This research was an attempt to identify and provide a phylogeny of Vanilla orchids using PCR sequencing/ fingerprinting.Traditional classification methods haved relied heavily on morphological traits and are often contradictory, subjective and incomplete. This research attempted to discover an objective and reliable method for identification and classification of selected tropical orchids species using molecular techniques. Vanilla orchids were chosen for their commercial importance in the scent and flavoring industry.Reconstruction of phylogenetic data is possible using relatively new molecular techniques: Polymerase Chain Reaction (PCR) fingerprinting and sequencing. PCR fingerprinting reveals restriction fragment length polymorphisms (RFLPs) within an organism's genome. Thesevariations can be used to construct genetic maps in a variety of species. PCR sequencing reveals genetic variation at an even greater level: nucleotide sequence.The literature suggests that these methods are fairly quick and simple; however, the crucial step is obtaining high molecular weight DNA digestable with restriction enzymes or amplifiable by the PCR. DNA isolation has proven to be difficult with Vanilla orchids due to their numerous phenolic compounds, tough fibrous tissue and high number of polysaccharides. This research developed a method of isolating high molecular weight DNA from orchids. This DNA was digestible with restriction enzymes. The DNA was subjected to DNA fingerprinting with primers specific to the 18S-26S ribosomal RNA gene and with RAPD primers. The DNA was also sequenced using the PCR technique.Variation between Vanilla species genomes was discovered and compared to traditional phylogenetic information. It was found that banding patterns and nucleotide sequences were almost identical for Vanilla planifolia and planifolia varegata. The banding patterns for Vanilla barbellata were similar to those of the two unknown Vanilla orchids. Vanilla humboltii exhibited a banding pattern far different from either barbellata or planifolia. These results confirm the hypothesis that PCR fingerprinting/ sequencing is a useful technique for the identification and phylogenetic analyses of Vanilla orchids. / Department of Biology

There are ~12 supergroups of complex-celled organisms (eukaryotes), but relationships among them (including the root) remain elusive. For Paper I, I developed a dataset of 37 eukaryotic proteins of bacterial origin (euBac), representing the conservative protein core of the proto-mitochondrion. This gives a relatively short distance between ingroup (eukaryotes) and outgroup (mitochondrial progenitor), which is important for accurate rooting. The resulting phylogeny reconstructs three eukaryote megagroups and places one, Discoba (Excavata), as sister group to the other two (neozoa). This rejects the reigning “Unikont-Bikont” root and highlights the evolutionary importance of Excavata. For Paper II, I developed a 150-gene dataset to test relationships in supergroup SAR (Stramenopila, Alveolata, Rhizaria). Analyses of all 150-genes give different trees with different methods, but also reveal artifactual signal due to extremely long rhizarian branches and illegitimate sequences due to horizontal gene transfer (HGT) or contamination. Removing these artifacts leads to strong consistent support for Rhizaria+Alveolata. This breaks up the core of the chromalveolate hypothesis (Stramenopila+Alveolata), adding support to theories of multiple secondary endosymbiosis of chloroplasts. For Paper III, I studied the evolution of cox15, which encodes the essential mitochondrial protein Heme A synthase (HAS). HAS is nuclear encoded (nc-cox15) in all aerobic eukaryotes except Andalucia godoyi (Jakobida, Excavata), which encodes it in mitochondrial DNA (mtDNA) (mt-cox15). Thus the jakobid gene was postulated to represent the ancestral gene, which gave rise to nc-cox15 by endosymbiotic gene transfer. However, our phylogenetic and structure analyses demonstrate an independent origin of mt-cox15, providing the first strong evidence of bacteria to mtDNA HGT. Rickettsiales or SAR11 often appear as sister group to modern mitochondria. However these bacteria and mitochondria also have independently evolved AT-rich genomes. For Paper IV, I assembled a dataset of 55 mitochondrial proteins of clear α-proteobacterial origin (including 30 euBacs). Phylogenies from these data support mitochondria+Rickettsiales but disagree on the placement of SAR11. Reducing amino-acid compositional heterogeneity (resulting from AT-bias) stabilizes SAR11 but moves mitochondria to the base of α-proteobacteria. Signal heterogeneity supporting other alternative hypotheses is also detected using real and simulated data. This suggests a complex scenario for the origin of mitochondria.

Vertebral development patterns have been well characterised in the Paleozoic "lepospondyls" and "labyrinthodonts", as well as in modern amniotes, frogs and caecilians. Each of those groups consistently develop either the neural arches before the centra or the centra before neural arches. Preliminary studies confirmed that members of the Urodela exhibit both developmental patterns. To understand if there is any consistency in patterns of vertebral development within and between families, as well as to investigate the distribution of patterns within the order, 120 salamander larvae from the ten living salamander families were cleared, stained and examined for osteological development. In order to provide a basis of comparison between different developmental stages observed in different families, a staging table was constructed. The complete osteological development of every cleared and stained specimen used in this study was then described. Finally, the general pattern of vertebral development was examined and characteristic patterns for each family were mapped on an accepted phylogeny of salamander relationships.

The North American antlion genus Paranthaclisis is comprehensively revised for the first time. Four species are recognized: P. congener (Hagen), P. floridensis Stange & Miller, P. hageni (Banks) and P. nevadensis Banks. Redescriptions, distribution maps and figures of diagnostic morphological characters are provided for adults of each species. A key to adults of Paranthaclisis is also included. Paranthaclisis californica Navas (1922) is recognized as a new synonym of P. hageni Banks. The monophyly of, and interspecific relationships within, the antlion genus Paranthaclisis, and its relationships to other genera within the tribe Acanthaclisini, are investigated using multiple datasets. Fifteen datasets were produced and analyzed to explore the effects of inference method, alignment strategy and data partitioning on phylogenetic estimates using morphological, molecular and mixed data inputs. Eighteen unordered and unweighted morphological characters were coded from across adult body regions. Molecular sequence data generated for this study consisted of two ribosomal genes, 16S and 18S. Paranthaclisis was recovered as monophyletic in analyses using 14 of 15 datasets, with low to moderate support in maximum parsimony and maximum likelihood analyses and high support from Bayesian inference methods. A sister-group relationship between Paranthaclisis and Vella, the only other New World acanthaclisine genus, was also recovered in analysis of 13 of 15 datasets, with low to moderate support in all phylogenetic inference methods tested. Choice of phylogenetic inference method and partitioning of gene datasets had the most influence on resulting topologies and support values. Choice of alignment strategy resulted in few topological differences, but Clustal datasets generally had higher clade support values, compared to MAFFT-aligned sequences.

Thesis (Ph. D.)--University of Hawaii at Manoa, 2004. / Includes bibliographical references (leaves 349-373). / Also available by subscription via World Wide Web / x, 373 leaves, bound ill. 29 cm

Corrigenda pasted on verso of leaf 267. / Bibliography: leaves 239-253. / xii, 267 leaves : ill. ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / This study focuses on the phylogenetic status of Diolcogaster within the Cotesia-complex. The Cotesia-complex is not resolved as a monophyletic group though most of the included genera are so resolved. Diolcogaster is revised for the Australasian region and recorded for the first time fron New Zealand. A total of 26 species are now known from Australasia. / Thesis (Ph.D.)--University of Adelaide, Dept. of Crop Protection, Faculty of Agriculture and Natural Resource Sciences, 1997

Diss. (sammanfattning) Uppsala : Univ., 2007. / Härtill 4 uppsatser.

Diss. (sammanfattning) Uppsala : Univ., 2007. / Härtill 6 uppsatser.

Thesis (Ph. D.)--University of Hong Kong, 2008. / Also available in print.

Diss. (sammanfattning) Uppsala : Uppsala universitet, 2006. / Härtill 6 uppsatser.