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 …

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.

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 …

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 …

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 …

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.

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.

This service has been set up …

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 …

Divergent Functions Of The Myotubularin (Mtm) Homologs Atmtm1 And Atmtm2 In Arabidopsis Thaliana: Evolution Of The Plant Mtm Family, Yong Ding, Ivan Ndamukong, Yang Zhao, Yuannan Xia, Jean-Jack Riethoven, David R. Jones, Nullin Divecha, Zoya Avramova

School of Biological Sciences: Faculty Publications

Myotubularin and myotubularin-related proteins are evolutionarily conserved in eukaryotes. Defects in their function result in muscular dystrophy, neuronal diseases, and leukemia in humans. In contrast to the animal lineage, where genes encoding both active and inactive myotubularins (phosphoinositide 3-phosphatases) have appeared and proliferated in the basal metazoan group, myotubularin genes are not found in the unicellular relatives of green plants. However, they are present in land plants encoding proteins highly similar to the active metazoan enzymes. Despite their remarkable structural conservation, plant and animal myotubularins have significantly diverged in their functions. While loss of myotubularin function causes severe disease phenotypes …

Inbreeding-Stress Interactions: Evolutionary And Conservation Consequences, David H. Reed, Charles W. Fox, Laramy S. Enders, Torsten N. Kristensen

Department of Entomology: Faculty Publications

The effect of environmental stress on the magnitude of inbreeding depression has a long history of intensive study. Inbreeding-stress interactions are of great importance to the viability of populations of conservation concern and have numerous evolutionary ramifications. However, such interactions are controversial. Several meta-analyses over the last decade, combined with omic studies, have provided considerable insight into the generality of inbreeding-stress interactions, its physiological basis, and have provided the foundation for future studies. In this review, we examine the genetic and physiological mechanisms proposed to explain why inbreeding-stress interactions occur. We specifically examine whether the increase in inbreeding depression with …

Genome Sequencing Of Ovine Isolates Of Mycobacterium Avium Subspecies Paratuberculosis Offers Insights Into Host Association, John Bannantine, Chia-Wei Wu, Chungyi Hsu, Shiguo Zhou, David C. Schwartz, Darrell O. Bayles, Michael L. Paustian, David P. Alt, Srinand Sreevatsan, Vivek Kapur, Adel M. Talaat

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Background: The genome of Mycobacterium avium subspecies paratuberculosis (MAP) is remarkably homogeneous among the genomes of bovine, human and wildlife isolates. However, previous work in our laboratories with the bovine K-10 strain has revealed substantial differences compared to sheep isolates. To systematically characterize all genomic differences that may be associated with the specific hosts, we sequenced the genomes of three U.S. sheep isolates and also obtained an optical map.

Results: Our analysis of one of the isolates, MAP S397, revealed a genome 4.8 Mb in size with 4,700 open reading frames (ORFs). Comparative analysis of the MAP S397 isolate showed …

Natural Selection: A Concept In Need Of Some Evolution?, Charles H. Smith

DLPS Faculty Publications

In some respects natural selection is a quite simple theory, arrived at through the logical integration of three propositions (the presence of variation within natural populations, an absolutely limited resources base, and procreation capacities exceeding mere replacement numbers) whose individual truths can hardly be denied. Its relation to the larger subject of evolution, however, remains problematic. It is suggested here that a scaling-down of the meaning of natural selection to “the elimination of the unfit,” as originally intended by Alfred Russel Wallace (1823-1913), might ultimately prove a more effective means of relating it to larger-scale, longer-term, evolutionary processes.

Evolving Possibilities: Postembryonic Axial Elongation In Salamanders With Biphasic (Eurcyea Cirrigera, Eurycea Longicauda, Eurycea Quadridigitata) And Paedomorphic Life Cycles (Eurycea Nana And Ambystoma Mexicanum), Janet L. Vaglia, Kurt White '09, Alison Case '09

Biology Faculty publications

Typically, the number of vertebrae an organism will have postembryonically is determined during embryogenesis via the development of paired somites. Our research investigates the phenomenon of postembryonic vertebral addition in salamander tails. We describe body and tail growth and patterns of postsacral vertebral addition and elongation in context with caudal morphology for four plethodontids ( Eurycea) and one ambystomatid. Eurycea nana and Ambystoma mexicanum have paedomorphic life cycles; Eurcyea cirrigera, Eurycea longicauda and Eurycea quadridigitata are biphasic. Specimens were collected, borrowed and/or purchased, and cleared and stained for bone and cartilage. Data collected include snout-vent length (SVL), tail length (TL), …

Analysis Of The Lactobacilluscasei Supragenome And Its Influence In Species Evolution And Lifestyle Adaptation, Jeff Broadbent, E. C. Neeno-Eckwall, B. Stahl, K. Tandee, H. Cai, W. Morovic, P. Horvath, J. Heidenreich, N. T. Perna, R. Barrangou, J. L. Steele

Nutrition, Dietetics, and Food Sciences Faculty Publications

The broad ecological distribution of L. casei makes it an insightful subject for research on genome evolution and lifestyle adaptation. To explore evolutionary mechanisms that determine genomic diversity of L. casei, we performed comparative analysis of 17 L. casei genomes representing strains collected from dairy, plant, and human sources. Results Differences in L. casei genome inventory revealed an open pan-genome comprised of 1,715 core and 4,220 accessory genes. Extrapolation of pan-genome data indicates L. casei has a supragenome approximately 3.2 times larger than the average genome of individual strains. Evidence suggests horizontal gene transfer from other bacterial species, particularly lactobacilli, …

Prospects For The Study Of Evolution In The Deep Biosphere, Jennifer F. Biddle, Jason B. Sylvan, William J. Brazelton, Katina J. Edwards, Craig L. Moyer, John F. Heidelberg, William C. Nelson

Biology Faculty and Staff Publications

Since the days of Darwin, scientists have used the framework of the theory of evolution to explore the interconnectedness of life on Earth and adaptation of organisms to the ever-changing environment. The advent of molecular biology has advanced and accelerated the study of evolution by allowing direct examination of the genetic material that ultimately determines the phenotypes upon which selection acts. The study of evolution has been furthered through examination of microbial evolution, with large population numbers, short generation times, and easily extractable DNA. Such work has spawned the study of microbial biogeography, with the realization that concepts developed in …

Observed And Simulated Time Evolution Of Hcl, Clono2, And Hf Total Column Abundances, R Kohlhepp, R Ruhnke, M P Chipperfield, M De Maziere, J Notholt, S Barthlott, R L. Batchelor, R D. Blatherwick, Th Blumenstock, M T. Coffey, P Demoulin, H Fast, W Feng, A Goldman, D W. T Griffith, K Hamann, J W. Hannigan, F Hase, N B. Jones, A Kagawa, I Kaiser, Y Kasai, O Kirner, W Kouker, R Lindenmaier, E Mahieu, R L. Mittermeier, B Monge-Sanz, I Morino, I Murata, H Nakajima, M Palm, Clare Paton-Walsh, U Raffalski, Th Reddmann, M Rettinger, C P. Rinsland, E Rozanov, M Schneider, C Senten, C Servais, B M. Sinnhuber, D Smale, K Strong, R Sussmann, J R. Taylor, G Vanhaelewyn, T Warneke, C Whaley, M Wiehle, S W. Wood

Faculty of Science - Papers (Archive)

Time series of total column abundances of hydrogen chloride (HCl), chlorine nitrate (ClONO2), and hydrogen fluoride (HF) were determined from ground-based Fourier transform infrared (FTIR) spectra recorded at 17 sites belonging to the Network for the Detection of Atmospheric Composition Change (NDACC) and located between 80.05° N and 77.82° S. By providing such a near-global overview on ground-based measurements of the two major stratospheric chlorine reservoir species, HCl and ClONO2, the present study is able to confirm the decrease of the atmospheric inorganic chlorine abundance during the last few years. This decrease is expected following the 1987 Montreal Protocol and …