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Barcode identification is a method that uses genetic information to differentiate species. Because of its general versatility it can be applied to contexts from archaeology to the food industry. Atlantic salmon (Salmo salar) is a fish species commonly hunted in modern times and has been found in archaeological settings. However, barcoding requires enough quality DNA for amplification and abiotic exposure tends to degrade it. High temperatures, such as when boiling, can diminish DNA quality. The extent of DNA degradation between fresh and boiled tissues and whether all tissues retain the same amount of DNA is unclear. In this study DNA was extracted from S. salar tissues fins, muscle, bones and scales without treatment and with boiling treatment. DNA concentrations between fresh and boiled bones were not significantly different, nor were comparisons between samples with the same treatments. Muscles had higher DNA concentrations when boiled and fins had higher when fresh. These findings show that regarding certain tissue types can be expected to better retain DNA concentrations after boiling.

In part I, MgO and Co1-xO powders in 9:1 and 1:9 molar ratio (denoted as M9C1 and M1C9 respectively) were sintered and homogenized at 1600oC followed by annealing at 850 and 800oC, respectively to form defect clusters and precipitates. Analytical electron microscopic (AEM) observations indicated the protoxide remained as rock salt structure with complicated planar diffraction contrast for M9C1 sample, however with spinel paracrystal precipitated from the M1C9 sample due to the assembly of charge- and volume-compensating defects of the 4:1 type, i.e. four octahedral vacant sites surrounding one Co3+-filled tetrahedral interstitial site. The spacing of such defect clusters is 4.5 times the lattice spacing of the average spinel structure of Mg-doped Co3-dO4, indicating a higher defect cluster concentration than undoped Co3-dO4. The {111} faulting of Mg-doped Co3-dO4/Co1-xO in the annealed M1C9 sample implies the possible presence of zinc blend-type defect clusters with cation vacancies assembled along oxygen close packed (111) plane. In part II, the Mg2TiO4/MgO composites prepared by reactive sintering MgO and TiO2 powders (9:1 molar ratio) at 1600oC and then air-cooled or further aged at 900oC were studied by X-ray diffraction and (AEM) in order to characterize the microstructures and formation mechanism of nanosized Mg2TiO4 spinel precipitated from Ti-doped MgO. Expulsion of Ti4+ during cooling caused the formation of (001)-specific G.P. zone under the influence of thermal/sintering stress and then the spinel precipitates, which were about 30 nm in size and nearly spherical with {111} and {100} facets to minimize coherency strain energy and surface energy. Secondary nano-size spinel was precipitated and became site saturated during aging at 900oC, leaving a precipitate free zone at the grain boundaries of Ti-doped MgO. The intergranular spinel became progressively Ti-richer upon aging 900oC and showed <110>-specific diffuse scatter intensity likely due to short range ordering and/or onset decomposition. In part III, the Co1-xO/Co2TiO4 composite prepared by reactive sintering CoO and TiO2 powders (9:1 molar ratio) at 1450oC and then air-cooled were studied by X-ray diffraction and AEM in order to characterize the microstructures and formation mechanism of nanosized Co2TiO4 spinel precipitated from Ti-doped Co1-xO. Slight expulsion of Ti4+ during cooling caused the precipitation of nanosize Co2TiO4 spinel. Bulk site saturation also caused impingement of the Co2TiO4 precipitates upon growth. The Co3-dO4 spinel, as an oxidatin product of Co1-xO, was found to form at free surface and the Co1-xO/Co2TiO4 interface. The Co2TiO4 spinel particles formed by reactive sintering rather than precipitation were able to detach from the Co1-xO grain boundaries to reach parallel epitaxial orientation with respect to the host Co1-xO grains via Brownian-type rotation of the embedded particles. In part IV, AEM was used to study the defect microstructures of Zr-dissolved TiO2 prepared via reactive sintering the ZrO2 and TiO2 powders (8:92 in molar ratio, designated as Z8T92) at 1600oC for 24 h and then aged at 900oC for 2-200 h in air. The Zr-dissolved TiO2 with rutile structure showed dislocation arrays, defect clusters, G.P. zone, superlattice, nanometer-size domains incommensurate and commensurate superstructure, may be the precursor of ZrTi2O6 precipitates at 900oC. The rutile showed diffuse diffractions along [001] direction as a result of Zr4+ substitution for Ti4+ with volume compensating defect clusters. Incommensurate and commensurate structures, as indicated by diffraction splitting and extra diffraction along <100> and <010> directions may be attributed to the ordering and clustering process of Zr and Ti atoms in these directions. Part V, deals with the reactive sintering of ZrO2 and TiO2 powders (1:4 molar ratio) at 1400 to 1600oC in air to form orthorhombic ZrTiO4 (a-PbO2-type structure, denoted as a) and to study its epitaxial reorientation in the matrix of tetragonal TiO2 (rutile) grains with Zr4+ (15 mol %) dissolution. The epitaxial relationship of intragranular ZrTiO4 and Zr-dissolved rutile (denoted as r) was determined by electron diffraction as [010]a//[011]r; (001)a // (011)r (i.e. [100]a // [100]r; (001)a // (011)r). The reorientation of the intragranular particles in the composites can be reasonably explained by rotation of the nonepitaxial particles above a critical temperature (T/Tm > 0.8) and below a critical particle size for anchorage release at interface with respect to the host grain. Reactive sintering facilitated the reoreientation process for the particles about to detach from the grain boundaries. The Brownian rotation of the confined ZrTiO4 particles in rutile grains was activated by a beneficial lower interfacial energy for the epitaxial relationship, typically forming lath-like ZrTiO4 with (101)a/(211)r habit plane having fair match of oxygen atoms at the interface. Further aging at 900oC for 50 h in air caused modulated and periodic antiphase domains in ZrTiO4 matrix, as likely precursor of equilibrium ZrTi2O6.

An almost unbroken fringing reef runs along the east coast of Africa, the lagoon inside the reef is the foundation of almost all artisanal fisheries. It is a low-tech fishery conducted by many people. Some areas can have up to 19 fishermen per square kilometer. High fishing pressures, coupled with declining fish stocks has led to changes in mean size and reproductive age of many exploited species. There is a vital and urgent need for scientifically based management systems, including the utilization of genetic information to guide management practices. This thesis aims to investigate the presence of genetic structures in the western Indian Ocean. In order to do that we first investigated the historical patterns of connectivity throughout the region (paper I). In papers II and III we focused on local scale connectivity in Kenya and Tanzania and finally in paper IV we investigate the large-scale contemporary gene flow throughout the Western Indian Ocean. In paper III we also investigate the temporal genetic variation at one site and compare it to the small-scale genetic variation along a stretch of the Kenyan coastline. Some overall conclusions that can be drawn from my body of work are: there are genetic structures present in the western Indian Ocean even though the apparent lack of physical barriers. Major oceanic currents aid evolutionary dispersal patterns. A single geographic site need not be genetically homogenous or temporally stable. Island sites are genetically more homogenous than mainland sites. In conclusion, there are clear and distinct genetic structures present especially in Siganus sutor, the most targeted fish for the artisanal fishery in East Africa. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.</p>

Diseases like malaria claim the lives of millions of people every year. This deadly disease can result in considerable morbidity, which presently affects countries in Africa, Eurasia, and South America. Anopheline mosquitoes transmit this disease. Studies look at the identification first of the species to accurately determine their distribution. For identification, sequencing of the Internal Transcribed Spacer 2 region of the ribosomal DNA is analyzed. Although African Anophelines are very well studied species, there has been no recent significant research for Holarctic Anophelines. In particular, in North America and Eurasia, because of the eradication of malaria in the northern territories and the focus on other diseases transmitted by Aedes and Culex mosquitoes. In this study, we first look at the Holarctic species Anopheles punctipennis in North America from the Midwest to the eastern United States. Then we look at samples received from Eurasia, in particular Russia and Iran. We physically harvested 500 mosquitoes from ten breeding sites to analyze the identity and distribution of An. punctipennis. We received 110 samples from Russia and 180 samples from Iran to examine the identification and geographic distribution of An. daciae and An. persiensis. Mosquito ITS2 ribosomal DNA was extracted and amplified using polymerase chain reaction (PCR) methods. The PCR products were then sequenced and analyzed based on GenBank information obtained. An analysis by Restriction Fragment Length Polymorphism using ITS2 PCR products on An. punctipennis was conducted. Seven hundred ninety samples were processed to look at the identity and geographic distribution of Holarctic Anophlines. An. puntipennis has no current ITS2 records in GenBank. The distribution of An. daciae and An. persiensis was analyzed by ITS2 and location data. The identity and presence of a malaria vector in new areas or existing areas would prove to be vital if the disease were to re-emerge due to climate changes. / Master of Science in Life Sciences / Diseases like malaria claims the lives of millions of people every year. This deadly disease can result in considerable morbidity which presently affects countries in Africa, Eurasia, and South America. Anopheline mosquitoes transmit this disease. African Anophelines are very well studied species however, there has been no recent significant research for Holarctic Anophelines, in particular in the United States because of the eradication of malaria in the northern territories and the focus on other diseases transmitted by Aedes and Culex mosquitoes. One of the understudied neglected malaria vectors that has an extensive geographic distribution throughout the United States is Anopheles punctipennis. This species can transmit both forms of human malaria Plasmodium falciparum and Plasmodium vivax. Accurate morphological or molecular identification of mosquitoes is important for proper surveillance, control and diagnostic measures. Identifying this mosquito on a molecular level is pivotal for future genomic research in identifying vector competence, and insecticide resistant genes associated with this species. Internal Transcribe Spacer 2 sequencing is an efficient molecular tool for the identification of Anopheline mosquitoes. This tool has been successfully developed for species from the Maculipennis group and A. crucians complex but not for An. punctipennis type species. The goal of this study was to develop simple and robust molecular tools for identifying this species in the fields. Anopheline mosquito collections were made from multiple locations in the Mid-west to eastern U.S. Sequencing on the ribosomal DNA internal transcribed spacer 2 region (ITS2) of the genome provides positive and accurate identification of An. punctipennis. Developing a Restriction Fragment Length Polymorphism (RFLP) assay using the ITS2 PCR products reduces time and cost in molecular identification and proves to be an accurate method of identification. This research will enable future population genetic studies that are important for the development of mosquito population control.

Abstract This research is designed to investigate the occurrence of interdiffusion-induced mesopores, Brownian motion, cleaving and healing and defect clusters in three binary composites, i.e. Ni1-xO/Co1-xO, Ni1-xO/ZrO2 and Co1-xO/ZrO2 of the Ni1-xO-Co1-xO-ZrO2 system. Firstly, the (NimCo1-m)1-£_O/Ni-doped Co3-dO4 composites prepared by reactive sintering Ni1-xO and Co1-xO powders (1:2 molar ratio, denoted as N1C2) at 1000oC with or without further annealing at 720oC in air were studied by X-ray diffraction and electron microscopy to clarify the formation mechanism of mesoporous spinel precipitates. Submicron-sized inter- and intragranular pores, due to incomplete sintering and grain boundary detachment, prevails in (Ni0.33Co0.67)1-£_O protoxide with rock salt structure; whereas nanosize pores due to Kirkendall effect were restricted to the spinel precipitates having Ni component progressively expelled upon annealing. A rapid net vacancy flux and a tensile misfit stress perpendicular to the protoxide/spinel interface caused the formation of elongated and aligned {100}-faceted mesopores in the spinel precipitates with a relatively low equilibrium vacancy concentration. Aligned mesopores in diffusion zone of nonstoichiometric metal oxides have potential applications on thermal barrier bond coating and mass-transport limited heterogeneous catalysis. Also, this thesis deals with the reorientation and shape change of low-crystal-symmetry (non-cubic) ZrO2 within the high-crystal-symmetry grains of Co1-xO/Ni1-xO cubic rock salt-type structure. ZrO2/Co1-xO composites 1:99 and ZrO2/Ni1-xO composites 1:9 in molar ratio were sintered and then annealed at 1650oC for 24 and 100 h in air to induce reorientation of the embedded particles. Transmission electron microscopic observations in both systems indicated that the submicron tetragonal/monoclinic (t/m) ZrO2 particles fell into three topotaxial relationships with respect to the host Co1-xO/Ni1-xO grain: (1) parallel topotaxy, (2) ¡§eutectic¡¨ topotaxy i.e. [100]Z//[111]C,N, [010]Z//[0 1]C,N and (3) ¡§occasional¡¨ topotaxy [100]Z//[111]C,N, [01 ]Z//[0 1]C,N. The parallel topotaxy has a beneficial low energy for the family of {100}Z/C,N and {111}Z/C,N interfaces. The change from the occasional topotaxy to an energetically more favorable eutectic topotaxy was likely achieved by a rotation of the ZrO2 particles over a specific (100)Z/(111)C,N interface. Brownian-type rotation is probable for the embedded t-ZrO2 particles in terms of anchorage release at the interphase interface with the Co1-xO/Ni1-xO host. Detachment or bypassing of rock salt type grain boundaries could also cause orientation as well as shape changes of intergranular ZrO2 particles. Zirconia-polymorphism-induced cleaving and spontaneous healing by precipitation was studied in Co1-xO polycrystals containing a dispersion of ZrO2 particles. Conventional, analytical, and high-resolution transmission electron microscopy indicated that the Co1-xO matrix cleaves parallel to {100} and {110} planes and heals itself by co-precipitation of parallel-topotaxial ZrO2/Co3-£_O4 particles upon cooling. Due to size effect and matrix constraint, nanometer-size ZrO2 precipitates at cleavages were able to retain tetragonality upon further cooling to room temperature. Paracrystalline array of defect cluster was shown to form in Zr-doped Ni1-xO and Co1-xO polycrystals while prepared by sintering at relative high temperature, i.e., 1650oC to increase the defect concentration. Paracrystalline array of defect clusters in Co3-£_O4 spinel structure also occurred when doped with Zr4+ at high temperature or cooled below 900oC to activate oxy-precipitation of Co3-dO4 at dislocations. transmission electron microscopic observations indicated the spinel precipitate and its paracrystal predominantly formed at the ZrO2/Co1-xO interface and the cleavages/dislocations of the Co1-xO host. Defect chemistry consideration suggests the paracrystal is due to the assembly of charge- and volume-compensating defects of the 4:1 type with four octahedral vacant sites surrounding one Co3+-filled tetrahedral interstitial site. The spacing of paracrystalline distribution is 3.3, 2.9 and 4.9 times the lattice parameter for Zr-doped Ni1-xO, Zr-doped Co1-xO and Zr-doped Co3-dO4. This spacing between defect clusters is about 0.98 times that of the previously studied undoped Co3-dO4. There is much larger (3.4 times difference) paracrystalline spacing for Zr-doped Co3-£_O4 than its parent phase of Zr-doped Co1-xO.

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Summary: The thesis comprises from the introduction and five main parts: three of them are published papers, the rest two are manuscripts prepared for submitting to the scientific journals. The first two are published phylogenetic studies of the cichlasomatine cichlids based on (1) molecular characters, and (2) both morphological and molecular data with the description of a new genus Andinoacara. The third (3) is the already published description of the new species Andinoacara stalsbergi from Peru combining both morphological and phylogenetic approaches and including the detailed phylogeny of the genus Andinoacara. The next unpublished manuscript (4) is the more detailed comprehensive phylogeography of the two non-relative genera (including Andinoacaras) of the trans-Andean cichlids. Including all valid species from the majority of their distribution areas it was reconstructed the ancestral area of both genera in the Choco region, Colombia, and revealed the directions of their distribution spreading. The last (5) unpublished manuscript is the phylogeographical study of the cichlid genus Serranochromis from the headwaters of the totally unknown Central Angola. It showed several evidences of the faunal exchange among the adjacent river systems. Lastly, the thesis is supplemented by several appendices...