Polyploidy, base composition bias, and incomplete lineage sorting in fish phylogenetics

Thesis (Ph.D.) University of Alaska Fairbanks, 2014.Understanding the evolutionary relationships between organisms is of fundamental importance in biology. Originally based on overall similarity in morphological traits, depiction of evolutionary relationships is now often pursued by constructing trees based on molecular data- molecular phylogenetics. Molecular phylogenetic inference uses variation in molecular data in a variety of frameworks to produce hypothetical relationships between organisms. As with many practices making use of biological data, the inherent noise and complexity challenges phylogeneticists. In this dissertation, I examine three empirical datasets while addressing three possible issues in phylogenetic inference: polyploidy, base composition bias and incomplete lineage sorting. Polyploidy leads to incorrect genes (paralogs) being analyzed, since it is often impossible to distinguish between gene copies generated as a result of polyploidization. My analysis indicates that incorrect assumptions of orthology have led to incorrect conclusions being drawn from phylogenetic studies including the polyploid salmons (Salmoniformes). Results indicate that pikes (Esociformes) and the polyploid salmons are not only sister taxa, but that the graylings (Thymallinae) and whitefishes (Coregoninae) are most closely related to each other. Base composition bias misleads inference through the overall similarity between sequences being a result of changes in base composition, not shared evolutionary history. Incomplete lineage sorting refers to the fact that the reconstructed relationships of different genes do not agree. Genetic variants may persist through speciation events and are not completely "sorted" between lineages, and require a methodology to reconcile the different genealogies. In two chapters I focused on base composition bias and incomplete lineage sorting in a detailed study of flatfish (Pleuronectiformes) origins. A major issue in fish phylogenetics is the question of whether flatfish are monophyletic with poor support from both morphological and molecular data. Often it appears that cranial asymmetry is the only characteristic uniting the group. I found very little evidence for a single evolutionary origin of the extant flatfishes. Base composition bias appears not to be a major contributor to flatfish non-monophyly; however incomplete lineage sorting likely results in the inability to generate robust statistical support for inferred relationships of flatfishes and relatives. Results of my work indicate that more care should be exercised in phylogenetics in determining orthology of genes. I also find that not acknowledging the presence of paralogs does indeed mislead analyses. With increased data availability and computational capabilities, non-neutral models of nucleotide evolution should be developed and included in further studies. Presenting the heterogeneity of datasets and actively accounting for incomplete lineage sorting will definitively improve the field of phylogenetics as well.Chapter 1. Introduction -- Chapter 2. Pike and Salmon as Sister Taxa: Detailed Intraclade Resolution and Divergence Time Estimation of Esociformes + Salmoniformes Based on Whole Mitochondrial Genome Sequences -- Chapter 3. Are Flatfishes (Pleuronectiformes) Monophyletic? -- Chapter 4. Mitochondrial Genomic Investigation of Flatfish (Pleuronectiformes) Monophyly -- Chapter 5. Conclusion

Local Guided Wavefield Analysis for Characterization of Delaminations in Composites

Delaminations in composite laminates resulting from impact events may be accompanied by minimal indication of damage at the surface. As such, inspection techniques are required to ensure defects are within allowable limits. Conventional ultrasonic scanning techniques have been shown to effectively characterize the size and depth of delaminations but require physical contact with the structure. Alternatively, a noncontact scanning laser vibrometer may be used to measure guided wave propagation in the laminate structure. A local Fourier domain analysis method is presented for processing guided wavefield data to estimate spatially-dependent wavenumber values, which can be used to determine delamination depth. The technique is applied to simulated wavefields and results are analyzed to determine limitations of the technique with regards to determining defect size and depth. Finally, experimental wavefield data obtained in quasi-isotropic carbon fiber reinforced polymer (CFRP) laminates with impact damage is analyzed and wavenumber is measured to an accuracy of 8.5% in the region of shallow delaminations. Keywords: Ultrasonic wavefield imaging, Windowed Fourier transforms, Guided waves, Structural health monitoring, Nondestructive evaluatio

Phylogeography and population genetics of a Beringian endemic: Dallia (Esociformes: Teleostei)

Thesis (M.S.) University of Alaska Fairbanks, 2011In this thesis I examine the population genetics of an endemic Beringian freshwater fish genus, Dallia (blackfish). The current distribution of blackfish was heavily influenced by paleoclimatic instability during the Pleistocene. Beringian paleoclimatic changes during the Pleistocene included the fluctuating growth and decline of glaciers and an overall decrease in temperature and increased aridity in areas not adjacent to the Bering Sea. Pleistocene glacial advances resulted in the cyclical emergence of the Bering land bridge. The effects of paleoclimatic instability on blackfish distribution and abundance can be inferred through the distribution of genetic variation across the Beringian landscape. I address three basic questions: 1: Are separate populations of blackfish taxonomically distinct entities? I found that while there is clear genetic structuring and isolation, there is insufficient information to make a strong statement in this regard. 2: Did blackfish survive Pleistocene glaciations within multiple Beringian refugia? My results indicate that blackfish persisted in at least four broad geographic areas. 3: How did the Bering land bridge influence intercontinental aquatic interchange? My evidence points to close genetic relationships and potentially high exchange of blackfish across the Bering land bridge, which supports the Bering land bridge as conduit for freshwater aquatic migration.1. Introduction -- Blackfish -- Scientific classification and relationships to other fishes -- History of blackfish in Beringia -- Thesis research and organization -- References -- 2. Mitochondrial phylogeography of a Beringian endemic: Dallia -- Abstract -- Introduction -- Materials and methods -- Results -- Discussion -- Acknowledgements -- References -- 3. Population genetics of Dallia in Beringia -- Abstract -- Background -- Methods -- Results -- Discussion -- Conclusions -- Authors' contributions -- Acknowledgements -- References -- 4. Conclusion

Oxidation state of a polyurethane membrane after plasma etching

Low moduli cell culture substrates can be used to apply dynamic mechanical strain to cells, by surface deformation. Understanding the surface interaction with cells is critical to improving cell adhesion and normal growth. A medical grade polyurethane (PU), Chronoflex AL 80A, was modified by oxygen plasma etching and characterised by X-ray photoelectron spectroscopy. Etching resulted in increased cross-linking at the isocyanate bond and formation of new oxygen moieties. The model, derived from patent data and XPS data of the unetched PU, indicated that the additional oxygen was likely to be hydroxyl and carbonyl groups. Etched membranes enhanced protein adhesion, resulting in full surface coverage compared to unetched PU. The etched PU supported cell adhesion and spreading, while the unetched PU was not conducive to monolayer formation

Performance Metrics for the Objective Assessment of Capacitive Deionization Systems

In the growing field of capacitive deionization (CDI), a number of performance metrics have emerged to describe the desalination process. Unfortunately, the separation conditions under which these metrics are measured are often not specified, resulting in optimal performance at minimal removal. Here we outline a system of performance metrics and reporting conditions that resolves this issue. Our proposed system is based on volumetric energy consumption (Wh/m$^3$) and throughput productivity (L/h/m$^2$) reported for a specific average concentration reduction, water recovery, and feed salinity. To facilitate and rationalize comparisons between devices, materials, and operation modes, we propose a nominal standard testing condition of removing 5 mM from a 20 mM NaCl feed solution at 50% water recovery for CDI research. Using this separation, we compare the desalination performance of a flow-through electrode (fte-CDI) cell and a flow between membrane (fb-MCDI) device, showing how significantly different systems can be compared in terms of generally desirable desalination characteristics. In general, we find that performance analysis must be considered carefully so to not allow for ambiguous separation conditions or the maximization of one metric at the expense of another. Additionally, for context we discuss a number of important underlying performance indicators and cell characteristics that are not performance measures in and of themselves but can be examined to better understand differences in performance

Changes in dietary patterns and body composition within 12 months of liver transplantation

Background: Cardiometabolic risk factors are increasing in liver transplant recipients (LTR). Influencing dietary factors have not been assessed. The aim of this observational study was to assess changes in weight, metabolic function, dietary intake and eating behaviours in the first year after orthotopic liver transplantation (OLT). Methods: Consecutive recruitment of 17 patients (14 males) awaiting OLT at a single tertiary hospital. Dietary intake, food behaviours and anthropometry were recorded at baseline, and 6 and 12 months posttransplant. Results: By 12 months, patients had gained on average 7.3% of body weight. The prevalence of overweight or obesity increased from baseline 53% to 77% (P=0.001). By 6 months, 65% (n=11/17) of patients had altered glucose metabolism. Dietary intake was consistent with a Western-style dietary pattern with high saturated fat. Over half of the patients (69%, n=11/16) reported low to no depressive feelings and rated their self-esteem as good (53%, n=9/16). The Power of Food Scale increased between pre and post-transplant, indicating a stronger appetitive drive. Conclusions: Weight gain occurs early post-transplant, with significant metabolic dysfunction present within 6 months, however is not associated with significant psychological distress. Early dietary intervention designed to limit weight gain and target cardiometabolic health is recommended for this unique patient population