Differential gene expression between sexes is the main contributor of the morphological and behavioral differences observed between them. Studying the signatures of these differences at the genetic level will help us understand the forces acting on them. The existence of androdioecious and gonochoristic species in the genus Caenorhabditis makes it suitable for sex-biased gene expression studies. In this thesis, I have assembled the transcriptome of C. sp. 9 and C. sp. 5 using de novo and reference-based techniques. Evolutionary analysis of the assembled contigs showed that genes with male-biased expression evolve faster than those with a female bias, as observed in other taxa. Furthermore, I found a positive correlation between gene expression and codon usage bias.

Differential gene expression between sexes is the main contributor of the morphological and behavioral differences observed between them. Studying the signatures of these differences at the genetic level will help us understand the forces acting on them. The existence of androdioecious and gonochoristic species in the genus Caenorhabditis makes it suitable for sex-biased gene expression studies. In this thesis, I have assembled the transcriptome of C. sp. 9 and C. sp. 5 using de novo and reference-based techniques. Evolutionary analysis of the assembled contigs showed that genes with male-biased expression evolve faster than those with a female bias, as observed in other taxa. Furthermore, I found a positive correlation between gene expression and codon usage bias.

No description available.

Thesis (Ph.D. 1974) from the Dept. of Botany, University of Adelaide.

Thesis (doctoral)--Universität Bonn, 2004. / Downloaded and printed Sept. 10, 2008. Includes bibliographical references (leaves 152-165). Also available via the internet.

Thesis (Ph. D.)--University of Missouri-Columbia, 2002. / Typescript. Vita. Includes bibliographical references (leaves 111-120). Also available on the Internet.

Thesis (Ph. D.)--University of Missouri-Columbia, 2002. / Typescript. Vita. Includes bibliographical references (leaves 111-120). Also available on the Internet.

The accurate identification of fish species, their life stages and their products enables the correct management of fisheries, research and conservation of distinctive populations for long-term survival and sustainability. Mesobola brevianalis Boulenger, 1908, commonly known as the river sardine, is found in many river systems in southern Africa. Because it exhibits widely separated populations showing subtle differences, particularly in colour, it is thought that there may be cryptic species involved. Standard phylogenetic techniques using three genetic markers (mitochondrial COI, nuclear protein RAG1 and nuclear ribosomal 28S rRNA), enabled the building of phylogenetic networks for M. brevianalis and some outgroup species. Consistent patterns of relationship were seen with 28S supporting monophyly. COI and RAG1 suggested that populations that are currently identified as M. brevianalis in fact represent several species. There was sufficiently strong support for the evolutionary independence of the M. brevianalis populations from the Rovuma, Kunene and Orange River Systems to consider them as independent species. The independence of the genus Mesobola was brought into question because Engraulicypris sardella and Rastrineobola argentea were placed within it phylogenetically.Morphometric methods in the form of multivariate truss network analyses, were performed to locate morphological markers for populations. There was little to no variation among most of the populations synonymized under M. brevianalis. Furthermore, neither latitude nor longitude had an effect on the morphological characters that might be linked to functional evolution. A molecular clock analysis of COI data was used to calibrate a paleobiogeographical model which entailed a divergence of lineages starting from an easterly reigning Paleo-Congo Basin, via a hypothetical Paleo-Kalahari Lake that was fragmented by a series of uplifts and drying events beginning ~65 million years ago. Complete evidence supported the synonymisation of the genera Engraulicypris and Mesobola, the resurrection of the species name gariepinus for the Orange River Systempopulation, and the description of two new species: E. ngalala from the Rovuma River System and E. howesi from the Kunene River System.

Gastropods are a highly diverse clade of molluscs that includes limpets, snails and slugs, and the only molluscan lineage with members that have successfully colonized land. Amphibious operculate freshwater gastropods, Ampullariidae, exhibit various morphological and physiological adaptations to their respective habitats, which make them ideal candidates for studying the mechanisms underlying adaptive evolution in gastropods. In the last two decades, there have been interests in the diverse reproductive behaviors of ampullariids: while most genera of apple snails deposit their eggs in a jelly mass underwater, two genera (i.e., Pomacea and Pila) deposit calcareous egg clutches above the waterline. The shift from aquatic to aerial oviposition required the concerted evolution of the adult snail's egg laying behavior as well as the composition of the egg. Today, only limited genomic information is available for this ecologically important family, except in the genus Pomacea, which hinders the investigation of its evolutionary history and mechanism. I have, therefore, developed the publicly accessible transcriptome database, AmpuBase, as molecular resources to support various transcriptomic and proteomic analyses. The database comprise de novo transcriptome assembly of eight species that belong to five representative genera of Ampullariidae. For each species there were 20,730 to 35,828 unigenes with predicted open reading frames, with an N50 ranging from 1,320 to 1,803 bp and 69.7% to 80.2% with functional annotation. Since the ability of laying out-of-water eggs is one of the key steps of terrestrialisation for aquatic snails, I analysed the proteome of perivitelline fluid (PVF) for the eggs of Marisa cornuarietis that were laid underwater. The PVF proteome of P. diffusa also investigated to reveal and compare the biochemical adaptation between P. diffusa clade and P. canaliculata clade. Using LC-MS/MS coupled with transcriptome database, I identified a total of 36 and 32 PVF proteins from M. cornuarietis and P. diffusa, respectively. Comparison of PVF proteomes among the aquatic (M. cornuarietis) and three aerial ovipositing ampullariids (P. diffusa, P. canaliculata and P. maculata) showed that the four species all contain several major perivitellins that are important for the nutrition of the embryos. M. cornuarietis invests heavier in protection against pathogens, whereas the unique presence of calcium binding protein and their high albumen gland expression in three Pomacea, implying the importance of the novel acquisition of this protein for forming the calcareous eggshell of terrestrial eggs. I also found the absence of a neurotoxin (PV2) in M. cornuarietis and P. diffusa PVF, indicating this protein was acquired after the divergence between the ancestors of P. diffusa clade and the P. canaliculata clade, and protects P. canaliculata and P. maculata eggs against terrestrial predators. Evolutionary analyses detected the involvement of gene duplication, positive selection and neofunctionalisation in the formation of several major PVF proteins. With the availability of ampullariid genomes and transcriptomes, I conducted an integrated evolutionary analysis of Pomacea PVF with an aim to understand the molecular adaptations underlying the transition from underwater to terrestrial egg deposition. There were many expanded gene families in the New World ampullariids; some of them may be important for their evolution towards terrestrial egg laying. The PV1 oligomer protein was a novel protein acquired by the common ancestor of New World species to nourishing their terrestrial eggs. Meanwhile, gene duplication followed by neofunctionalisation of MACPF-tachylectin paralogs has contributed to the novel acquisition of the toxic PV2 protein in the P. canaliculata species complex. Overall, using Ampullariidae as an example, my study has demonstrated the power of integrative genomics to address various fundamental questions in evolutionary biology. The findings have enhanced our mechanistic understanding of invasion of terrestrial habitats by aquatic gastropods.

<p> There has been an increasing value in the ability to describe the world's diversity for the purpose of enhancing research and conservatory efforts. Characterizing the level of heterogeneity of particular molecular markers and verifying its suitability as an identifier of new specimens provides a way of quantifying biodiversity. One such molecular marker is the mitochondrial cytochrome c oxidase subunit I (COl). An analysis of the evolutionary rates among and within taxonomic groupings of 13,641 insect COl sequences revealed that the evolutionary rate of some species increased or decreased, sometimes by an order of a magnitude. Furthermore, the increased evolutionary rates of two species, from the Lepidopteran and Orthopteran orders, may be explained by the influence of positive selection but further analyses would be required to rule out other explanations. Overall, we deem that the rate of substitution generates enough change for COl to work sufficiently as a barcode marker in insects. As COl is not suitable for specimen identification in plants, it would be useful to be able to quickly determine if there is enough variation in COl or other molecular markers for specimen identification. In response, a visualization tool, Fingerprint, was developed to graphically depict 11 different types of sequence diversity. An application of the tool to Lepidopteran COl data verified the genetic diversity in insect COl and the tool's ability to sensitively detect different types of heterogeneity. </p> / Thesis / Master of Science (MSc)