Master of Arts, Miami University, 2024, Psychology

Alcohol use disorders (AUDs) are a prevalent and significant public health issue, with hundreds of thousands of people dying from alcohol-related deaths across the United States of America each year. Interestingly, there are sex differences that exist in both human and rodent models of AUD. These sex differences are not well understood, and the influences of sex chromosomes and/or hormones are just beginning to be studied. This project used ovariectomized (OVX) Four Core Genotypes (FCG) mice in a limited access, drinking in the dark (DID) paradigm to assess the separate influences of sex chromosomes and hormones on binge drinking. Mice successfully escalated consumption throughout the paradigm, and decreased consumption and preference in the presence of aversion-resistant quinine, however, there were no significant differences found across sex chromosome (XX vs. XY) or treatment (OVX vs. sham) conditions. The findings from this study may suggest that FCG mice, uniquely, do not differ in EtOH consumption following the surgical removal of ovaries. Additional research needs to be completed in order to better understand why this effect was not found.

Committee: Anna Radke PhD (Advisor); Haifei Shi PhD (Committee Member); Jennifer Quinn PhD (Committee Member) Subjects: Neurosciences; Psychology

Master of Science, University of Akron, 2021, Biology

Sex chromosomes have evolved independently numerous times in many lineages spanning the tree of life. The study of these various evolutionary paths has led to the development of general sex chromosome evolutionary theory; despite the large number of diverse and varying systems, autosomes are thought to follow a convergent evolutionary trend with discrete steps towards sex chromosome formation. These steps include the occurrence of sex determining genes, the suppression of recombination, accumulation of transposable elements, and finally the degeneration of the chromosome itself. However, aspects of this general theory have not been thoroughly tested due to the diversity and complexity of sex chromosomal systems. Here I show that the sex chromosomal system of the clam shrimp Eulimnadia texana does exhibit the pattern of transposable element accumulation predicted by general sex chromosome evolutionary theory. Because recombination is usually suppressed during the evolution of sex chromosomes, transposable elements cannot be easily purged from the genome; this leads to accumulation and the ultimate degeneration of the sex-limited chromosome. The W chromosome of E. texana was analyzed using RepeatMasker in order to measure the levels of repetitive element accumulation – transposable elements in particular. The results of said analysis showed little to no accumulation occurring, however. The androdioecious mating system of clam shrimp – populations consisting of males and hermaphrodites – likely explains this deviation from the general evolutionary trend; by exhibiting the sex-limited chromosome in homogametic form (WW), repetitive elements may be exposed to selection and purged from the genome. I view these data as a valuable and unique lens under which the tenets of sex chromosome evolution can be tested.

Committee: Stephen Weeks (Advisor); Zhong-Hui Duan (Committee Member); Robert Duff (Committee Member) Subjects: Biology

Master of Science (MS), Wright State University, 2016, Biological Sciences

Sex chromosomes are thought to be an important component of the genome associated with speciation and the buildup of reproductive isolation. Recent advances in sequencing technologies and improvements in population genetics and modeling techniques have made it possible to better assess genomic signatures of selection, genetic drift and gene flow in diverging lineages. Recent studies have shown elevated differentiation on the Z sex-chromosome between the Australian grey teal (Anas gracilis) and chestnut teal (Anas castanea). Here, we used next generation sequencing to scan ~3,400 autosomal loci and ~190 Z loci to examine genomic differentiation and signatures of selection and gene flow between grey and chestnut teals. We also inferred demographic history to assess gene flow and signatures of selection. We found weak differentiation in autosomal loci (mean FST = 0.008), but ~ 28-times higher differentiation on the Z-chromosome (mean FST =0.23). We also found that this higher differentiation was localized on the q-arm of the Z chromosome between 15-million and 40-million base pairs. Whereas we could not reject a strict isolation model on the Z chromosome, models that incorporated gene flow provided a significantly better fit for autosomal loci, which is consistent with reduced local gene flow as expected under a speciation with gene flow model. However, nucleotide diversity within chestnut teal was reduced within the region of elevated differentiation on the Z chromosome, which is more consistent with a selective sweep rather than reduced effective gene flow. Furthermore, linkage disequilibrium within this region was elevated with respects to other regions on the Z chromosome as well as more significantly elevated in chestnut teal than in grey teal. Although we cannot fully reject a model of speciation with gene flow, recent speciation seems a more plausible explanation of the nearly absent divergence of mitochondrial and autosomal DNA. Rather, these data suggest that (open full item for complete abstract)

Committee: Jeffrey Peters Ph.D. (Advisor); Scott Baird Ph.D. (Committee Member); John Stireman Ph.D. (Committee Member) Subjects: Biology

Doctor of Philosophy, Miami University, 2013, Botany

Plants possess sex chromosomes at all stages of sex chromosome evolution. Carica papaya has become a model for early stages of sex chromosome evolution. The papaya sex-determining region (SDR) spans the centromere and is approximately 10% the length of Chromosome 1. The objectives of this dissertation are to investigate which mechanisms have driven sex chromosome evolution in papaya by comparing the patterns of polymorphism in the male-specific region of the Y (MSY) and the corresponding X region to low-recombining autosomal regions in the genome. In Chapter 2, patterns of nucleotide polymorphism were measured for regions of various levels of recombination within the papaya genome in order to determine whether strong patterns of selection are present within regions of low recombination. No significant correlations between nucleotide polymorphism (Watterson's theta) and divergence (KS [JC]) versus recombination rate (cM/Mbp) were found. This lack of relationship suggests little to no selection driving evolution of papaya regions of low recombination, inferred to be pericentromeric regions. From this, I concluded that levels of diversity and any patterns of selection occurring within papaya sex chromosomes are products of sex chromosome evolution, rather than their pericentromeric nature. In Chapters 3 and 4, patterns of selection were assessed at 19 X/Y gene pairs and two pseudoautosomal loci. X-linked loci, in general, exhibited low nucleotide diversity. Two regions were identified that exhibit signatures of selective sweeps, indicated by an excess of rare alleles and low diversity. In contrast, Y-linked loci had an excess of diversity, which is localized within three regions of balancing selection. When the regions of selection for the X region and MSY are plotted against each other, the regions overlap, with the selective sweeps for the X coinciding with the sites of balancing selection along the Y. Together, these results suggest that X-driven meiotic (open full item for complete abstract)

Committee: Richard Moore PhD (Advisor); David Gorchov PhD (Committee Member); Daniel Gladish PhD (Committee Member); Susan Hoffman PhD (Committee Member); David Berg PhD (Committee Member) Subjects: Botany; Evolution and Development; Molecular Biology; Plant Biology

Master of Science, Miami University, 2013, Botany

The sex chromosomes of Carica papaya are characterized by a small region of suppressed recombination flanked by two larger, recombining pseudoautosomal regions (PARs). To better understand the evolution of the sex chromosomes, I analyzed polymorphism across the entire X chromosome using next generation resequencing. In addition, I used traditional sequencing to analyze polymorphism at nine loci close to the PAR boundary. Two of these nine loci exhibit clear molecular signatures of X/Y-linkage. The other seven loci have autosomal patterns of polymorphism. By mapping these along the X chromosome, I was able to identify a ~95kb region where the boundary between the PAR and X lies, reducing the previous estimated size of the X by ~2Mbp. A clearly defined PAR border will allow for further investigation into the evolution of expansion of the PAR, especially when studied in a subject that has relatively young sex chromosomes like that of papaya.

Committee: Richard Moore (Advisor); Micheal Vincent (Committee Member); Chun Liang (Committee Member); Bruce Cochrane (Committee Member) Subjects: Biology; Botany; Genetics

Master of Science, Miami University, 2010, Botany

The sex chromosomes of the tropical crop papaya (Carica papaya) are young and consequently allow for the examination of evolutionary forces that affect early sex chromosome formation. We sequenced four X/Y gene pairs from a collection of natural papaya populations and examined the data for molecular signatures of selection and other evolutionary forces that govern sex chromosome formation. In most sex chromosome systems, the Y chromosome displays significantly reduced polymorphism levels while the X chromosome maintains a level of polymorphism that is comparable to autosomal loci. However, the four papaya sex-linked loci that we examined display diversity patterns that are opposite to this trend. The X alleles exhibit significantly reduced polymorphism levels while the Y alleles maintain expected or greater than expected levels of diversity. We hypothesize that the X chromosome has recently undergone a selective sweep while elevated Y polymorphism is due to population structure.

Committee: Richard C. Moore PhD (Advisor); Chun Liang PhD (Committee Member); Martin Henry H. Stevens PhD (Committee Member) Subjects: Botany; Genetics