Find research datasets worth reusing

opencc-by-4.0Dec 2023View details →

Data for the article "Tidal heating in a subsurface magma ocean on Io revisited"

The data files for the figures in the article "Tidal heating in a subsurface magma ocean on Io revisited". The structure of the files are given in the first row of each file. The file "figure2.dat" only consists of the data for Figure 2a, where Figure 2b andFiguresFigurec are part of Figure 1is.

opencc-by-4.0Jul 2023View details →

UKESM1 data supporting manuscript "Marine isoprene emissions in the Southern Ocean are significantly larger than expected"

Model output and README from simulations performed for study "Marine isoprene emissions in the Southern Ocean are significantly larger than expected" (Ferracci and Weber et al)

opencc-by-4.0Dec 2023View details →

Data For "Impact of dust and temperature on primary productivity in Late Miocene oceans"

Impact of dust and temperature on primary productivity in Late Miocene oceans   This dataset contains marine biogeochemical outputs (NetCDF files) from modeling experiments with realistic late Miocene paleogeography, different CO2 levels and dust concentrations. The simulations focus on the evolution of primary productivity in response to aridification and global cooling. The simulations were carried out using the IPSL-CM5A2 general circulation model (Sepulchre et al. 2020 - IPSL-CM5A2 - an Earth system model designed for multimillennial climate simulations, GMD) and the PISCES-v2 biogeochemistry model (Aumont et al. 2015). It includes four simulations: Mio300Dust (300 ppm, dust concentration equal to pre-industrial level), Mio420Dust2 (420 ppm, dust concentration equal to pre-industrial level divided by 2), Mio420Dust10 (420 ppm, dust concentration equal to pre-industrial level divided by 10) and Mio420NoDust (420 ppm, dust concentration equal to pre-industrial level divided by 1000). The data are monthly averages over the last 100 years of the simulations.   Contact: quentin.pillot@gmail.com   Experiments , see Pillot et al. (2024), Methods ans supplementary Informations for details.   INTPP : Vertically integrated primary production by phyto (mol/m2/s) EPC100 : Export of carbon particles at 100 m (mol/m2/s) LNlight : Light limitation term in Nanophyto (between 0 and 1) LNnut : Nutrient limitation term in Nanophyto (between 0 and 1) PPPHY : Primary production of nanophyto (mol/m3/s) PPPHY2 : Primary production of diatoms (mol/m3/s) Ndep : Nitrogen deposition from dust (mol/m2/s) Pdep : Phosphorus deposition from dust (mol/m2/s) Sidep : Silice deposition from dust (mol/m2/s) Irondep : Iron deposition from dust (mol/m2/s)   Keywords: Late Miocene, marine primary productivity, aridification, dust, CO2, cooling, oceans, modelling, IPSL-CM5A2, PISCES-v2

opencc-by-4.0Dec 2023View details →

Ocean bottom seismometer data of the OBS2020-1 profile at the northern continental margin of the South China Sea

Ocean bottom seismometer hydrophone data in SEG-Y format of 11 OBS stations along the OBS2020-1 profile and travel times used for the forward modeling and tomographic inversion. The travel times include the primary phases and secondary phases which are seawater layer multiples at the receiver side. Meanwhile, the OBS locations are also submitted to this repository.

opencc-zeroJan 2024View details →

Data from: Same places, same stories? Genomics reveals similar structuring and demographic patterns for four Pocillopora coral species in the southwestern Indian Ocean

Aim Efficiently protecting species requires knowing their ecological, life history and reproductive traits. This is particularly decisive for scleractinian corals, key components of coral reefs, which are experiencing critical declines. Yet their connectivity remains insufficiently documented. Here, we focused on four distinct species of the coral genus Pocillopora found in diverse habitats of the southwestern Indian Ocean and presenting various reproductive strategies. We aimed to understand whether these traits affect species connectivity. Location Archipelagos and islands of the southwestern Indian Ocean. Taxon Pocillopora spp. Methods We used target-capture to collect single-nucleotide polymorphisms (SNPs) from over a thousand colonies sampled across nine localities. From the ca. 1,400 SNPs retained per species, Bayesian clustering methods, networks and demographic inferences were applied to first infer the population genetic structure and connectivity of each species, then the demographic history of each population. Results All four Pocillopora species exhibited almost the same genetic structuring pattern, reflecting the sampled ecoregions (Madagascar and surrounding islands vs. Mascarene Islands). However, the genetic differentiation was stronger ( FST about 10 times higher) for P. acuta, the species inhabiting more enclosed habitats, such as lagoons and shallow waters, and reproducing mainly asexually. Similarly, all populations, except those from P. acuta, showed a signature of population expansion ca. 100,000 years ago, following the penultimate glacial period. Main conclusions These results indicate reduced gene flow between Madagascar and the Mascarenes, probably linked to currents, suggesting distinct connectivity networks that should be considered independently when setting up conservation plans. In addition, shared demographic histories reflect that populations from these species have probably met the same environmental constraints and reacted similarly, something that should be considered in light of the ongoing rapid climate change.

opencc-zeroJan 2024View details →

Data from: Early diversification dynamics in a highly successful insular plant taxon are consistent with the general dynamic model of oceanic island biogeography

The general dynamic model (GDM) of oceanic island biogeography views oceanic islands predominantly as sinks rather than sources of dispersing lineages. To test this, we conducted a biogeographic analysis of a highly successful insular plant taxon, Cyrtandra and inferred directionality of dispersal and founder events throughout the four biogeographical units of the Indo-Australian Archipelago (IAA), namely Sunda, Wallacea, Philippines, and Sahul. Sunda was recovered as the major source area, followed by Wallacea, a system of oceanic islands. The relatively high number of events originating from Wallacea is attributed to its central location in the IAA and its complex geological history selecting for increased dispersibility. We also tested if diversification dynamics in Cyrtandra follow predictions of adaptive radiation, which is the dominant process as per the GDM. Diversification dynamics of dispersing lineages of Cyrtandra in the Southeast Asian grade showed early bursts followed by a plateau, which is consistent with adaptive radiation. We did not detect signals of diversity-dependent diversification, and this is attributed to Southeast Asian cyrtandras occupying various niche spaces, evident by their wide morphological range in habit and floral characters. The Pacific clade, which arrived at the immaturity phase of the Pacific Islands, showed diversification dynamics predicted by the Island Immaturity Speciation Pulse (IISP) model, wherein rates increase exponentially, and their morphological range is controlled by the least action effect favoring woodiness and fleshy fruits. Our study provides a first step toward a framework for investigating diversification dynamics as predicted by the GDM in highly successful insular taxa.

opencc-zeroJan 2024View details →

Data from: Cross ocean-basin population genetic dynamics in a pelagic top predator of high conservation concern, the oceanic whitetip shark, Carcharhinus longimanus

The oceanic whitetip shark, Carcharhinus longimanus, is a Critically Endangered, circumtropical, and highly migratory, pelagic shark. Yet, little information exists on its population genetic dynamics to guide conservation management practice. We present a first worldwide, mitochondrial and nuclear DNA assessment of the population genetic status of this imperiled species based on sequences of the complete mitochondrial control region (n = 173) and partial ND4 gene (n = 172), and genotypes from 12 nuclear microsatellites (n = 164). Statistically significant mitochondrial and nuclear DNA population genetic differentiation was detected across all marker datasets between Western Atlantic and Indo-Pacific oceanic whitetip sharks. Additionally, our data, combined with previously published, partial (701-base pairs) mitochondrial control region sequences from additional locations in the Atlantic and Indian Oceans, confirmed significant matrilineal population structure between the Western and Eastern Atlantic. The combined data also provisionally (i.e., with FST but not ΦST) indicated differentiation between Western North and Central-South Atlantic sharks, pointing to the need for further assessment in this region. Matrilineal differentiation was also detected between Indian and Pacific Ocean sharks via pairwise analyses, albeit with the ND4 gene sequence only (ΦST = 0.051; FST = 0.092). Limited sampling in the Pacific leaves open questions about the connectivity dynamics in this large region. Despite the presence of geographic population genetic structure, the mitochondrial data showed no evidence of across ocean basin phylogeographic lineages. A provisional assessment of mitochondrial and nuclear genetic diversity indicated the oceanic whitetip shark's status falls in the middle to upper ranges compared to other shark species, potentially lending some optimism for the present adaptability and resiliency of this species if strong conservation measures are effectively implemented.

opencc-zeroFeb 2024View details →

Data from: Combining mesocosms with models to unravel the effects of global warming and ocean acidification on a temperate marine ecosystem

Ocean warming and species exploitation have already caused large-scale reorganization of biological communities across the world. Accurate projections of future biodiversity change require a comprehensive understanding of how entire communities respond to global change. We combined a time-dynamic integrated food web modelling approach (Ecosim) with previous data from community-level mesocosm experiments to determine the independent and combined effects of ocean warming and acidification, and fisheries exploitation, on a well-managed temperate coastal ecosystem. The mesocosm parameters enabled important physiological and behavioural responses to climate stressors to be projected for trophic levels ranging from primary producers to top predators, including sharks. Through model simulations, we show that under sustainable rates of exploitation, near-future warming or ocean acidification in isolation could benefit species biomass at higher trophic levels (e.g., mammals, birds, and demersal finfish) in their current climate ranges, with the exception of small pelagic fish. However, under warming and acidification combined biomass-increases at higher trophic levels will be lower or absent, whilst in the longer term reduced productivity of prey species is unlikely to support the increased biomass at the top of the food web. We also show that increases in exploitation will suppress any positive effects of human-driven climate change, causing individual species biomass to decrease at higher trophic levels. Nevertheless, total future potential biomass of some fisheries species in temperate areas might remain high, particularly under acidification, because unharvested opportunistic species will likely benefit from decreased competition and show an increase in biomass. Ecological indicators of species composition such as the Shannon diversity index declined under all climate change scenarios, suggesting a trade-off between biomass gain and functional diversity. By coupling parameters from multi-level mesocosm food web experiments with dynamic food web models, we were able to simulate the generative mechanisms that drive complex responses of temperate marine ecosystems to global change. This approach, which blends theory with experimental data, provides new prospects for forecasting climate-driven biodiversity change and its effects on ecosystem processes.

opencc-zeroDec 2023View details →

Data from: Phylogenomic position of eupelagonemids, abundant and diverse deep-ocean heterotrophs

Eupelagonemids, formerly known as Deep Sea Pelagic Diplonemids I (DSPD I), are among the most abundant and diverse heterotrophic protists in the deep ocean, but little else is known about their ecology, evolution, or biology in general. Originally recognized solely as a large clade of environmental ribosomal subunit RNA gene sequences (SSU rRNA), branching with a smaller sister group DSPD II, they were postulated to be diplonemids, a poorly-studied branch of Euglenozoa. Although new diplonemids have been cultivated and studied in depth in recent years, the lack of cultured eupelagonemids has limited data to a handful of light micrographs, partial SSU rRNA gene sequences, a small number of genes from single amplified genomes (SAGs), and only a single formal described species, Eupelagonema oceanica. To determine exactly where this clade goes in the tree of eukaryotes and begin to address the overall absence of biological information about this apparently ecologically important group, we conducted single-cell transcriptomics from two eupelagonemid cells. A SSU rRNA gene phylogeny shows these two cells represent distinct subclades within eupelagonemids, each different from E. oceanica. Phylogenomic analysis based on a 125-gene matrix contrasts with the findings based on ecological survey data, and shows eupelagonemids branch sister to the diplonemid subgroup Hemistasiidae.

opencc-zeroApr 2024View details →

Data from: Isotopic composition of particulate black carbon in the northern Indian Ocean

The dataset contains the concentration and stable isotopic composition of particulate black carbon (PBC) in the surface waters of the northern Indian Ocean. Samples were collected during multiple cruises to the Northern Indian Ocean (locations, date and time are provided in the datasheet) along with end member sampling of riverine particulate. Surface water samples were filtered onto 0.7 micron GF/F filters (precombusted at 400 degree Celsius) and oven-dried. Particulate black carbon was estimated following the chemothermal oxidation (CTO - 375) method. Briefly, samples were treated using HCl fumes to remove inorganic carbon fractions followed by heating at 400 degree celsius for 24 hours in active airflow to remove the organic carbon fraction. The residual carbon (BC in micromoles per litre) and its isotopic composition (represented by delta notation in permil) was measured using an elemental analyzer (EA: Flash 2000, Thermo Scientific) connected to an isotope ratio mass spectrometer (IRMS: Delta V, Thermo Scientific). The precision of measurement by repeated analysis of standards was better than 10 % for PBC concentration and 0.1 permil for its isotopic composition. The data is associated with the manuscript accepted in Geophysical Research Letters titled, 'Isotopic evidence for degradation of particulate black carbon in the ocean.

opencc-by-4.0Apr 2024View details →

Idealized wave data in support of Directional Breaking Kinematics Observations from 3D Stereo Reconstruction of Ocean Waves

You will find the WaveWatchIII data output from idealized solutions of Romero 2019, ST4 and ST6 Data are in Netcdf format and include metadata. Each file corresponds to a duration-limited solution with constant wind speed of 13 m/s

opencc-by-4.0Sep 2024View details →

An improved long-term high-resolution surface pCO2 data product for the Indian Ocean using machine learning

This dataset contains two improved surface pCO2 products, along with surface pCO2  from the INCOIS-BIO-ROMS model (pCO2_model) and other input variables. It is a long-term, high-resolution dataset developed for the Indian Ocean region (30°E - 120°E, 30°S - 30°N), covering the period from 1980 to 2019. The dataset features a monthly temporal resolution and a spatial resolution of 1/12 degree.  The file includes INCOIS-BIO-ROMS model outputs (sea surface temperature (SST), sea surface salinity (SSS), mixed layer depth (MLD), nitrate (NO3), dissolved inorganic carbon (DIC), and chlorophyll-a (CHL)). These variables are used as inputs for machine learning models to improve the pCO2_model. The machine learning model predicts the surface pCO2 deviants (pCO2_obs - pCO2_model). The file also provides spatiotemporally varying uncertainties associated with the predicted pCO2 deviants. **Users are advised to download Version v2 of the data product, as Version v1 has been deprecated and is no longer recommended for use.

opencc-by-4.0Dec 2024View details →

Data for the article 'Love numbers for Io with a magma ocean'

Data sets for the article 'Love numbers of Io with a magma ocean'.  The given file has the following structure and can be used to generate figures 2-5 in the manuscript Depth l (km)      log10(visocisty (Pa s))      Ocean thickness (km)      Dissipation (TW)     k20      k22c     k22s      Delta_t20 (h)     Delta_t22c (h)     Delta_t22s (h). In case of any inquiries, please send an email to aygun@karel.troja.mff.cuni.cz.

opencc-by-4.0Jun 2023View details →

Data files for "Genomic-to-space measurements reveal global ocean nutrient stress"

Data files to be used with the following code: https://github.com/ljustick/genomic_to_space_nut_stress

Supporting Data: The Effect of Ocean Salinity on Climate and its Implications for Earth's Habitability

Data supporting "The Effect of Ocean Salinity on Climate and its Implications for Earth's Habitability" by SL Olson, MF Jansen, DS Abbot, I Halevy, and C Goldblatt, submitted to GRL on April 18, 2022. The ROCKE-3D rundecks and input files required to reproduce these results are also included.

Data used in "Storms drive outgassing of CO2 in the Subpolar Southern Ocean"

Description:  The data included in this repository were used to generate the analysis and resulting figures for the paper "Storms drive outgassing of CO2 in the subpolar Southern Ocean" in Nature Communications. Abstract: "The subpolar Southern Ocean is a critical region where CO2 outgassing influences the global mean air-sea CO2 flux (FCO2). However, the processes controlling the outgassing remain elusive. We show, using an unprecedented multi-glider dataset combining FCO2 and ocean turbulence, that the air-sea gradient of CO2 (∆pCO2) is modulated by synoptic storm-driven ocean variability (20 µatm, 1-10 days) through two processes. Ekman transport explains 60% of the variability, and entrainment drives strong episodic CO2 outgassing events of 2-4 mol m-2 yr-1. Extrapolation across the subpolar Southern Ocean using a process model shows how ocean fronts spatially modulate synoptic variability in ∆pCO2 (6 µatm2 average) and how spatial variations in stratification influence synoptic entrainment of deeper carbon into the mixed layer (3.5 mol m-2 yr-1 average). These results not only constrain aliased-driven uncertainties in FCO2 but also the effects of synoptic variability on slower seasonal or longer ocean physics-carbon dynamics." In this study, we first use a two-month dataset from the Southern Ocean Seasonal Cycle Experiment (SOSCEx) which utilised multiple autonomous platforms to simultaneously observe the coupled atmosphere - ocean system, in high-resolution, in the Atlantic sector of the subpolar Southern Ocean. Corresponding processed data for this experiment used by this study is provided in the folder /Data/SOSCEx_STORM2_Glider_Data. Using these data we explain how storms influence, through ocean mixed layer physics (advection and mixing), the direction and magnitude of the air-sea CO2 gradient (∆pCO2) and flux (FCO2) over the duration of the experiment. We construct a conceptual ocean mixed layer model that captures the observed synoptic variability of ∆pCO2 in the observations, we estimate the synoptic variability around the entire subpolar Southern Ocean. The relating data for this second step can be found under /Data/Generalisation Related code: The data files provided are those that are required to create the figures for this study and/or perform key analyses. Each figure or analysis has an associated python script. Auxiliary data that are not provided in this repository are available in other public repositories and have been referred to in the main study manuscript and in each of the python scripts where they are used. The python scripts for this study are found at the corresponding authors GitHub at <a href="https://github.com/sarahnicholson/SouthernOceanStormsCO2">https://github.com/sarahnicholson/SouthernOceanStormsCO2</a>.

Data in support of manuscript "Impacts of storm surge barriers on drag, mixing, and exchange flow in a partially mixed estuary" submitted to JGR-Oceans

Data set in support of manuscript "Impacts of storm surge barriers on drag, mixing, and exchange flow in a partially mixed estuary" submitted to JGR-Oceans in November 2021.  Matlab script (makeFigs_barDragMix_upload.m) is used to generate the figures from the manuscript.  Data files (*.mat) correspond with each figure (*.png).  For questions or additional information please contact D. Ralston.

Environmental and AIS data collected during the EUMarineRobots Trans-National Access activities experiments using the NATO STO-CMRE Littoral Ocean Observatory Network testbed (Release 2)

Environmental and AIS data collected during the second phase of EUMR TNA experiments using the CMRE LOON testbed. Environmental data consists of temperature measured across the water column; sound velocity measured close to the surface and close to the sea bottom; meteorological data at the surface (i.e., pressure, temperature, wind speed and direction, humidity and rain). The environmental dataset is complemented with Automatic Identification System (AIS) data for the ships transiting close to  the LOON area (Gulf of La Spezia, Italy) Temperature measured across the water column in the LOON area (Gulf of La Spezia, Italy). The dataset includes measurements for: i) June 9-11, 17-18, 25-26 - 2021 ii) July 5-7, 21-27, 30-31 - 2021 iii) August 3-5, 10-14, 19-21, 23-24, 28-30 - 2021 Meteorological data at the surface (i.e., pressure, temperature, wind speed and direction, humidity and rain) in the LOON area (Gulf of La Spezia, Italy). The dataset includes measurements for: i) June 9-11, 17-18, 25-26 - 2021 ii) July 5-7, 21-27, 30-31 - 2021 iii) August 3-5, 10-14, 19-21, 23-24, 28-30 - 2021 Sound velocity measured close to the surface (SVP1) and close to the sea bottom (SVP2) in the LOON area (Gulf of La Spezia, Italy). The dataset includes measurements for: i) June 9-11, 17-18, 25-26 - 2021 ii) July 5-7, 21-27, 30-31 - 2021 iii) August 3-5, 10-14, 19-21, 23-24, 28-30 - 2021 SVP1 data  missing for  June 17-18 (2021) and July 5-7 (2021). Automatic Identification System (AIS) data for the ships transiting close to  the LOON area (Gulf of La Spezia, Italy). The dataset includes AIS data for: i) June 9-11 - 2021 AIS recorded data not available after June 11, 2021 For reference, see: "Environmental data collected on the CMRE LOON tested during the EUMR project: dataset description",  Petroccia, Roberto; Zappa, Giovanni; Cimino, Giampaolo; Grati, Alberto; Alves, João. CMRE-DA-2021-001. July 2021, available  at https://www.cmre.nato.int/research/publications/latest-techreports/1638-cmre-da-2021-001

opencc-by-4.0Jan 2021View details →

Adiabatic and diabatic signatures of ocean temperature variability - ACCESS-CM2 processing/plotting code and processed data

Contains processed data and processing/plotting code for the figures in the article: Holmes, R.M., Sohail, T. and Zika, J.D. (2022): Adiabatic and diabatic signatures of ocean temperature variability, Journal of Climate, <a href="https://doi.org/10.1175/JCLI-D-21-0695.1">https://doi.org/10.1175/JCLI-D-21-0695.1</a> For more information please see the published article, as well as the github repository where the code is described in more detail: <a href="https://github.com/rmholmes/CM2_HCvar/tree/JCLI-D-21-0695">https://github.com/rmholmes/CM2_HCvar/tree/JCLI-D-21-0695</a>