cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.30k44/8
title: Scan B: Protasterina flexuosa (CMC 25001)

description: Micro-CT scan of Protasterina flexuosa (CMC 25001) using a Nikon XTek XT H225 scanner (Tokyo, Japan). 3200 two-dimensional images were generated with a voxel size of 6.0 microns at a voltage of 85 kV and current of 90 microamps. Volume was reconstructed using Nikon CTPro 3D (Tokyo, Japan). Users should contact authors prior to file use other than corroborating data presented in paper.
DOI: 10.5061/dryad.30k44/9
title: Scan C

description: Micro-CT scan of Protasterina flexuosa (CMC 25001) using a Nikon XTek XT H225 scanner (Tokyo, Japan). 3200 two-dimensional images were generated with a voxel size of 10.4 microns at a voltage of 85 kV and current of 90 microamps. Volume was reconstructed using Nikon CTPro 3D (Tokyo, Japan). Users should contact authors prior to file use other than corroborating data presented in paper.
DOI: 10.5061/dryad.40nv6/1
title: Exposed porpoise GPS data

description: This is the full dataset collected by GPS tags fitted on four harbor porpoise individuals. Large positional errors were removed as described in the article. The data also contains the calculated horizontal movement parameters and distance variables to produce figure 1 in the main article and the figures in the Supplementary material. The data contains 10 variables:
“id” gives the name of the harbor porpoise individual
“datetime” gives the date and time of the GPS location
columns “x” and “y” are the coordinates of the GPS location in the projection CRS("+proj=utm +zone=32 +ellps=intl +towgs84=-87,-98,-121,0,0,0,0 +units=m +no_defs")
“steplength” is the Euclidian distance (m) between GPS locations
“speed” is the speed (m/sec) between GPS locations
“turing_angle” is the turning angle (degrees) between GPS locations
“hour_since_release” is the time (hours) since the individual was released into the water after GPS tagging
“dist_to_exposure_site” is the Euclidian distance (m) of the individual porpoise relative to the airgun exposure site 
“dist_to_release_site” is the Euclidian distance (m) of the individual porpoise relative to the GPS tagging and release site
DOI: 10.5061/dryad.40nv6/2
title: Exposed porpoise dive data

description: This is the full dataset collected by dive-loggers fitted on four harbor porpoise individuals. Impossible values were removed as described in the article. It is the underlying data used to produce figures in the Supplementary material and contains 6 variables:
“id” gives the name of the harbor porpoise individual
“datetime” gives the date and time of the start of each dive
“dive_duration” gives the difference in time (sec) between the start and end of each dive
“max_depth” provides the maximum depth (m) reached during each dive
“wiggliness” provides the sum of absolute depth differences (m) while at the bottom of each dive; measure of amount of “wiggling” while at bottom
“post_dive_duration” provides the time (sec) spent at the surface after each dive
DOI: 10.5061/dryad.40nv6/3
title: residual_data_horizontal_movements

description: Contains the residuals of the GAM analyses on the horizontal movement data, which was used in the piecewise regression analyses. It is the underlying data used to produce figure 3 in the main article and contains 5 variables:
“id” gives the name of the harbor porpoise individual
“hour_since_release” is the time (hours) since the individual was released into the water after GPS tagging
“residuals_steplength” are the residuals of the Euclidian distance (m) between GPS locations
“residuals_speed” are the residuals of the speed (m/sec) between GPS locations
“residuals_turing_angle” are the residuals of the turning angle (degrees) between GPS locations
DOI: 10.5061/dryad.40nv6/4
title: residual_data_vertical_movements

description: Contains the residuals of the GAM analyses on the vertical movement data, which was used in the piecewise regression analyses. It is the underlying data used to produce figure 4 in the main article and contains 6 variables:
“id” gives the name of the harbor porpoise individual
“hour_since_release” is the time (hours) since the individual was released into the water after GPS tagging
“dive_duration” are the residuals of the difference in time (sec) between the start and end of each dive
“max_depth” are the residuals of the maximum depth (m) reached during each dive
“wiggliness” are the residuals of the sum of absolute depth differences (m) while at the bottom of each dive
“post_dive_duration” are the residuals of the time (sec) spent at the surface after each dive
DOI: 10.5061/dryad.40nv6/5
title: R-code

description: The file contains the R-code for the piecewise linear regression analyses and model selection used to assess capture/tagging and airgun noise-induced movement responses in harbour porpoises
DOI: 10.5061/dryad.9k1h0/11
title: ITProcessedPartI

description: Processed Ion Torrent data part I
DOI: 10.5061/dryad.9k1h0/12
title: ITProcessedPartJ

description: Processed Ion Torrent data part J
DOI: 10.5061/dryad.9k1h0/13
title: ITProcessedPartK

description: Processed Ion Torrent data part K
DOI: 10.5061/dryad.9k1h0/14
title: ITProcessedPartL

description: Processed Ion Torrent data part L
DOI: 10.5061/dryad.9k1h0/15
title: ITRawPartA

description: Raw Ion Torrent data part A
DOI: 10.5061/dryad.9k1h0/16
title: ITRawPartB

description: Raw Ion Torrent data part B
DOI: 10.5061/dryad.9k1h0/17
title: ITRawPartC

description: Raw Ion Torrent data part C
DOI: 10.5061/dryad.9k1h0/9
title: ITProcessedPartG

description: Processed Ion Torrent data part G
DOI: 10.5061/dryad.b9d2cg7/1
title: distribution data for three Onomsa species
DOI: 10.5061/dryad.d87v3.2/1.2
title: Herrero-Jáuregui & Oesterheld 2017_Dryad

description: Data on species richness and diversity under different stocking rates of domestic herbivores in 48 studies all throughout the planet
DOI: 10.5061/dryad.fc827/10
title: Genomic prediction script

description: Perl wrapper script (forks to run multiple jobs) to run the genomic prediction option in gemma. This is sued after the standard BSLMM has been fit.
DOI: 10.5061/dryad.fc827/11
title: Scripts for processing BSLMM output

description: This compressed directory contains a series of perl scripts used to summarize the output from gemma's BSLMM. The calpost* scripts summarize the hyperparameter estimates (e.g., pve, pge, etc.), get Bvs* extract breeding values from the standard BSLMM (based only on the polygenic term), getPrdtBvs* extract breeding values from genomic prediction that include SNPs with measurable effects, and grabCalsEffects* extract and summarize the SNP effect estimates. All summaries are across MCMC chains.
DOI: 10.5061/dryad.fc827/12
title: QLT summaries and scripts

description: This compressed directory contains three files. sortedCombinedPips.txt contains the SNP posterior inclusions probabilities for all traits and biological levels, averaged across MCMC chains. This is the needed input for the other two files/scripts. pipColocal.R quanties correlations in PIPs across traits, and plotPipLgs.R runs the QTL number/density analyses per LG, along with making some plots.
DOI: 10.5061/dryad.fc827/13
title: G- and P-matrix infiles and analyses

description: This compressed directory includes the genome estimated breeding values from genomic prediction (catbv*csv) for each groups, phenotypic data for P-matrixes (resid*) and a R script that runs analyses on these files, matcomp.R (which has annotations throughout). The R script runs the comparisons of P and G-matrixes and the evolvability/constraint analyses, as well as making related plots.
DOI: 10.5061/dryad.fc827/9
title: Phenotypic data

description: This files contains the wing pattern data, including area and position measurements. Individual IDs and groups are given in the first and second column, respectively.
DOI: 10.5061/dryad.gd290/2
title: Processed data and covariates for each bird sister species pair

description: This file contains all data (variability of body mass across species ranges) and covariates assembled for each tropical-nontropical bird sister species pair identified from a global bird phylogeny. Detailed metadata for each column, including description, units, and data source, are in another associated file: bird_sister_species_column_metadata.txt.
DOI: 10.5061/dryad.gd290/3
title: Column metadata for bird sister species data

description: This is a tab-delimited .txt file with column metadata (description, data source, and units) for each of the columns in the bird_sister_species_data.csv file also archived with this submission.
DOI: 10.5061/dryad.gd290/4
title: Raw body mass data for bird species

description: These are raw body mass measurements from the vertnet.org specimen database that have already been subject to extensive quality control. All columns other than species binomial and mass in grams have been stripped away; this is the minimal information required to do the bootstrap resampling to recreate the analysis in the manuscript.
DOI: 10.5061/dryad.r8q72/1
title: Gene alignments

description: FASTA format alignments for 151 protein-coding using three assembly methods: consensus, ambiguity (iupac), and allele phasing. Alleles for each individual are annotated as _h1 or _h2; for SVDQuartets all SNPs are randomly assigned to _h1 or _h2. For the alleles dataset, alleles have been phased within the longest phaseable block. Outside this block, ambiguity codes are retained. Also contains partition files for RAxML, with each gene partitioned by codon position.
DOI: 10.5061/dryad.r8q72/2
title: Phyparts Output

description: Output of Phyparts, a bipartition analysis method. Rooted gene trees were reconciled with the ASTRAL species tree produced for each of the assembly methods: consensus (default), ambiguity (IUPAC) and alleles.
DOI: 10.5061/dryad.r8q72/3
title: Species Trees

description: Species phylogenies for the three assembly methods: consensus (default), ambiguity (iupac), and alleles. For the coalescent-based methods, two types of gene trees were used as input: one with fully bifurcating gene trees, and one where branches were collapsed if they had less than 33% gene tree bootstrap support.
DOI: 10.5061/dryad.r8q72/4
title: scripts

description: Bash shell and python scripts used to prepare alignments for gene tree inference, phase alleles, and extract introns and exons for multiple-sequence alignment.
DOI: 10.5061/dryad.r8q72/5
title: Gene_trees

description: Gene trees from three data assembly methods. The identity of each gene can be found in final_genelist.txt
DOI: 10.5061/dryad.r8q72/6
title: taxon_subst_artocarpus

description: Table for translating accession IDs into taxon names.
DOI: 10.5061/dryad.ts57v.1
title: Data from: Breeding bird species diversity across gradients of land use from forest to agriculture in Europe
DOI: 10.5061/dryad.ts57v.2
title: Data from: Breeding bird species diversity across gradients of land use from forest to agriculture in Europe
DOI: 10.5061/dryad.ts57v.2/1.2
title: Bioassess bird data

description: Landscape variables and avian point-count species richness data collected in the BioAssess project 2001-2002 in eight European countries
DOI: 10.5061/dryad.vj72f/1
title: Mantella_TI

description: Data on TI responses from captive and wild golden mantella
DOI: 10.5061/dryad.vs044/6
title: Supplementary Figure 6

description: Fig. S6: 3D interactive model of the Limulus polyphemus chilaria, as modelled from iodine staining and micro-CT-scanning.
DOI: 10.5061/dryad.vs044/7
title: Supplementary Figure 7

description: Fig. S7: 3D interactive model of the Limulus polyphemus genital operculum, as modelled from iodine staining and micro-CT-scanning.
DOI: 10.5061/dryad.vs044/8
title: Supplementary Figure 8

description: Fig. S8: 3D interactive model of the Limulus polyphemus gill operculum, as modelled from iodine staining and micro-CT-scanning.
DOI: 10.5061/dryad.08pv2/1
title: Data S1

description: Catch data for age-1 Walleye Sander vitreus sampled by nighttime electrofishing and mini-fyke nets in spring 2013 (South Buffalo Lake) and 2014 (Lake Kampeska, Lake Madison, and Roy Lake).
DOI: 10.5061/dryad.08pv2/2
title: Data S2

description: Total length (mm) and total weight (g) of fall age-0 and corresponding spring age-1 Walleye Sander vitreus collected from South Buffalo Lake (2012 and 2013) and Lake Kampeska, Lake Madison, and Roy Lake (2013 and 2014).
DOI: 10.5061/dryad.14sr463/13
title: Phocoena phocoena Mid-Span Slices
DOI: 10.5061/dryad.14sr463/14
title: Phocoena phocoena Tail Base Slices
DOI: 10.5061/dryad.14sr463/15
title: Phocoena phocoena Tail Tip Slices
DOI: 10.5061/dryad.14sr463/16
title: Tursiops truncatus Mid-Span Slices
DOI: 10.5061/dryad.14sr463/17
title: Tursiops truncatus Tail Base Slices
DOI: 10.5061/dryad.14sr463/18
title: Tursiops truncatus Tail Tip Slices
DOI: 10.5061/dryad.1c3k32r/1
title: Mandible descriptors and PCs for comparison

description: Sheet 1: Mandible area and Fourier coefficients from A0 to B7 describing size and shape of the mandible. Sheet 2: Mechanical advantages (MAs) and axes for comparisons: PCclimate, PC for D-loop analysis, and PC for mitochondrial analysis.
DOI: 10.5061/dryad.2jp32/1
title: Sumatran Rhinoceros occurence data

description: Georeferenced occurrence data for Sumatran Rhinoceros (Dicerorhinus sumatrensis) compiled from literature and including recent, historical and putative fossil occurrences.
DOI: 10.5061/dryad.37m5c/1
title: larvae_unsum_fulldata_rawcounts

description: Larvae: Raw sequence counts assigned to OTUs (97% identity threshold) without any filtering or summarizing. Post Wolbachia sequence removal.
DOI: 10.5061/dryad.3b04j/1
title: Landmarks coordinates of pronota and forewing

description: This ZIP file includes the raw coordinates of the landmarks employed to characterize the shape variation of the forewing and pronota. Trait shape was characterized separately for each sex. The landmarks are stored in TPS format.
DOI: 10.5061/dryad.3b04j/2
title: SVDquartets and SNAPP input files

description: This ZIP file includes the different inputs files for SVDquartets and SNAPP to species tree estimation. For SVDquartets analyses, six SNP matrices were employed which were obtained by setting in PyRAD different values of clustering thresholds (Wclust = 0.85 and 0.90) and minimum taxon coverage in a given locus (minCov = 4, 10 and 20). SNAPP analyses were performed employing a SNP matrix generated using Wclust = 0.90 and minCov = 10.
DOI: 10.5061/dryad.4188b/1
title: Data from Sloan et al

description: Excel spreadsheet containing gene expression and morphometric data for males from two treatment groups
DOI: 10.5061/dryad.4g9g0/1
title: Cleptoparasite density data

description: Data used for the analyses described in publication titled "Simplifying understory complexity in oil palm plantations is associated with a reduction in the density of a cleptoparasitic spider, Argyrodes miniaceus (Araneae: Theridiidae), in host (Araneae: Nephilinae) webs". Data includes information about each individual host (Nephila spp.) web as follows: "Plot" = assigned plot code for each treatment plot; "Treatment" = understory complexity treatment, including "E" (enhanced complexity), "N" (standard complexity), and "R" (reduced complexity); "Date" = date of survey; "Time" = time of survey; "Weather" = weather during survey; "Spider Height" = height of host (Nephila spp.) spider from the ground; "Spider size" = length of host (Nephila spp.) spider; "Web L" = host web length; "Web W" = host web width; "# cleptos" = the number of Argyrodes miniaceus cleptoparasites present in the host web; and "# males" = the number of males present in the host web.
DOI: 10.5061/dryad.58gn0/1
title: TableS4_Bagel_Dunlap_MBE_new

description: Results of BAGEL analyses for microarray data GSE8932. Relative gene expression analysis of 10 microarrays from Chen et al. (2009). Abbreviations: WT: wild type, nop: nop-1 knockout, Ref: pooled RNA reference, D: dark (DD), S: short light exposure (15–30 minutes, LL15, LL30), and L: long light exposure (60–120 minutes, LL60 and LL120).
DOI: 10.5061/dryad.58gn0/3
title: FigS2_nop1_phenotypes

description: Triplet crossing plates between the wild type strains (A and B) and between the nop-1 knockout and the wild type strains (C and D) when cultured under constant light with sealed (A and C) and unsealed plates (B and D). Wild type crosses produced perithecia earlier when cultured under constant white light on sealed plates (A) than when cultured under constant white light on unsealed plates (B). matA ∆nop-1 cross with mata wild type exhibited wild type perithecial development when cultured under constant white light on sealed plates (C), but exhibited earlier and more abundant production of perithecia for ∆nop-1 when cultured under constant white light on unsealed plates (D). Conidiation (visible as orange pigment) is much more abundant on unsealed plates in all comparisons
DOI: 10.5061/dryad.58gn0/4
title: Fungal opsin sequences analyzed

description: Sequences used in the evolutionary analyses
DOI: 10.5061/dryad.5n0c3/1
title: Watershed Invertebrate Diversity Data for 1995 MBSS

description: Data accompanying the analyses in Patrick & Brown 2017, Species pool functional diversity plays a hidden role in generating β-diversity.  Eight columns by 266 rows.  Each row corresponds to a community type in a particular watershed.  Community type is designated by the "group" column (P= Predator, H=Herbivore, F=Filterer, C=Collector-Gatherer, S = Shredder, all = Whole Community).  Watershed is denoted in the "MDE8Digit" column by a code referring to a Maryland 8 Digit watershed code (corresponds to USGS HUC12).  The average within stream alpha richness for the watershed is in the "alpha" column.  The total gamma richness for the watershed is in the "gamma" column.  The functional diversity, expressed as RaoQ, for the species pool of the watershed is in the "fdiv" column. The beta diversity, expressed as mean bray curtis dissimilarity, of the watershed is in the "bdiv" column.  The environmental dispersion, expressed as multivariate dispersion among environmental variables, is in the "envdisp" column.  Please see Patrick & Brown 2017 for detailed methods.
DOI: 10.5061/dryad.60p50/1
title: perrier-genotypes-parus-major

description: VCF file containing genotypes of the Parus major individuals. Individual names can be matched with the names found in the individuals.txt file in order to extract site of origin, coordinates, and urbanization scores.
DOI: 10.5061/dryad.60p50/2
title: perrier-individuals.txt-parus-major

description: TEXT file containing information (coordinates, site, urbanization scores ) regarding Parus major individual genotyped found in the VCF file.
DOI: 10.5061/dryad.68pc2/1
title: Determination of dimethylsulfoniopropionate (DMSP) in Ulva

description: (1) Raw file: DMSP can be directly quantified in Ulva mutabilis using liquid chromatography coupled to mass spectrometry (HILIC-ESI-Q-ToF-MS). A representative raw data file (MassLynx V4.1) was uploaded. DMSP (M+H = m/z 135) was produced by blade cells of the Ulva thallus. [2H6]-DMSP (M+H = m/z 141) was added as an internal standard for reference and quantification. (2) Excel file: Values of the DMSP quantification and the uptake experiment.
DOI: 10.5061/dryad.6nq0d/1
title: Data for Gross ammonification and nitrification rates

description: Data for "Soil gross N ammonification and nitrification from tropical to temperate forests in eastern China"
DOI: 10.5061/dryad.75b406n/1
title: Alignments and positively selected sites

description: The package contains visualizations of alignments and positively selected sites for all genes and branches that were analyzed in the corresponding article.
DOI: 10.5061/dryad.7rf7q/1
title: 2006-2011

description: SPSS 20 file containing anonymised data
DOI: 10.5061/dryad.7rf7q/2
title: 2012-2013 Cohort

description: SPSS 20 file containing anonymised patient data.
DOI: 10.5061/dryad.9238j7f/1
title: PlasticityRecombinatioRaw

description: This is the raw data file from this experiment. We report the number of each phenotype for each replicate at each temperature.
DOI: 10.5061/dryad.9k1h0/18
title: ITRawPartD

description: Raw Ion Torrent data part D
DOI: 10.5061/dryad.9k1h0/19
title: ITRawPartE

description: Raw Ion Torrent data part E
DOI: 10.5061/dryad.9k1h0/20
title: ITRawPartF

description: Raw Ion Torrent data part F
DOI: 10.5061/dryad.9k1h0/21
title: ITRawPartG

description: Raw Ion Torrent data part G
DOI: 10.5061/dryad.9k1h0/22
title: MEGA

description: Files associated with the MEGA analysis
DOI: 10.5061/dryad.9k1h0/23
title: STRUCTURE-MainK4run

description: Files associated with the Structure analysis determining K
DOI: 10.5061/dryad.9k1h0/24
title: STRUCTURE-referencePartA

description: Files associated with the Structure analysis on the full data set part A
DOI: 10.5061/dryad.9k1h0/25
title: STRUCTURE-referencePartB

description: Files associated with the Structure analysis on the full dataset part B
DOI: 10.5061/dryad.9k1h0/26
title: Exclave_sampling

description: Sampling (kmz file for Google Earth)
DOI: 10.5061/dryad.b9d2cg7/2
title: Original data for measuring mophological characters
DOI: 10.5061/dryad.d87v3.1
title: Data from: Effects of grazing intensity on plant richness and diversity: a meta-analysis
DOI: 10.5061/dryad.d87v3.1/1.1
title: Herrero-Jáuregui & Oesterheld 2017_Dryad

description: Data on species richness and diversity under different stocking rates of domestic herbivores in 48 studies all throughout the planet
DOI: 10.5061/dryad.d87v3.2
title: Data from: Effects of grazing intensity on plant richness and diversity: a meta-analysis
DOI: 10.5061/dryad.f1858/1
title: Diabetes mellitus and risk of colorectal cancer

description: The Korean Multi-center Cancer Cohort is a population-based prospective cohort study designed to investigate the relationship between exposures to environmental factors, lifestyle factors, and the risk of cancer in Korea. A total of 20,636 participants (8,235 men and 12,401 women) were recruited from six geographic areas of Korea from 1993 to 2005. For these analyses, we excluded participants who had no information on age at cohort recruitment (1,182 men and 1,792 women), whose FSG level information was incomplete or who had no information about history of diabetes mellitus (1,007 men and 1,575 women), who were aged 20 years or younger (156 men and 334 women), who had a prior diagnosis of colorectal cancer (6 men and 13 women), or who were censored within one month from the baseline survey (1 man). After these exclusions, 14,570 participants (5,883 men and 8,687 women) were included in the final analysis. Data were created using SAS software version 9.4 (SAS Institute Inc., Cary, North Carolina, United States).
DOI: 10.5061/dryad.fg189/1
title: Data for inbreeding depression in sperm performance (Losdat et al. 2017)
DOI: 10.5061/dryad.g8d1v/1
title: Moran & Fuller 2017 Current Zoology Dryad data

description: The Excel file contains two tabs with raw behavioral data. The first tab has data from trials that measured male competition and female mate choice and the second tab has data from trials that measured male mate choice. Further details on the experimental design and interpretation of the variables are provided in the document.
DOI: 10.5061/dryad.gd290/5
title: stepAICc R function

description: This is a modified version of the stepAIC() function from the R package MASS which uses AICc (Akaike's corrected information criterion) rather than AIC to select the predictor to add at each step.
DOI: 10.5061/dryad.gd290/6
title: Code to reproduce analyses in paper

description: This R script was tested with R version 3.3.3 on 13 December 2017. It loads the two .csv files also archived with this submission and reproduces the analyses in the paper: t-test, bootstrap sampling of the individual measurements to correct for unequal sample sizes, multiple regression, and model selection.
DOI: 10.5061/dryad.hd7j7kv/1
title: Robart_and_Sinervo_2018_BehavEcol