39 Works

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: 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: 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: 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: \"De novo assembly transcriptome for the rostrum dace (Leuciscus burdigalensis, Cyprinidae: fish) naturally infected by a copepod ectoparasite\" in Genomic Resources Notes accepted 1 December 2014 to 31 January 2015

Olivier Rey, Géraldine Loot, Olivier Bouchez, Simon Blanchet, Maria Jose Ruiz-Lopez, Nelson Ting, Paul D. Etter, Eric A. Johnson, Tony L. Goldberg, Colin A. Chapman, James H. Jones, Patrick A. Omeja & William M. Switzer
The emergence of pathogens represents substantial threats to public health, livestock, domesticated animals, and biodiversity. How wild populations respond to emerging pathogens has generated a lot of interest in the last two decades. With the recent advent of high-throughput sequencing technologies it is now possible to develop large transcriptomic resources for non-model organisms, hence allowing new research avenues on the immune responses of hosts from a large taxonomic spectra. We here focused on a wild...

Data from: The adaptive capacity of lake food webs: from individuals to ecosystems

Bailey C. McMeans, Kevin S. McCann, Tyler D. Tunney, Aaron T. Fisk, Andrew M. Muir, Nigel Lester, Brian Shuter & Neil Rooney
Aquatic ecosystems support size structured food webs, wherein predator-prey body sizes span orders of magnitude. As such, these food webs are replete with extremely generalized feeding strategies, especially among the larger bodied, higher trophic position taxa. The movement scale of aquatic organisms also generally increases with body size and trophic position. Together, these body size, mobility, and foraging relationships suggest that organisms lower in the food web generate relatively distinct energetic pathways by feeding over...

Data from: Quantifying risk and resource use for a large carnivore in an expanding urban-wildland interface

Wynne E. Moss, Mathew W. Alldredge & Jonathan N. Pauli
Large carnivores, though globally threatened, are increasingly using developed landscapes. However, most of our knowledge of their ecology is derived from studies in wildland systems; thus, for effective conservation and management, there is a need to understand their behavioural plasticity and risk of mortality in more developed landscapes. We examined cougar Puma concolor foraging ecology and survival in an expanding urban–wildland system in Colorado from 2007 to 2013. For GPS-collared individuals, we related diet (n...

Data from: Bouncing Back: plant-associated soil microbes respond rapidly to prairie establishment

Randall D. Jackson, Anna J. Herzberger & David S. Duncan
It is well established that soil microbial communities change in response to altered land use and land cover, but less is known about the timing of these changes. Understanding temporal patterns in recovering microbial communities is an important part of improving how we assess and manage reconstructed ecosystems. We assessed patterns of community-level microbial diversity and abundance in corn and prairie plots 2 to 4 years after establishment in agricultural fields, using phospholipid fatty acid...

Data from: Land-use legacies and present fire regimes interact to mediate herbivory by altering the neighboring plant community

Philip G. Hahn & John L. Orrock
Past and present human activities, such as historic agriculture and fire suppression, are widespread and can create depauperate plant communities. Although many studies show that herbivory on focal plants depends on the density of herbivores or the composition of the surrounding plant community, it is unclear whether anthropogenic changes to plant communities alter herbivory. We tested the hypothesis that human activities that alter the plant community lead to subsequent changes in herbivory. At 20 sites...

Registration Year

  • 2015

Resource Types

  • Dataset


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