Life Sciences Commons^™

The Evolution Of Host Specificity In The Vertebrate Gut Symbiont Lactobacillus Reuteri, Steven Frese

Department of Food Science and Technology: Dissertations, Theses, and Student Research

The vertebrate gut is home to one of the densest populations of life on Earth. This microbial community has a profound effect on host health, nutrition, development, behavior, and evolution. However, very little is known about how these microbes have evolved with their vertebrate hosts, how and whether they select hosts or how they remain associated with their hosts. Recent work identified Lactobacillus reuteri as an organism that is composed of host-specific sub-populations, each population associated with a different host animal. Representatives from each host-associated population were tested for their ability to colonize gnotobiotic mice, which only rodent strains could …

Sharing And Re-Use Of Phylogenetic Trees (And Associated Data) To Facilitate Synthesis, Arlin Stoltzfus, Brian C. O'Meara, Jamie Whitacre, Ross Mounce, Emily L. Gillespie, Sudhir Kumar, Dan F. Rosauer, Rutger A. Vos

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

Recently, various evolution-related journals adopted policies to encourage or require archiving of phylogenetic trees and associated data. Such attention to practices that promote sharing of data reflects rapidly improving information technology, and rapidly expanding potential to use this technology to aggregate and link data from previously published research. Nevertheless, little is known about current practices, or best practices, for publishing trees and associated data so as to promote re-use.

Findings

Here we summarize results of an ongoing analysis of current practices for archiving phylogenetic trees and associated data, current practices of re-use, and current barriers to re-use. We find …

Comparative Mitogenomic Analysis Of Damsel Bugs Representing Three Tribes In The Family Nabidae (Insecta: Hemiptera), Hu Li, Haiyu Liu, Fan Song, Aimin Shi, Xuguo Zhou, Wanzhi Cai

Entomology Faculty Publications

BACKGROUND: Nabidae, a family of predatory heteropterans, includes two subfamilies and five tribes. We previously reported the complete mitogenome of Alloeorhynchus bakeri, a representative of the tribe Prostemmatini in the subfamily Prostemmatinae. To gain a better understanding of architecture and evolution of mitogenome in Nabidae, mitogenomes of five species representing two tribes (Gorpini and Nabini) in the subfamily Nabinae were sequenced, and a comparative mitogenomic analysis of three nabid tribes in two subfamilies was carried out.

METHODOLOGY/PRINCIPAL FINDINGS: Nabid mitogenomes share a similar nucleotide composition and base bias, except for the control region, where differences are observed at the …

Aspm And The Evolution Of Cerebral Cortical Size In A Community Of New World Monkeys, Fernando A. Villanea, George H. Perry, Gustavo A. Gutiérrez-Espeleta, Nathaniel J. Dominy

Dartmouth Scholarship

The ASPM (abnormal spindle-like microcephaly associated) gene has been proposed as a major determinant of cerebral cortical size among primates, including humans. Yet the specific functions of ASPM and its connection to human intelligence remain controversial. This debate is limited in part by a taxonomic focus on Old World monkeys and apes. Here we expand the comparative context of ASPM sequence analyses with a study of New World monkeys, a radiation of primates in which enlarged brain size has evolved in parallel in spider monkeys (genus Ateles) and capuchins (genus Cebus). The primate community of Costa Rica is perhaps a …

Sequencing And Analysis Of The Gastrula Transcriptome Of The Brittle Star Ophiocoma Wendtii, Roy Vaughn, Nancy Garnhart, James R. Garey, W. Kelley Thomas, Brian T. Livingston

Hubbard Center for Genome Studies (HCGS)

Background

The gastrula stage represents the point in development at which the three primary germ layers diverge. At this point the gene regulatory networks that specify the germ layers are established and the genes that define the differentiated states of the tissues have begun to be activated. These networks have been well-characterized in sea urchins, but not in other echinoderms. Embryos of the brittle star Ophiocoma wendtii share a number of developmental features with sea urchin embryos, including the ingression of mesenchyme cells that give rise to an embryonic skeleton. Notable differences are that no micromeres are formed during cleavage …

A Tale Of Two Haplotypes: The Eda2r/Ar Intergenic Region Is The Most Divergent Genomic Segment Between Africans And East Asians In The Human Genome, Amanda M. Casto, Brenna M. Henn, Jeffery M. Kidd, Carlos D. Bustamante, Marcus W. Feldman

Human Biology Open Access Pre-Prints

Single nucleotide polymorphisms (SNPs) with large allele frequency differences between human populations are relatively rare. The longest run of SNPs with an allele frequency difference of one between the Yoruba of Nigeria and the Han Chinese is found on the long arm of the X chromosome in the intergenic region separating the EDA2R and AR genes. It has been proposed that the unusual allele frequency distributions of these SNPs are the result of a selective sweep affecting African populations that occurred after the Out-of-Africa migration. To investigate the evolutionary history of the EDA2R/AR intergenic region, we characterized the haplotype structure …

Evolution And Sustainability Of The Helping Hands Volunteer Program: Consumer Recovery And Mental Health Comparisoins Six Years On, Frank P. Deane, Retta Andresen

Frank Deane

The Helping Hands program commenced in 1999 and partners volunteers with mental health consumers for support and to increase social contact, recreational and friendship opportunities. The aim of the present study is to describe the evolution and sustainability of the program over the first 6 years. A description of consumers accessing the program using recovery-oriented measures and traditional measures of behavioural functioning is also provided. Service data was collected on the development of the program, service utilisation, volunteer participation and funding patterns. Cross-sectional measures of recovery and baseline and follow-up Health of the Nation Outcome Scales (HoNOS) were collected on …

Discovery Of Novel Dsrna Viral Sequences By In Silico Cloning And Implications For Viral Diversity, Host Range And Evolution, Huiquan Liu, Yanping Fu, Jiatao Xie, Jiasen Cheng, Said A. Ghabrial, Guoqing Li, Xianhong Yi, Daohong Jiang

Plant Pathology Faculty Publications

Genome sequence of viruses can contribute greatly to the study of viral evolution, diversity and the interaction between viruses and hosts. Traditional molecular cloning methods for obtaining RNA viral genomes are time-consuming and often difficult because many viruses occur in extremely low titers. DsRNA viruses in the families, Partitiviridae, Totiviridae, Endornaviridae, Chrysoviridae, and other related unclassified dsRNA viruses are generally associated with symptomless or persistent infections of their hosts. These characteristics indicate that samples or materials derived from eukaryotic organisms used to construct cDNA libraries and EST sequencing might carry these viruses, which were not easily detected by the researchers. …

Scopes, John Thomas, 1900-1970 (Mss 419), Manuscripts & Folklife Archives

MSS Finding Aids

Finding aid and scans (Click on "Additional Files" below) for Manuscripts Collection 419. Letters and clippings removed from a scrapbook belonging to John T. Scopes or his wife and relating primarily to the 1925 Scopes trial, his subsequent notoriety, and later publicity and commemorations surrounding the controversy.

Celebrating Darwin's Legacy: Evolution In The Galapagos Islands And The Great Plains, Paul A. Johnsgard

Paul Johnsgard

An exhibition of photographs by Linda R. Brown, Josef Kren, Paul A. Johnsgard, Allison Johnson, and Stephen Johnson; paintings by Allison Johnson; drawings by Paul A. Johnsgard; and related Darwiniana. Sponsored by the Center for Great Plains Studies, James Stubbendieck, director, and the Great Plains Art Museum, Amber Mohr, curator, in honor of the bicentennial of Charles Darwin's birth (1809-2009) and the 150th anniversary of The Origin of Species (1859). EXHlBlTORS Linda R. Brown, Lincoln, Nebraska. B.S. (Pharmacy) University of Nebraska-Lincoln, Lincoln, NE, 1965. Paul A. Johnsgard, Lincoln, Nebraska. Foundation Professor Emeritus, University of Nebraska-Lincoln. B.S. (Zoology) North Dakota State …

Quail Music: The Complex Calls Of A Bird Contain Clues To Its Evolution, Paul A. Johnsgard

Paul Johnsgard

Ethological research has revealed that the vocal communications of birds are highly specialized behavioral adaptations that can shed light on evolutionary processes. The calls of the quails of the New World are a good example. This group of birds includes some thirty species, about half of which are limited to the tropical forests of Central and northern South America. The other species are North American, ranging as far north as southern Canada. Morphological evidence favors the view that the most generalized, or “primitive,” of these species are the tree quails of Mexico’s moist mountain forests. The more open-country and arid-adapted …

It Pays To Cheat: Tactical Deception In A Cephalopod Social Signalling System, Culum Brown, Martin P. Garwood, Jane E. Williamson

Communication Skills Collection

Signals in intraspecific communication should be inherently honest; otherwise the system is prone to collapse. Theory predicts, however, that honest signalling systems are susceptible to invasion by cheats, the extent of which is largely mediated by fear of reprisal. Cuttlefish facultatively change their shape and colour, an ability that evolved to avoid predators and capture prey. Here, we show that this ability is tactically employed by male mourning cuttlefish (Sepia plangon) to mislead conspecifics during courtship in a specific social context amenable to cheating 39 per cent of the time, while it was never employed in other social contexts. Males …

The Human Phosphotyrosine Signaling Network: Evolution And Hotspots Of Hijacking In Cancer., Lei Li, Chabane Tibiche, Cong Fu, Tomonori Kaneko, Michael F. Moran, Martin Schiller, Shawn Shun-Cheng Li, Edwin Wang

Life Sciences Faculty Research

Phosphotyrosine (pTyr) signaling, which plays a central role in cell-cell and cell-environment interactions, has been considered to be an evolutionary innovation in multicellular metazoans. However, neither the emergence nor the evolution of the human pTyr signaling system is currently understood. Tyrosine kinase (TK) circuits, each of which consists of a TK writer, a kinase substrate, and a related reader, such as Src homology (SH) 2 domains and pTyr-binding (PTB) domains, comprise the core machinery of the pTyr signaling network. In this study, we analyzed the evolutionary trajectories of 583 literature-derived and 50,000 computationally predicted human TK circuits in 19 representative …

Two Boundaries Separate Borrelia Burgdorferi Populations In North America, Gabriele Margos, Jean I. Tsao, Santiago Castillo-Ramirez, Yvette A. Girard, Anne G. Hoen

Dartmouth Scholarship

Understanding the spread of infectious diseases is crucial for implementing effective control measures. For this, it is important to obtain information on the contemporary population structure of a disease agent and to infer the evolutionary processes that may have shaped it. Here, we investigate on a continental scale the population structure of Borrelia burgdorferi, the causative agent of Lyme borreliosis (LB), a tick-borne disease, in North America. We test the hypothesis that the observed d population structure is congruent with recent population expansions and that these were preceded by bottlenecks mostly likely caused by the near extirpation in the 1900s …

Evolutionary Genomics Of Mycovirus-Related Dsrna Viruses Reveals Cross-Family Horizontal Gene Transfer And Evolution Of Diverse Viral Lineages, Huiquan Liu, Yanping Fu, Jiatao Xie, Jiasen Cheng, Said A. Ghabrial, Guoqing Li, Youliang Peng, Xianhong Yi, Daohong Jiang

Plant Pathology Faculty Publications

BACKGROUND: Double-stranded (ds) RNA fungal viruses are typically isometric single-shelled particles that are classified into three families, Totiviridae, Partitiviridae and Chrysoviridae, the members of which possess monopartite, bipartite and quadripartite genomes, respectively. Recent findings revealed that mycovirus-related dsRNA viruses are more diverse than previously recognized. Although an increasing number of viral complete genomic sequences have become available, the evolution of these diverse dsRNA viruses remains to be clarified. This is particularly so since there is little evidence for horizontal gene transfer (HGT) among dsRNA viruses.

RESULTS: In this study, we report the molecular properties of two novel dsRNA mycoviruses that …

Evolution Of The National Disease Prevention And Health Promotion Strategy: Establishing A Role For The Schools, Donald Iverson, Lloyd Kolbe

Don C. Iverson

The history and evolution, during the past decade, of the national disease prevention and health promotion strategy is recounted, culminating with a description of the national prevention objectives. Objectives that directly could be attained by: (1) school health education; (2) school health services; (3) efforts to ensure healthy school environments; and (4) school physical education programs are delineated, as are objectives that could be influenced in important ways by school health programs. The nation's schools could contribute significantly and measurably toward improving the health of all Americans, if school health professionals, individually as well as within their various organizations, could …

Transcendental Thermodynamics, Richard E. Morel, George Fleck

Kahn Institute Projects

Thermodynamics is often viewed as a narrow, introspective discipline, trapped by its origins in the 18th and 19th centuries. By dramatic contrast, we show that the Fourth Law of Thermodynamics provides explanations and interpretations of all natural events, extending across artificial boundaries of tradition- al academic disciplines. The Fourth Law of Thermodynamics states that far-from-equilibrium systems increase entropy at the maximum rate available to them. This broadly inclusive paradigm applies to systems from molecules, to organisms, to the biosphere. The Fourth Law is the Law of Evolution. All systems that communicate with their environment exhibit self-organization and self-optimization, enabling the …

Extreme Environments Select For Reproductive Assurance: Evidence From Evening Primroses (Oenothera), Margaret Evans, David Hearn, Kathryn Theiss, Karen Cranston, Kent Holsinger, Michael Donoghue

Kent E Holsinger

• Competing evolutionary forces shape plant breeding systems (e.g. inbreeding depression, reproductive assurance). Which of these forces prevails in a given population or species is predicted to depend upon such factors as life history, eco- logical conditions, and geographical context. Here, we examined two such predictions: that self-compatibility should be associated with the annual life history or extreme climatic conditions.

• We analyzed data from a clade of plants remarkable for variation in breeding system, life history and climatic conditions (Oenothera, sections Anogra and Kleinia, Onagraceae). We used a phylogenetic comparative approach and Bayesian or hybrid Bayesian tests to account …

Natural Selection And Moral Sentiment: Evolutionary Biology's Challenge To Moral Philosophy, Charles W. Wright

Headwaters

No abstract provided.

Evolution And Biogeography Of Fire-Eye Antbirds (Genus Pyriglena): Insights From Molecules And Songs, Marcos Maldonado Coelho

Dissertations

The importance of climatic and geologic factors as drivers of population differentiation and speciation in the Neotropical region has long been appreciated. However, many questions remain regarding their roles underlying the processes and patterns of diversification. Studies conducted in distinct regions containing a suite of geological and ecological conditions constitute ideal scenarios to assess the role of Pleistocene climatic changes, rivers, and mountain building as historical diversification mechanisms. In chapters 1 and 2, I used an integrative approach combining molecular phylogenetics, phylogeography and population genetics to elucidate the importance of climatic and geological factors as engines of diversification. I focused …

Drag Reduction In Wave-Swept Macroalgae: Alternative Strategies And New Predictions, Patrick T. Martone, Laurie Kost, Michael L. Boller

Biology Faculty/Staff Publications

Premise of the study: Intertidal macroalgae must resist extreme hydrodynamic forces imposed by crashing waves. How does frond flexibility mitigate drag, and how does flexibility affect predictions of drag and dislodgement in the field? Methods: We characterized flexible reconfiguration of six seaweed species in a recirculating water flume, documenting both shape change and area reduction as fronds reorient. We then used a high-speed gravity-accelerated water flume to test our ability to predict drag under waves based on extrapolations of drag recorded at slower speeds. We compared dislodgement forces to drag forces predicted from slow- and high-speed data to generate new …

Paleobiological Assessment Of Controls Underlying Long-Term Diversity Dynamics, Andrés L. Cárdenas

USF Tampa Graduate Theses and Dissertations

Deciphering the factors underlying both long-term patterns of diversity and taxonomic turnover rates (i.e., extinction, and origination) has been one of Paleobiology's major foci for the past three decades. The importance of documenting these components is that they will expand our ability to interpret and model the evolutionary processes underlying those trends, highlight the evolutionary impact of historical events, and contribute to the formulation of robust predictions about the future of global diversity in response to the current anthropologically driven environmental changes. Accordingly, the first part of this study examines the possible occurrence of global marine evolutionary environmental controls into …

From A Rodent To A Rhetorician: An Ideological Analysis Of George Alexander Kennedy's Comparative Rhetoric, James Begley

Masters Theses

George Alexander Kennedy, a professor of classics at the University of North Carolina at Chapel Hill, has given birth to a new understanding of rhetorical studies: he argues for the evolution of rhetoric from animals to humans. Using Sonja Foss's methodology of "ideological criticism," this thesis examined Kennedy's case as presented in his book, Comparative Rhetoric: an Historical and Cross-Cultural Introduction. This study discovered that the book was heavily influenced by a secular, pro-evolutionary ideology which dually contributed to its selective use of scientific evidences and production of inconsistent arguments. Evaluated on the basis of Biblical principles, this thesis concluded …

Proteins: Form And Function, Roy D. Sleator

Department of Biological Sciences Publications

An overwhelming array of structural variants has evolved from a comparatively small number of protein structural domains; which has in turn facilitated an expanse of functional derivatives. Herein, I review the primary mechanisms which have contributed to the vastness of our existing, and expanding, protein repertoires. Protein function prediction strategies, both sequence and structure based, are also discussed and their associated strengths and weaknesses assessed.

The Chicken Challenge – What Contemporary Studies Of Fowl Mean For Science And Ethics, Carolynn L. Smith, Jane Johnson

Between the Species

Studies with captive fowl have revealed that they possess greater cognitive capacities than previously thought. We now know that fowl have sophisticated cognitive and communicative skills, which had hitherto been associated only with certain primates. Several theories have been advanced to explain the evolution of such complex behavior. Central to these theories is the enlargement of the brain in species with greater mental capacities. Fowl present us with a conundrum, however, because they show the behaviors anticipated by the theories but do not have the expected changes in the brain. Consequently fowl present two challenges of interest to us here. …

Evolution Of Plant Sucrose Uptake Transporters, Anke Reinders, Alicia B. Sivitz, John M. Ward

Dartmouth Scholarship

In angiosperms, sucrose uptake transporters (SUTs) have important functions especially in vascular tissue. Here we explore the evolutionary origins of SUTs by analysis of angiosperm SUTs and homologous transporters in a vascular early land plant, Selaginella moellendorffii, and a non-vascular plant, the bryophyte Physcomitrella patens, the charophyte algae Chlorokybus atmosphyticus, several red algae and fission yeast, Schizosaccharomyces pombe. Plant SUTs cluster into three types by phylogenetic analysis. Previous studies using angiosperms had shown that types I and II are localized to the plasma membrane while type III SUTs are associated with vacuolar membrane. SUT homologs were …

Some Biogeographers, Evolutionists And Ecologists: Chrono-Biographical Sketches, Charles H. Smith, Joshua Woleben, Carubie Rodgers

DLPS Faculty Publications

Each name in the following list of naturalists is linked to a corresponding capsule "chrono-biographical" sketch of that individual prepared by the authors. Coverage extends from approximately 1950 backward in time as far as the eighteenth century; figures from all over the world are included (though there is admittedly a decided Anglo-American bias). The target subject here is biogeography, but this being a broad field there are many persons on the list who are better known as climatologists, zoologists, botanists, ecologists, oceanographers, paleontologists, etc.--in other words, who made their main reputations in cognate disciplines.

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Cryo-Em Structure Of The Archaeal 50s Ribosomal Subunit In Complex With Initiation Factor 6 And Implications For Ribosome Evolution, Basil J. Greber, Daniel Boehringer, Vlatka Godinic-Mikulcic, Ana Crnkovic, Michael Ibba, Ivana Weygand-Durasevic, Nenad Ban

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Translation of mRNA into proteins by the ribosome is universally conserved in all cellular life. The composition and complexity of the translation machinery differ markedly between the three domains of life. Organisms from the domain Archaea show an intermediate level of complexity, sharing several additional components of the translation machinery with eukaryotes that are absent in bacteria. One of these translation factors is initiation factor 6 (IF6), which associates with the large ribosomal subunit. We have reconstructed the 50S ribosomal subunit from the archaeon Methanothermobacter thermautotrophicus in complex with archaeal IF6 at 6.6 Å resolution using cryo-electron microscopy (EM). The …

The Complete Mitochondrial Genome And Novel Gene Arrangement Of The Unique-Headed Bug Stenopirates Sp. (Hemiptera: Enicocephalidae), Hu Li, Hui Liu, Aimin Shi, Pavel Stys, Xuguo Zhou, Wanzhi Cai

Entomology Faculty Publications

Many of true bugs are important insect pests to cultivated crops and some are important vectors of human diseases, but few cladistic analyses have addressed relationships among the seven infraorders of Heteroptera. The Enicocephalomorpha and Nepomorpha are consider the basal groups of Heteroptera, but the basal-most lineage remains unresolved. Here we report the mitochondrial genome of the unique-headed bug Stenopirates sp., the first mitochondrial genome sequenced from Enicocephalomorpha. The Stenopirates sp. mitochondrial genome is a typical circular DNA molecule of 15, 384 bp in length, and contains 37 genes and a large non-coding fragment. The gene order differs substantially from …

Phylogeny Of Shiga Toxin-Producing Escherichia Coli O157 Isolated From Cattle And Clinically Ill Humans, James L. Bono, Timothy P. L. Smith, James E. Keen, Gregory P. Harhay, Tara G. Mcdaneld, Robert E. Mandrell, Woo Kyung Jung, Thomas E. Besser, Peter Gerner-Smidt, Martina Bielaszewska, Helge Karch, Michael L. Clawson

Roman L. Hruska U.S. Meat Animal Research Center: Reports

Cattle are a major reservoir for Shiga toxin-producing Escherichia coli O157 (STEC O157) and harbor multiple genetic subtypes that do not all associate with human disease. STEC O157 evolved from an E. coli O55:H7 progenitor; however, a lack of genome sequence has hindered investigations on the divergence of human- and/or cattle-associated subtypes. Our goals were to 1) identify nucleotide polymorphisms for STEC O157 genetic subtype detection, 2) determine the phylogeny of STEC O157 genetic subtypes using polymorphism-derived genotypes and a phage insertion typing system, and 3) compare polymorphism-derived genotypes identified in this study with pulsed field gel electrophoresis (PFGE), the …