cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.23td2/8
title: CEFAS G6A pelagic cormorant files (Part 1b)

description: Text files downloaded from the accelerometers attached to pelagic cormorants (first of five folders). Each folder refers to one individual bird (cross-referenced with doubly-labelled water data). The file name within each folder refers to the CSV file created by the CEFAS program and has the logger ID and the date the file was created (downloaded). The data file provides date/time, depth (pressure in dbars which is generally equivalent to depth in m) and acceleration in three dimensions at 25 Hz (in g), after a preamble generated by the logger that includes the daylog. Note that data is partitioned into two sections. The first section has data every 1 s, the second section has data at 25 Hz in the "fast log"; for five files, the fine-scale (25 Hz) data was only recorded when the bird was diving. The CEFAS G6A manual is here: https://www.cefastechnology.co.uk/downloads/file.aspx?file=33.
DOI: 10.5061/dryad.23td2/9
title: CEFAS G6A pelagic cormorant files (Part 5a)

description: Text files downloaded from the accelerometers attached to pelagic cormorants (first of five folders). Each folder refers to one individual bird (cross-referenced with doubly-labelled water data). The file name within each folder refers to the CSV file created by the CEFAS program and has the logger ID and the date the file was created (downloaded). The data file provides date/time, depth (pressure in dbars which is generally equivalent to depth in m) and acceleration in three dimensions at 25 Hz (in g), after a preamble generated by the logger that includes the daylog. Note that data is partitioned into two sections. The first section has data every 1 s, the second section has data at 25 Hz in the "fast log"; for five files, the fine-scale (25 Hz) data was only recorded when the bird was diving. The CEFAS G6A manual is here: https://www.cefastechnology.co.uk/downloads/file.aspx?file=33.
DOI: 10.5061/dryad.277g0/3
title: EcJME_R1-part1

description: This is part 1 of the forward raw reads from Illumina sequencing.  Please download all three parts and recombine them using the following command in Terminal or Command Prompt:    cat xaa xab xac &gt; EcJME_R1.fastqsanger
DOI: 10.5061/dryad.27d0g/1
title: alns

description: The dataset was constructed for near universal single copy genes from all 36 cyanobacterial genomes found in version 5 the HOGENOM database. For each family sequences were aligned using MUSCLE with default parameters. The multiple alignment was subsequently cleaned using GBLOCKS as described in the Appendix.
DOI: 10.5061/dryad.41131ns8/2
title: analysis script

description: R script for data analysis using CfE2_data.csv
DOI: 10.5061/dryad.565r1/1
title: analyses

description: R codes and data files.
DOI: 10.5061/dryad.5fc56/1
title: Phenotypic traits

description: This file contains data of phenotypic traits and MHC genotype of ring-necked pheasant males included in the study
DOI: 10.5061/dryad.6vk6f/6
title: Genotype data

description: This file contains the genotype data for all trees examined in this study. The data have been formated for input into Structure for admixture analysis.
DOI: 10.5061/dryad.7c7q0/1
title: Dikow&Smith_trees

description: Phylogenetic trees presented in the paper
DOI: 10.5061/dryad.84m54/3
title: Volumetric data from a micro-CT scan of Eunice sp., PTA-stained
DOI: 10.5061/dryad.8906j/1
title: Head et al_Paternal Effects Data
DOI: 10.5061/dryad.8d8h7/1
title: tracking_data

description: This zip files contains data from tracking experiments in the ant Camponotus fellah. There are 268 files (described in the READMD.txt) containing data on the social networks, behavior, spatial structure, expected and observed interaction frequencies, and information spread from all ants in six colonies of Camponotus fellah.
DOI: 10.5061/dryad.93p4q/6
title: AlyrataNorSpMaQTL
DOI: 10.5061/dryad.970b3/1
title: dataset for all 114 strains

description: The whole dataset is available for download(114 strains). Note that the observed 106 unique haplotypes (i.e.  the clone-corrected dataset used for all the analyses; see the Methods section) are labeled with a "0". Excluded clones are labeled with a "1".
DOI: 10.5061/dryad.9ck52/1
title: Proportion mating behaviour

description: Data collected in the field during the austral spring in South Africa. Male flies were tested on floral arrays of two sexually deceptive floral morphotypes of the daisy, Gorteria diffusa. The proportion of visits to inflorescences by male flies that including mating behaviour is shown.
DOI: 10.5061/dryad.9ck52/2
title: Visitation details per male fly

description: Data collected in the field. Same experiment as Proportion mating behaviour file. Details of visitation, such as number inflorescences visited and the time spent on various behaviours by experimental male flies.
DOI: 10.5061/dryad.b4d75m52/1
title: Sequences after initial processing in QIIME (seqs.fna, library 1)

description: Raw sequence data from the Roche 454 GS FLX sequencer, region 1 (split_library_output_1).  These data are the output of the command:  split_libraries.py -m 454_Map.txt -f 1.TCA.454Reads.fna -q 1.TCA.454Reads.qual -o split_library_output_1/ -l 100 -L 700 -H 9 -M 2 -b 10
DOI: 10.5061/dryad.bq7q0/5
title: DRYAD_5_MartinezAquino_et_al_PLOS1_lagrange_Margo_loc_3.lagrange
DOI: 10.5061/dryad.bq7q0/6
title: DRYAD_6_MartinezAquino_et_al_PLOS1_lagrange_Margo_host.lagrange
DOI: 10.5061/dryad.bq7q0/7
title: DRYAD_7_MartinezAquino_et_al_PLOS1_lagrange_Margo_host2.lagrange
DOI: 10.5061/dryad.c598v/1
title: Warmuth et al. PNAS 2012
DOI: 10.5061/dryad.cn946/1
title: Hawaii Wet Forest Plants

description: To determine which plant species occur within each region, we drew from a database of angiosperm distributions (Price, 2004), with additional data for ferns (Palmer, 2003) to represent all vascular plants. These data come from numerous sources, including herbarium specimens, species lists, historical accounts, and field records from numerous biologists. Where possible, specific localties place a species solidly within a given biogeographic region or moisture zone according to maps developed by Price et al. (2007); in some cases more general records were necessary, such as presence noted in a checklist from a given area or general herbarium label information ("Kohala Mountains"). We followed Price (2004) and considered a species to inhabit a wet forest habitat region if it was recorded from any of the volcanoes that make up the region and is known to occur in wet forest somewhere within its range.
DOI: 10.5061/dryad.cn946/2
title: D. sproati collection information

description: Detailed collection information for all D. sproati individuals sequenced in this study.
DOI: 10.5061/dryad.d2c619hd/1
title: Recruitment data for experimental populations

description: Recruitment data for experimental populations of Chamaecrista fasciculata established in 2009 at 5 sites: interior (CERA), west edge (RNHA), north edge (SCRS), beyond west (CPBS) and beyond north (ACNW). At each site, I established 5 blocks with either 20 (interior and edge site) or 10 (beyond edge) experimental populations per block. Each experimental population consisted of 4 seeds from the same population. The experimental populations were planted in spring 2009 and survival and reproduction recorded. The plants, including seed pods, were left in the field. In June 2010, I returned to each site and recorded the number of seedlings found within 60cm of the center of each experimental population. The attached ReadMe file is the R script (R Project for Statistical Computing) that more fully explains the data and can be used to recreate the analysis included in the paper.
DOI: 10.5061/dryad.d2c619hd/2
title: Fitness data for natural populations (2007-09)

description: Data from neighbor removal experiment performed from 2007-2009 in six natural populations of Chamaecrista fasciculata. The attached ReadMe file is the R script (R Project for Statistical Computing) for the analysis with information on column headers and provides the complete analysis.
DOI: 10.5061/dryad.d2c619hd/3
title: Weather data for natural populations

description: Weather data needed for analysis of the natural populations. Data on total precipitation and average temperature during the growing season (1 May to 30 September) for each year from the weather station nearest to each site; either a weather station on site (IA and KS) or the nearest airport weather station (data downloaded from wunderground.com)
DOI: 10.5061/dryad.d2c619hd/4
title: Fitness data for experimental populations

description: Seeds were planted into 5 sites at different geographic range locations: the range interior (CERA), western edge (RNHA), northern edge (SCRS), beyond western edge (CPBS), beyond northern edge (ACNW). Because of poor germination, likely due to drought conditions in spring 2009, the first 5 blocks of the SCRS site were replanted in June and thus are included as a sixth site, SCRSb. Five plant seed source populations were used: Missouri (TYS), Kansas (KZA), Illinois (GRE), Iowa (CRA) and Minnesota (GCD).  Eighty seeds at the interior and edge sites, and forty seeds at they beyond edge sites were planted into 10 blocks at each site.  Within each block, 4 seeds from the same population were planted into experimental patches, with seeds located 20cm from each other in each patch, and a meter between patches.  The patches were randomly assigned to either natural competition (competition) or reduced competition by neighbor removal (removal). Early-season survival, reproductive stage, plant height and leaf number at the middle of the season, and reproductive stage, height, and seed pod number were recorded.  In early summer 2010, I returned to each site and recorded the number of seedlings recruiting into the 1 meter area surrounding each experimental patch (separate data file = CfE3_recruitment.csv). | DATA | id: plant identifier | site: site (see above) | block: block, 1-10 at each site | patch: patch within block. 1-20 at interior and edge sites, 1-10 at beyond edge sites | p.pos: position of seed within patch (4 positions, see Fig 1 in paper). | pop: seed source population (see above) | fam: seed source family within population. | esurv: early-season survival (0 - dead/not present, 1 - alive) | july.stage: life-history stage in July:  0 - dead/not present, 1 - vegetative, 2 - flowering, 3 - flower and pods, 4 - pods, 5 - completely senesced | july.height: height (cm) in July | july.leaf, leaf number in July | herbivory.category: percent category of leaf herbivory in July.  1: 0%, 2: 1-25%, 3: 26-75%, 4: 76-100% | For plants with &lt;20 leaves, this was determined either by counting the number of leaves with herbivory, dividing by total leaves and placing in category. For plants with &gt;20 leaves, the % category was visually estimated. | disease.category: percent category for disease in July. values same as herbivory | fall.stage: life-history stage at time of fall measurements, same as july.stage | branch.number: branch number at end of season | seed.pods: number of pods (counting pedicels where pods had broken off) | browsed: whether a plant was browsed. 0-not browsed, 1-plant browsed at some point in season (integrates across observation of browsing in July or at end-of-season) | The attached ReadMe file is the R script (R Project for Statistical Computing) that can be used to recreate the analysis performed in the paper.
DOI: 10.5061/dryad.d41v4/1
title: Periodontitis diseased sample, patient 1, 16S rRNA sequences

description: Bacterial 16S rRNA sequences from patient 1 diseased periodontal sites. Sequences are read 1 and read 2 from MiSeq sequencing joined with the script fastq-join.
DOI: 10.5061/dryad.d41v4/2
title: Periodontitis diseased sample, patient 2, 16S rRNA sequences

description: Bacterial 16S rRNA sequences from patient 2 diseased periodontal sites. Sequences are read 1 and read 2 from MiSeq sequencing joined with the script fastq-join.
DOI: 10.5061/dryad.d41v4/3
title: Periodontitis diseased sample, patient 3, 16S rRNA sequences

description: Bacterial 16S rRNA sequences from patient 3 diseased periodontal sites. Sequences are read 1 and read 2 from MiSeq sequencing joined with the script fastq-join.
DOI: 10.5061/dryad.d41v4/4
title: Periodontitis diseased sample, patient 4, 16S rRNA sequences

description: Bacterial 16S rRNA sequences from patient 4 diseased periodontal sites. Sequences are read 1 and read 2 from MiSeq sequencing joined with the script fastq-join.
DOI: 10.5061/dryad.d41v4/5
title: Periodontitis diseased sample, patient 5, 16S rRNA sequences

description: Bacterial 16S rRNA sequences from patient 5 diseased periodontal sites. Sequences are read 1 and read 2 from MiSeq sequencing joined with the script fastq-join.
DOI: 10.5061/dryad.d7639/8
title: Supplemental Figure 6

description: Partial output summarizing the results of 100 search replicates for the best tree. Among the results of the post-processing displayed here are summary statistics that characterize the distribution of log-likelihood scores, symmetric tree distances (raw and normalized), and estimates of the number of search replicates required to recover the best tree topology at three probability levels.
DOI: 10.5061/dryad.dd65d/1
title: Mouse activity data WT_2684
DOI: 10.5061/dryad.dd65d/23
title: Mouse activity data P1C1_2069
DOI: 10.5061/dryad.dh7kh/1
title: 44_taxon_dataset_large_chromosome

description: Alignment of large chromosome LCB for 44-taxon dataset
DOI: 10.5061/dryad.ds3v4/1
title: isotria_data

description: The file provides fragment lengths generated by PCR at three microsatellite loci. For each locus, the first column gives one allele, and the "het" column gives the second allele if the plant was a heterozygote. Populations are numbered north to south.
DOI: 10.5061/dryad.gd93s/1
title: Silene nutans and otites GS

description: Alignment of chloroplastic GS sequence
DOI: 10.5061/dryad.hj7h2/4
title: Ceratosolen appendiculatus temp 26- 34

description: Survival data for Ceratosolen appendiculatus, pollinator of F. variegata for temperatures from 26 to 34 degree celsius at 85% relative humidity.
DOI: 10.5061/dryad.k3311/1
title: Individual data

description: This .csv file contains a list of all known individuals (“Band”).  For each individual, other variables are – “Cohort”: breeding season (cohort) in which individuals were hatched. “Surv1yr”: whether or not they survived their first winter.  “F”: individual inbreeding coefficient.  “H”: standardised multilocus heterozygosity, calculated using R package ‘Rhh’ (“NA” indicates values that cannot be calculated due to insufficient genotyping data).  “Rbm” and “Rwm”: relatedness coefficient to “blue-metal” and “white-metal”.  Genotypes for each of the seven TLR loci (missing data are blanks) are also provided.
DOI: 10.5061/dryad.mk471/23
title: runSAPSonPermutedData

description: runSAPSonPermutedData.R – This R script generates the P_pure, P_random, and P_enrichment on random gene sets. This "biologically null" set of SAPS scores is used to compute the SAPS_q_values on the msigdb gene sets.
DOI: 10.5061/dryad.mk471/24
title: saps

description: saps.R – This R script provides R commands for loading data, applying the SAPS method, and generating the SAPS p values. The script is interactive, and the user must specify the working directory, and if the analysis is on the ovarian or breast data.
DOI: 10.5061/dryad.mk471/26
title: computeSAPS.Permute.PValue.R

description: computeSAPS.Permute.PValue.R – This script generates permutation-based p and q values for the SAPSscores obtained in breast and ovarian cancer.
DOI: 10.5061/dryad.n872j/1
title: Lacey et al. - cum spike production csv2012
DOI: 10.5061/dryad.nh3d2/9
title: Test_lizard_1

description: .jpg image which can be used for testing the matlab script.
DOI: 10.5061/dryad.pv24v/1
title: Category_SNPs
DOI: 10.5061/dryad.pv24v/2
title: FET
DOI: 10.5061/dryad.r13f5/2
title: Maturation data for D. pulex

description: Age (a1, a2) and size (s1, s2) intervals of 5 Daphnia pulex clones very instar until primiparity (eggs). Columns: preova, mature and eggs refer to achieving IM-1, IM-2 and IM-3 respectively (see manuscript). Column: trt refers to concentration of food (not required for analysis).
DOI: 10.5061/dryad.s0n20/1
title: Phenotype and Fitness data

description: This file provides the raw phenotype and fitness (survivorship and fecundity) data for each of the transplanted Nearly Isogenic Lines as described in Mojica et al 2012.
DOI: 10.5061/dryad.sc193/1
title: High resolution Fig. 2
DOI: 10.5061/dryad.sc193/2
title: High resolution Fig. 3
DOI: 10.5061/dryad.sc193/3
title: High resolution Fig. 4
DOI: 10.5061/dryad.sc193/4
title: High resolution Fig. 5
DOI: 10.5061/dryad.sc193/5
title: High resolution Fig. 6
DOI: 10.5061/dryad.sc193/6
title: High resolution Fig. 7
DOI: 10.5061/dryad.sc193/7
title: High resolution Fig. 8
DOI: 10.5061/dryad.sc193/8
title: High resolution Fig. 9
DOI: 10.5061/dryad.sc6k5/3
title: Bellamy et al. File 3
DOI: 10.5061/dryad.th251/1
title: Male_Trial_Data

description: Male behavioural and phenotypic data recorded from interspecific mate choice tests in Control and BPA treatments.
DOI: 10.5061/dryad.14214/2
title: Cymbidium_CP genomes
DOI: 10.5061/dryad.14214/3
title: Cymbidium_Coding regions
DOI: 10.5061/dryad.18v85/1
title: Hoedjes et al 2014_Heredity_MemoryIntrogression

description: Data from all memory retention test as described in the manuscript and results from the genotyping microarray.
DOI: 10.5061/dryad.1pg3n/2
title: Fournier-Leveletal_DataSEM

description: Input file and R scripts used to perform the SEM analysis.
DOI: 10.5061/dryad.20r9k/3
title: Ailuropoda_melanoleuca_genomicORs

description: ORs found in the giant panda genome
DOI: 10.5061/dryad.364j2/3
title: Proctoporus_ND4

description: Sequence alignment for the ND4 rRNA mitochondrial gene region. Please refer to Table 1 of the associated manuscript for specimen information.
DOI: 10.5061/dryad.3sd60/1
title: Replacement networks

description: Adjacency matrices of 10 plant-plant replacement networks.
DOI: 10.5061/dryad.53356/1
title: datatables

description: Excel file with three tables; the first table lists details for all matings evaluated, including all mating partner IDs and associated information from the monitoring surveys. The second table is a subset of the first table restricted to all matings among F1 animals that were born in the enclosure. The third table is a subset of the second table, restricted to all first matings only.
DOI: 10.5061/dryad.5c6v7/1
title: Key for Figure 2

description: Accession numbers for all sequences used in Figure 2 and the short name used in sequence files for PAML and alignments (Appendix S1).
DOI: 10.5061/dryad.5c6v7/3
title: Supplementary Fig1

description: Teleost Na+, K+ ATPase α1 (ATP1A1) gene tree reconstructed using Bayesian inference (BI) with MrBayes version 3.2.1 (Ronquist et al. 2012) and the GTR+I+Γ model of nucleotide evolution.
DOI: 10.5061/dryad.6df73/1
title: assay_control_lines
DOI: 10.5061/dryad.6df73/2
title: assay_selection_lines_gradient_trial
DOI: 10.5061/dryad.6df73/3
title: historical_assay_sexual_lines
DOI: 10.5061/dryad.6df73/4
title: reciprocal_transplants
DOI: 10.5061/dryad.73g3d/2
title: MLTR input for the savannah woodland

description: This file contains the genotype for 17 mothers and its progeny in closed savannah woodland, ready to use in Ritland's (2002) MLTR program.
DOI: 10.5061/dryad.74j5g/2
title: Online Appendix 2

description: COI dataset
DOI: 10.5061/dryad.7c7q0/5
title: lcb 175

description: fasta files for genes in LCB 175
DOI: 10.5061/dryad.7m6kg/7
title: Figs. 2b & 9e: ROM 60079 – Nectocaris pteryx from the Burgess Shale
DOI: 10.5061/dryad.8f74d/1
title: Input data for pGLS

description: Coding for both habitat and breeding biology used in the phylogenetic generalized squares (pGLS) analysis using the R package "ape". The file contains all the different input files used in this study saved as different tabs inside the excel file. see README file and supplementary materials of publication for more details.
DOI: 10.5061/dryad.8ps58rp2/1
title: TCM_001

description: Animal and Plant Sequences from Traditional Chinese Medicine Sample No. 1
DOI: 10.5061/dryad.8ps58rp2/2
title: TCM_002

description: Plant Sequences from Traditional Chinese Medicine Sample No. 2
DOI: 10.5061/dryad.9cp1f/2
title: R script

description: R script used for R/qtl mapping of "Dissecting the genetic architecture of F1 hybrid sterility in PWD/Ph andC57BL/6J backcross" dataset
DOI: 10.5061/dryad.b70pn/3
title: Representative ITS1 sequences for OTUs

description: Includes the extracted ITS1 sequences for each operational taxonomic unit resulting from OTU picking as described in the text.
DOI: 10.5061/dryad.bq7q0/8
title: DRYAD_8_MartinezAquino_et_al_PLOS1_TreeMap.tgl
DOI: 10.5061/dryad.d15d4/1
title: Anopheles melas genotype data for 15 microsatellite loci

description: The datafile is in GENEPOP format, and comprises genotype scores for 15 Anopheles melas-specific microsatellite loci. A total of 617 wild-caught specimens from 11 populations are included in the datafile. Locus names are listed at the beginning of the file under the title line, and correspond with the lines of data, left to right. Missing genotypes are coded as "000". Allele scores for each locus are concatenated into six digits, with the first three letters representing allele "A", and the second three letters representing allele "B".
DOI: 10.5061/dryad.d41v4/10
title: Periodontitis diseased sample, patient 10, 16S rRNA sequences

description: Bacterial 16S rRNA sequences from patient 10 diseased periodontal sites. Sequences are read 1 and read 2 from MiSeq sequencing joined with the script fastq-join.
DOI: 10.5061/dryad.d41v4/11
title: Paired healthy sample, patient 1, 16S rRNA sequences

description: Bacterial 16S rRNA sequences from patient 1 healthy periodontal sites. Sequences are read 1 and read 2 from MiSeq sequencing joined with the script fastq-join.
DOI: 10.5061/dryad.d41v4/12
title: Paired healthy sample, patient 2, 16S rRNA sequences

description: Bacterial 16S rRNA sequences from patient 2 healthy periodontal sites. Sequences are read 1 and read 2 from MiSeq sequencing joined with the script fastq-join.
DOI: 10.5061/dryad.d41v4/13
title: Paired healthy sample, patient 3, 16S rRNA sequences

description: Bacterial 16S rRNA sequences from patient 3 healthy periodontal sites. Sequences are read 1 and read 2 from MiSeq sequencing joined with the script fastq-join.
DOI: 10.5061/dryad.d41v4/14
title: Paired healthy sample, patient 4, 16S rRNA sequences

description: Bacterial 16S rRNA sequences from patient 4 healthy periodontal sites. Sequences are read 1 and read 2 from MiSeq sequencing joined with the script fastq-join.
DOI: 10.5061/dryad.d41v4/6
title: Periodontitis diseased sample, patient 6, 16S rRNA sequences

description: Bacterial 16S rRNA sequences from patient 6 diseased periodontal sites. Sequences are read 1 and read 2 from MiSeq sequencing joined with the script fastq-join.
DOI: 10.5061/dryad.d41v4/7
title: Periodontitis diseased sample, patient 7, 16S rRNA sequences

description: Bacterial 16S rRNA sequences from patient 7 diseased periodontal sites. Sequences are read 1 and read 2 from MiSeq sequencing joined with the script fastq-join.
DOI: 10.5061/dryad.d41v4/8
title: Periodontitis diseased sample, patient 8, 16S rRNA sequences

description: Bacterial 16S rRNA sequences from patient 8 diseased periodontal sites. Sequences are read 1 and read 2 from MiSeq sequencing joined with the script fastq-join.
DOI: 10.5061/dryad.d41v4/9
title: Periodontitis diseased sample, patient 9, 16S rRNA sequences

description: Bacterial 16S rRNA sequences from patient 9 diseased periodontal sites. Sequences are read 1 and read 2 from MiSeq sequencing joined with the script fastq-join.
DOI: 10.5061/dryad.g4n13/7
title: Site03-01