23 Works

A roadmap to durable BCTV resistance using long-read genome assembly of genetic stock KDH13

Paul Galewski & Imad Euyjal
PacBio Sequence data associated with genetic stock KDH13.Datasets include genome resources and annotated files associated with the manuscript "Long-read genome assembly of Double Haploid Sugar Beet KDH13 provides roadmap for durable genetic resistance to Beet Curly Top Virus". This includes genome assembly, ordered genome assembly, protein predictions, variant call format files for an F1 hybrid (KDH13xKDH19-17).

Vegetation characteristics and precipitation jointly influence grassland bird abundance beyond the effects of grazing management

Kristin Davis, David Augustine, Adrian Monroe & Cameron Aldridge
Grassland birds have experienced some of the steepest population declines of any guild of birds in North America. The shortgrass steppe contains some of North America’s most-intact grasslands, which makes the region particularly important for these species. Grassland birds differentially respond to variation in vegetation structure generated by spatiotemporally-varying disturbance like grazing management. However, understanding how species respond to characteristics beyond vegetation structure or grazing could better inform management for these species in the shortgrass...

Phylogenomics in the hard pines (Pinus subsection Ponderosae; Pinaceae) confirms paraphyly in Pinus ponderosa, and places Pinus jeffreyi with the California big cone pines

Ann Willyard, David S. Gernandt, Blake Cooper, Connor Douglas, Kristen Finch, Hassan Karemera, Erik Lindberg, Stephen K. Langer, Julia Lefler, Paula Marquardt, Dakota Pouncey & Frank Telewski
We sampled 130 individuals (2 to 25 per taxon) of subsections Ponderosae and Sabinianae. Nucleotide sequences were obtained by targeting 703 low copy nuclear genes. From the unenriched portion of the short reads, we assembled nearly complete plastome nucleotide sequences. We used 600 nuclear genes and the plastome sequences to create phylogenies and species trees that we compared to evaluate cytonuclear concordance and reticulation. We found that Pinus jeffreyi belongs with subsect. Sabinianae based on...

Temporal nitrogen dynamics in intensively managed loblolly pine early stand development

Gabriel Ferreira, Benjamin Rau & Doug Aubrey
Forest production is strongly dependent on nutrient uptake; however, sustainable management of intensively managed plantations requires an improved understanding of this relationship when fertilization occurs frequently across short rotations. Here, we studied temporal nitrogen (N) concentration ([N]) and content (Nc) dynamics under different silvicultural practices (herbicide, fertilization, and planting density) throughout early loblolly pine (Pinus taeda) stand development (5 years). We describe relationships of [N] and Nc of different stand components (foliage, branches, stem, roots,...

DRP Visualization Challenge: Belgian Fieldstone

Devin Rippner
I took a stack of images of Belgian Fieldstone collected by Tom Bultreys at Ghent University and segmented them, generating masks of the fieldstone grains with quartz in (white), glauconite (yellow), and pore spaces (blue). The masks can be analyzed for surface area/volumetric information and allow for complete control over data visualization enabling each component of the column to be visualized independently.

Invasion and Global Change Meta-analysis Data

Bianca E. Lopez, Jenica M. Allen, Jeffrey S. Dukes, Jonathan Lenoir, Montserat Vila, Dana M. Blumenthal, Evelyn M. Beaury, Emily J. Fusco, Toni Lyn Morelli, Cascade J. B. Sorte & Bethany A. Bradley
We conducted a global meta-analysis to investigate invasions, abiotic global environmental changes, and their combined effects on native species, communities, and ecosystems.We searched the Web of Science Core Collection for articles and reviews that were available in English through September 30, 2020. Search terms were chosen to identify papers reporting impacts of invasions with one of six abiotic global environmental changes (GECs: warming, nitrogen deposition, O2 depletion, drought, CO2 addition, and altered pH). We assessed...

Introduced plants induce outbreaks of a native pest and facilitate invasion in the plants’ native range: Evidence from the emerald ash borer

Yingqiao Dang, Ke Wei, Xiaoyi Wang, Jian Duan, David Jennings & Therese Poland
1. Biological invasions are among the most serious threats to native forest ecosystems worldwide due to ever-increasing international trade and global change. Understanding the invasion processes and ecology of invasive pests in both newly invaded and native habitats is necessary to effectively manage the risks they pose. 2. The emerald ash borer (EAB), Agrilus planipennis, is one of the most devastating invasive forest insect pests in North America and has also invaded European Russia and...

Coffee Berry Borer (Hypothenemus hampei Ferrari) trap catch and associated weather variables on Hawaii Island

Melissa Johnson & Nicholas Manoukis
We sampled flying female CBB adults bi-weekly over a three-year period using red funnel traps baited with an alcohol lure at 14 commercial coffee farms on Hawaii Island to characterize seasonal phenology and the relationship between flight activity and five weather variables. We captured almost 5 million scolytid beetles during the sampling period, with 81-93% of the trap catch comprised of CBB. Of the captured non-target beetles, the majority were tropical nut borer, black twig...

Northern Bobwhite juvenile survival southwest Missouri 2016-2018

Emily Sinnott, Frank Thompson, Mitch Weegman & Thomas Thompson
These data and code are associated with the publication in Ornithological Applications entitled "Northern Bobwhite juvenile survival is greater on native grasslands managed with fire and grazing, and lower in non-native field borders and strip crop fields." We evaluated the influence of brood age, vegetation cover type, woody vegetation structure, habitat management, and landscape cover on juvenile survival in southwest Missouri 2016-2018.

Files used to develop and test SLAG, Seeded Local Assembly of Genes

Charles Crane, Christie Williams, Jill Nemacheck, Subhashree Subramanyam & Stephen Goodwin
This dataset consists of configuration files and results files involved in developing and testing SLAG, an iterative Perl pipeline to construct local assemblies seeded on query sequences. SLAG is intended for situations where a full genome assembly is economically or technically infeasible, and thus it emphasizes methods that can deal with shallow read depth. SLAG and its user-runnable test suite have been deposited at https://github.com/cfcrane/SLAG. This Dryad repository contains files that were used in preparing...

Data from: Biomass production and stability of five energycane cultivars at two latitudes in Georgia, USA

Joseph Knoll, William Anderson, Ali Missaoui, Anna Hale & Wayne Hanna
Energycane (Saccharum hyb.) could be a viable bioenergy crop for the Southeast USA. Five energycane cultivars were planted in 2008 at a northern (Watkinsville, GA) and a southern (Tifton, GA) site, and were grown for seven years to compare biomass yields. Plots were arranged in a four replicate randomized complete block design at each site. Energycane was grown under rainfed conditions with 90–112 kg ha-1 N applied annually. Plant height was recorded at least monthly,...

Blueprint for phasing and assembling the genomes of heterozygous polyploids: Application to the octoploid genome of strawberry

Michael Hardigan, Mitchell Feldmann, Randi Famula, Michaela Vachev, Mary Madera, Philipp Zerbe, Kristin Mars, Paul Peluso, David Rank, Shujun Ou, Christopher Saski, Charlotte Acharya, Glenn Cole, Alan Yocca, Patrick Edger & Steven Knapp
The challenge of allelic diversity for assembling haplotypes is exemplified in polyploid genomes containing homoeologous chromosomes of identical ancestry, and significant homologous variation within their ancestral subgenomes. Cultivated strawberry (Fragaria × ananassa) and its progenitors are outbred octoploids in which up to eight homologous and homoeologous alleles are preserved. This introduces significant risk of haplotype collapse, switching, and chimeric fusions during assembly. Using third generation HiFi sequences from PacBio, we assembled the genome of the...

Litter commensal bacteria can limit the horizontal gene transfer of antimicrobial resistance to Salmonella in chickens

Adelumola Oladeinde
Fostering a 'balanced' gut microbiome through the administration of beneficial microbes that can competitively exclude pathogens has gained a lot of attention and use in human and animal medicine. However, little is known on how microbes affect the horizontal gene transfer of antimicrobial resistance (AMR). To shed more light on this question, we challenged neonatal broiler chicks raised on reused broiler chicken litter – a complex environment made up of decomposing pine shavings, feces, uric...

Modeling phenological reaction norms over an elevational gradient reveals contrasting strategies of Dusky Flycatchers and Mountain Chickadees in response to early season temperatures

John Rotenberry, Sharon Coe & Kathryn Purcell
We developed an approach to distinguish among three alternative strategies birds may employ relating the timing of egg-laying across elevations to annual variation in spring temperature (phenological reaction norms), which we applied to analyze breeding phenology of two species over an elevational gradient in the Sierra Nevada, California. In a “simple offset” strategy, birds at different elevations initiate breeding relative to environmental temperature in a consistent manner, in that breeding onset is triggered by a...

Optical maps refine the bread wheat Triticum aestivum cv Chinese Spring genome assembly

Tingting Zhu, Le Wang, Hélène Rimbert, Juan Rodriguez, Karin Deal, Romain De Oliveira, Frédéric Choulet, Gabriel Keeble-Gagnère, Josquin Tibbits, Jane Rogers, Kellye Eversole, Rudi Appels, Yong Gu, Martin Mascher, Jan Dvorak, Ming-Cheng Luo, Juan C. Rodriguez, Karin R. Deal, Gabriel Keeble‐Gagnère, Yong Q. Gu & Ming‐Cheng Luo
This dataset contains a single whole-genome optical map file (.CMAP) for bread wheat (Triticum aestivum) cv Chinese Spring (CS). The methods for constructing this optical map and the properties of this map are described below. The definition of the CMAP format is documented in https://bionanogenomics.com/wp-content/uploads/2017/03/30039-CMAP-File-Format-Specification-Sheet.pdf. The extracted ultra-high-molecular weight DNA molecules of CS were labeled with the DLE-1 enzyme (Bionano Genomics, San Diego, CA, USA) and were then stained with the Bionano PrepTM DLS Kit...

Sustainable use of groundwater may dramatically reduce irrigated production of maize, soybean, and wheat

Jose R. Lopez, Jonathan M. Winter, Joshua Elliott, Alex C. Ruane, Cheryl Porter, Gerrit Hoogenboom, Martha Anderson & Christopher Hain
Groundwater extraction in the United States (US) is unsustainable, making it essential to understand the impacts of limited water use on irrigated agriculture. Here, we integrate a gridded crop model with satellite observations, recharge estimates, and water survey data to assess the effects of sustainable groundwater withdrawals on US irrigated agricultural production. Our model agrees with satellite-based estimates of evapotranspiration (R2 = 0.68), as well as survey production estimates from the United States Department of...

GapAnalysis: An R package to calculate conservation indicators using spatial information

Julian Ramirez-Villegas, Daniel Carver, Chrystian Sosa, Colin Khoury, Harold Achicanoy, Maria Victoria Diaz, Steven Sotelo & Nora Castaneda-Alvarez
Effective assessments of the current status of biodiversity conservation are needed to support planning, policy, and action, from local to global levels. Of particular use would be well documented, reproducible methods based on openly accessible data and tools. Such methods should provide an accurate estimate of the state of conservation of diversity, identifying gaps in current conservation systems, while providing a benchmark against which to measure success, including determining when conservation goals have been met....

Performance and refinement of nitrogen fertilization tools

Curtis Ransom, Jason Clark, Gregory Bean, Christopher Bandura, Matthew Shafer, Newell Kitchen, James Camberato, Paul Carter, Richard Ferguson, Fabián Fernández, David Franzen, Carrie Laboski, David Myers, Emerson Nafziger & John Sawyer
Improving corn (Zea mays L.) N management is pertinent to economic and environmental objectives. However, there are limited comprehensive data sources to develop and test N fertilizer decision aid tools across a wide geographic range of soil and weather scenarios. Therefore, a public-industry partnership was formed to conduct standardized corn N rate response field studies throughout the U.S. Midwest. This research was conducted using a standardized protocol at 49 site-years across eight states over the...

Supporting Data and Code for \"Managing to Climatology: Improving semi-arid agricultural risk management using crop models and a dense meteorological network\"

Steven Mauget & Donna Mitchell-McCallister
Without reliable seasonal climate forecasts, farmers and managers in other weather-sensitive sectors might adopt practices that are optimal for recent climate conditions. To demonstrate this principle, crop simulation models driven by a dense meteorological network were used to identify climate-optimal planting dates for U.S. Southern High Plains (SHP) un-irrigated agriculture. This method converted large samples of SHP growing season weather outcomes into climate-representative cotton and sorghum yield distributions over a range of planting dates. Best...

Environmental impacts on diapause and survival of the alfalfa leafcutting bee, Megachile rotundata

Elisabeth Wilson, Claire Murphy, Covey Wong, Joseph Rinehart, George Yocum & Julia Bowsher
Megachile rotundata exhibits a facultative prepupal diapause but the cues regulating diapause initiation are not well understood. Possible cues include daylength and temperature. Megachile rotundata females experience changing daylengths over the nesting season that may influence diapause incidence in their offspring through a maternal effect. Juvenile M. rotundata spend their developmental period confined in a nesting cavity, potentially subjected to stressful temperatures that may affect diapause incidence and survival. To estimate the impact of daylength...

Feather corticosterone reveals developmental challenges in a long‐term study of juvenile northern spotted owls

Ashlee Mikkelsen, Katie Dugger, Kathleen O'Reilly & Damon Lesmeister
1. Corticosterone is a steroid hormone integral to a variety of physiological pathways and is strongly associated with the vertebrate stress–response. In avian species, circulating corticosterone is sequestered into developing feathers and is used as an indicator of energy allocation during feather growth and widely applied in conservation physiology. 2. The northern spotted owl (Strix occidentalis caurina) is a federally threatened old–growth forest obligate of conservation concern endemic to the Pacific Northwest of the United...

Effect of data source on estimates of regional bird richness in northeastern United States

Roi Ankori-Karlinsky, Ronen Kadmon, Michael Kalyuzhny, Katherine F. Barnes, Andrew M. Wilson, Curtis Flather, Rosalind Renfrew, Joan Walsh & Edna Guk
Standardized data on large-scale and long-term patterns of species richness are critical for understanding the consequences of natural and anthropogenic changes in the environment. The North American Breeding Bird Survey (BBS) is one of the largest and most widely used sources of such data, but so far, little is known about the degree to which BBS data provide accurate estimates of regional richness. Here we test this question by comparing estimates of regional richness based...

Unifying community detection across scales from genomes to landscapes

Andrii Zaiats, Stephanie F. Hudon, Anna Roser, Anand Roopsind, Cristina Barber, Brecken C. Robb, Britt A. Pendleton, Meghan J. Camp, Patrick E. Clark, Merry M. Davidson, Jonas Frankel-Bricker, Marcella Fremgen-Tarantino, Jennifer Sorensen Forbey, Eric J. Hayden, Lora A. Richards, Olivia K. Rodrigues & T. Trevor Caughlin
Biodiversity science encompasses multiple disciplines and biological scales from molecules to landscapes. Nevertheless, biodiversity data are often analyzed separately with discipline-specific methodologies, constraining resulting inferences to a single scale. To overcome this, we present a topic modeling framework to analyze community composition in cross-disciplinary datasets, including those generated from metagenomics, metabolomics, field ecology, and remote sensing. Using topic models, we demonstrate how community detection in different datasets can inform the conservation of interacting plants and...

Registration Year

  • 2021
    23

Resource Types

  • Dataset
    23

Affiliations

  • Agricultural Research Service
    23
  • University of Georgia
    2
  • United States Geological Survey
    2
  • Texas Tech University
    2
  • Iowa State University
    2
  • North Dakota State University
    2
  • Michigan State University
    2
  • University of California, Davis
    2
  • Estación Biológica de Doñana
    1
  • University of Massachusetts Amherst
    1