Dissertations / Theses: 'Molecular systematics'

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Mullins, Josef Thomas. "Molecular systematics of Nepenthaceae." Thesis, University of Reading, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.271202.

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The tropical carnivorous pitcher-plant family, Nepenthaceae, is represented by the single dioecious genus Nepenthes. Whilst South East Asia represents the centre of diversity of the group several species have disjunct biogeographical distributions. Due to the highly polymorphic nature of Nepenthes and its distinct lack of discrete morphological characters no revision to date has been able to construct a phylogenetic classification. To address this issue, this study analyses nucleotide sequences from two independent regions, including chloroplast DNA (the trnL-F intron and intergenic spacer) and the nontranscribed spacer region from nuclear DNA (5S-NTS), together with a suite of morphological characters traditionally used to describe and group species. A total of 87 species are represented with the objectives of i) testing the monophyly of the genus and constructing a hypothesis of species relationships, ii) evaluating the taxonomic circumscription of poorly known species and iii) investigating character evolution and biogeographic patterns. In addition, for 25 species, multiple accessions were sequenced. Two artificial hybrids (of known sexual parentage), representing three geographically and taxonomically distinct species, were also included to test prevalent theories of hybrid origin and maternal inheritance. Cladistic analyses of these data strongly support the monophyly of the genus in which the disjunctly distributed species (including the easterly Nepenthes danseri from Waigeo Island and Halmahera) were found to form a grade while the South East Asian taxa form a clearly monophyletic group. Incongruence was found between the phylogenetic histories inferred from independent genetic markers and provides strong evidence to support natural hybridization as an important evolutionary process in the speciation of Nepenthes. The results support an ancient circum-Indian Ocean origin for Nepenthes, indicating the disjunct species to represent relictual taxa, with a geologically recent and rapid expansion into South East Asia. A phylogenetically consistent classification of the species is proposed.

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Tsyganov-Bodounov, Anton. "Molecular systematics of Bryozoa." Thesis, Swansea University, 2008. https://cronfa.swan.ac.uk/Record/cronfa43148.

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Osaloo, Shahrokh Kazempour. "Molecular Systematics of Trilliaceae." 京都大学 (Kyoto University), 1999. http://hdl.handle.net/2433/181996.

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Thureborn, Olle. "New insights into the deep divergences of Ephedra (Gnetales) using molecular data." Thesis, Stockholms universitet, Institutionen för ekologi, miljö och botanik, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-171411.

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Hovmöller, Rasmus. "Molecular phylogenetics and taxonomic issues in dragonfly systematics (Insecta: Odonata)." Doctoral thesis, Stockholm University, Department of Zoology, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-1065.

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Dragonflies (Odonata) are one of the ancestral groups of extant insects. They represent one of the three most basal branches in the phylogeny of winged insects. The other two groups are the Ephemeroptera, mayflies, and Neoptera, the latter which covers the remaining winged insects. The first paper is about the phylogenetic position of Odonata in relation to the other basal insect clades using 18S and 28S rDNA sequences. It was demonstrated that there are under certain parameters a strong statistical support for a sister-group relationship between Odonata and Neoptera forming the group Palaeoptera. The second paper is about the phylogeny of the Holarctic dragonfly Leucorrhinia. Dragonfly larvae are frequently equipped with spines on the abdomen, with great variation in spinyness between species. From an analysis of sequences of ITS and 5.8S rDNA it was found that spines have been lost at least twice in Leucorrhinia, in the European L. rubicunda and again in a clade of North American species. The third paper is on the subfamily Ischnurinae (Odonata: Coenagrionidae), a group dominated by the two larger genera Ischnura and Enallagma along with several mono- or oligotypic genera. From the presented molecular study, using mitochondrial 16S rDNA and COII sequences, it is demonstrated that Ischnurinae, and Ischnura are monophyletic. Enallagma is not monophyletic, and the genus name Enallagma should be restricted to the E. cyathigerum clade. he fourth paper is a catalog of the genus Coenagrion, with full information on synonymy, type material and bibliographical data. The fifth paper is an appeal to the International Commission on Zoological Nomenclature to suppress the genus group name Agrion. The letter of appeal elucidates the priority of Agrion, and demonstrates why it has fallen out of use. A case if made for why Agrion should be placed on the list of unavailable names, and Calopteryx given full validity.

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James, Stephen Alan. "Molecular systematics of ascomycetous yeasts." Thesis, University of East Anglia, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.267723.

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Brown, Susan. "Molecular systematics of Vahlkampfid amoebae." Thesis, University of Liverpool, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.363946.

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Unwin, Matthew M. "Molecular Systematics of the Eriocaulaceae Martinov." View electronic version of this work, 2004. http://www.ohiolink.edu/etd/send-pdf.cgi?miami1082582823.

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Waddell, Victor Garry. "Higher level molecular systematics of mammals." Thesis, Queen's University Belfast, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.394601.

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Teeling, E. C. "A molecular perspective on chiropteran systematics." Thesis, Queen's University Belfast, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.390864.

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Roberts, Peter James. "Morphological and molecular systematics of ceratobasidiales." Thesis, King's College London (University of London), 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.285829.

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Siripun, Kunsiri Chaw. "Molecular systematics of North American Eupatorium." View online version of this work, 2004. http://etd.utk.edu/2004/SiripunKunsiri.pdf.

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Thesis (Ph. D.)--University of Tennessee, Knoxville, 2004.
Title from title page screen (May 20, 2004). Thesis advisor: Edward E. Schilling. Document formatted into pages (xiv, 225 p. : ill. (some col.), maps). Vita. Includes bibliographical references (p. 117-128).

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Bygrave, Paul C. "Molecular systematics of the Annonaceae Juss." Thesis, University of Reading, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.367691.

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Pell, Susan Katherine. "Molecular systematics of the cashew family (Anacardiaceae) /." View online version of this work, 2004. http://etd.lsu.edu/docs/available/etd-04152004-101232/.

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Moulton, John Kevin 1966. "Molecular systematics of the Simuliidae (Diptera: Culicomorpha)." Diss., The University of Arizona, 1997. http://hdl.handle.net/10150/282408.

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Relationships within Simuliidae, or black flies, are inferred from molecular sequences from four nuclear loci -the large ribosomal subunit (28S rDNA), elongation factor one alpha (EF-1α), dopa decarboxylase (DDC), and phosphoenolpyruvate carboxykinase (PEPCK) - and two mitochondrial loci - the small ribosomal subunit (12S rDNA) and subunit two of NADH dehydrogenase (ND2). Analyses of all genes provide varying degrees of support for subfamily and tribal limits within Simuliidae that are completely concordant with those inferred from the most intensive analysis of morphological data. Additionally, 28S and PEPCK suggest thaumaleids are more closely related to simuliids than are chironomids. Relationships within Simuliidae below the level of tribe were inferred from independent and simultaneous analyses of these data. Phylogenetic trees thought to represent best estimates of simuliid relationships were used to trace the evolution of several morphological characters and of natural partitions of these sequences, particularly codon positions in the four protein coding genes. The rather poor performance of these genes at intermediate taxonomic depths within Simuliidae is hypothesized to be the result of explosive diversification, properties of these genes, or a combination of the two. Potential hypotheses for the rather poor performance of these genes are proposed, and two types of genes hypothesized to be more informative in cases of explosive radiation are described.

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Steane, D. A. "Molecular systematics of Clerodendrum L. s.l. (Lamiaceae)." Thesis, University of Oxford, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.259827.

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Shojaei, Hasan. "Molecular systematics of some medically important actinomycetes." Thesis, University of Newcastle Upon Tyne, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.326085.

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Ferguson, Carolyn Jeannine. "Molecular systematics of eastern Phlox L. (Polemoniaceae) /." Digital version accessible at:, 1998. http://wwwlib.umi.com/cr/utexas/main.

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De, Roo Ryan Thomas. "Molecular systematics of the genus Widdringtonia Endl." Thesis, University of Cape Town, 2002. http://hdl.handle.net/11427/23938.

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Varhol, Richard Joseph. "The molecular systematics of Southern African Testudinidae." Master's thesis, University of Cape Town, 1998. http://hdl.handle.net/11427/26918.

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Sixteen of the world's 42 species of land tortoises occur in Africa, 10 of which are endemic to southern Africa. South Africa itself, which occupies 0.8% of the earth's total land mass, has the highest tortoise biodiversity in the world, with 13 species. This is the first study to use molecular techniques to investigate the evolutionary history of this group, which displays an unusually high level of speciation on the continent. Four hundred and fifty base pairs of mtDNA cytochrome b sequence were obtained, using direct PCR-based sequencing, from 32 individual tortoise blood samples, comprising 13 different species from 6 genera. PAUP 3. 1.1, and MEGA were used to infer a phylogeny using Chrysemys scripta elegans (an Emydid) an outgroup. Both phenetic and cladistic methods generated similar results. With the exception of Malacochersus, both morphological and molecular work show largely congruent results. When intra-specific relationships, using the molecular results, were compared to the existing morphological data, Psammobates was the only genus with a consistent topology. Proposals for the re-evaluation of Homopus, Kinixys and Geochelone have been made. Suggestions, based on molecular results, include the distinction between Chersobius and Homopus (Hewitt 1937), incorporating Malacochersus tornieri into Kinixys, and the elevation of Geochelone pardalis pardalis and G.p. babcocki to species level. Sequencing a further nine individuals within Homopus areolatus showed a higher than expected sequence variation, suggesting a distinct population structure and possibly cryptic species.

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Ng, Y. P. "Molecular systematics and evolution of Eria (orchidaceae)." Thesis, Birkbeck (University of London), 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.492378.

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Hayashi, Kazuhiko. "Molecular Systematics of Liliales and Allied Groups." 京都大学 (Kyoto University), 1999. http://hdl.handle.net/2433/182016.

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Persson, Nannie. "Phylogenetic relationships of the "Briza complex" to other members of the subfamily Pooideae (Poaceae) : Based on molecular data from the nuclear regions ITS and GBSSI, and the chloroplast gene matK." Thesis, Stockholms universitet, Institutionen för ekologi, miljö och botanik, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-170406.

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Sivakumaran, Swarna. "Molecular systematics of the genera Cryptococcus and Filobasidiella." Thesis, Birkbeck (University of London), 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.407405.

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A molecular systematic study of the genera Cryptococcus and Filobasidiella was undertaken through PCR-RFLP and DNA sequence data analysis. The closely related genera in the orders Tremellales, Filobasidiales and Cystofilobasidiales included in the study were the anamorphic genera Trichosporon, Tsuchiyaea, Bullera and Fellomyces, together with the teleomorphic genera Tremella, Sirobasidium, Filobasidium and Cystofilobasidium. RFLP of PCR products was employed for an initial screening of the taxa to determine DNA variation. PCR-RFLP analysis of the ITS region in the ribosomal RNA gene cluster identified that Cryptococcus, Filobasidiella and other related taxa consisted of 64 groups or ITS-RFLP types. The DNA sequence data analyses were based on a multiple gene approach. Nuclear small subunit ribosomal DNA sequences (1682bp) and the ITS and 5.8S region of ribosomal DNA sequences (629bp) from 164 taxa were analysed using parasimony and Bayesian methods to show the ribosomal phylogeny of the genera Cryptococcus and Filobasidiella with other related taxa. As an additional gene region a defined section of the protein-encoding ,6-tubulin gene sequences (1147bp) from 76 taxa was analysed and compared with the ribosomal phylogeny. Combined analysis of the 18S and ITS ribosomal gene regions was also included, to support and strengthen the independent analysis. The results showed that in general there was a good agreement between the taxonomic relationships of the genera Filobasidiella and Cryptococcus with other related taxa based 3 on the ribosomal and ,3-tubulin phylogeny. All three analyses independently supported the positioning of the genus Filobasidiella within the Tremellales lineage and supported the monophyly of the genus Filobasidiella. The anamorphic genus Cryptococcus was shown to be an aggregate of several diverse taxa belonging to different genera. The present study provided sufficient evidence for determining the grouping of the Cryptococcus species and thus serves as a foundation for a new classification of this anamorphic genus.

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McIvor, Lynne Margaret. "Molecular systematics of the red algal order Ceramiales." Thesis, Queen's University Belfast, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.247387.

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Neubig, Kurt Maximillian. "Molecular systematics of the genus Dichaea (Zygopetalinae : Orchidaceae)." [Gainesville, Fla.] : University of Florida, 2005. http://purl.fcla.edu/fcla/etd/UFE0012820.

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Shrestha, Sangita. "Molecular systematics of weedy sporobolus species of Australia /." St. Lucia, Qld, 2001. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe16398.pdf.

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Bodine, Deanna Martinez. "Molecular systematics of Baird's pocket gopher (Geomys breviceps)." Thesis, University of North Texas, 2010. https://digital.library.unt.edu/ark:/67531/metadc30438/.

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Baird's pocket gopher (Geomys breviceps) is found in eastern Texas, eastern Oklahoma, central and western Arkansas, and western Louisiana. The cytochrome-b gene was sequenced and analyzed for 16 pocket gophers from throughout the range of the species. Similar phylogenetic trees were obtained using maximum-parsimony, maximum-likelihood, neighbor-joining, and Bayesian analyses. Two major clades were formed with northern individuals belonging to clade I and southern individuals belonging to clade II. G. b. sagittalis was paraphyletic in relation to G. b. breviceps in all analyses. Based on inconsistencies between the taxonomic classification and systematic relationships within Baird's pocket gopher, a taxonomic restructuring appears warranted.

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Carol. "Molecular and morphological systematics of heteroscleromorpha (Demospongiae : Porifera)." Thesis, Queen's University Belfast, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.680371.

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Heteroscleromorpha with approximately 5000 species is the largest and most important group of Demospongiae in terms of number of species. The aim of this project was to reconstruct a robust phylogeny of Heteroscleromorpha using 28S rRNA and mitochondrial COI barcoding fragments. The phylogenies derived from the 28S and COI sequences were congruent but conflicted with the morphological classification of Systema Porifera (Hooper & van Soest, 2002). Fourteen well supported clades were recovered and formed the basis for a new hypothesis for relationships of taxa allocated to Heteroscleromorpha. At the time of publication this was the largest and most comprehensive study of Heteroscleromorpha. Several important taxonomic changes were proposed including the resurrection ofAxinellida for a clade containing Axinellidae, Raspailiidae and Stelligeridae. The decision to abandon Axinellida arid distribute its families among other orders was based on the more parsimonious assumption that an axially condensed skeleton had evolved independently in separate lineages in preference to the less parsimonious assumption that asters, acanthostyles and sigmata each evolved more than once. In an attempt to understand the underlying causes of the incongruence between the morphology based classification Systema Porifera and the molecular classification, the distribution of asters, acanthostyles, sigmata and axially condensed skeletons were mapped onto phylogenetic trees derived from combined full length 18S rRNA, partial 28S rRNA (03-08 region) and COI barcoding sequences. From their distribution on the tree it was demonstrated that asters, acanthostyles, sigmata and axially condensed architectures are all homoplasious characters. The family Stelligeridae was resurrected for a strongly supported clade containing Halicnemia spp. (currently classified as Heteroxyidae), Stelligera spp. and Paratimea spp. (both genera classified as Hemiasterellidae). The surprising discovery that taxa from such distant parts of the classification appeared to be closely related on the 28S, 18S and COI trees led to a more extensive investigation of Heteroxyidae and Hemiasterellidae. Several species assigned to Heteroxyidae (on the basis of the possession of smooth or acanthose microxea) and Hemiasterellidae (on the basis of the possession of smooth or partially microspined euasters) were shown to be more closely related to other heteroscleromorph families.

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Semaan, Myrna. "Conservation and molecular systematics of the genus Cedrus." Thesis, University of Reading, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.394488.

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Cedrus is a long-lived forest tree whose extant distribution is limited to a disjunct occurrence at the southern margin of the wide expansion range of its family Pinaceae. Its taxonomy is marked with conflicting inferences. The position of Cedrus within Pinaceae is unresolved between the major subfamily groupings. The infrageneric classification of Cedrus taxa, which is based on indistinct phenotypic characters, remains highly controversial. Within its narrow geographical boundaries, Cedrus has long been, and is still, threatened with a diversity of degrading pressures that raise questions on the viability of the dispersed remnant populations. The unsettled taxonomic dispute, compounded with gaps and uncertainties in the information available on the genus, impede potential efforts toward the conservation and sustainable management of this ancient heritage. This study employed molecular systematics to establish a better understanding of the phylogenetic relationships of Cedrus at the different organizational levels from genus to species and populations. The phylogeny of Pinaceae, reconstructed from chloroplast DNA sequences, establishes Cedrus as a monophylum and resolves its position as sister to the rest of the Pinaceae genera. A DNA-based phylogeny of the interrelationships within Cedrus delimits five evolutionary units which are recognized as species, emphasizing the significance of their geographical disjunction. The evolutionary sequence of these units defines an east-west migration trend from the Himalayas toward the Mediterranean. At the population level, fingerprinting of the genetic diversity in the remnant Cedrus isolates of Lebanon infers a substantial level of diversity distributed within populations with no indication of interpopulation divergence. These findings are instrumental at defining the future conservation of Cedrus as a genetic resource

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Porter, James Mark. "Phylogenetic systematics of Gilia section Giliandra." Diss., The University of Arizona, 1993. http://hdl.handle.net/10150/186416.

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Nuclear ribosomal internal transcribed spacer (ITS) DNA sequences are used to (1) estimate the phylogeny of thirty-six members of Polemoniaceae and (2) estimate the phylogeny of twenty-five populations, representing fifteen named species of Gilia section Giliandra. Analyses evaluating robustness estimations suggest that the earliest branching events are not resolvable using ITS sequences. Evidence is presented to suggest that the genus Gilia, as currently interpreted, is polyphyletic, comprised of at least three independent lineages. Species currently included in Gilia sect. Giliandra represent a monophyletic lineage, independent of the "true Gilias," but sharing common ancestry with G. latifolia. The evolution of reproductive systems is evaluated, using a phylogeny of the fifteen diploid species of Giliandra, derived from a combined sequences and morphological data. Although P/O differs significantly between autogamous and xenogamous classes of species, there is no major changes in P/O associated with the transition from xenogamy to autogamy relative to changes in P/O within xenogamous and autogamous lineages. There is a major decrease in pollen production associated with this transition. It is also shown that changes in pollen and ovule production are uncorrelated.

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Carnicero, Campmany Pau. "Evolution, biogeography and systematics of the genus Cymbalaria Hill." Doctoral thesis, Universitat Autònoma de Barcelona, 2017. http://hdl.handle.net/10803/405371.

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Des de temps ancestrals la diversitat d’éssers vius del planeta ha fascinat i intrigat la humanitat. Com s’originen les espècies? Com han assolit la distribució geogràfica actual? En les darreres dècades, el gran avenç de les tècniques de sistemàtica molecular ha permès anar resolent aquests interrogants de manera satisfactòria. En aquesta tesi, desenvolupem un estudi sistemàtic del gènere Cymbalaria, un grup de plantes rupícoles endèmiques de la conca Mediterrània. Hem utilitzat principalment tècniques moleculars de filogènia i filogeografia i anàlisis morfològiques per inferir la seva història evolutiva i biogeogràfica, i proposar una nova classificació taxonòmica des de la perspectiva de la taxonomia integrativa. Cymbalaria va originar-se al voltant de 4 milions d’anys i va diversificar durant i després de l’establiment del clima mediterrani per mitjà de processos d’especiació al·lopàtrica, simpàtrica i poliploide. Com a mínim, dues dispersions a llarga distància des de Còrsega-Sardenya a les Balears van ocórrer, tot i no observar-se adaptacions específica a la dispersió en aquest cas. Les barreres marines han interromput exitosament el flux genètic en alguns casos, estimulant l’especiació al·lopàtrica, mentre que, en altres, les espècies han aconseguit mantenir el flux genètic entre poblacions separades pel mar. Les fluctuacions del nivell del mar del Pleistocè probablement van contribuir a la distribució actual dels tàxons i van afavorir l’especiació. La combinació de dades moleculars i morfològiques ens han permès apropar la classificació del gènere al concepte de taxonomia integrativa i identificar els caràcters morfològics amb valor diagnòstic. Així doncs, proposem una nova circumscripció per C. fragilis per incloure poblacions que, degut a l’ornamentació de les llavors, s’havien identificat com a C. aequitriloba. Per altra banda, descrivim la nova subespècie parafilètica C. muelleri subsp. villosa, de la qual s’originà per especiació anacladogenètica C. muelleri subsp. muelleri. Així, discutim la importància de reconèixer tàxons no monofilètics, que són el reflex d’una història evolutiva que no sempre produeix relacions purament dicotòmiques entre les espècies. Finalment, proposem un nou tractament taxonòmic per a les espècies de la Mediterrània oriental, en què dividim l’antiga C. microcalyx en quatre espècies, descrivim la nova espècie C. spetae i proposem dues noves combinacions.
Since ancient times the diversity of life forms has fascinated and intrigued humanity. How do species originate? How did they achieve their present geographic distributions? In the last decades, the progress of molecular systematics tools has allowed for successfully answering these questions. In this thesis, we perform a systematic study of the genus Cymbalaria, a group of rupicolous plants endemic to the Mediterranean Basin. Mainly, we used phylogenetic and phylogeographic methods and morphological analyses to infer their evolution and biogeographic history, and to propose a new taxonomic classification from the perspective of integrative taxonomy. Our results show that Cymbalaria originated ca. 4 million years ago and diversified during and after the establishment of Mediterranean type climate, through allopatric, sympatric and polyploid speciation. At least, two long-distance dispersal events from Corsica-Sardinia to the Balearic Islands occurred, although no apparent adaptations for dispersal exist in this case. Marine barriers successfully interrupted gene flow and allowed allopatric speciation to take place in some cases, while, in others, species successfully maintained gene flow between populations separated by the sea. Pleistocene sea-level fluctuations could have contributed to the present distribution of taxa and triggered speciation. By combining molecular and morphological data, we bring the classification of Cymbalaria closer to the integrative taxonomy concept and identify valuable diagnostic morphological characters. Here, we propose a new circumscription of C. fragilis to include specimens misidentified as C. aequitriloba due to the variability of seed ornamentation. Also, we describe the new paraphyletic subspecies C. muelleri subsp. villosa, from which C. muelleri subsp. muelleri originated through anacladogenetic speciation. Thus, we discuss the need for recognizing non-monophyletic taxa, since evolution does not always result in purely dichotomous branching patterns. Finally we suggest a new taxonomic treatment for the eastern Mediterranean species, in which we split C. microcalyx into four species, describe the new species C. spetae and propose two new combinations.

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Guo, Yuelong. "Molecular Systematics of Philadelphus and Molecular Evolution of LFY in the Core Eudicots." NCSU, 2010. http://www.lib.ncsu.edu/theses/available/etd-03262010-121851/.

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Phylogenetic analysis is a powerful tool for elucidate evolutionary relationships of organisms and genes and for testing taxonomic and evolutionary hypotheses. I conducted phylogenetic analyses of DNA sequences from five gene regions to evaluate the classification scheme of Philadelphus and used phylogenetic analysis to provide a framework for examining molecular evolution of the LFY gene in plants. Results from my study suggested that Philadelphus is a paraphyletic group with the single species genus Carpenteria nested within. Three evolutionary distinct clades were identified in this large Carpenteria-Philadelphus complex, the subgenus Deutzoides clade, the genus Carpenteria clade, and the remaining Core-Philadelphus clade, each merits the recognition of a genus. Our results mostly agreed with the most recent treatment of genus Philadelphus on the placement of Deutzoides, with the exception of P. hirsutus. However, our result does not support the classification scheme proposed for the rest Philadelphus species. Biogeographic analysis using the Statistical Bayes-DIVA method (S-DIVA) and divergence time dating with the BEAST method resolved the origin of Philadelphus s. l. in southwestern North America in the Oligocene. Several intercontinental migrations from North America to Asia and to Europe occurred at the different times of the later Tertiary to reach a worldwide distribution of the genus. For the molecular evolution study of LFY gene, our results revealed that the evolution of LFY was under strong functional constraint, with the C domain under the strongest selection force and the intervening domain being the most relaxed. Our study also showed that the detection of positive selection using the Branch Site Model was robust to taxon sampling density, but sensitive to sequence length and alignment ambiguity. Our analyses under various conditions consistently detected positive selection in Fabaceae, where FLO/LFY evolved a role of the KNOX1 gene function in regulating compound leaf development. Under the best alignment, we detected adaptive selection at several sites in Asterales, Brassicaceae, and Fabaceae where gene duplication and/or novel function of LFY have been reported.

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Farid, Arian. "Molecular Phylogenetics of Floridian Boletes." Scholar Commons, 2018. https://scholarcommons.usf.edu/etd/7618.

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The boletes are macrofungi which have undergone extensive taxonomic revisions since the advent of molecular tools. To further our understanding of the boletes in peninsular Florida, we sequenced two common Floridian boletes, and analyzed them with molecular phylogenetic tools. Boletus rubricitrinus, a common Florida bolete often found in lawns under Quercus, and likely has a distribution that extends to Texas. Based on ITS and LSU sequences and morphological studies, this species belongs in the genus Pulchroboletus. As the holotype is in poor condition, an epitype is established here. A thorough description of macroscopic and microscopic features is also provided for the species. Fungi in the genus Phylloporus are lamellate boletes that occur worldwide, but primarily in the tropics. Phylloporus boletinoides is a species which was described from Florida, and is found growing near Pinus spp. Based on ITS, LSU, and RPB1 sequences, we establish the novel genus Pseudophylloporus, which is allied to Bothia and Solioccasus. Morphological data are also provided from our collections, and one from Belize. Based on molecular data and a review of bolete literature, the delimitation of this genus suggests that there are three distinct lineages of boletes that have a lamellate hymenium in the Boletaceae. These molecular and morphological data will be useful to further improve our understanding of bolete taxonomy.

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Feng, Min. "Floral Morphogenesis and Molecular Systematics of the Family Violaceae." Ohio University / OhioLINK, 2005. http://www.ohiolink.edu/etd/view.cgi?ohiou1125497936.

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Sraml, Michaela, and n/a. "Molecular systematics of the native Australian waterfowl (Aves: Anseriformes)." University of Canberra. Resource, Environmental & Heritage Sciences, 1994. http://erl.canberra.edu.au./public/adt-AUC20061113.155232.

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A consensus classification for the waterfowl (order Anseriformes) has never been reached. There have been many revisions of the relationships within the order including those of the monotypic Australian genera. The Southern Hemisphere anseriforms comprise a large number of monotypic, endemic genera which have traditionally been linked to the established genera and tribes of the Northern Hemisphere. More recently, however, with the recognition of endemic Australian radiations of marsupial mammals (Main and Bakker 1981) and passerine birds (Cracraft 1976; Sibley and Ahlquist 1985; Christidis et al. 1988; Christidis and Schodde 1991), the affinities of the six monotypic Australian genera of anseriforms have been questioned (Delacour 1954; Frith 1955, 1964a, b, 1982; Johnsgard 196la, b, 1966; Davies and Frith 1964; Fullager 1990). In particular, whether they are more closely related to one another, or whether some or all of these monotypic genera have closer affinities with the Northern Hemisphere genera. Classification of the taxonomic relationships of the aberrant Australian endemic species may also corroborate or refute the recently advanced hypothesis of a Southern Hemisphere origin for the Anseriformes (Cracraft 1976, 1980; Livezey 1986; Olson 1988). A 307bp fragment of the mitochondrial cytochrome b gene of the 19 native Australian anseriforms and four Northern Hemisphere species was enzymatically amplified by PCR and manually sequenced. The Chicken (Gallus gallus) and Muscovy Duck (Cairinia moschatd) cytochrome b sequences were obtained from Genbank. The patterns of evolutionary dynamics within the cytochrome b gene of Anseriformes appear to conform to those reported in studies of avian and other vertebrate mtDNA. A new phylogenetic classification for the Anseriformes is proposed. The phylogenetic trees generated in this study indicate that the monotypic Australian genera, the pygmygeese and the swans and geese are members of the subfamily Anserinae which appears to represent a Southern Hemisphere radiation. Within the Anserinae, the Cape Barren Goose and Freckled Duck link most closely with each other, the Pink-eared Duck appears to be closely related to the true geese, the Musk Duck is a sister taxon to the Pink-eared Duck and may be less closely related to the Oxyura than previously thought and the Magpie Goose is the most divergent member of the Anseriformes included in this study. The Maned Duck and the remaining native Australian anseriforms are members of the established European genera and tribes of waterfowl. These species probably represent a secondary radiation of recent Northern Hemisphere invaders of Australia. Finally, the data provides some support for the theory of a Southern origin for the Anseriformes.

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Irestedt, Martin. "Molecular systematics of the antbird-ovenbird complex (Aves: Furnariida) /." Stockholm : Zoologiska institutionen, Univ, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-209.

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Ward, Barbara Ann. "The systematics of Ceramium : a molecular and morphological approach." Thesis, Queen's University Belfast, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.247395.

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Gladwell, Gilbert Wesley. "Molecular systematics of Rhinichthys bowersi and its taxonomic status." Huntington, WV : [Marshall University Libraries], 2002. http://www.marshall.edu/etd/descript.asp?ref=141.

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Januszewska, Nina. "Molecular systematics of dictyostelids : a case for single genus." Thesis, Anglia Ruskin University, 2011. http://arro.anglia.ac.uk/297202/.

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The cellular slime moulds or dictyostelids, are a major group of edaphic (soil-dwelling) unicellular eukaryotic micro-organisms which feed on bacteria in the humus layer of tropical and temperate soils. The extraordinary behaviour of dictyostelids where solitary, predatory amoebae become social, forming a multi-cellular spore-producing ‘organism’ when their food supply becomes limited has fascinated generations of researchers. Since their discovery the taxonomy of the cellular slime moulds has been largely based on morphological features, revised many times, but still remains unresolved and controversial. One focus of discussion is the controversial relationship between the two principal genera of Dictyostelium and Polysphondylium, which by virtue of a common amoeba type are placed in the same family - Dictyosteliaceae. Despite the current distinction between Dictyostelium and Polysphondylium it is impossible to definitively resolve these genera, or indeed the broader classification of cellular slime moulds, using only morphological features. Given that dictyostelids are both of major ecological importance and often used as a model eukaryotic system, it has become imperative to resolve these taxonomic uncertainties and to finally establish the validity of one or two genera. This study used two PCR based techniques: (1) direct sequencing of the ITS 1 and ITS 2 regions of the rDNA complex together with (2) ISSR-PCR, a standard molecular technique but rarely applied to the dictyostelids. The latter requiring the development of a working protocol before it could be implemented. The sequence data from 51 different dictyostelid species and isolates was aligned with CLUSTAL and analysed via PAUP. This study clearly demonstrates that molecular markers cannot distinguish Dictyostelium (sensu stricto) from Polysphondylium (sensu stricto): indeed it presents evidence to support the existence of a single genus. The implications of these results are unequivocal: the current systematics of cellular slime moulds, based on morphological characters, must be revised.

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De, Roo Ryan Thomas. "Molecular systematics of the leafy liverwort family Lophoziaceae cavers." Doctoral thesis, University of Cape Town, 2009. http://hdl.handle.net/11427/12425.

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Includes bibliographical references.
Includes abstract.
Many recent workers have included it in Jungermanniaceae, and even in its strictest sense, internal classification has varied widely among different treatments. Here an analysis of the variation in DNA sequences of the chloroplast rps4 gene and the trnG intron provides resolution of phylogenetic relationships in the leafy liverworts with emphasis on the various elements usually placed in Lophoziaceae. The following conclusions are drawn.

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Cox, S. C. "Molecular systematics and diversification of African Zosteropidae (Aves: Passeriformes)." Thesis, University College London (University of London), 2013. http://discovery.ucl.ac.uk/1397762/.

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The hyper-diverse avian family Zosteropidae (~100 species) is renowned for its exceptional colonising ability and rapid recent diversification. The genus Zosterops dominates within the family, including over 70% of all recognised species, and is notorious for the phenotypic uniformity that has traditionally made designation of taxon boundaries within the genus difficult. While the last decade has seen an abundance of research focusing on colonisation abilities and speciation patterns of insular taxa, relationships between continental forms, specifically mainland African taxa, remain subject to great uncertainty. This thesis focuses on uncovering the relationships, origin and evolutionary history of African Zosteropidae. Chapter 1 introduces the family Zosteropidae, reviews the current literature that is based predominantly on insular systems. In introducing the African Zosteropidae complex, this chapter highlights questions associated with this group and presents the aims of the thesis. Chapter 2 focuses in on one of the most geographically complex areas within the African system, to explore the relative importance of past climatic fluctuations as a driver of diversification in Zosterops endemic to the isolated montane massifs of East Africa. Results provide the first molecular assessment of mainland African Zosteropidae and are used to examine alternative models of speciation. A dated molecular phylogeny demonstrates that divergence within African Zosteropidae is very recent (<5Ma) coinciding with periods of climatic instability during the Plio-Pleistocene. Furthermore, the non-monophyly of mainland taxa, specifically the polyphyletic nature of Z. poliogaster, leads to the rejection of a widely held assumption that the montane endemics of East Africa are relics of a previously widespread population. Instead results provide evidence for evolutionary model based on ancestrally adaptive populations. Chapter 3 attempts to further investigate relationships within the East African Zosterops and explores the usefulness of amplified fragment length polymorphism (AFLPs) in revealing inter- and intra-specific relationships. Resolution of relationships across the AFLP phylogeny is generally poor which is attributed to the low information content of the AFLP matrix generated. Bayesian hypothesis testing failed to provide support for various topological constraints tested and consequently this study was unable to confirm or reject the non-monophyly of East African montane endemics. Chapter 4 builds upon the molecular phylogeny of Chapter 2, by substantially increasing the taxonomic sampling of African species using DNA obtained from museum specimens. The use of both archive and fresh material enabled the largest genetic assessment of western Zosteropidae to date. Extensive sampling across Sub-Saharan Africa, the Indian Ocean region, the Arabian Peninsula and the Gulf of Guinea region reveals six major clades within the African Zosteropidae complex. Results confirm the widespread non-monophyly of mainland African species rendering current taxonomic arrangements invalid. GMYC (General mixed Yule-coalescent) analysis recovers 14 distinct evolutionary lineages within the African Zosteropidae system and provides a framework for further work using model-based species delimitation approaches. Finally, Chapter 5 draws together key findings from Chapters 2-4, and reviews how this work advances our understanding of the African Zosteropidae system. This chapter also highlights new gaps in our understanding of the western Zosteropidae and discusses several areas for future research.

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Ntsohi, Refiloe. "Molecular phylogeny of Tribolium (Danthonioideae: Poaceae) and its taxonomic implications." Bachelor's thesis, University of Cape Town, 2003. http://hdl.handle.net/11427/25689.

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Molecular sequence data from two noncoding regions of DNA (ITS AND TRNL-F) were used to produce a phylogeny for the genus Tribolium and its African and Australasian allies. Topological comparisons of the combined molecular data with the appended existing morphological tree were made. A significant incongruence was revealed. Molecular data indicate that Tribolium is paraphyletic. The formally defined sections: Uniolae, Acutiflorae and Tribolium have been retrieved by the molecular data. The analysis retrieved Karroochloa as polyphyletic. Monophyly of Schismus is strongly supported. The Australasian species form a monophyletic clade. Data support early divergence of the Merxmuellera species and Pseudopentameris macrantha.

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Rai, Hardeep Singh. "Molecular phylogenetic studies of the vascular plants." Thesis, University of British Columbia, 2008. http://hdl.handle.net/2429/3889.

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To investigate vascular-plant phylogeny at deep levels of relationship, I collected and analyzed a large set of plastid-DNA data comprising multiple protein-coding genes and associated noncoding regions. I addressed questions relating to overall tracheophyte phylogeny, including relationships among the five living lineages of seed plants, and within two of the largest living gymnosperm clades (conifers and cycads). I also examined relationships within and among the major lineages of monilophytes (ferns and relatives), including their relationship to the remaining vascular plants. Overall, I recovered three well-supported lineages of vascular plants: lycophytes, monilophytes, and seed plants. I inferred strong support for most of the phylogenetic backbones of cycads and conifers. My results suggest that the cycad family Stangeriaceae (Stangeria and Bowenia) is not monophyletic, and that Stangeria is instead more closely related to Zamia and Ceratozamia. Within the conifers, I found Pinaceae to be the sister-group of all other conifers, and I argue that two conifer genera, Cephalotaxus and Phyllocladus (often treated as monogeneric families) should be recognized under Taxaceae and Podocarpaceae, respectively. Systematic error likely affects inference of the placement of Gnetales within seed-plant phylogeny. As a result, the question of the relationships among the five living seed-plant groups still remains largely unresolved, even though removal of the most rapidly evolving characters appears to reduce systematic error. Phylogenetic analyses that included these rapidly evolving characters often led to the misinference of the “Gnetales-sister” hypothesis (Gnetales as the sister-group of all other seed plants), especially when maximum parsimony was the inference method. Filtering of rapidly evolving characters had little effect on inference of higher-order relationships within conifers and monilophytes, and generally resulted in reduced support for backbone relationships. Within the monilophytes, I found strong support for the majority of relationships along the backbone. These were generally congruent with other recent studies. Equisetaceae and Marattiaceae may be, respectively, the sister-groups of the remaining monilophytes and of the leptosporangiate ferns, but relationships among the major monilophyte lineages are sensitive to the outgroups used, and to long branches in lycophytes.

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Nuhn, Mitchell E. "Molecular ecology of Boletinellus merulioides and systematics of the Boletineae." Thesis, Clark University, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10090330.

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This work focuses on members of the Boletales. This order is comprised of a morphological and ecologically diverse set of species. While the vast majority of species are pileate-stipitate with pores and have a mutualistic nutritional strategy ectomycorrhal (ECM), there are resupinate and gilled species, and saprotrophs and mycoparasites as well. In the first chapter, we review the ecological niche occupied by Boletinellus merulioides. This species was originally considered to be ECM, the symbiont to Fraxinus americana. This hypothesis was rejected, and replaced by the possibility of a mutualism with an F. americana aphid pest, Prociphilus fraxinifolii. We present the first study that observed all three species, since the original publication, the first molecular data for each species, and isotopic fractionation results for B. merulioides and P. fraxinifolii. Additionally, we describe a new morphology for sclerotia of B. merulioides. In total, we are unable to reject the possibility of a facultative mutualism between B. merulioides and P. fraxinifolii.

Chapters two through five review systematics in the Boletineae. Chapter two presents the most comprehensive phylogenetic review of the Boletineae, at the time publication, and remains one of the most inclusive Boletineae phylogenies. Three genes, nuclear large subunit, translation elongation factor 1-alpha, and DNA directed RNA polymerase II largest subunit, were used. This chapter is a summary of Boletineae taxonomy and morphological characteristics, with a clade by clade analysis. We present compelling evidence for the mycoparasitic nutritional mode of Buchwaldoboletus lignicola. Additionally, we found that Chalciporus piperatus, a close relative of B. lignicola, is likely to be a mycoparasite. We present strong evidence that the genus Boletus is limited to single clade that contains approximately 10% of the validly published Boletus species.

A subset of the taxa sampled in chapter two was used in the phylogenies presented in chapters three, four, and five. Each of these chapters reviews the phylogenetic placement of traditionally problematic species/genera; Surotius eximius, Harrya chromapes and allies, and the Boletaceae species with longitudinally striated spores. These groups have been in multiple. Our results show that Sutorius and Harrya species are distinct from other Boletacaea species and that the longitudinally striated species have been lumped together. By correcting taxonomic confusion and using a multigene data set we are able to resolve these problematic species, and provide a path for future systematics and evolutionary analysis.

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Wanke, Stefan. "Evolution of the genus Aristolochia - Systematics, Molecular Evolution and Ecology." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2007. http://nbn-resolving.de/urn:nbn:de:swb:14-1169634459488-35651.

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Evolution of Piperales – matK gene and trnK intron sequence data reveal lineage specific resolution contrast. Piperales are one of the largest basal angiosperm orders with a nearly worldwide distribution. The order includes three species rich genera, Piper (ca. 1,000 species), Peperomia (ca. 1,500-1,700 species), and Aristolochia s. l. (ca. 500 species). Sequences of the matK gene and the non-coding trnK group II intron are analysed for a dense set of 105 taxa representing all families (except Hydnoraceae) and all generic segregates (except Euglypha within Aristolochiaceae) of Piperales. A large number of highly informative indels are found in the Piperales trnK/matK dataset. Within a narrow region approximately 500 nt downstream in the matK coding region (CDS), a length variable simple sequence repeat (SSR) expansion segment occurs, in which insertions and deletions have led to short frame-shifts. These are corrected shortly afterwards, resulting in a maximum of 6 amino acids being affected. Furthermore, additional non-functional matK copies were found in Zippelia begoniifolia, which can easily be discriminated from the functional open reading frame (ORF). The trnK/matK sequence data fully resolve relationships within Peperomia, whereas they are not effective within Piper. The resolution contrast is correlated with the rate heterogenity between those lineages. Parsimony, Bayesian and likelihood analyses result in virtually the same topology, and converge on the monophyly of Piperaceae and Saururaceae. Lactoris gains high support as sister to Aristolochiaceae subf. Aristolochioideae, but the different tree inference methods yield conflicting results with respect to the relationships of subfam. Asaroideae. In Piperaceae, a clade formed by the monotypic genus Zippelia and the small genus Manekia (=Sarcorhachis) is sister to the two large genera Piper and Peperomia. Systematics of pipevines – Combining morphological and fast-evolving molecular characters to investigate the relationships within subfamily Aristolochioideae (Aristolochiaceae) A combined phylogenetic analysis of the Aristolochioideae was conducted based on 72 morphological characters and molecular datasets (matK gene, trnK intron, trnL intron, trnL-trnF spacer). The analysis sampled 33 species as the ingroup, including two species of Thottea and 30 species of Aristolochia and the monotypic genus Euglypha, which represent all the infrageneric taxa formally described; Saruma henryi and Asarum caudatum were used as the outgroup. The results corroborate a sister-group relationship between Thottea and Aristolochia, and the paraphyly of Aristolochia with respect to Euglypha that consequently should be included into Aristolochia. Two of the three subgenera within Aristolochia (Isotrema and Pararistolochia) are shown to be monophyletic, whereas the signal obtained from the different datasets about the relationships within subg. Aristolochia is low and conflicting, resulting in collapsed or unsupported branches. The relationship between the New World and the Old World species of subgenus Aristolochia is conflictive because morphological data support these two groups as monophyletic, whereas molecular data show the monophyletic Old World species of Aristolochia nested within the New World species. A sister group relationship is proposed between A. lindneri and pentandrous species, which suggests that a group of five species from central and southern South America (including A. lindneri) could be monophyletic and sister to Aristolochia subsection Pentandrae, a monophyletic taxon consisting of about 35 species from southern USA, Mesoamerica, and the West Indies. Colonisation, phylogeography and evolution of endemism in Mediterranean Aristolochia (Aristolochiaceae). This study provides evidence for a multiple colonisation of the western Old World from Asian ancestors within Aristolochia section Diplolobus (subsection Aristolochia and Podanthemum). Within subsection Podanthemum it is assumed, that the colonisation of the African continent happened at least two times independently. In contrast, for subsection Aristolochia, a rapid morphological radiation in the Near East (or close to this area) with subsequent star like colonisation of the different current distribution areas, which is not paralleled on the molecular level, appears to be more likely. Phylogenetic tree reconstruction is unsupported for these clades, but most clades are highly supported as monophyletic. Interestingly the Mediterranean and temperate Eurasian species, which are morphologically distinct (A. pistolochia, A. clematitis) are not clustering within the main clades, but are independent lineages. Analogue, A. rigida a species from Somalia is well-supported sister to the subsection Aristolochia. Within subsection Podanthemum the colonisation event from an Asian ancestor is clearly traceable, whereas in subsection Aristolochia the path is not traceable, since the ancestors are extinct or not present in the connecting areas. Within the Mediterranean, Near East and Caucasian species of subsection Aristolochia two morphologically and biogeographically well supported groups can be identified: the Near East/Caucasian species and the West Mediterranean species. The previous groupings for the latter, based on morphological characters, could be substantiated only partly by our results. This study provides the first phylogeny of all West Mediterranean species. In addition an independent complex is established including some micro endemic species. The phylogenetic results are discussed with respect to biogeography, and morphology, to give a first insight into the radiation and colonisation of the genus Aristolochia in the Mediterranean region. Universal primers for a large cryptically simple cpDNA microsatellite region in Aristolochia. We provide a new and valuable marker to study species relationships and population genetics in order to trace evolutionary, ecological, and conservational aspects in the genus Aristolochia. Universal primers for amplification and subsequent sequencing of a chloroplast microsatellite locus inside the trnK intron are presented. Utility of the primers has been tested in 32 species representing all clades of Aristolochia, including population studies within the A. pallida complex, A. clusii and A. rotunda. The microsatellite region is characterized as a (AnTm)k repeat of 22–438 bp containing a combination of different repeats arranged as ‘cryptically simple’. Trapped! Pollination of Aristolochia pallida Willd. in the Mediterranean A first study of the pollination biology of a Mediterranean Aristolochia species in its natural habitat is presented. 183 flowers of Aristolochia pallida were investigated, which in total contained 73 arthropods, dominated by two groups of Diptera, Sciaridae (37%) and Phoridae (19%). However, only Phoridae are regarded as potential pollinators, since pollen has been found exclusively on the body surfaces of these insects. All Phoridae belong to the genus Megaselia and are recognised as four undescribed species. The measurements of flower and insect dimensions suggest that size is an important constrain for successful pollination: 1) the insects must have a definitive size for being able to enter the flower and 2) must be able to get in touch with the pollen. Only very few insect groups found in Aristolochia pallida fulfil these size requirements. However, size alone is not a sufficient constrain as too many fly species of the same size might be trapped but not function as pollinators. Instead, specific attraction is required as otherwise pollen is lost. Since all trapped Phoridae are males, a chemical attraction (pheromones) is proposed as an additional constrain. Since A. pallida flowers are protogynous, the record of Megaselia loaded with pollen found in a flower during its female stage proves that this insect must have been visited at least one different flower during its male stage before. Further on, this observation provides strong evidence that the flowers are cross-pollinated. All these factors indicate a highly specialised pollination of Aristolochia pallida by Megaselia species.

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Smythe, Ashleigh Brooke. "Refining the systematics of Cephalobina with molecular and morphological tools /." For electronic version search Digital dissertations database. Restricted to UC campuses. Access is free to UC campus dissertations, 2005. http://uclibs.org/PID/11984.

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Thesis (Ph. D.)--University of California, Davis, 2005.
Degree granted in Plant Pathology. Library has photocopied, separately signed title page, in addition to original title page. Also available via the World Wide Web. (Restricted to UC campuses)

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Furtado-Neto, Manuel Antonio de Andrade. "Molecular systematics and population genetics of marine vertebrates from Brazil." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp02/NQ36203.pdf.

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Geleta, Mulatu. "Genetic diversity, phylogenetics and molecular systematics of Guizotia Cass. (Asteraceae) /." Alnarp : Department of Plant Protection Biology, Swedish University of Agricultural Sciences, 2007. http://epsilon.slu.se/200727.pdf.

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Hovmöller, Rasmus. "Molecular phylogenetics and taxonomic issues in dragonfly systematics (Insecta: Odonata) /." Stockholm : Department of Zoology, Stockholm university, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-1065.

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Dissertations / Theses on the topic 'Molecular systematics'

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