cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dp2ms/1
title: Lesser Black-backed Gull flight height data

description: This file was created with R. 'Bird.id', 'date_time', 'latitude', 'longitude', 'altitude', 'positiondop' and 'speed' were collected by GPS tags. 'Positiondop' is dilution of precision. 'Altitude' is measured in m and 'speed' in km/h. 'Marine' denotes observations over land (0) or sea (1), derived from overlaying the GPS measurements on a map in ArcGIS. 'Coastal' donates observations at sea but within 200 m of the coast (1) or further from the coast (0), again derived in ArcGIS. Tidal data ('tidal.state' in m) were from the British Oceanographic Data Centre (https://www.bodc.ac.uk/data/online_delivery/ntslf/), using tide gauge from Harwich. Surface elevation ('land_height' in m) was obtained from the Shuttle Radar Topography Mission 90 m digital elevation data (http://srtm.csi.cgiar.org/http://srtm.csi.cgiar.org/), aggregated at the 1 km square level. Sunrise and sunset information was obtained using the NOAA Sunrise/Sunset Calculator (http://www.srrb.noaa.gov/highlights/sunrise/sunrise.html).
DOI: 10.5061/dryad.dp2ms/2
title: Great Skua flight height data

description: This file was created with R. 'Bird.id', 'date_time', 'latitude', 'longitude', 'altitude', 'positiondop' and 'speed' were collected by GPS tags. 'Positiondop' is dilution of precision. 'Altitude' is measured in m and 'speed' in km/h. 'Marine' denotes observations over land (0) or sea (1), derived from overlaying the GPS measurements on a map in ArcGIS. Tidal data ('tidal.state' in m) were from the British Oceanographic Data Centre (https://www.bodc.ac.uk/data/online_delivery/ntslf/), using tide gauge from Lerwick and Wick. Surface elevation ('land_height' in m) was obtained from the Shuttle Radar Topography Mission 90 m digital elevation data (http://srtm.csi.cgiar.org/http://srtm.csi.cgiar.org/), aggregated at the 1 km square level. Sunrise and sunset information was obtained using the NOAA Sunrise/Sunset Calculator (http://www.srrb.noaa.gov/highlights/sunrise/sunrise.html).
DOI: 10.5061/dryad.g48pb/1
title: First record of Cyclanorbis senegalensis for Ethiopia_Supporting_Information

description: Materials and Methods (Sampling and laboratory procedures, Phylogenetic analyses), including Tables S1-S3
DOI: 10.5061/dryad.j47h4/1
title: 42alldatayule

description: This is the XML file used for the BEAST analyses. This file contains both mitochondrial and nuclear sequence data for all 34 loci analyzed here.
DOI: 10.5061/dryad.j47h4/2
title: 42mtDNA.yule.xml

description: This is the XML file used in the BEAST analyses. This file contains mtDNA sequences only.
DOI: 10.5061/dryad.j47h4/3
title: 42nuDNAYule

description: This is the XML file used in the BEAST analyses. This file contains sequence data from nuclear loci only.
DOI: 10.5061/dryad.j65n9/1
title: Black Sparrowhawk Breeding and Survival

description: Resightings data used for survival analysis and reproductive performance data used to examine breeding success, productivity, body condition, brood size,  lay date in the Black Sparrowhawk
DOI: 10.5061/dryad.k5k7n/1
title: Sperm measurements (morphology and velocity) of two Passer species

description: Included in this data set are three .csv files containing data, one .xlsx file with information on the naming of columns in the data files (information for each data file is in a separate tab in the .xlsx file), and R code. However, this R script should be sufficient to understand exactly how analyses were performed. Justification for analysis decisions is indicated in the manuscript.
DOI: 10.5061/dryad.k5n4k/2
title: Fig2

description: Colony forming unit counts for a ten day evolution experiment, where proportions of all three strain (loner, cooperator, and defector) cycle over time.
DOI: 10.5061/dryad.k5n4k/3
title: Fig3

description: Colony forming unit counts of a 4-strain evolution competition tracking the proportions of cooperator, defector, loner, and loner defector strains for five days.
DOI: 10.5061/dryad.nd7c8/1
title: Brain size and migration distance in birds

description: This table contain data on 1,475 globally distributed  bird species. Data covers: brain mass (g), body mass (g), minimum body mass (g), maximum body mass (g), migration distance (km), non-breeding range minimum monthly mean temperature (°C), breeding range temperature seasonality (°C), mean non-breeding latitude (absolute value). Additionally, coordinates of the breeding and wintering range geographic centroids (latitude and longitude), and monthly mean temperatures for both the breeding and wintering grounds are given.
DOI: 10.5061/dryad.p71bv/1
title: Xinghui Lu et al. 2016. Biotropica.Data Base

description: Data description of plot species and environment factors
DOI: 10.5061/dryad.tt78r/1
title: Data from: Evolutionary patterns and processes: lessons from ancient DNA

description: Whole mitochondrial genomes from present-day and ancient horses used for the reconstruction of the Bayesian skyline plot shown in figure 2b
DOI: 10.17632/tbp45pm92x.1
title: Solid state NMR spectra of brain-seeded Abeta40 and Abeta42 fibrils

description: Two-dimensional solid state NMR spectra of Abeta40 and Abeta42 fibrils, prepared from synthetic, isotopically labeled peptides by seeding with extracts from brain tissue. Spectra are *.ucsf files, suitable for viewing with Sparky software, available at https://www.cgl.ucsf.edu/home/sparky/ .
DOI: 10.5061/dryad.1s6v2/1
title: Raw Microsatellite Scores

description: Microsatellite genotypes for Strauzia flies reported in this study. "X" indicates no data.
DOI: 10.5061/dryad.1s6v2/2
title: Adult Strauzia collection data for temporal isolation study

description: Collection numbers for three varieties of Strauzia flies collected on H. tuberosus plants in the Iowa City, IA area from 2011-2014.
DOI: 10.5061/dryad.1s6v2/3
title: Mating Data

description: Results of 892 mating crosses between Strauzia flies. Included are information on collection site, number of observations, and the proportion of observations that flies were observed mating.
DOI: 10.5061/dryad.2435k/28
title: Dryad LOCAL Mustang Creek 1 Local

description: Mustang Creek, Mustang, Oklahoma
DOI: 10.5061/dryad.2435k/29
title: Dryad LOCAL S Canadian 1976-77

description: South Canadian River near Norman, Oklahoma
DOI: 10.5061/dryad.2435k/30
title: Dryad LOCAL Salt Fork RR

description: Salt Fork of Red River, Greer County, Oklahoma
DOI: 10.5061/dryad.2435k/31
title: Dryad LOCAL Tyner Creek

description: Tyner Creek, Adair County, Oklahoma
DOI: 10.5061/dryad.2bm21/1
title: Phylogenetic_data_sets

description: fasta formatted sequence files for 200 random RAD loci
DOI: 10.5061/dryad.2bm21/2
title: BEAST_xml_files

description: XML files used in *BEAST analysis
DOI: 10.5061/dryad.2bm21/3
title: Pupfish_contigs.fa

description: de-novo partial reference genome for Cyprinodon diabolis containing 793,068 RAD contigs ranging between 300 - 796 bp.
DOI: 10.5061/dryad.2bm21/4
title: cramfiles

description: Individual alignment files in CRAM format.
DOI: 10.5061/dryad.4291s/11
title: Data File S11. Nonessential and essential GI hub functional enrichment analysis

description: This file lists GO biological process, molecular function and cellular component terms that are enriched among of 10% of array strains with the most negative and 10% of array strains with the most positive interactions identified in the ExE network. Enrichments are also included for the 5% of array strains with the most negative interactions and 5% of array strains with the most positive interactions in the NxN genetic interaction network.
DOI: 10.5061/dryad.4291s/12
title: Data File S12. Protein complex standard

description: This file provides a list of protein complexes compiled from two sources: Baryshnikova 2010 (5) and Benschop 2010 (117).
DOI: 10.5061/dryad.4291s/14
title: Data File S14. D. melanogaster S2 cell fitness

description: This file provides D. melanogaster S2 cell fitness upon RNAi-mediated 26S proteasome depletion and Bortezomib treatment.
DOI: 10.5061/dryad.4291s/16
title: Data File S16. Genetic suppression analysis

description: This file includes raw data from spot dilution growth assays to identify positive interactions that can be classified as genetic suppression. The suppression score is based on visual assessment of double mutant strain growth relative to a wild type and single mutant control strains. The score reflects strength of suppression with a score of 4 indicative of a strong suppression interaction where double mutant growth exceeded growth of the sickest single mutant and a score of 0 indicates failure to confirm a suppression interaction.
DOI: 10.5061/dryad.4291s/17
title: Data File S17. YNL181W chemical genetics data

description: Relative growth of a YNL181W-DAmP strain (CG score) measured in the presence of 92 different compounds.
DOI: 10.5061/dryad.4291s/19
title: Data File S13. Genetic interaction enrichment among protein complexes

description: This file lists all possible pairs of protein complexes tested in the ExE, NxN and ExN networks. Enrichment for negative and positive interactions between genes in the same complex or between genes in different complexes is indicated. In addition, enrichment for genetic interaction in general (Combined interaction enrichment) regardless of the type is also indicated. Finally, Interaction Sign Bias indicates the distribution of interactions between genes within the same complex or between genes in different complexes. The interaction sign bias is computed as the mean over all interactions for within a given complex or between a pair of complexes. For example, an interaction sign bias of -1 indicates that all interactions identified between a set of genes encoding complexes members are negative, whereas a score of 1 indicates that only positive interactions were identified between a particular set of protein complex encoding genes. Rows highlighted in blue indicated complex-complex pairs enriched for negative interactions where greater than 75% of all interactions detected were negative. Rows highlighted in yellow indicated complex-complex pairs enriched for negative interactions where greater than 75% of all interactions detected were positive. The analysis shown in Fig. 7 is based on subset of complexes composed of 75% essential genes (i.e. considered essential complexes) or 75% nonessential genes (i.e. considered nonessential complexes). The complexes used for this analysis and their enrichment results are listed in the tabs labeled, “_filtered”. The tabs named “all” list within and between complex enrichment for all protein complexes without prior filtering of complexes composed of less than 75% essential or 75% nonessential genes.
DOI: 10.5061/dryad.4291s/20
title: Data File S15. Protein complex interaction enrichment and bias

description: This file indicates fold enrichment and biases in positive vs. negative interaction frequency for protein complexes and is described in detail above (see ìAnalysis of protein complexes exhibiting a positive interaction enrichment biasî). Rows highlighted in yellow indicate protein complexes that show &gt; 1.5X enrichment for positive interactions (ìE_fold_pos) stronger enrichment for positive versus negative interactions when screened against the essential TSA. The file consists of the following columns:(A) Protein complex name(B) Number of complex member-encoding query genes screened against the DMA (ìqueries_vs_DMAî).(C) Number of complex member-encoding query genes screened against the TSA (ìqueries_vs_TSAî).(D) Nonessential-negative GI fold enrichment (ìN_fold_negî): negative interaction fold enrichment for a complex of interest with nonessential genes not in the complex.(E) Essential-negative GI fold enrichment (ìE_fold_negî): negative interaction fold enrichment for a complex of interest with essential genes not in the complex.(F) Nonessential-positive GI fold enrichment (ìN_fold_posî): positive interaction fold enrichment for a complex of interest with nonessential genes not in the complex.(G) Essential-positive GI fold enrichment (ìE_fold_posî): positive interaction fold enrichment for a complex of interest with essential genes not in the complex. Complexes with a positive GI enrichment &gt; 1.5X are highlighted in yellow. These values were used to generate Fig. 8C.(H) Positive GI bias with essential genes (ìposGI_bias_with_Eî): the relative positive:negative enrichment ratio of essential to nonessential genes for the complex of interest (calculated as [D/E]/[F/G]). Complexes with a positive GI enrichment &gt; 1 and a positive GI bias &gt; 1.5 are highlighted in yellow. These values were used to generate Fig. 8D.(I) Positive GI bias with nonessential genes (posGI_bias_with_Nî): the relative positive:negative enrichment ratio of nonessential to essential genes for the complex of interest (calculated as [F/G]/[D/E]).
DOI: 10.5061/dryad.4n2th/1
title: JAV-01020.R2

description: Data used in the article
DOI: 10.5061/dryad.5ds98/1
title: Intervention rate over time in fallow deer

description: This is the datafile used in the paper. I did not change the variable names as these are used in the model descriptions in the code provided as supplementary material. If you want more details then please email me.
DOI: 10.5061/dryad.6rk67/1
title: data for Dryad

description: This file contain data on the flight performance of flies in a standard assay. The variables are described as follows: 1) selection "treatment" (C, H, or T); 2) experimental "population" within the selection treatment (1-5); 3) isofemale line within the population (#.#); 4) temperature at which flies were reared (16 or 25C); 5) temperature at which flies were tested (16 or 25C); and whether flies successfully demonstrated flight (0 or 1).
DOI: 10.5061/dryad.72591/2
title: File 2

description: Results of the MANOVA with pairwise comparisons between samples based on the first twelve relative warps
DOI: 10.5061/dryad.72591/3
title: File 3

description: Relative Warp scores of lateral view
DOI: 10.5061/dryad.75dg8/1
title: Alignment of genes from twenty-five fungi

description: Alignment of genes used to generate phylogenetic tree of twenty-five fungal taxa for modelling genome and chromosome evolution.
DOI: 10.5061/dryad.75dg8/2
title: Partitioning scheme for alignment file

description: A RAxML formatted partition file for the sequence alignment file.
DOI: 10.5061/dryad.75dg8/3
title: Genome size and inferred ancestral states from Mesquite

description: Observed genome sizes and inferred ancestral states in a nexus file for use with Mesquite from twenty-five fungi.
DOI: 10.5061/dryad.75dg8/4
title: Chromosome counts from fungi

description: Chromosome counts for the twenty-five fungi from the sequence alignment, for use with ChromEvol software.
DOI: 10.5061/dryad.7g1m9/1
title: Houetal_Supplementary Data 1

description: Supposed protaspid and meraspides of Zhangshania typica from the Hongjingshao Formation, in Kunming, Yunnan Province, southern China: (1), supposed protaspid of this species, YKLP 12249; (2), same specimen of YKLP 12249 photographed under different lighting; (3), Meraspid degree 2, YKLP 12250; (4), enlargement of pygidium of specimen YKLP 12250; (5), Meraspid degree 3, YKLP 12251; (6), enlargement of pygidium of specimen YKLP 12251. p, pygidial segment; t, thoracic segment. Same abbreviations seen below. Scale bars are (1, 2, 4, 6) 200 µm; (3, 5) 500 µm.
DOI: 10.5061/dryad.7g1m9/2
title: Houetal_Supplementary Data 2

description: Meraspides of Zhangshania typica from the Hongjingshao Formation, in Kunming, Yunnan Province, southern China: (1), Meraspid degree 4, YKLP 12252; (2), enlargement of cephalon of specimen YKLP 12252; (3), enlargement of pygidium of specimen YKLP 12252; (4), Meraspid degree 5, YKLP 12253;(5), Meraspid degree 6, YKLP 12254; (6), enlargement of pygidium of specimen YKLP 12254; (7), Meraspid degree 7, YKLP 12255; (8), enlargement of pygidium of specimen YKLP 12255; (9), Meraspid degree 8, YKLP 12256; (10), enlargement of pygidium of specimen YKLP 12256; (11), Meraspid degree 9, YKLP 12257; (12), enlargement of pygidium of specimen YKLP 12257. Scale bars are (3, 6, 8, 10, 12) 200 µm; (1–2, 4–5) 500 µm; (7, 9, 11) 1.0 mm.
DOI: 10.5061/dryad.7g1m9/3
title: Houetal_Supplementary Data 3

description: Meraspides and early holaspides of Zhangshania typica from the Hongjingshao Formation, in Kunming, Yunnan Province, southern China: (1), Meraspid degree 10, YKLP 12319; (2), Meraspid degree 11, YKLP 12259; (3), Meraspid degree 12, YKLP 12260; (4), Meraspid degree 13, YKLP 12261; (5), enlargement of pygidium of specimen YKLP 12261; (6), Holaspid stage 1, YKLP 12262; (7), enlargement of pygidium of specimen YKLP 12262; (8), Holaspid stage 2, YKLP 12263; (9), enlargement of pygidium of specimen YKLP 12263. Scale bars are (5, 7, 9) 200 µm; (1–3) 500 µm; (4, 6, 8) 1.0 mm.
DOI: 10.5061/dryad.808g7/1
title: Table 1 data
DOI: 10.5061/dryad.968vr/1
title: TP53.xml

description: .xml file used for BEAST
DOI: 10.5061/dryad.968vr/2
title: TP53.nex

description: Nexus file used in MrBayes
DOI: 10.5061/dryad.968vr/3
title: TP53.phy

description: .phy file used in PhyML
DOI: 10.5061/dryad.9gs8k/1
title: Data for Alp clone cold reaction for Dryad.xlsx

description: The row data is in "data" sheet.	The description of the data is in "read.me" sheet.		The description of the data:	1 row indicates 1 plant for which chlorophyll fluorescence was measured.		Column "source".	Which plants were derived from "seed" (i.e. seedling) or "clone" (i.e. tissule cultured plantlet).Column "w.genotype".	If clone, name of genotype is provided. Otherwise, "half-sib".Column "pop".	Name of populations. Either "ardal" in Norway, "notsand" in Sweden, or "sandfell" in Iceland.Column "treat".	Experimental treatments. "pre": pre-cold treatment. "post": post-cold treatment.Column "ind".	Number of plants.Column "block".	Name of blocks. Chlorophyll fluorescence of plants in the same block was measured at the same time.Column "fvfm".	Fv/Fm, chlorophyll fluorescence.Column "phy".	Fv’/Fm’, chlorophyll fluorescence.Column "fvfm2". ФPSII, chlorophyll fluorescence.
DOI: 10.5061/dryad.b55tv/1
title: Lucon-Xiccato et al. 2016 Behav Ecol - Data

description: Excel file with the data of the two experiments. Experiment 1: effect of predation risk on lateralization. Experiment 2: predator recognition learning test. Descriptive name of each variable is provided within the file.
DOI: 10.5061/dryad.c3q5c/3
title: Prior and Posterior Samples

description: The prior and posterior samples (and column headers) used for the hABC coexpansion models for each tetrapod group
DOI: 10.5061/dryad.c3q5c/4
title: Supporting Material; Table S1

description: Table S1: Columns show species used for demographic reconstruction, citations for original studies, Bayesian Skyline Plot profiles and slopes, mutation rate priors (low and high locus mutation rate) used in hABC analyses, Ne priors (low and high Ne) used in hABC analyses, generation times with citations, and genetic summary statistics used in the hABC models. This file is a CSV file and can be opened for viewing in Excel, Google Sheets, or any other spreadsheet software.
DOI: 10.5061/dryad.cq2rb/1
title: DC1
DOI: 10.5061/dryad.cq2rb/2
title: DC2
DOI: 10.5061/dryad.d75hq/1
title: spatial raster with cockle densities corresponding to Fig3A

description: The coordinate reference system is EPSG:32631 - WGS 84 / UTM zone 31N, and cockle density is presented in numbers per square meter.
DOI: 10.5061/dryad.d75hq/2
title: Spatial raster with relative AFDMflesh corresponding to Fig3B

description: The coordinate reference system is EPSG:32631 - WGS 84 / UTM zone 31N. Relative AFDMflesh is presented as the ratio of AFDMflesh to average AFDMflesh for cockles of identical length (see main article).
DOI: 10.5061/dryad.d75hq/3
title: spatial raster with predicted intake rates corresponding to Fig3C

description: The coordinate reference system is EPSG:32631 - WGS 84 / UTM zone 31N, and predicted intake rates are presented in mg AFDMflesh per second. These intake rates correspond to foragers without a digestive constraint.
DOI: 10.5061/dryad.g56g1/1
title: Transmission data for Keiser et al 2016, Biology Letters

description: Individual spider measurements and colony-wide bacterial transmission data.
DOI: 10.5061/dryad.m5n5b/1
title: All Data Kin Recognition in Amazons

description: Excel file contains all raw data separated by each individual study
DOI: 10.5061/dryad.mv88m/1
title: Additional file 4

description: Additional file 4: Table S4. Dataset of 1,745 polymorphic DArT and TRAP markers scored on the 88 sugarcane accessions and used to estimate genetic relationship among clones.  Table S5. Dice distances matrix. Table S6.  Ultrametric distances matrix.
DOI: 10.5061/dryad.mv88m/2
title: Figure 1

description: Figure 1. Neighbour-joining tree based on the Dice dissimilarity index calculated from 1,745 polymorphic markers data (103 TRAP and 1,642 DArT) assembling the 88 sugarcane genotypes.
DOI: 10.5061/dryad.nf01p/3
title: 1.Moyle.oscine.UCE.completematrix

description: Complete (loci common to all taxa) matrix of oscine UCE data. Date were produced with the tetrapod UCE 5K probe kit from Mycroarray. Data aligned with MAFFT, and trimmed with Gblocks. Number after taxon name refers to sample number.
DOI: 10.5061/dryad.r1mc3/1
title: Hainan gibbon microsatellite genotypes

description: Hainan gibbon genotypes for 13 polymorphic microsatellite loci with associated sample information (sample years, locations, number of samples/individual, number of DNA extractions/individual, final consensus genoptypes), plus microsatellite multiplex mixes used for genotyping.
DOI: 10.5061/dryad.r2t49/1
title: Tree A concatenate

description: Fasta files, alignments and Gblock output for the concatenate used to create the Tree A.
DOI: 10.5061/dryad.t4k7h/1
title: Hypsibius dujardini genome assembly

description: Genome sequence assembly of a single individual of Hypsibius dujardini Z151 sequencing reads (Illumina MiSeq 300bp paired end), using MaSuR-CA 3.1.3 software.
DOI: 10.5061/dryad.vr666/1
title: Ruuskanen: heritability of egg components
DOI: 10.5061/dryad.00fs2/1
title: CrossSectionMeasurements

description: Cross section data generated from leaf cross sections, imaged using a Zeiss microscope and analyzed in ImageJ.
DOI: 10.5061/dryad.00fs2/2
title: Gene trees

description: Gene trees produced from 272 single copy genes, using RAxML. Trees are the consensus of 500 bootstrap replicates (RAxML_bipartitions.*).
DOI: 10.5061/dryad.00fs2/3
title: Gene alignments

description: Nucleotide alignments of 272 single copy genes.
DOI: 10.5061/dryad.00fs2/4
title: Chloroplast tree

description: RAxML bipartition tree from chloroplast alignment. 500 bootstrap replicates.
DOI: 10.5061/dryad.00fs2/5
title: Chloroplast alignment

description: Chloroplast alignment file.
DOI: 10.5061/dryad.0n624/1
title: Mean laydate per species per year (1961-2012)

description: Laydates for 26 common breeding bird species in Finland were estimated based on nest-card data. The data here contains mean laydates (and standard deviation) per bird species per year for the period 1961-2012, including the number of nestcards on which each mean laydate was based on.
DOI: 10.5061/dryad.1q7j5/2
title: code_for_dryad

description: SAS code for analyzing data on ear hole closure
DOI: 10.5061/dryad.1q7j5/3
title: data_for_analysis

description: Excel file of raw data to be analyzed with SAS
DOI: 10.5061/dryad.1q7j5/4
title: data_for_comparing_contrasts

description: Raw data for analysis with SAS
DOI: 10.5061/dryad.3s7rd/1
title: Systematic review of CKD Prevalence Worldwide

description: The datafile contains the results from a systematic review and meta-analysis.  The full details of the search startegy, study selection and data extractions are detailed in the publication with which this dataset is associated. Each line in the datafile represent one population of data that were extracted. A value of -999 was used if data were unavailable.