cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s1f95/1
title: Atrium green roof temperature, moisture, seedling density, and species richness 2014 data

description: Data pertaining to Tables 2 & 3 and Figure 4. Includes data from the Atrium green roof collected in June and September of 2014. Data measured per quadrat (100cm2), with experimental quadrats assigned to 12 distinct microsite types relating to substrate depth (shallow, control, deep) and substrate features (none, logs, pebble pile center, pebble pile edge); abiotic data: substrate temperature (degrees Celsius), substrate volumetric water content (VWC, %), biotic data:  seedling density (number of seedlings/100cm2), and species richness (species/100cm2). Covariate data (% cover of vegetation, total solar radiation) are also included here.
DOI: 10.5061/dryad.s1f95/2
title: Atrium green roof species richness data 2014 - EstimateS output

description: Species richness output from EstimateS - used to create Figure 5. Microsites categorized as seeded controls (homogeneous conditions) or heterogeneous (mixed microsites). Combined homogeneous area sampled = 2400 cm2, combined heterogeneous area sampled = 9600 cm2.
DOI: 10.5061/dryad.s1f95/3
title: glasshouse module temperature, moisture, seedling density, species richness 2015

description: Data from glasshouse modules, used to create Figure 6. Contains data according to treatment (surface feature type) and time, including substrate temperature (degrees Celsius), volumetric moisture content (VWC, %), seedling density (seedlings/1296 cm2), and species richness (per 1296 cm2).
DOI: 10.5061/dryad.v7m05/1
title: Unedited plastome alignment from MAFFT

description: 131 plastomes aligned using MAFFT by major region (LSC, SSC, IR) and then concatenated. No further modifications to alignment made.
DOI: 10.5061/dryad.v7m05/2
title: All Gaps Plastome Alignment

description: 131 plastomes aligned using MAFFT by major region and then trimmed using the 'All Gaps' option in Gblocks.
DOI: 10.5061/dryad.v7m05/3
title: Half Gaps Plastome Alignment

description: 131 plastomes aligned using MAFFT by major regions and then trimmed using the 'Half Gaps' option in Gblocks.
DOI: 10.5061/dryad.v7m05/4
title: No Gaps Plastome Alignment

description: 131 plastomes aligned using MAFFT by major regions and then trimmed using the 'No Gaps' option in Gblocks.
DOI: 10.5061/dryad.v7m05/5
title: Unedited ML Phylogeny

description: RAxML phylogeny of plastome alignment not trimmed with Gblocks.
DOI: 10.5061/dryad.v7m05/6
title: All Gaps ML Phylogeny

description: RAxML phylogeny of plastome alignment trimmed with the 'All Gaps' option in Gblocks
DOI: 10.5061/dryad.v7m05/7
title: Half Gaps ML Phylogeny

description: RAxML phylogeny of plastome alignment trimmed with 'Half Gaps' option in Gblocks
DOI: 10.5061/dryad.v7m05/8
title: No Gaps ML Phylogeny

description: RAxML phylogeny of plastome alignment trimmed with 'No Gaps' option in Gblocks
DOI: 10.5061/dryad.vs27p/1
title: Apoptosis at maternal-fetal interface during type 2 PRRSV infection

description: File contains data from our study of the apoptosis at maternal-fetal placental interface (MFI) in late gestation pregnant gilts experimentally challenged with type 2 PRRS virus: counts of TUNEL (apoptotic) positive cells at MFI, uterine endometrium, area size tissue measurements used for counting of TUNEL positive cells, RT-qPCR results of concentration of PRRS virus in uterus and fetal thymus, fetal preservation status and microscopy.
DOI: 10.5061/dryad.vt2b3/1
title: JApEcol_Hastie_etal_observation_data_Dryad

description: Land based observer data (.xlsx) used in the analysis of seal responses to tidal turbine sounds. This is effectively counts of seals observed in the water during acoustic playbacks of tidal turbine sound and silent controls. Data were collected by a series of observers located on a clifftop overlooking the study area (Kyle Rhea, Isle of Skye, Scotland)  README file is provided as a tab in the file.
DOI: 10.5061/dryad.vt2b3/2
title: JApEcol_Hastie_etal_seal_telemetry_data_Dryad

description: Harbour seal telemetry data (.xlsx) used in the analysis of changes in usage with distance from the location of playbacks of tidal turbine sound. The data are regularised lat-lon locations from 10 individual harbour seals tagged with GPS telemetry devices. README is provided as a tab in the file.
DOI: 10.5061/dryad.vt2b3/3
title: STIMweighted_J11_1hour_withRamp

description: Sound file (.wav) used during playbacks of simulated tidal turbine sound to harbour seals to investigate avoidance responses. The file has a 10 second ramp at the start and end of the file, and is frequency weighted for use with a J11 underwater speaker.
DOI: 10.5061/dryad.10g95/11
title: SL_ms_final_results_Si_ESM_calculating_attraction

description: Copy of SPSS code and analyses for calculating attraction variables
DOI: 10.5061/dryad.10g95/12
title: SL_Ms_public_dataset

description: Excel copy version of SPSS dataset
DOI: 10.5061/dryad.10g95/9
title: SL_ms_final_results_Supp_info_correlations_TableS1

description: Copy of SPSS analyses for Results Section ESM TABLE 1
DOI: 10.5061/dryad.1k7h7/1
title: SR_2017

description: The data included in this directory was used for analysis in the publication "A predation cost to bold fish in the wild".
DOI: 10.5061/dryad.1n50j/1
title: Carbon and Nitrogen storage and CO2 fluxes in alpine plant communities

description: Field data of C and N pools (in above-ground vegetation, litter, roots, and soil separated into organic and mineral horizons) and CO2 fluxes (including Net Ecosystem Exchange, Ecosystem Respiration and Gross Ecosystem Photosynthesis) and the environment (such as light, moisture, and air, surface, and soil temperature) during measurements. The data is processed in R core Team 2015.
DOI: 10.5061/dryad.275d4/3
title: RCT Protocol for: A randomized synbiotic trial to prevent sepsis among infants in rural India

description: Study protocol: A double-blind, randomized, placebo-controlled study to test the effectiveness of a prophylactic oral administration of a L. plantarum + FOS preparation to community-born neonates in reducing the incidence of neonatal sepsis.
DOI: 10.5061/dryad.275d4/4
title: Data from: A Randomized Synbiotic Trial to Prevent Sepsis Among Infants in Rural India

description: Deidentified SEPSISF clean data set from randomized Synbiotic Trial with all variables used in SAS analysis.                       
Reference file: Data dictionary, please click on the appended "Readme file" below for study codes used in this analysis.
DOI: 10.5061/dryad.2v0f7/1
title: Suppl_Table1_Pfaff et al

description: Raw data, Scan settings, species informations
DOI: 10.5061/dryad.3275s/1
title: Montreal_IDENT_2012_SMC

description: The data are associated to the publication "Do temperate tree species diversity and identity influence soil microbial community function and composition?" by Khlifa, Rim, Paquette, Alain, Messier, Christian, Reich, Peter, Munson, Alison. They report measurements of soil microbial community function (analysed using the MicroResp method) and structure (using the PLFA analysis). The data also report mineral soil properties (0-15 cm depth). The samples are from the IDENT experiment of Montreal (Quebec, Canada), and were collected and analysed in 2012. A "read me" file is incorporated in the data file.
DOI: 10.5061/dryad.3600k/1
title: Supplemental Data and Analysis Script

description: A zip files containing csv, xls and Rmd formats.
DOI: 10.5061/dryad.42856/1
title: isolation_by_distance

description: The dataset utilized for calculating isolation by distance (Figure 2b)
DOI: 10.5061/dryad.47n27/4
title: Micro-CT scan volume renderings of Avalofractus abaculus (Rangeomorpha) cast ROM 63005 and scan information

description: Micro-CT volume renderings generated with the program Drishti and CT scan information file
DOI: 10.5061/dryad.48s16/1
title: ORCID public profiles

description: This file contains 2.8 million public profiles from ORCID in both XML and JSON format. You will need 300 GB of free space to decompress the data and work with it.
DOI: 10.5061/dryad.48s16/2
title: IPython Notebook to process ORCID profiles

description: This IPython Notebook provides code for processing the data from public_profiles.tar into manageable data files for analysis.
DOI: 10.5061/dryad.48s16/3
title: ORCID migrations

description: This file contains all affiliations (education and employment) and associated data. It is part of the output of the IPython Notebook above.
DOI: 10.5061/dryad.48s16/4
title: ORCID migrations by person

description: This file is an aggregation of affiliation data for each person. It is part of the output of the IPython Notebook above.
DOI: 10.5061/dryad.48s16/5
title: IPython Notebook to analyze migrations

description: This IPython Notebook provides analysis of the CSV files above.
DOI: 10.5061/dryad.48s16/6
title: ResearchGate - researcher movements from 2006

description: This file was provided to Science magazine by ResearchGate. It was described as being based on "over one million of our members who display education and employment affiliation on their profiles" with the data representing "percentages of total movements of researchers from country to country since 2006."
DOI: 10.5061/dryad.4rq73/1
title: All supplemental data for the analysis in this study

description: The observation and eDNA data in this study
DOI: 10.5061/dryad.4vs00/1
title: DRYAD_Data_Bretman_E&E_2017

description: All raw data for the analyses presented in this MS.
DOI: 10.5061/dryad.69dh9/1
title: data.striders

description: This file contains all the scan observations on all individuals during the experiment. Read the metadata file for more details.
DOI: 10.5061/dryad.69dh9/2
title: R script used to generate all results and figures

description: This script provides all the results presented in the paper and generates all the figures it contains.
DOI: 10.5061/dryad.6f2h4/1
title: Genotypes

description: Column 1 : individuals, Columns 2 - 16 : genotypes, 1 allele is coded by 3 digits
DOI: 10.5061/dryad.6tc06/10
title: FileS4 - habitats Cave hisse

description: Habitat state data used for HiSSE analysis, derived from Table S2
DOI: 10.5061/dryad.6tc06/9
title: FileS3 - habitats Cave geosse

description: Habitat state data used for GeoSSE analysis, derived from Table S2
DOI: 10.5061/dryad.7n731/1
title: Individual genotypes (SNP-markers)

description: Genotypes (SNPs markers) of all individuals in this study. Columns are SNP markers and rows are individuals. This matrix contains a header with SNP-marker names. Identities of the individuals can be found in the "list of individuals in the genotype matrix".
DOI: 10.5061/dryad.7n731/3
title: List of candidate genes

description: List of candidate genes. This file contains a header. marker_name corresponds to the marker identities (columns) in the " individual genotypes" matrix. gene_cat are the categories investigated in this study. candidate_gene are the corresponding gene names.
DOI: 10.5061/dryad.8j3s3/1
title: Lion FIV metadata

description: Metadata associated for 'pride or density' (Tab 1), within pride (Tab 2) and between pride (Tabs 3-12) analyses. Associated sequence data  can be found on GenBank  (accession numbers AY549217-537 AY549304, AY552614 to AY552683, and AY552684 - AY552748, and AY878208 - AY878235). "Ple numbers" attached to sequence data match to the first column of Tab 1. Please see README for information about each tab.
DOI: 10.5061/dryad.8m0q0/2
title: Electronic Appendix 2

description: Supplemental figure - phylomorphospace of total flower dry mass and dry mass investment ratio.
DOI: 10.5061/dryad.8mv2j.1/1.1
title: CHSP and WCSP Song Means DRYAD

description: Original data used in publication
DOI: 10.5061/dryad.9cp00/1
title: Maximum likelihood analysis

description: Maximum likelihood analysis was undertaken using RAxML on the BlackBox server for the combined six gene, 4118 character, 36 taxa dataset. COI, H3 and XPNPEP3 partitioned by codons and ITS1, 5.8S, ITS2 and 28S partitioned individually, with the GTR + G model used for all genes. This analysis resolved the genera Moggridgea and Bertmainius as reciprocally monophyletic, with M. rainbowi from KI clearly embedded within the African Moggridgea lineage and sister to M. intermedia (bootstrap value 100) (Fig 1). Furthermore, M. rainbowi formed a monophyletic group, but showed phylogeographic structure, with haplotypes reflecting the two geographic locations (Western River and American River). The MrBayes analysis of the same dataset produced a completely concordant tree.
DOI: 10.5061/dryad.9v46k/1
title: Spatial similarity index

description: This folder contains contains R code and data to calculate the spatial similarity index (SSI), and to compute and map the ‘distrib(t)’ and ‘counts(t)’ variables, as described in Appendix 2 of the paper. See the README file for further information and file descriptions.
DOI: 10.5061/dryad.9v46k/2
title: Space time models

description: This folder contains R code and data to run all models described in the paper, in addition to model output for plotting Figures. 3-5, A7 and reproducing Tables 2, 3, A1-A3. See the README file for further information and file descriptions.
DOI: 10.5061/dryad.bg08n/1
title: R_simulation_code

description: simulation code for phenotypic experimental evolution and power analysis (written by Thiago Guzella, guzella@biologie.ens.fr)
DOI: 10.5061/dryad.c5p1f/1
title: Unfiltered transcriptome

description: Raw output from the trinity assembly
DOI: 10.5061/dryad.c5p1f/2
title: Filtered transcriptome

description: Transcriptome filtered (Isopct ≥ 51, FPKM ≥ 0.1, length ≥ 600 bp)
DOI: 10.5061/dryad.ds543/1
title: Character Taxon Matrix

description: A character-taxon matrix for analysis of stegosaurian dinosaur relationships
DOI: 10.5061/dryad.ds543/2
title: Character List

description: A character list to accompany the character-taxon matrix
DOI: 10.5061/dryad.ds543/3
title: Raven&MaidmentOSI

description: A file containing characters, justifications for changes made to characters, and synapomorphies
DOI: 10.5061/dryad.dt4jq/1
title: ARES soil variables

description: This dataset describes soil variables (0-10-cm depth) measured in subplots with daily applications of root exudate solution (RE) or a procedural control solution (CP), applied using the Automated Root Exudate System (ARES) within experimental litter removal (0L) and control plots (1L) in an old-growth deciduous woodland in Wytham, Oxfordshire, UK. Full descriptions of the study site and experimental design are given in the paper and appendices. 

Data included in this file are: soil water content, soil pH and microbial biomass carbon and nitrogen measured in the subplots at the end of the growing season in the first and second year of treatments (September 2015 and 2016) as well as fine root biomass in the second year of the study (July 2016).

Column headings and abbreviations are as follows:
block = replicate block A-E; Plot = unique experimental plot identifier P1-P15; treatm = litter manipulation treatment, where 0L is litter removal and 1L is control; ARES = subplot treatment, where RE is root exudate solution and CP is procedural control; year = year of study; swc = gravimetric soil water content in %; pH = soil pH; MBC and MBN = microbial biomass carbon and nitrogen, respectively, in ug g-1;  fine.roots = fine root biomass in g m-2.
DOI: 10.5061/dryad.dt4jq/2
title: ARES soil respiration data

description: This dataset describes monthly measurements of soil CO2 efflux,  soil water content, and soil temperature in subplots with daily applications of root exudate solution (RE) or a procedural control solution (CP), applied using the Automated Root Exudate System (ARES) within experimental litter removal (0L) and control plots (1L) in an old-growth deciduous woodland in Wytham, Oxfordshire UK. Full descriptions of the study site and experimental design are given in the paper and appendices. 

Column headings and abbreviations are as follows:
block = replicate block A-E; Plot = unique experimental plot identifier P1-P15; treatm = litter manipulation treatment, where 0L is litter removal and CT is control; ARES = subplot treatment, where RE is root exudate solution, CP is procedural control and 'plot' is the main litter manipulation plot; year = year of study; month = month of measurement; nom.date = nominal date of measurement (set at 1st of the month); time = consecutive time point during the study; swc = soil water content at 0-6 cm depth in %; temp10 = soil temperature at 0-10 cm depth; Rsoil = soil CO2 efflux in mg C m2-1 h-1; Flux = soil CO2 efflux in umol m-2 s-1; Comments = reasons for outliers and missing values; ObsDateTime = actual date and time of each measurement.
DOI: 10.5061/dryad.fn0f4/1
title: costs of inflammatory responses in Kenyan house sparrows

description: These data are for a study of the energetic, oxidative damage, and nutritional costs of an inflammatory response in house sparrows from Kenya
DOI: 10.5061/dryad.gd489/1
title: Wombat abundance and mange severity data

description: This file contains average wombat abundance across different sections of the park over time (tab labelled "Presence Data") and mange severity scores from mange surveys (tab labelled "Mange Data")
DOI: 10.5061/dryad.gh721/2
title: R code used in Bolstad et al. (2017, Nature Ecology & Evolution)
DOI: 10.5061/dryad.gh721/3
title: C++ code needed for running R code
DOI: 10.5061/dryad.jd5j3/1
title: foliar traits in turnera

description: Dataset of foliar traits used to estimate phenotypic integration of 24 genotypes in juvenile and reproductive plants of Turnera velutina.
DOI: 10.5061/dryad.mc270/1
title: de novo assemblies for each taxa and a master reference for the genus

description: This includes de novo assembly of a "master reference" using all reads in the study, then filtered assemblies for each taxa using a 1 TPM threshold.
DOI: 10.5061/dryad.mc270/2
title: Nuclear_gene_alignments

description: MAFFT gene alignments for 89 putatively single copy nuclear genes, with a concatenated file in both .phy and .nex formats.  Genes were sequenced using MYbaits exon capture kit, sequenced on Illumina platform, and then analyzed using HybPiper.
DOI: 10.5061/dryad.mr556/11
title: P89 wing spanwise

description: PIV measurements of the P89 wing at all tested angles of attack
DOI: 10.5061/dryad.n49p1/1
title: Measurements of the optic lobes

description: All measurements of the optic lobes described in the paper
DOI: 10.5061/dryad.nb115/10
title: scripts

description: R scripts to create all figures, tables, data cleaning, SDM creation and assignment
DOI: 10.5061/dryad.nb115/7
title: Data Files

description: input files for monitoring data, stable isotope data, maping inputs for figures and sdm models saved in .Rdata files.
DOI: 10.5061/dryad.nb115/9
title: Shapefiles

description: Shapefiles for each species
DOI: 10.5061/dryad.r08t9/1
title: Feasible set analysis for host-parasite Taylor's Power Law
DOI: 10.5061/dryad.r43d0/1
title: Experiment 1 Species Data

description: Experiment 1 - Site vs. Plant-soil Feedback Experiment.  Above-ground biomass (g) of nine plant species grown in soils originating from four sites and conditioned by one of nine plant species.
DOI: 10.5061/dryad.r43d0/2
title: Experiment 2 Species Data

description: Experiment 2 - AMF & Rhizobia Experiment. Above-ground biomass (g) of ten plant species grown in soils originating from one site and conditioned by one of ten plant species.
DOI: 10.5061/dryad.r43d0/3
title: AMF

description: Experiment 2 - AMF hyphae, vesicle and arbuscule abundance in soils conditioned by one of ten plant species.
DOI: 10.5061/dryad.r43d0/4
title: Nodulation

description: Experiment 2 - Nodule formation on Baptisia and Melilotus seedlings in soils conditioned by one of ten plant species.
DOI: 10.5061/dryad.rr36r/1
title: atpB-rbcL intergenic spacer, partial sequence chloroplast

description: AR1-AR8 are identified from Sophora davidii,AR9, AR10 and AR11 are from Sophora moorcroftiana,Sophora alopecuroides and Sophora tomentosa,respectively.
DOI: 10.5061/dryad.rr36r/2
title: atpI-atpH intergenic spacer, partial sequence chloroplast

description: IH1-IH7,IH8-IH11,IH12 and IH13 are from Sophora davidii,Sophora moorcroftiana,Sophora alopecuroides and Sophora tomentosa,respectively.
DOI: 10.5061/dryad.rr36r/3
title: Internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence

description: R1-R9 are both from Sophora moorcroftiana
DOI: 10.5061/dryad.t7kp7/1
title: STN probability atlas

description: This atlas takes advantage of ultra-high resolution 7T MRI to provide unprecedented levels of detail on structures of the basal ganglia in-vivo. The atlas includes a disease-specific probability map of the subthalamic Nucleus based on Parkinson's Disease patients. The atlas is based either on QSM or T2*-weighted structural scans.
DOI: 10.5061/dryad.v7m05/10
title: Bayesian All Gaps Phylogeny

description: MrBayes phylogeny of plastome alignment trimmed with the 'All Gaps' option in Gblocks
DOI: 10.5061/dryad.v7m05/11
title: BEAST Run Logs

description: Combined logs from 5 runs of 100 million generations each in BEAST.
DOI: 10.5061/dryad.v7m05/12
title: BEAST Trees

description: Trees from 5 combined runs of 100 million generations each in BEAST
DOI: 10.5061/dryad.v7m05/9
title: BEAST Input File

description: Input XML file for each of 5 BEAST runs 100 million generations each.
DOI: 10.5061/dryad.vs078/1
title: urban_flight_endurance_EVA
DOI: 10.5061/dryad.15500/1
title: RSOS-170162_R1_data
DOI: 10.5061/dryad.2601h/1
title: 3-D model of Parvancorina minchami from South Australia in STL format

description: A freely-available reconstruction of Parvancorina minchami from South Australia in dorsal view (https://en.wikipedia.org/wiki/Parvancorina#/media/File:Parvancorina_species.png) was imported into the open-source 3-D creation program Blender (http://www.blender.org) and used as a reference to guide box modelling of the shield-shaped base. The file was exported from Blender in STL format and converted into a non-uniform rational basis spline (NURBS) surface (IGES format) in Geomagic Studio 2012 (http://www.geomagic.com). This IGES format file was then imported into the commercial simulation software COMSOL Multiphysics (https://uk.comsol.com/), where the raised T-shaped ridge was digitally modelled with a half torus, a cylinder, and three spheres. The final model was exported from COMSOL in STL format.
DOI: 10.5061/dryad.2601h/2
title: 3-D model of Parvancorina minchami from Russia in STL format

description: A freely-available reconstruction of Parvancorina minchami from Russia in dorsal view (https://en.wikipedia.org/wiki/Parvancorina#/media/File:Parvancorina_species.png) was imported into the open-source 3-D creation program Blender (http://www.blender.org) and used as a reference to guide box modelling of the shield-shaped base. The file was exported from Blender in STL format and converted into a non-uniform rational basis spline (NURBS) surface (IGES format) in Geomagic Studio 2012 (http://www.geomagic.com). This IGES format file was then imported into the commercial simulation software COMSOL Multiphysics (https://uk.comsol.com/), where the raised T-shaped ridge was digitally modelled with a half torus, a cylinder, and three spheres. The final model was exported from COMSOL in STL format.
DOI: 10.5061/dryad.2s590/1
title: Nile perch metabolic traits and CTmax

description: Sheet 1 contains standard and maximum metabolic rates (SMR and MMR), aerobic scope (AS), excess post-exercise oxygen consumption (EPOC), and recovery time (RT) data for Nile perch acutely exposed to a range of treatment temperatures. Sheet 2 contains the same data for Nile perch acclimated for 21 days (3-weeks) plus standard growth rate (SGR) and condition data. Sheet 3 contains CTmax data for both acclimated and acutely exposed Nile perch. Final fish mass (W), standard length (SL) and total length (TL) are included in each sheet.