cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0vt58q0/1
title: St.John_McGirr_Martin_2018

description: This file contains 5 tabs. The first tab contains a description of the file along with descriptions for any codes found in the remainder of the document. The second and third tab contain data for mirror assays. The fourth tab contains data for paired aggression assays. The fifth tab contains data for boldness assays.
DOI: 10.5061/dryad.1fm52vv.1
title: Data from: Taxonomic and evolutionary pattern revisions resulting from geometric morphometric analysis of Pennsylvanian Neognathodus conodonts, Illinois Basin
DOI: 10.5061/dryad.1fm52vv.1/2.1
title: Supplementary Table 1 (Specimen collection numbers)

description: Supplementary Table 1. Table showing the stratigraphic distribution of Neognathodus specimens selected to test morphotype group affinities. Specimens were chosen between multiple stratigraphic boundaries. For example, to select the 30-specimen sample of N. bassleri, 27 N. bassleri specimens were chosen from the Perth Limestone Member, two were chosen from the Mecca Quarry Shale and Velpen Limestone members, and one was chosen from the Alum Cave Limestone Member. LS = limestone, SH = shale and Mbr = member. The number of specimens chosen from each unit is proportional to the total number of morphotype group occurrences in that unit.
DOI: 10.5061/dryad.1fm52vv.1/3.1
title: Supplementary Table 2 (Total occurrences of Neognathodus)

description: Supplementary Table 2. Summary table showing the number of occurrences of each Neognathodus morphotype group in all examined stratigraphic intervals. Data are compiled for six previous studies (Brown et al. 1991; Rexroad et al. 1996; Rexroad et al. 1998; Rexroad et al. 2001; Brown and Rexroad 2009; Brown et al. 2016).
DOI: 10.5061/dryad.1fm52vv.2
title: Data from: Taxonomic and evolutionary pattern revisions resulting from geometric morphometric analysis of Pennsylvanian Neognathodus conodonts, Illinois Basin
DOI: 10.5061/dryad.1fm52vv.2/1.2
title: Supplementary Figure 1 (Neognathodus plate)

description: Figure 1. Images of type specimens for synonymized Neognathodus species N. medadultimus/N. medexultimus and N. dilatus/N. metanodosus. Pairs are synonymized here to N. medadultimus and N. dilatus, respectively. All images are re-illustrated from previous studies. Scale bar represents one mm. Conodont element identification is fol¬lowed by repository number (if available) and photo reference, stratigraphic unit and the county and state location. See README file for more specific details.
DOI: 10.5061/dryad.1fm52vv.2/2.2
title: Supplementary Table 1 (Specimen collection numbers)

description: Supplementary Table 1. Table showing the stratigraphic distribution of Neognathodus specimens selected to test morphotype group affinities. Specimens were chosen between multiple stratigraphic boundaries. For example, to select the 30-specimen sample of N. bassleri, 27 N. bassleri specimens were chosen from the Perth Limestone Member, two were chosen from the Mecca Quarry Shale and Velpen Limestone members, and one was chosen from the Alum Cave Limestone Member. LS = limestone, SH = shale and Mbr = member. The number of specimens chosen from each unit is proportional to the total number of morphotype group occurrences in that unit.
DOI: 10.5061/dryad.1fm52vv.2/3.2
title: Supplementary Table 2 (Total occurrences of Neognathodus)

description: Supplementary Table 2. Summary table showing the number of occurrences of each Neognathodus morphotype group in all examined stratigraphic intervals. Data are compiled for six previous studies (Brown et al. 1991; Rexroad et al. 1996; Rexroad et al. 1998; Rexroad et al. 2001; Brown and Rexroad 2009; Brown et al. 2016).
DOI: 10.5061/dryad.1fm52vv.2/4.2
title: Systematic Paleontology

description: Systematic Paleontology section that official synonymizes Neognathodus the species pairs of N. medadultimus and N. medexultimus to N. medadultimus, and and N. dilatus and N.metanodosus to N. dilatus. This synonymy is based on our geometric morphometric results that show there is no statistically significant shape difference between the species pairs of N. medadultimus/N. medexultimus and between N. dilatus/N. metanodosus.
DOI: 10.5061/dryad.28hv53f/1
title: Ramos-Fabiel et al DataBase

description: The data contained in this data base are from nine tropical dry forest secondary plots (30 × 30 m; 0.09 ha) representing a successional chronosequence, with ages ranging between 2 and 67 years after abandonment. The plots are located around the village of Nizanda, Oaxaca state, southern Mexico. The format is an Excel Book. Page 'SITES' contains the characteristics of these plots, including geographical location and elevation. Page 'VEGETATION ATTRIBUTES' contains structural and diversity attributes of the vegetation at each sampling site. Page 'BEE FUNCTIONAL ATTRIBUTES' contains information for bee guild, nesting habit and body size for each bee species. Page 'BEE ABUNDANCES' contains the numbers of individuals for each bee species at each sampling site. Page 'BEE FAMILIES BY PLANT SPECIES' contains the numbers of individuals belonging to each of five bee families that were trapped on each plant species over the study period.
DOI: 10.5061/dryad.2f7h7t6/1
title: Hydrologic metrics

description: Hydrologic metrics for sites used in analysis. Metrics were predicted using hydrologic modelling procedure described in Leasure et al. (2016), "Natural Flow Regimes of the Ozark–Ouachita Interior Highlands Region". X and Y coordinates are provided in meters projected using NAD 1983 Albers.
DOI: 10.5061/dryad.2f7h7t6/2
title: Fish Assemblage Data

description: Presence (1) and absence (0) of fish species across sample sites in AR, USA. Data is compiled samples taken between 1980-2009 by various state and federal agencies, universities, and museums. Data was compiled by the Arkansas GAP analysis project and was obtained from the Nature Conservancy. X and Y coordinates are provided in meters projected using NAD 1983 Albers.
DOI: 10.5061/dryad.34jc0m7/1
title: Paternity data

description: Complete data set from competitive paternity assay
DOI: 10.5061/dryad.34jc0m7/2
title: Fecundity Data

description: Complete data set from fecundity assay
DOI: 10.5061/dryad.34jc0m7/3
title: Means

description: Computed means of all measurements, including fecundity, paternity success on all days, and body mass
DOI: 10.5061/dryad.3f9r8r6/1
title: SCD-HeFT Heart Rate Variability Data Recorded by ICDs
DOI: 10.5061/dryad.4461jj8/1
title: Adolescent Anemia in Nepal 2014

description: Collected in the field of public health, the data set provides information on adolescent anemia in Nepal, obtained from the Adolescent Nutrition Survey 2014, carried out by Nepal Health Research Council in 2014 in Nepal
DOI: 10.5061/dryad.4p3f8c8/1
title: 174 genotyped individuals from Siberian Herefords and Kazakh Whiteheaded breeds

description: 174 cattle individuals from Siberian Hereford (150) and Kazakh Whiteheaded (24) breeds. These samples were genotyped on the GGP HD150K bovine SNP array, filtered for unmapped SNPs, SNPs on sex chromosomes, MAF&lt;0.05, low genotyping success and HW equilibrium. This resulted in 107 550 SNPs present in this file.
DOI: 10.5061/dryad.4th3p35/3
title: Chapman_seed.data

description: This is the seed rain dataset we used to compare against our small mammal density data. It comprises landscape-scale monthly means of pooled seed and fruit mass (g m3) against the relevant grids trapped in each month. For fuller details of how these data were derived, see the README.
DOI: 10.5061/dryad.57vf3fr/2
title: Concatenated Data of Nuclear DNA Sequences

description: Concatenated data of ITS (base 1-674) and at103 (base 675-1210)
DOI: 10.5061/dryad.57vf3fr/3
title: Concatenated Data of Chloroplast DNA Sequences

description: Concatenated data of matK (base 1-1042), trnLcd (base 1043-1679), trnLef (base 1680-2047) and ndhF (2048-2748)
DOI: 10.5061/dryad.60jv067.2
title: Data from: Moth body size increases with elevation along a complete tropical elevational gradient for two hyperdiverse clades
DOI: 10.5061/dryad.60jv067.2/1.2
title: Brehm_etal_ecog_03917_Moth_images

description: This zip file contains images of almost all specimens in the study with body weight data (27 species of Arctiinae and 57 species of Geometridae; each a male and a female). Scale bar = 10 mm
DOI: 10.5061/dryad.60jv067.2/2.2
title: Appendix_Raw_EVI-data

description: This file contains the raw EVI (Enhanced Vegetation Index) data from the study
DOI: 10.5061/dryad.60jv067.2/3.2
title: Appendix_Raw_Female Proportions

description: This file contains the raw data for female proportions of Arctiinae and Geometridae moths in the study
DOI: 10.5061/dryad.60jv067.2/4.2
title: Appendix_Raw_FWL-area-mass

description: This file contains the raw data for forewing lengths (FWL), wing area and mass of Arctiinae (27 males and 27 females of 27 species) and Geometridae (57 males and 57 females of 57 species) moths in the study
DOI: 10.5061/dryad.60jv067.2/5.2
title: Appendix_Raw_Winglength

description: This file contains the raw data for fore wing lengths (FWL) of all Arctiinae and Geometridae moths in the study.
DOI: 10.5061/dryad.60jv067.2/6.2
title: Appendix_Histograms

description: This file contains raw data and histograms of Arctiinae and Geometridae moths at 12 sites along the elevational gradient.
DOI: 10.5061/dryad.6363bk7/1
title: Delaney and Janzen_Behavioral Ecology_Dataset 1

description: This file contains data collected in the field during a dispersal experiment for hatchling Chelydra serpentina. Methods are discussed in detail in Delaney and Janzen (in press in 2018 in Behavioral Ecology).
DOI: 10.5061/dryad.6363bk7/2
title: Delaney and Janzen_Behavioral Ecology_Dataset 2

description: This file contains data collected from field observations of Chelydra serpentina. Methods are described in Delaney and Janzen (in press in Behavioral Ecology in 2018). Specifically, this dataset was used to compare female distance to water with her offsprings' performance and average size.
DOI: 10.5061/dryad.74r4q8p/1
title: SPSS data bank

description: The de-identified data presented here has been used for the analyses reported in the manuscript "NIGHTTIME INTENSIVE CARE UNIT DISCHARGE AND OUTCOMES: A PROPENSITY MATCHED RETROSPECTIVE COHORT STUDY", including  baseline characteristics of study participants and the main clinical outcomes before propensity score matching.
DOI: 10.5061/dryad.7jf0vp5/1
title: Oyster size distribution and abundance data

description: This file contains the raw survey data from size-abundance surveys at each site from 2004-2009. Each row corresponds to an observation of a single oyster on one face of one rock on one transect at a site in a given year. If multiple oysters were observed on a given rock face, each oyster is listed on a separate row with the same spatial label.                               
 Full meta-data can be accessed at the following GitHub site: 
  https://github.com/jwilsonwhite/IPM_statespace/tree/master/Kimbro_etal_Oikos
DOI: 10.5061/dryad.7jf0vp5/2
title: Post-settlement mortality experiment

description: Results of experiment that evaluated post-settlement mortality of oysters in Tomales Bay, CA. Results of the experiment are illustrated in Figure 1.  In file, column 1 "site" refers to each individual site and is a factor. Column 2, "region" refers to outer, mid, or inner area of Tomales Bay. Column 3 "unit" refers to individual experimental unit randomly assigned among sites. Column 4 "treatment" refers to one of three levels of the factor predation. Column 5 "number" refers to number of oysters on tile. Column 6 "revised" refers to corrected number of oysters on tiles.Column 7 "surv" refers to proportional survival at end of experiment (initial/final oysters). Columns 8 and 9 refer to number of alive and dead oysters. Column 10 refers to distance (km) of site from mouth of the bay. Column 11 "mort" refers to proportional mortality of oysters (1-initial/final).
DOI: 10.5061/dryad.7t3j55p/1
title: Ne_G_pallida

description: Genotypic data (Genepop format) for each initial (Pi_A to Pi_G) and final Globodera pallida populations (Pf-01 to Pf-24).
DOI: 10.5061/dryad.8717pg9/1
title: Protein expression under heat wave conditions

description: Protein ratios from quantitative proteomics of leaf samples collected after a four-day heat wave (42 degree) and control (28 degree) treatment for Eucalyptus grandis. Protein identity and quantity were determined using Proteome Discoverer V1.3 software (Thermo Scientific, United States) run from a local MASCOT server (Matrix Science, London, U.K.). The E. grandis protein sequences available through UniProt (http://www.uniprot.org, n = 44,150 proteins; October 2016) were used as a reference search database. The following parameters were used for peptide to spectrum matching in MASCOT: MS tolerance, ±10 ppm; enzyme, trypsin with one missed cleavage; fragment mass error, 0.1 Da; static modifications, carbamidomethylation of cysteine and 10-plex TMT tags on lysine residues and peptide N-termini; variable modifications, oxidation of methionine and deamidation of asparagine and glutamine. Spectra were also searched against a reversed-sequenced decoy database to determine false discovery rates (FDR) and filtered at a maximum FDR cut-off of 1% at the protein level. Only peptides below the MASCOT significance threshold filter of p = 0.05 were included in the final dataset, and proteins with at least two unique peptides were regarded as confident identifications. Relative quantification of proteins was achieved by pairwise comparison of TMT intensities, using the ratio of the labels for each of the treatment replicates (numerator) versus the labels of their corresponding pooled control reference (denominator).
DOI: 10.5061/dryad.b1366vs/1
title: Stott et al Python code

description: Python code to calculate stimulus parameters of a disc and sphere based on experimenter input to GUI.
DOI: 10.5061/dryad.b1366vs/2
title: Stott et al Matlab code

description: Matlab code to autodetect DCMD firing parameters
DOI: 10.5061/dryad.b9j94n3/1
title: Rubin et al. Ecology and Evolution Data

description: Phenotypic data for each replicate Mimulus guttatus plant in the parental (greenhouse) and progeny (growth chamber) generations.
DOI: 10.5061/dryad.bn796qq/17
title: 4_pgls_phylo_d_code

description: R code for running Phylo-D and PGLS tests
DOI: 10.5061/dryad.bn796qq/18
title: 2015 Cohen dates

description: Text file of dates used for time periods
DOI: 10.5061/dryad.bn796qq/19
title: ML taxa-matched trees

description: IQTREE output phylogenies with synonymous taxa matched, suitable for R analysis
DOI: 10.5061/dryad.bn796qq/20
title: Proposed supertrees

description: Eight proposed supertree topologies, suitable for R analysis
DOI: 10.5061/dryad.bn796qq/21
title: readme

description: Summary of appendices and supplementary data contents
DOI: 10.5061/dryad.c90m738/1
title: Data_from_MacDonald_et_al_Welsh_AES_species_J_Appl_Ecol

description: These are the data files used in the analysis for the article: Have Welsh agri-environment schemes delivered for focal species? Results from a comprehensive monitoring programme, by MacDonald et al.
DOI: 10.5061/dryad.cq2862k/1
title: data zip

description: Contains all data (pre-processed and in raw format) as well as scripts (matlab) used to analyze the data. A main readme file is contained in the main folder and individualized readme files are provided in each sub-folder for different experiments/codes.
DOI: 10.5061/dryad.f8n8p13/1
title: Supplementary Table 1

description: Character matrix data of several naticid genera and species to distinguish subfamilies within Naticidae and the out group Ampullospirinae. Major sources are Popenoe et al., 1987 (1); Aronowsky, 2003 (2), Marincovich, 1977(3), Majima, 1989 (4), Kilburn, 1976 (5).
DOI: 10.5061/dryad.f8n8p13/2
title: Supplementary Table 2

description: List of all Jurassic naticid genera reported in the Paleobiology Database (PBDB; www.paleobiodb.org) from different parts of the world. Only genus-level information has been listed. ‘Indet.’ forms are excluded from the list.
DOI: 10.5061/dryad.gm17ct8/1
title: Burress and Wainwright Supplementary Materials

description: This file contains all Supplementary Tables and Figures referenced in the article.
DOI: 10.5061/dryad.gm17ct8/2
title: Burress and Wainwright Supplementary Data

description: This file contains the data used in the article, including the functional innovation and trophic guild designations and morphological traits.
DOI: 10.5061/dryad.h2q3d96/1
title: Raw data - Kjernsmo et al 2018

description: Raw data from Experiment 1 and 2. Contains attack latency and side of prey attacked for each fish and trial. L = large spot, S = small spot, HC = High contrast and LC = Low contrast.
DOI: 10.5061/dryad.hk2p481/1
title: Chrysolaena cytogeography

description: Populations of Chrysolaena species analysed cytogeographically, with data on ploidy levels, geographical coordinates and bioclimatic variables.
DOI: 10.5061/dryad.k42t7g2/5
title: FennvilleApple.fq.gz

description: Fastq file containing demultiplexed sequences for samples from apple fruits at Fennville, MI.
DOI: 10.5061/dryad.k42t7g2/6
title: GrantHawthorn.fq.gz

description: Fastq file containing demultiplexed sequences for samples from hawthorn fruits at Grant, MI.
DOI: 10.5061/dryad.k42t7g2/7
title: GrantApple.fq.gz

description: Fastq file containing demultiplexed sequences for samples from apple fruits at Grant, MI.
DOI: 10.5061/dryad.k42t7g2/8
title: UrbanaHawthorn.fq.gz

description: Fastq file containing demultiplexed sequences for samples from hawthorn fruits at Urbana, IL.
DOI: 10.5061/dryad.k42t7g2/9
title: UrbanaApple.fq.gz

description: Fastq file containing demultiplexed sequences for samples from apple fruits at Urbana, IL.
DOI: 10.5061/dryad.n08c0t7/1
title: Supplementary Tables
DOI: 10.5061/dryad.pq269b0/1
title: SNP_coverage.tab

description: Coverage data for each of the 1,588,558 SNPs in each BAM file (2 per host race, ALF: alfalfa, CLO: clover, PEA: Pea). Coordinates on the v2 assembly (SCAFFOLD_POSITION) are given as row names.
DOI: 10.5061/dryad.pq269b0/2
title: SNP_refcounts.tab

description: Reference allele count data for each of the 1,588,558 SNPs in each BAM file (2 per host race, ALF: alfalfa, CLO: clover, PEA: Pea). Coordinates on the v2 assembly (SCAFFOLD_POSITION) are given as row names.
DOI: 10.5061/dryad.pq269b0/3
title: SelEstim output

description: Full output from the SelEstim analysis, see the README file for the command used.
DOI: 10.5061/dryad.pq269b0/4
title: coordinates_CS_salivary_candidates

description: Genomic coordinates of all chemosensory and salivary candidates (v2 assembly).
DOI: 10.5061/dryad.pq269b0/5
title: top_SNP_per_hotspot

description: Coordinates of the top 1 SNP per hotspot (based on KLD values from the SelEstim analysis) on the v2 assembly.
DOI: 10.5061/dryad.pq269b0/6
title: X-A_assignment

description: Coordinates (v2 assembly) of the X chromosome or autosome blocks identified by Jaquiéry et al. 2018 GBE.
DOI: 10.5061/dryad.r3k7m3c/1
title: ESM_appendices

description: Appendices 1-4 referenced in main text
DOI: 10.5061/dryad.r3k7m3c/2
title: dissimilarity_functions

description: R script with functions for calculating dissimilarity matrices using Wills' GED, Gower's coefficient, and the new family of metrics proposed in the associated publication
DOI: 10.5061/dryad.r3k7m3c/3
title: myriapods_final_final

description: Nexus file with character matrix for empirical example. Also available from MorphoBank (http://morphobank.org/permalink/?P3189).  See Appendix 3 for more information.
DOI: 10.5061/dryad.r3k7m3c/4
title: myriapods_type_205

description: Table with information about hierarchical structure of character matrix used in empirical example.  Required for calculating a dissimilarity matrix based on the new family of metrics proposed in the associated paper using the supplied R function.
DOI: 10.5061/dryad.r4688p7/1
title: Heinen & Harvey_Ecological Entomology

description: Total hyperparasitism data (counts and proportions, sheet1) and hyperparasitoid community data (sheet 2)
DOI: 10.5061/dryad.rs467t5/1
title: datafordryad

description: Data on community composition and environmental characterisitics from Ligurian shores
DOI: 10.5061/dryad.s6j1822/1
title: Welti et al. 2018_Online data_Network metrics

description: Climate, fire and grazing treatment and network metrics for plant-grasshopper networks.
DOI: 10.5061/dryad.sb7nb51/1
title: EOH PLOS One CSF Biomarkers in Hip Fracture Patients

description: CSF AD biomarkers in hip fracture patients
DOI: 10.5061/dryad.t48p8c0/1
title: dryad data_RSPB-2018-2193

description: Data for ms RSPB-2018-2193 by Barbaro et al.: site-variables, site-bird species, bird species traits, site-bat species and bat species traits tables
DOI: 10.5061/dryad.t76fk80/10
title: Supplementary file - settings files for demographic inferences
DOI: 10.5061/dryad.t76fk80/11
title: si_files_SA.tar

description: SLiM simulations
DOI: 10.5061/dryad.t76fk80/18
title: Main README

description: This dryad page provides the data and the source code for the figures in " Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences " by Pouyet F,* Aeschbacher S*, Thiery A and Excoffier L. 
* first co-authors 

It contains as compressed files: 
-- 1 -- Genotype tables and annotations from 1000G and SGDP data 1000G_genot-table.zip SGDP_genotypetable-annotation.zip with README files that describe the data and how to use them.   
-- 2 -- the R scripts to perform the figures of INDA figures_INDA_Rscripts.zip  
-- 3 -- the confidence intervals of the estimates as well as the source code to estimate them confidenceIntervals.zip  
-- 4 -- the scripts (R and python) to make the SFS figures as well as estimate confidence intervals and compute the SFS figures_data_SFS_Rscripts.zip  
-- 5 -- the setting parameters for FastSimCoal demographic inferences Supplementary file - settings files for demographi ...  
-- 6 -- the scripts for SLiM simulations and analyses (bash and R code) + a table with parameters used in the SLiM simulations (.csv) + the scripts and raw data that I used to make the figures (.txt and .R) si_files_SA.tar.gz 

Extra READMEs describe the files and how to launch them to compute the statistics or to make the figures.
DOI: 10.5061/dryad.t76fk80/6
title: SGDP_genotypetable-annotation

description: It contains as compressed files:
 
 - Genotype tables and annotations from SGDP see the file README_columns genotypeTables
 
 README files describe the files and how to launch them.
DOI: 10.5061/dryad.t76fk80/8
title: confidence Intervals

description: Files with 95% CI
DOI: 10.5061/dryad.v275qv6/1
title: Master_Data

description: 3 tabs with data (plant, larvae, genomics) and 3 tabs explaining the meaning of the various columns in the data sheets
DOI: 10.5061/dryad.vq05124/1
title: Sequences of two MHC class I loci

description: View File Details
DOI: 10.17632/c5bc68f2f7.1
title: Data for: A Stochastic Method in Simulating Particles Transport and Deposition in Wall-bounded Turbulent Flow

description: Data and figures of the manuscript
DOI: 10.5061/dryad.016gp34/1
title: Supplemental Materials

description: Supplemental Methods, Supplemental Figure S1, Supplemental Tables S1 and S2
DOI: 10.5061/dryad.14rr125/1
title: Figure1-Data

description: Source data and plot data points in Figure 1
DOI: 10.5061/dryad.14rr125/2
title: Figure2-Data

description: Source data and plot data points in Figure 2
DOI: 10.5061/dryad.14rr125/3
title: Figure3-Data.zip

description: Source data and plot data points in Figure 3. Combine with Figure3-Data.zip.002.
DOI: 10.5061/dryad.14rr125/5
title: Figure3-Data_STLC

description: Source data and plot data points in Figure 3 (STLC treated cells).