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Neutral And Adaptive Genetic Variation In North American Hardwood Tree Species, Sudhir Khodwekar

Dissertations, Master's Theses and Master's Reports

'Northern Hardwoods,’ are a characteristic composition of multiple tree species and a part of the rich and diverse northeastern forests. Hardwoods e.g. oaks (Quercus: Fagaceae and Sugar maple), serve as foundation species and offer ecological and economical gains to wildlife and humans. Most of the forest trees go through many biotic and abiotic stresses, for example climate change in their long life span. To overcome these threats and to adapt to changing conditions, tree species need to maintain variation especially in adaptive genes. Therefore, it is necessary to analyze genetic diversity within forest tree populations and take appropriate …

The Effect Of The Chromoshadow Domains Of Hhp1, Hpl1, And Hpl2 On Heterochromatin Protein Localization In Tetrahymena Thermophila, Claire Bagnani

Scripps Senior Theses

In the nucleus, post-translational modifications on histone N-terminal tails can determine how local DNA is packaged. In one case, T. thermophila proteins Hhp1, Hpl1, and Hpl2, all related to the Heterochromatin Protein 1 (HP1) family, are associated with heterochromatin and thus gene silencing. They may do this by binding to trimethylated lysine 9 and lysine 27, located on the tail of histone H3. One distinct region of these proteins, the chromodomain (CD), may bind these marks, while another region, the chromoshadow domain (CSD) homodimerizes to interact with other proteins. This study explores what effect, if any, the CSD has on …

Plantcv V2: Image Analysis Software For High-Throughput Plant Phenotyping, Malia A. Gehan, Noah Fahlgren, Arash Abbasi, Jeffrey C. Berry, Steven T. Callen, Leonardo Chavez, Andrew N. Doust, Max J. Feldman, Kerrigan B. Gilbert, John G. Hodge, J. Steen Hoyer, Andy Lin, Suxing Liu, César Lizárraga, Argelia Lorence, Michael Miller, Eric Platon, Monica Tessman, Tony Sax

Department of Agronomy and Horticulture: Faculty Publications

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the diversity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV) software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here we present the details and rationale for major …

An Analysis Of White-Tailed Deer, Odocoileus Virginianus, Killed In Deer Vehicle Accidents On Bulloch County, Ga Roadways, Mackenzie P. Payne 4003933

Honors College Theses

White-tailed deer, Odocoileus virginianus, are native to Georgia. With over 1.2 million individuals in the state, White-tailed deer have been implicated in a large number of motor vehicle collisions (ca. 1 million) each year. It is unknown, however, if deer are more likely to be killed: 1) if they are of particular ages (or classes), and 2) in areas with specific road characteristics. We addressed these two questions by collecting the remains of 20 White-tailed deer killed in deer vehicle collisions (“deer vehicle accidents” - DVAs) in Bulloch County, GA. When a deer was located, the road characteristics were …

Michigan Academician, Volume 45, Issue 1

Michigan Academician

No abstract provided.

Chimpanzee (Pan Troglodytes) Space Use In A Sanctuary Setting, Holly Soubiea

All Master's Theses

Studies of chimpanzee space use can provide information about chimpanzees’ preferences and welfare. This study examined the space use of 12 chimpanzees at Fauna Foundation, a chimpanzee sanctuary located in Carignan, Québec, Canada. Observers recorded the chimpanzees’ location, elevation, perimeter, and substrate using a scan sampling procedure. In total, there were 93 hours of data and 3,190 scans. The author used Geographical Information System (GIS) to plot the chimpanzees’ location for each scan. The chimpanzees used the largest rooms most often, were inside 61% (n = 1,942) of the time, an arm’s reach away from the perimeter 90% (n = …

The Social Behavior Of Rehabilitated Spider Monkeys (Ateles Geoffroyi), Anthony Denice

All Master's Theses

The welfare of captive primates in laboratories, sanctuaries, and zoos is affected by various aspects of their environments. Although space restrictions increase aggression and stress-related behaviors in most captive animals, primates show diverse mechanisms for displacing stress and mitigating conflict. Many primates, including wild spider monkeys (genus Ateles), use these mechanisms flexibly to cope with social and environmental stressors. I investigated whether or not captive black-handed spider monkeys (Ateles geoffroyi) use behavioral strategies to cope with potential stressors in captivity. In particular, I tested whether an affiliative or avoidant strategy was used in response to changes in …

Collective Decision Making In Tibetan Macaques: How Followers Affect The Rules And Efficiency Of Group Movement, Amanda Rowe

All Master's Theses

Primate societies must undergo successful collective decision making during group movement to stay cohesive and provide the ecological and evolutionary benefits of sociality. This study investigates how a fan structure facilitates successful group movement in the YA1 group of Tibetan macaques (Macaca thibetana) at Mt. Huangshan National Reserve in Anhui, China. We used structural equation modeling (SEM) to determine the relative influences of sex, age, maternal kinship, dominance, and social network centrality on the number of fans (consistent followers) an individual had, and the number of group members an individual was a fan of (fandom). SEM revealed that …

Enrichment Use & Social Interactions In A Mixed-Species Enclosure Of Sumatran (Pongo Abelij) & Bornean Orangutans (P. Pygmaeus) & Northern White-Cheeked Gibbons (Nomascus Leucogenys), Emily Veitia

All Master's Theses

Enrichment is an aspect of captive husbandry that has been shown to positively impact animals’ well-being and can be designed to encourage species-typical behaviors, such as foraging and arboreality. Enrichment can include housing together multiple compatible species. Orangutans are sympatric with siamangs and agile and Bornean gibbons, so several zoos house these four Asian ape species in the same enclosure, in part, as social enrichment. In my study, I observed enrichment use and social interactions in a mixed-species enclosure at the Oregon Zoo, which housed two Sumatran (Pongo abelii) and two Bornean (P. pygmaeus) orangutans with …

Process-Based Modelling Shows How Climate And Demography Shape Language Diversity, Michael C. Gavin, Thiago F. Rangel, Claire Bowern, Robert K. Colwell, Kathryn R. Kirby, Carlos A. Botero, Michael Dunn, Robert R. Dunn, Joe Mccarter, Marco Tulio Pacheco Coelho, Russell D. Gray

Biology Faculty Research

Aim

Two fundamental questions about human language demand answers: why are so many languages spoken today and why is their geographical distribution so uneven? Although hypotheses have been proposed for centuries, the processes that determine patterns of linguistic and cultural diversity remain poorly understood. Previous studies, which relied on correlative, curve-fitting approaches, have produced contradictory results. Here we present the first application of process-based simulation modelling, derived from macroecology, to examine the distribution of human groups and their languages.

Location

The Australian continent is used as a case study to demonstrate the power of simulation modelling for identifying processes shaping …

Front Matter

The Synapse: Intercollegiate science magazine

No abstract provided.

The Progression Of Lyme Disease In The State Of Virginia, Margaret Michel

Honors Theses

Lyme disease has spread in the United States from the northeast to more southern and western parts of the country. It has been shown that the tick which most often carries the Lyme disease pathogen (Borrelia burgdorferi) in North America, Ixodes scapularis, has also spread to these new areas of concern. In Virginia, the disease has progressed from the eastern shore to the western, more mountainous regions. Through obtaining historical museum specimens of mice from 11 locations in Virginia, we seek to determine whether the Lyme disease causing pathogen, B. burgdorferi, has always been present in …

Fitness Costs And Inheritance Of Bt Cry2ab2 Resistance In Fall Armyworm, Spodoptera Frugiperda (J.E. Smith), Binod Acharya

LSU Master's Theses

Evolution of resistance in target pest populations is a major threat to the sustainability of transgenic crops expressing Bacillus thuringiensis (Bt) proteins. Fall armyworm, Spodoptera frugiperda (J.E. Smith), is a cross-crop target pest of Bt corn, Bt cotton, and Bt soybean. This pest, thus far, is the only target pest species that has developed field resistance to Bt crops in multiple areas across countries. Cry2Ab2 is a common Bt protein expressed in transgenic corn and cotton targeting lepidopteran pests including S. frugiperda. The objective of this study was to characterize fitness costs and inheritance of Cry2Ab2 resistance in S. frugiperda. …

Ancient Dna Extraction From Stone Tools, Clare Super

Undergraduate Theses, Professional Papers, and Capstone Artifacts

Proteins and DNA can be trapped in the microcracks on the surface of stone tools, which can then be extracted and analyzed to aid in inferring the use of the tool (Shanks et al. 2001; 2005). This nondestructive method involves the use of sonication to release DNA from the microcracks, then amplification of regions of mitochondrial DNA that are species specific. This technique was applied to stone tools from the Bridge River site in British Columbia by researchers at UMT’s Ancient and Modern Molecular Anthropology labs. Bridge River archaeologists have designated the tools as used in “food processing or tool …

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. …

Communicating Canine And Human Emotions, Juliane Bräuer, Karine Silva, Stefan R. Schweinberger

Animal Sentience

Kujala (2017) reviews a topic of major relevance for the understanding of the special dog-human relationship: canine emotions (as seen through human social cognition). This commentary draws attention to the communication of emotions within such a particular social context. It highlights challenges that need to be tackled to further advance research on emotional communication, and it calls for new avenues of research. Efforts to disentangle emotional processes from cognitive functioning might be necessary to better comprehend how they contribute, alone and/or in combination, to the communication of emotions. Also, new research methods need to be developed to account for the …

Managing Sociality Of A Captive Female Bornean Orangutan From Breeding To Post-Partum At The Smithsonian's National Zoo, Marie Vergamini

Theses and Dissertations

The Association of Zoos and Aquariums’ Orangutan Species Survival Plan® aims to maintain 100 Bornean orangutans (Pongo pygmaeus) in captivity. Because investment in breeding these lineages is high, properly managing sociality of potential mothers is essential. This study assessed how behaviors of a captive breeding female at the Smithsonian’s National Zoo changed from pre-gestation through the offspring’s sixth month of age to improve breeding recommendations.

The infant Bornean orangutan was born September 2016. Results indicate that during breeding, the mother socialized most with two adult females. During pregnancy, the pregnant female socialized in less energy-consuming ways, i.e. grooming. …

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. …

Gender Perception Of The Rationales Behind Vegetarianism, Nicholas Tallant

Honors Theses

No abstract provided.

The Database Of The Predicts (Projecting Responses Of Ecological Diversity In Changing Terrestrial Systems) Project, Lawrence N. Hudson, Tim Newbold, Sara Contu, Samantha L.L. Hill, Igor Lysenko, Adriana De Palma, David J. Flaspohler, Et. Al.

Michigan Tech Publications, Part 1

The PREDICTS project—Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)—has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in …

Shoring Up The Precautionary Bar, Jon Mallatt

Animal Sentience

I offer four ways to reinforce Birch’s precautionary principle so it can be used effectively and practically in deciding which animals to cover by legislation for humane treatment: (1) add one more credible indicator of sentience to the BAR rule; (2) use phylogenetic classification, not the outdated Linnaean classification, to test which animal clades have sentience; (3) disentangle the pain of suffering from sentience; and (4) reconsider the sentient status of decapods and insects to remove potential inconsistencies in the proposed framework.

Support For The Precautionary Principle, Jennifer Mather

Animal Sentience

The precautionary principle gives the animal the benefit of the doubt when its sentient status is not known. This is necessary for advanced invertebrates such as cephalopods because research and evidence concerning the criteria for sentience are scattered and often insufficient to give us the background for the decision.

Scientific Uncertainty And The Animal Sentience Precautionary Principle, Michael L. Woodruff

Animal Sentience

Jonathan Birch offers the animal sentience precautionary principle (ASPP) as a framework for assigning sentience to animals. In doing this, he defines a BAR which when crossed will lead to action (ACT) and implementation of the ASPP. His effort to create a clear empirical basis for implementation of the precautionary principle in the area of animal welfare regulation is important. I argue, however, that his BAR is so low that the evidence supporting ACT is in danger of being overwhelmed by the problems of induction and the underdetermination of theory by evidence. If this happens, policy makers might well disregard …

Direct Perception Of Animal Mind, Paul Morris

Animal Sentience

Kujala’s (2017) target article is ostensibly focused on how everyday folk (fail to) make sense of canine emotions. However, the theories outlined in the article apply to making sense of all aspects of the mentality of both human and non-human animals. The target article neglects the fundamental arguments surrounding the problem of other minds. I explore the relevant arguments and briefly review approaches suggesting that our everyday-life sense that both human and non-human animals are thinking, feeling, emotional beings has a secure epistemological basis.

Sentience In Living Tissue, Alfredo Pereira Jr.

Animal Sentience

I agree with Woodruff’s concept of sentience but must disagree about what he proposes as the biological correlates of feeling. Based on the interpretation of brain function originally presented by Camilo Golgi, I assume that feelings are instantiated by hydro-ionic waves in living tissue. From this viewpoint, the anatomical, physiological and behavioural criteria of Woodruff would not be necessary to argue for sentience in fish.

Nagel-Ing Worries About Fish Sentience, Hugh Lafollette

Animal Sentience

Woodruff (2017) argues that teleosts’ more sophisticated behaviors make sense only if they are sentient. Moreover, their neuroanatomy, although different from mammalian, is sufficiently complex to support sentience. I answer some potential objections to Woodruff’s argument, and try to trace its moral significance. In so doing, I briefly address Birch’s (2017) target article as well.

Mental Representations Are Not Necessary For Fish Consciousness, Luis H. Favela

Animal Sentience

Woodruff (2017) argues that teleost fishes are capable of phenomenal consciousness. Central to his argument is the assumption that phenomenal consciousness is representational in nature. I think the commitment to a representational theory of consciousness undermines Woodruff’s case for teleost phenomenal consciousness. The reason is that organisms do not need to perceive the world indirectly via mental images/representations in order to have phenomenological experiences. My argument is based on considerations of ecological psychology and comparative ethology.

Animal Models, Agendas And Sentience, Thomas Creson

Animal Sentience

Woodruff’s target article on teleost consciousness is a well-organized logical argument for considering the fish as a sentient being. This becomes more important for animal ethical discussion as the fish becomes a more important and legitimate animal model for investigating animal states and traits associated with higher levels of behavior such as learning and memory.

Anecdotes Can Be Evidence Too, Heather Browning

Animal Sentience

Birch’s criterion for the precautionary principle imposes a high evidential standard that many cases will fail to meet. Reliable, relevant anecdotal evidence suggestive of animal sentience should also to fall within the scope of the precautionary principle. This would minimize potential suffering (as happened in the case cephalopods) while further evidence is gathered.

Canine Emotions And The Bond Between Humans And Dogs, Robert G. Franklin Jr.

Animal Sentience

I explore how the findings reviewed by Kujala (2017) influence our understanding of the human-dog bond. The special social cognitive abilities of dogs may be unique among animal species, probably influenced by the circumstances surrounding canine domestication. The bond has influenced animal welfare policies, giving dogs a privileged place among animals. To determine what protections other species should have in a rational animal welfare policy, more research is needed on whether other species have similar social cognitive abilities.