No description available.

No description available.

No description available.

No description available.

Around 375 million years ago, the first tetrapods appeared, marking one of the most important events in vertebrate evolutionary history. The fin to limb transition saw the appearance of fingers and a weight bearing pelvic girdle. While very little research has been done on the evolution of the tetrapod pelvic girdle, a fair amount has been done on the origins of fingers but some aspects remained controversial. A combination of palaeontology, developmental biology and comparative morphology was therefore used in this thesis to better understand the fin to limb transition. The pectoral fin of Panderichthys, a sarcopterygian fish closely related to tetrapods was CT-scanned and modeled in three dimensions and its pelvic girdle and fin were examined with traditional techniques. This information from the fossil record was integrated with comparisons of the development of the Australian lungfish, Neoceratodus forsteri, our closest living fish relative and the axolotl (Ambystoma mexicanum), a salamander representing well the condition of early tetrapods. Development of bone and cartilage was studied through clearing and staining and development of skeletal muscles through immunostaining. In situ hybridizations were performed on the lungfish to study the expression of Hoxd13, associated with the formation of digits in tetrapods. This work shows that the late expression phase of Hoxd13 is present in Neoceratodus and is associated with the formation of radials. Redescription of the pectoral fin of Panderichthys reveals that distal radials are present, which, in addition to other information, lead us to conclude that digits are not novelties in tetrapods but rather have evolved from the distal radials present in the fins of all sarcopterygian fish. The earliest tetrapods lack a full set of wrist + carpals/ankle + tarsal bones. Here, we propose that this region of the limbs evolved after fingers and toes through an expansion of the region between the proximal limb bones and the digits. As for the pelvic girdle, it is very primitive in Panderichthys but comparison of its development in Neoceratodus and Ambystoma suggest that the ischium evolved through the posterior expansion of the pubis and the ilium, through an elongation of the iliac process already present in sarcopterygian fishes. The results of this thesis help to better understand the fin to limb transition and show that it is more gradual than previously believed.

No description available.

No description available.

Finding the approximate location of short read genome sequences by comparing them to an already available closely related organism's complete genome sequence is a challenging research issue. Predicting intron locations in the short form of mRNA called Expressed Sequence Tags (ESTs) and the variability of intron lengths are the major challenges. More specifically, finding the intron positions in an EST sequence by comparing it with a reference genome sequence is a time consuming task, as currently it is done manually. In my thesis, I designed a pipeline that can predict the intron positions in ESTs of non-model organisms. Initially, I compared the ESTs to the closest completely sequenced genome. The pipeline then finds the alignment of the ESTs, the reference genome sequence, and the coding region of the gene (known as Coding DNA Sequence or CDS) from the reference genome.

The form of an organism is often closely linked to its function, and this relationship may be particularly important in organisms where individual form is highly flexible due to the repeated iteration of minute multicellular modules. In many modular taxa, including the bryozoans discussed in this thesis, each module is able to function as largely independent units; an individual module can feed independently, has a separate gut, and has the potential to reproduce. These characteristics mean that the number of modules in a bryozoan colony, and hence its size, is a reasonably accurate measure of the colony’s ability to both capture resources and to produce sexually developed larvae. Size is therefore a more appropriate measure of colony demography than age, the criterion traditionally used for unitary organisms. However, processes that can complicate the demography of modular organisms such as colony damage, fission or fusion also mean that the age structure of the component modules in a colony or fragment remains an important predictor of colony functioning, interacting with the effects of colony size. (For complete abstract open document)

The plasmodiophorid organism, Spongospora subterranea f. sp. nasturtii, is the causal agent of crook root disease of watercress (Rorippa nasturtium-aquaticumy. The only current control measure is zinc, used such that levels do not exceed 0.07S~g mrl in effluent water. Laboratory results indicated that zinc acts by actively lysing zoospores of S. subterranea, but does not cause 100% mortality at field concentrations. At 8ug ml", around 20 % of zoospores were seen to survive compared to controls. Of other cations investigated as potential control agents, none were as effective as zinc at equivalent levels. Only cobalt was capable of significant zoospore lysis. Attraction of zoospores to watercress roots and total root extracts appeared to be non-specific when compared to attraction to tobacco (Nicotiana rustica), tomato (Lycopersicon esculentum), and mustard (Brassica napus). Results implied that a general plant attractant was present, and that this did not mask a more specific attractant. A molecular, PeR-based diagnostic test was developed for S. subterranea f. sp. nasturtii. The internal transcribed spacer (ITS) and I8S ribosomal DNA were used to design specific peR primers, capable of detecting DNA directly from zoospores. As little as Sng genomic DNA or 100 zoospores were required as template. Efforts to develop a sampling technique for zoospores in watercress beds were successful based on washing root material followed by peR. DNA analysis also identified a Chytridiomycete-like organism as being consistently associated with crooked roots. However, preliminary studies showed that it did not have a direct role in crook root disease. The I8S ribosomal DNA sequence was' used to infer phylogeny of S. subterranea f. sp. nasturtii, and plasmodiophorids generally, by performing parsimonious and distance-based analyses. Within the plasmodiophorid grouping, S. suhterranea f. sp. nasturtii appeared to be closely related to S. suhterranea f. sp. suhterranea and Plasmodiophora brassicae, based on 270 bases at the 3' end of the gene, whilst Polymyxa species aligned on a separate branch. Based on a complete I8S ribosomal DNA analysis, plasmodiophorids seemed to form a discrete taxonomic grouping, not closely linked to either protists or fungi.