cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.70s5t/2
title: repro_raw

description: These are the studies that compared productivity (mostly number of fledged young per pair or per nest) to either timber harvest or tree size. We report the individual effects reported in each study and our derivation of the standard effect size ‘r’.
DOI: 10.5061/dryad.70s5t/3
title: repro_per-study_average

description: For each study listed in repro_raw, we have calculated an average effect size (both r and Zr), corresponding average sample size (n) and average variance corresponding with Zr (vz).
DOI: 10.5061/dryad.7cq0k/1
title: Breed Pig Genotypes

description: 1670 Individual genotypes, belonging to 45 pig breeds from the Iberian Peninsula (Spain and Portugal), Europe (local and commercial breeds), and America, for a panel of 24 microsatellites
DOI: 10.5061/dryad.7dq0j/1
title: Appendix S1 - TNT files

description: Zip file containing all 100 matrices generated from our MK model of morphological change.
DOI: 10.5061/dryad.7dq0j/2
title: Appendix S2 – Trees

description: Zip file containing pdfs of all consensus trees generated from equal and implied weighting analyses for all 100 matrices. The files have been commented on to denote correct and incorrect node relationships with checks and x's respectively.
DOI: 10.5061/dryad.7dq0j/3
title: Appendix S3 - Spreadsheet of Node Counts

description: Excel spreadsheet with raw counts of correct, incorrect, and unknown relationships for all runs of equal and implied weighting, as well standardized counts of implied weighting relative to equal weighting, and overall counts of the relative proportions of the data which increase or decrease error.
DOI: 10.5061/dryad.7dq0j/4
title: Appendix S4 – Run Counts of Repeated Errors

description: A checklist of the 100 runs counting off the number of times an error in equal weighting was repeated in 1, 2, 3, and all 4 implied weights runs.
DOI: 10.5061/dryad.7dq0j/5
title: Appendix S5 - Character Weights Test NEXUS files

description: Zip folder containing all 100 nexus files used in the character weights tests. These matrices contain the same 4 characters (Character 56-59), generated with known rates of evolution.
DOI: 10.5061/dryad.7dq0j/6
title: Appendix S6 - Character Weights

description: Excel spreadsheet of the weights/fits generated for our four characters in all 100 matrices for four values of k (1,3,5,10).
DOI: 10.5061/dryad.g0874/11
title: Alpha

description: Estimates of alpha, the genome-wide proportion of adaptive substitutions, at different minor allele frequency thresholds.
DOI: 10.5061/dryad.g0874/12
title: PSMC results

description: [12 files] PSMC results for twelve selected samples.
DOI: 10.5061/dryad.g0874/13
title: SweeD Results

description: [42 files] SweeD output for each of the 21 chromosomes, run for the Eastern and Western populations separately.
DOI: 10.5061/dryad.g0874/14
title: Analyses of chromosomes 11 and 12

description: [2 files] Statistics calculated in 50kb sliding windows for chromosomes 11 and 12. Nucleotide diversity, absolute divergence and Kst.
DOI: 10.5061/dryad.g0874/15
title: Genotypes 4D sites

description: Genotype calls for all individuals at all fourfold degenerate (4D) sites.
DOI: 10.5061/dryad.g0874/16
title: Genotypes Codon Pos 1

description: Genotype calls for all individuals at first codon positions.
DOI: 10.5061/dryad.g0874/17
title: Genotypes Codon Pos 2

description: Genotype calls for all individuals at second codon positions.
DOI: 10.5061/dryad.hf040/1
title: mtPIrtv in Andalusian 2-2-2016
DOI: 10.5061/dryad.kf4t9/1
title: Soil, litter, macrofauna and nematode data from Berenstecher et al. 2016

description: This data file contains unanalysed data from soil and litter characteristics, macrofaunal abundance and composition, nematode abundance and decomposition, litter and soil enzymatic activities and litter decomposition at sampling points before and after the massive  Puyehue volcanic eruption of June 2011 in Patagonia, Argentina
DOI: 10.5061/dryad.mb2tj/1
title: VCF file for experimental and natural populations

description: This is the VCF file for the experimental and natural population comparisons. To test for differentiation genome wide among sympatric populations, we contrasted our apple7 and haw7 groups; for a response to selection in our experiment, we compared haw7 and haw30. Haw or apple represents the host plant from which the flies were collected; the number - 7 or 30 - represents the pre-winter warm period experienced by larvae/pupae prior to overwintering to match that found in nature on haw or apple plants. See txt file to match individual MID labels in the VCF file with the experimental group they were part of.
DOI: 10.5061/dryad.mb2tj/2
title: R_pomonella_denovo_assembly

description: This file is the de novo assembly of Illumina sequence reads (20 million reads; 3% of total data) generated by Seqman NGen 4.0.0 (DNASTAR) using parameter values described in Gompert et al. 2012. See methods for more details.
DOI: 10.5061/dryad.mb2tj/3
title: R. pomonella Linkage Map

description: Linkage map giving the linear order of SNPs on each of the five chromosomes/linkage groups. Column labels: chromosome (1 to 5), Sn = SNP number ID (1-N by chromosome), locus = location of SNP in our de novo assembly by contig, then by location along contig, separated by an underscore, Position = distance along each linkage group/chromosome in centiMorgans.
DOI: 10.5061/dryad.r3s14/1
title: CrushSnailSheet

description: This was the data sheet used to examine the explanatory variables influencing crush resistance. Columns included are: "Snail.ID.no" = snail ID number, "Newton" = force required to break shell, "line" = maternal snail line, "numberincup" = snail density in each housing arena, "Dvpop" = divergence vector, "centroid" = size
DOI: 10.5061/dryad.s4h26/10
title: Simulation data on mobile pastoralists in northeastern Nigeria 10

description: This dataset contains the simulation output data generated by an agent-based model of mobile pastoralists.
DOI: 10.5061/dryad.s4h26/11
title: Simulation data on mobile pastoralists in northeastern Nigeria 11

description: This dataset contains the simulation output data generated by an agent-based model of mobile pastoralists.
DOI: 10.5061/dryad.s4h26/12
title: Simulation data on mobile pastoralists in northeastern Nigeria 12

description: This dataset contains the simulation output data generated by an agent-based model of mobile pastoralists.
DOI: 10.5061/dryad.s4h26/13
title: Simulation data on mobile pastoralists in northeastern Nigeria 13

description: This dataset contains the simulation output data generated by an agent-based model of mobile pastoralists.
DOI: 10.5061/dryad.sk3p7/1
title: freedman_2014_plosgenetics_vcffiles

description: Included in the tarball are merged vcf files, for individual autosomes, for the 6 canid genomes sequenced for and described in "Genome Sequencing Highlights the Dynamic Early History of Dogs", Freedman et al, PLoS Genetics 2014. Those are: Chinese wolf, Israeli wolf, Croatian wolf, Golden jackal, Dingo and Basenji.These files have been converted to boxer reference genome CanFam 3.1 coordinates (the original paper was in v. 3.0 coordinates). See Freedman et al. 2014 for a detailed description of filters.
DOI: 10.5061/dryad.v5k62/1
title: SAS laktation3

description: Time taking for the nursing suckling interaction
DOI: 10.5061/dryad.v5k62/2
title: Datablad dödlighet pek

description: Piglet mortality on sow level
DOI: 10.5061/dryad.v5k62/3
title: Avvlidna vikter och var

description: Where and weight of dead piglets in each managament routine and repeat
DOI: 10.5061/dryad.17m17/1
title: commands_ML_Blackwell
DOI: 10.5061/dryad.17m17/2
title: ML_Blackwell_keep
DOI: 10.5061/dryad.17m17/3
title: ML_Blackwell_map_cat
DOI: 10.5061/dryad.17m17/4
title: ML_Blackwell_map
DOI: 10.5061/dryad.17m17/5
title: parameters_core_diversity
DOI: 10.5061/dryad.17m17/6
title: parameters_jackknife
DOI: 10.5061/dryad.17m17/7
title: ML_Blackwell_97

description: Supporting data analysis for Richmond et al., Nat Comm 2016
DOI: 10.5061/dryad.35010/1
title: Willow height and position

description: Position and height of each willow measured. "ID" is the willow ID, "height", the willow height, "date", the time of measurement, "exclosure", weather the willow is inside or outside the cow exclosure, "Latitude" and "Longitude" are straightforward, "distance", is the distance from the closest willow within the dataset, and "dataset" is the group of data collected together.
DOI: 10.5061/dryad.35010/2
title: probe_depth

description: Depth of the Probe, one day in 2014.
DOI: 10.5061/dryad.35010/3
title: probe_attributes

description: Probe attributes: "Meadow", is the Meadow ID, "Probe2", the Probe ID, "Lat" and "Long", are lattitude and longitude coordinates, "Veg" is the dominant type of vegetation, "Hab" is the type of habitat, "Dep", the depth of the probe when set, "Elevation", the elevation of the probe, "Exclosure", exclosure if the probe is within or outside the exclosure.
DOI: 10.5061/dryad.35010/4
title: temperature data

description: "Probe2", is the probe ID, "Date", is the day of the measurement, "Tmed", median temperature value for a particular probe and day, "Tmean", mean temperature value for a particular probe and day, "Tmax", maximal temperature value for a particular probe and day,"Tmin", minimal temperature value for a particular probe and day,"Tsd", standard deviation of temperature for a particular probe and day, "T7sd.mean", 7-days moving average for the standard deviation, "T7med.mean", 7-days moving average for the median,"T7mean.mean", 7-days moving average for the mean, "T7min.mean", 7-days moving average for the minimum, "T7max.mean", 7-days moving average for the maximum, "T7sd.med", 7-days moving median for the sd, "T7med.med", 7-days moving median for the median, "T7mean.med", 7-days moving median for the mean, "T7min.med", 7-days moving median for the minimum, "T7max.med", 7-days moving median for the maximum, "year"        "date",  "day",  "Meadow" and "week" are straightforward.
DOI: 10.5061/dryad.3hq89/1
title: Species traits and variables - data table

description: Species trait data and environmental variables used for analysis of correlates of extinction risk in 1,139 squamate reptiles. For each species, data on extinction risk, range size, reproductive mode and output, body size, trophic group, biogeographical realm and island endemism is given. In addition, the file holds environmental data extracted across each species' range from spatial data layers on climate, net primary productivity (NPP) and human pressures (population density, human appropriation of NPP, accessibility, etc.).
DOI: 10.5061/dryad.3hq89/2
title: Composite phylogeny of squamate reptiles

description: Non-dated composite phylogeny of squamate reptiles (1,139 species + Sphenodon punctatus as outgroup) as used in our analysis of extinction risk correlates of squamate reptiles. This zip file contains the data file holding the phylogeny in text format, and a Word document describing how the phylogeny was constructed, as well as literature citations.
DOI: 10.5061/dryad.3rf1k/1
title: Fire, land-cover, weather data

description: R data file containing data about fire counts, land cover and weather. Spatial resolution of the data: 10 km. Data span from 2000 to 2010 and over 200,000 km2.
DOI: 10.5061/dryad.478t9/1
title: Phylogenetic tree for V6 30hpf embryo #7

description: A tree created with the PHYLIP Mix package from DNA sequenced from a 30hpf zebrafish embryo with an integrated GESTALT barcode, exposed to CRISPR/Cas9 editing reagents.
DOI: 10.5061/dryad.49rs8/2
title: Dfr, sequence alignments

description: Sequences from a total of 22 Iochrominae species were generated from floral bud cDNA prepared from greenhouse or field-collected material. Sequences from six outgroup taxa were retrieved from Genbank or Solgenomics (solgenomics.net).
DOI: 10.5061/dryad.49rs8/3
title: F3h, sequence alignments

description: Sequences from a total of 22 Iochrominae species were generated from floral bud cDNA prepared from greenhouse or field-collected material. Sequences from six outgroup taxa were retrieved from Genbank or Solgenomics (solgenomics.net).
DOI: 10.5061/dryad.664cp/12
title: FigureS2.1.PBGD
DOI: 10.5061/dryad.664cp/14
title: FigureS2.3.PPOX
DOI: 10.5061/dryad.664cp/15
title: FigureS2.4.FeCH
DOI: 10.5061/dryad.664cp/16
title: FigureS2.5.FeCH
DOI: 10.5061/dryad.664cp/17
title: FigureS2.6.FeCH
DOI: 10.5061/dryad.664cp/18
title: FigureS2.7.FeCH
DOI: 10.5061/dryad.664cp/19
title: FigureS2.8.UROS
DOI: 10.5061/dryad.664cp/20
title: FigureS2.9.FeCH
DOI: 10.5061/dryad.664cp/21
title: FigureS2.10.FeCH
DOI: 10.5061/dryad.6bs01/1
title: Greenhouse gas fluxes

description: Cumulative (interpolated) fluxes of CH4, N2O, and CO2 from each dung mesocosm, which is associated with cow ID, the presence/absence of beetles, and treatment (antibiotic / control). Note that there were missing readings due to technical mishaps: two per compound from mesocosm 39 (antibiotic treatment + with beetles); one per compound from mesocosm 49 (control treatment + no beetles) and one per compound from mesocosm 51 (control + with beetles). These missing values were replaced by the appropriate treatment-and-day-specific means for each compound.
DOI: 10.5061/dryad.6bs01/2
title: Number of beetle offspring

description: The total number of dung beetle offspring collected from dung mesocosms over the course of the experiment. Each mesocosm is associated with a cow ID and treatment (antibiotic or control).
DOI: 10.5061/dryad.6bs01/3
title: Performance measurements of beetle offspring

description: The average head capsule size and fresh weight of larval dung beetle offspring collected from each dung mesocosm. Each mesocosm is associated with cow ID and treatment (antibiotic or control). No head size measurement was available for mesocosm #25.
DOI: 10.5061/dryad.6bs01/4
title: Mapping file for sequence data

description: The metadata associated with sequenced samples.
DOI: 10.5061/dryad.6bs01/5
title: Replace Demultiplexed sequences

description: Demultiplexed paired-end 16S rRNA sequence reads (forward and reverse). These sequences are the output of the UPARSE script prep_fastq_for_uparse_paired.py (they have not been merged or quality-filtered). Note that this sequence run was a combination of additional samples/projects not included in the paper (not in the associated mapping file).
DOI: 10.5061/dryad.6bs01/6
title: OTU table

description: The OTU table used in analyses (previous sequence data processing steps described in the Methods). This dataset has not been rarefied or filtered (e.g. to remove mitochondria, chloroplasts, OTUs in negative controls - see Methods). The Greengenes-assigned taxonomy strings associated with each OTU are in the right-most columns.
DOI: 10.5061/dryad.70s5t/4
title: Occupancy_raw

description: These are the studies that compared the occupancy of nest sites or clusters of nest sites to either timber harvest or tree size. We report the individual effects reported in each study and our derivation of the standard effect size ‘r’.
DOI: 10.5061/dryad.70s5t/5
title: occupancy_continent_study_av

description: For each study listed in occupancy_raw, we have calculated an average effect size (both r and Zr), corresponding average sample size (n) and average variance corresponding with Zr (vz).
DOI: 10.5061/dryad.70s5t/6
title: occupancy_variable_study_av

description: For each study listed in occupancy_raw, we have calculated an average effect size (both r and Zr), corresponding average sample size (n) and average variance corresponding with Zr (vz). There is only one small difference with occupancy_continent_study_av above. One of the studies examined the correlations between occupancy and both timber harvest history and average tree size. Thus for this study, we calculated two average effects on this sheet, one corresponding to timber harvest and the other corresponding to average tree size. This facilitates comparing effects of tree size to effects of timber harvest.
DOI: 10.5061/dryad.77kj5/1
title: N&C_content

description: Nitrogen and carbon content are assayed separately on female flowers, acorns and cupules collected in 30 oak trees (Quercus petraea) in 2013.
DOI: 10.5061/dryad.bq5rj/1
title: dryad_ovda

description: Genetic data at 15 microsatellite loci, Dall's sheep, Wrangell-St. Elias National Park and Preserve, Alaska, USA
DOI: 10.5061/dryad.dc8nn/1
title: Supplemental Materials

description: The following reports were generated for each taxa based on the curated matrices and ‘monographs’ from the Phenoscape Knowledgebase. These reports list the entities and qualities used in each EQ statement from these works. These data were used to (1) compare the overlap of entities (E) and phenotypes (EQs) for monographs and matrices for each of the four taxa, and (2) calculate the anatomical entities (E), qualities (Q), and phenotypes (EQ) that were unique to monographs and matrices.
DOI: 10.5061/dryad.dc8nn/2
title: Supplementary Table 1

description: Relative proportions of different character types in datasets derived from monographs and matrices.
DOI: 10.5061/dryad.dc8nn/3
title: Supplementary Table 2

description: Breakdown of EQ complexity scores across EQ statements from matrices (A) and ‘monographs’ (B).
DOI: 10.5061/dryad.fh6d9/1
title: Inbreeding coefficients and all fitness and phenotypic data: genomic analysis reveals depression due to both individual and maternal inbreeding in a free-living mammal population.
DOI: 10.5061/dryad.g0874/18
title: Genotypes Codon Pos 3

description: Genotype calls for all individuals at third codon positions.
DOI: 10.5061/dryad.g0874/19
title: Genotypes Intronic

description: Genotype calls for all individuals at intronic sites.
DOI: 10.5061/dryad.g0874/20
title: Genotypes 4D lowCUB

description: Genotypes for all individuals at 4D sites in genes showing minimal codon usage bias.
DOI: 10.5061/dryad.g0874/21
title: Genotypes All Sites Part 1 of 4

description: Genotype calls for all individuals at all sites. Part 1 of 4.
DOI: 10.5061/dryad.g0874/22
title: Genotypes All Sites Part 2 of 4

description: Genotype calls for all individuals at all sites. Part 2 of 4.
DOI: 10.5061/dryad.g0874/23
title: Genotypes All Sites Part 3 of 4

description: Genotype calls for all individuals at all sites. Part 3 of 4.
DOI: 10.5061/dryad.g0874/24
title: Genotypes All Sites Part 4 of 4

description: Genotype calls for all individuals at all sites. Part 4 of 4.
DOI: 10.5061/dryad.g0874/25
title: Genotypes Intergenic Part 1 of 3

description: Genotype calls for all individuals at intergenic sites. Part 1 of 3.
DOI: 10.5061/dryad.g529s/1
title: Dataset FE-2016-00107

description: Data from: Positive species diversity and above-ground biomass relationships are ubiquitous across forest strata despite interference from overstorey trees. Functional Ecology
DOI: 10.5061/dryad.r3s14/2
title: F2_Behavior_WMorphology

description: This file contains the results of anti-predator behavioral trials and morphological measures for those individuals. "snail.ID" = individual snail ID, "Condition" = pre- or post-cue addition, "check.number" = observation number before or after the addition of cue, "centroid" = size, "Dvpop" = divergence vector, "numberincup" = snail density in home arena, "line" = maternal line, "Treatment" = F2 treatment (C = control, P = predator), "Treatment.parent" = F1 treatment (C = control, P = predator)
DOI: 10.5061/dryad.r3s14/3
title: morphoanalysisF2DVs

description: This file was used to look for a treatment (F1 and F2) on morphology (shape and size). Columns included are: "centroid" = size, "Dvpop" = divergence vector, "line" = maternal line, "treatment" = F2 treatment (C = control, P = predator), "ptreatment" = F1 treatment (C = control, P = predator), "numberincup" = snail density in home arenas
DOI: 10.5061/dryad.sh8b4/1
title: characterCompat

description: R script compiled for compatibility test
DOI: 10.5061/dryad.061tr/1
title: Bat activity data with environmental variables and geographic locaitons

description: Data includes all data used in bat models. Columns 1-2 give random effects (site and management unit), column 3 is thinning category. Columns 4:5 are the univariate bat response variables (total activity and foraging activity). Columns 6:28 are multivariate response variables: taxa activity (cols 6:16), guild activity (cols 17:22) and guild foraging activity (cols 23:28). All bat activity are in calls per night (foraging activity measures represent foraging calls or 'feeding buzzes' per night). Columns 29:41 are environmental variables described in Table S1 of the supplementary material of the paper (see attached README file). Columns 42:43 are geographic coordinates (latitude and longitude, WGS84) for each site.
DOI: 10.5061/dryad.061tr/2
title: Insect biomass data with environmental variables and geographic locations

description: Data includes all data used in insect models. Columns 1-2 give random effects (site and management unit), column 3 is thinning category. Column 4 is the univariate insect response variables (total insect biomass). Columns 5:15 are multivariate response variables including biomass for each order. All insect biomass measures are in grams. Columns 16:28 are environmental variables described in Table S1 of the supplementary material of the paper (see attached README file). Columns 29:30 are geographic coordinates (latitude and longitude, WGS84) for each site.
DOI: 10.5061/dryad.11c40/1
title: JEV-AllHosts-Phylogeo

description: This file contains all sequence data and the discrete character coding used for the ancestral reconstruction of geographic states
DOI: 10.5061/dryad.1ct66/1
title: Data_PONE-D-15-53646

description: Data of body mass, feather growth rate and flightlessness duration of common eiders (Somateria mollissima dresseri) exposed to warm and cold water treatments.
DOI: 10.5061/dryad.27m7h/1
title: GPA bats

description: Average coordinates and centroid sizes from Generalized Procrustes Analysis of bats in each of the skull views (cranium ventral, cranium lateral, and mandible lateral). Values were averaged across individuals for each species.
DOI: 10.5061/dryad.2vj5h/1
title: Data for the ns gene mapping

description: The information of molecular markers and candidate genes were listed in Table 1 and Table 3. Table 2 was the validity results of the SSRns-127 marker for MAS breeding. The pictures in Figure 1 showed the phenotypes of parental lines. Figure 2 was the genetic map of the ns gene.
DOI: 10.5061/dryad.330c1/1
title: NPF_paper_raw_data_Dryad_Biol_Letters

description: The raw cycle threshold (CT) values and associated identifiers of biological replicate and treatment for the analyses preformed in the linked paper.
DOI: 10.5061/dryad.478t9/10
title: embryos_1_7 data matrix

description: data matrix input to PHYLIP Mix for embryo #7, a v6 30hpf embryo
DOI: 10.5061/dryad.478t9/2
title: fish_ADR1_PHYLIP_MIX_gte5

description: a maximum parsimony tree of GESTALT barcodes collected from adult zebrafish ADR1.  The tree was assembled using the PHYLIP Mix software package and annotated into a JSON data object for visualization
DOI: 10.5061/dryad.478t9/3
title: fish_ADR2_PHYLIP_MIX_gt5

description: a maximum parsimony tree of GESTALT barcodes collected from adult zebrafish ADR2.  The tree was assembled using the PHYLIP Mix software package and annotated into a JSON data object for visualization
DOI: 10.5061/dryad.478t9/4
title: cell_culture_gte2

description: a maximum parsimony tree of GESTALT barcodes collected from cell culture lineages.  The tree was assembled using the PHYLIP Mix software package and annotated into a JSON data object for visualization
DOI: 10.5061/dryad.478t9/5
title: embryos_1_7

description: the raw maximum parsimony tree set output of GESTALT barcodes collected from embryo #7, a 30hpf zebrafish embryo.  The file contains the all of the raw PHYLIP Mix software package output trees
DOI: 10.5061/dryad.478t9/6
title: fish_ADR2_PHYLIP_MIX_gte5_output

description: the raw maximum parsimony tree set output of GESTALT barcodes collected from adult zebrafish ADR2.  The file contains the all of the raw PHYLIP Mix software package output trees