cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.32665/7
title: P2

description: Paternity and sperm count data. Variables:  Cross - Species identity of first and second male to mate with a D. simulans female, where "s" indicates D. simulans and "m" indicates D. mauritiana, such that "ss" indicates that both males were D. simulans, "ms" indicates that the first male was D. mauritiana and the second male was D. simulans, etc. Treat – time after mating for which paternity and sperm numbers in the female reproductive tract were quantified. ThoraxF - female thorax length, in arbitrary units. ThoraxM1 - thorax length of the first male, in arbitrary units. ThoraxM2 - thorax length of the second male, in arbitrary units. Cop1 – duration in minutes of the first copulation. Cop2 – duration in minutes of the second copulation. Remate – day after first mating (day 0) on which female remated. PriorProg – number of progeny produced by female before remating. P2Prog1 - number of progeny produced after remating sired by the first male. P2Prog2 - number of progeny produced after remating sired by the second male. P2 – proportion of progeny produced after remating sired by the second male. Bursa1 – number of first-male sperm in the bursa. Bursa2 – number of second-male sperm in the bursa. SR1 – number of first-male sperm in the SR. SR2 – number of second-male sperm in the SR. Sp1 – number of first-male sperm in the spermathecae. Sp2 – number of second-male sperm in the spermathecae.
DOI: 10.5061/dryad.3v0n3/5
title: Supp data-PAO1-LasI, lasB OD600, RLU-gene expressions
DOI: 10.5061/dryad.4411b/1
title: species_matrices_SCT-1_1m²_&_25m²_plots

description: Given are the cover values [in %] of the vascular species and bryophytes recorded on the permanent plots at the SCT-1 part of the Chicken Creek catchment (see fig. 1) in the study period.
DOI: 10.5061/dryad.4411b/2
title: species_matrices_SCT-2_1m²_&_25m²_plots

description: Given are the cover values [in %] of the vascular species and bryophytes recorded on the permanent plots at the SCT-2 part of the Chicken Creek catchment (see fig. 1) in the study period.
DOI: 10.5061/dryad.4411b/3
title: environment_matrices_SCT-1_1m²+25m²

description: Given are the environmental parameters measured on the permanent plots at the SCT-1 part of the Chicken Creek catchment  after its construction in 2005 (see methods).
DOI: 10.5061/dryad.4411b/4
title: environment_matrices_SCT-2_1m²+25m²

description: Given are the environmental parameters measured on the permanent plots at the SCT-2 part of the Chicken Creek catchment  after its construction in 2005 (see methods).
DOI: 10.5061/dryad.4b5c4/1
title: whole_head

description: Raw landmark coordinate data for whole-head landmark set for three populations of Alaskan threespine stickleback. Population Identifiers: 53=Boot Lake, 54=BearPaw Lake, 56=Rabbit Slough
DOI: 10.5061/dryad.4b5c4/2
title: four_ops

description: Raw landmark coordinate data for four-opercular-bone dataset for three populations of Alaskan threespine stickleback.  Population Identifiers: 53=Boot Lake, 54=BearPaw Lake, 56=Rabbit Slough
DOI: 10.5061/dryad.5248s/18
title: 2-hydroxymuconic semialdehyde hydrolase ARB output.nex
DOI: 10.5061/dryad.5248s/19
title: 2-oxopent-4-enoate hydratase ARB output.nex
DOI: 10.5061/dryad.5248s/20
title: 4-hydroxy-2-oxopentanoate aldolase ARB output.nex
DOI: 10.5061/dryad.5248s/21
title: 4-hydroxy-2-oxopentanoate aldolase DmpG-like domain ARB output.nex
DOI: 10.5061/dryad.5248s/22
title: 4-hydroxy-2-oxopentanoate aldolase HMGL-like domain ARB output.nex
DOI: 10.5061/dryad.5248s/23
title: acetaldehyde dehydrogenase ARB output.nex
DOI: 10.5061/dryad.5248s/24
title: acetaldehyde dehydrogenase dimerisation domain ARB output.nex
DOI: 10.5061/dryad.5j2v6/1
title: SNP genotype file for validation

description: Data was generated on the MassARRAY 4 analyzer system (Sequenom, Inc., San Diego, CA) and tissue was collected in the field from the authors and other personnel listed in the acknowledgements.  The SNP ID's and primer sequences are added in the supplementary information of the manuscript for reference. The top rows indicate species specific genotypes for Hypophthalmichthys nobilis (BH) and H. molitrix (SV).  The remaining rows and columns give the location, field ID, genetic ID, and genotypes of individual fishes at 57 SNP loci.
DOI: 10.5061/dryad.6dn5p/1
title: mtDNA Alignment

description: Nexus file containing 66 unique haplotypes of cytochrome b from Southeast Asian shrews. This alignment was used to generate the gene tree in Figure 2.
DOI: 10.5061/dryad.6dn5p/2
title: ApoB Alignment

description: Nexus file containing phased alleles from Apolipoprotein B sequences of Javan Crocidura.  This alignment was used to generate the gene tree in Figure S1.
DOI: 10.5061/dryad.6dn5p/3
title: BDNF Alignment

description: Nexus file containing phased alleles from BDNF sequences of Javan Crocidura.  This alignment was used to generate the gene tree in Figure S1.
DOI: 10.5061/dryad.6j9v0/1
title: Mol_Eco_qPCR_data

description: This file contains all the data from the qPCR analyses described in the paper.
DOI: 10.5061/dryad.7fr20/10
title: Supplementary Dataset 8: Normalized RSEM-estimated counts

description: Supplemental Dataset 8. Normalized RSEM-estimated counts for all replicates of each dodder tissue used for transcript clustering and differential expression analysis. There were eight replicates for stems, prehaustoria, haustoria and flowers (four replicates each from dodder grown on two host plants, tomato and tobacco) and four replicates for seeds and seedlings.Column titles: (1) Contig ID, (2) Trinity identifier, (3 - 10) eight replicates of flowers, (11 - 18) eight replicates of haustoria, (19 - 26) eight replicates of prehaustoria, (27 - 30) four replicates of seedlings, (31 - 34) four replicates of seeds and (35 - 42) eight replicates of stem.
DOI: 10.5061/dryad.7fr20/11
title: Supplementary Dataset 9: Enriched GO-categories for PCA-SOM clusters

description: Supplemental Dataset 9. Enriched GO-categories, both overall GO and GOslim, for all clusters generated from principal component analysis with self-organizing map. Cluster 1– 12 are shown sequentially on sheet 1 – 12.
DOI: 10.5061/dryad.7fr20/12
title: Supplementary Dataset 10: Differentially expressed transcripts for each pair-wise comparison

description: Supplemental Dataset 10. Differentially expressed transcripts (logFC " 1; FDR &lt; 0.05) for each pair-wise comparison for all dodder tissues: flowers_vs_haustoria (sheet 1); flowers_vs_prehaustoria (sheet 2); flowers_vs_seedlings (sheet 3); flowers_vs_seeds (sheet 4); flowers_vs_stems (sheet 5); haustoria_vs_prehaustoria (sheet 6); haustoria_vs_seedlings (sheet 7); haustoria_vs_seeds (sheet 8); haustoria_vs_stems (sheet 9); prehaustoria_vs_seedlings (sheet 10); prehaustoria_vs_seeds (sheet 11); prehaustoria_vs_stems (sheet 12); seedlings_vs_seeds (sheet 13); seedlings_vs_stems (sheet 14) and seeds_vs_stems (sheet 15). Column titles: (1) Contig ID, (2) Trinity identifier, (3) logFC (FoldChange), (4) logCPM (Counts Per Million), (5) PValue, (6) FDR (False discovery rate), (7) Sequence description from Blast2GO, (8) Top hit sequence ID from nr database, (9) Top hit gene ID from TAIR10, (10) Top hit gene name from TAIR10 and (11) Top hit gene description from TAIR10.
DOI: 10.5061/dryad.7fr20/13
title: Supplementary Dataset 11: Up-regulated and down-regulated transcripts at prehaustorial stage

description: Supplemental Dataset 11. Shared up-regulated and down-regulated transcripts at prehaustorial stage compared to seedlings and stems and associated enriched GO categories: up-regulated transcripts (sheet 1); down-regulated transcripts (sheet 2); enriched GO-terms in up-regulated transcripts (sheet3) and enriched GO-terms in downregulated transcripts (sheet4). Column titles for sheet 1 and sheet2: (1) Contig ID, (2) Trinity identifier, (3) Sequence description from Blast2GO, (4) gene name from TAIR10 and (5) gene description from TAIR10.
DOI: 10.5061/dryad.7fr20/14
title: Supplementary Dataset 12: Up-regulated and down-regulated transcripts at haustorial stage

description: Supplemental Dataset 12. Shared up-regulated and down-regulated transcripts at haustorial stage compared to prehaustoria, seedlings and stems and associated enrichedGO-categories: up-regulated transcripts (sheet 1); down-regulated transcripts (sheet 2); enriched GO-terms in up-regulated transcripts (sheet3) and enriched GO-terms in downregulated transcripts (sheet4). Column titles for sheet 1 and sheet2: (1) Contig ID, (2) Trinity identifier, (3) Sequence description from Blast2GO, (4) gene name from TAIR10 and (5) gene description from TAIR10.
DOI: 10.5061/dryad.7fr20/6
title: Supplementary Dataset 4. Annotation of transcripts form Dodder_final_transcriptome

description: Supplemental Dataset 4. Combined annotation of dodder transcripts obtained from BLASTX against nr and TAIR10 database. Column titles: (1) Contig_id, (2) Trinity identifier, (3) length of contig, (4) sequence description from Blast2GO, (5) top hit sequence ID from nr database, (6) top hit gene ID from TAIR10, (7) top hit gene name from TAIR10 and (8) gene description from TAIR10.
DOI: 10.5061/dryad.7fr20/7
title: Supplementary Dataset 5: GO chart data

description: Supplemental Dataset 5. GO chart data i.e. number of annotated transcripts in each GO-category along with GO-level, score and parent GO-terms for each category under biological process (sheet1), molecular function (sheet2) and cellular component (sheet3). Columns titles: (1) GO-level, (2) GO-term (Accession), (3) GO-term (Name), (4) Number of contigs belonging to the GO-term, (5) Score, (6) Parents GO-term (Accession) and (7) Parents GO-term (Name).
DOI: 10.5061/dryad.7fr20/8
title: Supplementary Dataset 6: GO-ids for annotated dodder transcripts

description: Supplemental Dataset 6. GO-ids for all annotated dodder transcripts: all GO-ids (sheet1) and GO-slim ids (sheet2). Column titles: (1) Contig ID, (2) Trinity identifier and (3) GO-term (Accession).
DOI: 10.5061/dryad.7fr20/9
title: Supplementary Dataset 7: Enzyme code distribution from KEGG

description: Supplemental Dataset 7. Enzyme code distribution from KEGG for all annotated dodder transcripts. Column titles: (1) Enzymatic Pathway, (2) Number of sequences in the pathway, (3) Enzyme class, (4) Enzyme ID/EC (Enzyme Code) number, (5) Number of annotated contigs in the class, (6) Trinity identifiers of the contigs and (7) Enzymatic Pathway ID.
DOI: 10.5061/dryad.832k336g/1
title: Climbing Adaptations Data

description: This table contains characters associated with tree-trunk climbing observed in study skins of 290 of the 293 currently recognized species of Furnariidae. Most specimens were examined at the Louisiana State University Museum of Natural Science. For each specimen, I recorded the morphology of seven characters of the tail and one character of the foot that have functional significance for tail-assisted climbing. For each character, states were coded such that 0 represents no specialization for climbing (the predominant state in passerines) and the other states represent an increasing degree of specialization. Character and character states are described in Table 1 of the associated article. Ambiguous and polymorphic conditions were coded with standard symbols (/ and & respectively). In addition to discrete characters, I used measurements of the length of one of the central tail feathers and the diameter (dorso-ventral) of its rachis at the midpoint to calculate relative rachis thickness as a percentage of the total length of the feather. Finally, a composite index of climbing adaptations for each species was calculated as the sum of the eight discrete characters plus relative rachis thickness all divided by 16.
DOI: 10.5061/dryad.832k336g/2
title: Table of Specimens for the Analysis of ND2 Divergence in Woodcreepers
DOI: 10.5061/dryad.832k336g/3
title: Specimens Used for the Analysis of ND2 divergence in Picidae
DOI: 10.5061/dryad.832k336g/4
title: Dendrocolaptidae Maximum Likelihood Clock Tree
DOI: 10.5061/dryad.832k336g/5
title: Picidae Maximum Likelihood Clock Tree
DOI: 10.5061/dryad.bj8ck/1
title: Yavno_Fox_DATA

description: Raw morphological measurements of traits associated with both the traditional centroid, and swimming. Trait names are listed at the top of each column; population and water treatment are listed in the first two columns.
DOI: 10.5061/dryad.ct40s/42
title: Sitta 241779
DOI: 10.5061/dryad.ct40s/43
title: Spizella 241938
DOI: 10.5061/dryad.ct40s/44
title: Struthio fem R1716
DOI: 10.5061/dryad.ct40s/45
title: Struthio hum R1716
DOI: 10.5061/dryad.ct40s/46
title: Turdus 241899
DOI: 10.5061/dryad.ct40s/47
title: Vermivora femur 242012
DOI: 10.5061/dryad.ct40s/48
title: Vireo 240779
DOI: 10.5061/dryad.ct40s/49
title: Zonotrichia 241280
DOI: 10.5061/dryad.ct40s/50
title: Dromaius R1717 cervical vert
DOI: 10.5061/dryad.d3mb4/1
title: Alignment of 10 nuclear genes in nexus format

description: Aligned DNA sequence data of 10 nuclear genes, interleaved. Taxa missing from individual genes are scored as missing data, e.g., "?"
DOI: 10.5061/dryad.g26k9/1
title: Selz et al. 2013

description: See ReadMe file.
DOI: 10.5061/dryad.j08jp/1
title: Dataset S3 - Genome assemblies in fasta format

description: Genome assemblies of six halophilic archaea. Organisms were obtained from culture collections, grown, and then each genome was shotgun sequenced using 454 pyrosequencing. The genomes were then assembled into contigs and scaffolds. Data for each organism is in a separate file in fasta format. Each scafold is labelled with a header delineated by the '&gt;' character.
DOI: 10.5061/dryad.j08jp/2
title: Dataset_S1 Syntenic Halophilic Tribes matrix

description: In order to determine phylogenetic distribution of haloarchaeal genes, a gene presence/absence matrix was constructed by the following process. Independent multi-genome alignments were made for the Haloferax and Haloarcula genera using the whole genome alignment method progressiveMauve [64]. The contigs for each alignment were reordered to match the published genomes of Haloferax volcanii [19] and Haloarcula marismortui [18], respectively, using Mauve’s built-in contig reordering program (Figures S3 and S4). Sets of functionally homologous genes (orthologs), referred to hereafter as Syntenic Halophile Tribes (SHTs), were determined from alignments and joined by the following process. The proteins in each SHT from the Haloferax alignment were searched against all proteins in each SHT from the Haloarcula genomes using BLAST [37] and a bit score for each pair of SHTs was calculated by averaging the bit scores from each BLAST hit. A traditional reciprocal best hit (RBH) BLAST approach was used to produce one-to-one mappings between SHTs in the two genera. Each joined SHT was assigned a function using the most commonly occurring functional annotation of the protein products of the genes in the SHT. This resulted in a set of 398 SHTs present in all nine genomes.

Hidden Markov Models (HMMs) were generated for each SHT using HMMER 3, resulting in 13,276 HMMs. The 1,303 completed archaeal and bacterial genomes available from NCBI as of March 15, 2011 were downloaded and a single genome from each genus selected at random, resulting in 396 genomes. Each SHT HMM was searched against these 396 genomes and the eight halophile genomes generated for this study using HMMER 3. Each gene was counted as belonging to the HMM if it had an E-value below 0.0001 and the hit covered greater than 80% of the length of both the gene and the HMM. If a gene hit more than one HMM it was counted only for the HMM with the best E-value. These hits were then used to generate a 13,276 x 405 presence/absence matrix. The genomes and HMMs were clustered using the ‘ctc’ library in R [65] with manhattan distance and complete linkage clustering. The clustering was viewed with the Java Treeview program [66]. Cluster file can be accessed at our website [60] and as Dataset S1 and Figure S5.
DOI: 10.5061/dryad.j08jp/3
title: Dataset S2. Full alignment of Proliferating Cell Nuclear Antigen (PCNA) homologs

description: Untrimmed alignment of sixty-one PCNA homologs from fifty-seven archaeal and eukaryotic species constructed with MUSCLE.
DOI: 10.5061/dryad.j512f21p/1
title: clinicaltrials.gov_search

description: This is complete original dataset.
DOI: 10.5061/dryad.j512f21p/2
title: identify completed trials

description: This is the R script which  when run on "clinicaltrials.gov_search.txt" will produce a .csv file which lists all the completed trials.
DOI: 10.5061/dryad.j512f21p/3
title: FDA_table_with_sens

description: This is the final dataset after cross referencing the trials. An explanation of the variables is included in the supplementary file "2011-10-31 Prayle Hurley Smyth Supplementary file 3 variables in the dataset".
DOI: 10.5061/dryad.j512f21p/4
title: analysis_after_FDA_categorization_and_sens

description: This R script reproduces the analysis from the paper, including the tables and statistical tests. The comments should make it self explanatory.
DOI: 10.5061/dryad.jd183/10
title: fasta_files36-40
DOI: 10.5061/dryad.jd183/11
title: fasta_files41-45
DOI: 10.5061/dryad.jd183/12
title: fasta_files46-50
DOI: 10.5061/dryad.jd183/2
title: fasta_files1-5
DOI: 10.5061/dryad.jd183/4
title: fasta_files6-10
DOI: 10.5061/dryad.jd183/5
title: fasta_files11-15
DOI: 10.5061/dryad.jd183/6
title: fasta_files16-20
DOI: 10.5061/dryad.jd183/7
title: fasta_files21-25
DOI: 10.5061/dryad.jd183/8
title: fasta_files26-30
DOI: 10.5061/dryad.jd183/9
title: fasta_files31-35
DOI: 10.5061/dryad.jn7b2/1
title: Cytochrome b nexus file for Gadopsis
DOI: 10.5061/dryad.jn7b2/2
title: S7 sequence nexus file for Gadopsis and outgroups
DOI: 10.5061/dryad.jn7b2/3
title: Combined Cytochrome b and S7 sequence data in nexus format

description: The codes for each OTU are in the readme file.  The first number is the population, the second is the name of the population and the third is the specific individual.  Note that the readme file contains the codes for samples that are not in the nexus file.
DOI: 10.5061/dryad.jn7b2/4
title: *beast xml file for Gadopsis (S7 and cytb)

description: The codes for each OTU are in the readme file.  The first number is the population, the second is the name of the population and the third is the specific individual.
DOI: 10.5061/dryad.jp2rm/1
title: Survival data binary format

description: Survival data are arranged for offspring from each family, with zeros denoting deaths, and ones denoting survivors.
DOI: 10.5061/dryad.jp2rm/2
title: Fertilisation data in binary format

description: Fertilisation data are arranged in binary format, with zeros denoting unfertilised eggs, and ones denoting fertilised eggs.
DOI: 10.5061/dryad.nr787/6
title: BEAST input files

description: Input files for BEAST analysis
DOI: 10.5061/dryad.rs4v1/1
title: genepop_western_alaska_chinook_RAD

description: Genepop formatted file containing genotypes from the 10,944 SNPs and 265 individuals used in this study.  SNP names are radtag_snp position i.e. a SNP named 12_46 would be on radtag number 12 and the SNP would be at position 46 in the tag.  Population abbreviations are collection year _ individual.  For example Koktuli10_0002 would be from the Koktuli River, collected in 2010, and would be individual 2.
DOI: 10.5061/dryad.rs4v1/2
title: sequences_for_10944_SNPs

description: Fasta file containing the sequences for each allele for each SNP discovered in this study.  Sequences are designated by rad tag_allele_SNP position(s).  Tags may contain multiple SNPs, for example &gt;84_AT_40-84 would designate the sequence for rad tag 84 which has SNPs at positions 40 and 84.  Since we only used one SNP per tag for the study, not all SNPs in this file are found in the genotypes file.  To obtain the positions of the SNPs that we did use, please see the locus names in the genepop file.
DOI: 10.5061/dryad.s11b6/1
title: DataDryad_PopulationData

description: Individual (GenotypeID) and Population data for individuals genotyped and phenotyped from common garden experiment. TenYR_Height is height at 10 years of age (mm) and ColdInjury.8 and ColdInjury.18 is a proportion of injury at -8C and -18C. respectively
DOI: 10.5061/dryad.t66ns/1
title: Haplotype Genomes with known karyotypes.

description: The ZIP archive contains whole chromosome haplotypes in Multi FASTA format, which were reconstructed for 15 individuals with known karyotypes. These were randomly picked from populations of a selection experiment. See Material and Methods for more details.
DOI: 10.5061/dryad.v2c17/1
title: DetectionNondetectionData

description: Data used in the hierarchical multispecies occupancy model with detection/non-detection data in the BUGS language
DOI: 10.5061/dryad.v2c17/2
title: TimeToDetectionData

description: Data used in the hierarchical multispecies time-to-detection occupancy model in the BUGS language
DOI: 10.5061/dryad.vs49s/1
title: S1

description: Gapped alignment of 40553 positions in length used to produce the OV alignment
DOI: 10.5061/dryad.077vm/1
title: DeLong et al Functional Ecology data

description: This Excel file includes three tabs. In first tab is the population density (cells per mL) data for Didinium and Paramecium together and Paramecium alone (control cultures). In the second tab is a list of cell sizes (length, width, and volume in cubic microns) for Didinium through time. In the third tab is functional response data, with prey density, predator density, and prey eaten per predator per day, along with a block identifier.
DOI: 10.5061/dryad.10154/1
title: Fitness measurements

description: See ReadMe file
DOI: 10.5061/dryad.36951/1
title: BighornEweGrowthFitness

description: First sheet: mass of ewes when caught as lambs, with ID of mother, population density, age of primiparity.   Second sheet: for each year of life of each ewe, mass and reproductive successThird sheet: codes for reproductive successs
DOI: 10.5061/dryad.41h46j37/1
title: Data Traoré et al. (2012) BMC Genetics

description: Genotypes, for 19 microsatellites, of 520 goat sampled in 23 different locations of Burkina Faso. Genotypes are given in MolKin format (similar to GENEPOP).
DOI: 10.5061/dryad.4bq08/1
title: Data from: Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol

description: 1. Milleretal2013DutchSpiderBarcodeDwC.txt. Occurrence data for all specimens in the study presented as a tab delimited text file with Darwin Core fields, plus custom fields for recording destructive and nondestructive sequencing success, DNA sequences, DNA concentration data, and hyperlinks to records on BOLD (http://www.boldsystems.org/).   2. Milleretal2013DutchSpiderBarcode.kml. Occurrence data in KML (keyhole markup language) format that can be opened using Google Earth (http://earth.google.com/) to display an interactive map plotting Dutch spider specimens included in this study. Data can be filtered by taxon using the Places directory.   3. Milleretal2013DutchSpiderBarcode.fasta. All sequence data for this study in fasta format.   4. Milleretal2013DutchSpiderBarcodeDestructiveExtractions.nex. Nexus files generated using Mesquite (http://mesquiteproject.org) for the independent contrasts analyses testing the relationship between body size and oldest success after accounting for phylogeny. Oldest success calculated based on destructive extractions only.   5. Milleretal2013DutchSpiderBarcodeAllExtractions.nex. Nexus files generated using Mesquite (http://mesquiteproject.org) for the independent contrasts analyses testing the relationship between body size and oldest success after accounting for phylogeny. Oldest success calculated based on all extractions (regardless of destructive vs. nondestructive method).   6. Milleretal2013DutchSpiderBarcodeElectronicSupplementaryDocuments.doc. Figure S1. Correlations based on independent contrasts.
DOI: 10.5061/dryad.5248s/25
title: acetaldehyde dehydrogenase NAD binding domain ARB output.nex
DOI: 10.5061/dryad.5248s/26
title: catechol 2,3-dioxygenase ARB output.nex
DOI: 10.5061/dryad.5248s/27
title: catechol 2,3-dioxygenase C-terminal domain ARB output.nex