Find research datasets worth reusing

Data from: Three-dimensional post-glacial expansion and diversification of an exploited oceanic fish

Vertical divergence in marine organisms is being increasingly documented, yet much remains to be carried out to understand the role of depth in the context of phylogeographic reconstruction and the identification of management units. An ideal study system to address this issue is the beaked redfish, Sebastes mentella – one of four species of 'redfish' occurring in the North Atlantic – which is known for a widely distributed 'shallow-pelagic' oceanic type inhabiting waters between 250 and 550 m, and a more localized 'deep-pelagic' population dwelling between 550 and 800 m, in the oceanic habitat of the Irminger Sea. Here, we investigate the extent of population structure in relation to both depth and geographic spread of oceanic beaked redfish throughout most of its distribution range. By sequencing the mitochondrial control region of 261 redfish collected over a decadal interval, and combining 160 rhodopsin coding nuclear sequences and previously genotyped microsatellite data, we map the existence of two strongly divergent evolutionary lineages with significantly different distribution patterns and historical demography, and whose genetic variance is mostly explained by depth. Combined genetic data, analysed via independent approaches, are consistent with a Late Pleistocene lineage split, where segregation by depth probably resulted from the interplay of climatic and oceanographic processes with life history and behavioural traits. The ongoing process of diversification in North Atlantic S. mentella may serve as an 'hourglass' to understand speciation and adaptive radiation in Sebastes and in other marine taxa distributed across a depth gradient.

opencc-zeroDec 2016View details →

Data from: Three-dimensional morphological analysis of a Parahaentzschelinia-like trace fossil

Serial grinding and three-dimensional reconstruction of aff. Parahaentzschelinia trace fossils from the Ordovician Winterhouse Formation reveals complex tiered network systems associated with more typical Parahaentzschelinia-like conical bundles of sub-vertical tubes. The morphological complexity of the burrow system is interpreted as an indication of the diverse behaviour of the trace-making organism. This organism is inferred to have exploited organic matter within the sand-rich event beds as well as in muddier beds above and below the sandstone beds using a variety of behaviours. Potential burrow irrigation and microbial cultivation associated with gardening behaviour is also inferred. The trace-making organism is unknown, but comparisons are drawn between the structures observed herein and those produced by both modern polychaetes and bivalves.

Data from: Combined use of GPS and accelerometry reveals fine scale three-dimensional foraging behaviour in the short-tailed shearwater

Determining the foraging behaviour of free-ranging marine animals is fundamental for assessing their habitat use and how they may respond to changes in the environment. However, despite recent advances in bio-logging technology, collecting information on both at-sea movement patterns and activity budgets still remains difficult in small pelagic seabird species due to the constraints of instrument size. The short-tailed shearwater, the most abundant seabird species in Australia (ca 23 million individuals), is a highly pelagic procellariiform. Despite its ecological importance to the region, almost nothing is known about its at-sea behaviour, in particular, its foraging activity. Using a combination of GPS and tri-axial accelerometer data-loggers, the fine scale three-dimensional foraging behaviour of 10 breeding individuals from two colonies was investigated. Five at-sea behaviours were identified: (1) resting on water, (2) flapping flight, (3) gliding flight, (4) foraging (i.e., surface foraging and diving events), and (5) taking-off. There were substantial intra- and inter- individual variations in activity patterns, with individuals spending on average 45.8% (range: 17.1–70.0%) of time at sea resting on water and 18.2% (range: 2.3–49.6%) foraging. Individuals made 76.4 ± 65.3 dives (range: 8–237) per foraging trip (mean duration 9.0 ± 1.9 s), with dives also recorded during night-time. With the continued miniaturisation of recording devices, the use of combined data-loggers could provide us with further insights into the foraging behaviour of small procellariiforms, helping to better understand interactions with their prey.

opencc-zeroDec 2017View details →

Data from: Multi-dimensional patterns of variation in root traits among coexisting herbaceous species in temperate steppes

1. Characterizing patterns of variation in plant traits across species and environmental gradients is critical for understanding performance of species in ecosystems. One-dimensional pattern of variation has been demonstrated in leaf traits, which is known as the leaf economic spectrum. However, it is unclear whether such a spectrum exists for root traits. 2. For roots of 15 species from temperate grasslands, we determined respiration rate, relative growth rate, lifespan as well as 10 morphological, chemical and anatomical root traits. We further evaluated pairwise and multiple-trait relationships by the Pearson's correlation and principle component analysis including phylogenetic contrasts. 3. We found that root functions were related to three clusters of variation. Root respiration rate and relative growth rate were positively correlated with average root diameter, but they were negatively correlated with specific root length. In contrast, root lifespan was not correlated with average root diameter, but it was positively correlated with specific root length. These results are inconsistent with the presumption of the root economic spectrum. 4. The principle components analysis revealed a multi-dimensional pattern of variation in root traits among the 15 coexisting herbaceous species. Moreover, species within the same phylogenetic clades tended to have similar root trait syndromes. Most of the root traits exhibited a significant phylogenetic signal. 5. Synthesis. Our results do not support a one-dimensional root economic spectrum in the coexisting herbaceous species of temperate grasslands. In contrast, the pattern of variation in root traits was multi-dimensional. We further demonstrated that species in different phylogenetic clades possess diverse root trait syndromes for efficient resource acquisition. Our findings provide a next step in understanding root functions and plant strategies in temperate grasslands.

Data from: Three dimensional tracking of a wide-ranging marine predator: flight heights and vulnerability to offshore wind farms

A large increase in offshore wind turbine capacity is anticipated within the next decade, raising concerns about possible adverse impacts on birds as a result of collision risk. Birds' flight heights greatly influence this risk, yet height estimates are currently available only using methods such as radar- or ship-based observations over limited areas. Bird-borne data-loggers have the potential to provide improved estimates of collision risk and here, we used data from Global Position System (GPS)-loggers and barometric pressure loggers to track the three-dimensional movements of northern gannets rearing chicks at a large colony in south-east Scotland (Bass Rock), located <50 km from several major wind farm developments with recent planning consent. We estimated the foraging ranges and densities of birds at sea, their flight heights during different activities and the spatial variation in height during trips. We then used these data in collision-risk models to explore how the use of different methods to determine flight height affects the predicted risk of birds colliding with turbines. Gannets foraged in and around planned wind farm sites. The probability of flying at collision-risk height was low during commuting between colonies and foraging areas (median height 12 m) but was greater during periods of active foraging (median height 27 m), and we estimated that ˜1500 breeding adults from Bass Rock could be killed by collision with wind turbines at two planned sites in the Firth of Forth region each year. This is up to 12 times greater than the potential mortality predicted using other available flight-height estimates. Synthesis and applications: The use of conventional flight-height estimation techniques resulted in large underestimates of the numbers of birds at risk of colliding with wind turbines. Hence, we recommend using GPS and barometric tracking to derive activity-specific and spatially explicit flight heights and collision risks. Our predictions of potential mortality approached levels at which long-term population viability could be threatened, highlighting a need for further data to refine estimates of collision risks and sustainable mortality thresholds. We also advocate raising the minimum permitted clearance of turbine blades at sites with high potential collision risk from 22 to 30 m above sea level.

Data from: Nitrogen deposition and multi-dimensional plant diversity at the landscape scale

Estimating effects of nitrogen (N) deposition is essential for understanding human impacts on biodiversity. However, studies relating atmospheric N deposition to plant diversity are usually restricted to small plots of high conservation value. Here, we used data on 381 randomly selected 1 km2 plots covering most habitat types of Central Europe and an elevational range of 2900 m. We found that high atmospheric N deposition was associated with low values of six measures of plant diversity. The weakest negative relation to N deposition was found in the traditionally measured total species richness. The strongest relation to N deposition was in phylogenetic diversity, with an estimated loss of 19% due to atmospheric N deposition as compared with a homogeneously distributed historic N deposition without human influence, or of 11% as compared with a spatially varying N deposition for the year 1880, during industrialization in Europe. Because phylogenetic plant diversity is often related to ecosystem functioning, we suggest that atmospheric N deposition threatens functioning of ecosystems at the landscape scale.

Data from: Conservation versus livelihoods: spatial management of non-timber forest product harvests in a two-dimensional model

Areas of high biodiversity often coincide with communities living in extreme poverty. As a livelihood support, these communities often harvest wild products from the environment. But harvest activities can have negative impacts on fragile and globally important ecosystems. This paper examines trade-offs in ecological protection and community welfare from the harvest of wild products. With a novel model and empirical evidence, I show that management of harvest activity does not always resolve these trade-offs. In a model of continuous harvests in a two-dimensional landscape, managed harvest activity improves welfare, but is uniformly bad for other ecosystem services that are sensitive to the presence (as opposed to the intensity) of human activity. Empirical results from a unique dataset of mushroom harvesters in Yunnan, China suggest more experienced, poorer, and more vulnerable individuals tend to rely on more distant harvests. Thus, policies that limit the extent of forest travel, such as protected areas, may protect fragile ecosystems but can have a disproportionately negative effect on those most vulnerable.

opencc-zeroJun 2015View details →

Knowledge base of two- and three-dimensional activity cliffs

The result of up-to-date surveys and systematic analyses of 2D-cliffs including clusters, 3D-cliffs, and extensions of 3D-cliffs is made freely available in four separate data files. These files contain the list of 2D-cliffs and cliff clusters, 3D-cliffs, 3D-cliff-MMPs, and superpositions of complex X-ray structures and 3D ligands for selected targets. The data organization and information is detailed in README.doc.

opencc-zeroJun 2016View details →

Supplementary files of Jorge M G, Brennand T A. Measuring (subglacial) bedform orientation, one-dimensional size, and directional shape - method accuracy. PLOS ONE, revision phase.

S1: shapefile of longitudinal subglacial bedform dataset. S2: spreadsheet with Fig. 6 signed error distributions.

FIGURE 5 in Applying n-dimensional hypervolumes for species delimitation: unexpected molecular, morphological, and ecological diversity in the Leaf-Toed Gecko Phyllodactylus reissii Peters, 1862 (Squamata: Phyllodactylidae) from northern Peru

FIGURE 5. Dorsal and ventral views of the holotype of Phyllodactylus pachamama sp. nov. (ZFMK 90886). Scale bars represent 5 mm.

FIGURE 3. N in Applying n-dimensional hypervolumes for species delimitation: unexpected molecular, morphological, and ecological diversity in the Leaf-Toed Gecko Phyllodactylus reissii Peters, 1862 (Squamata: Phyllodactylidae) from northern Peru

FIGURE 3. N-dimensional hypervolumes of morphological data show the position of the delimited species in the Phyllodactylus reissii group in multidimensional morphological space. Circles mark PCA-derived observations.

FIGURE 2 in Applying n-dimensional hypervolumes for species delimitation: unexpected molecular, morphological, and ecological diversity in the Leaf-Toed Gecko Phyllodactylus reissii Peters, 1862 (Squamata: Phyllodactylidae) from northern Peru

FIGURE 2. Bayesian consensus tree of Ecuadorian and Peruvian Phyllodactylus based on 835 bp of mitochondrial DNA (12S and 16S rRNA). Node support in terms of Bayesian posterior probabilities is indicated by circles at nodes (nodes with a BPP ≥ 0.90 are white, BPP ≥ 0.95 are grey, BPP> 0.99 are black, values <0.90 are not marked). Outgroup (Phyllopezus maranjonensis) not shown for clarity. Results of the species delimitations in the P. reissii group are illustrated by vertical bars. Each bar represents a species detected by the respective approach. Coloration of the bars is according to the species resulting from the consensus of all species delimitation hypotheses.

FIGURE 1 in Applying n-dimensional hypervolumes for species delimitation: unexpected molecular, morphological, and ecological diversity in the Leaf-Toed Gecko Phyllodactylus reissii Peters, 1862 (Squamata: Phyllodactylidae) from northern Peru

FIGURE 1. Geographical distribution of the different clades of Phyllodactylus reissii and related species. Colors refer to delimited species (see Fig. 2). Insets show clades endemic to the inter-Andean valley of the upper Marañón River. Circles mark occurrence records used for climatic niche distribution modeling. Localities with a thick margin were also genetically sampled.

FIGURE 6 in Applying n-dimensional hypervolumes for species delimitation: unexpected molecular, morphological, and ecological diversity in the Leaf-Toed Gecko Phyllodactylus reissii Peters, 1862 (Squamata: Phyllodactylidae) from northern Peru

FIGURE 6. Phyllodactylus pachamama sp. nov. from the type locality (Balsas, Amazonas, Peru) in life.

FIGURE 4. N in Applying n-dimensional hypervolumes for species delimitation: unexpected molecular, morphological, and ecological diversity in the Leaf-Toed Gecko Phyllodactylus reissii Peters, 1862 (Squamata: Phyllodactylidae) from northern Peru

FIGURE 4. N-dimensional hypervolumes representing the climatic niches of the delimited species in the Phyllodactylus reissii group. Circles mark centroids and outlines are the 90% confidence interval of the hypervolumes (note that these only approximate the actual hypervolumes and are only used for a more clear illustration).

FIGURES 33–40. Three dimensional vesica structure for Catocala didenko, C. gansan & C in A new species of Catocala Schrank, 1802 (Lepidoptera: Noctuidae) from Primorsky Krai, Russia

FIGURES 33–40. Three dimensional vesica structure for Catocala didenko, C. gansan & C. duplicata.

opencc-by-4.0May 2017View details →

Effects of individualized Electrical Impedance Tomography and image reconstruction settings upon the assessment of regional ventilation distribution: Comparison to 4-dimensional Computed Tomography in a porcine model

Reconstruction Models used for identification of optimal settings for comparison to CT images. Forward models are available in the supplement of the article but were removed form the inverse models due to redundance storage within each model. Prior reconstruction in EIDORS, forward models have to be added again to imdl.fwd_model and imdl.jacobian_background.fwd_model.

openJan 2024View details →

G4D-DOC: A global four-dimensional gridded dataset of ocean dissolved oxygen concentrations retrieval from Argo profiles

Based on temperature and salinity observations from Argo floats, this dataset uses machine-learning methods to reconstruct global ocean dissolved oxygen (DO) concentrations. This version only provides monthly-scale netCDF format data for everyone's use. If you need other time scales, please check previous versions. <h2>Spatiotemporal Characteristics</h2> <ul> <li> Time range: 2005–2022, monthly fields. </li> <li> Geographic range: Global oceans excluding the Arctic Ocean, from 90°S to 84°N and 180°W to 180°E. </li> <li> Horizontal resolution: 1° × 1° (regular grid). </li> <li> Vertical levels (26): 10, 20, 30, 40, 50, 75, 100, 125, 150, 200, 250, 300, 400, 500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, 1750, 1995dbar . </li> </ul> <h2>Data Format & Conventions</h2> <ul> <li> Format: NetCDF4 </li> <li> Coordinate conventions: <ul> <li> <code>lat</code> (Y axis): 89.5 → −89.5 (descending) </li> <li> <code>lon</code> (X axis): converted to −180 → 180 (1° centers) </li> <li> <code>depth</code>: ascending (matching the 26 target levels) </li> </ul> </li> <li> Units: DO in μmol/kg (<code>umol kg-1</code>). </li> </ul> <h2>Variables & Dimensions</h2> <ul> <li> Variables kept: <code>DO</code>, <code>depth</code>, <code>lat</code>, <code>lon</code> (with a single-valued <code>time</code> coordinate). </li> <li> DO dimensions: <code>(time, depth, lat, lon)</code>. </li> </ul> <h2>Filenames</h2> <ul> <li> Pattern: <code>G4D_DOC_YYYY_MM.nc</code> Example: <code>G4D_DOC_2005_07.nc</code> contains the field for July 2005. </li> </ul> <h2>Citation & Disclaimer</h2> Please cite the dataset and relevant literature when using it in publications or products. Recommended citation (example): <blockquote> Xue, C., & Wang, Z. (2025). A global four-dimensional gridded dataset of ocean dissolved oxygen concentrations retrieval from Argo profiles (Monthly NetCDF version). Zenodo. <a target="_new" rel="noopener">https://doi.org/</a>10.5281/zenodo.13920233 </blockquote> The data producers are not responsible for any losses arising from data use. Map boundaries or masks do not imply official positions. <h2>Contacts</h2> <ul> <li> Cunjin Xue — <a rel="noopener">xuecj@aircas.ac.cn</a> </li> <li> Zhenguo Wang — <a rel="noopener">zgwang24@m.fudan.edu.cn</a> </li> </ul>

opencc-by-4.0Nov 2023View details →

Simulation data in "Intense magnetic reconnection process embedded in three-dimensional turbulent current sheet"

Simulation data and program used for the research "Intense magnetic reconnection process embedded in three-dimensional turbulent current sheet".