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384 results for “assemblage data”
Anatoxin concentrations, algal assemblages, and water quality data for the South Fork Eel, Salmon, and Russian Rivers in northern California, 2022-2023
We collected this data to better understand the timing of peak benthic cyanobacterial mat occurrence (specifically taxa associated with anatoxin production, Microcoleus and Anabaena) and mat anatoxin concentrations in rivers. We sampled in northern California on the South Fork Eel, Salmon, and Russian Rivers biweekly in 2022, and the Salmon River biweekly and South Fork Eel weekly in 2023. During each sampling event, we conducted benthic cover surveys, measured in-situ water quality parameters (temperature, pH, dissolved oxygen, conductivity), and collected surface water samples and targeted cyanobacteria samples. In 2022 on all rivers and in 2023 at the Salmon River, we also collected distributed non-targeted periphyton samples to characterize full-reach community compositions. All sampling was completed in 150-m reaches upstream of sensors recording continuous dissolved oxygen, conductivity, and temperature data. We analyzed surface water samples for nitrate, ammonium, soluble reactive phosphate, total dissolved carbon, and dissolved organic carbon. We also analyzed surface water samples from 2022 for major anions (Cl, SO4, Br) and cations (Na, K, Mg, Ca). Targeted-cyanobacteria and non-target periphyton samples were analyzed for anatoxins (and two other classes of toxins, microcystins and cylindrospermopsins), relative abundance of algal taxa (via microscopy), ash-free dry mass, and chlorophyll-a. To estimate mean river depth within the dissolved oxygen footprint upstream of sensors, we kayaked portions of the river and collected river depth measurements. We also measured discharge at each river excluding the Salmon River (due to high discharge) and completed pebble counts at the South Fork Eel River to obtain sediment grain size distributions. Lastly, we estimated daily reach-scale river metabolism (gross primary productivity and ecosystem respiration) using data from dissolved oxygen sensors with the "streamMetabolizer" package in R at all sensor placements.
Ten years (2013-2023) of fish assemblage data collected seasonally with underwater visual surveys on paired artificial and natural reefs
<p>The study of assembly patterns and dynamics of organisms has long remained a foundational theme in ecology. Further, the relationship between assemblages and different habitats can provide important insight on ecological processes and guide management and conservation efforts (e.g., restoration, protected areas). We conducted underwater visual surveys of reef fish assemblages at 14 sites in the eastern Gulf of Mexico, including eight that were paired artificial and natural reefs. By using a paired design, we controlled biotic (e.g., larval supply), abiotic (e.g., depth), and socio variables (e.g., fishing access) to isolate the effect of reef type. Trained scientific SCUBA divers with extensive experience with reef fishes from the broader tropical western Atlantic region conducted two to four 10-minute stationary surveys on the paired reefs each season (i.e., calendar quarters) for 10 years from spring 2013 to spring 2023. We also surveyed six additional artificial reefs from winter 2020 to spring 2023 that lacked natural reef pairs. During each survey, the divers identified and estimated the total lengths of all taxa<strong> </strong>observed within an imaginary cylinder around them. The imaginary cylinders had a radius up to 7.5 meters (depending on horizontal visibility) and extended from the seafloor to the highest visible water above the diver. During the period of study, we conducted a total of 1,349 surveys and counted 544,736 fish that represented 171 taxa (most at the species level). Analyses of these data have revealed habitat-specific heterogeneity of the fish assemblages at both taxonomic and functional trait levels, the importance of herbivory in structuring the benthos, and socio-ecological interactions in the system, among other findings. These data may be useful for other researchers interested in patterns and dynamics of populations and communities, functional traits, taxa-habitat relationships, and for parameterizing statistical, joint distribution, metacommunity, and ecosystem models. In addition, because many of the observed taxa<strong> </strong>are of management concern, they may be useful for researchers interested in fisheries science. The data are free to use, are not copyright restricted, and we ask users to cite this data paper.</p>
Background data: Untangling the effects of multiple human stressors and their impacts on fish assemblages in European running waters
<p>This dataset presents some backkground data from the EFI+ database. Related work addresses human stressors and their impacts on fish assemblages at pan-European scale by analysing single and multiple stressors and their interactions. Based on an extensive dataset with 3105 fish sampling sites, patterns of stressors, their combination and nature of interactions, i.e. synergistic, antagonistic and additive were investigated. </p> <p>Data were derived within the EU-project "Improvement and Spatial extension of the European Fish Index (EFI+)". EFI+, an EU FP6 research project from 2007-2009 was designed to gain new knowledge and to further develop and improve new biological assessment methods to meet needs of the Water Framework Directive (WFD). </p> <p>Background data are available for boxplots and barplots shown in the related research article in STOTEN.</p>
Raw data of "Seasonal fluctuations of ichthyoplankton assemblage in the northeastern South China Sea influenced by the Kuroshio intrusion"
<p>The uploaded data here is the raw data of the manuscript "Seasonal fluctuations of ichthyoplankton assemblage in the northeastern South China Sea influenced by the Kuroshio intrusion" submitted to the Journal of Geophysical Research-Oceans. The CTD file (.cnv) is the data recorded by a Sea-Bird conductivity, temperature and depth (CTD) in the sampling stations. This data is used to analyze the water masses during the study period. It can be analyzed with free software of the Ocean Data View 4 (http://odv.awi.de/) or the MATLAB R2017 (http://www.mathworks.com/products/matlab/). The sequence data (.fasta) is used to evaluate the species composition. The data can be analyzed with free software of the BOLD Identification tool (http://www.boldsystems.org/), the basic local-alignment search tool (BLAST) (https://www.ncbi.nlm.nih.gov/), the Clustal X 2.1 (http://www.clustal.org/) and the MEGA 7 (http://www.megasoftware.net/). In additon, the .nc files are the data of surface temperature during the sampling periods. The data can be analyzed with the MATLAB R2017 (http://www.mathworks.com/products/matlab/).</p>
Data for: Deriving early hydration cement paste phase assemblage, microstructure development and elastic properties using thermodynamic simulation and multi-scale material modeling
<h2>Description</h2> <p>DATA REPOSITORY FOR</p> <p>Title: Deriving early hydration cement paste phase assemblage, microstructure development and elastic properties using thermodynamic simulation and <br> multi-scale material modeling<br>By: Eva Jägle, Jithender J. Timothy, Daniel Jansen, Alisa Machner<br>Accepted by: Cement and Concrete Research</p> <p>This dataset presents the data of the paper 'Deriving early hydration cement paste phase assemblage, microstructure development and elastic properties using thermodynamic simulation and multi-scale material modeling' submitted to and accepted by Cement and Concrete Research. The dataset follows the structure of the paper such that the calculations described therein can be reproduced.</p> <p>Data is available on three types of cement: Two ordinary Portland cements of different grinding fineness (CEM I 42.5 R und CEM I 52.5 R) and one limestone-containing blended cement (CEM II/A-LL 42.5 R). The data refer to the first 24 hours of hydration and temperature conditions of 20°C (for CEM I 42.5 R, CEM I 52.5 R, CEM II/A-LL 42.5 R) and 35°C (for CEM I 52.5 R). All data were retrieved for cement pastes with a water-to-cement ratio of 0.45.</p> <p>The dataset contains raw and processed data from quantitative X-ray diffraction, 5PL cement dissolution fitting, thermodynamic simulation with GEMS, multi-scale material modeling, ultrasonic testing and Vicat penetration tests. The data is mainly available in .xlsx files together with short descriptions in ReadMe.txt files.</p>
Harmonized data and code for "Plankton response to global warming is characterized by non-uniform shifts in assemblage composition since the last ice age"
<p>Harmonized data and R code for "Plankton response to global warming is characterized by non-uniform shifts in assemblage composition since the last ice age" by Tonke Strack, Lukas Jonkers, Marina C. Rillo, Helmut Hillebrand and Michal Kucera (in <em>Nature Ecology & Evolution</em>, 2022, https://doi.org/10.1038/s41559-022-01888-8).</p> <p>Analyse planktonic foraminifera species assemblages from the North Atlantic Ocean over the past 24,000 years.</p> <p>Scripts written by Tonke Strack</p> <p>DATA SOURCES<br>* WOA18: Locarnini, R. A. et al. World Ocean Atlas 2018, Volume 1: Temperature. A. Mishonov, Technical Editor. NOAA Atlas NESDIS 81, 52 (2019).<br>* LGMR: Osman, M. B. et al. Globally resolved surface temperatures since the Last Glacial Maximum. Nature 599, 239-244, doi:10.1038/s41586-021-03984-4 (2021).<br>* MARGO: Kucera, M., Rosell-Melé, A., Schneider, R., Waelbroeck, C. & Weinelt, M. Multiproxy approach for the reconstruction of the glacial ocean surface (MARGO). Quat. Sci. Rev. 24, 813-819, doi:10.1016/j.quascirev.2004.07.017 (2005). Kucera, M. et al. Reconstruction of sea-surface temperatures from assemblages of planktonic foraminifera: multi-technique approach based on geographically constrained calibration data sets and its application to glacial Atlantic and Pacific Oceans. Quat. Sci. Rev. 24, 951-998, doi:10.1016/j.quascirev.2004.07.014 (2005).<br>* planktonic foraminifera assemblage data: individual citations provided in CoreList_PlanktonicForaminifera.csv</p> <p>DATA<br>1. Harmonized assemblage data*: FullDataTable_PF_harmonized.txt<br>2. Core list with additional information to time series: CoreList_PlanktonicForaminifera.csv<br>3. Reference list for PF names: ReferenceList_PlanktonicForaminifera.csv</p> <p>CODE<br>1. 01_DataAnalysis_PCA.R: principal component analysis on assemblage data of individual time series as well as on whole dissimilarity matrix (results shown in Fig. 1 and 2)<br>2. 02_DataAnalysis_LocalBiodiversityChange.R: local biodiversity change analysis of individual time series (results shown in Fig. 3 and Extended Data Fig. 1); also recalculates resolution of time-series<br>3. 03_DataAnalysis_NoAnalogueAssemblages.R: calculates compositional dissimilarity to the nearest LGM sample to analyse existence of no-analogues (results shown in Fig. 4, as well as Extended Data Fig. 3 and 4)<br>4. 04_DataAnalysis_LDG_LGMresiduals.R: visualises latitudinal diversity gradient through time and the difference between richness and Shannon diversity to their respective LGM mean values (results shown in Fig. 5)</p> <p>*Assemblage data of individual time series were manually downloaded, checked and harmonized following the taxonomy of Siccha and Kucera (2017) and combined into one data file. Species not reported in the time series data were assumed to be absent (i.e., zero abundance). We merged <em>Globigerinoides ruber ruber</em> and <em>Globigerinoides ruber albus</em>, because some studies only reported them together as <em>Globigerinoides ruber</em>. Also, P/D intergrades (an informal category of morphological intermediates between <em>Neogloboquadrina incompta</em> and <em>Neogloboquadrina dutertrei</em>) were merged with <em>Neogloboquadrina incompta</em>. In total, 41 species of planktonic foraminifera were included in this study.</p> <p>Siccha, M. & Kucera, M. ForCenS, a curated database of planktonic foraminifera census counts in marine surface sediment samples. <em>Sci. Data</em> 4, 170109, doi:10.1038/sdata.2017.109 (2017).</p>
R code and data for "Flake selection and scraper retouch probability: an alternative model for explaining Middle Paleolithic assemblage retouch variability"
<p>R code and data used for "Flake selection and scraper retouch probability: an alternative model for explaining Middle Paleolithic assemblage retouch variability" (Archaeological and Anthropological Sciences, Volume 10, Issue 7, pp 1791–1806)</p>
Data and code: Kuipers et al. (2023) Land use diversification may mitigate on-site land use impacts on mammal popultions and assemblages. Global Change Biology
<p>Zip folder conaining the data and code that support the findings of <em>Kuipers et al. (2023) Land use diversification may mitigate on-site land use impacts on mammal popultions and assemblages. Global Change Biology.</em></p> <p>The <em>Data_code.zip</em> folder contains four subfolders with the following files:</p> <ul> <li>Data_raw <ul> <li>AgriDiv_data.csv</li> <li>AgriDiv_metadata.docx</li> <li>Species_data.csv</li> <li>Species_metadata.docx</li> <li>Landscape_data.csv</li> <li>Landscape_metadata.docx</li> </ul> </li> <li>Data_derived <ul> <li>RIA_RSR_effect_sizes.csv</li> <li>MSA_effect_sizes.csv</li> </ul> </li> <li>Data_output <ul> <li>Response_estimation.csv</li> </ul> </li> <li>R_scripts <ul> <li>01_Effect_size_calculation.R</li> <li>02_Null_model_analysis.R</li> <li>03_Model_selection.R</li> <li>04_Model_analysis.R</li> <li>05_Response_estimation.R</li> <li>06_Figures.R</li> <li>README.md</li> </ul> </li> </ul>
Supplementary data for "Ecological assessment of combined sewer overflow management practices through the analysis of benthic and hyporheic sediment bacterial assemblages of an intermittent stream"
<p><strong>Supplementary data for the Pozzi <em>et al.</em> paper entitled "Ecological assessment of combined sewer overflow management practices through the analysis of benthic and hyporheic microbial assemblages and a tracking of exogenous bacterial taxa in a peri-urban intermittent stream".</strong></p> <p># Created by Dr Adrien C. MEYNIER POZZI on June, 29th, 2023<br> # Part of DOmic research project funded by the Agence de l’Eau - Rhône Méditerranée Corse [AE-RMC, Project 2020 0702 DOmic, 2020-2023], and of the DOmic extension funded by the EUR H2O'Lyon [ANR-17-EURE-0018] of Université de Lyon<br> # Part of the Chaudanne river long-term experiment site belonging to the Observatoire de Terrain en Hydrologie Urbaine (OTHU)<br> # Part of the work conducted in the team on Opportinistic Bacterial Pathogen in the Environment (BPOE) led by Dr. Benoit Cournoyer<br> # Samples were obtained in 2 campaigns, corresponding to periods before (2010-2011) or after (2018) the implementation of the 91/271/EEC European Directive that limited Combined-Sewer Overflow (CSO) discharges to the Chaudanne river<br> # Samples consisted in surface water, benthic and hyporheic sediments taken in run, riffle and pool geomorphologic features, either upstream or downstream the CSO outlet, plus positive and negative controls</p> <table> <tbody> <tr> <td><strong>Metadata. Name and description of data tables provided as supplementary information</strong></td> </tr> <tr> <td><strong>Data Name</strong></td> <td><strong>Description</strong></td> </tr> <tr> <td>Data S1. River hydrology variables and hydraulic gradients at surveyed transects</td> <td>Array to describe the hydrologic variables and gradients at the studied transects. Top line is header, second line is metadata for each recorded variable, and third line is the unit of the variable, if any.</td> </tr> <tr> <td>Data S2. Environmental variables (water physical-chemistry, nutrients, FIBs, MTEs, PAHs) with metadata</td> <td>An array to list environmental variables for all true samples (n=90) included in the study. Sample identifiers and dates are provided. First 8 rows list the CAS number, SANDRE number, unit, method, limit of quantification and norm for each variable, if any.</td> </tr> <tr> <td>Data S3. Hydrological indices and synthetic variables computed with ClustOfVar</td> <td>Hydrological indices computed for the river flow, precipitations and CSO overflows computed over a 3-week period preceding each sampling date.</td> </tr> <tr> <td>Data S4. Discharge events selected to compute CSO dilution ratios</td> <td>An array to describe CSO events included for the computation of the CSO dilution ratio (SI Data 6A) together with 6 tables and 3 figures (SI Data 6B to 6J) describing the CSO event ratio all year round over the studied period, as well as for events that occurred before or after the CSO was modified and during low flow or high flow season. In SI Data 6A, top line is header and second line is metadata for each recorded variable.</td> </tr> <tr> <td>Data S5. Raw environmental matrix for use in R</td> <td>An array to list experimental design and environmental variables for all true samples and controls. Several environmental variables were synthetized using the ClustOfVar method (Chavent et al (2012) 10.18637/jss.v050.i13). Format is directly usable in R software.</td> </tr> </tbody> </table> <p> </p>
Online supplementary data linked to the publication "Aubenas-les-Alpes (S-E France). Part III – Last and final part of the mammalian assemblage with some comments on the palaeoenvironment and palaeobiogeography" doi:10.1016/j.annpal.2019.03.001
<p>Online supplementary appendix including the list of Oligocene localities and associated faunal lists compared to Aubenas-les-Alpes, and the size estimation of the non-predatory species for the construction of Fig.10.</p>
Data 1 for "Population- and age-specific patterns of haemosporidian assemblages and infection levels in European Bee-eaters (Merops apiaster)"
<p>Data related to the article "Population- and age-specific patterns of haemosporidian assemblages and infection levels in European Bee-eaters (<em>Merops apiaster</em>)" in the format .xlsx. The 1st sheet contains all variables for analyses done with the R script (see 10.5281/zenodo.3968360). The 2nd sheet contains explanations about the variables in sheet 1.</p>
Dinoflagellate cyst assemblage data from core JM09-020
<p>Absolute abundances (cysts g<sup>-1</sup>) of dinoflagellate cysts (dinocysts) species, total dinocyst abundance (cysts g<sup>-1</sup>), relative abundance of dinocysts produced by auto- and heterotrophic dinoflagellate species (%), and dry bulk density (g cm<sup>-3</sup>) for flux calculation in core JM09-020.</p>
Data from: Monitoring microarthropods assemblages along a pH gradient in a forest soil over a 60 years' time period
<p>The goal of this study was to assess the development, over 60 years, of microarthropod communities over a pH gradient in forest soil.</p> <p>Site Description</p> <p>Hackfort is an oak coppice grove in the East-Southeast of the city of Zutphen in the province of Gelderland, the Netherlands, 52°06′09.7″ N, 6°15′56.0″ E (see Figure 1). The experimental area is about 1.5 ha and is divided in a 10 m × 10 m grid. Vegetation is dominated by common oak (<em>Quercus robur</em>), mixed with birch (<em>Betula pendula</em>), and had in 1959, an understory of wood sage plugs (<em>Teucrium scorodonia</em>), wood anemone (<em>Anemone nemorosa</em>), bracken (<em>Pteridium aquilinum</em>), and wavy-hair grass (<em>Deschampsia flexuosa</em>). In later years, the understory became more dominated by bramble species (<em>Rubus fruticosus </em>and<em> R. idaeus</em>) and common nettles (<em>Urtica dioica</em>) at the edges of the forest, due to increased N deposition from adjacent farmland. The forest is situated at the transition from western riverine deposits and eastern periglacial cover sands. The soil is a riverine deposit with a few elevation differences, making a number of gradients in clay and loam content, which results in many short-distance gradients in soil types, varying from typic haplaquolls with the largest loam contents, via psammaquentic haplorthods to humaqueptic spodic psammaquents, slightly elevated and low in loam contents.</p> <p>Microarthropod Sampling and pH Measurement</p> <p>In 1959, samples were taken at three subsequent dates: 11 September, 9 October, and 30 October. Samples in 1987 were taken on one date, 9 October, just as on 30 October 2019. Samples were taken following a standard procedure, developed at the Institute for Applied Biological Research in Nature, Wageningen, the Netherlands (later merged into the Research Institute for Nature management, Institute for Forestry and Nature Research and Alterra resp., now known as Wageningen Environmental Research); this procedure has been published by Siepel and van de Bund in 1988 (Siepel and van de Bund, 1988). Each mineral soil sample has 100 cc: a volume of 5 cm diameter and 5 cm depth plus litter on top. In 1959, two samples per date were taken on each plot, making a total of 6 samples (only pooled data are available); in 1987 and in 2019, 4 and 5 samples for each plot were taken on, respectively (data per sample available).</p> <p>Soil cores were put on a Tullgren funnel for 1 week, during which temperature was increased from 35 to 45 °C, and then, microarthropods were collected in 70% alcohol and later put into 20% lactic acid for clarification and identification (Siepel, 1990; Siepel and van de Bund, 1988). The Tullgren funnel used for extraction (Siepel, 1990) has been used ever since 1936 and efficiency has not changed as the tool and protocol was the same all over the years.</p> <p>Identification was done to the species level as much as possible using at present the keys for Oribatida(Weigmann and G., 2006), for Gamasina (Lehtinen, 1994), for Uropodina (Karg, 1989), and for Collembola (Hopkin, 2007). Material from the extractions of 1959 and 1987 was re-examined as far as possible to check the correct species identification. In the 1959 and 1987 samples, only oribatid mites were identified to the species level, whereas in 1959, all species of <em>Quadroppiidae, Oppiidae</em>, and <em>Suctobelbidae</em> were pooled. In 2019, all microarthropods were identified to the species level.</p> <p>Sorting and identification of the 1959 microarthropods was carried out by an experienced acarologist (J.G. de Gunst), in 1987, this was done by a student (C. Arnold) and completed and checked by the second author. For the 2019 samples, we decided to demonstrate the potential difference in picking out the microarthropods from the extraction fluid into the slides for identification as part of the experiment: the first author made a first series of slides including all distinguished animals (dataset 2019 a), while the second author made an extra set of slides with the animals missed by the first (dataset 2019 b). The first author did know since the beginning that the second author would check all samples after her sorting session. In this way, we intended to demonstrate the potential difference in this crucial part of the procedure by a starting and an experienced professional. In the analysis, we compare dataset (2019 a) with (2019 a + b), in order to highlight the difference between a starting and an experienced acarologist. Nomenclature adopted was updated according to current standards, following, e.g., the checklists for Oribatida (Siepel et al., 2009), for Astigmatina (Siepel et al., 2016), and for Mesostigmata (Siepel, 2018). Values of pH-KCl were measured in the core material after the extraction of the microarthropods, both in 1959, 1987, and 2019.</p> <p> </p> <p>We have four data files:</p> <p>1959 hackfort microarthropods data.csv</p> <p>1989 hackfort microarthropods data.csv</p> <p>2019 hackfort microarthropods data.csv</p> <p>pH data Hackfort 1959-2019.csv.</p> <p> </p> <p>Explanation of the variables in the datasets:</p> <p>higher taxon: Oribatida, Astigmata, Mesostigmata, Prostigmata, Collembola or Protura</p> <p>Name in De Gunst 1959: taxonomic identification by De Gunst in 1959</p> <p>Valid name: Henk Siepel re-checked these species names in 2019</p> <p>Plot: plot 1, plot 2, plot 3, plot 4, plot 5</p> <p>a: identified by Yuxi Guo</p> <p>b: re-checked by Henk Siepel from remaining soil microarthropods in slide</p> <p>pH(KCL) and pH(H2O): pH values based on indicated methods</p> <p> </p>
Data from: Restoration of native saltmarshes can reverse arthropod assemblages and trophic interactions changed by a plant invasion
<p><span>Plant invasions profoundly impact both</span> <span>natural and managed ecosystems, and removal of the invasive plants addresses only part of the problem of restoring impacted areas. The rehabili</span><span>tation of diverse communities and their ecosystem functions following removal of invasive plants is an important goal of ecological restoration. Arthropod assemblages and trophic interactions are important indicators of the success of restoration, but have largely been overlooked in saltmarshes. We determined how arthropod assemblages and trophic interactions changed with the invasion of the exotic plant <em>Spartina</em> <em>alterniflora</em> and with the restoration of the native plant <em>Phragmites australis</em> following <em>Spartina </em>removal in a Chinese saltmarsh. We investigated multiple biotic and abiotic variables to gain insight into the factors underlying the changes in arthropod assemblages and trophic structure. We found that </span><span>although <em>Spartina</em> invasion had changed arthropod diversity, community structure, feeding-guild composition, and the diets of arthropod natural enemies in the saltmarsh, these changes could be reversed by the restoration of native <em><span>Phragmites</span></em> vegetation following removal of the invader. </span><span>The v</span><span>ariation in arthropod assemblages and </span><span>trophic structure </span><span>were </span><span>critically </span><span>associated with four biotic and abiotic variables (aboveground biomass, plant density, leaf N, and soil salinity)<span>. </span></span><span>Our findings demonstrate the positive effects of controlling invasive plants on biodiversity and nutrient cycling, and </span><span>provide a foundation </span><span>for assessing the efficacy of ecological restoration projects in saltmarshes.</span></p>
Hierarchical trait filtering at different spatial scales determines beetle assemblages in deadwood: Additional data
<p>Contains data used in the following publication:</p> <p>Felix Neff, Jonas Hagge, Rafael Achury, Didem Ambarlı, Christian Ammer, Peter Schall, Sebastian Seibold, Michael Staab, Wolfgang W. Weisser, Martin M. Gossner (2022). <em>Hierarchical trait filtering at different spatial scales determines beetle assemblages in deadwood. </em>Functional Ecology. <a href="https://doi.org/10.1111/1365-2435.14186">https://doi.org/10.1111/1365-2435.14186</a></p> <p>These are complementary data, which are needed to reproduce the analyses. Most data are archived in the Biodiversity Exploratories Information System (<a href="https://doi.org/10.17616/R32P9Q">https://doi.org/10.17616/R32P9Q</a>).</p> <p>The following data are included:</p> <ul> <li><strong>BELongDead_Subplots_Normal.csv</strong>: List of <em>normal</em> subplots within the BELongDead projects (only these were included in the analyses)</li> <li><strong>Body_length.csv</strong>: Body length data for study species assembled from Freude et al. (1965-1998)</li> <li><strong>Lightness_completion.csv</strong>: Colour lightness recorded from measured individuals and photos from coleonet.de (Lompe, 2002)</li> <li><strong>Name_standardisation.csv</strong>: Dataset used to standardise taxonomic names from different sources</li> <li><strong>Saproxylic_species_sub.csv</strong>: List of saproxylic species (according to Schmidl & Bussler (2004)), which were recorded in the project</li> <li><strong>Similar_Species.csv</strong>: List of similar species for species with missing traits. Based on these, missing traits were estimated</li> </ul> <p><strong>References</strong></p> <p>Freude, H., Harde, K. W., & Lohse, G. A. (1965–1998). <em>Die Käfer Mitteleuropas Band 1-15</em>. Goecke und Evers.</p> <p>Lompe, A. (2002). <em>Käfer Europas</em>. <a href="http://coleonet.de/">http://coleonet.de/</a></p> <p>Schmidl, J., & Bussler, H. (2004). Ökologische Gilden xylobionter Käfer Deutschlands. <em>Naturschutz und Landschaftsplanung</em>, <em>36</em>(7), 202–218.</p>
The Meltwater Pulse1A Triggered an Extreme Cooling Event: Evidence From Southern China. Meltwater Pulse Cooling Event (MCE). Winter temperature data during the last deglacial of Huguangyan Maar lake, Surface water temperature and seasonal diatom assemblage data of Huguangyan and Yunlong Lake.
<p>Here we present results of The lake averaged monthly mean surface water temperature over the period from September 2013 to August 2015 from Yunlong Tianchi Lake(YL)(25°52.2′N, 99°16.8′E, altitude: 2551 m a.s.l), southwestern China. The dataset include sediment trap main diatom percentages over the period from September 2013 to August 2015 from YL. Lake water temperature profiles at different depths (1, 3, 6, 9, 11, 13, 16 m) from November 2008 to May 2009 in Huguang Maar Lake (HML)(21°9′N, 110°17′E), Southern China. AMS radiocarbon dates of plant remains and bulk sediment samples for Huguangyan Maar Lake over the last ~17 cal ka BP. The main diatom assemblage percentages (%) from 17 to 10 cal ka BP at Huguangyan Maar Lake. Diatom-based reconstruction of winter temperature (WT) from 17 to 10 cal ka BP at Huguangyan Maar Lake.</p>
Data from: Active restoration accelerates recovery of tropical forest bird assemblages over two decades
<p>Choosing effective methods to restore habitat for the diverse faunal assemblages of tropical forests is hampered by lack of long-term data comparing multiple restoration treatments. We conducted area counts of bird assemblages over 12 years (~5-17 years since restoration) in a blocked experiment with two active planted treatments (tree plantations and applied nucleation) and a passive restoration treatment (natural regeneration) replicated at 11 sites in Costa Rica. We also surveyed six pastures and five remnant forest sites to assess recovery of avian species richness, composition, forest specialists, and range-restricted species in restoration plots relative to degraded and reference systems. Restoration treatments showed increased resemblance of avian assemblages to remnant forest over time. Applied nucleation proved equally effective as plantation, despite a reduced planted area, whereas natural regeneration recovered more slowly. Assemblage-level trends in avian species richness and compositional similarity to reference forest are underpinned by reductions in use by pasture birds and by gradual increases in richness of forest-affiliated species. Because forest-affiliated species tend to have narrower distributions than the open-country species they replace, forest restoration can reduce biotic homogenization at the local scale. Restoration practitioners should consider applied nucleation as an alternative to standard plantations if seeking rapid recovery of bird assemblages. However, the ecological return on investment from natural regeneration increases over a couple of decades. Managers should monitor trends in forest-affiliated and range-restricted species to track the recovery of the full avian assemblages, since coarse metrics like species richness and overall compositional similarity may plateau relatively quickly.</p>
Data from: Rapid shift in benthic assemblages following coral bleaching at an upper mesophotic habitat in Taiwan
<p>Mesophotic coral ecosystems (MCEs; typically, 30–150 m depths) have traditionally been considered potential refuges for shallow-water organisms, but recent evidence suggests that this role is context-dependent. Here, we document a singular habitat at the upper mesophotic depth (- 30 m) in Xiaoliuqiu, Taiwan, and assess the changes in the benthic assemblage one year after a heatwave affected the reefs. In the habitat studied, abundant branching depth-specialist corals were found free-living and thriving on the sandy-rubble bottom amidst dense filamentous turf algae. In 2022, 63.6% of the corals were observed bleached, which was associated with severe heat stress affecting shallow reefs. The dominant coral at the time, <em>Acropora tenella</em>, suffered the most from the bleaching, with only 9.7% of its population remaining healthy. After one year, there was a noticeable shift in dominance from <em>A. tenella</em> to the previously cryptic <em>Anacropora</em> spp. without an obvious change in coral cover. We hypothesize that this rapid shift is driven by <em>Anacropora</em> spp., benefiting from the dense canopy provided by <em>A. tenella</em>. This suggests that the composition of understory organisms may play an important role in the resilience of some reefs affected by disturbance. The characteristics of this habitat, which consists mainly of deep-water specialists, and its susceptibility to stressors indicate that this habitat is unlikely to serve as a refuge for most shallow-water taxa. Our findings reinforce that the effectiveness of MCEs as refuges is not universal, and emphasize the importance of incorporating these unique habitats into conservation strategies and gaining a deeper understanding of their functions before they are lost.</p>
Data and Code from: Wildfire influences species assemblage and habitat utilisation of boreal wildlife after more than a decade in northern Sweden
<p>Data and Code supporting the analyses presented in: Fredriksson, Cromsigt & Hofmeester - Wildfire influences species assemblage and habitat utilisation of boreal wildlife after more than a decade in northern Sweden as published in Wildlife Biology</p> <p><strong>Abstract</strong></p> <p><span>Fires can strongly change the vegetation structure and the availability of resources for wildlife, but fire suppression has long affected the natural role of fire in shaping boreal ecosystems in northern Europe. Recently, wildfires have increased in frequency, possibly due to global warming. In contrast to the boreal systems in North America, there have been few studies on responses of wildlife to wildfires in northern Europe. Based on the findings from North America, we predict that responses of wildlife to wildfire vary among wildlife species: where mammalian herbivores, such as moose (<em>Alces alces</em>) and mountain hare (<em>Lepus timidus</em>), will be attracted to burnt areas following an increase in food availability, other species, such as reindeer (<em>Rangifer tarandus</em>), are negatively impacted due to fire reducing their preferred food. We then tested our predictions by contrasting wildlife utilization of sites that burnt by wildfire in 2006 with nearby unburnt control sites in three areas in northern Sweden. To measure wildlife utilization, we used 72 camera traps, equally divided between the burnt and control sites, with two placement strategies: random and on wildlife trails. The cameras recorded 27 mammal and bird species during summer 2018. Species assemblage differed between burnt and control sites. Fieldfare (<em>Turdus pilaris</em>) used burnt sites more than control sites, while pine marten (<em>Martes martes</em>) and western capercaillie (<em>Tetrao urogallus</em>) used control sites more than burnt sites. We however did not find support for a positive effect of past forest fires on any of the observed wild mammals. We discuss how, due to the impact of forestry, forage-rich habitat may not be as limiting in Scandinavia as in the North-American context, potentially leading to recently burnt sites being less attractive to herbivores such as moose.</span></p>
Data for: Modeling the transition of death assemblages through the mixed layer predicts a downcore increase in time averaging
<p>Understanding how time averaging changes during the burial is essential for using Holocene and Anthropocene cores to analyze ecosystem change, given the many ways in which the time averaging affects biodiversity measures. Here, we use transition-rate matrices to explore how time averaging changes downcore when shells transit through a taphonomically-complex mixed layer into permanently-buried historical layers: this is a null model, without any temporal changes in rates of sedimentation or bioturbation, to contrast with downcore patterns that might be produced by human activity. Assuming stochastic burial and exhumation movements of shells between increments within the mixed layer and stochastic disintegration within increments, almost all combinations of net sedimentation, mixing, and disintegration produce a downcore increase in time averaging (interquartile range, IQR), typically associated with a decrease in kurtosis and skewness and with a shift from right-skewed to symmetrical age distributions. A downcore increase in time averaging is a null expectation wherever bioturbation generates an internally-structured mixed layer (i.e., a surface well-mixed layer is underlain by an incompletely-mixed layer), so that shells are mixed throughout the entire mixed layer at slower rate than they are buried below it by sedimentation. This downcore trend created by mixing is further amplified by the downcore decline in disintegration rate. Using data from the southern California shelf, we find that transition-rate matrices accurately reproduce the downcore changes in IQR, skewness, and kurtosis observed in sediment cores. The right-skewed distributions typical of surface death assemblages – the focus of most actualistic research – might be fossilized under exceptional conditions of episodic anoxia or sudden burial. However, such right-skewed assemblages will not typically transfer into subsurface historical layers and thus will be geologically transient. The deep-time fossil record will be dominated instead by more time-averaged assemblages with weakly skewed age distributions that form in the lower parts of the mixed layer.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.