Ecology and Evolutionary Biology Commons^™

Phylogenomic Analysis Of Copepoda (Arthropoda, Crustacea) Reveals Unexpected Similarities With Earlier Proposed Morphological Phylogenies, Seong-Il Eyun

Nebraska Center for Biotechnology: Faculty and Staff Publications

Background: Copepods play a critical role in marine ecosystems but have been poorly investigated in phylogenetic studies. Morphological evidence supports the monophyly of copepods, whereas interordinal relationships continue to be debated. In particular, the phylogenetic position of the order Harpacticoida is still ambiguous and inconsistent among studies. Until now, a small number of molecular studies have been done using only a limited number or even partial genes and thus there is so far no consensus at the order-level.

Results: This study attempted to resolve phylogenetic relationships among and within four major copepod orders including Harpacticoida and the phylogenetic position of …

Influence Of Mature Overstory Trees On Adjacent 12-Year Regeneration And The Woody Understory: Aggregated Retention Versus Intact Forest, Miranda T. Curzon, Susan C. Baker, Christel C. Kern, Brian J. Palik, Anthony W. D'Amato

Aspen Bibliography

No abstract provided.

Record Breaking Achievements By Spiders And The Scientists Who Study Them, Stefano Mammola, Peter Michalik, Eileen Hebets, Marco Isaia

Eileen Hebets Publications

Organismal biology has been steadily losing fashion in both formal education and scientific research. Simultaneous with this is an observable decrease in the connection between humans, their environment, and the organisms with which they share the planet. Nonetheless, we propose that organismal biology can facilitate scientific observation, discovery, research, and engagement, especially when the organisms of focus are ubiquitous and charismatic animals such as spiders. Despite being often feared, spiders are mysterious and intriguing, offering a useful foundation for the effective teaching and learning of scientific concepts and processes. In order to provide an entryway for teachers and students—as well …

Dna Markers Identify Genetic Heritage Between Chickadees Near A Contact Zone In Illinois, Fahad M. Alshammari

Masters Theses

I studied the genetic interactions of Black-capped (Poecile atricapilus) (BCCH) and Carolina (P. carolinensis) (CACH) Chickadees in and near the largest hybrid contact zone in Illinois. Biologists have assumed Carolina and Black-capped Chickadees hybridize in their large contact zone in Bond and Fayette Counties, based on intermediate morphological measurements, plumage characteristics and the production of aberrant vocalizations. In determining hybridization, however, diagnostic genetics may be more useful than any other criterion. The genetic and environmental factors that have contributed to the survival of this chickadees hybrid zone have underscored the genetic integrity of both species. We …

Guide To Quaking Aspen Ecology And Management With Emphasis On Bureau Of Land Management Lands In The Western United States, Paul C. Rogers

Aspen Bibliography

No abstract provided.

Genotypic Variability In Populus Tremula L. Affects How Anthropogenic Nitrogen Enrichment Influences Litter Decomposition, Franziska Bandau, Benedicte Riber Albrectsen, Riitta Julkunen-Tiitto, Michael J. Gundale

Aspen Bibliography

No abstract provided.

Can Carbon Fluxes Explain Differences In Soil Organic Carbon Storage Under Aspen And Conifer Forest Overstories?, Antra Boca, Helga Van Miegroet

Aspen Bibliography

No abstract provided.

Aspen Health On National Forests In The Northern Rocky Mountain Region, James T. Blodgett, Kurt K. Allen, Kendra Schotzko, Al Dymerski

Aspen Bibliography

No abstract provided.

Climatic Sensitivity Of A Mixed Forest Association Of White Spruce And Trembling Aspen At Their Southern Range Limit, Sophan Chhin, G. Geoff Wang

Aspen Bibliography

No abstract provided.

Post-Glacial Biogeography Of Trembling Aspen Inferred From Habitat Models And Genetic Variance In Quantitative Traits, Chen Ding, Stefan G. Schreiber, David R. Roberts, Andreas Hamann, Jean S. Brouard

Aspen Bibliography

No abstract provided.

Maintaining Ecosystem Resilience: Functional Responses Of Tree Cavity Nesters To Logging In Temperate Forests Of The Americas, Jose Tomas Ibarra, Michaela Martin, Kristina L. Cockle, Kathy Martin

Aspen Bibliography

Logging often reduces taxonomic diversity in forest communities, but little is known about how this biodiversity loss affects the resilience of ecosystem functions. We examined how partial logging and clearcutting of temperate forests influenced functional diversity of birds that nest in tree cavities. We used point-counts in a before-after-control-impact design to examine the effects of logging on the value, range, and density of functional traits in bird communities in Canada (21 species) and Chile (16 species). Clearcutting, but not partial logging, reduced diversity in both systems. The effect was much more pronounced in Chile, where logging operations removed critical nesting …

Quaking Aspen In The Northern Rockies Retention And Restoration, Camille Stevens-Rumann, Penelope Morgan, Eva Strand, Diane Abendroth

Aspen Bibliography

No abstract provided.

Assessment Of Aspen Ecosystem Vulnerability To Climate Change For The Uinta-Wasatch- Cache And Ashley National Forests, Utah, Janine Rice, Tim Bardsley, Pete Gomben, Dustin Bambrough, Stacey Weems, Allen Huber, Linda A. Joyce

Aspen Bibliography

No abstract provided.

Evolution Of Equine Arteritis Virus During Persistent Infection In The Reproductive Tract Of The Stallion And The Male Donkey, Bora Nam

Theses and Dissertations--Veterinary Science

Equine arteritis virus (EAV) establishes persistent infection in the stallion reproductive tract, and the carrier stallion continues to shed virus in semen for weeks to years or lifelong. The objective of this study was to elucidate the intra-host evolution of EAV during persistent infection in stallions. Seven EAV seronegative stallions were experimentally infected with EAV KY84 strain and followed for 726 days post-infection, and sequential clinical samples including semen were collected for virus isolation and next-generation sequencing (NGS). In addition, archived sequential semen samples from two stallions that were naturally infected with EAV KY84 for a long-period (up to 10 …

Perspectives Provided By Leopard And Other Cat Genomes: How Diet Determined The Evolutionary History Of Carnivores, Omnivores, And Herbivores, Soonok Kim, Yun Sung Cho, Jong Bhak, Stephen J. O'Brien, Joo-Hong Yeo

Biology Faculty Articles

Recent advances in genome sequencing technologies have enabled humans to generate and investigate the genomes of wild species. This includes the big cat family, such as tigers, lions, and leopards. Adding the first high quality leopard genome, we have performed an in-depth comparative analysis to identify the genomic signatures in the evolution of felid to become the top predators on land. Our study focused on how the carnivore genomes, as compared to the omnivore or herbivore genomes, shared evolutionary adaptations in genes associated with nutrient metabolism, muscle strength, agility, and other traits responsible for hunting and meat digestion. We found …

Distribution Changes, Genetic Population Structure, And A Novel Environmental Dna (Edna) Detection Method For Darters (Subgenus Nothonotus) In The Upper Ohio River Watershed, Anthony S. Honick

Electronic Theses and Dissertations

In the upper Ohio River watershed three species of small-bodied benthic fish the Bluebreast Darter, Etheostoma (Nothonotus) camurum (Cope), the Tippecanoe Darter, Etheostoma (Nothonotus) tippecanoe Jordan and Evermann, and the Spotted Darter, Etheostoma (Nothonotus) maculatum Kirtland previously existed in disjunct distributions due to poor water quality and habitat degradation. Signs of recovery indicated that these species were moving from areas of refugia into the deeper mainstem waters of the Allegheny and Ohio rivers and expanding their distributions. To provide information for the proper conservation management of these species this dissertation was divided into three stages: 1) distribution records were updated …

Mitochondrial And Nuclear Patterns Of Conflict And Concordance At The Gene, Genome, And Behavioral Scales In Desmognathus Salamanders, Justin D. Kratovil

Theses and Dissertations--Biology

Advancements in molecular sequencing have revealed unexpected cryptic genetic diversity and contrasting evolutionary histories within genes and between genomes of many organisms; often in disagreement with recognized taxonomy. Incongruent patterns between the mitochondrial and nuclear evolutionary history can have several plausible explanations, but widespread systematic conflict inevitably challenges our conceptions of species boundaries when there is discordance between coevolving and coinherited genomes. It is unknown to what degree mitonuclear conflict drives the process of divergence, or how ubiquitous these patterns are across the tree of life. To understand the evolutionary relevance of intergenomic discordance we must identify the conflicting patterns …

Genomic Perspectives On Amphibian Evolution Across Multiple Phylogenetic Scales, Paul Michael Hime

Theses and Dissertations--Biology

Genomes provide windows into the evolutionary histories of species. The recent accessibility of genome-scale data in non-model organisms and the proliferation of powerful statistical models are now providing unprecedented opportunities to uncover evolutionary relationships and to test hypotheses about the processes that generate and maintain biodiversity. This dissertation work reveals shallow-scale species boundaries and population genetic structure in two imperiled groups of salamanders and demonstrates that the number and information content of genomic regions used in species delimitation exert strong effects on the resulting inferences. Genome scans are employed to test hypotheses about the mechanisms of genetic sex determination in …

Evaluation Of Smartstax And Smartstax Pro Maize Against Western Corn Rootworm And Northern Corn Rootworm: Efficacy And Resistance Management, Graham P. Head, Matthew W. Carroll, Sean P. Evans, Dwain M. Rule, Alan R. Willse, Thomas L. Clark, Nicholas P. Storer, Ronald D. Flannagan, Luke W. Samuel, Lance Meinke

Department of Entomology: Faculty Publications

Background: Cases of western corn rootworm (WCR) field-evolved resistance to Cry3Bb1 and other corn rootworm (CRW) control traits have been reported. Pyramid products expressing multiple CRW traits can delay resistance compared to single trait products. We used field studies to assess the pyramid CRW corn products, SmartStax (expressing Cry3Bb1 and Cry34Ab1/Cry35Ab1) and SmartStax PRO (expressing Cry3Bb1, Cry34Ab1/Cry35Ab1 and DvSnf7), at locations with high WCR densities and possible Cry3Bb1 resistance, and to assess the reduction in adult emergence attributable to DvSnf7 and other traits. Insect resistance models were used to assess durability of SmartStax and SmartStax PRO to WCR resistance.

Results: …

Evolution Of Antagonistic Relationships In Proteins: A Case Study Of Radialis- And Diviricata-Like Genes, Ao Gao

Theses and Dissertations

The antagonistic relationship of proteins describes the opponent interactions that result in one protein suppressing the function of another. Developmental genetic studies of Antirrhinum majus demonstrated that two transcription factors from the MYB gene family, RAD and DIV, interact through antagonism to regulate floral dorsoventral asymmetry. Interestingly, similar antagonistic interactions were found among proteins of FSM1 (RAD-like), MYBI (DIV-like), and DRIF in Solanum lycopersicum, which is involved in fruit development. Here, we report on the homology of these antagonistic MYB proteins based on reconstruction of the phylogeny of I-box-like and R-R-type clades, where RAD- and DIV-like belong, …

Evolutionary Linkage Of Mimetic And Non-Mimetic Color Traits In A Coral Snake Mimicry Complex, John D. Curlis Jr

College of Graduate Studies: Theses & Dissertations

Color polymorphism in aposematic mimicry systems is a perplexing phenomenon for evolutionary biologists, as theoretically the benefits of converging on a model phenotype should constrain the evolution of phenotypic diversity in these systems (i.e., color polymorphism should not occur). Nevertheless, color polymorphism in mimicry systems is prevalent throughout many taxa. In some of these systems, the evolution of color polymorphism results in the existence of non-mimetic morphs, such as those that are cryptic. The case of ground snakes (Sonora semiannulata) is unique in that color polymorphism encompasses both mimetic and cryptic morphs, as well as individual mimetic and …

A Phylogenetic And Environmental Analysis Of Brazilian Placosoma Lizards, Kai A. Farje-Van Vlack

Dissertations and Theses

Placosoma is a genus comprised of the Brazilian spectacled lizards P. champsonotus, P. cipoense, P. cordylinum, P. glabellum, and P. limaverdorum. While P. champsonotus, P. cordylinum, and P. glabellum occupy the southern coast of Brazil, P. cipoense is found in the montane grasslands north of that range, and P. limaverdorum was recently discovered in forest isolates that persist within the semi-arid Caatinga. This study elucidates the ecological and evolutionary relationships among these morphologically similar lizards. Using mitochondrial and nuclear gene sequences, genus-wide phylogenies were inferred through Bayesian inference and a species tree approach, …

Determining The Reproductive Patterns Of The Titan Acorn Barnacle (Megabalanus Coccopoma) In Its Introduced Range, Isabel L. Moran Ms.

Honors College Theses

Invasive species are a significant conservation concern given their contribution to native species decline. The barnacle, Megabalanus coccopoma, is a common invasive species in tropical and subtropical regions of both the Pacific and Atlantic oceans. Little is known about the life history and ecology of M. coccopoma, and data on reproductive biology could provide valuable insight into its propensity to establish introduced populations. Most species of barnacle (including M. coccopoma) are hermaphroditic, but self-fertilization is rare in species studied to date. A recent genetic study of introduced M. coccopoma populations in the southeastern US showed high levels of …

A Population Genetic Investigation Of The Reticulated Flatwoods Salamander (Ambystoma Bishopi) On Eglin Air Force Base, Alexander S. Wendt

College of Graduate Studies: Theses & Dissertations

The reticulated flatwoods salamander (RFS) is an endangered salamander with a unique life history. One of the largest known, best studied refuges for RFS is found on Eglin Air Force Base, and these RFS have been sampled and managed extensively since 2010. My thesis seeks to better understand RFS by using genetic techniques to address several unknowns, including: 1) determining the population structuring of RFS and the manageable units for species conservation, 2) estimating the size and status of populations, 3) understanding dispersal of RFS and factors that influence this, 4) exploring the breeding biology and recruitment patterns of RFS …

Red Snapper Distribution On Natural Habitats And Artificial Structures In The Northern Gulf Of Mexico, Mandy Karnauskas, John F. Walter Iii, Matthew D. Campbell, Adam G. Pollack, J. Marcus Drymon, Sean P. Powers

University Faculty and Staff Publications

In 2011, an intensive, multiple-gear, fishery-independent survey was carried out in the northern Gulf of Mexico (GOM) to collect comprehensive age and length information on Red Snapper Lutjanus campechanus. Based on this synoptic survey, we produced a spatial map of Red Snapper relative abundance that integrates both gear selectivity effects and ontogenetically varying habitat usage. Our methodology generated a spatial map of Red Snapper at a 10-km2 grid resolution that is consistent with existing knowledge of the species: Red Snapper occurred in relatively high abundances at depths of 50–90 m along the coasts of Texas and Louisiana and in smaller, …

Dna Metabarcoding Reveals Provisioning Of Pollution-Sensitive Aquatic Insects, Resource Partitioning, And Dietary Shifts Among Breeding Neotropical Migratory Songbirds In A Riparian Habitat, Brian K. Trevelline

Electronic Theses and Dissertations

Elucidating the diet of Neotropical migratory birds is essential to our understanding of their ecology and to their long-term conservation. Beyond broad taxonomic or morphological categories, however, the diet of Neotropical migrants is poorly documented. Using the molecular techniques of DNA barcoding and next-generation sequencing, we elucidated the diet of Neotropical migratory songbirds breeding in the riparian zones of headwater Appalachian streams. This approach resulted in a genus- or species-level description of diets that improved the current understanding of how songbirds utilize aquatic prey resources in riparian habitats. Furthermore, our approach revealed that breeding songbirds partition prey resources within a …

¬Multilocus Phylogeny Of The Lichen Family Megasporaceae, Tim B. Wheeler

Graduate Student Theses, Dissertations, & Professional Papers

The lichen symbiosis is one of the oldest studied mutualisms; in fact, Frank and De Bary coined the term "symbiosis" while studying lichens (Frank, 1877; De Bary 1879). The widespread, stable association between the mycobiont and photobiont in lichens offers an ideal system for the study of co-evolution. The recent application of molecular data to lichens has begun to unveil the complexities involved in these associations (Upreti et al. 2015, Spribille et al. 2016). Lichenized fungi make up a huge fraction of fungal diversity (Nash 2008), yet very little is known of their genetic diversity. Fungal taxonomy is notoriously difficult …

Evolution Of Molt Phenology In Dwarf Hamsters, Zachary Clare-Salzler

Graduate Student Theses, Dissertations, & Professional Papers

Environmental seasonality presents many challenges for survival. In response, organisms from across the tree of life exhibit adaptive phenology, which can facilitate survival from season to season. In particular, many species are white in the winter and brown in the summer where winter snow cover alters the visual environment. There is an extensive body of literature describing the physiological and cellular regulation of this trait in the Siberian dwarf hamster (Phodopus sungorus), but there are major shortcomings in our understanding concerning the evolution and molecular regulation of mammalian skin phenology. Notably, little is known about the genetic basis …

Contributions Of Gene Copy Number Variation To Genome Evolution And Local Adaptation Of The Cyanobacterium Acaryochloris, Amy L. Gallagher

Graduate Student Theses, Dissertations, & Professional Papers

Acaryochloris is a recently discovered genus of cyanobacteria, unique in its use of an uncommon chlorophyll as its major photosynthetic pigment, and in its peculiar genome dynamics. Members of this genus exhibit increased genic copy number variation (CNV), which is thought to be primarily derived from gene duplications and horizontal gene transfer (HGT). Acaryochloris provides an ideal system to explore mechanisms behind maintenance of gene duplicates and the influence of CNV in local adaptation. Here, I propose a mechanism for retention of gene duplicates of the bacterial recombinase, RecA, in Acaryochloris genomes and provide preliminary evidence that these paralogs are …

K-Mer Analysis Pipeline For Classification Of Dna Sequences From Metagenomic Samples, Russell Kaehler

Graduate Student Theses, Dissertations, & Professional Papers

Biological sequence datasets are increasing at a prodigious rate. The volume of data in these datasets surpasses what is observed in many other fields of science. New developments wherein metagenomic DNA from complex bacterial communities is recovered and sequenced are producing a new kind of data known as metagenomic data, which is comprised of DNA fragments from many genomes. Developing a utility to analyze such metagenomic data and predict the sample class from which it originated has many possible implications for ecological and medical applications. Within this document is a description of a series of analytical techniques used to process …