cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m3t8r8v/7
title: E301-E350 raw illumina files

description: Raw Illumina data files for the Illumina Miseq sequencing of a library of tagged specimens of Microgastrinae (Hymenoptera: Braconidae) for COI (in two amplicons), Wingless and ITS2. This file contains Extraction codes E301-E350. Sample information for all specimens can be found as supporting information at: https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.12904 . The original data was generated for the paper:  Fagan-Jeffries, E.P., Cooper, S.J.B., Bertozzi, T., Bradford, T.M. & Austin, A.D. (2018) DNA barcoding of microgastrine parasitoid wasps (Hymenoptera: Braconidae) using high-throughput methods more than doubles the number of species known for Australia. Molecular Ecology Resources 18, 1132–1143.
DOI: 10.5061/dryad.m3t8r8v/8
title: E351-E450 raw illumina files

description: Raw Illumina data files for the Illumina Miseq sequencing of a library of tagged specimens of Microgastrinae (Hymenoptera: Braconidae) for COI (in two amplicons), Wingless and ITS2. This file contains Extraction codes E351-E450. Sample information for all specimens can be found as supporting information at: https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.12904 . The original data was generated for the paper:  Fagan-Jeffries, E.P., Cooper, S.J.B., Bertozzi, T., Bradford, T.M. & Austin, A.D. (2018) DNA barcoding of microgastrine parasitoid wasps (Hymenoptera: Braconidae) using high-throughput methods more than doubles the number of species known for Australia. Molecular Ecology Resources 18, 1132–1143.
DOI: 10.5061/dryad.mf4h560/1
title: foglets_days

description: Contains data on numbers of metamorphs leaving the pond per day (days are defined from median date of clutch deposition 2013/04/11 untill day of metamorphosis) and date.
DOI: 10.5061/dryad.mf4h560/2
title: all_froglets_111017

description: Contains data on date the metamorph was sampled, metamorph ID, body size (SVL in mm), Mass in g, day of emergence from the pond, day of migration (starts with the first metamoph collected). Total number of sampled metamorphs is 1943.
DOI: 10.5061/dryad.mf4h560/3
title: meta_traits_cluster

description: Contains metamorph ID, probability of sibship calculated by Colony software, father ID, mother ID, cluster number, size of the metamorph (SVL in mm), Mass in g, day of metamorphosis (defined as days from 2013/04/11 onwards), day of migration (starts with the first metamophs found on 2013/07/08), date, fathers (same or all) and Matriline number. Total number of metamorphs is 733 (same father= 294, all fathers= 439).
DOI: 10.5061/dryad.mf4h560/4
title: temp_rain_air_temp

description: Contains environmental variables. The date of measurement, daily mean water temperature in the pond (av_temp), daily standard deviation of mean water temperature in the pond (sd_temp, measurement of temperature every 3 hours), daily amount of rain in mm and mean air temperature in 2m above ground.
DOI: 10.5061/dryad.pv814j1/10
title: Specimen 4_1 cut_Part B
DOI: 10.5061/dryad.pv814j1/11
title: Specimen 4_1 cut_Part C
DOI: 10.5061/dryad.pv814j1/12
title: Specimen 5 Control
DOI: 10.5061/dryad.pv814j1/13
title: Specimen 5_1 cut
DOI: 10.5061/dryad.pv814j1/14
title: Specimen 5_2cut
DOI: 10.5061/dryad.pv814j1/15
title: Specimen 6 Control
DOI: 10.5061/dryad.pv814j1/16
title: Specimen 6_1cut
DOI: 10.5061/dryad.pv814j1/9
title: Specimen 4_1 cut_Part A
DOI: 10.5061/dryad.sv67kd4/1
title: Butterfly microbiome and community metabolic profiling data (open format)

description: Butterfly metadata, microbiome data (16s and ITS OTU tables; microbial taxonomic identifications; and representative fasta sequences for the OTUs) and gut community metabolic profiling (Biolog assay) data in .csv and .txt formats. See README file for additional information about individual files.
DOI: 10.5061/dryad.sv67kd4/2
title: R script and R-formatted data

description: This directory includes an R script that generates the figures from the associated manuscript, as well as butterfly metadata, microbiome (16s and ITS) data, and community metabolic profiling data in the .Rdata format. See the README for more information about individual files.
DOI: 10.5061/dryad.v6p96q5/1
title: LCMS annotated peaks

description: Spreadsheet contains LCMS identified and unidentified peaks. Includes relative concentrations.
DOI: 10.5061/dryad.v6p96q5/2
title: NMR Diversity & EcologicalData

description: Spreadsheet contains NMR diversity indices for each sample. The ecological data is included.
DOI: 10.5061/dryad.17hf071/1
title: Observed Flight dates

description: This file contains the first flight date information for adult Common green darners (Anax junius) used to generate Fig 1.
DOI: 10.5061/dryad.17hf071/2
title: Green Darner Isotope data

description: This file contains isotope data used to make natal geographic assignments to reveal the annual cycle and migration of the Common green darner (Anax junius).
DOI: 10.5061/dryad.1gv57s0/1
title: Captures_By_Trap_PEMA_REME

description: Capture data for deer mice and harvest mice.
DOI: 10.5061/dryad.1gv57s0/2
title: Ellis_Cushman_MICA

description: Capture data for meadow voles (Microtus californicus)
DOI: 10.5061/dryad.1gv57s0/3
title: seedremoval

description: Data for seed removal experiment
DOI: 10.5061/dryad.26c0m59/1
title: DATA_pilosocereus_leucocephalus_frugivory_records

description: Records of frugivory of Pilosocereus leucocephalus by birds and bats
DOI: 10.5061/dryad.26c0m59/2
title: METADATA_pilosocereus_leucocephalus_frugivory_records

description: METADATA or README file to interpret dataset
DOI: 10.5061/dryad.2pm2j8j/1
title: ITS_alignment_for_mrbayes.nexus

description: NEXUS-formatted ITS alignment for use with MrBayes
DOI: 10.5061/dryad.2pm2j8j/2
title: AFLP_data_matrix

description: Fasta-formatted AFLP data matrix. Individual abbreviations as in the Table S1 in the manuscript.
DOI: 10.5061/dryad.45873cg/1
title: R script

description: Fully annotated R code corresponding to 1) the IPM; 2) the 3 density-dependence models shown in the paper.
DOI: 10.5061/dryad.45873cg/2
title: Data files

description: For the 11 sites included in the study (see Appendix S1 for a map), for both great tit (GT) and blue tit populations (BT), the year of breeding "YearOfBreeding", the female identity "MotherID", its age "AgeMother", its status "StatusMother" ("I" immigrant; "R" locally recruited; "S" survived from previous year) and the number of daughters locally recruited "NumDaughtersLocal" are provided.
DOI: 10.5061/dryad.55nk147/1
title: DahlEtal_DataDryad
DOI: 10.5061/dryad.7519042/10
title: Nothoprocta_perdicaria_scan_data_16bit

description: Novaehollandiae perdicaria CT scan data - 16 bit
DOI: 10.5061/dryad.7519042/11
title: Pachyornis_elephantopus_scan_data_16bit

description: Pachyornis elephantopus CT scan data - 16 bit
DOI: 10.5061/dryad.7519042/12
title: Rhea_americana_scan_data_8bit

description: Rhea americana CT scan data - 8 bit
DOI: 10.5061/dryad.7519042/13
title: Rhea_americana_scan_data_16bit

description: Rhea americana CT scan data - 16 bit
DOI: 10.5061/dryad.7519042/14
title: Rhynchotus_rufescens_Tinamus_solitarius_scan_data_8bit

description: Rhynchotus rufescens and Tinamus solitarius CT scan data - 8 bit
DOI: 10.5061/dryad.7519042/15
title: Rhynchotus_rufescens_Tinamus_solitarius_scan_data_16bit

description: Rhynchotus rufescens and Tinamus solitarius CT scan data - 8 bit
DOI: 10.5061/dryad.7519042/16
title: Struthio_camelus_scan_data_a_8bit

description: Struthio camelus (first scan) CT scan data - 8 bit
DOI: 10.5061/dryad.7519042/17
title: Struthio_camelus_scan_data_a_16bit

description: Struthio camelus (first scan) CT scan data - 16 bit
DOI: 10.5061/dryad.7519042/9
title: Nothoprocta_perdicaria_scan_data_8bit

description: Novaehollandiae perdicaria CT scan data - 8 bit
DOI: 10.5061/dryad.cf0468k/1
title: Sperm allocation with variation in female quality.

description: To test for differences in sperm allocation by SR and ST males, we examined sperm storage by females after a single mating. Males were tested with large and small females to test whether sperm allocation varied with female quality. Allocation was assessed through counts of sperm stored in the spermathecae.
DOI: 10.5061/dryad.cf0468k/2
title: Sperm movement to the site of fertilisation.

description: We examined sperm that migrated to the ventral receptacle (VR), the site of egg fertilisation, when females were mated to an SR or ST male. Males were tested with large and small females, and the proportion of VR pouches that were filled (contained a sperm) or empty were counted.
DOI: 10.5061/dryad.cf0468k/3
title: Sperm allocation across sequential matings (multiple mating).

description: To examine SR and ST male sperm number across successive matings, sperm allocation was assessed through counts of sperm stored in spermathecae after a male’s first, second, and third mating. In this experiment, we did not vary female size, but selected mid-sized females with eyespan between 5.25mm – 5.95mm.
DOI: 10.5061/dryad.cf0468k/4
title: Sperm allocation across sequential matings (third mating).

description: To examine sperm number after successive matings, sperm allocation was assessed through counts of sperm stored in spermathecae on a male’s third mating. Females were mid-sized as before.
DOI: 10.5061/dryad.ct362tv/1
title: Supplementary File 1

description: Bash scripts used to handle raw sequence data, identify loci, and call genotypes.
DOI: 10.5061/dryad.ct362tv/2
title: Supplementary File 2

description: List of samples examined by collection.  Samples that were removed during analysis, and the reason for each, are indicated.
DOI: 10.5061/dryad.ft4sn88/1
title: Dryad Supplementary File 1. Exclude terms used in NCBI queries for Formicidae accessions.
DOI: 10.5061/dryad.ft4sn88/2
title: Dryad Supplementary File 2. Alignment used to infer Formicidae ML tree.

description: Dryad Supplementary File 2. Alignment used to infer Formicidae ML tree.
DOI: 10.5061/dryad.ft4sn88/3
title: Partition file used in Formicidae ML tree inference.

description: Partition file used in Formicidae ML tree inference.
DOI: 10.5061/dryad.ft4sn88/4
title: Dryad Supplementary File 4. ML phylogeny of Formicidae.

description: Dryad Supplementary File 4. ML phylogeny of Formicidae.
DOI: 10.5061/dryad.ft4sn88/5
title: Dryad Supplementary File 5. treePL configuration file (with prime function) used.

description: Dryad Supplementary File 5. treePL configuration file (with prime function) used.
DOI: 10.5061/dryad.ft4sn88/6
title: Dryad Supplementary File 6. treePL configuration file (with cross validation) used.

description: Dryad Supplementary File 6. treePL configuration file (with cross validation) used.
DOI: 10.5061/dryad.js42579/3
title: Hartmann_etal_MEC_Fig_3_data

description: The behavioral responses of Orbicella faveolata larvae to photosymbiont infection with cells obtained from conspecific adults on the natal reef and presented in Figure 3.
DOI: 10.5061/dryad.js42579/4
title: Hartmann_etal_MEC_Fig_4_data

description: The behavioral responses of Orbicella faveolata larvae to photosymbiont infection with cells obtained from two cultured species and presented in Figure 4. The photosymbiont species include Breviolum minutum and Symbiodinium microadriaticum.
DOI: 10.5061/dryad.kd1qt0p.2/24.2
title: Figure 6 - figure supplement 3 - source data 2

description: This zip archive contains the original z-stacks used for Figure 6 - figure supplement 3, 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 6 - figure supplement 3, panels B and D.
DOI: 10.5061/dryad.kd1qt0p.2/25.2
title: Table 2 - source data 1

description: This zip archive contains the chromatography data that was used to calculate the values displayed in Table 2. “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.2/26.2
title: Table 3 - source data 1

description: This zip archive contains the chromatography data that was used to calculate the values displayed in Table 3. “WT_LSI_raw_data.xlsx” contains the data for the wild-type lower small intestine, “KO_LSI_raw_data.xlsx” contains the data for the MUC2 knockout 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 S2 – 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.2/27.2
title: Table 4 - source data 1

description: This zip archive contains the chromatography data that was used to calculate the values displayed in Table 4. “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.2/28.2
title: Table 5 - source data 1

description: This zip archive contains the chromatography data that was used to calculate the values displayed in Table 5. “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.2/29.2
title: Table 6 - source data 1

description: This zip archive contains the chromatography data that was used to calculate the values displayed in Table 6. “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.2/30.2
title: Table 7 - source data 1

description: This zip archive contains the chromatography data that was used to calculate the values displayed in Table 7. “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.2/31.2
title: Table 8 - source data 1

description: This zip archive contains the chromatography data that was used to calculate the values displayed in Table 8. “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.
DOI: 10.5061/dryad.kd1qt0p.2/32.2
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.m3t8r8v/11
title: E651-E727 raw illumina files

description: Raw Illumina data files for the Illumina Miseq sequencing of a library of tagged specimens of Microgastrinae (Hymenoptera: Braconidae) for COI (in two amplicons), Wingless and ITS2. This file contains Extraction codes E651-E727, plus duplicates of earlier extractions (numbers appended with a 2). Sample information for all specimens can be found as supporting information at: https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.12904 . The original data was generated for the paper:  Fagan-Jeffries, E.P., Cooper, S.J.B., Bertozzi, T., Bradford, T.M. & Austin, A.D. (2018) DNA barcoding of microgastrine parasitoid wasps (Hymenoptera: Braconidae) using high-throughput methods more than doubles the number of species known for Australia. Molecular Ecology Resources 18, 1132–1143.
DOI: 10.5061/dryad.m3t8r8v/12
title: Blank samples raw illumina files

description: Raw Illumina data files for the Illumina Miseq sequencing of a library of tagged specimens of Microgastrinae (Hymenoptera: Braconidae) for COI (in two amplicons), Wingless and ITS2. This file contains blank extractions and PCRs as negative controls. Sample information for all specimens can be found as supporting information at: https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.12904 . The original data was generated for the paper:  Fagan-Jeffries, E.P., Cooper, S.J.B., Bertozzi, T., Bradford, T.M. & Austin, A.D. (2018) DNA barcoding of microgastrine parasitoid wasps (Hymenoptera: Braconidae) using high-throughput methods more than doubles the number of species known for Australia. Molecular Ecology Resources 18, 1132–1143.
DOI: 10.5061/dryad.m3t8r8v/13
title: All ITS2 variants (greater than 10 reads)

description: This folder contains ITS2 variants with greater than 10 reads, clustered at 98% read sequence identity. The files are labelled with the extraction code (See supplementary data 2 of the paper) and within the files, each variant contains the numbers of reads (size= ). There is also a file of the alignment of all variants from all specimens that were sequenced in greater than 1% relative abundance within an individual specimen.
DOI: 10.5061/dryad.m3t8r8v/9
title: E451-E550 raw illumina files

description: Raw Illumina data files for the Illumina Miseq sequencing of a library of tagged specimens of Microgastrinae (Hymenoptera: Braconidae) for COI (in two amplicons), Wingless and ITS2. This file contains Extraction codes E451-E550. Sample information for all specimens can be found as supporting information at: https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.12904 . The original data was generated for the paper:  Fagan-Jeffries, E.P., Cooper, S.J.B., Bertozzi, T., Bradford, T.M. & Austin, A.D. (2018) DNA barcoding of microgastrine parasitoid wasps (Hymenoptera: Braconidae) using high-throughput methods more than doubles the number of species known for Australia. Molecular Ecology Resources 18, 1132–1143.
DOI: 10.5061/dryad.mf4h560/5
title: froglets_genetics_NA

description: Contains microsatellite data on the 7 loci used in the study. Given are metamorph ID and allel per locus. Total number of genotyped metamorphs is 707.