59 Works

Data from: Organic matter loading by hippopotami causes subsidy overload resulting in downstream hypoxia and fish kills

Christopher L. Dutton, Amanda L. Subalusky, Stephen K. Hamilton, Emma J. Rosi & David M. Post
Organic matter and nutrient loading into aquatic ecosystems affects ecosystem structure and function and can result in eutrophication and hypoxia. Hypoxia is usually attributed to anthropogenic pollution and is rarely documented in unpolluted systems, particularly in rivers. Here we show that organic matter loading from hippopotami causes the repeated occurrence of hypoxia in the Mara River, East Africa. We documented 49 high flow events over three years that caused dissolved oxygen decreases, including 13 events...

Data from: Local interactions and self-organized spatial patterns stabilize microbial cross-feeding against cheaters

Simon Maccracken Stump, Evan Curtis Johnson & Christopher A. Klausmeier
Mutualisms are ubiquitous, but models predict they should be susceptible to cheating. Resolving this paradox has become relevant to synthetic ecology: cooperative cross-feeding, a nutrient exchange mutualism, has been proposed to stabilize microbial consortia. Previous attempts to understand how cross-feeders remain robust to non-producing cheaters have relied on complex behavior (e.g., cheater punishment) or group selection. Using a stochastic spatial model, we demonstrate two novel mechanisms that can allow cross-feeders to outcompete cheaters, rather than...

Data from: Early accumulation of active fraction soil carbon in newly established cellulosic biofuel systems

Christine D. Sprunger & G. Philip Robertson
We examined relative changes in soil C pools shortly after the establishment of six perennial and two annual bioenergy cropping systems that differed in diversity (monoculture vs. polyculture). Perennial systems included two monocultures (switchgrass, Panicum virgatum; and miscanthus, Miscanthus × giganteus) and four polycultures including hybrid poplar (Populus sp.) + herbaceous understory; mixed native grasses, successional vegetation, and restored prairie. Two annual systems included no-till continuous corn (Zea mays) and rotational corn (corn-soybean (Glycine max)-canola...

Data from: Eco-evolutionary rescue promotes host-pathogen coexistence

Graziella V. DiRenzo, Elise F. Zipkin, Evan H. Campbell Grant, J. Andrew Royle, Ana V. Longo, Kelly R. Zamudio & Karen R. Lips
Emerging infectious pathogens are responsible for some of the most severe host mass-mortality events in wild populations. Yet, effective pathogen control strategies are notoriously difficult to identify, in part because quantifying and forecasting pathogen spread and disease dynamics is challenging. Following an outbreak, hosts must cope with the presence of the pathogen, leading to host-pathogen coexistence or extirpation. Despite decades of research, little is known about host-pathogen coexistence post-outbreak when low host abundances and cryptic...

Data from: Phylogenomics clarifies repeated evolutionary origins of inbreeding and fungus farming in bark beetles (Curculionidae, Scolytinae)

Andrew Johnson, McKenna, Bjarte H. Jordal, Anthony I. Cognato, Sarah M. Smith, Alan R. Lemmon, Emily L. Moriarty Lemmon & Jiri Hulcr
Bark and ambrosia beetles (Curculionidae, Scolytinae) display a conspicuous diversity of unusual genetic and ecological attributes and behaviors. Reconstructing the evolution of Scolytinae, particularly the large and ecologically significant tribe Cryphalini (pygmy borers), has long been problematic. These challenges have not adequately been addressed using morphological characters, and previous research has used only DNA sequence data from small numbers of genes. Through a combination of anchored hybrid enrichment, low-coverage draft genomes, and transcriptomes, we addressed...

Data from: Candidate variants for additive and interactive effects on bioenergy traits in switchgrass (Panicum virgatum L.) identified by genome-wide association analyses

Guillaume P. Ramstein, Joseph Evans, Aruna Nandety, Malay C. Saha, E. Charles Brummer, Shawn M. Kaeppler, C. Robin Buell & Michael D. Casler
Switchgrass is a promising herbaceous energy crop, but further gains in biomass yield and quality must be achieved to enable a viable bioenergy industry. Developing DNA markers can contribute to such progress, but depiction of genetic bases should be reliable, involving not only simple additive marker effects but also interactions with genetic backgrounds, e.g., ecotypes, or synergies with other markers. We analyzed plant height, carbon content, nitrogen content, and mineral concentration in a diverse panel...

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: Inferring continuous and discrete population genetic structure across space

Gideon S. Bradburd, Graham M. Coop & Peter L. Ralph
A classic problem in population genetics is the characterization of discrete population structure in the presence of continuous patterns of genetic differentiation. Especially when sampling is discontinuous, the use of clustering or assignment methods may incorrectly ascribe differentiation due to continuous processes (e.g., geographic isolation by distance) to discrete processes, such as geographic, ecological, or reproductive barriers between populations. This reflects a shortcoming of current methods for inferring and visualizing population structure when applied to...

Data from: Genomic differentiation during speciation-with-gene-flow: comparing geographic and host-related variation in divergent life history adaptation in Rhagoletis pomonella

Meredith M. Doellman, Gregory J. Ragland, Glen R. Hood, Peter J. Meyers, Scott P. Egan, Thomas H.Q. Powell, Peter Lazorchak, Mary M. Glover, Cheyenne Tait, Hannes Schuler, Daniel A. Hahn, Stewart H. Berlocher, James J. Smith, Patrik Nosil, Jeffrey L. Feder, Daniel Hahn, Stewart Berlocher, Peter Meyers, Scott Egan, Jeffrey Feder, Glen Hood, Thomas Powell & Gregory Ragland
A major goal of evolutionary biology is to understand how variation within populations gets partitioned into differences between reproductively isolated species. Here, we examine the degree to which diapause life history timing, a critical adaptation promoting population divergence, explains geographic and host-related genetic variation in ancestral hawthorn and recently derived apple-infesting races of Rhagoletis pomonella. Our strategy involved combining experiments on two different aspects of diapause (initial diapause intensity and adult eclosion time) with a...

Data from: The effects of agent hybridization on the efficacy of biological control of tansy ragwort at high elevations

Marianna Szucs, Patricia E. Salerno, Brittany J. Teller, Urs Schaffner, Jeffrey L. Littlefield & Ruth A. Hufbauer
The success rate of weed biological control programs is difficult to evaluate and the factors affecting it remain poorly understood. One aspect which is still unclear is whether releases of multiple, genetically distinct populations of a biological control agent increase the likelihood of success, either by independent colonization of different environmental niches or by hybridization that may increase the agent’s fitness and adaptive ability. Since hybridization is often invoked to explain the success of unintentionally...

Data from: Limited phenological and dietary overlap between bee communities in spring flowering crops and herbaceous enhancements.

Thomas J. Wood, Jason Gibbs, Nikki Rothwell, Julianna K. Wilson, Larry Gut, Julia Brokaw & Rufus Isaacs
Wild bee populations have undergone declines in recent years across much of the Western world, and these declines have the potential to limit yield in pollination-dependent crops. Highbush blueberry, Vaccinium corymbosum, and tart cherry, Prunus cerasus, are spring-blooming crops that rely on the movement of pollen by bees and other insects for pollination. Wild bee populations can be increased on farmland by providing floral resources, but whether the addition of these plants translates into increased...

Data from: Genetic variation in mutualistic and antagonistic interactions in an invasive legume

Casey P. TerHorst, Camdilla Wirth & Jennifer A. Lau
Mutualists may play an important role in invasion success. The ability to take advantage of novel mutualists or survive and reproduce despite a lack of mutualists may facilitate invasion by those individuals with such traits. Here, we used two greenhouse studies to examine how soil microbial communities in general and mutualistic rhizobia in particular affect the performance of a legume species (Medicago polymorpha) that has invaded five continents. We performed two plant growth experiments with...

Data from: Assessing impact of exogenous features on biotic phenomena in the presence of strong spatial dependence: a lake sturgeon case study in natural stream settings

Andrew O. Finley, Patrick S. Forsythe, James A. Crossman, Edward A. Baker & Kim T. Scribner
Modeling spatially explicit data provides a powerful approach to identify the effects of exogenous features associated with biological processes, including recruitment of stream fishes. However, the complex spatial and temporal dynamics of the stream and the species' reproductive and early life stage behaviors present challenges to drawing valid inference using traditional regression models. In these settings it is often difficult to ensure the spatial independence among model residuals---a key assumption that must be met to...

Data from: Associative nitrogen fixation (ANF) in switchgrass (Panicum virgatum) across a nitrogen input gradient

Sarah S. Roley, David S. Duncan, Di Liang, Aaron Garoutte, Randall D. Jackson, James M. Tiedje & G. Philip Robertson
Associative N fixation (ANF), the process by which dinitrogen gas is converted to ammonia by bacteria in casual association with plants, has not been well-studied in temperate ecosystems. We examined the ANF potential of switchgrass (Panicum virgatum L.), a North American prairie grass whose productivity is often unresponsive to N fertilizer addition, via separate short-term 15N2 incubations of rhizosphere soils and excised roots four times during the growing season. Measurements occurred along N fertilization gradients...

Data from: Prediction of cooking time for soaked and unsoaked dry beans (Phaseolus vulgaris L.) using hyperspectral imaging technology

Fernando A. Mendoza, Jason A. Wiesinger, Renfu Lu, Susan Nchimbi-Msolla, Phillip N. Miklas, James D. Kelly & Karen A. Cichy
The cooking time of dry beans varies widely by genotype and is also influenced by the growing environment, storage conditions and cooking method. Thus, high throughput phenotyping methods to assess cooking time would be useful to breeders interested in developing cultivars with desired cooking time. The objective of this study was to evaluate the performance of hyperspectral imaging technology for predicting dry bean cooking time. Fourteen dry bean (Phaseolus vulgaris L.) genotypes with a wide...

Data from: Disentangling the genetic effects of refugial isolation and range expansion in a trans-continentally distributed species

Brendan N. Reid, Jamie M. Kass, Seth Wollney, Evelyn L. Jensen, Michael A. Russello, Ella M. Viola, Jenna Pantophlet, John B. Iverson, Marcus Z. Peery, Christopher J. Raxworthy & Eugenia Naro-Maciel
In wide-ranging taxa with historically dynamic ranges, past allopatric isolation and range expansion can both influence the current structure of genetic diversity. Considering alternate historical scenarios involving expansion from either a single refugium or from multiple refugia can be useful in differentiating the effects of isolation and expansion. Here, we examined patterns of genetic variability in the trans-continentally distributed painted turtle (Chrysemys picta). We utilized an existing phylogeographic dataset for the mitochondrial control region and...

Data from: An updated gene atlas for maize reveals organ-specific and stress-induced genes

Genevieve M. Hoopes, John P. Hamilton, Joshua C. Wood, Eddi Esteban, Asher Pasha, Brieanne Vaillancourt, Nicholas J. Provart & C. Robin Buell
Maize(Zea mays L.), a model species for genetic studies, is one of the two most important crop species worldwide.The genome sequence of the reference genotype, B73, representative of the stiff stalk heterotic group was recently updated (AGPv4) using long‐read sequencing and optical mapping technology. To facilitate the use of AGPv4 and to enable functional genomic studies and association of genotype with phenotype, we determined expression abundances for replicated mRNA‐sequencing datasets from 79 tissues and five...

Data from: Climate-mediated hybrid zone movement revealed with genomics, museum collection and simulation modeling

Sean F. Ryan, Jillian M. Deines, J. Mark Scriber, Michael E. Pfrender, Stuart E. Jones, Scott J. Emrich & Jessica J. Hellmann
Climate-mediated changes in hybridization will dramatically alter the genetic diversity, adaptive capacity and evolutionary trajectory of interbreeding species. Our ability to predict the consequences of such changes will be key to future conservation and management decisions. Here we tested through simulations how recent warming (over a 32-year period) is affecting the geographic extent of a climate-mediated developmental threshold implicated in maintaining a butterfly hybrid zone (Papilio glaucus and Papilio canadensis; Lepidoptera: Papilionidae). These simulations predict...

Data from: Brassicales phylogeny inferred from 72 plastid genes: a reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses

Patrick P. Edger, Jocelyn C. Hall, Alex Harkess, Michelle Tang, Jill Coombs, Setareh Mohammadin, M. Eric Schranz, Zhiyong Xiong, James Leebens-Mack, Blake C. Meyers, Kenneth J. Systma, Marcus A. Koch, Ihsan A. Al-Shehbaz, J. Chris Pires & Kenneth J. Sytsma
PREMISE OF THE STUDY - Previous phylogenetic studies employing molecular markers have yielded various insights into the evolutionary history across Brassicales, but many relationships between families remain poorly supported or unresolved. A recent phylotranscriptomic approach utilizing 1155 nuclear markers obtained robust estimates for relationships among 14 of 17 families. Here we report a complete family‐level phylogeny estimated using the plastid genome. METHODS - We conducted phylogenetic analyses on a concatenated data set comprising 44,926 bp...

Data from: Individual-level trait variation and negative density dependence affects growth in tropical tree seedlings

Maria Natalia Umana, Elise F. Zipkin, Caicai Zhang, Min Cao, Luxiang Lin & Nathan G. Swenson
1. Individual-level interactions with neighbours and their surrounding environments are key factors influencing performance that ultimately shape and maintain diversity in tropical plant communities. Theory predicts that the strength of these interactions depends on the similarity among neighbours, the turnover in composition caused by individuals that enter as new recruits and individuals that die, and fitting to local conditions. Despite considerable phenotypic variation among individuals and high community dynamics, these three factors have rarely been...

Data from: Host cues mediate growth and establishment of oak mistletoe (Phoradendron leucarpum, Viscaceae), an aerial parasitic plant.

Christopher P. Randle, Brandi C. Cannon, Amber L. Faust, Angela K. Hawkins, Sarah E. Cabrera, Stephen Lee, Amy A. Perez, Michelle L. Lewis, James Sopas, Timothy J. Verastegui, Justin K. Williams & Sara E. Cabrera
The oak mistletoe (Phoradendron leucarpum, Viscaceae) is well-documented to exhibit preference for a few potential host species in a given locality, even when many potential host species are present. In trying to explain this distribution, we examined the mechanisms by which mistletoe seedlings recognize potentially suitable hosts in the Piney Woods ecoregion of east Texas. An initial survey of patterns of infection on the campus of Sam Houston State University revealed that water oak (Quercus...

Data from: Landscape heterogeneity is key to forecasting outcomes of plant reintroduction

T. Trevor Caughlin, Ellen I. Damschen, Nick M. Haddad, Douglas J. Levey, Christopher Warneke & Lars A. Brudvig
Conservation and restoration projects often involve starting new populations by introducing individuals into portions of their native or projected range. Such efforts can help meet many related goals, including habitat creation, ecosystem service provisioning, assisted migration, and the reintroduction of imperiled species following local extirpation. The outcomes of reintroduction efforts, however, are highly variable, with results ranging from local extinction to dramatic population growth; reasons for this variation remain unclear. Here, we ask whether population...

Data from: Population genetics reveals high connectivity of giant panda populations across human disturbance features in key nature reserve

Maiju Qiao, Thomas Connor, Xiaogang Shi, Jie Huang, Yan Huang, Hemin Zhang & Jianghong Ran
The giant panda is an example of a species that has faced extensive historical habitat fragmentation and anthropogenic disturbance, and is assumed to be isolated in numerous subpopulations with limited gene flow between them. To investigate the population size, health and connectivity of pandas in a key habitat area, we noninvasively collected a total of 539 fresh wild giant panda fecal samples for DNA extraction within Wolong Nature Reserve, Sichuan, China. Seven validated tetra-microsatellite markers...

Data from: Genome-wide search for quantitative trait loci controlling important plant and flower traits in petunia using an interspecific recombinant inbred population of Petunia axillaris and Petunia exserta

Zhe Cao, Yufang Guo, Qian Yang, Yanhong He, Mohammed Fetouh, Ryan M. Warner, Zhanao Deng & Mohammed I. Fetouh
A major bottleneck in plant breeding has been the much limited genetic base and much reduced genetic diversity in domesticated, cultivated germplasm. Identification and utilization of favorable gene loci or alleles from wild or progenitor species can serve as an effective approach to increasing genetic diversity and breaking this bottleneck in plant breeding. This study was conducted to identify quantitative trait loci (QTL) in wild or progenitor petunia species that can be used to improve...

Data from: 18S rRNA metabarcoding diet analysis of the predatory fish community across seasonal changes in prey availability

Justin M. Waraniak, Terence L. Marsh & Kim T. Scribner
Predator-prey relationships are important ecological interactions, affecting biotic community composition and energy flow through a system, and are of interest to ecologists and managers. Morphological diet analysis has been the primary method used to quantify the diets of predators, but emerging molecular techniques using genetic data can provide more accurate estimates of relative diet composition. This study used sequences from the 18S V9 rRNA barcoding region to identify prey items in the gastrointestinal (GI) tracts...

Registration Year

  • 2018

Resource Types

  • Dataset


  • Michigan State University
  • University of Wisconsin-Madison
  • Cornell University
  • University of Michigan-Ann Arbor
  • University of Notre Dame
  • University of Vermont
  • United States Department of Agriculture
  • University of Florida
  • Great Lakes Science Center
  • California State University, Northridge