Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
178
datasets available to search
ShareScore release 0.9.0
Dataset results
178 results for “Florida Keys”
Orbicella faveolata and O. franksi coral metagenome assemblies from the Lower Florida Keys region of Florida, USA
<div> <p>The enclosed files include mostly <em>Orbicella faveolata</em> and three <em>Orbicella franksi</em> coral metagenome assemblies collected from the Lower Keys in Florida’s Coral Reef, USA. Metadata for the files is included in this repository. Apparently healthy coral tissue cores were collected between May 28 and June 21, 2021. The DNA was extracted from the host and associated microorganisms and sequenced in a paired-end 150 bp format on an Illumina NovaSeq. Trimming and quality filtering of DNA sequence reads proceeded, followed by host and photoendosymbiotic dinoflagellate DNA removal. The host-cleaned reads were assembled individually by coral sample into longer contigs using MegaHit v1.1.4. The “Assembly_Fastas” zipped file contains 41 metagenome assemblies from the individual <em>Orbicella faveolata</em> corals and 3 assemblies from the individual <em>Orbicella franksi </em>colonies for a total of 44 assemblies. In addition, these assemblies were annotated with eggnog-mapper v2.1.6 to generate both predicted gene regions and annotation output files. The “Predicted_Gene_Fastas” zipped file contains nucleotide fasta files of the predicted gene regions for all 44 coral metagenome assemblies. The fasta header of each gene includes the contig ID it originated from in the associated “Assembly_Fasta”. The “Predicted_Gene_Annotations” zipped file contains either .csv or .xlsx files with the eggnog-mapper-based annotations. These files contain a “query contig” that corresponds to the contig ID in the fasta header of the “Predicted_Gene_Fasta”. </p> <p>In addition to individual assemblies, a co-assembly was generated that included all 41 <em>Orbicella faveolata</em> coral samples. Prior to co-assembly, further removal of eukaryotic DNA proceeded by splitting the indiviudual assemblies into eukaryotic and prokaryotic content with the program EukRep v0.6.7, followed by mapping of the host-clean reads to the eukaryotic DNA to remove them. The eukaryote-clean reads from all 41 corals were input into MegaHit to generate a co-assembly. The co-assembly is included (FLK_OFAV_MG_coassembly_final.contigs.fa). Predicted genes from the co-assembly were generated with Prodigal v2.6.3 and the nucleotide fasta of the output is included in this repository (FLK_OFAV_MG_pred.fna). Like with the indiviudal assemblies, eggnog-mapper was used to generate annotations of the predicted genes from Prodigal (FLK_OFAV_MG.emapper.annotations.xlsx). Additionally, the abundance of each predicted gene was generated using Salmon to map the eukaryote-clean reads to the predicted genes. The number of reads (counts) for each gene across each coral sample were aggregated as integers into one table and included in this repository (FLK_OFAV_MG_pred_NumReads.tsv). </p> </div> <div> <p>These data were processed and generated by Julie Meyer’s Lab at the University of Florida, using funding from the Florida Department of Environmental Protection. </p> </div>
NOAA Monthly Mean Sea Level Summary Data for the Key West Water Level Station (NOAA/NOS Co-OPS ID 8724580), Florida, USA, January 1913 - ongoing
Monthly Mean Sea Level Summary Data for the Key West, Florida, Water Level Station (NOAA/NOS CO-OPS ID 8724580). Data is in meters relative to the STND-Key West Station Datum.
Evaporation Estimates for Long Key C-MAN Weather Station, Florida Bay (FCE) from July 1998 to May 2004
This file contains data from the National Data Buoy Office Coastal-Meteorological Automated Network (C-MAN) weather station near Long Key, in Florida Bay (LONF1, 24deg 50min 36sec N, 80deg 51min 42sec W). The time period is 1600 EST February 6, 2004 through 0700 EST May 28, 2004. The record is a combination of NDBO data (wind speed, air pressure, air temperature water temperature) and Harbor Branch data (relative humidity) needed to calculate evaporative water loss. The file is one of several from this location. Together, they can be used to estimate of hourly, daily, monthly, seasonal and annual evaporation rates. Calculations include hourly water loss and cumulative water loss. Times are Eastern Standard.
Radiation measurements at Key Largo Ranger Station, South Florida (FCE) for July 2001
Basic radiation data, including Infra-red canopy temperatures, collected as 1 minute averages from a 5 m tower at Key Largo Ranger Station, South Florida, near Everglades National Park.
Meteorological measurements at Key Largo Ranger Station, South Florida (FCE) for July 2001 to August 2001
Basic radiation data, including Infra-red canopy temperatures, collected as 1 minute averages from a 5 m tower at Key Largo Ranger Station, South Florida, near Everglades National Park.
Mangrove leaf physiological response to local climate at Key Largo, Watson River Chickee, Taylor Slough, and Little Rabbit Key, South Florida (FCE) from July 2001 to August 2001
Determine the red mangrove leaf physiological response to the local climate to understand the local controls on plant physiology. Data were collected in the Key Largo Ranger Station, Watson River Chickee and Taylor Slough research Sites, South Florida.
Rubisco limited photosynthesis rates of Red mangrove leaves at Key Largo, Watson River Chickee, Taylor Slough, and Little Rabbit Key, South Florida (FCE) from July 2001 to August 2001
Determine the Rubisco limited carboxylation rates of red mangrove ( species Rhizophora mangle) leaves. This information will be used to model carbon sequestration by Red mangroves.
Light limited carboxylation rates of Red mangrove leaves at Key Largo, Watson River Chickee, Taylor Slough, and Little Rabbit Key, South Florida (FCE) from July 2001 to August 2001
Our goal is to determine light limited carboxylation rates of red mangrove (specie sRhizophora mangle) leaves. This information will be used to model carbon sequestration by Red mangroves.
Gastropod Biomass and Densities found at Rabbit Key Basin, Florida Bay (FCE) from March 2000 to April 2001
Grazing gastropod biomass and shell morphology were measured from 1 m2 plots within Thalassia seagrass meadow in Rabbit Key Basin, Florida Bay, Everglades National Park.
Seagrass Epiphyte Accumulation: Epiphyte Loads on Thalassia testudinum in Rabbit Key Basin, Florida Bay (FCE) from March 2000 to April 2001
Total epiphyte and epiphyte chlorophyll-a loads and leaf nutrients were measured on Thalassia seagrass short-shoots from Rabbit Key Basin, Florida Bay.
Thalassia leaf morphology and productivity measurements from arbitrary plots located in a Thalassia seagrass meadow in Rabbit Key Basin, Florida Bay (FCE) from March 2000 to April 2001
Thalassia leaf morphology and productivity were measured from six arbitrary 200 cm2 plots within a Thalassia seagrass meadow in Rabbit Key Basin, Florida Bay.
Annual Water Quality in Everglades National Park, Florida Bay, West Florida Shelf, and Florida Keys National Marine Sanctuary, Florida, USA: 1994-2019
Annual (water year basis) geometric mean concentrations of total phosphorus (TP), soluble-reactive phosphorus (SRP), total nitrogen (TN), dissolved inorganic nitrogen (DIN; calculated as nitrate + nitrite + ammonia), chlorophyll-a (Chl-a), and total organic carbon (TOC) concentrations across Everglades National Park (ENP), Florida Keys National Marine Sanctuary (FKNMS), West Florida Shelf and Florida Bay. This dataset is composed of data from multiple sources including Florida Coastal Everglades, Florida International University Southeast Research Center (FIU SERC), South Florida Water Management District (SFWMD), and National Oceanic and Atmospheric Administration Atlantic Oceanographic and Meteorological Laboratory (NOAA AOML). All values reported less than the laboratory minimum detection limit (MDL) were set to one-half the MDL. Annual geometric mean concentrations were computed for monitoring locations with greater than five years of data and four samples per year with a minimum of one sample in the wet and dry seasons. This dataset was created to evaluate long-term spatial and temporal trends in nutrients, chlorophyll-a, and total organic carbon at the landscape scale relative to freshwater and marine ecosystems.
Non-continous meteorological data from Butternut Key Weather Tower, Florida Bay, Everglades National Park (FCE LTER), April 2001 through August 2013
The following abstract is from Price, R.M., Nuttle, W.K., Cosby, B.J., and Swart, P.K. 2007. Variation and Uncertainty in Evaporation from a Subtropical Estuary: Florida Bay, Estuaries and Coasts. 30(3): 497-506: Variation and uncertainty in estimated evaporation was determined over time and between two locations in Florida Bay, a subtropical estuary. Meteorological data were collected from September 2001 to August 2002 at Rabbit Key and Butternut Key within the Bay. Evaporation was estimated using both vapor flux and energy budget methods. The results were placed into a long-term context using 33 years of temperature and rainfall data collected in south Florida. Evaporation also was estimated from this long-term data using an empirical formula relating evaporation to clear sky solar radiation and air temperature. Evaporation estimates for the 12-mo period ranged from 144 to 175 cm yr21, depending on location and method, with an average of 163 cm yr21 (6 9%). Monthly values ranged from 9.2 to 18.5 cm, with the highest value observed in May, corresponding with the maximum in measured net radiation. Uncertainty estimates derived from measurement errors in the data were as much as 10%, and were large enough to obscure differences in evaporation between the two sites. Differences among all estimates for any month indicate the overall uncertainty in monthly evaporation, and ranged from 9% to 26%. Over a 33-yr period (1970 to 2002), estimated annual evaporation from Florida Bay ranged from 148 to 181 cm yr21, with an average of 166 cm yr21. Rainfall was consistently lower in Florida Bay than evaporation, with a long-term average of 106 cm yr21. Rainfall considered alone was uncorrelated with evaporation at both monthly and annual time scales; when the seasonal variation in clear sky radiation was also taken into account both net radiation and evaporation were significantly suppressed in months with high rainfall.
Mangrove soil phosphorus addition experiment from June 2013 to August 2013 at the mangrove peat soil mesocosms (FCE), Key Largo, Florida - Nutrients in Porewater, Soil and Roots
Sea levels in South Florida are conservatively predicted to rise by 0.60 m by 2060. The key mechanisms that maintain coastal peatland elevation against increasing sea level are organic matter accumulation via plant production and mineral sedimentation rates (Smoak et al. 2013). Although coastal mangrove soils are regularly inundated with seawater, little is know about the drivers of carbon sequestration (above or below ground) versus atmospheric efflux under different conditions of salinity and elevated phosphorus (P) associated with sea-level rise and storm surge. A recent study using mangrove peat soils found that seawater inundation reduced soil carbon efflux losses and salinity concentration had little effect on carbon retention or loss pathways. The next logical steps are to understand how plant-soil interactions affect above and below ground carbon processes, as well as how increases in P associated with storm surge from the Gulf of Mexico will influence physical, chemical and biological components of mangrove soils that are associated with above and belowground carbon processes. We will manipulate P in inundated peat soil mesocosms with disturbed and undisturbed red mangrove (Rhizophora mangle) seedlings to identify some of the fundamental mechanisms of soil elevation and carbon cycling given expected increases in seawater-based P availability in South Florida coastal mangroves.
Mangrove soil phosphorus addition experiment from July 2013 to August 2013 at the mangrove peat soil mesocosms (FCE), Key Largo, Florida - Nutrients in Surface Water and Aboveground Biomass
Sea levels in South Florida are conservatively predicted to rise by 0.60 m by 2060. The key mechanisms that maintain coastal peatland elevation against increasing sea level are organic matter accumulation via plant production and mineral sedimentation rates (Smoak et al. 2013). Although coastal mangrove soils are regularly inundated with seawater, little is know about the drivers of carbon sequestration (above or below ground) versus atmospheric efflux under different conditions of salinity and elevated phosphorus (P) associated with sea-level rise and storm surge. A recent study using mangrove peat soils found that seawater inundation reduced soil carbon efflux losses and salinity concentration had little effect on carbon retention or loss pathways. The next logical steps are to understand how plant-soil interactions affect above and below ground carbon processes, as well as how increases in P associated with storm surge from the Gulf of Mexico will influence physical, chemical and biological components of mangrove soils that are associated with above and belowground carbon processes. We will manipulate P in inundated peat soil mesocosms with disturbed and undisturbed red mangrove (Rhizophora mangle) seedlings to identify some of the fundamental mechanisms of soil elevation and carbon cycling given expected increases in seawater-based P availability in South Florida coastal mangroves.
Figures 2-6. Calusamyia hribari. 2 in A New Genus and Species of North American Robsonomyiini (Diptera: Sciaroidea: Keroplatidae: Macrocerinae) from the Florida Keys Edward I. Coher Emeritus Prof. Long Island Univ. 10203 Greentrail Drive N. Boynton Beach, FL 33436
Figures 2-6. Calusamyia hribari. 2) Wing. 3) Thorax, lateral. 4) Male terminalia, dorsal view. 5) Female terminalia, ventral view. 6) Female terminalia, lateral view.
Capturing local nuisance flooding events with HOBO pendant G data loggers in Key West, Florida US
<p>Flooding impacts social, economic, and landscape systems globally. Changing climate and growing coastal populations exacerbate the outcomes of environmental hazards. Due to the spatial variability in exposure and vulnerability, coastal flooding must be understood at high spatial and temporal resolutions. This paper presents a novel deployment technique using inexpensive accelerometers to measure local floods. The technique is tested in Key West, FL, USA using storm drains to deploy HOBO pendant G data loggers. The feasibility of the method is tested by a team of local stakeholders and researchers through four deployments between July 2019 – November 2021. All deployments resulted in 22 sensors successfully recording data, with 15 of these sensors recording flooding. Sensors captured an average of 13.58 inundation events causing the storm drains to be inundated on average 12.07% of the deployment time. Measured inundation events coincide with local National Oceanic and Atmospheric Administration (NOAA) water level measurements of high tides, which shows that high-tide inundation is captured by the accelerometers. Accelerometers are easy to deploy and accurately capture the duration of local flooding. Access to an effective and inexpensive sensor for measuring flood events can increase opportunities to measure local-scale hazards and collect important information with participation by interested parties (e.g., local governments, homeowners, schools etc.). The ease of use and successful recording of loggers can give communities access to flooding data, and in turn, increase their capacity to make data-informed decisions surrounding sea level rise adaptation. </p>
Balancing carnivore conservation and sustainable hunting of a key prey species: a case study on the Florida panther and white-tailed deer
<p>1. Large carnivore restoration programs are often promoted as capable of providing ecosystem services. However, these programs rarely measure effects of successful restoration on other economically and ecologically important species. In South Florida, while the endangered Florida panther (Puma concolor coryi) population has increased in recent years due to conservation efforts, the population of its main prey, the white-tailed deer (Odocoileus virginianus), has declined in some regions. The extent to which panther predation has affected deer populations has been difficult to assess because several other factors have changed during this period, including hydrology and hunting regulations.</p> <p>2. We collected known-fate survival data on 241 GPS-collared adult deer (156 females and 85 males) from 2015 to 2018 in the Florida Panther National Wildlife Refuge and the Big Cypress National Preserve in Florida, USA, to assess effects of panther predation on the deer population, while also evaluating the impacts of hunting and hydrology.</p> <p>3. Predation was the primary cause of death (110 of 134 mortalities), and 87% of predation events were attributed to panthers, a much greater rate than reported by studies conducted before the panther genetic restoration effort initiated in 1995. One deer was legally harvested, and two were likely killed by poachers. Increasing water depth decreased female survival but had little impact on male survival, and drowning was never a cause of mortality.</p> <p>4. Females had greater survival probability than males, except during fawning season. From 2015 to 2018, annual survival rates increased from 0.61 (0.52-0.70) to 0.86 (0.79-0.91) for females, and from 0.45 (95% CI: 0.33-0.58) to 0.79 (0.69-0.86) for males.</p> <p>5. Synthesis and applications – High predation rates, coupled with previous evidence of low recruitment of deer in South Florida, suggest that it will be challenging to meet society's competing demands for large predator restoration and sustainable deer harvest. Deer hunting in the area must remain tightly controlled, for now, if it is to be sustainable, and managers should seek to mitigate effects of high waters and improve deer habitat quality to increase deer population viability. Future work should closely monitor the deer population to assess if management actions can increase vital rates and abundance in the context of high predation rates.</p>
Fig. 3 in A newly established non-native praying mantis species, Liturgusa maya (Mantodea: Liturgusidae) in Florida, USA, and a key to Florida mantis genera
Fig. 3. Praying mantis genera in Florida: (A) Mantoida maya female (photograph by Cheryl Harleston (www.inaturalist.org, CC BY-NC-SA); (B) Brunneria borealis female (photograph by Gary L. Dearman); (C) Oligonicella scudderi female (photograph by Jennifer Thompson); (D) Thesprotia graminis female (photograph by Sturgis McKeever, Georgia Southern University (www.Bugwood.org, CC-BY-NC); (E) Gonatista grisea female (photograph by Scott D. Nelson); (F) Liturgusa maya female (photograph by Brian Fridie Jr.); (G) Stagmomantis carolina female (photograph by Wendy Garfinkel-Gold); (H) Stagmomantis floridensis female (photograph by Andrew Nisip).
Fig. 2 in A newly established non-native praying mantis species, Liturgusa maya (Mantodea: Liturgusidae) in Florida, USA, and a key to Florida mantis genera
Fig. 2. Liturgusa maya specimens were collected in and near Long Key Natural Area and Nature Center (red star on large map) in Davie, Florida. The inset map indicates the proximity of the 2 collection sites (adjacent red stars) to National Parks and Preserves. (Maps modified from www.freemapsonline.com and www.nps.gov).
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.