main aim was to identify pathogenic viruses, several insect-specific viruses belonging to Alphavirus and Flavivirus genera were also detected and these are described in Chapter 6. The numerous arboviruses detected in Culicine mosquitoes, including Aedes species, demonstrate that some species are likely maintaining natural cycling of these arboviruses. Noteworthy, is that mosquito species positive for arboviruses are often the most abundant in the selected sampling locations and that these species blood feed mostly on the larger vertebrates present in the area. Outbreaks possibly occur when the prevalence of certainmosquito species are high due to favourable climatic conditions. Highest arbovirus detections occurred in peri-urban, rural, and conservation areas, indicating that livestock and wildlife likely play an important role in the amplification of these arboviruses. This study highlights the importance of a continues mosquito-based surveillance for arboviruses in South Africa, and the role that Aedes species might be playing in the circulation of these arboviruses. Surveillance for the species that tested positive for pathogenic arboviruses during the arbovirus season may act as an early warning system and can also help to avoid spill over in animals and humans in the area surveyed.
Thesis (PhD)--University of Pretoria, 2020.
Centres for Disease Control and Prevention National Research Foundation
Medical Virology
PhD
Unrestricted

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41

Zhen, Zhao. "The Qphyl System: a web-based interactive system for phylogenetic analysis". Thesis, The University of Sydney, 2008. http://hdl.handle.net/2123/2691.

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Phylogenetic tree reconstruction is a prominent problem in computational biology. Currently, all computational methods have their limitations and work well only for simple problems of small size. No existing method can guarantee that trees constructed for real-world problems are true phylogenetic trees for large and complex problems mainly because the existing computational models are not very biologically realistic. It has become a serious issue for many important real-life applications which often desire accurate results from phylogenetic analysis. Thus, it is very crucial to effectively incorporate multi-disciplinary analyses and synthesize results from various sources when answering real-life questions. In this thesis, a novel web-based phylogeny reconstruction system with a real-time interactive environment, called Qphyl (short for quartet-based phylogenetic analysis) is introduced. The Qphyl system uses a new interactive approach to enable biologists to greatly improve the final results through effectively dynamic interaction with the computation, e.g., to move the computation back and forth to different stages so users can check the intermediate results, compare results from different methods and carry out certain manual refinements using their biological domain-specific knowledge in the decision making on how a tree should be reconstructed. Currently the alpha version of this web-based interactive system has been released and accessible through the URL: http://ww-test.it.usyd.edu.au/sogrid/qphyl/.

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42

Zhen, Zhao. "The Qphyl System: a web-based interactive system for phylogenetic analysis". University of Sydney, 2008. http://hdl.handle.net/2123/2691.

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Master of Science
Phylogenetic tree reconstruction is a prominent problem in computational biology. Currently, all computational methods have their limitations and work well only for simple problems of small size. No existing method can guarantee that trees constructed for real-world problems are true phylogenetic trees for large and complex problems mainly because the existing computational models are not very biologically realistic. It has become a serious issue for many important real-life applications which often desire accurate results from phylogenetic analysis. Thus, it is very crucial to effectively incorporate multi-disciplinary analyses and synthesize results from various sources when answering real-life questions. In this thesis, a novel web-based phylogeny reconstruction system with a real-time interactive environment, called Qphyl (short for quartet-based phylogenetic analysis) is introduced. The Qphyl system uses a new interactive approach to enable biologists to greatly improve the final results through effectively dynamic interaction with the computation, e.g., to move the computation back and forth to different stages so users can check the intermediate results, compare results from different methods and carry out certain manual refinements using their biological domain-specific knowledge in the decision making on how a tree should be reconstructed. Currently the alpha version of this web-based interactive system has been released and accessible through the URL: http://ww-test.it.usyd.edu.au/sogrid/qphyl/.

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43

Jong, Yde Sijbrand Diederick Maria de. "Systematic, phylogenetic and biogeographic studies of Atlantic seaweeds". [Leiden] The Netherlands : Rijksherbarium/Hortus Botanicus, Leiden University, 1998. http://catalog.hathitrust.org/api/volumes/oclc/40701628.html.

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44

Garcia, Michael R. "Identification of novel nuclear markers for use in phylogenetic analysis". Tallahassee, Fla. : Florida State University, 2010. http://purl.fcla.edu/fsu/lib/digcoll/undergraduate/honors-theses/2181925.

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Thesis (Honors paper)--Florida State University, 2010.
Advisor: Dr. Gavin J.P. Naylor, Florida State University, College of Arts and Sciences, Dept. of Biology. Includes bibliographical references.

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45

Dunne, Emma Maria. "Investigations in trypanosome diversity and evolution using molecular phylogenetic analysis". Thesis, University of Bristol, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.289775.

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46

Gooder, Stephen John. "A phylogenetic and vicariance analysis of some African forest mammals". Thesis, University of Liverpool, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.359167.

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47

Costa, Helena Sofia Gomes. "Molecular and phylogenetic analysis of parapoxvirus in north American pinnipeds". Master's thesis, Universidade de Lisboa, Faculdade de Medicina Veterinária, 2019. http://hdl.handle.net/10400.5/18138.

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Dissertação de Mestrado Integrado em Medicina Veterinária
Parapoxvirus causes nodular lesions in the skin and mucosal membranes of diverse species of pinnipeds, worldwide. Seal parapoxvirus is currently categorized as a tentative species of the Parapoxvirus genus. Between 2009 and 2018, 22 samples were collected from 12 pinnipeds representing 5 different species (grey seal, harp seal, harbor seal, California sea lion and northern elephant seal) with clinical suspicion of parapoxvirus infection, from rehabilitation facilities on the east and west coast of the United States of America. The aims of this study were to confirm the presence of parapoxvirus in the clinical samples by PCR, to resolve evolutionary relationships to other members of the genus and to determine whether pinnipeds from different species and locations are infected with the same parapoxvirus strains. Parapoxvirus DNA was detected in 11 of the 12 animals. The sequence analysis showed that the parapoxvirus sequences from the seal samples differed significantly from parapoxviruses found in terrestrial hosts and that the pinniped parapoxviruses formed a separated cluster within the genus. Five distinct parapoxvirus variants were detected. Parapoxviruses from harbor seals from the Atlantic and Pacific coast clustered separately, indicating different virus variants in the two subspecies. One variant of parapoxvirus was found in both a California sea lion (Otariidae family) and a northern elephant seal (Phocidae family) housed in the same facility. Therefore, the results of this study support the classification of Seal parapoxvirus as a separate species within the genus Parapoxvirus and give further insight into the phylogenetic relationships between the different circulating Seal parapoxvirus strains.
RESUMO - Análise molecular e filogenética de parapoxvirus em pinípedes norte-Americanos - Os parapoxvírus causam lesões nodulares na pele e mucosa de diferentes espécies de pinípedes, por todo o mundo. O Seal parapoxvirus ainda não se encontra incluído como uma espécie do género Parapoxvirus. Entre 2009 e 2018, foram colhidas 22 amostras de 12 pinípedes de 5 espécies diferentes (foca cinzenta, foca da Groenlândia, foca-comum, leão-marinho Californiano e elefante marinho do norte) com suspeita clínica de infecção por parapoxvírus, internados em diferentes em centros de recuperação nas costas Este e Oeste dos Estados Unidos da América. Os objectivos deste trabalho consistiram em confirmar a presença de parapoxvírus nas amostras por PCR, estudar a relação evolutiva deste vírus com outros membros do género e determinar se pinípedes de diferentes espécies e locais estão ou não infectados com a mesma variante de parapoxvírus. Foi detectado ADN de parapoxvírus em 11 dos 12 animais. A análise das sequências revelou que as sequências virais obtidas a partir das amostras de focas diferiram significativamente dos parapoxvírus encontrados em hospedeiros terrestres e que os parapoxvírus dos pinípedes formaram um agregado separado dentro do género. Foram detectadas cinco variantes distintas de parapoxvirus. Parapoxvírus da espécie foca-comum da costa do Atlântico e do Pacífico agruparam-se separadamente, indicando diferentes variantes de vírus nas duas subespécies. Uma variante de parapoxvirus foi detectada tanto num leão-marinho Californiano (família Otariidae) como num elefante marinho do norte (família Phocidae) alojados na mesma instalação. Desta forma, os resultados deste estudo suportam a classificação do Seal parapoxvirus como uma nova espécie pertencente ao género Parapoxvirus e fornecem uma visão adicional sobre as relações filogenéticas entre as diferentes variantes circulantes de parapoxvírus de pinípedes.
N/A

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48

Curtis, Sarah Maureen. "Enhanced phylogenetic analysis and targeted search for the genus Kribbella". Doctoral thesis, University of Cape Town, 2015. http://hdl.handle.net/11427/15757.

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49

Deng, Ziling. "Phylogenetic analysis of aquatic microbiomes : Evolution of the brackish microbiome". Thesis, KTH, Skolan för kemi, bioteknologi och hälsa (CBH), 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-278730.

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Microorganisms play crucial roles in aquatic environments in determining ecosystemstability and driving the turnover of elements essential to life. Understanding thedistribution and evolution of aquatic microorganisms will help us predict how aquaticecosystems will respond to Global Change, and such understanding can be gained bystudying these processes of the past. In this project, we investigate the evolutionaryrelationship between brackish water bacteria from the Baltic Sea and Caspian Seawith freshwater and marine bacteria, with the goal of understanding how brackishwater bacteria have evolved. 11,276 bacterial metagenome-assembled genomes(MAGs) from seven metagenomic datasets were used to conduct a comparativeanalysis of freshwater, brackish and marine bacteria. When clustering the genomes bypairwise average nucleotide identity (ANI) at the approximate species level (96.5%ANI), the Baltic Sea genomes were more likely to form clusters with the Caspian Seagenomes than with Swedish lakes genomes, even though geographic distancesbetween Swedish lakes and the Baltic Sea are much smaller. Phylogenomic analysisand ancestral state reconstruction showed that approximately half of the brackishMAGs had freshwater ancestors and half had marine ancestors. Phylogeneticdistances were on average shorter to freshwater ancestors, but when subsampling thetree to the same number of freshwater and marine MAG clusters, the distances werenot significantly different. Brackish genomes belonging to Acidimicrobiia,Actinobacteria and Cyanobacteriia tended to originate from freshwater bacteria, whilethose of Alphaproteobacteria and Bacteroidia mainly had evolved from marinebacteria.
Mikroorganismer spelar avgörande roller i akvatiska ekosystem där de driverkretsloppen av näringsämnen. En ökad förståelse för hur mikroorganismer anpassarsig till miljöförändringar är viktigt för att förutsäga hur akvatiska ekosystem kommeratt förändras som en konsekvens av global uppvärmning, och sådan förståelse kanuppnås genom att studera tidigare skeenden i evolutionen. I detta projekt undersökervi det evolutionära förhållandet mellan brackvatten-bakterier från Östersjön ochKaspiska havet med sötvattens- och marina bakterier, med målet att förstå hurbrackvatten-bakterier har utvecklats. 11,276 bakteriella arvsmassor somrekonstruerats med metagenomik från sju data-set användes för att utföra enjämförande analys av bakterie-genom från söt-, brack och havsvatten. Klustring avgenomen baserat på parvis genomsnittlig nukleotididentitet (ANI) på ungefärligartnivå (96,5% ANI), grupperade Östersjöns bakterier tillsammans med Kaspiskahavets bakterier mer än med bakterier från svenska sjöar, trots att det geografiskaavståndet mellan svenska sjöar och Östersjön är mycket mindre. Fylogenetisk analysvisade att ungefär hälften av brackvatten arterna hade anfäder från sötvatten ochhälften från havsvatten. De fylogenetiska avstånden var i genomsnitt kortare tillanfaderna i sötvatten, men när man reducerade trädet till att ha samma antal sötvattenoch marina arter var avstånden inte längre signifikant olika. Brackvatten-arter somtillhörde Acidimicrobiia, Actinobacteria och Cyanobacteriia tenderade att härstammafrån sötvattenbakterier, medan de från Alphaproteobacteria och Bacteroidia främsthärstammade från marina bakterier.

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50

Dale, D. "Comparisons of parsimony and likelihood-based methods in phylogenetic analysis". Thesis, University College London (University of London), 2006. http://discovery.ucl.ac.uk/1445406/.

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This work provides a defence of the claim that likelihood based methods provide a better framework for performing phylogenetic analyses on molecular sequences than do parsimony based methods under the conditions studied. Novel work introduced in the thesis includes simulation studies that examine the performance oflikelihood based and parsimony based methods at high evolutionary distances. At these distances, many changes accumulate at a single site causing a catastrophic collapse in the performance of the parsimony analysis. In contrast a well understood mathematical theory involving the use of Fisher's information measure describes the decline in performance oflikelihood methods. Further work compares the performance oflikelihood based methods and parsimony methods under heterotachous conditions, i.e. conditions under which a single site will alter its rate of evolution relative to other sites. A recent claim that parsimony based analyses outperform likelihood is rebutted and a likelihood model is introduced and its performance analysed. Finally likelihood based methods are defined in terms of rates. A method for turning these rates into a probability distribution describing the number of changes of interest across a phylogeny is described. This is then compared to the number of changes inferred under a parsimony analysis. When the true model is known, it is shown that the counts of changes inferred under a parsimony based analysis have a low probability of being correct. It is argued that this accounts for the poor performance of parsimony.

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