MS, Kent State University, 2023, College of Arts and Sciences / Department of Biological Sciences

Eastern redcedar (Juniperus virginiana L. var. virginiana) is a native species currently invading open areas and grasslands outside of its original range in the United States. I studied the eastern redcedar's (ERC) invasion patterns in the Lakeside Daisy State Nature Preserve (LDSNP), a short grass prairie located on the Marblehead Peninsula in Ohio, examining the changes in the genetic diversity and structure of the encroaching population. I investigated the relative importance of long-distance dispersal vs. diffusion in the invasion of this short grass prairie by ERC. I used eight microsatellite marker loci and a database of single nucleotide polymorphisms to infer gene flow from external sources vs. within-population recruitment. I found that the older trees in this preserve were less than fifty-years-old, indicating that the population was established between 1970 and 1980. When I grouped trees into five age categories of 10-year increments, we found that the allelic diversity, as indicated by the average number of alleles per locus, increased as the age of the trees decreased. Principal Coordinate Analysis showed two distinct groups of trees in the LDSNP that I investigated further using soil type. Analysis of the population structure of the ERC trees using ADMIXTURE revealed three ancestral clusters in the ERC populations. All ancestral clusters are present in all age groups, suggesting that there is continual input of genetic information from the ancestral clusters. Overall, my findings indicate that ERC encroachment of the LDSNP results from multiple and reiterated gene flow events from the edge of the range through animal-mediated seed dispersal at short and intermediate distances.

Committee: Oscar Rocha (Advisor); David Ward (Committee Member); Sangeet Lamichhaney (Committee Member) Subjects: Bioinformatics; Conservation; Genetics; Natural Resource Management; Plant Biology; Plant Sciences; Range Management

Master of Science, Miami University, 2020, Biology

The prairie vole (Microtus ochrogaster) is a monogamous rodent currently classified into seven subspecies across central United States and south-central Canada. However, conflicting data from recent morphological and nuclear DNA analyses suggest further phylogeographic study is warranted. The primary objective of my study was to conduct the first phylogeographic analysis of prairie voles using mitochondrial DNA sequence data. I sequenced an approximately 505 base pair region of cytochrome b from 40 individuals across the species range that represented six of the seven current subspecies. A spatial genetic cluster analysis yielded three clusters. The largest cluster contained 73% of the individuals sequenced including representatives from the six subspecies. A haplotype network and phylogenetic reconstruction suggested further substructuring within the smaller clusters. Overall, my results, and a prior analysis of nuclear data, suggest panmixia with high gene flow throughout the species range. Interestingly, the genetic structure from the mitochondrial data does not match the structure from the nuclear data. This discordance is likely caused by incomplete lineage sorting due to recent range expansion. Furthermore, the mitochondrial genetic structure is not consistent with the currently accepted geographic ranges of the seven described subspecies and suggests that past subspecies classifications need to be reevaluated.

Committee: Brian Keane (Advisor); Nancy Solomon (Advisor); David Berg (Committee Member); Meixia Zhao (Committee Member) Subjects: Biology; Ecology; Evolution and Development; Genetics

MS, University of Cincinnati, 2017, Medicine: Biostatistics (Environmental Health)

The success of genome-wide association study (GWAS) depends on genotyping a large number of SNPs and determining which of these SNPs are significantly associated with the outcome of disease. While studying for these associations, it is important to take into account the effects caused by differences of ethnicities and population groups. The study of human population genetic structure focused on analyzing the human genetic variations between different populations and on assigning individuals to subpopulations based on the degree of human genetic variations. Currently the leading statistical method for uncovering population structure in GWAS is Principal Component Analysis (PCA). However one major problem of using PCA on SNPs data is that the principal components that are defined do not correspond to actual SNP variables, we need to find ways that can map the principal components to measure the importance of actual SNP variables in terms of ancestry information. To overcome these limitations, Sparse Principal Component Analysis (SPCA) has been proposed to identify a small set of structure informative markers more efficiently by modifying the alternating regression equation for PCA with including a penalty term during optimization that encourages SNPs with negligible loadings to vanish. Yet the computation costs of selecting a small subset of actual ancestry informative SNP variables via SPCA can still be expensive, especially where a large number of non-zero loadings across multiple principal components are required for structure analysis. Given these limitations, it is desirable to find some methods which not only achieve the population classification but also reduce the number of explicitly used variables and can select actual SNP variables that are ancestry informative markers in a cost-effective manner. The goals of this study will not only focus on making inferences on the application of major data mining methods in human population genetics structure analysis (open full item for complete abstract)

Committee: Marepalli Rao Ph.D. (Committee Chair); Tesfaye Mersha Ph.D. (Committee Member); Changchun Xie Ph.D. (Committee Member) Subjects: Biostatistics

Master of Science (MS), Ohio University, 2017, Industrial and Systems Engineering (Engineering and Technology)

In a hospital, there are many factors that must be considered when determining inventory levels and frequency of ordering. Many supplies in a hospital are perishable, so they must be disposed of if they are not used before their expiration date. In addition, multiple hospitals in an area are often owned by the same organization, so they could potentially benefit from joint purchasing in larger quantities and redistributing to the individual hospitals. This inventory model determines the inventory level and reorder point for supplies to minimize total cost. The total cost includes holding cost, distribution cost, purchasing cost, stockout cost and discarding expired product cost. To reflect the fact that hospitals can jointly take advantage of bulk purchasing, a discount cost structure is utilized. To validate the model small-sized numerical examples are solved using the CPLEX solver within GAMS software. And for large-sized problems a Genetic Algorithm is presented. The model is also tested on a case based on data from the catheterization laboratory of a large hospital. Also, a sensitivity analysis of optimal solution is conducted and some important observations are drawn.

Committee: Dale Masel (Advisor); Diana Schwerha (Committee Member); Felipe Aros-Vera (Committee Member); Ashley Metcalf (Committee Member) Subjects: Industrial Engineering

Master of Science, Miami University, 2016, Botany

The biodiversity of wild crop species can be threatened by genetic introgression of cultivated traits from co-occurring cultivated varieties. The tropical fruit crop, papaya (Carica papaya L.), is a model organism to study questions related to crop-to-wild gene flow because it is cultivated in Central America alongside natural populations. Morphological and genetic diversity was assessed for a collection of naturally occurring papaya individuals from four regions in Panama', which is the southern-most extent of papaya's range. Significant morphological variation was limited, and fruit characteristics align with typical wild-type traits; fruits are small and round with a thin mesocarp and yellow flesh. Genetic analyses indicated a deficiency in heterozygosity in all regions except the Northeast region. We found moderate levels of population differentiations and regional structuring. This study provides further insight into the natural biodiversity of a tropical crop cultivated in close proximity to its wild counterparts.

Committee: Richard Moore (Advisor) Subjects: Botany

Master of Science (MS), Wright State University, 2014, Chemistry

The Ozobranchidae family is the smallest and least studied hirudinean taxon. Our research includes the largest molecular dataset yet reported for marine ozobranchids (Ozobranchus margoi and Ozobranchus branchiatus) with the most number of documented turtle hosts (57) from the Atlantic and Pacific Oceans to date of any marine turtle epibiont study. Turtle species sampled in this study include loggerheads (Caretta caretta), hawksbill (Eretmochelys imbricata), olive ridley (Lepidochelys olivacea), and green turtles (Chelonia mydas). Phylogenetic analyses of mitochondrial (COI) and nuclear ribosomal (18S and 28S) genes all support the monophyly of marine Ozobranchidae leeches with speciation occurring over an extensive period of time, likely prior to the Isthmus of Panama. Histone H3 data suggests at least three histone H3 genes for O. margoi. In addition, mtDNA analyses show higher genetic structure in the Atlantic for O. branchiatus existing in both ocean basins. The small tropical family of turtle annelids was also used to examine the limitations of DNA barcoding on taxa with incomplete taxonomic sampling and to assess whether these issues can be adequately resolved using the character-based approach. The ability to assign ocean basin origin of leech specimens using character-based DNA barcoding suggests the potential for this tool to be integrated with other applications besides species identification.

Committee: Audrey McGowin Ph.D. (Advisor); Daniel Ketcha Ph.D. (Committee Member); Ioana Sizemore Ph.D. (Committee Member) Subjects: Conservation; Ecology; Genetics; Molecular Biology; Parasitology

PhD, University of Cincinnati, 2010, Arts and Sciences: Biological Sciences

Biological invasions have received considerable attention because of the increasing frequency with which they occur and the damage they can inflict on ecosystems. However, invasions are ideal study systems not only because of the insight they provide about management and preservation of biodiversity, but also because they can be used to answer a variety of ecological and evolutionary questions. In this series of studies I used the invasions of tropical geckos in urban habitats to address questions about range expansion and species replacement during invasion of an occupied niche. I used both the invasion of A-clones and replacement of B-clones of Lepidodactylus lugubris in Hawaii and the invasion of Hemidactylus mabouia and replacement of H. garnotii in Florida as models to test hypotheses about the process of range expansion and species replacement. To test hypotheses about the mechanisms and consequences of range expansion at multiple spatial scales, I developed 12 novel microsatellite markers in H. mabouia and used them to determine patterns of gene flow at both a very fine scale (tens of meters) and at a very large scale (statewide). To test hypotheses about species replacement, I used both laboratory studies and field studies to document mechanisms and timing of species replacement during invasion. In L. lugubris, I used controlled laboratory experiments to determine the behavioral mechanisms underlying the advantage of A-clones in the human environment. In H. mabouia, I used field census data from many locations in Florida to determine the rate at which H. garnotii was displaced during invasion. I found that dispersal was limited at a very fine spatial scale in H. mabouia, and that population structure arises at the leading edge of range expansion but erodes as the populations approach migration-drift equilibrium. I also demonstrated that human-mediated dispersal at the statewide scale plays a role in the rapid range expansion of H. mabouia. These findings dem (open full item for complete abstract)

Committee: Kenneth Petren PhD (Committee Chair); Eric Maurer PhD (Committee Member); Stephen Matter PhD (Committee Member); Michal Polak PhD (Committee Member); George Uetz PhD (Committee Member); Gisela Garcia-Ramos PhD (Committee Member) Subjects: Ecology

Doctor of Philosophy, University of Toledo, 2011, Biology (Ecology)

One of the most pertinent questions in conservation management is how to discern a species' genetic structure, notably the degree of genetic diversity, composition, and divergence among its component populations. These measures may be used to assess migration patterns, biogeographic variability, recruitment success, and the effects of anthropogenic exploitation and habitat loss. Additionally, comparisons of a species' genetic diversity and divergence patterns across large connected populations versus those in isolated relict areas may provide important data for understanding its distributional response to changes in habitat connectivity and other perturbations. Aquatic taxa offer ideal case studies for interpreting these patterns because their dispersal and gene flow often are constrained through narrow connectivity channels that have changed over geological time and from contemporary anthropogenic alterations. This dissertation's research objective is to understand the interplay between historic (climate change, lake basin formation, and channel connectivity shifts during and after the Pleistocene glaciations) and modern-day factors (fishery exploitation, stocking supplementation, and habitat loss) in shaping population genetic patterns of the yellow perch Perca flavescens (Percidae: Teleostei) across its native North American range. A dual genome and modified landscape genetic approach is employed, analyzing complete sequences from the mitochondrial DNA control region (912 base pairs) and 15 nuclear DNA microsatellite loci. Results support contribution from three primary glacial refugia to contemporary northern populations: the Missourian refugium founded the Northwest Lake Plains region (37% assignment probability) and western Lake Superior (96% assignment), the Mississippian refugium colonized most of the Great Lakes (83-100% assignment), and the Atlantic refugium contributed to the lower Great Lakes and founded the northern Atlantic seaboard (82-100% assignment (open full item for complete abstract)

Committee: Carol Stepien PhD (Committee Chair); Johan Gottgens PhD (Committee Member); Ann Krause PhD (Committee Member); Stuart Ludsin PhD (Committee Member); Edward Roseman PhD (Committee Member) Subjects: Aquatic Sciences; Ecology; Genetics

Doctor of Philosophy, Miami University, 2010, Zoology

Woodland mice of the genus Peromyscus are broadly distributed throughout North America, where they interact with a wide variety of landscape features, climates, and biological communities. Each of the central chapters of this dissertation examines genetic heterogeneity in a species of Peromyscus in relation to landscape features of the Great Lakes region, in order to illuminate the biogeographical constraints facing small mammals in this region. Chapter 1, General introduction Chapter 2, MtDNA genetic structure transcends natural boundaries in Great Lakes populations of deer mice (Peromyscus maniculatus gracilis), examines the genetic structure of deer mice to describe the effect of the Great Lakes on the colonization of northern Michigan from southern refugial sources after the end of the last glacial cycle. Analyses reveal a complex structure indicating occasional migration across Lake Michigan during the 10,000-year history of mouse habitation in the region. Chapter 3, Landscape fragmentation and geographical isolation define microsatellite genetic structure in Great Lakes populations of deer mice (Peromyscus maniculatus gracilis), describes the genetic structure of deer mice using nuclear microsatellite markers. In contrast to Chapter 2, which examines the Great Lakes as barriers to postglacial colonization, Chapter 3 considers the role of the lakes in promoting the differentiation of populations through genetic drift, after expansion from a common source. Chapter 4, Landscape-scale fragmentation and genetic structure in populations of the northern white-footed mouse (Peromyscus leucopus noveboracensis), describes the genetic structure of white-footed mice along a transect from southern Ohio to northern Michigan. Because this transect covers a heterogeneous landscape and climatic gradient, habitat fragmentation and biogeographical range limitation are considered as possible determinants of genetic patterns. Chapter 5, Conclusion

Committee: Susan Hoffman PhD (Advisor); David Berg PhD (Committee Member); Brian Keane PhD (Committee Member); Douglas Meikle PhD (Committee Member); Emily Murphree PhD (Committee Member) Subjects: Biology; Ecology; Genetics; Zoology

Doctor of Philosophy, Miami University, 2004, Zoology

Fragmentation of forests has led to the creation of forest patches that differ in size, proportion of edge habitat, and degree of isolation. Although densities of many mammalian species are positively related to patch area, there appears to be a general negative relationship between density of white-footed mice (Peromyscus leucopus) and patch area. In Chapters 2 – 5, I investigated both resource-based (i.e., vegetation characteristics) and dispersal-based (i.e., inhibited dispersal and sink) hypotheses to explain the negative density – area relationship using live-trapping data and DNA-microsatellite analyses. As an extension of how forest fragmentation may affect movements by this habitat generalist into and out of habitats, in Chapter 6 I focused on how patch isolation influences population genetic structure. Data were collected from 1999 to 2001 in 15 different patches of various sizes and degrees of isolation. I confirmed that relative abundance of P. leucopus was negatively related to forest patch area (Chapter 2). My results indicated that relative abundance of P. leucopus was positively related to structural complexity of understory vegetation and total basal area of trees, and tended to be negatively related to the species richness of trees (Chapter 2 and 3). Although I was unable to differentiate whether understory vegetation results in higher relative abundances due to food or cover, the results suggest that vegetation characteristics contribute to the negative density – area relationship. Based on live-trapping data and DNA-microsatellite analyses, I rejected both dispersal-based hypotheses to explain the effect of patch area on relative abundance of P. leucopus (Chapters 4 and 5). Within-population genetic variation was high across populations, and only 50% of individuals could be assigned to their population of capture based on multilocus genotypes, suggesting high rates of gene flow. Degree of isolation and landscape structure had a small but significa (open full item for complete abstract)

Committee: Douglas Meikle (Advisor) Subjects:

PHD, Kent State University, 2010, College of Arts and Sciences / Department of Biological Sciences

The introduction of exotic species is the inevitable consequence of an expanding global society that relies heavily on international trade of goods and services. These introduced species have negative effects on biodiversity and disrupt native communities. In fact, the spread of non-native species is the second greatest threat to the loss of biodiversity next to habitat destruction. The emerald ash borer (EAB), Agrilus planipennis Fairmaire (Buprestidae), is a recent example of an exotic forest pest species. EAB completes its life cycle on ash trees (Fraxinus spp.) including larvae feeding on cambium tissue which interferes with water and nutrient translocation. Once ash trees become infested with EAB, mortality is >99%. This dissertation was initiated after EAB was discovered and attempts to understand how EAB affects long-term forest community dynamics in order to provide practical applied conservation strategies. These research projects are designed to identify the ecological impacts of EAB and to determine long-term community changes to native deciduous forests. The research objectives are: (1) to identify consequences of EAB eradication efforts, (2) to determine altered community composition under different disturbance intensities (tree removal management recommendations) and (3) to design effective ex situ conservation protocols for future ash tree preservation. EAB causes a disturbance to native forest by creating large light gaps through ash tree dieback; yet, EAB eradication efforts magnified the scale of disturbance through time and space which facilitated the establishment of invasive plant species. The tracked vehicles used during eradication also caused significant soil compaction. Management efforts applied to EAB-infested forests should prioritize appropriate tree removal techniques to minimize the disturbance to the surrounding community. Ash stands in close proximity to roads or edges, or near established invasive populations may benefit from (open full item for complete abstract)

Committee: Oscar Rocha PhD (Advisor); Andrea Case PhD (Committee Member); Daniel Herms PhD (Committee Member); Marilyn Norconk PhD (Committee Member); Alison Smith PhD (Committee Member) Subjects: Biology; Botany; Ecology; Environmental Management; Forestry; Molecular Biology; Plant Biology

Master of Science (MS), Bowling Green State University, 2012, Biological Sciences

The lark sparrow (Chondestes grammacus) is a ground-nesting passerine that breeds across much of the central North American steppe and sand barrens. Through genotyping and sequencing of avian malaria parasites we examined levels of malaria prevalence and determined the distribution of Haemoproteus and Plasmodium lineages across the breeding range of the lark sparrow. Analysis of 459 birds collected from five breeding locations revealed relatively high levels of malaria prevalence in adults (80.3%) and juveniles (45.9%), with infections being primarily of Haemoproteus (88.3% of sequenced samples). Levels of genetic diversity and genetic structure of malaria parasites with respect to the avian host populations revealed distinct patterns for Haemoproteus and Plasmodium, most likely as a result of their distinct life histories, host specificity, and transmission vectors. With the exception of one common Haemoproteus haplotype detected in all populations, all other haplotypes were population-specific. A hierarchical analysis of molecular variance of Haemoproteus sequences revealed that 46-51% of the genetic variation can be explained by differences among host populations (p<0.001). In contrast to the regional patterns of genetic differentiation detected for the lark sparrow populations, Haemoproteus parasites showed high levels of population-specific variation and no significant differences among regions, which suggest that the population dynamics of the parasites may be driven by evolutionary processes operating at small spatial scales (e.g., at the level of host populations). These results highlight the potential effects of host population structure on the demographic and evolutionary dynamics of parasites.

Committee: Juan Bouzat L. (Advisor); Jeffrey Miner (Committee Member); Moira van Staaden (Committee Member) Subjects: Biology