cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f420m4q/4
title: Comparison_noConstraint_Diploporita_Templeton

description: Coding for Templeton test comparing forced monophyletic grouping of  Diploporita versus no constraints
DOI: 10.5061/dryad.gj8jv50/3
title: Sequencing files for Figure 5
DOI: 10.5061/dryad.gj8jv50/4
title: Sequencing files for Figure 6
DOI: 10.5061/dryad.gj8jv50/5
title: Data-sets used to identify motifs J4 and H4
DOI: 10.5061/dryad.gj8jv50/6
title: Sequencing data for starting pools used in RNA ligation / recombination experiments
DOI: 10.5061/dryad.h52h5t7/1
title: Lochmuller et al UX001 CL301 MS supp materials protocol 13Dec2018

description: Supplemental Material for Lochmuller et al Neurology: Table e-1. Change from Baseline to Week 48 in UEC and LEC Individual Muscle Groups with Hand-Held Dynamometry; Figure e-1. UX001-CL301 CONSORT Flow Diagram; UX001-CL301 Protocol
DOI: 10.5061/dryad.jm5251f/1
title: RAXML_input

description: Input files used for phylogenetic genetic inference using RAXML.
DOI: 10.5061/dryad.jm5251f/4
title: Mitochondrial_partitioned_alignments

description: Alignments used for phylogenetic inference, separated by mitochondrial partition in both .fasta and .phy format. Unstable blocks in these alignments were removed through the Gblocks program.
DOI: 10.5061/dryad.jm5251f/5
title: Mitogenomes

description: Final mitogenomes reconstructed in .fasta format.
DOI: 10.5061/dryad.m097580/1
title: Lymbery et al 2018 Full dataset

description: Contains all the data used in the statistical analyses for the associated manuscript. The file contains two spreadsheets: one containing the data and one containing a legend relating to column titles.
DOI: 10.5061/dryad.m097580/2
title: Lymbery et al 2018 Reduced dataset 1

description: Contains data used in the attached manuscript following the removal of three outliers for the purposes of data distribution, as described in the associated R code. The file contains two spreadsheets: one containing the data and one containing a legend relating to column titles.
DOI: 10.5061/dryad.m097580/3
title: Lymbery et al 2018 Reduced dataset 2

description: Contains the data used in the statistical analyses for the associated manuscript, after the removal of all outliers stated in the manuscript and associated R code. The file contains two spreadsheets: one containing the data and one containing a legend relating to column titles.
DOI: 10.5061/dryad.nv3846b/2
title: carnivora_beast_xml

description: XML file for beast
DOI: 10.5061/dryad.nv3846b/3
title: carnivora_phylo_data

description: R data object containing species means and standard errors for ecomorphological data, family level assignments, and phylogeny
DOI: 10.5061/dryad.nv3846b/4
title: basic_trait_analyses

description: R script to perform basic trait evolutionary model fitting analyses
DOI: 10.5061/dryad.nv3846b/5
title: lasso output functions

description: utility functions to process the output of L1OU
DOI: 10.5061/dryad.nv3846b/6
title: l1OU

description: code to run L1OU on carnivore rlga data
DOI: 10.5061/dryad.nv3846b/7
title: RateMatrixFunctions

description: utility functions to process rate matrix output
DOI: 10.5061/dryad.nv3846b/8
title: RateMatrix_by_diet

description: script to run rate matrix on carnivore data
DOI: 10.5061/dryad.nv3846b/9
title: PMC

description: uses phylogenetic Monte Carlo procedure of Boettiger et al. to assess support for EB or SSP in family level clades.
DOI: 10.5061/dryad.r1t6fj5/1
title: ARGOS_LocationData

description: The file contains ARGOS satellite telemetry locations for the 26 elephant seals included in the analysis. Each location is associated with an ARGOS location class (lc).
DOI: 10.5061/dryad.r1t6fj5/3
title: Diving data and lean mass

description: The file contains the diving data for each individual on each day of the foraging trip: median time spent at the bottom during a dive (Bottom_time), median dive duration (Dive_duration), median descent rate (Descent_rate), median ascent rate (Ascent_rate), total number of dives per day (N_dives), number of drift dives per day (N_Drift_dives) and daily median drift rate (Drift_rate). The lean mass on each day for the two assumed functional forms (Lean_mass_1 and Lean_mass_2) and a variable indicating whether the median drift rate on that day was positive or negative (Indicator) are also included.
DOI: 10.5061/dryad.r2dm56s/1
title: Osmia_iridis_summer_duration_expt_2013-14

description: Please see README file.
DOI: 10.5061/dryad.r2dm56s/2
title: Osmia_iridis_summer_duration_expt_2014-15

description: Please see README file.
DOI: 10.5061/dryad.r2dm56s/4
title: Osmia_iridis_2016_summer_incubator_expt

description: Data used to generate Fig. 3C-D. Please see README file for details.
DOI: 10.5061/dryad.r2dm56s/5
title: Osmia_iridis_development_by_DD_2015-16

description: Data used to generate Fig. 4. Please see README file for details.
DOI: 10.5061/dryad.rk26g0n/1
title: All_data_R_ants-connectivity

description: CSV file containing ant activity on coffee plants and CBB removal before and after the placement of strings. Rows are plants. Each site contains 6 plants. trans columns refer to transformed data from densiometer. This dataset does not contain data from ant activity on the trees.
DOI: 10.5061/dryad.rs7d7q7/2
title: Supplementary Archive 2

description: Files included in Supplementary Archive 2
DOI: 10.5061/dryad.rs7d7q7/3
title: Supplementary Archive 3

description: Files included in Supplementary Archive 3
DOI: 10.5061/dryad.rs7d7q7/4
title: Supplementary Archive 4

description: Files included in Supplementary Archive 4
DOI: 10.5061/dryad.rs7d7q7/5
title: Supplementary Archive 5

description: Files included in Supplementary Archive 5
DOI: 10.5061/dryad.rs7d7q7/6
title: Supplementary Archive 1

description: Files included in Supplementary Archive 1
DOI: 10.5061/dryad.rs7d7q7/7
title: Supplementary Archive 6

description: Files included in Supplementary Archive 6
DOI: 10.5061/dryad.tq2f566/1
title: Data of all three rounds of the quantitative genetics experiment

description: Refer to the Readme file for variable descriptions.
DOI: 10.5061/dryad.08mg597/1
title: H.fraxineus data from Orton et al., Forest Pathology doi 10.1111/efp.12484

description: Data on in vitro growth rates, lesion lengths and disease progress scores.
DOI: 10.5061/dryad.0ds81v1/1
title: Frog tissue sanger sequences generated by EGETER-2019-16S primer pair
DOI: 10.5061/dryad.0ds81v1/2
title: EGETER_2019_FINAL_OTUS_FROM_FIELD_COLLECTED_RAT_STOMACH_SAMPLES
DOI: 10.5061/dryad.1nh877d/1
title: SupplementarySoftware

description: R code.
DOI: 10.5061/dryad.1nh877d/2
title: seaAge_analysis

description: This is a c++ file required to run the sea age analysis. The user does not need to open the cpp file, but the cpp file must be in the same working directory as the R code.
DOI: 10.5061/dryad.1nh877d/3
title: SourceData

description: This file contains source data to reproduce all tables and figures. The file contains 3 data sets. Readme information is included in the xlsx file. Save the respective work sheets as txt files to use as Source data for the accompanying R code.
DOI: 10.5061/dryad.205823j/1
title: Patch size and isolation

description: Patch size and patch isolation data for the 84 sampling sites.

id: sample point identification
patch: patch size (m2)
for_dist: distance to the next forest patch (m)
nfor_dist: distance to the next non-forest patch (m)
DOI: 10.5061/dryad.20p4g44/1
title: male sexual selection data across reproductive episodes--manning&mcloughin

description: Data are from an empirical study of counts and demographic rates of spatially explicit segments of a feral horse population and associated distances to nearest permanent freshwater sources on Sable Island, Canada (2008-2013). Field Labels Year=year, Itotal= georeferenced estimate of standardized variance in male mating success (variance/[mean mating success2]) for a given dominant male horse during a specific breeding season, Iband= georeferenced estimate of opportunity for male sexual selection associated with acquiring a harem, Imaresperband= georeferenced estimate of opportunity for male selection associated with acquiring mates once a male attained a harem, Band=name of band (group) of breeding feral horses consisting of a dominant male (stallion) with a harem of females, TotASR=adult sex ratio (mean number of adult males/[adult males + adult females] with ≥1 buffered locations that overlapped ≥1 locations of the ith band over the course of the field season in the jth year), NrstWater=source of nearest freshwater (hole dug by horses or naturally occurring permanent pond), AdultFemales=count of adult female horses, AveDNrstPond=distance to nearest permanent freshwater pond (meters), AveDensAllhorses=average density of all horses over an entire breeding season per km2 of terrestrial area across a band’s buffered locations, DensSumBachD= total number of unpaired adult males over an entire breeding season per km2 of terrestrial area across a band’s buffered locations, SummerTotalPrecipCM=total summer precipitation from June through August
DOI: 10.5061/dryad.2f7g889/1
title: Seed production of plants in screen houses

description: Raw and summary data for field experiment investigating male reproductive success in the presence or absence of pollinators for plants differing in stamen natural frequency.
DOI: 10.5061/dryad.2f7g889/2
title: Wind tunnel assay of pollen release

description: Data for wind tunnel assay of pollen release from flowers differing in stamen natural frequency. Flowers were exposed to two wind speeds, high and low. File includes raw data for each trial, and summary data used to produce Figure 2.
DOI: 10.5061/dryad.2f7g889/3
title: Measurements of stamen and floral traits

description: Data used in population comparison and repeatability measurements of stamen natural frequency.
DOI: 10.5061/dryad.3rj81.2
title: Data from: Different phylogenetic and environmental controls of first-order root morphological and nutrient traits: evidence of multidimensional root traits
DOI: 10.5061/dryad.4c7s325/1
title: Manuscript Appendices
DOI: 10.5061/dryad.4r34m7b/2
title: Raw data for Figure 3

description: Contains raw flow cytometry data for Figure 3. A description of this data can be found in the Excel sheet containing data for the remaining figures.
DOI: 10.5061/dryad.50t6sq6/1
title: Spiny lobster functional response analysis

description: Functional response analysis for California spiny lobsters consuming purple and red sea urchins
DOI: 10.5061/dryad.50t6sq6/14
title: ReadMe File describing all scripts and datasets

description: This text file provides a description and some metadata for each of the datasets and analysis scripts associated with the paper: Experiments reveal limited top-down control of key herbivores in Southern California kelp forests by Dunn & Hovel in Ecology
DOI: 10.5061/dryad.56q7c2k/1
title: Tracking data for hawkmoths in wind

description: The zip file contains 5 data files (described in detail in the README text file). These include the raw tracked points (in the x- and y-directions) for hawkmoth and flower motion during the wind tunnel experiments. A conversion factor from pixel values to real units is included. There is also a file for the frequency response found for hawkmoths tracking flowers in wind.
DOI: 10.5061/dryad.606fq59/1
title: Otolith_data

description: Tab delimited text file containing genotype data of five diagnostic loci  for reference Platichthys solemdali and Platichthys flesus samples and for the otolith samples genotyped in this study. These are the raw data used for the Bayesian assignment tests. The file also contains the results of the assignment tests (the posterior probabilities of each sample being P. flesus and P.solemdali). Comment lines start with ###
DOI: 10.5061/dryad.606fq59/2
title: Environmental Data

description: Environmental and fishery landings data. These include time series of the reproductive volume in the Eastern Gotland Basin (from Ustups et al, 2013), estimated proportion of P. flesus in the Gulf of Finland and the Western Åland Sea (this study) and commercial landings of flounder in the Gulf of Finland (from ICES). Comment lines start with ###
DOI: 10.5061/dryad.6963pj3/1
title: Pyoverdine production

description: Pyoverdine production of isolates sampled from cystic fibrosis patients. For each sample is given: the Patient ID, the clone type, the absolute pyoverdine production as RFU/OD, the sample location, the length of infection of the clone type and overall in the patient, the pyoverdine type, the pyoverdine production relative to the first isolate of the clone type from the patient, and classification as pyoverdine non-, super-, or producer.
DOI: 10.5061/dryad.6g24f6k/1
title: INVERTS

description: Excel file showing bulk delta13C and delta15N isotope values from macroinvertebrates collected in freshwater steams in the region of Zagreb, Croatia in April to May of 2016. Other columns include taxonomic and functional information about each sample that was analysed for isotopes, site name, stream name, and the land use classification for each sampling station.
DOI: 10.5061/dryad.6g24f6k/2
title: SOURCES

description: Excel file showing bulk delta13C and delta15N isotope values from food source materials collected in freshwater steams in the region of Zagreb, Croatia in April to May of 2016. Other columns include the type of resource, the classification of the resource in terms of allocthonous or autochthonous,  and the site name, stream name, and the land use classification for each sampling station.
DOI: 10.5061/dryad.6k417tm/1
title: Post-laying clutch reduction Dryad Dataset

description: The attached Excel file provides data for "An avian equivalent of selective abortion: post-laying clutch reduction under resource limitation". The first sheet contains data on the natural occurrence of last-egg abandonment under high and low food conditions in red-necked grebes. The second sheet contains data on the occurrence of prolonged incubation. The third sheet contains data used for calculation of the scaled mass index in juvenile birds. The scaled mass index (SMI) was computed using the equation of Peig & Green (2009). The fourth sheet contains data on the effect of experimentally increased hatching asynchrony on last-egg abandonment rates.
DOI: 10.5061/dryad.73d9482/1
title: BehavProxiesData

description: Correlative data between pairs and true genetic reproductive success
DOI: 10.5061/dryad.840j728/3
title: Drosophila_distribution_climate_data

description: <i>Drosophila</i> distribution data linked to climate variables.
DOI: 10.5061/dryad.8jh08mp/1
title: Griebeler_Klein_Supplementary_Information

description: Supporting Information with growth records of nothosaurs, additional statistical analysis on differences in life-history strategies of extant squamates, a detailed description of our growth curve fitting method, tables with equations fitted to the growth record of nothosaur specimens, and life-history traits inferred from nothosaur growth curves.
DOI: 10.5061/dryad.8p003sg/2
title: RSF data

description: Data supporting resource selection functions
DOI: 10.5061/dryad.92jr204/1
title: Daily group foraging data

description: Daily group foraging data for all 8 study sites (4 Urban (U) and 4 Rural (R)), including number of indiviudals (n), number of visits (nvisit), number of events (nevent), clumpiness of arrival (c.arrival), clumpiness of event (c.event), day and month (both continous count from the first day of data collection).
DOI: 10.5061/dryad.92jr204/2
title: Individual foraging data

description: Individual data file of recorded visits to electronic feeder. Included site (8 sites), individual id (unique PIT tag code per bird), time arrived at the feeder (arrivetime), time of departure from feeder (departtime), duration of visit (totaltime), gap between visits (difftime), and habitat type of site (urban (U) or Rural (R)).
DOI: 10.5061/dryad.cm94q95/1
title: DBH of trees per plot

description: This is the raw dbh data collected n the field per plot
DOI: 10.5061/dryad.cm94q95/2
title: Remnant Trees Data

description: Ths is the AGB calculations for the remnant trees per plot.
DOI: 10.5061/dryad.g87871r/1
title: wilkinson_et_al._plant_aphid_AMF_responses

description: This csv. file contains the physiological and chemical data acquired during the experiment. This file was used in 'R' for statistical analysis and contains the raw counts and data output of appropriate variables as well as the post calculation data used in statistical tests.
DOI: 10.5061/dryad.g87871r/2
title: wilkinson_et_al._organic_patch_IRMS_analysis

description: This data file contains the results of IRMS analysis on the organic patch material used in the study.
DOI: 10.5061/dryad.g87871r/3
title: wilkinson_et_al._raw_plant_aphid_IRMS_data

description: This data file includes the entire output from the IRMS analysis of the plant and aphid tissue. This includes carbon related analysis not used in the final statistical analysis reported.
DOI: 10.5061/dryad.h015320/1
title: Raw_reads_fasta_files.tar.gz

description: Genomic DNA was extracted from whole blood or tissue samples of 52 koalas.  DNA concentrations were quantified using a Nanodrop spectrophotometer and stock solutions were standardized at 5 ng/uL, with the exception of individual (ZIMS# 501277), which had a concentration of 2.5 ng/uL.  We amplified primer sets previously characterized from the expressed MHC transcripts in three SDZ koalas [Abts et al. 2015], and 4 additional primer sets from Lau et al. 2013.  
We began with eleven primer sets:  DAA, DAB, DBA, DBB, DCB, DMA, DMB, UAB1, UB1, UE, and UK, named according to the guidelines set forth in Klein [1990]. Each set of PCR primers was optimized and used to amplify the target regions and each individual was amplified twice at each primer set in a modified Lenz-Becker approach to minimize artifact alleles.  Barcoded TruSeq front-end adaptors then were added to the amplicons to uniquely identify each replicate.  The products were then quantified using a Qubit fluorometer and pooled in equal concentrations of approximately 10 nM.  Then the pool was sequenced using 2x300bp chemistry and an Illumina MiSeq sequencer.
The reads from each replicate were separated using the barcoded front-end adaptors.  These reads are arranged by individual-replicate (indicated by the three digits - one digit after the initial six digit unique identifier).  R1 or R2 represents the forward and reverse reads, respectively.
DOI: 10.5061/dryad.h015320/2
title: Filtered_reads_fastq_files.tar.gz

description: Beginning with the reads in Raw_reads_fasta_files.tar.gz, the adaptor sequences were trimmed and both ends of the read were trimmed for quality (Q = 20), using cutadapt [version 1.1b, Martin 2011].  These reads are arranged by individual-replicate (indicated by the three digits - one digit after the initial six digit unique identifier).  R1 or R2 represents the forward and reverse reads, respectively.
DOI: 10.5061/dryad.h015320/3
title: Filtered_merged_reads_fastq_files.tar

description: Starting from the reads in Filtered_reads_fastq_files.tar.gz, paired reads were then merged together using pandaseq [version 2.8.1, Masella et al. 2012] and separated by amplicon using a custom perl script.  The primer sets that were larger than 600 bp did not merge correctly and were not used in the final genotype sets.  These reads are arranged by individual-replicate (indicated by the three digits - one digit after the initial six digit unique identifier).
DOI: 10.5061/dryad.h015320/4
title: AmpliSAS_Results

description: Barcode sequences were reincorporated into the completely filtered reads, and 1000 reads were randomly sampled from each replicate-amplicon combination for computational tractability.  Preliminary genotypes were created using the AmpliSAS pipeline [Sebastian et al. 2016] with the default parameters for Illumina sequencing, except for the following:  minimum dominant frequency threshold = 50%, minimum amplicon depth = 10.  
Since it is thought that artifact alleles should be rare and arise from a true allele close in sequence [Babik et al. 2009], the genotypes for each amplicon were refined by filtering the alleles.  For our novel primer sets, any allele that composed less than 10% of the amplicon coverage in any individual was removed.  If any of these alleles always co-occurred with the same more dominant allele, the less abundant allele was removed even if it composed more than 10% of the amplicon coverage in some individuals.   For the Lau et al 2013 primer sets, the AmpliSAS alleles were trimmed to match the length of those alleles presented in Lau et al 2013.  Any allele that was not presented in Lau et al. 2013 was flagged and removed if it always co-occurred with the same dominant allele.
DOI: 10.5061/dryad.h0g0kf0/2
title: Backcross family (F1 female x G. pennsylvanicus male) - JoinMap Format and SNPs

description: Tab 1: Genotype data for all mapped individuals at all loci not excluded due to lack of sequence data. Data is presented in the format used by JoinMap 4.1 in which  represent loci in which the father is homozygote and the F1 mother is heterozygote and  represent loci in which both parents are heterozygotes. Tab 2: Same data in raw SNP format including mother (F1) and father (G. pennsylvanicus) information.
DOI: 10.5061/dryad.h27n3bk/1
title: mec_perspectives_gender_anon

description: Gender of authors/reviewers of perspectives pieces
DOI: 10.5061/dryad.h27n3bk/2
title: mec-9year_reviewer_gender_40_10-RSB_anon

description: A subsample of papers from Scholar one to assess editor and reviewer gender of papers submitted to MEC
DOI: 10.5061/dryad.h27n3bk/3
title: mec-9year_reviewer_gender_10_10_anon

description: Same as file ‘Mec-9year_reviewer_gender_40_10-RSB_anon’ but subsampled for first 10 women/men editors.
DOI: 10.5061/dryad.hn626p7/1
title: GPR_TWT_2017_WRRmethods

description: Two way traveltime data of ground penetrating radar wave from the snow surface to the ground surface at two sites in the Colorado Rocky Mountains.
DOI: 10.5061/dryad.jm5251f/10
title: Turnix_velox

description: Shotgun data: all merged NextSeq reads for Turnix velox, unfiltered. Unmerged reads are available upon request from the corresponding author.
DOI: 10.5061/dryad.jm5251f/11
title: Extraction_control

description: Shotgun data: all merged NextSeq reads for the extraction control, unfiltered. Unmerged reads are available upon request from the corresponding author.
DOI: 10.5061/dryad.jm5251f/2
title: Mitochondrial_partitions_gblocks

description: Alignments of mitochondrial partitions in NEXUS format. Unstable blocks were removed using the Gblocks program.
DOI: 10.5061/dryad.jm5251f/3
title: Barcodes

description: Raw: Barcode sequence data, sorted by index and trimmed but not filtered; Filtering_pipeline: Pipeline used to quality filter, chimera filter, and abidance filter barcode data before BLAST; Filtered: Barcode data, post-filtering, that was then BLAST as described in the main manuscript.
DOI: 10.5061/dryad.jm5251f/6
title: Filtered_mapped_reads

description: Reads used to reconstruct the final mitogenomes of each organism. The pipeline used to quality filter mapped reads after de novo assembly (as described in the main manuscript) is included as a .sh file.
DOI: 10.5061/dryad.jm5251f/7
title: Subset_for_BLAST

description: Unfiltered: a random selection of 1,000,000 merged sequences for blast, not quality filtered; Shotgun_filtering_pipeline.sh: the pipeline used to quality filter shotgun reads prior to BLAST; Filtered: the final selection of filtered sequences that were BLAST as outlined in the main manuscript.
DOI: 10.5061/dryad.jm5251f/8
title: Aquila_audax

description: Shotgun data: all merged NextSeq reads for Aquila audax, unfiltered. Unmerged reads are available upon request from the corresponding author.
DOI: 10.5061/dryad.jm5251f/9
title: Cracticus_tibicen

description: Shotgun data: all merged NextSeq reads for Cracticus tibicen, unfiltered. Unmerged reads are available upon request from the corresponding author.