441 Works

Data from: Temperature effects on long-term population dynamics in a parasitoid-host system

Anthony R. Ives, Matthew H. Meisner & Jason P. Harmon
Long-term environmental changes will likely alter the strengths of interactions between species and consequently their population dynamics, leading to changes in the stability of ecological systems. While an increasing number of empirical studies have shown that environmental changes can alter the strengths of species interactions, these studies are typically short (<1–2 generations) and therefore give only partial information about longer term population dynamics. To focus on longer term dynamics, we investigated population cycles of pea...

Data from: Extensive genetic diversity is present within North American switchgrass germplasm

Joseph Evans, Millicent D. Sanciangco, Kin H. Lau, Emily Crisovan, Kerrie Barry, Chris Daum, Hope Hundley, Jerry Jenkins, Megan Kennedy, Govindarajan Kunde-Ramamoorthy, Brieanne Vaillancourt, Ananta Acharya, Jeremy Schmutz, Malay Saha, Shawn M. Kaeppler, E. Charles Brummer, Michael D. Casler & C. Robin Buell
Switchgrass (Panicum virgatum L.) is a perennial native North American grass present in two ecotypes: upland, found primarily in the northern range of switchgrass habitats, and lowland, found largely in the southern reaches of switchgrass habitats. Previous studies focused on a diversity panel of primarily northern switchgrass, so to expand our knowledge of genetic diversity in a broader set of North American switchgrass, exome capture sequence data were generated for 632 additional, primarily lowland individuals....

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: Defining the role of Prolamin-box binding factor1 gene during maize domestication

Zhihong Lang, David M. Wills, Zachary H. Lemmon, Laura M. Shannon, Robert Bukowski, Yongrui Wu, Joachim Messing & John F. Doebley
The prolamin-box binding factor1 (pbf1) gene encodes a transcription factor that controls the expression of seed storage protein (zein) genes in maize. Prior studies show that pbf1 underwent selection during maize domestication although how it affected trait change during domestication is unknown. To assay how pbf1 affects phenotypic differences between maize and teosinte, we compared nearly isogenic lines (NILs) that differ for a maize versus teosinte allele of pbf1. Kernel weight for the teosinte NIL...

Data from: Puma predation subsidizes an obligate scavenger in the high Andes

Paula L. Perrig, Emiliano Donadio, Arthur D. Middleton & Jonathan N. Pauli
The ungulate–carnivore–vulture complex is a key trophic module of many terrestrial ecosystems, but one that is globally under threat. Few have explored cross-species dependencies in this module, and the degree to which vultures rely on trophic facilitation by apex carnivores is rarely known and almost never quantified. We investigated the importance of puma Puma concolor predation on its native camelid prey, vicuñas Vicugna vicugna and guanacos Lama guanicoe, in food provisioning for Andean condors Vultur...

Data from: Distinctive fungal communities in an obligate African ant-plant mutualism

Christopher C.M. Baker, Dino J. Martins, Julianne N. Pelaez, Johan P.J. Billen, Anne Pringle, Megan E. Frederickson, Naomi E. Pierce, Christopher C. M. Baker & Johan P. J. Billen
Three ant species nest obligately in the swollen-thorn domatia of the African ant-plant Vachellia (Acacia) drepanolobium, a model system for the study of ant-defence mutualisms and species coexistence. Here we report on the characteristic fungal communities generated by these ant species in their domatia. First, we describe behavioural differences between the ant species when presented with a cultured fungal isolate in the laboratory. Second, we use DNA metabarcoding to show that each ant species has...

Data from: Hallauer's Tusón: a decade of selection for tropical- to-temperate phenological adaptation in maize

Juliana E. C. Teixeira, Teclemariam Weldekidan, Natalia De Leon, Sherry Flint-Garcia, James B. Holland, Nick Lauter, Seth C. Murray, Wenwei Xu, David A. Hessel, Adrienne E. Kleintop, James A. Hawk, Arnel R. Hallauer & Randall J. Wisser
Crop species exhibit an astounding capacity for environmental adaptation, but genetic bottlenecks resulting from intense selection for adaptation and productivity can lead to a genetically vulnerable crop. Improving the genetic resiliency of temperate maize depends upon the use of tropical germplasm, which harbors a rich source of natural allelic diversity. Here, the adaptation process was studied in a tropical maize population subjected to 10 recurrent generations of directional selection for early flowering in a single...

Data from: Avoided heat-related mortality through climate adaptation in three US cities

, Jason Vargo, Peng Liu, Dana Habeeb, Anthony DeLucia, Marcus Trail, Yongtao Hu, Armistead Russell & Brian Stone
Heat-related mortality in US cities is expected to more than double by the mid-to-late 21st century. Rising heat exposure in cities is projected to result from: 1) climate forcings from changing global atmospheric composition; and 2) local land surface characteristics responsible for the urban heat island effect. The extent to which heat management strategies designed to lessen the urban heat island effect could offset future heat-related mortality remains unexplored in the literature. Using coupled global...

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: Early- and late-flowering guilds respond differently to landscape spatial structure

Jesse E.D. Miller, Anthony R. Ives, Susan P. Harrison, Ellen I. Damschen & Jesse E. D. Miller
1. Species with unique phenologies have distinct trait syndromes and environmental affinities, yet there has been little exploration of whether community assembly processes differ for plants with different phenologies. In this study, we ask whether early- and late-blooming species differ in the ways that dispersal, persistence, and resource-acquisition traits shape plant occurrence patterns in patchy habitats. 2. We sampled plant communities in 51 Ozark dolomite glade grasslands, which range in size from <1 ha to...

Data from: Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)

Carlos I. Arbizu, Shelby L. Ellison, Douglas Senalik, Philipp W. Simon & David M. Spooner
Background: The majority of the subspecies of Daucus carota have not yet been discriminated clearly by various molecular or morphological methods and hence their phylogeny and classification remains unresolved. Recent studies using 94 nuclear orthologs and morphological characters, and studies employing other molecular approaches were unable to distinguish clearly many of the subspecies. Fertile intercrosses among traditionally recognized subspecies are well documented. We here explore the utility of single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing...

Ordered phylogenomic subsampling enables diagnosis of systematic errors in the placement of the enigmatic arachnid order Palpigradi

Jesús Ballesteros, Carlos Santibáñez López, Ľubomír Kováč, Efrat Gavish-Regev & Prashant Sharma
The miniaturized arachnid order Palpigradi has ambiguous phylogenetic affinities, due to its odd combination of plesiomorphic and derived morphological traits. This lineage has never been sampled in phylogenomic datasets because of its small body size and fragility of most species, a sampling gap of immediate concern to recent disputes over arachnid monophyly. To redress this gap, we sampled a population of the cave-inhabiting species Eukoenenia spelaea from Slovakia and inferred its placement in the phylogeny...

Data from: Forest structure and snow depth alter the movement patterns and subsequent expenditures of a forest carnivore, the Pacific marten

Marie Martin, Katie Moriarty & Jonathan Pauli
Energetic balance is central to the survival and persistence of free-ranging animals. Quantifying expenditures and identifying factors that drive energetics informs our understanding of species’ ecology and their responses to shifting environmental conditions. Approaches used to estimate energetic expenditures of free-ranging species, such as doubly-labelled water (DLW), are precise but difficult to implement. Global positioning system (GPS) collars and accelerometers have emerged as alternatives for estimating expenditures, but these techniques have few applications in terrestrial...

­­Evolution of floral morphology and symmetry in the Miconieae (Melastomataceae): multiple generalization trends within a specialized family

Maria Gavrutenko, Marcelo Reginato, Ricardo Kriebel, Antoine M. Nicolas & Fabián A. Michelangeli
Premise of the Research:Analyses of evolution of floral morphology and symmetry broaden our understanding of the drivers of angiosperm diversification. Integrated within a flower, labile floral characters produce different phenotypes that promote variable interactions with pollinators. Thus, investigation of floral evolution may help infer potential historic transitions in pollinator modes and ecological pressures that generated present diversity. This study aims to explore morphological evolution of flowers in Miconieae, a species-rich Neotropical tribe within the Melastomataceae....

Data from: Large-scale patterns of seed removal by small mammals differ between areas of low vs. high wolf occupancy

Jennifer L. Chandler, Timothy R. Van Deelen, Nathan P. Nibbelink & John L. Orrock
Because most tree species recruit from seeds, seed predation by small-mammal granivores may be important for determining plant distribution and regeneration in forests. Despite the importance of seed predation, large-scale patterns of small-mammal granivory are often highly variable and thus, difficult to predict. We hypothesize distributions of apex predators can create large-scale variation in the distribution and abundance of mesopredators that consume small-mammals, creating predictable areas of high and low granivory. For example, because gray...

Data from: Pollinator shifts, contingent evolution, and evolutionary constraint drive floral disparity in Salvia (Lamiaceae): evidence from morphometrics and phylogenetic comparative methods

Ricardo Kriebel, Bryan Drew, Jesús G. González-Gallegos, Ferhat Celep, Luciann Heeg, Mohamed M Mahdjoub & Kenneth Sytsma
Switches in pollinators have been argued to be key drivers of floral evolution in angiosperms. However, few studies have tested the relationship between floral shape evolution and switches in pollination in large clades. In concert with a dated phylogeny, we present a morphometric analysis of corolla, anther connective, and style shape across 44% of nearly 1,000 species of Salvia (Lamiaceae) and test four hypotheses of floral evolution. We demonstrate that floral morphospace of New World...

Data from: Demography, life history trade-offs, and the gastrointestinal virome of wild chimpanzees

Jacob D. Negrey, Melissa Emery Thompson, Kevin E. Langergraber, Zarin P. Machanda, John C. Mitani, Martin N. Muller, Emily Otali, Leah A. Owens, Richard W. Wrangham & Tony L. Goldberg
In humans, senescence increases susceptibility to viral infection. However, comparative data on viral infection in free-living non-human primates—even in our closest living relatives, chimpanzees and bonobos (Pan troglodytes and P. paniscus)—are relatively scarce, thereby constraining an evolutionary understanding of age-related patterns of viral infection. We investigated a population of wild eastern chimpanzees (P. t. schweinfurthii), using metagenomics to characterize viromes (full viral communities) in the feces of 42 sexually mature chimpanzees (22 males, 20 females)...

Data from: De novo gene birth, horizontal gene transfer and gene duplication as sources of new gene families associated with the origin of a symbiosis in Amanita

Yen-Wen Wang
By introducing novel capacities and functions, new genes and gene families may play a crucial role in ecological transitions. Mechanisms generating new gene families include de novo gene birth, horizontal gene transfer and neofunctionalization following a duplication event. The ectomycorrhizal (ECM) symbiosis is a ubiquitous mutualism and the association has evolved repeatedly and independently many times among the fungi, but the molecular dynamics enabling its emergence remain elusive. We developed a phylogenetic workflow to first...

Phylogenomic resolution of sea spider diversification through integration of multiple data classes

Jesus Ballesteros, Emily Setton, Carlos Santibáñez-López, Claudia Arango, Georg Brenneis, Saskia Brix, Kevin Corbett, Esperanza Cano-Sánchez, Merai Dandouch, Geoffrey Dilly, Marc Eleaume, Guilherme Gainett, Cyril Gallut, Sean McAtee, Lauren McIntyre, Randy Moran, Pablo López-González, Gerhard Scholtz, Clay Williamson, Arthur Woods, Jakob Zehms, Ward Wheeler & Prashant Sharma
Despite significant advances in invertebrate phylogenomics over the past decade, the higher-level phylogeny of Pycnogonida (sea spiders) remains elusive. Due to the inaccessibility of some small-bodied lineages, few phylogenetic studies have sampled all sea spider families. Previous efforts based on a handful of genes have yielded unstable tree topologies. Here, we inferred the relationships of 89 sea spider species using targeted capture of the mitochondrial genome, 56 conserved exons, 101 ultraconserved elements, and three nuclear...

Greater Prairie-chicken data used in \"Responses to land cover and grassland management vary across life-history stages for a grassland specialist\"

Michael Hardy, Matthew Broadway, Christopher Pollentier, Volker Radeloff, Jason Riddle & Scott Hull
Grassland birds have exhibited dramatic and widespread declines since the mid-20th century. Greater Prairie-Chickens (Tympanuchus cupido pinnatus) are considered an umbrella species for grassland conservation and are frequent targets of management, but their responses to land use and management can be quite variable. We used data collected during 2007-2009 and 2014-2015 to investigate effects of land use and grassland management practices on habitat selection and survival rates of Greater Prairie-Chickens in central Wisconsin, USA. We...

Temporal flexibility of gene regulatory network underlies a novel wing pattern in flies

Cédric Finet
Organisms have evolved endless morphological, physiological, and behavioral novel traits during the course of evolution. Novel traits were proposed to evolve mainly by orchestration of preexisting genes. Over the past two decades, biologists have shown that co-option of gene regulatory networks (GRNs) indeed underlies numerous evolutionary novelties. However, very little is known about the actual GRN properties that allow such redeployment. Here we have investigated the generation and evolution of the complex wing pattern of...

Data from: Soil microbes alter herbivore-induced volatile emissions in response to cereal cropping systems

Shealyn Malone, Amy Trowbridge, David Weaver, Fabian Menalled, Tim Seipel & Megan Hofland
Soil microbes can influence the emissions of plant volatile organic compounds (VOCs), which serve as host-location cues for insect pests and their natural enemies. Agricultural practices steer unique soil microbial communities, but how this influences crop VOCs and subsequent insect attraction remains unknown. The aim of this study was to investigate the effect of diversified agricultural practices on constitutive and herbivore-induced VOC emissions by crops through soil-microbe legacy effects. In a full factorial experiment, we...

Data from: Arctic and boreal paleofire records reveal drivers of fire activity and departures from Holocene variability

Tyler Hoecker, Philip Higuera, Ryan Kelly & Feng Sheng Hu
Boreal forest and tundra biomes are key components of the Earth system because the mobilization of large carbon stocks and changes in energy balance could act as positive feedbacks to ongoing climate change. In Alaska, wildfire is a primary driver of ecosystem structure and function, and a key mechanism coupling high-latitude ecosystems to global climate. Paleoecological records reveal sensitivity of fire regimes to climatic and vegetation change over centennial-millennial time scales, highlighting increased burning concurrent...

A basic ddRADseq two-enzyme protocol performs well in herbarium and silica-dried tissues across four genera

Ingrid Jordon-Thaden, James Beck, Catherine Rushworth, Michael Windham, Nicolas Diaz, Jason Cantley, Chris Martine & Carl Rothfels
Premise of the study: The ability to sequence genome-scale data from herbarium specimens would allow for the economical development of broad datasets with taxonomic and geographic sampling not otherwise possible. Here we evaluate the utility of a basic restriction site-associated DNA (ddRADseq) protocol with DNAs from four genera extracted from both silica-dried and herbarium tissue. Methods: DNAs from Draba, Boechera, Solidago, and Ilex were processed with a double-digest restriction-site associated DNA sequencing (ddRADseq) protocol. The...

Ruffed Grouse Resource Selection Function and Survival Datasets

Amy Shipley
For overwintering species, individuals’ ability to find refugia from inclement weather and predators likely confers strong fitness benefits. How animals use their environment can be mediated by their personality (e.g., risk-taking), but does personality mediate how overwintering species select refugia? Snow cover is a dynamic winter characteristic that can influence crypsis or provide below-the-snow refugia. We explored how wintering ruffed grouse (Bonasa umbellus) selected snow roosting sites, a behavior that reduces stress and cold exposure....

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