298 Works

Data from: Effects of grasshoppers on prairies: herbivore composition matters more than richness in three grassland ecosystems

Angela N. Laws, Chelse M. Prather, David H. Branson & Steven C. Pennings
1. Understanding how biodiversity affects ecosystem processes is a key question in ecology. Previous research has found that increasing plant diversity often enhances many ecosystem processes, but less is known about the role of consumer diversity to ecosystem processes, especially in terrestrial ecosystems. Furthermore, we do not know how general biodiversity responses are among ecosystem types. 2. We examined the role of insect herbivore (Orthoptera) diversity on plant production using parallel field experiments in three...

Data from: The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

Lei Gao, Itay Gonda, Honghe Sun, Qiyue Ma, Kan Bao, Denise M. Tieman, Elizabeth A. Burzynski-Chang, Tara L. Fish, Kaitlin A. Stromberg, Gavin L. Sacks, Theodore W. Thannhauser, Majid R. Foolad, Maria Jose Diez, Joaquin Canizares, Yimin Xu, Esther Van Der Knaap, Sanwen Huang, Harry J. Klee, James J. Giovannoni & Zhangjun Fei
Modern tomatoes have narrow genetic diversity limiting their improvement potential. We present a tomato pan-genome constructed using genome sequences of 725 phylogenetically and geographically representative accessions, revealing 4,873 genes absent from the reference genome. Presence/absence variation analyses reveal substantial gene loss and intense negative selection of genes and promoters during tomato domestication and improvement. Lost or negatively selected genes are enriched for important traits, especially disease resistance. We identify a rare allele in TomLoxC promoter...

Data from: Attract or defend? Pollen and vegetative secondary chemistry of three pollen-rewarding lupines

Jacob M. Heiling, Daniel Cook, Stephen T. Lee & Rebecca E. Irwin
PREMISE OF THE STUDY: Optimal Defense Theory predicts that selection should drive plants to differentially allocate resources for herbivore defense to tissues with high fitness values. As pollen’s primary role is the transport of gametes, plants may be expected to defend it from herbivory. However, for many animal-pollinated plants, pollen serves a secondary role as a pollinator reward. This may present a conflict between selection to defend pollen from herbivores and selection to reward pollinators....

Data from: Distance, elevation, and environment as drivers of diversity and divergence in bumble bees across latitude and altitude

Jason M. Jackson, Meaghan L. Pimsler, Kennan Jeannet Oyen, Jonathan B. Koch-Uhuad, James D. Herndon, James P. Strange, Michael E. Dillon & Jeffrey D. Lozier
Identifying drivers of dispersal limitation and genetic differentiation is a key goal in biogeography. We examine patterns of population connectivity and genetic diversity using Restriction-site Associated DNA sequencing (RADseq) in two bumble bee species, Bombus vosnesenskii and Bombus bifarius across latitude and altitude in mountain ranges from California, Oregon, and Washington, U.S.A. Bombus vosnesenskii, which occurs across a broader elevational range at most latitudes, exhibits little population structure while B. bifarius, which occupies a relatively...

Data from: Extreme site fidelity as an optimal strategy in an unpredictable and homogeneous environment

Brian D. Gerber, Mevin B. Hooten, Christopher P. Peck, Mindy B. Rice, James H. Gammonley, Anthony D. Apa & Amy J. Davis
1. Animal site fidelity structures space-use, population demography, and ultimately gene flow. Understanding the adaptive selection for site fidelity patterns provides a mechanistic understanding to both spatial and population processes. This can be achieved by linking space-use with environmental variability (spatial and temporal) and demographic parameters. However, rarely is the environmental context that drives the selection for site fidelity behavior fully considered. 2. We use ecological theory to understand whether the spatial and temporal variability...

Conspecific leaf litter induces negative feedbacks in Asteraceae seedlings

Max Zaret & Briana Whitaker
The plant soil feedback (PSF) framework has been instrumental in quantifying soil microbial impacts on plant fitness and mechanisms for species coexistence. The recent extension of the PSF framework to microbes associated with aboveground tissues of plants, termed here as plant phyllosphere feedbacks (PPFs), can also help determine the role of aboveground microbes as drivers of plant-plant interactions. However, experimental tests of PPFs in wild hosts is nascent and their prevalence across diverse hosts remains...

Unraveling the complex hybrid ancestry and domestication history of cultivated strawberry

Michael Hardigan, Anne Lorant, Dominique Pincot, Mitchell Feldmann, Randi Famula, Charlotte Acharya, Seonghee Lee, Sujeet Verma, Vance Whitaker, Nahla Bassil, Jason Zurn, Glenn Cole, Kevin Bird, Patrick Edger & Steven Knapp
Cultivated strawberry (Fragaria × ananassa) is one of our youngest domesticates, originating in early eighteenth-century Europe from spontaneous hybrids between wild allo-octoploid species (F. chiloensis and F. virginiana). The improvement of horticultural traits by 300 years of breeding has enabled the global expansion of strawberry production. Here, we describe the genomic history of strawberry domestication from the earliest hybrids to modern cultivars. We observed a significant increase in heterozygosity among interspecific hybrids and a decrease...

QTL mapping and marker development for tolerance to sulfur phytotoxicity in melon (Cucumis Melo)

Sandra Branham, James Daley, Amnon Levi, Richard Hassell & Patrick Wechter
Elemental sulfur is an effective, inexpensive fungicide for many foliar pathogens, but severe phytotoxicity prohibits its use on many melon varieties. Sulfur phytotoxicity causes chlorosis and necrosis of leaf tissue, leading to plant death in the most sensitive lines, while other varieties have little to no damage. A high-density, genotyping-by-sequencing (GBS)-based genetic map of a recombinant inbred line (RIL) population segregating for sulfur tolerance was used for a quantitative trait loci (QTL) mapping study of...

Pierce's disease vector transmission-preference experiment on PdR1 resistant grapevines

Adam Zeilinger, Dylan Beal, Anne Sicard, Christopher Wallis, M. Andrew Walker & Rodrigo Almeida
Host defense against vector-borne plant pathogens is a critical component of integrated disease management. However, theory predicts that traits that confer tolerance or partial resistance can, under certain ecological conditions, enhance the spread of pathogens and spillover to more susceptible populations or cultivars. A key component driving such epidemic risk appears to be variation in host selection behavior of vectors based on infection status of the host. While recent theory has further emphasized the importance...

Comprehensive phylogenomic analyses re-write the evolution of parasitism within cynipoid wasps

Bonnie B Blaimer, Dietrich Gotzek, Seán G Brady & Matthew L Buffington
Background Parasitoidism, a specialized life strategy in which a parasite eventually kills its host, is frequently found within the insect order Hymenoptera (wasps, ants and bees). A parasitoid lifestyle is one of two dominant life strategies within the hymenopteran superfamily Cynipoidea, with the other being an unusual plant-feeding behavior known as galling. Less commonly cynipoid wasps exhibit inquilinism, a strategy where some species have adapted to usurp other species’ galls instead of inducing their own....

Influence of voltine ecotype and geographic distance on genetic and haplotype variation in the Asian corn borer

Brad Coates & Yangzhou Wang
Diapause is an adaptive dormancy strategy by which arthropods endure extended periods of adverse climatic conditions. Seasonal variation in larval diapause initiation and duration in the Asian corn borer, Ostrinia furnacalis, influences adult mating generation number (voltinism) across local environmental conditions. Degree of mating period overlap between sympatric voltinism ecotypes influence hybridization level, but impact on O. furnacalis population genetic structure and evolution of divergent adaptive phenotypes remains uncertain. Genetic differentiation was estimated between voltinism...

VCF file of multiple single-cyst-derived Ro1 and Ro2 lines of New York fields on Globodera rostochiensis genome

Xiaohong Wang, Huijun Yang, Pierre-Yves Véronneau, David Thurston & Benjamin Mimee
The potato cyst nematode, Globodera rostochiensis, is a regulated pest posing a serious threat to potato production worldwide. Although the endemic pathotype (Ro1) of G. rostochiensis has been confined to New York State for several decades as a result of quarantine regulations and management with resistant potato cultivars, a virulent pathotype, Ro2, has emerged, for which control measures are scarce. The ability to detect Ro2 early in fields is necessary to sustain the success of...

Data from: Collapse, reorganization, and regime identity: breaking down past management paradigms in a forest-grassland ecotone

Victoria Donovan, Caleb Roberts, Carissa Wonkka, Daniel Uden, David Angeler, Craig Allen, David Wedin, Rhae Drijber & Dirac Twidwell
The identity of an ecological regime is central to modern resilience theory and our understanding of how systems collapse and reorganize following disturbance. However, resilience-based models used in ecosystem management have been criticized for their failure to integrate disturbance outcomes into regime identity. Assessments are needed to understand how well these classifications represent ecosystem responses that occur over management relevant time scales. We tracked post-wildfire forest and grassland dynamics 27 years after wildfire in eastern...

Assessment of biogeographic variation in traits of Lewis flax (Linum lewisii) for use in restoration and agriculture

Peter Innes, André Gossweiler, Scott Jensen, Derek Tilley, Loren St. John, Thomas Jones, Stanley Kitchen & Brent S. Hulke
Lewis flax (Linum lewisii) is widely distributed across western North America and is currently used in native ecosystem restoration. There is also growing interest in de novo domestication of Lewis flax as a perennial oilseed crop. To better understand this species and facilitate both restoration and domestication, we used common gardens to assess bio-geographical variation in a variety of seed and growth traits from 37 flax accessions, consisting of 35 wild populations from the Intermountain...

Root Production and Morphological Traits During and After Single and Repeated Extreme Droughts in a Mesic Grassland

Ingrid Slette, David Hoover, Melinda Smith & Alan Knapp
Global climate change is expected to cause more frequent extreme droughts in many parts of the world. Despite the crucial role of roots in water acquisition and plant survival, our understanding of ecosystem vulnerability to drought is primarily based on aboveground impacts. As return intervals between droughts decrease, root responses to one drought might alter responses to subsequent droughts, but this remains unresolved. We conducted a 7-year experiment that imposed extreme drought (growing season precipitation...

Alien insect dispersal mediated by the global movement of commodities

Gyda Fenn-Moltu, Gyda Fenn-Moltu, Sébastien Ollier, Barney Caton, Andrew Liebhold, Helen Nahrung, Deepa Pureswaran, Rebecca Turner, Takehiko Yamanaka & Cleo Bertelsmeier
Globalization and economic growth are recognized as key drivers of biological invasions. Alien species have become a feature of almost every biological community worldwide, and rates of new introductions continue to rise as the movement of people and goods accelerates. Insects are among the most numerous and problematic alien organisms, and are mainly introduced unintentionally with imported cargo or arriving passengers. However, the processes occurring prior to insect introductions remain poorly understood. We used a...

Data from: Rocky Mountain forests are poised to recover following bark beetle outbreaks, but with altered composition

Kyle Rodman, Robert Andrus, Amanda Carlson, Trevor Carter, Teresa Chapman, Jonathan Coop, Paula Fornwalt, Nathan Gill, Brian Harvey, Ashley Hoffman, Katharine Kelsey, Dominik Kulakowski, Daniel Laughlin, Jenna Morris, José Negrón, Katherine Nigro, Gregory Pappas, Miranda Redmond, Charles Rhoades, Monique Rocca, Zoe Schapira, Jason Sibold, Camille Stevens-Rumann, Thomas Veblen, Jianmin Wang … & Sarah Hart
Amplified by warming temperatures and drought, recent outbreaks of native bark beetles (Curculionidae: Scolytinae) have caused extensive tree mortality throughout Europe and North America. Despite their ubiquitous nature and important effects on ecosystems, forest recovery following such disturbances is poorly understood, particularly across regions with varying abiotic conditions and outbreak effects. To better understand post-outbreak recovery across a topographically complex region, we synthesized data from 16 field studies spanning subalpine forests in the Southern Rocky...

Data from: Genetic evidence for high propagule pressure and long-distance dispersal in monk parakeet (Myiopsitta monachus) invasive populations

Anders Gonçalves Da Silva, Jessica Eberhard, Timothy Wright, Michael Avery & Michael Russello
The monk parakeet (Myiopsitta monachus) is a successful invasive species that does not exhibit life history traits typically associated with colonizing species (e.g., high reproductive rate or long-distance dispersal capacity). To investigate this apparent paradox, we examined individual and population genetic patterns of microsatellite loci at one native and two invasive sites. More specifically, we aimed to evaluate the role of propagule pressure, sexual monogamy, and long-distance dispersal in monk parakeet invasion success. Our results...

Data from: Molecular evolution of shattering loci in U.S. weedy rice

Carrie Thurber, Michael Reagon, Briana Gross, Kenneth Olsen, Yulin Jia & Ana Caicedo
Cultivated rice fields worldwide are plagued with weedy rice, a conspecific weed of cultivated rice (Oryza sativa L.). The persistence of weedy rice has been attributed, in part, to its ability to shatter (disperse) seed prior to crop harvesting. In the United States, separately evolved weedy rice groups have been shown to share genomic identity with exotic domesticated cultivars. Here, we investigate the shattering phenotype in a collection of U.S. weedy rice accessions, as well...

Data from: Hybridization and invasion: an experimental test with diffuse knapweed (Centaurea diffusa Lam.)

Amy C Blair, Dana Blumenthal & Ruth A Hufbauer
A number of studies have suggested a link between hybridization and invasion. In this study, we experimentally test the potential for hybridization to influence invasion through a greenhouse common garden study. Diffuse knapweed (Centaurea diffusa Lam.) was introduced to North America with admixture from spotted knapweed (Centaurea stoebe subsp. stoebe L.). Comparisons between North American diffuse knapweed (including hybrid phenotypes) and native (European) diffuse knapweed in a common garden did not reveal enhanced performance or...

Data from: Microsatellite primers for the Pacific Northwest endemic conifer Chamaecyparis lawsoniana (Cupressaceae)

Tara N. Jennings, Brian J. Knaus, Scott Kolpak & Richard Cronn
Microsatellite primers were developed for the Pacific Northwest conifer, Chamaecyparis lawsoniana (A. Murray) Parl. (Cupressaceae), to enhance efficiencies in disease-resistance breeding and germplasm screening for gene conservation of this rare species. Using multiplexed massively parallel Illumina sequencing, we identified over 300,000 microsatellite-containing sequences from 2 million paired-end microreads. After stringent filtering and primer evaluation, we selected 11 primer pairs and used these to screen variation in 4 populations of C. lawsoniana. Loci show between three...

Data from: Divergence estimates and early evolutionary history of Figitidae (Hymenoptera: Cynipoidea)

Matthew L. Buffington, Seán G. Brady, Shelah I. Morita & Simon Van Noort
matrix08REDUCEDBayes04The combined molecular and morphological dataset analyzed using MrBayes.cynipoid_dating_all_calibrationsThe molecular dataset analyzed using BEAST.

Data from: Patterns of primary succession of native and introduced plants in lowland wet forests in eastern Hawai‘i

Naupaka Zimmerman, R. Flint Hughes, Susan Cordell, Patrick Hart, Heather Kalei Chang, David Perez, Ryan Kaipoalohaakala Like & Rebecca Ostertag
The majority of Hawaii’s lowland wet forests no longer exist, with many of the last remaining patches found on the eastern, windward sides of the largest islands. To better understand successional patterns and invasion in these native systems, we quantified basal area (BA) and densities of woody species and understory cover at nine sites in the Puna district on the Island of Hawai‘i, representing age gradients of native stand development on both ‘a’ā and pāhoehoe...

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