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When this study commenced in early 2004, only five Phaeophleospora species. had been reported from eucalypts of which only two; P. destructans (STE-U 1336) and P. epicoccoides (STE-U 1346) had been sequenced. In a former study, Phaeophleospora species emerged in two separate clades suggesting that Phaeophelospora is polyphyletic. The appearance and severity of lesions on eucalypt leaves are generally used to recognise the species of Phaeophleospora responsible for disease. However, depending on host and climate, the symptoms associated with infection by P. epicoccoides, P. eucalypti and P. destructans can be almost identical and incorrect diagnosis is a common problem. Thus, Phaeophleospora species were compared based on DNA sequences and multi gene genealogies were constructed. In addition species- specific primers were designed and tested on leaf material. Many isolates of Phaeophleospora spp. were collected and sequenced, and all Phaeophleospora spp. from eucalypts were shown to cluster together and are closely related to the most important leaf pathogens associated with eucalypts namely Colletogloeopsis zuluensis, Mycosphaerella cryptica and M. nubilosa. In contrast, these fungi are distantly related to the type specimen of the genus Phaeophleospora, P. eugeniae. Furthermore, all DNA sequences of isolates of P. destructans examined in this thesis, including the ex-type culture, were identical but different to one previously lodged in GenBank. This phylogenetic separation led to a morphological study of the species assigned to Phaeophleospora and compared the species from eucalypts with P. eugeniae the type specimen of Phaeophleospora. The phylogenetic and morphological studies show that P. eugeniae is well separated from Phaeophleospora spp. occurring on eucalypts and led to the resurrection of the previous generic name, Kirramyces for Phaeophleospora spp. occurring on eucalypts. Furthermore, phylogenetic analysis and morphological observation of Kirramyces spp. and Colletogloeopsis spp. occurring on eucalypts showed considerable overlap between these two genera. Therefore, Colletogloeopsis was reduced to synonymy with Kirramyces. Consequently, the genus Kirramyces was expanded from five to 14 species, and included the description of two new species, K. angophorae and K. corymbiae. In order to assist with their identification a key based on morphology of conidia for Kirramyces species was developed. Kirramyces destructans is a devastating pathogen originally described from Indonesia in 1996 and has since been found throughout Asia where all common tropical and subtropical plantation eucalypt species and hybrids are susceptible. K. destructans is considered a major biosecurity threat in Australia, both to native eucalypt forests and the tropical plantation industry. Prior to the current study, there had been no investigation into the origin and movement of this important pathogen. Thus, five gene regions and six microsatellite loci were sequenced for 43 representative isolates of K. destructans from a range of geographical locations and hosts. Two microsatellite markers detected very low nucleotide polymorphism (three haplotypes for each loci); five other gene regions, including four microsatellite region were uniform. This low level of genetic diversity provides strong evidence that K. destructans was introduced into Indonesia as a founder population and that it has subsequently been spread throughout Asia via human-mediated movement of germplasm. Timor and Northern Australia were considered to be a possible source of origin of this fungus, but the high susceptibility of native E. urophylla to K. destructans in Timor indicates that the pathogen is unlikely to be endemic to Timor. The current distribution of Kirramyces eucalypti is New South Wales, Queensland, Victoria, Tasmania and New Zealand (North Island). The main host of this pathogen is E. nitens which is native to Victoria and New South Wales. Kirramyces eucalypti has not been found in South Africa, yet it causes a severe disease on eucalypt hybrids originating from South Africa growing in New South Wales indicating movement to these hybrids from either native eucalypts or nearby plantations. As such, K. eucalypti poses a threat for the plantation industry in sub-tropical and tropical Australia. The phylogeography of K. eucalypti in Australia and New Zealand was studied by sequencing three gene regions and one microsatellite locus of fifty-seven representative isolates of K. eucalypti from Queensland, New South Wales, Victoria, Tasmania and New Zealand. The highest genetic variation was found among isolates from NSW suggesting that K. eucalypti originates from NSW. Isolates in New Zealand appear to have been introduced from NSW. Isolates from Queensland were consistently different to those from other regions and may in fact represent a cryptic species or a hybrid. During monitoring of eucalypt taxa trials in far North Queensland, infected leaves resembling symptoms typical of K. destructans were collected and examined. Phylogenetic data based on three gene regions and some morphological characteristics revealed a new taxon described in this study as K. viscidus. Kirramyces viscidus was also shown to be closely related to the devastating pathogen K. destructans. Kirramyces viscidus had been found to cause extensive damage to eucalypt hybrids originating from South America, and less damage to E. grandis from Australia, indicating that this pathogen is probably endemic to Australia. Kirramyces viscidus has the potential to seriously damage tropical eucalypt plantations, especially if clonal and planted off-site. In conclusion, this study resurrected genus Kirramyces for the Phaeophleospora and Coletoglloeopsis spp. occurring on eucalypts. It also studied the phylogeography and gene flow of the two most important Kirramyces species, K. destructans and K. eucalypti and describes three new Kirramcyes spp. found on eucalypts in Australia. Very recently, K. destructans has been discovered in Northern Australia. This raises a whole series of new issues as there are now several pathogens, K. eucalypti, K. viscidus and K. destructans present in Australia that known to cause serious damage on plantation eucalypts. Recent investigations have also revealed several undescribed Kirramyces spp. in Northern Australia. Their impact, distribution, movement and potential for hybridization now need to be examined.

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Phylogenetics is the study of evolutionary relationships. It is a scientific endeavour to discover history, and it is not easy. Massive amounts of data together with computationally difficult optimization problems mean that heuristics are prevalent, and ever better techniques are sought. New approaches are valuable if they are more accurate, but are considered even more so if they are faster than pre-existing methods. Improvements to existing algorithms, whether in terms of space requirements, or faster running times, are also worthwhile. This dissertation explores three new techniques, each of which is valuable according to the previous definitions. The first contribution is TASPI, a system for storing collections of phylogenetic trees, and performing post-tree analyses. TASPI stores collections of trees more compactly than the previous method, and this compact structure lends itself to post-tree analyses. This results in the ability to compute strict and majority consensus trees faster than common alternatives. As an added benefit, TASPI is written in ACL2, which allows properties of the algorithms and data structures to be formally verified. The second contribution is an improved method to generate phylogenetic trees. A common methodology involves two steps, first estimating a Multiple Sequence Alignment (MSA), and then estimating a tree using that MSA. This method changes the way in which the MSA is estimated, and this leads to improved accuracy of the resultant trees. Also, in some cases, the time required is also reduced. The third contribution is BLuTGEN, a method by which a phylogenetic tree is estimated from sequence data, but without ever generating an MSA for the full dataset. BLuTGEN is as accurate as one of the best published tree estimation techniques (SATé), but takes a novel approach which allows it to be applied to much larger datasets. / text

<p>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 <i>Leucorrhinia</i>. 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 <i>Leucorrhinia,</i> in the European<i> L. rubicunda</i> 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 <i>E. cyathigerum </i>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.</p>

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The focus of this thesis has been the phylogenomics and evolution of the Alphaproteobacteria. This is a very diverse group which encompasses bacteria from intraceullar parasites, such as the Rickettsiales, to freeliving bacteria such as the most abundant bacteria on earth, the SAR11. The genome sizes of the Alphaproteobacteria range between 1 Mb and 10 Mb. This group is also connected to the origin of the mitochondria. Several studies have placed the SAR11 clade together with the Rickettsiales and mitochon- dria. Here I have shown that this placement is an artifact of compositional heterogeneity. When choosing genes or sites less affected by heterogeneity we find that the SAR11-clade instead groups with free-living alphaproteobacteria. Gene-content analysis showed that SAR11 was missing several genes for recombination and DNA-repair. The relationships within the SAR11- clade has also been examined and questioned. Specifically, we found no support for placing the taxon referred to as HIMB59 within the SAR11. Ocean metagenomes have been investigated to determine whether the SAR11-clade is a potential relative of the mitochondria. No such relationship was found. Further I have shown how important it is to take the phylogenetic relationships into account when doing statistical analyzes of genomes. The evolution of LD12, the freshwater representative of SAR11, was investigated. Phyloge- nies and synonymous substitution frequencies showed the presence of three distinct subclades within LD12. The recombination to mutation rate was found to be extremely low. This is re- markable in light of the very high rate in the oceanic SAR11. This is may be due to adaptation to a more specialized niche. Finally we have compared structure-based and sequence-based methods for orthology pre- diction. A high fraction of the orfan proteins were predicted to code for intrinsically disordered proteins. Many phylogenetic methods are sensitive to heterogeneity and this needs to be taken into ac- count when doing phylogenies. There have been at least three independent genome reductions in the Alphaproteobacteria. The frequency of recombination differ greatly between freshwater and oceanic SAR11. Forces affecting the size of bacterial genomes and mechanisms of evolu- tionary change depend on the environmental context.

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