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Theoretical And Practical Utility Of Gene Sequences In Phylogenetic And Phylogeographic Analysis, Robert Aaron Makowsky

Biology Dissertations - Archive

Phylogenetics, or the study of evolutionary relationships among organisms, is a rapidly changing field due primarily to the dramatic increase in available molecular characters and increasingly sophisticated theoretical and computational methods. Current phylogenetic methods, though, poorly handle such large datasets due to the extremely large number of calculations required. In this dissertation, I focus on a method that can reduce datasets with a large number of molecular characters and at the same time optimize the performance of phylogenetic methods. Chapter 1 provides background information about phylogenetic methods, with a specific emphasis on Bayesian phylogenetic methods. MrBayes is the most common …

Intensity Of Herbivory On Kelp By Fish And Sea Urchins Differs Between Inshore And Offshore Reefs, Mathew Vanderklift, Paul Lavery, Kris Waddington

Research outputs pre 2011

Interactions between water motion, primary productivity, and herbivory are complex. Rates of grazing by fish on tropical coral reefs and by sea urchins on temperate rocky reefs are usually high, but can be low in areas of extreme water motion. Some herbivores can switch between mobile (grazing) and sedentary (drift-feeding) behaviours, and this can be influenced by water motion. We compared the relative consumption of the kelp Ecklonia radiata at rocky reefs in western Australia with different wave exposures (inshore versus offshore). No herbivory was recorded offshore, suggesting that wave exposure might inhibit herbivory. We also compared grazing by fish …

Detection Of Mycoplasma Hyopneumoniae In Pigs In Turkey, Arzu Funda Bağcigi̇l, Serkan İki̇z, N. Yakut Özgür

Turkish Journal of Veterinary & Animal Sciences

Mycoplasma hyopneumoniae is the primary agent of enzootic pneumonia in pigs. The aim of this study was to investigate the occurrence of M. hyopneumoniae in pigs raised in Turkey. Samples were obtained from the lungs of 286 pigs, which had already been separated from the carcasses at slaughter. Lung tissues were homogenized in 5 ml of Friis medium, the suspensions were inoculated into Friis medium, and then incubated at 37 °C until they developed an acid color change or for 21 days. Cultures were identified by M. hyopneumoniae-specific PCR. M. hyopneumoniae was recovered from 2 (0.70%) of the 286 lung …

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 …

Gordie News, January 2009, West Chester University Of Pennsylvania

Gordon Natural Area History & Strategic Plan Documents

No abstract provided.

Gordon Natural Area (Gna) - (2009) - An Ecological Treasure Island In A Sea Of Development, Gerard Hertel

Gordon Natural Area History & Strategic Plan Documents

No abstract provided.

Land Resources Series No 21 - Tambellup-Borden Area Land Resources Survey, Angela Stuart-Street, Rohan Marold

Natural resources published reports

AGDEX 526

Land Resources Series No. 21

This report presents results from soil-landscape mapping at a scale of 1: 100,000 in the Tambellup- Borden area of Western Australia. It is accompanied by a soil-landscape map covering almost 511,000 hectares.

Most of the survey occurs within the upper Frankland-Gordon, Kent, North Stirlings Basin and upper reaches of the Pallinup and Kalgan River catchments. The survey falls within the Katanning and Albany Department of Agriculture and Food advisory districts.

Seventeen soil-landscape systems have been identified and are represented on the map on the accompanying CD-ROM. These systems have been further divided into …

The Eradication Of Invasive Mammal Species: Can Adaptive Resource Management Fill The Gaps In Our Knowledge?, Sugoto Roy, Graham C. Smith, James C. Russell

Human–Wildlife Interactions

Invasive alien species (IAS) threaten global biodiversity; they are the major cause of species extinction on offshore islands. Management of IAS requires data on the ecology of species in their new environment, how these species respond to management, and how these processes interact. Often, however, there is a paucity of information on key biological parameters that are critical to making management decisions. We sent a questionnaire to professionals and organizations managing invasive species and asked the respondents to prioritize a list of information they required to carry out eradication of invasive species. We analysed responses to assess the level of …

The Self Reported Aggravating Activities Of Chronic Non Specific Low Back Pain Patients Do Not Demonstrate A Consistent Directional Pattern: An Observational Study, Benedict M. Wand, Rebecca Hunter, Neil E. O'Connell, Louise Marston, James Mcauley

Health Sciences Papers and Journal Articles

Question: Do the self-reported aggravating activities of chronic non-specific low back pain patients demonstrate a consistent directional pattern?

Design: Cross-sectional observational study. Participants: 240 chronic non specific low back pain patients.

Outcome measure: We invited experienced clinicians to classify each of the three self-nominated aggravating activities from the Patient Specific Functional Scale by the direction of lumbar spine movement. Patients were described as demonstrating a directional pattern if all nominated activities moved the spine into the same direction. Analyses were undertaken to determine if the proportion of patients demonstrating a directional pattern was greater than would be expected by chance. …

Ancient Leishmaniasis In A Highland Desert Of Northern Chile, Maria Antonietta Costa, Carney Matheson, Lucia Iachetta, Otto Appenzeller

Harold W. Manter Laboratory of Parasitology: Library Materials

Background

Leishmaniasis is an infectious disease endemic today in many areas of South America.

Methodology

We discovered morphologic and molecular evidence of ancient infections in four female skulls in the archaeological cemetery of Coyo Oriente, in the desert of San Pedro de Atacama, northern Chile. The boney facial lesions visible in the skulls could have been caused by a number of chronic infections including chronic Leishmaniasis. This diagnosis was confirmed using PCR-sequenced analyses of bone fragments from the skulls of the affected individuals. Leishmaniasis is not normally found in the high-altitude desert of northern Chile; where the harsh climate does …

Agroecology As A Science, A Movement And A Practice: A Review, A. Wezel, S. Bellon, T. Doré, Charles A. Francis, D. Vallod, C. David

Department of Agronomy and Horticulture: Faculty Publications

Agroecology involves various approaches to solve actual challenges of agricultural production. Though agroecology initially dealt primarily with crop production and protection aspects, in recent decades new dimensions such as environmental, social, economic, ethical and development issues are becoming relevant. Today, the term ‘agroecology’ means either a scientific discipline, agricultural practice, or political or social movement. Here we study the different meanings of agroecology. For that we analyse the historical development of agroecology. We present examples from USA, Brazil, Germany, and France. We study and discuss the evolution of different meanings agroecology. The use of the term agroecology can be traced …

Nagmia Rodmani N. Sp., Nagmia Cisloi N. Sp. And Probolitrema Richiardii (López, 1888) (Gorgoderidae: Anaporrhutinae) From Elasmobranchs In The Gulf Of California, Mexico, Stephen S. Curran, Charles K. Blend, Robin M. Overstreet

Harold W. Manter Laboratory of Parasitology: Faculty Publications

The generic diagnosis of Nagmia Nagaty, 1930, is emended to include species having some vitelline follicles extending into the extracecal space. Two new species belonging in the genus are described from the Gulf of California: Nagmia rodmani n. sp. from the body cavity of the giant electric ray, Narcine entemedor Jordan and Starks, 1895, and Nagmia cisloi n. sp. from the body cavity of the smoothtail mobula, Mobula thurstoni (Lloyd, 1908). Both species are distinguished from each other and the 13 other known congeners by the number of testicular follicles, ratio of widths of oral sucker to ventral sucker, and …

Integration Of Modified Universal Soil Loss Equation (Musle) Into A Gis Framework To Assess Soil Erosion Risk, Yanli Zhang, J. Degroote, Calvin Wolter, Ramanathan Sugumaran

Faculty Publications

Soil erosion is an important economic and environmental concern throughout the world. In order to assess soil erosion risk and conserve water and soil resources, soil erosion modeling at the watershed scale is urgently needed. This study integrated the Modified Universal Soil Loss Equation (MUSLE) in a Geographic Information System (GIS) framework in the form of a tool called ArcMUSLE, an extension of ArcGIS® software, to assist soil and water conservation agencies in soil erosion risk assessment and prioritization of critical areas for soil erosion control practices. With widely available spatial data, this tool can be applied to determine curve …

Determining The Role Of Environmental Factors And Disturbance In The Distribution Of Reed Canary Grass Within Wetlands, Kathryn M. Marlor

Dissertations, Master's Theses and Master's Reports - Open

Reed canary grass (Phalaris arundinacea L.) is an invasive species originally from Europe that has now expanded to a large range within the United States. Reed canary grass possesses a number of traits that allow it to thrive in a wide range of environmental factors, including high rates of sedimentation, bouts of flooding, and high levels of nutrient inputs. Therefore, the goals of our study were to determine if 1) certain types of wetland were more susceptible to Reed canary grass invasion, and 2) disturbances facilitated Reed canary grass invasion.

This study was conducted within the Keweenaw Bay Indian …

A Revision Of The Freshwater Crabs Of Mt. Kenya And The Aberdare Mountains , Neil Cumberlidge

Journal Articles

No abstract provided.

"A Revision Of The Freshwater Crabs Of Mt Kenya And The Aberdare Mountains, Kenya, East Africa" , Neil Cumberlidge

Journal Articles

No abstract provided.

The Taxonomic Designation Of Eriogonum Corymbosum Var. Nilesii (Polygonaceae) Is Supported By Aflp And Cpdna Analyses, M. W. Ellis, J. M. Roper, R. Gainer, J. P. Der, Paul G. Wolf

Biology Faculty Publications

We examined populations of perennial, shrubby buckwheats in the Eriogonum corymbosum complex and related Eriogonum species in the subgenus Eucycla, to assess genetic affiliations of the recently named E. corymbosum var. nilesii. The known populations of this varietyare all located in Clark County, Nevada, U. S. A. We compared AFLP profiles and chloroplast DNA sequences of plants sampled from populations of E. corymbosum var. nilesii with those of plants representing other E. corymbosum varieties and related Eriogonum species from Colorado,Utah, northern Arizona, and northern New Mexico. We found evidence of genetic cohesion among the Clark County populations as well astheir …

Global Chloroplast Phylogeny And Biogeography Of Bracken (Pteridium: Dennstaedtiaceae), J. P. Der, J. A. Thomson, J. K. Stratford, Paul G. Wolf

Biology Faculty Publications

Bracken ferns (genus Pteridium) represent an ancient species complex with a natural worldwide distribution. Pteridium has historically been treated as comprising a single species, but recent treatments have recognized several related species. Phenotypic plasticity, geographically structured morphological variation, and geographically biased sampling have all contributed to taxonomic confusion in the genus. We sampled bracken specimens worldwide and used variable regions of the chloroplast genome to investigate phylogeography and reticulate evolution within the genus. Our results distinguish two major clades within Pteridium, a primarily northern hemisphere Laurasian/African clade, which includes all taxa currently assigned to P. aquilinum, and a primarily southern …

Adiantum Viridimontanum, Aspidotis Densa, Minuartia Marcescens, And Symphyotrichum Rhiannon: Additional Serpentine Endemics From Eastern North America, T B. Harris, N Rajakaruna

Faculty Publications, Biological Sciences

Serpentine outcrops around the world are known to harbor disproportionately high rates of plant endemism. Remarkable cases of serpentine endemism occur in New Caledonia and Cuba, with 3178 and 920 endemic taxa, respectively, found solely on serpentine. Despite the patchy occurrence of serpentine in eastern North America from Québec and Newfoundland south to Alabama, only one taxon, Cerastium velutinum var. villosissimum, has been broadly recognized as a serpentine endemic for the region. Based on reports in the literature, we suggest that Adiantum viridimontanum, Minuartia marcescens, and Symphyotrichum rhiannon be considered endemic to serpentine soils from the east coast of North …

Historical Review Of Elk-Agriculture Conflicts In And Around Riding Mountain National Park, Manitoba, Canada, Ryan K. Brook

Human–Wildlife Interactions

Conflicts between elk (Cervus elaphus) and farmers have been occurring since the 1880s when agriculture began around what is now Riding Mountain National Park (RMNP). Initially, the conflicts were related to low elk numbers caused primarily by unregulated harvest of elk. The creation of RMNP in 1930 and the associated ban on hunting allowed elk numbers to reach critically high levels. Since farming began, elk have been associated with considerable damage to fences and crops around RMNP, with annual damage often >$240,000. Hunting on agricultural lands has been the most common approach to mitigating elk impacts, despite its …

Potential Export Of Unattached Benthic Macroalgae To The Deep Sea Through Wind Driven Langmuir Circulation, H. M. Dierssen, Richard C. Zimmerman, Lisa A. Drake, David J. Burdige

OES Faculty Publications

Carbon export to the deep sea is conventionally attributed to the sinking of open ocean phytoplankton. Here, we report a Langmuir supercell event driven by high winds across the shallow Great Bahama Bank that organized benthic non-attached macroalgae, Colpomenia sp., into visible windrows on the seafloor. Ocean color satellite imagery obtained before and after the windrows revealed a 588 km² patch that rapidly shifted from highly productive macroalgae to bare sand. We assess a number of possible fates for this macroalgae and contend that this event potentially transported negatively buoyant macroalgae to the deep Tongue of the Ocean …

Honors Convocation Speech (Text And Audio), Jonathan Dey

Honorees for Teaching Excellence

No abstract provided.

A Phylogeographic Analysis Of Fiddler Crabs, Uca Longisignalis And U. Pugnax, Cydney Brooks

Dissertations and Theses @ UNI

Uca pugnax and U. longisignalis are fiddler crabs commonly found in the southeastern United States. These sibling species occupy distinct regions. Uca pugnax is found on the Atlantic and U. longisignalis on the Gulf coasts. Their distributions are separated by the Florida peninsula. Many different taxa with similar distributions in this region have been the focus of phylogeographic studies. In these studies, it appears there is no simple pattern to explain genetic variability. Previous studies of Uca pugnax and U. longisignalis reveal no significant morphological or physiological differences within either species across its respective region. The purpose of this study …

Multivariate Morphometric Study On Apis Florea Distributed In Iran, Ayça Özkan, Mohammed M. Gharleko, Berna Özden, İrfan Kandemi̇r

Turkish Journal of Zoology

Multivariate Morphometric and Spatial Autocorrelation Analyses were performed to determine the morphometric variation in Apis florea colonies representing 13 localities from 4 states on the coastal north-south diagonal in Iran. New morphometric characters (hind wing length, hind wing width, and hind wing angles) were also measured to determine the usefulness of these characters for Apis florea. Analysis of variance of new morphometric characters showed that 7 out of the 8 hind wing variables displayed statistically significant differences among populations (P < 0.05). The scatter plot from Canonical Variate Analysis revealed that the colonies from north (Ilam, Khuzestan, and Bushehr states) showed an overlapping distribution. The colonies from south (Hormuzgan state) formed a non-overlapping distant cluster. Based on the spatial autocorrelation analysis, 14 correlograms were significant for morphometric characters (According to the Bonferroni criterion). Six characters (CuB, C.Ind, HWW, B4, D7, and I13) showed clinal type correlogram.

Problems With The Claim Of Ecotype And Taxon Status Of The Wolf In The Great Lakes Region, Matthew A. Cronin, L. David Mech

United States Geological Survey, Northern Prairie Wildlife Research Center: Publications

Koblmuller et al. (2009) analyzed molecular genetic data of the wolf in the Great Lakes (GL) region of the USA and concluded that the animal was a unique ecotype of grey wolf and that genetic data supported the population as a discrete wolf taxon. However, some of the literature that the researchers used to support their position actually did not, and additional confusion arises from indefinite use of terminology. Herein, we discuss the problems with designation of a wolf population as a taxon or ecotype without proper definition and assessment of criteria.

Koblmuller et al. (2009) wrote ‘The GL …

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 …

Recent Occurrence Of An American Black Bear In Nebraska, Justin D. Hoffman, Sam Wilson, Hugh H. Genoways

University of Nebraska State Museum: Mammalogy Papers

We report on a young male, cinnamon-phase American black bear (Ursus americanus) that was collected in northwestern Nebraska on May 12, 2008. This specimen represents the first black bear taken in Nebraska since 1907. Cranial characteristics and mass of the individual indicated a 15–16-month old bear. This bear may have dispersed from the Laramie Mountains in southeastern Wyoming along the North Platte River into western Nebraska. This record adds to the growing number of cases where large carnivores are reinvading previously occupied territory in the Great Plains. These reinvasions potentially have broad ecological implications to local prey populations …

Pollen-Based Biome Reconstructions For Latin America At 0, 6000 And 18 000 Radiocarbon Years Ago, Rob A. Marchant, Antoine M. Cleef, Sandy P. Harrison, Henry Hooghiemstra, Vera Markgraf, John H. Van Boxel, Thomas A. Ager, Lucia Almeida, R. Anderson, C. Baied, H. Behling, J. C. Berrio, R. Burbridge, S. Bjorck, R. Byrne, Mark B. Bush, J. Duivenvoorden, J. Flenley, P. De Oliveira, B. Van Geel, K. Graf, W. D. Gosling, S. Harbele, T. Van Der Hammen, B. Hansen, S. Horn, P. Kuhry, M.-.P Ledru, F. Mayle, B. Leyden, S. Lozano-Garcia, A. M. Melief, P. Moreno, N. T. Moar, A. Prieto, G. Van Reenen, M. Salgado-Labouriau, F. Schabitz, E. J. Schreve-Brinkman, M. Wille

Ocean Engineering and Marine Sciences Faculty Publications

The biomisation method is used to reconstruct Latin American vegetation at 6000±500 and 18 000±1000 radiocarbon years before present (14C yr BP) from pollen data. Tests using modern pollen data from 381 samples derived from 287 locations broadly reproduce potential natural vegetation. The strong temperature gradient associated with the Andes is recorded by a transition from high altitude cool grass/shrubland and cool mixed forest to mid-altitude cool temperate rain forest, to tropical dry, seasonal and rain forest at low altitudes. Reconstructed biomes from a number of sites do not match the potential vegetation due to local factors such as human …

Spectral Reflectance And Digital Image Relations Among Five Aquatic Weeds, James H. Everitt, Kenneth R. Summy, Chenghai Yang

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

This study reports on the use of an artificial quartz halogen lighting source to facilitate the acquisition of spectral light reflectance measurements and digital imaging of invasive aquatic weeds. Spectral leaf or leaf/stem reflectance measurements were made on five aquatic weeds: Eurasian watermilfoil (Myriophyllum spicatum L.), hydrilla [Hydrilla verticillata (L. F.) Royle], parrotfeather [Myriophyllum aquaticum (Vall.), waterhyacinth [Eichhornia crassipes (Mart.) Solms], and waterlettuce (Pistia stratiotes L.). Reflectance measurements were studied at five wavelengths of the electromagnetic spectrum: 450 nm (visible blue), 550 nm (visible green), 650 nm (visible red), 680 nm (visible red edge), and 850 nm (near-infrared). Reflectance values …