Doctor of Philosophy (PhD), Ohio University, 2023, Biological Sciences (Arts and Sciences)

Gene flow and geography are critically influential factors in shaping the genetic history of a species. Gene flow can have beneficial effects on a population that may allow for new adaptations to occur, such as increasing genetic variation. However, gene flow may also result in negative consequences for populations if their fitness is decreased through the introduction of non-optimized traits or through selection resulting in a reduction of locally adapted individuals. Asymmetrical gene flow can even prevent local adaptation in edge populations when gene flow from central populations adapted to central conditions swamps locally adapted populations. This phenomenon can prevent a species from expanding its range, as it is unable to adapt to local conditions at the range edges. Thus, patterns of gene flow can determine the extent to which gene flow slows or promotes adaptation. Gene flow can also create problems for the inference of species relationships, because it is a source of gene tree-species tree discordance. While speciation is commonly modeled as a finite event, divergence is a process. Even after divergence, hybridization is common, and neglecting to account for it can lead to incorrect species tree inference. Nonetheless, the development of species tree inference methods that account for gene flow remains in its infancy. Even with the addition of more loci from genomic-scale data, gene flow misleads phylogenetic reconstruction. Thus, it is vital to account for gene flow with phylogenetic networks when inferring species relationships. This dissertation examines the role of gene flow in constraining adaptation in the Cumberland Plateau Salamander, Plethodon kentucki, a cryptic species with respect to the sympatric Northern Slimy Salamander, Plethodon glutinosus. After its description in 1983 by Highton and MacGregor using allozyme data, its taxonomic status was unclear, as the authors reported extreme levels of genetic differentiatio (open full item for complete abstract)

Committee: Shawn Kuchta (Advisor); John Schenk (Committee Member); Diego Alvarado-Serrano (Committee Member); Susan Williams (Committee Member) Subjects: Biology; Evolution and Development

Doctor of Philosophy (PhD), Ohio University, 2023, Biological Sciences (Arts and Sciences)

Patterns in the distributions of species result from numerous ecological and evolutionary processes, including competitive interactions, evolved physiological tolerances, and the historical environmental fluctuations that have caused ranges to shift, expand, or contract over long time periods. For some groups of species, these processes have resulted in an elaborate diversification of traits. For other groups, however, such as woodland salamanders (genus Plethodon), closely related species may be phenotypically similar or even identical. It is less clear what drives the formation of such species, whether and how they maintain their identities and interact after initial divergence, and how such similar species might have evolved ecologically in subtle ways to differentially utilize the landscape. The Eastern Red-backed Salamander (Plethodon cinereus) is a small, fully terrestrial woodland salamander notable for its wide distribution and high phylogeographic diversity in the eastern United States and southeastern Canada. Most of its current distribution, however, was covered by ice sheets at the end of the Pleistocene, suggesting recent and rapid post-glacial expansion. It is not yet clear how P. cinereus colonized these landscapes, and what ecological characteristics made P. cinereus so successful in its range expansion compared to other species. Some studies comparing narrowly-distributed montane Plethodon to their lowland counterparts have suggested a combination of physiological specialization and competitive superiority of montane species relative to generalist lowland species such as P. cinereus, but it is unknown if this asymmetry applies to sets of lowland species outside of montane systems. In this dissertation, I explore the biogeography of woodland salamanders, with special attention to P. cinereus, at ecological and evolutionary time scales to uncover the processes that shape genetic diversity and species distributions. Chapters 1 and 2 concern the hi (open full item for complete abstract)

Committee: Shawn Kuchta (Advisor); John Schenk (Committee Member); Diego Alvarado-Serrano (Committee Member); Viorel Popescu (Committee Member) Subjects: Ecology; Evolution and Development

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

Doctor of Philosophy, The Ohio State University, 2020, Evolution, Ecology and Organismal Biology

My dissertation aims to understand the history of divergence and speciation in terrestrial gastropods from the Pacific Northwest of North America (PNW). Speciation is the driving force behind the diversity on earth, but most of what we know about speciation has been learned from a small number of model systems. In my dissertation, I extend knowledge about how species form in an understudied system, pulmonate gastropods, using genomic and ecological data. Temperate rainforests in the PNW are disjunct and are separated by the arid Columbia Basin (CB). In many rainforest endemics, genetic data suggest that the formation of the CB led to speciation. I set out to test whether this barrier drove speciation in terrestrial gastropods. In Chapter 2, I collected subgenomic data from the robust lancetooth snail (Haplotrema vancouverense) using a restriction-associated-digest (RADseq) technique. While phylogeography has moved away from descriptive work towards model-based approaches in recent years, many approaches perform poorly on large datasets with thousands of loci, or, at least, require that much of the information content of the data is sacrificed. I developed a novel approach that uses Machine Learning to compare hypothesis-driven models using genome-scale data. I applied this framework to H. vancouverense and found evidence of recent dispersal between coastal and inland populations; speciation across the CB was not supported (Smith et al., 2017). In Chapter 3, I expanded this work to several species of taildropper slugs (Genus Prophysaon) with this disjunct distribution. I leveraged an approach described by Espindola et al. (2016) to predict phylogeographic patterns based on taxonomy and environmental data, and predicted that these species would lack deep divergence across the CB. Molecular data and model-based approaches did not support speciation across the CB, and suggested a different distribution of cryptic diversity (Smith et al., 2018). In Chapter 4, I e (open full item for complete abstract)

Committee: Bryan Carstens (Advisor); Marymegan Daly (Committee Member); Laura Kubatko (Committee Member); Andreas Chavez (Committee Member); Jack Sullivan (Committee Member); David Tank (Committee Member) Subjects: Biology; Genetics; Zoology

Master of Science, The Ohio State University, 2018, Evolution, Ecology and Organismal Biology

In marine environments, phylogeographic approaches have the power to counteract the difficulties of studying small, highly mobile organisms that live in a fluid environment. These analyses are particularly useful for studying exploited species, as understanding connectivity and processes governing gene flow between populations is essential to sustainable management of fisheries. Among the most vulnerable of exploited species are marine invertebrates collected for the ornamental aquarium trade, as commercial culture techniques are largely not addressed and vital data on larval biology is inadequate or remain unknown. The Caribbean blue-legged hermit crab (Clibanarius tricolor) is heavily collected for its role as an aquarium cleaner; however, despite its economic and ecological importance, little is known about their population structure or genetic diversity. Here, we investigate the phylogeography and genetic diversity of C. tricolor by comparing structure across four well-defined phytogeographic breaks throughout their range in the Caribbean and west Atlantic: the Florida Straits, Mona Passage, Central America, and central Bahamas breaks. We also explore additional factors (e.g. reproductive strategies, life-history traits, habitat preference, demographic history, biogeographic processes) that may influence whether structure is present in marine organisms within this region. Prior to analyzing structure throughout C. tricolor's entire range, a preliminary study was done to determine whether high throughput sequencing approaches (i.e. double digest Restriction-site Associated DNA sequencing) were necessary for detecting phylogeographic patterns in C. tricolor. Findings indicated that Sanger sequencing of traditional loci used in decapod studies (mtDNA: cytochrome c oxidase subunit 1, 16S-rDNA; nuDNA: Histone 3) were sufficient for this study. To infer C. tricolor structure and connectivity, analyses investigating genetic diversity (# segregating sites, # haploty (open full item for complete abstract)

Committee: Marymegan Daly (Advisor); Bryan Carstens (Committee Member); John Freudenstein (Committee Member) Subjects: Biology; Conservation; Genetics

Doctor of Philosophy, The Ohio State University, 2018, Evolution, Ecology and Organismal Biology

Speciation is one of the central topics in evolutionary biology. To understand speciation processes and diversification patterns it is necessary to study the interaction between genotype and environment and their effect on phylogenetic divergence and phenotypic variation among taxa. Myotis (Chiroptera: Vespertilionidae), the most diverse genus of bats by species number, represents an exceptional system to study drivers of speciation and the genomic mechanisms underlying processes of adaptive radiations and morphological convergence. Species of this genus have colonized all biogeographic regions and adapted to a wide variety of biomes, yet the phenotypic variation among the more than 100 species is restricted to three ecomorphs associated with foraging strategies that have apparently evolved several times. This work contributes to our understanding of divergence processes, speciation with gene flow and, phenotypic convergence in this evolutionary labile group. My approach goes from a broad genomic and biogeographic perspective to infer phylogenetic relationships and patterns of morphologic convergence among nearly 90% of extant Myotis species throughout the world (Chapter 2), to specific model-based phylogeographic approaches to co-estimate species limits, species relationships and interspecific gene flow in species complexes of North American Myotis, the western long-eared bats and the little brown bat (Chapters 3 and 4). I then summarize the results of former chapters and discuss the main conclusions of this work (Chapter 5).

Committee: Bryan Carstens (Advisor); Laura Kubatko (Committee Member); Marimegan Daly (Committee Member); John Hunter (Committee Member); Manuel Ruedi (Committee Member) Subjects: Biology; Genetics

Doctor of Philosophy, The Ohio State University, 2017, Evolution, Ecology and Organismal Biology

Understanding the patterns and processes that generate and maintain biodiversity is the key pursuit of evolutionary biology. The field of phylogeography attempts to bridge the gap between phylogenetics and populations genetics, and reveal the underlying historical and biogeographic mechanisms of the divergence process itself. In a comparative framework, phylogeography seeks to identify the shared historical processes that promote population and species level diversification. Largely missing from the comparative phylogeographic literature are experimental frameworks that account for abiotic and biotic factors, as many taxa engage in highly specialized interactions that can have profound impacts on evolutionary history. Accounting for biological traits can thus identify the relative contributions of abiotic versus biotic process across ecosystems, the origin and maintenance of ecological communities, and increased power to evaluate top-down hypotheses about the generation of biodiversity. Tropical coral reefs are among the most biodiverse ecosystems on the planet, and inherently reliant on highly specialized symbioses that represent millions of years of evolutionary interactions. Long-term, stable, ecological associations generate an a priori hypothesis of concordant phylogeographic history among interacting species, yet the degree of specificity and fidelity within these associations should lead to varying degrees of shared biogeographical histories. Using a common sea anemone symbiosis on coral reefs from the Tropical Western Atlantic, I test the hypothesis that variation in host specificity, across five co-occurring crustacean species symbiotic with sea anemones, predicts levels of phylogeographic concordance with their shared host, the corkscrew anemone Bartholomea annulata. First, in Chapters 2-6, using DNA barcodes and high-throughput DNA sequencing, I demonstrate that three of the five nominally described, focal crustacean species, are actually cryptic species (open full item for complete abstract)

Committee: Marymegan Daly (Advisor); John Freudenstein (Committee Member); Bryan Carstens (Committee Member) Subjects: Biology

Doctor of Philosophy (PhD), Ohio University, 2016, Biological Sciences (Arts and Sciences)

The Diamondback Terrapin (Malaclmeys terrapin) is a turtle found in brackish water habitats along the Gulf and Atlantic coastlines of the North American continent. Historically, terrapins have had a complex relationship with humans, including over- harvesting, habitat loss and degradation, and translocations. Furthermore, ecological and molecular studies of terrapins yield conflicting results with respect to terrapin population biology. Resolving these conflicts is integral to understanding how past human activities have influenced the contemporary distribution and abundance of terrapin genetic diversity. In Chapter 1, I surveyed the terrapin literature and identified incongruences between ecological and molecular studies. I finish Chapter 1 with recommendations for future molecular and ecological terrapin studies. In Chapter 2, I demarcated metapopulation structure and quantified gene flow between populations in Chesapeake Bay. I detected four populations with weak structure, high admixture, high genetic diversity, and genetic signatures of anthropogenic translocation. In Chapter 3, I quantified the effective population sizes of the Chesapeake Bay populations, with both ecological and molecular approaches. Using mark-recapture, Bayesian model testing, and approximate Bayesian computation, I recovered incongruent results among methods. I then used mark-recapture data to rule out spurious molecular estimates, finding that coalescent models more accurately estimate effective population size in Chesapeake Bay. In Chapter 4, I used a range-wide dataset to locate major terrapin populations, quantified historical and contemporary gene flow, and tested for bottlenecks. I used Bayesian model testing and discriminant analysis of principal components (DAPC) as well as historical terrapin literature to show the terrapin's phylogeographic structure was best explained by anthropogenic translocation events in the early 1900's. In Chapter 5, I revisited a classic terrapin phylogeo (open full item for complete abstract)

Committee: Shawn Kuchta (Advisor); Willem Roosenburg (Advisor); Morgan Vis (Committee Chair); Harvey Ballard (Committee Member); Matthew White (Committee Member) Subjects: Biology; Genetics

Doctor of Philosophy, The Ohio State University, 2016, Evolution, Ecology and Organismal Biology

Interactions among species are driving forces behind the formation, structure, and persistence of ecological communities. The nature of species interactions that characterize communities, however, has long been debated by ecologists, varying from communities as fluid entities to communities as evolving units. For species with obligate interactions (e.g., host and parasite, plant and pollinator), we might expect these ecologically dependent associations to be reflected in a shared evolutionary history, yet relatively few studies have demonstrated this process in nature. To address this central tenet in ecology and evolutionary biology, my research explores co-diversification in the Sarracenia alata pitcher plant system. Sarracenia alata (family Sarraceniaceae) is a carnivorous pitcher plant distributed along the Gulf Coast of the American southeast, bisected by the Mississippi River. Leaves of this plant are tube-shaped and filled with fluid, adapted for the capture and digestion of prey items. The breakdown of prey provides inorganic compounds to the plant, necessary in the nutrient-poor habitats where these plants are found. In addition to prey capture, the plant's modified leaves harbor a unique biota of associated organisms (i.e., inquilines)—diverse species that share ecological relationships and often provide important services (e.g., secrete digestive enzymes) for the plant. My dissertation tests coevolution theory, exploring how a host plant may influence the population genetic structure of associated species. Shared structure would suggest stable ecological relationships through evolutionary time, and would provide evidence that ecologically interacting lineages can evolve as a unit. I first analyzed DNA sampled directly from the pitcher fluid to identify microorganisms contained within the community (Chapter 2). My results recover a diverse set of taxa found within the pitcher fluid, and demonstrate that roughly half of the small eukaryotes (e.g., fungi, (open full item for complete abstract)

Committee: Bryan Carstens (Advisor); Laura Kubatko (Committee Member); John Freudenstein (Committee Member) Subjects: Biology

Doctor of Philosophy, The Ohio State University, 2016, Evolution, Ecology and Organismal Biology

The Neotropics is the most species-rich region in the world. The current diversity and distribution of lineages present in this region is in part the result of complex ecological and evolutionary trends determined by environmental variables that have operated at diverse spatial and temporal scales. In addition, demographic processes have also influenced the structure of present-day phylogeographic patterns. Several studies have used Neotropical pitvipers as model organisms to explore historical diversification patterns and ecological processes that produce diversity in this region. However, few of those studies have explored patterns of diversification for groups of pitvipers likely influenced by one of the most salient features of the South American continent: The Andes. Here, I use a combination of molecular, morphological, and geographical data to explore diversification patterns and the evolutionary mechanisms implicated in the divergence of two distinct members of the genus Bothrops. First, I examine cryptic diversity present in the widespread and medically important snakes of the B. asper species complex (Chapter 2). Using a genomic and morphological dataset collected across the distribution of the group, I identified extensive phylogeographic structure, suggesting the influence of geographic barriers and/or differences in ecological niches in the recent diversification in the group. A deep divergence between a Central and South American clade is evident, but more recently diverged groups in South America show complicated patterns suggestive of recent divergence and/or gene flow among lineages. Next, I use this information to perform model-based analyses to investigate the demographic processes involved in the recent origin of two Ecuadorian montane lineages of these pitvipers (Chapter 3). This approach allowed me to resolve some of the discrepancies of evolutionary relationships found in Chapter 2. I found evidence for the isolation of one of the montane line (open full item for complete abstract)

Committee: H. Lisle Gibbs (Advisor); Paul A. Fuerst (Committee Member); Thomas Hetherington (Committee Member); John Freudenstein (Committee Member) Subjects: Ecology; Evolution and Development; Zoology

Bachelor of Science (BS), Ohio University, 0, Biological Sciences

Phylogeography is the study of the principles and processes which influence the geographic distributions of genealogical lineages. An understanding of phylogeography can help us to understand the contributions of historical and contemporary process that shape that distribution. Information uncovered in phylogeogaphic analyses can be used to advise on fisheries management. The walleye (Sander vitreus) is one of the most widely stocked fishes in North America. Historic stocking has led to introgression between walleye native to the Central Highlands (“Highlands walleye”) and nonnative Lake Erie stocks of walleye. Introgression can have deleterious effects on native populations, and modern stocking aims to reduce the amount of nonnative fish in Highlands ecosystems. Analyses of the mitochondrial gene cytochrome b show that there are two distinct clades of walleye in the Allegheny and Ohio River watersheds. Each clade corresponds to fishes of the Highlands and Lake Erie haplotypes. The majority of the tested populations contain Lake Erie alleles to varying degrees. It is possible that pure native populations exist at East Brady, Oil City, and Templeton.

Committee: Matthew White Ph.D. (Advisor) Subjects: Biology

Doctor of Philosophy, The Ohio State University, 2015, Evolution, Ecology and Organismal Biology

Plethodon salamanders are fully terrestrial, lungless salamanders found in forested areas throughout North America. My dissertation focuses on five of these salamander species located in the Pacific Northwest (PNW). The PNW has a complex geologic history including events such as volcanism and repeated glaciations. This complexity makes studying biodiversity patterns informative as to what evolutionary processes shape current population and species structure. The five species that are the focus of my dissertation are used to learn about Plethodon salamanders in general, but because these salamanders are at different stages of divergence within and among species, they can further be used to explore methods in phylogeography, which help us better understand the process of evolution. First, I explore demographic model selection using genetic data in P. idahoensis (Chapter 2). The best demographic model for this species is one with population divergence, expansion, and migration. Furthermore, the evaluation of Approximate Bayesian computation techniques highlights the complexities of this method for model selection in phylogeography. Next, I test species boundaries in P. vandykei, P. larselli, and P. idahoensis (Chapter 3). Results of this study were opposite of those expected, in that the current range of the species did not accurately predict species boundaries. In other words, geographic proximity and connectivity did not produce species hypotheses that were supported by genetic data. Alternatively, distributions estimated from historical species distribution models were better predictors of current genetic patterns. Finally, I explore range expansion dynamics in P. dunni and P. vehiculum using genetic, environmental, and morphological data (Chapter 4). Both species underwent recent rapid range expansions since the Pleistocene and share similar population structure, but one species has a much larger geographic range than the other. The best explanations for (open full item for complete abstract)

Committee: Bryan Carstens Dr. (Advisor); Laura Kubatko Dr. (Committee Member); Lisle Gibbs Dr. (Committee Member); John Freudenstein Dr. (Other) Subjects: Biology; Ecology; Evolution and Development

Doctor of Philosophy, University of Akron, 2015, Integrated Bioscience

Euhrychiopsis lecontei (milfoil weevils) have been used as a native, augmentative biological control agent in the management of the invasive aquatic weed, Myriophyllum spicatum (Eurasian watermilfoil), since the 1990's. Although much research has been conducted on E. lecontei's life history and effectiveness as a biological control agent, detailed genetic characterization of the weevil and its close relatives has been lacking in the literature. The current studies sought to fill this gap in knowledge by collecting molecular genetic data for this important native insect. Characterization of interspecific diversity, via the examination of mitochondrial DNA of E. lecontei and other members of the tribe Phytobiini, suggest that the North American members of this group are sister species (E. lecontei and Parenthis vestitus) as are European members (Eubrychius velutus and Phytobius leucogaster) of the group. This study therefore supports the hypothesis that this group of milfoil specialists shares a recent common ancestor that colonized aquatic habitats and utilized one or more Myriophyllum species as a host. Intraspecific studies utilizing mitochondrial and microsatellite DNA of E. lecontei were also performed. These data indicate that while the species shows some geographic structuring on a continental scale, population-level studies indicate high levels of panmixia with relatively high rates of inbreeding. Since the continued management of Eurasian watermilfoil represents a large economic and ecological burden across the United States and Canada, studies such as these are of particular value in determining if E. lecontei has suitable viability as a native biological control agent for this invasive plant.

Committee: Stephen Weeks Dr. (Advisor); Randall Mitchell Dr. (Committee Member); R. Joel Duff Dr. (Committee Member); Francisco Moore Dr. (Committee Member); Shanon Donnelly Dr. (Committee Member) Subjects: Biology; Entomology; Evolution and Development; Freshwater Ecology; Genetics

Master of Science (MS), Ohio University, 2015, Biological Sciences (Arts and Sciences)

Climatic oscillations during the Pleistocene repeatedly formed glacial boundaries, shifted suitable habitat, and caused significant geological changes in the major drainage systems of Eastern North America. Contemporary drainage systems were heavily impacted by these cycles of glacial advancement and retreat. These impacts, in conjunction with ongoing stream capture, caused the fragmentation and fusion of many major pre-Pleistocene drainage systems. In this study, I investigated the contribution of historic and contemporary drainage systems in shaping the phylogeographic patterns of genetic diversity in the stream dwelling salamander Gyrinophilus porphyriticus. I used nucleotide sequence data from two protein coding genes, one nuclear (Rag-1) and one mitochondrial (Cytochrome b), to generate a phylogenetic hypothesis of population-level relationships and utilized both matrix and linear based approaches to test for the role of isolation by distance and drainage system connectivity on phylogenetic patterns. My results show that while both historic and contemporary river systems have played a role in structuring phylogeographic relationships, historic river systems have played a greater role.

Committee: Shawn Kuchta (Advisor); Matthew White (Committee Member); Harvey Ballard Jr. (Committee Member) Subjects: Biology

Doctor of Philosophy (PhD), Wright State University, 2014, Environmental Sciences PhD

Speciation is primarily regarded as an ancestral split that results in two distinct taxonomic units, and proceeds in stages along a continuum from initiation (i.e., population divergence) to completion (i.e., reproductively isolated species). Establishing how and why populations diverge, including the primary mechanisms influencing these events is a major objective for evolutionary scientists. Focusing on incipient forms, researchers attempt to disentangle the antagonistic nature of selection, genetic drift, and gene flow in the speciation process. In chapter 1, I investigate the phylogenetic relationships of 14 closely related taxa within the mallard complex (Anas spp.) that underwent a radiation within the past one million years. Using mitochondrial DNA (mtDNA) and 20 nuclear loci for one to five individuals per taxon, I further examine how recombination and hybridization affect species tree reconstructions. In general, relationships within major clades were robust to treatment of recombination (i.e., ignoring or filtering) and inclusion or exclusion of hybridizing taxa, but branch lengths and posterior support were sensitive to both treatments. Of the 14 taxa, the most confounded relationships were those within the New World (NW) group comprising the sexually dichromatic mallard (Anas platyrhynchos) and the monochromatic American black duck (A. rubripes; "black duck"), mottled duck (A. fulvigula), and Mexican duck (A. [p.] diazi). Finally, I address discordance between nuclear, morphometric, and mitochondrial trees, particularly with regard to the placement of the Hawaiian duck (A. wyvilliana), Philippine duck (A. luzonica), and two spot-billed ducks (A. zonorhyncha and A. poecilorhyncha) and discuss how alternative modes of speciation (i.e., hybrid speciation) may lead to variance in these relationships. In Chapter 2, I attempt to disentangle the evolutionary relationships of the New World (NW) group using mtDNA and 17 nuclear loci for a larger per taxon s (open full item for complete abstract)

Committee: Jeffrey Peters Ph.D. (Advisor); John Stireman III Ph.D. (Committee Member); Volker Bahn Ph.D. (Committee Member); Christopher Barton Ph.D. (Committee Member); Lisle Gibbs Ph.D. (Committee Member) Subjects: Biology; Conservation; Genetics; Molecular Biology; Wildlife Conservation; Wildlife Management

Bachelor of Sciences, Ohio University, 2014, Environmental and Plant Biology

The freshwater red alga, Batrachospermum gelatinosum (L.) DC., inhabits streams of Europe and North America having been collected frequently on both continents. A study of this species showed evidence of a glacial refugium in the southeastern US with little genetic variation throughout its more northern range in eastern North America. This study was initiated to investigate its phylogeography throughout Europe. Specimens were collected from Belgium, Estonia, Finland, France, Great Britain, Italy, Latvia, Lithuania, Poland and Spain. Of the 70 individuals analyzed, there were 12 cox1 haplotypes. In addition, ITS variation of 68 individuals was surveyed and showed 22 haplotypes. The haplotype network of cox1 data showed 54 individuals distributed among three common haplotypes. The other nine haplotypes only differed from the commons ones by 1-2 base pair and were represented by 1-5 individuals. For the ITS data, the network had a star appearance with common haplotype (16 individuals) and many closely related haplotypes with few individuals per haplotype. Compared to North America, there are more haplotypes present in Europe and the relationship among haplotypes is more complex. The geographic distribution of haplotypes did not appear to follow a glaciation pattern, but rather the common haplotypes were widely spread suggesting a recent expansion.

Committee: Morgan Vis-Chiasson (Advisor) Subjects: Plant Biology

Doctor of Philosophy, The Ohio State University, 2013, Evolution, Ecology and Organismal Biology

The genus Viola is a large and diverse group of flowering plants. The objectives of this study were to develop and explore new morphological and molecular tools with horticultural and systematic applications. Chapter 1 employed digital image analysis software, Tomato Analyzer, for flower morphology analysis of a 127 accession collection of sect. Melanium violets ("pansy group"). Seventy-seven traits associated with shape, size, and color were scored separately as categorical or continuous variables. The qualitative analysis was favored, capturing more of the variation and receiving higher bootstrap support in cluster analysis dendrograms. Cluster and ordination analyses indicated that the presence of blotch was the primary grouping factor, and secondarily, measures of color and shape (e.g., petal width). Uniformity across accessions of some hybrid morphotypes (e.g., "white with blotch") led to tight clustering across analyses. There were no significant correlations between clustering patterns and accessions' originating country or parent company, as had been previously reported. Chapter 2 builds on the morphological analysis described in Chapter 1 by utilizing sequence-related amplified polymorphism (SRAP) markers to further characterize the collection of Melanium violets. Here, SRAP fragments indicated no significant differences between the horticultural classes of violets, though more were generated from species types than hybrid types of the same ploidy. Bayesian analysis suggested distinctive structure clusters within the collection, but was obscured by high levels of admixture. Some color forms (white, white with blotch, yellow with blotch, and orange) tended to cluster strongly together. Correlation analysis of morphological and molecular datasets, as well as analysis of a combined dataset, underscored the conclusion that some genetic lines could be generalized by blotch presence and flower color. The relationship between these data may help in (open full item for complete abstract)

Committee: Andrea Wolfe (Advisor); Pablo Jourdan (Committee Member); Laura Kubatko (Committee Member); Harvey Ballard (Committee Member) Subjects: Conservation; Horticulture; Plant Sciences

Doctor of Philosophy (PhD), Wright State University, 2012, Environmental Sciences PhD

Genetic diversity and divergence at a locus are the result of interactions among the fundamental evolutionary forces of mutation, genetic drift, gene flow and natural selection. Variation in the strength of these forces can cause high heterogeneity in diversity and divergence across the genome. The overall objective of this thesis was to examine the role of population history vs. selection in generating heterogeneity in genetic diversity and differentiation. In Chapter 1, I examine the role of dispersal behavior in causing genetic differentiation and population structure within and between two morphologically distinct Australian duck species that differ in ecology and life history characteristics. A five-locus nuclear dataset revealed nearly no divergence and similar values of genetic diversity between species. However, as predicted, I found significant population structure in the sedentary chestnut teal (Anas castanea) but no structure within the vagile grey teal (A. gracilis). In Chapter 2, a more rigorous examination of differentiation among nineteen autosomal loci also failed to uncover a genetic distinction between these two species. However, DNA sequences from seven loci sampled from the Z-chromosome revealed strong differentiation between chestnut and grey teal. Furthermore, the most divergent loci are clustered on the shorter p-arm of the chromosome, close to the centromere, suggesting this region as an island of differentiation that may have been important in the speciation process. These two species of Australian teal are perhaps the most recently diverged taxa examined to date that reveal a large Z-effect. In Chapter 3, I quantitatively tested the contribution of gene flow and introgression to the heterogeneity of genetic diversity and differentiation in two deeply divergent taxa, the falcated duck (A. falcata) and the gadwall (A. strepera). Consistent with previously published mitochondrial DNA analyses, 19 nuclear loci revealed the introgression of (open full item for complete abstract)

Committee: Jeffrey Peters PhD (Advisor); John Stireman III PhD (Committee Member); Volker Bahn PhD (Committee Member); Michael Raymer PhD (Committee Member); Kevin Omland PhD (Committee Member) Subjects: Molecular Biology

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, University of Toledo, 2009, Biology (Ecology)

The study of biodiversity, at multiple hierarchical levels, provides insight into the evolutionary history of taxa and provides a framework for understanding patterns in ecology. This is especially poignant in invasion biology, where the prevalence of invasiveness in certain taxonomic groups could be related to their evolutionary history. In this dissertation, I examined the systematics, phylogeography, population genetics, and biogeography of a group of Ponto-Caspian endemic gobies that includes multiple introduced species in Europe and North America. In Chapters 2 and 4 I found highly divergent genetic lineages within two morphologically defined species (Neogobius fluviatilis and Proterorhinus marmoratus) that are widespread throughout the Ponto-Caspian region. Statistical analyses of morphology identified significant differences according to genetic lineage within each morphospecies, indicating species level divergence among regional taxa. In Chapter 3 I constructed the phylogeny of the Ponto-Caspian gobies, finding broad paraphyly in Neogobius sensu Miller & Vasil'eva (2003), and identifying a novel relationship between the “neogobiin” gobies (Babka, Mesogobius, Neogobius, Proterorhinus, and Ponticola) and the tadpole gobies (Anatirostrum, Benthophiloides, Benthophilus, Caspiosoma) as a distinct group highly divergent from other gobiids. I redefined the taxonomy and nomenclature according to the molecular phylogeny, and redescribed the subfamily Benthophilinae to comprise all Ponto-Caspian endemic gobies. In all three chapters, I estimated divergence times among genetic lineages at multiple taxonomic levels, and found gross concordance between the timing of diversification events within the Ponto-Caspian gobies and major geologic changes in the evolution of the Ponto-Caspian basin. Additionally, in Chapters 2 and 4, I identified potential source locations in the northwestern Black Sea for introduced goby populations in northern/central Europe and North America. (open full item for complete abstract)

Committee: Carol Stepien PhD (Committee Chair); Christine Mayer PhD (Committee Member); Elliot Tramer PhD (Committee Member); David Jude PhD (Committee Member); Juan Bouzat PhD (Committee Member) Subjects: Biology; Ecology; Environmental Science; Zoology