cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.04t19/13
title: Slow Flow - narrowgrid, binaral transversal

description: contains ("sample_L_0" - "sample_L_8") and ("sample_R_0" - "sample_R_8") which correspond to 4 minute epochs at two locations (left and right).
DOI: 10.5061/dryad.1fp259b/1
title: eDNA Data by month and water body

description: Samples are provided by month and water body with corresponding covariate information (water body type, pH, water sample depth, days since last pig visit, number of pictures of pigs per month, and average pig group size).  The qPCR results are shown (simplified to zeros and ones that were used in this analysis). The first six columns of the qPCR results are from the pooled sample data (first 3 are pre-inhibitor removal, next 3 are post-inhibitor removal).  The next 40 columns are the qPCR results by sample (first 20 are pre-inhibitor removal, next 20 are post-inhibitor removal).
DOI: 10.5061/dryad.20md774/1
title: Zip file of matlab code

description: Zip files of the matlab code used to generate the results in the paper
DOI: 10.5061/dryad.343nt5s/1
title: 2018-Jan-31 WCE Combined Final Sessions

description: This SPSS data file provides all of the survey responses and background characteristics of the participants in the World Climate Exercise as covered in the article.
DOI: 10.5061/dryad.3528sj6/1
title: README

description: ddRAD sequences and metadata from Eucera (Peponapis) pruinosa (Hymenoptera: Apidae) males used in: 

Anthony D. Vaudo, Megan L. Fritz, and Margarita  M. Lopez-Uribe (2018) Opening the door to the past: Accessing phylogenetic, pathogen, and population data from museum curated bees. Insect Systematics and Diversity
DOI: 10.5061/dryad.5cr07/2
title: T1_brain_PLOS1
DOI: 10.5061/dryad.5f88r9m/2
title: Martin et al 2018 MEE R code
DOI: 10.5061/dryad.5q9q697/1
title: (Table 1) Direction of Growth

description: The data that was used to show the preferential growth direction in figure 1 and 2.
DOI: 10.5061/dryad.5q9q697/2
title: (Table 2) Sr Transects

description: Data for figure 3
DOI: 10.5061/dryad.6447n78/16
title: README

description: README file describing contents of the other files.
DOI: 10.5061/dryad.712kj7v/1
title: Example_simulated_fd_run_scripts
DOI: 10.5061/dryad.712kj7v/2
title: BarombiMbo_corrected_dxy_pi

description: Sliding window values of pairwise Dxy and Pi, corrected for missing invariant sites in the vcf, for Barombi Mbo cichlids and riverine outgroups
DOI: 10.5061/dryad.712kj7v/3
title: Bmbo.MAF0.05.MaxMiss0.9.DP5.GQ20.recode.vcf

description: Filtered vcf of Sarotherodon Barombi Mbo species, riverine outgroups and Coptodon outgroup
DOI: 10.5061/dryad.712kj7v/4
title: BarombiMbo_treemixoutput.tar

description: Treemix output of genome-wide estimates of migration events into Barombi Mbo from riverine outgroups
DOI: 10.5061/dryad.712kj7v/5
title: BarombiMbo_fd_50kslide_and_simulation_output.tar

description: Csv file output of the fd tests of introgression for the empirical Barombi Mbo data and the sequences simulated under a model of no migration
DOI: 10.5061/dryad.712kj7v/6
title: BarombiMbo_Saguaro_SNP_filtered_output

description: Saguaro output files containing the segments assigned to 75 cacti. This folder contains three versions of SNP filtering: with segments with less than 1, 10 and 20 SNPs removed.
DOI: 10.5061/dryad.712kj7v/7
title: BarombiMbo_Saguaro_tree_files.tar

description: .TRE for all 75 topologies assigned across genome using Saguaro
DOI: 10.5061/dryad.72cg113/1
title: Faria_et_al_Wavefamilies_filtered_GT_FORMAT

description: Genotypes of the Wave families.
DOI: 10.5061/dryad.7h62c8t.1
title: Data from: Prey diversity, prey composition, and predator population dynamics in experimental microcosms
DOI: 10.5061/dryad.7h62c8t.1/1.1
title: Population abundance data

description: day - the day of the experiment the observation in the row belongs to.
jar - a number that uniquely identifies each experimental unit.
prey.composition - a number that identifies the combination of prey species added to the jar.
prey.richness - the number of prey species added to the jar.
replicate - a replicate identifier, unique within prey composition.
species - a numeric code for the species that the observation in the row belongs to.
count - the number of individuals counted in the sample; used to calculate density per ml. Counts were made by eye, looking down a microscope.
w1 - the volume of liquid in ml removed from the community for sampling abundance, used to calculate density per ml.
w2 - the volume of diluent added to the volume sampled.
w3 - the volume of the sub-sample taken of the mixture of diluent and sample removed (i.e. w1 + w2).
DOI: 10.5061/dryad.7h62c8t.2
title: Data from: Prey diversity, prey composition, and predator population dynamics in experimental microcosms
DOI: 10.5061/dryad.7h62c8t.2/1.2
title: Population abundance data

description: day - the day of the experiment the observation in the row belongs to.
jar - a number that uniquely identifies each experimental unit.
prey.composition - a number that identifies the combination of prey species added to the jar.
prey.richness - the number of prey species added to the jar.
replicate - a replicate identifier, unique within prey composition.
species - a numeric code for the species that the observation in the row belongs to.
count - the number of individuals counted in the sample; used to calculate density per ml. Counts were made by eye, looking down a microscope.
w1 - the volume of liquid in ml removed from the community for sampling abundance, used to calculate density per ml.
w2 - the volume of diluent added to the volume sampled.
w3 - the volume of the sub-sample taken of the mixture of diluent and sample removed (i.e. w1 + w2).
DOI: 10.5061/dryad.bs154q0/1
title: Data for Berson and Simmons 2018 Condition dependence of CHCs

description: File containing the treatment, morphological and CHC data.
DOI: 10.5061/dryad.cb51t54/1
title: Validation NIM-MetS
DOI: 10.5061/dryad.cm86089/1
title: DRYAD-J-alignment-Evolution
DOI: 10.5061/dryad.dc28m/2
title: Zinger_et_al_metabar_PP1_Bacteria.uniq.fasta

description: This gz contains a fasta file of pre-filtered sequencing data (i.e. assembled and dereplicated reads assigned to their original sample), corresponding to amplicons of soil bacteria.
DOI: 10.5061/dryad.dc28m/3
title: Zinger_et_al_metabar_PP1_Eukaryota.uniq.fasta

description: This gz contains a fasta file of pre-filtered sequencing data (i.e. assembled and dereplicated reads assigned to their original sample), corresponding to amplicons of soil eukaryotes
DOI: 10.5061/dryad.dc28m/4
title: Zinger_et_al_metabar_PP1_Plants.uniq.fasta

description: This gz contains a fasta file of pre-filtered sequencing data (i.e. assembled and dereplicated reads assigned to their original sample), corresponding to amplicons of plants
DOI: 10.5061/dryad.dc28m/5
title: Zinger_et_al_metabar_PP1_samples

description: This file contains all samples/pcrs characteristics.
DOI: 10.5061/dryad.dc28m/6
title: Zinger_et_al_metabar_PP1_filtered_tabs

description: This zip file contains 4 txt files (tab delim) of filtered sequencing data (i.e. after sequence clustering and spurious OTUs removal), corresponding each to Archaea, Bacteria, Eukaryota and Plants amplicons.
DOI: 10.5061/dryad.dd64hf3/1
title: offspring.xlsx

description: Data obtained from a common garden admixture experiment with three subpopulations of anadromous pike (Esox lucius) from the Baltic Sea. In the experiment, gametes were stripped from ripe individuals from each of the three populations, and artificial fertilization utilized to create all possible pairwise population combinations (three pure and six admixed treatments). Three offspring quality traits was quantified (hatching success, fry survival, and fry length). Data on two out of the three offspring quality traits (hatching success and fry survival) is presented in this data file, and data on individual fry lengths can be found in the ‘fry.xlsx’ data file.
DOI: 10.5061/dryad.dd64hf3/2
title: fry.xlsx

description: Data obtained from a common garden admixture experiment with three subpopulations of anadromous pike (Esox lucius) from the Baltic Sea. In the experiment, gametes were stripped from ripe individuals from each of the three populations, and artificial fertilization utilized to create all possible pairwise population combinations (three pure and six admixed treatments). Three offspring quality traits was quantified (hatching success, fry survival, and fry length). Data on individual fry lengths is presented in this data file, and data on the other two offspring quality traits (hatching success and fry survival) can be found in the ‘offspring.xlsx’ data file.
DOI: 10.5061/dryad.dg31k/2
title: Data Figure 6

description: #######------- Data accessibility note for:

Rocchini, D., Luque, S., Pettorelli, N., Bastin, L., Doktor, D., Faedi, N., Feilhauer, H., Féret, J.-B., Foody, G.M., Gavish, Y., Godinho, S., Kunin, W.E., Lausch, A., Leitao, P.J., Marcantonio, M., Neteler, M., Ricotta, C., Schmidtlein, S., Vihervaara, P., Wegmann, M., Nagendra, H. (2017). Measuring $\beta$-diversity by remote sensing: a challenge for biodiversity monitoring. 
Methods in Ecology and Evolution. [5years-IF: \IFmethodsecolevol]


#---- Figure 6 (section 6. Rao's Q diversity)

The image used to build Figure 6 is a Sentinel-2A L1C from 8 August 2016 (tile 29 SND) and has been downloaded from the ESA Sentinel Scientiﬁc Data Hub (https://scihub.copernicus.eu/).

We added to the Dryad doi the NDVI input image and the resulting Shannon and RAO's Q indices.
DOI: 10.5061/dryad.f0s23r8/45
title: Donor 71 - Bw6

description: fcs files for ABC donor 71
DOI: 10.5061/dryad.f0s23r8/79
title: Donor64_Part3/3: Bw6 Stability

description: This corresponds to the HLA-Bw6 stability flow cytometry fcs files for Donor 64.
DOI: 10.5061/dryad.f0s23r8/80
title: Donor24_Part3/3: Bw6 Stability

description: This corresponds to the HLA-Bw6 stability flow cytometry fcs files for Donor 24.
DOI: 10.5061/dryad.f0s23r8/81
title: Donor64_Part2/3: Bw6 Stability

description: This corresponds to the HLA-Bw6 stability flow cytometry fcs files for Donor 64.
DOI: 10.5061/dryad.f0s23r8/82
title: Donor64_Part1/3: Bw6 Stability

description: This corresponds to the HLA-Bw6 stability flow cytometry fcs files for Donor 64.
DOI: 10.5061/dryad.f0s23r8/83
title: Donor55: Bw6 Stability

description: This corresponds to the HLA-Bw6 stability flow cytometry fcs files for Donor 55.
DOI: 10.5061/dryad.f0s23r8/84
title: Donor121: Bw6 Stability

description: This corresponds to the HLA-Bw6 stability flow cytometry fcs files for Donor 121.
DOI: 10.5061/dryad.f0s23r8/85
title: Donor71: Bw6 Stability

description: This corresponds to the HLA-Bw6 stability flow cytometry fcs files for Donor 71.
DOI: 10.5061/dryad.f4g56/10
title: IPYRAD parameters file - Shared by Min. 35 Taxa

description: IPYRAD parameters file used for processing data files; Loci must be shared by a minimum of 35 taxa to be retained.
DOI: 10.5061/dryad.f4g56/11
title: Datasets and Alignments (Updated 9-11-18)

description: A selection of key data sets and sequence alignments used for the associated project. VCF files generated using IPYRAD and STACKS pipelines. Conversions between VCF and other formats using PGDSpider. '.data' and '.xlsx' files used for MOMMENTS and GenAlEx respectively. COI sequence data set used for biotype assessment derived from Sanger sequencing. Please see associated manuscript for further details.
DOI: 10.5061/dryad.f4g56/12
title: Momments_Script_Palau1xPalau2

description: Python script used to perform the MOMMENTS analysis described in this report.
DOI: 10.5061/dryad.f4g56/8
title: Stacks Script

description: Script (command line) used for running STACKS for data filtering and assembly. Flag settings and parameters vary based on filtering requirements and desired outputs.
DOI: 10.5061/dryad.f4g56/9
title: IPYRAD parameters file - Shared by Min. 4 Taxa

description: IPYRAD parameters file used for processing data files; Loci must be shared by a minimum of 4 taxa to be retained.
DOI: 10.5061/dryad.h8r2629/1
title: README file for Puttick et al. 2018
DOI: 10.5061/dryad.h8r2629/2
title: supplementalCode

description: R code to simulate data matrices
DOI: 10.5061/dryad.h8r2629/3
title: empirical.CI

description: Data from the survey of Consistency Indices from empirical matrices of morphological data
DOI: 10.5061/dryad.h8r2629/4
title: RCode_example

description: Example of how data were simulated in the manuscript
DOI: 10.5061/dryad.h8r2629/5
title: simulateBinary

description: R code to simulate all binary matrices
DOI: 10.5061/dryad.h8r2629/6
title: simulateMultiState

description: R code to simulate all binary + multistate matrices
DOI: 10.5061/dryad.h8r2629/7
title: Puttick_et_al_supp_figures

description: All supplementary figures referenced in Puttick et al. 2018
DOI: 10.5061/dryad.jg81r80/1
title: Barcode_Files

description: Barcode files associated with each of the 21 fastq data files used in AftrRAD run.
DOI: 10.5061/dryad.jg81r80/2
title: RAD3_fastq

description: Fastq dataset associated with RAD3 barcode file
DOI: 10.5061/dryad.jg81r80/3
title: RAD4_fastq

description: Fastq dataset associated with RAD4 barcode file
DOI: 10.5061/dryad.m276f51/1
title: Modified GotoOrectolbiformMatrix

description: Phylogenetic matrix for orectolobiform sharks used in Gates et al. paper. The file is a Mesquite file containing character descriptions and codings.
DOI: 10.5061/dryad.n0vr7d0/1
title: Mean Flight Data for Spatial Frequency and Contrast Experiments

description: This file contains the mean flight data (lateral position and 2D ground speed) for each flight in each of the experimental conditions presented in the paper. Please note that the Bombus terrestris data is taken from Chakravarti et al. 2017.
DOI: 10.5061/dryad.n6sc718/1
title: Cozzarolo_et_al_2018_YRW_haemosporidians

description: Excel file (4 sheets) containing yellow-rumped warblers (Setophaga coronata) data collected on the field in 2005-2007 and 2015, including body measurements, as well as diagnosis of infection by haemosporidian parasites.
DOI: 10.5061/dryad.q2s7q8m/1
title: pep_FcC_supermatrix.fas
DOI: 10.5061/dryad.q2s7q8m/2
title: CDS12_FcC_supermatrix
DOI: 10.5061/dryad.q2s7q8m/3
title: CDS_FcC_supermatrix
DOI: 10.5061/dryad.q2s7q8m/4
title: Phylogenetic Tree
DOI: 10.5061/dryad.qf0ft85/1
title: SSU-Align input and output files

description: Input and output files for the 18S aligment using the software SSU-ALIGN
DOI: 10.5061/dryad.qf0ft85/2
title: Phylogenetic tree files

description: This file contains RAxML and MrBayes tree files for the 'raphid' and 'Aneumastus' datasets as well as BEAST MCC tree files for both the relaxed- and strict-clock analyses
DOI: 10.5061/dryad.r18b12m/1
title: Kangaroo Rat Musculoskeletal Model (One Hindlimb)

description: This zip file contains all of the data files required to view the kangaroo rat musculoskeletal model in SIMM (Musculographics, Inc).
DOI: 10.5061/dryad.r18b12m/2
title: Jumping and Hopping Motion Files

description: These files contain the joint angle histories for a hopping and jumping motion of a desert kangaroo rat. The files are meant to be used and viewed with the musculoskeletal model included in this data set.
DOI: 10.5061/dryad.r18b12m/3
title: Muscle Architecture Data

description: This is a Microsoft Excel file containing the muscle architecture data underlying the information presented in Table 2 of the paper.
DOI: 10.5061/dryad.t358vv1.2
title: Data from: Impacts of inference method and dataset filtering on phylogenomic resolution in a rapid radiation of ground squirrels (Xerinae: Marmotini)
DOI: 10.17632/67n9j3fgk3.1
title: Data for: Nutrients and herbivory, but not sediments, have opposite and independent effects on the tropical macroalga, Padina boryana
DOI: 10.17632/rp35s24v27.1
title: Data for: The development of face expertise: Evidence for a qualitative change in processing

description: Cross-sectional and longitudinal data for face recognition (upright and inverted faces)
DOI: 10.5061/dryad.1k7d35q/1
title: Supplementary material

description: Supplementary tables (E- tables 1, 2, 3)
DOI: 10.5061/dryad.1k7d35q/2
title: Near-SUDEP Event in Patient 1

description: Video 1
DOI: 10.5061/dryad.1k7d35q/3
title: Near-SUDEP Event in Patient 2
DOI: 10.5061/dryad.1k7d35q/4
title: Legend for the videos

description: Description of videos 1 and 2
DOI: 10.5061/dryad.3528sj6/2
title: Eucera pruinosa museum specimen ddRAD reads

description: This file contains the demultiplexed, trimmed and quality filtered ddRAD reads from museum curated Eucera (Peponapis) pruinosa males. See README file for specific information about sample metadata.
DOI: 10.5061/dryad.3sm0340/1
title: Root turnover in grasslands
DOI: 10.5061/dryad.56mh682/1
title: LoCoD data

description: data in txt and raw format for upload in DDMT LoCoD behaivour building. Includes data from four species with their different behaviours: Penguin walking, Sheep biting, Condor thermalling and a Cheetah stalking. DDMT software can be found at the URL http://ggluck.swan.ac.uk/ftp/DDMT%20new%20version/
DOI: 10.5061/dryad.5q9q697/10
title: Appendix

description: Supplementary statistical data for the manuscript.
DOI: 10.5061/dryad.5q9q697/3
title: (Table 3) Sr line transect data

description: Data for figure 4
DOI: 10.5061/dryad.5q9q697/4
title: (Table 4) Dark and Light band thickness

description: Supplement outlining thicknesses of dark and light bands.
DOI: 10.5061/dryad.5q9q697/5
title: Fig. 1 Normal conodont

description: Large, high resolution image of the normal conodont.
DOI: 10.5061/dryad.5q9q697/6
title: Fig. 2 Pathological conodont
DOI: 10.5061/dryad.5q9q697/9
title: S1

description: Alternative version of figure 3 with parallel axes, and the required graphs plotted away from the original image.
DOI: 10.5061/dryad.63sj6f0/1
title: FE-2018-00702-DataAccessibility

description: Raw data for analyses in "From Salmon to Salmonberry: the effect of salmon-derived nutrients on the stomatal density of leaves of the nitriphillic shrub Rubus spectabilis:.
DOI: 10.5061/dryad.6pg15js/1
title: Variants for 55 California white oak taxa and 3 outgroup taxa

description: Non-biallelic and QD&lt;2.0 variants have been excluded.  Reference genome is a collapsed and concatenated Quercus lobata draft assembly (v0.5.100Mcat), see associated file.
DOI: 10.5061/dryad.6pg15js/2
title: Qlobata.v0.5.100Mcat.fasta

description: Quercus lobata draft assembly version 0.5, concatenated into 8 approximately 100Mb psuedo-contigs,  Original contig positions are listed in associated file Qlobata.v0.5.100Mcat.bed.   This assembly has been aggressively haplotype reduced, resulting in very few genome regions represented more than once, but also approximately 100 Mb missing entirely. Due to high heterozygosity, typical assembly methods fail to collapse haplotypes for as much as half of the genome. We found this version of the genome to be particularly useful for variant calling prior to completion of our final chromosome level genome assembly (v3.0 now available at valleyoak.ucla.edu).
DOI: 10.5061/dryad.6pg15js/3
title: Qlobata.v0.5.100Mcat.bed

description: This file lists the positions of the original contigs on the 8 psuedo-contigs of the concatenated Q. lobata reference genome, Qlobata.v0.5.100Mcat.fasta
DOI: 10.5061/dryad.712kj7v/10
title: Bmbo.MAF0.05.DP5.GQ20.geno

description: Geno formated file for using ABBABABA.py and popGenWindows.py from https://github.com/simonhmartin/genomics_general.
DOI: 10.5061/dryad.712kj7v/8
title: BarombiMbo_raxml_runs.tar

description: Raxml analyses input and output for largest region assigned to introgression topologies focused on in the manuscript (FigS2-S4).
DOI: 10.5061/dryad.712kj7v/9
title: BarombiMbo_msmc_output_scripts

description: Scripts used to run msmc, output, and figures
DOI: 10.5061/dryad.7m5cv66/1
title: Aquatic insect captures in relation to color and polarization of light

description: We captured aquatic insects in oil-filled trays in 6 treatments. They were composed of lamps of three different spectra (blue-red LED, High-pressure sodium, metal-halide) that were polarized or left unpolarized by reflection with an oil-filled tray. Aerial terrrestrial and aquatic insects were captured in oil.
DOI: 10.5061/dryad.f0s23r8/86
title: Donor28_Part1/2: Bw6 Stability

description: This corresponds to the HLA-Bw6 stability flow cytometry fcs files for Donor 28.
DOI: 10.5061/dryad.f0s23r8/87
title: Donor28_Part2/2: Bw6 Stability

description: This corresponds to the HLA-Bw6 stability flow cytometry fcs files for Donor 28.
DOI: 10.5061/dryad.f0s23r8/88
title: Donor31_Part1/3: Bw6 Stability

description: This file corresponds to flow cytometry data for HLA-Bw6 stability of Donor 31.
DOI: 10.5061/dryad.f0s23r8/89
title: Donor91: Bw6 Stability

description: This file corresponds to flow cytometry data for HLA-Bw6 stability of Donor 91.
DOI: 10.5061/dryad.f0s23r8/90
title: Donor111: Bw6 Stability

description: This file corresponds to flow cytometry data for HLA-Bw6 stability of Donor 111.
DOI: 10.5061/dryad.f0s23r8/91
title: Donor31_Part2/3: Bw6 Stability

description: This file corresponds to flow cytometry data for HLA-Bw6 stability of Donor 31.
DOI: 10.5061/dryad.f0s23r8/92
title: Donor31_Part3/3: Bw6 Stability

description: This file corresponds to flow cytometry data for HLA-Bw6 stability of Donor 31.
DOI: 10.5061/dryad.f0s23r8/93
title: Donor94_Part1/2: Bw6 Stability

description: This file corresponds to flow cytometry data for HLA-Bw6 stability of Donor 94.
DOI: 10.5061/dryad.g0h04s1/2
title: dose_response_normal_dist
DOI: 10.5061/dryad.g0h04s1/3
title: Data for figure 8

description: CSV file contains 12 data set together with mean, standard deviation and 95% confidence interval.
DOI: 10.5061/dryad.g0h04s1/4
title: matlab program/code to generate the figure 8

description: The program uses data from the CSV file 'Dataforfigure8'
DOI: 10.5061/dryad.h8r2629/8
title: Puttick_et_al_supp_tables

description: All supplementary tables referenced in Puttick et al. 2018
DOI: 10.5061/dryad.jg81r80/10
title: RAD15_fastq

description: Fastq dataset associated with RAD15 barcode file
DOI: 10.5061/dryad.jg81r80/11
title: RAD16_fastq

description: Fastq dataset associated with RAD16 barcode file
DOI: 10.5061/dryad.jg81r80/12
title: RAD18_fastq

description: Fastq dataset associated with RAD18 barcode file
DOI: 10.5061/dryad.jg81r80/4
title: RAD5_fastq

description: Fastq dataset associated with RAD5 barcode file
DOI: 10.5061/dryad.jg81r80/5
title: RAD7_fastq

description: Fastq dataset associated with RAD7 barcode file
DOI: 10.5061/dryad.jg81r80/6
title: RAD9a_fastq

description: Fastq dataset associated with RAD9a barcode file
DOI: 10.5061/dryad.jg81r80/7
title: RAD10_fastq

description: Fastq dataset associated with RAD10 barcode file
DOI: 10.5061/dryad.jg81r80/8
title: RAD14-1_fastq (1 of 2)

description: Partial fastq dataset associated with RAD14 barcode file. Combine with RAD14-2 prior to analysis.
DOI: 10.5061/dryad.jg81r80/9
title: RAD14-2_fastq (2 of 2)

description: Partial fastq dataset associated with RAD14 barcode file.  Combine with RAD14-1 prior to analysis.