Life Sciences Commons^™

Phylogenetic Analysis Of The Nearctic Blepharicera Macquart (Diptera: Blephariceridae) With An Emphasis On The Eastern Blepharicera Tenuipes Group Hogue, Amanda Jane Jacobson

Doctoral Dissertations

The eastern Nearctic fauna of Blepharicera Macquart (Diptera: Blephariceridae) is revised to include twenty-three species, six of which are new to science. Descriptions of the larvae, pupae, and adults of B. amnicula n. sp., B. conifera n. sp., B. crista n. sp., B. enoristera n. sp., B. hillabee n. sp., and B. opistera n. sp. are presented. Keys to instar IV larvae, pupae, and adults of all eastern Blepharicera (except B. caudata Courtney) are provided. Phylogenetic studies were conducted to determine the relationships between eastern and western Nearctic Blepharicera and among species within these groups. Larvae, pupae, and adults were …

Micrornas Reveal The Interrelationships Of Hagfish, Lampreys, And Gnathostomes And The Nature Of The Ancestral Vertebrate, Alysha M. Heimberg, Richard Cowper-Sal{Middle Dot}Lari, Marie Semon, Philip C. J. Donoghue, Kevin J. Peterson

Dartmouth Scholarship

Hagfish and lampreys are the only living representatives of the jawless vertebrates (agnathans), and compared with jawed vertebrates (gnathostomes), they provide insight into the embryology, genomics, and body plan of the ancestral vertebrate. However, this insight has been obscured by controversy over their interrelationships. Morphological cladistic analyses have identified lampreys and gnathostomes as closest relatives, whereas molecular phylogenetic studies recover a monophyletic Cyclostomata (hagfish and lampreys as closest relatives). Here, we show through deep sequencing of small RNA libraries, coupled with genomic surveys, that Cyclostomata is monophyletic: hagfish and lampreys share 4 unique microRNA families, 15 unique paralogues of more …

Retention And Loss Of Rna Interference Pathways In Trypanosomatid Protozoans, Lon-Fye Lye, Katherine Owens, Huafang Shi, Silvane M. F. Murta, Ana Carolina Vieira, Salvatore J. Turco, Christian Tschudi, Elisabetta Ullu, Stephen M. Beverley

Molecular and Cellular Biochemistry Faculty Publications

RNA interference (RNAi) pathways are widespread in metaozoans but the genes required show variable occurrence or activity in eukaryotic microbes, including many pathogens. While some Leishmania lack RNAi activity and Argonaute or Dicer genes, we show that Leishmania braziliensis and other species within the Leishmania subgenus Viannia elaborate active RNAi machinery. Strong attenuation of expression from a variety of reporter and endogenous genes was seen. As expected, RNAi knockdowns of the sole Argonaute gene implicated this protein in RNAi. The potential for functional genetics was established by testing RNAi knockdown lines lacking the paraflagellar rod, a key component of the …

Utilization Of Phylogenetic Systematics, Molecular Evolution, And Comparative Transcriptomics To Address Aspects Of Nematode And Bacterial Evolution, Scott M. Peat

Theses and Dissertations

Both insect parasitic/entomopathogenic nematodes and plant parasitic nematodes are of great economic importance. Insect parasitic/entomopathogenic nematodes provide an environmentally safe and effective method to control numerous insect pests worldwide. Alternatively, plant parasitic nematodes cause billions of dollars in crop loss worldwide. Because of these impacts, it is important to understand how these nematodes evolve, and, in the case of entomopathogenic nematodes, how their bacterial symbionts evolve. This dissertation contains six chapters. Chapter one is a review of DNA markers and their use in the phylogenetic systematics of entomopathogenic and insect-parasitic nematodes as well as a review of phylogenetic, co-phylogenetic, and …

Comparative Mitogenomics Of Braconidae (Insecta: Hymenoptera) And The Phylogenetic Utility Of Mitochondrial Genomes With Special Reference To Holometabolous Insects, Shu-Jun Wei, Min Shi, Michael J. Sharkey, Cornelis Van Achterberg, Xue-Xin Chen

Entomology Faculty Publications

BACKGROUND: Animal mitochondrial genomes are potential models for molecular evolution and markers for phylogenetic and population studies. Previous research has shown interesting features in hymenopteran mitochondrial genomes. Here, we conducted a comparative study of mitochondrial genomes of the family Braconidae, one of the largest families of Hymenoptera, and assessed the utility of mitochondrial genomic data for phylogenetic inference at three different hierarchical levels, i.e., Braconidae, Hymenoptera, and Holometabola.

RESULTS: Seven mitochondrial genomes from seven subfamilies of Braconidae were sequenced. Three of the four sequenced A+T-rich regions are shown to be inverted. Furthermore, all species showed reversal of strand asymmetry, suggesting …

Behavioural Display Systems Across Nine Anolis Lizard Species: Sexual Dimorphisms In Structure And Function, Michele A. Johnson, J. Wade

Biology Faculty Research

Relationships between structure and function are a primary focus in biology, yet they are most often considered within individual species. Sexually dimorphic communication behaviours and the morphology of associated structures can vary widely, even among closely related species, and these traits provide an ideal opportunity to investigate the evolution of structure-function patterns. Using nine Anolis lizard species, we addressed a series of questions regarding sex differences in and the evolution of relationships between extension of the throat fan (dewlap) and morphology of the muscles and cartilage controlling it. The main results indicated that within species, males displayed the dewlap more …

The Challenge Of A Siberian Bluegrass (Poa) Phylogeny, Marina V. Olonova

Aliso: A Journal of Systematic and Floristic Botany

In Siberia, the bluegrass genus (Poa) comprises 43 species and 61 subspecies in 12 sections. Diverse modes of speciation, including polyploidy and hybridization, have led to reticulate evolution and adaptive radiation. Cladistic methods that ignore hybridization and reticulate evolution may not be appropriate for morphological data. The number of morphological characters suitable for bluegrass analysis is limited, a majority does not have clear adaptive significance, and the character states cannot be readily polarized, rendering phylogenetic reconstruction very difficult in this group. Other methods of estimating phylogenetic relationships should be used to test hypotheses about relationships and hybridization. Biochemical …

Identification And Phylogenetic Characterization Of Select Species Of Buprestidae (Coleoptera) And Sesiidae (Lepidoptera) Wood Boring Insect Families Occuring Across The Southeastern United States., Jason A. Hansen

Doctoral Dissertations

A brief overview of the importance of wood boring insects is provided. Background on the two wood boring insect families Buprestidae (Coleoptera) and Sesiidae (Lepidoptera) is given. Keys and checklists to Tennessee’s buprestid fauna as presently known are furnished. Photomicrographs depicting characteristics separating Tennessee buprestid taxa to the level of species are provided for select couplets to aid those unfamiliar with buprestid morphology and terminology. Distribution and flight data of many species within the state are also featured. Results of a phylogenetic analysis of the Chrysobothris femorata (Olivier) species complex is presented based on the nuclear gene arginine kinase and …

Diversity Of Bacteria And Glycosyl Hydrolase Family 48 Genes In Cellulolytic Consortia Enriched From Thermophilic Biocompost, Javier A. Izquierdo, Maria V. Sizova, Lee R. Lynd

Dartmouth Scholarship

The enrichment from nature of novel microbial communities with high cellulolytic activity is useful in the identification of novel organisms and novel functions that enhance the fundamental understanding of microbial cellulose degradation. In this work we identify predominant organisms in three cellulolytic enrichment cultures with thermophilic compost as an inoculum. Community structure based on 16S rRNA gene clone libraries featured extensive representation of clostridia from cluster III, with one cluster sharing as little as 73% sequence similarity with the closest known relative. In all, 14 new GHF48 gene sequences were added to the known diversity of 35 genes from cultured …

An Examination Of The Dna Content, Taxonomy And Phylogeny Of Penstemon (Plantaginaceae), Shaun R. Broderick

Theses and Dissertations

Penstemon is the largest genus in North America with more than 270 reported species. However, little is known about the genome size of this genus and how this information may be useful in selecting species in developing hybrids for landscape use. Using flow cytometry, we estimated the genome size of approximately 40% of the genus (117 specimens from 104 different species.) Genome sizes for the putative diploids ranged from 2C = 0.94 – 1.89 pg (1C = 462 – 924 Mbp) and the putative polyploids ranged from 2.57 – 6.54 pg (1C = 1,257 – 3,156 Mbp). Chromosome counts were …

Distinct Evolutionary Histories Of The Dna-A And Dna-B Components Of Bipartite Begomoviruses, Rob W. Briddon, Basavaprabhu L. Patil, Basavaraj Bagewadi, Muhammad Shah Nawaz-Ul-Rehman, Claude M. Fauquet

Plant Pathology Faculty Publications

BACKGROUND: Viruses of the genus Begomovirus (family Geminiviridae) have genomes consisting of either one or two genomic components. The component of bipartite begomoviruses known as DNA-A is homologous to the genomes of all geminiviruses and encodes proteins required for replication, control of gene expression, overcoming host defenses, encapsidation and insect transmission. The second component, referred to as DNA-B, encodes two proteins with functions in intra- and intercellular movement in host plants. The origin of the DNA-B component remains unclear. The study described here was initiated to investigate the relationship between the DNA-A and DNA-B components of bipartite begomoviruses with a …

Mitochondrial Phylogenomics Of The Bivalvia (Mollusca): Searching For The Origin And Mitogenomic Correlates Of Doubly Uniparental Inheritance Of Mtdna, Hélène Doucet-Beaupré, Sophie Breton, Eric G. Chapman, Pierre U. Blier, Arthur E. Bogan, Donald T. Stewart, Walter R. Hoeh

Entomology Faculty Publications

BACKGROUND: Doubly uniparental inheritance (DUI) is an atypical system of animal mtDNA inheritance found only in some bivalves. Under DUI, maternally (F genome) and paternally (M genome) transmitted mtDNAs yield two distinct gender-associated mtDNA lineages. The oldest distinct M and F genomes are found in freshwater mussels (order Unionoida). Comparative analyses of unionoid mitochondrial genomes and a robust phylogenetic framework are necessary to elucidate the origin, function and molecular evolutionary consequences of DUI. Herein, F and M genomes from three unionoid species, Venustaconcha ellipsiformis, Pyganodon grandis and Quadrula quadrula have been sequenced. Comparative genomic analyses were carried out on these …

Convergent Evolution Of Sequestrate Forms In Amanita Under Mediterranean Climate Conditions, Alfredo Justo, Ingo Morgenstern, Heather E. Hallen-Adams, David S. Hibbett

Department of Food Science and Technology: Faculty Publications

The systematic position of secotioid (Torrendia) and gasteroid (Amarrendia) forms within the agaricoid Amanita lineage (Agaricales, Basidiomycota) was studied with molecular (nLSU, ITS) data. Secotioid and gasteroid forms occur in four independent clades nested within agaricoid forms. One clade corresponds to the secotioid T. pulchella from southern Europe and northern Africa. The others correspond to Torrendia and Amarrendia species from Australia. Mediterranean climatic conditions are postulated as a force driving the convergent evolution of these secotioid and at least one of the gasteroid forms in geographically distant areas. Species formerly placed in Torrendia and Amarrendia are …

Mechanisms Of Apoptosis In Crustacea: What Conditions Induce Versus Suppress Cell Death?, Michael A. Menze, Grady Fortner, Suman Nag, Steven C. Hand

Michael Menze

Arthropoda is the largest of all animal phyla and includes about 90% of extant species. Our knowledge about regulation of apoptosis in this phylum is largely based on findings for the fruit fly Drosophila melanogaster. Recent work with crustaceans shows that apoptotic proteins, and presumably mechanisms of cell death regulation, are more diverse in arthropods than appreciated based solely on the excellent work with fruit flies. Crustacean homologs exist for many major proteins in the apoptotic networks of mammals and D. melanogaster, but integration of these proteins into the physiology and pathophysiology of crustaceans is far from complete. Whether apoptosis …

Preliminary Phylogeny Of The Thrips Parasitoids Of Turkey Based On Some Morphological Scales And 28s D2 Rdna, With Description Of A New Species, Oguzhan Doğanlar, Mi̇kdat Doğanlar, Anne Frary

Turkish Journal of Zoology

Species of the Ceranisus thrips-attacking genus are difficult to distinguish morphologically. The phylogenetic relationships within the Ceranisus species were explored using nucleotide sequences of the 28S D2 expansion region of the rDNA gene. Bayesian, maximum likelihood, and parsimony inference methods were employed to construct the phylogenetic relationships. Principal component analysis on the Turkish species of Ceranisus, namely antalyacus, menes, bozovaensis, hirsutus, planitianus (a new record for Turkey), pacuvius, and a new species, provided supporting evidence. All known data concerning hosts and geographical distribution are presented. A new species, C. onuri O. Doganlar, sp.n., was described from Turkey.

Mechanisms Of Apoptosis In Crustacea: What Conditions Induce Versus Suppress Cell Death?, Michael A. Menze, Grady Fortner, Suman Nag, Steven C. Hand

Faculty Research & Creative Activity

Arthropoda is the largest of all animal phyla and includes about 90% of extant species. Our knowledge about regulation of apoptosis in this phylum is largely based on findings for the fruit fly Drosophila melanogaster. Recent work with crustaceans shows that apoptotic proteins, and presumably mechanisms of cell death regulation, are more diverse in arthropods than appreciated based solely on the excellent work with fruit flies. Crustacean homologs exist for many major proteins in the apoptotic networks of mammals and D. melanogaster, but integration of these proteins into the physiology and pathophysiology of crustaceans is far from complete. Whether apoptosis …

Systematics Of The Genus Ptychadena Boulenger, 1917 (Anura: Ptychadenidae) From Democratic Republic Of The Congo, Katrina Marie Weber

Open Access Theses & Dissertations

This thesis increases the scope of previous phylogenetic analyses that revealed high levels of genetic differentiation within the anuran genus Ptychadena. Herein, I increase sampling of Central African populations of Ptychadena by over six times to examine their relationships to other African populations and to search for cryptic species. This study represents the most comprehensive molecular phylogeny of Ptychadena to date. A total of three mitochondrial (12S, 16S, and cyt b) and two nuclear (RAG1 and rhodopsin) genes were sequenced for 67 specimens of Ptychadena. Maximum parsimony, maximum likelihood, and Bayesian analyses were conducted. These analyses revealed …

Internal Transcribed Spacer (Its) Polymorphism In The Wild Primula (Primulaceae) Taxa Of Turkey, Mutlu Gültepe, Uğur Uzuner, Kami̇l Coşkunçelebi̇, Ali̇ Osman Beldüz, Sali̇h Terzi̇oğlu

Turkish Journal of Botany

Twenty-three populations belonging to 10 wild Primula L. (Primulaceae) taxa of Turkey, some of which are morphologically quite similar, were investigated based on nrDNA ITS regions. The plant materials were collected from different geographical areas of Anatolia in vegetation periods of 2005 and 2006. Total genomic DNAs were isolated from the healthy leaves of each population. The entire ITS regions of the populations were amplified by universal primers with the aid of a polymerase chain reaction (PCR), and then the PCR products were sequenced. Neighbour-Joining (NJ) and Maximum Parsimony (MP) trees were constructed in order to identify the relationships among …

Morphological, Karyological And Phylogenetic Evaluation Of Cyclotrichium: A Piece In The Tribe Mentheae Puzzle, Tuncay Di̇rmenci̇, Ekrem Dündar, Görkem Deni̇z, Turan Arabaci, Esra Marti̇n, Zi̇ba Jamzad

Turkish Journal of Botany

The genus Cyclotrichium, a member of the tribe Mentheae subtribe Menthinae (Lamiaceae, Nepetoideae), was analysed with respect to morphological revision, phylogenetic analysis, and cytogenetic properties. All species of the genus were investigated for morphological characters and ITS (internal transcribed spacers) of nrDNA sequence comparison (except C. hausknechtii for ITS). Six members of the genus were also analysed for chromosome numbers. The combined results strongly suggested that Cyclotrichium is a separate genus in Nepetoideae with distinct morphological, phylogenetic, and cytogenetic characteristics. For intrageneric phylogeny of Cyclotrichium, 3 groups were recognised: 1. C. niveum; 2. C. origanifolium; and 3. the remaining 6 …

Phylogenetic Relationships Of Elymus L. And Related Genera (Poaceae) Based On The Nuclear Ribosomal Internal Transcribed Spacer Sequences, Ayten Di̇zkirici, Zeki̇ Kaya, Evren Cabi̇, Musa Doğan

Turkish Journal of Botany

To help in the clarification of the taxonomic status of Elymus L. and related genera Agropyron Gaertn., Leymus Hochst., Hordelymus (Jess.) Harz, and Brachypodium P.Beauv., the sequence diversity in the internal transcribed spacer (ITS) region of nuclear ribosomal DNA was studied. ITS data of 64 Triticeae accessions including 40 Elymus, 12 Agropyron, 7 Leymus, and 4 Hordelymus, and 1 Brachypodium as an out-group were analysed. The molecular diversity statistics indicated that the most diverse genus is Elymus among the studied genera. The constructed phylogenetic tree by the maximum parsimony method revealed that one specimen of Elymus, E. pycnanthus (Godr.) Melderis, …

Mechanisms Of Apoptosis In Crustacea : What Conditions Induce Versus Suppress Cell Death?, Michael Menze, Grady Fortner, Suman Nag, Steven Hand

Faculty Scholarship

Arthropoda is the largest of all animal phyla and includes about 90% of extant species. Our knowledge about regulation of apoptosis in this phylum is largely based on findings for the fruit fly Drosophila melanogaster. Recent work with crustaceans shows that apoptotic proteins, and presumably mechanisms of cell death regulation, are more diverse in arthropods than appreciated based solely on the excellent work with fruit flies. Crustacean homologs exist for many major proteins in the apoptotic networks of mammals and D. melanogaster, but integration of these proteins into the physiology and pathophysiology of crustaceans is far from complete. Whether apoptosis …