cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6gb90.2/14.2
title: Protected_AZEs_IPBES

description: Percentage of AZE sites wholly covered by protected areas, over time, for each IPBES region and subregion
DOI: 10.5061/dryad.6gb90.2/7.2
title: IBAs_AZEs_GEO

description: Total numbers, mean sizes, and percentage coverages of IBAs and AZEs in each GEO region and subregion
DOI: 10.5061/dryad.6gb90.2/8.2
title: IBAs_AZEs_IPBES

description: Total numbers, mean sizes, and percentage coverages of IBAs and AZEs in each IPBES region and subregion
DOI: 10.5061/dryad.6gb90.2/9.2
title: PAs_GEO

description: Percentage protected area coverage of land and sea, for each GEO region and subregion
DOI: 10.5061/dryad.6hc8q/1
title: Species_x_Traits

description: This file contains the species by trait matrix for all observed species included in the study. The trait scoring follows the fuzzy coding procedure as described in the manuscript. Species names are abbreviated by the first three letters of their genus. The functional traits are sorted by number (1-9) and followed by their trait-categories. See the "Abbreviations species and traits. csv" file below and the manuscript for details.
DOI: 10.5061/dryad.6hc8q/2
title: Abbreviations species and traits

description: This file contains details to the abbreviations of included species and traits
DOI: 10.5061/dryad.6hc8q/3
title: Station_x_Species

description: This file contains the station by species abundance matrix. Stations are labeled by their exposure classification (E = exposed, S = sheltered), their station ID, and their collection year. Species abundances are the mean abundance of five Ekman-Birge grab samples per site. Species names are abbreviated by the first three letters of their genus. See manuscript for details.
DOI: 10.5061/dryad.6hc8q/4
title: CWM_PERMANOVA

description: This file contains the matrix of community weighted means of trait category expression (CWM) for all included sampling stations and years. CWM values were calculated from the species by trait matrix and station by species matrix and used for the CWM PERMANOVA. See manuscript for details.
DOI: 10.5061/dryad.871db/7
title: Genotypic data (input file) for Bayesian cluster analysis using STRUCTURE.

description: Project input file containing genotypic data for Bayesian cluster analysis using STRUCTURE.  Site IDs, 1-47, are defined in companion file with this data package.
DOI: 10.5061/dryad.871db/8
title: Site location information file, including site IDs, date of collection, and geographic coordinates.

description: Site, collection year, sample ID, and within population microsatellite DNA genetic diversity [sample size (N), observed heterozygosity (Ho), Hardy-Weinberg expected heterozygosity (He), allelic richness (A), rarified allelic richness (Ar), rarified number of private alleles (Ap), inbreeding effective size (Nei) and 95% confidence interval (CI)] for northern California tidewater goby populations (listed from north to south).  Also included are site reference numbers for analysis using PHYLIP (1-36) and STRUCTURE (1-47).
DOI: 10.5061/dryad.87r18/2
title: Zea mays ssp. parviglumis unigenes' sequences

description: Due to lack of available reference genome, clean reads from 3 Zea mays ssp. parviglumis were first de novo assembled into contigs using Trans-ABySS. After discarding the contigs &lt;200 bp, the remaing contigs were then assembled into unigenes, whcih represented the individual transcriptome at the seedling stage. To obtain the transcriptomes from Zea mays ssp. parviglumis, individual transcriptomes were pooled to reconstruct the transcriptome using CD-HIT-EST with a word length of 8 and an identity threshold ≥ 0.98. Sequentially, CAP3 was used to discard the redundancy transcripts, and the resulting contigs and singlets were combined to represent Zea mays ssp. parviglumis transcriptome.
DOI: 10.5061/dryad.87r18/3
title: Zea mays ssp. mexicana unigenes'sequences

description: Due to lack of available reference genome, clean reads from 3 Zea mays ssp. mexicana were first de novo assembled into contigs using Trans-ABySS. After discarding the contigs &lt;200 bp, the remaing contigs were then assembled into unigenes, whcih represented the individual transcriptome at the seedling stage. To obtain the transcriptomes from Zea mays ssp. mexicana, individual transcriptomes were pooled to reconstruct the transcriptome using CD-HIT-EST with a word length of 8 and an identity threshold ≥ 0.98. Sequentially, CAP3 was used to discard the redundancy transcripts, and the resulting contigs and singlets were combined to represent Zea mays ssp. mexicana transcriptome.
DOI: 10.5061/dryad.87r18/4
title: Annotation information of teosinte unigenes

description: Functional annnotation was conducted using InterProScan against Pfam database.
DOI: 10.5061/dryad.9pp6q/1
title: Protein sequences for constructing phylogenetic tree

description: Amino acid sequences of all the TCP transcription factors in Arabidopsis thaliana(24), watermelon(27) and rice(21) were listed to construct phylogenetic tree.
DOI: 10.5061/dryad.9pp6q/2
title: Data of relative chlorophyll content in Arabidopsis leaves
DOI: 10.5061/dryad.9pp6q/3
title: Inflorescence height data of transgenic Arabidopsis
DOI: 10.5061/dryad.9pp6q/4
title: Plant height data of watermelon treated by GA and CCC
DOI: 10.5061/dryad.ct5q3/10
title: filtered_SNPs_convexa

description: Filtered SNP dataset for Crepidula convexa. Filtering was done as described in the main text. SNPs are reported using the IUPAC codes.
DOI: 10.5061/dryad.ct5q3/11
title: filtered_SNPs_fornicata

description: Filtered SNP dataset for Crepidula fornicata. Filtering was done as described in the main manuscript text. SNPs are reported using IUPAC codes.
DOI: 10.5061/dryad.ct5q3/8
title: input_hierfstat_fornicata

description: This file is the input file for Hierfstat for Crepidula fornicata. It was used for both Hierfstat and Adegenet analyses.
DOI: 10.5061/dryad.ct5q3/9
title: input_hierfstat_convexa

description: This file was used as input for the Hierfstat package in R, and downstream analyses in Adegenet, for Crepidula convexa.
DOI: 10.5061/dryad.d3459/48
title: ITS

description: ITS sequences alignment
DOI: 10.5061/dryad.h617h/1
title: Transcriptome assembly for American lobster Homarus americanus

description: Transcriptome assembly for the American lobster, Homarus americanus. Assembly conducted in Trinity (version 8-14-2013) from 145 million single-end reads (Illumina HiSeq 2000) from mRNA extracted from nervous system, heart, and muscle tissues of Homarus americanus (2012). For additional information, please email Lara McGrath at lara.l.mcgrath [at] gmail.com
DOI: 10.5061/dryad.m1bm5/1
title: 2bRAD_Listeria_ package_Pauletto

description: It contains a copy of Structure and Phyloviz input files exactly as used for this paper. In additionit includes Stacks and Panseq output files and provides the files required for performing an integratedanalysis of additional L. monocytogenes isolates, as described in the supplemental figure S2.
DOI: 10.5061/dryad.n818s/1
title: SNP_flanking_sequence

description: Genotyped SNPs names with their flanking sequences
DOI: 10.5061/dryad.n818s/2
title: SNP_sample_matrix

description: Genotyped SNPs by sample matrix with information on sample ID, sampling area, latitude and longitude
DOI: 10.5061/dryad.sk7q8/10
title: Arachniodes ochropteroides3

description: SEM spore photo of Arachniodes ochropteroides. Voucher: Colombia, Sanin 5088 (NY). Scale bar = 10 micrometers.
DOI: 10.5061/dryad.sk7q8/11
title: Arachnoides ochropteroides4

description: SEM photo of Arachnoides ochropteroides. Voucher: Surinam, T. Hawkins 1906 (NY). Scale bar = 10 micrometers.
DOI: 10.5061/dryad.sk7q8/12
title: Arachniodes ochropteroides5

description: SEM spore photo of Arachnoides_ochropteroides. Voucher: Suriname, T. Hawkins 1906 (NY). Scale bar = 10 micrometers.
DOI: 10.5061/dryad.sk7q8/13
title: Cyclodium inerme2

description: SEM spore photo of Cyclodium inerme. Voucher: Guyana, Tillett et al. 44942 (NY). Scale bar = 10 micrometers.
DOI: 10.5061/dryad.sk7q8/7
title: Polybotrya aequatoriana2

description: SEM spore image of Polybotrya aequatoriana. Voucher: Bolivia, S. Beck 3060 (NY). Scale bar = 10 micrometers.
DOI: 10.5061/dryad.sk7q8/8
title: Polystichopsis chaerophylloides2

description: SEM spore image of Polystichopsis chaerophylloides. Voucher: Puerto Rico, Britton & Marble 1082 (NY). Scale bar = 10 micrometers.
DOI: 10.5061/dryad.sk7q8/9
title: Arachniodes ochropteroides2

description: SEM spore image of Arachniodes ochropteroides. Voucher: Colombia, Sanin 5088 (NY). Scale bar = 10 micrometers.
DOI: 10.5061/dryad.ss368/1
title: CC_microsatellites_genotypes

description: This file contains the microsatellites genotypes for the 503 specimens of Centroscymnus coelolepis (CC). The file is in genepop 3 digits format, which is widely used and can be easily converted in other types of files. It contains the genotypes for the 11 nuclear loci screened in the 8 localities studied: AZ-Azores; SAZ-South of Azores; UKIRE-United Kingdom and Ireland; MAU-Mauritania; MED-Western Mediterranean; PT-Portugal mainland; MAD-Madeira; AUS-Australia.
DOI: 10.5061/dryad.ss368/2
title: CC_CR_aligment_all

description: This file contains all the 347 mtDNA Control Region sequences used in the above studied. The file is in fasta format with all the aligned sequences with 497bp.Localities codes: AZ-Azores; MAR-Mid-Atlantic Ridge; SAZ-South of Azores; UK-United Kingdom; IRE-Ireland; MAU-Mauritania; MED-Western Mediterranean; PT-Portugal mainland; MAD-Madeira; AUS-Australia; SAF-South Africa.
DOI: 10.5061/dryad.ss368/3
title: CC_CR_aligment_haplotypes

description: This file contains all 27 haplotypes found in the studied areas for Centroscymnus coelolepis. The file is in fasta format. Haplotypes frequencies: H1-121; H2-144; H3-3; H4-1: H5-20; H6-1; H7-1;H8-1; H9-1; H10-7; H11-1; H12-1; H13-6; H14-4; H15-2; H16-1; H17-1; H18-8; H19-10; H20-4; H21-1; H22-1; H23-1; H24-1; H25-1; H26-2; H27-2.
DOI: 10.5061/dryad.ss368/4
title: CC_DB_biologic_data

description: This file in excel format contains the biological data used in the life-history analyses. Each line refers to one sampled specimen and the columns refer to: Cruise/Source- Code for the scientific cruise where the samples were collected or in other case provenience of the samples; Data provider- Person responsible/owner for the collection of the biological data; Genetic code- Sample genetic code, specimens without a genetic code were not screened with genetic markers; Area- Geographic region of the specimens collected: Atlantic, Mediterranean, Australia; Date: specimen capture date; Depth: specimen capture depth in meters; Total length: Specimen total length in centimeters; Total weight: specimen total weight in kilograms; Sex: Male or female; Mature/immature; Source: data from this study or retrieved from the literature (only for some Australian samples).
DOI: 10.5061/dryad.ss368/5
title: IMa_parameter_file

description: This file contains the command lines with all the parameters used to run IMa2 software.Input file was constructed from individual sequences and microsatellite genotypes for the subset of C. coelolepis samples. The subset consists of 53 samples drawn randomly from both Atlantic and Mediterranean groups (altogether 106 samples) and only samples with available microsatellite genotypes and mtDNA sequences were considered. The mutation rate was obtained from the DIYABC analysis.
DOI: 10.5061/dryad.tn6vn/1
title: LR0Rre.LSU401.Mock.fasta

description: Fasta file containing repetitiveness sequences of OTUs described using the primer pair LR0R(Rehner)-nuLSU401.
DOI: 10.5061/dryad.tn6vn/2
title: LR0R.LR3.Mock.fasta

description: Fasta file containing repetitiveness sequences of OTUs described using the primer pair LR0R-LR3.
DOI: 10.5061/dryad.tn6vn/3
title: ITS1F.ITS2.Mock.fasta

description: Fasta file containing repetitiveness sequences of OTUs described using the primer pair ITS1F-ITS2.
DOI: 10.5061/dryad.v089t/1
title: Garwood et al 2016, SI File 1.

description: A 3D model of I. brasieri - provided in the VAXML interchange format [39]. Can be open with the freely available software SPIERS (spiers-software.org).
DOI: 10.5061/dryad.v089t/2
title: Garwood et al 2016, SI File 2.

description: A video showing the 3D model of I. brasieri from both laboratory and synchrotron scans, plus slices from synchrotron scans demonstrating the lack of ventral opisthosomal spinnerets.
DOI: 10.5061/dryad.0bn55/1
title: Molecular Data Scores for G. hirsutum and G. barbadense

description: SSR fragment presence/absence matrix of molecular data originally collected from 1971 G. hirsutum and G. barbadense accessions obtained from the US National Cotton Germplasm Collection (NCGC) using 105 SSR markers.  Please see ReadMe file for further information.
DOI: 10.5061/dryad.16860/1
title: Experiment data DOI 10.1038_NPLANTS.2016.38

description: Experimental data used for the comparative growth analysis reported by Atkinson et al. (2016) DOI 10.1038_NPLANTS.2016.38. The phylogeny used for this analysis is included as supplementary data with the paper.
DOI: 10.5061/dryad.1cc85/1
title: Figure 3 left panel spore production

description: Figure 3 left panel: spore production under control and toxic conditions comparing seven non-farmers and seven farmers carrying 4 different types of non-food bacteria
DOI: 10.5061/dryad.1cc85/2
title: Figure 3 right panel spore viability

description: Figure 3 right panel: spore viability under control and toxic conditions comparing seven non-farmers and seven farmers carrying 4 different types of non-food bacteria
DOI: 10.5061/dryad.2d6h4/1
title: climate_ARPEGE

description: One of the A1B climate files that we used to simulate Kalkalpen National Park. The spatial location of the climate tables was defined in the file "environment".
DOI: 10.5061/dryad.42tr5/1
title: Daphnia metabolic rates

description: Metabolic rate data from laboratory experiments on Daphnia magna and Daphnia pulex
DOI: 10.5061/dryad.48012/1
title: All basic data

description: Includes data worksheet that detail: 1. the natural nest data and parasitism rates, 2. the laying fate of the cuckoo eggs documented, 3. the outcome of the artificial parasitism experiments, and 4. the fates of the cuckoo chicks
DOI: 10.5061/dryad.52504/1
title: Simple Sequence Repeat Data

description: This file contains the genotypes for 16 nuclear (nuSSR) and 5 chloroplast (cpSSR) simple sequence repeat loci and 812 individuals from six Californian scrub oak species (Quercus berberidifolia, Quercus durata, Quercus cornelius-mulleri, Quercus john-tuckeri, Quercus dumosa and Quercus pacifica) collected in 87 localities.
DOI: 10.5061/dryad.55nb0/1
title: liu ting ting-sequencing RawData
DOI: 10.5061/dryad.57gj4/19
title: ML_RAxML_bestTree_CES_dataset

description: Maximum likelihood tree obtained using the CES (Cremolobeae, Eudemeae, Schizopetaleae) dataset in RAxML 8.1.11 (Stamatakis, 2006)
DOI: 10.5061/dryad.57gj4/20
title: MCCT_CES_dataset

description: Maximum clade credibility tree obtained in BEASTv2.2 analyses using the CES (Cremolobeae, Eudemeae, Schizopetaleae) dataset.
DOI: 10.5061/dryad.57gj4/21
title: 1000_trees_CES_dataset

description: 1000 posterior trees from the BEASTv2.2 analyses using the CES (Cremolobeae, Eudemeae, Schizopetaleae) dataset.
DOI: 10.5061/dryad.57gj4/22
title: Materials&Methods

description: Materials & Methods for data analyses
DOI: 10.5061/dryad.6b1h8/1
title: Adult preference - Laying site

description: The file ‘Adult preference - Laying site’ contains the data of the laying site in the ‘oviposition experiment’. - The first column, entitled ‘ID_eggmasses’, gives the unique identifer of each egg-mass sampled in the experimental cages. - The second column, entitled ‘ID_cage’, gives the unique numerical identifier of each experimental cage. - The third column, entitled ‘Ostrinia_species’, refer to O. nubilalis (ECB) and O. scapulalis (ABB) species used in the experiment. - The fourth column, called ‘Setup’, corresponds to the three experimental set-ups tested in the oviposition experiment: choice (with maize and mugwort plants), maize_only (with maize plants only) and mugwort_only (with mugwort plants only). - the fifth column, entitled ‘Laying_site’, corresponds to the three laying sites where adult females laid eggs: mugwort, maize or the netting cage. - the sixth column, entitled ‘Sampling_Date’, corresponds to the sampling date of egg-masses. - the seventh column, called ‘Hatching’ is a binomial variable, with 0 corresponding to not hatched egg-masses and 1 to hatched egg-masses. - the eighth column, called ‘Hatching_Date’, corresponds to the date of egg-masses hatching (‘NA’ for the egg-masses that did not hatch).
DOI: 10.5061/dryad.6b1h8/2
title: Adult preference - resting sites

description: The file ‘Adult preference – resting sites’ contains the data obtained of the adult resting site in the ‘oviposition experiment’. - The first column, entitled ‘ID_adult’, gives the unique identifer for each adult (male and female) recovered in the experimental cages. - The second column, entitled ‘ID_cage’, gives the unique numerical identifier of each experimental cage. - The third column, entitled ‘Ostrinia_species’, refer to O. nubilalis (ECB) and O. scapulalis (ABB) species used in the experiment. - The fourth column, called ‘Setup’, corresponds to the three experimental set-ups tested in the oviposition experiment: choice (with maize and mugwort plants), maize_only (with maize plants only) and mugwort_only (with mugwort plants only). - the fifth column, entitled ‘Sex’, corresponds to sex of each individual: female or male. - the sixth column, entitled ‘Deposit_Date’, corresponds to the release date of the adult males and females in the cages. - the seventh column, entitled ‘Sampling_Date’, corresponds to the sampling date of adults in the cages. - the eighth column, entitled ‘Resting_site’, corresponds to the three resting sites where the adults were recovered : mugwort, maize, or the netting cage.
DOI: 10.5061/dryad.6cj8h/1
title: tufA database

description: TufA database for OTU annotation (sequences span the length of the metabarcode, i.e. the second half of tufA). Annotation consists of fields separated by '|' and include Genbank Accession, Category (Phototroph, Heterotroph), Domain, Phylum, Class, Order, Family and Genus.
DOI: 10.5061/dryad.6cj8h/2
title: Annotated OTUs (Phototrophs)

description: Annotated Core OTUs clustered with UPARSE and SWARM. Annotation are found in fields separated by '|' and include OTU number, Domain, Phylum, Class, Order, Family and Genus.
DOI: 10.5061/dryad.6gb90.1
title: Data from: Analysing biodiversity and conservation knowledge products to support regional environmental assessments
DOI: 10.5061/dryad.6gb90.2/15.2
title: EEZ_WVS_layer

description: Dataset combining Exclusive Economic Zones (EEZ; VLIZ 2014) and terrestrial country boundaries (World Vector Shoreline, 3rd edition, National Geospatial-Intelligence Agency) with their corresponding GEO and IPBES regions/subregions
DOI: 10.5061/dryad.7440s/1
title: ms code for admixture simulation

description: bash script to evaluate accuracy of ancestry estimation from allele frequency data.
DOI: 10.5061/dryad.7440s/2
title: Population trees for all sampled D. mel populations in Newick format

description: Trees are partitioned based on chromosome and inversion status.
DOI: 10.5061/dryad.7440s/4
title: Distance matrices for population trees

description: Nei's genetic distance matrices for populations used in this study. A separate file for each chromosome & inversion type is provided.
DOI: 10.5061/dryad.7440s/5
title: Allele frequencies for world-wide D. melanogaster populations

description: Allele frequency information for ~500,000 SNPs genome-wide from D. melanogaster populations sampled throughout the world. See Readme for detailed information
DOI: 10.5061/dryad.86fj0/1
title: 2_Body_Mass
DOI: 10.5061/dryad.86fj0/2
title: 1_No_Of_Survivors
DOI: 10.5061/dryad.86fj0/3
title: 3_No_Of_Competitors
DOI: 10.5061/dryad.8r351/1
title: TBset all data - article Rebollo et al - Plos One - 2015

description: all data generated for the 50 compounds released in the article
DOI: 10.5061/dryad.b5g97/1
title: MEE Data 2 Browne et al

description: Data for figures and tables in paper.
DOI: 10.5061/dryad.bg41s/1
title: R source, markdown and helper file

description: The zip file contains all the source code used in our study (Guerrero_etal_source.R), as well as the R markdown file (Guerrero_etal_SuppInfo.Rmd) used to produce the Supporting Information (the .pdf output is also included). Two more files necessary for running the scripts (isNIL_bool_*) are included. These have the information on the state of each gene in the S. lycopersicum genome with respect to the introgressed regions in each introgression line. An allele can be introgressed (coded "true") or background (coded "false")
DOI: 10.5061/dryad.bg41s/5
title: Gene expression in vegetative tissue

description: Processed data generated from RNA-Seq data from apices of 74 S. lycopersicum x S. pennellii introgression lines, and the two parents, from Chitwood et al. (2013; The Plant Cell, 25). Please see Readme.txt for further details on how to obtain the raw data.
DOI: 10.5061/dryad.c69n0/1
title: T.nylanderi contigs

description: de novo assembled contigs. Trimmed reads were assembled to contigs for each of the worker groups in CLC workbench. A meta-assembly on these contigs was conducted in MIRA.
DOI: 10.5061/dryad.c69n0/2
title: Tnyl_read-counts

description: normalized read counts as obtained from eXpress.
DOI: 10.5061/dryad.c69n0/3
title: Tnylanderi_morphological_measurements

description: Morphological measures as well as number of parasites for parasitized and unparasitized workers.
DOI: 10.5061/dryad.d670p/1
title: Supplementary Material
DOI: 10.5061/dryad.dv4rg/1
title: agnp

description: Experimental treatments, parent IDs, and observations made on embryos raised individually in 24-well plates.
DOI: 10.5061/dryad.fv8jv/1
title: An .zip archive of article raw data

description: Data are organised in self-explanatory nested folders. Vibrometry and neurophysiology data are in separate folders.
DOI: 10.5061/dryad.gs228/1
title: Copy of GenotypeData_DRYAD_Adams.etal.2016

description: Individual genotype data for 14 microsatellite loci.
DOI: 10.5061/dryad.h617h/2
title: Read Counts for Homarus americanus transcriptome samples

description: Read counts from read mapping conducted in Bowtie (version 0.12.7) against de novo assembled Homarus americanus transcriptome. For identification of samples: U= untreated, P=proctolin-treated, M=muscle, B= brain, H= heart, A= abdominal ganglia, and number indicates individual lobster. For more information, email Lara McGrath at lara.l.mcgrath [at] gmail.com
DOI: 10.5061/dryad.h617h/3
title: Annotations for Homarus americanus transcriptome

description: Protein annotations from tBlast of de novo assembled Homarus americanus transcriptome against NCBI, and UniprotKB Swiss-Prot and TrEMBL databases. For more information, email Lara McGrath at lara.l.mcgrath [at] gmail.com
DOI: 10.23728/b2share.1b9cb216fab543aa96fc7c49d770f61e
title: Air quality data from the LIFE+RESPIRA project in Pamplona, Spain: PM1, PM2.5 and PM10 (dataset)

description: csv file including air quality data from the LIFE+RESPIRA project (http://www.liferespira.eu/) in Pamplona, Spain, with measures of PM1, PM2.5 and PM10 particles. Full condensation of all available data for the specified conditions.
DOI: 10.17026/dans-xht-ry34
title: Victimization in Psychiatric Patients

description: The project studied victimization rates and risk factors among persons with severe mental illness (SMI). A nationwide multi-site cross-sectional survey among 956 SMI patients was conducted. At each site (i.e. GGZ InGeest, BavoEuropoort, Parnassia, GGZ Dijk en Duin, Mondriaan, Altrecht) a random sample was selected. A structured interview was used to assess experiences and consequences of (criminal) victimisation, discrimination and self stigmatization, perpetration of violence, childhood trauma, symptom severity and co-morbid psychopathology (e.g. anger, PTSD).