Digital Commons Network^™

Primate Phylogenomics: Developing Numerous Nuclear Non-Coding, Non-Repetitive Markers For Ecological And Phylogenetic Applications And Analysis Of Evolutionary Rate Variation, Zuogang Peng, Navin Elango, Derek E. Wildman, Soojin V. Yi

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Genetic analyses are often limited by the availability of appropriate molecular markers. Markers from neutrally evolving genomic regions may be particularly useful for inferring evolutionary histories because they escape the constraints of natural selection. For the majority of taxa however, obtaining such markers is challenging. Advances in genomics have the potential to alleviate the shortage of neutral markers. Here we present a method to develop numerous markers from putatively neutral regions of primate genomes.

Results

We began with the available whole genome sequences of human, chimpanzee and macaque. Using computational methods, we identified a total of 280 potential …

Peptide Hydrolysis And The Uptake Of Dipeptides By Phytoplankton, Margaret R. Mulholland, Cindy Lee

OES Faculty Publications

Rates of peptide hydrolysis (using the fluorescent substrate, lucifer yellow anhydride-labeled tetra-alanine) and dipeptide uptake (using dually labeled, ¹⁵N and ¹³C, dialanine) were measured in phytoplankton cultures and in natural populations during algal blooms dominated by one or two taxa. During most sampling events, both peptide hydrolysis and dipeptide uptake were greatest in the size fraction containing the dominant phytoplankter, suggesting that phytoplankton contribute substantially to or may even dominate observed extracellular peptide hydrolysis and dipeptide uptake in the environment. These are the first data suggesting that dipeptides may be taken up directly by phytoplankton and this may …

Ecology Of Neotropical Arboreal Snakes And Behavior Of New World Mollusk-Eating Snakes, Julie M. Ray

Biological Sciences Theses & Dissertations

The Neotropics is a biologically diverse region that provides man opportunities for ecological and behavioral studies. I utilized the speciose ophidian fauna of central Panama to explore the general ecology of arboreal snakes, the defensive behaviors of the snake community, and the diet of mollusk-eating snakes. I studied arboreal species to understand interspecilic relationships in several morphometric characters and to examine preferences in habitat. There were significant morphometric differences in relative length of jaw, mass, tail length, and size at midbody. The arboreal realm was partitioned among species by distance to ground, distance to water, and diameter of the perch. …

Patterns Of Spiny Lobster (Panulirus Argus) Postlarval Recruitment In The Carribbean: A Crtr Project, Mark J. Butler Iv, Angela M. Mojica, Eloy Sosa-Cordero, Marines Millet, Paul Sanchez-Navarro, Miguel A. Maldonado, Juan Posada, Bladimir Rodriguez, Carlos M. Rivas, Adrian Oviedo, Marcio Arrone, Martha Prada, Nick Bach, Nilda Jimenez, Maria Del Carmen Garcia-Rivas, Kirah Forman, Donald C. Behringer Jr., Thomas Matthews, Claire Paris, Robert Cowen

Biological Sciences Faculty Publications

As part of the Coral Reef Targeted Research (CRTR) Program, a partnership between the Global Environment Facility and the World Bank, our research team examined the recruitment patterns of Caribbean spiny lobster (Panulirus argus) postlarvae among regions in the Caribbean, with a particular focus on Mesoamerica. Our goal was to collect comparable information on postlarval supply among regions and to provide data to test predictions of connectivity generated from a coupled biophysical oceanographic model of lobster larval dispersal. Here we present the results of the postlarval recruitment monitoring program. We monitored the catch of postlarvae on Witham-style collectors …

Fundamentals For Using Geographic Information Science To Measure The Effectiveness Of Land Conservation Projects, Robert G. Pontius Jr., Shaily Menon, Joseph Duncan, Shalini Gupta

Other Scholarly Publications

Some humans spend a tremendous amount of effort to change landscapes from a “natural” state to a “developed” state for a variety of desirable economic uses, such as urban, agriculture, transportation, and mining. Others spend a tremendous amount of effort to prevent such development in order to conserve the landscapes for a variety of important environmental uses, such as biodiversity maintenance, carbon storage, water filtration, and landslide prevention. It would be efficient in theory if a society were to focus its development efforts at locations that give the largest economic utility per area developed, and to focus its conservation efforts …

Nutrient Dynamics In A Created Desert Wetland: Implications For The Rio Bosque Wetlands Park, Ruth Rodriguez

Open Access Theses & Dissertations

Rio Bosque Wetland Park is an arid wetland currently under restoration, which primarily receives water inputs from the Bustamante Waste Water Treatment Plant (WWTP) during the non-irrigation season. Understanding the ability of a desert wetland to remove nutrients from the water column through uptake by primary producers or sediment transformations is key to justifying the protection and creation of other similar wetland sites. Nitrate concentrations tended to be reduced, relative to the inflow, near the outflow of the wetland.To further understand these trends, sediment nutrient release experiments and algal nutrient limitation experiments were completed. Sediment phosphorus release experiments indicated that …

Assemblage Of Hymenoptera Arriving At Logs Colonized By Ips Pini (Coleoptera: Curculionidae: Scolytinae) And Its Microbial Symbionts In Western Montana, Celia K. Boone, Diana Six, Steven J. Krauth, Kenneth F. Raffa

Ecosystem and Conservation Sciences Faculty Publications

Colonization of a tree by bark beetles and their symbionts creates a new habitat for a diverse assemblage of arthropods, including competing herbivores, xylophages, fungivores, saprophages, predators, and parasitoids. Understanding these assemblages is important for evaluating nontarget effects of various management tactics and for subsequently evaluating how changes in climate, the presence of invasive species, and altered forestry practices and land-use tenure may affect biodiversity. We characterized the assemblage of hymenopterans attracted to logs of ponderosa pine (Pinus ponderosa C. Lawson (Pinaceae)) colonized by the bark beetle Ips pini (Say) and its microbial symbionts. In one experiment, the composition and …

Controls Over Leaf Litter Decomposition In Wet Tropical Forests, William R. Wieder, Cory C. Cleveland, Alan R. Townsend

Ecosystem and Conservation Sciences Faculty Publications

Tropical forests play a substantial role in the global carbon (C) cycle and are projected to experience significant changes in climate, highlighting the importance of understanding the factors that control organic matter decomposition in this biome. In the tropics, high temperature and rainfall lead to some of the highest rates of litter decomposition on earth, and given the near-optimal abiotic conditions, litter quality likely exerts disproportionate control over litter decomposition. Yet interactions between litter quality and abiotic variables, most notably precipitation, remain poorly resolved, especially for the wetter end of the tropical forest biome. We assessed the importance of variation …

Transport Of Fungal Symbionts By Mountain Pine Beetles, K. P. Bleiker, S. E. Potter, C. R. Lauzon, Diana Six

Ecosystem and Conservation Sciences Faculty Publications

The perpetuation of symbiotic associations between bark beetles (Coleoptera: Curculionidae: Scolytinae) and ophiostomatoid fungi requires the consistent transport of fungi by successive beetle generations to new host trees. We used scanning electron microscopy and culture methods to investigate fungal transport by the mountain pine beetle (MPB), Dendroctonus ponderosae Hopkins. MPB transports its two main fungal associates, Grosmannia clavigera (Robinson-Jeffrey and Davidson) Zipfel, de Beer and Wingfield and Ophiostoma montium (Rumbold) von Arx, in sac-like mycangia on the maxillary cardines as well as on the exoskeleton. Although spores of both species of fungi were observed on MPB exoskeletons, often in pits, …

Estrogenic Compounds Downstream From Three Small Cities In Eastern Nebraska: Occurrence And Biological Effect, Marlo K. Sellin, Daniel D. Snow, Debbie L. Akerly, Alan S. Kolok

Biology Faculty Publications

Recent studies have detected estrogenic compounds in surface waters in North America and Europe. Furthermore, the presence of estrogenic compounds in surface waters has been attributed, in some cases, to the discharge of wastewater treatment plant (WWTP) effluent. The primary objective of the current study was to determine if WWTP effluent contributes estrogens to the surface waters of Nebraska. A second objective of this study was to determine if estrogens were found in concentrations sufficient enough to manifest feminizing effects on fish. These objectives were satisfied by deploying polar organic chemical integrative samplers (POCIS) and caged fathead minnows at eight …

Letter From The Dean, Lalit Verma

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

No abstract provided.

Integrated Responses Of Crustaceans Inhabiting Estuaries To The Challenges Of Feeding And Digestion In Low Salinity, Daniel Luke Curtis

UNLV Theses, Dissertations, Professional Papers, and Capstones

Estuaries are highly productive and serve as vital habitats for numerous decapod crustacean species. However, the environmental conditions within estuaries are often highly dynamic and subject to large changes in salinity and temperature that occur on seasonal and tidal scales. Not all of the species occupying these habitats are adept in coping with changes in these environmental conditions. This dissertation describes the influence of low salinity conditions on the 1) habitat preference, 2) feeding behaviour and 3) digestive physiology of crustaceans inhabiting estuaries. I have primarily focussed on a weak osmoregulator, the Dungeness crab, Cancer magister , but have also …

Effects Of Plant Uptake And Micro-Topography On Chloride Transport In Arid Soils, Wenming Nie

UNLV Theses, Dissertations, Professional Papers, and Capstones

Chloride concentration profiles to depths of 1 m were evaluated on a young alluvial fan in Eldorado Valley, NV. It was found that chloride beneath plant canopies were 11 to 222 times higher than adjacent (1 - 2 m away) bare soil locations. Two-dimensional numerical simulations using HYDRUS 2D/3D model were used to further explore the impact of plants on chloride transport. The simulation results indicated that lateral flow driven by root uptake concentrated chloride toward root zones, leading to the accumulation of chloride under plant canopies. Results also suggest that locally micro-topography can have a substantial impact on chloride …

Molecular Systematics And Phylogeography Of The Genus Richardsonius, Derek Dee Houston

UNLV Theses, Dissertations, Professional Papers, and Capstones

The complex geological and climatic events that significantly altered the landscape throughout the Cenozoic Era impacted the diversification of many North American taxa, including freshwater fishes. Here, I employ an array of phylogenetic analyses using a multiple gene tree approach to address several questions regarding the phylogenetic relationships of the North American cyprinid genus Richardsonius and two other closely related genera, Clinostomus and Iotichthys. I also use divergence time estimates generated using fossil calibrations to qualitatively assess the phylogeographic implications of evolution within and among these three genera. Mitochondrial and nuclear DNA sequences show a sister relationship between Iotichthys and …

What's Up With Fiddler Crabs: Does Larval Dispersal Render Genetic Similarity In The Disjunct Distribution Of Uca Minax (Uca: Ocypodidae)?, Alexa Warwick

Honors Program Theses

The red-jointed fiddler crab, Uca minax, has a disjunct distribution along the Atlantic and Gulf coasts in North America. Previous studies have not found any significant discrepancies in morphology, physiology, or allozymes between the two groups of U.minax. The primary objective of this study was to use DNA sequence data to test whether genetic variation is consistent with patterns of morphological, physiological, and allozyme variation of the disjunct populations. We collected mitochondrial cytochrome oxidase subunit I and nuclear internal transcribed spacer sequences from approximately 100 individuals distributed across the range. Phylogenetic analyses of the haplotypes revealed no genetic differentiation …

Pervasive Hitchhiking At Coding And Regulatory Sites In Humans, James J. Cai, J. Michael Macpherson, Guy Sella, Dmitri A. Petrov

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Much effort and interest have focused on assessing the importance of natural selection, particularly positive natural selection, in shaping the human genome. Although scans for positive selection have identified candidate loci that may be associated with positive selection in humans, such scans do not indicate whether adaptation is frequent in general in humans. Studies based on the reasoning of the MacDonald–Kreitman test, which, in principle, can be used to evaluate the extent of positive selection, suggested that adaptation is detectable in the human genome but that it is less common than in Drosophila or Escherichia coli. Both positive and purifying …

The Distribution Of Unpaired During Drosophila Oogenesis, Travis Sexton

University of Kentucky Doctoral Dissertations

Janus Kinase (JAK) activity specifies the cell fates of the follicular epithelium during Drosophila oogenesis by establishing a gradient of JAK activity with highest levels at the A/P poles. Unpaired (Upd), a ligand for the pathway, is expressed and secreted exclusively from the polar cells potentially establishing the JAK activity gradient. This project proposed that Upd acts as a morphogen to directly establish the JAK activity gradient, specifying the fates of the follicular epithelium. The aims of this work were to investigate the extracellular distribution of Upd and, in addition, factors that may be involved. Furthermore, upd3, a gene …

Unionoida (Mollusca: Margaritiferidae, Unionidae) In Arkansas, Third Status Review, John L. Harris, William R. Posey Ii, C. L. Davidson, Jerry L. Farris, S. R. Oetker, J. N. Stoeckel, B. G. Crump, M. S. Barnett, H. C. Martin, J. H. Seagraves, M. W. Matthews, R. Winterringer, C. Osborne, Alan D. Christian, N. J. Wentz

Journal of the Arkansas Academy of Science

We analyzed stream inventories, phylogeographic studies, community and population estimates, life history and reproductive biology research, and suitable habitat investigations conducted from 1997-2008, as well as the Arkansas Natural Heritage Commission mussel database, to update the conservation status for all native freshwater unionoid bivalves thought to occur in Arkansas. Prior to this study, Harris et al. (1997) reviewed the distribution and status of 75 freshwater mussels considered native to Arkansas and ranked 22 species as endangered, threatened or special concern. We now recognize 85 mussel taxa in Arkansas; however, some of those have yet to be described or their nomenclature …

Mussel Inventory And Population Status Of The Federally Endangered Potamilus Capax (Green 1832) In The Tyronza River, Arkansas, N. J. Wentz, John L. Harris, Jerry L. Farris, Alan D. Christian

Journal of the Arkansas Academy of Science

Currently, few data exist for the mussel assemblages of the Tyronza River, Arkansas. The goal of this project was to inventory the freshwater mussel assemblages of the Tyronza River and determine the status of the federally endangered Potamilus capax. We qualitatively and quantitatively sampled mussel assemblages and documented the occurrence of S1 (extremely rare), S2 (very rare), and S3 (rare to uncommon) species. A total of 70.4 river kilometers were sampled in 2006 and 2007 resulting in 363 sampling sites, 4030 live individuals, and 25 species. We observed a total of 1 S1, 2 S2, and 9 S3 species. Mean …

Tidal Influences On Bacterial And Phytoplankton Abundances And The Resulting Effects On Patterns Of Dissolved Oxygen In The Skidaway River Estuary, Casey Colleen Brazell

College of Graduate Studies: Theses & Dissertations

Two studies were conducted to investigate the physical and biological processes contributing to the dissolved oxygen (DO) availability in the Skidaway River Estuary (SRE), Savannah, GA during the summer of 2005. A temporal study looked at changes in DO concentrations, Chlorophyll a concentrations, bacterial abundance, water depth, and salinity, every hour, for 26 hours, over both a neap and a spring tide. A spatial study looked at changes in the above variables at 5 sites along the SRE while following the tide inland during a neap high and low tide, and a spring high and low tide. DO concentrations varied …

Effects Of Habitat Quality On Reproduction In Two Georgia Populations Of Gopherus Polyphemus, Jaqueline W. Entz

College of Graduate Studies: Theses & Dissertations

Author's Abstract: The purpose of this study was to examine differences in maternal investment by examining variation in the habitat structure and reproductive parameters for two populations of Gopherus polyphemus in Southeast GA. Both habitat structure and reproductive parameters for these populations are known from a previous study, thus this study expands upon the previous one and addresses four main questions. (1) Has habitat quality changed in the past ten years within and between population sites? (2) Could a change of habitat have affected female morphology or female reproductive parameters within or between populations? (3) Is female body size shaping …

Surface Mining And Reclamation Effects On Flood Response Of Watersheds In The Central Appalachian Plateau Region, Todd R. Lookingbill, Joseph R. Ferrari, B. Mccormick, P. A. Townsend, K. N. Eshleman

Geography and the Environment Faculty Publications

Surface mining of coal and subsequent reclamation represent the dominant land use change in the central Appalachian Plateau (CAP) region of the United States. Hydrologic impacts of surface mining have been studied at the plot scale, but effects at broader scales have not been explored adequately. Broad-scale classification of reclaimed sites is difficult because standing vegetation makes them nearly indistinguishable from alternate land uses. We used a land cover data set that accurately maps surface mines for a 187-km2 watershed within the CAP. These land cover data, as well as plot-level data from within the watershed, are used with HSPF …

Altered Ecological Flows Blur Boundaries In Urbanizing Watersheds, Todd R. Lookingbill, Sujay S. Kaushal, Andrew J. Elmore, Robert Gardner, Keith N. Eshleman, Robert H. Hilderbrand, Raymond P. Morgan, Walter R. Boynton, Margaret A. Palmer, William C. Dennison

Geography and the Environment Faculty Publications

The relevance of the boundary concept to ecological processes has been recently questioned. Humans in the post-industrial era have created novel lateral transport fluxes that have not been sufficiently considered in watershed studies. We describe patterns of land-use change within the Potomac River basin and demonstrate how these changes have blurred traditional ecosystem boundaries by increasing the movement of people, materials, and energy into and within the basin. We argue that this expansion of ecological commerce requires new science, monitoring, and management strategies focused on large rivers and suggest that traditional geopolitical and economic boundaries for environmental decision making be …

Demographics And Habitat Selection For The Western Meadowlark (Sturnella Neglecta) In The Nebraska Sandhills, Matthew D. Giovanni

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

The prairie ecosystems of the Great Plains region in North America have largely been replaced and fragmented with industrial agriculture and invasive herbaceous and woody plant species. The concurrent and large-scale suppression of wildfire and elimination of grazing by native ungulates may have further decreased the availability and quality of habitat for wildlife. Indeed, 2004 estimates indicate only 30% of historic grasslands in the Great Plains still exist, while the trends of decreased land area enrolled in the Conservation Reserve Program and increased land area in commercial agriculture indicate continued loss of habitat. This decrease in habitat availability continues to …

Planted Grasslands And Native Sod Prairie: Equivalent Habitat For Grassland Birds, Kristel K. Bakker, Kenneth F. Higgins

Natural Resource Management Faculty Publications

Little is known about how avian relationships to tracts of native sod prairie compare with avian relationships to single and multiple species of cool- and warm-season grassland plantings. We compared grassland bird species richness and density in 5 grassland cover types (n = 97) in the tallgrass prairie region of eastern South Dakota and western Minnesota, 2001–2004. Grassland bird species richness was significantly higher in native sod prairies than it was in all planted cover types except warm-season mixes. Grasslands dominated by exotic species did not support as many grassland bird species or have species densities as high as grasslands …

Dietery Response Of Sympatric Deer To Fire Using Stable Isotope Analysis Of Liver Tissue, W. D. Walter, T. J. Zimmerman, D. M. Leslie Jr., J. A. Jenks

Natural Resource Management Faculty Publications

Carbon (δ13C) and nitrogen (δ15N) isotopes in biological samples from large herbivores identify photosynthetic pathways (C3 vs. C4 ) of plants they consumed and can elucidate potential nutritional characteristics of dietary selection. Because large herbivores consume a diversity of forage types, δ13C and δ15N in their tissue can index ingested and assimilated diets through time. We assessed δ13C and δ15N in metabolically active liver tissue of sympatric mule deer (Odocoileus hemionus) and white-tailed deer (O. virginianus) to identify dietary disparity resulting from use of burned and unburned areas in a largely forested landscape. Interspecific variation in dietary disparity of deer …

Direct And Indirect Effects Of Climate Change On A Prairie Plant Community, Peter B. Adler, James Leiker, Jonathan M. Levine

Wildland Resources Faculty Publications

Background

Climate change directly affects species by altering their physical environment and indirectly affects species by altering interspecific interactions such as predation and competition. Recent studies have shown that the indirect effects of climate change may amplify or counteract the direct effects. However, little is known about the the relative strength of direct and indirect effects or their potential to impact population persistence.

Methodology/Principal Findings

We studied the effects of altered precipitation and interspecific interactions on the low-density tiller growth rates and biomass production of three perennial grass species in a Kansas, USA mixed prairie. We transplanted plugs of each …

The Fourth Level Of Social Structure In A Multi-Level Society: Ecological & Social Functions Of Clans In Hamadryas Baboons, Amy Schreier, Larissa Swedell

Publications and Research

Hamadryas baboons are known for their complex, multi-level social structure consisting of troops, bands, and one-male units (OMUs) [Kummer, 1968]. Abegglen [1984] observed a 4^th level of social structure comprising several OMUs that rested near one another on sleeping cliffs, traveled most closely together during daily foraging, and sometimes traveled as subgroups independently from the rest of the band. Abegglen called these associations “clans” and suggested that they consisted of related males. Here we confirm the existence of clans in a second wild hamadryas population, a band of about 200 baboons at the Filoha site in lowland Ethiopia. During …

Male Aggression Towards Females In Hamadryas Baboons: Conditioning, Coercion And Control, Larissa Swedell, Amy Schreier

Publications and Research

No abstract provided.

Mckillop Library Electricity Use, Impacts And Solutions, Nellie Tarini, Marisa Volo, Carly Ouellette, Other Students

BIO140 Carbon Footprint Project

A few weeks ago, our class went on a guided tour of the library, which taught us about what goes on in the library, how resources are used, and basically how the library operates. From our tour, we saw many problem areas that could use improvements. One of these areas is the library’s use of electricity. Our group focused on the computers, printers, copiers, lights, and elevators in the library and how the library could use their electricity more efficiently. We have found that the library is not always using electricity effectively and efficiently. There are lights on when nobody …