96 Works

Data from: Phylogeny and photosynthesis of the grass tribe Paniceae

Jacob D. Washburn, James C. Schnable, Gerrit Davidse & J. Chris Pires
PREMISE OF THE STUDY: The grass tribe Paniceae includes important food, forage, and bioenergy crops such as switchgrass, napiergrass, various millet species, and economically important weeds. Paniceae are also valuable for answering scientific and evolutionary questions about C4 photosynthetic evolution, drought tolerance, and spikelet variation. However, the phylogeny of the tribe remains incompletely resolved. METHODS: Forty-five taxa were selected from across the tribe Paniceae and outgroups for genome survey sequencing (GSS). These data were used...

Data from: Seasonal variation in life history traits in two Drosophila species

Emily L. Behrman, Samuel S. Watson, Katherine R. O'Brien, Shane M. Heschel, Paul S. Schmidt, K. R. O'Brien, E. L. Behrman, P. S. Schmidt & S. S. Watson
Seasonal environmental heterogeneity is cyclic, persistent and geographically widespread. In species that reproduce multiple times annually, environmental changes across seasonal time may create different selection regimes that may shape the population ecology and life history adaptation in these species. Here, we investigate how two closely related species of Drosophila in a temperate orchard respond to environmental changes across seasonal time. Natural populations of Drosophila melanogaster and D. simulans were sampled at four timepoints from June...

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...

Data from: Globally, functional traits are weak predictors of juvenile tree growth, and we do not know why

C. E. Timothy Paine, Lucy Amissah, Harald Auge, Christopher Baraloto, Martin Baruffol, Nils Bourland, Helge Bruelheide, Kasso Daïnou, Roland C. De Gouvenain, Jean-Louis Doucet, Susan Doust, Paul V. A. Fine, Claire Fortunel, Josephine Haase, Karen D. Holl, Hervé Jactel, Xuefei Li, Kaoru Kitajima, Julia Koricheva, Cristina Martínez-Garza, Christian Messier, Alain Paquette, Christopher Philipson, Daniel Piotto, Lourens Poorter … & Andy Hector
1. Plant functional traits, in particular specific leaf area (SLA), wood density and seed mass, are often good predictors of individual tree growth rates within communities. Individuals and species with high SLA, low wood density and small seeds tend to have faster growth rates. 2. If community-level relationships between traits and growth have general predictive value, then similar relationships should also be observed in analyses that integrate across taxa, biogeographic regions and environments. Such global...

Data from: Correction of location errors for presence-only species distribution models

Trevor J. Hefley, David M. Baasch, Andrew J. Tyre & Erin E. Blankenship
1. Species distribution models (SDMs) for presence-only data depend on accurate and precise measurements of geographic and environmental covariates that influence presence and abundance of the species. Some data sets, however, may contain both systematic and random errors in the recorded location of the species. Environmental covariates at the recorded location may differ from those at the true location and result in biased parameter estimates and predictions from SDMs. 2. Regression calibration is a well-developed...

Data from: The tree of life and a new classification of bony fishes

Ricardo Betancur-R., Adela Roa-Varon, Nancy I. Holcroft, W. Calvin Borden, Terry Grande, Kent Carpenter, Millicent Sanciangco, Chenhong Li, Dahiana Arcila, Jesus A Ballesteros, Guillermo Ortí, J. Andrés López, Matthew A. Campbell, Edward O. Wiley, Gloria Arratia, Guoqing Lu, Stuart Willis, Richard E. Broughton, Cureton II, James C, Feifei Zhang & Daniel J. Hough
The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The situation is most critical for a large clade of spiny-finned fishes, traditionally referred to as percomorphs, whose uncertain relationships have plagued ichthyologists for over a century. Most of what we know about the higher-level relationships among fish lineages has been based on morphology, but rapid influx of molecular studies is...

Data from: Species limits and phylogenomic relationships of Darwin’s finches remain unresolved: potential consequences of a volatile ecological setting

Robert M. Zink, Hernán Vázquez-Miranda & Robert M Zink
Island biotas have become paradigms for illustrating many evolutionary processes. The fauna of the Galapagos Islands includes several taxa that have been focal points for evolutionary studies. Perhaps their most famous inhabitants, Darwin’s finches, represent a go-to icon when thinking about how species originate and adapt to the environment. However, unlike other adaptive radiations, past morphological and molecular studies of Darwin’s finches have yielded inconsistent hypotheses of species limits and phylogenetic relationships. Expecting that idiosyncrasies...

Data from: High soil test phosphorus effect on corn yield

Charles Wortmann, Charles Shapiro, Tim Shaver & Michael Mainz Retired
Phosphorus removal in crop harvest has increased as yields have increased. Fertilizer P use guidelines are based on calibrations often developed for much lower yield levels and may need recalibration. Corn yields may be greater with higher than recommended soil test P when springs are relatively wet and cool. Research was conducted across 12 irrigated and five rainfed siteyr in Nebraska with initial Bray-1 P ≤ 11 mg kg–1 to evaluate P application strategies for...

Data from: Mitochondrial dysfunction and infection generate immunity-fecundity tradeoffs in Drosophila

Justin L. Buchanan, Colin D. Meiklejohn, Kristi L. Montooth, Justin L Buchanan, Colin D Meiklejohn & Kristi L Montooth
Physiological responses to short-term environmental stressors, such as infection, can have long-term consequences for fitness, particularly if the responses are inappropriate or nutrient resources are limited. Genetic variation affecting energy acquisition, storage, and usage can limit cellular energy availability and may influence resource-allocation tradeoffs even when environmental nutrients are plentiful. Here, we utilized Drosophila mitochondrial-nuclear genotypes to test whether disrupted mitochondrial function interferes with nutrient-sensing pathways, and whether this disruption has consequences for tradeoffs between...

Data from: Lake regionalization and diatom metacommunity structuring in tropical South America

Xavier Benito, Sherilyn C. Fritz, Miriam Steinitz-Kannan, Maria I. Vélez & Michael M. McGlue
Lakes and their topological distribution across Earth’s surface impose ecological and evolutionary constraints on aquatic metacommunities. In this study, we group similar lake ecosystems as metacommunity units influencing diatom community structure. We assembled a database of 195 lakes from the tropical Andes and adjacent lowlands (8ºN–30ºS and 58–79ºW) with associated environmental predictors to examine diatom metacommunity patterns at two different levels: taxon and functional (deconstructed species matrix by ecological guilds). We also derived spatial variables...

Data from: Spatial heterogeneity in species composition constrains plant community responses to herbivory and fertilization

Dorothee Hodapp, Elizabeth T. Borer, W. Stanley Harpole, Eric M. Lind, Eric W. Seabloom, Peter B. Adler, Juan Alberti, Carlos A. Arnillas, Jonathan D. Bakker, Lori Biederman, Marc Cadotte, Elsa E. Cleland, Scott Collins, Philip A. Fay, Jennifer Firn, Nicole Hagenah, Yann Hautier, Oscar Iribarne, Johannes M.H. Knops, Rebecca L. McCulley, Andrew MacDougall, Joslin L. Moore, John W. Morgan, Brent Mortensen, Kimberly J. La Pierre … & Johannes M. H. Knops
Environmental change can result in substantial shifts in community composition. The associated immigration and extinction events are likely constrained by the spatial distribution of species. Still, studies on environmental change typically quantify biotic responses at single spatial (time series within a single plot) or temporal (spatial beta-diversity at single time points) scales, ignoring their potential interdependence. Here, we use data from a global network of grassland experiments to determine how turnover responses to two major...

Data from: Maize-nutrient response information applied across Sub-Saharan Africa

Charles S. Wortmann, Maribeth Milner, Kayuki C. Kaizzi, Maman Nouri, Athanase R. Cyamweshi, Mohammed K. Dicko, Catherine N. Kibunja, Martin Macharia, Ricardo Maria, Patson C. Nalivata, Negash Demissie, Davy Nkonde, Korodjouma Ouattara, Catherine J. Senkoro, Bitrus Dawi Tarfa & Francis M. Tetteh
The profit potential for a given investment in fertilizer use can be estimated using representative crop nutrient response functions. Where response data is scarce, determination of representative response functions can be strengthened by using results from homologous crop growing conditions. Maize (Zea mays L.) nutrient response functions were selected from the Optimization of Fertilizer Recommendations in Africa (OFRA) database of 5500 georeferenced response functions determined from field research conducted in Sub-Saharan Africa. Three methods for...

Data from: Evaluation of acoustic telemetry grids for determining aquatic animal movement and survival

Richard T. Kraus, Christopher M. Holbrook, Christopher S. Vandergoot, Taylor R. Stewart, Matthew D. Faust, Douglas A. Watkinson, Colin Charles, Mark Pegg, Eva C. Enders & Charles C. Krueger
1. Acoustic telemetry studies have frequently prioritized linear configurations of hydrophone receivers, such as perpendicular from shorelines or across rivers, to detect the presence of tagged aquatic animals. This approach introduces unknown bias when receivers are stationed for convenience at geographic bottlenecks (e.g., at the mouth of an embayment or between islands) as opposed to deployments following a statistical sampling design. 2. We evaluated two-dimensional acoustic receiver arrays (grids: receivers spread uniformly across space) as...

Data from: Mesotocin influences pinyon jay prosociality.

Juan F. Duque, Whitney Leichner, Holly Ahmann, Jeffrey R. Stevens, J. F. Duque & J. R. Stevens
Many species exhibit prosocial behavior, in which one individual’s actions benefit another individual, often without an immediate benefit to itself. The neuropeptide oxytocin is an important hormonal mechanism influencing prosociality in mammals, but it is unclear whether the avian homologue mesotocin plays a similar functional role in birds. Here, we experimentally tested prosociality in pinyon jays (Gymnorhinus cyanocephalus), a highly social corvid species that spontaneously shares food with others. First, we measured prosocial preferences in...

Data from: Parasites favor intermediate nestling masses and brood sizes in cliff swallows

Charles R. Brown, Mary B. Brown & Mary Bomberger Brown
A challenge of life-history theory is to explain why animal body size does not continue to increase, given various advantages of larger size. In birds, body size of nestlings and the number of nestlings produced (brood size) have occasionally been shown to be constrained by higher predation on larger nestlings and those from larger broods. Parasites also are known to have strong effects on life-history traits in birds, but whether parasitism can be a driver...

Data from: Effects of light and topography on regeneration and coexistence of evergreen and deciduous tree species in a Chinese subtropical forest

Yi Jin, Sabrina E. Russo & Mingjian Yu
1. Evergreen broad-leaved forests are widely distributed in eastern Asia with evergreen (EBL) and deciduous (DBL) broad-leaved tree species coexisting under the same climatic regime, raising questions as to the underlying mechanisms. Since EBL and DBL species differ in leaf lifespan, a key component of resource economic strategies, their coexistence might be attributed to regeneration niche partitioning across habitats varying in resource supply. 2. We investigated the effects of variation in insolation and topography on...

Data from: The roles of ecology, behavior and effective population size in the evolution of a community

Chih-Ming Hung, Sergei V. Drovetski & Robert M. Zink
Organismal traits such as ecological specialization and migratory behavior may affect colonization potential, population persistence, and degree of isolation, factors that determine the composition and genetic structure of communities. However, studies focusing on community assembly rarely consider these factors jointly. We sequenced 16 nuclear and one mitochondrial genes from Caucasian and European populations of 30 forest-dwelling avian species that represent diverse ecological (specialist-generalist) and behavioral (migratory-resident) backgrounds. We tested the effects of organismal traits on...

Data from: Evolutionary history of chemosensory-related gene families across the Arthropoda

Seong-Il Eyun, Ho Young Soh, Marijan Posavi, James B. Munro, Daniel S. T. Hughes, Shwetha C. Murali, Jiaxin Qu, Shannon Dugan, Sandra L. Lee, Hsu Chao, Huyen Dinh, Yi Han, HarshaVardhan Doddapaneni, Kim C. Worley, Donna M. Muzny, Eun-Ok Park, Joana C. Silva, Richard A. Gibbs, Stephen Richards & Carol Eunmi Lee
Chemosensory-related gene (CRG) families have been studied extensively in insects, but their evolutionary history across the Arthropoda had remained relatively unexplored. Here, we address current hypotheses and prior conclusions on CRG family evolution using a more comprehensive data set. In particular, odorant receptors were hypothesized to have proliferated during terrestrial colonization by insects (hexapods), but their association with other pancrustacean clades and with independent terrestrial colonizations in other arthropod subphyla have been unclear. We also...

Data from: Genome-wide differentiation in closely related populations: the roles of selection and geographic isolation

Rebecca J. Safran, Elizabeth S. C. Scordato, Matthew R. Wilkins, Joanna K. Hubbard, Brittany R. Jenkins, Tomas Albrecht, Samuel M. Flaxman, Hakan Karaardic, Yoni Vortman, Arnon Lotem, Patrik Nosil, Péter Pap, Sheng-Feng Shen, Shih-Fan Chan, Thomas L. Parchman, Nolan C. Kane, M. R. Wilkins, J. K. Hubbard, S. Shen, S.-F. Chan, P. Nosil, T.L. Parchman, R. J. Safran, E. S. C. Scordato, B. R. Jenkins … & T. Albrecht
Population divergence in geographic isolation is due to a combination of factors. Natural and sexual selection may be important in shaping patterns of population differentiation, a pattern referred to as ‘isolation by adaptation’ (IBA). IBA can be complementary to the well-known pattern of ‘isolation by distance’ (IBD), in which the divergence of closely related populations (via any evolutionary process) is associated with geographic isolation. The barn swallow Hirundo rustica complex comprises six closely related subspecies,...

Data from: Reflections of the social environment in chimpanzee memory: applying rational analysis beyond humans

Jeffrey R. Stevens, Julian N. Marewski, Lael J. Schooler & Ian C. Gilby
In cognitive science, the rational analysis framework allows modelling of how physical and social environments impose information-processing demands onto cognitive systems. In humans, for example, past social contact among individuals predicts their future contact with linear and power functions. These features of the human environment constrain the optimal way to remember information and probably shape how memory records are retained and retrieved. We offer a primer on how biologists can apply rational analysis to study...

Data from: Phylogenetic patterns of trait and trait plasticity evolution: Insights from amphibian embryos

Rick Relyea, Patrick R. Stephens, Lisa N. Barrow, Andrew Blaustein, Paul Bradley, Julia Buck, Ann Chang, Brian I Crother, James Collins, Julia Earl, Stephanie Gervasi, Jason T. Hoverman, Olliver Hyman, Emily Claire Moriarty Lemmon, Thomas Luhring, Moses Michelsohn, Christopher M. Murray, Steven Price, Raymond Semlitsch, Andy Sih, Aaron Stoler, Nick VandenBroek, Alexa Warwick, Greta Wengert, John Hammond … & Stephanie S. Gervasi
Environmental variation favors the evolution of phenotypic plasticity. For many species, we understand the costs and benefits of different phenotypes, but we lack a broad understanding of how plastic traits evolve across large clades. Using identical experiments conducted across North America, we examined prey responses to predator cues. We quantified five life history traits and the magnitude of their plasticity for 23 amphibian species/populations (spanning three families and five genera) when exposed to no cues,...

Data from: Individual resource limitation combined with population-wide pollen availability drives masting in the valley oak (Quercus lobata)

Walter D. Koenig, Mario B. Pesendorfer, Ian S. Pearse, Johannes M. H. Knops & Kyle A. Funk
1. Masting, the synchronized production of variable seed crops, is widespread among woody plants, but there is no consensus about the underlying proximate mechanisms. To understand this population-level behavior, it is necessary to dissect the behavior of individual trees as well as the interactions that synchronize them. 2. Here we test a model of masting in which variability in seed set is driven by resource limitation within trees and synchrony is driven by pollen limitation...

Data from: Climate variability predicts thermal limits of aquatic insects across elevation and latitude

Alisha A. Shah, Brian A. Gill, Andrea C. Encalada, Alexander S. Flecker, W. Chris Funk, Juan M. Guayasamin, Boris C. Kondratieff, N. LeRoy Poff, Steven A. Thomas, Kelly R. Zamudio & Cameron K. Ghalambor
Janzen's extension of the climate variability hypothesis posits that increased seasonal variation at high latitudes should result in greater temperature overlap across elevations, and favor wider thermal breadths in temperate organisms compared to their tropical counterparts. We tested these predictions by measuring stream temperatures and thermal breadths (i.e. the difference between the critical thermal maximum and minimum) of 62 aquatic insect species from temperate (Colorado, USA) and tropical (Papallacta, Ecuador) streams spanning an elevation gradient...

Data from: Genetic variation in the Yolk protein expression network of Drosophila melanogaster: sex-biased negative correlations with longevity

Aaron M. Tarone, Lauren M. Mcintyre, Lawrence G. Harshman, Sergey V. Nuzhdin, A M Tarone, L G Harshman, L M McIntyre & S V Nuzhdin
One of the persistent problems in biology is understanding how genetic variation contributes to phenotypic variation. Associations at many levels have been reported, and yet causal inference has remained elusive. We propose to rely on the knowledge of causal relationships established by molecular biology approaches. The existing molecular knowledge forms a firm backbone upon which hypotheses connecting genetic variation, transcriptional variation and phenotypic variation can be built. The sex determination pathway is a well-established molecular...

Data from: Nestling and adult sparrows respond differently to conspecific dialects

Emily Jane Hudson, Matthew Hahn & Daizaburo Shizuka
Understanding the causes and consequences of divergence in mate recognition traits has long been a fundamental question in evolutionary biology. In songbirds, songs are culturally transmitted, and cultural divergence can generate discrete geographic variation in song (i.e., dialects). Understanding how responses to within- versus across-species variation in songs changes across life stages may shed light on the functional significance of population divergence in learned traits. Here, we use a novel combination of song playbacks to...

Registration Year

  • 2010
  • 2011
  • 2012
  • 2013
  • 2014
  • 2015
  • 2016
  • 2017
  • 2018

Resource Types

  • Dataset


  • University of Nebraska–Lincoln
  • University of California System
  • Cornell University
  • University of Colorado Boulder
  • Texas A&M University
  • Stanford University
  • University of Minnesota
  • University of Chicago
  • Max Planck Institute for Human Development
  • Tel Aviv University
  • Iowa State University
  • Michigan State University
  • University of Kansas
  • Howard Hughes Medical Institute
  • University of Pennsylvania