Digital Commons Network^™

Hiding In Plain Sight: Accounting For Rate Heterogeneity In Trait Evolution Models, James Boyko

Graduate Theses and Dissertations

Within the last four decades, phylogenetic comparative methods have become the defacto method of analysis for comparative biologists. The availability of high-quality comparative datasets has been matched by an explosion of possible phylogenetic models. In large part, the efforts to increase the realism of phylogenetic comparative methods has been successful as evidenced by their widespread use. To this extensive literature, my contributions are modest. I have focused my dissertation work on two main themes. First, most phenotypic evolution is not independent of other phenotypes. Changes in a particular character may influence changes in another and modeling these characters in isolation …

Genome Architecture And Diverged Selection Shaping Pattern Of Genomic Differentiation In Wild Barley, Wenying Zhang, Cong Tan, Haifei Hu, Rui Pan, Yuhui Xiao, Kai Ouyang, Gaofeng Zhou, Yong Jia, Xiao-Qi Zhang, Camilla Beate Hill, Penghao Wang, Brett Chapman, Yong Han, Le Xu, Yanhao Xu, Tefera Angessa, Hao Luo, Sharon Westcott, Darshan Sharma, Eviatar Nevo, Roberto A. Barrero, Matthew I. Bellgard, Tianhua He, Xiaohai Tian, Chengdao Li

Grain and Other Field Crops Research Articles

Summary

Divergent selection of populations in contrasting environments leads to functional genomic divergence. However, the genomic architecture underlying heterogeneous genomic differentiation remains poorly understood. Here, we de novo assembled two high-quality wild barley (Hordeum spontaneum K. Koch) genomes and examined genomic differentiation andgene expression patterns under abiotic stress in two populations. These two populations had a shared ancestry and originated in close geographic proximity but experienced different selective pressures due to their contrasting micro-environments. We identified structural variants that may have played significant roles in affecting genes potentially associated with well-differentiated phenotypes such as flowering time and drought response between …

B.R. Wells Arkansas Rice Research Studies 2021, J. Hardke, X. Sha, N. Bateman

Arkansas Agricultural Experiment Station Research Series

Arkansas is the leading rice producer in the United States. The state represents 47.5% of total U.S. rice production and 47.8% of the total acres planted to rice in 2021. Rice cultural practices vary across the state and across the U.S. However, these practices are also dynamic and continue to evolve in response to changing political, environmental, and economic times. This survey was initiated in 2002 to monitor and record changes in the way Arkansas rice producers approach their livelihood. The survey was conducted by polling county extension agents in each of the counties in Arkansas that produce rice. Questions …

Chromosome Number Evolution, Phylogeography, And The Effects Of Climate Change On Species Distributions In Polyploid Plant Systems, Courtney H. Babin

LSU New Orleans Theses and Dissertations

Polyploidy, a term used to describe organisms with cells having more than two paired sets of chromosomes, is a significant driver of diversification among land plants. Over a century of research has advanced our understanding of polyploidization in some taxa, but polyploid organisms remain understudied. In this dissertation, I investigate chromosome number evolution, phylogeographic structure, genetic differentiation, and the effects of climate change on ploidy level distribution using polyploid plant systems. In the first chapter, I inferred a molecular phylogeny of Allium, an economically important genus that includes cultivated crops and ornamentals, to investigate evolutionary transitions in chromosome number …

Environmental Weed Risk Assessment Protocol For Growing Non-Indigenous Plants In The Western Australian Rangelands, Geoff A. Moore Mr, Christine Munday Ms, Papori Barua Dr

Bulletins 4000 -

This bulletin is a post-border environmental weed risk assessment (WRA) protocol which is based on the Environmental WRA Protocol developed for the Future Farm Industries Co-operative Research Centre (FFI CRC), but with some changes to reflect the different environment and objectives.

The WRA protocol was developed specifically as a post-border assessment of non-indigenous species that may have agricultural value in the WA rangelands and the risk that they may become environmental weeds. Weeds can occur in many land-use systems including agriculture, horticulture and forestry; however, the focus of this protocol is on the risk that non-indigenous agricultural plants may become …

Tree Ring Reconstructions Of Streamflow For The Lower Rio Grande Valley Of Texas, Adedolapo Mutiyat Adeyanju

Theses and Dissertations

The Rio Grande River is a major water source for people living within the USA-Mexico border. The Rio Grande River has its headwaters in the San Juan Mountains in Colorado and the Sierra Madre Occidental in Mexico before flowing into Texas through El-Paso. The water supply issues facing the Lower Rio Grande Basin (LRGB) are extremely complex from international restrictions to severe climate change. The river shares its flow between the U.S.A and Mexico based on the provisions of the 1944 treaty between the U.S.A and Mexico. The LRGB flow is regulated by releases from Falcon and Amistad Reservoirs managed …

De Novo Transcriptome Analysis Of Orange Jasmine (Murraya Paniculata) Infected With Citrus Greening Disease, Jeffrey Aquino Gomez

Theses and Dissertations

Citrus greening disease, also known as Huanglongbing, is one of the most devastating citrus diseases in the world. Candidatus Liberibacter asiaticus (CLas) is a non-culturable, phloem-limited bacterium that serves as one of two vectors for the transmission of any of the three kinds of greening disease. In cooler climates, the African variant transmitted by the African citrus psyllid (Trioza erytreae) is more prevalent. The Asian form transmitted by the Asian citrus psyllid (Diaphorina citri) where is predominant in warmer conditions and recently discover the American form who is also transmit by Diaphorina citri, was discover in Brazil but has also …

Revealing The Effects Of Climate Change And Fungicides On Soil Microbial Communities In The Lower Rio Grande Valley, Texas, Armida Rivera

Theses and Dissertations

Fungicide applications are effective to prevent fungal pathogens that are known to cause crop damage and decrease yields. However, these pesticides can exert toxic or inhibitory effects on non-targeted organisms such as soil microbial communities. In addition, it is unknown to what extent shifts in temperature and soil moisture resulting from global climate change, alter the activities of non-targeted soil organisms. The aim of this study was to evaluate soil biological parameters such as soil respiration and enzyme activities involved in the cycling of carbon, nitrogen, and phosphorous (Beta-glucosidase, Fluorescein Diacetate (FDA) Hydrolysis, urease, alkaline phosphatase, acid phosphatase, and N-acetyl-Beta-glucosaminidase) …

Examination Of The Realized Host Range Of North American Lacebug (Gargaphia Arizonica Drake & Carvalho) And Texas False Potato Beetle (Leptinotarsa Texana Schaeffer) As A Potential Biocontrol Agents For Silverleaf Nightshade (Solanum Elaeagnifoli Cav.), Samikshya Subedi

Theses and Dissertations

Silverleaf nightshade (Solanum elaeagnifolium Cav.) is a perennial forb native to South Texas and Central and South America, but it has become a serious agricultural weed across the world. Because silverleaf nightshade (SLN) is difficult and expensive to manage using chemical and mechanical controls, there is growing attention and research focused on biological control options. In this project, we used both field and laboratory studies to examine the suitability of two North American insects, namely North American lacebug (Gargaphia arizonica Drake & Carvalho) and Texas false potato beetle (Leptinotarsa texana Schaeffer) as prospective biological control agents for …

18s-Nemabase: Curated 18s Rrna Database Of Nematode Sequences, Kaitlin Gattoni, Eli M. S. Gendron, Rebeca Sandoval- Ruiz, Abigail Borgemeier, J. Parr Mcqueen, Rachel M. Shepherd, Dieter Slos, Tom Powers, Dorota L. Porazinska

Department of Plant Pathology: Faculty Publications

Nematodes are the most abundant and diverse animals on the planet but lack representation in biodiversity research. This presents a problem for studying nematode diversity, particularly when molecular tools (i.e., barcoding and metabarcoding) rely on well-populated and curated reference databases, which are absent for nematodes. To improve molecular identification and the assessment of nematode diversity, we created and curated an 18S rRNA database specific to nematodes (18S-NemaBase) using sequences sourced from the most recent publicly available 18S rRNA SILVA v138 database. As part of the curation process, taxonomic strings were standardized to contain a fixed number of taxonomic ranks relevant …

Potassium Level Prediction Of Peach Tree Leaves Using A Hyperspectral Camera And Multivariate Analysis, Megan Io Ariadne Salimbangon Abenina

All Theses

The use of hyperspectral imaging is a valuable piece of technology used in precision agriculture. Hyperspectral imaging system could help farmers and researchers alike in analyzing tissue samples quicker compared to the current way of running a plant tissue analysis on the different nutrient levels that often takes time in generating results. The objective of this research was to measure the potassium level of peach trees using its leaves with a hyperspectral camera. The Senop HSC-2 was used to capture images of peach tree leaves during the fall of 2020 and 2021. The collected data were used to create a …

Cover Cropping To Improve The Sustainability Of Agronomic Production Systems, Ricardo St Aime

All Dissertations

The adoption rate of cover cropping among farmers in the Southeast is low due to the lack of knowledge regarding the suitable cover crop species and their management practices and the concerns of resource depletion for the subsequent cash crop. To generate information addressing the above knowledge gap, the present research was conducted with the following objectives: (1) to determine the optimal planting method for winter cover crops in the upstate of SC and whether it is influenced by the seeding rates (Project-1); (2) to determine suitable winter cover crops for the region based on biomass production, water use efficiency …

Flora Of Doe Mountain Recreation Area, Johnson County, Tennessee, Benjamin Mccullough

Electronic Theses and Dissertations

A botanical inventory of Doe Mountain Recreation Area (DMRA) in northeastern Tennessee was conducted to help guide conservation-based management. A total of 484 species were found in DMRA, comprising 94 families, and 285 genera, 10 species listed in the state rare plant list, and 76 exotic species. Two species, Liatris virgata and Lycopodiella inundata, were new state records. Water in the Lycopodiella seep was an order of magnitude more acid than at other sites. An analysis of the wildland-urban interface showed that only 13% of the area was classified as uninhabited. The inventory-invasion index, introduced to quantify the relative …

Using Condensed Tannin To Mitigate Tall Fescue Toxicosis, Ally Jo Grote

Graduate Theses and Dissertations

Endophyte-infected (Neotyphodium coenophialum) tall fescue, [Schedonorus arundinaceus (Shreb.)] produces ergot alkaloids. Condensed tannins could bind to ergot alkaloids and render them ineffective. The first objective was to improve the health of sheep offered endophyte-infected tall fescue by binding toxins in the rumen with condensed tannins. Non-toxic novel-endophyte infected tall fescue (NE) or toxic endophyte-infected tall fescue forage was harvested, baled at targeted moisture of 55%, wrapped within 8 hours of baling with 2 layers of net wrap and 20 layers of plastic, and ensiled for at least 60 days. Prior to feeding, forages were chopped and packed into plastic trash …

Management Of Garlic Mustard (Alliaria Petiolata), Sahara Mustard (Brassica Tournefortii), And Elongated Mustard (Brassica Elongata) In Utah, Natalie Layne Fronk

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The invasive mustard species Sahara mustard (Brassica tournefortii), garlic mustard (Alliaria petiolata) and elongated mustard (Brassica elongata) negatively impact a variety of ecological systems across the state of Utah. The distribution of these species in Utah is relatively limited at the current time. If prompt action is taken, it may be possible to contain and manage these species before irreparable ecological and agricultural damage occurs. For this reason, all three mustards are listed by the State of Utah as weeds of high priority for management.

This project tested multiple strategies to determine effective species-specific …

Soil Genesis Across A Climo-Lithosequence Of Western Haleakalā, Maui, Ryan C. Hodges

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The soils of western Haleakalā are incredibly diverse due to two primary reasons: 1) they receive varying levels of rainfall based on location relative to Haleakalā, and 2) volcanic vents upwind of the area indicate that volcanic ash has blanketed much of western Haleakalā in the past. Ash can weather to form short-range-order materials, which contribute to the classification of andic soil properties. Due to their structure, short-range-order materials impart soil behavior that creates benefits and challenges in land management. Therefore, an understanding of how these soils formed and differ, and where andic soils occur is crucial.

The objectives of …

Intestinal Microbiota Analysis Of Broiler Chickens Under Necrotic Enteritis Challenge And Tributyrin Supplementation, Taylor Nicole Mckinney

Graduate Theses and Dissertations

Poultry is a staple protein source for most of the planet. Until recently, antibiotic growth promoters (AGPs) were used to prevent illnesses in commercial chicken production. Currently, this is not possible due to regulations and consumer concern, but without such a preventative, diseases like necrotic enteritis (NE) have reemerged, posing a threat to bird health, and ultimately, our food source. Necrotic enteritis is a severe gastrointestinal disease caused by the gram-positive pathogen, Clostridium perfringens. Clinical features of this disease are diarrhea, intestinal lesions, and death, with a high transmission rate. In a subclinical form, growth performance is diminished and is …

Investigating Hops Production In Arkansas To Support Specialty Crop Growth, James Oliver Mcclellan

Graduate Theses and Dissertations

The hop plant (Humulus lupulus L.) is a perennial, climbing species within the Cannabaceae family that produces cones used for brewing. Hops are grown worldwide. In the United States most hops production occurs in the Pacific Northwest, but growth in the craft beer industry is driving efforts for hops production in other U.S. regions. Recommendations on hops cultivar suitability, fertility, and management are needed for the U.S. mid-south region. Objectives of this research on Arkansas-grown hops were to 1) assess the impact of cultivar and fertility rate on plant and cone attributes of six cultivars of Arkansas-grown hops and 2) …

Optimization Techniques For Soil Organic Carbon Prediction Using Mid-Infrared Spectroscopy, Minerva J. Dorantes

Graduate Theses and Dissertations

Resource-efficient techniques for accurate soil carbon estimation are necessary to satisfy the increasing demand for spatiotemporal data. In the last thirty years, mid-infrared (MIR) soil spectroscopy has developed as an accurate, rapid, cost-effective, and non-destructive technique for soil organic carbon (SOC) analysis. In soil spectroscopy, a calibration model relates spectral data to a corresponding measured soil property and is subsequently used to predict this value from new spectral data. Various optimization techniques have been used to improve the statistical performance of calibrations; however, there is little consensus on the conditions that make these techniques effective. The objectives of this research …

Evaluating Flavor And Aroma Attributes Of Arkansas-Grown Horticultural Crops, Jordan Chenier

Graduate Theses and Dissertations

Arkansas has a climate and geography that allows for the production of unique horticultural crops, including hops (Humulus lupulus L.), blackberries (Rubus subgenus Rubus), and muscadine grapes (Vitis rotundifolia). These crops not only have potential for growers in Arkansas but have unique flavor and aroma attributes that impact marketability. Volatile compounds present in many different agricultural plants are the primary source of biologically-derived aromas and flavors. Therefore, the volatile and other quality attributes of hops, blackberries, and muscadine grapes were evaluated at the University of Arkansas (UA System) Division of Agriculture. The quality, volatile, and sensory attributes of four hops …

The Influences Of Disperser Behavior, Host Availability, And Environmental Conditions On The Distribution Of Oak Mistletoe [Phoradendron Leucarpum (Raf.) Reveal & M. C. Johnst.] In Eastern Virginia And North Carolina, Nicholas Pearce Flanders

Biological Sciences Theses & Dissertations

Mistletoes are shrubs that typically parasitize the branches of host trees and rely on avian frugivores for seed dispersal. Because mistletoes are restricted to a narrow range of suitable recruitment sites and avian frugivores are more visible than other guilds of seed dispersers, mistletoe-frugivore systems afford opportunities for assessing the roles of dispersal limitation and local environment in determining plant distribution. These mechanisms have been proposed as determinants of the observed association of oak mistletoe [Phoradendron leucarpum (Raf.) Reveal & M. C. Johnst.] with forested wetlands in eastern Virginia and North Carolina, USA. I tested the alternative hypothesis that …

Effect Of Irrigation Regime And Fertilization On Recovery Of Dicamba Injured Soybean, Wesley France, Jason K. Norsworthy, Trenton Roberts, Jeremy Ross, L. Tom Barber, Edward E. Gbur

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

With the release of the dicamba-resistant crop technology and subsequent increase in dicamba off-target movement to non-dicamba-resistant crops, discovering means of mitigating yield loss through studying dicamba injury to soybean and interactions with factors such as irrigation regime and fertilization would prove beneficial. Field experiments were conducted in 2019 in Fayetteville and Colt, Arkansas, to evaluate the effect of irrigation regime to non-dicamba-resistant soybean that was injured by dicamba at a low dose at multiple timings. Another experiment was conducted in Fayetteville in 2019 and 2020 evaluating the impact of nitrogen (N) and potassium (K) fertilization on soybean recovery following …

Comparison Of Plant Richness And Density In Crp-42 Fields Between 2018 And 2022, Liz Wilgenbusch, Ai Wen Ph.D.

Summer Undergraduate Research Program (SURP) Symposium

Recently, the number of pollinators have decreased dramatically throughout the United States. Pollinators play an important role in food production with around ⅓ of the world’s food crops being dependent on pollinators. Providing a high-forage habitat for pollinators is a proposed solution to combat their decline. In the upper Midwest United States, the Conservation Reserve Program (CRP) helps protect pollinator habitats by providing farmers with annual payments to retire their old farmland. The purpose of this study was to compare plant density and richness in CRP fields between year 3 and year 7 post planting to find trends in the …

Quantification And Machine Learning Based N2o–N And Co2–C Emissions Predictions From A Decomposing Rye Cover Crop, Deepak R. Joshi, David E. Clay, Sharon A. Clay, Janet Moriles-Miller, Aaron L. M. Daigh, Graig Reicks, Shaina Westhoff

Department of Agronomy and Horticulture: Faculty Publications

Cover crops improve soil health and reduce the risk of soil erosion. However, their impact on the carbon dioxide equivalence (CO_2e) is unknown. Therefore, the objective of this 2-yr study was to quantify the effect of cover crop-induced differences in soil moisture, temperature, organic C, and microorganisms on CO_2e, and to develop machine learning algorithms that predict daily N₂O–N and CO₂–C emissions. The prediction models tested were multiple linear regression, partial least square regression, support vector machine, random forest (RF), and artificial neural network. Models’ performance was accessed using R², …

Limited Effects Of Precipitation Manipulation On Soil Respiration And Inorganic N Concentrations Across Soil Drainage Classes In Northern Minnesota Aspen Forests, Anna B. Stockstad, Robert A. Slesak, Alan J. Toczydlowski, Charles R. Blinn, Randall K. Kolka, Stephen D. Sebestyen

Aspen Bibliography

It is critical to gain insight into the responses of forest soils to the changing climate. We simulated future climate conditions with growing season throughfall reduction (by 50%) and winter snow removal using a paired-plot design across a soil drainage class gradient at three upland, Populus-dominated forests in northern Minnesota, USA. In situ bulk soil respiration and concentrations of extractable soil N were measured during the summers of 2020–2021. Soil respiration and N concentrations were not affected by throughfall reduction and snow removal, which was largely attributed to the limited treatment effects on soil moisture content and soil temperature. …

Registration Of Lcs ‘Valiant’ Hard Red Winter Wheat, P. Stephen Baenziger, S. D. Masterson, J. D. Boehm Jr., Vikas Belamkar, M. D. Barnett, Devin J. Rose, Lan Xu, Stephen N. Wegulo, T. Regassa, Amanda Easterly, Cody F Creech, Dipak K. Santra, G. R. Kruger, G. W. Hergert, R. N. Klein, J. Kolmer, J. Kolmer, M.-S. Chen, Gary L. Hein, R. L. Bowden, M. J. Guttieri, G. Bai, El-Basyoni Salah, J. Poland

Department of Agronomy and Horticulture: Faculty Publications

Historically cultivars developed jointly by the University of Nebraska-Lincoln and USDA-ARS wheat (Triticum aestivum L.) improvement project tend to be late and better adapted to the northern Great Plains. LCS ‘Valiant’ (Reg. no. CV-1196, PI 693223; tested as NE10478-1) was released based on the merits of its earliness, agronomic performance, relevant disease resistances, and end-use quality characteristics and its adaptation to the central Great Plains. As such, the line was licensed to Limagrain Cereal Seeds for their ability to market outside of Nebraska. LCS Valiant hard red winter wheat was released in March 2020 by the developing institutions and …

Effects Of Elevated Co2 Concentrations And Elevated Temperatures On Isoprene Emissions Of Rhamnus Cathartica (European Buckthorn), Quercus Rubra (Red Oak) And Quercus Michauxii (Swamp Chestnut Oak), Janet G. Núñez

DePaul Discoveries

Tropospheric ozone is a ground-level pollutant and is produced from primary air pollutants like nitrogen oxides and volatile organic compounds (VOCs). While many VOCs are anthropogenic, isoprene is emitted from certain species of plants and reacts with nitrogen oxides to form ozone. Previous studies have found that isoprene can be suppressed by CO₂, but such suppression can be reduced under conditions of increased temperature. However, this pattern is not seen in all plants capable of emitting isoprene. The focus of this is study is to determine if similar patterns are present in the invasive tree species of buckthorn …

Association Analyses Of Host Genetics, Root-Colonizing Microbes, And Plant Phenotypes Under Different Nitrogen Conditions In Maize, Michael A. Meier, Gen Xu, Martha G. Lopez-Guerrero, Guangyong Li, Christine Smith, Brandi Sigmon, Joshua R. Herr, James R. Alfano, Yufeng Ge, James C. Schnable, Jinliang Yang

Department of Agronomy and Horticulture: Faculty Publications

The root-associated microbiome (rhizobiome) affects plant health, stress tolerance, and nutrient use efficiency. However, it remains unclear to what extent the composition of the rhizobiome is governed by intraspecific variation in host plant genetics in the field and the degree to which host plant selection can reshape the composition of the rhizobiome. Here, we quantify the rhizosphere microbial communities associated with a replicated diversity panel of 230 maize (Zea mays L.) genotypes grown in agronomically relevant conditions under high N (+N) and low N (-N) treatments. We analyze the maize rhizobiome in terms of 150 abundant and consistently reproducible …

The Biological Activity Of Tea Tree Oil And Hemp Seed Oil, Lakatos Lakatos, Samuel Obeng Apori, Julie Dunne, Furong Tian

Articles

The interest in hemp seed oil (HSO) and tea tree oil (TTO) in the medical and food industries is increasing. The current study compares their bioactivity to other plant oils, mainly focusing on hemp seed oils (HSOs) with various cannabidiol (CBD) contents. A DPPH assay was employed to evaluate the antioxidant activity. The antimicrobial activity against Escherichia coli, Staphylococcus aureus, and Salmonella enteritidis was evaluated using time–kill, minimum inhibition concentration (MIC), and Kirby–Bauer disk diffusion methods. Tea tree oil showed significantly higher antimicrobial activity against S. enteritidis compared to E. coli and S. aureus (p < 0.05). The antioxitant activity range (lowest to highest) was sesame < vetiver < rosehip < tea tree < organic hemp < pure hemp < 5% CBD < vitamin C. Tea tree oil and 5% CBD showed antioxidant activity at IC50 of 64.45 μg/mL and 11.21 μg/mL, respectively. The opposing antimicrobial and antioxidant results for TTO and HSO indicate that these activities arise from different components within the oil compositions.

Orthotrichum Lyellii As An Active Moss Biomonitor: Examining The Interplay Between Ambient Pm10, Bulk Deposition And Heavy Metals In An Urban Environment, Scott Bradley Kiel

Dissertations and Theses

The importance of monitoring and preventing pollution in the environment is a globally recognized issue. Of the criteria pollutants outlined by the United States Environmental Protection Agency, particulate matter is among these least understood in relation to toxicity and most wide-spread. Many governments have employed continuous air quality monitoring networks to track ambient levels of particulate matter, but are often too widespread to capture the heterogeneity of the urban environment, especially for heavy metal deposition. In Portland, OR, the epiphytic moss Orthotrichum lyellii was successfully used as a low-cost passive biomonitor to increase the spatial resolution of pollution around the …