cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c9086/5
title: bulks

description: ## -- Table bulks -- ##
Information about `bulks' (mixtures) of DNA from individual samples.

       row_id: Numerical identifier (unique per row)
      updated: Date / Time of last update for the information.
         bulk: Bulk identifier.
 well_in_bulk: Well of plate where the sample is stored.
bulk_accesion: Identifier of accession / bulk.
        indiv: Number of individual DNA sample.
   indiv_well: Well of individual DNA sample.
indiv_mic_lit: Quantity stored.


** - Technical description of columns - **
Field	Type	Null	Key	Default	Extra
row_id	int(5)	NO	PRI	NULL	auto_increment
updated	timestamp	NO		CURRENT_TIMESTAMP	on update CURRENT_TIMESTAMP
bulk	varchar(5)	YES		NULL	
well_in_bulk	varchar(3)	YES		NULL	
bulk_accesion	varchar(7)	YES		NULL	
indiv	int(2)	YES		NULL	
indiv_well	varchar(3)	YES		NULL	
indiv_mic_lit	int(3)	YES		NULL
DOI: 10.5061/dryad.c9086/6
title: fingerprint (DNA profile for each bulk)

description: ## -- Table fingerprint -- ##
Information about all marker types of each bulk within accession.
NOTE: Each one of the marker types is a numerical variable, with 0 if the sample
      was negative for that marker type and 1 otherwise. 

          acc: Accession identifier.
        batch: Bulk (batch) identifier.
 : Combination marker / allele (contents 0 or 1; see above)
...
[There are 328 posible marker / allele columns]

** - Technical description of columns - **
Field	Type	Null	Key	Default	Extra
acc	varchar(5)	NO	MUL	NULL	
batch	int(1)	NO	MUL	NULL	
PHI015_0	int(1)	YES		0	
PHI015_63	int(1)	YES		0	
...
[There are 328 marker / allele columns]
DOI: 10.5061/dryad.c9086/7
title: fingerprint_acc (DNA profile per accession)

description: ## -- Table fingerprint_acc -- ##
Information about  about all marker types (fingerprint) in a given accession.
NOTE: Each one of the marker types is a numerical variable, with the number of bulks
      (batches) that were positive for each particular marker type, thus the variables
      can take values 0, 1, 2 or 3.

          acc: Accession identifier.
     PHI015_0: value for allele 0 of marker PHI015; can be 0, 1, 2 or 3.
In general:
 : Combination marker / allele (contents 0 or 1; see above)
...
[There are 328 marker / allele columns]

** - Technical description of columns - **
Field	Type	Null	Key	Default	Extra
acc	varchar(5)	NO	MUL	NULL	
PHI015_0	int(1)	YES		0	
...
[There are 328 posible marker / allele columns]
DOI: 10.5061/dryad.c9086/8
title: lecturas (assignation of marker genotype per bulk)

description: ## -- Table lecturas -- ##
Information about the readings for each batch (bulk)

    lec_id: Numerical identifier (unique per row)
  accesion: Full accession identifier = state_id acces_id
  state_id: State identifier (two characters).
  acces_id: Accession identifier within state (three digits)
  id_group: Batch (bulk) identifier.
    marker: SSR Marker.
  alelo_bp: Allele identified.
reading_bp: Raw lecture.

** - Technical description of columns - **
Field	Type	Null	Key	Default	Extra
lec_id	int(5)	NO	PRI	NULL	auto_increment
accesion	varchar(5)	YES	MUL	NULL	
state_id	varchar(2)	YES		NULL	
acces_id	varchar(3)	YES		NULL	
id_group	int(1)	YES	MUL	NULL	
marker	varchar(15)	YES	MUL	NULL	
alelo_bp	float	YES		NULL	
reading_bp	float	YES		NULL
DOI: 10.5061/dryad.c9086/9
title: plates (where DNA samples are stored)

description: ## -- Table plates -- ##
Information about plates where the DNA samples are stored.

plate_id: Numerical identifier (unique per row)
 updated: Last time information was updated.
   plate: Plate identifier.


** - Technical description of columns - **
Field	Type	Null	Key	Default	Extra
plate_id	int(5)	NO	PRI	NULL	auto_increment
updated	timestamp	NO		CURRENT_TIMESTAMP	on update CURRENT_TIMESTAMP
plate	varchar(100)	YES		NULL
DOI: 10.5061/dryad.j315n/11
title: DTdadi

description: Demographic  inferences (Figure S5a and b): SNP data set for wine and Jura/Hungary flor strains, and wine and Spain/Italy flor strains at dadi format for demographic inference. Obtained with script Vcf-to-dadi.pl
DOI: 10.5061/dryad.j315n/12
title: Vcf-to-dadi perl  script

description: Demographic  inferences (Figure S5a and b): Perl script that converts a vcf file including 2 or 3 pop with Ancestral Allele field (not necessary if folded)  to a file for diffusion approximation demographic inference (dadi,  Gutenkunst 2015, PLoS Genetics). Requires Bioperl, reference sequence fasta file, and variant file at VCF format (only with strains required for the analysis)
DOI: 10.5061/dryad.j315n/13
title: TranslocationsCompilation_outputs_delly

description: Compilation of delly  V 0.1.1 outputs  for each strain. This file contrains only events that occured more than 40 times.
DOI: 10.5061/dryad.j315n/14
title: XPCLR selection test: Script prepares ms data and runs XPLCR
DOI: 10.5061/dryad.j315n/15
title: Data XPCLR of Wine and Spain Italy Flor strain

description: XPCLR selection test: Data for XPCLR of Wine and Spain and Italy Flor strain recombination rate 403 M. Window= 0.1 cM, window 1kb
DOI: 10.5061/dryad.j315n/16
title: Data XPCLR of Wine and France and Hungary Flor strain

description: XPCLR selection test: Data for XPCLR of Wine and French (Jura) and Hungarian Flor strain recombination rate 403 M. Window= 0.1 cM, window 1kb
DOI: 10.5061/dryad.j315n/17
title: Combined set of SNPS including wine and flor strains and strains from other origins(Allyeast-set)

description: Data for Phylogeny and population structure (Figure 1, Figure2A and B). Compressed Vcf file containing a set of biallelic variant with less than 20 % missing position among all strains, obtained from the genotyping  of 20 flor and wine strains  compared to 82 strains with available genome sequences (obtained from Saccharomyces genome database (http://www.yeastgenome.org/), of from the SGRP project (http://www.sanger.ac.uk/research/projects/genomeinformatics/sgrp.html) (Liti et al. 2009, Population genomics of domestic and wild yeasts. Nature, 458, 337–41)
DOI: 10.5061/dryad.jb4dh/1
title: Restio-insect herbivore interaction network data for the CFR

description: Insect species were sampled from Restionaceae plant species in the CFR. Except for the Cephalelini, insects were identified to family and then assigned to a morphospecies group. Columns depict insects, rows, depict plant species, and cells are filled with interaction frequencies. Data for sites and seasons are given separately.
DOI: 10.5061/dryad.ns143/1
title: Data for Trait-matching and mass effect determine the functional response of herbivore communities to land use intensification, Le Provost, Gaëtane, Gross, Nicolas, Börger, Luca, Deraison, Hélène, Roncoroni, Marilyn, Badenhausser, Isabelle

description: File containing means and variances for grasshopper body size and incisor strength, local abiotic variables, local plant community variables and landscape variables
DOI: 10.5061/dryad.pp176/1
title: 28S_alignment

description: Alignment of 169 partial 28S rDNA nucleotide sequences from amphipods in genus Niphargus. Sequences were highly variable in their length and were aligned in MAFFT ver. 6 using the E-INS-i option for sequences with multiple conserved domains and long gaps.
DOI: 10.5061/dryad.pp176/2
title: COI_alignment

description: Alignment of 117 nucleotide sequences of mitochondrial gene cytochrome oxidase subunit I (COI), partial cds, from amphipods in genus Niphargus.  Sequences were aligned with a simple alghoritm (Geneious alignment).
DOI: 10.5061/dryad.pp176/3
title: H3_alignment

description: Alignment of 109 nucleotide sequences of nuclear gene histone H3, partial cds, from amphipods in genus Niphargus. All sequences were the same length and were aligned using a simple alghoritm (Geneious alignment).
DOI: 10.5061/dryad.pp176/4
title: Concatenated alignments

description: Concatenated alignments of all three genes (28S, H3, COI).
DOI: 10.5061/dryad.pp176/5
title: MrBayes output

description: Output files from MRBAYES for each gene(28S, H3, COI) analysed separately and a concatenated analysis.
DOI: 10.5061/dryad.q3h85/10
title: TPC2016-00768-LSBR1_Supplemental_Data_Set_10

description: Supplemental Data 10. The peptide identification data for each time point for peptides at T=0 days in the spiked in 15N reference experiment
DOI: 10.5061/dryad.q3h85/11
title: TPC2016-00768-LSBR1_Supplemental_Data_Set_11

description: Supplemental Data 11. The peptide identification data for each time point for peptides at T=1 day in the spiked in 15N reference experiment.
DOI: 10.5061/dryad.q3h85/12
title: TPC2016-00768-LSBR1_Supplemental_Data_Set_12

description: Supplemental Data 12. The peptide identification data for each time point for peptides at T=3 days in the spiked in 15N reference experiment
DOI: 10.5061/dryad.q3h85/14
title: TPC2016-00768-LSBR1_Supplemental_Data_Set_14

description: Supplemental Data 14. Determination of labelled protein fraction (LPF) for peptides by 15N progressively labelling in 27 individual leaf samples.
DOI: 10.5061/dryad.q3h85/15
title: TPC2016-00768-LSBR1_Supplemental_Data_Set_15

description: Supplemental Data 15. The peptide identification data for 15N progressively labelled peptides at all time points.
DOI: 10.5061/dryad.q3h85/6
title: TPC2016-00768-LSBR1_Supplemental_Data_Set_6

description: Supplemental Data 6. Comparison of protein degradation rate (KD) and leaf growth rates in leaf 3, leaf 5 and leaf 7
DOI: 10.5061/dryad.q3h85/7
title: TPC2016-00768-LSBR1_Supplemental_Data_Set_7

description: Supplemental Data 7. Calculation of ATP costs for protein synthesis and degradation in leaf 3, leaf 5 and leaf 7.
DOI: 10.5061/dryad.q3h85/8
title: TPC2016-00768-LSBR1_Supplemental_Data_Set_8

description: Supplemental Data 8. Comparison of protein degradation rate and protein abundance for selected proteins of interest.
DOI: 10.5061/dryad.q3h85/9
title: TPC2016-00768-LSBR1_Supplemental_Data_Set_9

description: Supplemental Data 9. Determination of protein abundance fold change relative to a 15N reference in 36 individual leaf samples.
DOI: 10.5061/dryad.r7r01/1
title: Kindinger data_Uploaded PlosOne

description: Anonymised individual cervical length and outcome data of pregnant women who had been treated by excision cervical cervical treatment for cervical intraepithelial neoplasia, pre-pregnancy.
DOI: 10.5061/dryad.rh2cf/1
title: Sauroscaptor phylogenetic character data

description: Anomodont data matrix (in TNT format) used in phylogenetic analysis of Sauroscaptor tharavati.
DOI: 10.5061/dryad.rh2cf/2
title: Cistecephalid Measurements

description: Measurements of total dorsal skull length, anterior and posterior intertemporal width, and post-pineal skull length in cistecephalid dicynodonts.
DOI: 10.5061/dryad.t2d38/1
title: Supplement

description: Supplemental Tables 1-3 for the paper.
DOI: 10.5061/dryad.057b7/1
title: Trinity assembly

description: Trinity assembly of filtered paired-end reads (phred score &gt;30, both pairs passed QC control) pooling all samples.
DOI: 10.5061/dryad.057b7/2
title: blastx table for all reconstructed transcripts

description: Blastx table against human for all reconstructed transcripts. Includes the perecentage of the human protein covered by the lemur transcript.
DOI: 10.5061/dryad.057b7/3
title: GTEx rpkm table

description: GTEX rpkm table for the 2 human adipose tissue samples analyzed:  GTEX9N7MS903269SM94E3K2 and GTEX9NFK9903269SM93MJGV)
DOI: 10.5061/dryad.2m2r2/4
title: Chicks

description: Details of all offspring in this study including results from parentage analysis.
DOI: 10.5061/dryad.2m2r2/5
title: Nest data for Spatial EPP analysis

description: All breeding observations in nestboxes and hollows (without genetic samples) at Wyndham in 2008-2009, including anonymised co-ordinates for nest locations, where inter nest differences are preserved but do not reflect the real position on the globe. README file also includes the code used to calculate the number of synchronous nests and how far away they are.
DOI: 10.5061/dryad.2m2r2/6
title: Genotypes of Wild and Captive birds

description: Genotypes of the wild and captive birds in Arlequin format. Readme file includes the key that will allow the ID numbers to be broken down into which morph they are.
DOI: 10.5061/dryad.320h5/1
title: Topper et al. Raw coordinates used in ventral valve analyses

description: Raw landmark coordinates used in ventral valve analyses exported directly from MorphoJ. This data has not been transformed using Generalized Procrustes Analysis.
DOI: 10.5061/dryad.320h5/2
title: Topper et al. Raw coordinates for dorsal valves

description: Raw landmark coordinates used in dorsal valve analyses exported directly from MorphoJ. This data has not been transformed using Generalized Procrustes Analysis.
DOI: 10.5061/dryad.320h5/3
title: Table S1

description: Table S1 Details of Micromitra burgessensis specimens included in the analysis, including information regarding attachments, locality and individual measurements. WQ denotes the Walcott Quarry Shale Member, RQ denotes, the slightly younger Raymond Quarry Shale Member and Ta refers to material collected as talus.
DOI: 10.5061/dryad.320h5/4
title: Table S2

description: Table S1 Details of Micromitra burgessensis dorsal valve specimens included in the analysis, including information regarding attachments, locality and individual measurements. WQ denotes the Walcott Quarry Shale Member and RQ denotes, the slightly younger Raymond Quarry Shale Member.
DOI: 10.5061/dryad.38c5g/1
title: Raw Ct values qPCR

description: Contains information on raw Ct values for all used genes used in this study. Additionally the file contains information on the individuals used to obtain these Ct values in the study.
DOI: 10.5061/dryad.3h4m5.2/19.2
title: C6_1clock_paramConvergence

description: File_C6 (plain text).  Convergence diagnostics for numerical parameters from MrBayes [9] for the analysis in Files C2-4.  PSRFs (ratio of within-run to between-run variance) is approximately 1 for all parameters, consistent with the view the MCMC runs are sampling from the same posterior and consistent with good convergence [10].
DOI: 10.5061/dryad.3h4m5.2/21.2
title: C8_8clocks_PostburninTrees&Params_folder

description: File_C8 (zipped, plain text).  The full MCMC tree and parameter output files from the MrBayes analysis in file C7.   Only post-burnin samples for each of the 4 runs (last 10 million, see below) are included to reduce file sizes. Run the MrBayes file in C7 (first disabling the MCMC command) and setting burnin to 0 to generate consensus trees and statistics. Run the relevant MrBayes file (disabling the MCMC command) and setting burnin to 0 to generate consensus statistics.
DOI: 10.5061/dryad.3h4m5.2/22.2
title: C9_8clocks_con_fig

description: File_C9 (approximate nexus format).  The majority-rule consensus tree from the MrBayes analysis in files C6-7.
DOI: 10.5061/dryad.3h4m5.2/23.2
title: C10_8clocks_topolConvergence

description: File_C10 (pdf). Convergence diagnostics for tree topologies sampled in C8.  (A) AWTY [20] plots demonstrating relatively good correlation (albeit with substantial variance) for all clades across 4 runs, and (A) high variation at different stages in a single run, but no obvious directional trends.   The topology convergence statistics from MrBayes and AWTY (standard deviation of split frequencies across runs) were also relatively good ie being &lt;0.093 across all comparisons (see top right cells of panel A).   These results are consistent with convergence or near-convergence, i.e. runs sampling similar distributions but cycling very slowly through parameter space.
DOI: 10.5061/dryad.3h4m5.2/24.2
title: C11_8clocks_param_summary

description: File_C11 (plain text).  Convergence diagnostics for numerical parameters from MrBayes [10] for the analysis in Files C7-9.  PSRFs (ratio of within-run to between-run variance) is very  1 for most numerical parameters, but approaches ~1.7 for a single parameter (due to variance in 1 run).  This single outlier is slightly higher than desirable.  These diagnostics do not indicate convergence, though are consistent with convergence being approached.
DOI: 10.5061/dryad.3h4m5.2/25.2
title: C12_NodeAges

description: File_C12 (Word docx).  Comparison of divergence dates obtained from the single-clock and multi-clock analyses, and two previous studies [6,9].  Numerical dates were not published in [9] so dates were retrieved from a detailed time-tree (Figure S1) and are thus shown as estimated (e.g. ~56).
DOI: 10.5061/dryad.437t2/1
title: Recordingdata2013allspecies

description: The data was collected in the field from 15 April to 15 May (from 27 April to 15 May for the Voorstonden location). The first column shows the 7 sites (from 1 to 7) used in the models as random effects. Site 1 corresponds to a location called ‘Lebret’s Hoeve’, site 2 to ‘Voorstonden’, site 3 to ‘Radio Kootwijk’, and site 7 to ‘Hijkerveld’. Sites 4 and 5 are adjacent spatially and correspond to a location called ‘ASK Doornspijk’. Finally, site 6 consists of two sites merged together because they overlap in a location called ‘Klaterweg’. The onsets (column 7) have therefore been obtained from the mean onsets in the two former sites for each light treatment on each day.The second column shows the 3 levels of 'Treatment', which represents the transects where the data has been collected (green, red, or white light transect). The third column shows the 'Formal date', i.e.,  the date at which the bird was singing (in calendar days).The fourth column shows the (relative) ‘date', which is the date relative to 15 April (0 = 15 April), and which has been used in the models as a random slope.The fifth column shows the 'onset relative to control'. This variable is calculated for each species, at each site and on each day, as the difference (in min) in the onset of dawn song between each light treatment (red/green/white) and the dark control. The sixth and last column shows the 'species' for which the onset is shown (14 levels, vernacular names shown).
DOI: 10.5061/dryad.5kq4r/3
title: Macquaria_australasica_field_ratios

description: Contains the data of the calculated ratios between nuclear and mitochondrial environmental DNA concentrations for the field study.
DOI: 10.5061/dryad.5kq4r/4
title: Rscript_Bylemans et al (MEE)

description: This is the R script which when run on "Macquaria_australasica_experimental.csv", "Macquaria_australasica_ratios.csv" and "Macquaria_australasica_field_ratios.csv" will produce and print Figure 3, 4 and 5 contained within the main manuscript.
DOI: 10.5061/dryad.5kq4r/5
title: ReadMe

description: This readme file describes the data files accompanying the publication "An environmental DNA (eDNA) based method for monitoring spawning activity: a case study using the endangered Macquarie perch (Macquaria australasica)" by Bylemans et al. For any further queries please contact Jonas.Bylemans@canberra.edu.au
DOI: 10.5061/dryad.6qk05/1
title: Oncology data_30 Jan 2017

description: Excel sheet containing the control and cases for the oncology including demographics and bacteriology
DOI: 10.5061/dryad.73s68/2
title: Population_density
DOI: 10.5061/dryad.73s68/3
title: Challenge_data
DOI: 10.5061/dryad.7f55p/1
title: Behavioral, developmental, and eye size data

description: This excel sheet contains: 1) individual-level summary of performance in behavioral trials, 2) raw data for individuals choosing correct colored sponges versus making mistakes in behavioral trials, 3) all individuals that attempted the behavioral trial (including those that did not participate), 4) development time and survival data for all individuals transferred onto control and lead diets, and 5) eye size and wing size data for individuals reared on control and lead diets.
DOI: 10.5061/dryad.8182t/1
title: Bananaquit (Coereba flaveola) genome annotation

description: Structural and functional annotation (.gff) file for the genes, exons, and CDS from bananaquit genome sequencing and assembly (NCBI Bioproject ID: PRJNA353240).
DOI: 10.5061/dryad.8182t/2
title: Bananaquit (Coereba flaveola) transcripts

description: Fasta file for the annotated transcripts from bananaquit genome sequencing and assembly (NCBI Bioproject ID: PRJNA353240).
DOI: 10.5061/dryad.8182t/3
title: Bananaquit (Coereba flaveola) proteins

description: Fasta file for the annotated proteins from bananaquit genome sequencing and assembly (NCBI Bioproject ID: PRJNA353240).
DOI: 10.5061/dryad.832t8/5
title: b120haplotypes

description: Alignment of haplotypes found at B120 (S-locus lectin kinase 9; At4g21390).  Individual sequences have been deposited to Genbank.
DOI: 10.5061/dryad.832t8/6
title: b160haplotypes

description: Alignment of haplotypes at B160 (transcription factor; At4g21430).  Sequences were deposited to Genbank for a previous project (Popset accession: 374282986).
DOI: 10.5061/dryad.9qt80/1
title: Data Oecologia Fuchs et al

description: Aphid numbers and aphid predator numbers per week and pot. qPCR data from quantifying fungal DNA weekly. UPLC-MS data for endophyte derived alkaloids in the grass per week.
DOI: 10.5061/dryad.bv3nf/1
title: Dietrich_Mothur_Phylotype_table

description: This file contains the phylotype table of the 18 bat samples and 2 negative controls, after processing with MOTHUR.
DOI: 10.5061/dryad.bv3nf/2
title: Dietrich_reads

description: This folder contains the FASTQ.GZ files with the 16S rRNA sequences generated for the 18 bat samples and the 2 negative controls. Forward and reverse primers were removed at 100% nucleotidic identity and sequences were quality trimmed when Q score &lt; 30.
DOI: 10.5061/dryad.c9086/11
title: wells (within plate where DNA samples are stored)

description: ## -- Table wells -- ##
Information about the wells (within plate) where the DNA sample is stored.

 well_id: Numerical identifier (unique per row)
 updated: Last time the information was updated.
plate_id: Numerical identifier of plate.
   plate: Identifier of plate.
    well: Identifier of well (within plate).

** - Technical description of columns - **
Field	Type	Null	Key	Default	Extra
well_id	int(5)	NO	PRI	NULL	auto_increment
updated	timestamp	NO		CURRENT_TIMESTAMP	on update CURRENT_TIMESTAMP
plate_id	int(5)	YES		NULL	
plate	varchar(100)	YES		NULL	
well	varchar(100)	YES		NULL
DOI: 10.5061/dryad.c9d3j/1
title: Cotesia rubecula Data

description: Data from mother-son crosses, outcrosses, and field-gathered Cotesia rubecula cocoons is available in Microsoft Excel format, “Weis et al. Evolution Cotesia.xlsx”, and is accompanied with a metadata description on the first worksheet.  The first data worksheet contains summary information on mother-son and outcrosses of Cotesia rubecula conducted at the University of Minnesota in 2015.  The second data worksheet contains detailed information on the offspring of mother-son and outcrosses.  The third data worksheet contains detailed information on Cotesia rubecula cocoons gathered near the University of Minnesota campus in the 2015 and 2016 growing seasons.
DOI: 10.5061/dryad.c9d3j/2
title: Figures 2 and 3 Simulation Data

description: Simulated data presented in Figures 2, and 3 is available here in Microsoft Excel format, “Weis et al. Evolution Fig2 Fig3.xlsx”, and is accompanied with a metadata description on the first worksheet.
DOI: 10.5061/dryad.c9d3j/3
title: Supporting Information F1 Data

description: Expanded data presented in Supporting Information F is available here in text file format: “SIF1.Data.txt” (Supporting Information F1).
DOI: 10.5061/dryad.cs128/1
title: Genetic and phenotypic matrices

description: Sheet 1 contains Genetic data and Sheet 2 contains Phenotypic data that were used for the analysis. Sheet three contains the code (equivalent to a readme) explaining the layout of both sheets.
DOI: 10.5061/dryad.cs128/2
title: Sequence data

description: This file contains the sequences data that was used to construct the phylogenetic tree
DOI: 10.5061/dryad.dd00m/1
title: CTvsEXT fat measurements
DOI: 10.5061/dryad.dd00m/2
title: CT measurements table