cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pr907/3
title: STRUCTURE_file

description: This is the input file for the structure analyses that includes genotype data for 923 individuals, and also contains marker names in the top row.
DOI: 10.5061/dryad.pr907/8
title: README
DOI: 10.5061/dryad.119f80q/5
title: VIDEO_5_100_MICRON_MRI_SYNTHESIZED_FLASH25_CORONAL

description: This is a 100 micron isotropic resolution magnetic resonance imaging (MRI) scan of an ex vivo human brain specimen. The brain specimen was donated by a 58-year-old woman who had no history of neurological disease and died of non-neurological causes. Her family provided written informed consent. We imaged her brain for 5 days continuously on a 7 Tesla MRI scanner using a custom-built 31-channel receive array coil. The images shown here are from the synthesized FLASH25 volume.
DOI: 10.5061/dryad.119f80q/6
title: VIDEO_6_100_MICRON_MRI_SYNTHESIZED_FLASH25_CORONAL

description: This is a 100 micron isotropic resolution magnetic resonance imaging (MRI) scan of an ex vivo human brain specimen. The brain specimen was donated by a 58-year-old woman who had no history of neurological disease and died of non-neurological causes. Her family provided written informed consent. We imaged her brain for 5 days continuously on a 7 Tesla MRI scanner using a custom-built 31-channel receive array coil. The images shown here are from the synthesized FLASH25 volume.
DOI: 10.5061/dryad.1m7n014/2
title: Campephagidae alignment txt

description: See details in Table S1.1 in Appendix S1 in the online Supporting Information.
DOI: 10.5061/dryad.37jj6t9/20
title: Appendix S7

description: Appendix S7. The trees resulting from the analysis of molecular data. Strict consensus tree of the two most parsimonous trees; numbers at nodes represent bootstrap supports (A); Fifty per cent majority rule consensus tree from Bayesian analysis; numbers at nodes represent posterior probabilities (B).
DOI: 10.5061/dryad.3ng4kr8/1
title: Stable isotopes and immune markers from Isle of May mice

description: The data file contains data associated with the publication Taylor et al. 2019 "Immune state is associated with natural dietary variation in wild mice Mus musculus domesticus" Functional Ecology.
Data refer to 74 individual mice Mus musculus domesticus that were trapped on the Isle of May, Scotland on 9th-12th October 2015. For full details of methodology, please refer to the above publication. Missing data are indicated by NA.
DOI: 10.5061/dryad.3ng4kr8/2
title: R script for analysis of diet and immunity from Isle of May mice

description: This script accompanies the data file "IoM_mousedata_dietandimmunity.csv" and carries out the analysis and plots described in the paper Taylor et al. 2019 "Immune state is associated with natural dietary variation in wild mice Mus musculus domesticus" Functional Ecology.
DOI: 10.5061/dryad.46cg87c/1
title: analysis_scripts_and_functions

description: Processing scripts for state-dependent detection analysis of cortical LFP in awake mouse.
DOI: 10.5061/dryad.46cg87c/2
title: csd_allchannels

description: evoked responses and pre-stimulus activity across all channels  (CSD)
DOI: 10.5061/dryad.46cg87c/3
title: lfp_dimReduce

description: evoked responses and pre-stimulus activity across all channels (LFP)
DOI: 10.5061/dryad.46cg87c/4
title: lfp_cont_l4channels
DOI: 10.5061/dryad.4j2c7h6/1
title: VCF for Urochloa spp. hybrids

description: Created from GBS data with GATK, using an Urochloa mock reference genome for alignment
DOI: 10.5061/dryad.4j2c7h6/2
title: List of 267 hybrids included in the analysis
DOI: 10.5061/dryad.5qg30sd/10
title: R code to prepare porpoise responses & construction activity data

description: R code to prepare the data file for analyses of porpoise responses to pile-driving, acoustic deterrent device (ADD) use and vessel activity. 
Filename = "Graham_BOWL_cMMMP_R_code_to_prepare_porpoise_response_data_2019-01-18.R"
DOI: 10.5061/dryad.5qg30sd/12
title: Readme.txt file for data packages associated with paper on “Harbour porpoise responses to pile-driving diminish over time”

description: Description of data packages
DOI: 10.5061/dryad.5qg30sd/2
title: Zip folder with 100 data files on porpoise occurrence

description: Zip folder with 100 CPOD data files on porpoise occurrence for analyses of responses of porpoises to construction activity. 
Filename = "Graham_BOWL_cMMMP_CPOD_porpoise_ClickCounts_data_2019-01-18.zip”
Each file has the data from a single CPOD deployment, cropped to remove data up to 23:59 on the day of deployment and from 00:00 on the day of retrieval. 
Each file has five columns = File, ChunkEnd, Nfiltered, Nall, MinsOn
File is the filename of the original CPOD data file.
ChunkEnd is the time in minutes.
Nfiltered is the number of high and moderate quality porpoise clicks for each minute.
Nall is the total number of unfiltered clicks for each minute.
MinsOn indicates whether the CPOD was recording during that minute (1) or not (0).
DOI: 10.5061/dryad.5qg30sd/3
title: Data on piling activity by turbine/OTM location

description: Data on the piling activity summarised by turbine/OTM location (see Table S1).
Filename = “Graham_BOWL_cMMMP_Piling_summary_by_turbine_data_2019-01-18.csv”
Twelve columns = turbine, start_time, end_time, piling_duration, piling_duration_hours, total_blow_count, max_energy, interval_days, daystocomplete, piling_order, lat, long.
Turbine is the code for the turbine/OTM location.
Start_time is the time when piling of the first pile started.
End_time is the time when piling of the fourth pile ended.
Piling_duration is the duration of active piling in minutes.
Piling_duration_hours is the duration of active piling in hours.
Total_blow_count is the total number of hammer blows.
Max_energy is the maximum hammer energy (kJ).
Interval_days is the time difference (in days) between the end of piling at the previous location and the start of piling at the current location.
Daystocomplete is the number of days from the start to the end of piling.
Piling_order is the order in which locations were piled, equivalent to the cumulative number of locations piled at the end of piling at that location.
Lat is the latitude in decimal degrees.
Long is the longitude in decimal degrees.
DOI: 10.5061/dryad.5qg30sd/4
title: Data on piling activity by turbine/OTM location & day

description: Data on the piling activity summarised by turbine/OTM location and day.
Filename = “Graham_BOWL_cMMMP_Piling_summary_by_day_data_2019-01-18.csv”
Twenty-two columns = julian, start_time, end_time, total_duration, total_duration_hours, total_blow_count, max_energy, no_turbines_piled, turbine1, start_time1, end_time1, duration1, duration_hours1, blow_count1, max_energy1, turbine2, start_time2, end_time2, duration2, duration_hours2, blow_count2, max_energy2.
DOI: 10.5061/dryad.5qg30sd/5
title: Data on CPOD deployments

description: Data on the CPOD deployments.
Filename = “Graham_BOWL_cMMMP_POD_deployment_data_2019-01-18.csv”
Eight columns = Dep_no, POD_number, Deployment_date, Location_ID, Latitude, Longitude, Retrieval_date, Data_end_date.
Dep_no is the unique number assigned to each CPOD deployment.
POD_number is the unique individual number for the CPOD used in that deployment.
Deployment_date is the date when that CPOD was deployed at sea.
Location_ID is the numeric identifier for the location at which that CPOD was deployed.
Latitude is the latitude in decimal degrees for that deployment.
Longitude is the longitude in decimal degrees for that deployment
Retrieval_date is the date when that CPOD was retrieved at sea.
Data_end_date is the date when the data on the CPOD’s SD card ended.
DOI: 10.5061/dryad.5qg30sd/6
title: Data on AIS detections within 1km of CPODs

description: Data on the Automatic Identification System (AIS) vessel detections within 1km of each CPOD. Raw AIS data for 2017 for the Moray Firth were supplied to BOWL by Astra Paging Ltd., Sliven, Bulgaria. This AIS data consisted of the location (latitude and longitude) of each AIS vessel at 5 minutes intervals. These data were processed in R to select only those AIS vessel locations within 1 km of each CPOD when the CPOD was operational (i.e. deployed and recording data).
Filename = “Graham_BOWL_cMMMP_5min_boat_withineach_1kmCPODbuffer _data_2019-01-18.csv”
Five columns = MMMSI.x, DATE.TIME.x, Deployment.number, BOAT.LATITUDE, BOAT.LONGITUDE.
MMMSI.x is the unique 9 digit vessel identifier.
DATE.TIME.x is the time of the vessel detection.
Deployment.number is the CPOD deployment to which that vessel detection refers.
BOAT.LATITUDE is the latitude in decimal degrees for that vessel detection.
BOAT.LONGITUDE is the longitude in decimal degrees for that vessel detection.
DOI: 10.5061/dryad.609g597/1
title: PONE-D-18-20002-data

description: EEG data from subjects during the speech imagery tasks described in PONE-D-18-20002
DOI: 10.5061/dryad.6rn879c/1
title: Sodhi et al 2019 - Trait & abundance data

description: This excel spreadsheet contains functional trait and abundance data for herbaceous plants in Rouge National Urban Park. Information on the study sites is also included.
DOI: 10.5061/dryad.805cp7g/1
title: Bird occurrence, ecological traits and landscape predictors in southeast Brazil

description: This database provide data on bird species occurrence in forest edges, pastures and eucalyptus plantation across a wide region of fragmented Atlantic Forest, southeastern Brazil. Additonally, information on species ecological traits, sampling geographical coordinates, and landscape attributes are available. Detailed information on how these data were collated are found in the Methods section of the manuscript.
DOI: 10.5061/dryad.b412jp5/22
title: Tamer_Interproscan_GO

description: Gene ontology annotations of all contigs of the transcriptome of T. americanus generated using InterProScan v.5.25-64.0.
DOI: 10.5061/dryad.b412jp5/23
title: Tamer_Interproscan_KEGG

description: KEGG pathways of all contigs of the transcriptome of T. americanus generated using InterProScan v.5.25-64.0.
DOI: 10.5061/dryad.b412jp5/24
title: Tamer_transcriptome_filtered

description: Transcriptome of T. americanus after all filtering steps prior to gene expression analysis generated using Trinity v.2.4.0, TransDecoder TransDecoder v.3.0.1, R package DESeq2 v.1.16.1.
DOI: 10.5061/dryad.b412jp5/25
title: Tamer_Trinity_Transcriptome

description: Transcriptome of T. americanus created by Trinity without any filtering steps generated using Trinity v.2.4.0.
DOI: 10.5061/dryad.b412jp5/26
title: Tlongi_BLAST_transcriptome

description: BLAST annotations of all contigs in the Trinity transcriptome of T. longispinosus generated using blastx, NCBI BLAST v2.6.0.
DOI: 10.5061/dryad.b412jp5/27
title: Tlongi_Interproscan_GO

description: Gene ontology annotations of all contigs of the transcriptome of T. longispinosus generated using InterProScan v.5.25-64.0.
DOI: 10.5061/dryad.b412jp5/28
title: Tlongi_Interproscan_KEGG

description: KEGG pathways of all contigs of the transcriptome of T. longispinosus generated using InterProScan v.5.25-64.0.
DOI: 10.5061/dryad.b412jp5/29
title: Tlongi_transcriptome_filtered

description: Transcriptome of T. longispinosus after all filtering steps prior to gene expression analysis generated using Trinity v.2.4.0, TransDecoder TransDecoder v.3.0.1, R package DESeq2 v.1.16.1.
DOI: 10.5061/dryad.b412jp5/30
title: Tlongi_Trinity_Transcriptome

description: Transcriptome of T. longispinosus created by Trinity without any filtering steps generated using Trinity v.2.4.0.
DOI: 10.5061/dryad.b412jp5/31
title: ReadMe

description: This file describes all supplementary material provided alongside: Tandem-Running and Scouting Behavior is Characterized by Up-Regulation of Learning and Memory formation genes within the Ant Brain 
(A. Alleman, M. Stoldt, B. Feldmeyer, S. Foitzik) 2019
DOI: 10.5061/dryad.fv278qs/1
title: Table S1
DOI: 10.5061/dryad.fv278qs/2
title: Table S2
DOI: 10.5061/dryad.fv278qs/3
title: Table S3
DOI: 10.5061/dryad.j27h930/1
title: code

description: "main text.nb" (written in Mathematica) reproduces all five figures in the main text.

"Supplement 7.R" (written in R) reproduces Supplement 7.
DOI: 10.5061/dryad.kb135g6/1
title: Culshaw et al, dataset for BDR paper

description: Spreadsheet containing raw data and statistical analyses for Figures 1, 4, 5, 6 and 8.
DOI: 10.5061/dryad.m173s71/2
title: Figure 2B_2D
DOI: 10.5061/dryad.m173s71/3
title: Figure3
DOI: 10.5061/dryad.m173s71/4
title: Figure4
DOI: 10.5061/dryad.m173s71/5
title: FigureEV3
DOI: 10.5061/dryad.m173s71/6
title: FigureEV4
DOI: 10.5061/dryad.m173s71/7
title: FigureEV5
DOI: 10.5061/dryad.n34d4m7/3
title: Supplemental Table 1

description: The data for all samples included in the three RADseq libraries.
DOI: 10.5061/dryad.n34d4m7/4
title: Supplemental Table 2

description: The data for all samples included in the 16 pairs of populations analyzed in this study. This is a subset of the data in Supplemental Table 1.
DOI: 10.5061/dryad.n34d4m7/5
title: Animation from Supplemental Figure 2

description: Animation of approximate sea-level changes in the Philippine Islands over the last 430,000 years. Sea-level estimates are from the projection of Spratt and Lisiecki (2016) based on seven reconstructions. Bathymetry data are from the ETOPO1 1-arc-minute global relief model (Amante and Eakins, 2009). Animation generated using marmap version 1.0.2 (Pante and Simon-Bouhet, 2013), ggplot2 Version 2.2.1 (Wickham, 2009), ImageMagick Version 6.9.10-8 Q16 x86_64 20180723, and FFmpeg Version 4.0.2-2. The source code for generating the plot is available at https://github.com/phyletica/animating-sea-level-change. This animation can also be viewed at https://youtu.be/NjGdCezUvw8.
DOI: 10.5061/dryad.nc38t01/1
title: Buchloë dactyloides SSR genotypes

description: Alleles observed at 14 SSR loci in 364 Buchloë dactyloides individuals. Collector names and numbers match those presented in Appendix S1.
DOI: 10.5061/dryad.pj8c6g2/1
title: Zipped data and scripts

description: This is a folder of all of the data and script files from the paper (as outlined in the README).
DOI: 10.5061/dryad.pr907/4
title: Structure_Harvester_Results_All_SNPs

description: This folder contains the results from the Structure Harvester analyses of all 5 replicates (K1-K10) for the entire SNP data set (all 923 individuals).
DOI: 10.5061/dryad.pr907/5
title: Structure_Harvester_Results_Northern

description: This folder contains the results from the Structure Harvester analyses of all 5 replicates (K1-K10) for the Northern group (516 individuals) only.
DOI: 10.5061/dryad.pr907/6
title: Structure_Harvester_Results_Southern

description: This folder contains the results from the Structure Harvester analyses of all 5 replicates (K1-K10) for the Southern group (391 individuals) only.
DOI: 10.5061/dryad.pr907/7
title: Treemix_input_file

description: This file contains the SNP genotype data formatted for input into TreeMix.
DOI: 10.5061/dryad.s1725t6/1
title: Data and Analysis Scripts

description: Contains data and analysis scripts to produce figures presented in paper.
DOI: 10.5061/dryad.sc26m6c/1
title: GPS locations of bottlenose dolphins

description: File contains GPS locations of individual sightings of bottlenose dolphins in the western gulf of Shark Bay (Western Australia) between 2007 and 2018 (WGS84).
DOI: 10.5061/dryad.sc26m6c/3
title: Association network

description: Matrix with association strength (simple ratio association index) among bottlenose dolphins in the western gulf of Shark Bay between 2007-2018. All mother-offspring association were set to 0.
DOI: 10.5061/dryad.sc26m6c/4
title: Genetic relatedness network

description: Matrix containing dyadic genetic relatedness (TrioML) based on 27 microsatellite markers in the bottlenose dolphin population in the western gulf of Shark Bay using biopsy samples collected between 2007 and 2018. Relatedness for dyads with no genetic information were set to population average of 0.043.
DOI: 10.5061/dryad.sc26m6c/5
title: Home range overlaps (dolphins)

description: Matrix containing 95% dyadic home range overlap (utilization distribution overlap index) of bottlenose dolphins in the western gulf of Shark Bay based on GPS locations of individual sightings between 2007 and 2018. Home ranges were based on kernel densities with a customized smoothing factor.
DOI: 10.5061/dryad.sc26m6c/7
title: Land contours - western Gulf of Shark Bay (Australia)

description: shape file containing land contours in the western gulf of Shark Bay in Western Australia (UTM zone 49S)
DOI: 10.5061/dryad.tk47202/1
title: MicroCT Raw Data

description: µCT Data Set for Sympetrum striolatum including labels data
DOI: 10.17632/2nwt2d9k8y.1
title: Data for: Neonatal transport clinician performed ultrasound evaluation of cardiac function

description: Excel sheet with raw data
DOI: 10.5061/dryad.0c3cn5f/1
title: Pollination data of ten Galapagos Islands

description: The pollination data consists of a survey of pollination events on 10 islands, including Fernandina, Pinta, San Cristóbal, Santa Cruz and Santiago (reported in Traveset et al. 2013 Proc R Soc B; surveyed in February 2010 and 2011); and Española, Floreana, Genovesa, Isabela and Marchena (reported in this paper; surveyed from 2012 to 2015).
DOI: 10.5061/dryad.10b64m4/1
title: Resetarits et al. 2019 American Naturalist data

description: Experimental data on patch size and perceived predation risk.
DOI: 10.5061/dryad.23jr5h2/1
title: De Mendoza Appendix I character list

description: Character list for the phylogenetic analysis of Anatidae, including Cayaoa bruneti.
DOI: 10.5061/dryad.23jr5h2/2
title: De Mendoza Appendix II data matrix table

description: Character matrix in word format
DOI: 10.5061/dryad.23jr5h2/3
title: De Mendoza data matrix

description: Character matrix in nexus format
DOI: 10.5061/dryad.23jr5h2/4
title: De Mendoza Appendix III specimens used

description: Specimens used in the analyses
DOI: 10.5061/dryad.38gk4m6/1
title: batch_1.structure_Oregon_1100_repeat_1

description: Subset of 1100 loci for individuals from Oregon populations formatted for Structure.
DOI: 10.5061/dryad.38gk4m6/2
title: batch_1.structure_Oregon_1100_repeat_2

description: Subset of 1100 loci for individuals from Oregon populations formatted for Structure
DOI: 10.5061/dryad.38gk4m6/3
title: batch_1.structure_Oregon_1100_repeat_3

description: Subset of 1100 loci for individuals from Oregon populations formatted for Structure
DOI: 10.5061/dryad.38gk4m6/4
title: batch_1.structure_Oregon_Alaska_1100_repeat_1

description: Subset of 1100 loci for individuals from Oregon and Alaska populations formatted for Structure.
DOI: 10.5061/dryad.3gm4500/2
title: Fig 2

description: 2D-PAGE analysis of proteins extracted from upper parts of pistils of pin and thrum plants. Total proteins from stigmas and styles were separated by 2D-PAGE and silver-stained. SP1 and SP2, thrum-specific spots.
DOI: 10.5061/dryad.3gm4500/3
title: Fig 3

description: Amino-acid sequence of SP1 (FePG1) and multiple sequence alignment analysis. The predicted amino-acid sequence of FePG1 was aligned with those of four PG orthologues from Arabidopsis thaliana (At), Brassica napus (Bn), Solanum lycopersicum (Sl), and Turnera subulata (Ts). Conserved domains of PGs are indicated as regions I to IV. N-terminal and internal amino-acid sequences obtained by Edman sequencing and MS/MS analysis are indicated as N1, Int1, Int2, MS1, and MS2. The putative cleavage site was predicted by ExPASy.
DOI: 10.5061/dryad.3gm4500/4
title: Fig 4

description: Relative expression levels of FePG1. (A) The mRNA abundances of FePG1 in different organs of four floral morphotypes were detected by semi-qRT-PCR (40 cycles). The housekeeping gene Histone H3 (H3) was used as a loading control. L, leaves; S, stems; R, roots; F, flowers. (B) The mRNA abundances of FePG1 in pin and thrum styles were compared by real-time qRT-PCR. Values are relative to the H3 transcript level. Data are means ± s.e. for three technical replicates (bulked RNA from at least four independent plants). *P &lt; 0.05 (Student’s t test)
DOI: 10.5061/dryad.3gm4500/5
title: Fig 5

description: DNA polymorphism of the FePG1 genomic region in ‘KSC7’ (long homostyle). (A) Gene structure of FePG1 of ‘KSC7’. ‘KSC7’ has a 692-bp insertion in the 3rd exon. Black boxes, exons; bars, introns. (B) DNA polymorphism at the insertion region detected by agarose gel electrophoresis. P, pin; T, thrum; LH, long homostyle; SH, short homostyle
DOI: 10.5061/dryad.3gm4500/6
title: Fig 6

description: Cis-elements of FePG1 and Fes_sc0001894.1.g000002.aua.1 A 2-kb region upstream of the translation initiation site and intron regions were analyzed. Triangles indicate cis-elements: LUX-binding site (LBS), evening element (EE), morning element (ME), and G-box (G). The lowercase letters are sequences different from the consensus sequence of each cis-element; +, forward strand; –, reverse strand
DOI: 10.5061/dryad.3gm4500/7
title: Supplementary Fig. S1

description: Phylogenetic tree constructed with the sequences of glycoside hydrolase family 28 domains of 51 buckwheat PG and 56 PG proteins from various plant species. Bootstrap values (1000 replicates) are shown under the branches. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The PG proteins used in this analysis are listed in Supplementary Tables S3 and S4
DOI: 10.5061/dryad.3gm4500/8
title: Sup Table S1

description: Plant materials used in proteomic analysis, quantitative RT-PCR, and linkage analysis.
DOI: 10.5061/dryad.3gm4500/9
title: Sup Table S2

description: Sequences of primers used for cloning, quantitative RT-PCR, and linkage analysis.
DOI: 10.5061/dryad.40sf920/1
title: Step1_WGCNA

description: This zip file contains all of the required R.code to run the WGCNA analysis used to identify the UPRmt of O. faveolata.
DOI: 10.5061/dryad.40sf920/2
title: Step2_GoMWU

description: This zip folder contains the gene_ids and the module membership scores for the identified O. faveolata UPRmt genes, as well as the GO terms for those genes.
DOI: 10.5061/dryad.40sf920/4
title: Step3_Transcription_factors
DOI: 10.5061/dryad.45482t5/1
title: Short tandem repeat (STR) data set for: Genetic changes caused by restocking and hydroelectric dams in demographically bottlenecked brown trout in a transnational subarctic riverine system

description: This is a the short tandem repeat (STR) data set for the article: Genetic changes caused by restocking and hydroelectric dams in demographically bottlenecked brown trout in a transnational subarctic riverine system
DOI: 10.5061/dryad.4pf04c0/1
title: Rchickadees_Repeatability

description: Data associated with the trait repeatability portion of our study. We evaluated the degree to which among-individual variation in corticosterone, scaled mass index, and fat score is attributable to individual identity or, conversely, due to environmental plasticity by using estimates of agreement repeatability. In all repeatability calculations, we only included data from individuals caught twice during the winter (2nd measurements were done at least 6 days after first measurements).
DOI: 10.5061/dryad.4pf04c0/2
title: Rchickadees_Cross_Seasons

description: Data associated with the cross-seasonal portion of our study. We evaluated whether initial corticosterone and estimates of body condition (i.e., scaled mass index and fat score) measured during winter predicted reproductive investment in the subsequent breeding season. Some birds were sampled twice during winter, but we only used the first measurement of winter CORT, fat, and scaled mass index to investigate these cross-seasonal relationships. The data file also contains a README tab containing variable definitions.
DOI: 10.5061/dryad.506p9k0/1
title: Data