126 Works

Data from: A thorny issue: woody plant defence and growth in an East African savanna

Benjamin J. Wigley, Corli Coetsee, David J. Augustine, Jayashree Ratnam, Dawood Hattas & Mahesh Sankaran
1. Recent work suggests that savanna woody plant species separate into two different strategies based on their defences against herbivory; a low nutrient/high chemical defence strategy and a nutrition paired with mostly architectural defences strategy. The concept that chemical and structural defences can augment each other and do not necessarily trade-off has emanated from this work. In this study we examine woody plant defence strategies, how these respond to herbivore removal and how they affect...

Data from: Declines in pinyon pine cone production associated with regional warming

Miranda D. Redmond, Frank Forcella & Nichole N. Barger
Global climate change is expected to produce large shifts in vegetation distribution and has already increased tree mortality, altering forest structure. However, long-term shifts will be partly dependent on the ability of species to reproduce under a novel climate. Few studies have examined the impact of climate change on the reproductive output of long-lived ‘masting' species, or species characterized by episodic reproductive events. Here, we show that seed cone production among pinyon pine (Pinus edulis),...

Data from: Climate change impacts on bumblebees converge across continents

Jeremy T. Kerr, Alana Pindar, Paul Galpern, Laurence Packer, Stuart M. Roberts, Pierre Rasmont, Oliver Schweiger, Sheila R. Colla, Leif L. Richardson, David L. Wagner, Lawrence F. Gall, Derek S. Sikes & Alberto Pantoja
For many species, geographical ranges are expanding toward the poles in response to climate change, while remaining stable along range edges nearest the equator. Using long-term observations across Europe and North America over 110 years, we tested for climate change–related range shifts in bumblebee species across the full extents of their latitudinal and thermal limits and movements along elevation gradients. We found cross-continentally consistent trends in failures to track warming through time at species’ northern...

Data from: High levels of diversity and population structure in the potato late blight pathogen at the Mexico center of origin

Jianan Wang, Sylvia P. Fernândez-Pavía, Meredith M. Larsen, Edith Garay-Serrano, Rosario Gregorio-Cipriano, Gerardo Rodríguez-Alvarado, Niklaus J. Grünwald & Erica M. Goss
Globally destructive crop pathogens often emerge by migrating out of their native ranges. These pathogens are often diverse at their center of origin, and may exhibit adaptive variation in the invaded range via multiple introductions from different source populations. However, source populations are generally unidentified or poorly studied compared to invasive populations. Phytophthora infestans, the causal agent of late blight, is one of the most costly pathogens of potato and tomato worldwide. Mexico is the...

Data from: Mapping and expression of candidate genes for development rate in rainbow trout (Oncorhynchus mykiss)

Matthew C. Hale, John A. Colletti, Scott A. Gahr, Julie Scardina, Frank P. Thrower, Matthew Harmon, Megan Carter, Ruth B. Phillips, Gary H. Thorgaard, Caird E. Rexroad & Krista M. Nichols
Development rate has important implications for individual fitness and physiology. In salmonid fishes, development rate correlates with many traits later in life, including life history diversity, growth, and age and size at sexual maturation. In rainbow trout (Oncorhynchus mykiss), a Quantitative Trait Locus (QTL) for embryonic development rate has been detected on chromosome 5 across populations. However, few candidate genes have been identified within this region. In this study, we use gene mapping, gene expression,...

Long-term evidence shows crop-rotation diversification increases agricultural resilience to adverse growing conditions in North America

Timothy Bowles, Maria Mooshammer, Yvonne Socolar, Franciso Calderón, Michel Cavigelli, Steve Culman, William Dean, Axel Garcia Y Garcia, Amélie Gaudin, W Scott Harkom, Michael Lehman, Shannon Osborne, G Philip Robertson, Jonathan Salerno, Marty Schmer, Jeffrey Strock, A Stuart Grandy & Craig Drury
A grand challenge facing humanity is how to produce food for a growing population in the face of a changing climate and environmental degradation. Though empirical evidence remains sparse, management strategies that increase environmental sustainability, like increasing agroecosystem diversity through crop rotations, may also increase resilience to weather extremes without sacrificing yields. We used multilevel regression analyses of long-term crop yield datasets across a continental precipitation gradient to assess how temporal crop diversification affects maize...

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....

Host plant defense produces species-specific alterations to flight muscle protein structure and flight-related fitness traits of two armyworms

Scott Portman
Insects manifest phenotypic plasticity in their development and behavior in response to plant defenses, via molecular mechanisms that produce tissue-specific changes. Phenotypic changes might vary between species that differ in their preferred hosts and these effects could extend beyond larval stages. To test this, we manipulated the diet of southern armyworm (SAW; Spodoptera eridania) and fall armyworm (FAW; Spodoptera frugiperda) using a tomatomutant for jasmonic acid plant defense pathway (def1), and wild-type plants, and then...

Data from: Influence of canopy openness, ungulate exclosure, and low-intensity fire for improved oak regeneration in temperate Europe

Linda Petersson, Daniel Dey, Annika Felton, Emile Gardiner & Magnus Löf
Failed oak regeneration is widely reported in temperate forests and has been linked in part to changed disturbance regimes and land-use. We investigated if the North American fire-oak hypothesis could be applicable to temperate European oaks (Q. robur, Q. petraea) using a replicated field experiment with contrasting canopy openness, protection against ungulate browsing (fencing/no fencing), and low-intensity surface fire (burn/no burn). Survival, relative height growth (RGRH), browsing damage on naturally regenerated oaks (≤300 cm tall),...

Data from: Latent developmental and evolutionary shapes embedded within the grapevine leaf

Dan Chitwood, Robert VanBuren, Zoë Migicovsky, Margaret Frank & Jason Londo
Across plants, leaves exhibit profound diversity in shape. As a single leaf expands, its shape is in constant flux. Plants may also produce leaves with different shapes at successive nodes. In addition, leaf shape varies among individuals, populations and species as a result of evolutionary processes and environmental influences. Because leaf shape can vary in many different ways, theoretically, the effects of distinct developmental and evolutionary processes are separable, even within the shape of a...

Data From: TERRA-REF, An open reference data set from high resolution genomics, phenomics, and imaging sensors

David LeBauer, Burnette Maxwell, Jeffrey Demieville, Noah Fahlgren, Andrew French, Roman Garnett, Zhenbin Hu, Kimberly Huynh, Rob Kooper, Zongyang Li, Maitiniyazi Maimaitijiang, Jerome Mao, Todd Mockler, Geoffrey Morris, Maria Newcomb, Michael Ottman, Philip Ozersky, Sidike Paheding, Duke Pauli, Robert Pless, Wei Qin, Kristina Riemer, Gareth Rohde, William Rooney, Vasit Sagan … & Charles Zender
The ARPA-E funded TERRA-REF project is generating open-access reference datasets for the study of plant sensing, genomics, and phenomics. Sensor data were generated by a field scanner sensing platform that captures color, thermal, hyperspectral, and active flourescence imagery as well as three dimensional structure and associated environmental measurements. This dataset is provided alongside data collected using traditional field methods in order to support calibration and validation of algorithms used to extract plot level phenotypes from...

Data from: Tropical understory herbaceous community responds more strongly to hurricane disturbance than to experimental warming

Deborah Kennard, David Matlaga, Joanne Sharpe, Clay King, Aura Alonso-Rodríguez, Sasha Reed, Molly Cavaleri & Tana Wood
The effects of climate change on tropical forests may have global consequences due to the forests’ high biodiversity and major role in the global carbon cycle. In this study, we document the effects of experimental warming on the abundance and composition of a tropical forest floor herbaceous plant community in the Luquillo Experimental Forest, Puerto Rico. This study was conducted within Tropical Responses to Altered Climate Experiment (TRACE) plots, which use infrared heaters under free-air,...

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...

Exploratory surveys in Taiwan of the roseau cane scale Nipponaclerda biwakoensis Kuwana and its associated parasitoids

, Cheng-Lung Chu, Hannah Broadley, Michael Gates, Yong-Sin Lo, Yu-Chun Chen, Kim Hoelmer, Juli Gould & Shaw-Yhi Hwang
Roseau cane (Phragmites australis (Cav). Trin. ex Steud.) is the dominant plant species of the Mississippi River Delta in Louisiana, USA, and protects marsh communities from erosion and storm-related impacts, maintaining shipping channels and oil infrastructure. Widespread dieback and thinning of P. australis were noted in the Mississippi River Delta in the fall of 2016. Invasive populations of the roseau cane scale (Nipponaclerda biwakoensis Kuwana), which is native to Asia, were found at outbreak levels...

UCE Phylogenomics resolves major relationships among Ectaheteromorph ants (Hymenoptera: Formicidae: Ectatomminae, Heteroponerinae): A new classification for the subfamilies and the description of a new genus

G P Camacho, W Franco, M G Branstetter, M R Pie, J T Longino, T R Schultz & R M Feitosa
Uncovering the evolutionary history of the subfamilies Ectatomminae and Heteroponerinae, or ectaheteromorphs, is key to understanding a major branch of the ant tree of life. Despite their diversity and ecological importance, phylogenetic relationships in the group have not been well explored. One particularly suitable tool for resolving phylogeny is the use of ultraconserved elements (UCEs), which have been shown to be ideal markers at a variety of evolutionary time scales. In the present study, we...

Data from: Chemical extraction of phosphorus from dairy manure and utilization of recovered manure solids

Ariel A. Szogi, Virginia H. Takata & Paul D. Shumaker
This is digital research data corresponding to a published manuscript, Chemical extraction of phosphorus from dairy manure and utilization of recovered manure solids. Agronomy 2020, 10, 1725; doi:10.3390/agronomy10111725 Repeated land application of dairy manure can increase soil phosphorus above crop requirements because of manure’s low nitrogen (N) to phosphorus (P) ratio (N:P < 4:1). This soil P build-up can lead to off-site P transport and impairment of surface water quality. We evaluated a treatment process...

Data from: Genetic susceptibility to infectious disease in East African Shorthorn Zebu: a genome-wide analysis of the effect of heterozygosity and exotic introgression

Gemma G. R. Murray, Mark E. J. Woolhouse, Miika Tapio, Mary N. Mbole-Kariuki, Tad S. Sonstegard, Samuel M. Thumbi, Amy E. Jennings, Ilana Conradie Van Wyk, Margo Chase-Topping, Henry Kiara, Phil Toye, Koos Coetzer, Barend M. De C. Bronsvoort & Olivier Hanotte
Genotyping 50kSNPs East African Shorthorn ZebuPlink files with no QC50kSNPs.ped

Data from: Genome-wide association study of Arabidopsis thaliana identifies determinants of natural variation in seed oil composition

Sandra E. Branham, Sara J. Wright, Aaron Reba & C. Randal Linder
The renewable source of highly reduced carbon provided by plant triacylglycerols (TAGs) fills an ever increasing demand for food, biodiesel, and industrial chemicals. Each of these uses requires different compositions of fatty acid proportions in seed oils. Identifying the genes responsible for variation in seed oil composition in nature provides targets for bioengineering fatty acid proportions optimized for various industrial and nutrition goals. Here, we characterized the seed oil composition of 391 world-wide, wild accessions...

Data from: Honeybee microbiome is stabilized in the presence of propolis

Perot Saelao, Renata S. Borba, Vincent Ricigliano, Marla Spivak & Michael Simone-Finstrom
Honey bees have developed many unique mechanisms to help ensure the proper maintenance of homeostasis within the hive. One specific method includes the collection of antimicrobial plant resins and wax to form propolis, which is deposited throughout the hive. Propolis is believed to play a significant role in reducing disease load in the colony due to its antimicrobial and antiseptic properties. However, little is known on how propolis may be interacting with the commensal bacteria...

Data from: Increased soil temperature and decreased precipitation during early life stages constrain grass seedling recruitment in cold desert restoration

Jeremy J. James, Roger Sheley, Elizabeth Leger, Peter B. Adler, Stuart Hardegree, Elise Gornish & Matt Rinella
1. Seed-based restoration is one of the most difficult challenges for dryland restoration. Identifying environmental conditions that drive variation in seed and seedling mortality across similar restoration efforts could increase understanding of when and where restoration outcomes are likely to be favorable and identify new tools and strategies to improve outcomes. 2. We asked how variation in a suite of environmental predictors influenced germination, emergence, seedling establishment, and juvenile survival of four commonly sown perennial...

Nitrate removal and N2O production from upflow and downflow column woodchip bioreactors

Gary Feyereisen, Kurt Spokas, Jeffrey Strock, David Mulla, Andry Ranaivoson & Jeffrey Coulter
Woodchip denitrifying bioreactors (WDBR) reduce off-field tile drainage nitrogen (N) losses from agricultural fields. Limited evaluation exists regarding the influence of flow direction through WDBRs. Changing flow direction could reduce short circuiting. This study evaluated the dependency of nitrate-nitrogen removal and dissolved nitrous oxide (dN2O) production rates on vertical flow direction in triplicate column bioreactors at 12-h (without carbon dosing) and 2-h (with carbon dosing) hydraulic residence times. Results presented demonstrate that there was no...

Coffee Leaf Rust monitoring data on Hawaii Island

Melissa Johnson
CLR was detected in Hawaii for the first time in 2020 and quickly spread across the state. We initiated a CLR monitoring program in Kona, West Hawaii Island to track the spread of this new invasive disease across a broad elevational gradient. The goals of the program were to assist growers in the early detection of CLR, to characterize patterns of disease incidence across the region, and to collect information on farm agronomics, management practices,...

Ecotypic variation in Elymus elymoides productivity and drought resistance traits across the western United States

Dana Blumenthal
Introduction: Understanding local adaptation to climate is critical for managing ecosystems in the face of climate change. While there have been many provenance studies in trees, less is known about local adaptation in herbaceous species, including the perennial grasses that dominate arid and semiarid rangeland ecosystems. Methods and Results: We used a common-garden study to quantify variation in growth and drought-resistance traits in 99 populations of Elymus elymoides from a broad geographic and climatic range...

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