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403 results for “Occurrence Data”
FIGURES 1–14. 1–4 in New data on recently described Chilean trophonines (Gastropoda: Muricidae), description of a new species and notes of their occurrence at a cold seep site
FIGURES 1–14. 1–4, Trophon condei Houart, 2003; 1, Chile, Ancud, trawled in 1350m, holotype IRSNBIG 29715/512, 61.4mm; 2, Chile, 36°21.65'S, 73°44.42'W, 900904m (AGT 5), JS, 41.6mm; 3–4, Chile, off Concepción, 36°21.46'S, 73°44.08'W, 930m, MNHNCL201646, 41.8mm; 5–10, Trophon ceciliae Houart, 2003; 5–6, Chile, trawled off Caldera, III Región, 434m, coll. E. Garcia, nr 25029, 43.9mm; 7–8, Chile, off Concepción, 36°21.46'S, 73°44.08'W, 930m, JS, 28.7mm (juvenile); 9, Chile, Antofagasta, 1000m, holotype MNHN Moll 4544, 41.5m; 10, Chile, Antofagasta, 1300m, paratype RH, 16.5mm (juvenile); 11–14, Trophon vangoethemi Houart, 2003; 11–12, Chile, trawled off Itata, north of Concepción, in about 350m, Holotype IRSNB IG 29715/ 513, 16.9mm; 13–14, Chile, off Concepción, 36º10.50' S, 73º35.95'W, 563–613m, JS, 13. 14.8mm; 14: 16.8mm.
FIGURES 27–35. 27–29 in New data on recently described Chilean trophonines (Gastropoda: Muricidae), description of a new species and notes of their occurrence at a cold seep site
FIGURES 27–35. 27–29, Coronium wilhelmense (RamírezBohme, 1981); 27–28, Chile, off Valdivia, 39°50'S, 74°30'W, 500m, JS, 18.4mm; 29, Protoconch. Scale bar: 0.5mm; 30, Protoconch of Trophon acanthodes (Watson, 1882) [syntype BM(NH)] 1887.2.9.570. Scale bar: 0.5mm; 31–32, Trophon vangoethemi; 31, Operculum, Chile, off Concepción, 36º10.50' S, 73º35.95' W, 563–613m (scale bar: 1.2mm); 32, Radula, male, same locality (scale bar: 60µm); 33, Radula of Trophon condei, female, off Concepción, Chile, (Sta. AGT 1, 11/30/2003), 36°21.46'S, 73°44.08'W, 930m, (scale bar: 120µm); 34–35, Radula of Pagodula concepcionensis n.sp., female, off Concepción, Chile, (Sta. AGT 1, 11/30/2003), 36°21.46'S, 73°44.08'W, 930m, (scale bar: 60µm).
DATA for Nano Ranking Analysis: determining NPF event occurrence and intensity based on the concentration spectrum of formed (sub-5 nm) particles
<p>data used for: </p><p>Nano Ranking Analysis: determining NPF event occurrence and intensity based on the concentration spectrum of formed (sub-5 nm) particles</p><p>https://doi.org/10.5194/ar-2023-5</p>
Data from "Elevation affects both the occurrence of ungulate browsing and its effect on tree seedling growth for four major tree species in European mountain forests"
<p>This repository contains the field data used in the paper from Bernard et al. on the interactive effect of elevation and ungulate browsing on tree regeneration. This dataset is associated with a github repository containing the code to run the analyses of the paper, publicly available at https://github.com/jbarrere3/BaccaraPaper</p>
Data from: Novel associations among insect herbivores and trees: drivers of occurrence and damage on pines and eucalypts
<p><span>List of novel associations beteween insects and pine and eucalypt trees recorded in these study (each row represents a single novel association). We detail characteristics of the insect species involved in each novel association, indicating their order, family, subfamily species, native biogeographic region (Afr: Afrotropic, AP: Austro-Pacific, IM: Indo-Malaya, Nea: Nearctic, Neo: Neotropic, Pal: Palearctic), non-native biogeographic region where it has established, feeding guild (W&PF: wood and phloem feeder, FF: foliage feeder, F&SF: fruit and seed feeders , SF: sap feeder, ShF: shoot feeder), specificity in host use (VP: very polyphagous, P: polyphagous, O: oligophagous, M: monophagous), impact (N: negligible, L-M: low-medium, H: high, LD: lack of data), and the tree condition (L: living, DD: dying or dead, D: exclusively dead). Information not available is indicated as N/A). We also detail the biogeographic region where the novel association was reported, the novel association type (NIET: native insect on exotic trees, EINT: exotic insect on native trees, EIET: exotic insect on exotic trees), the pine and eucalypt novel host involved in the association, and the phylogenetic relatedness between ancient and novel hostts both for pines and eucalypts (SG: same genus, SF: different genera of the same family, DF: different family). Colors were assigned for the<span> </span>insect species involved in: two new association (orange), three new association (yellow), four new association (pink), five new association (green).</span></p>
Moose occurrence data in Bohemian Forest Ecosystem
<p>This dataset contains all gathered spatial data for moose occurrence in our study area (see manuscript). In the table you can find these attributes: country of the occurrence, data quality according to SCALP classification, details about occurrence, coordinates for used S-JTSK (5514) reference system, locality and year of the record.</p>
Data for "Association of lightning occurrence with precipitation cloud column structure at a fixed position"
<p>Here are the data for the paper titled "Association of lightning occurrence with precipitation cloud column structure at a fixed position" and submitted to Atmospheric Research. The abstract is as follow.</p> <p> </p> <p>In this study, a C-band frequency-modulated continuous-wave (C-FMCW) radar, with its feature of vertical detection, was combined with lightning discharge recordings within a 3 km range to investigate the dependence of lightning occurrence on the structure of precipitation cloud columns (PCCs) from the perspective of a fixed position. The results show that, relative to PCCs without lightning, PCCs with lightning exhibit greater maximum reflectivity, maximum upward radial velocity, maximum velocity spectrum width, cloud top height, and vertically integrated liquid in terms of their average values, and wider-range distributions of these parameters. Using the Light Gradient Boosting Machine algorithm, a lightning diagnosis program that integrates multiple C-FMCW radar parameters was developed. Its hit rate of lightning occurrence is 93.5% and it has a threat score of 0.421. The maximum velocity spectrum width above the melting layer was found to be the most effective in distinguishing PCCs with or without lightning. It was suggested that the hydrometeor properties at a specific location, specifically the size diversity and content of ice-phase particles, should be the key elements determining the occurrence of lightning discharge in PCCs; meanwhile, the convection characteristics in the PCCs may be not the most critical.</p>
seltmann/taxonomy-darwin-core: A GitHub Approach to Publishing Darwin Core Formatted Occurrence Data for Taxonomic Studies
<p><strong>A GitHub Approach to Publishing Darwin Core Formatted Occurrence Data for Taxonomic Studies</strong></p> <p><strong>Description</strong><br> This repository contains a Darwin Core Archive template and instructions for revisionary taxonomists to use to publish their data as a Darwin Core Archive or Darwin Core Compliant CSV file. This repository contains the Darwin Core Archive for "A taxonomic revision of <em>Gryonoides</em> Dodd, 1920 (Hymenoptera: Scelionidae), with a review of the hosts of Teleasinae." The archive was produced by the authors from data contained in mx (Yoder et al. 2006–present).</p> <p><strong>Summary</strong><br> Darwin core archives have emerged as the accepted data-sharing standard for occurrence data about organisms. These occurrences could be observations or specimens in natural history collections. The standard is applied by natural history collections worldwide to share their data between various repositories, including Global Biodiversity Information Faculty (GBIF) and Integrated Digitized Bio collections (iDigBio). This repository can be repurposed as an example template for publishing material examined as a Darwin Core Archive, accessible for data aggregators, journals, and conforming to community standards. This method can be used for any occurrence dataset, such as material examined, species monitoring observation records, ecological observations, or natural history collection data.</p> <p><strong>How to Create a Darwin Core Archive Using this Repository</strong><br> 1- Fork repository on GitHub or download its contents.</p> <p>2- Use the occurrences.csv file as a template. Delete the *Gryonoides* data and add your own. Do not change the column number or order. It is ok to leave in extra columns that you do not use. The only columns that need to be filled out are <em>occurrenceID</em> and <em>BasisOfRecord</em>. Specific definitions of the field names can be found in the Darwin Core Documentation under the <a href="https://dwc.tdwg.org/terms/#occurrence">Occurrence Core</a>.</p> <p>3- Do not touch the meta.xml. This file describes the columns in the occurrences.csv file.</p> <p>4- Edit the eml.xml files to include information about your institution and project. </p> <p>5- Zip the folder to create the archive. If you are using GitHub you can use the zip function for the repository using Code -> Download ZIP.</p> <p>6- Validate the archive using the <a href="https://www.gbif.org/tools/data-validator">GBIF Data Validator tool</a>.</p> <p><strong>Citations</strong></p> <p>Yoder, M.J., Dole, K., Seltmann, K., and Deans, A. 2006-Present. Mx, a collaborative web based content management for biological systematists. http://mx.phenomix.org/index.php/Main_Page<br> </p>
Data and analysis for: Divergent occurrences of juvenile and adult trees are explained by both environmental change and ontogenetic effects
<p>This is a mirror of the github repository https://github.com/lukasheiland/Divergence at 2021-12-16, which provides code and aggregated data to reproduce the simulations and analyses in "Divergent occurrences of juvenile and adult trees are explained by both environmental change and ontogenetic effects". Session info is provided in 'DEF_sessionInfo__2020-11-02.*'.</p> <p>The simulations are contained in<br> - 'Sim ontogenetic stages.R'</p> <p>The main script for the empirical analysis<br> - 'Fit beta.R' performs the complete analysis with already aggregated data that is provided with 'Data/taxtables_pres_thresholdsubset.rds'.</p> <p>In addition, several other scripts are provided for reference, which can be explored interactively, but would need additional unanomyzed data to be run completely:<br> - 'Prepare data.R' had been run for wrangling the unanonymized data prior to the analysis.<br> - 'Publishing/Publish fit.R' creates maps, plots, and tables. (For maps, original coordinates would be necessary.)<br> </p>
Figs 1–5 in First record of Cylindrotoma distinctissima (Meigen, 1818) from Serbia and new data on the occurrence of Cylindrotomidae (Diptera) in Bulgaria and Romania
Figs 1–5. Cylindrotoma distinctissima distinctissima (Meigen, 1818) from Kopaonik Mountains (Serbia); 1 – dorsal view of male hypopygium, 2 – habitus, 3 – dorsal view of the head (antennae removed), 4 – lateral view of the head, 5 – wing. Photos by L.-P. Kolcsár.
Fig. 6 in New data on the occurrence of terrestrial true bugs (Hemiptera: Heteroptera) in Pieniny Mountains
Fig. 6. Distribution of Adelphocoris detritus (A) and Criocoris nigripes (B) in Poland; ● – literature data, ● – confirmed data.
Fig. 4 in New data on the occurrence of terrestrial true bugs (Hemiptera: Heteroptera) in Pieniny Mountains
Fig. 4. Comparison of Stenodema sericans and Stenodema holsata: A – S. sericans, female, B – S. holsata, female, C – S. sericans, male, D – S. holsata, male. Photo by A. Taszakowski.
Fig. 2 in New data on the occurrence of terrestrial true bugs (Hemiptera: Heteroptera) in Pieniny Mountains
Fig. 2. The distinguishing features of L. wagneri and L. punctatus. A – spiculum of vesica of L. wagneri; B – spiculum of vesica of L. punctatus, according Aglyamzyanov (2009), modified.; C – Structure of the middle part of right corium L. wagneri: yellow – clavus, green – corium (photo by A. Taszakowski & M. Kanturski).
Fig. 3 in New data on the occurrence of terrestrial true bugs (Hemiptera: Heteroptera) in Pieniny Mountains
Fig. 3. Distribution of Stenodema sericans in Poland; ● – literature data, ● – confirmed data, ● – new data.
Fig. 1 in New data on the occurrence of terrestrial true bugs (Hemiptera: Heteroptera) in Pieniny Mountains
Fig. 1. Eurycolpus flaveolus: A – Distribution in Poland; ● – confirmed data; B – dorsal habitus. Photo by A. Taszakowski
Figs 7 & 8. 7 in First record of Cylindrotoma distinctissima (Meigen, 1818) from Serbia and new data on the occurrence of Cylindrotomidae (Diptera) in Bulgaria and Romania
Figs 7 & 8. 7 – Occurrence of Cylindrotoma distinctissima distinctissima) in Bulgaria, Romania and Serbia; white cirlces – literature data, grey circles – new records. 8 – Occurrence of Diogma glabrata (triangles) and Triogma trisulcata (squares) in Romania; white and gray color applies respectively to literature data and new records.
Fig. 1 in New data on the occurrence of longhorn beetles (Coleoptera: Cerambycidae) in the Eastern Beskid Mountains (Poland)
Fig. 1. The research plots within the Eastern Beskid Mountains: 1 – Libusza and Lipinki, 2 – Bednarka, 3 – Wola Dębowiecka and Dobrynia, 4 – Nowy Żmigród, 5 – Wapienne, 6 – Mrukowa, 7 – Bartne, 8 – Gładyszów and Małastów, 9 – Wysowa-Zrój and Blechnarka; white line – border of the Low Beskids. The map of Poland was created based on gis.biomap.pl.
Data from: Fauxcurrence: simulating multi-species occurrences for null models in species distribution modelling and biogeography
<p>This dataset contains GPS coordinates of occurrences from 22 species from Sulawesi, Indonesia. It was used in the manuscript "Fauxcurrence: simulating multi-species occurrences for null models in species distribution modelling and biogeography" to demonstrate the utility of the fauxcurrence R package (<a href="https://github.com/ogosborne/fauxcurrence">https://github.com/ogosborne/fauxcurrence)</a>.</p>
Data from: Atmospheric N deposition alters co-occurrence, but not functional potential among saprotrophic bacterial communities
The use of co-occurrence patterns to investigate interactions between micro-organisms has provided novel insight into organismal interactions within microbial communities. However, anthropogenic impacts on microbial co-occurrence patterns and ecosystem function remain an important gap in our ecological knowledge. In a northern hardwood forest ecosystem located in Michigan, USA, 20 years of experimentally increased atmospheric N deposition has reduced forest floor decay and increased soil C storage. This ecosystem-level response occurred concomitantly with compositional changes in saprophytic fungi and bacteria. Here, we investigated the influence of experimental N deposition on biotic interactions among forest floor bacterial assemblages by employing phylogenetic and molecular ecological network analysis. When compared to the ambient treatment, the forest floor bacterial community under experimental N deposition was less rich, more phylogenetically dispersed and exhibited a more clustered co-occurrence network topology. Together, our observations reveal the presence of increased biotic interactions among saprotrophic bacterial assemblages under future rates of N deposition. Moreover, they support the hypothesis that nearly two decades of experimental N deposition can modify the organization of microbial communities and provide further insight into why anthropogenic N deposition has reduced decomposition, increased soil C storage and accelerated phenolic DOC production in our field experiment.
Genetic datasets, climatic conditions at sampled localities, and occurrence data to: Ice age-driven range shifts of diploids and expanding autotetraploids within a conserved niche (Grünig, Patsiou & Parisod, 2024, New Phytologist)
<div> <h3><strong>This repository includes</strong></h3> - An overview of the raw sequencing reads deposited in the European Nucleotide Archive (ENA) for the 370 individuals sampled in 17 diploid and 19 tetraploid field populations <div>- Scripts used to genotype diploids and autotetraploids samples of <em>Biscutella laevigata</em> from ddRADseq data</div> <div>- Input data (as vcf format) used in population genetic analyses</div> <div>- Scripts used to run the different genetic analyses</div> <div>- Dataset of extracted climatic conditions at sampled localities</div> <div>- Occurrence dataset used for the climatic niche modelling</div> <br> <h3><strong>Description of the data and file structure</strong></h3> <strong>00.ENA_samples_correspondance.txt: </strong>provides ENA project ID, run ID (i.e. raw fastq files), sample ID, and alias for each sample included in the study.<br> <div> </div> <div><strong>1.scripts_reads_to_vcf.zip:</strong> consists of the following:</div> - <strong>1.reads_to_vcf.md: </strong>md file with scripts documenting the read quality check, demultiplexing, mapping, SNP calling using GATK4, and filtering steps<br> <div>- Additional scripts called within <strong>1.reads_to_vcf.md</strong>:</div> <div>-- 1.3. Mapping: <strong>02_run_mapping_XXX.py</strong> and <strong>BWA-mem_bisc1_sg.py</strong> scripts</div> <div>-- 1.4.a. HaplotypeCaller: <strong>03_V1_gvcf.py</strong></div> <div>-- 1.4.b. GDBI + genotypeGVCF: <strong>03_V3_gdbi_genotype_per100scaf.py</strong></div> <br> <div><strong>2.datasets_genetics.tar.gz</strong> consists of the following</div> <br> <div>- <strong>bisc_all370_diminDP15_tetraminDP30.vcf.gz</strong>: "Initial SNPs dataset" = biallelic SNPs fulfilling GATK quality hard filtering recommendations, present in at least 50% of samples. Genotypes with DP<15 for diploids and DP<30 for tetraploids are set to no-call. This vcf was used as basis for fastsimcoal dataset preparation, and as basis for subsequent selection of loci fulfilling requirements of each analysis. It includes 2246701 biallelic SNPs for 370 samples</div> <br> <div>- <strong>bisc_all370_diminDP15_tetraminDP30_MD05_pruned.vcf.gz:</strong> subset of the "Initial SNPs dataset" retaining SNPs called in at least 50% of samples, and pruned for Linkage disequilibrium. This vcf includes 107574 biallelic SNPs for 370 samples and was used in the analysis of the proportion of diploids diagnostic alleles shared by tetraploids.</div> <br> <div>- <strong>bisc_all370_diminDP15_tetraminDP30_MD01_pruned.vcf.gz: </strong>subset of the "Initial SNPs dataset", retaining SNPs called in at least 90% of samples, and pruned for Linkage disequilibrium. This vcf includes 4444 biallelic SNPs for 370 samples and was used in the analyses of Population diversity and differentiation (SpaGeDi, GenoDive, PCA), and f3-statistics.</div> <br> <div>- <strong>bisc_all370_diminDP15_tetraminDP30_MD0.1_pruned_MAC3rm.vcf.gz:</strong> subset of the "Initial SNPs dataset", retaining SNPs called in at least 90% of samples, pruned for Linkage disequilibrium, and with a minor allele count of 3. This vcf includes 2593 biallelic SNPs for 370 samples and was used in STRUCTURE analysis</div> <br><br> <div><strong>3.pres_2x.txt:</strong> list of the 128 diploid occurrences used in climatic niche modelling</div> <br> <div><strong>3.pres_4x_strat_reg.txt:</strong> list of the 924 tetraploid occurrences used in climatic niche modelling</div> <br> <div><strong>biscall_chelsa_ordered_noDEM.txt:</strong> climatic data extracted from the CHELSA dataset at sampled localities</div> <br> <div><strong>4.plot_GTfreqs.md:</strong> markdown file including scripts to plot allele and genotype frequencies</div> <br> <div> </div> <h3><strong>Sharing/Access information</strong></h3> Raw sequencing reads have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under the accession number PRJEB48869:<a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB48869"> https://www.ebi.ac.uk/ena/browser/view/PRJEB48869</a></div>
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