155 Works

Pronghorn population genomics show connectivity at the core of their range

Melanie E.F. LaCava, Roderick B. Gagne, Sierra M. Love Stowell, Kyle D. Gustafson, C. Alex Buerkle, Lee Knox & Holly B. Ernest
Preserving connectivity in the core of a species’ range is crucial for long-term persistence. However, a combination of ecological characteristics, social behavior, and landscape features can reduce connectivity among wildlife populations and lead to genetic structure. Pronghorn (Antilocapra americana), for example, exhibit fluctuating herd dynamics and variable seasonal migration strategies, but GPS-tracking studies show that landscape features such as highways impede their movements, leading to conflicting hypotheses about expected levels of genetic structure. Given that...

Aerosol particle measurements taken during the airborn ARISTO 2016 campaign.

John Ortega, James Smith, Jefferson Snider & J. Michael Reeves
Several different types of measurements of particle size and concentration were compared during the 2016 Airborne Research Instrumentation Testing Opportunity (ARISTO) campaign. The scanning mobility particle sizer (SMPS) measured number-size distributions for mobility diameters between ~20-350 nm or ~8-110 nm, depending on the mobility analyzer chosen. Also included were two stand-alone condensation particle counters (CPC) for determining size-integrated particle concentrations. A wing-mounted and a rack-mounted Ultra-High Sensitivity Aerosol Spectrometer (UHSAS) were used to measure size...

Data from: A nested association mapping panel in Arabidopsis thaliana for mapping and characterizing genetic architecture

Marcus Brock
Linkage and association mapping populations are crucial public resources that facilitate the characterization of trait genetic architecture in natural and agricultural systems. We define a large nested association mapping panel (NAM) from 14 publicly available recombinant inbred populations (RILs) of Arabidopsis thaliana, which share a common recurrent parent (Col-0). Using a genotype-by-sequencing approach (GBS), we identified single nucleotide polymorphisms (SNPs; range 563-1525 per population) and subsequently built updated linkage maps in each of the 14...

Data from: Whole-genome duplication and host genotype affect rhizosphere microbial communities

Julian Bennett Ponsford, Charley Hubbard & Joshua Harrison
The composition of microbial communities found in association with plants is influenced by host phenotype and genotype. Yet, the ways in which specific genetic architectures of host plants shape microbiomes is unknown. Genome duplication events are common in the evolutionary history of plants, influence many important plant traits, and, thus, they may affect associated microbial communities. Using experimentally induced whole genome duplication (WGD), we tested the effect of WGD on rhizosphere bacterial communities in Arabidopsis...

Functional connectivity in a continuously distributed, migratory species as revealed by landscape genomics

Melanie E. F. LaCava, Roderick B. Gagne, Kyle D. Gustafson, Sara J. Oyler-McCance, Kevin L. Monteith, Hall Sawyer, Matthew J. Kauffman, Daniel J. Thiele & Holly B. Ernest
Maintaining functional connectivity is critical for the long-term conservation of wildlife populations. Landscape genomics provides an opportunity to assess long-term functional connectivity by relating environmental variables to spatial patterns of genomic variation resulting from generations of movement, dispersal, and mating behaviors. Identifying landscape features associated with gene flow at large geographic scales for highly mobile species is becoming increasingly possible due to more accessible genomic approaches, improved analytical methods, and enhanced computational power. We characterized...

Data from: Assortative flocking in crossbills and implications for ecological speciation

Julie W. Smith, Stephanie M. Sjoberg, Matthew C. Mueller & Craig W. Benkman
How reproductive isolation is related to divergent natural selection is a central question in speciation. Here we focus on several ecologically specialised taxa or “call types” of red crossbills (Loxia curvirostra complex), one of the few groups of birds providing much evidence for ecological speciation. Call types differ in bill sizes and feeding capabilities, and also differ in vocalizations, such that contact calls provide information on crossbill phenotype. We found that two call types of...

Data from: Population genetic structure of Picea engelmannii, P. glauca and their previously unrecognized hybrids in the central Rocky Mountains

Monia S. H. Haselhorst & C. Alex Buerkle
Areas of geographic overlap between potentially hybridizing species provide the opportunity to study interspecific gene flow and reproductive barriers. Here we identified hybrids between Picea engelmannii and P. glauca by their genetic composition at 17 microsatellite markers, and determined the broad-scale geographic distribution of hybrids in the central Rocky Mountains of North America, a geographic region where hybrids and isolation between species had not previously been studied. Parameter estimates from admixture models revealed considerable variation...

Data from: Mechanisms of plant–plant interactions: concealment from herbivores is more important than abiotic-stress mediation in an African savannah

Allison M. Louthan, Daniel F. Doak, Jacob R. Goheen, Todd M. Palmer & Robert M. Pringle
Recent work on facilitative plant–plant interactions has emphasized the importance of neighbours’ amelioration of abiotic stress, but the facilitative effects of neighbours in reducing plant apparency to herbivores have received less attention. Whereas theory on stress reduction predicts that competition should be more important in less stressful conditions, with facilitation becoming more important in harsh environments, apparency theory suggests that facilitation should be greater in the presence of herbivores, where it is disadvantageous to be...

Data from: Elephant damage, not fire or rainfall, explains mortality of overstorey trees in Serengeti

Thomas A. Morrison, Ricardo M. Holdo & T. Michael Anderson
Generalizations about the drivers of tree demography in tropical savannahs continue to prove difficult because of the complex and dynamic interactions involved, and because multi-year datasets spanning meaningful gradients in potential drivers are lacking. Overstorey trees play disproportionate roles in the long-term dynamics and functioning of savannah ecosystems. Understanding demographic patterns in these trees is complicated by their resprouting ability after being top-killed and few studies have attempted to separate top-kill from true mortality events....

Data from: Genome divergence and the genetic architecture of barriers to gene flow between Lycaeides idas and L. melissa

Zachariah Gompert, Lauren K. Lucas, Chris Clark Nice & C. Alex Buerkle
Genome divergence during speciation is a dynamic process that is affected by various factors, including the genetic architecture of barriers to gene flow. Herein we quantitatively describe aspects of the genetic architecture of two sets of traits, male genitalic morphology and oviposition preference, that putatively function as barriers to gene flow between the butterfly species Lycaeides idas and L. melissa. Our analyses are based on unmapped DNA sequence data and a recently developed Bayesian regression...

Data from: Rat eradication and the resistance and resilience of passerine bird assemblages in the Falkland Islands

Michael A. Tabak, Sally Poncet, Ken Passfield, Jacob R. Goheen & Carlos Martinez Del Rio
Norway rats (Rattus norvegicus) were introduced to the Falkland Islands and are detrimental to native passerines. Rat eradication programs are being used to help protect the avifauna. The present study assesses the effectiveness of eradication programs while using this conservation practice as a natural experiment to explore the ecological resistance, resilience, and homeostasis of bird communities. We conducted bird surveys on 230 islands: 85 in the presence of rats, 108 that were historically free of...

Data from: Interplanting annual ryegrass, wheat, oat, and corn to mitigate iron deficiency in dry beans

Emmanuel Chiwo Omondi & Andrew R. Kniss
This study evaluated whether grass intercropping can be used to alleviate Fe deficiency chlorosis in dry beans (Phaseolus vulgaris L.) grown in high pH, calcareous soils with low organic matter. Field studies were conducted at the University of Wyoming Sustainable Agriculture Research and Extension Center in 2009 and 2010. Black- and navy beans were grown alone or intercropped with annual ryegrass (Lolium multiflorum Lam.), oat (Avena sativa L.), corn (Zea mays L.), or spring wheat...

Data from: Willet be one species or two?: a genomic view of the evolutionary history of Tringa semipalmata

Jessica A. Oswald, Michael G. Harvey, Rosalind C. Remsen, DePaul U. Foxworth, Steven W. Cardiff, Donna L. Dittmann, Libby C. Megna, Matthew D. Carling & Robb T. Brumfield
The Willet (Tringa semipalmata; Scolopacidae) is composed of 2 morphologically and vocally distinct subspecies with broadly disjunct breeding distributions in North America. Nominate T. s. semipalmata breeds in coastal salt and brackish marshes along the Atlantic and Gulf coasts of eastern North America and the West Indies, and T. s. inornata breeds in wet grasslands and prairies in the northwestern interior of North America. To assess divergence and test for hybridization between the 2 subspecies,...

Data from: Matching habitat choice in nomadic crossbills appears most pronounced when food is most limiting

Craig W. Benkman
Of the various forms of non-random dispersal, matching habitat choice, whereby individuals preferentially reside in habitats where they are best adapted, has relatively little empirical support. Here I use mark-recapture data to test for matching habitat choice in two nomadic ecotypes of North American Red Crossbills (Loxia curvirostra complex) that occur in the lodgepole pine (Pinus contorta) forests in the South Hills, Idaho every summer. Crossbills are adapted for foraging on seeds in conifer cones,...

Data from: Anthropogenic ecosystem disturbance and the recovery debt

David Moreno Mateos, Edward B. Barbier, Peter C. Jones, Holly P. Jones, James Aronson, Jose A. Lopez-Lopez, Michelle L. McCrackin, Paula Meli, Daniel Montoya & José Rey Benayas
Ecosystem recovery from anthropogenic disturbances, either without human intervention or assisted by ecological restoration, is increasingly occurring worldwide. As ecosystems progress through recovery, it is important to estimate any resulting deficit in biodiversity and functions. Here we use data from 3,035 sampling plots worldwide, to quantify the interim reduction of biodiversity and functions occurring during the recovery process (that is, the ‘recovery debt’). Compared with reference levels, recovering ecosystems run annual deficits of 46–51% for...

Data from: Plasticity contributes to a fine-scale depth gradient in sticklebacks’ visual system

Thor Veen, Chad Brock, Diana Rennison & Daniel Bolnick
The light environment influences an animal’s ability to forage, evade predators, and find mates, and consequently is known to drive local adaptation of visual systems. However, the light environment may also vary over fine spatial scales at which genetic adaptation is difficult. For instance, in aquatic systems the available wavelengths of light change over a few meters depth. Do animals plastically adjust their visual system to such small-scale environmental light variation? Here, we show that...

Mechanisms of Anti-Obesity Effects of Capsaicin

Baskaran Thyagarajan
Obesity is a major metabolic disease. Currently, there are no effective strategies to counter obesity. Transient receptor potential vanilloid subfamily 1 (TRPV1), a non-selective cation channel protein expressed in metablically important tissues, has been pursued as a target to combat obesity. In our efforts to understand the mechanisms by which activation of TRPV1 by its selective agonist capsaicin counters obesity we discovered that mammalian white and brown adipose tissues (WAT and BAT, respectively) endgenously express...

Data from: Synergistic effects of fire and elephants on arboreal animals in an African savannah

Robert M. Pringle, Duncan M. Kimuyu, Ryan L. Sensenig, Todd M. Palmer, Corinna Riginos, Kari E. Veblen & Truman P. Young
1. Disturbance is a crucial determinant of animal abundance, distribution and community structure in many ecosystems, but the ways in which multiple disturbance types interact remain poorly understood. The effects of multiple-disturbance interactions can be additive, subadditive or super-additive (synergistic). Synergistic effects in particular can accelerate ecological change; thus, characterizing such synergies, the conditions under which they arise, and how long they persist has been identified as a major goal of ecology. 2. We factorially...

Data from: Worldwide evidence of a unimodal relationship between productivity and plant species richness

Lauchlan H. Fraser, Jason Pither, Anke Jentsch, Marcelo Sternberg, Martin Zobel, Diana Askarizadeh, Sandor Bartha, Carl Beierkuhnlein, Jonathan A. Bennett, Alex Bittel, Bazartseren Boldgiv, Ilsi I. Boldrini, Edward Bork, Leslie Brown, Marcelo Cabido, James Cahill, Cameron N. Carlyle, Giandiego Campetella, Stefano Chelli, Ofer Cohen, Anna-Maria Csergo, Sandra Diaz, Lucas Enrico, David Ensing, Alessandra Fidelis … & Talita Zupo
The search for predictions of species diversity across environmental gradients has challenged ecologists for decades. The humped-back model (HBM) suggests that plant diversity peaks at intermediate productivity; at low productivity few species can tolerate the environmental stresses, and at high productivity a few highly competitive species dominate. Over time the HBM has become increasingly controversial, and recent studies claim to have refuted it. Here, by using data from coordinated surveys conducted throughout grasslands worldwide and...

Data from: Deterministic and stochastic processes lead to divergence in plant communities 25 years after the 1988 Yellowstone fires

William H. Romme, Timothy G. Whitby, Daniel B. Tinker & Monica G. Turner
Young, recently burned forests are increasingly widespread throughout western North America, but forest development after large wildfires is not fully understood, especially regarding effects of variable burn severity, environmental heterogeneity, and changes in drivers over time. We followed development of subalpine forests after the 1988 Yellowstone fires by periodically re-sampling permanent plots established soon after the fires. We asked two questions about patterns and processes over the past 25 years: (1) Are plant species richness...

Data from: Genome divergence and diversification within a geographic mosaic of coevolution

Thomas L. Parchman, C. Alex Buerkle, Victor Soria-Carrasco & Craig W. Benkman
Despite substantial interest in coevolution's role in diversification, examples of coevolution contributing to speciation have been elusive. Here, we build upon past studies that have shown both coevolution between South Hills crossbills and lodgepole pine (Pinus contorta), and high levels of reproductive isolation between South Hills crossbills and other ecotypes in the North American red crossbill (Loxia curvirostra) complex. We used genotyping by sequencing to generate population genomic data and applied phylogenetic and population genetic...

Data from: Enhanced seed defenses potentially relax selection by seed predators against serotiny in lodgepole pine

Craig Benkman & Anna Parker
Serotiny, the retention of seeds in a canopy seed bank until high temperatures cause seeds to be released, is an important life history trait for many woody plants in fire-prone habitats. Serotiny provides a competitive advantage after fire but increases vulnerability to predispersal seed predation, due to the seeds being retained in clusters in predictable locations for extended periods. This creates opposing selection pressures. Serotiny is favored in areas of high fire frequency, but is...

Data from: Pathogens manipulate the preference of vectors, slowing disease spread in a multi-host system

Lauren G. Shoemaker, Evelyn Hayhurst, Christopher P. Weiss-Lehman, Alexander T. Strauss, Anita Porath-Krause, Elizabeth T. Borer, Eric W. Seabloom & Allison K. Shaw
The spread of vector‐borne pathogens depends on a complex set of interactions among pathogen, vector, and host. In single‐host systems, pathogens can induce changes in vector preferences for infected vs. healthy hosts. Yet it is unclear if pathogens also induce changes in vector preference among host species, and how changes in vector behaviour alter the ecological dynamics of disease spread. Here, we couple multi‐host preference experiments with a novel model of vector preference general to...

An experimental test of community-based strategies for mitigating human-wildlife conflict around protected areas

Ryan Long, Paola Branco, Jerod Merkle, Robert Pringle, Lucy King, Tosca Tindall & Marc Stalmans
Natural habitats are rapidly being converted to cultivated croplands, and crop-raiding by wildlife threatens both wildlife conservation and human livelihoods worldwide. We combined movement data from GPS-collared elephants with camera-trap data and local reporting systems in a before-after-control-impact design to evaluate community-based strategies for reducing crop raiding outside Mozambique’s Gorongosa National Park. All types of experimental fences tested (beehive, chili, beehive and chili combined, and procedural controls) significantly reduced the number of times elephants left...

Data from: Machine learning to classify animal species in camera trap images: applications in ecology

Micheal A. Tabak, Mohammad Sadegh Norouzzadeh, Michael A. Tabak, David W. Wolfson, Steven J. Sweeney, Paul A. Di Salvo, Ryan S. Miller, Jesse S. Lewis, Jeff Clune, Ryan K. Brook, Elizabeth G. Mandeville, Paul M. Lukacs, Anna K. Moeller, Raoul K. Boughton, Bethany Wight, James C. Beasley & Peter E. Schlichting
Motion‐activated cameras (“camera traps”) are increasingly used in ecological and management studies for remotely observing wildlife and are amongst the most powerful tools for wildlife research. However, studies involving camera traps result in millions of images that need to be analysed, typically by visually observing each image, in order to extract data that can be used in ecological analyses. We trained machine learning models using convolutional neural networks with the ResNet‐18 architecture and 3,367,383 images...

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  • University of Wyoming
  • Utah State University
  • Colorado State University
  • University of Nevada Reno
  • University of California, Davis
  • United States Geological Survey
  • Princeton University
  • University of Montana
  • Texas State University
  • United States Department of Agriculture