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1. Data for "Effects of Azteca trigona alarm pheromones on heterospecific ant behavior"

   https://doi.org/10.25422/azu.data.13963886  

   Frost, Christopher; Yanoviak, Stephen; Wells, Rachel (January 2021, University of Arizona Research Data Repository)

   Data and video files of behavioral responses of Canopy ant species individuals to volatile odors of Azteca trigona ants or control ambient air collected at Barro Colorado Island in Panama. Two videos provide a general examples of the experimental arena and protocol, and the difference between responses to control air and A. trigona headspace air. The single .csv file provides the specific behavioral responses of the individual ants observed and recorded during the behavioral trials.</div></div></div></div>For inquiries regarding the contents of this dataset, please contact the Corresponding Author listed in the README.txt file. Administrative inquiries (e.g., removal requests, trouble downloading, etc.) can be directed to data-management@arizona.edu</i></div></div> 

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2. Dataset: Spatiotemporal variability and origin of CO2 and CH4 tree stem fluxes in an upland forest

   https://doi.org/10.6084/m9.figshare.14885697.v2  

   Barba, Josep; Poyatos, Rafael; Capooci, Margaret; Vargas, Rodrigo (January 2021, figshare)

   The exchange of multiple greenhouse gases (i.e., CO₂and CH4</sub>) between tree stems and the atmosphere represents a knowledge gap in the global carbon cycle. Stem CO2</sub> and CH4</sub> fluxes vary across time and space and is unclear which are their individual or shared drivers. This dataset contains information of CO2</sub> and CH4</sub> fluxes at different stem heights combining manual (biweekly; n=678) and automated (hourly; n>38,000) measurements in a temperate upland forest.</div>This study was performed in an upland forested area at the St. Jones Reserve [39°5’20”N, 75°26’21”W], a component of the Delaware National Estuarine Research Reserve (DNERR).</div></div>The dominant vegetation species are bitternut hickory (Carya cordiformis</i>), eastern red cedar (Juniperus virginiana</i> L.), American holly (Ilex opaca</i> (Ashe)), sweet gum (Liquidambar styraciflua</i> L.) and black gum (Nyssa sylvatica</i> (Marshall)), with an overall tree density of 678 stems ha^-1 and mean diameter at breast height (DBH) of 25.7±13.9 cm (mean±sd). We studied bitternut hickory, which is one of the most important species in the study site, accounting for 24.9% of the total basal area.</div></div>For code </div></sup></sub> 

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3. Carbon Dioxide and Methane Emissions from a Temperate Salt Marsh Tidal Creek: Dataset

   https://doi.org/10.6084/m9.figshare.12340580  

   Trifunovic, Branimir; Vazquez-Lule, Alma; Capooci, Margaret; Seyfferth, Angelia; Moffat, Carlos; Vargas, Rodrigo (January 2020, figshare)

   Coastal salt marshes store large amounts of carbon but the magnitude and patterns of greenhouse gas (GHG; i.e., carbon dioxide (CO₂) and methane (CH4</sub>)) fluxes are unclear. Information about GHG fluxes from these ecosystems comes from studies of sediments or at the ecosystem-scale (eddy covariance) but fluxes from tidal creeks are unknown. </div>This dataset includes GHG concentrations in water, water quality, meteorology, sediment CO2</sub> efflux, ecosystem-scale GHG fluxes, and plant phenology; all at half-hour time-steps over one year.</div></div>This study was carried out in the St. Jones Reserve, a component of the Delaware National Estuarine Research Reserve in Dover, Delaware, U.S.A. The study site is part of the following networks:</div></div>- AmeriFlux (https://ameriflux.lbl.gov/sites/siteinfo/US-StJ) </div>- Phenocam (https://phenocam.sr.unh.edu/webcam/sites/stjones/) </div></div>The GHG concentration and efflux sampling point was located at Aspen Landing within a microtidal (mean tide range of 1.5 m), mesohaline (typical salinity of 5-18 ppt) salt marsh (Delaware Department of Natural Resources and Environmental Control, 2006) tidal creek.</div></div>Main reference:</div> Trifunovic, B., Vázquez‐Lule, A., Capooci, M., Seyfferth, A. L., Moffat, C., & Vargas, R. (2020). Carbon dioxide and methane emissions from a temperate salt marsh tidal creek. Journal of Geophysical Research: Biogeosciences, 125, e2019JG005558. https://doi.org/ 10.1029/2019JG005558 </p> </div> </div> </div></div></sub> 

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4. Plant neighborhood shapes diversity and reduces interspecific variation of the phyllosphere microbiome. Meyer et. al 2022. ISME-J.

   https://doi.org/10.6084/m9.figshare.16575194.v1  

   Meyer, Kyle (January 2022, figshare)

   This is the data archive for: Meyer et al. 2022. Plant neighborhood shapes diversity and reduces interspecific variation of the phyllosphere microbiome. ISME-J. Please cite this article when using these archived data.</div>DOI: 10.1038/s41396-021-01184-6</div></div>Included are raw genetic sequences of the V5-V7 region of the 16S rRNA gene derived from experimental leaf surfaces of tomato, pepper, and bean plants.</div></div>Included in this archive are:</div>Raw sequence data (RawFASTQ.zip)</div>Reproducible R scripts (MeyerEtAl2021_RScript.R, VarPartSupplement.R)</div>R objects corresponding to archived scripts (.RDS)</div>Data for generating certain plots (PermanovaRValues.txt, PermanovaValuesByHost.txt, NeutralModelRValuesByHarvest.txt, VarPartHostEffects.txt)</div>Sample metadata (NeighborhoodMetaData.txt)</div>Phylogenetic Tree file for sample ASVs (PhyloTree.tre)</div>Geographic distance matrix for distances between plots (GeodistNeighborhood.txt)</div>ddPCR (microbial abundance) data (ddPCR_Neighborhood.csv)</div>R script for rarefication function (Rarefy_mean.R)</div>Taxonomic assignments for all ASVs in study (Taxonomy_Neighborhood.txt)</div>R image files to load R environment instead of running script (MeyerEtAl2021_RScript.RData, VarPartSupplement.RData)</div></div></div></div> 

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5. Data Associated with PhyloFisher

   https://doi.org/10.6084/m9.figshare.15141900.v1  

   Brown, Matthew (January 2021, figshare)

   PhyloFisher is a software package, written in Python3, that contains a protocol designed for phylogenomic dataset assembly and data exploration. This software package aids in the construction and curation of protein sequence-based phylogenomic datasets, conducts post-assembly analyses, and allows visualization of the results. In addition, PhyloFisher currently includes a manually curated starting dataset of 240 proteins from 304 eukaryotic taxa representing the full breadth of known diversity in the eukaryotic tree of life. Importantly, this dataset also includes identified paralogs of each of the 240 proteins from all investigated taxa which is crucial for the identification of probable orthologs. Although PhyloFisher includes this pan-eukaryotic dataset, the tool is flexible and can work with any dataset consisting of protein sequences derived from eukaryotes. The combination of all of the foregoing features makes PhyloFisher a broadly-useful, user-friendly software tool for sophisticated phylogenomic analyses of eukaryotes.</div></div>PROJECT WEBSITE: http://amoeba.msstate.edu/phylofisher/ </div>PROJECT GITHUB: http://github.com/TheBrownLab/PhyloFisher</div></div>This dataset contains files for endusers to retrieve for installation of PhyloFisher as well as accompanying data from the PhyloFisher manuscript.</div></div>Tice_etal.PhyloFisher.archives.tar.gz | Installation requirements for PIP installation</div>Tice_etal.PhyloFisher1.FINAL_DATASET_RENAMED.tar.gz | File dataset associated with the manuscript including matrices and phylogenetic analyses</div>Tice_etal.PhyloFisher_v1.0_input_proteomes_LongNames.tar.gz | Input proteome data from taxa that was used to construct PhyloFisher v1.0</div>Tice_etal.PhyloFisherDatabase_v1.0_Jan.28.2021.tar.gz | PhyloFisher v1.0 starting database</div>Tice_etal.PhyloFisher_FOR_CUSTOM_DATASET_Jan.28.2021.tar.gz | Necessary files and directory structure to be used in custom database construction.</div>Tice_etal.PhyloFisher.DATA.tgz | All data associated with the figures (Fig 3, 4, A-Y) along with all phylogenomic trees and analyses. </div></div></div> 

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