Theses and Dissertations from UMD
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Item Multi-locus phylogenetic analysis of Amphipoda indicates a single origin of the pelagic suborder Hyperiidea(2019) Biancani, Leann M; Cummings, Michael P; Osborn, Karen J; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Hyperiidea is an exclusively pelagic suborder of amphipod crustaceans, exhibiting a wide array of unique adaptations to life in the dark, open expanse of the oceanic midwater. No common morphological synapomorphy unites approximately 350 described species. Instead, hyperiid amphipods are defined only by their pelagic existence. Hyperiidea exhibits many of the characteristics of an adaptive radiation and could represent a midwater example of this phenomenon. Previous morphological and molecular analyses have led to uncertainty in the shared ancestry of Hyperiidea. The evolutionary history of their diverse adaptations, as well as their relationship to other amphipods, remains unknown. Here we present results of a multi-locus phylogenetic analysis of publicly available amphipod sequences for three nuclear loci (18S, 28S, and H3) and two mitochondrial loci (COI and 16S) from over 300 amphipod genera, 40 of which are hyperiids. We recover strong support for a monophyletic Hyperiidea as well as reciprocally monophyletic hyperiid infraorders Physocephalata and Physosomata (with enigmatic genera Cystisoma and Paraphronima more closely related to Physosomata). We also identify several benthic, commensal amphipods representing potential sister groups for Hyperiidea. These taxa have not previously been considered close hyperiid relatives and include the genera Amphilochus, Colomastix, Anamixis, Paranamixis, and Leucothoe. Our results support the current definition of Hyperiidea and inform the phylogenetic placement of the suborder within Amphipoda.Item Research And Application Of Parallel Computing Algorithms For Statistical Phylogenetic Inference(2017) Ayres, Daniel L.; Cummings, Michael P; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Estimating the evolutionary history of organisms, phylogenetic inference, is a critical step in many analyses involving biological sequence data such as DNA. The likelihood calculations at the heart of the most effective methods for statistical phylogenetic analyses are extremely computationally intensive, and hence these analyses become a bottleneck in many studies. Recent progress in computer hardware, specifically the increase in pervasiveness of highly parallel, many-core processors has created opportunities for new approaches to computationally intensive methods, such as those in phylogenetic inference. We have developed an open source library, BEAGLE, which uses parallel computing methods to greatly accelerate statistical phylogenetic inference, for both maximum likelihood and Bayesian approaches. BEAGLE defines a uniform application programming interface and includes a collection of efficient implementations that use NVIDIA CUDA, OpenCL, and C++ threading frameworks for evaluating likelihoods under a wide variety of evolutionary models, on GPUs as well as on multi-core CPUs. BEAGLE employs a number of different parallelization techniques for phylogenetic inference, at different granularity levels and for distinct processor architectures. On CUDA and OpenCL devices, the library enables concurrent computation of site likelihoods, data subsets, and independent subtrees. The general design features of the library also provide a model for software development using parallel computing frameworks that is applicable to other domains. BEAGLE has been integrated with some of the leading programs in the field, such as MrBayes and BEAST, and is used in a diverse range of evolutionary studies, including those of disease causing viruses. The library can provide significant performance gains, with the exact increase in performance depending on the specific properties of the data set, evolutionary model, and hardware. In general, nucleotide analyses are accelerated on the order of 10-fold and codon analyses on the order of 100-fold.Item Development and the Early Animal Fossil Record: Evolution and Phylogenetic Applications(2016) Tweedt, Sarah Maureen; Delwiche, Charles F; Erwin, Douglas H; Cell Biology & Molecular Genetics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Although evolutionary developmental biology and paleontology are linked by the study of morphology, the application of development to paleontological questions has only recently become more prominent. The growth of a robust developmental genetic framework for studying the origin and evolution of morphological features, however, holds great promise for understanding ancient animal life. As paleontology provides the historical record as well as the temporal and environmental context of past morphological evolution, uniting knowledge of developmental genetic systems with this historical record will form a key synthetic approach to understanding the early evolution of developmental processes. Ultimately unraveling the sequence of ancient animal developmental evolution will require combining analysis of comparative developmental data, critical assessment of fossil morphology within a developmental framework, and the targeted exploration of specific geologic periods to fill in the missing record of key times in animal developmental evolution. This study addresses each of these three approaches. First, I provide a new compilation and evaluation of recent comparative and experimental developmental biology data to review the nature of developmental ‘toolkits’ at the origin of the most basal animal clades. I reconstruct early animal developmental capacities and integrate these data within a temporal framework to better understand the context of earliest animal development. Second, I assess longstanding evolutionary hypotheses about the origin of the panarthropod clade and the phylogenetic position of Cambrian ‘lobopod’ fossils by examining signal present within current morphological datasets. I apply new methods to fossil panarthropod phylogeny estimation and suggest strategies for developmentally-informed phylogenetic coding of morphological data. Third, I present the discovery of the oldest spicule-bearing fossil sponges in the rock record, which co-occur in latest Ediacaran strata with classic enigmatic Ediacaran fauna. I provide a formal systematic description of fossil material from localities in both Nevada and southern Namibia. The combined approaches presented herein are a first step towards a deeper integration of developmental principles in the study and discovery of ancient animal life, and contribute to our understanding of the evolution of ancient animal developmental processes.Item Diversity of Phytophthora Species in Costa Rica's Tropical Forest(2015) Wallace, Sydney F.; Balci, Yilmaz; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The fungus-like organism Phytophthora includes more than 130 species, most of which are destructive plant pathogens. Information about the occurrence and diversity of Phytophthora species in forest and protected areas are largely unknown. The purpose of this study was to fill in the scientific gap in species biodiversity by conducting a survey in tropical forest ecosystems. The survey was conducted at 10 sites across Costa Rica. Leaves with lesions attached to live plants (LP), fallen from tree canopies (LF), submerged in forest streams (LS) and soil was sampled. Isolate identification was based on a multi-locus (4 mitochondrial and 4 nuclear) phylogeny, and examination of morphological features. In total 258 isolates were characterized into 21 species: eight known and 13 novel species. Phylogenetically, species discovered were placed in seven different clades and clade 9 included the most number of species. Species were more common in transitional forests. The number of unknown species discovered suggests that tropical forests are a “hotspot “for Phytophthora diversity.Item Salmonella Newport: Genetic Diversity and Phylogenetic Analysis(2014) Cao, Guojie; Meng, Jianghong; Food Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Salmonella enterica subsp. enterica causes over 99% of human salmonellosis. Salmonella Newport has ranked in the top three Salmonella serotypes associated with foodborne outbreaks in the United States. S. Newport is ubiquitous in the environment. S. Newport consisted of three lineages. It is necessary to investigate and determine the evolution relationship between S. Newport and to identify the genetic diversities of this emerging foodborne pathogen. Whole genome sequencing has played important roles in food safety and public health providing the most accurate information for phylogenetic analysis and more comprehensive picture for comparative genomics. Total 26 S. Newport strains from diverse sources and geographic locations were selected and conducted pyrosequencing to obtain 16-24 × coverage of draft genomes. More than 140,000 SNPs were identified to construct parsimony tree. Phylogenetic analysis indicated that S. Newport was divided into two major groups, lineages II and III. Lineage II was further grouped into three subgroups, IIA, IIB, and IIC. Lineage III strains showed close relationship to each other. Moreover, lineages II and III displayed divergent distance. Comparative genomics identified the region around mutS as potential biomarkers to distinguish these two lineages, including ste fimbrial operon, transposase, and cas genes. Salmonella pathogenicity islands (SPIs) play essential roles in virulence, metabolism, and host adaptations in Salmonella. Due to the significant roles of SPI-5 and SPI-6, the genetic diversities in these two gene clusters may contribute to the various activities in different strains. Both indels and mutations were identified in SPI-5, including two large insertions with over 40 kb encoding phage genes and 146 single nucleotide polymorphisms (SNPs). The phylogenetic tree of SPI-5 genes showed that lineages II and III contained divergent distances. SPI-6 was not identified in Asian strains in subgroup IIA, indicating the potential differences in virulence and host adaptations. S. Newport multidrug resistant strains have been clinical important issue in the United States. Plasmids contributed to the MDR phenotypes. The common genetic characterizations of these strains could be help to understand the prevalence of MDR strains. In the current study, all MDR strains belonging to one node in IIC and contained unfunctional CRISPR systems.Item MOLECULAR PHYLOGENY AND TAXONOMIC REVISION OF FUNGI IN THE GENUS Thelonectria AND RELATED SPECIES WITH Cylindrocarpon-LIKE ANAMORPHS(2014) Salgado-Salazar, Catalina; Chaverri, Priscila; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The genus Thelonectria and related species with Cylindrocarpon-like anamorphs are a group of perithecial ascomycetes in the family Nectriaceae that occur as saprobes and in few cases as pathogens of hardwood trees, shrubs or other plant substrates. Despite of being a key component of forest ecosystems around the world, species relationships and distribution are largely unknown. The objectives of this study were to: 1) infer species level phylogenetic relationships of the genus Thelonectria and related species with Cylindrocarpon-like anamorphs with uncertain classification, testing monophyly of each one of the groups studied; 2) delimit taxa, establishing taxon circumscriptions and providing brief descriptions; 3) resolve nomenclatural issues by identifying redundantly used names and synonyms; 4) provide identification tools, specifically, diagnostic keys and molecular data that can be used further as molecular barcodes; 4) provide distribution data and to take the first steps into the identification of speciation patterns observed in these fungi. To achieve these goals, herbarium materials, as well as freshly collected material obtained from the field or from fungal repositories were compared using phylogenetic analyses of multiple loci, morphology and geographic distribution. This research resulted in the narrower circumscription of the genus Thelonectria, not to contain one of the most common species in the group, T. jungneri. According to the results of the phylogenetic analyses it was found T. jungneri is a segregating clade that needs to be recognized as a different genus. For the genus Thelonectria, a total of 31 new species were described, and three new genera, closely related to Thelonectria were created to accommodate the diversity of other species with Cylindrocarpon-like anamorphs: Cinnamonectria gen nov. with C. cinnamomea as type taxon, Macronectria gen. nov. with M. jungneri as type taxon, and Tumenectria gen. nov. with T. laetidisca as type taxon. Species in this group of fungi present extensive morphological conservationism, representing a challenge for species identification without the use of molecular techniques, however offering a great opportunity to explore mechanisms of speciation and evolutionary diversification.Item Molecular phylogenetics, biodiversity and life history evolution of Yponomeutoidea (Lepidoptera: Ditrysia), with a catalog and an overview of the lepidopteran fossils(2013) Sohn, Jae-Cheon; Mitter, Charles; Entomology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Yponomeutoidea, one of the earliest-branching superfamilies of advanced (ditrysian) Lepidoptera, comprise about 1,800 species worldwide, including notable pests and models of insect-plant interaction. Yponomeutoids were one of the earliest lepidopteran clades to evolve external feeding and to colonize extensively herbaceous angiosperms. Despite the group's economic importance, and its value for tracing early lepidopteran evolution, the biodiversity and phylogeny of Yponomeutoidea have been relatively little studied. Even the monophyly and composition of the superfamily have been in doubt. In this dissertation, the most detailed molecular phylogeny to date for Yponomeutoidea is presented (Chapter 1). The resulting phylogeny is compared to previous morphological evidence, and its implications for evolutionary trends in yponomeutoid host association and biogeography are explored. As a prerequisite to divergence dating in the Yponomeutoidea, which is necessarily based on outgroup fossils as none are known for yponomeutoids, a general summary and overview of the lepidopteran fossil record (Chapter 2) is provided, based a recent, comprehensive catalog of known fossils. For chapter 2, all known lepidopteran fossils have been catalogued with annotations of their preservation, specimen deposition, fossil localities and ages (Chapter 3). As a contribution toward better characterization of yponomeutoid biodiversity, taxonomic reviews are provided for the New World genera Eucalantica and Atemelia (Chapter 4). The molecular phylogeny estimate (Chapter 1) is based on 8-27 protein coding nuclear genes sequenced in 86 Yponomeutoidea and 53 outgroups. Monophyly for Yponomeutoidea is corroborated. Results from different analyses are highly congruent and relationships within Yponomeutoidea are well supported overall. There is strong support overall for monophyly of families (or major parts thereof) previously recognized on morphological grounds, including Yponomeutidae, Ypsolophidae, Plutellidae, Glyphipterigidae, Argyresthiidae, Attevidae, Praydidae, Heliodinidae, and Bedelliidae. The formerly yponomeutid subfamily Scythropiinae are elevated to family rank (Scythropiidae stat. rev.). Host plant family associations of yponomeutoid subfamilies and families are non-random, but show no trends suggesting parallel phylogenesis, and are less conserved than is mode of feeding (e.g. internal versus external). My analyses reveal previously unrecognized tropical clades in several families, and suggest that previous characterization of yponomeutoids as predominantly Palearctic/ Holarctic was based on insufficient sampling.Item Kinetic and Structual Characterization of Glutamine-Dependent NAD Synthetases(2010) Resto, Melissa; Gerratana, Barbara; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Multifunctional enzymes catalyzing successive reactions have evolved several mechanisms for the transport of intermediates between active sites. One mechanism, substrate channeling, allows the transport of the intermediate without releasing it into the solvent. Members of the glutamine amidotransferase (GAT) family often utilize substrate channeling for the transport of intermediates. GAT enzymes hydrolyze glutamine to ammonia, which is transported to an acceptor domain preventing wasteful hydrolysis of glutamine and increasing the efficiency of the reaction. Many GAT enzymes utilize molecular tunnels to shuttle ammonia between active sites. Often GAT enzymes synchronize the active site through conformational changes that occur during catalysis. Glutamine-dependent NAD synthetases are GAT enzymes and catalyze the last step in the biosynthesis of NAD, utilizing nicotinic acid adenine dinucleotide (NaAD), ATP and glutamine. Steady-state kinetic characterizations and stoichiometric analysis of NAD synthetase from Mycobacterium tuberculosis (NAD synthetaseTB) revealed a substrate channeling mechanism for ammonia transport and tight coordination of the active sites resulting in an enzyme that is highly efficient in the use of glutamine. The crystal structure of NAD synthetaseTB has revealed a 40 Å tunnel that connects the active sites and is postulated to play a role in the synchronized activities. Several regions of the enzyme were identified that may be important for regulation, such as the YRE loop which contacts the glutamine active site and key regions of the tunnel. Mutations of tunnel residues, such as D656A, show that interruption of important interactions can result in compromise in transfer of ammonia or active site communication. Phylogenetic analysis revealed that glutamine-dependent NAD synthetases have different levels of regulation. Three groups of enzymes were identified represented by NAD synthetase from M. tuberculosis, S. cerevisiae (NAD synthetaseYeast) and Thermotoga maritima (NAD synthetaseTM). Steady-state kinetic characterizations and stoichiometric analysis of NAD synthetaseTM has revealed a compromised coordination of the active sites compared to the highly synchronized NAD synthetaseTB and the moderate synchronization of NAD synthetaseYeast. Sequence alignment of these groups has allowed identification of residues that line the tunnel that may be responsible for the differences observed in active site coordination and are, therefore, important for active site communication.