cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j1t17/1
title: Sperm counts in the reproductive tract of doubly-mated females

description: Assays were performed to evaluate how sperm dynamics in the reproductive tract of doubly-mated females differs when the second male to mate lacks or carries the species-specific multigene family Sdic of Drosophila melanogaster in the genome.  Virgin females were first mated to a reference male and two days later to one of the two possible experimental males (with Sdic, Sdic+, or without Sdic, Sdic-).  Females were randomly assigned to one of three time points after the end of the second mating period (30 min, 1 h and 45 min, and 2 days) and subsequently flash frozen.  Female reproductive tracts were dissected and the sperm from the different males counted using a fluorescent microscope; the sperm from the reference and experimental males glow in red and green respectively.  Sperm counting was performed for both the bursa and the sperm storage organs, i.e. the paired spermatheca and the seminal receptacle.
DOI: 10.5061/dryad.kc835.3
title: Data from: Genome sequence of M6, a diploid inbred clone of the high glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity.
DOI: 10.5061/dryad.kc835.3/1.3
title: M6_v4.1_masked_PM.fa

description: Masked pseudomolecules of S. chacoense M6, containing 12 chromosomes
DOI: 10.5061/dryad.kc835.3/13.3
title: M6_v4.1_PM.fa

description: Pseudomolecules of S. chacoense M6, containing 12 chromosomes
DOI: 10.5061/dryad.kc835.3/14.3
title: Readme_v3.txt
DOI: 10.5061/dryad.kc835.3/2.3
title: 523_3_assembly_ALLPATHS_v4.1.fasta

description: Genome assembly of S. chacoense M6, containing 8,260 scaffold sequences
DOI: 10.5061/dryad.kc835.3/3.3
title: short_summary_BUSCO_output.txt

description: Output file from running BUSCO on the genome assembly
DOI: 10.5061/dryad.kc835.3/4.3
title: full_table_BUSCO_output.tsv

description: Output file from running BUSCO on the genome assembly
DOI: 10.5061/dryad.tf641/2
title: R-scripts for analysing heat tolerance data

description: R-script contains code to analyse and plot the data on heat tolerance and is programmed in R
DOI: 10.5061/dryad.tf641/3
title: Dataset on activation energy (Ea)

description: This dataset compiles published data on respiration rates for 6 different species, measured at different temperatures to calculate its thermal dependency, expressed as Activation Energy (Ea). Literature sources are given in full in the accompanying paper.
DOI: 10.5061/dryad.tf641/4
title: R-scripts for analyzing activation energy (Ea)

description: R-script contains code to analyse and plot the data on activation Energy and is programmed in R
DOI: 10.5061/dryad.tm06r/1
title: Main calculation

description: R script for calculating body temperature, developmental time, developmental viability and embryonic energy consumption.
DOI: 10.5061/dryad.tm06r/2
title: Make figures

description: R script for ploting developmental developmental time, developmental viability and embryonic energy consumption.
DOI: 10.5061/dryad.tm06r/3
title: Realistic distribution

description: R script for calculating and plotting the proportion of viviparity at globe.
DOI: 10.5061/dryad.tm06r/4
title: SRA_markdown

description: R markdown file for spatial regression analysis.
DOI: 10.5061/dryad.ts57v.1/1.1
title: Bioassess bird data

description: Landscape variables and avian point-count species richness data collected in the BioAssess project 2001-2002 in eight European countries
DOI: 10.17632/34fmvnrjzd.1
title: Data for: Dual Reduced Kernel Extreme Learning Machine for Aero-engine Fault Diagnosis

description: Seven benchmark datasets include the training samples and testing samples.
DOI: 10.17632/34fmvnrjzd.2
title: Data for: Dual Reduced Kernel Extreme Learning Machine for Aero-engine Fault Diagnosis

description: Seven benchmark datasets include the training samples and testing samples.
DOI: 10.5061/dryad.37m5c/10
title: adults_dotu_table_noWol_L4

description: Adults: QIIME OTU table summarized at L4 (order). Post Wolbachia removal. No filtering for low count OTUs.
DOI: 10.5061/dryad.37m5c/2
title: adults_unsum_fulldata_rawcounts

description: Adults: Raw sequence counts assigned to OTUs (97% identity threshold) without any filtering or summarizing. Post Wolbachia sequence removal.
DOI: 10.5061/dryad.37m5c/3
title: larvae_otu_table_noWol_L2

description: Larvae: QIIME OTU table summarized at L2 (phylum). Post Wolbachia removal. No filtering for low count OTUs.
DOI: 10.5061/dryad.37m5c/4
title: larvae_otu_table_noWol_L3

description: Larvae: QIIME OTU table summarized at L3 (class). Post Wolbachia removal. No filtering for low count OTUs.
DOI: 10.5061/dryad.37m5c/5
title: larvae_otu_table_noWol_L4

description: Larvae: QIIME OTU table summarized at L4 (order). Post Wolbachia removal. No filtering for low count OTUs.
DOI: 10.5061/dryad.37m5c/6
title: larvae_otu_table_noWol_L5

description: Larvae: QIIME OTU table summarized at L5 (family). Post Wolbachia removal. No filtering for low count OTUs.
DOI: 10.5061/dryad.37m5c/7
title: larvae_otu_table_noWol_L6

description: Larvae: QIIME OTU table summarized at L6 (genus). Post Wolbachia removal. No filtering for low count OTUs.
DOI: 10.5061/dryad.37m5c/8
title: adults_otu_table_noWol_L2

description: Adults: QIIME OTU table summarized at L2 (phylum). Post Wolbachia removal. No filtering for low count OTUs.
DOI: 10.5061/dryad.3b04j/3
title: BPP and iBPP input files

description: This ZIP file includes the genetic and morphological matrices that were used to perform the BPP and iBPP analyses.
DOI: 10.5061/dryad.3rk3h/1
title: raw data for upload_Eng

description: .opj files are for Origin software
DOI: 10.5061/dryad.42b68/1
title: Amanita afn lavendula taxon 1 cloned ITS sequences

description: Cloned Amanita afn lavendula taxon 1 ITS1-5.8S-ITS2 sequences
DOI: 10.5061/dryad.42b68/2
title: Amanita afn_lavendua Taxon 1  ITS consensus sequence

description: Amanita afn lavendula taxon 1 ITS consensus sequence
DOI: 10.5061/dryad.42b68/3
title: ML tree of Amanita afn lavendula taxon 1 ML1-2

description: Nexus file. PhyML tree based on Mitochondrial rRNA large subunit sequences amplified with primers ML1 and ML2
DOI: 10.5061/dryad.42b68/4
title: ML tree of Amanita afn lavendula taxon 1 ML5-6

description: Nexus file: PhyML analyses of mitochondrial rRNA large subunit sequences amplified with primers ML5 and ML6
DOI: 10.5061/dryad.42b68/5
title: ML tree of Amanita afn lavendula taxon 1 MS1-2

description: Nexus file: PhyML analysis of mitochondrial rRNA 16S sequences amplified with primers MS1 and MS2
DOI: 10.5061/dryad.42b68/6
title: ML tree of Amanita afn lavendula taxon 1 nrLSU

description: Nexus file: PhyML analysis of nuclear ribosomal LSU sequences  of Amanita afn lavendula taxon 1
DOI: 10.5061/dryad.67sf3/1
title: HUNTSUCCESS_input

description: This is the input file used in the Hunting Success analysis and contains appropriate covariate fields. This processed version has all geographic coordinate information removed to protect the precise locations of the subject pumas. Fields identified by ‘Animal_ID’, ‘ikid’, and ‘FEEDING’ are used as random effect, strata, and response terms in the model. Landscape predictor covariates follow the naming convention and accompanying description presented in Table S1.1 of the publication. Mule deer prey availability covariate is identified as ‘Util.muledeer’.
DOI: 10.5061/dryad.67sf3/2
title: SSF_input

description: This is the input file used in the patch-selection (Step Selection Function) analysis and contains appropriate covariate fields. This processed version has all geographic coordinate information removed to protect the precise locations of the subject pumas. Fields identified by ‘Animal_ID’, ‘ClusterID_8day’, and ‘SSF.used’ are used as random effect, strata, and response terms in the model. Landscape predictor covariates follow the naming convention and accompanying description presented in Table S1.1 of the publication. Mule deer prey availability covariate is identified as ‘Util.muledeer’.
DOI: 10.5061/dryad.c9h35/1
title: Station locations and elevations

description: Latitude, longitude, and elevation for all meteorological and precipitation phase observation stations used in the Jennings et al. (2018) manuscript.
DOI: 10.5061/dryad.c9h35/2
title: Precipitation phase and meteorological observations

description: Observations of precipitation phase and meteorological data used in the Jennings et al. (2018) manuscript. Please note, this is a cleaned, formatted version of the http://rda.ucar.edu/datasets/ds464.0/ dataset. Be sure to cite the original dataset as well if you choose to use these data in your work.
DOI: 10.5061/dryad.c9h35/3
title: Observed 50% rain-snow air temperature thresholds

description: 50% rain-snow air temperature thresholds for 6,883 Northern Hemisphere stations. Snow frequency was calculated per 1°C temperature bin using observations of precipitation phase. A hyperbolic tangent was then fit to the frequency data and used to calculate the 50% rain-snow air temperature threshold. All NA values indicate there were not enough data to fit the hyperbolic tangent.
DOI: 10.5061/dryad.c9h35/4
title: Simulated 50% rain-snow air temperature thresholds (hyperbolic tangent)

description: Map of simulated 50% rain-snow air temperature thresholds based on a bivariate binary logistic regression phase prediction model applied to 27 years of MERRA-2 reanalysis data. The probability of snowfall was predicted for each precipitation event in the record as a function of air temperature and relative humidity. For each MERRA-2 grid cell, the probabilities were binned by 1°C air temperature bins to produce a snow frequency curve. A hyperbolic tangent was then fit to the data and used to calculate the 50% rain-snow air temperature threshold.
DOI: 10.5061/dryad.c9h35/5
title: Simulated 50% rain-snow air temperature thresholds (linear regression)

description: Map of simulated 50% rain-snow air temperature thresholds based on a bivariate binary logistic regression phase prediction model applied to 27 years of MERRA-2 reanalysis data. The probability of snowfall was predicted for each precipitation event in the record as a function of air temperature and relative humidity. For each MERRA-2 grid cell, the probabilities were binned by 1°C air temperature bins to produce a snow frequency curve. The 50% rain-snow air temperature threshold was then calculated using a linear regression on snow frequency between 0.5°C and 6.5°C. This approach was used for grid cells without enough snow and rain events to compute the threshold using a hyperbolic tangent.
DOI: 10.5061/dryad.c9h35/6
title: R code for calculating observed 50% rain-snow air temperature thresholds

description: R code for computing the 50% rain-snow air temperature threshold using the station data in jennings_et_al_2018_file2_ppt_phase_met_observations.csv
DOI: 10.5061/dryad.c9h35/7
title: R code for evaluating precipitation phase methods

description: R code for evaluating the performance of different precipitation phase methods using the station data in jennings_et_al_2018_file2_ppt_phase_met_observations.csv
DOI: 10.5061/dryad.c9h35/8
title: R code for mapping simulated rain-snow thresholds

description: R code for creating the simulated 50% rain-snow air temperature threshold maps (jennings_et_al_2018_file4_temp50_raster.tif and jennings_et_al_2018_file5_temp50_linregr_raster.tif).
DOI: 10.5061/dryad.j327n/2
title: Parasite intensities in relation to anthelminitic treatment in reindeer

description: one row per observation. Each row is a separate individual. Columns provide date of culling, treatment group, age and various measures of the abundance of the different stages of the two main parasites. See READ ME file for definitions of the variables
DOI: 10.5061/dryad.kc835.3/10.3
title: pasa_m6.hc.gene_models.repr.pep.fa

description: Protein sequences of representative models of high-confidence genes in S. chacoense M6
DOI: 10.5061/dryad.kc835.3/11.3
title: M6_gene_expression_matrix.xlsx

description: Expression abundance of representative gene models
DOI: 10.5061/dryad.kc835.3/12.3
title: 523_3_assembly_ALLPATHS_v4.1.fasta.repeatmasker.gff

description: GFF file of the repeat-masked genome
DOI: 10.5061/dryad.kc835.3/5.3
title: pasa_m6.hc.gene_models.Chr.gff3

description: Generic feature format file (gff3) of high-confidence genes in S. chacoense M6
DOI: 10.5061/dryad.kc835.3/6.3
title: pasa_m6.hc.gene_models.cdna.fa

description: Transcript sequences (cDNA) of high-confidence genes in S. chacoense M6
DOI: 10.5061/dryad.kc835.3/7.3
title: pasa_m6.hc.gene_models.cds.fa

description: Coding sequences (CDS) of high-confidence genes in S. chacoense M6
DOI: 10.5061/dryad.kc835.3/8.3
title: pasa_m6.hc.gene_models.pep.fa

description: Protein sequences of high-confidence genes in S. chacoense M6
DOI: 10.5061/dryad.kc835.3/9.3
title: m6_gene_models.func_anno.txt

description: Functional annotation of working gene model set in S. chacoense M6
DOI: 10.5061/dryad.kc835/14
title: Readme_v3.txt
DOI: 10.5061/dryad.kc835/2
title: 523_3_assembly_ALLPATHS_v4.1.fasta

description: Genome assembly of S. chacoense M6, containing 8,260 scaffold sequences
DOI: 10.5061/dryad.kc835/3
title: short_summary_BUSCO_output.txt

description: Output file from running BUSCO on the genome assembly
DOI: 10.5061/dryad.kc835/4
title: full_table_BUSCO_output.tsv

description: Output file from running BUSCO on the genome assembly
DOI: 10.5061/dryad.kc835/5
title: pasa_m6.hc.gene_models.Chr.gff3

description: Generic feature format file (gff3) of high-confidence genes in S. chacoense M6
DOI: 10.5061/dryad.kc835/6
title: pasa_m6.hc.gene_models.cdna.fa

description: Transcript sequences (cDNA) of high-confidence genes in S. chacoense M6
DOI: 10.5061/dryad.kc835/7
title: pasa_m6.hc.gene_models.cds.fa

description: Coding sequences (CDS) of high-confidence genes in S. chacoense M6
DOI: 10.5061/dryad.p85q4.2
title: Data from: Breaking down the lithification bias: the effect of preferential sampling of larger specimens on the estimate of species richness, evenness, and average specimen size
DOI: 10.5061/dryad.tf641/5
title: Dataset on respiratory responses to hypoxia

description: This dataset compiles published data on respiration rates for 4 different species, measured at different levels of oxygen. Literature sources are given in full in the accompanying paper.
DOI: 10.5061/dryad.tf641/6
title: R-scripts for analysing respiratory responses to hypoxia

description: R-script contains code to analyse and plot the data on respiratory responses to hypoxia and is programmed in R
DOI: 10.5061/dryad.tr20q/1
title: data

description: Raw data file from manipulative field experiment.
DOI: 10.5061/dryad.tr20q/2
title: occurrences

description: Specimen data downloaded from Global Biodiversity Information Facility in Aug, 2014.
DOI: 10.5061/dryad.tr20q/3
title: r.code

description: R code for statistical analyses and figures.
DOI: 10.5061/dryad.03622/1
title: Aframomum_specimens Harris Wortley 2018

description: This text file contains data on herbarium specimens, herbaria where housed, and collecting localities.
DOI: 10.5061/dryad.03622/2
title: Aframomum_specimens_Harris Wortley 2018

description: This csv file saved in microsoft excel contains herbarium specimen data, herbaria where housed, and collecting localities. It is the same data as the txt file with the same name on dryad.
DOI: 10.5061/dryad.15dd2j2/1
title: TelegonyParentage_final_dryad
DOI: 10.5061/dryad.37m5c/11
title: adults_otu_table_noWol_L5

description: Adults: QIIME OTU table summarized at L5 (family). Post Wolbachia removal. No filtering for low count OTUs.
DOI: 10.5061/dryad.37m5c/12
title: adults_otu_table_noWol_L6

description: Adults: QIIME OTU table summarized at L6 (genus). Post Wolbachia removal. No filtering for low count OTUs.
DOI: 10.5061/dryad.37m5c/13
title: Larvae_unsum_edgeR_pooled_all

description: Differential relative abundance calculated using phyloseq/edgeR with collection sites pooled to compare all Wolbachia-negative samples to all Wolbachia-positive samples. Input files were QIIME OTU tables (unsummarized, 97% identity threshold) that have been filtered for Wolbachia and for low-count OTUs.
DOI: 10.5061/dryad.37m5c/14
title: Larvae_unsum_edgeR_glm_all

description: Differential relative abundance in Wolbachia-negative samples compared to Wolbachia-positive samples, calculated using phyloseq/edgeR with a linear model to include collection site as a factor. Input files were QIIME OTU tables (unsummarized, 97% identity threshold) that have been filtered for Wolbachia and for low-count OTUs.
DOI: 10.5061/dryad.37m5c/15
title: Larvae_L6sum_edgeR_pooled_all

description: Differential relative abundance calculated using phyloseq/edgeR with collection sites pooled to compare all Wolbachia-negative samples to all Wolbachia-positive samples. Input files were QIIME OTU tables (summarized at L6, genus) that have been filtered for Wolbachia and for low-count OTUs.
DOI: 10.5061/dryad.37m5c/16
title: Larvae_L6sum_edgeR_glm_all

description: Differential relative abundance in Wolbachia-negative samples compared to Wolbachia-positive samples, calculated using phyloseq/edgeR with a linear model to include collection site as a factor. Input files were QIIME OTU tables (summarized at L6, genus) that have been filtered for Wolbachia and for low-count OTUs.
DOI: 10.5061/dryad.37m5c/17
title: Adults_unsum_edgeR_pooled_all

description: Differential relative abundance calculated using phyloseq/edgeR with collection sites pooled to compare all Wolbachia-negative samples to all Wolbachia-positive samples. Input files were QIIME OTU tables (unsummarized, 97% identity threshold) that have been filtered for Wolbachia and for low-count OTUs.
DOI: 10.5061/dryad.37m5c/18
title: Adults_unsum_edgeR_glm_all

description: Differential relative abundance in Wolbachia-negative samples compared to Wolbachia-positive samples, calculated using phyloseq/edgeR with a linear model to include collection site as a factor. Input files were QIIME OTU tables (unsummarized, 97% identity threshold) that have been filtered for Wolbachia and for low-count OTUs.
DOI: 10.5061/dryad.37m5c/9
title: adults_otu_table_noWol_L3

description: Adults: QIIME OTU table summarized at L3 (class). Post Wolbachia removal. No filtering for low count OTUs.
DOI: 10.5061/dryad.42b68/7
title: ML tree of Amanita afn lavendula taxon 1 RPB2_trimmed

description: Nexus File: PhyML analysis of RPB2 (RNA polymerase 2nd largest subunit) amplified with primers bRPB2-6F and fRPB2-7cR (Matheny, PB 2005).
DOI: 10.5061/dryad.4hc42/1
title: Body size, sexual size dimorphism indices, and habitat classification

description: Excel file that includes mean body size of males and females from 135 turtle species. Also includes sexual size dimorphism indices, habitat classification, center of geographic range (latitude, longitude), and range associated climate data.
DOI: 10.5061/dryad.4hc42/2
title: Turtle species distribution climate data

description: Excel file that includes mean climate data collected via (http://www.worldclim.org/bioclim) for 330 turtle species' geographic distributions.
DOI: 10.5061/dryad.5qr6t/1
title: Median Joining Network
DOI: 10.5061/dryad.5qr6t/2
title: NADH1 gene alignment
DOI: 10.5061/dryad.64td7/1
title: Supplemental_Data_1

description: Supplemental Data Tables 1 and 2
DOI: 10.5061/dryad.b3ng3/3
title: License File
DOI: 10.5061/dryad.b3ng3/4
title: Raw Data and Analysis functions
DOI: 10.5061/dryad.c76pf34.2
title: Data from: Double-digest RAD sequencing outperforms microsatellite loci at assigning paternity and estimating relatedness: a proof of concept in a highly promiscuous bird
DOI: 10.5061/dryad.c76pf34.2/1.2
title: 2012-2016 MSAT Genotypes

description: Microsatellite genotypes of offspring and adult variegated fairy-wrens
DOI: 10.5061/dryad.c9h35/9
title: R code for snowfall frequency uncertainty

description: R code for analyzing the sensitivity of simulated snowfall frequency to 18 different precipitation phase methods.
DOI: 10.5061/dryad.cb83072/1
title: TaxonomicHypotheses

description: Taxonomic hypotheses output from the UNITE and Warcup training databases. SINTAX was used to assign taxonomy. Confidence in assignments is shown. UNITE was accessed May 3, 2017 and Warcup was accessed Dec 4, 2017
DOI: 10.5061/dryad.cb83072/2
title: Sequences of OTUs

description: FASTA file with sequences
DOI: 10.5061/dryad.cb83072/3
title: OTU table

description: OTU table, see main text and supplemental methods for details of how this table was made.
DOI: 10.5061/dryad.cb83072/4
title: Labelling key

description: Well to sample key. Samples were spread across eight 96 well plates (denoted p1–8 in field 1). Each well corresponded with a specific sample, the name of which is shown in field 2. The lane the sample was sequenced on is shown in field 3. Note that there were samples from a different project sequenced at the same time (see supplemental methods).
DOI: 10.5061/dryad.cb83072/5
title: Data for focal populations

description: Summary indices and abiotic information for each focal population. See "readme" file for information on what each field contains.
DOI: 10.5061/dryad.dh2hg/1
title: PublicationData

description: Data of the non-reproductive males with growth rate, body mass,  group size, disperser, group ID and sex for each individual.
DOI: 10.5061/dryad.dh2hg/2
title: PublicationGrowthData

description: Animal ID, group ID, growth rate, body mass, sex and tenure of philopatry (days) for each non-reproductive male.
DOI: 10.5061/dryad.dh2hg/3
title: PublicationTimeColonyData

description: Anima ID, group ID, time of philopatry (days) and disperse (yes-no) for each non-reproductive male.
DOI: 10.5061/dryad.f0285/1
title: Data for Leary and Crocker-Buta (2018) Functional Ecology

description: Data for effects of glucocorticoids on mating behavior and vocal attractiveness in male green treefrogs.
DOI: 10.5061/dryad.f6r55/1
title: Genotype file

description: This file contains genotype information for all 51633 SNPs coded as 0,1,2 (based on the number of minor alleles).
DOI: 10.5061/dryad.f6r55/2
title: SDM_locations

description: Filtered occurrence records for Core, Periphery & P. flexilis used in ENM.
DOI: 10.5061/dryad.f6r55/3
title: Demographic_Models

description: Python scripts used to run 11 demographic models for SWWP (core and periphery) & LP
DOI: 10.5061/dryad.kc835/10
title: pasa_m6.hc.gene_models.repr.pep.fa

description: Protein sequences of representative models of high-confidence genes in S. chacoense M6
DOI: 10.5061/dryad.kc835/11
title: M6_gene_expression_matrix.xlsx

description: Expression abundance of representative gene models
DOI: 10.5061/dryad.kc835/12
title: 523_3_assembly_ALLPATHS_v4.1.fasta.repeatmasker.gff

description: GFF file of the repeat-masked genome
DOI: 10.5061/dryad.kc835/13
title: M6_v4.1_PM.fa

description: Pseudomolecules of S. chacoense M6, containing 12 chromosomes
DOI: 10.5061/dryad.kc835/8
title: pasa_m6.hc.gene_models.pep.fa

description: Protein sequences of high-confidence genes in S. chacoense M6
DOI: 10.5061/dryad.kc835/9
title: m6_gene_models.func_anno.txt

description: Functional annotation of working gene model set in S. chacoense M6
DOI: 10.5061/dryad.n2048/1
title: By mating

description: Data organized by mating event
DOI: 10.5061/dryad.n2048/2
title: By male

description: Data organized by male
DOI: 10.5061/dryad.p85q4.1
title: Data from: Breaking down the lithification bias: the effect of preferential sampling of larger specimens on the estimate of species richness, evenness, and average specimen size
DOI: 10.5061/dryad.q3v30/1
title: tdc.data

description: Annual predictors of survival for time dependent covariate survival analysis.
DOI: 10.5061/dryad.q3v30/2
title: fixedeffects.data

description: Multi-year predictors for fixed effects survival analysis
DOI: 10.5061/dryad.q3v30/3
title: permuted strength-consistency class coefficients

description: Coefficients of fixed-effects survival models with strength consistency classes based on values of bond strength and partner consistency from permuted DSI matrices.