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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 …

Burbot Growth Rates In A Northern Mesotrophic Lake, Samuel J. Peterson

Journal of Earth and Life Science

Burbot Lota lota has a circumpolar distribution throughout cold-water areas and is the only freshwater member of the family Gadidae. There are currently very few management techniques applied to Burbot throughout their northern extent. Growth is an indicator of fish health, biomass, and habitat quality; therefore, the objective of this study was to determine the growth rate of Burbot in Lake Bemidji. Burbot (n = 45) were collected along three sites on Lake Bemidji for years 2015-2017. Age was determined from sagittal otoliths, the marginal zones of which were opaque from December to May and translucent from June to November. …

Effects Of Catch-And-Release Angling On Egg Densities In Largemouth Bass Nests, Tyler Robinson

Journal of Earth and Life Science

Predation during early life stages of Centrarchidae offspring are a major cause of decreased reproductive success. For five-weeks Largemouth Bass Micropterus salmoides defend their broods from invaders such as Yellow Perch Perca flavescens and Bluegill Lepomis macrochirus. The focus of this study was to determine if predation upon Largemouth Bass broods increased as removal time from the nest via catch-and-release angling increased. Sampling was conducted on the Whitefish Chain, MN from 7 May - 7 June 2016, where a total of 29 nests were located and sampled. Three treatment groups were used; immediate catch-and-release, three-minute, and a seven- minute …

Effect Of Abiotic Factors On Bluegill Size Structure In Nine Central Minnesota Lakes, Ryan Henry

Journal of Earth and Life Science

Bluegill are the most targeted species of fish in Minnesota. In recent years, the abundance of slow growing, small Bluegill has increased within the state. Angler harvest of Bluegill can reduce the average length of Bluegill up to four times the original length. Abiotic factors such as maximum depth, average water clarity, littoral area, and percent littoral area can influence the dynamics of a lake system. There has been limited research on whether these abiotic factors can influence the size structure of a Bluegill population. The objective of this study is to determine if there is a direct relationship between …

Investigation Of The Anthropogenic Factors Influencing Eastern Fox Squirrel, Sciurus Niger, Distribution And Abundance In Urban Residential Areas, Gabrielle Vinyard

Undergraduate Honors Thesis Collection

In this rapidly developing world, the relationship between humans and wildlife is becoming more strained. Despite the challenges, some animals respond better than others to the additional pressures present in urban environments, and squirrels are a prime example (McKinney, 2002). Several studies have focused on the distribution and abundance of tree squirrels in urban landscapes, but more information is needed to understand the connections between anthropogenic factors and population density (Shochat et al., 2006). Previous research that examined leaf nest densities within residential neighborhoods found a positive correlation between property value and nest density (Salsbury et al., unpublished data). The …

A Comparison Of Benthic Macroinvertebrate Assemblages Between Perennial And Intermittent Headwater Streams Of The Mattole River In Northern California, Usa, Mason S. London

Cal Poly Humboldt theses and projects

Intermittent streams are common throughout the world and comprise 60% or more of total river lengths in the conterminous United States. Despite their prevalence, intermittent streams are understudied, particularly first-order headwater streams, which are vital for maintaining the function, health and biotic diversity of river networks. In June 2016, I sampled five intermittent and five perennial headwater streams in the Mattole River watershed in northwestern coastal California, USA, to compare benthic macroinvertebrate (BMI) assemblages between intermittent and perennial streams. BMI samples were collected using a 500µm mesh D-net at eight randomly located riffles along a 150-m reach, and then composited, …

Chapter 16 - Birds, Janice M. Glime

Bryophyte Ecology Volume 2: Bryological Interaction

Explore the contents of Bryophyte Ecology, Volume 2, Chapter 16 - Birds by clicking the links above. For the Contents section of this ebook, as well as Volumes 1 through 5, please visit the Bryophyte Ecology Main Page.

Ebook sponsored by Michigan Technological University and the International Association of Bryologists.

Chapter 12 - Terrestrial Insects, Janice M. Glime

Bryophyte Ecology Volume 2: Bryological Interaction

Bryophyte Ecology, Volume 2, Chapter 12 - Terrestrial Insects is coming soon. For the Contents section of this ebook, as well as Volumes 1 through 5, please visit the Bryophyte Ecology Main Page.

Ebook sponsored by Michigan Technological University and the International Association of Bryologists.

Pteropus Voeltzkowi And The Understory: A Study Of The Behavioral Impacts Of The Pemba Flying Fox On The Vegetation And Soil Quality Of Pemba Island, Lea Davidson

Independent Study Project (ISP) Collection

This study examines the impact of Pteropus voeltzkowi , colloquially known as the Pemba Flying Fox, on biodiversity and health of the forest ground layer. Known to serve as reforesters, high concentrations of both fruit seeds and nutrient dense guano are introduced into specific environmental locations due to the bat's behavioral patterns. Working around two roost locations, one in Ngezi Forest and the other at the Kidike conservation site near Mjini Ole, diversity of juvenile vegetation was measured and quantified. In a laboratory setting, soil samples from both sites were analyzed for impacts of guano concentration on soil chemical properties. …

The Effects Of Thermal Stress On Fluorescent Protein Expression In An Indo-Pacific Scleractinian Coral Species, Acropora Tenuis, Anna Knochel

Independent Study Project (ISP) Collection

The scleractinian coral species that so heavily define tropical coral reefs are increasingly threatened by anthropogenic global warming. Rising sea surface temperatures in combination with light stress causes the photosynthetic breakdown of the coral’s algal symbiont, Symbiodinium. Corals have developed a number of physiological responses to handle acute stressors, such as the production of ultraviolet-protecting amino acids, heat shock proteins, the ability to shift symbionts, and the production of fluorescent proteins. The latter has been thought to play a photoprotective role in the coral holobiont, and studies have shown evidence that corals orient these pigments to divert harmful light away …

Large-Scale Surveillance Of Captive Naked Mole-Rat Colonies Shows Caste Differences In Space Utilization, Michael Kress, Edward F. Meehan, Dan Mccloskey

Publications and Research

African naked mole-rats are eusocial mammals that provide unique opportunity to study complex mammalian social behavior and large-group dynamics in a controlled vivarium setting. Previous reports of captive and wild naked mole-rats have identified a division of labor among non-reproductive colony members along a size polyethism, with large animals specializing in defense behaviors, and small animals performing foraging, nest building, and caretaking functions. This study utilized radio frequency identification (RFID) and advanced computational approaches to monitor the activity patterns and place preferences of all members in two naked mole-rat colonies (N = 36 and 37 animals) for a period of …

Habitat Use By Wintering Passerines In Fire-Managed Forests Along The U.S. Gulf Coast, Justin Michael Michaud

Online Theses and Dissertations

Coastal habitats are being impacted by land development, fragmentation, and disturbance related to climate change. The remaining natural areas need to use planned management that may, in some cases, include the use of prescribed fire to maintain habitat quality. Numerous species of passerines, including some with declining populations, use the Gulf Coast as a wintering area, and some depend on habitats managed by fire. To provide information for land managers, I studied the winter bird community at Naval Live Oaks in Gulf Islands National Seashore with two primary objectives: (1) to describe the distribution, abundance, and diversity of the non-breeding …

Are Mussel Shells Environmental Dna Time Capsules? A Comparison Of Extraction Methods For Obtaining Dna From Shell Material., Kelsey Elizabeth Rogers

Online Theses and Dissertations

Freshwater mussels have become some of the most imperiled species in North America and widespread populations have succumbed to pollution and many other anthropogenic-related factors. With molecular techniques evolving, a recent interest in ancient DNA and museum specimens has emerged and prompted a study to test the ability of several extraction methods to isolate DNA from museum mussel specimens. The purpose of this study was to determine if four DNA extraction methods had influence on total DNA yield (ng/mg) from mussel tissue. The hinge ligaments of freshwater mussels ranging in collection date (1984-2015) were used as the source of genetic …

Natural Environmental Gradients Predict The Microhabitat Use, Fine-Scale Distribution, And Abundance Of Three Woodland Salamanders In An Old-Growth Forest, Joseph Alex Baecher

Online Theses and Dissertations

Woodland salamanders (Plethodonidae: Plethodon)－a group of sensitive, direct developing, lungless amphibians－are particularly responsive to gradients in environmental conditions. Because of their functional dominance in terrestrial ecosystems, woodland salamanders are responsible for the transformation of nutrients and translocation of energy between highly desperate levels of trophic organization (detrital food webs and high‐order predators). However, the spatial extent of woodland salamanders' role in the ecosystem is likely contingent upon the distribution of their biomass throughout the forest. Therefore, a better understanding of woodland salamander spatial population dynamics is needed to further understand their role in terrestrial ecosystems. The objectives of this study …

Comparison Of Cytochrome B Variation And Morphological Features Of Isolated Banded Pygmy Sunfish (Elassoma Zonatum) Populations In The Lower Green River And Coastal Plain Systems In Western Kentucky, David Cravens

Online Theses and Dissertations

The banded pygmy sunfish Elassoma zonatum is a wide-ranging species found throughout the Southeastern Coastal Plain of North America. In Kentucky, the populations are found above and below the inner boundary of the Coastal Plain. Due to their geographical separation comparisons in body size and morphological features along with genetic comparisons using mitochondrial cytochrome-b (Cyt-b) were conducted to test relationships between populations. Two sites, Cypress Creek in the Lower Green River system and Rose Creek in the Tradewater River drainage, were sampled from above the inner boundary and two additional sites, Bayou de Chien and Running Slough in the Mississippi …

Sample Collection And Dna Extraction Methods For Environmental Dna Metabarcoding In Headwater Streams, Michael Triston Mullins

Online Theses and Dissertations

DNA is found to be free and ubiquitous in the environment where it is no longer associated with the source organism, and is also known as environmental-DNA (eDNA). Methods optimized for specific environments may be able supplement insight to local taxa richness. With the advent of high throughput sequencing and the proliferation of sequence data in public repositories, insights to the biodiversity of communities at the molecular level have been possible. Thus, this study compared commonly used DNA capture (water precipitation and filtration) and extraction (MoBio's PowerWater, Qiagen's DNeasy Blood and Tissue Kit, and a CTAB protocol) methods in their …

Glucocorticoids And Parental Effort In Tree Swallows (Tachycineta Bicolor), Mackenzie Prichard

Undergraduate Theses, Professional Papers, and Capstone Artifacts

All vertebrates respond to stressful situations through the release of hormones called glucocorticoids (CORT). These hormones alter processes within the body to prioritize long term survival over immediate reproduction. It is hypothesized that this is helps individuals survive until conditions become more favorable for successful reproduction. Historically, stress was hypothesized to primarily to pull organisms out of reproductive life history stages when unfavorable conditions made offspring survival slim (otherwise known as the “CORT-tradeoff hypothesis”). However, recent evidence suggests that birds actively feeding nestlings show elevated CORT levels, possibly due to the increased metabolic demands of parenthood. This relationship has been …

Invasion Dynamics Of The Exotic Liana Euonymus Fortunei (Turcz.) Hand.-Mazz. (Wintercreeper), Todd J. Rounsaville

Theses and Dissertations--Biology

Elevated atmospheric CO₂ has been implicated as a driver of increased liana abundance worldwide. Known as disturbance creators and beneficiaries, lianas possess the potential to significantly influence forest ecosystems. I investigated the early-invasion dynamics of Euonymus fortunei (wintercreeper), an evergreen liana that is invading forests in eastern North America, disrupting native plant communities and ecosystem functions.

Wintercreeper is widely cultivated as an ornamental groundcover, frequently invading natural areas via asexual stem growth. Invasion of remote natural areas is dependent upon seed transport and may occur less frequently. I examined the mechanisms of seed dormancy by conducting a ‘move-along’ experiment …

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 …

Using Genomics To Understand Population Demographics In The Context Of Amphibian Conservation, Schyler O. Nunziata

Theses and Dissertations--Biology

Understanding the demography of species over recent history (e.g., < 100 years) is critical in studies of ecology and evolution, but records of population history are rarely available. Large single nucleotide polymorphism datasets generated with restriction-site associated DNA sequencing (RADseq), in combination with demographic inference methods, are improving our ability to gain insights into the population history of both model and non-model species. However, to assess the performance of genetic methods it is important to compare their estimates of population history to known demography, in both simulation and empirical settings. Here, I used a simulation approach to examine the potential for RADseq datasets to accurately estimate effective population size (N_e) in Wright-Fisher populations over the course of stable and declining population trends, and distinguish stable from steadily declining populations over a contemporary time scale (20 generations). Overall, my results reveal that demographic inference using genome-wide data can be successfully applied to estimate N_e, and the detection of population-size declines. Next, I assess these methods in an empirical study from a wetland with 37 years of amphibian mark-recapture data to study the utility of genetically-based demographic inference on salamander species with documented population declines (Ambystoma talpoideum) and …

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 …

Nematodes Associated With Mammals In The Great American Biotic Interchange (Gabi), F. Agustin Jimenez, Juliana Notarnicola, Scott Lyell Gardner

Scott L. Gardner Publications

The Great American Biotic Interchange (GABI) is a large-scale zoogeographic event that illustrates the exchange and diversification of mammals between North and South America. This phenomenon was accelerated by the connection of both landmasses during the Pliocene. Support for this phenomenon includes the extant distribution of xenarthrans, didelphiomorph marsupials, hystricognath and cricetine rodents, sciurids and carnivores, as well as the distribution of fossils in the stratigraphic record and the coalescence of genotypes. Contrasting with the relatively well-documented role and history of mammals in GABI, the role of their parasites has been largely neglected. As a consequence, the reconstructions of the …

Rewiring Metabolism Under Oxygen Deprivation: Naked Mole-Rats Evolved A Means To Cope With Anoxia, Jay F. Storz, Grant B. Mcclelland

Jay F. Storz Publications

When faced with a reduced availability of oxygen in the environment (hypoxia), vertebrates can make a variety of respiratory, cardiovascular, and hematological adjustments to ensure an uninterrupted supply of oxygen to the cells of metabolizing tissues (1, 2). These are adaptive solutions for “aerobic organisms in an aerobic world” (3). Coping with the complete absence of oxygen (anoxia) requires more fundamental alterations of cellular metabolism that are typically nothing more than emergency stopgap measures to buy time until the oxygen supply is (hopefully) reestablished (4). On page 307 of this issue [Science 356 (6335)], Park et al. (5) identify a …

Biotic Interchange Has Structured Western Hemisphere Mammal Communities, Danielle Fraser, S. Kathleen Lyons

School of Biological Sciences: Faculty Publications

Aim.— Many hypotheses posit that species-rich tropical communities are dominated by speciesspecies interactions, apparent as competitive exclusion or character displacement, whereas species-poor temperate communities are dominated by species-environment interactions. Recent studies demonstrate a strong influence of macroevolutionary and biogeographic factors. We simultaneously test for the effects of species interactions, climate, and biotic interchange on Western Hemisphere mammal communities using a phylogenetic and functional diversity approach.

Location.— Western Hemisphere.

Time period.— Modern

Major taxa studied.— Mammalia

Methods.— Using Western Hemisphere mammal distributional and body mass data, we calculate body mass dispersion, phylogenetic diversity (Net Relatedness Index), and assemblage-averaged rates of co-occurrence …

Palynological Investigation Of Mummified Human Remains, Karl Reinhard, Marina Milanello Do Amaral, Nicole Wall

Karl Reinhard Publications

Pollen analysis was applied to a mummified homicide victim in Nebraska, U.S.A., to determine the location of death. A control sample showed the normal ambient pollen in the garage crime scene. Ambient windborne types, common in the air of the region, dominated the control. Internal samples were analyzed from the sacrum, intestine, and diaphragm. Microfossils were recovered from the rehydrated intestine lumen. The intestinal sample was dominated by Brassica (broccoli). The sacrum sample was high in dietary types but with a showing of ambient types. The pollen from the diaphragm was dominated by ambient pollen similar to the control samples. …

Impact Of Disease On The Survival Of Three Commercially Fished Species, John M. Hoenig, Maya L. Groner, Matthew W. Smith, Wolfgang K. Vogelbein, David M. Taylor, Donald F. Landers Jr., John T. Swenarton, David T. Gauthier

Biological Sciences Faculty Publications

Recent increases in emergent infectious diseases have raised concerns about the sustainability of some marine species. The complexity and expense of studying diseases in marine systems often dictate that conservation and management decisions are made without quantitative data on population-level impacts of disease. Mark-recapture is a powerful, underutilized, tool for calculating impacts of disease on population size and structure, even in the absence of etiological information. We applied logistic regression models to mark-recapture data to obtain estimates of disease-associated mortality rates in three commercially important marine species: snow crab (Chionoecetes opilio) in Newfoundland, Canada, that experience sporadic epizootics …

Effects Of Prescribed Fire On Cope’S Gray Treefrog (Hyla Chrysoscelis) Across Habitat Scales And Life Stages, Logan Mcdonald

Theses and Dissertations

Fire may alter both aquatic and terrestrial habitat used by all amphibian life stages, yet, our knowledge of its effects on amphibians is primarily limited to adult responses. I present an integrated approach to test the response of Cope’s Gray Treefrog (Hyla chrysoscelis) to fire by examining responses in tadpole performance and survivorship, adult abundance, and oviposition. Tadpoles raised with burned leaf litter had similar survival, but total mass and total length were 440% and 170% greater, respectively, for tadpoles raised in unburned litter. I assessed terrestrial and aquatic oviposition cues by embedding burned and unburned litter treatments within burned …

A Comparative Analysis Of Geometric Morphometrics Across Two Pseudemys Turtle Species In East Central Virginia, Kristin C. Dillard

Theses and Dissertations

The phylogeny of the turtle genus Pseudemys is poorly understood. In Virginia, many turtles have been found with indicator traits of both eastern river cooters (Pseudemys concinna concinna) and northern red bellied cooters (Pseudemys rubriventris). This study explores morphological evidence for hybridization between the two species across three riverine sites in east central Virginia.

Museum voucher groups for each species were analyzed for relative shell height and plastron length. The shape of the plastral scutes and upper jaw were analyzed using landmark-based morphometric software. These metrics were compared with measurements taken from 188 field-caught Pseudemys specimens. …

The Soundscape Of The St. Johns River And Its Potential Impacts On The Habitat Use Patterns Of Bottlenose Dolphins, Carissa Deeann King

UNF Graduate Theses and Dissertations

The development of effective management plans for animal populations relies on an understanding of how the population is utilizing the habitat as well as the identification of any critical habitat areas. The St. Johns River (SJR), an urban estuary with a high level of anthropogenic disturbance, is home to a resident population of bottlenose dolphins (Tursiops truncatus). In chapter one, SJR dolphin habitat use patterns, the factors that influenced these patterns, and the critical habitat areas were identified. Significant associations were found in most pair-wise comparisons between season, behavioral state, group size, water depth, and location, indicating that …

Persistence Of The Larval Environment On Post-Metamorphic Performance And Population Dynamics In Amphibians, Julie Charbonnier

Theses and Dissertations

Organisms with complex life cycles may experience diverse stressors during their development. Stressors experienced in early life stages may influence the quantity and quality of individuals in later life stages. However, it is unclear if these effects persist later in life and how they may influence population dynamics. This dissertation uses two amphibian species, the Western spadefoot toad (Pelobates cultripes) and the spotted salamander (Ambystoma maculatum) to explore how biotic and abiotic factors experienced in aquatic and terrestrial environments influence phenotype and survival. We use a combination of field mesoscosm studies, laboratory studies and modeling to …