Jacob N Barney

Jacob N Barney
Virginia Polytechnic Institute and State University | VT · School of Plant and Environmental Sciences

Ph.D.

About

140
Publications
30,302
Reads
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3,379
Citations
Additional affiliations
August 2016 - December 2016
Virginia Polytechnic Institute and State University
Position
  • Associate Professor of Invasive Plant Ecology
January 2007 - August 2010
University of California, Davis
Education
March 2007 - August 2010
University of California, Davis
Field of study
  • Invasive Plant Ecology
August 2003 - January 2007
Cornell University
Field of study
  • Weed Ecology
May 2000 - August 2003
Cornell University
Field of study
  • Weed Science

Publications

Publications (140)
Article
Full-text available
The sweet-basil (Ocimum basilicum L.) fruit/pericarp produces mucilage that engulfs the fruit and seed within minutes of hydration. Seed mucilage is produced by plant species that have adapted to arid, sandy soils. This study was conducted to determine how basil-seed mucilage improves ecological fitness. A second objective was to find ways to remov...
Article
Full-text available
Extreme cold plays a key role in the range boundaries of plants. Winter survival is central to their persistence, but not all structures are equally susceptible to frost kill and, therefore, limiting to distributions. Furthermore, we expect intraspecific variation in cold tolerance both within and among tissue types. In a laboratory setting, we det...
Article
Full-text available
Fruit house microbial communities that are unique from the rest of the plant. While symbiotic microbial communities complete important functions for their hosts, the fruit microbiome is often understudied compared to other plant organs. Fruits are reproductive tissues that house, protect, and facilitate the dispersal of seeds, and thus they are dir...
Article
Full-text available
Species niches have been defined in different ways, variably encompassing abiotic and biotic parameters limiting an organism’s spatial distribution. Climate is often the primary component of the abiotic (fundamental) niche, especially among terrestrial plants. In invasion biology, there is an ongoing debate on the prevalence of niche shifts, which...
Article
Full-text available
Weeds, plants that thrive in the face of disturbance, have eluded human's attempts at control for >12 000 years, positioning them as a unique group of extreme stress tolerators. The most successful weeds have a suite of traits that enable them to rapidly adapt to environments typified by stress, growing in hostile conditions or subject to massive d...
Article
Full-text available
Ailanthus altissima, the invasive forest tree commonly known as the tree-of-heaven, has been associated with decreased levels of plant species richness and native species diversity. However, this relationship with resident plants has been inconsistently found and the tree’s influence on the seedbank has yet to be studied. To further understand the...
Article
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Aim Introduced species often occupy different climates in their introduced than their native range, but to what degree do such ‘climatic niche shifts’ interfere with our ability to predict invasions? Answering this question is crucial if we are to understand the threat invasive species pose to human and natural systems, especially given the ever in...
Article
Aims Within-species genetic and phenotypic variations have well-known effects on evolutionary processes, but less is known about how within species variation may influence community-level processes. Ecologically meaningful intraspecific variation might be particularly important in the context of anthropogenic impacts on natural systems, such as agr...
Article
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The US native liana, poison ivy (Toxicodendron radicans), responsible for contact dermatitis in humans, is a competitive weed with great potential for expansion in disturbed habitats. To facilitate a better understanding of this threat, we sought to evaluate habitat suitability, population demography, and biotic interactions of poison ivy, using a...
Article
Full-text available
Invasive plants and agricultural weeds are a ubiquitous and ever-expanding threat to biosecurity, biodiversity, and ecosystem services. Many of these species are known to succeed through rapid adaptation to biotic and abiotic stress regimes, often in highly disturbed systems. Given the current state of evidence for selection of weedy genotypes via...
Article
Weedy and invasive plants threaten our food supply, native biodiversity, and the structure and function of ecosystems. The number and impact of these damaging plants are expected to continue to grow with ongoing global change. Some of the most common policy tools to help mitigate this threat are regulatory weed lists, which limit the importation an...
Article
Full-text available
From noble beginnings as a prospective forage, polyploid Sorghum halepense (‘Johnsongrass’) is both an invasive species and one of the world’s worst agricultural weeds. Formed by S. bicolor x S. propinquum hybridization, we show S. halepense to have S. bicolor-enriched allele composition and striking mutations in 5,957 genes that differentiate it f...
Article
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Despite their near ubiquity across global ecosystems, the underlying mechanisms contributing to the success of invasive plants remain largely unknown. In particular, ecophysiological traits, which are fundamental to plants' performance and response to their environment, are poorly understood with respect to geographic and climate space. We evaluate...
Article
Governments and conservation organizations worldwide are motivated to manage invasive species due to quantified and perceived negative ecological and economic impacts invasive species impose. Thus, determining which species cause significant negative impacts, as well as clear articulation of those impacts, is critical to meet conservation prioritie...
Article
Full-text available
Aims Exotic invasive species are often exposed to strong selection pressures in their new ranges that can often lead to substantial intraspecific variation. Population differentiation in the timing of life history events in response to climate gradients is thought to be an important mechanism facilitating the range expansion of many invasive specie...
Article
Cover crop residue can act as a mulch that will suppress weeds, but as the residue degrades, weed suppression diminishes. Biomass of cover crop residue is positively correlated to weed suppression, but little research is available regarding the composition of cover crop residue and its effect on weed suppression. Field experiments were conducted to...
Article
We compared the influence of biological traits (morphology, physiology, reproduction, and life history), ecological traits (geographic distribution, habitat associations, food habits), and introduction attributes (propagule pressure, human use of a species, residence time) on invasion success of native and introduced stream fishes during the coloni...
Article
Hairy vetch is a widely adopted cover crop in the United States. However, hairy vetch can become weedy in subsequent crops as seeds germinate after the cover crop growing season, which is largely attributed to seed dormancy. We conducted two field experiments to determine seed germination, viability and seed production phenology of two common hairy...
Article
Biological invasions are known drivers of biodiversity decline, yet the ecological impacts of invaders remain largely unmeasured in many contexts. Consequently, other measures of a species invasion (eg local abundance) are often used as surrogates (or “proxies”) to infer impact on recipient ecosystems. However, the use of surrogates for impact in i...
Article
Weeds pose severe threats to agricultural and natural landscapes worldwide. One major reason for the failure to effectively manage weeds at landscape scales is that current Best Management Practice guidelines, and research on how to improve such guidelines, focus too narrowly on property-level management decisions. Insufficiently considered are the...
Article
Horseweed is a problematic weed to control, especially in no-tillage production. Increasing cases of herbicide resistance have exacerbated the problem, necessitating alternative control options and an integrated weed management approach. Field experiments were conducted to evaluate horseweed suppression from fall-planted cover crop monocultures and...
Article
Biological invasions are one of the grand challenges facing society, as exotic species introductions continue to rise and can result in dramatic changes to native ecosystems and economies. The scale of the “biological invasions crisis” spans from hyperlocal to international, involving a myriad of actors focused on mitigating and preventing biologic...
Article
The Appalachian region of the United States is home to the largest temperate deciduous forest in the world, though surface mining has caused significant forest loss. Many former coal mines are now dominated by invasive plants, which often inhibit establishment of desirable species, especially slower-growing native trees. Autumn-olive ( Elaeagnus um...
Article
Surface mining has caused significant disturbance globally, and is responsible for the loss of >600,000 hectares of the world’s largest temperate deciduous forest in the Appalachian region of the US alone. Due to the heavy disturbance on mine lands, invasive plants have become dominant on many former coalfields, some of which were intentionally pla...
Data
Data S1. Materials and methods. Table S1. The 124 pre‐submitted research questions that address fundamental and applied issues in weed ecology, evolution and management
Article
Full-text available
Aims As an exotic species colonises a new continent, it must overcome enormous environmental variation in its introduced range. Local adaptation of introduced species has frequently been observed at the continent scale, particularly in response to latitudinal climatic variation. However, significant environmental heterogeneity can also exist at the...
Article
Full-text available
Weedy plants pose a major threat to food security, biodiversity, ecosystem services and consequently to human health and wellbeing. However, many currently used weed management approaches are increasingly unsustainable. To address this knowledge and practice gap, in June 2014, 35 weed and invasion ecologists, weed scientists, evolutionary biologist...
Article
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Deoxyribonucleic acid (DNA) methylation is an epigenetic alteration crucial for regulating stress responses. Identifying large-scale DNA methylation at single nucleotide resolution is made possible by whole genome bisulfite sequencing. An essential task following the generation of bisulfite sequencing data is to detect differentially methylated cyt...
Article
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Our understanding of how climate influences species distributions and our ability to assess the risk of introduced species depend on the assumption that species' climatic niches remain stable across space and time. While niche shifts have been detected in individual invasive species, one assessment of ~50 plants in Europe and North America conclude...
Article
The negative effects of invasive plant species on native ecosystems, which can be large and long-lasting, are the primary justifications for their research and management. Tremendous effort is focused on quantifying the ecological impacts of invasive plants, though two different methods are primarily used: observational (compare invaded and uninvad...
Article
Knowledge of expanding and contracting ranges is critical for monitoring invasions and assessing conservation status, yet reliable data on distributional trends are lacking for most freshwater species. We developed a quantitative technique to detect the sign (expansion or contraction) and functional form of range-size changes for freshwater species...
Article
Full-text available
Forests understories in Europe are known to generally resist invasion, though some alien plants do invade woodland communities. Here we focused on the impact of the widespread invasive annual Impatiens glandulifera, common along watercourses, but recently spreading in forests up to timberline. We investigated its impact on plant–soil feedback and e...
Article
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Continuous use of herbicides has resulted in the evolution of resistance to all major herbicide modes of action worldwide. Besides the well-documented cases of newly acquired resistance by genetic changes, epigenetic regulation may also contribute to herbicide resistance in weeds. Epigenetics involves processes that modify the expression of specifi...
Article
Full-text available
The emergence of herbicide-resistant weeds is a major threat facing modern agriculture. Over 470 weedy-plant populations have developed resistance to herbicides. Traditional evolutionary mechanisms are not always sufficient to explain the rapidity with which certain weed populations adapt in response to herbicide exposure. Stress-induced epigenetic...
Data
Table S1. Overview of sequencing results. Overview of sequencing results, breadth of coverage, and identification of methylated cytosines (mCs) following bisulfite sequencing of gDNA collected from newly formed cauline leaves at silique maturation of four A. thaliana individuals from each treatment where four-week-old rosettes were exposed to 0, 5,...
Data
Dataset S1. All differentially methylated positions (DMPs) identified by methylkit.
Data
Dataset S3. All differentially methylated regions (DMRs) identified using bsseq algorithm.
Data
Dataset S4. DMRs categorized by dose dependency.
Data
Dataset S6. GO term enrichment in DMR-associated genes.
Data
Dataset S7. All DMR-associated genes following glyphosate stress (this work), biotic stress mimic (1), or phosphate starvation (2). References: 1. Dowen RH, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, Nery JR, et al. Widespread dynamic DNA methylation in response to biotic stress. Proceedings of the National Academy of Sciences. 2012;109(32):E2183...
Data
Figure S2. Categorization of overlapping DMRs identified following treatment at 5 and 10% glyphosate. Categorization of overlapping DMRs identified following treatment at 5 and 10% of a 0.9 kg acid ha−1 glyphosate rate based on dose-dependency of methylation response. Using a 95% confidence interval cutoff, overlapping DMRs were classified as eithe...
Data
Dataset S5. DMR-associated transposable elements.
Data
Figure S1. Effect of increasing the number of replicates in limiting the number of DMRs called by the BSmooth/bsseq R package. Effect of increasing the number of replicates in limiting the number of DMRs called by the BSmooth/bsseq R package (Bioconductor) using less stringent qcutoff of 0.1 (left panel) and more stringent qcutoff of 0.01 (right pa...
Data
Figure S3. Pearson’s product moment correlation coefficients clustered for four replicates each of 3 treatments and within three sequence contexts. Treatments comprised percentages of a 0.9 kg acid equivalency ha−1 glyphosate rate applied to four-week-old A. thaliana rosettes.
Data
Figure S6. Gene ontology (GO) terms for molecular function enriched in DMR-associated genes for each of the three sequence contexts. Gene ontology (GO) terms for molecular function enriched (p<0.05) in DMR associated genes for each of the three sequence contexts. Rfi/Rfr represents the ratio of the relative frequency of GO terms in the input (glyph...
Data
Figure S4. Number of DMRs identified using eDMR across the three sequence contexts. Number of DMRs identified using eDMR across the three sequence contexts and separated by hypomethylation vs hypermethylation and whether or not the DMR was identified in the 5% glyphosate-treated samples only, the 10% glyphosate-treated samples only, or in both trea...
Data
Figure S5. Frequency of DMRs associated with transposable elements superfamilies. Frequency of DMRs associated with transposable elements superfamilies, identified from the TAIR10 genome release, across all contexts (CG, CHG, CHH). Panels separate hypomethylation vs hypermethylation and colors differentiate the 5% (orange) and 10% (maroon) glyphosa...
Data
Dataset S2. All differentially methylated regions (DMRs) identified using eDMR algorithm.
Data
Custom Perl script. Annotation of genomic features with DMRs. This custom Perl script identifies differentially methylated regions (DMRs) and provides genomic features annotation with TAIR10 gff file.
Article
The morphology and growth habit of Toxicodendron radicans (Poison Ivy) varies widely across North America. In this study, we evaluated the role of Poison Ivy accessionlevel diversity on growth habit and performance responses to light and nutrient stress in a common-garden greenhouse environment. We grew Poison Ivy seedlings derived from drupes coll...
Article
Many introduced species are capable of both sexual and vegetative reproduction. Our understanding of the ecology of such species depends on the trade-offs between vegetative and sexual reproduction and the ecological conditions that favor both modes of reproduction and how those factors influence the population ecology of introduced species. Here,...
Article
Ecological impacts from invasive plants that have been identified include reductions in biodiversity, changes in resource cycling, and disruptions of ecosystem function. To mitigate these negative ecological impacts, managers work to remove invasive plants. However, removal does not necessarily immediately lead to a return to the uninvaded ecologic...
Article
Full-text available
Exotic species can cause changes to their invaded ecosystems, which can be large and long lasting. Despite most landscapes being invaded by multiple exotic plant species, >90 % of impact studies only characterize the impacts of single species. Therefore, our knowledge of invasive plant impacts does not reflect the co-invaded nature of most landscap...
Article
Full-text available
Johnsongrass (Sorghum halepense) is a striking example of a post-Columbian founder event. This natural experiment within ecological time-scales provides a unique opportunity for understanding patterns of continent-wide genetic diversity following range expansion. Microsatellite markers were used for population genetic analyses including leaf-optimi...
Data
Figure A. Map of sampling sites and Principle Coordinate Analysis (PCoA) distribution of samples. Figure B. Principle Coordinate Analysis and locations of five groups at two extremes shown with number of genotypes in each group. Figure C. Mismatch distribution profiles (demographic expansion) from 12. Figure D. Mismatch distribution profiles (spati...
Data
Newick format file of N-J tree with bootrap values. (NWK)
Data
Overall averages of variance components in test for Linkage Disequilibrium for non-random association between pairs of loci in finite subdivided populations. (DOCX)
Data
Variances for every pairwise comparison of loci in Linkage Disequilibrium test for non-random association between pairs of loci in finite subdivided populations. (DOCX)
Article
Transdisciplinary weed research (TWR) is a promising path to more effective management of challenging weed problems. We define TWR as an integrated process of inquiry and action that addresses complex weed problems in the context of broader efforts to improve economic, environmental and social aspects of ecosystem sustainability. TWR seeks to integ...
Article
Full-text available
Sweet basil (Ocimum basilicum) is a warm-season herbaceous plant typically propagated from seed. Establishment of direct-seeded basil is oen difficult because seed germination may be limited, particularly in cold soils. To determine base, optimum, and ceiling germination temperatures and possible genetic variation, seeds of six cultivars of sweet...
Article
Full-text available
Transdisciplinary weed research (TWR) is a promising path to more effective management of challenging weed problems. We define TWR as an integrated process of inquiry and action that addresses complex weed problems in the context of broader efforts to improve economic, environmental and social aspects of ecosystem sustainability. TWR seeks to integ...
Article
Understanding impacts of invasive plants is necessary to achieve conservation goals. In this issue of Applied Vegetation Science, Kelemen et al. identify that a widespread invader reduces native abundance, but not richness, by displacing weak competitors as invader cover increased. An enhanced understanding of the multitude of ecological impacts sh...
Article
Successful invasions result from species functional traits interacting with the receiving community. Some have proposed that propagule pressure, or the size and number of introductions, can overcome high invasion resistance. However, few studies empirically investigate the relationship among functional traits, community composition, and propagule p...
Article
Full-text available
Weed Risk Assessments Can Be Useful, But Have Limitations - Volume 9 Issue 1 - Jacob N. Barney, Larissa L. Smith, Daniel R. Tekiela
Article
Full-text available
The ecological impacts of invasive plants have served to justify the cost of their management, which is estimated to exceed $1 billion annually in the US alone. However, our understanding of the ecological impacts of most invasive plants is extremely limited, and when known, interpretation is confounded with varied measurements and methods. While t...