39 Works

Data from: Diversity and population structure of northern switchgrass as revealed through exome capture sequencing

Joseph Evans, Emily Crisovan, Kerrie Barry, Chris Daum, Jerry Jenkins, Govindarajan Kunde-Ramamoorthy, Aruna Nandety, Chew Yee Ngan, Brieanne Vaillancourt, Chia-Lin Wei, Jeremy Schmutz, Shawn M. Kaeppler, Michael D. Casler, Carol Robin Buell & Chia-Lin Wei
Switchgrass (Panicum virgatum L.) is a polyploid, perennial grass species that is native to North America, and is being developed as a future biofuels feedstock crop. Switchgrass is present primarily in two ecotypes: a northern upland ecotype composed of tetraploid and octoploid accessions, and a southern lowland ecotype composed of primarily tetraploid accessions. We employed high-coverage exome capture sequencing (~2.4 Tb) to genotype 537 individuals from 45 upland and 21 lowland populations. From these data,...

Data from: The mouse universal genotyping array: from substrains to subspecies

Andrew Parker Morgan, Chen-Ping Fu, Chia-Yu Kao, Catherine E. Welsh, John P. Didion, Liran Yadgary, Leeanna Hyacinth, Martin T. Ferris, Timothy A. Bell, Darla R. Miller, Paola Giusti-Rodriguez, Randal J. Nonneman, Kevin D. Cook, Jason K. Whitmire, Lisa E. Gralinski, Mark P. Keller, Alan D. Attie, Gary A. Churchill, Petko Petkov, Patrick F. Sullivan, Jennifer R. Brennan, Leonard McMillan & Fernando Pardo-Manuel De Villena
Genotyping microarrays are an important resource for genetic mapping, population genetics, and monitoring of the genetic integrity of laboratory stocks. We have developed the third generation of the Mouse Universal Genotyping Array (MUGA) series, GigaMUGA, a 143,259-probe Illumina Infinium II array for the house mouse (Mus musculus). The bulk of the content of GigaMUGA is optimized for genetic mapping in the Collaborative Cross and Diversity Outbred populations, and for substrain-level identification of laboratory mice. In...

Data from: Environmental predictors of woody plant encroachment in calcareous fens are modified by biotic and abiotic land-use legacies

David Bart, Tara Davenport & Austin Yantes
Woody plant encroachment in grasslands is a world-wide concern. Assertions that abiotic stress reduction facilitates encroachment are not universally supported. To devise restoration and management strategies, the ability of stress reduction, in the context of co-occurring biotic land-use legacies, needs to be assessed to predict shrub cover. We determined whether legacy-induced reduction in Carex stricta (a potential facilitator of shrub encroachment and attractor of animal dispersers) and an increase in herbaceous invaders (potential competitors) altered...

Data from: Are attractive male crickets better able to pay the costs of an immune challenge?

Clint D. Kelly, Melissa S. C. Telemeco, Lyric C. Bartholomay & Melissa S.C. Telemeco
Reproduction and immunity are fitness-related traits that trade-off with each other. Parasite-mediated theories of sexual selection suggest, however, that higher-quality males should suffer smaller costs to reproduction-related traits and behaviours (e.g., sexual display) from an immune challenge because these males possess more resources with which to deal with the challenge. We used Gryllus texensis field crickets to test the prediction that attractive males should better maintain the performance of fitness-related traits (e.g., calling effort) in...

Data from: Long-term avian community response to housing development at the boundary of U.S. protected areas: effect size increases with time

Eric M. Wood, Anna M. Pidgeon, Volker C. Radeloff, David P. Helmers, Patrick D. Culbert, Nicholas S. Keuler & Curtis H. Flather
1. Biodiversity conservation is a primary function of protected areas. However, protected areas also attract people, and therefore, land use has intensified at the boundaries of these lands globally. In the USA, since the 1970s, housing growth at the boundaries (<1 km) of protected areas has increased at a rate far higher than on more distant private lands. Here, we designed our analyses to address our central hypothesis that increasing housing density in and near...

Data from: Controlling false discoveries in genome scans for selection

Olivier Francois, Helena Martins, Kevin Caye & Sean Schoville
Population differentiation (PD) and ecological association (EA) tests have recently emerged as prominent statistical methods to investigate signatures of local adaptation using population genomic data. Based on statistical models, these genome-wide testing procedures have attracted considerable attention as tools to identify loci potentially targeted by natural selection. An important issue with PD and EA tests is that incorrect model specification can generate large numbers of false positive associations. Spurious association may indeed arise when shared...

Data from: A major gene for bovine ovulation rate

Brian W. Kirkpatrick & Chris A. Morris
Half-sib daughters sired by a bull believed to be a carrier of a major gene for high ovulation rate were evaluated for ovulation rate and genotyped in an effort to both test the hypothesis of segregation of a major gene and to map the gene’s location. A total of 131 daughters were produced over four consecutive years at a University of Wisconsin-Madison research farm. All were evaluated for ovulation rate over an average of four...

Data from: Iconicity can ground the creation of vocal symbols

Marcus Perlman, Rick Dale & Gary Lupyan
Studies of gestural communication systems find that they originate from spontaneously created iconic gestures. Yet, we know little about how people create vocal communication systems, and many have suggested that vocalizations do not afford iconicity beyond trivial instances of onomatopoeia. It is unknown whether people can generate vocal communication systems through a process of iconic creation similar to gestural systems. Here, we examine the creation and development of a rudimentary vocal symbol system in a...

Data from: Nitrous oxide emissions during establishment of eight alternative cellulosic bioenergy cropping systems in the North Central United States

Lawrence G. Oates, David S. Duncan, Ilya Gelfand, Neville Millar, G. Philip Robertson & Randall D. Jackson
Greenhouse gas (GHG) emissions from soils are a key sustainability metric of cropping systems. During crop establishment, disruptive land-use change is known to be a critical, but under reported period, for determining GHG emissions. We measured soil N2O emissions and potential environmental drivers of these fluxes from a three-year establishment-phase bioenergy cropping systems experiment replicated in southcentral Wisconsin (ARL) and southwestern Michigan (KBS). Cropping systems treatments were annual monocultures (continuous corn, corn–soybean–canola rotation), perennial monocultures...

Data from: Signal diversification in Oecanthus tree crickets is shaped by energetic, morphometric, and acoustic trade-offs

Laurel B. Symes, Matthew P. Ayres, Colleen P. Cowdery & Robin A. Costello
Physiology, physics, and ecological interactions can generate trade-offs within species, but may also shape divergence among species. We tested whether signal divergence in Oecanthus tree crickets is shaped by acoustic, energetic, and behavioral trade-offs. We found that species with faster pulse rates, produced by opening and closing wings up to twice as many times per second, did not have higher metabolic costs of calling. The relatively constant energetic cost across species is explained by trade-offs...

Data from: A unique ecological niche fosters hybridization of oak-tree and vineyard isolates of Saccharomyces cerevisiae.

Katie J. Clowers, Jessica L. Will & Audrey P. Gasch
Differential adaptation to distinct niches can restrict gene flow and promote population differentiation within a species. However, in some cases the distinction between niches can collapse, forming a hybrid niche with features of both environments. We previously reported that distinctions between vineyards and oak soil present an ecological barrier that restricts gene flow between lineages of Saccharomyces cerevisiae. Vineyard isolates are tolerant to stresses associated with grapes while North American oak strains are particularly tolerant...

Data from: Genome assembly improvement and mapping convergently evolved skeletal traits in sticklebacks with genotyping-by-sequencing

Andrew M. Glazer, Emily E. Killingbeck, Therese Mitros, Daniel S. Rokhsar & Craig T. Miller
Marine populations of the threespine stickleback (Gasterosteus aculeatus) have repeatedly colonized and rapidly adapted to freshwater habitats, providing a powerful system to map the genetic architecture of evolved traits. Here, we developed and applied a binned genotyping-by-sequencing (GBS) method to build dense genome-wide linkage maps of sticklebacks using two large marine by freshwater F2 crosses of more than 350 fish each. The resulting linkage maps significantly improve the genome assembly by anchoring 78 new scaffolds...

Data from: Experimental evidence that the effectiveness of conservation biological control depends on landscape complexity

Mattias Jonsson, Cory S. Straub, Raphael K. Didham, Hannah L. Buckley, Bradley S. Case, Roddy J. Hale, Claudio Gratton & Steve D. Wratten
1. The expansion of intensive agricultural practices is a major threat to biodiversity and to the delivery of ecosystem services on which humans depend. Local-scale conservation management strategies, such as agri-environment schemes to preserve biodiversity, have been widely adopted to reduce the negative impacts of agricultural intensification. However, it is likely that the effectiveness of these local-scale management actions depend on the structure and composition of the surrounding landscape. 2. We experimentally tested the utility...

Data from: Pervasive and strong effects of plants on soil chemistry: a meta-analysis of individual plant ‘Zinke’ effects

Bonnie G. Waring, Leonor Álvarez-Cansino, Kathryn E. Barry, Kristen K. Becklund, Sarah Dale, Maria G. Gei, Adrienne B. Keller, Omar R. Lopez, Lars Markesteijn, Scott Mangan, Charlotte E. Riggs, Maria Elizabeth Rodríguez-Ronderos, R. Max Segnitz, Stefan A. Schnitzer & Jennifer S. Powers
Plant species leave a chemical signature in the soils below them, generating fine-scale spatial variation that drives ecological processes. Since the publication of a seminal paper on plant-mediated soil heterogeneity by Paul Zinke in 1962, a robust literature has developed examining effects of individual plants on their local environments (individual plant effects). Here, we synthesize this work using meta-analysis to show that plant effects are strong and pervasive across ecosystems on six continents. Overall, soil...

Data from: Orchid phylogenomics and multiple drivers of their extraordinary diversification

Thomas J. Givnish, Daniel Spalink, Mercedes Ames, Stephanie P. Lyon, Steven J. Hunter, Alejandro Zuluaga, William J. D. Iles, Mark A. Clements, Mary T. K. Arroyo, James Leebens-Mack, Lorena Endara, Ricardo Kriebel, Kurt M. Neubig, W. Mark Whitten, Norris H. Williams & Kenneth M. Cameron
Orchids are the most diverse family of angiosperms, with over 25 000 species, more than mammals, birds and reptiles combined. Tests of hypotheses to account for such diversity have been stymied by the lack of a fully resolved broad-scale phylogeny. Here, we provide such a phylogeny, based on 75 chloroplast genes for 39 species representing all orchid subfamilies and 16 of 17 tribes, time-calibrated against 17 angiosperm fossils. A supermatrix analysis places an additional 144...

Data from: Recognizing cross-ecosystem responses to changing temperatures: soil warming impacts pelagic food webs

Samuel B. Fey, Andrew N. Mertens, Lucas J. Beversdorf, Katherine D. McMahon & Kathryn L. Cottingham
The energy and materials that move across ecosystem boundaries influence food web structure and key ecosystem functions. Despite the acknowledged importance of such ecological subsidies, surprisingly little information is available regarding the role of environmental temperature in influencing subsidy quality and the response of the recipient ecosystem. We evaluated the impacts of temperature-mediated changes in leaves from deciduous trees, an important subsidy from terrestrial to freshwater ecosystems, on both the producer-based and detritivore-based components of...

Data from: Shared genomic regions between derivatives of a large segregating population of maize identified using bulked segregant analysis sequencing and traditional linkage analysis

Nicholas J. Haase, Timothy Beissinger, Candice N. Hirsch, Brieanne Vaillancourt, Shweta Deshpande, Kerrie Barry, C. Robin Buell, Shawn M. Kaeppler & Natalia De Leon
Delayed transition from the vegetative stage to the reproductive stage of development and increased plant height have been shown to increase biomass productivity in grasses. The goal of this project was to detect quantitative trait loci using extremes from a large synthetic population, as well as a related recombinant inbred line mapping population for these two traits. Ten thousand individuals from a B73 × Mo17 noninbred population intermated for 14 generations (IBM Syn14) were grown...

Data from: Modality interactions alter the shape of acoustic mate preference functions in gray treefrogs

Michael S. Reichert & Gerlinde Höbel
Sexual selection takes place in complex environments where females evaluating male mating signals are confronted with stimuli from multiple sources and modalities. The pattern of expression of female preferences may be influenced by interactions between modalities, changing the shape of female preference functions, and thus ultimately altering the selective landscape acting on male signal evolution. We tested the hypothesis that the responses of female gray treefrogs, Hyla versicolor, to acoustic male advertisement calls are affected...

Data from: Context matters: sexual signaling loss in digital organisms

Emily G. Weigel, Nicholas D. Testa, Alex Peer & Sara C. Garnett
Sexual signals are important in attracting and choosing mates; however, these signals and their associated preferences are often costly and frequently lost. Despite the prevalence of signaling system loss in many taxa, the factors leading to signal loss remain poorly understood. Here, we test the hypothesis that complexity in signal loss scenarios is due to the context-dependent nature of the many factors affecting signal loss itself. Using the Avida digital life platform, we evolved 50...

Data from: Predator experience overrides learned aversion to heterospecifics in stickleback species pairs

Genevieve M. Kozak & Janette W. Boughman
Predation risk can alter female mating decisions because the costs of mate searching and selecting attractive mates increase when predators are present. In response to predators, females have been found to plastically adjust mate preference within species, but little is known about how predators alter sexual isolation and hybridization among species. We tested the effects of predator exposure on sexual isolation between benthic and limnetic threespine sticklebacks (Gasterosteus spp.). Female discrimination against heterospecific mates was...

Data from: Drivers of bushmeat hunting and perceptions of zoonoses in Nigerian hunting communities

Sagan Friant, Sarah B. Paige & Tony L. Goldberg
Bushmeat hunting threatens biodiversity and increases the risk of zoonotic pathogen transmission. Nevertheless, limited information exists on patterns of contact with wildlife in communities that practice bushmeat hunting, especially with respect to social drivers of hunting behavior. We used interview responses from hunters and non-hunters in rural hunting communities in Nigeria to: 1) quantify contact rates with wildlife, 2) identify specific hunting behaviors that increase frequency of contact, 3) identify socioeconomic factors that predispose individuals...

Data from: Prioritizing land management efforts at a landscape scale: a case study using prescribed fire in Wisconsin

Tracy L. Hmielowski, Sarah K. Carter, Hannah Spaul, David P. Helmers, Volker C. Radeloff, Paul H. Zedler & David Helmers
One challenge in the effort to conserve biodiversity is identifying where to prioritize resources for active land management. Cost-benefit analyses have been used successfully as a conservation tool to identify sites that provide the greatest conservation benefit per unit cost. Our goal was to apply cost-benefit analysis to the question of how to prioritize land management efforts, in our case the application of prescribed fire to natural landscapes in Wisconsin, USA. We quantified and mapped...

Data from: Severity of mitral valve degeneration is associated with chromosome 15 loci in Whippet dogs

Joshua A. Stern, Weihow Hsue, Kun-Ho Song, Eric S. Ontiveros, Virginia Luis Fuentes & Rebecca L. Stepien
Mitral valve degeneration (MVD) is the most common form of heart disease in dogs, frequently leading to left-sided congestive heart failure and cardiac mortality. Although breed-specific disease characteristics and overrepresentation point towards a genetic origin for MVD, a causative mutation and complete molecular pathogenesis are unknown. Whippet dogs are overrepresented in incidence of MVD, suggesting an inherited component in this breed. Expressivity of this condition is variable with some dogs showing evidence of more severe...

Data from: Spatially varying selection shapes life history clines among populations of Drosophila melanogaster from sub-Saharan Africa

Daniel K. Fabian, Justin B. Lack, Vinayak Mathur, Christian Schlötterer, Paul S. Schmidt, John E. Pool & Thomas Flatt
Clines in life history traits, presumably driven by spatially varying selection, are widespread. Major latitudinal clines have been observed, for example, in Drosophila melanogaster, an ancestrally tropical insect from Africa that has colonized temperate habitats on multiple continents. Yet, how geographic factors other than latitude, such as altitude or longitude, affect life history in this species remains poorly understood. Moreover, most previous work has been performed on derived European, American and Australian populations, but whether...

Data from: Development of sound localization strategies in children with bilateral cochlear implants

Yi Zheng, Shelly P. Godar & Ruth Y. Litovsky
Localizing sounds in our environment is one of the fundamental perceptual abilities that enable humans to communicate, and to remain safe. Because the acoustic cues necessary for computing source locations consist of differences between the two ears in signal intensity and arrival time, sound localization is fairly poor when a single ear is available. In adults who become deaf and are fitted with cochlear implants (CIs) sound localization is known to improve when bilateral CIs...

Registration Year

  • 2015
    39

Resource Types

  • Dataset
    39

Affiliations

  • University of Wisconsin-Madison
    39
  • Michigan State University
    6
  • Stanford University
    2
  • University of Georgia
    2
  • University of Minnesota
    2
  • University of California, Berkeley
    2
  • University of Florida
    2
  • Swedish University of Agricultural Sciences
    2
  • Smithsonian Tropical Research Institute
    2
  • University of British Columbia
    2