UMD Theses and Dissertations
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Item Taxonomic revision, phylogenomic analyses, and natural history of the fungus-farming ant genus Sericomyrmex (Hymenoptera: Formicidae)(2016) Jesovnik, Ana; Mitter, Charles; Schultz, Ted R; Entomology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Fungus-farming ("attine") ants, a New World clade of nearly 300 species in 16 genera, are model systems for studies of symbiosis, coevolution, and advanced eusociality. All attine ants cultivate fungal symbionts for food. "Lower" attine ants cultivate facultatively symbiotic fungi, but in "higher" attine ants both ants and fungi are obligate, highly coevolved symbionts. Sericomyrmex is a poorly studied higher-attine genus known for its problematic taxonomy. This work represents the first comprehensive study of Sericomyrmex species and their fungal cultivars. For Chapter One I sequenced, assembled, and analyzed transcriptomes of three species of Sericomyrmex and a lower-attine-ant species, Apterostigma megacephala. I characterize the transcriptomes, conduct phylogenetic analyses, and search for genes of interest, most importantly arginine biosynthesis pathway genes, the absence of which in A. megacephala strongly suggests that attine ants became dependent on their fungi early in their evolution. In Chapter Two I address the phylogenomics of Sericomyrmex, sequencing ~990 ultra-conserved-element loci for 88 Sericomyrmex samples. Maximum-likelihood and species-tree phylogenetic methods recover nearly identical topologies across data sets, identifying nine species-level lineages. Divergence-dating analyses indicate that Sericomyrmex is the product of a recent, rapid radiation, with a crown-group age estimate of 4.3 million years. I sequence two nuclear ribosomal regions for 32 Sericomyrmex fungi. The fungal phylogeny indicates that Sericomyrmex cultivars are generalized higher-attine cultivars, which, rather than forming a separate clade, are interspersed with Trachymyrmex-associated fungi, indicating cultivar sharing and horizontal transfer between those genera. In Chapter Three, guided by my phylogenomic results, I study the morphology of Sericomyrmex workers, males, queens, and larvae and conduct a comprehensive taxonomic revision, including a key to the worker caste and species distribution maps. Sericomyrmex comprises 11 species, including three new species. The number of recognized species is lower than the previously recognized 19 species and three subspecies. In Chapter Four I review the literature of and report newly acquired data on the natural history of Sericomyrmex, with a focus on nesting biology, presenting data for 19 nests of seven Sericomyrmex species.Item Top-Down Analysis of Bacterial Proteins by High-Resolution Mass Spectrometry(2010) Wynne, Colin Michael; Fenselau, Catherine; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)In the biodefense and medical diagnostic fields, MALDI mass spectrometry-based systems are used for rapid characterization of microorganisms generally by detecting and discriminating the highly abundant protein mass-to-charge peaks. It is important that these peaks eventually are identified, but few bacteria have publicly available, annotated genome or proteome from which this identification can be made. This dissertation proposes a method of top-down proteomics using a high-resolution, high mass accuracy analyzer coupled with bioinformatics tools to identify proteins from bacteria with unavailable genome sequences by comparison to protein sequences from closely-related microorganisms. Once these proteins are identified and a link between the unknown target bacteria and the annotated related bacteria is established, phylogenetic trees can be constructed to characterize where the target bacteria relates to other members of the same phylogenetic family. First, the top-down proteomic approach using an Orbitrap mass analyzer is tested using a well known, well studied single protein. After this is demonstrated to be successful, the approach is demonstrated on a bacterium without a sequenced genome, only matching proteins from other organisms which are thought to have 100% homology with the proteins studied by the top-down approach. Finally, the proposed method is changed slightly to be more inclusive and the proteins from two other bacteria without publicly available genomes or proteomes are matched to known proteins that differ in mass and may not be 100% homologous to the proteins of the studied bacteria. This more inclusive method is shown to also be successful in phylogenetically characterizing the bacteria lacking sequence information. Furthermore, some of the mass differences are localized to a small window of amino acids and proposed changes are made that increase confidence in identification while lowering the mass difference between the studied protein and the matched, homologous, known protein.Item MATING COSTS, MALE CHOICE DISPLACEMENT, AND THE EFFECTS ON HYBRIDIZATION AND SPECIATION IN THE HAWAIIAN CRICKET LAUPALA (SUBFAMILY:TRIGONIDIINAE)(2009) Jadin, Jenna; Shaw, Kerry L; Behavior, Ecology, Evolution and Systematics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Contact zones between two closely-related species provide unique laboratories for studying the processes of speciation. This is because, within these zones, species barriers will be reinforced and speciation will reach completion, or the barriers will break down, causing the two species to become one. Which of these two alternatives will occur depends on the degree of genetic differentiation and behavioral isolation between the species. If there is significant and non-combinable genetic variation between species, but behavioral isolation between the two incipient taxa is incomplete and allows hybrid offspring to be produced, these hybrid offspring will have lower fitness relative to parental types and selection should act directly to eliminate those offspring and indirectly against parents with broad mating preferences or traits. If however the genetic architecture is similar and behavioral isolation is incomplete, the populations would be expected to turn into a hybrid swarm and eventually become one species. Patterns of behavioral isolation and genetic variation in several Laupala species pairs suggest that contact zones between closely related species are marked by conflicting patterns of behavioral isolation and genetic differentiation. Evidence also suggests that the complex courtship system of Laupala may allow male choice to play an important role in sexual selection and speciation. Therefore I tested several hypotheses about the genetic differentiation, sexual selection, and behavioral isolation in a contact zone between the closely-related and morphologically indistinguishable L. tantalus and L. pacifica species pair. First, by using the mitochondrial COI gene and AFLPs as genetic markers, I demonstrated that there appears to be mitochondrial DNA introgression between sympatric, but not allopatric congeners, which suggests contemporary hybridization in the contact zone. Next, I found that males experience post-mating resource-limitation and show a significant tendency to invest less into a second mating, however, their investment is dependent upon female size. Finally, I found that there is apparent displacement of male choice, decreased variation in spermatophore production, and asymmetrical mating isolation within the contact zone. This evidence all suggests that there is increased behavioral isolation in this contact zone, which may be consistent with a hypothesis of speciation by reinforcement. However, this evidence also suggests that male costs may result in male choice conflicting with other isolating mechanisms. If so, this study may be another putative case of reinforcement, or it may be an entirely novel report of conflicting selection pressures within a hybrid zone. I suggest that further studies are needed to measure hybrid fitness as well as to evaluate relative male and female mating costs within the complex mating system of this rapidly-diversifying genus.Item Patterns of Diversification in Phytophagous Insects: Phylogeny and Evolution of Phytomyza Leaf-mining Flies (Diptera: Agromyzidae)(2008-01-22) Winkler, Isaac Scott; Mitter, Charles; Scheffer, Sonja J.; Entomology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Plant-feeding insects account for about one fourth of macroscopic biodiversity. This study aims to document factors contributing to this diversity by investigating phylogenetic relationships within a large radiation of herbivorous insects, Phytomyza leaf-mining flies (Diptera: Agromyzidae). After a brief introduction (Chapter 1), a general overview of phylogenetic patterns in phytophagous insects is presented, based on over 200 phytophagous insect phylogenies from the recent literature (Chapter 2). A few salient results include 1) host use conservatism at the family level predominates, with shifts occurring at about 5% of speciation events; 2) host shifts are a major contributor to speciation, occuring in about half of 145 speciation events tabulated; 3) insect-host associations mostly reflect colonization of already diversified host plant clades; and 4) variation in diversification rates is not yet well-documented for phytophagous insects, except at the broadest scale. Chapter 3 is a phylogenetic study of the genus Phytomyza sensu lato, using over 3,000 nucleotides of DNA sequence data from three genes. Results indicate that the genus Chromatomyia, considered by some as synonymous with Phytomyza, is in fact polyphyletic and nested within Phytomyza. Possible parallelism in a biological trait (internal pupation in leaf tissue) which is one of the defining traits of species in the former Chromatomyia is discussed. In addition, the internal classification of Phytomyza is assessed and revised insofar as the data permit. Divergence times for the Agromyzidae, and also for Phytomyza and related genera, were estimated using a molecular phylogeny calibrated by three agromyzid fossils (Chapter 4). Results suggest that the temperate Phytomyza group of genera originated in the relatively warm Eocene epoch. Ranunculaceae, a primitive plant family, is inferrred as the ancestral host for a clade including most Phytomyza species, but is probably secondary to feeding on more derived plant families ("asterid clade"). Ten clades were identified for comparison of diversification rates between Ranunculaceae- and asterid-feeding lineages, which showed that asterid-feeding clades exhibit higher rates of diversification. Phytomyza originated approximately at the early Oligocene global cooling event, but contrary to expectations, diversification significantly slowed during the Oligocene cool period, when suitable habitats for Phytomyza were presumably widespread.Item Diversity of conjugating green algae; phylogenetic studies of a species-rich eukaryotic lineage(2007-12-21) Hall, John David; Delwiche, Charles F; Cell Biology & Molecular Genetics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)This thesis used molecular phylogenetic techniques to investigate diversity in the conjugating green algae. The conjugating green algae are closely related to land plants and evolution within the group provides a good analogy of how evolution may have proceeded in the lineage that gave rise to land plants. I developed a dataset of the genes coxIII, psaA and rbcL with 109 taxa to determine phylogenetic relationships of the families and genera. I found that the order Zygnematales is not monophyletic and that Spirogyra was the first to branch. The order Desmidiales is monophyletic if one includes the genus Roya. The family Peniaceae is not monophyletic. The genera Cosmarium, Cylindrocystis, Mesotaenium, Penium, Spondylosium, Staurodesmus and in later studies Desmidium and Hyalotheca were found to be paraphyletic or polyphyletic. Investigation of cell division syndromes among filamentous Desmidiaceae revealed greater diversity than was previously reported. Notable among these discoveries is that Spondylosium pulchrum displays the Desmidium-type cell division, Spondylosium pulchellum the Cosmarium-type, and Spondylosium tetragonum the newly described Teilingia-type cell division. The relationship among the syndromes was inferred from phylogenetic analysis of the species that revealed a single lineage comprising filamentous and colonial species and multiple modes of cell division. This suggests that even the fundamental process of cell division can be highly modified. Results from this study also resulted in the taxonomic resurrection of the genus Didymoprium, as well as the creation of the new genus Isthmocatena and the combinations Didymoprium grevillei, Desmidium pulchrum, and Isthmocatena pulchella. Investigations of the Gonatozygaceae revealed unexpected diversity in Gonatozygon brebissonii and G. kinahani. Structural measurements were sufficient to distinguish among strains of Gonatozygon species except for Gonatozygon brebissonii. We have probably underestimated genetic and species diversity in this family. In contrast, the structurally distinct species Triploceras gracile, was found to be closely related to Micrasterias. This relationship was confirmed by sequencing and phylogenetic analysis of the nuclear encoded EF1α, EIF4 and TUA. The results of this study indicate that Triploceras is probably actually bilaterally symmetric, although it has been treated as a radially symmetric species.