293 Works

Data from: Microsatellite primers for the Pacific Northwest conifer, Callitropsis nootkatensis (Cupressaceae)

Tara N. Jennings, Brian J. Knaus, Katherine Alderman, Paul E. Hennon, David V. D'Amore, Richard Cronn & David V. D' Amore
Premise of the study: Microsatellite primers were developed for Nootka cypress (Callitropsis nootkatensis) to provide quantitative measures for gene conservation that can assist in guiding management decisions for a species experiencing climate-induced decline. Methods and Results: Using multiplexed massively parallel sequencing, we identified 136,785 microsatellite-containing sequences from 489,625 paired-end 80 bp reads. After stringent filtering, we selected 144 primer pairs and screened variation at these loci in five populations of C. nootkatensis. Loci show between...

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: 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: 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: 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: 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: 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: 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...

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...

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...

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...

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...

Data and analysis code for \"Forest recovery following extreme drought in California, USA: natural patterns and effects of pre-drought management\"

Derek Young, Marc Meyer, Becky Estes, Shana Gross, Amarina Wuenschel, Christina Restaino & Hugh Safford
This repository contains data and code for the paper "Forest recovery following extreme drought in California, USA: natural patterns and effects of pre-drought management" by Young et al., published in Ecological Applications. The abstract of the paper is as follows. Rising temperatures and more frequent and severe droughts are driving increases in tree mortality in forests around the globe. However, in many cases, the likely trajectories of forest recovery following drought-related mortality are poorly understood....

Data from: Microbial functional diversity: from concepts to applications

Arthur Escalas, Lauren Hale, James Voordeckers, Yunfeng Yang, Mary Firestone, Lisa Alvarez-Cohen & Jizhong Zhou
Functional diversity is increasingly recognized by microbial ecologists as the essential link between biodiversity patterns and ecosystem functioning, determining the trophic relationships and interactions between microorganisms, their participation in biogeochemical cycles and their responses to environmental changes. Consequently, its definition and quantification have practical and theoretical implications. In this opinion paper, we present a synthesis on the concept of microbial functional diversity from its definition to its application. Initially, we revisit to the original definition...

Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (Anaxyrus canorus)

Paul A. Maier, Amy G. Vandergast, Steven M. Ostoja, Andres Aguilar & Andrew J. Bohonak
Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (Anaxyrus canorus) Species endemic to alpine environments can evolve via steep ecological selection gradients between lowland and upland environments. Additionally, many alpine environments have faced repeated glacial episodes over the past two million years, fracturing these endemics into isolated populations. In this “glacial pulse” model of alpine diversification, cycles of allopatry and ecologically divergent glacial refugia play a role in generating biodiversity, including...

Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts

Alyssa Burkhardt, Kevin Childs, Jie Wang, Marina Ramon & Frank Martin
Background: Macrophomina phaseolina is a fungal plant pathogen with a broad host range, but one genotype was shown to exhibit host preference/specificity on strawberry. This pathogen lacked a high-quality genome assembly and annotation, and little was known about genomic differences among isolates from different hosts. Results: We used PacBio sequencing and Hi-C scaffolding to provide nearly complete genome assemblies for M. phaseolina isolates representing the strawberry-specific genotype and another genotype recovered from alfalfa. The strawberry...

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...

Recent evolutionary history predicts population but not ecosystem level patterns

Sarah Fitzpatrick, Madison Miller & John Kronenberger
In the face of rapid anthropogenic environmental change, it is increasingly important to understand how ecological and evolutionary interactions affect the persistence of natural populations. Augmented gene flow has emerged as a potentially effective management strategy to counteract negative consequences of genetic drift and inbreeding depression in small and isolated populations. However, questions remain about the long-term impacts of augmented gene flow and whether changes in individual and population fitness are reflected in ecosystem structure,...

Diet quantity influences caste determination in honey bees (Apis mellifera)

Julia Bowsher, Garett Slater & George Yocum
In species that care for their young, provisioning has profound effects on offspring fitness. Provisioning is important in honey bees because nutritional cues determine whether a female becomes a reproductive queen or sterile worker. A qualitative difference between the larval diets of queens and workers is thought to drive this divergence; however, no single compound seems to be responsible. Diet quantity may have a role during honey bee caste determination yet has never been formally...

Local adaptation constrains drought tolerance in a tropical foundation tree

Kasey Barton, Casey Jones, Kyle Edwards, Aaron Shiels & Tiffany Knight
1. Plant species with broad climatic ranges might be more vulnerable to climate change than previously appreciated due to intraspecific variation in climatic stress tolerance. In tropical forests, drought is increasingly frequent and severe, causing widespread declines and altering community dynamics. Yet, little is known about whether foundation tropical trees vary in drought tolerance throughout their distributions, and how intraspecific variation in drought tolerance might contribute to their vulnerability to climate change. 2. We tested...

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...

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...

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