19 Works

Differential effects of nematode infection on pollinating and non-pollinating fig wasps: can shared antagonism provide net benefits to a mutualism?

Justin Van Goor, Finn Piatscheck, Derek Houston & John Nason
1. Species pairs that form mutualistic associations are also components of broader organismal community networks. These network-level associations have shaped the evolution of individual mutualisms through interspecific interactions ranging from secondarily mutualistic to intensely antagonistic. Our understanding of this complex context remains limited because characterizing the impacts of species interacting with focal mutualists is often difficult. How is the fitness of mutualists impacted by the co-occurring interactive network of community associates? 2. We investigate this...

Performance and refinement of nitrogen fertilization tools

Curtis Ransom, Jason Clark, Gregory Bean, Christopher Bandura, Matthew Shafer, Newell Kitchen, James Camberato, Paul Carter, Richard Ferguson, Fabián Fernández, David Franzen, Carrie Laboski, David Myers, Emerson Nafziger & John Sawyer
Improving corn (Zea mays L.) N management is pertinent to economic and environmental objectives. However, there are limited comprehensive data sources to develop and test N fertilizer decision aid tools across a wide geographic range of soil and weather scenarios. Therefore, a public-industry partnership was formed to conduct standardized corn N rate response field studies throughout the U.S. Midwest. This research was conducted using a standardized protocol at 49 site-years across eight states over the...


Carolyn Lawrence-Dill
This dataset generated by GOMAP is a high-coverage and reproducible functional annotation set based on Gene Ontology (GO) term assignments that covers all gene models in the NCBI Criollo_cocoa_genome_V2 genome that was made available in the July of 2016: https://www.ncbi.nlm.nih.gov/assembly/GCF_000208745.1/ with a median of 10 annotations per gene model with 99.65% coverage. This dataset was created in March of 2021.

Data and scripts for: Genetic dissection of seasonal vegetation index dynamics in maize through aerial based high-throughput phenotyping

Jinyu Wang, Guo Guo, Tingting Guo, Matthew Dzievit, Xiaoqing Xiaoqing, Peng Liu, Kevin Price & Jianming Yu
Plant phenotyping under field conditions plays an important role in agricultural research. Efficient and accurate high-throughput phenotyping strategies enable a better connection between genotype and phenotype. Unmanned aerial vehicle-based high-throughput phenotyping platforms (UAV-HTPPs) provide novel opportunities for large-scale proximal measurement of plant traits with high efficiency, high resolution, and low cost. The objective of this study was to use time series normalized difference vegetation index (NDVI) extracted from UAV-based multispectral imagery to characterize its pattern...

Nitrogen budget data

Tan Zou, Xin Zhang, Luis Lassaletta, Nathaniel Mueller, Francesco Tubiello, Matthew Lisk, Chaoqun Lu, Richard Conant, Christopher Dorich, James Gerber, Hanqin Tian, Tom Bruulsema, Tai Maaz, Kazuya Nishina, Benjamin Bodirsky, Alexander Popp, Lex Bouwman, Arthur Beusen, Jinfeng Chang, Petr Havlík, David Leclère, Josep Canadell, Robert Jackson, Patrick Heffer, Nathan Wanner … & Eric Davidson
Input-output estimates of nitrogen (N) on cropland are essential for improving N management and better understanding the global N cycle. Here, we compare 13 N budget datasets covering 115 countries and regions over 1961-2015. Though most datasets showed similar spatiotemporal patterns, some annual estimates varied widely among them, resulting in large ranges and uncertainty. In 2010, global medians (in Tg N yr-1) and associated min-max ranges were 73 (64-84) for global harvested crop N; 161...

Correcting parentage relationships in the endangered California condor: Improving mean kinship estimates for conservation management

Brigid M. Moran, Steven M. Thomas, Jessica M. Judson, Asako Navarro, Heidi Davis, Lindsay Sidak-Loftis, Marisa Korody, Michael Mace, Katherine Ralls, Taylor Callicrate, Oliver A. Ryder, Leona G. Chemnick & Cynthia C. Steiner
Maintaining the existing biodiversity of endangered species is a goal of conservation management programs, and a major component of many collaborative efforts undertaken by zoos, field biologists, and conservation scientists. Over the past three decades, the San Diego Zoo has performed long-term genetic studies in support of the recovery program for the critically endangered California condor (Gymnogyps californianus). This work has included sex determination of hatchlings and parentage confirmation using microsatellite genotyping. This paper describes...

Dual infection by respiratory syncytial virus and Streptococcus pneumoniae in an experimental lamb model

David Verhoeven
Respiratory syncytial virus (RSV) is the primary cause of viral bronchiolitis resulting in hospitalization and a frequent cause of secondary respiratory bacterial infection, especially by Streptococcus pneumoniae (Spn) in infants. While murine studies have demonstrated enhanced morbidity during a viral/bacterial co-infection, human meta-studies have conflicting results. Moreover, little knowledge about the pathogenesis of emerging Spn serotype 22F, especially the co-pathologies between RSV and Spn, is known. Here, colostrum-deprived neonate lambs were divided into four groups....

Blueprint for phasing and assembling the genomes of heterozygous polyploids: Application to the octoploid genome of strawberry

Michael Hardigan, Mitchell Feldmann, Randi Famula, Michaela Vachev, Mary Madera, Philipp Zerbe, Kristin Mars, Paul Peluso, David Rank, Shujun Ou, Christopher Saski, Charlotte Acharya, Glenn Cole, Alan Yocca, Patrick Edger & Steven Knapp
The challenge of allelic diversity for assembling haplotypes is exemplified in polyploid genomes containing homoeologous chromosomes of identical ancestry, and significant homologous variation within their ancestral subgenomes. Cultivated strawberry (Fragaria × ananassa) and its progenitors are outbred octoploids in which up to eight homologous and homoeologous alleles are preserved. This introduces significant risk of haplotype collapse, switching, and chimeric fusions during assembly. Using third generation HiFi sequences from PacBio, we assembled the genome of the...

Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus

Kevin Bird, Chad Niederhuth, Shujun Ou, Malia Gehan, J. Chris Pires, Zhiyong Xiong, Robert VanBuren & Patrick Edger
Interspecific hybridization and allopolyploidization merge evolutionarily distinct parental genomes (subgenomes) into a single nucleus. A frequent observation is that one subgenome is "dominant” over the other subgenome, having a greater number of retained genes and being more highly expressed. Which subgenome becomes dominantly expressed in allopolyploids remains poorly understood. Here we “replayed the evolutionary tape” with six isogenic resynthesized Brassica napus (rapeseed) allopolyploid lines and investigated subgenome dominance patterns over the first ten generations post...

Genetic tracking of density‐dependent adult recruitment: A case study in a subtropical oak

Xin Tong, John D. Nason, Yuan‐Yuan Ding & Xiao-Yong Chen
Density-dependent recruitment is fundamental to understanding species diversity and community dynamics in plants. Although there is compelling evidence that seeds and seedlings die from conspecific negative density dependence (CNDD) as predicted by the Janzen–Connell hypothesis, characterizing adult recruitment remains a challenge for long-living trees. Previous studies have used the decrease of fine-scale spatial genetic structure (FSGS) across life stages to indicate CNDD; however, this has not been tested rigorously. We addressed these challenges by integrating...

Data from: Asexuality associated with marked genomic expansion of tandemly repeated rRNA and histone genes

Kyle McElroy
How does asexual reproduction influence genome evolution? While is it clear that genomic structural variation is common and important in natural populations, we know very little about how one of the most fundamental of eukaryotic traits - mode of genomic inheritance - influences genome structure. We address this question with the New Zealand freshwater snail Potamopyrgus antipodarum, which features multiple, separately derived obligately asexual lineages that coexist and compete with otherwise similar sexual lineages. We...

Genomic variation within the maize Stiff Stalk heterotic germplasm pool

Nolan Bornowski, Kathryn J. Michel, John P. Hamilton, Shujun Ou, Arun S. Seetharam, Jerry Jenkins, Jane Grimwood, Chris Plott, Shengqiang Shu, Jayson Talag, Megan Kennedy, Hope Hundley, Vasanth R. Singan, Kerrie Barry, Chris Daum, Yuko Yoshinaga, Jeremy Schmutz, Candice N. Hirsch, Matthew B. Hufford, Natalia De Leon, Shawn M. Kaeppler & C. Robin Buell
The Stiff Stalk heterotic group is an important source of inbreds used in U.S. commercial hybrid production. Founder inbreds B14, B37, B73, and to a lesser extent B84, are found in the pedigrees of a majority of commercial seed parent inbred lines. We created high-quality genome assemblies of B84 and four ex-Plant Variety Protection lines LH145 representing B14, NKH8431 of mixed descent, PHB47 representing B37, and PHJ40 which is a Pioneer Hi-Bred early Stiff Stalk...

Evolutionary allometry of sexual dimorphism of jumping performance in anurans

Bryan Juarez & Dean Adams
Sexual dimorphism is a common feature in animals, yet the degree of sexual dimorphism is not constant across taxa. Sometimes the magnitude of sexual dimorphism varies systematically with body size, resulting in evolutionary allometry of sexual dimorphism. While such patterns are commonly investigated for traits such as overall size, allometric variation in sexual dimorphism of other traits remains underexplored. Here, we characterize the evolutionary allometry of sexual dimorphism in a functional phenotypic trait (jumping performance)...

Tree species of wet tropical forests differ in their tissue biochemistry and effects on soil carbon dynamics

Ann Russell, Rachel Marek & Daniel Olk
Given the hypothesized effects on soil organic matter (SOM) of polyphenols in plant tissues, differences among tree species in their biochemical composition could influence the turnover and accrual of SOM in various ways. The extent to which the biochemical composition of leaf and fine-root tissues differ among tropical tree species, and the effects on soil dynamics, are largely undocumented, however. We used cupric oxide analyses of plant tissues and soil in long-term, replicated, mono-dominant 15-yr-old...

White Sands desert lizard thermal data

Alex Gunderson, Eric Riddell, Michael Sears & Erica Bree Rosenblum
Traits often contribute to multiple functions, complicating our understanding of the selective pressures that influence trait evolution. In the Chihuahuan Desert, predation is thought to be the primary driver of cryptic light coloration in three White Sands lizard species relative to the darker coloration of populations on adjacent dark soils. However, coloration also influences radiation absorption and thus animal body temperatures. We combined comparative physiological experiments and biophysical models to test for thermal consequences of...

Balancing crop and ecosystem service production in the U.S. Corn Belt through spatially targeted conservation

Ellen Audia
This master's thesis tests and provides data and methodologies for spatially targeting conservation in the Corn Belt region of the U.S.

Mechanochemical exfoliation of graphite

Nicole Hashemi
A facile method to produce few-layer graphene (FLG) nanosheets is developed using protein-assisted mechanical exfoliation. The predominant shear forces that are generated in a planetary ball mill facilitates exfoliation of graphene layers from graphite flakes. The process employs a commonly known protein, Bovine Serum Albumin (BSA), which not only acts as an effective exfoliation agent but also provide stability by preventing restacking of the graphene layers. The latter is demonstrated by the excellent long-term dispersibility...

Resource limitation, intragroup aggression, and brain neuropeptide expression in a social wasp

Alexander Walton & Amy Toth
1. Nourishment can have profound effects on social behavior, including aggressive interactions between individuals. However, how nutritional resource availability and limitation affects intraspecific aggression remains somewhat contested. The prevailing theoretical and empirical understanding is that when nutritional resources are limited, inter-individual competition and aggression will increase. However, findings from several social animals suggest that limited nutrition can lead to increased cooperation, including by a reduction in inter-individual aggression. 2. We suggest that in social insect...

Online Appendix and Cetacean Datasets for: The Occurrence Birth-Death Process for combined-evidence analysis in macroevolution and epidemiology

Jérémy Andréoletti, Antoine Zwaans, Rachel Warnock, Gabriel Aguirre-Fernández, Joëlle Barido-Sottani, Ankit Gupta, Tanja Stadler & Marc Manceau
Phylodynamic models generally aim at jointly inferring phylogenetic relationships, model parameters, and more recently, the number of lineages through time, based on molecular sequence data. In the fields of epidemiology and macroevolution these models can be used to estimate, respectively, the past number of infected individuals (prevalence) or the past number of species (paleodiversity) through time. Recent years have seen the development of “total-evidence” analyses, which combine molecular and morphological data from extant and past...

Registration Year

  • 2021

Resource Types

  • Dataset
  • Output Management Plan


  • Iowa State University
  • University of Minnesota
  • Michigan State University
  • University of Wisconsin-Madison
  • Agricultural Research Service
  • Clemson University
  • Donald Danforth Plant Science Center
  • Stanford University
  • University of Erlangen-Nuremberg
  • Pacific Biosciences (United States)