Digital Commons Network^™

Comparative Genomics Reveals Insights Into Avian Genome Evolution And Adaptation, Guojie Correction Zhang, Cai Li, Qiye Li, Bo Li, Denis M. Larkin, Chul Lee, Jay F. Storz, Agostinho Antunes, Matthew J. Greenwold, Robert W. Meredith, Anders Ödeen, Jie Cui, Qi Zhou, Luohao Xu, Hailin Pan, Zongji Wang, Lijun Jin, Pei Zhang, Haofu Hu, Wei Yang, Jiang Hu, Jin Xiao, Zhikai Yang, Yang Liu, Qiaolin Xie, Hao Yu, Jinmin Lian, Ping Wen, Fang Zhang, Hui Li, Yongli Zeng, Zijun Xiong, Shiping Liu, Long Zhou

Faculty Publications

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses …

Whole-Genome Analyses Resolve Early Branches In The Tree Of Life Of Modern Birds, Erich D. Jarvis, Siavash Mirarab, Andre J. Aberer, Bo Li, Peter Houde, Cai Li, Simon Y.W. Ho, Brant C. Faircloth, Benoit Nabholz, Jason T. Howard, Alexander Suh, Claudia C. Weber, Rute R. Da Fonseca, Jianwen Li, Fang Zhang, Hui Li, Long Zhou, Nitish Narula, Liang Liu, Ganesh Ganapathy, Bastien Boussau, Md Shamsuzzoha Bayzid, Volodymyr Zavidovych, Sankar Subramanian, Toni Gabaldón, Salvador Capella-Gutiérrez, Jaime Huerta-Cepas, Bhanu Rekepalli, Kasper Munch, Mikkel Schierup, Bent Lindow, Wesley C. Warren, David Ray, Richard E. Green

Faculty Publications

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data.We recovered a highly resolved tree that confirms previously controversial sister or close relationships.We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as …

Membrane Potential-Dependent Integration Of Synaptic Inputs In Entorhinal Stellate Neurons., Economo Mn, Martínez Jj, White Ja

Faculty Publications

No abstract provided.

Webster's Geometry; Or, The Irreducible Duchess, Benjamin Bertram Phd

Faculty Publications

This study of geometry, gender, and skepticism in John Webster’s The Duchess of Malfi argues that the play leaves us in a hall of mirrors, a horror show of optical tricks, delusion, narcissism, and perspectivism from which there seems to be no escape, no masterpiece of God’s creation upholding reality beyond sensory images. In the absence of a transcendental referent, the Duchess’ willful and fearful journey «into the wilderness» – the life she leads as a result of her furtive marriage to her steward Antonio – becomes an alternative to both the public sphere mapped by divine patterns of order …

Intellectual Origins Of (Modern) Substantive Due Process, The, Joshua D. Hawley

Faculty Publications

Almost fifty years after the Supreme Court revived the doctrine, substantive due process remains a puzzle. Detractors insist it is nothing more than judicial policy making. Defenders say it accords with the deepest values of the Constitution. But on all sides, the present scholarly debate suffers from an impoverished understanding of modern substantive due process's intellectual history, which has led to an impoverished understanding of the doctrine's core normative content. It is time for a revisionist turn. This Article supplies that turn by excavating the intellectual origins of modern substantive due process and relating that history to the doctrine's development. …

Photoperiod And Temperature Effects On The Adult Eclosion And Mating Rhythms In Pseudopidorus Fasciata (Lepidoptera: Zygaenidae), Shaohui Wu, Roberto Refinetti, Loke T. Kok, Roger R. Youngman, Gadi V.P. Reddy, Fang Sen Xue

Faculty Publications

Daily distributions of eclosion and mating activities of Pseudopidorus fasciata Walker (Lepidoptera: Zygaenidae) were recorded under natural and various laboratory conditions. Eclosion of this insect exhibited circadian gating in constant darkness (DD) but not in constant light (LL) at 28°C. Under natural conditions, the majority of adults emerged in midmorning with an eclosion peak around 1000 hours. The eclosion distribution was significantly affected by ambient temperature but not by photoperiod under laboratory conditions. Eclosion was more spread out at 22°C than at higher temperatures, and peak eclosion times were advanced at higher temperatures up to 30°C. Under natural and laboratory …

Experimental Translocations: Pitfalls And Alternatives For Quantifying Animal Movement In Fragmented Landscapes, Luke L. Powell, Philip C. Stouffer

Faculty Publications

As anthropogenic change continues to fragment terrestrial habitats, conservation biologists are increasingly concerned with how wild animals move through fragmented landscapes. Experimental translocations have recently gained popularity as a technique to determine landscape permeability by wild animals in fragmented landscapes. In experimental translocations, researchers capture individuals — usually adults — and release them elsewhere in order to determine whether they are able to cross the landscape and return to their original location. We argue that most experimental translocations have two inherent confounding factors — age of the individual and homing ability — and that the narrow spatiotemporal scale of the …

Step Selection Techniques Uncover The Environmental Predictors Of Space Use Patterns In Flocks Of Amazonian Birds, Jonathan R. Potts, Karl Mokross, Philip C. Stouffer, Mark A. Lewis

Faculty Publications

Understanding the behavioral decisions behind animal movement and space use patterns is a key challenge for behavioral ecology. Tools to quantify these patterns from movement and animal-habitat interactions are vital for transforming ecology into a predictive science. This is particularly important in environments undergoing rapid anthropogenic changes, such as the Amazon rainforest, where animals face novel landscapes. Insectivorous bird flocks are key elements of avian biodiversity in the Amazonian ecosystem. Therefore, disentangling and quantifying the drivers behind their movement and space use patterns is of great importance for Amazonian conservation. We use a step selection function (SSF) approach to uncover …

Jellyfish, Forage Fish, And The World's Major Fisheries, Kelly L. Robinson, James J. Ruzicka, Mary Beth Decker, Richard D. Brodeur, Frank J. Hernandez, Javier Quiñones, E. Marcelo Acha, Shin-Ichi Uye, Hermes Mianzan, William M. Graham

Faculty Publications

A majority of the world’s largest net-based fisheries target planktivorous forage fish that serve as a critical trophic link between the plankton and upper-level consumers such as large predatory fishes, seabirds, and marine mammals. Because the plankton production that drives forage fish also drives jellyfish production, these taxa often overlap in space, time, and diet in coastal ecosystems. This overlap likely leads to predatory and competitive interactions, as jellyfish are effective predators of fish early life stages and zooplankton. The trophic interplay between these groups is made more complex by the harvest of forage fish, which presumably releases jellyfish from …

A Scale-Explicit Framework For Conceptualizing The Environmental Impacts Of Agricultural Land Use Changes, Iago Lowe Hale, Wilfred M. Wollheim, Richard G. Smith, Heidi Asbjornsen, Andre F. Brito, Kirk Broders, Andrew S. Grandy, Rebecca J. Rowe

Faculty Publications

Demand for locally-produced food is growing in areas outside traditionally dominant agricultural regions due to concerns over food safety, quality, and sovereignty; rural livelihoods; and environmental integrity. Strategies for meeting this demand rely upon agricultural land use change, in various forms of either intensification or extensification (converting non-agricultural land, including native landforms, to agricultural use). The nature and extent of the impacts of these changes on non-food-provisioning ecosystem services are determined by a complex suite of scale-dependent interactions among farming practices, site-specific characteristics, and the ecosystem services under consideration. Ecosystem modeling strategies which honor such complexity are often impenetrable by …

The Drivers Of Tropical Speciation, Brian Tilston Smith, John E. Mccormack, Andrés M. Cuervo, Michael J. Hickerson, Alexandre Aleixo, Carlos Daniel Cadena, Jorge Pérez-Emán, Curtis W. Burney, Xiaoou Xie, Michael G. Harvey, Brant C. Faircloth, Travis C. Glenn, Elizabeth P. Derryberry, Jesse Prejean, Samantha Fields, Robb T. Brumfield

Faculty Publications

© 2014 Macmillan Publishers Limited. All rights reserved. Since the recognition that allopatric speciation can be induced by large-scale reconfigurations of the landscape that isolate formerly continuous populations, such as the separation of continents by plate tectonics, the uplift of mountains or the formation of large rivers, landscape change has been viewed as a primary driver of biological diversification. This process is referred to in biogeography as vicariance. In the most species-rich region of the world, the Neotropics, the sundering of populations associated with the Andean uplift is ascribed this principal role in speciation. An alternative model posits that rather …

Population Genetics Of Seaside Sparrow (Ammodramus Maritimus) Subspecies Along The Gulf Of Mexico, Stefan Woltmann, Philip C. Stouffer, Christine M.Bergeon Burns, Mark S. Woodrey, Mollie F. Cashner, Sabrina S. Taylor

Faculty Publications

Seaside Sparrows (Ammodramus maritimus) along the Gulf of Mexico are currently recognized as four subspecies, including taxa in Florida (A. m. juncicola and A. m. peninsulae) and southern Texas (Ammodramus m. sennetti), plus a widespread taxon between them (A. m. fisheri). We examined population genetic structure of this ''Gulf Coast'' clade using microsatellite and mtDNA data. Results of Bayesian analyses (STRUCTURE, GENELAND) of microsatellite data from nine locations do not entirely align with current subspecific taxonomy. Ammodramus m. sennetti from southern Texas is significantly differentiated from all other populations, but we found evidence of an admixture zone with A. m. …

A Challenge For The Seed Mixture Refuge Strategy In Bt Maize: Impact Of Cross-Pollination On An Ear-Feeding Pest, Corn Earworm, Fei Yang, David L. Kerns, Graham P. Head, B. Rogers Leonard, Ronnie Levy, Ying Niu, Fangneng Huang

Faculty Publications

To counter the threat of insect resistance, Bacillus thuringiensis (Bt) maize growers in the U.S. are required to plant structured non-Bt maize refuges. Concerns with refuge compliance led to the introduction of seed mixtures, also called RIB (refuge-inthe-bag), as an alternative approach for implementing refuge for Bt maize products in the U.S. Maize Belt. A major concern in RIB is cross-pollination of maize hybrids that can cause Bt proteins to be present in refuge maize kernels and negatively affect refuge insects. Here we show that a mixed planting of 5% nonBt and 95% Bt maize containing the SmartStax traits expressing …

Using Phylogenetically-Informed Annotation (Pia) To Search For Light-Interacting Genes In Transcriptomes From Non-Model Organisms, Daniel Isaac Speiser, M Sabrina Pankey, Alexandera K. Zaharoff, Barbara A. Battelle, Heather D. Bracken-Grissom, Jesse W. Breinholt, Seth M. Bybee, Thomas W. Cronin, Anders Garm, Annie R. Lindgren, Nipam H. Patel, Megan L. Porter, Meredith E. Protas, Ajna S. Rivera, Jeanne M. Serb, Kirk S. Zigler, Keith A. Crandall, Todd H. Oakley

Faculty Publications

Background

Tools for high throughput sequencing and de novo assembly make the analysis of transcriptomes (i.e. the suite of genes expressed in a tissue) feasible for almost any organism. Yet a challenge for biologists is that it can be difficult to assign identities to gene sequences, especially from non-model organisms. Phylogenetic analyses are one useful method for assigning identities to these sequences, but such methods tend to be time-consuming because of the need to re-calculate trees for every gene of interest and each time a new data set is analyzed. In response, we employed existing tools for phylogenetic analysis …

Cry1f Resistance In Fall Armyworm Spodoptera Frugiperda: Single Gene Versus Pyramided Bt Maize, Fangneng Huang, Jawwad A. Qureshi, Robert L. Meagher, Dominic D. Reisig, Graham P. Head, David A. Andow, Xinzi Ni, David Kerns, G. David Buntin, Ying Niu, Fei Yang, Vikash Dangal

Faculty Publications

Evolution of insect resistance to transgenic crops containing Bacillus thuringiensis (Bt) genes is a serious threat to the sustainability of this technology. However, field resistance related to the reduced efficacy of Bt maize has not been documented in any lepidopteran pest in the mainland U.S. after 18 years of intensive Bt maize planting. Here we report compelling evidence of field resistance in the fall armyworm, Spodoptera frugiperda (J.E. Smith), to Cry1F maize (TC 3507) in the southeastern region of the U.S. An F2 screen showed a surprisingly high (0.293) Cry1F resistance allele frequency in a population collected in 2011 from …

The Living Earth: A Nineteenth-Century Latter-Day Saint Perspective, J. Michael Hunter

Faculty Publications

By studying the worldview of Mormons living in the nineteenth century, we can better understand their interpretation of nature and their relationship to it. For Mormons of that era, the earth was alive and deeply affected by the attitudes and actions of the humans living upon it. Nineteenth-century Latter-day Saints spoke frequently of the earth, its nature, and its relationship to humanity. They referred to the earth in anthropomorphic terms. It was a living orb endowed with intelligence and feelings. The earth’s life paralleled that of the humans who lived on it. So entwined were the lives of the earth …

Data For Henson Et Al. 2014, Shandelle M. Henson, James L. Hayward, Gordon Atkins, Amanda Sandler, Wadenerson Saint Martin

Faculty Publications

These data are archived for the paper "Changing sea surface temperature alters timescale of reproductive synchrony in seabirds" by Henson et al., currently submitted to Nature.

Self-Propagative Replication Of Aβ Oligomers Suggests Potential Transmissibility In Alzheimer Disease, Amit Kumar, Kayla M. Pate, Melissa A. Moss, Dexter N. Dean, Vijayaraghavan Rangachari

Faculty Publications

The aggregation of amyloid-β (Aβ) peptide and its deposition in parts of the brain form the central processes in the etiology of Alzheimer disease (AD). The low-molecular weight oligomers of Aβ aggregates (2 to 30 mers) are known to be the primary neurotoxic agents whose mechanisms of cellular toxicity and synaptic dysfunction have received substantial attention in the recent years. However, how these toxic agents proliferate and induce widespread amyloid deposition throughout the brain, and what mechanism is involved in the amplification and propagation of toxic oligomer species, are far from clear. Emerging evidence based on transgenic mice models indicates …

Viability Costs Of Reproduction And Behavioral Compensation In Western Mosquitofish (Gambusia Affinis), Clinton T. Laidlaw, Jacob M. Condon, Mark C. Belk

Faculty Publications

The cost of reproduction hypothesis suggests that current reproduction has inherent tradeoffs with future reproduction. These tradeoffs can be both in the form of energy allocated to current offspring as opposed to somatic maintenance and future reproduction (allocation costs), or as an increase in mortality as a result of morphological or physiological changes related to reproduction (viability costs). Individuals may be able to decrease viability costs by altering behavior. Female western mosquitofish, Gambusia affinis experience a reduction in swimming ability as a consequence of pregnancy. We test for a viability cost of reproduction, and for behavioral compensation in pregnant female …

Evaluating Gps Effectiveness For Natural Resource Professionals: Integrating Undergraduate Students In The Decision-Making Process, Daniel Unger, I-Kuai Hung, Yanli Zhang, David Kulhavy

Faculty Publications

Undergraduate students pursuing a Bachelor of Science in Forestry (BSF) degree at Stephen F. Austin State University (SFA) attend an intensive 6-week residential hands-on instruction in applied field methods. For students pursuing the BSF degree knowing the exact location of a forestland is crucial to the understanding and proper management of any related natural resource. The intensive 6-week instruction includes teaching how to use the Global Positioning System (GPS) to accurately record the spatial location of an earth’s surface feature. After receiving hands-on instructions during the summer of 2014, students were taken to the field to collect real-world locations. Students …

Increasing Label-Free Stem Cell Sorting Capacity To Reach Transplantation-Scale Throughput, Melinda Simon, Ying Li, Janahan Arulmoli, Lisa Mcdonnell, Adnan Akil, Jamison Nourse, Abraham Lee, Lisa Flanagan

Faculty Publications

Dielectrophoresis (DEP) has proven an invaluable tool for the enrichment of populations of stem and progenitor cells owing to its ability to sort cells in a label-free manner and its biological safety. However, DEP separation devices have suffered from a low throughput preventing researchers from undertaking studies requiring large numbers of cells, such as needed for cell transplantation. We developed a microfluidic device designed for the enrichment of stem and progenitor cell populations that sorts cells at a rate of 150,000 cells/h, corresponding to an improvement in the throughput achieved with our previous device designs by over an order of …

Exposure To Combustion Generated Environmentally Persistent Free Radicals Enhances Severity Of Influenza Virus Infection, Greg I. Lee, Jordy Saravia, Dahui You, Bishwas Shrestha, Sridhar Jaligama, Valerie Y. Hebert, Tammy R. Dugas, Stephania A. Cormier

Faculty Publications

© 2014 Lee et al. Background: Exposures to elevated levels of particulate matter (PM) enhance severity of influenza virus infection in infants. The biological mechanism responsible for this phenomenon is unknown. The recent identification of environmentally persistent free radicals (EPFRs) associated with PM from a variety of combustion sources suggests its role in the enhancement of influenza disease severity. Methods: Neonatal mice (< seven days of age) were exposed to DCB230 (combustion derived PM with a chemisorbed EPFR), DCB50 (non-EPFR PM sample), or air for 30 minutes/day for seven consecutive days. Four days post-exposure, neonates were infected with influenza intranasally at 1.25 TCID50/neonate. Neonates were assessed for morbidity (% weight gain, peak pulmonary viral load, and viral clearance) and percent survival. Lungs were isolated and assessed for oxidative stress (8-isoprostanes and glutathione levels), adaptive immune response to influenza, and regulatory T cells (Tregs). The role of the EPFR was also assessed by use of transgenic mice expressing human superoxide dismutase 2. Results: Neonates exposed to EPFRs had significantly enhanced morbidity and decreased survival following influenza infection. Increased oxidative stress was also observed in EPFR exposed neonates. This correlated with increased pulmonary Tregs and dampened protective T cell responses to influenza infection. Reduction of EPFR-induced oxidative stress attenuated these effects. Conclusions: Neonatal exposure to EPFR containing PM resulted in pulmonary oxidative stress and enhanced influenza disease severity. EPFR-induced oxidative stress resulted in increased presence of Tregs in the lungs and subsequent suppression of adaptive immune response to influenza.

A Single Intramuscular Vaccination Of Mice With The Hsv-1 Vc2 Virus With Mutations In The Glycoprotein K And The Membrane Protein Ul20 Confers Full Protection Against Lethal Intravaginal Challenge With Virulent Hsv-1 And Hsv-2 Strains, Brent A. Stanfield, Jacque Stahl, Vladimir N. Chouljenko, Ramesh Subramanian, Anu Susan Charles, Ahmad A. Saied, Jason D. Walker, Konstantin G. Kousoulas

Faculty Publications

© 2014 Stanfield et al. Herpes Simplex Virus type-1 (HSV-1) and type-2 (HSV-2) establish life-long infections and cause significant orofacial and genital infections in humans. HSV-1 is the leading cause of infectious blindness in the western world. Currently, there are no available vaccines to protect against herpes simplex infections. Recently, we showed that a single intramuscular immunization with an HSV-1(F) mutant virus lacking expression of the viral glycoprotein K (gK), which prevents the virus from entering into distal axons of ganglionic neurons, conferred significant protection against either virulent HSV-1(McKrae) or HSV-2(G) intravaginal challenge in mice. Specifically, 90% of the mice …

Seqassist: A Novel Toolkit For Preliminary Analysis Of Next-Generation Sequencing Data, Yan Peng, Andrew S. Maxwell, Natalie D. Barker, Jennifer G. Laird, Alan J. Kennedy, Nan Wang, Chaoyang Zhang, Ping Gong

Faculty Publications

Background: While next-generation sequencing (NGS) technologies are rapidly advancing, an area that lags behind is the development of efficient and user-friendly tools for preliminary analysis of massive NGS data. As an effort to fill this gap to keep up with the fast pace of technological advancement and to accelerate data-to-results turnaround, we developed a novel software package named SeqAssist ("Sequencing Assistant" or SA).

Results: SeqAssist takes NGS-generated FASTQ files as the input, employs the BWA-MEM aligner for sequence alignment, and aims to provide a quick overview and basic statistics of NGS data. It consists of three separate workflows: …

Why Russian Inflection Is And Isn't Complex: From A(Ckerman And Malouf) To Z(Aliznjak), Jeffery R. Parker

Faculty Publications

Why do we care about morphological complexity?

• Typologically languages vary in how many morphosyntactic properties they express; morphological systems can have a large number of inflection classes, morphological distinguishers (e.g. exponents) to express these properties

• Paradigm Cell Filling Problem

Residency Time As An Indicator Of Reproductive Restraint In Male Burying Beetles, Ashlee N. Smith, Mark C. Belk, J. Curtis Creighton

Faculty Publications

The cost of reproduction theory posits that there are trade-offs between current and future reproduction because resources that are allocated to current offspring cannot be used for future reproductive opportunities. Two adaptive reproductive strategies have been hypothesized to offset the costs of reproduction and maximize lifetime fitness. The terminal investment hypothesis predicts that as individuals age they will allocate more resources to current reproduction as a response to decreasing residual reproductive value. The reproductive restraint hypotheses predicts that as individuals age they will allocate fewer resources to current reproduction to increase the chance of surviving for an additional reproductive opportunity. …

“Much Dispute And Wonderful Contentions”: Modern First Amendment Values In The Book Of Mormon, Edward L. Carter

Faculty Publications

The First Amendment’s free speech clause, like the religious exercise clause, is profoundly counter-majoritarian. So the fact that a religious point of view is unpopular or out of step with a majority of society is not justification to suppress its expression. Rather, the unpopularity of religious views is the very reason why religious expression should be protected from government or private censorship. Free speech, including religious expression, strengthens and stabilizes society, enables the search for truth, provides a check on government power, facilitates self-governance and fosters autonomy. The Book of Mormon teaches Mormons to respect the contributions of free expression …

Further Changes In L2 Thinking For Speaking?, Gale Stam

Faculty Publications

Cross-linguistic research has shown that languages differ typologically in how motion events are indicated lexically and syntactically, and that speakers of these languages have different patterns of thinking for speaking (for a review, see Han and Cadierno, 2010). Spanish speakers express path linguistically on verbs, their path gestures tend to occur with path verbs, and their manner gestures may occur without manner in speech, whereas English satellite units, and their manner gestures rarely occur without manner in speech. Stam (2006b) has shown that the English narrations of Spanish learners of English have aspects of their first language (Spanish) and aspects …

Social Regulation Of Reproduction In Male Cichlid Fishes, Karen P. Maruska

Faculty Publications

© 2014 Elsevier Inc. Social interactions and relative positions within a dominance hierarchy have helped shape the evolution of reproduction in many animals. Since reproduction is crucial in all animals, and rank typically regulates access to reproductive opportunities, understanding the mechanisms that regulate socially-induced reproductive processes is extremely important. How does position in a dominance hierarchy impact an individual's reproductive behavior, morphology, and physiology? Teleost fishes, and cichlids in particular, are ideally-suited models for studying how social status influences reproduction on multiple levels of biological organization. Here I review the current knowledge on the reproductive behavioral and physiological consequences of …

The Early History Of Chance In Evolution, Charles H. Pence

Faculty Publications

Work throughout the history and philosophy of biology frequently employs ‘chance’, ‘unpredictability’, ‘probability’, and many similar terms. One common way of understanding how these concepts were introduced in evolution focuses on two central issues: the first use of statistical methods in evolution (Galton), and the first use of the concept of “objective chance” in evolution (Wright). I argue that while this approach has merit, it fails to fully capture interesting philosophical reflections on the role of chance expounded by two of Galton's students, Karl Pearson and W.F.R. Weldon. Considering a question more familiar from contemporary philosophy of biology—the relationship between …