Ecology and Evolutionary Biology Commons^™

Naturalization Of Salt Marsh Restoration Sites In The Elizabeth River, Virginia, Assessed By Feeding Activity And Trophic Level Of Mummichogs (Fundulus Heteroclitus), Moriah Anne Good

Biological Sciences Theses & Dissertations

Recent efforts to mitigate environmental issues within the Southern Branch of the Elizabeth River, Virginia, designated a “Region of Concern” by the Chesapeake Bay Program, include several salt marsh restorations. By examining gut contents and stable isotopes values (δ13C and δ15N) from mummichogs (Fundulus heteroclitus), the functional equivalency of restored salt marshes compared to natural marshes was measured. In July 2013 I collected mummichogs from three restored and three reference salt marshes in the Southern Branch. Fish were collected for gut content analysis and were analyzed for stable isotopes (δ13C and δ15N).

I removed gut contents from 16 fish per …

Acoustic Detection Reveals Fine-Scale Distributions Of Myotis Lucifugus, Myotis Septentrionalis, And Perimyotis Subflavus In Eastern Nebraska, Jeremy A. White, Cliff Lemen, Patricia Freeman

School of Natural Resources: Faculty Publications

ABSTRACT.—Before white-nose syndrome arrives in Nebraska, it is important to document the preexposure distributions of cave bats in the state. We examined the distributions of Myotis lucifugus (little brown myotis), Myotis septentrionalis (northern long-eared myotis), and Perimyotis subflavus (tri-colored bat) in eastern Nebraska by setting acoustic detectors for a single night at 105 sites in wooded habitats during summers of 2012 and 2014. We compared 2 methods of determining presence at each site. Results of our analyses are fine-scale distributional maps for these bats and some range extensions from published records. Results for M. septentrionalis and P. subflavus are largely …

Diversity-Dependent Cladogenesis Throughout Western Mexico: Evolutionary Biogeography Of Rattlesnakes (Viperidae: Crotalinae: Crotalus And Sistrurus), Christopher Blair, Santiago Sánchez-Ramírez

Publications and Research

Rattlesnakes (Crotalus and Sistrurus) represent a radiation of approximately 42 species distributed throughout the New World from southern Canada to Argentina. Interest in this enigmatic group of snakes continues to accrue due, in part, to their ecomorphological diversity, contributions to global envenomations, and potential medicinal importance. Although the group has garnered substantial attention from systematists and evolutionary biologists for decades, little is still known regarding patterns of lineage diversification. In addition, few studies have statistically quantified broad-scale biogeographic patterns in rattlesnakes to ascertain how dispersal occurred throughout the New World, particularly among the different major biomes of the …

Fine-Scale Spatial Ecology Drives Kin Selection Relatedness Among Cooperating Amoebae, Jeff Smith, Joan E. Strassmann, David C. Queller

Biology Faculty Research

Cooperation among microbes is important for traits as diverse as antibiotic resistance, pathogen virulence, and sporulation. The evolutionary stability of cooperation against “cheater” mutants depends critically on the extent to which microbes interact with genetically similar individuals. The causes of this genetic social structure in natural microbial systems, however, are unknown. Here, we show that social structure among cooperative Dictyostelium amoebae is driven by the population ecology of colonization, growth, and dispersal acting at spatial scales as small as fruiting bodies themselves. Despite the fact that amoebae disperse while grazing, all it takes to create substantial genetic clonality within multicellular …

New Clues To A Mass Extinction: Colby Geologist Robert Gastaldo And Student Researchers Unearth Evidence That Contradicts Prevailing Models About Ancient Die-Offs, Stephen Collins

Colby Magazine

Colby geologists are rewriting deep time history, altering the script of how scientists understand the mother of all mass extinctions—the End-Permian event that occurred approximately 252 million years ago. Or to suggest that they don’t, in fact, understand it.

The Line Drawn On Pain Still Holds, Bjorn H. Merker

Animal Sentience

The many substantive criticisms raised against Key by me and by many of the other commentators will not disappear by ignoring or waving them aside with meta-discourse about anthropomorphism, just-so stories, or celestial teapots. The conceptual edifice Key inhabits and defends with such gusto may look like an impregnable fortress from the inside – and Key behaves as if it were. From the outside, however, it looks more like a ramshackle structure gaping with holes and pieced together from imperfectly understood neuroscience and often faulty literature citations.

Slavery, Welfare And The Sixth Extinction, Stephen R. Clark

Animal Sentience

Ng’s laudable concern for animal welfare would be welcome to any sensible slave-owner wishing to preserve his investment. What welfarism – for slave-owners and animal husbandmen – fails to call into question is whether we have the right to breed, hold captive and kill animals at all: If it matters, as the widely recognized slogan of ‘Five Freedoms’ suggests, that animals have the chance to live a ‘normal’ life, then more matters than keeping them ‘happy’ in subjection. Their lives – and also the lives of wild things – also deserve respect.

Surveys For The Alabama Map Turtle (Graptemys Pulchra) In The Coosa River, Georgia, John B. Jensen

Georgia Journal of Science

The Alabama Map Turtle, found only in Mobile Bay drainages, is state-listed in Georgia as “rare” and has been petitioned for federal listing as “threatened.” Because this species has been poorly studied in Georgia and in the Coosa River especially, a survey was undertaken to determine its status in the Coosa to help inform the federal listing decision. The 2014-2015 survey involved counting basking turtles from a motorboat with the aid of binoculars. The Alabama Map Turtle was the third most abundantly observed turtle species during the survey, preceded by only the Slider and River Cooter. All size/age classes were …

Novel Techniques In Chemical Ecology To Examine Life Histories In Fishes, Orian Tzadik

USF Tampa Graduate Theses and Dissertations

Diet and movements in fishes are often logistically challenging to study. Trace element and stable isotope analyses have advanced these fields considerably, but are still constrained by methodological impediments, such as the tendency towards lethal sampling. Studying endangered fishes is particularly challenging as representative samples are difficult to obtain. However, the information gained from such studies is often critical to the recovery of endangered fishes as knowledge of life history attributes has the potential to greatly influence the success of management strategies.

I tested the viability of using fin rays in fishes as a non-lethal approach to study diet and …

Scorpions Of Sri Lanka (Scorpiones: Buthidae, Chaerilidae, Scorpionidae) With Description Of Four New Species Of The Genera Charmus Karsch, 1879 And Reddyanus Vachon, 1972, Stat. N., František Kovařík, Graeme Lowe, Kithsiri B. Ranawana, David Hoferek, V. A. Sanjeewa Jayarathne, Jana Plíšková, František Šťáhlavský

Euscorpius

Data about all 18 known scorpion species of Sri Lanka are summarized. All previously known species were newly collected and four new species discovered during a scorpiological expedition in 2015. Information is provided about their taxonomy, distribution, ecology, and reproductive biology, fully complemented with color photos of live and preserved specimens, as well as their habitat. Subgenus Isometrus (Reddyanus) Vachon, 1972 is elevated to genus level, Reddyanus stat. n., supported by new characters of setation on leg tarsomere II and hemi-spermatophore morphology. Charmus saradieli sp. n., Reddyanus ceylonensis sp. n., R. jayarathnei …

Acropora Habitat Evaluation And Restoration Site Selection Using A Species Distribution Modeling Approach, Katherine Wirt Ames

USF Tampa Graduate Theses and Dissertations

While populations of nearly all stony coral species along the Florida reef tract have exhibited decline, the most notable decline has occurred in the once-dominant acroporid species (Acropora cervicornis, A. palmata). Both species were listed in 2006 as threatened under the Endangered Species Act. This listing, combined with their continued decline, has resulted in large-scale restoration efforts throughout Florida and the Western Caribbean. Currently, there is little to no information regarding spatial prioritization of sites for these restoration efforts. The primary objective of this dissertation was to utilize species distribution modeling, informed by existing data from the …

Recovery Of Forest Floor Diversity After Removal Of The Nonnative, Invasive Plant Euonymus Fortunei, Kali Z. Mattingly, Ryan W. Mcewan, Robert D. Paratley, Sarah R. Bray, James R. Lempke, Mary A. Arthur

Biology Faculty Publications

The vine Euonymus fortunei (Turcz.) Hand.-Mazz. is invading forests of the eastern United States; as a result, removal of E. fortunei has become a priority of resource managers. This study examined the effectiveness of five techniques for eliminating E. fortunei, restoring plant species richness, and enhancing recolonization by woody species. In 2003, the following five treatments were applied: burn with a propane torch, light exclusion by plastic tarp, burn and glyphosate application, cut (simulated grazing) and glyphosate application, mow and glyphosate application, plus an untreated control. Each treatment was replicated four times in a randomized block design located in …

Wild Animal Suffering And Vegan Outreach, Eze Paez

Animal Sentience

Ng’s strategic proposal seems to downplay the potential benefits of advocacy for wild animals and omit what may be the most effective strategy to reduce the harms farmed animals suffer: vegan outreach.

To Minimize Animal Suffering, Broaden The Definition Of Animal Cruelty, Eleonora Gullone

Animal Sentience

Mandatory veterinary reporting of suspected abuse might discourage caregivers from seeking treatment for their injured animals. Animal abusers are more likely to be brought to justice by raising community awareness about the link between animal cruelty and human violence and its implications for the wellbeing of both humans and animals. Commonly accepted definitions of animal cruelty focus only on cruelty that is socially unacceptable, excluding an enormous amount of unnecessary animal suffering caused by humans. Only by broadening the definition of animal cruelty can we bring about the cultural change necessary to minimize this animal suffering.

Monitoring Macroalgae In The Great Bay Estuary For 2014, David M. Burdick, Arthur C. Mathieson, Sydney Nick

PREP Reports & Publications

Four more intertidal fixed transect sites were added to the long5term macroalgal monitoring array, resulting in a total of eight sites for the Great Bay Estuary. Monitoring results from 2014 show high levels of cover of nuisance green and red algae (Ulva and Gracilaria, respectively) at all sites except near the mouth of the Estuary. Seasonal sampling of algal cover confirmed earlier work that showed mid5summer accumulations of green algae (primarily Ulva)lactuca) were largely replaced in late summer and fall by red algae (two species of Graciliaria, one native and the other introduced). A determination of whether intertidal macroalgal populations …

Review Paper: The Shape Of Phylogenetic Treespace, Katherine St. John

Publications and Research

Trees are a canonical structure for representing evolutionary histories. Many popular criteria used to infer optimal trees are computationally hard, and the number of possible tree shapes grows super-exponentially in the number of taxa. The underlying structure of the spaces of trees yields rich insights that can improve the search for optimal trees, both in accuracy and in running time, and the analysis and visualization of results. We review the past work on analyzing and comparing trees by their shape as well as recent work that incorporates trees with weighted branch lengths.

Declining Frequency Of Road-Killed Rabbits In Central Georgia, Anna M. Bosch, Katelyn J. Benson, Alfred J. Mead

Georgia Journal of Science

Cottontail rabbits (Sylvilagus floridanus, Sylvilagus aquaticus, Sylvilagus palustris) are a common component of the mammal fauna of the southeastern United States, yet their numbers have been in decline for at least the past 40 years. Urban sprawl, land use changes, forest maturation, and increased predation have contributed to the decline in Georgia. In the current study we explore the proposition that long-term changes in roadkill frequency track changes in wildlife populations as a whole. Using comparisons of historical data collected by Georgia Department of Natural Resources personnel and recent roadkill census data from Baldwin County, it appears that the overall …

Population Genetic Divergence Of Isle Royale Pearl Dace, Margarita Margariscus (Cyprinidae)., John F. Elder Jr., Jack R. Martin, Isaac J. Schlosser, Larry Kallemeyn

Georgia Journal of Science

In 1949, Hubbs and Lagler described morphological variation among pearl dace (Margariscus margarita) of inland lakes on Isle Royale, Michigan. For Harvey Lake, Hubbs and Lagler, proposed that pearl dace were sufficiently morphologically distinct to warrant subspecific status. They argued that divergence of the Harvey Lake pearl dace was due to allopatric differentiation in isolation from lower elevation lakes. Harvey Lake has been isolated by elevation from lower elevation lakes for approximately 10 to 15 thousand years. No genetic studies have been done on Isle Royale pearl dace to evaluate this hypothesis to date. Here we report the analysis of …

Developing Probability Maps For Locating And Scouting Unprotected Areas Of Gravel Hill Prairies On Rodman Soils Along The Wabash River Valley Near Lafayette, Indiana, Ryan W.R. Schroeder

Engagement & Service-Learning Summit

No abstract provided.

Molecular Evolution And Functional Divergence Of Trace Amine–Associated Receptors, Seong-Il Eyun, Hideaki Moriyama, Federico G. Hoffmann, Etsuko N. Moriyama

School of Biological Sciences: Faculty Publications

Trace amine-associated receptors (TAARs) are a member of the G-protein-coupled receptor superfamily and are known to be expressed in olfactory sensory neurons. A limited number of molecular evolutionary studies have been done for TAARs so far. To elucidate how lineage-specific evolution contributed to their functional divergence, we examined 30 metazoan genomes. In total, 493 TAAR gene candidates (including 84 pseudogenes) were identified from 26 vertebrate genomes. TAARs were not identified from non-vertebrate genomes. An ancestral-type TAAR-like gene appeared to have emerged in lamprey.We found four therian-specific TAAR subfamilies (one eutherian-specific and three metatherian- specific) in addition to previously known nine …

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 …

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 …

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. …

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 …