cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s2405/3
title: SNP primer sequences

description: List of 12 markers that were individually validated using seven individuals by PCR and Sanger sequencing.
DOI: 10.5061/dryad.s2405/4
title: Alignments

description: Sanger sequencing alignments are in BioEdit (*.bio) and Fasta format (*.fas).
DOI: 10.5061/dryad.v6726/1
title: Allele Frequency Data

description: This file contains allele frequency data for each of the 14 populations used in the fst-pst analyses. The format of the file format for each population is as follows, for each line: locus number, the total number of genes in the population for the locus, the number of alleles for the locus,  the number of copies of each allele in the population.
DOI: 10.5061/dryad.v6726/2
title: Barcodes

description: This file contains information on the barcode sequence assigned to each individual in our study.
DOI: 10.5061/dryad.v6726/3
title: Structure

description: This is a structure formatted file containing genotypic data for each individual used in the study.
DOI: 10.5061/dryad.v6726/4
title: BEDASSLE

description: This is an R object file that was used to run the BEDASSLE analyses.
DOI: 10.5061/dryad.v6726/5
title: Bootstrap

description: This R script contains the code for the bootstrapping procedure for obtaining confidence intervals for the global pst data as described in the manuscript.
DOI: 10.5061/dryad.v6726/6
title: Calculate_Fsts

description: This python script contains the code for calculating global Fst's for each locus as described in the manuscript.
DOI: 10.5061/dryad.v6726/7
title: FastSimCoal

description: This archive contains the files used to run fastsimcoal2 to obtain the isolation-migration parameter estimates as in the manuscript.
DOI: 10.5061/dryad.0fg55/1
title: Mud_Per1

description: Individual 1 Lateral and Ventral external 500 Hz
DOI: 10.5061/dryad.0fg55/2
title: Mud_Per2

description: Individual 2 Lateral and Ventral external 500 Hz
DOI: 10.5061/dryad.0fg55/3
title: Mud_Per4

description: Individual 3 Lateral and Ventral external 500 Hz
DOI: 10.5061/dryad.0fg55/4
title: Mud_Per5

description: Individual 4 Lateral and Ventral external 500 Hz
DOI: 10.5061/dryad.0fg55/5
title: WaterAbsorb

description: Periophthalmus absorption
DOI: 10.5061/dryad.0fg55/6
title: xrayvids

description: Comparison Highspeed X-ray Video of Lepomis gibbosus and Triturus carnifex Hyoid movements
DOI: 10.5061/dryad.0fg55/7
title: HyoidXR

description: Highspeed X-ray videos of Hyoid movement in Periophthalmus
DOI: 10.5061/dryad.0fg55/8
title: CT_Buccal_Volume

description: CT-Scan internal buccal cavity volume WRL file
DOI: 10.5061/dryad.0fg55/9
title: Readme

description: Read this file for information on the files presented here
DOI: 10.5061/dryad.0h584/5
title: AppendixS1

description: Blast results, GO annotations, GO annotation terms, associated microsatellites (including motif, primer and product size for each SSR) for each of the contigs and for both taxa
DOI: 10.5061/dryad.30qm1/1
title: Soil Test Results for 2009 PLOS

description: Data collected in the field in 2009. Column headings include the following: 1) Year – Year that study was conducted. 2) Stage: Refers to the stage of dry bean development when data was collected including; Plant (Planting Stage) and 2-4TL (two to four trifoliolate leaf stage. 3) Bean: Refers to the bean market class used in the intercropping treatment plots including B - for black beans, N for Navy beans, NONE for when beans were not presents in a plot. 4) Grass: refers to grass species used in the intercropping treatment plot including R (Annual Ryegrass), O (Oats), C (Corn), W (Wheat), and NONE (when grass species was not present in the plot). 5) Rep: refers to replication or block number. 5) Salt - Refers to the soluble salt content in ppm. 6) OM - soil organic matter content in LOI percentage 7) Zn - soil zinc concentration in ppm 8) Fe - soil iron concentration in ppm 8) Mn - soil manganese concentration in ppm 9) Cu - soil copper concentration in ppm 10) NO - soil nitrate nitrogen concentration in ppm.
DOI: 10.5061/dryad.30qm1/2
title: Soil Test Results for 2010 PLOS

description: Data collected in the field in 2010. Column headings include the following: 1) Year – Year that study was conducted. 2) Stage: Refers to the stage of dry bean development when data was collected including; Plant (Planting Stage); 2-4, 4-8, or 8-16 TL (trifoliolate leaf stage); Flower (flowering stage). 3) Bean: Refers to the bean market class used in the intercropping treatment plots including B - for black beans, N for Navy beans, NONE for when beans were not presents in a plot. 4) Grass: refers to grass species used in the intercropping treatment plot including R (Annual Ryegrass), O (Oats), C (Corn), W (Wheat), and NONE (when grass species was not present in the plot). 5) Rep: refers to replication or block number. 5) Salt - Refers to the soluble salt content in ppm. 6) OM - soil organic matter content in LOI percentage 7) Zn - soil zinc concentration in ppm 8) Fe - soil iron concentration in ppm 8) Mn - soil manganese concentration in ppm 9) Cu - soil copper concentration in ppm 10) NO - soil nitrate nitrogen concentration in ppm.
DOI: 10.5061/dryad.49q24/1
title: All sequences and alignments used in study

description: Zipped sequences (fasta) and alignments (multiple formats) for all genes used in analyses
DOI: 10.5061/dryad.8m65n/1
title: Data

description: Behaviour metrics calculated for each fish for each day, together with environmental data (temperature, precipitation and upwelling) for those days.
DOI: 10.5061/dryad.9d030/13
title: Supplementary file 14

description: The crossing information of RILs to generate IMF2s.
DOI: 10.5061/dryad.9d030/14
title: Supplementary file 1

description: The statistics of reads after quality filtering, size filtering, ncRNA filtering and genome mapping for redundant and distinct reads for 98 crosses in the IMF2 population, the parents Zhenshan 97, Minghui 63 and their F1 hybrid.
DOI: 10.5061/dryad.9d030/15
title: Supplementary file 7

description: The QTL analysis results of s-traits, sc-traits and e-traits.
DOI: 10.5061/dryad.9d030/16
title: Supplementary file 8
DOI: 10.5061/dryad.9d030/17
title: Supplementary file 10
DOI: 10.5061/dryad.9d030/18
title: Supplementary file 11
DOI: 10.5061/dryad.9d030/19
title: Supplementary file 12
DOI: 10.5061/dryad.9d030/20
title: Supplementary file 13

description: Genetic effects of the sQTLs and scQTLs.
DOI: 10.5061/dryad.fj276/1
title: ESM1 Symbiodinium genomic data

description: Electronic supplementary material 1. Fasta file containing the Symbiodinium genomic data used to filter the Orbicella faveolata metatranscriptome. This file includes contigs from Symbiodinium types A, A3, B1 and C1. For further details on the A3 and C1 data contact Dr. Todd C. LaJeunesse at The Pennsylvania State University.
DOI: 10.5061/dryad.fj276/2
title: ESM2 Bleaching metatranscriptome transcriptome

description: Electronic supplementary material 2. Fasta file containing 442294 contigs of the assembled Orbicella faveolata metatranscriptome.
DOI: 10.5061/dryad.hr4g0/1
title: dryad-12-23-14

description: Genotypes and geographic coordinates of Bombus vosnesesnkii workers collected from 21 populations in California in 2011.
DOI: 10.5061/dryad.hv431/1
title: Spawning location and phenotypic data for parents and offspring
DOI: 10.5061/dryad.hv431/2
title: Wenatchee River Chinook salmon genetic and phenotypic data
DOI: 10.5061/dryad.j7090/1
title: DeLisle&Rowe_Data

description: Data set of amphibian body sizes (previously published) as well as Redlist extinction risk and approximate latitudinal midpoint of species ranges, compiled from the IUCN and Amphibiaweb, respectively
DOI: 10.5061/dryad.j7090/2
title: DeLisle&Rowe_Chronogram

description: Pyron and Wiens 2011 molecular phylogeny of the Amphibia, dated by penalized maximum likelihood under a strict-clock model with fossil calibration points.
DOI: 10.5061/dryad.rq120/2
title: Populations Exposed
DOI: 10.5061/dryad.v6726/10
title: Maxent ASCII

description: This is the habitat suitability output file from Maxent.
DOI: 10.5061/dryad.v6726/11
title: Morphological Data

description: This file contains the morphological data used for calculating Psts.
DOI: 10.5061/dryad.v6726/12
title: Population Coordinates

description: This file contains the geographic coordinates (WGS84) for each population used in the landscape genetic analyses.
DOI: 10.5061/dryad.v6726/8
title: Fst_Bootstrap

description: This R script contains the code for calculating bootstrapped confidence intervals for global Fst as described in the manuscript.
DOI: 10.5061/dryad.v6726/9
title: IBDWS

description: This text file contains the distance matrix information used for testing for isolation by distance using the Isolation by distance web server.
DOI: 10.5061/dryad.30qm1/3
title: Tissue Results for 2009 and 2010 PLOS

description: Data collected in the field in 2009 and 2010. Column headings include the following: 1) Year – Year that study was conducted. 2) Stage: Refers to the stage of dry bean development when data was collected including; 2-4 or 8-16 TL (trifoliolate leaf stage). 3) Bean: Refers to the bean market class used in the intercropping treatment plots including B - for black beans, N for Navy beans, NONE for when beans were not presents in a plot. 4) Grass: refers to grass species used in the intercropping treatment plot including R (Annual Ryegrass), O (Oats), C (Corn), W (Wheat), and NONE (when grass species was not present in the plot). 5) Rep: refers to replication or block number. 6) Zn – dry bean tissue zinc concentration in ppm 7) Fe - dry bean tissue iron concentration in ppm 8) Mn - dry bean tissue manganese concentration in ppm 9) Cu - dry bean tissue copper concentration in ppm 10) Mo - dry bean tissue molybdenum concentration in ppm 11) NO - dry bean tissue nitrate nitrogen concentration in ppm.
DOI: 10.5061/dryad.30qm1/4
title: Chlorophyll 2009 and 2010 PLOS

description: Data collected in the field in 2009 and 2010. Column headings include the following: 1) Year – year that study was conducted. 2) Stage: Refers to the stage of dry bean development when data was collected including; 2-4 or 8-16 TL (trifoliolate leaf stage). 3) Rep: refers to replication or block number. 4) Bean: Refers to the bean market class used in the intercropping treatment plots including B - for black beans, N for Navy beans, NONE for when beans were not presents in a plot. 5) Grass: refers to grass species used in the intercropping treatment plot including R (Annual Ryegrass), O (Oats), C (Corn), W (Wheat), and NONE (when grass species was not present in the plot). 6) Chloro – Chlorophyll intensity in SPAD units.
DOI: 10.5061/dryad.30qm1/5
title: Bean Yields 2009 and 2010

description: Data collected in the field in 2009 and 2010. Column headings include the following: 1) Year – year that study was conducted. 2) Bean: Refers to the bean market class used in the intercropping treatment plots including B - for black beans, N for Navy beans, NONE for when beans were not presents in a plot. 3) Rep: refers to replication or block number. 4) Grass: refers to grass species used in the intercropping treatment plot including R (Annual Ryegrass), O (Oats), C (Corn), W (Wheat), and NONE (when grass species was not present in the plot). 5) Bean Yield per sub-sample per plot in Kg.
DOI: 10.5061/dryad.427v8/1
title: Host density VS parasite density

description: The file provides densities (per m2) for 310 parasite populations, from 16 freshwater localities in New Zealand, as well as local densities of their hosts.
DOI: 10.5061/dryad.8s96r/1
title: Growth data 0-5y
DOI: 10.5061/dryad.8s96r/2
title: Growth data 5-18y
DOI: 10.5061/dryad.8s96r/3
title: Growth data 0-5y breastfeeding
DOI: 10.5061/dryad.fj276/3
title: ESM3 Bleaching "O. faveolata" transcriptome

description: Electronic supplementary material 3. Fasta file containing 178943 contigs that constitute the ‘Orbicella faveolata’ transcriptome.
DOI: 10.5061/dryad.fj276/4
title: ESM4 Bleaching "Symbiodinium spp." transcriptome

description: Electronic supplementary material 4. Fasta file containing 130217 contigs that constitute the ‘Symbiodinium spp.’ transcriptome.
DOI: 10.5061/dryad.fj276/5
title: ESM5 Bleaching "Other-eukaryotes" transcriptome

description: Electronic supplementary material 5. Fasta file containing 202236 contigs that constitute the ‘other-eukaryotes’ transcriptome.
DOI: 10.5061/dryad.fj276/6
title: ESM6 Annotations metatranscriptome

description: Electronic supplementary material 6. Blast results for all genes found in the Orbicella faveolata metatranscriptome.
DOI: 10.5061/dryad.fj276/7
title: ESM7 Annotations of 1368 coral genes with different expression levels

description: Electronic supplementary material 7. List of 1368 genes from the ‘Orbicella faveolata’ transcriptome with significant differences in expression levels. Of the 1368 genes, 729 were annotated.
DOI: 10.5061/dryad.kb874/1
title: README_Runemark_et_al

description: Readme file containing descriptions of the files deposited for this manuscript
DOI: 10.5061/dryad.kb874/2
title: Geographic_locations_Runemark_et_al

description: A table of the geographic coordinates and population names.
DOI: 10.5061/dryad.kb874/3
title: Microsatellite_data_Runemark_et_al

description: A file containing the raw microsatellite data Fst calculations for the paper were based on. Population affinity is denoted by the codes used on the map in Figure 1 in the paper and the table in Geographic_locations_Runemark_et_al.txt
DOI: 10.5061/dryad.kb874/4
title: SVL_headwidth_Runemark_et_al

description: Contains information on Snout-vent length and head width per individuals. Population affinity is denoted by the population codes from Figure 1 in the manuscript and Geographic_locations_Runemark_et_al.txt
DOI: 10.5061/dryad.kb874/5
title: Dorsal_headshape_RWs_Runemark_et_al

description: Relative warps (RWs) reflecting dorsal head shape of individuals. These were obtained from the tpsRelw software. Population affinity of individuals is denoted by letter combinations as in Figure 1 in the manuscript and Geographic_locations_Runemark_et_al.txt
DOI: 10.5061/dryad.kb874/6
title: Biteforce_headwidth_Runemark_et_al

description: Data on biteforce (unitless measure) in relation to head width for individuals from different populations. Population abbreviations are as in Figure 1 in the manuscript and Geographic_locations_Runemark_et_al.txt
DOI: 10.5061/dryad.kb874/8
title: Available_diet_Runemark_et_al

description: Data on available diet. Taxonomic composition per pitfall trap. The localities are the same as the populations in Figure 1 in the paper and Geographic_locations_Runemark_et_al.txt
DOI: 10.5061/dryad.m1s8s/1
title: Blenckner et al model forcing data

description: This file contains the data which have been used to build the different models (Fig 3). The first column is year, second the cod fishing pressure (Cod F47), third column the cod biomass (TOTALBIO_COD), fourth column the herring fishing pressure (HerF36), fifth column the herring biomass (TOTALBIO_HER), sixth column the sprat biomass (TOTALBIO_SPR), the seventh column the Pseudocalanus accuses biomass in spring (PseudoSpr) , the eight column the cladocerans biomass in summer (CladSum), the ninth column the sea surface temperature in summer (SSTGBSum),  the tenth column the  temperature 40-60 m (T60Sum) and the eleventh column the salinity between 80-100m (S100GB).
DOI: 10.5061/dryad.m1s8s/2
title: Blenckner model simulation results

description: These are the results from the model simulation, where the mean and confidence intervalls are shown in Fig 4. The data file contains the results from the forward (black in Fig 4a-, 100 simulation for each F) and backward (red in Fig 4a-c, 100 simulation for each F) for cod, sprat, herring and Pseudocalanus accuses biomass.
DOI: 10.5061/dryad.n6sn0/1
title: Heterozygosity-Fitness correlation in European Shag

description: Data file includes 3 spreadsheets:1) Micros spreadsheet; Number: numeric code for each bird; year: year of capture; colony: island of capture, Sex: sex of each bird; Phaari02 to Phaari16: alleles at seven microsatellite loci; HL: homozygosity weighted by locus by using CERNICALIN2) Survival spreadsheet;Number: numeric code for each bird; year: year of capture; colony: island of capture; HL: homozygosity weighted by locus by using CERNICALIN; Sex: sex of each bird; V2007toV2013: capture recapture data 3) Reproduction spreadsheet;Number: numeric code for each bird; RS: Reproductive success; year: year of capture; colony: island of capture; Sex: sex of each bird; HL: homozygosity weighted by locus by using CERNICALIN
DOI: 10.5061/dryad.nd154/1
title: Maximum Likelihood Tree (Newick Format) for 51 Pseudomonas Genomes using Azotobacter vinelandii CA as outgroup.

description: Conserved genes (400) based phylogenetic tree of strain RL and representative Pseudomonas genotypes constructed at 1000 bootstrap with Azotobacter vinelandii CA as an out-group. Branch lengths are drawn to scale, with scale bar indicating the number of amino acid substitutions. Numbers on branches are the bootstrap values of the clusters on the right.
DOI: 10.5061/dryad.nd154/2
title: Maximum Likelihood Tree (Nexus Format) for 51 Pseudomonas Genomes using Azotobacter vinelandii CA as outgroup.

description: Conserved genes (400) based phylogenetic tree of strain RL and representative Pseudomonas genotypes constructed at 1000 bootstrap with Azotobacter vinelandii CA as an out-group. Branch lengths are drawn to scale, with scale bar indicating the number of amino acid substitutions. Numbers on branches are the bootstrap values of the clusters on the right.
DOI: 10.5061/dryad.t2f47/1
title: Risk-conditions chronic Q fever vaccination datasets

description: The IPCI-dataset contains all extracted patients from a 5% sample of the population based general practice database, based on selection criteria described in the article. Patients age, sex and risk conditions are supplied with level of diagnostic certainty. The Q fever vaccination dataset contains accepted referrals and registered chronic Q fever risk conditions with sex, age and living area of patients. Code books are included.
DOI: 10.5061/dryad.t7m5v/1
title: SimCoal simulations

description: This compressed folder contains SimCoal simulations of 1-species datasets.
DOI: 10.5061/dryad.t7m5v/2
title: DendroPy simulations

description: This compressed folder contains simulations of 3-species and 6-species datasets obtained using DendroPy.
DOI: 10.5061/dryad.v051c/1
title: invader_fitness_in_pristine_env

description: Invader fitness in pristine environment (Figure 2)
DOI: 10.5061/dryad.v051c/2
title: effect_of_manipulated_env_deg_on_invader_growth

description: Effect of manipulated environmental degradation on invader growth rate (column headings refer to time in 0.5 h increments) (Raw data for Figure 3A)
DOI: 10.5061/dryad.v051c/3
title: effect_of_evolved_res_on_growth_rate

description: Effect of evolved resident on invader growth rate (column headings refer to time in 0.5 h increments) (Raw data for Figure 3B)
DOI: 10.5061/dryad.v051c/4
title: effect_of_evolved_res_on_env_deg

description: Effect of evolved resident on environmental degradation experienced by invader (computed data for Figure 3B)
DOI: 10.5061/dryad.05478/1
title: Simulation Data and AUTO Files

description: This .zip archive contains an .xlsx spreadsheet of data used to plot Figures 7 and 8 of the paper "Use of elastic stability analysis to explain the stress-dependent nature of soil strength". This archive also contains sets of AUTO input files for these simulations (∗.f and c.∗) and the associated AUTO output files (fort.7, fort.8, fort.9).
DOI: 10.5061/dryad.0dk3n/1
title: Chaudhary et al. public data

description: Data used for analysis in: Polygyny without wealth: popularity in gift games predicts polygyny in BaYaka Pygmies (Chaudhary et al. 2015).
DOI: 10.5061/dryad.42711/1
title: Rhizophora mucronata-stylosa genotype data in Genalex format

description: Rhizophora mucronata and R. stylosa population samples genotyped by 20 SSR loci
DOI: 10.5061/dryad.42tr0.1
title: Data from: New World cattle show ancestry from multiple independent domestication events
DOI: 10.5061/dryad.42tr0.2
title: Data from: New World cattle show ancestry from multiple independent domestication events
DOI: 10.5061/dryad.42tr0.2/1.2
title: SNP data
DOI: 10.5061/dryad.4tj59/1
title: Don_PP_IMRnotwins_IMRpaperDryad
DOI: 10.5061/dryad.bv247/1
title: Marques et al Active diet mixing, data Fig. 1a
DOI: 10.5061/dryad.bv247/2
title: Marques et al Active diet mixing, data Fig. 1b
DOI: 10.5061/dryad.bv247/3
title: Marques et al Active diet mixing, data Fig. 1c
DOI: 10.5061/dryad.bv247/4
title: Marques et al Active diet mixing, data Fig. 1d
DOI: 10.5061/dryad.bv247/5
title: Marques et al Active diet mixing, data Fig. 2a
DOI: 10.5061/dryad.bv247/6
title: Marques et al Active diet mixing, data Fig. 2b
DOI: 10.5061/dryad.c194d/1
title: Recombination breakpoints in the 3rd chromosome introgression lines

description: Recombination breakpoints calculated using the MSG pipeline (Andolfatto et al. 2011). Coordinates in the gff files correspond to the D. simulans w501 genome (Hu et al. 2013). File names refer to chromosome and introgression ID.
DOI: 10.5061/dryad.cp8pj/6
title: S1 Stock assessment model information

description: Stock, Spawning Stock Biomass model, Source
DOI: 10.5061/dryad.cp8pj/7
title: S1 Dataset Stock assessment data per species

description: Research Vessel Data of the spatial distribution of fish species, including total number, total weight, time and location
DOI: 10.5061/dryad.cp8pj/8
title: S2 Dataset SSB and source data

description: Year, Spawning Stock Biomass in tonnes, Spawning Stock Number tonnes (x1000), Area, Strata, Species and Data source
DOI: 10.5061/dryad.fb80v/1
title: ERP in isolated rat hearts

description: SPSS data (.sav) file. It contains the effective refractory periods at different loading conditions (0, 20, 40mmHg LVEDP) and with and without GsMtx4 in isolated rat hearts.
DOI: 10.5061/dryad.fb80v/2
title: Induced arrhythmias in rat hearts

description: SPSS data (.sav) file. It contains the number of TV runs (and the sum of ventricular beats in these runs) induced by programmed stimulation in isolated rat hearts at 0, 20, 40 mmHg LVEDP and with and without GsMtx4.
DOI: 10.5061/dryad.kb874/7
title: Realized_diet_composition_Runemark_et_al

description: Contains data on realized diet composition from fecal samples. Contains a table with the realized diet composition of the seven populations included in the study. The first column entitled 'population' includes the population abbreviations (D refers to Mesa Diavates; DII to Exo Diavates; L to Lakonisi; IA to Island of Atsitsa; AF to Agios Fokas; PA to Palamari; N to Nyfi) as illustrated in Figure 1 and given in Figure 3 in the manuscript, the second column denotes the habitat ('I' for islet or 'M' for mainland) and the third the sex of the individual. In the following columns we provide the 19 taxonomic prey categories and the number of each prey item found in the stomach of each individual.
DOI: 10.5061/dryad.mv95p/1
title: Lee et al AmNat 55827

description: Data set for choice and no-choice tests, including performance, body composition, and intake data.
DOI: 10.5061/dryad.nd154/3
title: Alignment Files for protein coding sequences of bacterial conserved marker genes (n=400) for 51 representative Pseudomonas genomes.

description: Phylogenetic status of strain RL was determined using 400 conserved bacterial marker genes and representative whole genome sequences from 40 diverse Pseudomonas species as available in NCBI database (http://www.ncbi.nlm.nih.gov/genome/browse/representative/). A phylogenetic tree was hence constructed using maximum likelihood (ML) methodology on the basis of protein coding bacterial conserved gene (400) sequences [39] determined for Pseudomonas sp. RL and 50 other Pseudomonas strains with Azotobacter vinelandii being the outgroup.
DOI: 10.5061/dryad.qk26v/1
title: ELISA

description: Raw data form TGF-b activation performed by ELISA assays