289 Works

Data from: Signatures of selection for environmental adaptation and zebu x taurine hybrid fitness in East African Shorthorn Zebu

Hussain Bahbahani, Abdulfatai Tijjani, Christopher Mukasa, David Wragg, Faisal Almathen, Oyekanmi Nash, Gerald N. Akpa, Mary Mbole-Kariuki, Sunir Malla, Mark Woolhouse, Tad Sonstegard, Curtis Van Tassell, Martin Blythe, Heather Huson & Olivier Hanotte
The East African Shorthorn Zebu (EASZ) cattle are ancient hybrid between Asian zebu × African taurine cattle preferred by local farmers due to their adaptability to the African environment. The genetic controls of these adaptabilities are not clearly understood yet. Here, we genotyped 92 EASZ samples from Kenya (KEASZ) with more than 770,000 SNPs and sequenced the genome of a pool of 10 KEASZ. We observe an even admixed autosomal zebu × taurine genomic structure...

Data from: Use of simulation-based statistical models to complement bioclimatic models in predicting continental scale invasion risks

Ranjan Muthukrishnan, Nicholas R. Jordan, Adam S. Davis & James D. Forester
Invasive species represent one of the greatest risks to global biodiversity and economic productivity of agroecosystems. The development of certain novel crops—e.g., herbaceous perennial biomass crops—may create a risk of novel invasions by these crops. Therefore, potential benefits and risks need to be weighed in making decisions about their introduction and subsequent management. Ideally, such a weighing will be based on good estimates of invasion risks in realistic scenarios pertaining to actual landscapes of concern...

Data from: Tracking the origins of fly invasions; using mitochondrial haplotype diversity to identify potential source populations in two genetically intertwined fruit fly species (Bactrocera carambolae and Bactrocera dorsalis [Diptera: Tephritidae])

Michael San Jose, Camiel Doorenweerd, Luc Leblanc, Norman Barr, Scott Geib & Daniel Rubinoff
Bactrocera carambolae Drew and Hancock and B. dorsalis (Hendel) (Diptera: Tephritidae) are important pests of many fruits. These flies have been spread across the world through global travel and trade, and new areas are are at risk of invasion. Whenever new invasive populations are discovered, quick and accurate identification is needed to mitigate the damage they can cause. Determining invasive pathways can prevent further spread of pests as well as subsequent reinvasions through the same...

Data from: The genetic architecture of ecological adaptation: intraspecific variation in host plant use by the lepidopteran crop pest Chloridea virescens

Sara J. Oppenheim, Fred Gould & Keith R. Hopper
Intraspecific variation in ecologically important traits is a cornerstone of Darwin’s theory of evolution by natural selection. The evolution and maintenance of this variation depends on genetic architecture, which in turn determines responses to natural selection. Some models suggest that traits with complex architectures are less likely to respond to selection than those with simple architectures, yet rapid divergence has been observed in such traits. The simultaneous evolutionary lability and genetic complexity of host plant...

Data from: Character evolution and missing (morphological) data across Asteridae

Gregory W. Stull, Melanie Schori, Douglas E. Soltis & Pamela S. Soltis
Premise of the study: Our current understanding of flowering plant phylogeny provides an excellent framework for exploring various aspects of character evolution through comparative analyses. However, attempts to synthesize this phylogenetic framework with extensive morphological datasets have been surprisingly rare. Here, we explore character evolution in Asteridae (asterids), a major angiosperm clade, using an extensive morphological data set and a well-resolved phylogeny. Methods: We scored 15 phenotypic characters (spanning chemistry, vegetative anatomy, and floral, fruit,...

Data from: The genomes of two key bumblebee species with primitive eusocial organisation

Ben M. Sadd, Seth M. Barribeau, Guy Bloch, Dirk C. De Graaf, Peter Dearden, Christine Elsik, Jurgen Gadau, Cornelius Grimmelikhuijzen, Martin Hasselmann, Jeffrey Lozier, Hugh Robertson, Guy Smagghe, Eckart Stolle, Matthias Van Vaerenbergh, Robert Waterhouse, Erich Bornberg-Bauer, Steffan Klasberg, Anna Bennett, Francisco Camara, Roderic Guigo, Katharina Hoff, Marco Mariotti, Monica Munos-Torres, Terence Murphy, Didac Santesmasses … & Kim C. Worley
Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome...

Data from: High precipitation and seeded species competition reduce seeded shrub establishment during dryland restoration

Matthew J. Rinella, Darcy H. Hammond, Ana-Elisa M. Bryant & Brian J. Kozar
Drylands comprise 40% of Earth's land mass and are critical to food security, carbon sequestration, and threatened and endangered wildlife. Exotic weed invasions, overgrazing, energy extraction, and other factors have degraded many drylands, and this has placed an increased emphasis on dryland restoration. The increased restoration focus has generated a wealth of experience, innovations and empirical data, yet the goal of restoring diverse, native, dryland plant assemblages composed of grasses, forbs, and shrubs has generally...

Data from: Genomics assisted ancestry deconvolution in grape

Jason K. Sawler, Bruce Reisch, Mallikarjuna K. Aradhya, Bernard Prins, Gan-Yuan Zhong, Heidi Schwaninger, Charles Simon, Edward Buckler, Sean Myles & Jason Sawler
The genus Vitis (the grapevine) is a group of highly diverse, diploid woody perennial vines consisting of approximately 60 species from across the northern hemisphere. It is the world’s most valuable horticultural crop with ~8 million hectares planted, most of which is processed into wine. To gain insights into the use of wild Vitis species during the past century of interspecific grape breeding and to provide a foundation for marker-assisted breeding programmes, we present a...

Data from: Leaf nutrients, not specific leaf area, are consistent indicators of elevated nutrient inputs

Jennifer Firn, James M. McGree, Eric Harvey, Habacuc Flores-Moreno, Martin Schütz, Yvonne M. Buckley, Elizabeth T. Borer, Eric W. Seabloom, Kimberly J. La Pierre, Andrew M. MacDougall, Suzanne M. Prober, Carly J. Stevens, Lauren L. Sullivan, Erica Porter, Emma Ladouceur, Charlotte Allen, Karine H. Moromizato, John W. Morgan, W. Stanley Harpole, Yann Hautier, Nico Eisenhauer, Justin P. Wright, Peter B. Adler, Carlos Alberto Arnillas, Jonathan D. Bakker … & Anita C. Risch
Leaf traits are frequently measured in ecology to provide a ‘common currency’ for predicting how anthropogenic pressures impact ecosystem function. Here, we test whether leaf traits consistently respond to experimental treatments across 27 globally distributed grassland sites across 4 continents. We find that specific leaf area (leaf area per unit mass)—a commonly measured morphological trait inferring shifts between plant growth strategies—did not respond to up to four years of soil nutrient additions. Leaf nitrogen, phosphorus...

Data from: Development and evaluation of 200 novel SNP assays for population genetic studies of westslope cutthroat trout and genetic identification of related taxa

Nathan R. Campbell, Stephen J. Amish, Victoria L. Pritchard, K. M. McKelvey, Michael K. Young, Michael K. Schwartz, John C. Garza, Gordon Luikart & Shawn R. Narum
DNA sequence data were collected and screened for single nucleotide polymorphisms (SNPs) in westslope cutthroat trout (Oncorhynchus clarki lewisi) and also for substitutions that could be used to genetically discriminate rainbow trout (O. mykiss) and cutthroat trout, as well as several cutthroat trout subspecies. In total, 260 expressed sequence tag-derived loci were sequenced and allelic discrimination genotyping assays developed from 217 of the variable sites. Another 50 putative SNPs in westslope cutthroat trout were identified...

Data from: Conditional vulnerability of plant diversity to atmospheric nitrogen deposition across the United States

Samuel M. Simkin, Edith B. Allen, William D. Bowman, Christopher M. Clark, Jayne Belnap, Matthew L. Brooks, Brian S. Cade, Scott L. Collins, Linda H. Geiser, Frank S. Gilliam, Sarah E. Jovan, Linda H. Pardo, Bethany K. Schulz, Carly J. Stevens, Katharine N. Suding, Heather L. Throop & Donald M. Waller
Atmospheric nitrogen (N) deposition has been shown to decrease plant species richness along regional deposition gradients in Europe and in experimental manipulations. However, the general response of species richness to N deposition across different vegetation types, soil conditions, and climates remains largely unknown even though responses may be contingent on these environmental factors. We assessed the effect of N deposition on herbaceous richness for 15,136 forest, woodland, shrubland, and grassland sites across the continental United...

Data from: HiMAP: robust phylogenomics from highly multiplexed amplicon sequencing

Julian R. Dupuis, Forest T. Bremer, Angela Kauwe, Michael San Jose, Luc Leblanc, Daniel Rubinoff & Scott M. Geib
High-throughput sequencing has fundamentally changed how molecular phylogenetic datasets are assembled, and phylogenomic datasets commonly contain 50-100-fold more loci than those generated using traditional Sanger-based approaches. Here, we demonstrate a new approach for building phylogenomic datasets using single tube, highly multiplexed amplicon sequencing, which we name HiMAP (Highly Multiplexed Amplicon-based Phylogenomics), and present bioinformatic pipelines for locus selection based on genomic and transcriptomic data resources and post-sequencing consensus calling and alignment. This method is inexpensive...

Data from: Novel forests maintain ecosystem processes after the decline of native tree species

Joseph Mascaro, R. Flint Hughes & Stefan A. Schnitzer
The positive relationship between species diversity (richness and evenness) and critical ecosystem functions, such as productivity, carbon storage, and nutrient cycling, is often used to predict the consequences of extinction. At regional scales, however, plant species richness is mostly increasing rather than decreasing because successful plant species introductions far outnumber extinctions. If these regional increases in richness lead to local increases in diversity, a reasonable prediction is that productivity, carbon storage, and nutrient cycling will...

Data from: Process-based simulation of prairie growth

Cody J. Zilverberg, Jimmy Williams, Curtis Jones, Keith Harmoney, Jay Angerer, Loretta J. Metz & William Fox
When field research is cost- or time-prohibitive, models can inform decision-makers regarding the impact of agricultural policy on production and the environment, but process-based models that simulate animal-plant-soil interaction and ecosystem services in grazing lands are rare. In the U.S.A., APEX (Agricultural Policy/Environmental eXtender) is a model commonly used to inform policy on cropland, but its ability to simulate grazinglands was less robust. Therefore, we enhanced the APEX model’s plant growth module to improve its...

Data from: Sorption and desorption of bicyclopyrone on soils

Kurt Spokas, Bea Gamiz, Sharon Schneider, Kathleen Hall & Wenlin Chen
Bicyclopyrone is a herbicide that is targeted for the control of herbicide-resistant weeds. However, there is a lack of extensive data on its sorption and factors that control its sorption in the soil system. In this study, we evaluated a series of 25 different soils, with a variety of soil properties to assess if an empirical relationship could be developed to predict the sorption coefficient for bicyclopyrone. Overall, there were no statistically significant relationships observed...

Variation in host home range size decreases rabies vaccination effectiveness by increasing the spatial spread of rabies virus

Katherine McClure, Amy Gilbert, Richard Chipman, Erin Rees & Kim Pepin
1. Animal movement influences the spatial spread of directly-transmitted wildlife disease through host-host contact structure. Wildlife disease hosts vary in home range-associated foraging and social behaviors, which may increase the spread and intensity of disease outbreaks. The consequences of variation in host home range movement and space use on wildlife disease dynamics are poorly understood, but could help to predict disease spread and determine more effective disease management strategies. 2. We developed a spatially-explicit individual-based...

Assessing intrastate cattle shipments from interstate data and expert opinion

Peter Brommesson, Stefan Sellman, Lindsay Beck-Johnson, Clayton N Hallman, Deedra Murieta, Colleen Webb, Ryan Miller, Katie Portacci & Tom Lindström
Live animal shipments are a potential route for transmitting animal diseases between holdings and are crucial when modeling spread of infectious diseases. Yet, complete contact networks are not available in all countries, including the United States. Here, we considered a 10% sample of Interstate Certificate of Veterinary Inspections from one year (2009). We focused on distance dependence in contacts and investigated how different functional forms affect estimates of unobserved intrastate shipments. To further enhance our...

Testing the potential contribution of Wolbachia to speciation when cytoplasmic incompatibility becomes associated with host‐related reproductive isolation

Daniel Bruzzese, Hannes Schuler, Thomas Wolfe, Mary Glover, Joseph Mastroni, Meredith Doellman, Cheyenne Tait, Wee Yee, Juan Rull, Martin Aluja, Glen Hood, Robert Goughnour, Christian Stauffer, Patrik Nosil, Jeffery Feder, Daniel J. Bruzzese, Thomas M. Wolfe, Mary M. Glover, Meredith M. Doellman, Wee L. Yee, Glen R. Hood & Jeffery L. Feder
Endosymbiont induced cytoplasmic incompatibility (CI) may play an important role in arthropod speciation. However, whether CI consistently becomes associated or coupled with other host-related forms of reproductive isolation (RI) to impede the transfer of endosymbionts between hybridizing populations and further the divergence process remains an open question. Here, we show varying degrees of pre- and post-mating RI exist among allopatric populations of two interbreeding cherry-infesting tephritid fruit flies (Rhagoletis cingulata and R. indifferens) across North...

Large herbivores suppress liana infestation in an African savanna

Tyler C. Coverdale, Ryan D. O'Connell, Matthew C. Hutchinson, Amanda Savagian, Tyler R. Kartzinel, Todd M. Palmer, Jacob R. Goheen, David J. Augustine, Mahesh Sankaran, Corina E. Tarnita & Robert M. Pringle
African savannas are the last stronghold of diverse large-mammal communities, and a major focus of savanna ecology is to understand how these animals affect the relative abundance of trees and grasses. However, savannas support diverse plant life-forms, and human-induced changes in large-herbivore assemblages—declining wildlife populations and their displacement by livestock—may cause unexpected shifts in plant community composition. We investigated how herbivory affects the prevalence of lianas (woody vines) and their impact on trees in an...

Eight generations of native seed cultivation reduces plant fitness relative to the wild progenitor population

Riley Pizza, Erin Espeland & Julie Etterson
Native seed for restoration is in high demand, but widespread habitat degradation will likely prevent enough seed from being sustainably harvested from wild populations to meet this need. While propagation of native species has emerged in recent decades to address this resource gap, few studies have tested whether the processes of sampling from wild populations, followed by generations of farm cultivation, reduces plant fitness tolerance to stress over time. To test this, we grew the...

Ants adjust their tool use strategy in response to foraging risk

Aiming Zhou, Yuzhe Du & Jian Chen
1. Ants are among a few invertebrates that can use certain tools. For example, some ants can use debris and soil grains to transport liquid food. Although there has been evidence showing that ants can select the most efficient tools in transporting liquid food, little is known about their flexibility in using a specific tool under environmental pressure. 2. Black imported fire ants, Solenopsis richteri Forel, can use sands as a tool for foraging. We...

Onion (Allium cepa) pseudoreference genome

Joanne Labate, Jeffrey Glaubitz & Michael Havey
Onion (Allium cepa) is not highly tractable for development of molecular markers due to its large (16 gigbases per 1C) nuclear genome. Single nucleotide polymorphisms (SNPs) are useful for genetic characterization and marker-aided selection of onion because of codominance and common occurrence in elite germplasm. We completed genotyping by sequencing (GBS) to identify SNPs in onion using 46 F2 plants, parents of the F2 plants (Ailsa Craig 43 and Brigham Yellow Globe 15-23), two doubled...

Critical PO2 as a diagnostic biomarker for the effects of low-oxygen modified and controlled atmospheres on phytosanitary irradiation treatments in the Cabbage Looper Trichoplusia ni (Hübner)

Chao Chen, Catriona Condon, Leigh Boardman, Robert Meagher, Laura Jeffers, Andrea Beam, Woodward Bailey & Daniel Hahn
BACKGROUND: Phytosanitary irradiation is a sustainable alternative to chemical fumigants for disinfesting fresh commodities from insect pests. However, irradiating insects in modified atmospheres with very low oxygen (<1 kPa O2) has repeatedly been shown to increase radioprotective response. Thus, there is a concern that modified atmosphere packaging could reduce the efficacy of phytosanitary irradiation. One hurdle slowing the widespread application of phytosanitary irradiation is a lack of knowledge about how moderate levels of hypoxia relevant...

Data from: Crop production in the USA is frequently limited by a lack of pollinators

James Reilly, Derek Artz, David Biddinger, Kyle Bobiwash, Natalie Boyle, Claire Brittain, Julia Brokaw, Josh Campbell, Jaret Daniels, Elizabeth Elle, Jamie Ellis, Shelby Fleischer, Jason Gibbs, Robert Gillespie, Knute Gundersen, Larry Gut, George Hoffman, Neelendra Joshi, Ola Lundin, Keith Mason, Carley McGrady, Steve Peterson, Theresa Pitts-Singer, Sujaya Rao, Nikki Rothwell … & Rachael Winfree
Most of the world’s crops depend on pollinators, so declines in both managed and wild bees raise concerns about food security. However, the degree to which insect pollination is actually limiting current crop production is poorly understood, as is the role of wild species (as opposed to managed honey bees) in pollinating crops, particularly in intensive production areas. We established a nation-wide study to assess the extent of pollinator limitation in seven crops at 131...

The tepary bean genome provides insight into evolution and domestication under heat stress

Samira Mafi Moghaddam, Atena Oladzad, Chu Shin Koh, Larissa Ramsay, John Hart, Sujan Mamidi, Genevieve Hoopes, Avinash Sreedasyam, Andrew Wiersma, Dongyan Zhao, Jane Grimwood, John P. Hamilton, Jerry Jenkins, Brieanne Vaillancourt, Joshua C. Wood, Jeremy Schmutz, Sateesh Kahale, Tiomothy Porch, Kirstin E. Bett, C. Robin Buell & Phillip E. McClean
Tepary bean (Phaseolus acutifolis A. Gray), native to the Sonoran Desert, is highly adapted to heat and drought. It is a sister species of common bean (Phaseolus vulgaris L.), the most important legume protein source for direct human consumption, and whose production is threatened by climate change. Analysis of the tepary genome revealed mechanisms for resilience to moderate heat stress and a reduced disease resistance gene repertoire, consistent with adaptation to arid, hot environments. Extensive...

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