published_or_final_version / Computer Science and Information Systems / Master / Master of Philosophy

The Archiborborinae comprise a diverse clade of flies in the family Sphaeroceridae. This thesis presents the first phylogenetic analysis and a thorough taxonomic revision of the subfamily. The phylogenetic revision includes morphological data from all species, and molecular data from a subset of 21 ingroup species. Although the group here treated as the Archiborborinae has been traditionally treated as a tribe within the subfamily Copromyzinae, analysis of morphological, molecular, and combined datasets supports the monophyly of the Archiborborinae and shows that the Archiborborinae and Copromyzinae are not sister taxa. The Copromyzinae are more closely related to the Sphaerocerinae and possibly to the enigmatic genus Pycnopota than they are to the Archiborborinae. The elevation of the clade to subfamily rank is supported on the basis of this evidence. Basal relationships within the Archiborborinae are difficult to resolve, but the phylogenetic evidence generally supports a division of the subfamily into the following 8 genera: Antrops Enderlein 1909, Penola Richards 1941, Frutillaria Richards 1961, Boreantrops gen. nov., Coloantrops gen. nov., Maculantrops gen. nov., Photantrops gen. nov., and Poecilantrops gen. nov. The genus Archiborborus, until recently a paraphyletic assemblage including most of the described species in the subfamily, is treated as a junior synonym of Antrops (syn. nov.) All genera are described and a generic key is provided. A total of 122 species, including 25 previously described and 89 new, are fully described and illustrated; another 8 new species are diagnosed but not formally named.

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<p>This thesis explored species-level phylogenetic relationships of the African cycad genus Encephalartos, which is one of the eleven genera of cycads. The genus is confined to Africa and comprises approximately 65 species, 38 of which are found naturally in South Africa. The phylogenetic studies on Encephalartos to date still result in many unresolved polytomies so it is not possible to fully understand the relationships between different taxa. In this study, AFLPs were used together with DNA sequencing to reconstruct the phylogenetic relationships of the genus. This study was the first to be presented with aims of resolving the relationships of Encephalartos using AFLPs together with DNA sequences.</p>

In this study, mitochondrial transcript information from a recent EST project wasextended to obtain complete mitochondrial genome sequence for 5 tiger salamandercomplex species (Ambystoma mexicanum, A. t. tigrinum, A. andersoni, A. californiense,and A. dumerilii). For the first time, aspects of mitochondrial transcription in arepresentative amphibian are described, and then complete mitochondrial sequencedata are used to examine salamander phylogeny at both deep and shallow levels ofevolutionary divergence. The available mitochondrial ESTs for A. mexicanum (N=2481)and A. t. tigrinum (N=1205) provided 92% and 87% coverage of the mitochondrialgenome, respectively. Complete mitochondrial sequences for all species were rapidlyobtained by using long distance PCR and DNA sequencing. A number of genomestructural characteristics (base pair length, base composition, gene number, geneboundaries, codon usage) were highly similar among all species and to other distantlyrelated salamanders. Overall, mitochondrial transcription in Ambystoma approximatedthe pattern observed in other vertebrates. From the mapping of ESTs onto mtDNA it wasinferred that transcription occurs from both heavy and light strand promoters andcontinues around the entire length of the mtDNA, followed by post-transcriptionalprocessing. However, the observation of many short transcripts corresponding to rRNAgenes indicates that transcription may often terminate prematurely to bias transcriptionof rRNA genes; indeed an rRNA transcription termination signal sequence was observedimmediately following the 16S rRNA gene. Phylogenetic analyses of salamander familyrelationships consistently grouped Ambystomatidae in a clade containingCryptobranchidae and Hynobiidae, to the exclusion of Salamandridae. This robust resultsuggests a novel alternative hypothesis because previous studies have consistentlyidentified Ambystomatidae and Salamandridae as closely related taxa. Phylogeneticanalyses of tiger salamander complex species also produced robustly supported trees.The D-loop, used in previous molecular phylogenetic studies of the complex, was foundto contain a relatively low level of variation and we identified mitochondrial regions withhigher rates of molecular evolution that are more useful in resolving relationships amongspecies. Our results show the benefit of using complete mitochondrial genomeinformation in studies of recently and rapidly diverged taxa.

Anthracnose of lentil caused by the fungal pathogen Colletotrichum lentis is an economically important disease in Western Canada. The pathogen population is divided into two races (0 and 1) and two sexual incompatibility groups (IG-1 and IG-2). Resistance to anthracnose race 1 is found in cultivated Lens cultivars whereas for the more aggressive race 0, higher levels of resistance have been reported only from wild Lens species. Furthermore, C. lentis seems to only possess one (MAT1-2) of the two mating type idiomorphs commonly present in heterothallic ascomycete fungi with the typical bipolar mating system. The purpose of this study was to verify the phylogenetic relationship between race 0 and 1 isolates of C. lentis and to sequence and characterize the MAT1-2 of C. lentis. A morphological, multi-locus phylogenetic and host-range study was conducted with isolates of C. lentis, C. truncatum (from various host species and the epitype), C. destructivum, C. dematium, C. higginsianum, C. linicola and C. lindemuthianum. Sequence data from six conserved loci displayed 100% identity for C. lentis isolates of both races that formed a single cluster separate from other Colletotrichum species including C. destructivum, the epitype of C. truncatum and isolates from other hosts identified as C. truncatum. Conidia of C. lentis were slightly falcate with obtuse apices compared to cylindrical conidia with rounded ends of C. destructivum, and longer lunate to falcate conidia of the epitype C. truncatum. Host range tests undertaken on Lens culinaris, Pisum sativum, Cicer arietinum, Vicia faba, Glycine max, Phaseolus vulgaris, Phaseolus lunatus, Trifolium pratense, Medicago sativa, Medicago truncatula, Brassica chinensis and Arabidopsis thaliana under controlled environmental conditions revealed that the host ranges of C. linicola and C. higginsianum overlapped with that of lentil isolates. In contrast, the epitype specimen of C. truncatum was pathogenic on Pisum sativum, Phaseolus vulgaris, T. pratense and Medicago sativa, but not on L. culinaris. All Colletotrichum spp. infected Medicago truncatula and all but the lentil isolates caused disease on G. max. The mating type gene MAT1-2 of C. lentis contained two introns and three exons and an open reading frame of 726 bp coding for a putative protein of 241 amino acids including the high mobility group (HMG) domain characteristic of the MAT1-2 in fungi. The MAT1-2 nucleotide sequences of C. lentis isolates were identical irrespective of IG. An isolate from each of the two IGs, CT-21 (IG-2), CT-30 (IG-1) and a co-culture of CT-21 and CT-30 was used to study the expression levels of MAT1-2 at seven different in vitro time points (0h, 6h, 12h, 18h, 24h, 36, 48h after inoculation in glucose yeast media) and investigate for possible alternative splicing events. MAT1-2 expression for CT-21, CT-30 and the co-culture was observed at all seven time points indicating that it is constitutively expressed, and no differences in the transcript size were seen, ruling out the possibility of a splicing event.

The phylogeny of lampreys is controversial, because they possess few taxon-distinctive morphological characters. This is especially true of the relationships among the genus Lethenteron and the closely related genera Eudontomyzon and Lampetra. Thus, the first objective of this thesis was to use DNA sequences of the mitochondrial cytochrome b gene and two nuclear gene introns to infer the phylogeny among these three genera. I found that: 1) Lethenteron plus Eudontomyzon morii without Lethenteron ninae, Lethenteron zanandreai, and Lethenteron sp. S (a distinct cryptic species in the Lethenteron reissneri complex) was monophyletic; 2) Lampetra from the Pacific drainage of North America and Lampetra aepyptera should each be separated, as distinct genera, from Lampetra (including Lethenteron ninae and Lethenteron zanandreai) from the Atlantic drainage of Eurasia; and 3) the remaining Eudontomyzon and the Atlantic Lampetra clustered together in all analyses. The second objective of this thesis was to resolve the relationship among closely related Lethenteron species. Lampreys are either parasitic or non-parasitic, and each non-parasitic (satellite) species is believed to have been derived independently from the parasitic (stem) ancestor. In the phylogenetic analysis, the parasitic Arctic lamprey Lethenteron camtschaticum and its four satellite species were not reciprocally monophyletic. Since network methods are generally more useful for closely related haplotypes than bifurcating trees, a haplotype network of these five Lethenteron species was generated using the cytochrome b gene sequences; Lethenteron appendix showed haplotype frequency distribution differences but there was little support for recognizing the other four taxa as distinct species.

The species pool for a site is defined as that set of species which have a non-zero probability of maintaining viable populations under the prevailing environmental conditions. it may contain many more species than are actually present in the community of the site. The science of community assembly attempts to understand how particular communities arise from the welter of possible species combinations. The assembly of a grassland plant community from the local species pool was examined in a phylogenetically corrected trait-based study. Competition theory suggests coexisting species should be less similar than expected by chance, whilst environmental sorting theory suggests they should be more similar. This work suggests that, at the whole community scale, species tend to be more similar and that their likelihood of occurrence in communities can to an extent be predicted from their traits. Experimental studies revealed a complicated picture. Species naturally occurring in the community did not show convincing signs of outperforming their absent congeners. Community composition appears to depend in considerable measure upon chance events such as seed dispersal coinciding with the availability of vacant microsites in the community, rather than just a sorting process in which the best suited species are invariably present. These findings suggest that it modelling community assembly is possible, but that it is unlikely ever to be an exact science because it is influenced to a large extent by unpredictable events.

The snake genus Oligodon, known for its egg-eating feeding behaviour, is a taxonomically and systematically challenging group from South and Southeast Asia. This work provides the first phylogenetic hypothesis for the genus, and includes a checklist and key to the species. I use approximately 1900 base pairs of mitochondrial DNA sequence data to infer the relationships of these snakes, and I examine congruence between the molecular phylogeny and hemipenial characters. A hypothesis for the position of Oligodon within the Colubridae is also proposed. I discuss the implications of the phylogeny for previous taxonomic groupings, and consider the usefulness of the trees in analysis of behaviour and biogeography.

The snake genus Oligodon, known for its egg-eating feeding behaviour, is a taxonomically and systematically challenging group from South and Southeast Asia. This work provides the first phylogenetic hypothesis for the genus, and includes a checklist and key to the species. I use approximately 1900 base pairs of mitochondrial DNA sequence data to infer the relationships of these snakes, and I examine congruence between the molecular phylogeny and hemipenial characters. A hypothesis for the position of Oligodon within the Colubridae is also proposed. I discuss the implications of the phylogeny for previous taxonomic groupings, and consider the usefulness of the trees in analysis of behaviour and biogeography.