Find research datasets worth reusing

DNA-HDXMS_XchangeDB: A dataset of Hydrogen-Deuterium eXchange native Mass Spectrometry experiments on DNA oligonucleotides

The DNA-HDXMS_XchangeDB dataset contains HDX/native MS exchange kinetics and metadata of a reference set of DNA oligonucleotides.

Distribution of functionally distinct native and non-indigenous species within marine urban habitats

This data file (.xls) is composed of 5 sheets: <ol> <li>The “Taxon labels”: Taxon code, full name, authority and status/type (Abiotic, Unassigned, Native, Cryptogenic, Non-Indigenous Species)</li> <li>The “Trait labels”: Trait modality and labels and correspondences.</li> <li>The “Taxon-by-Trait matrix”: Fuzzy coded scores for each trait modality and taxon</li> <li>The “Taxon-by-sample matrix”: Abundance data of retained taxa in samples</li> <li>The “Sample labels and description”: Site and experimental factors (Habitat, Age, Experimental Unit, Replicate, nested within site) corresponding to each sample.</li> </ol> Sheets 4 and 5 are extracted from a published dataset, which cannot be shared at this stage of revision without revealing the name of several of the manuscript authors. This is done in respect with the journal guidelines about data storage.

Distribution of functionally distinct native and non-indigenous species within marine urban habitats

opencc-zeroMar 2023View details →

US National Native Bee Monitoring RCN Data Management Workshop: Public Domain Videos

The US National Native Bee Monitoring Research Coordination Network (RCN) held a two-day workshop on data management best practices for native bee inventory, survey, and monitoring data on March 28 and 30, 2023. Videos in this data set were played at the workshop. These videos are released into the public domain. This data set includes the following videos: <ul> <li>Ecological Metadata Standards to Enable Data Reuse by Julien Brun</li> <li>Useful Photo Management for Bee Species by Sam Droege</li> <li>Trait Data Models and Vocabulary by Jen Hammock</li> <li>Symbiota: open-source community portals for insect data management by Andrew Johnston</li> <li>Moving data from the field to the world by Jonathan Koch</li> <li>Exploring data using Discover Life by Clare Maffei</li> <li>USDA Data Sharing Policies and Opportunities by Cynthia Sims Parr</li> <li>Why Share Species Interaction Data? by Jorrit H. Poelen</li> <li>Big-Bee: Sharing Bee Interactions & Traits by Katja C. Seltmann</li> <li>Let’s talk about data by Katja C. Seltmann</li> <li>Responsible use of museum specimens & their data by Erika M. Tucker</li> </ul>

US National Native Bee Monitoring RCN Data Management Workshop: CC BY Videos

The US National Native Bee Monitoring Research Coordination Network (RCN) held a two-day workshop on data management best practices for native bee inventory, survey, and monitoring data on March 28 and 30, 2023. Videos in this data set were played at the workshop. These videos are released with a CC BY license. Please cite the presenter(s) of the video(s) you use. This data set includes the following videos: <ul> <li>The ABeeCs of Data Attribution: Please use your magic words by David Bloom</li> <li>Darwin Core Geography: How to make your locality data complete and accurate by David Bloom</li> <li>Best Practices for Managing Native Bee Molecular Data by Michael G. Branstetter</li> <li>A Trait Database for Bees by Elizabeth A. Crisfield</li> <li>Biotic interaction data and invasive species assessment by Quentin Groom</li> <li>OpenTraits Network (OTN) & TRY Plant Trait Database by Jens Kattge</li> <li>Semantics modeling of phenotypic trait data with ontologies by Diego S. Porto</li> <li>WorldFAIR: towards making plant-pollinator data FAIR by Maarten Trekels</li> </ul>

opencc-by-4.0Jun 2023View details →

Native North American Silene (L.) Occurrences Filtered from GBIF

This is a dataset including all Native Silene species accepted in taxonomic nomenclature and considered to inhabit the North American range. Data was downloaded using rgbif::occ_download and accessed from R via rgbif (https://github.com/ropensci/rgbif) on 2023-03-29. The original unfiltered GBIF occurrences can be download at https://doi.org/10.15468/dl.g89y2y, and https://api.gbif.org/v1/occurrence/download/request/0128277-230224095556074.zip. The data is filtered to have coordinates in North America, no geospatial issues, no spatial duplicates filtered to the infraspecific epithet, no coordinate uncertainty greater than 100000 meters, and no occurrences lying within 1km of a college or university. This dataset is incomplete as it does not include ALL observations that occur in North American countries as observations lacking a continent field of "north_america" in GBIF are not included.

openCustomMay 2025View details →

Data for "Pollinator Conservation Paradox: Exotic Forbs Support Native Pollinators Under Global Changes" by Nelson, Seabloom and Borer 2025, California grasslands, 2023-2024

Data for analysis on how plant provenance mediates plant-pollinator interaction responses to fertilization and herbivore exclusion, associated with Nelson, Seabloom, and Borer 2025. Data on pollinator visitation and floral abundance were collected in plots that received factorial experimental treatments of combined nitrogen, phosphorus and potassium with micronutrients by herbivore exclusion fencing in three California grasslands in 2023-2024.

openCC (other)Jun 2020View details →

Effects of experimental manipulation of light and nutrients on establishment of seedlings of native and invasive woody species in Long Island, NY, USA forests 2000 - 2003

While several studies on the process of invasion often focused on single factors or on the general explanation of ‘disturbance,' recent work has attempted to move towards a more mechanistic understanding of the factors that promote plant community invasion. Manipulative experiments provide a means for discerning causal relationships and interactive effects of environmental factors in promoting invasion. This dataset contains the results of multifactor manipulative experiments in forest communities, which compared factors influencing early seedling establishment for native and invasive woody plants. In an earlier study, we found that in Long Island, NY, invasion patterns are correlated with forest community type (pine barrens or hardwood), light availability, and soil N and Ca. Therefore, we conducted manipulative field experiments in two different years to determine the relative importance and interaction of experimental gaps and N and Ca addition in pine barrens and hardwood forests in promoting invasion. We used seedlings of seven common native and invasive species in the first experiment, and 16 native and invasive species paired phylogenetically in the second experiment. This was done in the years 2000 and 2003 respectively.

openCC (other)Dec 2020View details →

Native seedlings recorded on field plots with and without invasive buffel grass during the monsoon season of 2013 near Tucson, Arizona, USA

Although buffel grass (Cenchrus ciliaris) invasions on several continents have significant ecological impacts, little information is available on its effect on seedling emergence and establishment of native vegetation. In highly impacted areas of the Sonoran Desert of North America, perennial plants are particularly vulnerable during their seedling stage. We studied the impact of buffel grass on the emergence and early survival of native seedlings in a field experiment. We marked out 2m x 2m field plots at three locations near Tucson, Arizona, with and without buffel grass. We removed the buffel grass from half of those with the invasion, and censused and marked native perennial seedlings that emerged in each plot for ten weeks during July-September (monsoon season) of 2013. Emergence and survival of native perennials in the field were both significantly higher where mature buffel grass was removed or had never invaded than where it remained. Our results highlight the need for more manipulative studies of density to improve mechanistic understanding of population dynamics, and to forecast how populations and communities will respond in the long term to perturbations such as invasion.

openCC (other)Feb 2021View details →

Emerging fungal pathogen of an invasive grass: Implications for competition with native plant species

This data package includes data and code from an experiment testing the effects of a leaf spot fungal infection and competition from the invasive (to the U.S.) grass Microstegium vimineum on the performance of three native grass species: Dichanthelium clandestinum, Elymus virginicus, and Eragrostis spectabilis. The experiment was performed between June and September of 2019 in a greenhouse on the University of Florida campus in Gainesville, FL, USA. The leaf spot infection is caused by the fungal pathogen Bipolaris gigantea, which has recently emerged on populations of M. vimineum in the U.S. We tested the hypothesis that infection of B. gigantea would both directly and indirectly affect the native grass species by measuring the change in biomass of each species with and without pathogen inoculation (direct effects) and by measuring the effect of pathogen inoculation on M. vimineum competition through changes in native grass biomass across a density gradient of M. vimneum (indirect effects). The code includes statistical analyses and figures. The code was run using R (version 4.0.1).

openCustomJan 2020View details →

The effects of agricultural land-use history on non-native plant invasion in Bent Creek Experimental Forest in 2006

The researchers considered the effects of agricultural land-use legacies on the distribution of non-native invasive plants a century after abandonment in a watershed in western North Carolina, USA. The study was conducted at the Bent Creek Experimental Forest (BCEF) 15 km southwest of Asheville, North Carolina, USA, in the Pisgah National Forest. Forest sites that were previously in cultivation and abandoned ca. 1905 were compared with nearby reference sites that were never cultivated. The most common invasive plants were Celastrus orbiculatus Thunb., Microstegium vimineum Trin., and Lonicera japonica Thunb. (Kuhman, Pearson, and Turner 2011). Disentangling the cause–effect relationships between land-use history, the biotic community, and the abiotic template presents a challenge, but understanding the role of land-use legacies may provide important insights regarding the mechanisms underlying the establishment and spread of invasive plants in forest ecosystems (Kuhman, Pearson, and Turner 2011). A total of 86 plots were established at Bent Creek Experimental Forest during the summer of 2006. Specifically, the study was conducted between June and August 2006. Half of these were established in historic agricultural plots and half in reference plots that were not formerly used for agriculture (pasture or rowcrops) based on the 1941 Forest Service Report by William Nesbitt and the appended land-use history map (History of early settlement and land use on the Bent Creek Experimental Forest Buncombe County, NC. 1941). Historic agriculture and reference plots were paired based on similarities in topography and bedrock geology (typically in relatively close proximity to one another). Within sites, two plots were established, one adjacent to the road and one 50 m away from the road (labeled as "A" and "B", respectively, in the "Plot #").

openCustomJan 2020View details →

Does land-use history facilitate non-native plant invasion? A field experiment with Celastrus orbiculatus in the Bent Creek Experimental Forest in the southern Appalachians from 2008 to 2009

Although historic land use is often implicated in non-native plant invasion of forests, little is known about how land-use legacies might actually facilitate invasion. The researchers conducted a 2-year field seeding experiment in western North Carolina, USA, to compare germination and first-year seedling survival of Celastrus orbiculatus Thunb. in stands that had been cultivated and abandoned a century earlier and were dominated by tulip poplar (Liriodendron tulipifera L.), and in paired stands that had never been cultivated and were dominated by oaks (Quercus spp.). Experiments were conducted at five sites with paired tulip poplar and oak stands by varying litter mass (none, low, or high) and litter type (tulip poplar or oak).

openCC (other)Aug 2023View details →

Throw trap and electrofishing data collected during 1996–2022 from the Everglades, Florida, United States for the publication "Contrasting invasion histories and effects of three non-native fishes observed with long-term monitoring data"

This dataset was used to analyze the effects of three non-native fishes in the Florida Everglades for a publication in the journal Biological Invasions. The dataset incorporates plot-level mean densities (# of individuals per square meter) of common aquatic animals collected during 1996–2022 from 17 sites across three regions of the Everglades: Taylor Slough, Shark River Slough, and Water Conservation Area 3A. Prey species included are nine common small fishes and three common decapod species (two crayfish species and grass shrimp). The dataset includes throw trap data on three predator taxa: African Jewelfish (Hemichromis letourneuxi), Mayan Cichlids (Mayaheros uruphthalmus), and sunfishes (Lepomis spp.). Annual indices of mean wet season electrofishing catch-per-unit-effort of Asian Swamp Eels (Monopterus albus/javanesis), Mayan Cichlids, sunfishes, and the three other large 'top predator' fishes (Amia calva, Lepisosteus platyrhincus, Micropterus salmoides) are included for plots where electrofishing was performed from 1997-2021. Hydrologic measures used in analyses and R code used to conduct analyses are also included.

openCC0May 2023View details →

CSM09 Small mammal host-parasite sampling data associated with the Consume herbivore exclusion plots across two burned and native-grazed watersheds at Konza Prairie

Data set contains summaries of the number of individuals of each species of small mammal captured (relative abundance) on each trapping grid. Each record contains date, treatment, grid, trap station, species, specimen number, recapture status, specimen disposition, external body measurements (where applicable), reproductive information, and miscellaneous associated comments. These sampling records are based on nightly captures during one 4-night trapping period in fall (October concurrent with annual bison roundup activites) for each of 4 permanent trapping grids established on two fire/grazing treatments (two grids per treatment). These treatments are both grazed by native grazers (bison) and include one treatment burned annually (N1A) and one treatment burned every 4 years (N4B). In each treatment, sampling grids are arranged as 5 x 10 permanent stakes spaced 10m apart and labeled numerically between 1-50 for grid A and 51-100 for grid B. One grid per treatment (grid A) is sampled using capture-mark-release methods and the other grid in each treatment (grid B) is sampled using specimen removal and subsequent whole body processing and curation.

opencc-by-4.0Sep 2019View details →

Fig. 8 in Foraging behavior interactions between the invasive Nile Tilapia (Cichliformes: Cichlidae) and three large native predators

Fig. 8. Activity (inactive, swimming and avoidance) by the Nile Tilapia (mean ± SD) in the tanks with Pseudoplatystoma corruscans (white circles), Salminus brasiliensis (white squares) and Brycon orbignyanus (black triangles), for 0%, 50%, 100% and RD treatments. The three-way ANOVA for these data suggested interaction (P =0.029) among species, structural complexity and activity. The avoidance activity was not observed.

opencc-by-4.0May 2020View details →

Video S4 - Angling for Restored Native Cutthroat Trout

Video S4. Yellowstone cutthroat trout recovery results in large adults returning to tributaries of the upper Yellowstone River to spawn. Sustained gillnetting suppression of invasive lake trout is allowing for a recovery of native Yellowstone cutthroat trout. Although abundances remain below target levels, the relative weights (condition) of cutthroat trout have increased, large individuals (400+ mm) are more prevalent, and individual weights have more than doubled over the past four decades. Cutthroat trout from Yellowstone Lake make long-distance (> 40 km) spawning migrations upstream from Yellowstone National Park and into the remote headwaters of the upper Yellowstone River in the Bridger-Teton Wilderness, Wyoming, USA. Here, Liz Storer, Wyoming Storer Foundation and Jason Burckhardt, Wyoming Game and Fish Department are fly-fishing for the migratory cutthroat trout in Atlantic Creek during early July, 2019. The cutthroat trout transport lake-derived nutrients into these remote headwaters in U.S. Forest Service lands, highlighting the importance of large, unfragmented, highly protected watersheds such as those of Greater Yellowstone. Partnerships with the Storer Foundation, the Wyoming Game and Fish Department, and numerous others developed over the past 25 years were the driving force behind the initial recovery of cutthroat trout and restoration of this ecosystem.

opencc-by-4.0May 2020View details →

Video S1 - Native Cutthroat Trout and the Yellowstone Lake Ecosystem

Video S1. The Yellowstone Lake ecosystem in Yellowstone National Park. Following glacial recession, cutthroat trout evolved as the sole salmonid and dominant fish within Yellowstone Lake and its connected river network. Yellowstone Lake is a large aquatic system on the Yellowstone Plateau (2,357 m in elevation) with a highly protected watershed (> 3200 km2) located within Yellowstone National Park and the Bridger-Teton Wilderness of Wyoming, USA. Powerboat access is limited to only two locations, and most of the shoreline lies in protected (federally proposed) wilderness. Thermal structure of the lake is typically unstable with a weak and variable thermocline at a depth of 12–15 m during July-September. Surface water temperatures rarely exceed 18°C. The lake freezes over by late December and can remain frozen until late May or early June. In winter, ice about 1 m thick covers much of the lake except where shallow water covers active hot springs. During spring (May-July), cutthroat trout spawn in tributaries around Yellowstone Lake, where they are important prey for grizzly bears, black bears, river otters, and numerous avian predators.

opencc-by-sa-4.0May 2020View details →

Cryo-OrbiSIMS for 3D molecular imaging of a bacterial biofilm in its native state

We developed a method for analysis and imaging of biological samples in their native state, by combining a cryo-OrbiSIMS instrument with cryogenic sample handling and high-pressure freezing. By using this method, we did analysis and imaging of frozen-hydrated mature Pseudomonas aeruginosa biofilm, which allows the identification and map of quorum sensing signaling molecules, nucleobases and bacterial membrane molecules with high spatial-resolution and high mass-resolution.  Some of quorum sensing signaling molecules were further confirmed by MS/MS. By comparing the analysis of frozen-hydrated Pseudomonas aeruginosa biofilm with the freeze-dried one,  we dicover that signal intensity of all interesting molecules get enhanced in the frozen-hydrated state. Especially for polar molecules, such as amino acid, it could even achieve 10,000 fold increasing. Here, we provide the original OrbiSIMS data including MS and MS/MS spectra, depth profile and images of frozen-hydrated and freeze-dried Pseudomonas aeruginosa biofilm. The data could be open by using SurfaceLab Version 7.0 (ION-TOF, Germany).

opencc-by-4.0Jul 2015View details →

Figure 1 in Helminth fauna of the invasive American red-eared slider Trachemys scripta in eastern Spain: potential implications for the conservation of native terrapins

Figure 1. Sampling localities of the American red-eared slider, Trachemys scripta in eastern Spain. (A) Protected wetland 'Marjal de Peñíscola'; (B) 'Cabanes-Torreblanca' Natural Park; (C) Protected Landscape 'Desembocadura del Mijares'; (D) Protected wetland 'Marjal de Gandía'; (E) Site of Community Importance 'Marjal de La Safor'.