396 Works

Data from: The use of functional data analysis to evaluate activity in a spontaneous model of degenerative joint disease associated pain in cats

Margaret E. Gruen, Marcela Alfaro-Córdoba, Andrea E. Thomson, Alicia Worth, Ana-Maria Staicu, B. Duncan X. Lascelles & Alicia C. Worth
Accelerometry is used as an objective measure of physical activity in humans and veterinary species. In cats, one important use of accelerometry is in the study of therapeutics designed to treat degenerative joint disease (DJD) associated pain, where it serves as the most widely applied objective outcome measure. These analyses have commonly used summary measures, calculating the mean activity per-minute over days and comparing between treatment periods. While this technique has been effective, information about...

Data from: Continuous corn and corn–soybean profits over a 45-year tillage and fertilizer experiment

Andrew Trlica, Maninder K. Walia, Ron Krausz, Silvia Secchi & Rachel L. Cook
Studies comparing profitability of tillage systems often examine narrow historic windows or exclude annual price fluctuations. This study uses a continuous corn (Zea mays L.) (CC; 1970–1990) and corn–soybean [Glycine max (L.) Merr.] (CS; 1991–2014) Tillage × Fertilizer study in somewhat poorly drained soils in southern Illinois to reconstruct partial annual budgets with historical prices for crops, fertilizers, lime, herbicides, fuel, labor, and machinery. Combinations of tillage (moldboard plow [MP], chisel tillage [ChT], alternate tillage...

Data from: Human-caused habitat fragmentation can drive rapid divergence of male genitalia

Justa L. Heinen-Kay, Holly G. Noel, Craig A. Layman & R. Brian Langerhans
The aim of this study rests on three premises: 1) humans are altering ecosystems worldwide, 2) environmental variation often influences the strength and nature of sexual selection, and 3) sexual selection is largely responsible for rapid and divergent evolution of male genitalia. While each of these assertions has strong empirical support, no study has yet investigated their logical conclusion that human impacts on the environment might commonly drive rapid diversification of male genital morphology. We...

Data from: How shrub encroachment under climate change could threaten pollination services for alpine wildflowers: a case study using the alpine skypilot, Polemonium viscosum

Jessica A. Kettenbach, Nicole Miller-Struttmann, Zoë Moffett & Candace Galen
Under climate change, shrubs encroaching into high altitude plant communities disrupt ecosystem processes. Yet effects of encroachment on pollination mutualisms are poorly understood. Here, we probe potential fitness impacts of interference from encroaching Salix (willows) on pollination quality of the alpine skypilot, Polemonium viscosum. Overlap in flowering time of Salix and Polemonium is a precondition for interference and was surveyed in four extant and 25 historic contact zones. Pollinator sharing was ascertained from observations of...

Data from: Evolution of male coloration during a post-pleistocene radiation of Bahamas mosquitofish (Gambusia hubbsi)

Ryan A. Martin, Rüdiger Riesch, Justa Lee Heinen-Kay & R. Brian Langerhans
Sexual signal evolution can be complex because multiple factors influence the production, transmission, and reception of sexual signals, as well as receivers’ responses to them. To grasp the relative importance of these factors in generating signal diversity, we must simultaneously investigate multiple selective agents and signaling traits within a natural system. We use the model system of the radiation of Bahamas mosquitofish (Gambusia hubbsi) inhabiting blue holes to test the effects of resource availability, male...

Data from: The individual and combined effects of snowmelt timing and frost exposure on the reproductive success of montane forbs

Gabriella L. Pardee, Isaac O. Jensen, David W. Inouye & Rebecca E. Irwin
1. Changes from historic weather patterns have affected the phenology of many organisms worldwide. Altered phenology can introduce organisms to novel abiotic conditions during growth and modify species interactions, both of which could drive changes in reproduction. 2. We explored how climate change can alter plant reproduction using an experiment in which we manipulated the individual and combined effects of snowmelt timing and frost exposure, and measured subsequent effects on flowering phenology, peak flower density,...

Data from: Tissue storage and primer selection influence pyrosequencing-based inferences of diversity and community composition of endolichenic and endophytic fungi

Jana M. U'Ren, Jakob M. Riddle, James T. Monacell, Ignazio Carbone, Jolanta Miadlikowska & A. Elizabeth Arnold
Next-generation sequencing technologies have provided unprecedented insights into fungal diversity and ecology. However, intrinsic biases and insufficient quality control in next-generation methods can lead to difficult-to-detect errors in estimating fungal community richness, distributions, and composition. The aim of this study was to examine how tissue storage prior to DNA extraction, primer design, and various quality-control approaches commonly used in 454 amplicon pyrosequencing might influence ecological inferences in studies of endophytic and endolichenic fungi. We first...

Data from: Climate mediates the effects of disturbance on ant assemblage structure

Heloise Gibb, Nathan J. Sanders, Robert R. Dunn, Simon Watson, Manoli Photakis, Silvia Abril, Alan N. Andersen, Elena Angulo, Inge Armbrecht, Xavier Arnan, Fabricio B. Baccaro, Tom R. Bishop, Raphael Boulay, Cristina Castracani, Israel Del Toro, Thibaut Delsinne, Mireia Diaz, David A. Donoso, Martha L. Enríquez, Tom M. Fayle, Donald H. Feener, Matthew C. Fitzpatrick, Crisanto Gómez, Donato A. Grasso, Sarah Groc … & C. Gomez
Many studies have focused on the impacts of climate change on biological assemblages, yet little is known about how climate interacts with other major anthropogenic influences on biodiversity, such as habitat disturbance. Using a unique global database of 1128 local ant assemblages, we examined whether climate mediates the effects of habitat disturbance on assemblage structure at a global scale. Species richness and evenness were associated positively with temperature, and negatively with disturbance. However, the interaction...

Data from: Ecological effects on metabolic scaling amphipod responses to fish predators in freshwater springs

Douglas S. Glazier, Eric M. Butler, Sara A. Lombardi, Travis J. Deptola, Andrew J. Reese & Erin V. Satterthwaite
Metabolic rate is commonly thought to scale with body mass to the 3/4-power as a result of universal body-design constraints. However, recent comparative work has shown that the metabolic scaling slope may vary significantly among species and higher taxa, apparently in response to different lifestyles and ecological conditions, though the precise mechanisms involved are not well understood. To better understand these under-appreciated ecological effects and their causes, it is important to control for extraneous phylogenetic...

Data from: Taxon cycle predictions supported by model-based inference in Indo-Pacific trap-jaw ants (Hymenoptera: Formicidae: Odontomachus)

Pável Matos-Maraví, Nicholas J. Matzke, Fredrick J. Larabee, Ronald M. Clouse, Ward C. Wheeler, Daniela Magdalena Sorger, Andrew V. Suarez & Milan Janda
Non-equilibrium dynamics and non-neutral processes, such as trait-dependent dispersal, are often missing from quantitative island biogeography models despite their potential explanatory value. One of the most influential non-equilibrium models is the taxon cycle, but it has been difficult to test its validity as a general biogeographical framework. Here, we test predictions of the taxon-cycle model using six expected phylogenetic patterns and a time-calibrated phylogeny of Indo-Pacific Odontomachus (Hymenoptera: Formicidae: Ponerinae), one of the ant genera...

Data from: Betweenness centrality as predictor for forces in granular packings

Jonathan E. Kollmer & Karen E. Daniels
A load applied to a jammed frictional granular system will be localized into a network of force chains making inter-particle connections throughout the system. Because such systems are typically under-constrained, the observed force network is not unique to a given particle configuration, but instead varies upon repeated formation. In this paper, we examine the ensemble of force chain configurations created under repeated assembly in order to develop tools to statistically forecast the observed force network....

Data from: Environmental and historical imprints on beta diversity: insights from variation in rates of species turnover along gradients

Matthew C. Fitzpatrick, Nathan J. Sanders, Signe Normand, Jens-Christian Svenning, Simon Ferrier, Aaron D. Gove, Robert R. Dunn, N. J. Sanders, S. Normand, R. R. Dunn, J.-C. Svenning, A. D. Gove & S. Ferrier
A common approach for analysing geographical variation in biodiversity involves using linear models to determine the rate at which species similarity declines with geographical or environmental distance and comparing this rate among regions, taxa or communities. Implicit in this approach are weakly justified assumptions that the rate of species turnover remains constant along gradients and that this rate can therefore serve as a means to compare ecological systems. We use generalized dissimilarity modelling, a novel...

Data from: Tethered homing gene drives: a new design for spatially restricted population replacement and suppression

Sumit Dhole, Alun L. Lloyd & Fred Gould
Optimism regarding potential epidemiological and conservation applications of modern gene drives is tempered by concern about the possibility of unintended spread of engineered organisms beyond the target population. In response, several novel gene drive approaches have been proposed that can, under certain conditions, locally alter characteristics of a population. One challenge for these gene drives is the difficulty of achieving high levels of localized population suppression without very large releases in the face of gene...

Data from: Extensive sex-specific nonadditivity of gene expression in Drosophila melanogaster

Greg Gibson, Rebecca Riley-Berger, Larry Harshman, Artyom Kopp, Scott Vacha, Sergey Nuzhdin & Marta Wayne
Assessment of the degree to which gene expression is additive and heritable has important implications for understanding the maintenance of variation, adaptation, phenotypic divergence, and the mapping of genotype onto phenotype. We used whole-genome transcript profiling using Agilent long-oligonucleotide microarrays representing 12,017 genes to demonstrate that gene transcription is pervasively nonadditive in Drosophila melanogaster. Comparison of adults of two isogenic lines and their reciprocal F1 hybrids revealed 5820 genes as significantly different between at least...

Dityrosine formation via reactive oxygen consumption yields increasingly recalcitrant humic-like fluorescent organic matter in the ocean

Ryan Paerl, Iliana Claudio, Michael Shields, Thomas Bianchi & Christopher Osburn
Marine dissolved organic matter (DOM) is a massive elemental pool on Earth and is thought to consist of a chemically complex mixture of molecules. Part of marine DOM is fluorescent (FDOM) and includes humic-like compounds. The chemical composition of, and biochemical pathways that yield, autochthonous humic-like FDOM in the ocean is largely unknown. Inspired by medical and biochemical research detailing the formation of colored and fluorescent dityrosine via peroxidase mediated reactions, we used fluorometry and...

Multiple traits and multifarious environments: integrated divergence of morphology and life history

Rüdiger Riesch, Ryan A. Martin & R. Brian Langerhans
Understanding complex responses of multiple character suites (e.g., behaviour, life history, morphology) to multifarious environments is a challenging task. Here we use a multivariate approach (partial least squares structural equation modelling) to disentangle drivers (i.e., predation, resource availability, and population demographics) of phenotypic divergence among populations of Bahamas mosquitofish (Gambusia hubbsi) inhabiting blue holes. We further employ a two-block partial least squares analysis in a novel approach to uncovering integrated and independent aspects of divergence...

Maintaining historic disturbance regimes increases species’ resilience to catastrophic hurricanes

Erica H Henry, Martha O Burford Reiskind, Aerin Land & Nick M Haddad
As habitat loss and fragmentation, urbanization, and global climate change accelerate, conservation of rare ecosystems increasingly relies on human intervention. However, any conservation strategy is vulnerable to unpredictable, catastrophic events. Whether active management increases or decreases a system’s resilience to these events remains unknown. Following Hurricane Irma’s landfall in our habitat restoration study sites, we found that rare ecosystems with active, human-imposed management suffered less damage in a hurricane’s path than unmanaged systems. At the...

Genomic evidence of introgression and adaptation in a model subtropical tree species, Eucalyptus grandis

Marja Mostert-O'Neill, Sharon Reynolds, Juan Acosta, David Lee, Justin Borevitz & Alexander Myburg
The genetic consequences of adaptation to changing environments can be deciphered using landscape genomics, which may help predict species’ responses to global climate change. Towards this, we used genome-wide SNP marker analysis to determine population structure and patterns of genetic differentiation in terms of neutral and adaptive genetic variation in the natural range of Eucalyptus grandis, a widely cultivated subtropical and temperate species, serving as genomic reference for the genus. We analysed introgression patterns at...

Experimental N and P additions relieve stoichiometric constraints on organic-matter flows through five stream food webs

Lee Demi, Jonathan Benstead, Amy Rosemond & John Maerz
1. Human activities have dramatically altered global patterns of nitrogen (N) and phosphorus (P) availability. This pervasive nutrient pollution is changing basal resource quality in food webs, thereby affecting rates of biological productivity and the pathways of energy and material flow to higher trophic levels. 2. Here, we investigate how the stoichiometric quality of basal resources modulates patterns of material flow through food webs by characterizing the effects of experimental N and P enrichment on...

Do dog breeds differ in pain sensitivity? Veterinarians and the public believe they do

Margaret Gruen, Brian Hare & Philip White
Humans do not respond to the pain of all humans equally; physical appearance and associated group identity affect how people respond to the pain of others. Here we ask if a similar differential response occurs when humans evaluate different individuals of another species. Beliefs about pain in pet dogs (Canis familiaris) provide a powerful test, since dogs vary so much in size, shape, and color, and are often associated with behavioral stereotypes. Using an on-line...

Parasites, niche modification and the host microbiome: A field survey of multiple parasites

Kayleigh R. O'Keeffe, Fletcher W. Halliday, Corbin D. Jones, Ignazio Carbone & Charles E. Mitchell
Parasites can affect and be affected by the host's microbiome, with consequences for host susceptibility, parasite transmission, and host and parasite fitness. Yet, two aspects of the relationship between parasite infection and host microbiota remain little understood: the nature of the relationship under field conditions, and how the relationship varies among parasites. To overcome these limitations, we performed a field survey of the within-leaf fungal community in a tall fescue population. We investigated how diversity...

Robustness of the Dorsal morphogen gradient with respect to morphogen dosage

Gregory Reeves, Hadel Al Asafen, Sophia Carrell-Noel, Allison Schloop, Jeramey Friedman & Prasad Bandodkar
In multicellular organisms, the timing and placement of gene expression in a developing tissue assigns the fate of each cell in the embryo in order for a uniform field of cells to differentiate into a reproducible pattern of organs and tissues. This positional information is often achieved through the action of spatial gradients of morphogens. Spatial patterns of gene expression are paradoxically robust to variations in morphogen dosage, given that, by definition, gene expression must...

PacBio IsoSeq reference transcriptomes for Pinus taeda L.

Edwin Lauer & Fikret Isik
Fusiform rust disease, caused by the endemic fungus Cronartium quercuum f. sp. fusiforme, is the most damaging disease affecting economically important pine species in the southeast United States. In this report, we detail the genomic localization and sequence-level discovery of candidate race-nonspecific broad-spectrum fusiform rust resistance genes in Pinus taeda L. Two full-sib families, each with ~1000 progeny, were challenged with a complex inoculum consisting of over 150 pathogen isolates. High-density linkage mapping revealed three...

Resolving the phylogenetic relationship among recently diverged members of the rockfish subgenus Sebastosomus

Martha Burford Reiskind, Emma Wallace, Emily Reed & Andres Aguilar
Rapid speciation is an important aspect of adaptive radiations, but can obfuscate phylogenetic relationships among taxa. For recent radiations, there are challenges to reconstructing the relationships among the species due to often shorter branch lengths. Resolution of these relationships is further confounded when studies only use a few genetic markers. Double digest restriction-site associated DNA sequencing (ddRADseq) is a method of next generation sequencing that identifies many single nucleotide polymorphisms (SNPs) throughout the genome. This...

Data from: Seed fate in ant-mediated dispersal: Seed dispersal effectiveness in the Ectatomma ruidum (Formicidae) - Zanthoyxlum ekmanii (Rutaceae) system

Selina A. Ruzi & Andrew V. Suarez.
Plants are often dispersal limited relying on passive or active agents to find suitable microhabitats for germination. Seeds of pioneer tree species, for example, require light gaps for growth but have short median dispersal distances and often do not provide a food reward to encourage animal dispersal. Zanthoxylum ekmanii seeds are frequently moved by ants but evaluating the effectiveness of ant-mediated seed removal requires knowledge of the species moving the seeds, how far they are...

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