cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kd1qt0p.1/21.1
title: Figure S2 - source data 1

description: This zip archive contains the original z-stacks used for Figure S2 - source data 1, panels A and C. These are provided as TIF files. All imaging parameters are included in the image metadata. They are labeled as follows: 
A7PS302_s1_t1 = WT USI, Dilution factor = 1
A7PS302_s2_t1 = WT USI, Dilution factor = 1/2
A7PS302_s3_t1 = WT USI, Dilution factor = 1/4
A7PS302_s4_t1 = WT USI, Dilution factor = 1/8
A7PS302_s17_t1 = MUC2KO USI, Dilution factor = 1
A7PS302_s18_t1 = MUC2KO USI, Dilution factor = 1/2
A7PS302_s19_t1 = MUC2KO USI, Dilution factor = 1/4
A7PS302_s20_t1 = MUC2KO USI, Dilution factor = 1/8
A7PS284_s13_t1 = HBSS

Additionally, this file contains .csv files of all the statistics on particle sizes collected by the ImageJ macro. These are labeled in the format “zstackname_automated_counting_statistics”, where “zstackname” is the title of the associated z-stack. It also contains a .csv file of the particle # IDs of the singlet particles that were used to get the average singlet size, which was then used to normalize the ECDFs (as explained in detail in Materials and Methods). These are labeled in the format “zstackname_singlet_IDs”, where “zstackname” is the title of the associated z-stack. These .csv files were used in combination with the Jupyter notebooks (provided with this submission) to generate Figure S2 - source data 1, panels A and C.
DOI: 10.5061/dryad.kd1qt0p.1/22.1
title: Figure S2 - source data 2

description: This zip archive contains the original z-stacks used for Figure S2 - source data 2, panels B and D. These are provided as TIF files. All imaging parameters are included in the image metadata. They are labeled as follows: 
A7PS302_s9_t1 = WT LSI, Dilution factor = 1
A7PS302_s10_t1 = WT LSI, Dilution factor = 1/2
A7PS302_s11_t1 = WT LSI, Dilution factor = 1/4
A7PS302_s12_t1 = WT LSI, Dilution factor = 1/8
A7PS302_s25_t1 = MUC2KO LSI, Dilution factor = 1
A7PS302_s26_t1 = MUC2KO LSI, Dilution factor = 1/2
A7PS302_s27_t1 = MUC2KO LSI, Dilution factor = 1/4
A7PS302_s28_t1 = MUC2KO LSI, Dilution factor = 1/8
A7PS284_s13_t1 = HBSS

Additionally, this file contains .csv files of all the statistics on particle sizes collected by the ImageJ macro. These are labeled in the format “zstackname_automated_counting_statistics”, where “zstackname” is the title of the associated z-stack. It also contains a .csv file of the particle # IDs of the singlet particles that were used to get the average singlet size, which was then used to normalize the ECDFs (as explained in detail in Materials and Methods). These are labeled in the format “zstackname_singlet_IDs”, where “zstackname” is the title of the associated z-stack. These .csv files were used in combination with the Jupyter notebooks (provided with this submission) to generate Figure S2 - source data 2, panels B and D.
DOI: 10.5061/dryad.kd1qt0p.1/27.1
title: Table S3 - source data 1

description: This zip archive contains the chromatography data that was used to calculate the values displayed in Table S3. “WT_USI_raw_data.xlsx” contains the data for the wild-type upper small intestine, “Rag1KO_USI_raw_data.xlsx” contains the data for the immunoglobulin-deficient (Rag1KO) upper small intestine. In both the excel files, RI = refractive index, RALS = Right-angle light scattering, LALS = low-angle light scattering, DP = differential pressure (the viscometer). All values are measured in millivolts except for retention volume, which is measured in milliliters (mL). 
The file “Table S3 – source data 1.OmnisecArchive” contains all this data, along with the data for the pullulan and dextran standard that were used to calibrate the instrument. This can be used in conjunction with Malvern OMNISEC v10.20 software to reproduce the calculations displayed in the table. LALS data was not used for these calculations because of the noisiness of the signal from the detector.
DOI: 10.5061/dryad.kd1qt0p.1/32.1
title: Aggregate Image Analysis Code

description: These FIJI ImageJ macros were used to determine volumes of aggregates of particles in z-stacks.

"Aggregate_Counting_Macro_1.2.4_for_publication.ijm" takes in a z-stack and generates various statistics about aggregates including volume, surface area, and position. Results for Test_dataset_08_01_18 are located in the Results folder.

"Average_Singlet_Size_Macro_1.0.0_for_publication.ijm" takes the object map output from the Aggregate_Counting_Macro and prompts the user to record the ID number associated with 10 single particles. The singlets can then be used to convert aggregate volumes from the Aggregate_Counting_Macro into particle counts.
Written in the ImageJ macro language.

Test dataset was run in FIJI version 2.00-rc-68/1.52e, Build:bad6864e55 using macOS Version 10.13.4.
DOI: 10.5061/dryad.kd1qt0p.1/33.1
title: Bootstrap confidence intervals code

description: This zip folder contains the source code to generate 95% empirical bootstrap confidence intervals. The .html and .ipynb files are identical. The code was written with Python version 3.6.4. It has been verified to work with numpy version 1.13.3, pandas version 0.21.1, scipy version 1.0.0, bokeh version 0.12.15, holoviews version 1.9.1, and numba version 0.36.2. 

 

The test data folder provides data that can be used to verify that the code is working. Make sure to change the file paths to what is appropriate for your computer. The test data will reproduce Figure 7G from the main text. This data was also provided as part of “Figure 7 – source data 4”.
DOI: 10.5061/dryad.kd1qt0p.1/34.1
title: volume-weighted ECDF code

description: This zip folder contains the source code to generate 95% empirical bootstrap confidence intervals The .html and .ipynb file are identical. The code was written with Python version 3.6.4. It has been verified to work with numpy version 1.13.3, pandas version 0.21.1, scipy version 1.0.0, bokeh version 0.12.15, and holoviews version 1.9.1. 

 

The test data folder provides data that can be used to verify that the code is working. Make sure to change the file paths to what is appropriate for your computer. The test data will reproduce Figure 5, Panel A from the main text. This data was also provided as part of “Figure 5 – source data 1”.
DOI: 10.5061/dryad.kd1r166/1
title: AllSpeciesPhenology
DOI: 10.5061/dryad.kd1r166/2
title: AllSpeciesVisitation
DOI: 10.5061/dryad.kd1r166/5
title: Mertensia_SeedSet
DOI: 10.5061/dryad.kd1r166/6
title: Potentilla_SeedSet
DOI: 10.5061/dryad.kd1r166/7
title: MetaDataFile

description: This file gives the project description and the column description for each file.
DOI: 10.5061/dryad.nh773s0/1
title: reptile DDR

description: Grazing intensity and reptile trait group richness
DOI: 10.5061/dryad.pv814j1/53
title: Specimen 24 Control
DOI: 10.5061/dryad.pv814j1/54
title: Specimen 24_2cut
DOI: 10.5061/dryad.pv814j1/55
title: Specimen 25 Control
DOI: 10.5061/dryad.pv814j1/56
title: Specimen 25_2cut
DOI: 10.5061/dryad.pv814j1/57
title: Specimen 26 Control
DOI: 10.5061/dryad.pv814j1/58
title: Specimen 26_1cut
DOI: 10.5061/dryad.pv814j1/59
title: Specimen 27 Control
DOI: 10.5061/dryad.pv814j1/60
title: Specimen 27_1cut
DOI: 10.5061/dryad.qh4fd46/1
title: data used for the IPM

description: Contains the data used in the IPM and its description
DOI: 10.5061/dryad.qh4fd46/2
title: Rdata

description: Contains all data in a format ready to use in order to run the IPM in jags (script of the IPM available in the Appendix section).
DOI: 10.17632/kz555pcr99.1
title: Data for: Study on properties of anti-reflective and superhydrophobic films prepared by magical sol
DOI: 10.17632/xfwwscyvn9.1
title: Data for: Rheological study of W/O oil emulsion by low-field NMR

description: Petroleum chemistry
DOI: 10.5061/dryad.114j8m1/1
title: VCF file of full, filtered dataset

description: VCF file of 13,424 single nucleotide polymorphisms (SNPs) derived from genotype-by-sequencing of 117 Olympia oysters (Ostrea lurida) sampled across 19 populations, filtered for a minor allele frequency of 2.5% and no more than 75% missing data.
DOI: 10.5061/dryad.114j8m1/2
title: Fasta file of outlier GBS loci

description: Fasta file of 129 genotype-by-sequencing loci potentially involved in local adaptation, as determined by at least two methods (pcadapt, OutFLANK, or BayeScan). The 18 loci with positive BLASTx hits are annotated.
DOI: 10.5061/dryad.114j8m1/3
title: VCF file of putative neutral SNPs

description: VCF file of 13,073 putative neutral SNPs derived from genotype-by-sequencing data of 117 Olympia oysters (Ostrea lurida) sampled across 19 populations. Obtained by filtering the full dataset of any SNP found on a locus containing at least one outlier SNP.
DOI: 10.5061/dryad.2m9r762/1
title: Doi&Hillebrand-FCL-data

description: The data used in this study, experimental setup (inputted pellet mass and species sequence), the number of individuals in the species at the final day (28 days) of the experiment, food-chain length (FCL) from d15N of copepod, and copepod biomass.
DOI: 10.5061/dryad.4d72h89/1
title: Behavioural plasticity for parent-offspring coadaptation

description: We measured parent-offspring interactions in canaries (Serinus canaria) at two different levels of nestling hunger (30 minutes and 60 minutes) in order to be able to separate between- and within-nest covariances.
DOI: 10.5061/dryad.4t46jj6/2
title: distance_between_plots

description: Pairwise distances (in meters) between all 94 plots. "trans1" and "trans2" give the plot numbers, and "dist" the distance between the two plots in meters.
DOI: 10.5061/dryad.61r43kd/2
title: Supplementary_OTUtable

description: OTUtable with OTUs generated during this study. For each sample, sequence ID matching that of Supplementary_Metadata, the total number of OTUs belonging to different bacterial taxonomic groups as assigned by the RDP classifier, are listed.
DOI: 10.5061/dryad.6kv7k29/1
title: Files to perform the working example of bioclimatic consistency strategy

description: Map of bioclimatic congruence (congruence.grd) and the SDM prediction of Litucranius walleri (pr_Litocranius_walleri.grd) to perform the working example of bioclimatic consistency strategy.
DOI: 10.5061/dryad.70955d1/1
title: alignment files

description: Alignment files used in the article "Increased evolutionary rates and conserved transcriptional response following allopolyploidisation in brown algae"
DOI: 10.5061/dryad.73rj625/6
title: Restriction Site Associated DNA data (ddRAD) - for fineRADstructure

description: Stacks output that can be converted into the fineRADstructure input file using the Stacks2fineRAD.py script available at http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html
DOI: 10.5061/dryad.73rj625/7
title: Restriction Site Associated DNA data (ddRAD) - STACKS assembly

description: Final STACKS assembly. Includes two population maps: 1) all samples; 2) samples with low missing data that are in the paper.
Files in different formats (structure, vcf, genpop, etc) can be exported using the "populations" module from stacks.
DOI: 10.5061/dryad.73rj625/8
title: Restriction Site Associated DNA data (ddRAD) - fastq files

description: A folder containing 36 fastq files named after the samples to which the sequences belong.
It includes samples that were discarded because of high levels of missing data.
DOI: 10.5061/dryad.7bp65gp/1
title: S10189

description: Aligned nucleotide sequences. Data also available in TreeBASE at accession S10189  . First deposited for Bell C. 2010. Towards a Species Level Phylogeny of Symphoricarpos (Dipsacales), Based on Nuclear and Chloroplast DNA. Systematic Botany, 35(2): 442-450. https://doi.org/10.1600/036364410791638351
DOI: 10.5061/dryad.92dj50c/5
title: Preisler et al. 2019_ Bucket model results_Figure 5

description: The bucket model simulation results output.
DOI: 10.5061/dryad.980538t/1
title: winlose_production_line_bic

description: The production line scripts were made in order to turn a file describing colony battle outcomes and the species of the two colonies into a response, explanation variable file fit for regression analysis. The explanation variables are trait differences (thus ensuring reshuffling symmetry) made using a separate trait file describing the traits of each species. Interaction terms are made in addtion, before a random subset of battles are reshuffled, meaning that the outcome and each explanation variable is reversed. This in order to make sure there are both wins and losses in the output file, which then can be used in regression. This production line was used for making a single regression file, usable for for instance (but not restricted to) BIC-based model search on regression models (as opposed to a training-validation-test-based model search).
DOI: 10.5061/dryad.980538t/2
title: winlose_production_line_tvt

description: See the description for winlose_production_line_bic for details concerning turning a battle outcome and species trait file into a reshuffled regressison file. The training-validation-test (tvt) version of this production line separates the species into a training set (battles are in the training set if both combatants are in the training species set), a validation set (battles are in the validation set if at least one combatant is in the validation species set and none are in the test species set) and a test set (battles are in the test set if at least one combatant is in the test species set). Instead of one regression files, three are thus produced.
DOI: 10.5061/dryad.980538t/3
title: winlose_analyze_bic

description: This collection of files contains the regression data (the result of running the production line scripts) and the analysis scripts for BIC-based model search. It contains one analysis script for the set of simple explanation variables and another for the full explanation variable set (including interaction terms and using random search). It also contains similar analysis scripts for the 3 external datasets.
DOI: 10.5061/dryad.980538t/4
title: winlose_analyze_tvt

description: This collection of files contains the training, validation and test regression data files (the result of running the production line scripts) and the analysis scripts for training-validation-test-based model search. It contains one analysis script for the set of simple explanation variables and another for the full explanation variable set (including interaction terms and using random search).
DOI: 10.5061/dryad.980538t/5
title: winlose_present

description: This contains an R script (and accompanying regression datasets) for presenting the result of the BIC-based model selection search, including regression coefficient estimates for the best model, variance decomposition, prediction strength assessment and tests on external datasets.
DOI: 10.5061/dryad.980538t/6
title: winlose_reselection

description: This set of scripts resamples the data in various ways in order to answer whether the results of the BIC model selection could come about due to pure chance, random species effects or random species-species pair effects.
DOI: 10.5061/dryad.980538t/9
title: FormationAges

description: Contains a description of each site and the age it represents. Used for assigning age numbers in the trait-age interaction terms.
DOI: 10.5061/dryad.f6s45p7/1
title: Acoustic, morphometric, and ecological data of glassfrogs (Centrolenida)

description: We obtained acoustic data from analyses of audio recordings gathered from personal and museum collections for 67 species and from the bibliography for 5 species. We obtained morphometric data for 67 glassfrog species from the literature, and for 11 species from fellow researchers. We compiled the predominant calling site of each species from the literature (72 species) and complemented it with field observations provided by fellow researchers. We compiled parental care (i.e., prolonged attendance) data from Delia et al. (2017). See Escalona et al., Journal of Evolutionary Biology, for more details.
DOI: 10.5061/dryad.f6s45p7/2
title: Dataset S1. Sound records analyzed per species, with the corresponding authorship, locality, and coordinates with its source.
DOI: 10.5061/dryad.j0s643c/1
title: Data_Fowler et al_Starling

description: Data on 14 physiological variables and measures of workload, current productivity, future fecundity, and survival measured in 93 female European starlings (Sturnus vulgaris) at two breeding stages (incubation, chick-rearing), for first-and second-broods over two years (152 observations).
DOI: 10.5061/dryad.k73988d/1
title: Lifespan and reproductive data for temperature and sexual conflict level treatments
DOI: 10.5061/dryad.kd1qt0p.1/24.1
title: Figure S5 - source data 2

description: This zip archive contains the original z-stacks used for Figure S5, panels B and D. These are provided as TIF files. All imaging parameters are included in the image metadata. They are labeled as follows: 
A7PS308_s9_t1 = WT LSI, Dilution factor = 1
A7PS308_s10_t1 = WT LSI, Dilution factor = 1/2
A7PS308_s11_t1 = WT LSI, Dilution factor = 1/4
A7PS308_s12_t1 = WT LSI, Dilution factor = 1/8
A7PS308_s25_t1 = Rag1KO LSI, Dilution factor = 1
A7PS308_s26_t1 = Rag1KO LSI, Dilution factor = 1/2
A7PS308_s27_t1 = Rag1KO LSI, Dilution factor = 1/4
A7PS308_s28_t1 = Rag1KO LSI, Dilution factor = 1/8
A7PS284_s13_t1 = HBSS

Additionally, this file contains .csv files of all the statistics on particle sizes collected by the ImageJ macro. These are labeled in the format “zstackname_automated_counting_statistics”, where “zstackname” is the title of the associated z-stack. It also contains a .csv file of the particle # IDs of the singlet particles that were used to get the average singlet size, which was then used to normalize the ECDFs (as explained in detail in Materials and Methods). These are labeled in the format “zstackname_singlet_IDs”, where “zstackname” is the title of the associated z-stack. These .csv files were used in combination with the Jupyter notebooks (provided with this submission) to generate Figure S5, panels B and D.
DOI: 10.5061/dryad.kd1qt0p.1/25.1
title: Table S1 - source data 1

description: This zip archive contains the chromatography data that was used to calculate the values displayed in Table S1. “WT_USI_raw_data.xlsx” contains the data for the wild-type upper small intestine, “KO_USI_raw_data.xlsx” contains the data for the MUC2 knockout upper small intestine. In both the excel files, RI = refractive index, RALS = Right-angle light scattering, LALS = low-angle light scattering, DP = differential pressure (the viscometer). All values are measured in millivolts except for retention volume, which is measured in milliliters (mL). 
The file “Table S1 – source data 1.OmnisecArchive” contains all this data, along with the data for the pullulan and dextran standard that were used to calibrate the instrument. This can be used in conjunction with Malvern OMNISEC v10.20 software to reproduce the calculations displayed in the table.
DOI: 10.5061/dryad.kd1qt0p.1/28.1
title: Table S4 - source data 1

description: This zip archive contains the chromatography data that was used to calculate the values displayed in Table S4. “WT_LSI_raw_data.xlsx” contains the data for the wild-type lower small intestine, “Rag1KO_LSI_raw_data.xlsx” contains the data for the immunoglobulin-deficient (Rag1KO) lower small intestine. In both the excel files, RI = refractive index, RALS = Right-angle light scattering, LALS = low-angle light scattering, DP = differential pressure (the viscometer). All values are measured in millivolts except for retention volume, which is measured in milliliters (mL). 
The file “Table S4 – source data 1.OmnisecArchive” contains all this data, along with the data for the pullulan and dextran standard that were used to calibrate the instrument. This can be used in conjunction with Malvern OMNISEC v10.20 software to reproduce the calculations displayed in the table. LALS data was not used for these calculations because of the noisiness of the signal from the detector.
DOI: 10.5061/dryad.kd1qt0p.1/29.1
title: Table S5 - source data 1

description: This zip archive contains the chromatography data that was used to calculate the values displayed in Table S5. “pectin_raw_data.xlsx” contains the data for pectin, “fibersol-2_raw_data.xlsx” contains the data for Fibersol-2. In both the excel files, RI = refractive index, RALS = Right-angle light scattering, LALS = low-angle light scattering, DP = differential pressure (the viscometer). All values are measured in millivolts except for retention volume, which is measured in milliliters (mL). 
The file “Table S5 – pectin source data” contains all the data for pectin, along with the data for the pullulan and dextran standard that were used to calibrate the instrument for this run. The file “Table S5 – fibersol-2 source data” contains all the data for Fibersol-2, along with the data for the pullulan and dextran standard that were used to calibrate the instrument for this run. This can be used in conjunction with Malvern OMNISEC v10.20 software to reproduce the calculations displayed in the table. LALS data was not used for these calculations because of the noisiness of the signal from the detector.
DOI: 10.5061/dryad.kd1qt0p.1/30.1
title: Table S6 - source data 1

description: This zip archive contains the chromatography data that was used to calculate the values displayed in Table S6. “pectin_USI_raw_data.xlsx” contains the data for the upper small intestine of pectin-fed mice, “Fibersol-2_USI_raw_data.xlsx” contains the data for the upper small intestine of Fibersol-2-fed mice. In both the excel files, RI = refractive index, RALS = Right-angle light scattering, LALS = low-angle light scattering, DP = differential pressure (the viscometer). All values are measured in millivolts except for retention volume, which is measured in milliliters (mL). 
The file “Table S6 – source data 1” contains all the data, along with the data for the pullulan and dextran standard that were used to calibrate the instrument. This can be used in conjunction with Malvern OMNISEC v10.20 software to reproduce the calculations displayed in the table. LALS data was not used for these calculations because of the noisiness of the signal from the detector.
DOI: 10.5061/dryad.kd1qt0p.1/31.1
title: Table S7 - source data 1

description: This zip archive contains the chromatography data that was used to calculate the values displayed in Table S7. “pectin_LSI_raw_data.xlsx” contains the data for the lower small intestine of pectin-fed mice, “Fibersol-2_LSI_raw_data.xlsx” contains the data for the lower small intestine of Fibersol-2-fed mice. In both the excel files, RI = refractive index, RALS = Right-angle light scattering, LALS = low-angle light scattering, DP = differential pressure (the viscometer). All values are measured in millivolts except for retention volume, which is measured in milliliters (mL). 
The file “Table S7 – source data 1” contains all the data, along with the data for the pullulan and dextran standard that were used to calibrate the instrument. This can be used in conjunction with Malvern OMNISEC v10.20 software to reproduce the calculations displayed in the table. LALS data was not used for these calculations because of the noisiness of the signal from the detector.