cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m88g7/2
title: Functional Traits

description: Measurements of five ecologically relevant functional traits (seed mass, maximum height, specific leaf area, leaf size, and nitrogen content) for each species occurring on the islands sampled
DOI: 10.5061/dryad.m88g7/3
title: Island Metadata

description: Metadata and summaries of species richness for all 80 islands sampled in the San Juan Island archipelago, Washington, USA
DOI: 10.5061/dryad.m88g7/4
title: San Juan Islands Community Phylogeny

description: Time-calibrated maximum likelihood mega-phylogeny of the vascular flora of the San Juan Islands
DOI: 10.5061/dryad.mt57r/1
title: Supplementary Information 1: Surface mesh distance script

description: The script surf_dist.py computes the surface-to-surface distance between two aligned STL models and displays the result as color-coded distance maps. It also computes the mean absolute distance (MAD), the root-mean square (RMS) distance, and the max absolute (Hausdorff) distance between the models and writes the resulting distance values to a text file.
DOI: 10.5061/dryad.mt57r/2
title: Supplementary Information 2: Surface mesh distance animation

description: Surface mesh distance animation, showing Endocast, Brain, Overlay, Signed Distance Map and Unsigned Distance Map of the Australian lungfish, Neoceratodus.
DOI: 10.5061/dryad.n3h6d/1
title: RAE CHC, mating success and SNP data

description: File contains individual level CHC mating success data plus denormalised family level SNP data. Spreadsheet has explanatory tabs for variable names.
DOI: 10.5061/dryad.n3h6d/2
title: Corrected Supplementary Table 1

description: The published Sup Table 1 contained errors. Posted in this file is a corrected version.
DOI: 10.5061/dryad.n9c88/1
title: N2 On Food Recording

description: A sample tracker recording of a wild-type (N2) strain C. Elegans animal, moving freely on a 150mm diameter agar plate with a bacterial lawn of E. Coli.
DOI: 10.5061/dryad.n9c88/2
title: N2 Off Food Recording

description: A sample tracker recording of a wild-type (N2) strain C. Elegans animal, moving freely on a 150mm diameter agar plate.
DOI: 10.5061/dryad.n9c88/3
title: tph-1 Strain On Food Recording

description: A sample tracker recording of a tph-1 mutant strain C. Elegans animal, moving freely on a 150mm diameter agar plate with a bacterial lawn of E. Coli.
DOI: 10.5061/dryad.n9c88/4
title: tph-1 Strain Off Food Recording

description: A sample tracker recording of a tph-1 mutant strain C. Elegans animal, moving freely on a 150mm diameter agar plate.
DOI: 10.5061/dryad.q0h473vr.1
title: Data from: Latitudinal patterns in rodent metabolic flexibility
DOI: 10.5061/dryad.q0h473vr.2
title: Data from: Latitudinal patterns in rodent metabolic flexibility
DOI: 10.5061/dryad.q0h473vr.2/1.2
title: Naya_Dataset

description: Basal and maximum metabolic rates for rodents
DOI: 10.5061/dryad.s492m/1
title: congruent evolution data

description: Data from Manipulative and Natural experiments, including plant growth, resistance, leaf and root secondary metabolite data.
DOI: 10.5061/dryad.tr87v/1
title: 29196_Reference_Picea_mariana_contigs

description: Reference Picea mariana contigs used for read mapping: contig number, length and nucleotide sequences.
DOI: 10.5061/dryad.tr87v/2
title: SNP_dataset_Varscan_software_part_01

description: SNP dataset from Varscan software, part 1: contig number, SNP position, reference and variant alleles and number of reads, variant frequency (VarFreq), Varscan P value, contig length, annotation with Picea glauca paired transcript and percent of homology.
DOI: 10.5061/dryad.tr87v/3
title: SNP_dataset_Varscan_software_part_02

description: SNP dataset from Varscan software, part 2: contig number, SNP position, reference and variant alleles and number of reads, variant frequency (VarFreq), Varscan P value, contig length, annotation with Picea glauca paired transcript and percent of homology.
DOI: 10.5061/dryad.tr87v/4
title: SNP_dataset_Varscan_software_part_03

description: SNP dataset from Varscan software, part 3: contig number, SNP position, reference and variant alleles and number of reads, variant frequency (VarFreq), Varscan P value, contig length, annotation with Picea glauca paired transcript and percent of homology.
DOI: 10.5061/dryad.v0np1/1
title: Corvides alignment

description: Corvides alignment with partitions
DOI: 10.5061/dryad.v0np1/2
title: Corvides Maximum Clade Credibility (MCC) Tree

description: Corvides Maximum Clade Credibility (MCC) Tree
DOI: 10.5061/dryad.v0np1/4
title: temporal banding function R script

description: This function identifies where to cut the tree to cause least taxonomic disruption at a particular taxonomic rank.
DOI: 10.5061/dryad.v9f16/1
title: EEG resting state data

description: Data used in paper "Large-scale Functional Networks Indentified from Resting-state EEG Using Spatial ICA"data_EEG: raw data on 64 electrodes - 1 run per subject - the last 300 seconds were used in this paper - (BrainAmps system)        xxx.eeg  &gt;&gt;&gt; EEG binary        xxx.vhdr &gt;&gt;&gt; EEG header        xxx.vrmk &gt;&gt;&gt; EEG markers        polhemus.pol  &gt;&gt;&gt; polhemus file - electrodes localization
DOI: 10.5061/dryad.vg446/2
title: EndleinFederle_Data_PONE-D-15-22788

description: Raw data for all figures presented in the manuscript.
DOI: 10.5061/dryad.19dj5/1
title: Behavioral Field Study

description: Responses to a "predatory threat" by 57 Furcifer viridis and 4 Calumma gastrotaenia specimens collected between 9-19th January 2011 in the Makay Massif, Madagascar at three sites: Antsoha Forest 21.596°S, 45.114°E; Androtsy Forest 21.569°S, 45.076°E; and Ankilytsoky 21.674°S, 44.993°E.  Presence or absence of lateral and ventral line markings are recorded for each specimen in addition to their response to a predatory threat.
DOI: 10.5061/dryad.19dj5/2
title: Image Analyses from Behavioral Study

description: Chameleons were collected between 9-19th January 2011 in the Makay Massif, Madagascar at three sites: Antsoha Forest 21.596°S, 45.114°E; Androtsy Forest 21.569°S, 45.076°E; and Ankilytsoky 21.674°S, 44.993°E. Video from behavioral trials were used to take snapshots of various chameleon views and analyzed using ImageJ. SVL is the snout-vent length. Specimen is a specific identification number assigned to each specimen that is composed of the date and number.
DOI: 10.5061/dryad.1rr87/1
title: Vonfrey Acetone and RotaRod Data Paclitaxel

description: Contains raw data for the paclitaxel graphs and expiriments as well as rotarod data averages. Group A is the NMNAT2 +/- group and B is the wild-type group.
DOI: 10.5061/dryad.1rr87/2
title: Capsascin

description: The capsaicin spreadsheet contains raw data for each timepoint following capsaicin administration, as well as a tab for nocifensive behavior. The animals are the same as the paclitaxel spreadsheet.
DOI: 10.5061/dryad.1rr87/3
title: NMNAT Vonfrey Acetone Vincristine 9 29 14

description: Contains raw data for the Vincristine graphs and experiments. Group A is the NMNAT2 +/- group and B is the wild-type group.
DOI: 10.5061/dryad.1rr87/4
title: MTT data

description: Contains average output for three experiments for WT vs HET vs KO as well as the graph template for Figure 1.
DOI: 10.5061/dryad.1rr87/5
title: NMNATGraphPad

description: The primary graph file used to generate figures 2-5. Contains averages of each subject throughout the necessary timecourse (via the spreadsheets).
DOI: 10.5061/dryad.1rr87/6
title: DRGEXP

description: DRG quantification data from western blots and NAD/NADH activity.
DOI: 10.5061/dryad.21s55/1
title: Full Wader Avian Malaria Prevalence Datafile

description: Sample size, sampling location and number of individuals infected with avian malaria for migratory and resident waders (Charadriiformes)
DOI: 10.5061/dryad.21s55/2
title: Full Wader Gene Tree

description: Phylogeny of waders used in phylogenetic comparative analyses. Gene sequences uploaded in the Oikos supplementary files were used to create a Bayesian consensus tree. Wader species without molecular data were grafted onto the consensus tree as polytomies using taxonomic information.
DOI: 10.5061/dryad.2k4b7/1
title: Sample locations, microsatellite data and clustering assignment

description: Complete genetic profiles at 15 microsatellite loci (Ruiz-Gonzalez et al. 2014), geographic coordinates and Bayesian clustering assignment according to STRUCTURE and GENELAND for the 140 pine marten individuals. The genetic raw data is provided in CONVERT data format (Glaubitz, 2004).
DOI: 10.5061/dryad.2k4b7/2
title: Landscape resistance maps

description: Raw '.asc' files of the optimal resistance models (IBR; i.e. EN, LandFB_100 and LandFb_50) produced with ARCGIS version 9.3 (ESRI 2009), with a raster cell size set to 50 m. The three different landscape resistance models were previously optimized for the study species at the Basque country level (Ruiz-González et al. 2014). Land_Fb100 and Land_Fb50: Binary landscape resistance maps indicating that pine marten gene flow in is facilitated by forests, forestry plantations, scrubland, agroforestry mosaics and pastures and meadows, and that crops have roughly 100 (LandFb_100) or 50 (LandFb_50) times higher resistance than optimal habitat and the existence of a barrier effect of national roads, highways, urban areas, reservoirs and quarries. Ecological Network resistance map; EN: a resistance map analogous to that used in the design of the ecological network of the Basque country (Gurrutxaga et al. 2010a). Land use information was obtained in vector format from the most recent forest map of Spain (Spanish Ministry of the environment, 2006) and from national road network maps (Spanish National Geographic Institute (2008). Full methodological details for model construction are reported in Table 1 and Appendix S2 (Supporting information).
DOI: 10.5061/dryad.2k4b7/3
title: Genetic_LCD_Matrices

description: Genetic distance (Rousset’s a) matrix and least-cost distance (LCD) matrices for IBD, IBR and IBB models. 1) IBD-Isolation by distance; 2) IBR-Isolation by landscape resistance models optimized by Ruiz-González et al. (2014); Land_Fb100 and Land_Fb50: Binary landscape resistance maps indicating that pine marten gene flow in is facilitated by forests, forestry plantations, scrubland, agroforestry mosaics and pastures and meadows, and that crops have roughly 100 (LandFb_100) or 50 (LandFb_50) times higher resistance than optimal habitat and the existence of a barrier effect of national roads, highways, urban areas, reservoirs and quarries. Ecological Network resistance map; EN: a resistance map analogous to that used in the design of the ecological network of the Basque country (Gurrutxaga et al. 2010a); and 3) IBB-Isolation by barriers or clusters obtained from both Bayesian clustering approaches (i.e. IBB_Geneland and IBB_Structure). The effective and Euclidean distances between each pair of individuals were calculated with PATHMATRIX 1.1 (Ray 2005), following the resistances values outlined in Table 1. Pair-wise effective distances between individuals were calculated as the accumulated cost through the least cost paths (LCP) throughout each resistance surface (Adriaensen et al. 2003; Ray 2005). Full methodological details for model construction are reported in Appendix S2 (Supporting information).
DOI: 10.5061/dryad.4q3d3/3
title: Song_DCC_PlosOne_datadryad9.16.15
DOI: 10.5061/dryad.6394c/1
title: Results of tree analyses

description: MrBayes results: (1) mt+nc combined matrix and tree (161 samples); (2) mt matrix and tree (161 samples); and (3) nc matrix and tree (59 samples). BEAST results using reduced matrices (51 samples): (1) molecular clock calibrated tree and (2) geological event calibrated tree. RAxML result using reduced matrix.
DOI: 10.5061/dryad.68184/1
title: Hua_et_al-Phenology and weather data

description: 1. Raw time series on the first and last sighting of 50 animal taxa collected from 360 meteorological observatories between 1981 and 2009. 2. Weather data from the same sites where phenological data were collected, including records on the daily maximum, minimum, and mean temperature, and daily precipitation. In all, weather data for 349 sites within China were presented.
DOI: 10.5061/dryad.78b22/1
title: Illumina CanineHD Beadchip data

description: Illumina CanineHD Beadchip data of whippets - traditional ped based format for PLINK
DOI: 10.5061/dryad.8070m/1
title: RADseq data for the earthworm Lumbricus rubellus sampled in Poland

description: The file includes RADseq data for Lumbricus rubellus earthworm, 100 individuals, sampled from four populations in Southern Poland. The data were generated with the double digest RADseq approach. The file includes output of the denovo_map.pl program of the Stacks software. Detailed description is available in the attached ReadMe file.
DOI: 10.5061/dryad.83004/1
title: Total articles published for Bangladesh Rwanda and South Africa

description: We analyzed each country’s leading national English-language newspaper: Bangladesh's The Daily Star, Rwanda's The New Times/The Sunday Times, and South Africa's Sunday Times/The Times. We searched the electronic archives of each country’s newspapers described above from January 1, 2008 to March 31, 2013.  We chose a January 1, 2008 start date because the searchable online archive of South Africa’s Sunday Times only goes as far back as January 1, 2008. We searched for articles on maternal health (including family planning) using the strategy detailed in Appendix A. The collected articles were entered on an Excel spreadsheet.
DOI: 10.5061/dryad.83004/2
title: Coded articles Bangladesh

description: For the content analysis, we used a “constructed week” sampling technique, in which sample dates are stratified by day of the week to account for systematic variation due to day of the week. Through this “constructed week” sampling method, we sampled 75 articles from The Daily Star (Bangladesh).
DOI: 10.5061/dryad.83004/3
title: Coded articles Rwanda

description: For the content analysis, we used a “constructed week” sampling technique, in which sample dates are stratified by day of the week to account for systematic variation due to day of the week. Through this “constructed week” sampling method, we sampled 64 articles from Rwanda’s The New Times/The Sunday Times .
DOI: 10.5061/dryad.83004/4
title: Coded articles South Africa

description: For the content analysis, we used a “constructed week” sampling technique, in which sample dates are stratified by day of the week to account for systematic variation due to day of the week. Through this “constructed week” sampling method, we sampled 51 articles from South Africa’s Sunday Times/The Times.
DOI: 10.5061/dryad.83004/5
title: Sampled articles to code

description: For the content analysis, we used a "constructed week" sampling technique, in which sample dates are stratified by day of the week to account for systematic variation due to day of the week. Through this “constructed week” sampling method, we sampled 75 articles from The Daily Star (Bangladesh), 64 articles from Rwanda’s The New Times/The Sunday Times and 51 articles from South Africa’s Sunday Times/The Times— a total of 190 articles published from October 1, 2010 to March 31, 2013
DOI: 10.5061/dryad.83004/6
title: Inter-rater Reliability

description: Two coders (Frey Gugsa and Ellora Karmarkar) developed the codebook from relevant existing work, supplemented with additional themes that emerged from the three newspapers (Appendix B). We followed an iterative process of reading randomly selected articles, assessing themes, and adjusting the codebook until we achieved inter-rater reliability (Cohen’s Kappa &gt; 0.82). All articles were recoded using the finalized codebook.
DOI: 10.5061/dryad.8787m/13
title: Loxodonta africana_heart

description: Interactive PDF model of Loxodonta africana heart. To activate the 3D feature click the model. Using the cursor it is now possible to rotate, zoom, pan the model and in the model tree all segments of the model can be turned on/off or made transparent.
DOI: 10.5061/dryad.8787m/15
title: Melanosuchus niger_head

description: Interactive PDF model of Melanosuchus niger head. To activate the 3D feature click the model. Using the cursor it is now possible to rotate, zoom, pan the model and in the model tree all segments of the model can be turned on/off or made transparent.
DOI: 10.5061/dryad.8787m/16
title: Melanosuchus niger_C2_150%

description: Ready to 3D print STL file of Melanosuchus niger C2 (axis).
DOI: 10.5061/dryad.8787m/17
title: Phoca vitulina_head

description: Interactive PDF model of Phoca vitulina head. To activate the 3D feature click the model. Using the cursor it is now possible to rotate, zoom, pan the model and in the model tree all segments of the model can be turned on/off or made transparent.
DOI: 10.5061/dryad.8787m/18
title: Phoca vitulina_C2_150%

description: Ready to 3D print STL file of Phoca vitulina C2 (axis).
DOI: 10.5061/dryad.8787m/19
title: Phocoena phocoena_fulbody

description: Interactive PDF model of Phocoena phocoena full body. To activate the 3D feature click the model. Using the cursor it is now possible to rotate, zoom, pan the model and in the model tree all segments of the model can be turned on/off or made transparent.
DOI: 10.5061/dryad.8787m/20
title: Phocoena phocoena_brain_80%

description: Ready to 3D print STL file of Phocoena phocoena brain.
DOI: 10.5061/dryad.8787m/21
title: Phocoena phocoena_lungs_80%

description: Ready to 3D print STL file of Phocoena phocoena lungs.
DOI: 10.5061/dryad.8787m/22
title: Pogona sp._head

description: Interactive PDF model of Pogona sp. head. To activate the 3D feature click the model. Using the cursor it is now possible to rotate, zoom, pan the model and in the model tree all segments of the model can be turned on/off or made transparent.
DOI: 10.5061/dryad.91kk8/1
title: Species data

description: Occurrences of 244 bird species (following the taxonomy by Jetz et al. 2012) at 106 sample points in Colombia. Each cell contains the highest abundance of birds recorded at each sample point.
DOI: 10.5061/dryad.bt5v6/15
title: Ch10 alignment

description: Alignment file of Chromosome 10 sanger sequencing
DOI: 10.5061/dryad.bt5v6/16
title: Ch9 tree file

description: MrBayes tree file for Chromosome 9
DOI: 10.5061/dryad.bt5v6/17
title: Ch10 tree file

description: MrBayes tree file for Chromosome 10
DOI: 10.5061/dryad.d4p7n/1
title: Thompson et al. deadwood foraging and structural property data
DOI: 10.5061/dryad.d9p4v/1
title: z_results_coarse_data_southern_savonia

description: The results contained in this data package describe the spatial conservation priorities generated by the analysis software Zonation. The analyses and the results produced are based on a set of forest conservation indices derived from freely available, but relatively coarse multi-source forest inventory data produced and distributed by the Natural Resources Institute Finland. The original publication deals with comparing prioritizations based on coarse forest inventory data to those based on more detailed data. The authors compare the results to each other and to a set of independent validation datasets and conclude that while prioritizations based on coarse data are informative on larger spatial extents, using more detailed data is superior especially in finer scales. This data package only includes results of four out of the six analysis variants used in the study, namely the ones based on the coarser forest inventory data ("coarse", "coarseCon", "coarseClass", "coarseClassCon"). The results based on the more detailed forest inventory data cannot be share due to privacy issues. Please see the original publication for instructions on how to gain access to the raw data used in the analyses.
DOI: 10.5061/dryad.fg4v1/1
title: Data for Dryad

description: Data used to create Figures 1 and 2.
DOI: 10.5061/dryad.g3g65/1
title: DADI.INPUT.FILES

description: Ready-run dadi files for 3 models that includes isolation-with-migration (IM), neutral-no-divergence (neutral.model), and split with secondary contact (Split.Mig) using the folded frequency spectrum of only minor alleles for greater (N = 64) and lesser (N = 47) scaup. The site-frequency spectrum is based on bi-allelic single nucleotide polymorphisms from 3448 autosomal ddRAD-seq markers.
DOI: 10.5061/dryad.g3g65/2
title: INIDIVIDUAL & CONCATENATED FASTA FILES

description: Individual and concatenated fasta files for 3448 Autosomal and 140 Z linked markers identified using ddRAD-seq protocols for greater (N = 64) and lesser (N = 47) scaup. A fasta file with mitochondrial sequences is also provided.
DOI: 10.5061/dryad.g3g65/3
title: PCA & ADMIXTURE FILES

description: Run-ready input files of 140 Z-linked and 3448 autosomal ddRAD-seq markers for PCA (*.4.PCA.stru) and ADMIXTURE (*.map & *.ped) analyses for greater (N = 64) and lesser (N = 47) scaup.
DOI: 10.5061/dryad.g3g65/4
title: R Code for Simulations

description: R Code ("R.code.4.hybrid.Simulations.r") is provided to run simulations from ADMIXTURE style .ped files. Missing data across individuals is first replaced with a randomly chosen allele from their respective population ("impute.gen"), and then hybridization and X backcrossing events are simulated ("sim.hybrid").
DOI: 10.5061/dryad.k8hr0/1
title: Bianchi, Dahlgren et al., Canine Hypothyroidism data
DOI: 10.5061/dryad.m0m6r/3
title: Hermsen_Gandolfo_Juglandaceae_morphology

description: Morphological matrix for extant and fossil Juglandaceae.
DOI: 10.5061/dryad.m0qc8/4
title: Phylogenetic tree of all bZIP proteins from Arabidopsis thaliana and six legume genomes

description: The PDF file was the phylogenetic tree of all bZIP proteins from Arabidopsis thaliana and six legume genomes, which corresponds to the Figure 1 and Additional file 3 in publication
DOI: 10.5061/dryad.m3685/1
title: DESeq2_ColorMorphGE

description: R script for all DESeq2 analysis. allcounts_Jan102015.txt is loaded into this script.
DOI: 10.5061/dryad.m3685/2
title: allcounts_Jan102015

description: Table of count data from processed reads. Columns are samples and rows are genes.
DOI: 10.5061/dryad.m3685/3
title: VSDandPVALS_All

description: Variance stabilized gene expression data for each sample (columns 1-18) and pvalues/FDR corrected pvalues (columns 19-33) associated with each statistical test. Rows are genes. Extensions .c, .t, and .i are results of LRT tests for fluroescent phenotype, light treatment and the interation, respectively. Extensions .Only are Wald test results comparing one color larvae to the other two. Extensions .V are Wald test results comparing only two of the morphs.
DOI: 10.5061/dryad.m88g7/5
title: Alignments

description: Sequence alignments for each gene region with GenBank accession numbers for each species and the concatenated sequence alignment
DOI: 10.5061/dryad.m88g7/6
title: Treefiles

description: Maximum likelihood phylograms for each gene region and the concatenated alignment
DOI: 10.5061/dryad.p33fm/1
title: Irwin et al JEcol 2015 Nectar robbing direct vs indirect effects

description: This datafile contains worksheets in an excel file describing three experiments testing for direct effects of robbing on plant reproduction, and one experiment testing for indirect effects of robbing. The focal plant was Ipomopsis aggregata that is pollinated by hummingbirds and nectar robbed by bumble bees.
DOI: 10.5061/dryad.pk16b/1
title: Fig 2 data

description: Data for Fig 2
DOI: 10.5061/dryad.sq134/1
title: Data S2

description: Interactive three-dimensional digital reconstruction of the early post-metamorphic, Carboniferous blastoid (NIGP 163236). The reconstruction is in VAXML format, compressed in a ZIP archive, and has been downsampled to reduce triangle count. To view: unpack the .zip file, install the SPIERS software suite (program and documentation available from www.spiers-software.org), and double-click the unpacked .vaxml file.
DOI: 10.5061/dryad.sq134/2
title: Video S1

description: Video showing a three-dimensional digital reconstruction of the early post-metamorphic, Carboniferous blastoid (NIGP 163236).