To see the other types of publications on this topic, follow the link: Phylogenetic relationship.
Dissertations / Theses on the topic 'Phylogenetic relationship'
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the top 50 dissertations / theses for your research on the topic 'Phylogenetic relationship.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Browse dissertations / theses on a wide variety of disciplines and organise your bibliography correctly.
1
Yamada, Shunsuke. "Phylogenetic relationship of prophages is affected by CRISPR selection in Group A Streptococcus." Kyoto University, 2019. http://hdl.handle.net/2433/242419.
Full text
2
Liu, Hui. "Interspecific hybridization in Leucadendron : capacity building and phylogenetic insights." University of Western Australia. School of Plant Biology, 2007. http://theses.library.uwa.edu.au/adt-WU2007.0181.
Full textAbstract:
Flowers from members of the genus Leucadendron have colourful bracts and long vase life that make them highly desirable cut-flowers. Breeding programs based on interspecific hybridization would encounter difficulty if pre- or post-fertilization barriers exist in the distant crosses. Embryo rescue is one of the commonly used approaches to overcome post-fertilization barriers in wide hybridization. In this study, intersectional and intersubsectional hybridization of Leucadendron was attempted. Observation of pollen-pistil interactions revealed that post-zygotic rejection was the main reason for the incompatibility of the crosses, therefore embryo rescue was adopted and a protocol was developed to raise the hybrids. To better understand the genome structure in the genus, karyotypes of selected species were analyzed. Chromosome examination indicated that all (27) Leucadendron species examined were diploid and had a chromosome number of 2n = 26. The chromosomes were small in size and had predominantly median to submedian centromeres. The karyotypes of the species were rather symmetrical and seemed to be primitive according to Stebbins' karyotype classification. DNA based PCR-RFLP and RAMP markers were developed to identify Leucadendron hybrids at an early age. RAMP analysis showed more discrimination in identifying Leucadendron hybrids than did PCR-RFLP. The occurrence of PCR recombination also proved to be a troublesome issue when using the PCR-RFLP method, whereas the clarity of the interpretion of the RAMP method was not influenced by PCR recombination. Interspecific hybridization in a breeding program can provide valuable information on grouping of the species for systematic purposes. Regression analysis between cross success rate and cpDNA character difference revealed that there was a highly significant correlation between them. Patterns of success for intersectional hybridizations in Leucadendron were generally consistent with current taxonomic hypotheses regarding the sectional division of the genus. Success was generally lower for intersectional crosses than for intrasectional crosses.
3
Ibrahim, Douglas George. "The C₃ and C₄ subspecies of Alloteropsis semialata : phylogenetic relationship and climatic responses." Thesis, University of Sheffield, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.443894.
Full text
4
Crowe, Celeste T. "Using the psbA gene as a measure in determining the phylogenetic relationship among bryophytes." [Johnson City, Tenn. : East Tennessee State University], 2002. http://etd-submit.etsu.edu/etd/theses/available/etd-0516102-110619/restricted/crowect053102a.pdf.
Full text
5
Knauss, Georgia Ellen. "A morphological description of Baptemys wyomingensis and an analysis of its phylogenetic relationship within Kinosternoidea." Thesis, University of Iowa, 2014. https://ir.uiowa.edu/etd/4665.
Full textAbstract:
The clade Kinosternoidea consists of the extant mud and musk turtles (Kinosternidae) and the Central American river turtle Dermatemys mawii. Baptemys, an Eocene turtle taxon from North America, has historically been allied to D. mawii within Dermatemydidae, but this relationship has never been rigorously tested in a global analysis.
Molecular data and multiple morphological characters support monophyly of Kinosternoidea, but kinosternids and D. mawii are vastly different in their morphology, and the relationships of Dermatemys are controversial. Dermatemys mawii is highly adapted to consuming aquatic vegetation and is thus much more similar in gestalt to some emydids than to kinosternids. Dermatemys mawii was historically placed among tortoises (Testudinoidea) by a number of traits pertaining to their fully ossified shell and the development of a secondary palate. Different placements of D. mawii indicate radically different historical biogeographic scenarios and sequences of character evolution. Few relevant morphological characters have been used in global analyses of turtle relationships, and several fossil taxa are known that could prove critical to resolving this debate.
Baptemys wyomingensis is the best-sampled fossil dermatemydid. A detailed description of B. wyomingensis, along with a consideration of its phylogenetic relationships, indicates additional morphological support for a close relationship with Dermatemys and a placement for D. mawii and Baptemys within Kinosternoidea, as well as an unexpected close relationship with Hoplochelys and Agomphus to the exclusion of the Kinosternids. A review of the alpha taxonomy of Baptemys reveals that the relationships between the species, other than B. wyomingensis and B. garmanii remain unclear due to a lack of published descriptions and it appears likely that Baptemys may be paraphyletic in regard to D. mawii.
6
Choi, Young-A. "Cytogenetic analysis of the phylogenetic relationship between persimmon(Diospyros kaki Thunb..) and several wild relatives(Diospyros spp.)." Kyoto University, 2003. http://hdl.handle.net/2433/148581.
Full textAbstract:
Kyoto University (京都大学)<br>0048<br>新制・課程博士<br>博士(農学)<br>甲第10472号<br>農博第1372号<br>新制||農||881(附属図書館)<br>学位論文||H15||N3853(農学部図書室)<br>UT51-2003-T298<br>京都大学大学院農学研究科農学専攻<br>(主査)教授 米森 敬三, 教授 矢澤 進, 教授 遠藤 隆<br>学位規則第4条第1項該当
7
Arendse, Clement. "On the phylogenetic relationship of South African species of Cladophora (Chlorophyta) based on the 26S (LSU) gene region." Bachelor's thesis, University of Cape Town, 2004. http://hdl.handle.net/11427/26496.
Full textAbstract:
In order to delineate the genus Cladophora in South Africa, several sites along the Cape peninsula were sampled and sequences for the partial26S region of the rRNA were obtained and a phylogram was constructed. The aims of this study were to provide a robust phylogenetic tree describing the relationship between members of the genus Cladophora and related taxa and to determine the origins of South Africa's estuarine species of Cladophora. After DNA extraction and cycle sequencing of products, sequences were aligned and compared to several east coast species (obtained from GENBANK) and a phylogram was constructed. The results yielded several clades within Cladophora; Clad. capensis grouping with Clad. isaacii, Clad sericea and Clad. dalmatica; Cheatomorpha forming a polyphyletic group within Cladophora; and Clad. vagabunda and Clad. laetevirens grouping with the estuarine species. As no Clad. vagabunda or Clad. laetevirens are found along the coast of South Africa, the origins of its estuarine species still remain a mystery and needs further investigation.
8
Gebler, Glenn Frederick. "Phylogenetic relationship among polymorphic oligohymenophorean ciliates, with gene expression in life-history stages of (miamiensis avidus) (ciliophora, oligohymenophorea)." College Park, Md.: University of Maryland, 2007. http://hdl.handle.net/1903/7752.
Full textAbstract:
Thesis (Ph. D.) -- University of Maryland, College Park, 2007.<br>Thesis research directed by: Dept. of Biology. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.
9
Farrell, Sam Hanno. "Adaptive evolution in the Pseudomonas fluorescens Wsp signalling pathway : exploring the relationship between genetic cause and phenotypic effect." Thesis, University of Manchester, 2013. https://www.research.manchester.ac.uk/portal/en/theses/adaptive-evolution-in-the-pseudomonas-fluorescens-wsp-signalling-pathway-exploring-the-relationship-between-genetic-cause-and-phenotypic-effect(d4fc7a28-6da0-477b-9315-34f4b4d71f76).html.
Full textAbstract:
When provided with spatial niches by growth in static nutrient medium, Pseudomonas fluorescens diversifies through adaptive radiation into several well-defined phenotype classes. One of these classes, named wrinkly spreader (WS) for its morphology on agar medium, forms a biofilm at the air-liquid interface through mutations in one of several loci including the genes wspF and awsX. These genes code for negative regulators of di-guanylate cyclases (DGCs). These DGCs catalyse synthesis of cyclic-di-GMP, a second messenger, overproduction of which effects physiological changes leading to overproduction of a cellulose polymer and the WS phenotype. Intriguingly, a diverse range of wspF mutations leads to diversity both in colony morphology and strain fitness.In this study, I investigate genetic and fitness diversity in wrinkly spreaders with the aim of identifying the causal factors that link genetic diversity and physiological factors with diversity in fitness. I approach the subject from several directions, examining the historical context of genetic diversity in wspF and awsX, distribution of control over output in the Wsp pathway and overall fitness effects of different causal factors. I investigate the genetic basis of wrinkly spreader evolution through generation of a large number of novel WS strains and exploration of the distribution of mutations in the wspF and awsX genes. In combination with this I calculate estimates of the past rates of mutation in these genes, derived from a phylogenetic investigation of a group of orthologues. I examine the response of the Wsp pathway to change in WspF function through a novel computational analysis that is capable of revealing valuable information on control in a biological system based purely on model structure. In addition I show how this analysis can be refined through specification of broad estimates of system parameters, thereby avoiding issues related to over-reliance on specific parameter values. Finally, I investigate the fitness implications of these factors, as well as a variety of others, through assays of fitness in a group of WS strains combined with machine learning analyses of predictive relationships between protein and mutation characteristics and experimentally measured strain fitness, and consider the implications of this analysis in the context of intermediate physiological effects.I find that mutations in the WspF protein that lead to the WS phenotype tend to be located in regions of historically strong conservation, the first time that any such pattern to WS mutations has been identified. Mutations in AwsX, on the other hand, do not fit such a pattern. Computational analysis of the Wsp pathway shows that, regardless of model parameters, pathway output is always more sensitive to changes in methylesterase activity by WspF than to changes in phosphorylation of WspF, which may explain the greater frequency of mutations fixed in vivo seen in the methylesterase domain. Despite these patterns, none of a wide range of mutation and sequence-based biochemical characteristics, including local rates of past evolution and size and position of mutations, exhibited any predictive power over WS fitness. Overall, the findings in this study point towards an essential role for complex pleiotropic effects in strongly modulating the fitness effect of different mutations in wspF.
10
Gonzalez, Malinda Wallentine. "Phylogenetic relationship of forest spiny pocket mice (Genus Heteromys) inferred from mitochondrial and nuclear markers with implications for species boundaries." BYU ScholarsArchive, 2005. https://scholarsarchive.byu.edu/etd/263.
Full textAbstract:
I constructed a best estimate phylogeny based on congruence of multiple data sources. In recent years molecular data has been used both to construct phylogenies of taxonomic groups and to aid in the delimitation of new species. I generated and analyzed sequence data for forest spiny pocket mice (Genus Heteromys) for the mitochondrial gene cyt b (1143 bp) and two nuclear gene segments MYH2 (252 bp) and EN2 (189 bp). I used maximum parsimony and Bayesian analyses to infer relationships among species and to provide a framework for using a species delimitation method to investigate the possibility of multiple species within the widespread Heteromys desmarestianus. I found several well-supported lineages within the H.desmarestianus complex, including H. goldmani and H. oresterus. Incorporating karyotype and allozyme data from earlier studies, I found sufficient supporting evidence to justify maintaining H. goldmani and H. oresterus as species as well as identifying four lineages as candidate species. I present a revised taxonomic arrangement within the genus; the subgenus Heteromys should be divided into three species groups: anomalus (H. anomalus and H. australis), gaumeri (H. gaumeri), and desmarestianus (H. desmarestianus, H. goldmani, H. oresterus, and the four candidate species).
11
Peyer, Karin. "A reevaluation of the French Compsognathus of the Tithonian of southeastern France and its phylogenetic relationship with other compsognathids and coelurosaurs." Paris, Muséum national d'histoire naturelle, 2004. http://www.theses.fr/2004MNHN0039.
Full textAbstract:
Les compsognathides sont représentés dans les sédiments du Jurassique supérieur et du Crétacé inférieur d'Europe, de Chine, de Mongolie et d'Amérique du Sud. Actuellement, le genre Compsognathus inclut C. Longipes et C. Corallestris. Une réévaluation du Compsognathus de Canjuers (France) nous fournit, grâce à de nouvelles données crâniennes et postcrâniennes, une information cruciale pour une meilleure compréhension du genre Compsognathus et de l'estimation phylogénétique des Coelurosauria basaux et des Compsognathidae. Le Compsognathus français est quasiment complet et, comme tous les compsognathides, il a une main courte et spécialisée, des épines neurales dorsales en forme d'éventail, un pied pubien non étendu antérieurement et ne possède pas de fenêtre mandibulaire. De plus, l'architecture de son squelette ressemble fortement à celle des coelurosaures non-spécialisés. Les caractères anatomiques révélés chez le Compsognathus bavarois sont quasiment identiques à ceux du spécimen de Canjuers. Les différences peuvent être attribuées à des stades ontogénétiques différents des deux spécimens. Par conséquent, cette étude soutient que C. Corallestris est un synonyme “junior” de Compsognathus longipes. A partir de propres observations et de données déjà publiées, la matrice de données pour l'analyse phylogénétique est composée de 30 taxons terminaux et 347 caractères. L'enracinement a été fait par comparaison avec des extra-groupes composés des genres Herrerasaurus et Coelophysis. L'analyse phylogénétique au niveau espèce montre que le groupe des Compsognathidae est monophylétique près de la base des Maniraptoriformes et plus dérivé que les Ornithomimosauria. Le consensus strict, résultant de deux arbres parcimonieux, a 917 pas, un indice de cohérence de 0,47 et un indice de rétention de 0,63. Dans le clade des Compsognathidae, Scipionyx se retrouve à la base suivi de Sinosauropteryx, Huaxiagnathus, Mirischia et un clade incluant les Compsognathus bavarois et français<br>Compsognathids are represented in Late Jurassic and Early Cretaceous sediments of Europe, China, Mongolia, and South America. The genus Compsognathus currently includes C. Longipes and C. Corallestris. A reevaluation of the French Compsognathus from the Portlandian lithographic limestones of the Tithonian of South-eastern France provides us with new cranial and postcranial information crucial for a better understanding of the genus Compsognathus and the phylogenetic assessment of basal Coelurosauria and Compsognathidae. The French Compsognathus is nearly complete and like all compsognathids has a short and specialized manus, no mandibular fenestra, fan-shaped dorsal neural spines, an anteriorly unexpanded pubic boot, but otherwise has a relatively unspecialized coelurosaurian body plan. Anatomical characters of the Bavarian specimen of Compsognathus are nearly identical to the same characters in the Canjuers specimen. Differences can be attributed to different ontogenetic stages of the two specimens. Therefore this study supports that C. Corallestris is a junior synonym of Compsognathus longipes from Bavaria. The data matrix is based on own my observations and previously published data of 30 (31 including Aristosuchus pusillus, respectively) terminal taxa and 347 characters. Rooting was done by outgroup comparisons with Herrerasaurus and Coelophysis. The species-level phylogenetic analysis shows that the Compsognathidae, consisting of six genera and ten specimens, is a monophyletic group. The phylogenetic analysis resulted in two most parsimonious trees and places the Compsognathidae near the base of the Maniraptiformes more derived than Ornithomimosauria. The resulting strict consensus tree with 920 steps has a consistency index of 0. 47 and a retention index of 0. 63. Scipionyx takes the most basal position within Compsognathidae, followed by Sinosauropteryx, Huaxiagnathus, and Mirischia; the latter is the sister taxon to the clade including the German and French Compsognathus
12
Keivany, Yazdan. "Phylogenetic relationships of Gasterosteiformes (Teleostei, Percomorpha)." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp02/NQ59608.pdf.
Full text
13
Fuentes, Carvajal Andreina. "Phylogenetic relationships within Coleeae (Bignoniaceae juss.)." Click here to access thesis, 2007. http://www.georgiasouthern.edu/etd/archive/fall2007/carvajal_a_fuentes/carvajal_andreina_f_200708_MS.pdf.
Full textAbstract:
Thesis (M.S.)--Georgia Southern University, 2007.<br>"A thesis submitted to the Graduate Faculty of Georgia Southern University in partial fulfillment of the requirements for the degree Master of Science." In Biology, under the direction of Michelle Zjhra. ETD. Electronic version approved: December 2007. Includes bibliographical references (p. 38-42)
14
Figueroa, Alex. "Phylogenetic Relationships and Evolution of Snakes." ScholarWorks@UNO, 2016. http://scholarworks.uno.edu/td/2222.
Full textAbstract:
Snakes represent an impressive evolutionary radiation of over 3,500 widely-distributed species, categorized into 515 genera, encompassing a diverse range of morphologies and ecologies. This diversity is likely attributable to their distinctive morphology, which has allowed them to populate a wide range of habitat types within most major ecosystems. In my first chapter, I provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61). I then use this phylogeny to test hypotheses regarding heterogeneity in diversification rates and how this shaped overall patterns of snake diversity in Chapter 2. I also used the species-level phylogeny to test the evolution of habitat use in snakes, morphological variation, and whether distantly-related species exhibit morphological convergence in Chapter 3. Finally, in Chapter 4 I investigate how prehensile tails effect striking performance in arboreal snakes.
15
Orr, James Wilder. "Phylogenetic relationships of gasterosteiform fishes (Teleostei: Acanthomorpha) /." Thesis, Connect to this title online; UW restricted, 1995. http://hdl.handle.net/1773/5276.
Full text
16
Nyberg, Kruys Åsa. "Phylogenetic relationships and species richness of coprophilous ascomycetes." Doctoral thesis, Umeå University, Ecology and Environmental Science, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-625.
Full textAbstract:
<p>Coprophilous ascomycetes are a diverse group of saprobes, of which many belong to three families, Delitschiaceae, Phaeotrichaceae and Sporormiaceae, within the large order Pleosporales. The natural relationships and circumscription of these families are unclear, especially within the family Sporormiaceae, where the generic delimitation have been questioned. There is also a need to understand how different ecological processes affect species richness and occurrence of coprophilous ascomycetes in general. The aim of this thesis was therefore to test earlier classifications of coprophilous taxa within Pleosporales, using phylogenetic analyses of DNA sequences; and to study how the habitat, dung type and herbivores´ food choice may affect the species richness and species composition of coprophilous ascomycetes.</p><p>A phylogenetic study shows that coprophilous taxa have arisen several times within Pleosporales. Sporormiaceae and Delitschiaceae are separate monophyletic groups and should continue to be recognized as two distinct families within Pleosporales. Phaeotrichaceae forms a monophyletic group, and is, unexpectedly, a strongly supported sister-group to Venturiaceae, but if they belong to Pleosporales or not, remains unresolved. Testudinaceae and Zopfiaceae, which previously had an unclear position in Ascomycota, are shown to be members of Pleosporales and should be treated as two separate families. The genus <i>Eremodothis</i> is, however, not related to Testudinaceae, but is nested within Sporormiaceae and should be transferred to <i>Westerdykella</i>.</p><p>The natural relationships within Sporormiaceae are still not fully resolved and consequently, I suggest a rather conservative generic classification, accepting <i>Preussia, Sporormia, Westerdykella</i>, as well as <i>Sporormiella</i>, despite that the latter is not conclusively well supported as monophyletic. Characters previously used in the taxonomy and classification of Sporormiaceae, as choice of substrate, presence or absence of an ostiole, presence or absence of germ slits, and spore ornamentation, were all homoplastic and not very useful for circumscribing monophyletic groups.</p><p>Field-studies of moose (<i>Alces alces</i>), mountain hare (<i>Lepus timidus</i>) and roe deer (<i>Capreolus capreolus</i>) dung resulted in several new species records, which suggests that coprophilous ascomycetes in boreal Sweden are poorly known. Fungal species richness and occurrence on moose dung varied significantly between habitats. Species diversity was negatively associated with amount of insect attack, and insects feeding either on the dung and/or the fungi may be an important factor explaining the observed pattern. Species richness of coprophilous fungi varied also significantly between different dung types. A study of moose, mountain hare, and roe deer dung did not show any consistent patterns in respect to the animals´ digestive system. There was, however, a general strong positive relationship between the total number of ascomycete species and the number of plant species foraged by the three herbivores. Fungal species with large spores (≥ 50 µm) were over-represented on roe deer dung, and under-represented on moose dung, while the reverse was found for species with small spores (<10µm). This suggests that the foraging level of the herbivore, which in turn mirrors species-specific differences in spore dispersal of the fungi, may be an important factor in explaining species richness and diversity of the coprophilous community.</p>
17
Nyberg, Kruys Åsa. "Phylogenetic relationships and species richness of coprophilous ascomycetes /." Umeå : Univ, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-625.
Full text
18
Cox, Cymon John. "Phylogenetic relationships of the Eubryalean mosses (Bryineae, Musci)." Thesis, University of Reading, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.270904.
Full text
19
Porto, Diego Sasso. "Phylogenetic relationships of corbiculate bees (Hymenoptera: Apidae: Apini)." Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/59/59131/tde-29122015-125541/.
Full textAbstract:
Bees are aculeate hymenopterans, which, altogether, comprise approximately 20,000 valid species divided into seven families, among which Apidae is one of the best known groups. In addition to the species richness, a remarkable diversity of social behaviors is known to exist within this group, ranging from strict solitary taxa (over 80% of bee species) to groups showing highly sophisticated behaviors related to life in society. One of the most fascinating groups of bees in this respect is that of corbiculate bees (Apidae: Apinae: Apini). Amongst its four subtribes, Apina and Meliponina comprise the so-called \"fixed-caste eusocial\" groups. Phylogenetic relationships of corbiculate bees have been under intense controversy for the last two decades, thus hampering a robust understanding of the evolution of eusocial traits. Most hypotheses based on morphological/behavioral data point to a clade uniting Apina + Meliponina, thus favoring a single origin scenario for the evolution of fixed-caste eusociality. Molecular datasets, on the other hand, consistently indicated independent origins for this cluster of traits. In this contribution, the main goal was to re-evaluate the phylogenetic relationships between the major lineages of corbiculate bees exploring new sources of information from internal skeletal structures of exoskeleton. It were provided descriptions/discussions on some important morphological complexes of the head capsule, mandibles, sitophore, propectus, meso/metafurca and mesophragma of bees. Also, it was attempted to standardize the current morphological terminology used for bees to that used for other Hymenoptera. A set of different phylogenetic analysis with the main lineages of Apidae emphasizing the corbiculate clade was conducted. The complete morphological matrix with 93 characters from external morphology and 42 from internal structures of exoskeleton resulted into two most parsimonious trees with 376 steps, CI=45 and RI=78, which were congruent with the current morphological/behavioral scenario for the corbiculate relationships: Euglossina + (Bombina + (Apina + Meliponina)). It was demonstrated that characters extracted from internal structures of exoskeleton, although poorly explored, can provide critical evidence to elucidate the corbiculate controversy. Moreover, despite the inclusion of new sources of data is fundamental to elucidate this issue, some efforts should be made to reevaluate many characters currently in (re)use. Also, the inclusion of fossil information and use of new technologies for phenotypic studies can open new windows for future comparative morphological studies in bees<br>Abelhas são himenópteros aculeados que, ao todo, compreendem aproximadamente 20.000 espécies válidas distribuídas em sete famílias, das quais Apidae é um dos grupos mais conhecidos. Além da diversidade de espécies, uma notável diversidade de comportamentos sociais é conhecida para esse grupo, desde táxons estritamente solitários (mais de 80% das espécies de abelhas) a grupos exibindo comportamentos altamente sofisticados relacionados à vida em sociedade. Um dos grupos mais fascinantes nesse aspecto é o das abelhas corbiculadas (Apidae: Apinae: Apini). Dentre suas quatro subtribos, Apina e Meliponina compreendem os chamados grupos eussociais de casta-fixa. As relações filogenéticas entre abelhas corbiculadas têm estado sob intensa controvérsia nas duas últimas décadas, o que dificulta a compreensão robusta da evolução dos atributos da eussocialidade. A maioria das hipóteses baseadas em dados morfológicos/comportamentais apontam para um clado unindo Apina + Meliponina, portanto favorecendo um cenário de origem única para a eusocialidade de casta-fixa. Conjuntos de dados moleculares, por outro lado, indicam consistentemente origens independentes para esse conjunto de atributos. Nesta contribuição, o objetivo principal foi reavaliar as relações filogenéticas entre as principais linhagens de abelhas corbiculadas, explorando novas fontes de informação das estruturas internas do exoesqueleto. Foram fornecidas descrições/discussões sobre alguns importantes complexos morfológicos da cabeça, mandíbulas, sitóforo, meso/metafurca e mesofragma de abelhas. Além disso, buscou-se padronizar a atual terminologia morfológica usada para abelhas com aquela usada para outros Hymenoptera. Um conjunto de diferentes análises com as principais linhagens de Apidae, enfatizando o clado das corbiculadas, foi conduzido. A matrix morfológica completa com 93 caracteres de morfologia externa e 42 de estruturas internas do exoesqueleto resultou em duas árvores mais parcimoniosas com 376 passos, CI=45 e RI=78, que são congruentes com o cenário morfológico/comportamental atual para as relações filogenéticas das corbiculadas: Euglossina + (Bombina + (Apina + Meliponina)). Foi demonstrado que caracteres de estruturas internas do exoesqueleto, apesar de pouco explorados, podem fornecer evidências críticas para elucidar a controvérsia das corbiculadas. Ademais, apesar da inclusão de novas fontes de dados ser fundamental para essa questao, algum esforço deve ser feito para se reavaliar muitos caracteres atualmente em (re)uso. Além disso, a inclusão de informação de fósseis e uso de novas tecnologias para estudos fenotípicos podem abrir novas janelas para futuros estudos morfológicos em abelhas
20
Bik, Holly Marie. "Resolving phylogenetic relationships within the order Enoplida (Phylum Nematoda)." Thesis, University of Southampton, 2010. https://eprints.soton.ac.uk/168993/.
Full textAbstract:
The Order Enoplida (Phylum Nematoda) has been proposed as a divergent nematode lineage—Enoplid nematodes are thought to exhibit morphological and developmental characteristics present in the ‘ancestral nematode’. However, previous molecular phylogenies have failed to unequivocally confirm the position of this group. The Enoplida is primarily comprised of free-living marine species; if these taxa represent close relatives of the nematode ancestor, this relationship would presumably imply a marine origin for the phylum. Prior to this investigation, few publically available gene sequences existed for Enoplid nematodes, and published sequences represented only shallow water fauna from Northwest Europe. This study has aimed to improve resolution at the base of the nematode tree, using drastically increased taxon-sampling within the previously neglected Enoplid clade. Morphological identifications, nuclear gene sequences (18S and 28S rRNA), and mitochondrial gene sequences (Cox1) were obtained from marine specimens representing a variety of deep-sea and intertidal habitats. Molecular data were used to assess the phylogenetic placement of the Enoplid clade, resolve internal taxonomic relationships within this group, and investigate relationships between shallow water and deep-sea fauna. Despite rigorous empirical testing and comprehensive taxon sampling, large-scale phylogenetic analyses based on 18S rRNA sequences (using both Maximum Likelihood and Bayesian Inference methods) failed to provide added resolution at the base of the nematode tree. Molecular data from the 18S rRNA gene was unable to confirm the placement of Enoplida as a divergent lineage representing the sister taxon to all other nematodes. These findings highlight the limitations of the 18S gene for resolving the deepest evolutionary splits amongst nematode clades. Analysis of internal relationships reveals that the Enoplida is split into two main clades, with groups consisting of terrestrial and primarily marine fauna, respectively. For marine taxa, deep-sea and shallow-water specimens from the same genus consistently appear as sister taxa. Deep-sea nematode species may have arisen via several evolutionary routes; some deep-sea clades appear to represent recently derived forms, while other groups seem to have radiated much earlier. Nematodes from deep-sea sites exhibit no obvious clustering according to depth or geographic location, and specimens represent a wide taxonomic range within the Enoplida. In addition, there seems to be some molecular evidence for purportedly cosmopolitan nematode species; identical gene sequences were recorded between distant shallow water locations, as well as between deep-sea and shallow water habitats. Data from Enoplid nematodes suggests an intriguing pattern for nematode species distributions—validating these preliminary insights will require a large amount of molecular data from many additional geographic locations. Future studies will also need to incorporate data from additional genetic loci (or use phylogenomic methods) in order to build robust deep phylogenies.
21
Medeiros, Nathalia Maira Cabral de. "An?lise filogen?tica e funcional de dois genes de reparo hom?logos a AP endonuclease em cana-de-a??car: ScARP1 e ScARP3." Universidade Federal do Rio Grande do Norte, 2014. http://repositorio.ufrn.br:8080/jspui/handle/123456789/12627.
Full textAbstract:
Made available in DSpace on 2014-12-17T14:03:44Z (GMT). No. of bitstreams: 1
NathaliaMCM_DISSERT.pdf: 2544480 bytes, checksum: eab320fea2fc6e6b04c8d45099041a93 (MD5)
Previous issue date: 2014-03-21<br>Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior<br>The genome of all organisms constantly suffers the influence of mutagenic factors from endogenous and/or exogenous origin, which may result in damage for the genome. In order to keep the genome integrity there are different DNA repair pathway to detect and correct these lesions. In relation to the plants as being sessile organisms, they are exposed to this damage frequently. The Base Excision DNA Repair (BER) is responsible to detect and repair oxidative lesions. Previous work in sugarcane identified two sequences that were homologous to Arabidopsis thaliana: ScARP1 ScARP3. These two sequences were homologous to AP endonuclease from BER pathway. Then, the aim of this work was to characterize these two sequence using different approaches: phylogenetic analysis, in silico protein organelle localization and by Nicotiana tabacum transgenic plants with overexpression cassette. The in silico data obtained showed a duplication of this sequence in sugarcane and Poaceae probably by a WGD event. Furthermore, in silico analysis showed a new localization in nuclei for ScARP1 protein. The data obtained with transgenic plants showed a change in development and morphology. Transgenic plants had slow development when compared to plants not transformed. Then, these results allowed us to understand better the potential role of this sequence in sugarcane and in plants in general. More work is important to be done in order to confirm the protein localization and protein characterization for ScARP1 and ScARP3<br>O genoma de todos os organismos sofre constantemente a influ?ncia de fatores mutag?nicos que podem ser de origem end?gena e/ou ex?gena, estes podem resultar em danos ao material gen?tico. Se esses danos n?o forem corrigidos pode levar ao aparecimento de muta??es. As plantas por serem organismos sesseis est?o continuamente expostas a estes fatores. Considerando isto, os organismos (animais e vegetais) possuem diferentes vias de reparo de DNA para manter a integridade do material gen?tico. Dentro destas vias, h? a via de Reparo por Excis?o de Bases (BER) que ? composta por diferentes enzimas, e dentro dessa via h? a enzima AP endonuclease que ? alvo deste estudo. Trabalhos anteriores em cana-de-a??car identificaram duas sequ?ncias de cDNA hom?logas a esta prote?na que foram denominadas ScARP1 e ScARP3. Com isso, o objetivo deste trabalho foi caracterizar estas duas sequ?ncias por meio de an?lises filogen?ticas utilizando sequ?ncias presentes dentro do reino Plantae, e de an?lises estruturais dos genes de AP endonuclease por an?lise in silico e por plantas transg?nicas contendo cassetes de super-express?o. Al?m disso, foi realizado transforma??es e a obten??o plantas transg?nicas de Nicotiana tabacum contendo cassetes de super-express?o em orienta??o anti-senso. Foi tamb?m analisado a rela??o filogen?tica de genes DNA ligase I presentes no organismo vegetal de estudo. Os resultados obtidos permitiram verificar que as sequ?ncias ScARP1 e ScARP3 correspondem a uma duplica??o, provavelmente devido a um processo de duplica??o do genoma como um todo (WGD) que deve ter ocorrido no grupo das gram?neas (Poaceae). Refor?ando estes dados, foi verificado um poss?vel direcionamento da prote?na para organelas diferentes, sendo que a ScARP1 pode ser encontrada no n?cleo e a ScARP3 em mitocondrias e/ou cloroplasto. Com rela??o as plantas transg?nicas contendo o cassete em orienta??o anti-senso foi observado que estas apresentaram crescimento lento quando comparado com a planta selvagem (n?o transformada). Al?m disso, seu fen?tipo abrange altera??es morfol?gicas no crescimento foliar, baixa estatura e diminui??o na produ??o de sementes. Entretanto, ainda se faz necess?rio a obten??o da linhagem homozigota para aprofundar essas observa??es. Desta forma, estes resultados permitem compreender um pouco melhor do poss?vel papel da enzima AP endonuclease em cana-de-a??car e em plantas
22
Bleidorn, Christoph. "Phylogenetic relationships of sedentary polychaetes (Annelida) inferred from molecular data." [S.l. : s.n.], 2004. http://www.diss.fu-berlin.de/2004/248/index.html.
Full text
23
Dnyansagar, Rohit. "Investigation of phylogenetic relationships using microRNA sequences and secondary structures." Thesis, Högskolan i Skövde, Institutionen för vård och natur, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-4478.
Full textAbstract:
MicroRNAs are important biomolecules for regulating biological processes. Moreover, the secondary structure of microRNA is important for its activity and has been used previously as a mean for finding unknown microRNAs. A phylogenetic study of the microRNA secondary structure reveals more information than its primary sequence, because the primary sequence can undergo mutations that give rise to different phylogenetic relationships, whereas the secondary structure is more robust against mutations and therefore sometimes more informative. Here we constructed a phylogenetic tree entirely based on microRNA secondary structures using tools PHYLIP (Felsenstein, 1995) and RNAforester (Matthias Höchsmann, 2003, Hochsmann et al., 2004), and compared the overall topology and clusters with the phylogenetic tree constructed using microRNA sequence. The purpose behind this comparison was to investigate the sequence and structure similarity in phylogenetic context and also to investigate if functionally similar microRNA genes are closer in their structure-derived phylogenetic tree. Our phylogenetic comparison shows that the sequence similarity has hardly any effect on the structure similarity in the phylogenetic tree. MicroRNAs that have similar function are closer in the phylogenetic tree based on secondary structure than its respective sequence phylogeny. Hence, this approach can be very useful in predicting the functions of the new microRNAs whose function is yet to be known, since the function of the miRNAs heavily relies on its secondary structure.
24
Zaki, Shama Abdul Halim. "Life history parameters and phylogenetic relationships of the European bitterling." Thesis, University of Leicester, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.491089.
Full textAbstract:
Bitterling fishes lay their eggs on the gills of living freshwater mussels and are valuable models in behavioural and evolutionary ecology. To develop a fuller understanding of the coevolutionary relationship between European bitterling and mussels an aim of this study was to conduct a phylogenetic reconstruction of the colonisation of Europe by bitterling, and to resolve the taxonomic question of whether eastern and western populations ofbitterling represent the same species using genetic and traditional morphological/meristic methods. A second aim was to obtain a better understanding of the life-history parameters of R. amarus in Europe, including larval growth parameters. Previous studies have suggested the European bitterling is either a single species with a wide but discontinuous geographic distribution, or a complex of species. Morphometric and meristic data identified differences between three putative species; with a clear distinction between the eastern Asian Rhodeus sericeus sensu stricto, western European bitterling R. amarus and colchian bitterling, R. colchicus. Polymorphism. in the mitochondrial DNA control region was predominantly due to insertion/deletion events, making phylogenetic inference difficult. Cytochrome b data produced a phylogeny with strongly-supported differentiation between a clade of two R. sericeus haplotypes and a clade of six R. amarus/colchicus haplotypes. The starlike topology of the R. amarus/colchicus haplotypes in a minimum spanning network suggested a rapid radiation in this clade. The results are consistent with an hypothesis of relatively ancient divergence of R. sericeus from R. a11larus/colchicus and more recent and rapid differentiation between R. a11larus and R. colchicus. Analysis of otolith microstructure demonstrated a relationship between mussel availability for spawning and length of spawning season. In addition, these data strongly suggest the onset of exogenous feeding by larval R. amarus while still in their mussel host.
25
李麗瑩 and Lai-ying Rosita Lee. "Genetic diversity and phylogenetic relationships of sweetclovers (Melilotus) germplasm resources." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1999. http://hub.hku.hk/bib/B31221269.
Full text
26
Van, Wyk Marelize. "Phylogenetic relationships and taxonomy of species in ceratocystis sensu lato." Thesis, University of Pretoria, 2013. http://hdl.handle.net/2263/32957.
Full textAbstract:
Ceratocystis is a genus of Ascomycete fungi residing in the family Ceratocystidaceae (Order:
Microascales; Class: Sordariomycetes). Species of Ceratocystis are best-known as woundinfecting
fungi, which are mostly carried by insects. Little is known regarding the basis of the
relationship between insects and Ceratocystis spp., but in some cases it might extend to levels of
mutualism. The taxonomic history of the genus is complex and has, during the course of more
than 100 years, been intertwined with several other genera. However, in recent years, the
resolution arising from DNA sequence comparisons has resulted in the recognition of at least four
major groups within Ceratocystis. major groups within Ceratocystis.
Ceratocystis species in the broad sense (including Ambrosiella) represent ecologically diverse
assemblages, including four very clearly defined groups. One of these groups, which I refer to as
the C. coerulescens sensu lato (s.l.) group, which mainly cause blue-stain in timber, is the only
group that is known to have a very close association with conifer-infesting bark beetles. Perhaps
the best-known group is the C. fimbriata s.l. assemblage of species, which includes a large
number of serious pathogens of angiosperms, mostly trees. This group also includes nonpathogenic
wound-infecting species. There are no specific insect vectors of these species but they
produce fruity aromas, which attract a wide range of insects such as flies, ants, mites and nitidulid
beetles that aid in their dissemination to fresh wounds. The majority of the species in the C.
fimbriata s.l. group are primary pathogens causing cankers that can girdle and eventually kill the
affected areas. The third group of fungi in the broadly defined Ceratocystis s.l. is the C.
moniliformis s.l. group. This group includes only saprophytes that, similar to species in C.
fimbriata s.l., produce fruity odours and they are thus vectored by opportunistic insects including
flies and nitidulid beetles. Ambrosiella spp. are broadly included in the assemblage
accommodating Ceratocystis spp. These fungi have no known sexual state and they live in
obligate symbioses with ambrosia beetles (Scolytinae). Ceratocystis and its relatives have had a complex taxonomic history ever since the genus was
first described by Halstead in 1890. Much of the confusion regarding their taxonomy has arisen
from a dependence on morphology for classification and the fact that these and other fungi have
undergone convergent evolution related to their association with insects. Until the late 1990s,
genera and species in this group were described based only on morphology, although the importance of various morphological features was strongly debated. However, between 1950-
1999, a turning point arose in the way that these fungi were recognised. This change emerged
first from the inclusion of various chemical approaches and then later the application of
molecular techniques to identify them. The most dramatic changes have come with the
widespread application of DNA sequence comparisons, which were first applied to the group in
the early 1990’s. This made it possible to define higher-order relationships and brought the first
clear evidence that species in Ceratocystis and Ophiostoma were phylogenetically unrelated. A
complete taxonomic history of this group is provided in the timeline presented in Table 1. This thesis deals primarily with two groups in the broadly defined Ceratocystis. These are species
in the C. moniliformis s.l. and the C. fimbriata s.l. complexes, but with a considerably greater
focus on the C. fimbriata s.l. complex. Morphologically, species in the two complexes are easy to
distinguish from each other even though they share some common characteristics. Species in both
complexes have hat-shaped ascospores and both have the anamorphic characteristics typical of
species in the genus Thielaviopsis. The ascomatal bases are mostly globose to sub-globose with
elongated necks. There are two main features that species in the C. moniliformis s.l. complex
have that are not observed in the C. fimbriata s.l. complex. One is a very distinct “collar-like”
structure at the base of the ascomatal necks of species in the C. moniliformis s.l. complex. These
“collar-like” structures result in the necks being fragile and they dislodge from the ascomatal
bases very easily. The other distinct characteristic is that these fungi have conical spines on their
ascomatal bases, giving the structures a textured appearance. This is in contrast to the ascomatal
bases in the C. fimbriata complex that are smooth. Species in the C. moniliformis s.l. complex are
non-pathogenic and cause only some sap-stain in the host tissues. The C. fimbriata s.l. complex
includes a large number of primary pathogens, mainly of trees but also including root crops. A
phylogenetic tree including all species in the C. fimbriata s.l and C. moniliformis s.l. complexes
is presented in Figure 1-3. In generating this tree, three gene regions i.e. the Internal Transcribed
Spacer Region including the 5.8S rRNA operon (ITS), part of the the Beta-Tubulin 1 (BT) gene
and part of the Transcription Elongation Factor 1 alpha (TEF) gene have been combined to
represent species in the two complexes. Both Bootstrap as well as Bayesian analyses were run to
obtain confidence intervals. More detailed methods are presented in the legends to the trees. Chapter one of this thesis presents a review of the groups in Ceratocystis. With the aid of DNA
sequence comparisons, three phylogenetically distinct groups are identified. These groups are
characterised by three well-known species each now defined as a species complex i.e. the
Ceratocystis coerulescens complex, the C. moniliformis s.l. complex and the C. fimbriata s.l.
complex. Species of Ambrosiella are also recognised as representing a discrete and related group.
These three species complexes are not only differentiated based on DNA sequence comparison
but have distinct morphological features that distinguish them from each other. They are also
defined by having very distinct ecological roles in nature. Chapter 2 specifically reviews the key
literature dealing with the taxonomy of species in the C. fimbriata complex. This group is defined
by Ceratocystis fimbriata s.s., which was first described as a pathogen causing black rot on sweet
potato. Subsequent to the emergence of DNA sequencing techniques to define species, many new
species in the C. fimbriata s.l. complex have been defined and described. Chapters three and four of this thesis deal with a species of Ceratocystis collected from dying
Mango trees in Oman. A very serious disease known as Mango Sudden Decline disease was first
observed in Oman and has recently been subjected to intensive investigation. This led to a
recognition that a species related to C. fimbriata might be responsible for the disease of
Mangifera indica. As part of the process of identifying the causal agent of Mango Sudden
Decline, two Ceratocystis spp. were described. One is the previously described and nonpathogenic
C. omanensis residing in the C. moniliformis s.l. complex and the other is C.
manginecans, a virulent pathogen residing in the C. fimbriata s.l. complex (Chapter 4).
Chapters five through eleven of this thesis include the descriptions of new species in the C.
fimbriata complex that have emerged over a seven year period. These descriptions have all relied
strongly on DNA sequence based phylogenetic inference as well as morphology. It is important
to recognise, however, that the morphological features are very similar in most species and that
differences rely on the size ranges of key features in this group.
The genus Ceratocystis represents a complex of many species and is set to be sub-divided into at
least three discrete genera, not including Ambrosiella, which is also closely related and already
well-defined. Studies in this thesis began at a time when it became possible to define species of Ceratocystis based strongly on a phylogenetic concept. Thus, while morphological and ecological
features were taken into account, there has been a heavy reliance on DNA sequence comparisons.
It is likely that in coming years, new gene regions will be recognised that will allow a refinement
of genus and species boundaries. Furthermore, having access to whole-genome sequencing will
add deeply to our understanding of taxonomic relationships between these important and
fascinating fungi. It is my hope that the foundation provided by the studies incorporated in this
thesis will be useful as this new wave of study emerges.<br>Thesis (PhD)--University of Pretoria, 2013.<br>gm2013<br>Genetics<br>unrestricted
27
Chang, Ying Carleton University Dissertation Earth Sciences. "Determination of phylogenetic relationships between foraminiferal suborders; a cladistic approach." Ottawa, 1994.
Find full text
28
Lee, Lai-ying Rosita. "Genetic diversity and phylogenetic relationships of sweetclovers (Melilotus) germplasm resources /." Hong Kong : University of Hong Kong, 1999. http://sunzi.lib.hku.hk/hkuto/record.jsp?B21090208.
Full text
29
Bortiri, Pedro Esteban. "Phylogenetic relationships and evolution of morphology in Prunus L. (Rosaceae) /." For electronic version search Digital dissertations database. Restricted to UC campuses. Access is free to UC campus dissertations, 2002. http://uclibs.org/PID/11984.
Full text
30
ARRIGONI, ROBERTO. "Systematics, taxonomy and phylogenetic relationships of the coral family Lobophylliidae." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2015. http://hdl.handle.net/10281/69739.
Full textAbstract:
Traditional classification of scleractinian corals (Cnidaria, Anthozoa, Scleractinia) have been conducted on the basis of skeleton macromorphology. However, the commonly used skeletal characters are plagued by phenotypic plasticity, intraspecific variation, and morphological convergence that fail to recognize most natural evolutionary lineages. Recent molecular studies have revolutionized the conventional taxonomic schemes, suggesting remarkably different phylogenetic relationships when compared with those based on macromorphology. In the last decade, the integration of this increasing amount of genetic data and new micromorphological and microstructural traits has led to a better understanding of evolutionary relationships between hard corals and opened the way to the new era of coral taxonomy.
The Indo-Pacific family Lobophylliidae potentially represents an interesting case study of “reciprocal illumination” between genetics and morphology. This taxon has been defined on a combination of phylogenetic analyses and micromorphological observations, although it still remains poorly understood.This dissertation aims to fill this gap in knowledge through the investigation of evolutionary relationships of the Lobophylliidae and starting the impending process of taxonomic revision of this family as a result of an integrated molecular and micromorphological approach.
A molecular phylogeny of one of the three major groups recovered in the order Scleractinia, the Robusta, to which the Lobophylliidae belong is presented. The representatives of this family were recovered in a cohesive lineage for the first time and the phylogenetic relationships with the other closely related families were discussed. The analysis was then expanded analyzing more species and samples and focused exclusively on the Lobophylliidae in order to produce the most comprehensive molecular phylogeny reconstruction of this group to date. The monophyly of the family was strongly supported and nine main monophyletic genus-level lineages were recovered within the Lobophylliidae. All analyzed polytypic genera, were not monophyletic and resulted in need of a formal taxonomic revision.
Subsequently, the complete mitochondrial genome of Acanthastrea maxima was sequenced. This species based on a combination of data including its restricted geographic distribution, evolutionary distinctiveness, and small population size was revealed be a case of priority for future conservation strategies. Being 18,278 bp in length, it is the longest sequence among the robust corals sequenced mitogenome to date, while the GC content and the gene arrangement are similar to those of the other scleractinian corals.
Finally, integrating multi-locus molecular phylogenies and detailed gross- and fine-scale morphologic observations three cases analyzed in the family provided examples of how reverse taxonomy can be useful in understanding the evolutionary history of the Lobophylliidae: I) a taxonomic revision for the monotypic genus Australomussa, revealed to be a junior synonym of Parascolymia, was proposed; II) the long-ignored monospecific genus Sclerophyllia was resurrected and the unforeseen sister relationships between Sclerophyllia margariticola and A. maxima led to the placement of the latter species in Sclerophyllia; III) the closely related genera Homophyllia and Micromussa were revised with the description of two new species of Micromussa and Symphyllia wilsoni, an Australian endemism, was placed in a new genus based on an unique combination of molecular and micromorphological data.
Overall, the results stemming from the results obtained in the framework of my thesis significantly improve our understanding of evolution of the family Lobophylliidae and provide a solid case for the importance of an integrated morpho-molecular approach in resolving taxonomy of this group of marine animals.
31
Banks, Jill. "Genetic variation of avian influenza viruses relationship to their virulence and epidemiology." Thesis, Open University, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.343751.
Full text
32
Crary, Monica J. "Genetic Variability and its Relationship to Acanthamoeba Pathogenesis." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1343831120.
Full text
33
Day, Julia Jane. "Comparative morphology and evolutionary relationships of the Sparidae (Teleostei: Percoidei)." Thesis, University College London (University of London), 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.326234.
Full text
34
Silva, Riviane Garcez da. "Filogenia da família Cynodontidae sensu Lucena & Menezes, 1998 (Ostariophysi, Characiformes) e história demográfica de Rhaphiodon vulpinus (Cynodontinae) baseadas em marcadores moleculares." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/41/41131/tde-11072012-084328/.
Full textAbstract:
Cynodontidae (sensu Lucena & Menezes, 1998) é uma família de Characiformes com 14 espécies válidas divididas em duas subfamílias (Cynodontinae e Roestinae). As espécies de Cynodontinae sempre foram classificadas em um mesmo grupo, enquanto que Roestinae já foi classificada junto com Characidae. Com o objetivo de testar o monofiletismo de Cynodontidae, realizamos uma análise de máxima parcimônia com o algoritmo TBR em 42 táxons representando 12 famílias de Characiformes. A análise foi realizada com três regiões nuclearas e três genes mitocondriais; entretanto, o íntron da RPS7 foi retirado da análise final por questões de homologia do alinhamento. A árvore consenso obtida com 9842 passos (IC = 0,351 e IR = 0,358) evidencia o não monofiletismo de Cynodontidae, com Cynodontinae relacionada a um clado composto por Serrasalmidae, Prochilodontidae, Hemiodontidae e Parodontidae, enquanto que Roestinae aparece dentro de Characidae relacionada à Heterocharacinae. Acestrorhynchidae foi recuperada na base do clado Roestinae/Heterocharacinae, o que condiz com outras filogenias moleculares e difere das filogenias morfológicas. As relações entre as espécies de Roestes e de Hydrolycus também foram recuperadas. As outras relações encontradas condizem com dados recentes da literatura, fortalecendo o conhecimento sobre a ictiofauna de água doce. A espécie Rhaphiodon vulpinus se destaca entre os Cynodontíneos por apresentar uma ampla distribuição geográfica, sendo encontrada em sistemas atualmente separados como as bacias do Paraná e do Amazonas. Por isso, uma análise da variabilidade e da estrutura populacional desta espécie foi realizada com o intuito de ampliar o conhecimento sobre a influência do passado geológico na distribuição da ictiofauna Neotropical, além de fornecer áreas prioritárias de conservação. Inicialmente, o estudo foi realizado com sequencias do gene da ATPase do mtDNA, e os resultados evidenciaram a existência de três grupos genéticos que foram considerados UES distintas (Bacia do Paraná, oeste da Amazônia e leste da Amazônia). Entretanto, a hipótese de contato secundário com mistura de fauna entre a Bacia do Paraná e o Rio Madeira foi postulada para explicar os resultados. Para testar tal hipótese, foi desenvolvida a biblioteca de microssatélites de R. vulpinus, já que este marcador é mais sensível para a detecção de estruturas populacionais. Foram obtidos 11 locos polimórficos, sendo que sete funcionaram em outros gêneros de Cynodontinae. A análise com microssatélites confirmou a conexão entre o oeste da Amazônia e a Bacia do Paraná, provavelmente devido à captura de riachos para a sub bacia do Rio Madeira. Uma grande diferença entre as análise é a subdivisão UES do leste da Amazônia (rios Araguaia e Xingu) devido à grande diferenciação do alto Xingu. Além disso, esta localidade parece ter contribuído no pool gênico do Araguaia após a estruturação, o que pode indicar outro evento de captura de cabeceiras. Estes eventos, no entanto, seriam relativamente recentes na história evolutiva de R. vulpinus, assim como é a barreira estabelecida pela Cachoeira do Teotônio no Rio Madeira, já que a mesma não foi detectada como barreira na análise do mtDNA. A história demográfica de Rhaphiodon vulpinus parece estar intimamente relacionada a eventos geológicos, já que a estruturação encontrada reflete o conhecimento atual sobre a formação das bacias hidrográficas. Além disso, R. vulpinus parece ser uma espécie bastante antiga, especialmente pela estruturação encontrada dentro da Bacia Amazônica. Por isso, tanto a diminuição do tamanho populacional (detectada no leste da Amazônia pelos microssatélites) quanto a expansão populacional (detectada no oeste da Amazônia pela ATPase) podem ter acontecido nesta espécie. R. vulpinus parece ser uma espécie com grande capacidade migratória, já que apresenta isolamento pela distância e estruturação relacionada à barreiras históricas. Em relação aos padrões de diversidade, ambos os marcadores evidenciaram uma diversidade moderadamente alta na Amazônia (com os maiores valores no oeste) e uma baixa diversidade na Bacia do Paraná, provavelmente devido à colonização da bacia aliado às alterações ambientais ocorridas na região. O conjunto de dados obtidos contribuirá para o esclarecimento das relações filogenéticas em Characiformes e também para a compreensão de aspectos da história evolutiva e da dinâmica de populações de R. vulpinus, uma espécie que parece ser mais antiga do que a formação atual dos sistemas de drenagem.<br>Cynodontidae (sensu Lucena & Menezes, 1998) is a Characiform family with 14 valid species which are divided in two subfamilies (Cynodontinae and Roestinae). Cynodontinae species were always classified in the same group meanwhile Roestinae has already been classified together with Characidae. In order to test the monophylestism of Cynodontidae, we have conducted a Maximum Parsimony Analysis using the algorithm TBR in 42 taxa, which represent 12 Characiform families. The analysis was performed with three nuclear regions and three mitochondrial genes; the first intron of RPS7 was removed from the final analysis due to problems related to alignment homology. The consensus tree obtained with 9842 steps (IC = 0,351 and IR = 0,358) does not support the monophylestism of Cynodontidae, which appears in a clade composed by Serrasalmidae, Prochilodontidae, Hemiodontidae, and Parodontidae; Roestinae appears within Characidae, close-related to Heterocharacinae. Acestrorhynchidae was recovered at the base of Roestinae/Heterocharacinae clade, which is in agreement with other molecular phylogenies and in disagreement with the morphological ones. The relationship between Roestes and Hydrolycus species was also recovered. Other relationships obtained are in agreement with recent data described elsewhere, which reinforces the knowledge on the freshwater fish fauna. The species Rhaphiodon vulpinus stands out from other Cynodontinae species due to its wide geographic distribution, occurring in basins that are currently separated as is the case of Paraná and Amazon. Within this context, population variability and structure analyses were conducted with the aim of expanding the knowledge related to the influence of geological history on the distribution of Neotropical fish fauna as well as to provide priority areas for conservation means. Initially, the study was carried out with ATPase gene sequences from mtDNA and the results evidenced the existence of three genetic groups which were considered as different ESUs (Evolutionary Significant Units; Paraná, Western Amazon, and Eastern Amazon). However, a secondary contact hypothesis with fauna mixture between Paraná and Madeira river basins was formulated in order to explain the results. In order to test such hypothesis, a microsatellite library was developed for R. vulpinus, once this marker is more sensitive for the detection of population structure. 11 polymorphic loci were obtained and among them, seven showed to be useful in other Cynodontinae genus. The microsatellite analysis confirmed the connection between the Western Amazon and the Paraná basin, which probably occurred as a result of headwaters capture by the Madeira river sub-basin. The major difference between the analyses comprises the ESU sub-division in Easter Amazon (Araguaia and Xingu rivers) due to the high differentiation of Upper Xingu. Moreover, this locality may have contributed on the Araguaia gene pool after its structuration process, which may be an indicative of another headwaters capture event. However, those events would be relatively recent in the R. vulpinus evolutive history, likewise the barrier formed by Teotônio Falls in Madeira river, once it was not detected as a barrier by mtDNA analysis. The demographic history of R. vulpinus seems to be tightly related to geologic events, once the structure obtained reflects the current knowledge on the formation of hydrographic basins. Furthermore, R. vulpinus seems to be a very old species, mainly due to the structure found within the Amazon basin. Thus, both the reduction of population size (detected in Eastern Amazon by microsatellite) and the population expansion (detected in Western Amazon by ATPase) may have occurred in this species. R. vulpinus seems to be a species with a high migration capacity, once it presents isolation by the distance and structuration related to historical barriers. Regarding the diversity patterns, both markers evidenced a slightly high diversity in the Amazon (high values on Western) and low diversity in the Paraná basin, possibly due to the occupation of the basin modulated by environmental changes that occurred in the region. Those data will contribute to resolve the phylogenetic relationships in Characiform and for the understanding of some aspects of the evolutive history and population dynamics of R. vulpinus, a species that seems to be older than the current drainage systems.
35
Jeewon, Rajesh. "Pestalotiopsis taxonomy : molecular phylogenetics, species nomenclature and teleomorph relationships /." Thesis, Hong Kong : University of Hong Kong, 2001. http://sunzi.lib.hku.hk/hkuto/record.jsp?B24367394.
Full text
36
Salim, Anna. "The origins and relationships of the pathogenic strains of Vibrio cholerae." Thesis, The University of Sydney, 2015. http://hdl.handle.net/2123/12644.
Full textAbstract:
Sporadic cholera cases had been reported worldwide and that the remnants of the 6th pandemic clone, the 7th pandemic clone and other closely related pathogenic strains are of great importance in their roles to cholera. Sequencing 26 housekeeping genes from V. cholerae isolates that are representatives of the 6th pandemic clone, the 7th pandemic clone, the U.S. Gulf Coast clone, the Australian clone and the pre-7th pandemic strains showed that all of these pathogenic O1 V. cholerae strains evolved from the same lineage, in which during divergence between the 6th pandemic clone and the node for the 7th pandemic clone and the remaining pathogenic O1 El Tor V. cholerae strains, there were eight recombination events and two single mutations. The sequencing of selected seven housekeeping genes (adk, mdh, purM, gyrB, pntA and metE) from 26 V. cholerae isolates (11 pathogenic O1 and 15 non-pathogenic non-O1 non-O139 V. cholerae strains), which consequently led to the generation of seven MLST sequence defined region (416 bp to 591 bp) for each of the seven respective genes, has resulted in a MLST scheme for V. cholerae. This system was able to identify all of the 26 V. cholerae isolates, able to distinguish the O1 from the non-O1 non-O139 V. cholerae strains and was also able to differentiate the pathogenic O1 V. cholerae strains into their five unique groups. The MLST scheme was applied to 19 sporadic strains (one O1 and 18 non-O1 non-O139 V. cholerae strains) and was able to identify 16 of these sporadic strains. The system failed to amplify one, two and five of the selected MLST genes from strains M2551, M2548 and M2550 respectively. Amplification of five virulence-associated genes (ctxA, tcpA, rtxA, acfB and sto/stn) from these 19 sporadic strains by PCR revealed that only one strain M2557 (O1) carries all of these genes, while strains M2548, M2550 and M2551 do not carry any of these genes. The remaining 15 sporadic strains were shown to carry only the rtxA gene.
37
Geiger, Matthias. "Phylogenetic relationships and evolutionary ecology of nicaraguan midas-cichlids(Amphilophus SPP.)." Diss., lmu, 2011. http://nbn-resolving.de/urn:nbn:de:bvb:19-138206.
Full text
38
Zaki, Shama Abdul Haleem. "Phylogenetic relationships and some life history parameters of the European bitterling." Thesis, University of Leicester, 2007. http://hdl.handle.net/2381/29744.
Full textAbstract:
Bitterling fishes lay their eggs on the gills of living freshwater mussels and are valuable models in behavioural and evolutionary ecology. To develop a fuller understanding of the coevolutionary relationship between European bitterling and mussels an aim of this study was to conduct a phylogenetic reconstruction of the colonisation of Europe by bitterling, and to resolve the taxonomic question of whether eastern and western populations of bitterling represent the same species using genetic and traditional morphological/meristic methods. A second aim was to obtain a better understanding of the life-history parameters of R. amarus in Europe, including larval growth parameters. Previous studies have suggested the European bitterling is either a single species with a wide but discontinuous geographic distribution, or a complex of species. Morphometric and meristic data identified differences between three putative species; with a clear distinction between the eastern Asian Rhodeus sericeus sensu stricto, western European bitterling R. amarus and colchian bitterling, R. colchicus. Polymorphism in the mitochondrial DNA control region was predominantly due to insertion/deletion events, making phylogenetic inference difficult. Cytochrome b data produced a phylogeny with strongly-supported differentiation between a clade of two R. sericeus haplotypes and a clade of six R. amarus/colchicus haplotypes. The starlike topology of the R. amarus/colchicus haplotypes in a minimum spanning network suggested a rapid radiation in this clade. The results are consistent with an hypothesis of relatively ancient divergence of R. sericeus from R. amarus/colchicus and more recent and rapid differentiation between R. amarus and R. colchicus. Analysis of otolith microstructure demonstrated a relationship between mussel availability for spawning and length of spawning season. In addition, these data strongly suggest the onset of exogenous feeding by larval R. amarus while still in their mussel host.
39
Rolph, Helen Jane. "Investigation of phylogenetic relationships between penicillin producing fungi using molecular methods." Thesis, University of Sheffield, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.265587.
Full text
40
Lester, Ntsikelelo Blessings. "Preliminary investigations into the phylogenetic relationships in the genus Erica L." Thesis, Stellenbosch : University of Stellenbosch, 2006. http://hdl.handle.net/10019.1/17376.
Full textAbstract:
Thesis (MSc)--University of Stellenbosch, 2006.<br>ENGLISH ABSTRACT: Erica is a genus of about 860 species world wide, with 700 of these found in South Africa’s
southwestern and southern Cape, making it by far the most speciose genus in the Cape Floristic
Region. This poses a particular challenge in the construction of a molecular phylogeny of the
genus. The choice of suitably variable gene regions is a crucial decision on which the successful
phylogenetic reconstruction of this important genus is critically dependent.
The aim of this project was therefore to determine which DNA regions, both chloroplast and
nuclear, would be sufficiently variable to give adequate informative characters that may be useful
at the species level phylogenetic reconstruction. A subset of 30 species, representing the range of
morphological diversity and pollinator preference within Erica, was selected for study. For each of
these species the variability in eight chloroplast regions (trnL-F, matK, trnS-G, rps12- rpl20, psbAtrnH,
trnC-D, rps4-trnT and trnT-L) and the nuclear ITS region was investigated.
The psbA-trnH, trnC-D, rps4-trnT and trnT-L chloroplast regions were found to be problematic to
amplify and to possess too few Parsimony Informative Characters to be of use in phylogenetic
reconstruction. Four of the chloroplast regions, trnS-G, trnL-F, matK and rpS12-rpL20 and the
nuclear ITS region could be amplified and sequenced with success. The ITS region was found to
be reasonably variable, with the chloroplast genes showing less variability.
The DNA extraction method employed showed itself to be of critical importance in the success of
the study. Two DNA extraction protocols, both modified from the original Doyle and Doyle (1987)
method, were tested. The one included double the amount of β-mercaptoethanol and
Polyvinylpyrrolidone (PVP) and the other included an extended phenol: chloroform: isoamylalcohol
step. These variables, together with the effectiveness of these methods on fresh vs. silica dried
plant samples, were investigated to determine which of the two would yield high quantities and
qualities of DNA and result in the best method for the extraction of DNA from Erica species.<br>AFRIKAANSE OPSOMMING: Erica is ‘n genus van omtrent 860 spesies wêreldwyd, met 700 van hierdie spesies aanwesig in die
suidwes en suid Kaap van Suid Afrika, wat dit by verre die mees spesieryke genus in die Kaapse
Floristiese Streek maak. Dit stel ’n besondere uitdaging in die konstruksie van ’n molekulêre
filogenie van die genus. Die keuse van geskikte variërende geen-areas is ‘n belangrike besluit
waarvan die suksesvolle filogenetiese rekonstruksie van hierdie belangrike genus krities afhanklik
sal wees.
Die doel van hierdie projek was dus om te bepaal watter DNS areas, buide chloroplas en kern,
genoegsaam varieer om voldoende informatiewe kenmerke te lewer om bruikbaar te wees in ’n
spesie-vlak molekulêre rekonstruksie. ’n Subgroep van 30 spesies, wat die reeks van morfologiese
diversiteit en bestuiwer voorkeure in Erica verteenwoordig, is dus vir die studie geselekteer. Vir elk
van hierdie spesies is die variasie in agt chloroplast areas (trnL-F, matK, trnS-G, rps12- rpl20,
psbA-trnH, trnC-D, rps4-trnT en trnT-L) en die kern ITS area ondersoek.
Dit was problematies om die psbA-trnH, trnC-D, rps4-trnT en trnT-L chloroplast areas te
amplifiseer, en daar is gevind dat hulle te min Parsimonie Informatiewe Kenmerke besig om
bruikbaar te wees in filogenetiese rekonstruksie. Vier van die chloroplas areas, trnS-G, trnL-F,
matK en rpS12-rpL20 en die kern ITS kon suksesvol geamplifiseer word en die basisvolgordes kon
suksesvol bepaal word. Daar is gevind dat die ITS area redelik variërend is, terwyl chloroplas
areas minder variasie getoon het.
Die DNS ekstraksie metode wat gebruik is het die kritiese belang van die ekstraksie metode in die
sukses van die studie bewys. Twee DNS protokolle, beide gemodifiseer van die oorspronklike
Doyle en Doyle (1987) metode, is getoets. Die een het dubbel die hoeveelheid β-mercaptoetanol
en Polyvinylpyrrolidone (PVP) bevat, en die het ’n uitgebruide fenol: chloroform: isoamylalkohol
stap ingesluit. Hierdie veranderlikes, saam met die effektiwiteit van hierdie metodes op vars
teenoor silika-gedroogde plant monsters, is ondersoek om vas te stel watter een van die twee die
hoogste kwaliteit en kwantiteit DNS sou lewer en dus sal lei tot die beste DNS ekstraksie metode
vir Erica spesies.
41
Dludlu, Meshack N. "Cyperaceae tribe Cyperae : phylogenetic relationships and evolutionary patterns of diagnostic characters." Bachelor's thesis, University of Cape Town, 2007. http://hdl.handle.net/11427/26187.
Full textAbstract:
Phylogenetic relationships in Cyperus and allied genera in the tribe Cypereae (family Cyperaceae) have been reconstructed using parsimony and Bayesian analyses of a combined data matrix, which consisted of plastid DNA (rbcL, trnL-F intergenic spacer, and rps16), nuclear ribosomal DNA (internal transcribed spacer ITS) sequences and morphological data. From both analyses, tribe Cypereae were resolved into a very strongly supported clade (Posterior probability =98%; Bootstrap= 100%) characterised by the Cyperus-type of embryo and the absence of perianth segments. Cyperus sensu stricto is not monophyletic as currently resolved as several cyperoid genera are embedded within it. The Cyperoid clade splits into two distinct clades which are diagnosed by the Eucyperoid (C₃) and Chlorocyperoid (C₄) anatomy. The evolution of key morphological characters used to diagnose genera is discussed and genera whose classification needs to be revisited are highlighted.
42
Mandiwana, Tshifhiwa G. "Taxonomy, phylogenetic and biogeographical relationships of African grassland Francolins (Genus: Scleroptila)." Master's thesis, University of Cape Town, 2003. http://hdl.handle.net/11427/8615.
Full textAbstract:
Bibliography: leaves 23-28.<br>The potential for using a combination of molecular and whole-organismal data has opened up new avenues for avian taxonomy, phylogenetics and biogeography. Such a multifaceted approach is used here to identify diagnosable taxa within the Orange River Francolin Scleroptila levaillanloides species complex and resolve evolutionary relationships between these taxa and other mono-and polytypic forms within the Red-winged Group of francolins (= genus Scleroplila sensli lalo). Mitochondrial cytochrome-b DNA sequence data (±250 b.p.) from 50 individuals and 19 morphological characters extracted from reports in published literature were employed to achieve these aims. These characters were analysed separately and also in combination using maximum parsimony (DNA sequences and organismal data), maximum likelihood (DNA sequences) and distance (DNA sequences) analyses. Monophyly of the Red-winged Group plus the Ring-necked Francolin Dendroperdix slreptophorus was supported by all the analyses (bootstrap support ranged from 50%-94%) except distance analysis. The Orange River Francolin complex was found to be non-monophyletic. Two distinct clades were identified, one comprising taxa from southwestern and the other from northeastern Africa. Morphological analysis yielded a distinct clade of the southwestern Orange River Francolin. The other polytypic species and assemblages thereof show poor resolution. The results of this study clearly demonstrate a need for further assessment of the taxonomic status of Scleroptila spp. and their phylogenetic relationships.
43
Koutsovoulos, Georgios D. "Reconstructing the phylogenetic relationships of nematodes using draft genomes and transcriptomes." Thesis, University of Edinburgh, 2015. http://hdl.handle.net/1842/10558.
Full textAbstract:
Nematoda is a very diverse animal phylum. Within Nematoda, species display a multitude of life styles, different reproductive strategies and parasitism has arisen independently several times. Furthermore, morphological conservation and a high rate of homoplasy have impeded the resolution of nematode systematics. To address these issues, single gene (usually the nuclear ribosomal small subunit gene) and mitochondrial gene phylogenies have been used, but the information contained within the sequence of these genes is not enough to resolve the topological relationships between clades that emerged during rapid cladogenesis. Next generation sequencing data have been shown to produce high quality genomic and transcriptomic assemblies at low cost, as a result more and more nematode species are being sequenced. Sequences were gathered or generated for 53 nematode species from ESTs, gene predictions from full genome assemblies and transcripts from RNA-Seq experiments. These sequences were screened for orthologous gene clusters, which were concatenated into a supermatrix with thousands of aminoacid sites. The analysis of the supermatrix with maximum likelihood and Bayesian inference methods sheds light into the early splitting clades of the phylogenetic tree of nematodes and the derived clades III, IV and V. Furthermore, the phylogenetic relationships within the parastitic family Onchocercidae were resolved, unveiling the evolutionary history of these important taxa. Finally, data produced in this work will be useful for subsequent evolutionary studies of the phylum Nematoda.
44
Eiadthong, Wichan. "PHYLOGENETIC RELATIONSHIPS OF SOME MANGIFERA SPECIES AND MANGO CULTIVARS IN THAILAND." Kyoto University, 2000. http://hdl.handle.net/2433/181039.
Full textAbstract:
Kyoto University (京都大学)<br>0048<br>新制・課程博士<br>博士(農学)<br>甲第8410号<br>農博第1094号<br>新制||農||798(附属図書館)<br>学位論文||H12||N3367(農学部図書室)<br>UT51-2000-F314<br>京都大学大学院農学研究科農学専攻<br>(主査)教授 杉浦 明, 教授 中坪 文明, 教授 矢澤 進<br>学位規則第4条第1項該当
45
Liu, Jy-lin, and 劉芝麟. "The Molecular Phylogenetic Relationship among Hexatrygon fishes of Taiwan." Thesis, 2002. http://ndltd.ncl.edu.tw/handle/89581512105206263411.
Full textAbstract:
碩士<br>國立清華大學<br>生命科學系<br>91<br>Abstract
Hexatrygon fishes of Taiwan are represented by three species in the previous records, including H. taiwanensis、H. brevirostra and H. yangi respectively, which have been found on the north-eastern and south-western coast of Taiwan. Nowadays the classification of the three species depends mainly on the external morphology: the posterior tip of tail of H. yangi is naked, and snout angle is 45 degree. H. taiwanensis and H. brevirostra do not have a naked tail. H. brevirostra is similar to H. taiwanensis but distinguishable by having large percentage of snout length and disc width, longer snout and shorter tail. Because of the difficulty in catching Hexatrygon fishes, and the great differences between juveniles and adults, which give rise to the controversy of classification. Combining a total evidence of morphological features and 12S mtDNA data, the results follow (1) According to the newly recorded species of Hexatrygon longirostra, it increases to four species of Hexatrygon in Taiwan. However, the phylogenetic analyses show that four species have a high similarity in 12S rRNA sequence. The difference in genetic distance is very limited. It shows that the fishes of Hexatrygon in Taiwan are synonyms. (2) Snout is a limited organ for classification. The shape of snout, including width and thick, may be a perceptible feature for classification. But the snout angles of Hexatrygon overlap at interspecies level. (3) Besides the snout, other morphologic characters such as total length and disc width do not have obvious difference at interspecies level. Like snout, those characters fail to be the useful traits for classification.
46
Jang-Liaw, Nain-Hong, and 張廖年鴻. "Phylogenetic relationship of family Pomacentridae by using mt DNA sequences." Thesis, 1995. http://ndltd.ncl.edu.tw/handle/31770688822661597976.
Full text
47
Liu, Yu Shan, and 劉育姍. "Studies of Phylogenetic and Molecular Relationship in the Genus Citrus." Thesis, 2007. http://ndltd.ncl.edu.tw/handle/35718708166753850386.
Full textAbstract:
博士<br>國立臺灣大學<br>園藝學研究所<br>95<br>The discovery and development of citrus genus has a long history, however, in most of the past studies, citrus classification was mainly based on appearance and chemical characteristics. Citrus hybrids and branch mutations have made us difficult to distinguish their origins and species using traditional methods. Following to the advancement of molecular technology, the molecular markers have become the most important methods at taxonomy in past decade. The cpDNA (chloroplast DNA) has become one of the most useful markers for classification due to its characters such as maternal inheritance and slow evolution, which suitable for genetic variation analysis. The region commonly used for phylogenetic relationship of cpDNA is trnL-trnL-trnF noncoding region. The other regions were less used in the researches of phylogenetic relationship and genetic variation. In this study, nuclear DNA and cpDNA were used for the analysis of genetic variation. The noncoding regions of cpDNA were used to study their phylogenetic relationship. The genetic variation of two nuclear genes related to the environment adatpation and the fruit characteristic after processing were also compared.
In the first part, 9 noncoding regions of cpDNA were used for the analysis of phylogenetic relationship of citrus. It was found out that the trnL intron and trnL-trnF IGS which frequently analyzed in the past showed high haplotype diversity. Nevertheless, the sweet oranges, grapefruits and pummelos have the same haplotype in these regions. Accordingly, both trnL intron and trnL-trnF IGS could only used to distinguish mandarins and sweet oranges. To address different evolutional rates of different regions at cpDNA and accuracy for analysis, we further combined several other DNA sequences.
Secondly, the cytosolic classI small heat shock protein (sHSP) was used to analyze citrus genetic variation. It was found that most of the nucleotide variations in the coding regions were transversion and transition, and there was no indel in these regions. Therefore, the amino acid sequences of cytosolic classI sHSP were rather conservative. There was an indel in the 3’-UTR (3’-untranlated region) of this gene. According to this variation, the pummelos, grapefruits and tangelos which originated from different regions and grow in different climates could be distinguished into different groups. Nevertheless, this finding was not similar in the groups of mandarins, sweet oranges, lemons and limes. Latter citrus species were rapidly worldwide distributed and genetically hybridized and adatped to different climate patterns. These situations made the DNA sequences of cytosolic classI sHSP in citrus not an optimum marker for phylogenetic analysis.
The final part in this study was to analyze the genetic variation of LGTase (limonoid glucosyltransferase). Most of the citrus, such as sweet oranges, mandarins and grapefruit, have 2 types of LGTase gene. However, 2 pummelos (Siam and Shatianyu) and one citron (Bergamot) only have 1 type of LGTase gene. Comparing the DNA sequences of LGTase from 24 citrus, it was found that the bitterness of limonoids was caused by several other factors instead of LGTase alone, thus its variation did not contribute much on limonoid bitterness.
48
Meng-Chuan, Ho, and 何孟娟. "Phylogenetic relationship between Papilio paris Linnaeus and P. hermosanus Rebel." Thesis, 2000. http://ndltd.ncl.edu.tw/handle/78135986195018437479.
Full textAbstract:
碩士<br>國立臺灣師範大學<br>生物研究所<br>88<br>The systematic status between Papilio paris and P. p. hermosanus are controversial, and so far no convincing evidence has been available to elucidate this problem. Characters based upon morphology, ecology, allozyme allele frequency and mtDNA sequence variation were surveyed P. p. nakaharai and P. p. hermosanus from Taiwan, which were compared with P. p. paris from the Asiatic continent. Using samples of P. bianor thrasymedes and P. dialis tatsuta of the bianor-paris species group in Taiwan were served as outgroup taxa in these analyses.
Data from male genital morphology, androconial patch size, eggs size and feeding tests provided clear distinction between P. paris nakaharai and P. p. hermosanus. On the other hand, genetic distance ( D＝0.373, calculated from allozyme data ) between the two taxa revealed that they should be regarded as distinct species. By analyzing a fragment of the mitochondrial COI gene sequence, the phylogenetic relationship of the two taxa also showes they represent independent evolutionary lineages. Consequently two distinct species could be recognized based upon these data, namely, P. paris ranging across Asiatic continent to north Taiwan and the islands where the Sundaland located, and P. hermosanus endemic to Taiwan.
The results of this study suggest that the hypothesis of allopatric speciation was supported. In other words, P. paris might be derived from a recent dispersal to Taiwan during last glacial stage of Quarternary, but they were already genetically and phenotypically isolated from P. hermosanus, which were descents of previous invasion at the time
49
Ni, Yu-Han, and 倪郁涵. "The relationship between chironomid phylogenetic diversity and environment in stream ecosystem." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/f8k4c5.
Full textAbstract:
碩士<br>國立中興大學<br>昆蟲學系所<br>101<br>Flies in the familiy Chironomidae have a worldwide distribution and their larvae are ideal indicators of the quality of aquatic ecosystems. Prior to this study, chironomid larvae had not been studied in stream ecosystems in Taiwan. From 2003-2012, a total of 28,896 chironomid larvae, belonging to four subfamilies, 14 genera and 21 species, were collected from 3 streams in central Taiwan. Larval abundance and the number of morphological types were higher in the dry season than in the wet season. The sample density ratio between Yousheng, Cijiawan and Gaoshan Streams was 3: 2: 1. The highest number of larvae belonged to the subfamily Orthocladiinae, followed by the Chironominae, Diamesinae and Tanypodinae. Only 1% of Tanypodinae larvae came from Gaoshan Stream, probably because the lower water temperature. In Gaoshan Stream, the most abundant genus was Orthocladius (21% of total) and the least common genus was Cricotopus (less than 1%). The chironomid phylogenetic tree indicates that the Diamesinae evolved first and was closely related to the Tanypodinae, which were, in turn, closely related to the Orthocladiinae. Within the Orthocladiinae, Corynoneura was most closely related to the Chironominae. At the generic level, the Orthocladiinae was a multi-branched, paraphyletic group, but the Chironominae, closely related genus were clustered in same branch, was monophyletic. Diversity was low in years with high discharge because the chironomid larvae were washed away. Larval diversity in the three streams varied distinctly from the dry to the wet season. Extreme floods occurred in 2005, 2007, and 2009, and the diversity of chironmid larvae was relatively low in these years. Multiple regression analysis indicates that characteristics of the physical environment (wet and dry season, conductivity, temperature, turbidity) had the highest relationship with the phylogenetic diversity index. Discharge was the most important factor in the wet and dry seasons. Changes in the phylogenetic diversity index paralleled changes in stream discharge. The phylogenetic diversity index did not overestimate or underestimate the stream ecosystems like biodiversity indices, and, therefore, it can be used to explore more of the relationship between environmental factors than other diversity indices.
50
Liao, Te-Yu, and 廖德裕. "The Molecular Phylogenetic Relationship among Populations of Sinogastromyzon puliensis of Taiwan." Thesis, 2000. http://ndltd.ncl.edu.tw/handle/36172392329400013615.
Full textAbstract:
碩士<br>國立清華大學<br>生命科學系<br>88<br>To uncover the phenomenon of genetic differentiation among populations of Sinogastromyzon puliensis in Taiwan, we sequenced the mitochondrial D-loop region from samples collected from all basins and derived genetic distances among local populations. Two major deletions were found in samples from Ta-Tu River, Cho-Shuei River and Tsen-Wen River, as referenced by the Kao-Ping River samples. The largest genetic distance between Ta-Tu River and Cho-Shuei River populations is only 1.14% nucleotides substitution. If we combine the three deletion-bearing river basins together, the genetic distance of this Central Taiwan composite is 2.07％ from the Tsen-Wen River, and 2.42％ from the Kao-Ping River population. The genetic structure of Sinogastromyzon puliensis also points to similar grouping: the Nm value between Ta-Tu River and Cho-Shuei River is 24.29, and the others among all the other populations are lower than 0.17. Obviously these populations are genetically distinct. The nucleotide diversity within the Cho-Shuei River and the Tsen-Wen River populations are the lowest among all. This result is concordant with the morphological statistics. Morphologically Sinogastromyzon puliensis may be divided into two subspecies based on the number of lateral line scales. The Tsen-Wen River and the Kao-Ping River populations belong to the southern type, while the others belong to the central type. On the other hand, despite the remarkable genetic differentiation between the Tsen-Wen River and the Kao-Ping River populations, no traits with significantly discerning resolution have been found. These two populations of the southern type can not be distinguished by morphology only.