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106 results for “vertical distribution”
Data and Analysis for Kaplanis, Denny, and Raimondi 2024, "Vertical distribution of rocky intertidal organisms shifts with sea-level variability on the Northeast Pacific Coast".
<p>This repository contains all the data and R scripts used to produce all analyses and figures for Kaplanis, Denny, and Raimondi 2024, as well as all intermediate outputs and final figures. To access this content, download and unzip the intertidalvertdist folder (for intertidal vertical distribution). The R Project is titled "intertidalvertdist". All pertinent information needed to access data, replicate the analyses, and produce figures is contained within the README file, but a brief desciption is below.</p> <p><br>Directory Architecture:</p> <p>Data:<br>Contains all data. Within this folder are two subdirectories - Raw Data, and Processed Data. Raw Data are unmanipulated, straight from the data source. Processed Data are outputs from scripted data wrangling and transformations. </p> <p>Within each of these folders are two more subdirectories: Tide Gauge Data, and MARINe Data. These are the two data sources used in this manuscript - monthly sea-level data from The National Oceanic and Atmospheric Administration Center for Operational Oceanographic Products and Services (NOAA CO-OPS) tide gauge stations, and long-term rocky intertidal biological monitoring data from Multi-Agency Rocky Intertidal Network (MARINe) survey sites.</p> <p>Scripts:<br>All R scripts are contained within the Scripts folder. The scripts have the prefix IVD (for intertidal vertical distribution), then a name that indicates the major function of the code. The scripts either downloads data, manipulates data, conducts analyses, and/or produces a figure.</p> <p>Outputs:<br>Any figures and tables from preliminary analyses, but that are not used in the final manuscript, are saved in Outputs.</p> <p>Figures:<br>All final figures and tables are contained in the Figures folder. All figures are produced by scripts, except Figs. 1 and 2, which are schematics produced manually in a graphics editor. This folder contains two other folders: Supplemenatary Figures, and Partial Regression Plots. Partial Regression plots are the same as the final Figures 8-12, except they are grouped by taxa rather than by explanatory variable.</p> <p>Data Processing Workflow - Overview: <br>Tide Gauge Data (Data/Raw Data/Tide Gauge Data/individual stations) were downloaded using the NOAA Co-Ops API URL Builder (https://tidesandcurrents.noaa.gov/api-helper/url-generator.html), merged, then analyzed. Three MARINe data sets from the Coastal Biodiversity Survey (CBS) were accessed via data requests (https://marine.ucsc.edu/explore-the-data/contact/data-request-form.html). The first MARINe dataset (Data/Raw Data/MARINe Data/CBS_Percent Cover Data, both First Sample and Full Sample) was used to determine the top ten most abundant taxa (hereafter termed “dominant taxa”) across CBS survey sites during the monitoring period of 2001-01-01 to 2021-09-30. The second MARINe dataset (Data/Raw Data/MARINe Data/CBS_Elevation Data) was used to describe the upper limits of vertical distribution of dominant taxa through time. The third MARINe dataset (Data/Raw Data/MARINe Data/CBS_Presence Data) was used to visualize latitudinal distribution of taxa.</p> <p>Location information for Tide Gauge Stations and CBS Survey Sites were assembled into a table (Data/Raw Data/CBS_Tide Gauge_Data.csv)</p> <p>Tide Gauge Data were processed first, then MARINe Data. To replicate this workflow follow the steps described in the README file, in order.</p>
VDMBC_vertical_distribution_soil_microbial_biomass_carbon
<p>Soil microbial biomass carbon (SMBC) is important in regulating soil organic carbon (SOC) dynamics along soil profiles by mediating the decomposition and formation of SOC. The dataset (VDMBC) is about the vertical distributions of SOC, SMBC, and soil microbial quotient (SMQ = SMBC/SOC) and their relations to environmental factors across five continents. Data were collected from literature, with a total of 289 soil profiles and 1040 observations in different soil layers compiled. The associated environment data collectd include climate, ecosystem types, and edaphic factors. We developed this dataset by searching the the Web of Sciene and the China National Knowledge Infrastructure from the year of 1970 to 2019. All the data in this dataset met two creteria: 1) there were at least three mineral soil layers along a soil profile, and 2) SMBC was measured using the fumigation extraction method. The data in tables and texts were obtained from literature directly, and the data in figures were extracted by using the GetData Graph digitizer software version 2.25. When climate and soil properties were not available from publications, we obtainted the data from the World Weather Information Service (https://worldweather.wmo.int/en/home.html) and SoilGrids at a spatial resolution of 250 meters (version 0.5.3, https://soilgrids.org).</p> <p>The units of all the variables were converted to the standard international units or commonly used ones and the values were converted correspondingly. For example, the value of soil organic matter (SOM) was converted to SOC using the equation (SOC = SOM × 0.58). Soil depth was calculated as the arithmetic mean value of the upper and lower boundaries for a given soil layer.</p> <p>This dataset can be used in predicting global SOC change along soil profiles using the multi-layer soil carbon models. It can also be used to analyse how soil microbial biomass changes with plant roots as well as the composition, structure, and functions of soil microbial communities along soil profiles at large spatial scales. This dataset offers opportunities to improve our prediction of SOC dynamics under global changes and to advance our understanding of the environmental controls.</p>
Figure 4 in Inter-oceanic comparison of planktonic copepod ecology (vertical distribution, abundance, community structure, population structure and body size) between the Okhotsk Sea and Oyashio region in autumn
Figure 4. Copepod species composition (centre) and copepodid stage structures of the dominant species (left: Oyashio region, right: Okhotsk Sea). All data are integrated means of a 0– 500 m water column based on the IONESS samples in the Oyashio region (St. 19) and Okhotsk Sea (St. OK24) from October to November 1996. Error bars for the copepodid stage indicate standard deviations of each daily duplicate.
Figure 3 in Inter-oceanic comparison of planktonic copepod ecology (vertical distribution, abundance, community structure, population structure and body size) between the Okhotsk Sea and Oyashio region in autumn
Figure 3. Vertical distribution of zooplankton biovolume in the Oyashio region (upper panels) and Okhotsk Sea (lower panels) from September to December in 1996–1998. Note that the biovolume axes are not the same between panels. Tc: thermocline.
Vertical distribution of heterotrophic nanoflagellates in the Baltic Proper
<p>This dataset contains data on the abundance of prokaryotes, heterotrophic nanoflagellates (HNF), specific lineages of HNF and environmental factors in the Baltic Sea collected during four cruises of r/v Baltica (National Fisheries Research Institute) in 2021. The Excel file includes six sheets:</p> <ol> <li>The "Parameters-Data" sheet lists all parameters for data presented in the "Data" sheet. Column A (Name) contains the variables names, column B (Unit) contains units in which they were measured, column C (Method/Device) contains information on the methodology, and column D (Comments) contains additional information</li> <li>The "Data" sheet contains data in a wide format for all variables listed in the "Parameters-Data" sheet measured at sampling depths. The first row contains variable names (listed in Column A of the Parameters-Data sheet) with units in square brackets</li> <li>The "Parameter-Size" sheet lists parameters for data presented in the "Size" sheet in the same format as described for the "Parameters-Data" sheet. Starting from row 5 in columns A and B, the number of measured HNF cells for each sample is given </li> <li>The "Size" sheet contains size measurements of HNF in the samples in a long format. The number of cells measured in each sample is provided in the "Parameter-Size" sheet</li> <li>The "Parameters-CTD depth profiles" sheet lists parameters for data presented in the "CTD depth profiles" sheet in the same format as described for the "Parameters-Data" sheet.</li> <li>The "CTD depth profiles" sheet contains full-depth profiles of variables measured with a CTD probe with 1 m resolution.</li> </ol>
Figure 6 in Vertical distribution and migration of planktonic polychaete larvae in Onagawa Bay, north-eastern Japan
Figure 6. Box plots of vertical distribution of two spionid larvae: a, Pseudopolydora achaeta and b, Prionospio spp. The central line in the box represents the median, the upper and lower boundaries of the box represent the quartiles, and the vertical bar represents the 95% range of larval distribution (left axes). The dashed wavy lines and dark shaded areas represent the tidal level (right axes) and night-time, respectively.
Figure 5 in Vertical distribution and migration of planktonic polychaete larvae in Onagawa Bay, north-eastern Japan
Figure 5. Diel changes in vertical distribution of planktonic spionid larvae at St. 1 in Onagawa Bay from 8:00 a.m. on 20 August to 5:00 a.m. on 21 August 2012.
Figure 4 in Vertical distribution and migration of planktonic polychaete larvae in Onagawa Bay, north-eastern Japan
Figure 4. Diel changes in vertical distribution of planktonic polychaete (upper axes) and chlorophyll fluorescence (ppb) (lower axes) larvae at St. 1 in Onagawa Bay from 8:00 a.m. on 20 August to 5:00 a.m. on 21 August, 2012.
Figure 3 in Vertical distribution and migration of planktonic polychaete larvae in Onagawa Bay, north-eastern Japan
Figure 3. Vertical distribution of each species or genus of planktonic spionid larvae at St. 1 in Onagawa Bay from January to December 2012.
Figure 2 in Vertical distribution and migration of planktonic polychaete larvae in Onagawa Bay, north-eastern Japan
Figure 2. Vertical distribution of each family of planktonic polychaete larvae (upper axes) and chlorophyll a concentration (µg L−1) (lower axes) at St. 1 in Onagawa Bay from January to December 2012.
Fig. 3 in Seasonal and vertical distribution of Dalbulus maidis (Hemiptera: Cicadellidae) in Brazilian corn fields
Fig. 3. Abundance of Dalbulus maidis from yellow sticky card and yellow pan traps positioned at 2 heights in corn grown during (a, c) the rainy season and (b, d) the dry season.
Fig. 1 in Seasonal and vertical distribution of Dalbulus maidis (Hemiptera: Cicadellidae) in Brazilian corn fields
Fig. 1. Trends in capture of Dalbulus maidis, and weather variables, during the study at Teresina, Piauí, Brazil, in 2013.
Fig. 2 in Seasonal and vertical distribution of Dalbulus maidis (Hemiptera: Cicadellidae) in Brazilian corn fields
Fig. 2. Quality of fit of generalized linear mixed models used to assess the effect of trap type on capture of D. maidis at 2 heights, expressed as the ratio of values observed to values predicted by the models. Type 1 = yellow sticky card and type 2 = yellow water pan. (a) Rainy season. (b) Dry season.
Fig. 1 in The Vertical Distribution of the Ant Fauna (Hymenoptera: Formicidae) of the Samanlı Mountains, Turkey
Fig. 1: Map indicating the sampling sites on the Samanlı Mountains (Numbers in the map indicate localities, which are described in the Table 1).
Figure 4 in Diurnal vertical distribution of zooplankton in a newly formed reservoir (Tahtalı Reservoir, Kocaeli): the role of abiotic factors and chlorophyll a
Figure 4. The vertical distribution of A) K. cochlearis, B) P. vulgaris, C) P. sulcata, D) total Rotifera, E) B. longirostris, F) total Cladocera, G) copepod nauplii, and H) total Copepoda, denoted by the time of sampling.
Dataset to: Vertical distribution of ice nucleating particles over the boreal forest of Hyytiälä, Finland
<p>This repository contains the datasets used in the study 'Vertical distribution of ice nucleating particles over the boreal forest of Hyytiälä, Finland'. Detailed information and technical aspects of the data can be found in the publication.</p>
Determinants of the vertical distribution of the phyllosphere differ between microbial groups and the epi- and endosphere
<ul> <li>The assembly of phyllosphere microbial communities is under the control of stochastic and deterministic processes. In neotropical forests, the tree host identity and physiology together with strong heterogeneities of the environment within the canopy and at the leaf scale could potentially drive the assembly of phyllosphere microbial communities.</li> <li>We analyzed the assembly processes shaping the microbial communities living in the endophytic and epiphytic phyllosphere in tree species across vertical environmental gradients present from the top of the canopy to the ground. We used DNA metabarcoding to characterize microbial communities and described the microhabitats along the gradient by measuring morphological and chemical foliar traits of host trees.</li> <li>The results revealed that the assembly of both communities resulted from a balance of deterministic and stochastic effects with strong discrepancies between fungal and bacterial communities. Different effects of the host and of the vertical environmental gradient shaped epiphytic and endophytic communities. If fungal communities were mainly shaped by the host identity, different leaf morphological and chemical leaf traits drove the epi- and endophytic bacterial communities.</li> <li>Taken together, the phyllosphere represent a global selective pressure of the plant on microbial communities but the microhabitat at the leaf scale contribute also significantly to drive the assembly of microbial communities.</li> </ul>
Raw SP-ICP-MS data for the publication "Vertical distribution of inorganic nanoparticles in a Norwegian fjord"
<p>The compressed archive contains SP-ICP-MS data to reproduce results for the paper "Vertical distribution of inorganic nanoparticles in a Norwegian fjord"". F4 in the sample name denotes the outer station, F2 denotes the inner station. The suffix integer (1-6) indicates the depth position, lowest numbers nearest bottom. The letter A denotes acidified sampling, N neutral sampling. The data consists of integer intensity versus time data in .csv-format.</p> <p>The remaining data to produce all other results, visualizations and statistics for the paper is included in the supplementary or GitHub. Associated code is deposited in a GitHub repository, github.com/arebruvold/fordefjorden_distribution. Note that these data may have different licenses:</p> <ul> <li>The excel file "total_metals.xlsx" contains the total metal data.</li> <li>"sjovann_partikler_noytral.xls" and "sjovann_minste_partikler_2.xls" contains quantitative SEM-EDS data.</li> <li>"204473_F4.txt" and "204473_F2.txt" contains CTD data for salinity and temperature.</li> <li>"dens_comps_large.csv" and "dens_comps_large.csv" contain the particle compositions used for particle size calculations.</li> </ul>
Thermal stratification and fish thermal preference explain vertical eDNA distributions in lakes
<p>Significant advances have been made towards surveying animal and plant communities using DNA isolated from environmental samples. Despite rapid progress, we lack a comprehensive understanding of the "ecology" of environmental DNA (eDNA), particularly its temporal and spatial distribution and how this is shaped by abiotic and biotic processes. Here, we tested how seasonal variation in thermal stratification and animal habitat preferences influence the distribution of eDNA in lakes. We sampled eDNA depth profiles of five dimictic lakes during both summer stratification and autumn turnover, each containing warm- and cool-water fishes as well as the cold-water stenotherm, lake trout (<i>Salvelinus namaycush</i>). Habitat use by <i>S. namaycush</i> was validated by acoustic telemetry and was significantly related to eDNA distribution during stratification. Fish eDNA became "stratified" into layers during summer months, reflecting lake stratification and the thermal niches of the species. During summer months, <i>S. namaycush</i>, which rarely ventured into shallow waters, could only be detected at the deepest layers of the lakes, whereas the eDNA of warm-water fishes was much more abundant above the thermocline. By contrast, during autumn lake turnover, the fish species assemblage as detected by eDNA was homogenous throughout the water column. These findings contribute to our overall understanding of the "ecology" of eDNA within lake ecosystems, illustrating how the strong interaction between seasonal thermal structure in lakes and thermal niches of species on very localised spatial scales influences our ability to detect species.</p>
Vertical distribution of epiphytic lichens on Quercus laurina Humb. & Bonpl. in a remnant of cloud forest in the state of Veracruz, México
<p>It is considered that in the tropics, lichen richness and cover tend to increase from the trunk base to the top of the crown of trees. In this study we calculate total beta diversity of the lichen community along a vertical gradient on Quercus laurina. By comparing the richness and cover of the lichens by zone, we will be able to prove that the foliose and fruticose forms will be the minor component of the total lichen species richness; but with the highest cover with respect to the crustose lichens. Five zones were identified in each phorophyte (n=15) with a diameter at breast height > 40 cm. A total of 92 species were identified, of these, 38% were found only in a single zone, 51% were shared between the different zones, 11% occurred across all zones. Species richness and cover increased from the lowest to the highest zones of phorophytes. Dissimilarity in species composition between the zones, can be explained by species replacement. The Indicator Species Analysis revealed that only a few species such as Hypotrachyna vexans, H. cf. sublaevigata and Ramalina cf. sinaloensis preferred a particular zone. The results obtained to date show that the lichen community associated with Quercus laurina phorophytes is highly diverse. There is a high replacement of species across the different zones. Our results suggest that species richness and cover of the corticolous lichen community are related to the zone and the diverse growth forms.</p>
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