The fossil record is the only direct source of data for studying modes (patterns) and rates of morphological change over geologic time periods. Determining modes is critical for understanding macroevolutionary processes, but just how modes can vary within a taxon, and why, have hitherto been largely understudied. To address this, I examined patterns of morphological change in the shell of the Mesozoic marine bivalve genus Buchia over its geographic and temporal range. Buchia was chosen as a test subject because it is abundant, well-preserved across a variety of facies, and is widely distributed across the Northern Hemisphere where the likelihood of multiple lineages is low. While the focus of this thesis is on evolutionary patterns, it is also necessary to address issues of taxonomy and geographical variation, making this research applicable to a wide-variety of fields. Previous to this study there was no protocol for measuring buchiid valves, nor was the genus studied in a quantitative manner. Throughout this research I used ten morphological characters to describe shell shape and size. Multivariate methods (principle component and canonical variate analyses) were employed to discriminate between species of Buchia and examine how morphological characters change through time and space within the genus. Evolutionary patterns were delineated using two well-established programs that discriminate between multiple modes of evolution. Overall, nearly 2000 specimens from eight geographical locations around the world were studied for this thesis. I found the genus Buchia was a useful tool for evolutionary studies as it can be studied quantitatively in space and time. Specically I have found that buchiid species can be delineated using morphometrics; the genus is restricted to the Northern Hemisphere; while the environment significantly affects morphology, there is no evidence of a latitudinal gradient; diversity and disparity within Buchia are not correlated; most evolutionary modes conformed to random walks or stasis; and modes and rates vary across the geographical range of the genus. Overall, I have found that the environment plays an important role in shaping both morphology and modes.

The Contaya arch is an elongated topographic high that divides the Huallaga, Maranon and Ucayali basins in the Peruvian Amazonian plain. Its position well into the foreland basin and well inland from the main Andean thrust belt has proven to be enigmatic. Although it is often considered to be a single structural feature with a single origin, we show here that the Contaya arch is composed of distinct structures with different structural styles and different geologic histories: The main structures include the Contamana high, Contaya high, and Moa divisor. The Contamana high is limited by high angle reverse faults with a NW-SE orientation parallel to the Andean fold and thrust belt. This structure formed in the Tertiary, most probably in the Miocene after deposition of the Pozo Formation sands and shales. To the east of this is the Contaya high. This structure originally formed during the Triassic-Jurassic and was later reactivated in the Tertiary. The easternmost structure, the Moa divisor, separates the Ucayali basin from the Acre basin in Brazil. It is bounded by a high-angle, thick-skinned reverse fault. It appears to be a reactivated normal fault that formed in the Paleozoic during rifting and deposition of the Mitu Formation. From 10 to 4 Ma the subducted Nazca ridge was located beneath the Peruvian fold and thrust belt in the area where the Contamana high, Contaya high and Moa divisor are located. We suggest that the uplift of the Moa Divisor and the Contamana high as NW-SE oriented structures bounded by high-angle, thickskinned reverse faults and the reactivation of the Contaya high during the Miocene is related to the subduction of the Nazca ridge from 10 Ma to present.

The directionality and consistency of evolution has long been a subject of contention among evolutionary biologists since the days of Darwin. However, it is unknown how much can be quantified and how much results from more complex variables. It is also unknown whether evolution is consistent or whether it occurs differently in each system. My study focuses on predation and habitat as ecological gradients that may create convergent evolution in livebearing fishes. In Chapter I, I focus on predation as a mechanism for driving convergent evolution in Gambusia affinis. A suite of 7 microsatellite markers was used in order to determine independence of morphological evolution. Mantel tests were used to compare genetic, phenotypic, geographical and environmental distances among the six focal populations. These tests showed that there was a significant correlation between genetic and geographic distance but no significant correlation between genetic and phenotypic distances, which may indicate that phenotypic divergence has arisen independently in multiple instances. The second chapter focuses on a unique form of convergence that arose during speciation of three livebearing fishes, which we termed "convergent speciation." I focus on habitat type as a selective pressure in the lake system of Lake Catemaco, Mexico and the surrounding rivers. Lake Catemaco has been isolated from the surrounding rivers for approximately 1.2 million years and during that time several endemic species have evolved in the lake. This provides an excellent study system for studying convergent divergence. To test the theory of convergent speciation in this system, a MANOVA was conducted. The effect of habitat was an important source of variance in the system, indicating that habitat is a likely driving force responsible for convergent speciation in the system. Using discriminant functions I was able to correctly predict the habitat of fish of six different species between 68% and 71% of the time. This may indicate that evolutionary response to habitat is consistent across taxa (i.e., convergent divergence is taking place).

Transmissible spongiform encephalopathies (TSEs), or prion diseases, are a group of inevitably fatal neurodegenerative diseases that occur in mammalian species. Ovine susceptibility to scrapie, the prototypical TSE, is predominantly modulated by nonsynonymous polymorphisms within exon 3 of the ovine prion protein gene (PRNP). Investigation of PRNP exon 3 for two hair-sheep breeds revealed a novel predicted amino acid substitution (P116) associated with the ovine ARQ allele (P116A136R154Q171). Additionally, two novel ovine PRNP genotypes (PARQ/ARR; PARQ/ARQ) also were detected, and most of the hair sheep sampled possessed PRNP exon 3 genotypes associated with some degree of resistance to scrapie and/or experimental BSE (bovine spongiform encephalopathy). Unlike sheep, expression of bovine spongiform encephalopathy (BSE) in cattle and other bovids has not been associated with nucleotide variation within bovine PRNP exon 3. However, BSE susceptibility has been tentatively associated with specific insertion-deletion (indel) polymorphisms within the putative bovine PRNP promoter, and to a lesser extent intron 1, for a few German cattle breeds. Evaluation of the patterns of nucleotide variation associated with bovine PRNP exon 3 provided evidence that strong purifying selection has intensely constrained bovine exon 3 over the long-term evolutionary history of the subfamily Bovinae, as well as evidence for significant purifying selection in regions of bovine PRNP exon 3 that are considered to be of functional, structural, and pathogenic importance in other mammalian species. Evaluation of the frequencies of known indel polymorphisms within the putative bovine PRNP promoter for a panel of U. S. cattle sires revealed no significant differences in the distribution of promoter alleles and/or genotypes between U. S. cattle sires and BSEaffected German cattle. Notably, a nonsynonymous PRNP exon 3 polymorphism (T50C) identified in American bison (Bison bison) was tentatively associated with Brucella spp. seropositivity. Specifically, a significant overabundance (P = 0.021) of Yellowstone National Park bison possessing the CC genotype were Brucella spp. seropositive. Furthermore, the T-allele and TT genotype were observed at significantly higher frequencies in three bison populations that were either founded from Brucella spp. seronegative stock or previously subjected to test-and-slaughter management to eradicate brucellosis.

Phosphotriesterase (PTE) isolated from the soil bacterium Flavobacterium sp. is a member of the amidohydrolase superfamily. PTE catalyzes the hydrolysis of a broad spectrum of organophosphate triesters including the insecticide paraoxon, and the chemical warfare agents; GF, sarin, and soman. In addition, PTE has been shown to catalytically hydrolyze the lethal nerve agent, VX. However, the rate of VX hydrolysis is significantly slower. PTE was subjected to directed evolution studies to identify variants with enhanced activity towards VX hydrolysis. First generation libraries targeted amino acid residues in the substrate binding site. The H254A mutation displayed a 4-fold enhancement in kcat and a 2-fold enhancement in kcat/Km over wild type PTE. The double mutant H254Q/H257F was isolated from the second generation libraries and displayed a 10-fold enhancement in kcat and a 3-fold enhancement in kcat/Km. In addition, H254Q/H257F displayed a 9-fold enhancement in kcat/Km for the hydrolysis of the VX analog, demeton-S. An in vivo selection approach utilizing organophosphate triesters as the sole phosphorus source is discussed. The selection is based on co-expressing PTE with the phosphodiesterase (GpdQ) from E. aerogenes. Substrate specificity of GpdQ was investigated using a small library of structurally diverse organophosphate diesters and phosphonate monoesters. Results obtained from the in vivo growth assays showed that GpdQ enabled E. coli to utilize various organophosphate diesters and phosphonate monoesters as the sole phosphorus source. Cells co-expressing PTE and GpdQ were tested for their ability to utilize two different organophosphate triesters as the sole phosphorus source. The results from this experiment indicate that the growth rate is limited by the phosphotriesterase activity. Protein translocation to the periplasm was proven advantageous for in vivo selection since it overcomes the limitation of intercellular delivery of the substrate of interest. Translocation of PTE to the periplasmic space of E. coli was examined. Two signal peptides were tested; the native leader peptide from Flavobacterium sp. and the signal sequence of alkaline phosphatase. The results obtained from cellular fractionation indicated that neither signal peptides were able to translocate PTE to the periplasm and that the protein remained in the cytoplasm.

Thesis (Ph. D.)--University of California, San Diego, 2001. / Vita. Includes bibliographical references (leaves 231-269).

Thesis (Ph. D.)--Open University. BLDSC no. DXN116690.

Thesis (Ph. D.)--Rutgers University, 2009. / "Graduate Program in Ecology and Evolution." Includes bibliographical references.

Thesis (Ph. D.)--Rutgers University, 2009. / "Graduate Program in Ecology and Evolution." Includes bibliographical references.

Thesis (Ph.D.) -- University of Texas at Arlington, 2009.