• Phylogenomics: Molecular Evolution in the Genomics Era

      Seetharam, Arun Somwarpet (2012-10-19)
      Evolutionary studies in recent years have been transformed by the development of new, powerful techniques for investigating many mechanisms and events of molecular evolution. Large collections of many different complete genomes now available in the public domain offer great advantages to genomic scale evolutionary studies. Phylogenomics, a term often used to describe the use of genomic scale data to infer species phylogeny or to predict protein function through evolutionary history, is greatly benefitted by the revolutionary progress in DNA sequencing technology. In the present study we developed and utilized various phylogenomic methods on large genome-scale data. In the first study, we applied Singular Value Decomposition (SVD) analysis to reexamine current evolutionary relationships for 12 Drosophila species using the predicted proteins from whole genomes. An SVD analysis on unfiltered whole genomes (193,622 predicted proteins) produced the currently accepted Drosophila phylogeny at higher dimensions, except for the generally accepted, but difficult to discern, sister relationship between D. erecta and D. yakuba. Also, in accordance with previous studies, many sequences appear to support alternative phylogenies. In this case, we observed grouping of D. erecta with D. sechellia when approximately 55% to 95% of the proteins were removed using a filter based on projection values or by reducing resolution by using fewer dimensions. In the second study, we simulated restriction enzyme digestions on 21 sequenced genomes of various Drosophila species. Using the fragments generated by simulated digestion from the predicted targets of 16 Type IIB restriction enzymes, we sampled a large and effectively arbitrary selection of loci from these genomes. The resulting fragments were then used to compare organisms and to calculate the distance between genomes in pair-wise combination by counting the number of shared fragments between the two genomes. Phylogenetic trees were then generated for each enzyme using this distance measure, and the consensus was calculated. The consensus tree obtained agrees well with the currently accepted tree for these Drosophila species. We conclude that multi-locus sub-genomic representation combined with next generation sequencing, especially for individuals and species without previous genome characterization, can improve studies of comparative genomics and the building of accurate phylogenetic trees. The third study utilized the relatively new Daphnia genome in an attempt to identify 40 orthologous groups of C2H2 Zinc-finger proteins that were previously determined to be well conserved in bilaterians. We identified 58 C2H2 ZFP genes in Daphnia that belong to these 40 distinct families. The Daphnia genome appears to be relatively efficient with respect to these well-conserved C2H2 ZFP, since only 7 of the 40 gene families have more than one identified member. Worms have a comparable number of 6. In flies and humans, C2H2 ZFP gene expansions are more common, since these organisms display 15 and 24 multi-member families respectively. In contrast, only three of the well-conserved C2H2 ZFP families have expanded in Daphnia relative to Drosophila, and in two of these cases, just one additional gene was found. The KLF/SP family in Daphnia, however, is significantly larger than that of Drosophila, and many of the additional members found in Daphnia appear to correspond to KLF 1/2/4 homologs, which are absent in Drosophila, but present in vertebrates. The last study was conducted to investigate the conservation and distribution of 38 C2H2 ZNF gene families in Eukaryotes. We combined two popular approaches for homolog detection, Reciprocal Best Hit (RBH) and Hidden–Markov model (HMM) profile search, on a diverse set of complete genomes of 124 eukaryotic species ranging from excavates to humans. We succeeded in identifying 3,675 genes as distinct members of the 38 C2H2 gene families. This largely automated technique is much faster than manual methods and is able to detect homologs accurately and efficiently among a diverse set of organisms. Our analysis of the 38 evolutionarily conserved C2H2 ZNF gene families revealed a stepwise appearance of ZNF families, agreeing well with the phylogenetic relationship of the organisms compared and their presumed stepwise increase in complexity.
    • Physiological Responses to Temperature in the Lizard, Sceloporus Undulatus

      Ehrenberger, Joseph C. (2010-07-20)
      Temperature affects all organisms differently. Physiological processes, such as metabolism, interact with temperature to determine a minimal rate of energy loss. Physiological limits, such as heat and cold tolerances, likely constrain the activity and survival of organisms. Ultimately, these physiological processes and limits determine a species‘ geographical distribution. Through experiments, I sought to understand specifically how temperature affects the physiology of the lizard Sceloporus undulatus. This species is a model organism to answer such questions, as it is geographically widespread species and well-described phylogenetically. In the first experiment, I compared standard metabolic rates of lizards from three locales and interpreted these rates in the context of the metabolic theory of ecology—a set of models that describes the effects of body mass and body temperature on metabolic rate. My findings indicate that metabolic rate increases with body size, but that the exact nature of this relationship depends on temperature; this result contrasts a major assumption of the metabolic theory of ecology, which stresses the need to evaluate this theory through by examining intraspecific variation. In my second experiment, I measured the preferred body temperatures and critical thermal limits of S. undulatus. Existing theory indicates that physiological traits associated with temperature may be evolutionary static or labile. By measuring these traits from seven populations, which cover the majority of this species‘ range, I have provided one of the most comprehensive comparisons of thermal physiology in a single biological species. My results are consistent with the static view of thermal physiology, suggesting that thermal physiology has not adapted to local conditions in this species.
    • Place Construction, Identity, and Capital Investment: An investigation of two tourist landscapes in Michigan

      Stawarski, Andrew (2011-07-20)
      Tourist communities exist all over the world. They are areas that are focused on tourism and are often tailored to resemble specific regions or themes to better achieve capital gain. In this study, two cities in Michigan are examined to better understand how the cultural landscapes are experienced and what practices are employed throughout the landscape. Specifically, this thesis investigates the spatial practices that are involved in re-creating and re-presenting ―themed‖ landscapes. Another question analyzed is whether the ―themed‖ landscapes reflect the resident‘s daily lives and/or their histories. This thesis examines the two Michigan cities of Gaylord and Frankenmuth, re-presenting and re-creating Alpenfest and Frankenmuth, respectively, and their emphasis on tourism within their respective communities. To better understand the cultural environment and themed landscapes, digital images are used throughout this thesis of both cities. The data for these themed landscapes were geocoded and analyzed. Also, photographs of both cities were used to demonstrate that only modifications to the façade and additions to the structures were merely aesthetic in nature, and are not realistic but stereotypes of the regions they were representing.
    • Place names of Parke County, Indiana

      Seits, Laurence (2014-08-12)
      Not Available
    • Pollinator Deception and Plant Reproductive Success in Jack-In-The-Pulpit

      Pettit, Joseph L. (2010-07-20)
      I conducted a study of the deceptive pollination system of Jack-in-the-pulpit (Arisama triphyllum, Araceae) in forests of west-central Indiana. I focused on (a) determining the identities and abundances of insect visitors to spathes, (b) evaluating the success of female spathes in setting fruit, (c) determining the relative importance of pollinator visitation and plant size for fruit number, and (d) investigating the function of the female spathe’s lack of an exit hole, which has been hypothesized to improve pollination success. I found that (a) Jack-in-the-pulpit receives visits from both flies and thrips. Counts of fly corpses from spathes showed the most prevalent families to be Mycetophilidae and Sciaridae with other nematoceran families and a few brachyceran families present as well. Visitation by thrips, determined by visual inspection of spathes, was low, involving only 30% of plants. (b) Fifty-seven percent of female plants set fruit, with much variation among sites. (c) Mushroom flies, especially the families Mycetophilidae and Sciaridae, were found to be the primary pollinators of Jack-in-thepulpit based on pollen loads, visit rates, and an exclusion experiment. Pollination by thrips, though possible, probably had only a minor effect. (d) An experiment that created an exit hole in female spathes yielded no support for the hypothesis that lack of an exit hole (the natural condition) improves fruit set.
    • Population genetic structure of blanding's turtle(emydiodea blandingii)in New York.

      McCluskey, Eric M (2012-04-25)
      The loss of genetic diversity is a major concern in conservation biology.As wild populations decline and become more isolated from one another overall genetic diversity is influenced by inbreeding,genetic drift and gene flow.Some of the consequences of inbreeding and genetic drift and gene flow are a decrease in a specie's adaptability and accumulation of deleterious alleles.As wetlands vanish,aquatic species can be permanently isolated with no access to adjacent habitat.I investigated how habitat fragmentation and population isolation are affecting gene flow and genetic diversity in Blanding's turtle(Emydoidea blandingii)populations in New York State.Four county populations(Jefferson,St Lawrence,Saratoga,Dutchess)and an adjacent Ontario population were included in this study.These represent populations both peripheral(Jefferson,St Lawrence,Ontario)and disjunct(Saratoga,Dutchess) to the main range.I found evelated genetic diversity in the populations on the periphery of the main range in the northern section of the state compared to the two eastern,disjunct populations.Subpopulations structuring was also evident in the St Lawrence and Dutchess Co populations.
    • Raising African American student graduation rates:A best practices study of predominantly white liberals arts college.

      Pool, Robert W (2012-05-21)
      This qualitative study sought to explore best practices at small, private liberal arts institutions that experienced large increases in African American graduation rates. Particular focus was on institutions that enrolled less than 17% minority students whose overall enrollment fell within the middle 50% of all SAT scores and the middle 50% of institutional full time equivalent (FTE) spending. Two colleges were selected for study via one-on-one interviews of key personnel, focus groups of students, and institutional document analyses. Themes from the data which participants felt contributed to the unusually large African American graduation rate increases are discussed.
    • Remote Sensing of Tanzanian Volcano Oldoinyo Lengai: Verifying Detection Methods of Flow Activity

      Frystak, Scott Richard (2013-01-30)
      Every day volcanoes erupt with varying magnitudes across the globe, and remote sensing used to keep track of volcanic activity would be a useful application. One promising use of remote sensing to understand volcanoes at a distance is to distinguish gaseous or lava flow activity. Current methods for differentiating volcanic activity with remote sensing have only been applied at Mt. Etna, and research is still needed to verify that the detection of gaseous or lava flow activity is possible at volcanoes with different compositions. The subject of this study, the Oldoinyo Lengai volcano, is a natrocarbonatite stratovolcano with drastically different chemical composition from Mt. Etna. These composition differences allow for the verification of gaseous or lava flow activity remotely over time. Furthermore, looking closely at how volcano composition affects detection will allow us to understand the variables required to detect gaseous or lava flow activity. The results of the research are inconclusive, but provide useful information for this application of remote sensing. For Oldoinyo Lengai, the Landsat TM data were unable to resolve lava flows or degassing activity, due to a combination of the volcano’s small size, the lack of lava flows, and/or pixel saturation. Superior sensors such as hyperspectral sensors are needed to adequately perform the analysis, and would likely result in the capability to differentiate volcanic activity. Further applicability of the study is prudent due to the varying nature of volcanoes and sensors. Gathering additional detailed information should be at the forefront of volcanic monitoring research.
    • Sex-instruction as the core of a high school biology course

      Woodrow, Walter H. (2012-06-28)
      Not Available.
    • Sexual Selection and Plumage in the Polymorphic White-throated Sparrow

      Rathbun, Nathan (2010-07-20)
      Feather coloration has been known to be connected with sexual selection for many years. It also provides an opportunity to study evolution, focusing on sexual selection and natural selection. Plumage is affected by both of these forces and the equilibrium is where these forces balance. The white-throated sparrow gives us a unique opportunity to observe the effects of the different strengths of these forces within a species. First, I established that there were differences in plumage characteristics between the morphs and sexes. White males had the brightest white and darkest black feathers. White females and tan males were the next brightest, with tan females having the dullest white and lightest black head stripes. Using plumage characteristics I was able to predict the morph/sex class of the bird significantly more than by chance. With the exact differences between each morph/sex class now known, I looked at the relationship between fitness and plumage. White males with higher overall contrast (brighter white, darker black) were more successful than duller white males. This was attributed to the males displaying their quality to females. Duller tan males however, were more successful than brighter tan males. With duller plumage, they may reduce predation on their nest while they are feeding their offspring. The differences in reproductive strategy changed the relative strength of natural and sexual selection between the morphs. Observing this interaction in this system will let us judge the relative strength of these forces in other systems.
    • Some recent investigations in the teaching of mathematics

      Strong, Orvel E. (2012-08-20)
      Not Available.
    • Spatial decision support system for abandoned coal mine reclamation.

      Liu, Qian (2012-05-16)
      Abandoned coal mines and mining activities typically cause severe environmental problems related to erosion and pollutant transportation.Because of the lack of data integration,traditional methods and procedures of reclamation plan design must go through a time-consuming process.As new technologies from a variety of fields have been revolutionizing the way in which planning is conducted,it is practical to find a more efficient approach to deal with complex reclamation planning.In this research,a Geographic Information System(GIS),remotely sensed data,erosion modeling,and Multi-Criteria Decision Making(MCDM)methods were integrated to implement a Spatial Decision Support System(SDSS)for better reclamation planning.The newly developed Open Development Environment(ODE)and GIS componentware technology were adopted to provide GIS functions and to build the interface.The system was designed to facilitate the prioritizing of specific areas for reclamation within a region of abandoned coal mines.
    • Studies of Bee Diversity in Indiana: The Influence of Collection Methods on Species Captures, and a State Checklist Based on Museum Collection

      Jean, Robert P. (2011-03-29)
      Bees are among the most important of pollinators, but little is known about their status. I expand the knowledge of the bees of the Midwest by updating the bees of Indiana, the first update in over fifty years, by adding two local bee species inventories, in the black oak savannas of northeastern Indiana and another reconstructed based on museum specimens, and by comparing two methods for sampling bees. Bees from six families, 52 genera, and 416 species are represented in Indiana, an addition of over 200 species from precious lists. Species ranged from common to rare with a median abundance of 22 specimens. Distributions, life histories, flight decade, but several species have not been collected in the last 20-50 years. These are mainly rare or were last collected in an area or on a host flower species which has not been sampled recently. Four bumble bee species appear to be declining and another is likely extirpated. Bees are commonly sampled either by netting at flowers or by bowl trapping. The bases of these techniques were explored while inventorying black oak savannas. Netting at flowers collected more species at any given site, but using both methods gave the best picture of species richness. Both techniques collected all common species and differed mainly in the rare species collected. Smaller bees were significantly more likely to be captured in bowls, especially within the families Halictidae and Apidae. Bowls were also more likely to catch more bees when fewer flower resources were available for bees. These studies represent a significant addition to knowledge of bee distribution and abundance in the Midwest.
    • Summer Indiana Bat Ecology in the Southern Appalachians: An Investigation of Thermoregulation Strategies and Landscape Scale Roost Selection

      Hammond, Kristina (2014-03-18)
      In the southern Appalachians there are few data on the roost ecology of the federally endangered Indiana bat (Myotis sodalis). During 2008-2012, we investigated roosting ecology of the Indiana bat in ~280,000 ha in the Great Smoky Mountains National Park, Cherokee National Forest, and Nantahala National Forest in the southern Appalachians Mountains of Tennessee and North Carolina. We investigated 2 aspects of the Indiana bat’s roosting ecology: thermoregulation and the extrinsic factors that influence body temperature, and landscape-scale roost selection. To investigate thermoregulation of bats at roost, we used data gathered in 2012 from 6 female Indiana bats (5 adults and 1 juvenile) to examine how reproductive condition, group size, roost characteristics, air temperature, and barometric pressure related to body temperature of roosting bats. We found that air temperature was the primary factor correlated with bats’ body temperatures while at roost (P < 0.01), with few differences detected among reproductive classes in terms of thermoregulatory strategies. To understand how Indiana bats select roosts on a landscape-scale, we created a presence-only model through the program MaxENT using 76 known roost locations to identify areas important to summer roosting habitat within our study area and to identify important landscape-scale factors in habitat selection. The final model showed that Indiana bats selected roosts on the upper portion of ridges on south facing slopes in mixed pine-hardwood forests at elevations of 260-700 meters. Unfortunately, due to small sample size and the large effort required to fully investigate thermoregulation of Indiana bats in the southern Appalachians, we only were able run correlations with temperature data, and further investigation is needed to make concrete conclusions. However, the new advancements in resolution of landscape cover data and new programs in spatial modeling have enabled us to produce a large scale spatial model for identifying Indiana bat summer roosting habitat within our study area. Our findings have added to our understanding of Indiana bat roosting ecology, particularly in the southern Appalachian Mountains, and will aid land managers in effective management for this federally endangered species.