Find research datasets worth reusing

opencc-by-4.0Jan 2022View details →

Tropical extreme droughts drive long-term increase in atmospheric CO2 growth rate variability

This repository includes the code and the processed climate data used to examine the long-term change in atmospheric CO2 growth rate. The code will generate the main figures (Figure 1, 2 and 3) in the paper - Luo, X. & Keenan, T. F. (2022) Tropical extreme droughts drive long-term increase in atmospheric CO2 growth rate variability. Nature Communications, doi: 10.1038/s41467-022-28824-5. Please refer to the "Data Availability Statement" in the paper and cite the original sources if you need to use one or more datasets published here. There are three files in the repository: 1) CGR_analysis_input.mat is the processed data in matlab format to support the study; 2) master_figures_CGR_publish_v1.m is the main matlab routine that used to generate figures; 3) supporting code is a folder that contains third-party routines to support the main routine.

Data from: A shift from phenol to silica-based leaf defenses during long-term soil and ecosystem development

The resource availability hypothesis predicts that plants adapted to infertile soils have high levels of anti-herbivore leaf defenses. This hypothesis has been mostly explored for secondary metabolites such as phenolics, while it remains underexplored for silica-based defenses. We determined leaf concentrations of total phenols and silicon (Si) in plants growing along the 2-million-year Jurien Bay chronosequence, exhibiting an extreme gradient of soil fertility. We found that nitrogen (N) limitation on young soils led to a greater expression of phenol-based defenses, whereas old, phosphorus (P)-impoverished soils favored silica-based defenses. Both defense types were negatively correlated at the community and individual species level. Our results suggest a tradeoff among these two leaf defense strategies based on the strength and type of nutrient limitation, thereby opening up new perspectives for the resource availability hypothesis and plant defense research. This study also highlights the importance of silica-based defenses under low P supply.

Biological experimental raw data from: The Incubascope : A simple, compact and large field of view microscope for long-term

Optical imaging has rapidly evolved in the last decades. Sophisticated microscopes allowing optical sectioning for 3D imaging or sub-diffraction resolution are available. Due to price and maintenance issues, these microscopes are often shared between users in facilities. Consequently, long term access is often prohibited and does not allow to monitor slowly evolving biological systems or to validate new models like organoids. Preliminary coarse long-term data that do not require do acquisition of terabytes of high-resolution images are important as a first step. By contrast with expansive all-in-one commercialized stations standard microscopes equipped with incubator stages offer a more cost-effective solution despite imperfect long run atmosphere and temperature control. Here, we present the Incubascope, a custom-made compact microscope that fits into a table-top incubator. It is cheap and simple to implement user-friendly and yet provides high imaging performances. The system has a field of view of 5.5×8 mm2, a 3 µm resolution, a 10 frames/second acquisition rate, and is controlled with a Python-based graphical interface. We exemplify the capabilities of the Incubascope on biological applications such as the hatching of Artemia salina eggs, the growth of the slime mold Physarum polycephalum and of encapsulated spheroids of mammalian cells.

Data from: Harvest and density-dependent predation drive long-term population decline in a northern ungulate

The relative effect of top-down versus bottom-up forces in regulating and limiting wildlife populations is an important theme in ecology. Untangling these effects is critical for a basic understanding of trophic dynamics and effective management. We examined the drivers of moose (Alces alces) population growth by integrating two independent sources of observations within a hierarchical Bayesian population model. This analysis used one of the largest existing spatiotemporal datasets on ungulate population dynamics globally. We documented a 20% population decline over the period examined. Moose population growth was negatively density-dependent. Although the mechanisms producing density-dependent suppression of population growth could not be determined, the relatively low densities at which moose populations were documented suggests it could be due primarily to density-dependent predation. Predation primarily limited population growth, except at low density, where it was regulating. Harvest appeared to be largely additive and contributed to population declines. Our results, highlight how population dynamics are context dependent and vary strongly across gradients in climate, forest type, and predator abundance. These results help clarify long-standing questions in population ecology and highlight the complex relationships between natural and human-caused mortality in driving ungulate population dynamics.

Long-term monitoring in endangered woodlands shows effects of multi-scale drivers on bird occupancy

Occupancy predictor data, detection predictor data, and species detections from sites in remnant Box Gum Grassy Woodland patches in south-eastern Australia. Only sites, species, and predictors used in our statistical analysises included. For privacy, predictors have been standardised (mean = 0, standard deviation = 1) and latitude and longitude have been offset by random vectors.

A systematic review of long-term avian studies on phenological changes of birds and their food

Many organisms reproduce in seasonal environments, where selection on timing of reproduction is particularly strong as consumers need to synchronize reproduction with the peaked occurrence of their food. When a consumer species changes its phenology at a slower rate than its resources, this may induce a trophic mismatch, i.e. offspring growing up after the peak in food availability, potentially leading to reductions in growth and survival. However, there is large variation in the degree of trophic mismatches as well as in its effects on reproductive output. Here, we explore the potential causes for variation in the strength of trophic mismatches in published studies of birds. Specifically, we ask whether the changes in the degree of mismatch that have occurred over time can be explained by a bird's (1) breeding latitude, (2) migration distance, and/or (3) life-history traits. In particular, the script used contains the following analyses: (I) using linear mixed effect models we test whether the rate of change in food phenology, bird phenology and their difference (i.e. the rate of change in asynchrony) differed significantly from zero, (II) using linear mixed effect models we test whether the rate of change in asynchrony between birds and their food could be explained by breeding latitude, migratory behaviour and/or species life-history traits (body mass, clutch size and incubation duration). We found that none of these three factors explains changes in the degree of mismatch over time. Nevertheless, food phenology did advance faster at more northerly latitudes, while shifts in bird phenology did not show a trend with latitude. We argue that the lack of support in our results is attributable to the large variation in the metrics used to describe timing of food availability.

Effects of long-term nitrogen addition on water use by Cunninghamia lanceolate in a subtropical plantation

The deposition of reactive nitrogen (N) has substantially increased in subtropical regions due to human activities. However, the effects of long-term N addition on the water-use efficiency of subtropical forests are poorly understood. Here, we conducted an 11-year experiment in a subtropical Cunninghamia lanceolate plantation with four N-addition levels: N0, N1, N2, and N3 (equivalent to 0, 6, 12, and 24 g of N m-2 yr-1, respectively). A thermal dissipation probe system was used to calculate sap flow and plant biomass carbon was assessed by field investigation. The whole-plant water use and water-use efficiency were estimated. In addition, the δ13C of tree rings was used to indicate the plant intrinsic water-use efficiency. The results showed that N3 significantly increased the annual sap flow velocity, especially in summer and winter. Annual water use, plant growth, and water-use efficiency did not significantly differ among the N treatments, but water use tended to be higher in N3 than in N0. Furthermore, the reduction of δ13C between the pre-N treatment period and the post-N treatment period was 3.02%, 3.26%, 3.58%, and 5.28% for N0, N1, N2 and N3, respectively, which supported the inference that N addition could enhance water use. We conclude that long-term addition of high levels (but not of low levels) of N increased whole-plant water use in C. lanceolate plantations. Our results indicate that N deposition accompanied by high temperature and drought events may negatively affect water balance in subtropical forests.

opencc-by-4.0Nov 2021View details →

A calcium-based plasticity model for predicting long-term potentiation and depression in the neocortex

This dataset contains all (>1000) cell pairs as the Blue Brain Projects <a href="https://github.com/BlueBrain/EModelRunner">EModelRunner</a> packages as well as analysis code and analysed data used for the figures of our <a href="https://www.biorxiv.org/content/biorxiv/early/2020/04/20/2020.04.19.043117.full.pdf">preprint</a>: "A calcium-based plasticity model predicts long-term potentiation and depression in the neocortex". More documentation will follow in the upcoming days. Updates: v1.1 (31/12/2021): updated READMEs within cell_packages, added 2 extra authors for their contribution in EModelRunner. v1.2 (31/12/2021): same as v1.1 but w/o MacOS junk v1.3 (11/01/2022): added analysis notebooks v2.0 (11/01/2022): same as v1.3 but w/o MacOS junk and proper version number v2.1 (14/03/2022): fetching data from websites when possible instead of providing the downloaded csv files.

opencc-zeroMar 2022View details →

Supplementary material 1 from: Di Lorenzo T, Di Marzio W, Piccini L, Messana G, Sáenz M, Galassi D (2018) Survival, metabolic rates and locomotory activities of a groundwater-obligate copepod species under long-term exposures to tetrachloroethylene. ARPHA Conference Abstracts 1: e29966. https://doi.org/10.3897/aca.1.e29966

Survival, metabolic rates and locomotory activities of a groundwater-obligate copepod species under long-term exposures to tetrachloroethylene

opencc-zeroMar 2022View details →

Archive data supporting the results in the paper: Long-term soil warming alters fine root dynamics and morphology, and their ectomycorrhizal fungal community in a temperate forest soil"

Climate warming is predicted to affect temperate forests severely, but the response of fine roots, key to plant nutrition, water uptake, soil carbon and nutrient cycling is unclear. Understanding how fine roots will respond to increasing temperature is a prerequisite for predicting the functioning of forests in a warmer climate. We studied the response of fine roots and their ectomycorrhizal (EcM) fungal and root-associated bacterial communities to soil warming by 4 °C in a mixed spruce-beech forest in the Austrian Limestone Alps after 8 and 14 years of soil warming, respectively. Fine root biomass (FRB) and fine root production were 17% and 128% higher in the warmed plots, respectively, after 14 years. The increase in FRB (13%) was not significant after 8 years of treatment, whereas specific root length, specific root area, and root tip density were significantly higher in warmed plots at both sampling occasions. Soil warming did not affect EcM exploration types and diversity, but changed their community composition, with an increase in the relative abundance of Cenoccocum at 0 – 10 cm soil depth, a drought-stress tolerant genus, and an increase in short and long-distance exploration types like Sebacina and Boletus at 10 – 20 cm soil depth. Warming increased the root-associated bacterial diversity but did not affect their community composition. Soil warming did not affect nutrient concentrations of fine roots, though we found indications of limited soil phosphorus (P) and potassium (K) availability. Our findings suggest that, in the studied ecosystem, global warming could persistently increase soil carbon inputs due to accelerated fine root growth and turnover, and could simultaneously alter fine root morphology and EcM fungal community composition towards improved nutrient foraging.

opencc-byMar 2022View details →

Is switchgrass good for carbon savings? Long-term results in marginal land Running title: Switchgrass SOC storage capacity in marginal land Walter Zegada-Lizarazu 1, Federica Zanetti 1, Nicola Di Virgilio 2, Andrea Monti 1 1Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 44 – 40127, Bologna, Italy; 2CNR, Institute for the BioEcononomy, National Research Council of Italy, Via P Gobetti 101, I-40129 Bologna, Italy

Growing switchgrass in marginal land can be a valuable option to mitigate the risk of agricultural land abandonment whilst storing a significant amount of soil C. It was found a significant increase in SOC in a 13-years period. A significant positive correlation was observed between the C derived from switchgrass and SOC gain (the estimated switchgrass derived C was 12.7 Mg C ha-1). The increased SOC along the field, however, was patchy, with the highest increments registered in the center of the field, while the lowest ones in the top and bottom of the hill.

opencc-by-4.0Nov 2020View details →

AERA5-Asia: A long-term Asian precipitation dataset (0.1°, 1 hourly, 1951–2015, Asia) anchoring the ERA5-Land under the total volume control by APHRODITE (1967–1981)

AERA5-Asia: A long-term Asian precipitation dataset (0.1°, 1 hourly, 1951–2015, Asia) is developed by organically combining the ERA5-Land dataset with high spatiotemporal resolutions and continuity and the APHRODITE dataset with high quality. How to cite: Ma, Z., Xu, J., Ma, Y., Zhu, S., He, K., Zhang, S., Ma, W., Xu, X., 2022. AERA5-Asia: A long-term Asian precipitation dataset (0.1°, 1 hourly, 1951–2015, Asia) anchoring the ERA5-Land under the total volume control by APHRODITE. Bulletin of American Meteorological Society, 103 (4)., DOI: https://doi.org/10.1175/BAMS-D-20-0328.1. Data Format: GeoTIFF Spatial Coverage: 60°E–150°E, 15°S–55°N, land. AERA5-Asia (0.1°/ hourly, 1951–1966, Asia) is available at  <a href="https://doi.org/10.5281/zenodo.3609352">https://doi.org/</a><a href="https://doi.org/10.5281/zenodo.4266081">10.5281/zenodo.6367463</a> AERA5-Asia (0.1°/ hourly, 1982–1998, Asia) is available at  <a href="https://doi.org/10.5281/zenodo.3609352">https://doi.org/</a><a href="https://doi.org/10.5281/zenodo.4266081">10.5281/zenodo.4266081</a> AERA5-Asia (0.1°/ hourly, 1999–2015, Asia) is available at  <a href="https://doi.org/10.5281/zenodo.3609352">https://doi.org/</a><a href="https://doi.org/10.5281/zenodo.4264451">10.5281/zenodo.4264451</a>

opencc-by-4.0Nov 2020View details →

AERA5-Asia: A long-term Asian precipitation dataset (0.1°, 1 hourly, 1951–2015, Asia) anchoring the ERA5-Land under the total volume control by APHRODITE (1951–1966)

AERA5-Asia: A long-term Asian precipitation dataset (0.1°, 1 hourly, 1951–2015, Asia) is developed by organically combining the ERA5-Land dataset with high spatiotemporal resolutions and continuity and the APHRODITE dataset with high quality. How to cite: Ma, Z., Xu, J., Ma, Y., Zhu, S., He, K., Zhang, S., Ma, W., Xu, X., 2022. AERA5-Asia: A long-term Asian precipitation dataset (0.1°, 1 hourly, 1951–2015, Asia) anchoring the ERA5-Land under the total volume control by APHRODITE. Bulletin of American Meteorological Society, 103 (4)., DOI: https://doi.org/10.1175/BAMS-D-20-0328.1. Data Format: GeoTIFF Spatial Coverage: 60°E–150°E, 15°S–55°N, land. AERA5-Asia (0.1°/ hourly, 1962–1981, Asia) is available at  <a href="https://doi.org/10.5281/zenodo.3609352">https://doi.org/</a><a href="https://doi.org/10.5281/zenodo.4266081">10.5281/zenodo.6369796</a> AERA5-Asia (0.1°/ hourly, 1982–1998, Asia) is available at  <a href="https://doi.org/10.5281/zenodo.3609352">https://doi.org/</a><a href="https://doi.org/10.5281/zenodo.4266081">10.5281/zenodo.4266081</a> AERA5-Asia (0.1°/ hourly, 1999–2015, Asia) is available at  <a href="https://doi.org/10.5281/zenodo.3609352">https://doi.org/</a><a href="https://doi.org/10.5281/zenodo.4264451">10.5281/zenodo.4264451</a>

opencc-zeroMar 2022View details →

Data from: Determinants and long-term costs of early reproduction in males of a long-lived polygynous mammal

In long-lived polygynous species, male reproductive success is often monopolized by a few mature dominant individuals. Young males are generally too small to be dominant and may employ alternative tactics, however, little is known about the determinants of reproductive success for young males. Understanding the causes and consequences of variability in early reproductive success may be crucial to assess the strength of sexual selection and possible long-term trade-offs among life-history traits. Selective pressures driven by fluctuating environmental conditions may depend on age-class. We evaluated the determinants of reproduction in male bighorn sheep (Ovis canadensis) aged 2-4 years using 30 years of individual-level data. These young males cannot defend estrous ewes and use alternative mating tactics. We also investigated how the age of first detected reproduction was correlated to lifetime reproductive success and longevity. We found that reproductive success of males aged three years was positively correlated to body mass, to the proportion of males aged 2-4 years in the competitor pool and to the number of females available per adult male. These results suggest that reproductive success depends on both competitive ability and population age-sex structure. None of these variables, however, had significant effects on the reproductive success of males aged 2 or 4 years. Known reproduction before the age of five increased lifetime reproductive success but decreased longevity, suggesting a long-term survival cost of early reproduction. Our analyses reveal that both individual-level phenotypic and population-level demographic variables influence reproductive success by young males and provide a rare assessment of fitness trade-offs in wild polygynous males.

opencc-zeroApr 2022View details →

Heterogeneity in resource competition covaries with individual variation in long-term social relationships

Resource competition among conspecifics is central to social evolution, as it serves as one of the primary selective pressures of group living. This is because the degree of competition for resources impacts the costs and benefits of social interactions. Despite this, how heterogeneity in resource competition drives variation in the type and quantity of long-term social relationships individuals foster has been overlooked. By measuring male mating competition and female foraging competition in a highly social, long-lived mammal, we demonstrate that individual variation in long-term intrasexual social relationships covaries with preferred habitat and experienced resource competition, and this effect differs based on the sex of the individual. Specifically, greater resource competition resulted in fewer social preferences, but the magnitude of the effect varied by both habitat and sex, whereas for social avoidances, both the directionality and magnitude of the effect of resource competition varied by habitat and sex. Together our work shows how fine-scale variation in individual socioecological niches (i.e., unique physical and social environments) can drive extensive variation in individual social behavior (here long-term relationships) within a population, thereby broadening current theories of social evolution.

opencc-by-4.0May 2022View details →

Generation-dependent functional and numerical responses of Neoseiulus californicus (Phytoseiidae) long-term reared on thorn apple pollen

Raw data of Functional and numerical response of N. califrnicus on T. urticae in different generaaations

opencc-zeroMay 2022View details →

Interactions between local and global drivers determine long-term trends in boreal forest understory vegetation

Aim: Global change effects on forest ecosystems are increasingly claimed to be context dependent, indicated by interactions between global and local environmental drivers. Most examples of such context dependencies originate from temperate systems, while limited research comes from the boreal biome. Here we set out to test if interactions between climate warming, nitrogen deposition, land-use change resulting in increasing forest density and soil pH drive long-term changes of understory vegetation in boreal forests. Location: Sweden Time period: 1953-2012 Major taxa studied: Vascular plants Methods: We used long-term (50 years) National Forest Inventory data on forest understory vegetation in Sweden to model the combined effects of climate warming, nitrogen deposition, increase in forest density (tree basal area) and soil pH. Results: Our results identify increasing temperature, nitrogen deposition and denser, shadier forest conditions as main drivers of understory vegetation changes during this time period. More importantly, we found that these effects varied with local conditions, i.e. that the change towards a more nitrophilic understory vegetation was more pronounced at low than high soil pH. Forest density was an important modulator of nitrogen deposition and temperature increase, with effects generally decreasing with density. Decreased cover of ericaceous dwarf shrubs was driven by both forest density and nitrogen deposition, with a stronger effect at low than at high pH. Main conclusions: Our results highlight that to understand forest ecosystems´ response to global change, and to make adequate management decisions to mitigate the effects of global change, we need to understand how changes in local environmental factors (forest density and soil pH) interact with global-scale drivers (nitrogen deposition and climate warming). Neglecting such interactions will lead to incorrect estimations of effects. In our case, we would e.g. have underestimated the eutrophication effects on acid soils, which constitute a considerable part of the boreal biome. --

opencc-by-4.0May 2022View details →

A Long-Term Land Surface Hydrologic Fluxes and States Dataset for China

** VIC_forcings_4vars: 1/4 Degree Gridded Daily Meteorological VIC Forcing Data Set over China domain  1. Data sources This dataset is from 1/1/1952 to 12/31/2012, which were derived by interpolating gauged daily precipitation, maximum temperature, minimum temperature and wind speed of 756 ground mornitoring stations from Chinese Meteorological Administration (CMA).  ** This section provides only a very brief description of the data source. For a full explanation, the user need refer to the published papers in the references **  2. References to Cite We request that users of this data set cite Zhang et al.(2014) in any reports or publications using it.  Zhang, X., Tang, Q., Pan, M., Tang, Y., 2014. A Long-Term Land Surface Hydrologic Fluxes and States Dataset for China. Journal of Hydrometeorology. (Accepted) 3. Dataset format This data set is available in netCDF (which cannot be read directly by VIC).  Please click the year number in the table below to download the corresponding daily forcings (i.e., precipitation, maximum temperature, minimum temperature and wind speed).  ** VICoutput_fluxes: VIC Retrospective Land Surface Dadaset over China: 1952-2012 1. Background The Variable Infiltration Capacity (VIC) model was driven using the gridded daily observed forcings (including precipitation, maximum temperature, minimum temperature, and wind speed; if necessary, please download the VIC forcings from http://hydro.igsnrr.ac.cn/public/vic_forcings_4vars.html) to simulate the land surface hydrological cycle from 1952-2012 over China. The modeling study was done at a 3-hourly time step and at a spatial resolution of 0.25 degree. Details can be found in the journal article: Zhang, X., Q. Tang, M. Pan, and Y. Tang, 2014: A Long-Term Land Surface Hydrologic Fluxes and States Dataset for China. Journal of Hydrometeorology. doi: 10.1175/JHM-D-13-0170.1 2. Archived data information and format This website provides access to parts of the model derived variables(including the water balance variables and states and energy balance varibales) at daily scale. This dataset is available in netCDF format. Please click the varible names below to download the corresponding variable. 3. Download the dataset Model Derived Variables, 1952-2012 (Water Balance Variables and States) Evaporation Runoff Baseflow Soil Moisture Layer 1 Soil Moisture Layer 2 Soil Moisture Layer 3 Snow Water Equivalent Contact: tangqh@igsnrr.ac.cn

opennotspecifiedAug 2021View details →

Fig. 6 in The explosive radiation, intense host-shifts and long-term failure to speciate in the evolutionary history of the feather mite genus Analges (Acariformes: Analgidae) from European passerines

Fig. 6. The co-phylogenetic scenarios revealed by JANE analysis. Thin black lines are the Analges phylogenetic tree, wide grey lines are the bird tree. The legend shows the cost of each event (in parentheses) near every co-phylogenetic event and the number of reconstructed events. A, original analysis with the full set of taxa in multi-host Analges–bird associations.? – after speciation, the ancestral species still exists. B, dated best-cost scenarios of the multi-host associations reduced to a single host species and supplemented by spread events for remaining host species. Clades in multi-host species remained as in the original analysis, i.e. originated by failure to speciate. The circles near Analges species names designate the components of host nests: black circles, fine feathers and/or down in nest material; white circles, no feathers in nest material (after Gotzman & Jablonski, 1972 and Beuch, 2013).