Digital Commons Network^™

Three-Dimensional Interstitial Space Mediates Predator Foraging Success In Different Spatial Arrangements, Stephen Gregory Hesterberg

USF Tampa Graduate Theses and Dissertations

Habitat structure modifies the strength of predator-prey interactions, but it remains unclear how to describe the three-dimensional spatial arrangement of structural components in a way that consistently predicts outcomes. Interstitial space may provide a useful target for measurement, but most studies use only two-dimensional methods to describe 3D space, limiting their predictive power. Using a novel technology to produce identical components, this study tests whether the 3D interstitial space of oyster shell mimics modifies the ability of blue crabs (Callinectes sapidus) to capture their mud crab prey (Eurypanopeous depressus) in mesocosms and a variety of reef-associated …

Drought Responsive Gene Expression Regulatory Divergence Between Upland And Lowland Ecotypes Of A Perennial C4 Grass, John T. Lovell, Scott Schwartz, David B. Lowry, Eugene V. Shakirov, Jason E. Bonnette, Xiaoyu Weng, Mei Wang, Jenifer Johnson, Avinash Sreedasyam, Christopher Plott, Jerry Jenkins, Jeremy Schmutz, Thomas E. Juenger

Biological Sciences Faculty Research

Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; however, surprisingly few studies have examined how genome-wide patterns of gene expression G×E are manifested in response to environmental stress and other selective agents that cause climatic adaptation. Here, we characterize drought-responsive expression divergence between upland (drought-adapted) and lowland (mesic) ecotypes of the perennial C₄ grass, Panicum hallii, in natural field conditions. Overall, we find that cis-regulatory elements contributed to gene expression divergence across 47% of genes, 7.2% of which exhibit drought-responsive G×E. …

A Phylogenomic Assessment Of Ancient Polyploidy And Genome Evolution Across The Poales, Michael R. Mckain, Haibao Tang, Joel R. Mcneal, Et Al.

Faculty Articles

Comparisons of flowering plant genomes reveal multiple rounds of ancient polyploidy characterized by large intra-genomic syntenic blocks. Three such whole genome duplication (WGD) events, designated as rho (ρ), sigma (σ), and tau (τ), have been identified in the genomes of cereal grasses. Precise dating of these WGD events is necessary to investigate how they have influenced diversification rates, evolutionary innovations, and genomic characteristics such as the GC profile of protein coding sequences. The timing of these events has remained uncertain due to the paucity of monocot genome sequence data outside the grass family (Poaceae). Phylogenomic analysis of protein coding genes …

Session D-1: Science And Spaghetti Monsters: Addressing The Ethical Issues And Controversy Related To Genomics And Evolution In The Biology Classroom, Sarah O'Leary-Driscoll

Professional Learning Day

As science teachers, we may shy away from addressing the controversy surrounding particular topics in our classrooms in order to maintain focus on content. However, the real world context of knowledge is essential, and the performance expectations in the life sciences as outlined in the NGSS state that students should be able to discuss the ethical issues related to genetic modifications and the nature of science. We will discuss ideas for how to address these topics effectively and help our students understand their importance beyond academics in our global community.

Session C-1: Ecosystem Disruption: Using Lab And Real-World Examples To Bring Changes In Earth’S Ecosystems To Life, Crystal Randall, Sarah O'Leary-Driscoll, Sowmya Anjur, Don Dosch

Professional Learning Day

The magnitude of the changes occurring in Earth’s ecosystems seems difficult to tackle in the classroom and lab. Here we explore ways to demonstrate the changes in the Earth’s water and carbon cycles in the lab and bring them to life in real-world ecosystems in the classroom.

Upscaling Methane Emission Hotspots In Boreal Peatlands, Fabio Cresto Aleina, Benjamin R. K. Runkle, Tim Brucher, Thomas Kleinen, Victor Brovkin

Biological and Agricultural Engineering Faculty Publications and Presentations

Upscaling the properties and effects of small-scale surface heterogeneities to larger scales is a challenging issue in land surface modeling. We developed a novel approach to upscale local methane emissions in a boreal peatland from the micro-topographic scale to the landscape scale. We based this new parameterization on the analysis of the water table pattern generated by the Hummock–Hollow model, a microtopography resolving model for peatland hydrology. We introduce this parameterization of methane hotspots in a global model-like version of the Hummock–Hollow model that underestimates methane emissions. We tested the robustness of the parameterization by simulating methane emissions for the …

New Data On The Distribution Of Butheoloides Littoralis Lourenço, Touloun Et Boumezzough, 2011 (Scorpiones: Buthidae) Oulaid, Oulaid Touloun, Moulay Abdelmonaim El Hidan, Ali Boumezzough

Euscorpius

Morocco is the region in Africa with the highest diversity of Butheoloides Hirst, 1925 species. Until now, the total number of species of this genus known from Morocco is raised to five. A field study conducted in southern Morocco discovered a new specimen of Butheloides littoralis in the Tighmi region (southeast of Tiznit), the most continental site of this species in Morocco. This specimen is the third of this endemic species of Morocco but it is the first male discovered.

Animal Suffering And Human Bias, Stijn Bruers

Animal Sentience

Ng proposes concrete ways to decrease animal suffering on the basis of commonsense economic logic and research in welfare biology. But to reduce animal suffering effectively in livestock farming, animal experimentation or the natural environment we have to become more aware of our pervasive and spontaneous but unreliable intuitive moral judgments. These can generate biases that prevent us from decreasing animal suffering effectively.

Temporal Trends In Genetic Data And Effective Population Size Support Efficacy Of Management Practices In Critically Endangered Dusky Gopher Frogs ( Lithobates Sevosus ), Kristin M. Hinkson, Stephen C. Richter

Biological Sciences Faculty and Staff Research

Monitoring temporal changes in population genetic diversity and effective population size can provide vital information on future viability. The dusky gopher frog, Lithobates sevosus, is a critically endangered species found only in coastal Mississippi, with low genetic variability as a consequence of isolation and population size reduction. Conservation management practices have been implemented, but their efficacy has not been addressed. We genotyped individuals collected 1997–2014 to determine temporal trends in population genetic variation, structure, and effective size. Observed and expected heterozygosity and allelic richness revealed temporally stable, but low, levels of genetic variation. Positive levels of inbreeding were found in …

Investigating Physiological Collaborations Between A Lower Termite And Its Symbionts, Brittany F. Peterson

Open Access Dissertations

This project was completed in an effort to better understand the contributions of symbiotic microbes to the biology of Reticulitermes flavipes, the eastern subterranean termite. Lower-termites, like R. flavipes, house symbionts from all three domains of life within their hindgut paunch. This intimate association is reflected in nearly every aspect of termite biology. Here, I investigate these physiological collaborations as they relate to digestion and immunity. My efforts focused on 1) quantifying the role of bacteria in wood digestion within the termite gut, 2) evaluating the role of symbionts in protection against pathogens, and 3) identifying gene products that bacterial …

Marine Disease Impacts, Diagnosis, Forecasting, Management And Policy, Kevin D. Lafferty, Eileen E. Hofmann

CCPO Publications

(First paragraph) As Australians were spending millions of dollars in 2014 to remove the coraleating crown of thorns sea star from the Great Barrier Reef, sea stars started washing up dead for free along North America’s Pacific Coast. Because North American sea stars are important and iconic predators in marine communities, locals and marine scientists alike were alarmed by what proved to be the world’s most widespread marine mass mortality in geographical extent and species affected, especially given its mysterious cause. Investigative research using modern diagnostic techniques implicated a never-before-seen virus [1]. The virus inspired international attention to marine diseases, …

A Systems Approach To Animal Communication, Eileen A. Hebets, Andrew B. Barron, Christopher N. Balakrishnan, Mark E. Hauber, Paul H. Mason, Kim L. Hoke

Eileen Hebets Publications

Why animal communication displays are so complex and how they have evolved are active foci of research with a long and rich history. Progress towards an evolutionary analysis of signal complexity, however, has been constrained by a lack of hypotheses to explain similarities and/or differences in signalling systems across taxa. To address this, we advocate incorporating a systems approach into studies of animal communication—an approach that includes comprehensive experimental designs and data collection in combination with the implementation of systems concepts and tools. A systems approach evaluates overall display architecture, including how components interact to alter function, and how function …

Genetic Structure Of Micromeria (Lamiaceae) In Tenerife, The Imprint Of Geological History And Hybridization On Within-Island Diversification, Pamela Puppo, Manuel Curto, Harald Meimberg

Biological Sciences Faculty Research

Geological history of oceanic islands can have a profound effect on the evolutionary history of insular flora, especially in complex islands such as Tenerife in the Canary Islands. Tenerife results from the secondary connection of three paleo-islands by a central volcano, and other geological events that further shaped it. This geological history has been shown to influence the phylogenetic history of several taxa, including genus Micromeria (Lamiaceae). Screening 15 microsatellite markers in 289 individuals representing the eight species of Micromeria present in Tenerife, this study aims to assess the genetic diversity and structure of these species and its relation with …

Glyphosate Induces Neurotoxicity In Zebrafish, Nicole M. Roy, Bruno Carneiro, Jeremy Ochs

Biology Faculty Publications

Glyphosate based herbicides (GBH) like Roundup^® are used extensively in agriculture as well as in urban and rural settings as a broad spectrum herbicide. Its mechanism of action was thought to be specific only to plants and thus considered safe and non-toxic. However, mounting evidence suggests that GBHs may not be as safe as once thought as initial studies in frogs suggest that GBHs may be teratogenic. Here we utilize the zebrafish vertebrate model system to study early effects of glyphosate exposure using technical grade glyphosate and the Roundup^® Classic formulation. We find morphological abnormalities including cephalic and …

Ecosystem Services In Managing Residential Landscapes: Priorities, Value Dimensions, And Cross-Regional Patterns, Kelli L. Larson, Jennifer L. Morse, Peter M. Groffman, Neil D. Bettez, Tara Trammell

Environmental Science and Management Faculty Publications and Presentations

Although ecosystem services have been intensively examined in certain domains (e.g., forests and wetlands), little research has assessed ecosystem services for the most dominant landscape type in urban ecosystems—namely, residential yards. In this paper, we report findings of a cross-site survey of homeowners in six U.S. cities to 1) examine how residents subjectively value various ecosystem services, 2) explore distinctive dimensions of those values, and 3) test the urban homogenization hypothesis. This hypothesis posits that urbanization leads to similarities in the social-ecological dynamics across cities in diverse biomes. By extension, the thesis suggests that residents’ ecosystem service priorities for residential …

The Sea Among Us: The Amazing Strait Of Georgia By Richard Beamish And Gordon Mcfarlane, Dee Horne Dr.

The Goose

Review of The Sea Among Us: The Amazing Strait of Georgia by Richard Beamish and Gordon McFarlane.

Profiles Of Low Complexity Regions In Apicomplexa, Fabia U. Battistuzzi, Kristan A. Schneider, Matthew K. Spencer, David Fisher, Sophia Chadhry, Ananias A. Escalante

Harold W. Manter Laboratory of Parasitology: Library Materials

Background: Low complexity regions (LCRs) are a ubiquitous feature in genomes and yet their evolutionary history and functional roles are unclear. Previous studies have shown contrasting evidence in favor of both neutral and selective mechanisms of evolution for different sets of LCRs suggesting that modes of identification of these regions may play a role in our ability to discern their evolutionary history. To further investigate this issue, we used a multiple threshold approach to identify species-specific profiles of proteome complexity and, by comparing properties of these sets, determine the influence that starting parameters have on evolutionary inferences.

Results: …

An Animal Victim's Best Chance: Veterinary Legal Duty To Report Cruelty In The U.S., Lora Dunn

Animal Sentience

Legislation throughout the U.S. recognizes animal sentience and the importance of veterinary reporting to combat the ongoing suffering of these animal victims: All 50 states have felony penalties available for animal cruelty crimes, and veterinary reporting is permitted or required in the majority of states. The remaining minority of U.S. states should take action to require veterinarians to report animal cruelty and render veterinarians immune for good faith reporting.

Veterinary Medical Associations Need To Educate Veterinarians For Mandatory Reporting Of Suspected Animal Abuse, Melinda V. Merck

Animal Sentience

When animals are suffering, we have a duty to take action. With appropriate incentive and educational support mandatory veterinary reporting can be a great legal avenue to help ensure their safety and welfare.

Fish Pain's Burden Of Proof, Carl Safina

Animal Sentience

A hypothesis like Key’s, that fish cannot feel pain, should really be stated as a null hypothesis — an assumption that there is no difference in the things being compared. Then evidence — including anecdotal evidence — for and against rejecting the null hypothesis can be examined and weighed. Key (2016a) has proven only that fish lack mammalian brains.

Fire Was In The Reptile’S Mouth: Towards A Transcultural Ecological Poetics, Stuart Cooke

Landscapes: the Journal of the International Centre for Landscape and Language

This paper compares two creation narratives from indigenous peoples on either side of the Pacific Ocean, the relationships between which catalyse the theorisation of a transcultural approach to ecological poetics. The comparison of these narratives reveals important, rhizomatic similarities, and also unmistakable regional differences, concerning the origins of language and culture in Yanomami (Venezuela) and MakMak (Australia) communities. Concomitant with the centrality of indigenous thought in this theorisation of ecopoetics is the de­centrality of human-only conceptions of poetics. Accordingly, the paper considers non-semantic forms of poetics such as birdsong in order to de-centre classically Western, humanist conceptions of language …

Burden Of Proof Lies With Proposer Of Celestial Teapot Hypothesis, Brian Key

Animal Sentience

Bertrand Russell famously imagined the existence of a celestial teapot to highlight that the burden of proof of a hypothesis lay with its proposer and it was not the responsibility of others to refute it. Those who propose that fish feel pain must bear the burden of proof for their hypothesis. There are several common arguments adopted by those defending the position that fish feel pain. For instance, proponents envisage that pain is so important for human survival that they can’t imagine fish could exist without it. Out of this argument from incredulity emerges the idea that pain must have …

Swans: Their Biology And Natural History, Paul A. Johnsgard

Zea E-Books Collection

The seven species of swans of the world are an easily and universally recognized group of waterfowl, which have historically played important roles in the folklore, myths and legends in many of the world’s cultures. Among the largest of all flying birds, they have also almost universally been used as symbols of royalty, grace and beauty, and largely for these reasons swans have only rarely been considered acceptable as targets for sport hunting. Swans occur on all the continents except Africa, although most species are associated with the temperate and arctic zones of North America and Eurasia. Among birds, swans …

Animal Suffering In China, Peter J. Li

Animal Sentience

Chinese policy has been aimed at maximizing GDP; it is time to focus also on minimizing animal suffering.

Science And Sensibility, Bernard E. Rollin

Animal Sentience

The sentience and suffering of animals is obvious to common sense, even if science and industry claim to be agnostic. Economic incentives to reduce the suffering of animals are welcome, but it is not clear whether animals can turn to science for help.

Weathering The End Times, Donald W. Holdridge Sr.

Eruditio Ardescens

“Weathering the End Times” first addresses some of the major arguments for and against man-caused Climate Change, and then portrays where the various elements of Christendom fall within this debate. It goes on to examine the prophetic Scriptures that relate to the environments of the Tribulation, Millennial Kingdom and Eternal State, concluding that God-caused Climate Change is what believers truly need to focus on.

A Profusion Of Parallel Tracks: Why Mongolian Roads Of Dirt And Gravel Branch, Multiply, And Fuse Endlessly, Bill Yake

Landscapes: the Journal of the International Centre for Landscape and Language

A Profusion of Parallel Tracks: Why Mongolian Roads of Dirt and Gravel Branch, Multiply, and Fuse Endlessly

When The Client Is Not The Abuser, But One Of The Abused, Tania Signal

Animal Sentience

The question of client confidentiality and reporting animal abuse is complicated when the client is not the abuser, and when the abuse (of both people and animals) may escalate precisely because it has been (or may be) reported.

Two New Scorpions Of The Genus Chaneke Francke, Teruel Et Santibáñez-López, 2014 (Scorpiones: Buthidae) From Southern Mexico, František Kovařík, Rolando Teruel, Graeme Lowe

Euscorpius

Herein we describe two new species of the recently discovered buthid scorpion genus Chaneke Francke, Teruel et Santibáñez-López, 2014. Both are from Oaxaca State in southern Mexico: Chaneke hofereki sp. n. based upon adults of both sexes from a single coastal locality, and Chaneke baldazoi sp. n. based upon adult females and juveniles from a mountain site in the Sierra Madre. Additional information is given on their taxonomy, distribution, ecology, and reproductive biology, fully complemented with color photos of live and preserved specimens, and their habitat.

Eggshell Pigment Composition Covaries With Phylogeny, Kaat Brulez, Ivan Miksik, Christopher R. Cooney, Mark E. Hauber, Paul George Lovell, Golo Maurer, Steven J. Portugal, Douglas Russell, Silas James Reynolds, Phillip Cassey

Publications and Research

No single hypothesis is likely to explain the diversity in eggshell coloration and patterning across birds, suggesting that eggshell appearance is most likely to have evolved to fulfill many nonexclusive functions. By controlling for nonindependent phylogenetic associations between related species, we describe this diversity using museum eggshells of 71 British breeding passerine species to examine how eggshell pigment composition and concentrations vary with phylogeny and with life-history and nesting ecology traits. Across species, concentrations of biliverdin and protoporphyrin, the two main pigments found in eggshells, were strongly and positively correlated, and both pigments strongly covaried with phylogenetic relatedness. Controlling for …