60 Works

Probing the molecular basis of fruit firmness in southern highbush blueberry (Vaccinium corymbosum hybrid) through RNA sequencing

Lena Wilson & Hamid Ashrafi
Blueberries (Vaccinium corymbosum L.) benefit from increased fruit firmness because of consumer preference and machine harvestability. However, the genetic component of fruit texture and skin thickness and their relationship to firmness have yet to be deciphered. This study used bulked segregant RNA-seq (BSR-seq) for differential gene expression analysis. Previously an F1 population of a cross between firm-fruited southern highbush cv. 'Reveille' and soft-fruited cv. 'Arlen' was developed in our laboratory. The total RNA of the...

Effects of an alternative host on the prevalence and infection intensity of a bumble bee parasite

Rebecca Irwin & Simon Pinilla-Gallego
Several bee parasites are transmitted through flowers, and some of them can infect multiple host species. Given the shared use of flowers by bee species, parasites can potentially encounter multiple host species, which could affect the evolution of parasite virulence. We used the trypanosomatid parasite Crithidia bombi and its host, the common eastern bumble bee (Bombus impatiens), to explore the effect of infecting an alternative host, the alfalfa leaf-cutter bee (Megachile rotundata), on parasite infectivity...

Floral shape predicts bee-parasite transmission potential

Rebecca Irwin, Mario Pinilla-Gallego, Wee-Hao Ng & Victoria Amaral
The spread of parasites is one of the primary drivers of population decline of both managed and wild bees. Several bee parasites are transmitted by the shared use of flowers, turning floral resources into potential disease hotspots. However, we know little about how floral morphology and floral species identity affect different steps of the transmission process. Here, we used the gut parasite Crithidia bombi and its primary host, bumble bees (Bombus spp.), to examine whether...

Data from: AgMate: an optimal mating software versus other mate pair designing methods on long-term breeding of Pinus taeda L

Khushi Goda & Fikret Isik
Breeding objectives aim to optimize two crucial but contrasting goals of maximizing genetic gain while managing genetic diversity. In advanced generations, this becomes a challenge in monoecious conifer tree species breeding programs because they suffer from inbreeding. Developing an algorithm that maximizes genetic gain while maintaining genetic diversity for monoecious species is imperative. While methods and algorithms for animal breeding are well-established, an efficient algorithm suited to monoecious species remains elusive. Towards this goal, we...

Data from: Wild bee abundance declines with urban warming, regardless of floral density

Elsa Youngsteadt, April Hamblin & Steven Frank
As cities expand, conservation of beneficial insects is essential to maintaining robust urban ecosystem services such as pollination. Urban warming alters insect physiology, fitness, and abundance, but the effect of urban warming on pollinator communities has not been investigated. We sampled bees at 18 sites encompassing an urban warming mosaic within Raleigh, NC, USA. We quantified habitat variables at all sites by measuring air temperature, percent impervious surface (on local and landscape scales), floral density,...

Phylogenomics and biogeography of Castanea (chestnut) and Hamamelis (witch-hazel): Choosing between RAD-seq and Hyb-Seq approaches

Wenbin Zhou &
Target enrichment and RAD-seq are well-established high throughput sequencing technologies that have been increasingly used for phylogenomic studies. Each method has its own pros and cons. The choice between them is a practical issue for plant systematists studying the evolutionary histories of biodiversity of rela­tively recent origins. However, few studies have compared the congruence and conflict between results from the two methods within the same group of organisms in plants. In this study, we employed...

Life-history stage and the population genetics of the tiger mosquito Aedes albopictus at a fine spatial scale

Emily Reed, Michael Reiskind & Martha Burford Reiskind
As a widespread vector of disease, the mosquito species Aedes albopictus Skuse (Diptera: Culicidae) is a high priority for both public health and invasive species research and management. Like all mosquitoes, A. albopictus has a complex life history with aquatic egg, larval, and pupal stages and a terrestrial adult stage. This requires targeted management strategies for each life stage, coordinated across time and space. Researchers use population genetics to inform control of A. albopictus. However,...

Intensive hunting fundamentally changes human-wildlife relationships

Arielle Parsons, Martin Wikelski, Brigitta Keeves Von Wolff, Jan Dodel & Roland Kays
Wildlife alter their behaviors in a trade-off between consuming food and fear of becoming food themselves. The risk allocation hypothesis posits that variation in the scale, intensity, and longevity of predation threats can influence the magnitude of antipredator behavioral responses. Hunting by humans represents a threat to wildlife thought to be perceived as similar to those of a top predator, although hunting intensity and duration vary widely around the world. Here we evaluate the effects...

Toward a Contingency Theory of Relating Management: Exploring Organization-Public Relationships (OPRs) in Conflicts

Yang Cheng & Allison Fisk
This paper presents the theoretical rationale for a contingency theory of relating management. Thepurpose of building such a contingency approach is to assist organizations in assessing and managing the dynamics of relationships with their external andinternal publics when conflicts arise. Through integrating interdisciplinary literature from public relations and conflict management, this theoretical framework argues that contingent organization-public relationships (COPRs) inthe conflict management process are highly dynamic and complex. COPRs influence relationship qualities and depend on...

Parasites, niche modification and the host microbiome: A field survey of multiple parasites

Kayleigh R. O'Keeffe, Fletcher W. Halliday, Corbin D. Jones, Ignazio Carbone & Charles E. Mitchell
Parasites can affect and be affected by the host's microbiome, with consequences for host susceptibility, parasite transmission, and host and parasite fitness. Yet, two aspects of the relationship between parasite infection and host microbiota remain little understood: the nature of the relationship under field conditions, and how the relationship varies among parasites. To overcome these limitations, we performed a field survey of the within-leaf fungal community in a tall fescue population. We investigated how diversity...

Resolving the phylogenetic relationship among recently diverged members of the rockfish subgenus Sebastosomus

Martha Burford Reiskind, Emma Wallace, Emily Reed & Andres Aguilar
Rapid speciation is an important aspect of adaptive radiations, but can obfuscate phylogenetic relationships among taxa. For recent radiations, there are challenges to reconstructing the relationships among the species due to often shorter branch lengths. Resolution of these relationships is further confounded when studies only use a few genetic markers. Double digest restriction-site associated DNA sequencing (ddRADseq) is a method of next generation sequencing that identifies many single nucleotide polymorphisms (SNPs) throughout the genome. This...

Data from: Seed fate in ant-mediated dispersal: Seed dispersal effectiveness in the Ectatomma ruidum (Formicidae) - Zanthoyxlum ekmanii (Rutaceae) system

Selina A. Ruzi & Andrew V. Suarez.
Plants are often dispersal limited relying on passive or active agents to find suitable microhabitats for germination. Seeds of pioneer tree species, for example, require light gaps for growth but have short median dispersal distances and often do not provide a food reward to encourage animal dispersal. Zanthoxylum ekmanii seeds are frequently moved by ants but evaluating the effectiveness of ant-mediated seed removal requires knowledge of the species moving the seeds, how far they are...

Consuming sunflower pollen reduced pathogen infection but did not alter measures of immunity in bumble bees

Alison Fowler, Ben Sadd, Toby Bassingthwaite, Rebecca Irwin & Lynn Adler
Certain diets can benefit bee health by reducing pathogens, but the mechanism(s) driving these medicinal effects are largely unexplored. Recent research found that sunflower (Helianthus annuus) pollen reduces the gut pathogen Crithidia bombi in the common eastern bumble bee (Bombus impatiens). Here, we tested the effects of sunflower pollen and infection on two bee immune metrics to determine if sunflower pollen diet drives changes in host immunity that can explain this medicinal effect. Bees were...

Diet nutritional condition affects tergal gland secretion and courtship success of male cockroaches

Samantha McPherson, Ayako Wada-Katsumata, Eduardo Hatano, Jules Silverman & Coby Schal
An integral part of the courtship sequence of the German cockroach (Blattella germanica) involves the male raising his wings to expose tergal glands on his dorsum. When a female cockroach feeds on the secretion of these glands, she is optimally positioned for mating. Core chemical components have been identified, but the effect of male diet on the tergal gland secretion remains unexplored. After validating the pivotal role of tergal feeding in mating, we starved or...

Food for thought: Barro Colorado Island frugivore home range summaries

Shauhin Alavi, Roland Kays, Ben Hirsch, Rasmus Havmøller, Damien Caillaud & Margaret Crofoot
This dataset consists of home-range area summaries of four species of frugivores on Barro Colorado Island, Panama, including 12 kinkajou (Potos flavus), 16 white-nosed coati (Nasua narica), 8 white-faced capuchin monkey (Cebus capucinus), and 8 spider monkey (Ateles geoffroyi). Summaries include effective sample sizes (DOF) as well as parameter estimates (in hectares) including upper and lower confidence intervals. Metadata for each individual are provided including their indivdual ID and species ID. The summaries of the...

Data: Rapid evolution of an adaptive taste polymorphism disrupts courtship behavior

Ayako Wada-Katsumata, Eduardo Hatano, Samantha McPherson, Jules Silverman & Coby Schal
The evolution of adaptive behavior often requires changes in sensory systems. However, rapid adaptive changes in sensory traits can adversely affect other fitness-related behaviors. In the German cockroach, a gustatory polymorphism, ‘glucose-aversion (GA)’, supports greater survivorship under selection with glucose-containing insecticide baits and promotes the evolution of behavioral resistance. Yet, sugars are prominent components of the male’s nuptial gift and play an essential role in courtship. Behavioral and chemical analyses revealed that the saliva of...

Phylogenomics and biogeography of Torreya (Taxaceae) – Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD-seq

Wenbin Zhou, AJ Harris &
Restriction site-associated DNA sequencing (RAD-seq) enables obtaining thousands of genetic markers for phylogenomic studies. However, RAD-seq data are subject to allele dropout (ADO) due to polymorphisms at enzyme cutting sites. We developed a new pipeline, RADADOR, to mitigate the ADO in outgroups by recovering missing loci from previously published transcriptomes in our study of a gymnosperm genus Torreya. Using the supplemented RAD-seq data in combination with plastome and mitochondrial gene sequences, morphology, and fossil records,...

Water stages in a tidal marsh measured using images, visually and automatically, along with stages measured using pressure transducer and Doppler sensors

François Birgand
This data was acquired to evaluate the performance of an image based system to measure water stages in streams and rivers. It contains measurements performed visually and stored (NR_Visual_Data_120201_120724.csv) It contains the measurements performed automatically by the system studied corresponding to those done visually (NR_Gaugecam_Data_120201_120724.csv) It contains the measurements done automatically (GC) and those measured by ISCO, HOBO, and Sontek instruments (NR-GC-vs-ISCO.csv)

Data From: Fixed depth Hamiltonian simulation via Cartan decomposition

Efekan Kökcü, Thomas Steckmann, Yan Wang, James K. Freericks, Eugene F. Dumitrescu & Alexander F. Kemper
Simulating quantum dynamics on classical computers is challenging for large systems due to the significant memory requirements. Simulation on quantum computers is a promising alternative, but fully optimizing quantum circuits to minimize limited quantum resources remains an open problem. We tackle this problem presenting a constructive algorithm, based on Cartan decomposition of the Lie algebra generated by the Hamiltonian, that generates quantum circuits with time-independent depth. We highlight our algorithm for special classes of models,...

Data from: Optimal mating of Pinus taeda L. under different scenarios using differential evolution algorithm

Khushi Goda & Fikret Isik
A newly developed software, AgMate, was used to perform optimized mating for monoecious Pinus taeda L. breeding. Using a computational optimization procedure called differential evolution (DE), AgMate was applied under different breeding population sizes scenarios (50, 100, 150, 200, 250) and candidate contribution scenarios (max use of each candidate was set to 1 or 8), to assess its efficiency in maximizing the genetic gain while controlling inbreeding. Real pedigree data set from North Carolina State...

Data for: Effects of nutrient heterogeneity on root foraging and plant growth at the individual and community level

Peng Wang, Pu Mou, Lingyan Hu & Shuijin Hu
Plants can respond to heterogeneous nutrient distribution through selective root placement to enhance nutrient uptake. It is believed that nutrient heterogeneity can better promote plant growth than homogeneous nutrient distribution, but comprehensive analyses are relatively few. We meta-analyzed the data from 131 comparative studies and synthesized the effects of nutrient heterogeneity on root foraging and plant growth, and examined the roles of patch scale and contrast. Plant responses to nutrient heterogeneity was phylogenetically conserved, and...

A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component

Matthew T. Webster, Matthew J. Christmas, Julia C. Jones, Anna Olsson, Ola Wallerman, Ignas Bunikis, Marcin Kierczak, Kaitlyn M. Whitley, Isabel Sullivan, Jennifer C. Geib & Nicole E. Miller‐Struttmann
Over the last six decades, populations of the bumblebees Bombus sylvicola and Bombus balteatus in Colorado have experienced decreases in tongue length, a trait important for plant-pollinator mutualisms. It has been hypothesized that this observation reflects selection resulting from shifts in floral composition under climate change. Here we used morphometrics and population genomics to determine whether morphological change is ongoing, investigate the genetic basis of morphological variation, and analyse population structure in these populations. We...

CAREER: Design and Application of 2-Metallated Benzimidazoles as Robust Bifunctional Complexes for Sustainable Catalysis at the ppm Level

Vincent Lindsay
Transition metal-catalyzed cross-coupling reactions and related processes are among the most important transformations for the construction of organic compounds. While a number of advances have been made in terms of the scope of accessible products, significant challenges remain with regards to the sustainability of these processes, especially in palladium catalysis. This work proposes the design, synthesis and application of benzimidazolyl-metal complexes as a novel template in bifunctional catalysis, where a Lewis basic and nucleophilic N-functionality...

Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity

Genevieve Hoopes, Xiaoxi Meng, John P. Hamilton, Sai Reddy Achakkagari, Fernanda De Alves Freitas Guesdes, Marie E. Bolger, Joseph J. Coombs, Danny Esselink, Natalie R. Kaiser, Linda Kodde, Maria Kyriakidou, Brian Lavrijssen, Natascha Van Lieshout, Rachel Shereda, Heather K. Tuttle, Brieanne Vaillancourt, Joshua C. Wood, Jan M. De Boer, Nolan Bornowski, Peter Bourke, David Douches, Herman J. Van Eck, Dave Ellis, Max J. Feldman, Kyle M. Gardner … & Richard Finkers
Hoopes G., Meng X., Hamilton J.P., Achakkagari S.R., de Alves Freitas Guesdes F., Bolger M.E., Coombs J.J., Esselink D., Kaiser N.R., Kodde L., Kyriakidou M., Lavrijssen B., van Lieshout N., Shereda R., Tuttle H.K., Vaillancourt B., Wood J.C., de Boer J.M., Bornowski N., Bourke P., Douches D., van Eck H.J., Ellis D., Feldman M.J., Gardner K.M., Hopman J.C.P., Jiang J., De Jong W.S., Kuhl J.C., Novy R.G., Oome S., Sathuvalli V., Tan E.H., Ursum R.A.,...

Data from: Estimating bee abundance: Can mark-recapture methods validate common sampling protocols?

Emma Briggs, Christopher Baranski, Olivia Münzer Schaetz, Gabriela Garrison, Jaime Collazo & Elsa Youngsteadt
Wild bees can be essential pollinators in natural, agricultural, and urban systems, but populations of some species have declined. Efforts to assess the status of wild bees are hindered by uncertainty in common sampling methods, such as pan traps and aerial netting, which may or may not provide a valid index of abundance across species and habitats. Mark-recapture methods are a common and effective means of estimating population size, widely used in vertebrates but rarely...

Registration Year

  • 2022

Resource Types

  • Dataset
  • Audiovisual
  • Journal Article
  • Output Management Plan
  • Text


  • North Carolina State University
  • University of Minnesota
  • University of Florida
  • University of Massachusetts Amherst
  • Max Planck Institute of Animal Behavior
  • California Academy of Sciences
  • University of California, Riverside
  • Harvard University
  • Pennsylvania State University
  • Helmholtz Centre for Environmental Research