cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ms2np57/4
title: Pulse Chase Vegetation Mass

description: Contains dry weight biomass for all plant samples collected in pulse chase experiment. Note that treatment and plot number must be combined to generate unique plot ID. 'Sub' identifies replicate harvest swath collected at each harvest date (2 day and 7 day only, 32 day only had one swath and is thus identified as AA, as is the t=0 harvest of aboveground tissue immediately post pulse). 'Harvest' identifies time of harvest post pulse and is either 0 (immediately post pulse, aboveground tissue only), '2d' (2 day), '7d' (7 day), or '32day' (32 days). 'Pool' identifies the plant tissue and is either shoots ('Ag Veg'), roots ('Root') or rhizomes ('Rh'). Biomass is in grams. 'Standing dead' represents the senesced tissue sorted out of the sample prior to analysis, and is also in grams.
DOI: 10.5061/dryad.ms2np57/5
title: Pulse Chase Microbial Data

description: Microbial biomass and isotope ratio data. Note that treatment and plot number must be combined to generate a unique sample ID. Harvest indicates time since post pulse: '48' represents 2 days, '336' represents 7 days, and 4 represents 32 days. 'Sub' represents replicated harvest swath within a given harvest date (2 day and 7 day only). Column 'Rep' can be ignored. 'mgC/dry_mass_soil(g)' represents the carbon concentration of the extract, standardized per gram of soil extracted. 'd13c (permil, versus VPDB)' is the standard isotope delta 13C value, and 'Fumigated' identifies fumigated extracts (containing lysed microbial cell contents in addition to dissolved organic carbon, DOC) and 'unfumigated' extracts (which contain just DOC). Formulae for calculating microbial biomass and isotope enrichment are in the main paper, and are also explained in the open source code used to process and analyze data available at https://github.com/chwilson/GCB_2018).
DOI: 10.5061/dryad.n9882/1
title: FE-2017-00704_R scripts

description: R scripts for all structural equation models evaluated
DOI: 10.5061/dryad.n9882/2
title: FE-2017-00704_sampling sites

description: Google maps file with the location of the sampling sites
DOI: 10.5061/dryad.pn931/1
title: HumanDetection

description: 1 second prestimulus MEG dipole source localized to hand area of S1
DOI: 10.5061/dryad.pn931/2
title: HumanAttention

description: 1 second prestimulus MEG dipole source localized to hand area of S1
DOI: 10.5061/dryad.pn931/3
title: MouseDetection1

description: 1 second prestimulus LFP in mouse barrel cortex
DOI: 10.5061/dryad.pn931/4
title: MouseDetection2

description: 1 second prestimulus LFP in mouse barrel cortex
DOI: 10.5061/dryad.qr5vd/2
title: Boechera_experiment_phenology

description: This file contains individual-level  phenology data for the Boechera stricta experiment (Tables S8-S10).
DOI: 10.5061/dryad.qr5vd/3
title: Boechera_experiment_flowering_success

description: This file contains family-level flowering success data for the Boechera stricta experiment (Tables S11a-S11c).
DOI: 10.5061/dryad.qr5vd/4
title: Photoperiod

description: This file contains daylength data local to the study site for every day of the study period.
DOI: 10.5061/dryad.qr5vd/5
title: Observational_phenology

description: This file contains data of the date of first flower, date of snowmelt, accumulated growing degree days at first flower, and daylength at first flower for the six species monitored in the observational experiment.
DOI: 10.5061/dryad.qr5vd/6
title: Temperature

description: This file contains minimum temperature, maximum temperature, and average temperature, and growing degree day data for every day of the study period.
DOI: 10.5061/dryad.qr5vd/7
title: Snowmelt

description: This file contains data for the ordinal date of snowmelt for out study region from 1936-2016.
DOI: 10.5061/dryad.rg6k9/4
title: BED_file

description: Bed file generated in PLINK using the LD-pruned SNPs.
DOI: 10.5061/dryad.rg6k9/5
title: BIM_file

description: Bim file generated in PLINK using the LD-pruned SNPs.
DOI: 10.5061/dryad.rg6k9/6
title: FAM_file

description: Fam file generated in PLINK using the LD-pruned SNPs.
DOI: 10.5061/dryad.rg6k9/7
title: MAP_file

description: Map file with the original set of SNPs prior to LD-pruning.
DOI: 10.5061/dryad.rg6k9/8
title: PED_file

description: Ped file with the original set of SNPs prior to LD-pruning. Containing genotype data for 185 individuals.
DOI: 10.5061/dryad.tv210/1
title: Database used in the study
DOI: 10.5061/dryad.v1m95/1
title: Minimum data set to investigate use of environmental sites by mule deer

description: This data set contains two worksheets: (1) a column dictionary describing the contents of all columns in the data set, and (2) the data set used in the analyses of the published manuscript.
DOI: 10.17632/xwyg8pzvdd.2
title: Data for: Emplacement dynamics and hydrothermal alteration of the Atengo ignimbrite, southern Sierra Madre Occidental, northwestern Mexico

description: the files are raw, which are generated during hysteresis and FORC analysis
DOI: 10.5061/dryad.08c4c/2
title: Hayes MMR & range Dryad file - MMR, Mass & range data plus MMR & Mass references

description: Data for Hayes MMR & geographic range paper in comma separated variable format.  Same information as in MS-Word file but formatted for easier data handling.  Note for literature citations (references to data sources) please see the MS-Word file
DOI: 10.5061/dryad.11313/4
title: Client Flow Base Dataset 10 Oct 2014 (SPSS) (De-Identified)

description: Base dataset for client flow data collected under the study "A Descriptive Evaluation of Postpartum Family Planning Integration Models in Kenya and India," conducted in 2014 by the Maternal and Child Survival Program. SPSS version.
DOI: 10.5061/dryad.11313/5
title: Client Flow Base Dataset 10 Oct 2014 (Stata) (De-Identified)

description: Base dataset for client flow data collected under the study "A Descriptive Evaluation of Postpartum Family Planning Integration Models in Kenya and India," conducted in 2014 by the Maternal and Child Survival Program. Stata version.
DOI: 10.5061/dryad.14sr463/1
title: Delphinus delphis Mid-Span Slices
DOI: 10.5061/dryad.14sr463/2
title: Delphinus delphis Tail Base Slices
DOI: 10.5061/dryad.14sr463/3
title: Delphinus delphis Tail Tip Slices
DOI: 10.5061/dryad.250dt/1
title: UTP14a transcript sequence and UTP14 peptide sequence use.

description: Human UTP14a sequence data used for BLAST search of ENSEMBL species specific genome data ti identify UTP14 retrogenes. Primate UTP14a and UTP14 retrogene encoded peptide sequences used to generate phylogeny trees.
DOI: 10.5061/dryad.28d4t/1
title: prog_population
DOI: 10.5061/dryad.6v0j9/1
title: CRRTstudy_1144patients

description: 1144 patients with acute kidney injury who received continuous renal replacement therapy (CRRT) were enrolled. Phosphate levels were measured before (0 h) and 24 h after CRRT initiation. We assessed disease severity using various clinical parameters.
DOI: 10.5061/dryad.76tr6/1
title: Wolf monitoring genotype and phenotype data

description: This file contains the consensus multi-locus genotypes of all individual wolves identified and fitted in the pedigree, along with phenotypic data used to inform the pedigree.
DOI: 10.5061/dryad.86fr4/1
title: FASTA_CP_Ichthyoplankton

description: Raw (unedited) Sanger sequences (COI and 16S) obtained from ichthyoplankton collected from Cabo Pulmo National Park (Jan 2014- Dec 2014). Organized in rows by sequence ID.
DOI: 10.5061/dryad.96c43/1
title: Data used in our analyses.

description: The file contains 8 columns and 31 rows. The first row contains  the column headings and the remaining 30 rows are the data values arranged by year (i.e. one row for each of the 30 years of the study). The first column 'Year' is the year the data relate to (first year is 1984, last year is 2013). The second column 'HunterCPUE' is the mean number of sambar deer shot per hunter per day in each of the 30 years. The third column 'nDingoScats' is the number of dingo scats collected in each of the 30 years. The fourth column 'nRedFoxScats' is the number of red fox scats collected in each of the 30 years. The fifth column 'nSambDingoScats' is the number of dingo scats collected in each year that contained sambar deer. The sixth column 'nSambRedFoxScats' is the number of red fox scats collected in each year that contained sambar deer. The seventh column 'SambFoxScatsPerc' is the percentage of red fox scats collected in each year that contained sambar deer. The eighth column 'SambDingoScatsPerc' is the percentage of red fox scats collected in each year that contained sambar deer.
DOI: 10.5061/dryad.9k1h0/1
title: Files associated with the HZAR analysis

description: Files associated with the HZAR analysis
DOI: 10.5061/dryad.9k1h0/10
title: ITProcessedPartH

description: Processed Ion Torrent data part H
DOI: 10.5061/dryad.9k1h0/2
title: Ion Torrent output

description: Ion Torrent output
DOI: 10.5061/dryad.9k1h0/3
title: ITProcessedPartA

description: Processed Ion Torrent data part A
DOI: 10.5061/dryad.9k1h0/4
title: ITProcessedPartB

description: Processed Ion Torrent data part B
DOI: 10.5061/dryad.9k1h0/5
title: ITProcessedPartC

description: Processed Ion Torrent data part C
DOI: 10.5061/dryad.9k1h0/6
title: ITProcessedPartD

description: Processed Ion Torrent data part D
DOI: 10.5061/dryad.9k1h0/7
title: ITProcessedPartE

description: Processed Ion Torrent data part E
DOI: 10.5061/dryad.9k1h0/8
title: ITProcessedPartF

description: Processed Ion Torrent data part F
DOI: 10.5061/dryad.9v64t5f/1
title: FRET index versus shortening speed of  seam-seam junctions

description: Plot of FRET index for seam-seam junctions at 1.5-fold versus their shortening speed at the same stage (measured as % of change in length per minute) showing the absence of correlation.
DOI: 10.5061/dryad.cc202/1
title: Sirkiä et al. data for deposition
DOI: 10.5061/dryad.d21j6/1
title: FASTR model validation data

description: File contains water balance results generated with the FASTR hydrological model for three numerical validation experiments.
DOI: 10.5061/dryad.d21j6/2
title: FASTR experiment 1: role of the unsaturated zone moisture profile

description: File contains water balance results simulated with the FASTR hydrological model for 15,000 combinations of initial groundwater level, soil hydraulic parameters, saturated hydraulic conductivity, and precipitation structure.
DOI: 10.5061/dryad.d21j6/3
title: FASTR experiment 2: seasonal saturation excess runoff generation in fields with mesotopography

description: File contains water balance results simulated with the FASTR hydrological model for 1,080 combinations of mesotopography, soil hydraulic parameters, saturated hydraulic conductivity, and precipitation structure.
DOI: 10.5061/dryad.fc827/1
title: Genetic data (filtered vcf file)

description: This text file contains the filtered genetic data (SNP set) in variant call format (vcf). This included genetic data for 78,567 SNPs.
DOI: 10.5061/dryad.fc827/2
title: Variant filtering scripts

description: This compressed directory contains three perl scrips used for filtering and processing the genetic data (i.e., the vcf file). morefilter_filtered2x-70_varsLycGwa.vcf was generated by running the two filter scripts. Most filters described in the paper are impelemented in the main script, vcfFilter.pl, which was run first. The second script, filterSomeMore.pl applies maximum coverage filters and a filter to drop variants that are near each other (within 3 bp in this case). The final scrips, vcf2gl.pl, extracts the genotype likelihoods from the vcf file.
DOI: 10.5061/dryad.fc827/3
title: Variant calling script

description: Shell script used for variant calling with samtools and bcftools.
DOI: 10.5061/dryad.fc827/4
title: Alignment script

description: This perl script generates shell scripts to submit to a SLURM job scheduler to run bwa, which we used for DNA sequence alignments. Note that this depends on having a bwa module installed on a cluster running SLURM.
DOI: 10.5061/dryad.fc827/5
title: Lycaeides melissa reference genome

description: Reference genome for Lycaeides melissa as a fasta file.
DOI: 10.5061/dryad.fc827/6
title: Lycaeides melissa linkage map

description: Text file describing the L. melissa linkage map. There are three columns giving the linkage group (lg), scaffold number (scaf, these match the reference genome scaffold names), and position (pos) in centi Morgans along the relevant linkage group.
DOI: 10.5061/dryad.fc827/7
title: Gemma BSLMM infiles

description: This compressed directory contains the infiles for the genomic prediction/genome wide association mapping analysis. These are in BIMBAM format and include mean genotype (*geno*) and phenotype (*pheno*) files. We include files for size and position (*coord*) traits.  Files are included for all biological levels we considered and for all groups: AN = L. anna, GNP = L-ID-GNP, ID = L. idas, JA = Jackson hole, ME = L. melissa east, MW = L. melissa west, RI = L. anna ricei, SIN = L-ME-SIN, SN = Sierra Nevada, WA - Warner Mt., and YBG = L-AN-YBG. Files without prefixes are for the species-comples level analysis. We have also included a perl wrapper script used to fit the BSLMM in gemma = forkRunGemmaPop.pl.
DOI: 10.5061/dryad.fc827/8
title: PCA infile and scripts

description: This compressed directory contains the phenotype infile (resid-sizeANDcoord-6vi17-subgroups-NoNA.csv) used for the PCA, as well as the PCA script PCA_sizeANDposition-final.R and an additional script defining the Bayesian model that was used for the 95% PC mean ellipses (fitEllipse.R).
DOI: 10.5061/dryad.fk41r/12
title: cal_hc_repr_gene_models.rmscaff.gff3

description: Generic feature format (gff3) of representative models for high-confidence genes in C. gigantea
DOI: 10.5061/dryad.fk41r/13
title: cal_hc_gene_models.rmscaff.repr.pep.fa

description: Protein sequences of representative models for high-confidence genes in C. gigantea
DOI: 10.5061/dryad.fk41r/14
title: cal_hc_func_anno.txt

description: Functional annotation for high-confidence genes in C. gigantea
DOI: 10.5061/dryad.fk41r/15
title: cal_FPKM_matrix.txt

description: Table with FPKM expression values for high-confidence genes in C. gigantea
DOI: 10.5061/dryad.g8609/5
title: R commands for STRAPP

description: R commands used for STRAPP analysis to determine if floral sonication behavior was associated with increased diversification within bee lineages.
DOI: 10.5061/dryad.hc8k0/1
title: Copy of DatabasePaperV2
DOI: 10.5061/dryad.j47br/2
title: Raw data of 97 genes for cetacean analysis

description: 97 genes alignment in cetaceans
DOI: 10.5061/dryad.m8t2k/1
title: Stable isotopic values of different tissues from two gull species

description: Stable isotopic values from two gull species breeding at South Portugal
DOI: 10.5061/dryad.q3r52/1
title: GauthierMatrixTNT1st2ndAnalysis

description: TNT file including dataset made by Gauthier et al. (2012). Taxa added: Slavoia darevskii, Cryptolacerta hassiaca, Ardeosaurus brevipes, Yabeinosaurus robustus. This file was used for the1st and 2nd analysis.
DOI: 10.5061/dryad.q3r52/2
title: GauthierMatrixTNT3rdAnalysis

description: TNT file including dataset made by Gauthier et al. (2012) modified by Simoes et al. (2017). Taxa added: Slavoia darevskii, Cryptolacerta hassiaca, Ardeosaurus brevipes, Yabeinosaurus robustus. This file was used for the 3rd analysis.
DOI: 10.5061/dryad.q3r52/3
title: Talanda1stAnalysis

description: The strict consensus tree of the first analysis (matrix and settings from Gauthier et al. [2012]).
DOI: 10.5061/dryad.q3r52/4
title: Talanda2ndAnalysisImpliedWeighting

description: The most parsimonious tree of the second analysis (matrix from Gauthier et al. [2012] analyzed under implied weighting algoritm).
DOI: 10.5061/dryad.q3r52/5
title: Talanda_3rd_analysis

description: The majority rule (cut off 50) consensus tree of the third analysis (matrix and settings from Simões et al. [2017]).
DOI: 10.5061/dryad.qd450/1
title: Combined MammalDIET and MammalDIET 2 dataset

description: The combined mammal dietary dataset from Kissling et al. (2014) and the updated collected dietary information for 1261 mammalian species.
DOI: 10.5061/dryad.qp244/1
title: Infrared thermographs of flower species

description: This zipped dataset contains 136 folders, corresponding to the 136 species and subspecies thermographed as described in Harrap et al.  All the files contain three .jpg files.

Each folder contains two infrared images (which are identical to each other, except that the image marked with an ‘m’ has the hottest and coldest points identified as described in the text).

Each folder also contains an accompanying photograph taken in the visible spectrum, taken by the thermal camera at the same time as the infrared image.  The visible spectrum photographs are provided purely to give an indication of the floral form, and do not contribute any further data that is used in the paper.
DOI: 10.5061/dryad.qp244/2
title: Raw and processed data for figures 3 and 4

description: A zipped file containing nine .csv files. Three of these files each correspond to figures 3a, 3b and 4, and contain the raw data and processed versions that relate to the final figures. The readme file details the format of these files
DOI: 10.5061/dryad.rn420/2
title: Appendix S2. Modern birds' dataset.

description: Dataset of modern Neoaves used in the present study. Main flight modes were assigned following Viscor and Fuster (1987), Del Hoyo et al. (1992; vol 1-16) and Bruderer et al. (2010). Specimen code: Only number – Burke Museum of the University of Washington (Seattle, USA); UBCBM – Beaty Museum of the University of Bristish Columbia (Vancouver, Canada); BR – obtained from the dataset of Bruderer et al. (2010); VF - obtained from the dataset of Viscor and Fuster (1987); PN – obtained from the preset database of software Flight 1.24.
DOI: 10.5061/dryad.rn420/3
title: Appendix S3. Summary of Canonical Variates Analysis.

description: Summary of Canonical Variates Analysis: 1. Eigenvalues and % variance explained by the canonical functions; 2. Lambda Wilk’s test for mean groups’ differences; 3. Coefficients of the canonical functions; 4. Reclassification of modern birds’ dataset after leave-one-out validation. Group codes: continuous flapping (1); bounding (2); facultative gliding (3).
DOI: 10.5061/dryad.rn420/4
title: Appendix S4. Difference in power margin between two modern birds with similar body mass.

description: Flight reconstruction of two modern flying birds with similar BM to show difference in the power margin. Power curves indicating the relationship between Pmec and Vt were modeled for a continuous flapping strategy (i.e., q=1) with CDb calculated according the two approaches used in this study: A, CDb = 0.1; and B, CDb = 0.01 SL / Sb (see Methods). Pav is closely similar as both birds weighted almost the same, and thus the mean value of Pav was drawn (pointed horizontal line). The bar-tailed godwit Limosa lapponica (BM = 367g; CDb = 0.136) shows sufficient power margin to sustain flapping flight in the full-range of Vt, using the aerobic activity from the flight muscles. In contrast, the grey partridge Perdix perdix (BM = 372g; CDb = 0.125) cannot sustain a prolonged flapping flight because the Pav does not attain Pmec. Instead, partridges and other Galliformes fly using short bursts supported by anaerobic activity of the fiber muscles (see Bishop and Butler 2015).
DOI: 10.5061/dryad.rn420/5
title: Appendix S1. Concornis lacustris and Eoalulavis hoyasi measurements.

description: Measurements of the fossil specimens from Las Hoyas included in the present study. Following Serrano et al. (2017).
DOI: 10.5061/dryad.tb850/1
title: All data for this study
DOI: 10.5061/dryad.vs044/1
title: Supplementary Figure 2

description: Fig. S2: 3D interactive model of the Limulus polyphemus chelicera, as modelled from iodine staining and micro-CT-scanning.
DOI: 10.5061/dryad.vs044/2
title: Supplementary Figure 3

description: Fig. S3: 3D interactive model of the Limulus polyphemus walking leg, as modelled from iodine staining and micro-CT-scanning.
DOI: 10.5061/dryad.vs044/3
title: Supplementary Figure 4

description: Fig. S4: 3D interactive model of the Limulus polyphemus male pedipalp, as modelled from iodine staining and micro-CT-scanning.
DOI: 10.5061/dryad.vs044/4
title: Supplementary Figure 1

description: Fig. S1: 3D interactive model of the complete Limulus polyphemus specimen, as modelled from 
CT-scanning.
DOI: 10.5061/dryad.vs044/5
title: Supplementary figure 5

description: Fig. S5: 3D interactive model of the Limulus polyphemus pushing leg, as modelled from iodine staining and micro-CT-scanning.
DOI: 10.5061/dryad.11313/6
title: Client Flow Dataset BASE 2014.10.10 (CSV) (De-Identified)

description: Base dataset for client flow data collected under the study "A Descriptive Evaluation of Postpartum Family Planning Integration Models in Kenya and India," conducted in 2014 by the Maternal and Child Survival Program. CSV format.
DOI: 10.5061/dryad.11313/7
title: Client Flow Codebook

description: Codebook for the client flow dataset collected under the study "A Descriptive Evaluation of Postpartum Family Planning Integration Models in Kenya and India," conducted in 2014 by the Maternal and Child Survival Program.
DOI: 10.5061/dryad.14sr463/10
title: Lagenorhynchus albirostris Mid-Span Slices
DOI: 10.5061/dryad.14sr463/11
title: Lagenorhynchus albirostris Tail Base Slices
DOI: 10.5061/dryad.14sr463/12
title: Lagenorhynchus albirostris Tail Tip Slices
DOI: 10.5061/dryad.14sr463/4
title: Grampus griseus Mid-Span Slices
DOI: 10.5061/dryad.14sr463/5
title: Grampus griseus Tail Base Slices
DOI: 10.5061/dryad.14sr463/6
title: Grampus griseus Tail Tip Slices
DOI: 10.5061/dryad.14sr463/7
title: Kogia breviceps Mid-Span Slices
DOI: 10.5061/dryad.14sr463/8
title: Kogia breviceps Tail Base Slices
DOI: 10.5061/dryad.14sr463/9
title: Kogia breviceps Tail Tip Slices
DOI: 10.5061/dryad.30k44/1
title: 3D Maya model of Protasterina flexuosa Arm

description: 3D Maya model of portion of the arm of Protasterina flexuosa  constructed using extracted volumes of micro-CT scans of CMC 25001. See legend of figure 2 in main text of publication for details.
DOI: 10.5061/dryad.30k44/2
title: Ambulacral Ossicle Triangular Mesh

description: Raw STL triangular mesh of P. flexuosa ambulacral ossicle used in Maya model. See legend of figure 2 in main text of publication for details.
DOI: 10.5061/dryad.30k44/3
title: Lateral Ossicle Triangular Mesh

description: Raw STL triangular mesh of P. flexuosa lateral ossicle used in Maya model. See legend of figure 2 in main text of publication for details.
DOI: 10.5061/dryad.30k44/4
title: Ossicle A Triangular Mesh

description: Raw STL triangular mesh of P. flexuosa ossicle A used in Maya model. See main text of publication for ossicle description and legend of figure 2 for details regarding the creation of this file.
DOI: 10.5061/dryad.30k44/5
title: Structure B Triangular Mesh

description: Raw STL triangular mesh of P. flexuosa structure B used in Maya model. See main text of publication for structure description and legend of figure 2 for details regarding the creation of this file.
DOI: 10.5061/dryad.30k44/6
title: Water Vascular System

description: Raw STL triangular mesh of P. flexuosa water vascular system used in Maya model. See legend of figure 2 in the main text of publication for details.
DOI: 10.5061/dryad.30k44/7
title: Scan A: Protasterina flexuosa (CMC 25001)

description: Micro-CT scan of Protasterina flexuosa (CMC 25001) using the North Star Imaging micro-CT scanner housed at Vanderbilt University (Tennessee, USA). 1170 two-dimensional images were generated with a voxel size of 29.3 microns at a voltage of 100kV and current of 62 microamps. Volume was reconstructed using EFX-CT. Users should contact authors prior to file use other than corroborating data presented in paper.