The aqueous speciation and hydrolysis of actinides in both the presence and absence of organic ligands has been investigated in the pH range 1 - 13. The speciation and hydrolysis of Th4+, U4+ and UO22+ with H3thme, H3tea, H3bic, H3heidi, H3NTA, H2ADA and H3cit have been investigated using various analytical techniques (1H NMR, 13C NMR, IR, UV-Vis(-nIR) spectroscopy and potentiometric titrations). The PHREEQC interactive software suite was used to predict speciation with the formation constants for various complexes calculated in the Hyperquad software suite. Formation constants of Th4+, U4+ and UO22+ hydroxide species have been calculated showing the formation of polymeric complexes. Experiments showed no complexation of actinides by H3thme and H3tea in aqueous solutions. However, 1:3 (M:L) complexation of Th4+ and U4+ was observed with H3bic along with 1:2 (M:L) complexation of UO22+. A variety of 1:1 and 1:2 (M:L) complexes were observed with H3heidi, H3NTA, H2ADA and H3cit for the actinides. Formation constants for complexes of H3NTA with Th4+ and UO22+, H2ADA with Th4+ and H3cit with UO22+ were calculated in Hyperquad. Studies of Pu3+ with H3heidi showed little complexation but 5Me-HXTAH4 showed 1:3 (M:L) speciation. Complexation of PuO22+ by saldien(Et2N)2H2 and salterpyH2 was shown and a secondary band was observed at ~944 nm after multiple days. The functionalities of organic ligands have been shown to have a profound effect on the (partial) hydrolysis of the actinides.

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Order Acipenseriformes (sturgeons and paddlefishes) is an ancient lineage of bony fishes (> 200 million years old) with most extant species at conservation risk. The pallid sturgeon, Scaphirhynchus albus, is a federally endangered species native to the Mississippi and Missouri River basins. Hybridization with sympatric shovelnose sturgeon, S. platorynchus, is one of several threats to pallid sturgeon. Current molecular markers cannot reliably distinguish among pure species and multigenerational backcrosses. This information is critical for implementation of management strategies to increase populations through natural reproduction and artificial propagation. Genotypes from a large panel of unlinked single-nucleotide polymorphisms (SNPs) may provide greater resolution of the two species; however, paralogous sequence variants (PSVs) within individuals resulting from an ancient whole genome duplication event confound SNP development. The aim of this dissertation was to produce unlinked disomic SNPs that would increases resolution between pallid sturgeon and shovelnose sturgeon. This was achieved by producing haploid gynogens, which contain only DNA from the maternal parent, and then producing a reference from these haploid gynogens. Sequence assembly based on haploids informed the presence of multi-locus contigs. More than 11,000 disomic SNP markers were produced that differentiate between the two species by mapping 120 individuals of either species onto the haploid reference. A linkage map, based on three haploid families, was able to resolve some paralogs and can be used to inform which discriminatory SNP markers are linked. Future research should convert the disomic markers derived in this study to an applied form, such as that achieved by genotyping-by-thousands.

The X and Z chromosomes have unique characteristics that lead to unique evolutionary consequences. Lepidopterans have a well-known, disproportionately large-Z effect for behavioral and morphological traits that distinguish closely related species. A potential explanation for the Large-X effect is the faster evolution of the sex chromosome (Faster-X evolution). We use whole genome re-sequencing of Heliconius erato races and of the incipient species H. himera to test for faster-Z evolution between hybridizing populations at different reproductive isolation levels, by calculating divergence and nucleotide diversity. We show evidence for Faster-Z evolution in Heliconius butterflies at the early stages of speciation and along the speciation continuum. Evidence of higher divergence and lower nucleotide diversity suggests not only selection but also nonaptive process, like demographic changes, may be driving faster-Z evolution, especially in the incipient species.

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Repeated emergence of similar adaptations is often explained by parallel evolution of underlying genes. However, evidence of parallel evolution at amino acid level is limited. When the analyzed species are highly divergent, this can be due to epistatic interactions underlying the dynamic nature of the amino acid preferences: The same amino acid substitution may have different phenotypic effects on different genetic backgrounds. Distantly related species also often inhabit radically different environments, which makes the emergence of parallel adaptations less likely. Here, we hypothesize that parallel molecular adaptations are more prevalent between closely related species. We analyze the rate of parallel evolution in genome-size sets of orthologous genes in three groups of species with widely ranging levels of divergence: 46 species of the relatively recent lake Baikal amphipod radiation, a species flock of very closely related cichlids, and a set of significantly more divergent vertebrates. Strikingly, in genes of amphipods, the rate of parallel substitutions at nonsynonymous sites exceeded that at synonymous sites, suggesting rampant selection driving parallel adaptation. At sites of parallel substitutions, the intraspecies polymorphism is low, suggesting that parallelism has been driven by positive selection and is therefore adaptive. By contrast, in cichlids, the rate of nonsynonymous parallel evolution was similar to that at synonymous sites, whereas in vertebrates, this rate was lower than that at synonymous sites, indicating that in these groups of species, parallel substitutions are mainly fixed by drift.

Several subspecies of Monardella villosa (California Coyote Mint) have been distinguished on the basis of leaf thickness, shape, and trichome characteristics, yet many intermediates are known. We investigated morphological differences in natural populations of two subspecies (M. v. subsp. villosa and M. v. subsp. franciscana) in the Scott Creek watershed, north of Davenport, in Santa Cruz County, CA. Monardella villosa subsp. franciscana grows in coastal scrub in gulches and ocean terraces whereas subsp. villosa grows at more protected inland sites. Morphological difference between subspecies may be adaptations to these different habitats. I grew plants in a common garden at Cal Poly, San Luis Obispo to determine if the morphological differences were genetically based. I also conducted a reciprocal transplant of the two subspecies between inland and coastal populations to determine if they are locally adapted. The morphological differences (leaf hair density and length as well as leaf base angle) between subspecies were maintained in the common garden, yet no patterns of local adaptation were observed in germination or survival of the subspecies in reciprocal transplants in the first year. However, Monardella is a perennial plant and fitness differences may exist in later life stages that I have not yet measured.

Both crystalline and sedimentary rocks are being considered as potential host rocks for a deep geological repository in Canada. Deep-seated sedimentary rocks in the Michigan Basin, Ontario, Canada contain highly saline ground and pore waters. The relatively high I of these waters may influence speciation and rock matrix sorption properties. To this end, laboratory sorption experiments were conducted to examine sorption of Pd(II) on sodium bentonite, illite and Ordovician age shale as a function of pH and solution I and initial concentration of Pd. Solutions with pH values in the range of 5 to 9, I ranging from 0.1 to 4 M and initial concentration of Pd ranging from 5×10 −8 to 1×10 −6 M were considered. A sorption time of 14 days was used and the separation method was by centrifuge. Experiments were performed under aerobic conditions at 25 ◦ CC, and the Eh value of the solution ranged from 300 to 600 mV. The data from sorption experiments were used to validate surface complexation models developed in PHREEQC with the JAEA TDB. The sorption of Pd on bentonite, shale and illite all showed strong dependence on I and pH. The dependence on initial concentration of Pd was used to plot sorption isotherms. The slope of the isotherms showed that Pd was forming inner- and outer- sphere complexes inside the stern layer for sorption onto bentonite and illite. It also showed however that shale was most likely undergoing cooperative sorption. Strong fit was found between the single layer surface complexation model for montmorillonite (the major constituent clay mineral of sodium bentonite) and experimental data, but not for illite (the major constituent clay mineral of shale). / Thesis / Master of Applied Science (MASc)

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