69 Works

Data from: Application of CRISPR/Cas9 to Tragopogon (Asteraceae), an evolutionary model for the study of polyploidy

Shengchen Shan, Evgeny V. Mavrodiev, Riqing Li, Zhengzhi Zhang, Bernard A. Hauser, Pamela S. Soltis, Douglas E. Soltis & Bing Yang
Tragopogon (Asteraceae) is an excellent natural system for studies of recent polyploidy. Development of an efficient CRISPR/Cas9-based genome editing platform in Tragopogon will facilitate novel studies of the genetic consequences of polyploidy. Here, we report our initial results of developing CRISPR/Cas9 in Tragopogon. We have established a feasible tissue culture and transformation protocol for Tragopogon. Through protoplast transient assays, use of the TragCRISPR system (i.e. the CRISPR/Cas9 system adapted for Tragopogon) was capable of introducing...

Data from: Origin and macroevolution of micro-moths on sunken Hawaiian islands

Chris A. Johns, Emmanuel F.A. Toussaint, Jesse W. Breinholt, Akito Y. Kawahara & Emmanuel F. A. Toussaint
The origins and evolution of Hawaiian biodiversity are a matter of controversy, and the mechanisms of lineage diversification for many organisms on this remote archipelago remain unclear. Here we focus on the poorly-known endemic leaf-mining moth genus Philodoria (Lepidoptera, Gracillariidae), whose species feed on a diversity of Hawaiian plant lineages, many of which are critically endangered. We use anchored hybrid enrichment to assemble the first phylogenomic dataset (507 loci) for any Hawaiian animal taxon. To...

Data from: Phenotypic and transcriptomic responses to salinity stress across genetically and geographically divergent Tigriopus californicus populations

Melissa B. De Biasse, Yasmeen Kawji, Morgan W. Kelly & Melissa B. DeBiasse
Species inhabiting the North American west coast intertidal must tolerate an extremely variable environment, with large fluctuations in both temperature and salinity. Uncovering the mechanisms for this tolerance is key to understanding species’ persistence. We tested for differences in salinity tolerance between populations of Tigriopus californicus copepods from locations in northern (Bodega Reserve) and southern (San Diego) California known to differ in temperature, precipitation, and humidity. We also tested for differences between populations in their...

Data from: Trait-specific processes of convergence and conservatism shape ecomorphological evolution in ground-dwelling squirrels

Bryan S. McLean, Kristofer M. Helgen, H. Thomas Goodwin & Joseph A. Cook
Our understanding of mechanisms operating over deep timescales to shape phenotypic diversity often hinges on linking variation in one or few trait(s) to specific evolutionary processes. When distinct processes are capable of similar phenotypic signatures, however, identifying these drivers is difficult. We explored ecomorphological evolution across a radiation of ground-dwelling squirrels whose history includes convergence and constraint, two processes that can yield similar signatures of standing phenotypic diversity. Using 4 ecologically-relevant trait datasets (body size,...

Data from: Evolutionary history of the angiosperm flora of China

Li-Min Lu, Ling-Feng Mao, Tuo Yang, Jian-Fei Ye, Bing Liu, Hong-Lei Li, Miao Sun, Joseph T. Miller, Sarah Mathews, Hai-Hua Hu, Yan-Ting Niu, Dan-Xiao Peng, You-Hua Chen, Stephen A. Smith, Min Chen, Kun-Li Xiang, Chi-Toan Le, Viet-Cuong Dang, An-Ming Lu, Pamela S. Soltis, Douglas E. Soltis, Jian-Hua Li & Zhi-Duan Chen
High species diversity may result from recent rapid speciation in a ‘cradle’ and/or the gradual accumulation and preservation of species over time in a ‘museum’1,2. China harbours nearly 10% of angiosperm species worldwide and has long been considered as both a museum, owing to the presence of many species with hypothesized ancient origins3,4, and a cradle, as many lineages have originated as recent topographic changes and climatic shifts—such as the formation of the Qinghai–Tibetan Plateau...

Data from: Stream community richness predicts apex predator occupancy dynamics in riparian systems

Angela M. Holland, Eric M. Schauber, Clayton K. Nielsen & Eric C. Hellgren
Streams and adjacent riparian habitats represent linked terrestrial and aquatic ecosystems that exchange materials and energy. Recognized relationships among apex predators and ecosystem biodiversity led us to hypothesize that these predators in riparian-stream systems were more likely to be found in sites with high stream quality, defined as increased ecosystem function and integrity. In our freshwater study system, river otter (Lontra canadensis) and mink (Neovison vison) play critical roles as apex predators. We used multi-season...

Data from: Head-to-head comparison of three experimental methods of quantifying competitive fitness in C. elegans

Timothy A. Crombie, Sayran Saber, Ayush Shekhar Saxena, Robyn Egan & Charles F. Baer
Organismal fitness is relevant in many contexts in biology. The most meaningful experimental measure of fitness is competitive fitness, when two or more entities (e.g., genotypes) are allowed to compete directly. In theory, competitive fitness is simple to measure: an experimental population is initiated with the different types in known proportions and allowed to evolve under experimental conditions to a predefined endpoint. In practice, there are several obstacles to obtaining robust estimates of competitive fitness...

Data from: The complete mitochondrial genome of the sea urchin, Echinometra sp. EZ

Remi N. Ketchum, Melissa B. DeBiasse, Joseph F. Ryan, John A. Burt & Adam M. Reitzel
The complete mitogenome of Echinometra sp. EZ has been described and fully annotated in this study. Cytochrome subunit one phylogenetic analysis of six Echinometra species confirms that our sample is E. sp. EZ. The mitogenome is 15,698 bp in length and contains 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a non-coding region with an identical organization to other Echinoidea. The E. sp. EZ mitogenome shared ~99.1% identity to the published Echinometra mathaei mitogenome, differing...

Data from: Predictors of alcohol responsiveness in dystonia

Johanna Junker, Valerie Brandt, Brian D. Berman, Marie Vidailhet, Emmanuel Roze, Anne Weissbach, Cynthia Comella, Irene A. Malaty, Joseph Jankovic, Mark S. LeDoux, Alfredo Berardelli, Richard Barbano, Stephen G. Reich, Joel S. Perlmutter, Hyder A. Jinnah & Norbert Brüggemann
Objective: To determine predictors of alcohol responsiveness in a large cohort of dystonia patients. Methods: 2159 participants with dystonia were prospectively enrolled in the cross-sectional Dystonia Coalition multicenter study. Patients with secondary, combined or confirmed genetic dystonia (total n=164) or unknown alcohol responsiveness (n= 737) were excluded. Patients answered a standardized questionnaire and were clinically examined using a standardized video protocol and the Burke-Fahn-Marsden Dystonia Rating Scale. Alcohol responsiveness was determined by patients’ self-report. Results:...

Data from: Parental and offspring larval diets interact to influence life history traits and dengue virus infection of offspring in Aedes aegypti

Kylie Zirbel, Bradley Eastmond & Barry W. Alto
The environmental conditions experienced by parents can influence offspring phenotype along with the conditions experienced by offspring. These parental effects are clear in organisms that display parental care and are less clear in other organisms. Here we consider effects of parental and offspring larval nutrition on offspring development time, survivorship, and infection with dengue virus in Aedes aegypti, the mosquito vector of dengue, chikungunya, yellow fever and Zika. Parents were raised on either high or...

Data from: The hidden cost of sexually selected traits: the metabolic expense of maintaining a sexually selected weapon

Ummat Somjee, H. Arthur Woods, Meghan Duell & Christine W. Miller
Sexually selected weapons are among the most exaggerated traits in nature. Theory frequently assumes a high cost of this exaggeration; yet, those costs are rarely measured. We know very little about the energetic resources required to maintain these traits at rest and the difference in energetic costs for the largest relative to the smallest individuals. Knowledge in this area is crucial; resting metabolic rate can account for 30-40% of daily energy expenditure in wild animals....

Data from: Body size shifts influence effects of increasing temperatures on ectotherm metabolism

Kristina Riemer, Kristina J. Anderson-Teixeira, Felisa A. Smith, David J. Harris, S.K. Morgan Ernest & S. K. Morgan Ernest
Aim: Warmer temperatures directly increase metabolic rates of ectotherms, but temperature also indirectly affects metabolic rates. Higher temperatures result in smaller body sizes and associated decreases in metabolic rates, and it remains unknown whether this indirect effect of temperature increase could mitigate the direct positive effect of temperature on metabolic rate. Here, we assess whether temperature‐induced shifts in body size are likely to offset the direct influence of temperature on metabolic rate. Location: Global. Time...

Data from: Integrative identification of incipient lineages in Heuchera longiflora (Saxifragaceae)

Ryan F. Folk, Julian C. Ginori, Douglas E. Soltis & Aaron J. Floden
Following on emerging understanding of the diversification process, many recent workers have considered infraspecific taxa as valuable for formally recognizing incompletely speciated entities. The distinction between a species and an infraspecific taxon represents a fundamentally subjective weighting of evidence, yet this points further to the need for an evidential basis for these decisions. We explore these concepts in Heuchera longiflora (Saxifragaceae), which is morphologically variable and has a disjunct range across several physiographic provinces in...

Data from: Genome-wide exon-capture approach identifies genetic variants of Norway spruce genes associated with susceptibility to Heterobasidion parviporum infection

Mukrimin Mukrimin, Andriy Kovalchuk, Leandro G. Neves, Emad H. A. Jaber, Matti Haapanen, Matias Kirst & Fred O. Asiegbu
Root and butt rot caused by members of the Heterobasidion annosum species complex is the most economically important disease of conifer trees in boreal forests. Wood decay in the infected trees dramatically decreases their value and causes considerable losses to forest owners. Trees vary in their susceptibility to Heterobasidion infection, but the genetic determinants underlying the variation in the susceptibility are not well-understood. We performed the identification of Norway spruce genes associated with the resistance...

Data from: Divergent rates of change between tree cover types in a tropical pastoral region

Bryan C. Tarbox, Carlita Fiestas & T. Trevor Caughlin
Context: Forest cover change analyses have revealed net forest gain in many tropical regions. While most analyses have focused solely on forest cover, trees outside forests are vital components of landscape integrity. Quantifying regional-scale patterns of tree cover change, including non-forest trees, could benefit forest and landscape restoration (FLR) efforts. Objectives: We analyzed tree cover change in Southwestern Panama to quantify: 1) patterns of change from 1998-2014, 2) differences in rates of change between forest...

Data from: Integrating encounter theory with decision analysis to evaluate collision risk and determine optimal protection zones for wildlife

Bradley J. Udell, Julien Martin, , Mathieu Bonneau, Holly Edwards, Timothy A. Gowan, Stacie K. Hardy, Eliezer Gurarie, Charles Calleson, Charles J. Deutsch, Robert J. Fletcher & Charles S. Calleson
1. Better understanding human-wildlife interactions and their links with management can help improve the design of wildlife protection zones. One important example is the problem of wildlife collisions with vehicles or human-built structures (e.g. power lines, wind farms). In fact, collisions between marine wildlife and watercraft are among the major threats faced by several endangered species of marine mammals. Natural resource managers are therefore interested in finding cost-effective solutions to mitigate these threats. 2. We...

Data Papers are Witness to Trusted Resources in Grey Literature: A Project Use Case

Dominic Farace, Jerry Frantzen & PhD Smith II
In 2011, GreyNet embarked on an Enhanced Publications Project with DANS, Data Archiving and Networked Services in an effort to circumvent the data versus document camps entrenched in grey literature communities. The results of that two year project served to incorporate in GreyNet’s workflow the acquisition, indexing, and linking of research data with their full-text and accompanying metadata. Recently, GreyNet discussed with a data management librarian from UFL, University of Florida a proposed follow-up project...

Data from: The future of cold-adapted plants in changing climates: Micranthes (Saxifragaceae) as a case study

Rebecca L. Stubbs, Douglas E. Soltis & Nico Cellinese
As a result of changing climates, research has shown species undergoing range contractions and/or northward and higher elevational movements. Here, we evaluate how the distribution of a group of cold-adapted plant species with similar evolutionary histories changes in response to warming climates. We selected 29 species of Micranthes (Saxifragaceae) representing the mountain and Arctic biomes of the northern hemisphere. For this analysis, 24,755 data points were input into ecological niche models to assess both present...

Data from: Genome-wide search for quantitative trait loci controlling important plant and flower traits in petunia using an interspecific recombinant inbred population of Petunia axillaris and Petunia exserta

Zhe Cao, Yufang Guo, Qian Yang, Yanhong He, Mohammed Fetouh, Ryan M. Warner, Zhanao Deng & Mohammed I. Fetouh
A major bottleneck in plant breeding has been the much limited genetic base and much reduced genetic diversity in domesticated, cultivated germplasm. Identification and utilization of favorable gene loci or alleles from wild or progenitor species can serve as an effective approach to increasing genetic diversity and breaking this bottleneck in plant breeding. This study was conducted to identify quantitative trait loci (QTL) in wild or progenitor petunia species that can be used to improve...

Data from: Museum specimens provide phylogenomic data to resolve relationships of sack-bearer moths (Lepidoptera, Mimallonoidea, Mimallonidae)

Ryan A. St Laurent, Chris A. Hamilton & Akito Y. Kawahara
Mimallonidae, the sack‐bearer moths, are a family of predominantly Neotropical moths containing nearly 300 described species. Mimallonidae feed on over 40 host plant families and are found in a variety of environments, but phylogenetic relationships of species within the family have never been investigated. We sequenced 515 loci using anchored hybrid enrichment target capture on ethanol‐preserved and dried museum specimens, with dates of collection ranging from 1985 to 2017. We sampled 47 species, representing 32...

Data from: Do an ecosystem engineer and environmental gradient act independently or in concert to shape juvenile plant communities? Tests with the leaf-cutter ant Atta laevigata in a Neotropical savanna

Alan N. Costa, Emilio M. Bruna & Heraldo L. Vasconcelos
Background. Ecosystem Engineers are species that transform habitats in ways that influence other species. While the impacts of many engineers have been well described, our understanding of how their impact varies along environmental gradients remains limited. Although disentangling the effects of gradients and engineers on biodiversity is complicated – the gradients themselves can be altered by engineers – doing so is necessary to advance conceptual and mathematical models of ecosystem engineering. We used leaf-cutter ants...

Data from: Community assembly of the ferns of Florida

Emily B. Sessa, Sally M. Chambers, Daijiang Li, Lauren Trotta, Lorena Endara, J. Gordon Burleigh & Benjamin Baiser
Premise of the study: Many ecological and evolutionary processes shape the assembly of organisms into local communities from a regional pool of species. We analyzed phylogenetic and functional diversity to understand community assembly of the ferns of Florida at two spatial scales. Methods: We built a phylogeny for 125 of the 141 species of ferns in Florida using five chloroplast markers. We calculated mean pairwise dissimilarity (MPD) and mean nearest taxon distance (MNTD) from phylogenetic...

Data from: Rituximab vs placebo induction prior to glatiramer acetate monotherapy in multiple sclerosis

Justin M. Honce, Kavita V. Nair, Stefan Sillau, Brooke Valdez, Augusto Miravalle, Enrique Alvarez, Teri L. Schreiner, John R. Corboy & Timothy L. Vollmer
Objective: To examine whether rituximab induction followed by glatiramer acetate (GA) monotherapy is more effective than GA alone for the treatment of relapsing MS with active disease. Methods: This was a single center, double-blind, placebo-controlled study(NCT01569451). Fifty-five participants were randomly assigned (1:1ratio) to either rituximab (R-GA) or placebo induction (P-GA), followed by all participants initiating GA therapy. Participants were followed up to 3-years. The primary endpoint was the number of participants with no evidence of...

Data from: Insights into the genetic basis of blueberry fruit-related traits using diploid and polyploid models in a GWAS context

Luis Felipe V. Ferrão, Juliana Benevenuto, Ivone De Bem Oliveira, Catherine Cellon, James Olmstead, Matias Kirst, , Patricio Munoz & Marcio F. R. Resende
Polyploidization is an ancient and recurrent process in plant evolution, impacting the diversification of natural populations and plant breeding strategies. Polyploidization occurs in many important crops; however, its effects on inheritance of many agronomic traits are still poorly understood compared with diploid species. Higher levels of allelic dosage or more complex interactions between alleles could affect the phenotype expression. Hence, the present study aimed to dissect the genetic basis of fruit-related traits in autotetraploid blueberries...

Data from: Estimating field capacity from volumetric soil water content time series using automated processing algorithms

Eban Z. Bean, Ray G. Huffaker & Kati W. Migliaccio
Vadose zone measurements of volumetric soil water content (θ) using soil moisture sensors (SMSs) have become more common due to advances in technology and reduction of costs. Soil moisture sensor data exhibit a characteristic cyclical pattern reflecting water flux dynamics into and out of the observed soil volume. Expert review of SMS datasets to distinguish valid from corrupt or incomplete soil water cycles is arguably the most precise method for determining field capacity (θFC) but...

Registration Year

  • 2018

Resource Types

  • Dataset
  • Text


  • University of Florida
  • University of Georgia
  • Michigan State University
  • University of Michigan-Ann Arbor
  • Florida Museum of Natural History
  • Max Planck Institute for Ornithology
  • University of Montana
  • University of Adelaide
  • Rice University
  • Stanford University