Sex determination in mammals is regulated by the sex-determining region on the Y chromosome (SRY); the presence of SRY activates the male developmental pathway and suppresses the gene network necessary for female gonad development. Mutations in sex determination genes lead to various abnormal sexual phenotypes, including sex reversal syndrome in which the genetic and phenotypic sex do not match. Sex reversal syndrome has been reported in humans, mouse, and several domestic species. In horses, SRY-negative XY sex reversal syndrome has been well described and is caused by deletions on the Y chromosome. However, the molecular causes of the SRY-positive condition in horses and other mammals are not known. This research investigated five horses affected with SRY-positive XY sex reversal syndrome. Sequencing of the coding exon region of the SRY gene in the five cases showed 99-100% alignment with the sequences of normal males. Genotyping of two closely related individuals with 46 normal male controls on an equine SNP50 Beadchip identified two statistically significant SNPs in a ~16 Mb region on the long arm of horse chromosome 3 (ECA3q). The region was analyzed using Gene Ontology (GO) and Gene Relationships Across Implicated Loci (GRAIL) to select functionally relevant candidate genes for sequencing. Further analysis of the entire horse genome was done through array comparative genomic hybridization (aCGH), which investigated possible structural rearrangements, such as copy number variants (CNVs). Deletions of olfactory receptor genes were detected on multiple chromosomes and confirmed through quantitative real-time PCR (qPCR). A homozygous deletion on ECA29 in a region containing genes of the aldo-keto reductase gene family, known to play a role in interconverting sex hormones between active forms and inactive forms, was discovered in two sex reversed animals. The findings were confirmed through qPCR and fluorescence in situ hybridization (FISH), and experiments to define the specific breakpoints of the deletion through PCR have been initiated. This research represents the first systematic search in the horse genome for mutations and CNVs related to sex determination. The findings contribute to better understanding of the molecular mechanisms of sex determination in horses and other mammals, including humans.

The golden-winged warbler (Vermivora chrysoptera) inhabits lower elevations on reclaimed surface mines in Kentucky, an indication of recent range expansion in this imperiled species. In 2004 and 2005, I compared breeding habitat between the golden-winged warbler and blue-winged warbler (V. pinus) in eastern Kentucky at landscape, territory, and nest site scales. Distance to forest edge averaged 38 m for the golden-winged warbler and 33 m for the blue-winged warbler. Maximum territory size averaged 1.5 ha for the golden-winged warbler and 2.1 ha for the blue-winged warbler. The golden-winged warbler occurred at higher elevations (up to 912 m) than the blue-winged warbler (up to 693 m). Golden-winged warblers occurred on flatter slopes when coexisting with bluewinged warblers. A higher percentage of grass cover occurred in golden-winged warbler territories where blue-winged warblers were absent compared to territories of either species where the two coexisted. Golden-winged warblers coexisting with blue-winged warblers were more often found in shrub cover than when they established territories in absence of blue-winged warblers. Management for the golden-winged warbler should focus on enhancement of transition zones between forest edges and open grasslands, especially at higher elevations.

The isolation and characterization of the gene(s) associated with and potentially responsible for the regulation of apomixis (asexual) and sexual reproduction in the grass species Tripsacum dactyloides is quintessential to agricultural advancement. Apomixis is the mechanism by which plants can produce seed without fertilization, where all progeny are genetically identical to the maternal parent. In natural populations of the genus Tripsacum, lower ploidy forms (i.e., diploid, 2n=36) reproduce sexually and the higher ploidy forms (triploid, 3n=54; tetraploid, 4n=72; etc.) reproduce asexually via apomixis. In order to gain a better understanding of sexual reproductive processes in plants, subtractive hybridization was performed on early and late female inflorescence gene products. This procedure allows for the recovery of gene products in the form of complimentary DNA, cDNA molecules, which correspond to messenger RNA (mRNA) present. These cDNA molecules were then used to extract unique sequence messages from the early developmental stage ovule tissue of diploid T. dactyloides. These cDNA molecules will allow for the direct isolation of the original form of the gene(s) from a large fragment library of the Tripsacum genome. Isolation and characterization of these gene(s) is of pivotal importance to our understanding of alternate modes of reproduction in Tripsacum. / Department of Biology

This study developed an informative model of a nasal cavity of a Neanderthal and Anatomically Modern Human (AMH) hybrid based on the morphological measurements and nonmetric features of nonhuman primate hybrids. This study examined morphometric measurements and nonmetric traits of the interior nasal cavity of two species of baboons (olive and yellow) and their first generation hybrids to determine how hybridization affects the internal anatomy of the nasal cavity. The nasal cavity was chosen because the nasal cavities of Neanderthals and AMH are recognized as uniquely different in size and shape. This study found that functionally different regions within the baboon nasal cavity are altered in size and shape in response to hybridization. Changes in size and shape due to hybridization occurred in three regions, at the rhinion, choana, and mid-nasopharynx. In regions of more complex physiological function, the mid-bony cavity and the posterior nasopharynx, no size or shape response was observed, except a wider lateral recess. Males and females responded differently to hybridization; males showed heterosis and females showed heterosis in most areas, though dysgenesis in the inferior meatus. The opposing male and female trends may contribute to the greater sexual dimorphism observed in hybrids compared to parental taxa. This study found that frequencies of nonmetric traits in the baboon hybrid nasal cavity were no different from frequencies in parental taxa, nor were regional frequency differences observed because anterior and posterior nonmetric traits occurred at the same frequency. However, males expressed a significantly higher frequency of nonmetric traits than females. Assuming Neanderthal and AMH hybrid nasal cavities follow the trends observed in the baboon hybrid model, the Neanderthal and AMH hybrid nasal cavity would have a different shape and larger size at the rhinion, choana, and mid-nasopharynx, while the mid-bony cavity and posterior nasopharynx remained unchanged compared to parental taxa. However, because Neanderthals and AMH have been diverged for a longer time period, the traits of the nasal cavity may be very different in parental taxa due to adaptations to local conditions, which may result in hybrids with traits from one parent or the other. Further, an analysis of different hybridization scenarios between Neanderthals and AMH, based on observed hybridization in baboons and paleoanthropological evidence, suggests rapid gene swamping of the Neanderthal population by AMH during hybridization, as other authors have also concluded.

I investigated how orchid biology, floral morphology, and diversity of surrounding floral and pollinator communities affected reproductive success and hybridization of Cypripedium candidum and C. parviflorum. Floral dimensions, including pollinator exit routes were smallest in C. candidum, largest in C. parviflorum, with hybrids intermediate and overlapping with both. This pattern was mirrored in the number of insect visitors, fruit set, and seed set. Exit route size seemed to restrict potential pollinators to a subset of visiting insects, which is consistent with reports from other rewardless orchids. Overlap among orchid taxa in morphology, pollinators, flowering phenology, and spatial distribution, may affect the frequency and direction of pollen transfer and hybridization. The composition and abundance of co-flowering rewarding plants seems to be important for maintaining pollinators in orchid populations. Comparisons with orchid fruit set indicated that individual co-flowering species may be facilitators or competitors for pollinator attention, affecting orchid reproductive success.

Guppies exhibit color based sexual dimorphism and females generally prefer the most colorful males. It has also recently been found that guppies possess a large opsin repertoire. As opsins are the receptors responsible for color vision, this ten gene repertoire might have contributed to the evolution of extravagant male coloration in this species. My study starts by characterizing the opsin repertoire of Jenynsia onca, a noncolorful relative of the guppy belonging to the family Anablepidae (sister group to Poeciliidae, of which the guppy is a member). A PCR based survey indicated that J. onca had a very similar opsin repertoire to the guppy; J. onca had nine genes including orthologs of all but one of the guppy opsins. To gain further insight into the origin of the guppy repertoire, a bioinformatics based survey of ray-finned fish opsins was undertaken. This revealed that large opsin repertoires are common in ray-finned fish and are the product of gene duplication events, spanning the age of the taxon Teleostei. Given that the large opsin repertoire of the guppy did not appear to be perfectly correlated with the evolution of color based sexual selection in this lineage, I turned to investigating the expression of this opsin repertoire. In situ hybridization was used to characterize the pattern of opsin expression across the surface of the retina of adult male and female guppies. In situ hybridization demonstrated that most opsin genes had distinct expression profiles. These expression patterns also indicated that sensitivity and discrimination in the dorsal retina might differ from the ventral retina; the ventral retina appears to be tuned to middle-wavelength light (green), while the dorsal retina is predicted to have exceptional wavelength discriminatory ability and broad spectral sensitivity. This expression data was then used to evaluate models of sexual selection in the context of the predicted visual capacity of the guppy. / Graduate

The linear and nonlinear optical response of plasmon hybridized systems is the subject of study of this thesis. Plasmonic silver nanoprisms are able to confine light to a sub-wavelength volume, which provides local field enhancement. This confined field is promising for achieving an enhanced nonlinear optical response. For many of plasmon nanoparticles, however, the plasmonic resonance is not at the near-infrared wavelengths of a Ti:Sapphire laser, the most common source used for ultra-fast measurements. To achieve resonance at these wavelengths, a tuning mechanism is required. The plasmon hybridization between silver nanoprisms and a thin gold film provides this tuning mechanism, which allows for enhanced optical second harmonic generation. Overlapping the plasmon resonance of the system with excitation source, by varying the spacer layer between the nanoprisms and the gold film, enhances the second harmonic counts by approximately three orders of magnitude. The finite-difference time-domain calculations agree to within a factor of two with the experimental findings in terms of the predicted enhancement factor. This plasmon hybridization approach is promising for future applications, including enhanced multi-photon lithography and nonlinear sensing using metal nanoparticles. / Graduate

This dissertation is centered on problems within the history and philosophy of biology. The project identifies the philosophical roots of the current ecological movement and shows how a version of philosophical naturalism might be put to use within contemporary ethical issues in biology, and aid in the development of research programs. The approach is historically informed, but has application for current dilemmas. The traditions from which I primarily draw include classical American philosophy, particularly C.S. Peirce and John Dewey, as well as thinkers associated with the German Naturphilosophie movement, such as Goethe and Schopenhauer. There are deep, but often overlooked, resonances between these seemingly disparate traditions and contemporary biology that are located in the conflict between the developing organism and the ever-fluctuating environment. The dissertation makes the case for a shared description of nature among these traditions and proposes applications to burgeoning contemporary ecological interpretations of issues such as hybridization and epigenetics.

Copy of author's previously presented paper inserted. / Bibliography: leaves 187-218. / x, 219, [12] leaves, [10] leaves of plates : ill (some col.) ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / This thesis aims to increase knowledge essential for conservation biology and for focused and efficient breeding of banksias. Interspecific hybridisation is assessed as a potential breeding tool, and for the assessment of species relationships within the genus. Species relationships within Banksia are also assessed using molecular techniques. Random amplified polymorphic DNA (RAPD) markers are assessed for their usefulness at various taxonomic levels within the genus. The results indicate a close relationship between Banksia and Dryandra, which are sister genera in the tribe Banksiae, family Proteaceae. / Thesis (Ph.D.)--University of Adelaide, Dept. of Horticulture, Viticulture and Oenology, 1997

Diss. (sammanfattning) Göteborg : Univ. , 2009. / Härtill 4 uppsatser.