Ecology and Evolutionary Biology Commons^™

Competitive Interactions Between Appalachian Hardwoods And Different Groundcovers On Reclaimed Mine Sites, Adam David Klobucar

Masters Theses

Coal mining is a significant industry in Appalachia. Herbaceous groundcovers are commonly planted to reduce soil erosion and protect water quality during mine reclamation, but many groundcovers may be too competitive to be compatible with trees. The objectives of this research were to investigate the performance of trees planted within different groundcovers and to measure how different groundcovers influence resource availability, specifically soil moisture and light

Two studies were performed; one in a greenhouse and the other on 3 mine sites in east Tennessee where seedlings were planted and grown in competition with different groundcovers. Growth, biomass, leaf area, and …

Climate Change Alters Seedling Emergence And Establishment In An Old-Field Ecosystem, Aimée T. Classen, Richard J. Norby, Courtney E. Campany, Katherine E. Sides, Jake F. Weltzin

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

Ecological succession drives large-scale changes in ecosystem composition over time, but the mechanisms whereby climatic change might alter succession remain unresolved. Here, we asked if the effects of atmospheric and climatic change would alter tree seedling emergence and establishment in an old-field ecosystem, recognizing that small shifts in rates of seedling emergence and establishment of different species may have long-term repercussions on the transition of fields to forests in the future.

Methodology/Principal Findings

We introduced seeds from three early successional tree species into constructed old-field plant communities that had been subjected for 4 years to altered temperature, precipitation, and …

Explorations Volume 1 Fall 2010, Department Of Ecology & Evolutionary Biology

EEB Newsletter

No abstract provided.

Temporal Diversification Of Central American Cichlids, C Darrin Hulsey, Phillip R. Hollingsworth, James A. Fordyce

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

Cichlid fishes are classic examples of adaptive radiation because of their putative tendency to explosively diversify after invading novel environments. To examine whether ecological opportunity increased diversification (speciation minus extinction) early in a species-rich cichlid radiation, we determined if Heroine cichlids experienced a burst of diversification following their invasion of Central America.

Results

We first reconstructed the Heroine phylogeny and determined the basal node to use as the root of Central American Heroine diversification. We then examined the influence of incomplete taxon sampling on this group's diversification patterns. First, we added missing species randomly to the phylogeny and assessed …

Effect Of Correlated Tran Abundances On Translation Errors And Evolution Of Codon Usage Bias, Premal Shah, Michael A. Gilchrist

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Abstract

Despite the fact that tRNA abundances are thought to play a major role in determining translation error rates, their distribution across the genetic code and the resulting implications have received little attention. In general, studies of codon usage bias (CUB) assume that codons with higher tRNA abundance have lower missense error rates. Using a model of protein translation based on tRNA competition and intra-ribosomal kinetics, we show that this assumption can be violated when tRNA abundances are positively correlated across the genetic code. Examining the distribution of tRNA abundances across 73 bacterial genomes from 20 different genera, we find …

Steps Toward Butternut (Juglans Cinerea L.) Restoration, Sunshine L. Brosi

Doctoral Dissertations

Butternut (Juglans cinerea L.), a lesser-known relative of black walnut (Juglans nigra L.), is a native tree species beneficial for wildlife, valuable for timber, and part of the great diversity of species in the eastern forests of North America. Populations of butternut are being devastated by butternut canker disease, caused by the fungus Sirococcus clavigignenti-juglandacearum (V.M.G. Nair, Kostichka, & Kuntz), which is thought to be introduced to North America. The disease causes multiple branch and stem cankers that eventually girdle trees. Small population sizes, lack of sprouting, and shade intolerance exacerbates the disease and results in permanent losses of butternut …

Conservation Genetics And The Ctenosaura Palearis Clade, Stesha Ann Pasachnik

Doctoral Dissertations

We are now in the midst of a mass extinction crisis. The top threats to biodiversity include habitat destruction, pollution, over-harvesting, and invasive species. The field of conservation genetics seeks to understand these threats and devise management to preserve taxa with the ability to cope with environmental change. Preserving genetic variation and the processes in which variation is created and maintained is vital to long-term conservation goals. Limited conservation resources are cause for the prioritization of taxa and areas. Nine basic methods of prioritization have been developed. Though there are differences in these methods, and thus in the resulting target …

Spatiotemporal Dynamics In A Lower Montane Tropical Rainforest, Robert Michael Lawton

Doctoral Dissertations

Disturbance in a forest’s canopy, whether caused by treefall, limbfall, landslide, or fire determines not only the distribution of well-lit patches at any given time, but also the ways in which the forest changes over time. In this dissertation, I use a 25 year record of treefall gap formation find a novel and highly patterned process of forest disturbance and regeneration, providing a local mechanism by examining the factors that influence the likelihood of treefall. I then develop a stochastic cellular automaton for disturbance and regeneration based on the analysis of this long term data set and illustrate the potential …

Linking Community Ecology And Biogeography: The Role Of Biotic Interactions And Abiotic Gradients In Shaping The Structure Of Ant Communities., Jean-Philippe Lessard

Doctoral Dissertations

Understanding what drives variation in species diversity in space and time and limits coexistence in local communities is a main focus of community ecology and biogeography. My doctoral work aims to document patterns of ant diversity and explore the possible ecological mechanisms leading to these patterns. Elucidating the processes by which communities assemble and species coexist might help explain spatial variation in species diversity. Using a combination of manipulative experiments, broad-scale surveys, behavioral assays and phylogenetic analyses, I examine which ecological processes account for the number of species coexisting in ant communities. Ants are found in most terrestrial habitats, where …

Soil Nitrogen Amendments And Insect Herbivory Alter Above-And Belowground Plant Biomass In An Old-Field Ecosystem, Jarrod Dwayne Blue

Masters Theses

Nutrient availability and herbivory can regulate primary production in ecosystems, but little is known about how, or whether, they may interact with one another. Here I investigate how nitrogen availability and insect herbivory interact to alter above- and belowground plant community biomass in an old-field ecosystem. In 2004, 36 experimental plots were established in which soil nitrogen (N) availability (at three levels) was manipulated and insect abundance (at two levels) in a completely randomized plot design. In 2009, after six years of treatment, I measured aboveground biomass and assessed root production at peak growth. Overall, I found a significant effect …

Population Abundance And Genetic Structure Of Black Bears In Coastal South Carolina, John Michael Drewry

Masters Theses

Because of increasing frequency of bear sightings, vehicle collisions, and nuisance incidents in coastal South Carolina, the South Carolina Department of Natural Resources is developing a comprehensive black bear management plan. However, no reliable estimates of population abundance or density are available. I used genotypes of black bears determined from hair samples collected in Lewis Ocean Bay and Carvers Bay to estimate population abundance and density. I obtained hair samples from snares during 8 weekly sampling periods in 2008 and 2009. I used Huggins closed population models to estimate abundance and spatially explicit capture- recapture models to estimate density. Based …

Optimal Control Of Species Augmentation Conservation Strategies, Erin Nicole Bodine

Doctoral Dissertations

Species augmentation is a method of reducing species loss via augmenting declining or threatened populations with individuals from captive-bred or stable, wild populations. In this dissertation, species augmentation is analyzed in an optimal control setting to determine the optimal augmentation strategies given various constraints and settings. In each setting, we consider the effects on both the target/endangered population and a reserve population from which the individuals translocated in the augmentation are harvested. Four different optimal control formulations are explored. The first two optimal control formulations model the underlying population dynamics with a system of ordinary differential equations. Each of these …

Evaluating Ecological Restoration In Tennessee Hardwood Bottomland Forests, Elizabeth Anne Summers

Masters Theses

Hardwood bottomland ecosystems provide critical habitat for various wildlife among numerous ecosystem services. Since the 1800s, these forested wetlands have been logged and drained for agriculture. The federal government passed a series of legislative acts that protected wetlands and provided monetary support for restoration. The Wetlands Reserve Program (WRP) was established in 1990 with the goal of restoring ecological function in wetlands. Although several studies have measured plant and wildlife responses to WRP restorations, no standard protocol has been developed to monitor the state of ecological restoration at sites. Index of biotic integrity (IBI) models are commonly used to evaluate …

Interpreting The Γ Statistic In Phylogenetic Diversification Rate Studies: A Rate Decrease Does Not Necessarily Indicate An Early Burst, James A. Fordyce

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

Phylogenetic hypotheses are increasingly being used to elucidate historical patterns of diversification rate-variation. Hypothesis testing is often conducted by comparing the observed vector of branching times to a null, pure-birth expectation. A popular method for inferring a decrease in speciation rate, which might suggest an early burst of diversification followed by a decrease in diversification rate is the γ statistic.

Methodology

Using simulations under varying conditions, I examine the sensitivity of γ to the distribution of the most recent branching times. Using an exploratory data analysis tool for lineages through time plots, tree deviation, I identified trees with a …

Is Thermosensing Property Of Rna Thermometers Unique?, Premal Shah, Michael A. Gilchrist

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

A large number of studies have been dedicated to identify the structural and sequence based features of RNA thermometers, mRNAs that regulate their translation initiation rate with temperature. It has been shown that the melting of the ribosome-binding site (RBS) plays a prominent role in this thermosensing process. However, little is known as to how widespread this melting phenomenon is as earlier studies on the subject have worked with a small sample of known RNA thermometers. We have developed a novel method of studying the melting of RNAs with temperature by computationally sampling the distribution of the RNA structures at …

Retention Of Low-Fitness Genotypes Over Six Decades Of Admixture Between Native And Introduced Tiger Salamanders, Jarrett R. Johnson, Benjamin M. Fitzpatrick, Bradley H. Shaffer

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Abstract

Background

Introductions of non-native tiger salamanders into the range of California tiger salamanders have provided a rare opportunity to study the early stages of secondary contact and hybridization. We produced first- and second-generation hybrid salamanders in the lab and measured viability among these early-generation hybrid crosses to determine the strength of the initial barrier to gene exchange. We also created contemporary-generation hybrids in the lab and evaluated the extent to which selection has affected fitness over approximately 20 generations of admixture. Additionally, we examined the inheritance of quantitative phenotypic variation to better understand how evolution has progressed since secondary …

Evaluation Of Genetic Diversity Of Flowering Dogwood (Cornus Florida L.) In The Eastern United States Using Microsatellites., Denita Hadziabdic

Doctoral Dissertations

Flowering dogwood (Cornus florida L.) populations have experienced severe declines caused by dogwood anthracnose in the past three decades. Mortality has ranged from 48 to 98%, raising the concern that genetic diversity of this native tree has been reduced significantly. Microsatellite data were used to evaluate the level and distribution of genetic variation throughout much of the native range of the tree. In the first conducted study, we found that genetic variation in areas affected by anthracnose was as high as or higher than areas without die-offs. We found evidence of four widespread, spatially contiguous genetic clusters. However, there was …

Early Vessel Evolution And The Diversification Of Wood Function: Insights From The Malagasy Canellales, Patrick Joseph Hudson

Masters Theses

Xylem vessels have long been proposed as a key innovation for the ecological diversification of angiosperms by providing a breakthrough in hydraulic efficiency to support high rates of photosynthesis and growth. However, recent studies demonstrated that angiosperm woods with structurally ‘primitive’ vessels did not have greater whole stem hydraulic capacities as compared to vesselless angiosperms. As an alternative to the hydraulic superiority hypothesis, the heteroxylly hypothesis proposes that subtle hydraulic efficiencies of primitive vessels over tracheids enabled new directions of functional specialization in the wood. However, the functional properties of early heteroxyllous wood remain unknown. We selected the two species …

Seasonality, Variation In Species Prevalence, And Localized Disease For Ranavirus In Cades Cove (Great Smoky Mountains National Park) Amphibians, Megan Todd-Thompson

Masters Theses

World-wide amphibian declines sparked concern and encouraged investigation into potential causes beginning in the 1980’s. Infectious disease has been identified as one of the major potential contributors to amphibian declines. For example, Ranavirus has caused amphibian die-offs throughout the United States. Investigators isolated Ranavirus from dead or moribund amphibians during large-scale die-offs of amphibians in the Cades Cove area of Great Smoky Mountains National Park in 1999-2001. In 2009, after nearly a decade without follow-up monitoring, I undertook an investigation to determine if the virus persisted in the area, and if so, to assess spatial, temporal, and taxonomic patterns in …

Molecular Analysis Of Guano From Bats In Bat Houses On Organic Pecan Orchards, Veronica Angelelli Brown

Masters Theses

Bats are generalist predators of night flying insects, including many crop pests. Pecan nut casebearer (Acrobasis nuxvorella), hickory shuckworm (Cydia caryana), and several stink bug species are some of the most damaging crop pests in pecan orchards. Attracting bats to agricultural areas using bats houses may reduce the numbers of these pests and, consequently, their economic impact. This study uses quantitative polymerase chain reaction (QPCR) of mitochondrial DNA found in the guano of bats living in bat houses on organic pecan orchards to document the consumption of pecan nut casebearer, hickory shuckworm, and corn earworm ( …

Plant Genotype And Environment Interact To Influence Soil Carbon And Nitrogen Dynamics, Clara Christina Pregitzer

Masters Theses

Abiotic and biotic variation has been shown to be important in regulating nutrient cycling and belowground communities in natural systems. However, genetic variation in dominant plants as a driver of rates of nutrient cycling is still poorly understood and few studies have looked at genotype interactions across multiple environments. Using Populus angustifolia and a common garden approach, we hypothesized that all three factors: tree genetic variation, environmental conditions and genetic by environment (G x E) interactions would affect soil carbon (C) storage and nitrogen (N) cycling. Replicated copies of five different reciprocally planted Populus genotypes were studied in three separate …

Bias Correction And Bayesian Analysis Of Aggregate Counts In Sage Libraries, Russell L. Zaretzki, Michael A. Gilchrist, William M. Briggs, Artin Armagan

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Abstract

Background

Tag-based techniques, such as SAGE, are commonly used to sample the mRNA pool of an organism's transcriptome. Incomplete digestion during the tag formation process may allow for multiple tags to be generated from a given mRNA transcript. The probability of forming a tag varies with its relative location. As a result, the observed tag counts represent a biased sample of the actual transcript pool. In SAGE this bias can be avoided by ignoring all but the 3' most tag but will discard a large fraction of the observed data. Taking this bias into account should allow more of …

Non-Additive Effects Of Genotypic Diversity Increase Floral Abundance And Abundance Of Floral Visitors, Mark A. Genung, Jean-Philippe Lessard, Claire B. Brown, Windy A. Bunn, Melissa A. Cregger, Wm. Nicholas Reynolds, Emmi Felker-Quinn, Mary L. Stevenson, Amanda S. Hartley, Gregory M. Crutsinger, Jennifer A. Schweitzer, Joseph K. Bailey

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Background

In the emerging field of community and ecosystem genetics, genetic variation and diversity in dominant plant species have been shown to play fundamental roles in maintaining biodiversity and ecosystem function. However, the importance of intraspecific genetic variation and diversity to floral abundance and pollinator visitation has received little attention.

Methodology/Principal Findings

Using an experimental common garden that manipulated genotypic diversity (the number of distinct genotypes per plot) of Solidago altissima, we document that genotypic diversity of a dominant plant can indirectly influence flower visitor abundance. Across two years, we found that 1) plant genotype explained 45% and 92% …

The Delimitation Of Flammulina Fennae, Soňa Ripková, Karen Hughes, Slavomír Adamčík, Viktor Kučera, Katarína Adamčíková

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Multivariate morphometric analyses of micromorphological characters measured on 35 specimens of Flammulina fennae and related species show that only a combination of spore dimensions and ixohyphidia characters are suitable for delimitation of this species. In order to confirm species identifications based on micromorphology, ribosomal ITS DNA sequences were obtained and compared with those previously deposited in GenBank, and phylogenetic analyses were performed using an ITS dataset of all known Flammulina species. All six specimens morphologically determined as F. fennae were identified by molecular data. Two of twelve specimens morphologically assigned to F. velutipes had F. elastica sequences. One ITS sequence …

A New Genus To Accommodate Gymnopus Acervatus (Agaricales), Karen Hughes, David A. Mather, Ronald H. Peterson

Faculty Publications and Other Works -- Ecology and Evolutionary Biology

Phylogenies based on ITS and LSU nrDNA sequences show Agaricus (Gymnopus) acervatus as unique within the Gymnopus/Rhodocollybia complex. These phylogenies imply that a separate genus is necessary, and Connopus is proposed. Infraspecific morphological and DNA-based variation within C. acervatus suggests that a western North American clade might be reproductively isolated from the eastern North American/Scandinavian clade and that in this species complex the European and eastern North American clade might be conspecific. A Scandinavian exemplar is selected for bar-coding. Two GenBank sequences with name-phylogenetic placement inconsistencies are identified.