290 Works

Data from: Bioturbation by mammals and fire interact to alter ecosystem-level nutrient dynamics in longleaf pine forests

Kenneth L. Clark, Lyn C. Branch & Jennifer Farrington
Activities of ecosystem engineers can interact with other disturbances to modulate rates of key processes such as productivity and nutrient cycling. Bioturbation, movement of soil by organisms, is a widespread form of ecosystem engineering in terrestrial ecosystems. We propose that bioturbation by southeastern pocket gophers (Geomys pinetis), an abundant but declining ecosystem engineer in longleaf pine (Pinus palustris Mill.) forests, accelerates nutrient dynamics of the forest floor by burying litter and then reduces litter consumption...

Supplemental data to \"Estimating the Genetic Diversity of Pacific salmon and trout using Multi-gene eDNA Metabarcoding\"

Kevin Weitemier, Brooke E. Penaluna, Laura Hauck, Lucas J. Longway, Tiffany Garcia & Richard Cronn
This dataset contains DNA sequence data of Oncorhynchus species, isolated from environmental DNA (eDNA) from Pacific Northwest streams via microfluidic eDNA metabarcoding and high-throughput (Ilummina) sequencing (samples collected from 2017-09-22 to 2017-10-10). It is accompanied by scripts and commands for data analyses including: sequence denoising, calculation of entropy values by codon position, and calculation of diversity statistics and haplotype mapping. Intermediate outputs include denoised haplotypes, entropy calculations, and haplotype summaries following chimera removal.

Nitrous oxide emissions in a landscape transitioning from Conservation Reserve Program grassland to energy crops switchgrass and Miscanthus

A.R. Kemanian, D. Shaha, B.M. Rau, J.P. Kaye, F.R. Montes & P.R. Adler
uture liquid fuel demand from renewable sources may, in part, be met by converting the seasonally wet portions of the landscape currently managed for soil and water conservation to perennial energy crops. However, this shift may increase nitrous oxide (N2O) emissions, thus limiting the carbon (C) benefits of energy crops. Particularly high emissions may occur during the transition period when the soil is disturbed, plants are establishing, and nitrate and water accumulation may favor emissions....

Data from: Reproductive isolation and environmental adaptation shape the phylogeography of mountain pine beetle (Dendroctonus ponderosae)

Eddy J. Dowle, Ryan R. Bracewell, Michael E. Pfrender, Karen E. Mock, Barbara J. Bentz & Gregory J. Ragland
Chromosomal rearrangement can be an important mechanism driving population differentiation and incipient speciation. In the mountain pine beetle (MPB, Dendroctonus ponderosae), deletions on the Y chromosome that are polymorphic among populations are associated with reproductive incompatibility. Here we used RAD sequencing across the entire MPB range in western North America to reveal the extent of the phylogeographic differences between Y haplotypes compared to autosomal and X-linked loci. Clustering and gene flow analyses revealed three distinct...

Data from: Use of simulation-based statistical models to complement bioclimatic models in predicting continental scale invasion risks

Ranjan Muthukrishnan, Nicholas R. Jordan, Adam S. Davis & James D. Forester
Invasive species represent one of the greatest risks to global biodiversity and economic productivity of agroecosystems. The development of certain novel crops—e.g., herbaceous perennial biomass crops—may create a risk of novel invasions by these crops. Therefore, potential benefits and risks need to be weighed in making decisions about their introduction and subsequent management. Ideally, such a weighing will be based on good estimates of invasion risks in realistic scenarios pertaining to actual landscapes of concern...

Data from: Signatures of selection for environmental adaptation and zebu x taurine hybrid fitness in East African Shorthorn Zebu

Hussain Bahbahani, Abdulfatai Tijjani, Christopher Mukasa, David Wragg, Faisal Almathen, Oyekanmi Nash, Gerald N. Akpa, Mary Mbole-Kariuki, Sunir Malla, Mark Woolhouse, Tad Sonstegard, Curtis Van Tassell, Martin Blythe, Heather Huson & Olivier Hanotte
The East African Shorthorn Zebu (EASZ) cattle are ancient hybrid between Asian zebu × African taurine cattle preferred by local farmers due to their adaptability to the African environment. The genetic controls of these adaptabilities are not clearly understood yet. Here, we genotyped 92 EASZ samples from Kenya (KEASZ) with more than 770,000 SNPs and sequenced the genome of a pool of 10 KEASZ. We observe an even admixed autosomal zebu × taurine genomic structure...

Data from: Integrating transcriptional, metabolomic, and physiological responses to drought stress and recovery in switchgrass (Panicum virgatum L.)

Eli Meyer, Michael J. Aspinwall, David B. Lowry, Juan Diego Palacio-Mejía, Tierney L. Logan, Philip A. Fay & Thomas E. Juenger
Background: In light of the changes in precipitation and soil water availability expected with climate change, understanding the mechanisms underlying plant responses to water deficit is essential. Toward that end we have conducted an integrative analysis of responses to drought stress in the perennial C4 grass and biofuel crop, Panicum virgatum (switchgrass). Responses to soil drying and re-watering were measured at transcriptional, physiological, and metabolomic levels. To assess the interaction of soil moisture with diel...

Data from: Divergence in strategies for coping with winter embolism among co-occurring temperate tree species: the role of positive xylem pressure, wood type and tree stature

Cun-Yang Niu, Frederick C. Meinzer & Guang-You Hao
1. In temperate ecosystems, freeze-thaw events are an important environmental stress that can induce severe xylem embolism (i.e. clogging of conduits by air bubbles) in overwintering organs of trees. However, no comparative studies of different adaptive strategies among sympatric tree species for coping with winter embolism have examined the potential role of the presence or absence of embolism refilling by positive xylem pressure. 2. We evaluated the degree of winter embolism and hydraulic architecture traits...

Data from: Falcons using orchard nest boxes reduce fruit-eating bird abundances and provide economic benefits for a fruit-growing region

Megan E. Shave, Stephanie A. Shwiff, Julie L. Elser & Catherine A. Lindell
1. Suppression of pest species via a native predator is a regulating ecosystem service that has the potential to limit crop damage and produce economic benefits. American kestrels (Falco sparverius) are widespread, highly-mobile, generalist predators that hunt in human-dominated habitats and potentially provide previously undocumented ecosystem services in agricultural landscapes. 2. We hypothesized that kestrel activity associated with nest boxes and artificial perches acts to increase perceived predation risk that, in combination with direct predation,...

Data from: Patterns of primary succession of native and introduced plants in lowland wet forests in eastern Hawai‘i

Naupaka Zimmerman, R. Flint Hughes, Susan Cordell, Patrick Hart, Heather Kalei Chang, David Perez, Ryan Kaipoalohaakala Like & Rebecca Ostertag
The majority of Hawaii’s lowland wet forests no longer exist, with many of the last remaining patches found on the eastern, windward sides of the largest islands. To better understand successional patterns and invasion in these native systems, we quantified basal area (BA) and densities of woody species and understory cover at nine sites in the Puna district on the Island of Hawai‘i, representing age gradients of native stand development on both ‘a’ā and pāhoehoe...

Data from: Conditional vulnerability of plant diversity to atmospheric nitrogen deposition across the United States

Samuel M. Simkin, Edith B. Allen, William D. Bowman, Christopher M. Clark, Jayne Belnap, Matthew L. Brooks, Brian S. Cade, Scott L. Collins, Linda H. Geiser, Frank S. Gilliam, Sarah E. Jovan, Linda H. Pardo, Bethany K. Schulz, Carly J. Stevens, Katharine N. Suding, Heather L. Throop & Donald M. Waller
Atmospheric nitrogen (N) deposition has been shown to decrease plant species richness along regional deposition gradients in Europe and in experimental manipulations. However, the general response of species richness to N deposition across different vegetation types, soil conditions, and climates remains largely unknown even though responses may be contingent on these environmental factors. We assessed the effect of N deposition on herbaceous richness for 15,136 forest, woodland, shrubland, and grassland sites across the continental United...

Data from: Process-based simulation of prairie growth

Cody J. Zilverberg, Jimmy Williams, Curtis Jones, Keith Harmoney, Jay Angerer, Loretta J. Metz & William Fox
When field research is cost- or time-prohibitive, models can inform decision-makers regarding the impact of agricultural policy on production and the environment, but process-based models that simulate animal-plant-soil interaction and ecosystem services in grazing lands are rare. In the U.S.A., APEX (Agricultural Policy/Environmental eXtender) is a model commonly used to inform policy on cropland, but its ability to simulate grazinglands was less robust. Therefore, we enhanced the APEX model’s plant growth module to improve its...

Data from: The genetic architecture of ecological adaptation: intraspecific variation in host plant use by the lepidopteran crop pest Chloridea virescens

Sara J. Oppenheim, Fred Gould & Keith R. Hopper
Intraspecific variation in ecologically important traits is a cornerstone of Darwin’s theory of evolution by natural selection. The evolution and maintenance of this variation depends on genetic architecture, which in turn determines responses to natural selection. Some models suggest that traits with complex architectures are less likely to respond to selection than those with simple architectures, yet rapid divergence has been observed in such traits. The simultaneous evolutionary lability and genetic complexity of host plant...

Data from: Character evolution and missing (morphological) data across Asteridae

Gregory W. Stull, Melanie Schori, Douglas E. Soltis & Pamela S. Soltis
Premise of the study: Our current understanding of flowering plant phylogeny provides an excellent framework for exploring various aspects of character evolution through comparative analyses. However, attempts to synthesize this phylogenetic framework with extensive morphological datasets have been surprisingly rare. Here, we explore character evolution in Asteridae (asterids), a major angiosperm clade, using an extensive morphological data set and a well-resolved phylogeny. Methods: We scored 15 phenotypic characters (spanning chemistry, vegetative anatomy, and floral, fruit,...

Data from: Leaf nutrients, not specific leaf area, are consistent indicators of elevated nutrient inputs

Jennifer Firn, James M. McGree, Eric Harvey, Habacuc Flores-Moreno, Martin Schütz, Yvonne M. Buckley, Elizabeth T. Borer, Eric W. Seabloom, Kimberly J. La Pierre, Andrew M. MacDougall, Suzanne M. Prober, Carly J. Stevens, Lauren L. Sullivan, Erica Porter, Emma Ladouceur, Charlotte Allen, Karine H. Moromizato, John W. Morgan, W. Stanley Harpole, Yann Hautier, Nico Eisenhauer, Justin P. Wright, Peter B. Adler, Carlos Alberto Arnillas, Jonathan D. Bakker … & Anita C. Risch
Leaf traits are frequently measured in ecology to provide a ‘common currency’ for predicting how anthropogenic pressures impact ecosystem function. Here, we test whether leaf traits consistently respond to experimental treatments across 27 globally distributed grassland sites across 4 continents. We find that specific leaf area (leaf area per unit mass)—a commonly measured morphological trait inferring shifts between plant growth strategies—did not respond to up to four years of soil nutrient additions. Leaf nitrogen, phosphorus...

Data from: Complementarity of statistical treatments to reconstruct worldwide routes of invasion: the case of the Asian ladybird Harmonia axyridis

Eric Lombaert, Thomas Guillemaud, Jonathan Lundgren, Robert Koch, Benoît Facon, Audrey Grez, Antoon Loomans, Thibaut Malausa, Oldrich Nedved, Emma Rhule, Arnstein Staverlokk, Tove Steenberg & Arnaud Estoup
Inferences about introduction histories of invasive species remain challenging because of the stochastic demographic processes involved. Approximate Bayesian computation (ABC) can help to overcome these problems, but such method requires a prior understanding of population structure over the study area, necessitating the use of alternative methods and an intense sampling design. In this study, we made inferences about the worldwide invasion history of the ladybird Harmonia axyridis by various population genetics statistical methods, using a...

Data from: Population genomics of divergence among extreme and intermediate color forms in a polymorphic insect

Jeffrey D. Lozier, Jason M. Jackson, Michael E. Dillon & James P. Strange
Geographic variation in insect coloration is among the most intriguing examples of rapid phenotypic evolution and provides opportunities to study mechanisms of phenotypic change and diversification in closely related lineages. The bumble bee Bombus bifarius comprises two geographically disparate color groups characterized by red-banded and black-banded abdominal pigmentation, but with a range of spatially and phenotypically intermediate populations across western North America. Microsatellite analyses have revealed that B. bifarius in the USA are structured into...

Data from: Long-term impacts of variable retention harvesting on ground-layer plant communities in Pinus resinosa forests

Margaret W. Roberts, Anthony W. D'Amato, Christel C. Kern & Brian J. Palik
Concerns about loss of biodiversity and structural complexity in managed forests have recently increased and led to the development of new management strategies focused on restoring or maintaining ecosystem functions while also providing wood outputs. Variable Retention Harvest (VRH) systems, in which mature overstorey trees are retained in various spatial arrangements across harvested areas, represent one potential approach to this problem. However, long-term evaluations of the effectiveness of this strategy at sustaining plant community composition...

Data from: Conserved genetic regions across angiosperms as tools to develop single copy nuclear markers in gymnosperms: an example using cycads

Dayana E. Salas-Leiva, Alan W. Meerow, Javier Francisco-Ortega, Michael Calonje, M. Patrick Griffith, Dennis W. Stevenson & Kyoko Nakamura
Several individuals of the Caribbean Zamia clade and other cycad genera were used to identify single copy nuclear genes for phylogeographic and phylogenetic studies in Cycadales. Two strategies were employed to select target loci: 1) a tblastX search of Arabidopsis conserved ortholog sequence (COS) set and, 2) a tblastX search of Arabidopsis-Populus-Vitis-Oryza Shared Single Copy genes (APVO SSC) against the EST Zamia databases in Genbank. From the first strategy, 30 loci were selected, and from...

Data from: Elevated CO2 and water addition enhance nitrogen turnover in grassland plants with implications for temporal stability

Feike A. Dijkstra, Yolima Carrillo, Dana M. Blumenthal, Kevin E. Mueller, Daniel R. LeCain, Jack A. Morgan, Tamara J. Zelikova, David G. Williams, Ronald F. Follett, Elise Pendall & Dan R. LeCain
Temporal variation in soil nitrogen (N) availability affects growth of grassland communities that differ in their use and reuse of N. In a seven-year-long climate change experiment in a semiarid grassland, the temporal stability of plant biomass production varied with plant N turnover (reliance on externally acquired N relative to internally recycled N). Species with high N turnover were less stable in time compared to species with low N turnover. In contrast, N turnover at...

Data from: The genetic architecture of a complex ecological trait: host plant use in the specialist moth, Heliothis subflexa

Sara Jane Oppenheim, Fred Gould & Keith Roderick Hopper
We used genetic mapping to examine the genetic architecture of differences in host plant use between two species of noctuid moths, Heliothis subflexa, a specialist on Physalis spp., and its close relative, the broad generalist H. virescens. We introgressed H. subflexa chromosomes into the H. virescens background and analyzed 1,462 backcross insects. The effects of H. subflexa-origin chromosomes were small when measured as the percent variation explained in backcross populations (0.2 to 5%), but were...

Data from: Genetic architecture of sexual dimorphism in a subdioecious plant with a proto-sex chromosome

Rachel B. Spigler, Kim S. Lewers & Tia-Lynn Ashman
The rise of sexual dimorphism is thought to coincide with the evolution of sex chromosomes. Yet because sex chromosomes in many species are ancient, we lack empirical evidence of the earliest stages of this transition. We use QTL analysis to examine the genetic architecture of sexual dimorphism in subdioecious octoploid Fragaria virginiana. We demonstrate that the region housing the male-function locus controls the majority of quantitative variation in proportion fruit set, confirming the existence of...

Data from: Climate modifies response of non-native and native species richness to nutrient enrichment

Habacuc Flores-Moreno, Peter B. Reich, Eric M. Lind, Lauren L. Sullivan, Eric W. Seabloom, Laura Yahdjian, Andrew S. MacDougall, Lara G. Reichmann, Juan Alberti, Selene Báez, Jonathan D. Bakker, Marc W. Cadotte, Maria C. Caldeira, Enrique J. Chaneton, Carla M. D'Antonio, Philip A. Fay, Jennifer Firn, Nicole Hagenah, W. Stanley Harpole, Oscar Iribarne, Kevin P. Kirkman, Johannes M. H. Knops, Kimberly J. La Pierre, Ramesh Laungani, Andrew D. B. Leakey … & Elizabeth T. Borer
Ecosystem eutrophication often increases domination by non-natives and causes displacement of native taxa. However, variation in environmental conditions may affect the outcome of interactions between native and non-native taxa in environments where nutrient supply is elevated. We examined the interactive effects of eutrophication, climate variability and climate average conditions on the success of native and non-native plant species using experimental nutrient manipulations replicated at 32 grassland sites on four continents. We hypothesized that effects of...

Data from: Divergence estimates and early evolutionary history of Figitidae (Hymenoptera: Cynipoidea)

Matthew L. Buffington, Seán G. Brady, Shelah I. Morita & Simon Van Noort
matrix08REDUCEDBayes04The combined molecular and morphological dataset analyzed using MrBayes.cynipoid_dating_all_calibrationsThe molecular dataset analyzed using BEAST.

Data from: Not as ubiquitous as we thought: taxonomic crypsis, hidden diversity and cryptic speciation in the cosmopolitan fungus Thelonectria discophora (Nectriaceae, Hypocreales, Ascomycota)

Catalina Salgado-Salazar, Amy Y. Rossman & Priscila Chaverri
The distribution of microbial species, including fungi, has long been considered cosmopolitan. Recently, this perception has been challenged by molecular studies in historical biogeography, phylogeny and population genetics. Here we explore this issue using the fungal morphological species Thelonectria discophora, one of the most common species of fungi in the family Nectriaceae, encountered in almost all geographic regions and considered as a cosmopolitan taxon. In order to determine if T. discophora is a single cosmopolitan...

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