Chan, Ho Fai. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2008. / Includes bibliographical references (leaves 59-60). / Abstracts in English and Chinese. / Chapter 1 --- Introduction --- p.5 / Chapter 2 --- Current methods on Neighbor-Joining --- p.9 / Chapter 2.1 --- Introduction to graph theory --- p.9 / Chapter 2.2 --- General discussion on visualizing distance matrices by binary trees --- p.18 / Chapter 2.3 --- Original 0(N5) Neighbor-Joining algorithm --- p.21 / Chapter 2.4 --- Speedup of NJ --- p.22 / Chapter 2.4.1 --- 0(N3) NJ for arbitrary distance matrices --- p.23 / Chapter 2.4.2 --- 0(N2) NJ on additive matrices --- p.23 / Chapter 3 --- Finding neighbor pairs --- p.25 / Chapter 3.1 --- Properties of Binary trees --- p.25 / Chapter 3.2 --- Similar rows: finding all neighbor pairs in additive matrices --- p.28 / Chapter 4 --- Divide-and-Conquer Neighbor-Joining --- p.35 / Chapter 4.1 --- DCNJ Algorithm --- p.36 / Chapter 4.2 --- Theories of DCNJ on additive matrices: Correctness and Complexity --- p.44 / Chapter 5 --- Experimental Results --- p.56 / Chapter 6 --- Conclusions --- p.58

Culture independent studies have revealed a greater diversity of Archaea than the two kingdoms initially defined by Carl Woese. Culturing species from the newly discovered archaeal lineages, as with the majority of microbes, has been difficult. To overcome the culturing dilemma, metagenomics is being used to reconstruct environmental genomes. Two metagenomic studies are presented in this thesis, with the aim of recovering newly proposed archaeal genomes from the Nanoarchaeota and Korarchaeota. In the first study, a sediment sample, NZ13, was collected from a terrestrial New Zealand hot spring. Along with the sediment sample, two complex enrichments were sequenced on an Illumina MiSeq platform. Assembly and differential binning recovered two nearly complete genomes of a nanoarchaeote and a korarchaeote. The NZ13 nanoarchaeote is similar to other terrestrial nanoarchaeotes, which lack an ATP synthase and encode genes for glycolysis/gluconeogenesis and archaella. One notable difference is the NZ13 nanoarchaeote contains CRISPR genes, which are absent in other terrestrial nanoarchaeotes, although present in a marine nanoarchaeote, Nanoarchaeum equitans. The NZ13 korarchaeote mirrors Candidatus Korarchaeum cryptofilum, lacking genes for de novo synthesis of purines and several cofactors, while containing an abundance of peptide transporters and amino acid fermentation pathways. The second study focused on sulfide samples collected from deep-sea hydrothermal vent fields in southwestern Pacific Ocean along the Eastern Lau Spreading Center. Ten sulfide samples were sequenced on an Illumina HiSeq platform. Small subunit ribosomal RNA genes were extracted from the metagenome reads and aligned against the SILVA Ref NR 99 123 database. The preliminary results identified which samples could be prioritized for genome reconstruction of uncultured bacterial and archaeal lineages. Three uncultured bacteria, candidate division SR1, Gracilibacteria (GN02), and Parcubacteria (OD1) were identified in several samples. Many uncultured deep-sea hydrothermal archaeal lineages were identified in all samples. In particular, korarchaeotal sequences were in high relative archaeal abundances in two samples, ABE 1 and Vai Lili-2, while few nanoarchaeotal reads were classified.

Abstract not available

"December 2001" Bibliography: leaves 227-246.

Corrigenda pasted on verso of leaf 267. Bibliography: leaves 239-253. 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.

Graduation date: 1998

The relative role of cospeciation and host switching in the phylogenetic history of ascomycete foliar symbionts is addressed in the orders Leotiales and Rhytismatales, fungi associated predominantly with Pinaceae (Coniferales). Emphasis is placed on comparing the evolution of the sister genera Pseudotsuga and Larix (Pinaceae) with that of the pathogenic and endophytic fungi in the genus Rhabdocline. Pinaceae evolved during the Mesozoic and divergence of all extant genera and several infrageneric lineages (esp. in Pinus) occurred prior to the Tertiary, with subsequent species radiations following climatic changes of the Eocene. The youngest generic pair to evolve from Pinaceae, Larix and Pseudotsuga, diverged near the Cretaceous-Tertiary boundary in East Asia or western North America. Rhabdocline is comprised of seven species and subspecies, six known from two species of Pseudotsuga and one, the asexual species Meria laricis, from three species of Larix. Evidence from host distributions and from nuclear ribosomal DNA suggests that Rhabdocline speciated in western North America and has been involved in several host switches. The ancestor of Meria laricis appears to have switched from P. menziesii to its current western North American hosts, L. occidentalis, L. lyallii, and very recently may have extended its host range to the European species, L. decidua. The occurrence of two lineages of R. weirii ssp. weirii on both North American species of Pseudotsuga is also probably the result of a recent host switch. Evidence of hostmediated divergence is seen in R. parkeri, which has different internal transcribed spacer types in the geographically isolated coastal and interior forms of P. menziesii. The wide host ranges of fungal genera closely related to Rhabdocline indicates that host switching is a prevalent pattern in the evolution of foliar symbionts in Leotiales and Rhytismatales. The prevalence of host switching in this group relative to other endosymbiotic organisms can probably be attributed to differences in dispersal mechanisms. Spores of foliar fungi are dispersed horizontally by wind and rain, rather than vertically from parent to offspring. Over evolutionary time, this provides more opportunities to shift to new hosts, particularly when the hosts are closely related and have overlapping distributions. / Graduation date: 1998

We studied genetic polymorphism and phylogeny using nuclear random amplified polymorphic DNA markers (RAPDs) and mitochondrial DNA (mtDNA) restriction fragment length polymorphisms (RFLPs) in the three California Closed-Cone Pines: Pinus attenuata Lemm., P. muricata D. Don, and P. radiata D. Don. A total of 343 to 384 trees derived from 13 populations were analyzed using 13 mitochondria' gene probes and two restriction enzymes, and more than 90 RAPD loci generated by 22 primers. Southern hybridization was used to test homology among comigrating RAPD markers. Segregation analysis and Southern hybridization were carried out to distinguish between RAPD fragments of nuclear and organellar origin. Estimates of genetic diversity and population differentiation, and phylogenetic analyses based on RAPD and RFLP markers, were compared with those based on allozymes from a similar study. Twenty-eight distinct mtDNA haplotypes were detected among the three species. All three species showed limited variability within populations, but strong differentiation among populations. Based on haplotype frequencies, genetic diversity within populations (Hs) averaged 0.22, and population differentiation (GsT and 0) exceeded 0.78. Analysis of molecular variance (AMOVA) also revealed that more than 90% of the variation resided among populations. Species and populations could be readily distinguished by unique haplotypes, often using the combination of only a few probes. Twenty-eight of 30 (93%) comigrating RAPD fragments tested were homologous by Southern hybridization. Hybridization with enriched mtDNA, and chloroplast DNA (cpDNA) clones, identified one fragment as being of mtDNA origin and two as being of cpDNA origin, among 142 RAPD fragments surveyed. RAPD markers revealed moderately higher intrapopulation gene diversity and significantly higher total genetic diversity and population differentiation than did allozyme markers for each species. Simulation analysis to study effects of dominance on RAPD diversity suggested that dominance substantially depressed values of diversity within populations and inflated values of differentiation among populations. By comparison to our empirical analyses, we inferred that the underlying diversity of RAPD markers is substantially greater than that of allozymes. Results of phylogenetic analysis of RAPD markers were largely consistent with those from allozyme analysis, though they had many minor differences. Joint phylogenetic analysis of both the RAPD and allozyme markers strongly supported a common ancestor for P. radiata and P. attenuata, and south to north migration histories for all three species. Dendrograms based on mtDNA analysis, however, strongly disagreed with those based on allozymes, RAPDs, chloroplast DNA and morphological traits, suggesting convergent genome evolution. / Graduation date: 1999

A brief overview of the importance of wood boring insects is provided. Background on the two wood boring insect families Buprestidae (Coleoptera) and Sesiidae (Lepidoptera) is given. Keys and checklists to Tennessee’s buprestid fauna as presently known are furnished. Photomicrographs depicting characteristics separating Tennessee buprestid taxa to the level of species are provided for select couplets to aid those unfamiliar with buprestid morphology and terminology. Distribution and flight data of many species within the state are also featured. Results of a phylogenetic analysis of the Chrysobothris femorata (Olivier) species complex is presented based on the nuclear gene arginine kinase and the mitochondrial gene cox I. Implications of the resultant phylogenies are discussed. Phylogenetic relationships with the economically important sesiid tribe Synanthedonini are explored using cox I gene sequences. The cox I tree inferred provides interesting new insight into some ambiguous evolutionary relationships. Morphological characters that are used to distinguish genera within Synanthedonini are discussed and compared with the molecular data.

A taxonomic and phylogenetic study of the tribe Habrolepidini is described. A cladistic analysis was carried out in order to establish the phylogenetic relationships of the supraspecific taxa of the tribe. An illustrated key for the identification at the level of genera is included. Based on the results of the phylogenetic analysis, the diagnosis and taxonomic descriptions of the recognized taxa are presented. A single most parsimonius parsimony tree was obtained from the cladistic analysis based on 67 morphological characters, generated by a two-step procedure using PAUP. Initially, heuristic searches considering all characters with equal weights resulted in three equally parsimonious trees. Then the method of successive approximation weighting was applied to the three trees. The values of statistic parameters of the most parsimonious tree are: length = 582 steps; consistency index = 0.4966, retention index = 0.5850. The results support the hypothesis that the tribe Habrolepidini is monophyletic. It is defined by the presence of a specialized ventral mandibular tooth that is formed through modification of a seta into a stout socketed spine and three more unambiguous characters, clava length from 2.57 to 3.28, small hexagonal sculpture of scutellum and sensilla in three circles in a straight line. The inclusion of the genera Anthemus, Arrenophagoidea, Arrenophagus, Thomsonisca and Zaomma into Habrolepidini is supported by the presence of the mandibular tooth or by sister group relationships to other taxa with the mandibular tooth. The revision of the genera Ceraptroceroideus and Homalopoda is included; the taxonomic revision of each genus includes a key, diagnosis, descriptions and illustrations for all the species.