Find research datasets worth reusing

opencc-by-4.0Oct 2022View details →

Validation of a new spatially-explicit process-based model (HETEROFOR) to simulate structurally and compositionally complex stands in Eastern North-America : Dataset

This dataset is linked to the paper “Validation of a new spatially-explicit process-based model (HETEROFOR) to simulate structurally and compositionally complex stands in Eastern North-America" published in Geoscientific Model Development (https://doi.org/10.5194/gmd-16-1661-2023). It contains the installer of the model, its user guide, as well as all the input files (inventory, thinning, meteorology and soil horizons files for each stand used in the evaluation and calibration steps), the R scripts and associated data used to analyse the model outputs.

opencc-zeroNov 2022View details →

Temperature as a likely driver shaping global patterns in mineralogical composition in bryozoans: Implications for marine calcifiers under Global Change

The Southern Ocean is showing one of the most rapid responses to human-induced global change, thus acting as a sentinel of the effects on marine species and ecosystems. Ocean warming and acidification are already impacting benthic species with carbonate skeletons, but the magnitude of these changes to species and ecosystems remains largely unknown. Here we provide the largest carbonate mineralogical dataset to date for Southern Ocean bryozoans, which are diverse, abundant and important as carbonate producers, thus making them excellent for monitoring the effects of ocean warming and acidification. To improve our understanding of how bryozoans might respond to ocean warming and acidification, we assess latitudinal and seafloor temperature patterns of skeletal mineralogy using bryozoan species occurrences together with temperature data for the first time. Our findings, combining new mineralogical data with published data from warmer regions, show that the proportions of high-Mg calcite and bimineralic species increase significantly towards lower latitudes and with increasing seawater temperature. These patterns are consistent with the hypothesis that seawater temperature is likely a significant driver of variations in bryozoan mineralogy at a global scale.

opencc-zeroNov 2022View details →

Data for the article: Coupling of leaf elemental traits with root fungal community composition reveals a plant resource acquisition strategy in a desert ecosystem

Purpose: Plant-associated microbes enhance nutrient access and stress tolerance of the host species, and therefore, are crucial for plant traits and resource strategies. However, the links between aboveground plant traits and belowground microbes related to plant resource strategies under stressful conditions remain poorly understood. Methods: We tested the relationships between leaf traits linked to water (carbon isotopic composition, δ13C) and nutrient use (elemental concentrations and stoichiometry) with microbial compositions in roots and rhizospheres of two dominant species (Artemisia ordosica and Leymus secalinus) in the Mu Us Desert, northern China. Results: L. secalinus exhibited higher Mg and Mn concentrations, N:P ratios, stoichiometric flexibility, and root fungi:bacteria ratios, but lower foliar K and Ca concentrations and δ13C values than A. ordosica. The leaf N:P of L. secalinus increased with the root fungi:bacteria ratios, whereas the leaf N:P of A. ordosica decreased with the root fungi:bacteria ratios. The plant elemental levels (P, N, K, Ca, Mn, and δ13C) of L. secalinus but not A. ordosica were significantly related to their root fungal composition. Additionally, the random forest model identified four key fungal families in predicting leaf elemental traits for both plant species. Conclusion: The results suggested tight coupling and coordination between leaf elemental traits and root microbial compositions (especially fungal communities) related to plant resource acquisition strategies. By regulating aboveground and belowground feedback loops through trait flexibility and root microbial compositions, the studied plant species can sustain their resource strategies under stressful environmental conditions.

opencc-zeroNov 2022View details →

Functional impact of subunit composition and compensation on Drosophila melanogaster nicotinic receptors: Targets of neonicotinoids

Neonicotinoid insecticides target insect nicotinic acetylcholine receptors (nAChRs) and their adverse effects on non-target insects are of serious concern. We recently found that cofactor TMX3 enables robust functional expression of insect nAChRs in Xenopus laevis oocytes and showed that neonicotinoids (imidacloprid, thiacloprid, and clothianidin) exhibited agonist actions on some nAChRs of the fruit fly (Drosophila melanogaster), honeybee (Apis mellifera) and bumblebee (Bombus terrestris) nAChRs with more potent actions on the pollinator nAChRs. However, other subunits from the nAChR family remain to be explored. We show that the Dα3 subunit co-exists with Dα1, Dα2, Dβ1, and Dβ2 subunits in the same neurons of adult D. melanogaster, thereby expanding the possible nAChR subtypes in these cells alone from 4 to 12. The presence of Dα1 and Dα2 subunits reduced the affinity of imidacloprid, thiacloprid, and clothianidin for nAChRs expressed in Xenopus laevis oocytes, whereas the Dα3 subunit enhanced it. RNAi targeting Dα1, Dα2, or Dα3 in adults reduced expression of targeted subunits but commonly enhanced Dβ3 expression. Also, Dα1 RNAi enhanced Dα7 expression, Dα2 RNAi reduced Dα1, Dα6, and Dα7 expression and Dα3 RNAi reduced Dα1 expression while enhancing Dα2 expression, respectively. In most cases, RNAi treatment of either Dα1 or Dα2 reduced neonicotinoid toxicity in larvae, but Dα2 RNAi enhanced neonicotinoid sensitivity in adults reflecting the affinity-reducing effect of Dα2. Substituting each of Dα1, Dα2, and Dα3 subunits by Dα4 or Dβ3 subunit mostly increased neonicotinoid affinity and reduced efficacy. Therefore, functional expression studies and RNAi targeting of subunits show that neonicotinoid action and toxicity involve the integrated actions of multiple nAChR subunit combinations, counseling caution in interpreting toxicity to insects by subunit gene modification alone.

opencc-by-4.0Nov 2022View details →

Data from: Mixed Signals from the Stable Isotope Composition of Precipitation and Plant Waxes in the Northern Tropical Andes

These files are the supplementary information for Pérez‐Angel, L. C., Sepúlveda, J., Montes, C., Smith, J. J., Molnar, P., González-Arango, C., Snell, K., Dildar, N., Mixed Signals from the Stable Isotope Composition of Precipitation and Plant Waxes in the Northern Tropical Andes. Journal of Geophysical Research: Biogeosciences (In Revision).    This work was funded by the National Science Foundation NSF | GEO | Division of Earth Sciences (EAR): 1929199

opencc-by-4.0Nov 2022View details →

Lipid metabolism, fatty acid composition and meat quality in broilers supplemented with increasing levels of defrosted black soldier fly larvae

Dataset for the experiment to evaluate the effects of increasing levels of whole black soldier fly larvae (BSFL) in broiler diets on lipid metabolism, fatty acid composition, and meat quality of birds. Chicks received the whole BSFL at 10%, 20%, or 30% of the feed intake of control chickens that received no BSFL but only age-specific diets. <a href="https://doi.org/10.3920/JIFF2022.0125">https://doi.org/10.3920/JIFF2022.0125</a>

opencc-by-4.0Nov 2022View details →

Composite tracks of Mediterranean cyclones (1979-2020)

The composite tracks of Mediterranean cyclones have been produced by combining an ensembles of 10 independent track datasets, applied to ERA5 reanalysis for the period 1979-2020. Composite tracks describe more intense and longer-lasting cyclones with more distinguished early, mature and decay stages than cyclones coming from individual tracking methods. Composite tracks are ranked according to their confidence level, i.e. the number of individual cyclone tracking methods that tracked the same cyclone. For each confidence level, we provide a separate file that includes a matrix of eight columns and a number of rows that varies among the datasets. Each row corresponds to a single track point, while the eight columns provide the following information: - Column 1: A cumulatively increasing index that functions as an identifier of unique cyclone tracks. For instance, all information about the track of cyclone #456 are found in all rows starting with the number 456. - Column 2: Longitude of track points - Column 3: Latitude of track points. It is important to note that geographical coordinates are produced using Step 2 of our method and thus may not match the exact location of grid points of ERA5. - Column 4: Year of occurrence - Column 5: Month of occurrence - Column 6: Day of occurrence - Column 7: Hour of occurrence - Column 8: Lowest MSLP value (in hPa) within a 2.5 degrees radius from the geographical coordinates in columns 2 and 3. These values are only meant to function as an approximate reference of intensity.

Data from: DNA metabarcoding improves the taxonomical resolution of visually determined diet composition of beaked redfish (Sebastes sp.)

Beaked redfish, dominated by Sebastes mentella, have recently reached record abundance levels in the Gulf of St. Lawrence (GSL) and knowledge of their diet composition is essential to understand the trophic role that these groundfish play in the ecosystem. The objective of the present study was to compare the performance of the visual examination and DNA metabarcoding of stomach contents of the same individual redfish caught in the estuary and northern Gulf of St. Lawrence. Using a universal metazoan mitochondrial cytochrome c oxidase subunit I (COI) marker, a total of 27 taxonomic sequence matches, 16 at the species level considered as primary prey, were obtained from 185 stomachs with DNA metabarcoding and compared to the 26 prey types, 16 at genus or species level, obtained with stomach content analysis (SCA). While both techniques pointed to a similar definition of diet composition, our results also revealed that the SCA and DNA metabarcoding perform differently among prey categories, both in terms of detectability and taxonomical resolution, as well as in estimated contribution to diet. The use of DNA metabarcoding along with SCA improves the taxonomical resolution of visually determined prey, which supports the concept that both techniques provide useful complementary information that is best used together to gain a maximum level of information on the predator's diet.

Nonlinear responses of metals and composites

Dataset composed of two main parts     1. Material characterization of a metal (from lab test)         Single file: `metal-tensile.txt`         Material characteristics:             - isotropic elastoplastic material with isotropic hardening             - poisson ratio = 0.3         Geometrical characteristics:             - specimen geometry: bar             - initial length = 1000 mm             - initial cross section = 35.28 mm^2         Loading characteristics:             - uniaxial tension     2. Composite open-hole substructure characterization (from FE simulations)         Multiple files: `EaX_EbY_EsZ.txt` (see README.txt for nomenclature)         Layup:             - [45/90/-45/0]s         Damage criterion:             - Hashin with cohesive damage propagation             - No delaminations considered         Loading characteristics:             - Homogenized strain loading over the plate edges             - In plane loading: different combinations of (eps_1, eps_2, eps_12)             - In plane response: (sig_1, sig_2, sig_12), i.e. homogenized stresses

Mass spectrometry-based aerosolomics: a new approach to resolve sources, composition, and partitioning of secondary organic aerosol

Dataset of Thoma et al. published at Atmospheric Measurements and Techniques: Mass spectrometry-based aerosolomics: a new approach to resolve sources, composition, and partitioning of secondary organic aerosol

Experimental extensification of mountain grasslands restores plant species richness but not species composition in the mid-term

<ol> <li>The traditional grasslands that characterize the cultural landscapes of the palaeartic mountain massifs represent biodiversity hotspots. Yet, they are currently threatened by the intensification of farming practices, notably excesses in fertilization and irrigation.</li> <li>We experimentally investigated the passive restoration of montane and subalpine hay meadows after six years of management intensification, with different levels of fertilization and irrigation, followed by five years of release of intensive management, i.e. extensification. More specifically, relying on a full randomized block-design replicated at 11 Swiss study sites constituted of extensively-managed meadows, we exposed during six years (2010-2015) four 20 m diameter plots to three levels of intensification (low, medium and high inputs), while a fourth plot served as a control (no inputs). In the second phase of the experiment (2016-2020), all study meadows underwent farming extensification.</li> <li>We monitored total species richness and plant diversity (Simpson diversity), indicator plant species as well as the composition and variability of the plant communities based on Bray-Curtis dissimilarity distances.</li> <li>We found that total species richness decreased in the most intensified plots after six years of intensification, but all plots retrieved their baseline species richness after five years of re-extensification. Additionally, we found no difference between the years in plant diversity (Simpson diversity) among the treatments. Yet, intensification led to different plants communities' compositions in all three levels of intensification in 2015 compared to the extensive plots, and this structural difference remained after five years of re-extensification.</li> <li>Synthesis and applications. Land-use intensification induces a rapid impoverishment of the flora of mountain meadows. Our results demonstrate the potential of mountain hay meadows to passively restore plant species richness after re-extensification, however plants communities did not fully recover. We recommend maintaining fertilization inputs as low as possible and operating active restoration on grasslands formerly intensified.</li> </ol>

eDNA metabarcoding reveals high soil fungal diversity and variation in community composition among Spanish cliffs

Environments characterized by physical extremes harbor unique species diversity with particular adaptations. Cliffs are harsh environments for organisms but host a great diversity of specialized plants with many endemics, rare and even endangered species. It is, however, less known which fungal diversity the cliff habitats contain and whether it differs among different cliff locations. We thus sampled soil from three separate cliff locations in the North, Centre and South of Spain and used eDNA metabarcoding to determine fungal diversity. To better understand whether cliff specialist plants may promote particular fungal communities, we have sampled soil from crevices with cliff specialist plants and no apparent plants as controls. Major lifestyles found in cliff soils were saprotrophs, and major fungal orders were Dothideomycetes, Sordariomycetes, and Eurotiomycetes, while the amount of symbiotrophic fungi was relatively low. We found no significant differences in fungal amplicon sequence variant (ASV) richness among the three sampled locations, but the sites were significantly different in their community composition and their main indicator species. Overall, there were no significant differences in fungal ASV richness or composition between soils from cliff specialist plants and soils without plants, suggesting a unique fungal diversity in cliff soils independent from specialized plants. However, preliminary findings on soils of the specialist cliff plant Sedum dasyphyllum against control soils suggest that the presence of a specialist plant may be a relevant factor affecting the specificity of the fungal community in cliff soils. Our results indicate the existence of particular cliff fungal communities in each location, and that, despite limited and poorly developed soils and harsh conditions, cliffs can harbor a great diversity of fungal species, comparable to other ecosystems of Spain. This study points out that some fungi may be cliff-specific, shaping particular communities that mediate plant adaptations to cliffs' extreme conditions.

Major and trace element composition of IODP Site U1429 and Yellow River sediments and simulated rainfall changes in East-Southeast Asia during past 300 ka

This dataset includes major and trace element composition of IODP Site U1429 and Yellow River surface sediments. They are all analyzed based on the clay-sized fractions. It also includes the data of simulated rainfall changes in the northern and southern China, as well as in Southeast Asia during past 300 ka.

Indirect maternal effects via nest microbiome composition drives gut colonization in altricial chicks

The new version of the dataset includes the raw data and R scripts necessary to reproduce the analyses and figures explained in the manuscript "Indirect maternal effects via nest microbiome composition drives gut colonization in altricial chicks". The manuscript linked to this data has undergone a first round of peer-reviewed, which explains the differences between the first and second (current) version of the dataset. Notice that the manuscript has a new title and consequently the dataset title has been updated. This dataset includes: - ASV.xlxs: Complete ASV table of the field experiment. We collected cloacal swabs from parents and chicks in ten nests of Great tits (Parus major) and ten nests of Blue tis (Cyanistes caeruleus) together with nest and water microbiome. The Genbank accession numbers of the samples are given in each column (Bioproject: PRJNA800248). This file has been placed out of the folder "project data & code" for easy access. - README.docx: Complete explanation of the different raw data used for the statistical analyses, together with the link to the R script where data is analyzed. We recommend to read this document before diving into the data and scripts. - Project data & code: Two separate folders for raw data and code.

Data for: Species composition of shoreline wolf spider communities vary with salinity but their diets vary with wrack inflow

Wolf spiders are typically the most common group of arthropod predators on both lake and marine shorelines, because of the high prey availability in these habitats. However, shores are also harsh environments due to flooding and, in proximity to marine waters, to toxic salinity levels. Here, we describe the spider community, prey availabilities, and spider diets between shoreline sites with different salinities, albeit with comparatively small differences (5 vs. 7‰). Despite the small environmental differences, spider communities between low and higher-saline sites showed an almost complete species turnover. At the same time, differences in prey availability or spider gut contents did not match changes in spider species composition but rather changed with habitat characteristics within the region, where spiders collected at sites with thick wrack beds had a different diet than sites with little wrack. These data suggest that shifts in spider communities are due to habitat characteristics rather than prey availabilities, and the most likely candidate restricting species in high salinity would be saline sensitivity. At the same time, species' absences from low-saline habitats remain unresolved.

Data from: A mix of old British and modern European breeds: Genomic prediction of breed composition of smallholder pigs in Uganda

Pig herds in Africa comprise genotypes ranging from local ecotypes to commercial breeds. Many animals are composites of these two types and the best levels of crossbreeding for particular production systems are largely unknown. These pigs are managed without structured breeding programs and inbreeding is potentially limiting. The objective of this study was to quantify ancestry contributions and inbreeding levels in a population of smallholder pigs in Uganda. The study was set in the districts of Hoima and Kamuli in Uganda and involved 422 pigs. Pig hair samples were taken from adult and growing pigs in the framework of a longitudinal study investigating productivity and profitability of smallholder pig production. The samples were genotyped using the porcine GeneSeek Genomic Profiler (GGP) 50K SNP Chip. The SNP data was analyzed to infer breed ancestry and autozygosity of the Uganda pigs. The results showed that exotic breeds (modern European and old British) contributed an average of 22.8% with a range of 2–50% while "local" blood contributed 69.2% (36.9–95.2%) to the ancestry of the pigs. Runs of homozygosity (ROH) greater than 2 megabase (Mb) quantified the average genomic inbreeding coefficient of the pigs as 0.043. The scarcity of long ROH indicated low recent inbreeding. We conclude that the genomic background of the pig population in the study is a mix of old British and modern pig ancestries. Best levels of admixture for smallholder pigs are yet to be determined, by linking genotypes and phenotypic records.

Floristic composition, structure and diversity of riparian forests in southwestern Nigeria: Conservation is inevitable

The Nigerian riparian forest ecosystems had declined in extent and distribution and this had been attributed mainly to land use change. This study intended to provide an understanding of the links between plant diversity, composition, structures, and disturbances both anthropogenic and natural processes inducing the vegetation dynamics. Nine study sites were used for this study, within each site, five (5) plots (0.25 ha in size) were marked out and placed systematically at an interval of 10 m along the transect. A complete enumeration of plant species was carried out and identified at the species level. Diversity indices and structural parameters were determined and anthropogenic activities were ranked. A total number of 233 plant species were identified, belonging to 80 families; out of which, Euphorbiaceae and Apocynaceae were dominant families The density and basal area ranged from 2,200-6,000 ha-1 and 2.59-17.58 m2 ha-1 respectively across the study sites. Pterocarpus santalinoides, Alchornea cordiflora, Chassalia kolly, Tetracera spp, Fimbristylis, Bambusa vulgaris and Cyrtosperma senegalense were the dominant species. The Shannon diversity index ranged from (1.38-3.49), Simpson (0.66-0.97), and Evenness diversity (0.43-0.84). Fisher alpha (10.03-30.21) and Whittaker beta diversity (0.36-0.89) values were highest in Ipetumodu (site VIII) and lowest in Ilesha (site II). Seventy-three (73%) of the species in this study had a low important value index (IVI). The dominance of some lianas and herbaceous species in the riparian forest sites showed disturbances, stages of ecological succession, and regeneration of the vegetation. Conservation is inevitable towards maintaining and protecting species diversity, ecosystem roles, and services of these forests in Nigeria.

Data from: Hazard and catch composition of ghost fishing gear revealed by a citizen science clean-up initiative

Ghost fishing, the continued catch of fishes and invertebrates by lost fishing gear, represents an animal welfare issue as well as a waste of both potential food and ecosystem resources. Fishing gear is lost by both commercial and recreational fishers, and management authorities often lack an overview of gear loss and subsequently potential impact on coastal populations. To investigate the hazard and catch composition of lost fishing gear along the Norwegian coast, recreational divers in collaboration with scientists conducted systematic reporting of retrieved lost fishing gear. Through this citizen science project, a total of 12,101 gear items were retrieved and reported, including traps, gillnets and fyke nets. Combining both data on the catch ratio of the gear and its relative quantity, we identified the five most hazardous gear types to be parlor traps, gillnets, fyke nets, wrasse traps and square collapsible traps. The parlour trap was the most hazardous trap, due to high catchability and quantity. The correct classification of gear type could not be confirmed in 2.8 – 6.1 % of the pictures taken by divers, depending on reporting format, and divers reported the wrong gear type in 1.4 % of the reports. Brown crab (Cancer pagurus) was the species most often found in retrieved gear. Furthermore, the vulnerable species European lobster (Homarus gammarus) and Atlantic cod (Gadus morhua) were also common. These results can inform future clean up-initiatives and management responses to ghost fishing, including preventive measures against gear loss and gear restrictions and customization.

Monitoring of the physico-chemical composition of the Seine River based on the MeSeine network

In Europe, the management of freshwater ecosystem is governed by the Water Framework Directive (2000/60/CE) and its transposing legislation in France (2006-1772 of December 2006). The good ecological status of water are evaluated using a combination of several indicators such as biological and physico-chemical parameters. The Seine River crosses several important urbanized areas of France, including the Parisian conurbation (9 millions inhabitants). To ensure the good ecological status of the Seine River, the Greater Paris Conurbation Sanitation Authority (SIAAP), has constructed and operated the MeSeine network since 1990. MeSeine constitutes a tool for evaluating the quality of the Seine river and its tributaries (Marne, Oise) in terms of physico-chemistry, bacteriology, micro-contamination and faunal diversity. The MeSeine network extends along 125 km of the Seine River (from Choisy to Méricourt) and over 13 km along the Marne River (frome Champigny to Alfortville). It is structured around tree pillars: <ul> <li>Real time monitoring of the physico-chemical composition of the Seine river using in situ sensor, in particular dissolved oxygen and temperature sensors</li> <li>Sampling and laboratory analysis campaigns to monitor watercourses quality and comply with the quality standards as defined by the Water Framework Directive (good ecological and chemical parameters)</li> <li>Biota monitoring to appreciate the diversity of fish populations, macro-invertebrates and diatoms.</li> </ul> The aim of this work is to provide data on the physico-chemical quality of the Seine generated by the MeSeine observatory via the open platform Zenodo.

Cloud forests of the Orinoco River Basin (Colombia): Variation in vegetation and soil macrofauna composition along the hydrometeorological gradient

We present vegetation, soil macrofauna, soil, hydrometeorological and topographical data collected from Tropical Montane Cloud Forests in the Orinoco River basin. Specifically, from the municipality of Chámeza, department of Casanare, Colombia. These data sets were used to evaluate how vegetation and soil macrofauna diversity vary along the 1700–2200 m a.s.l. elevation range. Within this elevation range, we have previously described a hydrometeorological gradient largely driven by a fog incidence increase with elevation. Vegetation data were collected for all individuals with a diameter at breast height (DBH) > 5 cm in four vegetation plots (5 x 50 m; total: 0.1 ha) every 100 m in altitude between 1700–2200 m a.s.l. From each plot, we obtained three soil monoliths from the organic layer and three from the mineral horizon, and manually extracted their soil macrofauna, and soil samples for determining pH, organic matter content, and soil texture, among others in a soil laboratory. Topographical data was inferred from Digital Elevation Models. Hydrometeorological data was collected in a previous study, but it was interpolated to the sampling plots. Here we present the interpolated hydrometeorological data.