cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c8n18/1
title: ITS_taxonomy

description: Six oak bark pieces (~1g) from four oak trees (three pieces from oak 1 and one piece from each of the other trees) in Northern Germany were collected. In addition an infusion (20g oak bark in a sterile tea bag in 300 mL water for 24 hours) for each tree was prepared. DNA was extracted from all samples using the Soil DNA Kit from Omega Bio-Tek. The resulting DNA was sent to LGC Genomics (GmbH, Berlin, Germany) for amplification of the fungal ITS (ITS1, 5.8S and ITS2) sequences using ITS1f (CTTGGTCATTTAGAGGAAGTAA) and ITS4 (TCCTCCGCTTATTGATATGC) primers using the 454 GS FLX+ Titanium Sequencer (Roche). 
ITS sequences were processed with mothur and subsampled to 4000 sequences per sample. For taxonomic classification the mothur implementation of naive Bayesian classification was used with a threshold bootstrap value of 70% for each taxonomic level. The used fungal database was the “dynamic” mothur release from 08.12.2013 of the UNITE database.
DOI: 10.5061/dryad.c8n18/2
title: ITS_OTU

description: Six oak bark pieces (~1g) from four oak trees (three pieces from oak 1 and one piece from each of the other trees) in Northern Germany were collected. In addition an infusion (20g oak bark in a sterile tea bag in 300 mL water for 24 hours) for each tree was prepared. DNA was extracted from all samples using the Soil DNA Kit from Omega Bio-Tek. The resulting DNA was sent to LGC Genomics (GmbH, Berlin, Germany) for amplification of the fungal ITS (ITS1, 5.8S and ITS2) sequences using ITS1f (CTTGGTCATTTAGAGGAAGTAA) and ITS4 (TCCTCCGCTTATTGATATGC) primers using the 454 GS FLX+ Titanium Sequencer (Roche). We used the “pairwise.seqs” command in mothur for the OTU-based analysis with ignoring the penalization of the sequence ends. The shared file shows the distribution of OTUs in the ten groups at 97% and 95% identity level.
DOI: 10.5061/dryad.dj17c/1
title: Tsuda_Betulamaximowicziana_genotypes

description: SSR genotypes file of 1416 individuals (12loci) and 441 individuals (23loci). Please see readme file for detail information.
DOI: 10.5061/dryad.g75nq/2
title: tag-based RNAseq counts of larval families

description: The samples names identify the cross: first letter- dam, second letted - sire, number - culture replicate. The parents (from A to D) are the same as used for the heat stress experiment (see another tag-seq dataset). The parents A and B are from Orpheus Island (Central GBR), parents C and D are from Princess Charlotte Bay (Northern GBR). The annotations for the genes ("isogroups") are in the transcriptome bundle included with this submission.
DOI: 10.5061/dryad.g75nq/3
title: tag-based RNAseq counts for heat stress experiment in adult corals

description: Response of adult corals to heat stress. Letter identifies a coral colony, numbers 1 to 3 are controls fragments (ambient temperature, 28C), numbers 4 to 6 are heat-stressed fragments (3 days at 31.5C). Colonies A and B are from Orpheus Island (Central GBR), colonies C and D are from Princess Charlotte Bay (Northern GBR). These corals are the same as used as parents to produce larval cohorts (see another tag-seq dataset). The annotations for the genes ("isogroups") are in the transcriptome bundle included with this submission.
DOI: 10.5061/dryad.g75nq/4
title: Survival of coral larvae at 35.5C

description: The table contains counts of larvae surviving after a certain time at 35.5C, out of the initial number of 20 (the only exception is family AB replicate 2, which started with 40 larvae). The parental colonies (A through D) are the same as used for heat stress experiment (see tag-seq data set for heat stress in adults). Colonies A and B are from the Orpheus Island, colonies C and D are from Princess Charlotte Bay. Time is in hours.
DOI: 10.5061/dryad.g75nq/5
title: A.millepora transcriptome sequences and annotations

description: This transcriptome was published previously by Moya et al Mol. Ecol. 21, 2440–2454 (2012) and re-annotated for Dixon et al Science 2015 publication.
DOI: 10.5061/dryad.j18qs/1
title: Supplementary_Table_1

description: Taxa of the Tulip Beds with their respective abundance, ecological modes (tieirng level, motility and feeding mode), and phyla (or other higher taxonomic grouping)
DOI: 10.5061/dryad.j18qs/2
title: Supplementary_Table_2

description: Taxa of the Walcott Quarry with their respective abundance, ecological modes (tieirng level, motility and feeding mode), and phyla (or other higher taxonomic grouping). This dataset is adapted from Caron and Jackson (2008); see the original paper for details on data collection.
DOI: 10.5061/dryad.j18qs/3
title: Supplementary_Table_3

description: Taxa of Walcott Quarry with their respective abundances for each of 26 bedding assemblages. This data has been modified from Caron and Jackson (2008); see the original paper for details on data collection.
DOI: 10.5061/dryad.jm78g/1
title: Data files for Heyduk et al 2015 "Estimating species relationships within Sabal (Arecaceae) through multilocus analyses of sequence capture data."

description: README for data related to Heyduk et al 2015 "Estimating species relationships within Sabal (Arecaceae) through multilocus analyses of sequence capture data." A note about gene alignment/tree naming: File names refer to the geneID from which baits were designed from. For example, "Elaeis_1007" indicates that this gene matches the exons "Elaeis_1007_*" which we submitted to MySelect for bait design. Some genes are named "Sabal" or "Nypa" because sequences from those species were submitted for the initial bait design. Files in this repository: 1) alignments.zip - folder containing alignments for all 133 nuclear genes used in phylogenetic analyses. Naming as described above. 2) bootstraps.zip - folder containing bootstrap replicates, 500 per each of 133 genes, output from RAxML. Gene names are the same as described above. 3) genetrees.zip - bipartition tree for the 133 nuclear gene trees, output from RAxML. Naming as described above. 4) concat.align.fasta - supermatrix alignment from concatenation of the 133 nuclear genes for all 17 species. 5) plastid.align.fasta - alignment of 89kb of chloroplast sequence for all 17 species. 6) mpest.tre, star.tre, concat.tre, and plastid.tre - newick tree files for each respective phylogenetic analysis (MP-EST, STAR, supermatrix, and plastome). MP-EST and STAR trees are the output of the respective programs, whereas the supermatrix tree and the plastid tree are output of RAxML. 7) binaligns.zip - folder containing alignments (nexus formatted for BEAST) of each of 27 bins. 8) starBEAST.xml - xml run file for *BEAST
DOI: 10.5061/dryad.n3bb2/1
title: orpg_snpdev_glm_analysis

description: File contains an R script and set of data in a data folder. The R script contains descriptions of the data files, and reproduces the GLM analysis described in the paper
DOI: 10.5061/dryad.n3bb2/2
title: orpg_sevenLibrary_velvetAssembly

description: AFG formatted output of de novo Velvet assembly of seven orange roughy Illumina libraries. Methods described in the paper.
DOI: 10.5061/dryad.n3bb2/3
title: orpg_scaffolds_velvetAssembly

description: Contigs produced by de novo velvet assembly of seven orange roughy Illumina libraries. Contigs are scaffolded, separated by 20 or more Ns. SNP id matches the ContigID-_, where scaffold number increases from 0, and identified the fragment of the contig obtained after splitting it at the Ns. Assembly methods described in the paper.
DOI: 10.5061/dryad.n3bb2/4
title: perl_scripts

description: PERL scripts provided in zip file. Instructions for use, and README file included in package.
DOI: 10.5061/dryad.n3bb2/5
title: 454Contigs
DOI: 10.5061/dryad.n48q0/1
title: Experimental Matings

description: Column headers as follows: Female=Female genotype; Male= Male genotype; Male No= Individual male's ID; Time After Split (hrs)= Time (hrs) between mating and dissection; Plug (Y/N)= Indicating if the plug was still present at time of dissection; Mating (Y/N)= Indicates if a plug was present after experimental cross; Weight of Plug (g)= The absolute mass of the plug (NA indicates non successful mating); Weight of Female (g): Weight of female at dissection; Female DOB: Female's date of birth; Dissection Date= Date female was euthanized
DOI: 10.5061/dryad.n48q0/2
title: Male morphological data

description: Column headers are as follows:Male= Male genotype; Male No= Individual male's ID; Date of Birth= Male's date of birth; Body Weight (g)= Body weight at dissection; Seminal Vesicle Weight (g)=Absolute weight of the left seminal vesicle; Right Testis Weight (g)= Absolute weight of the right testis; Left Testis Weight (g)= Absolute weight of the left testis
DOI: 10.5061/dryad.n48q0/3
title: Protein quantification across genotypes

description: Column headers are as follows: Male=Male genotype; SVS1:SVS5=abundance of each protein band/sum of the abundances of the four protein bands; Total=Absolute value of abundance of 4protein bands
DOI: 10.5061/dryad.sn034/1
title: Compare_Stacks_vs_AftrRAD

description: Perl script to compare AftrRAD loci to Stacks loci.  Requires a series of output files that are listed in a comment at the beginning of the script.  Note that this script must be run prior to running Compare_PyRAD_vs_AftrRAD.pl.  Also note that both of these scripts are starting points for analysis, and that any loci identified as not shared among programs should be double-checked manually.  For questions regarding these scripts, visit the AftrRAD Google group.
DOI: 10.5061/dryad.sn034/2
title: Compare_PyRAD_vs_AftrRAD

description: Perl script to compare AftrRAD loci to PyRAD loci.  Note that the Compare_Stacks_vs_AftrRAD.pl script must be run prior to running Compare_PyRAD_vs_AftrRAD.pl.  Also note that both of these scripts are starting points for analysis, and that any loci identified as not shared among programs should be double-checked manually.
DOI: 10.5061/dryad.sn034/3
title: Mallard Data

description: Fastq file containing data from mallard (Anas platyrhynchos) used in comparisons of AftrRAD, Stacks, and PyRAD.
DOI: 10.5061/dryad.sn034/4
title: RAD5_data.txt.tar

description: Fastq file containing data from eastern massasauga rattlesnake (Sistrurus catenatus) used in comparisons of AftrRAD, Stacks, and PyRAD.
DOI: 10.5061/dryad.sn034/5
title: Rattlesnake_Barcode_Info

description: Barcode information for rattlesnake fastq dataset.
DOI: 10.5061/dryad.vt87n/2
title: ZooplanktonDataAllSamples_PLOSOne

description: Metadata for Cladoceran density, Copepod density, and rotifer density.
DOI: 10.5061/dryad.vt87n/3
title: GrayTreefrogTimetoMeta&Survival

description: Metadata for Gray treefrog time to metamorphosis and survival.
DOI: 10.5061/dryad.vt87n/4
title: GTFMetamorphMASSPLOSOne

description: Metadata for Gray treefrog mass.
DOI: 10.5061/dryad.078bn/1
title: PONE-D-14-48810

description: Raw data for PLOS ONE journal entitle: Morbidity rate prediction of dengue hemorrhagic fever (DHF) using the support vector machine and the Aedes aegypti infection rate in similar climates and geographical areas
DOI: 10.5061/dryad.1607t/1
title: Probabilistic Atlases

description: Nifty images containing population-averaged white matter atlases for 7 developmental time points in a preterm-born cohort. Each age group contains a mean fractional anisotropy (FA) map plus tract probability atlases for forceps major, forceps minor and corticospinal tracts. Age groups included are 25-28 weeks gestational age (GA), 29-30 weeks GA, 31-32 weeks GA, 33-35 weeks GA, 39-42 weeks GA, 1-year and 2-years of age.
DOI: 10.5061/dryad.1pj04/84
title: Figure 6 - Global G aflatoxin isolates
DOI: 10.5061/dryad.1pj04/85
title: Figure 6 - Global locality file
DOI: 10.5061/dryad.1pj04/86
title: Figure 6 - Global species file
DOI: 10.5061/dryad.1pj04/88
title: Figure 6 - RAxML file
DOI: 10.5061/dryad.1pj04/89
title: Figure 6 - RAxML multiple sequence alignment file
DOI: 10.5061/dryad.3jg57/2
title: article_data

description: Code and data to reproduce all figures of the article. In addition, information about where one can find additional code to run all simulations producing the data supplied here.
DOI: 10.5061/dryad.3v55p/1
title: Concatenated Dataset

description: A nexus file of all 8 nuclear loci concatenated.
DOI: 10.5061/dryad.3v55p/2
title: IMa2_6pop

description: IMa2 input file for the 6-population model
DOI: 10.5061/dryad.3v55p/3
title: Species Tree Diffusion xml file

description: BEAST xml needed to run species tree diffusion. Other files are needed to run this including a GPS coordinates file delimiting species boundaries, and a posterior distribution of species trees.
DOI: 10.5061/dryad.3v55p/4
title: horridus N .kml distribution file

description: KML file delineating S. horridus north distribution needed to run a species tree diffusion analysis.
DOI: 10.5061/dryad.3v55p/5
title: Posterior distribution of species trees

description: Posterior distribution of species trees generated in *BEAST needed to run the species tree diffusion analysis.
DOI: 10.5061/dryad.3v55p/6
title: STRUCTURAMA input file

description: Input file for the program STRUCTURAMA
DOI: 10.5061/dryad.75r70/1
title: Data_Lesmerises et al_PLoS One-2015

description: This dataset includes 1) the content of 139 fecal pellets found in 71 sites visited by 20 black bears collared with GPS/Argos telemetry devices, 2) black bear individual characteristics (age, sex, status) as well as 3) the proportion of different habitat types found in Brownian bridge ellipses covering the area potentially visited by bears in the hours preceding feces excretion, We used this dataset to link habitats that were visited to feces content and contrasted the foraging stratégies between groups of bears of similar age/sex/status.
DOI: 10.5061/dryad.7n1q4/1
title: Centroid size and uncorrected RW (relative warp) data of Cuvierina pteropods.

description: Centroid size and uncorrected RW data of all Cuvierina shells in ventral as well as apertural orientations. Relative contributions of RW axes to shell shape variation are included. The first sheet contains ventral data of 113 fresh, 712 reference museum, and 214 other museum specimens. The second sheet contains apertural data of 115 fresh, 352 reference museum, and 83 other museum specimens.
DOI: 10.5061/dryad.7n1q4/2
title: Photographs of Cuvierina shells in a ventral orientation.

description: Photographs of 1039 Cuvierina shells in a ventral orientation used for geometric morphometric analyses in this study.
DOI: 10.5061/dryad.7nb81/1
title: Pedigree Data

description: The .Rdata file containing two objects. 'ped' contains the full pedigree, with the columns of id (unique individual identity), dam (the mother), dad (the social father), sire (the genetic father), long (longitude position of brood), lat (latitude position of brood), brood (unique ID of the brood the individual was born in), year (the year the individual was born). 'males' contains all the males that could have potentially been the genetic sires of offspring for each year and includes columns of id (unique ID corresponding to the 'ped' dataframe), year (the year this ID could have sired genetic offspring), brood (the brood that this male was identified at this year - also corresponds to 'ped' dataframe), lat (latitude to brood position), long (longitude of brood position). The R script for simulating additional pedigrees using this data but with  different parameters is included in the manuscript Supplementary Information.
DOI: 10.5061/dryad.bh123/1
title: Supplementary Material

description: The file includes two figures and three tables.
DOI: 10.5061/dryad.c8n18/3
title: 16S_OTU

description: Six oak bark pieces (~1g) from four oak trees (three pieces from oak 1 and one piece from each of the other trees) in Northern Germany were collected. In addition an infusion (20g oak bark in a sterile tea bag in 300 mL water for 24 hours) for each tree was prepared. DNA was extracted from all samples using the Soil DNA Kit from Omega Bio-Tek. The resulting DNA was sent to LGC Genomics (GmbH, Berlin, Germany) for amplification of the bacterial 16S rRNA (V1 to V5) sequences using GM3 (AGAGTTTGATCMTGGC) and 926R (CCGTCAATTCMTTTGAGTTT) primers using the 454 GS FLX+ Titanium Sequencer (Roche).  16S sequences were processed with mother, aligned to the comprehensive seed database from SILVA downloaded on April 29, 2013 and subsampled to 4000 sequences per sample. We created a distance matrix of aligned sequences and clustered them into operational taxonomic units (OTUs) using the average neighbor clustering algorithm. The shared file shows the distribution of OTUs in the ten groups at 97% and 95% identity level.
DOI: 10.5061/dryad.c8n18/4
title: 16S_taxonomy

description: Six oak bark pieces (~1g) from four oak trees (three pieces from oak 1 and one piece from each of the other trees) in Northern Germany were collected. In addition an infusion (20g oak bark in a sterile tea bag in 300 mL water for 24 hours) for each tree was prepared. DNA was extracted from all samples using the Soil DNA Kit from Omega Bio-Tek. The resulting DNA was sent to LGC Genomics (GmbH, Berlin, Germany) for amplification of the bacterial 16S rRNA (V1 to V5) sequences using GM3 (AGAGTTTGATCMTGGC) and 926R (CCGTCAATTCMTTTGAGTTT) primers using the 454 GS FLX+ Titanium Sequencer (Roche).  16S sequences were processed with mother, aligned to the comprehensive seed database from SILVA downloaded on April 29, 2013 and subsampled to 4000 sequences per sample. Sequence classification was performed using the mothur implementation of naive Bayesian classification based on the RDP Classifier version 9, with a threshold bootstrap value of 70% for each taxonomic level.
DOI: 10.5061/dryad.d4863/1
title: MLSA Borrelia ML tree

description: A tree that shows the relationships of a number of Borrelia strains, including a subset of the Bbsl strains included in our PCR screen. A plus sign (+) next to the strain designation indicates that gene(s) from the Bor TOMM biosynthetic cluster (borB/borC/borD) was/were detected. WGS: whole genome sequence.
DOI: 10.5061/dryad.d4863/2
title: SLS like TOMM D alignment

description: This is the alignment file for the maximum-likelihood tree based on the D protein for the majority of known and putative producers of cytolytic TOMMs (as of December 2014).
DOI: 10.5061/dryad.d4863/3
title: Borrelia TOMM Alignment

description: BorB (A), borC (B) and borD (C) from Borrelia afzelii PKo (Bafz), B. spielmanii A14S (Bspi), and B. valaisiana VS116 (Bval) were aligned using ClustalW. Sites where PCR screening primers annealed are underlined. The primers used to detect borB/C/D were based on bvalB/C/D from B. valaisiana VS116
DOI: 10.5061/dryad.d4863/4
title: SLS like Precursor Alignment

description: Alignment using Clustal Omega [49] reveals that the SLS core region possesses a highly conserved N-terminus containing 9-10 contiguous heterocylizable residues (underlined), while the C-terminus is variable in terms of both identity of residues and length. The putative leader peptide cleavage sites are shown as carets. Residues of SagA from S. pyogenes are numbered.
DOI: 10.5061/dryad.d4863/5
title: SLS like TOMM D ML Tree

description: A maximum-likelihood tree based on the D protein for the majority of known and putative producers of cytolytic TOMMs (as of December 2014).
DOI: 10.5061/dryad.d4863/6
title: TOMM D Alignment

description: An alignment file for the maximum-likelihood tree of a representative sample of TOMMs based on the D protein from each cluster. Clades are color-coded based on the predicted class of TOMM natural product. NHLP, nitrile hydratase leader peptide; NHLP-Burk, NHLP from Burkholderia; PZN, plantazolicin; Balh, uncharacterized TOMM from Bacillus sp. Al Hakam; McB, microcin B from Gammaproteobacteria. SLS, streptolysin S; Bor TOMM, putative SLS-like cytolysin from Bbsl.
DOI: 10.5061/dryad.d4863/7
title: TOMM D ML Tree

description: A maximum-likelihood tree of a representative sample of TOMMs based on the D protein from each cluster. Clades are color-coded based on the predicted class of TOMM natural product. NHLP, nitrile hydratase leader peptide; NHLP-Burk, NHLP from Burkholderia; PZN, plantazolicin; Balh, uncharacterized TOMM from Bacillus sp. Al Hakam; McB, microcin B from Gammaproteobacteria. SLS, streptolysin S; Bor TOMM, putative SLS-like cytolysin from Bbsl.
DOI: 10.5061/dryad.dm132/1
title: LeePlosOne2015

description: The data are organized in the same way as in the figures of the paper. They are all in matlab format.
DOI: 10.5061/dryad.j18qs/4
title: Supplementary_Table_4A

description: Summary statistics for the co-occurrence (clustering) of specimens of the same species on a slab. See Appendix 4B for the raw data.
DOI: 10.5061/dryad.j18qs/5
title: Supplementary_Table_4B

description: Raw data for the co-occurrence (clustering) of specimens of the same species on a slab. See Appendix 4A for the summary statistics.
DOI: 10.5061/dryad.m5c7m/1
title: Phylogenetic Tree Original Data Set (Opens with MEGA 5.0 + MS Powerpoint)

description: All files were generated, and can be opened, on MEGA 5.0 (http://www.megasoftware.net/) + MS Powerpoint. Phylogenetic relationships among the 23 identified MOTUs from fungal endophytes isolated from Vanilla planifolia. The analysis was based on LSU rDNA sequences.
DOI: 10.5061/dryad.n0qr5/1
title: Matrix 1

description: Supermatrix of 136 orthologs and 26,337 sites. Occupancy: 93.0%. Criterion: At least 36 taxa present for every ortholog.
DOI: 10.5061/dryad.n0qr5/2
title: Partitions file for Matrix 1

description: Partitions file for Matrix 1.
DOI: 10.5061/dryad.n0qr5/3
title: Matrix 2

description: Supermatrix of 599 orthologs and 128,842 sites. Occupancy: 86.9%. Criterion: At least 33 taxa present for every ortholog.
DOI: 10.5061/dryad.qj120/1
title: Dietary Patterns and Household Food Insecurity in Rural Populations of Kilosa District, Tanzania

description: Data on food consumption and household food insecurity is contained in this file for the Rural Populations of Kilosa District, Tanzania. Repeated measurements were performed whereby same households were followed up in two rounds of the surveys across agricultural seasons. The first survey was conducted during the long rainy season (February–March) and a second survey post-harvest (September–October) in 2011.
DOI: 10.5061/dryad.qk461/1
title: Passerine bird morphological measurements

description: Average morphological measurements and distributions of 1,579 passerine bird species included in the study “THE EVOLUTION OF MORPHOLOGICAL DIVERSITY IN CONTINENTAL ASSEMBLAGES OF PASSERINE BIRD” by Jønsson KA, Lessard JP, Ricklefs RE. Species names are matched to the bird tree of life (birdtree.org).
DOI: 10.5061/dryad.sn034/6
title: Mallard_Barcode_Info

description: Barcode information for Mallard fastq dataset.
DOI: 10.5061/dryad.tg469/1
title: Supplementary Figure 1

description: Histogram of abundances and distributions of plant megafossils through the Hasty Bank plant bed. Modified from Spicer and Hill (1979).
DOI: 10.5061/dryad.tg469/2
title: Supplementary Figure 2

description: Relative abundance chart of all sporomorph taxa from the Hasty Bank plant bed. Relative abundances of Jurassic taxa are calculated from counts of at least 200 grains. Spiked Lycopodium count data is shown as a percentage of the indigenous Jurassic taxa plus the spiked Lycopodium itself.
DOI: 10.5061/dryad.tg469/3
title: Supplementary Table 1

description: Raw data set of all sporomorph taxa through the Hasty Bank plant bed. “p” indicates taxa which are present within slides but not in counts.
DOI: 10.5061/dryad.tg469/4
title: Supplementary Table 2

description: Raw data set of all palynofacies counts through the Hasty Bank plant bed.
DOI: 10.5061/dryad.tg469/5
title: Supplementary Table 3

description: Botanical affinities of sporomorphs from the Hasty Bank plant bed. The ages (period) of deposits from which sporomorphs were recovered from are provided in the “Reference” column. “–” indicates an unknown affinity or a lack of published information available.