cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rv77v/5
title: CPB1 barcode keyfile

description: Barcodes used to demultiplex "CPB1" GBS library deposited in the NCBI Short Read Archive: https://www.ncbi.nlm.nih.gov/biosample/6295597
DOI: 10.5061/dryad.rv77v/6
title: CPB2 barcode keyfile

description: Barcodes used to demultiplex "CPB2" GBS library deposited in the NCBI Short Read Archive: https://www.ncbi.nlm.nih.gov/biosample/6295598
DOI: 10.5061/dryad.rv77v/7
title: CPB3 barcode keyfile

description: Barcodes used to demultiplex "CPB2" GBS library deposited in the NCBI Short Read Archive: https://www.ncbi.nlm.nih.gov/biosample/6295599
DOI: 10.5061/dryad.sm95d/1
title: Caryophyllaceae_matK_Aligment

description: The Caryophyllaceae-wide matK alignment, used to produce the trees in Fig. 2 and Online Resource 2.  The names correspond to those in Voucher_Table.txt.  For our sequences, DNA numbers follow the names, while for sequences downloaded from GenBank, GB follows the names.
DOI: 10.5061/dryad.sm95d/2
title: Caryophyllaceae_matK-ConT_Fig_2

description: The consensus tree from the BEAST analysis of matK data, shown in Fig. 2 and Online Resource 2.  The names correspond to those in Voucher_Table.txt.  For our sequences, DNA numbers follow the names, while for sequences downloaded from GenBank, GB follows the names.
DOI: 10.5061/dryad.sm95d/3
title: Cherleria_cpDNA_Matrix

description: The Cherleria-wide alignment from the chloroplast trnQ-rps16 and psbD-trnT regions, used to produce the tree in Fig. 3.  The names correspond to those in Voucher_Table.txt.  DNA numbers follow the names.
DOI: 10.5061/dryad.sm95d/4
title: Cherleria_cpDNA_Gaps

description: The coded indels from the Cherleria-wide alignment from the chloroplast trnQ-rps16 and psbD-trnT regions, used to produce the tree in Fig. 3. The names correspond to those in Voucher_Table.txt.  DNA numbers follow the names.
DOI: 10.5061/dryad.sm95d/5
title: Cherleria_cpDNA+Indels_ConT_Fig_3

description: The consensus tree from the BEAST analysis of the trnQ-rps16 and psbD-trnT data, shown in Fig. 3. The names correspond to those in Voucher_Table.txt.  DNA numbers follow the names.
DOI: 10.5061/dryad.sm95d/6
title: Cherleria_cpDNA_SNPs+Gaps_TCS.nex

description: The Cherleria-wide alignment from the chloroplast trnQ-rps16 and psbD-trnT regions for the TCS analysis shown in Fig. 4. The names correspond to those in Voucher_Table.txt.  DNA numbers follow the names.
DOI: 10.5061/dryad.sm95d/7
title: Voucher_Table

description: The voucher table as a tab-delimitted text file including the full species name with authorities, the name in the tree, the DNA number (when we extracted the DNA sample), the voucher and country where it was collected (again, only for our samples), and the GenBank numbers for the sequences that are included in these alignments.
DOI: 10.5061/dryad.st3gt/1
title: 1_cds_genomes

description: CDS from 43 genomes
DOI: 10.5061/dryad.st3gt/2
title: 2_pep_genomes

description: Peptides from 43 genomes
DOI: 10.5061/dryad.v861k/2
title: SNP2271_batch_3_filtered_structure

description: 2271 SNP loci from 80 Plectropomus spp. including identified hybrids collected from the southern Great Barrier Reef, Australia.
DOI: 10.5061/dryad.vb051/1
title: Supplemental Data

description: online supplementary data showing the existing Tethyochonetes species, original data for the bivariate plots and regression analysis, original data for CATPCA analysis, original data for cladistics analysis and quantitative data for the revised genus Fusichonetes.
DOI: 10.5061/dryad.0550m/1
title: Raw data for GOX enzymatic activity, and GOX and Def1 gene expression

description: This excel file contains two sheets: (1) 'GOX_EnzymeActivity' contains the glucose oxidase activity values for the 3 replicates of all samples included in the study; (2) 'GeneExpression' contains gene expression values for the reference gene (Actin), GOX and Def1.
DOI: 10.5061/dryad.125g6/1
title: A list of genome contigs of E. mandarina that are homologous to B. mori genes

description: Raw data for Fig. 2M, Fig. 2N, Fig. 2O, Fig. S2.
DOI: 10.5061/dryad.125g6/2
title: Gene dose of Ket and Tpi in eggs laid by C females, CF females, and CF females treated with tetracycline

description: Raw data for Fig. 3A and Fig. S3.
DOI: 10.5061/dryad.125g6/3
title: Sexual phenotype of offspring produced by tetracycline-treated CF females

description: Raw data for Fig. 3B.
DOI: 10.5061/dryad.125g6/4
title: Gene dose of Ket in adult offspring produced by tetracycline-treated CF females

description: Raw data for Fig. 3C.
DOI: 10.5061/dryad.125g6/5
title: Survivorship data of offspring produced by tetracycline-treated CF females

description: Raw data for Fig. 3B and Fig. 3C.
DOI: 10.5061/dryad.125g6/6
title: Gene dose of Ket and Tpi in CF adults that were treated with tetracycline during larval stages

description: Raw data for Fig. 4I.
DOI: 10.5061/dryad.1vm8k/1
title: Data paper mastrus inbreeding compiled v2

description: File contains 5 sheets. Sheet 1 has data of offspring according to male crossing treatment, ploidy and generation. Sheet 2 is the data of ploidy of males, according to treatment and generation where the male originated (0 haploid; 1 diploid). Sheet 3 is the longevity of reproducing females according to crossing treatment, line and generation. Sheet 4 is the longevity of non-reproducing females according to crossing treatment, line and generation. Sheet 5 is data of offspring of selected females according to crossing treatment, line and generation.
DOI: 10.5061/dryad.24tm0/3
title: FemaleRecruit_Dryad_Tot

description: Females Recruits
DOI: 10.5061/dryad.24tm0/4
title: FemaleSurvival_Dryad_Tot

description: Females Survival
DOI: 10.5061/dryad.24tm0/5
title: MaleFledge_DryadTot

description: Males Fledged
DOI: 10.5061/dryad.24tm0/6
title: MaleRecruit_DryadTot

description: Males Recruits
DOI: 10.5061/dryad.24tm0/7
title: MaleSurv_DryadTot

description: Males Survival
DOI: 10.5061/dryad.2p2bh/1
title: salix and pv phenology data

description: Flowering phenology data (Julian day) for Salix spp. and Polemonium viscosum specimens collected from 25 sites in the Colorado Rocky Mountains between 1907 and 2009. The location, altitude, mean minimum June temperatures, and the latitude and longitude estimated using Google Earth are provided for each specimen.
DOI: 10.5061/dryad.2p2bh/2
title: 2016 population survey

description: Pollen counts on stigmas from naturally pollinated P. viscosum flowers. Pollen identified as Salix and P. viscosum (denoted by “pv” in the data file) were quantified using light microscopy. Salix pollen contamination was estimated as the frequency (proportion) of total pollen identified as Salix pollen. The site name, unique sample number (“sample ID), and the distance (m) from the focal plant to the nearest Salix spp. plant are included.
DOI: 10.5061/dryad.2p2bh/3
title: pollen purity vs seed set

description: Average seed set per flower for naturally pollinated plants at Pennsylvania Mountain, Colorado. Pollination success (conspecific pollen deposition and germination rates) and contamination (proportion of pollen from Salix spp.) were quantified for one flower per inflorescence.
DOI: 10.5061/dryad.2p2bh/4
title: pollination experiment

description: Data from the pollination contamination experiment. Individual plants found within groups of P. viscosum plants were randomly assigned to one of three pollination treatments: no pollen supplementation, conspecific (P. viscosum) pollen supplementation, and Salix spp. pollen supplementation. The plant number, group number, number of flowers pollinated, number of seeds produced, and average seeds per flower are provided.
DOI: 10.5061/dryad.327c2/1
title: Carbonate chemistry of the two study reefs - means over sites

description: Carbonate chemistry of the two study reefs - mean values per site at high CO2 at the CO2 seeps, and their adjacent control sites.
DOI: 10.5061/dryad.327c2/2
title: Carbonate chemistry of the two study reefs - means over tiles

description: Carbonate chemistry of the two study reefs - mean values for each of the settlement tiles.
DOI: 10.5061/dryad.327c2/3
title: Settlement choice experiments

description: Choice of larvae of Acropora tenuis to settle on settlement substrata from either High-CO2 or Control sites.
DOI: 10.5061/dryad.327c2/4
title: Settlement no-choice experiments

description: Settlement rates of Acropora tenuis larvae from parents originating from high CO2 or control sites.
DOI: 10.5061/dryad.327c2/5
title: Survival of A.tenuis recruits in field

description: Survival rates of A.tenuis recruits after returning into field settings at variable CO2 concentrations.
DOI: 10.5061/dryad.327c2/6
title: Substrata on settlement tiles

description: Substrata on settlement tiles including individual taxa of crustose coralline algae
DOI: 10.5061/dryad.327c2/7
title: Substrata on settlement tiles - summary variables

description: Substrata on settlement tiles - summary variables
DOI: 10.5061/dryad.33418/1
title: Script to call function that calculates f4 statistic in sliding windows across genome

description: Python script used to call the function that calculates f4 statistic in sliding windows across genome that is described in genomics_f4_ejredit.py. Modified from Simon H. Martin's script for calculating D and fd statistics in sliding windows (https://github.com/simonhmartin/genomics_general/ABBABABBA.py).
DOI: 10.5061/dryad.33418/2
title: Script to calculate f4 statistic in sliding window across genome

description: Script to calculate f4 statistic in sliding window across genome. Modified from Simon H. Martin's script to calculate D and fd statistics in sliding windows across genome (https://github.com/simonhmartin/genomics_general/genomics.py). See this website for details and options for running the function.
DOI: 10.5061/dryad.33418/3
title: SAGUARO input file

description: The feature file required for SAGUARO analysis consisting of information on SNPs from 43 pupfishes. This file was converted into this format from a vcf file.
DOI: 10.5061/dryad.33418/4
title: Sliding window f4 statistic file

description: Input file of SNP genotypes across 43 pupfishes used for calculating f4 statistic in sliding windows across genome. This file was converted into this format from a vcf file.
DOI: 10.5061/dryad.33418/5
title: Treemix input files for candidate adaptive introgression regions

description: The SNP matrix files used in the Treemix analysis of each candidate region. Files are labeled by scaffold and starting position of the region.
DOI: 10.5061/dryad.597ch/1
title: low data BMJ
DOI: 10.5061/dryad.5g39r/1
title: Data

description: Pollinator response to manually damaged strawberry flowers; Effects of herbivory on pollination success and fruit development; Woodland strawberry resistance against Galerucella sagittariae; and Woodland strawberry resistance to Galerucella tenella.
DOI: 10.5061/dryad.5q114/1
title: Temporal Beta-Diversity in weed communities

description: This data file provides two beta-diversity indices, namely Jaccard and Bray-Curtis, computed from successive weed communities growing in 493 arable fields distributed over the whole French national territory. Temporal environmental distances, environmental heterogeneity and temporal distance are also furnished. Weeds were surveyed in two kind of plots, without herbicide application (control, "c") and with herbicide application (sprayed, "s"). Each year, weeds were surveyed twice, at the begining (n1) and at the middle (n2) of the cropping season.
DOI: 10.5061/dryad.786r6.1
title: Data from: Techniques for estimating the size of low density gopher tortoise populations
DOI: 10.5061/dryad.786r6.1/1.1
title: FGtort_NE and NW datasets

description: Two distance sample projects - Download Program distance at http://distancesampling.org/. Tutorial in the readme for loading data and running analysis.
DOI: 10.5061/dryad.786r6.2
title: Data from: Techniques for estimating the size of low density gopher tortoise populations
DOI: 10.5061/dryad.786r6.2/1.2
title: FGtort_NE and NW datasets

description: Two distance sample projects - Download Program distance at http://distancesampling.org/. Tutorial in the readme for loading data and running analysis.
DOI: 10.5061/dryad.7f32h/1
title: Data for dryad

description: Evolutionary responses of Plodia interpunctella in sperm production, immunity, development, mating frequency and longevity in response to being reared at high (HD) or low (LD) population densities.
DOI: 10.5061/dryad.7gt44/2
title: BendectinFichesFDACombined

description: All FDA "fiche" files received. Some are not relevant.
DOI: 10.5061/dryad.7gt44/3
title: HealthCanadaA201100688_2012-11-19_09-21-37

description: Partially redacted documents from Health Canada
DOI: 10.5061/dryad.8nr8p/1
title: DeWitt et al - Capture History

description: Capture histories of porcupines at Sandhill Wildlife Area from 1996 to 2011. Each capture includes porcupine identity, date of capture, body mass at capture, the mean summer North Atlantic Oscillation (sNAO), the mean winter North Atlantic Oscillation (wNAO), the mean North Atlantic Oscillation measured between the start of winter and the date an individual was captured (NAO), and whether fishers were present within the study area during the capture year.
DOI: 10.5061/dryad.8sm32/3
title: Raeymaekers et al-NatCommun-2017_nine_spined_denovo_based_genotypes

description: de novo-based SNP genotypes of the nine-spined stickleback (VCF file). Individuals are labelled as Population_ID.
DOI: 10.5061/dryad.bs7sg/1
title: choice.all

description: average mate choice for all 291 F2 females with parentage assignment &gt;0.75 where 1=benthic and 0=limnetic
DOI: 10.5061/dryad.bs7sg/2
title: phenotypes.all

description: raw X and Y values for 17 morphological landmarks in all F2 females, wild benthic males and wild limnetic males
DOI: 10.5061/dryad.bs7sg/3
title: Morphology R script

description: script for statistical analysis and visualization of morphological data
DOI: 10.5061/dryad.bs7sg/4
title: landmarks R script

description: functions used in Morphology.R for scaling
DOI: 10.5061/dryad.bs7sg/5
title: pedigree.all

description: parentage assignments for all genotyped offspring
DOI: 10.5061/dryad.bs7sg/8
title: all.gen

description: SNP genotypes for input to Rqtl for 302 F2 females
DOI: 10.5061/dryad.g582t/2
title: Data File 2 LSU Clade G

description: Data File 2.  Nexus file of aligned sequences of the partial LSU rDNA used to generate phylogeny presented in Figure 2A.
DOI: 10.5061/dryad.g582t/3
title: Data File 3 cp23S Clade G

description: Data File 3.  Nexus file of aligned sequences of the partial chloroplast cp23S used to generate phylogeny presented in Figure 2A.
DOI: 10.5061/dryad.g582t/4
title: Data File 4 mitochondrial cob

description: Data File 4.  Nexus file of aligned sequences of the mitochondrial cob gene used to generate phylogeny presented in Figure 2A.
DOI: 10.5061/dryad.g582t/5
title: Data File 5 psbAncr Clade G

description: Data File 5.  Nexus file of aligned sequences of the partial 5’ (352 bases) and 3’ (237 bases) of the psbA gene for the D1 protein in the reaction center of photosystem II and the full sequence (~600-700 bases) of the non-coding region of the psbA minicircle used to generate phylogeny presented in Figure 3.
DOI: 10.5061/dryad.g9f5r/1
title: Index for VCF file

description: Index for VCF file
DOI: 10.5061/dryad.g9f5r/2
title: VCF file containing imputed genotype data belonging to 67 newly sequenced and publicly available ancient samples.

description: VCF file containing imputed genotype data belonging to 67 newly sequenced and publicly available ancient samples which we analysed in Martiniano et al. (2017).
DOI: 10.5061/dryad.g9f5r/3
title: README_Martiniano_et_al_2017

description: Description of the methods used for genotype imputation.
DOI: 10.5061/dryad.hf83v/1
title: Janzen-Connell patterns can be induced by fungal-driven decomposition and offset by ectomycorrhizal fungi accumulated under a closely related canopy

description: Data collected in the field
DOI: 10.5061/dryad.jn630/1
title: SNP dataset for 39 Kenyan honey bees (part 0)

description: This dataset contains the 8+ million SNPs that were detected between 39 Kenyan honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.

The original 39_kenyan_honeybees.vcf.gz input file has been split into four numbered parts (0 to 3). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 39_kenyan_honeybees.vcf.gz.{0..3}.split &gt; 39_kenyan_honeybees.vcf.gz

The VCF file can then be unzipped using the UNIX command: gunzip 39_kenyan_honeybees.vcf.gz
DOI: 10.5061/dryad.jn630/2
title: SNP dataset for 39 Kenyan honey bees (part 1)

description: This dataset contains the 8+ million SNPs that were detected between 39 Kenyan honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.

The original 39_kenyan_honeybees.vcf.gz input file has been split into four numbered parts (0 to 3). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 39_kenyan_honeybees.vcf.gz.{0..3}.split &gt; 39_kenyan_honeybees.vcf.gz

The VCF file can then be unzipped using the UNIX command: gunzip 39_kenyan_honeybees.vcf.gz
DOI: 10.5061/dryad.jn630/3
title: SNP dataset for 39 Kenyan honey bees (part 2)

description: This dataset contains the 8+ million SNPs that were detected between 39 Kenyan honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.

The original 39_kenyan_honeybees.vcf.gz input file has been split into four numbered parts (0 to 3). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 39_kenyan_honeybees.vcf.gz.{0..3}.split &gt; 39_kenyan_honeybees.vcf.gz

The VCF file can then be unzipped using the UNIX command: gunzip 39_kenyan_honeybees.vcf.gz
DOI: 10.5061/dryad.jn630/4
title: SNP dataset for 39 Kenyan honey bees (part 3)

description: This dataset contains the 8+ million SNPs that were detected between 39 Kenyan honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.

The original 39_kenyan_honeybees.vcf.gz input file has been split into four numbered parts (0 to 3). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 39_kenyan_honeybees.vcf.gz.{0..3}.split &gt; 39_kenyan_honeybees.vcf.gz

The VCF file can then be unzipped using the UNIX command: gunzip 39_kenyan_honeybees.vcf.gz
DOI: 10.5061/dryad.jn630/5
title: SNP dataset for 148 Kenyan, African and Eurasian honey bees (part 0)

description: This dataset contains the 13+ million SNPs that were detected between 148 Kenyan, African and Eurasian honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.

The original 148_honeybees.vcf.gz input file has been split into fourteen numbered parts (0 to 13). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 148_honeybees.vcf.gz.{0..13}.split &gt; 148_honeybees.vcf.gz

The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz
DOI: 10.5061/dryad.jn630/6
title: SNP dataset for 148 Kenyan, African and Eurasian honey bees (part 1)

description: This dataset contains the 13+ million SNPs that were detected between 148 Kenyan, African and Eurasian honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.

The original 148_honeybees.vcf.gz input file has been split into fourteen numbered parts (0 to 13). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 148_honeybees.vcf.gz.{0..13}.split &gt; 148_honeybees.vcf.gz

The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz
DOI: 10.5061/dryad.jn630/7
title: SNP dataset for 148 Kenyan, African and Eurasian honey bees (part 2)

description: This dataset contains the 13+ million SNPs that were detected between 148 Kenyan, African and Eurasian honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.

The original 148_honeybees.vcf.gz input file has been split into fourteen numbered parts (0 to 13). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 148_honeybees.vcf.gz.{0..13}.split &gt; 148_honeybees.vcf.gz

The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz
DOI: 10.5061/dryad.jn630/8
title: SNP dataset for 148 Kenyan, African and Eurasian honey bees (part 3)

description: This dataset contains the 13+ million SNPs that were detected between 148 Kenyan, African and Eurasian honey bees using FreeBayes and that passed quality filtering. Details for SNP processing, sample labels and quality control is provided in the paper and its supplementary information.

The original 148_honeybees.vcf.gz input file has been split into fourteen numbered parts (0 to 13). After downloading all parts, they can be joined to recreate the original file using the follwing UNIX command: cat 148_honeybees.vcf.gz.{0..13}.split &gt; 148_honeybees.vcf.gz

The VCF file can then be unzipped using the UNIX command: gunzip 148_honeybees.vcf.gz
DOI: 10.5061/dryad.k5m0s/1
title: ChristieEvolution2017Data

description: Scripts and data to generate Figs 1-3 and Table 1
DOI: 10.5061/dryad.p4238/1
title: Data from Kim et al 2017. Nat. Eco. Evol.
DOI: 10.5061/dryad.qn119/6
title: Coefficients and 95% confidence intervals for averaged consumer biomass models (Fig2)

description: Standardized coefficients and 95% confidence intervals for each of the ten predictors from each of 14 averaged consumer biomass models presented in Figure 2. Consumer groups are the ten selected taxonomic groups (ants, blattodea, chilopoda, coleoptera, diplopoda, isopoda, isoptera, opiliones, orthoptera, spiders), three functional feeding guilds (detritivores, predators, omnivores) and the complete consumer community (all). Predictor variables are litter mass (LM), plant species richness (prich), soil pH (pH), and litter carbon to element ratios for N, P, K, Ca, Mg, Na, and S. Coef gives the standardized coefficient of each predictor for each averaged model. Confint_lower_boundary and confint_upper_boundary give the 95% confidence interval for the coefficients. It should be noted that for all stoichiometric parameters, negative coefficients indicate a positive effect of the respective elemental availability as the models were run on C:element ratios. As such, a positive effect of e.g. C:N corresponds to a negative effect of N in main text Fig. 2.
DOI: 10.5061/dryad.r8591/1
title: Model outputs (R summaries and correlations)

description: The file contains the summary outputs saved from the software R for all the fitted models, including matrices reporting the correlation between the variables. Legend of variables and tree species, as well as a short explanation on how to read the model outputs, are included in the file.
DOI: 10.5061/dryad.rb0p7/1
title: Tables S1 and S10

description: Data used to complete analyses shown in Table S1 and S10
DOI: 10.5061/dryad.rb0p7/2
title: Effects of treatments on babysitting results

description: Data to assess how experimental treatments affect babysitting behaviour.