55 Works

Emergence rates of stink bugs and parasitoids under four heat wave conditions

Marianna Szucs & Olivia Simaz
Heat waves are becoming more frequent with climate change and their impact on lower and higher trophic levels can differ. Higher trophic levels, such as predators and parasitoids, are predicted to be more strongly affected by heat waves than herbivores because they may have smaller thermal windows and because of altered ecological interactions with lower trophic levels. We tested the effects of heat waves of varying intensity (36-42˚C), imposed for four hours during five consecutive...

Connectivity and edge effects increase bee colonization in an experimentally fragmented landscape

Sean Griffin & Nick Haddad
Though landscape corridors increase dispersal of many animals and plants, it remains unknown whether increased dispersal increases colonization and establishment of new populations in connected fragments. Working in experimentally fragmented landscapes, we tested how two aspects of habitat fragments altered by corridors- connectivity and edge-to-area ratio- determine patterns of colonization by a solitary, cavity-nesting bee (Megachile rotundata). We found that though higher connectivity initially increased rates of nest-site occupation, higher edge-to-area ratio ultimately increased patch...

Data from: Temporal dynamics of free‐living nitrogen fixation in the switchgrass rhizosphere

Darian Smercina, Sarah E. Evans, Maren L. Friesen & Lisa K. Tiemann
Here we present data associated with the manuscript, Temporal dyanmics of free-living nitrogen fixation in the switchgrass rhizosphere. Free-living nitrogen fixation (FLNF) represents an important terrestrial N source and is gaining interest for its potential to contribute plant available N to bioenergy cropping systems. Switchgrass, a cellulosic bioenergy crop, may be reliant on FLNF when particularly when grown on low N marginal lands. These potential contributions of FLNF to switchgrass and the controls on this...

Stickleback sensory morphology 2015 & 2017 measurements and analysis files

Robert Mobley
The peripheral sensory systems, whose morphological attributes help determine the acquisition of distinct types of information, provide a means to quantitatively compare multiple modalities of a species’ sensory ecology. We used morphological metrics to characterize multiple sensory modalities—the visual, olfactory, and mechanosensory lateral line sensory systems—for Gasterosteus aculeatus, the three‐spined stickleback, to compare how sensory systems vary in animals that evolve in different ecological conditions. We hypothesized that the dimensions of sensory organs and correlations...

Data from: Trait plasticity and tradeoffs shape intraspecific variation in competitive response in a foundation tree species

Olivia Cope, Richard Lindroth, Andrew Helm, Ken Keefover-Ring & Eric Kruger
The ability to tolerate neighboring plants (i.e., degree of competitive response) is a key determinant of plant success in high-competition environments. Plant genotypes adjust their functional trait expression under high levels of competition, which may help explain intraspecific variation in competitive response. However, the relationships between traits and competitive response are not well understood, especially in trees. In this study, we investigated among-genotype associations between tree trait plasticity and competitive response. We manipulated competition intensity...

The genetic architecture and evolution of life history divergence among perennials in the Mimulus guttatus species complex

Jennifer Coughlan, Maya Wilson Brown & John Willis
Ecological divergence is a main source of trait divergence between closely related species. Despite its importance in generating phenotypic diversity, the genetic architecture of most ecologically relevant traits is poorly understood. Differences in elevation can impose substantial selection for phenotypic divergence of both complex, correlated suites of traits (such as life history), as well as novel adaptations. Here, we use the Mimulus guttatus species complex to assess if divergence in elevation is accompanied by trait...

Drought-driven wildfire impacts on structure and dynamics in a wet Central Amazonian forest

Aline Pontes-Lopes, Camila V. J. Silva, Jos Barlow, Lorena M. Rincón, Wesley A. Campanharo, Cássio A. Nunes, Catherine T. De Almeida, Celso H. L. Silva Junior, Henrique L. G. Cassol, Ricardo Dalagnol, Scott C. Stark, Paulo M.L.A. Graça & Luiz E. O. C. Aragão
While climate and human-induced forest degradation is increasing in the Amazon, fire impacts on forest dynamics remain understudied in the wetter regions of the basin, which are susceptible to large wildfires only during extreme droughts. To address this gap, we installed burned and unburned plots immediately after a wildfire in the northern Purus-Madeira (central Amazon) during the 2015 El-Niño. We measured all individuals ≥10cm in diameter at breast height, and conducted recensuses to track the...

Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus

Kevin Bird, Chad Niederhuth, Shujun Ou, Malia Gehan, J. Chris Pires, Zhiyong Xiong, Robert VanBuren & Patrick Edger
Interspecific hybridization and allopolyploidization merge evolutionarily distinct parental genomes (subgenomes) into a single nucleus. A frequent observation is that one subgenome is "dominant” over the other subgenome, having a greater number of retained genes and being more highly expressed. Which subgenome becomes dominantly expressed in allopolyploids remains poorly understood. Here we “replayed the evolutionary tape” with six isogenic resynthesized Brassica napus (rapeseed) allopolyploid lines and investigated subgenome dominance patterns over the first ten generations post...

Gene modules lists of soybean in response to Fusarium virguliforme colonization

Amy Baetsen-Young, Huan Chen, Shin-Han Shiu & Brad Day
The broad host range of Fusarium virguliforme represents a unique comparative system to identify and define differentially-induced responses between an asymptomatic monocot host, maize (Zea mays), and a symptomatic eudicot host, soybean (Glycine max). Using a temporal, comparative transcriptome-based approach, we observed that early gene expression profiles of root tissue from infected maize suggest that pathogen tolerance coincides with the rapid induction of senescence dampening transcriptional regulators, including ANACs and Ethylene Responsive Factors. In contrast,...

Pastoralist cattle observations (vigilance and grouping behaviors)

Jacalyn Beck
Fear of predators fundamentally shapes the ecology of prey species and drives both inter- and intra-specific interactions. Extensive research has examined the consequences of predation risk from large carnivores on the behavior of wild ungulate prey species. However, many large carnivores not only hunt wild prey but also depredate domestic livestock, especially in pastoralist systems where livestock share land and resources with large carnivores. Northern Tanzania is a hotspot for human-carnivore conflict driven by livestock...

Anthropogenic noise alters parental behavior and nestling development, but not fledging condition

Meelyn Mayank Pandit, James Eapen, Gabriela Pineda-Sabilon, Margaret Caulfield, Alexander Moreno, Jay Wilhelm, Jessica Ruyle, Eli Bridge & Darren Proppe
Anthropogenic noise is a ubiquitous feature of the American landscape, and is a known stressor for many bird species, leading to negative effects in behavior, physiology, reproduction, and ultimately fitness. While a number of studies have examined how anthropogenic noise affects avian fitness, there are few that simultaneously examine how anthropogenic noise impacts the relationship between parental care behavior and nestling fitness. We conducted Brownian noise playbacks for six hours a day during the nesting...

Large ecosystem-scale effects of restoration fail to mitigate impacts of land-use legacies

Nash Turley & Lars Brudvig
Ecological restoration is a global priority, with potential to reverse biodiversity declines and promote ecosystem functioning. Yet, successful restoration is challenged by lingering legacies of past land-use activities, which are pervasive on lands available for restoration. Although legacies can persist for centuries following cessation of human land uses such as agriculture, we currently lack understanding of how land-use legacies affect entire ecosystems, how they influence restoration outcomes, or whether restoration can mitigate legacy effects. Using...

Mucilage-binding to ground protects seeds of many plants from harvester ants: a functional investigation

Vincent Pan, Marshall McMunn, Richard Karban, Jake Goidell, Eric LoPresti & Marjorie Weber
The seeds of many plant species produce mucilage on their surfaces that when wetted and dried, firmly adheres seeds to surfaces and substrates. Previous studies have demonstrated that seed anchorage to the ground can reduce seed predation, though only a few species have thus far been tested. Here we investigated whether binding to the ground reduces seed removal by harvester ants (Pogonomyrmex subdentatus), an important granivore, for 53 species with mucilaginous seeds. We also explored...

Data from: Spatial variation in bioclimatic relationships for a snow-adapted species along a discontinuous southern range boundary

Sean Sultaire
Documenting variation in the relationship between climate variables and species occurence at range boundaries can help reveal how species will respond to global climate change. We collected snowshoe hare (Lepus americanus) presence-absence data from snow-track surveys conducted in the U.S. states of Michigan and Wisconsin in winters from 2012-2014 at their southern range boundary in the region. A series of 125m transects were walked at each site within a week of fresh snowfall, and the...

X-Ray CT scans of barley panicles and their individual seeds from the Composite Cross II experiment

Erik Amézquita, Michelle Quigley, Tim Ophelders, Jacob Landis, Daniel Koenig, Elizabeth Munch & Daniel Chitwood
Shape plays a fundamental role in biology. Traditional phenotypic analysis methods measure some features but fail to measure the information embedded in shape comprehensively. To extract, compare, and analyze this information embedded in a robust and concise way, we turn to Topological Data Analysis (TDA), specifically the Euler Characteristic Transform. TDA measures shape comprehensively using mathematical representations based on algebraic topology features. To study its use, we compute both traditional and topological shape descriptors to...

Data from: Integrated SDM database: Enhancing the relevance and utility of species distribution models in conservation management

Veronica F. Frans, Amélie A. Augé, Jim Fyfe, Yuqian Zhang, Nathan McNally, Hendrik A. Edelhoff, Niko Balkenhol & Jan O. Engler
1. Species’ ranges are changing at accelerating rates. Species distribution models (SDMs) are powerful tools that help rangers and decision-makers prepare for reintroductions, range shifts, reductions, and/or expansions by predicting habitat suitability across landscapes. Yet, range-expanding or -shifting species in particular face other challenges that traditional SDM procedures cannot quantify, due to large differences between a species’ currently-occupied range and potential future range. The realism of SDMs is thus lost and not as useful for...

Data from: Multi-generation genomic prediction of maize yield using parametric and non-parametric sparse selection indices

Marco Lopez-Cruz, Yoseph Beyene, Manje Gowda, Jose Crossa, Paulino Perez-Rodriguez & Gustavo De Los Campos
Genomic prediction models are often calibrated using multi-generation data. Over time, as data accumulates, training data sets become increasingly heterogeneous. Differences in allele frequency and linkage disequilibrium patterns between the training and prediction genotypes may limit prediction accuracy. This leads to the question of whether all available data or a subset of it should be used to calibrate genomic prediction models. Previous research on training set optimization has focused on identifying a subset of the...

Confocal images from: Cell density, alignment, and orientation correlate with C-signal-dependent gene expression during Myxococcus xanthus development

Y Hoang, Joshua Franklin, Yann Dufour & Lee Kroos
Starving Myxococcus xanthus bacteria use short-range C-signaling to coordinate their movements and construct multicellular mounds, which mature into fruiting bodies as rods differentiate into spherical spores. Differentiation requires efficient C-signaling to drive the expression of developmental genes, but how the arrangement of cells within nascent fruiting bodies (NFBs) affects C-signaling is not fully understood. Here, we used confocal microscopy and cell segmentation to visualize and quantify the arrangement, morphology, and gene expression of cells near...

Complex landscapes stabilize farm bird communities and their expected ecosystem services

Olivia Smith, Christina M. Kennedy, Alejandra Echeverri, Daniel Karp, Christopher Latimer, Joseph Taylor, Erin Wilson-Rankin, Jeb Owen & William Snyder
1. Birds play many roles within agroecosystems including as consumers of crops and pests, carriers of pathogens, and beloved icons. Birds are also rapidly declining across North America, in part due to agricultural intensification. Thus, it is imperative to identify how to manage agroecosystems to best support birds for multi-functional outcomes (e.g., crop production and conservation). Both the average amounts of services/disservices provided and their temporal stability are important for effective farm planning. 2. Here,...

Genomic variation within the maize Stiff Stalk heterotic germplasm pool

Nolan Bornowski, Kathryn J. Michel, John P. Hamilton, Shujun Ou, Arun S. Seetharam, Jerry Jenkins, Jane Grimwood, Chris Plott, Shengqiang Shu, Jayson Talag, Megan Kennedy, Hope Hundley, Vasanth R. Singan, Kerrie Barry, Chris Daum, Yuko Yoshinaga, Jeremy Schmutz, Candice N. Hirsch, Matthew B. Hufford, Natalia De Leon, Shawn M. Kaeppler & C. Robin Buell
The Stiff Stalk heterotic group is an important source of inbreds used in U.S. commercial hybrid production. Founder inbreds B14, B37, B73, and to a lesser extent B84, are found in the pedigrees of a majority of commercial seed parent inbred lines. We created high-quality genome assemblies of B84 and four ex-Plant Variety Protection lines LH145 representing B14, NKH8431 of mixed descent, PHB47 representing B37, and PHJ40 which is a Pioneer Hi-Bred early Stiff Stalk...

Blueprint for phasing and assembling the genomes of heterozygous polyploids: Application to the octoploid genome of strawberry

Michael Hardigan, Mitchell Feldmann, Randi Famula, Michaela Vachev, Mary Madera, Philipp Zerbe, Kristin Mars, Paul Peluso, David Rank, Shujun Ou, Christopher Saski, Charlotte Acharya, Glenn Cole, Alan Yocca, Patrick Edger & Steven Knapp
The challenge of allelic diversity for assembling haplotypes is exemplified in polyploid genomes containing homoeologous chromosomes of identical ancestry, and significant homologous variation within their ancestral subgenomes. Cultivated strawberry (Fragaria × ananassa) and its progenitors are outbred octoploids in which up to eight homologous and homoeologous alleles are preserved. This introduces significant risk of haplotype collapse, switching, and chimeric fusions during assembly. Using third generation HiFi sequences from PacBio, we assembled the genome of the...

A recovery network leads to the natural recolonization of an archipelago and a potential trailing edge refuge

Matthew Smith, Jonathan Gilbert, Erik Olson, Kim Scribner, Timothy Van Deelen, Julie Van Stappen, Bronwyn Williams, James Woodford & Jonathan Pauli
Rapid environmental change is reshaping ecosystems and driving species loss globally. Carnivore populations have declined and retracted rapidly and have been the target of numerous translocation projects. Success, however, is complicated when these efforts occur in novel ecosystems. Identifying refuges, locations that are resistant to environmental change, within a translocation framework should improve population recovery and persistence. American martens (Martes americana) are the most frequently translocated carnivore in North America. As elsewhere, martens were extirpated...

List of papers reviewed to uncover trends in the use of model systems in infectious disease ecology & evolutionary biology

Nina Wale
Ever since biologists began studying the ecology and evolution of infectious diseases (EEID), laboratory-based ‘model systems’ have been important for developing and testing theory. Yet what EEID researchers mean by ‘model systems’ and what they want from them is unclear. This uncertainty hinders our ability to maximally exploit these systems, identify knowledge gaps, and establish effective new model systems. Here, we borrow a definition of model systems from the biomolecular sciences to assess how EEID...

Alignment-free methods for polyploid genomes: quick and reliable genetic distance estimation

Acer Van Wallendael
Polyploid genomes pose several inherent challenges to population genetic analyses. While alignment-based methods are fundamentally limited in their applicability to polyploids, alignment-free methods bypass most of these limits. We investigated the use of Mash, a k-mer analysis tool that uses the MinHash method to reduce complexity in large genomic datasets, for basic population genetic analyses of polyploid sequences. We measured the degree to which Mash correctly estimated pairwise genetic distance in simulated haploid and polyploid...

Infanticide by females is a leading source of juvenile mortality in a large social carnivore

Ally K Brown, Malit O Pioon, Kay E Holekamp & Eli D Strauss
Social animals benefit from their group-mates, so why do they sometimes kill each other’s offspring? Using 30 years of data from multiple groups of wild spotted hyenas, we address three critical aims for understanding infanticide in any species: (1) quantify the contribution of infanticide to overall mortality (2) describe the circumstances under which infanticide occurs and (3) evaluate hypotheses about the evolution of infanticide. We find that, although observed only rarely, infanticide is in fact...

Registration Year

  • 2021

Resource Types

  • Dataset


  • Michigan State University
  • University of Georgia
  • University of Wisconsin-Madison
  • Iowa State University
  • University of California, Davis
  • Stanford University
  • University of Minnesota
  • Ohio University
  • Indiana University
  • Agricultural Research Service