cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7nt8f/44
title: Appendix S2. SNP dataset

description: Every contig is represented by 18 lines, with two lines per individual in standard fasta format. Header line of each sequence contains: sampleID_genotype_contigID. Individuals' genotypes are indicated by letters as follows: LL, C. paludica; PP, C. pontica; EE, C. elongatoides; TT, C. taenia; NN, C. tanaitica. Variant positions are expressed using IUPAC notation and invariant positions are excluded.
DOI: 10.5061/dryad.7nt8f/45
title: Table S3. Summary of the coalescent models
DOI: 10.5061/dryad.7nt8f/46
title: Appendix S4. Summary of genetic divergences of fish species producing asexual hybrids
DOI: 10.5061/dryad.7nt8f/47
title: Table S5. Microsatellite allelic profiles of parents and their progeny within crossing experiments
DOI: 10.5061/dryad.7nt8f/48
title: Table S6. Oocyte analysis

description: For each female we indicate her biotype, origin, allozyme profile and the number of analyzed eggs.
DOI: 10.5061/dryad.854j2/1
title: dataset_S

description: Velocity trajectories and segmentation annotation.
DOI: 10.5061/dryad.854j2/4
title: classify_submodes_cmsec_degsec_30fps

description: MATLAB script to classify behavior elements (submodes, modes) in velocity time series of walking fruit flies.  Requires parameter file classification_params_r.mat.
DOI: 10.5061/dryad.854j2/5
title: classification_params_r

description: Parameter file for script classify_submodes_cmsec_degsec_30fps.m
DOI: 10.5061/dryad.854j2/6
title: mode_data_scripts

description: Scripts, parameter files, and data structures operating on segmented trajectories
DOI: 10.5061/dryad.b563d/1
title: Monitoring data

description: Pyrgus armoricanus abundance recorded in each site and each year
DOI: 10.5061/dryad.b563d/2
title: Site data

description: Location and characteristics of each monitored site
DOI: 10.5061/dryad.c134g/1
title: benthic composition summary data

description: Benthic surveys of reefs in the Atoll of Ulithi, Yap State, Micronesia
DOI: 10.5061/dryad.c197n/10
title: ABC Model 5 input files

description: Input files for ABC analysis with alternative divergence history of populations. These files were generated using ABCToolkit or manually. The files 'arl_run.txt' and 'arl_run.ars' were used to calculated summary statistics in Arlequin. The file 'hydromantesSTR.obs' contains summary statistics for observed data. The file 'hydromantesSTR.par' contains parameters  for the coalescence simulation program simcoal. 'hydromantes.input' is the input file for the program ABCSampler. 'ssDefs.txt' contains information on which summary statistics were calculated. The script 'Process_ABC_commands.R' was used to compare models and determine the posterior probability of each.
DOI: 10.5061/dryad.c197n/11
title: ABC Model 1 with population size change

description: Input files for ABC analysis of isolation with no migration model including population size changes. Subfolders correspond for to the model with a bottleneck in the population included in the folder name. These files were generated using ABCToolkit or manually. The files 'arl_run.txt' and 'arl_run.ars' were used to calculated summary statistics in Arlequin. The file 'hydromantesSTR.obs' contains summary statistics for observed data. The file 'hydromantesSTR.par' contains parameters  for the coalescence simulation program simcoal. 'hydromantes.input' is the input file for the program ABCSampler. 'ssDefs.txt' contains information on which summary statistics were calculated. The script 'Process_ABC_commands.R' was used to compare models and determine the posterior probability of each.
DOI: 10.5061/dryad.c197n/5
title: MSVAR input files

description: Input files for MSVAR analyses of bottlenecks for populations of Hydromantes platycephalus from the southern Sierra Nevada. The files were generated manually and analyzed using the program MSVAR to detect past demographic bottlenecks for each population. The results were summarized and visualized using the R script provided.
DOI: 10.5061/dryad.c197n/6
title: ABC Model 1 input files

description: Input files for isolation with no migration model for ABC analysis. These files were generated using ABCToolkit or manually. The files 'arl_run.txt' and 'arl_run.ars' were used to calculated summary statistics in Arlequin. The file 'hydromantesSTR.obs' contains summary statistics for observed data. The file 'hydromantesSTR.par' contains parameters  for the coalescence simulation program simcoal. 'hydromantes.input' is the input file for the program ABCSampler. 'ssDefs.txt' contains information on which summary statistics were calculated. The script 'Process_ABC_commands.R' was used to compare models and determine the posterior probability of each.
DOI: 10.5061/dryad.c197n/7
title: ABC model 2 input files

description: Input files for ABC analysis of Owens Valley refuge model. These files were generated using ABCToolkit or manually. The files 'arl_run.txt' and 'arl_run.ars' were used to calculated summary statistics in Arlequin. The file 'hydromantesSTR.obs' contains summary statistics for observed data. The file 'hydromantesSTR.par' contains parameters  for the coalescence simulation program simcoal. 'ssDefs.txt' contains information on which summary statistics were calculated. 'hydromantes.input' is the input file for the program ABCSampler. The script 'Process_ABC_commands.R' was used to compare models and determine the posterior probability of each.
DOI: 10.5061/dryad.c197n/8
title: ABC Model 3 input files

description: Input files for ABC analysis of High Sierra refuge model. 
These files were generated using ABCToolkit or manually. The files 'arl_run.txt' and 'arl_run.ars' were used to calculated summary statistics in Arlequin. The file 'hydromantesSTR.obs' contains summary statistics for observed data. The file 'hydromantesSTR.par' contains parameters  for the coalescence simulation program simcoal. 'hydromantes.input' is the input file for the program ABCSampler. 'ssDefs.txt' contains information on which summary statistics were calculated. The script 'Process_ABC_commands.R' was used to compare models and determine the posterior probability of each.
DOI: 10.5061/dryad.c197n/9
title: ABC model 4 input files

description: Input files for ABC analysis of model with persistence in both Owens Valley and High Sierra Nevada with migration between geographic neighbors. These files were generated using ABCToolkit or manually. The files 'arl_run.txt' and 'arl_run.ars' were used to calculated summary statistics in Arlequin. The file 'hydromantesSTR.obs' contains summary statistics for observed data. The file 'hydromantesSTR.par' contains parameters  for the coalescence simulation program simcoal. 'hydromantes.input' is the input file for the program ABCSampler. 'ssDefs.txt' contains information on which summary statistics were calculated. The script 'Process_ABC_commands.R' was used to compare models and determine the posterior probability of each.
DOI: 10.5061/dryad.cr65v/2
title: HTML output of simulation script

description: HTML output when knitting the file "Simulation_script_Fig.1Fig.S1-4.Rmd" using Rstudio
DOI: 10.5061/dryad.cr65v/3
title: DNA concentration data (Hoechst)

description: DNA concentration dataset (Hoechst) used to estimate the coefficient of variation when pooling samples before (CVbefore) or after (CVafter) DNA extraction.
DOI: 10.5061/dryad.cr65v/4
title: DNA concentration data (Picogreen)

description: DNA concentration dataset (Picogreen) used to estimate the coefficient of variation when pooling samples before (CVbefore) or after (CVafter) DNA extraction.
DOI: 10.5061/dryad.cr65v/5
title: Pipette calibration data
DOI: 10.5061/dryad.cr65v/6
title: CVbefore and CVafter estimation script

description: Script for estimating the coefficient of variation when pooling samples before (CVbefore) or after (CVafter) DNA extraction based on PipetteMetrology.csv and DataHoechst.csv or DataPicogreen.csv.
DOI: 10.5061/dryad.cr65v/9
title: Simulation script

description: Script for the simulations used to verify the analytical model.
DOI: 10.5061/dryad.d9n5d/1
title: locomotor_canetods

description: Records of distance ran by cane toads of different populations over 10 minutes on a circular track under different experimental conditions.
DOI: 10.5061/dryad.f13g4/1
title: Supporting Data
DOI: 10.5061/dryad.h21v2.2
title: Data from: The genetic architecture of UV floral patterning in sunflower
DOI: 10.5061/dryad.h21v2.2/1.2
title: Flowerheads photographed in UV

description: Zipped directory containing JPG files of Helianthus argophyllus flowerheads photographed with a Nikon D70s digital camera fitted with a Noflexar 35mm lens and a reverse-mounted 2 inch Baader U-Filter (restricting the transmission of light to 320–380 nm). Files are named according to the plant's location in the field and the photograph number (e.g. 'b1-11DSC_1586' is the plant from row 1, space 11, photograph 1586; exceptions are the F1 individuals which are labeled X3A-# or X3B-# instead of by field location). The archived data file with phenotypic measurements contains the key to translate field location to plant genotype.
DOI: 10.5061/dryad.h21v2.2/2.2
title: Custom Perl script for formatting paired-end GBS data for uneak pipeline

description: This script translates paired-end fastq sequencing files into two independent sets of individually barcoded reads with a custom Perl script, to be used in the uneak pipeline (which is built only for single-end reads, from TASSEL 3; Lu et al., 2013). usage: perl GBS_Fastq_BarcodeAdder.pl uneak_key_file.txt library_1.fq library_2.fq combined_library_out.fq
DOI: 10.5061/dryad.h21v2.2/3.2
title: Bash commands used to filter for final SNP matrix

description: This file contains the series of bash commands used to filter uneak output to call genotypes using more stringent filters. Starting with the HapMapCount file (for each individual at each tag pair: minimum of 10 tags, heterozygote if the ratio of the two tags &lt; 10, homozygote if the ratio of the two tags &gt; 50, otherwise N), filter the resulting file for sites with alternate homozygous genotypes in the two parent individuals (7,875 sites), filter those sites for a minimum coverage of 50% across all individuals and observed heterozygousity of 0.3–0.7, and then format these genotypes for import into R/qtl.
DOI: 10.5061/dryad.jc6r4/1
title: OGorman et al., _Pl. almanzai_Supp

description: Data set used in the phylogenetic analysis modified from Benson et al., 2013 "Benson, R. B., Evans, M., Smith, A. S., Sassoon, J., Moore-Faye, S., Ketchum, H. F., & Forrest, R. (2013). A giant pliosaurid skull from the Late Jurassic of England. PLOS One, 8(5), e65989"
DOI: 10.5061/dryad.jr0s5/1
title: Silk_et_al_2017_filtered_contact_data_for_seasonal_analysis

description: Data used for seasonal analysis of badger social contacts (filtered from raw data as described in the paper). Provided is the identity of both individuals in a proximity event, the date/time and length of the event, the month and season (as used in the analyses), time through the day in seconds, proportion of the time through the day (as described in the paper) and the social group of each individual (as defined in the paper)
DOI: 10.5061/dryad.jr0s5/2
title: Silk_et_al_2017_Data_for_Frequency_Analysis

description: Data used for monthly analysis of badger contact frequencies as described in the paper (within-group contacts only). Provided data are: the identity of both badgers in a dyad, their social group, the month, the frequency of contacts in that month, the number of days in the months on which both individuals were collared (-30 to centre to the results for dyads collared for roughly an entire month), and the values used for the time since collared term for each individual used in the analysis
DOI: 10.5061/dryad.kr856/1
title: HRBC23

description: Data Daphnia pulex reaction norm
DOI: 10.5061/dryad.kr856/2
title: Supplementary Table 1
DOI: 10.5061/dryad.kr856/3
title: Supplementary Table 2
DOI: 10.5061/dryad.q03d6/1
title: Dataset with Male size & immune measurements

description: This is the dataset belonging to the paper titled "Condition-dependent trade-off between weapon size and immunity in males of the European earwig"
DOI: 10.5061/dryad.qt000/1
title: Ellwood_MEE_RFID_BadgerData

description: See ReadMe file
DOI: 10.5061/dryad.rq560/1
title: Behavior data

description: Data recorded during mouse in vivo imaging and behavior sessions. Data saved as Python pickle files containing a dictionary of arrays of timestamped mouse behavior recordings and stimulus presentaitons. Data includes licking activity, treadmill position, and contextual stimuli presentation times. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.
DOI: 10.5061/dryad.rq560/2
title: Experiment metadata

description: Experiment metadata xml files containing a record of experimental parameters and links the locations of imaging and behavior data for a given experiment. Data recorded during mouse in vivo imaging and behavior sessions. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.
DOI: 10.5061/dryad.rq560/3
title: Place cell enrichment model data

description: Contains place cell data recorded during in vivo calcium imaging sessions of our goal-oriented learning task, as well as enrichment model parameters fit to the data, and saved simulations of the place cell enrichment model. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.
DOI: 10.5061/dryad.rq560/4
title: Imaging Data - Part 1

description: Calcium imaging data recorded during head-fixed awake in vivo two-photon imaging experiments. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.
DOI: 10.5061/dryad.rq560/5
title: Imaging Data - Part 2

description: Calcium imaging data recorded during head-fixed awake in vivo two-photon imaging experiments. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.
DOI: 10.5061/dryad.rq560/6
title: Imaging Data - Part 3

description: Calcium imaging data recorded during head-fixed awake in vivo two-photon imaging experiments. Data is designed to be read by corresponding figure code at https://github.com/losonczylab/Zaremba_NatNeurosci_2017.
DOI: 10.5061/dryad.tk5cq/1
title: Dryad data

description: Field data statistical results and mesocosm raw data.
DOI: 10.5061/dryad.2np32/1
title: Data from: Gut microbiota modifies olfactory-guided microbial preferences and foraging decisions in Drosophila

description: The file contains the raw data set for the Manuscript with the title mentioned above. Files are separated by figures, each in its individual tab within the Excel file. Variable names are self-explanatory.
DOI: 10.5061/dryad.33pm5/1
title: Hyla_femoralis_microsatellite_genotypes

description: Microsatellite data for 415 samples of Hyla femoralis at 17 loci. Loci names are in order across the top in row 1. See Table 2 for corresponding wetland identification.
DOI: 10.5061/dryad.4236t/1
title: Species in even-aged, uneven-aged and unmanaged beech forests

description: The data file comprises abundance, cover or presence of species from 15 taxonomic groups for even-aged, uneven-aged and unmanaged beech forest plots of the Hainich-Dün Biodiversity Exploratory (http://www.biodiversity-exploratories.de).

The work has been funded by the DFG Priority Program 1374 "Infrastructure-Biodiversity-Exploratories".
DOI: 10.5061/dryad.4m35m/3
title: Arlequin_files

description: Arlequin arp analyses and xml result files
DOI: 10.5061/dryad.4m35m/4
title: Haplotype_network_analyses

description: TCS network nex files (ITS1+2 and ITS2 only) used in Popart
DOI: 10.5061/dryad.4m35m/5
title: BEAST_analyses

description: xml and tree files for the different molecular dating analyses as used in BEAST. These include the two two-step dating analyses, one with (I1a + I2a) and one without (I1b + I2b) the fossil Eopolytrichum antiquum, and the molecular rate analysis (II).
DOI: 10.5061/dryad.4s3v1/11
title: Cybertype_Zasphinctus sarowiwai_CASENT0764654_holotype worker_4

description: Cybertype dataset for Zasphinctus sarowiwai (CASENT0764654) holotype worker 4: complete micro-CT scanning raw dataset of metasoma (DICOM format, 993 slices)
DOI: 10.5061/dryad.4s3v1/12
title: Cybertype_Zasphinctus sarowiwai_CASENT0764654_holotype worker_5

description: Cybertype dataset for Zasphinctus sarowiwai (CASENT0764654) holotype worker 5: 3D PDF and high-resolution 3D rotation video (mpg format) for scan of full body plus montage photos (full-face view, body in profile, and dorsal view of body) and microtomographic still images of diagnostic characters (tiff format)
DOI: 10.5061/dryad.4s3v1/13
title: Cybertype_Zasphinctus sarowiwai_CASENT0764654_holotype worker_6

description: Cybertype dataset for Zasphinctus sarowiwai (CASENT0764654) holotype worker 6: 3D PDFs and high-resolution 3D rotation videos (mpg format) for scans of head, mesosoma, and metasoma
DOI: 10.5061/dryad.4s3v1/14
title: Morphological dataset_Zasphinctus sarowiwai_CASENT0764654_muscles+sting

description: Morphological dataset for Zasphinctus sarowiwai (CASENT0764654) muscles+sting: high-resolution 3D video (mpg format) and still images (tiff format) of false-colour volume rendering of segmented mesosoma and metasoma musculature (red) and sting apparatus (green) superimposed on semitransparent surface model
DOI: 10.5061/dryad.4s3v1/15
title: Morphological dataset_Zasphinctus sarowiwai_CASENT0764652_mouthparts_1

description: Morphological dataset for Zasphinctus sarowiwai (CASENT0764652) mouthparts 1: complete micro-CT scanning raw dataset of anterior head (DICOM format, 992 slices)
DOI: 10.5061/dryad.4s3v1/16
title: Morphological dataset_Zasphinctus sarowiwai_CASENT0764652_mouthparts_2

description: Morphological dataset for Zasphinctus sarowiwai (CASENT0764652) mouthparts 2: 3D PDFs, high-resolution 3D rotation videos (mpg format), and microtomographic still images for segmented surface reconstructions of the mouthparts in open configuration (green= maxillae; yellow=labrum; orange=labium)
DOI: 10.5061/dryad.4s3v1/17
title: Cybertype_Zasphinctus wilsoni_MCZ-ENT-00512764_holotype worker_1

description: Cybertype dataset for Zasphinctus wilsoni (MCZ-ENT-00512764) holotype worker 1: complete micro-CT scanning raw dataset of full body (DICOM format, 993 slices)
DOI: 10.5061/dryad.4s3v1/18
title: Cybertype_Zasphinctus wilsoni_MCZ-ENT-00512764_holotype worker_2

description: Cybertype dataset for Zasphinctus wilsoni (MCZ-ENT-00512764) holotype worker 2: complete micro-CT scanning raw dataset of head (DICOM format, 991 slices)
DOI: 10.5061/dryad.4s3v1/19
title: Cybertype_Zasphinctus wilsoni_MCZ-ENT-00512764_holotype worker_3

description: Cybertype dataset for Zasphinctus wilsoni (MCZ-ENT-00512764) holotype worker 3: complete micro-CT scanning raw dataset of mesosoma (DICOM format, 992 slices)
DOI: 10.5061/dryad.4s3v1/20
title: Cybertype_Zasphinctus wilsoni_MCZ-ENT-00512764_holotype worker_4

description: Cybertype dataset for Zasphinctus wilsoni (MCZ-ENT-00512764) holotype worker 4: complete micro-CT scanning raw dataset of metasoma (DICOM format, 993 slices)
DOI: 10.5061/dryad.69bb2.1
title: Data from: Probabilistic distances between trees
DOI: 10.5061/dryad.69bb2.1/2.1
title: appendix

description: Online-only appendix
DOI: 10.5061/dryad.69bb2.2
title: Data from: Probabilistic distances between trees
DOI: 10.5061/dryad.69bb2.2/2.2
title: Appendix

description: Online-only appendix
DOI: 10.5061/dryad.69bb2.2/3.2
title: Software and data sets
DOI: 10.5061/dryad.69bb2/3
title: Software and data sets
DOI: 10.5061/dryad.760t1/1
title: DATAFILE_HAN_DINGEMANSE_2017_PRSB
DOI: 10.5061/dryad.7nt8f/49
title: Table S7. Microsatellite markers and cytochrome b gene haplotypes

description: This Table lists the alleles found in each sampled individual (specified by a respective ID number) on the basis of eight microsatellite markers. The cytochrome b gene haplotype is also specified.
DOI: 10.5061/dryad.7nt8f/50
title: Table S8. Summary statistics of microsatellite DNA analysis for three taxa based on eight loci
DOI: 10.5061/dryad.7nt8f/51
title: Table S9. SNP statistics

description: Summary statistics for within-species and between-species genetic distances.
DOI: 10.5061/dryad.7p511/1
title: Alignment and Partition

description: Alignment of 53 ultra-conserved element loci analyzed in the paper with a RAxML style partition file.
DOI: 10.5061/dryad.7p511/2
title: Assemblies

description: Newly generated assemblies from sequence capture data targeting 500 ultra-conserved element loci.
DOI: 10.5061/dryad.7p511/3
title: PartitionFinder

description: Partition Finder configuration file and partitioning scheme as described in the manuscript.
DOI: 10.5061/dryad.85641/1
title: WhitakerEtAl2017ELE_data

description: Data used to perform all analyses and create all figures in the published article Whitaker et al. 2017 Ecology Letters.
DOI: 10.5061/dryad.85641/2
title: 2015_AsterFB_sascode_SASs

description: SAS code used to perform all statistical analyses in the published article Whitaker et al. 2017 Ecology Letters.
DOI: 10.5061/dryad.85641/3
title: 2015_AsterFB_code&files

description: R Code used to create all data figures in the published article Whitaker et al. 2017 Ecology Letters.
DOI: 10.5061/dryad.8jj12/1
title: Jerusalen jittered data

description: This has the Jerusalen data described in the article, with X/Y jittered to prevent exact recognition of infested households (confidentiality issues). X: longitude in UTM, Y: longitude in UTM, OLDSTATUS: status (infested 0/1) in 2009, STATUS: status (infested 0/1) in 2011.
DOI: 10.5061/dryad.9m5h0/1
title: Amell_Ashby_casteFPKM

description: Column 1 has the A. mellifera gene IDs. Column 2 through 4 represents average FPKM for the respective caste (drone, queen, worker), across all samples. These expression levels were derived from Ashby et al.
DOI: 10.5061/dryad.9m5h0/2
title: Amell_SingleCopyGenes.txt

description: FIle with all the single copy genes in A. mellifera. Column 1(EOG) has the EOG id from OrthoDB v9.1 in which the single copy genes were derivived from. Column 1 (A. mellifera) has the single copy gene in A. mellifera and column 2 (B. terrestris) represents the sinlge copy ortholog in B. terrestris.
DOI: 10.5061/dryad.9m5h0/3
title: Amell_DupPairs.txt

description: File with all the duplicate genes in A. mellifera. Column 1(EOG) has the EOG id from OrthoDB v9.1 in which the gene duplicates were derivived from. Column 1 (Gene 1) and column 2 (Gene 2) represent the paralogs in A. mellifera in no particular order.
DOI: 10.5061/dryad.9m5h0/4
title: Amell_Bterr_EvoProc.txt

description: File that has the gene families used to identify the evolutionary processes maintaining paralogs in the A. mellifera genome. Column 1 (AMELL_D1) is the paralog with the highest sequence similarity to the single copy ortholog in B. terrestris, while column 2 (AMELL_D2) is the one with the lease sequence similarity. BTERR_ortho is the single copy ortholog of the duplicates in B. terrestris. Methods on how sequence similarity was measured can be found in the methods.
DOI: 10.5061/dryad.9m5h0/5
title: Bterr_caste_FPKM.txt

description: Column 1 has the B. terrestris gene IDs. Column 2 through 4 represents average FPKM for the respective caste, across all samples. These expression levels were derived from Harrison et al.