cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4h00t/21
title: dl;dl-mVenus/+

description: All lsm files (images taken with a Zeiss 710) of dl;dl-mVenus/+ embryos used in the analysis (quantitative or qualitative) in this paper. These embryos have zero copies of endogenous dl, and one copy of dl-mVenus.
DOI: 10.5061/dryad.4h00t/22
title: dl;dl-lacZ

description: All lsm files (images taken with a Zeiss 710) of dl;dl-lacZ embryos used in the analysis (quantitative or qualitative) in this paper. These embryos have zero copies of endogenous dl, and two copies of dl-lacZ.
DOI: 10.5061/dryad.4h00t/23
title: cact/+;cact-lacZ/+

description: All lsm files (images taken with a Zeiss 710) of cact/+;cact-lacZ/+ embryos used in the analysis (quantitative or qualitative) in this paper. These embryos have one copy of endogenous cact, and one copy of cact-lacZ
DOI: 10.5061/dryad.5081qr5/1
title: Pollinator-data-Table-1

description: Pollinator visitation to experimental arrays
DOI: 10.5061/dryad.5081qr5/2
title: Herkogamy-data-Table-2

description: Herkogamy data for arrays of Campanula americana from high and medium autogamy populations in placed in sun and shade environments.
DOI: 10.5061/dryad.5081qr5/3
title: Male-traits-Table-2

description: Male traits (dichogamy and pollen persistence) for arrays of Campanula americana from high and medium autogamy populations in placed in sun and shade environments
DOI: 10.5061/dryad.5081qr5/4
title: Pollen-limitation-Table-2

description: Pollen limitation for arrays of Campanula americana from high and medium autogamy populations in placed in sun and shade environments
DOI: 10.5061/dryad.5081qr5/5
title: Outcrossing-Table-3

description: Outcrossing rates for arrays of Campanula americana from high and medium autogamy populations that experience a range of pollen limitation.
DOI: 10.5061/dryad.5228g/1
title: Data Summary JEB O'Brien et al JEXBIO_2017_162503
DOI: 10.5061/dryad.5535h/1
title: Functional trait values, height and crown illumination index for each tree

description: This dataset gives the value of leaf functional traits (mean value for the three, or fewer, measured leaves), height and crown illumination index for 852 sapling trees belonging to 69 species of Costa Rican tropical dry forests.
DOI: 10.5061/dryad.5535h/2
title: Environmental factors in successional tropical dry forests of Costa Rica

description: This dataset gives the values of environmental factors (micro-climate, soil physical and chemical properties, forest structure) of 12 plots in successional tropical dry forests of Costa Rica.
DOI: 10.5061/dryad.5535h/3
title: Species codes

description: This file gives the list of species measured in a study of sapling in successional tropical dry forests of Costa Rica, their families, and the species code used in the dataset of functional traits.
DOI: 10.5061/dryad.739bs/10
title: SUPPLEMENTARY APPENDIX 10

description: Species delimitations estimated by bPTP-h for data sets from Scenario II. Panels show nine combinations of population size N and divergence time t along the top, and four values of sample size n on the right. The x-axis represents the number of loci. The y-axis represents the number of cases classified by correct delimitation (dark green), false positive (dark blue), complex false positive (light blue), and not available (grey) among the 10 replicates under each set of conditions.
DOI: 10.5061/dryad.739bs/11
title: SUPPLEMENTARY APPENDIX 11

description: Results of analyses of data sets from Scenario III.
DOI: 10.5061/dryad.739bs/12
title: SUPPLEMENTARY APPENDIX 12

description: Results of analyses of data sets from Scenario IV.
DOI: 10.5061/dryad.739bs/13
title: SUPPLEMENTARY APPENDIX 13

description: Results of analyses of full data sets from Scenario V.
DOI: 10.5061/dryad.739bs/5
title: SUPPLEMENTARY APPENDIX 5

description: Data files from the case study of Apidae bees.
DOI: 10.5061/dryad.739bs/6
title: SUPPLEMENTARY APPENDIX 6

description: Data files from the case study of Osmia bees.
DOI: 10.5061/dryad.739bs/7
title: SUPPLEMENTARY APPENDIX 7

description: Results of analyses of data sets from Scenario I. (a) Species delimitations estimated by the Bayesian coalescent method in BPP. Boxplots are shown for posterior probabilities of the one-species delimitation model (P1), across every 10 replicates under each set of conditions. Fifteen combinations of sample size n and population size N are shown along the top. The x-axis represents the number of loci. Probabilities are given on the y-axis. (b) Species delimitation estimated by the generalized mixed Yule-coalescent (GMYC) and the Poisson tree processes (PTP) methods. Stacked rows are shown for GMYC, Bayesian PTP heuristic (bPTP-h), Bayesian PTP maximum likelihood (bPTP-ML), and PTP heuristic (PTP-h), respectively. Twelve combinations of sample size n and population size N are along the top of the panels. The x-axis represents the number of loci. The y-axis represents the number of cases classified by false positive (dark blue) and not available (grey) among every 10 replicates under each set of conditions.
DOI: 10.5061/dryad.739bs/8
title: SUPPLEMENTARY APPENDIX 8

description: Results of supplementary data sets to Scenario II.
DOI: 10.5061/dryad.739bs/9
title: SUPPLEMENTARY APPENDIX 9

description: Species delimitations estimated by PTP-h for data sets from Scenario II. Panels show nine combinations of population size N and divergence time t along the top, and four values of sample size n on the right. The x-axis represents the number of loci. The y-axis represents the number of cases classified by correct delimitation (dark green), false positive (dark blue), complex false positive (light blue), and not available (grey) among the 10 replicates under each set of conditions.
DOI: 10.5061/dryad.9b3r0/4
title: Arrival data

description: Arrival of individuals to forage while feeder was in novel environment - restricted to each individual's first arrival only.
DOI: 10.5061/dryad.fk41r/1
title: README.txt

description: README.txt
DOI: 10.5061/dryad.fk41r/2
title: CAL_genome_asm_v2.2_1000_rmscaff.fasta

description: Final genome assembly for C. gigantea
DOI: 10.5061/dryad.fk41r/3
title: CAL_genome_asm_v2.2_1000_rmscaff_hard_masked.fasta

description: Final hard masked genome assembly for C. gigantea
DOI: 10.5061/dryad.h5r77/1
title: RADseq-derived SNP genotype data: 14,031 loci, 48 individuals, species = Leiopotherapon unicolor.

description: Data is R S4 class ‘genind’ object (adegenet R package): “unicolor_data.RData”. The data are RADseq-derived SNP genotypes scored for 14,031 loci in 48 individuals. Individual sample codes in this file include population identifier and  individual identifier. Please see Readme.txt file.
DOI: 10.5061/dryad.hp38ct1/1
title: Bison body size and climate change dataset

description: Locality information: name, geologic age, latitude, longitude, specimen numbers, specimen voucher list, locality summary statistics, GISP2 temperature, linear osteometrics, species, elevation, etc.
DOI: 10.5061/dryad.m5ct8/10
title: Count transitions between character states

description: R script for conducting stochastic character mapping (SIMMAP) on data to count transitions between character states, used in analysis of color polymorphism trait (three states: "similar coloration", "redder lowers", and "redder uppers").
DOI: 10.5061/dryad.m5ct8/11
title: Calculate correlations between morphological traits and altitude

description: R script for conducting phylogenetic generalized least squares (pgls) between continuous morphological traits and altitude or other continuous traits, as well as for utilizing brunch package to assess correlations between binary (primarily color-related) traits and altitude.
DOI: 10.5061/dryad.m5ct8/4
title: Character matrix

description: Character matrix of 89 taxa (including two outgroups) used for comparative phylogenetic methods described in Methods section 2; this additionally contains some data (peristome width, peristome slope, and wax coverage) taken from Bauer et al. (2012).
DOI: 10.5061/dryad.m5ct8/5
title: BEAST tree without ITS

description: Phylogenetic tree inferred by BEAST using trnK and PTR1 genes for 85 Nepenthes species and two outgroups (Ancistrocladus abbreviatus and Triphyophyllum peltatum), used in phylogenetic comparative analyses.
DOI: 10.5061/dryad.m5ct8/6
title: BEAST tree with ITS

description: Phylogenetic tree inferred by BEAST using trnK, PTR1, and ITS genes for 85 Nepenthes species and two outgroups (Ancistrocladus abbreviatus and Triphyophyllum peltatum)--not used in phylogenetic comparative analyses appearing in the manuscript.
DOI: 10.5061/dryad.m5ct8/7
title: BEAST tree (no ITS), annotated

description: Phylogenetic tree inferred with BEAST using trnK and PTR1 genes for 85 Nepenthes species and 2 outgroups (Ancistrocladus abreviatus and Triphyophyllum peltatum), annotated in TreeAnnotator to include posterior probabilities.
DOI: 10.5061/dryad.m5ct8/8
title: Ancestral state reconstruction

description: R script for conducting ancestral state reconstructions on the data.
DOI: 10.5061/dryad.m5ct8/9
title: Tests of correlated evolution

description: R script for conducting tests of correlated evolution on the data; includes Pagel's (1994) test and binary phylogenetic generalized linear mixed model (binary PGLMM).
DOI: 10.5061/dryad.qr5vd/1
title: Boechera_experiment_snowmelt

description: This file includes the snowmelt dates from the Boechera stricta experiment (Table S7).
DOI: 10.5061/dryad.rg6k9/1
title: Phenotype_Limb_Bone_Length_raw

description: Phenotype data for the length of each limb bone from the raw measurements.
DOI: 10.5061/dryad.rg6k9/2
title: Phenotype_Residuals_Age

description: Phenotype data for the length of each limb bone after linear regression on age (residual values).
DOI: 10.5061/dryad.rg6k9/3
title: Kinship_Matrix

description: Centered kinship matrix generated in GEMMA using LD-pruned SNPs from autosomes.
DOI: 10.5061/dryad.tb25q.1
title: Data from: Keeping pace with the Red Queen: identifying the genetic basis of susceptibility to infectious disease
DOI: 10.5061/dryad.tb25q.1/1.1
title: CoGWAS_Supplement

description: Mathematica notebook deriving analytical models, numerical simulations, and for producing figures 1-4 and S1.
DOI: 10.5061/dryad.tb25q.1/2.1
title: CoGWAS_Supplement

description: CDF version of Mathematica notebook covering analytical model derivation, numerical simulations, and for producing figures 1-4 and S1.
DOI: 10.5061/dryad.tb25q.1/3.1
title: CoGWAS_Supplement

description: PDF version of Mathematica notebook covering analytical model derivation, numerical simulations, and for producing figures 1-4 and S1.
DOI: 10.5061/dryad.tb25q.2/5.2
title: Fig. S2 - GWAS of *Daphnia magna* susceptibility

description: Genetic associations of each SNP with C1 (red circles), C19 (blue, squares), and "mixed'' susceptibility (green, triangles). Here, the mixed case was obtained by taking each host clone and randomly choosing the data upon exposure to C1 or C19 (not both, as incorporated in the overall analysis in figure 5).  Hence each SNP is represented three times, once for each genome wide scan. Note that closely linked SNPs often overlap with one another and are not all individually visible. Significant SNPs are shown in colour while those below the log-likelihood of 2 threshold or that are not clustered within a 10cM region of three other significant SNPs are shown in grey. The 10 linkage groups are delineated by vertical dashed lines.
DOI: 10.5061/dryad.tb25q/4
title: Fig. S1 - Matching-alleles model

description: Row 1: Estimated allelic effects as a function of pathogen allele frequency (black: \beta_0, solid red: \beta_{Hi}, dashed red: \beta_{H1,H2}, blue \beta_{Pi}, blue dashed: \beta_{P1,P2}, purple dashed: \beta_{Hi,Pj}). Row 2: Variation explained by host additive effects only (solid red), host additive and epistatic effects (dashed red), host and pathogen additive and epistatic effects (dashed blue, overlaps with dashed red), and a full host pathogen model (dashed purple).
DOI: 10.5061/dryad.tb25q/5
title: Fig. S2 - GWAS of *Daphnia magna* susceptibility

description: Genetic associations of each SNP with C1 (red circles), C19 (blue, squares), and "mixed'' susceptibility (green, triangles). Here, the mixed case was obtained by taking each host clone and randomly choosing the data upon exposure to C1 or C19 (not both, as incorporated in the overall analysis in figure 5).  Hence each SNP is represented three times, once for each genome wide scan. Note that closely linked SNPs often overlap with one another and are not all individually visible. Significant SNPs are shown in colour while those below the log-likelihood of 2 threshold or that are not clustered within a 10cM region of three other significant SNPs are shown in grey. The 10 linkage groups are delineated by vertical dashed lines.
DOI: 10.5061/dryad.vg71m/1
title: Mesodma p4 linear measurements

description: This file contains full locality information and linear measurements (length [L], length to maximum tooth height [L1], and height [H]) for all lower fourth premolars of Mesodma included in this study. All measurements are in millimeters. Diagram of measurements is shown in Figure 1 of publication. All locality numbers and specimen numbers are University of California Museum of Paleontology (UCMP) numbers.
DOI: 10.17632/jfcfmn6b43.1
title: Data for: Solid-Liquid equilibrium and heat capacity trend in the alkylimidazolium PF6 series

description: Data for: Solid-Liquid equilibrium and heat capacity trend in the alkylimidazolium PF6 series
DOI: 10.17632/jfcfmn6b43.2
title: Data for: Solid-Liquid equilibrium and heat capacity trend in the alkylimidazolium PF6 series

description: Data for: Solid-Liquid equilibrium and heat capacity trend in the alkylimidazolium PF6 series
DOI: 10.17632/srj2mb7k6w.2
title: Data for: Infection of Neuroblastoma Cells by Rabies Virus Is Modulated by Virus Titer

description: This is the data for this publication.
DOI: 10.5061/dryad.08c4c/1
title: Hayes MMR & range Dryad file - MMR, Mass & range data plus MMR & Mass references

description: Maximal metabolic rate, mass, and data source citations plus geographic range data
DOI: 10.5061/dryad.1r89hq8/1
title: Brachidontes_rawreads

description: Large file (~16Gb) containing raw reads in fastq format from all 125 individuals analysed in this study, sampled from seven marine lakes in Indonesia. Allocations of individuals to marine lakes can be found in the text file Populations.txt. In Brachidontes_Reference.fasta the obtained reference file can be found to which individuals were aligned.
DOI: 10.5061/dryad.1r89hq8/2
title: Populations

description: Simple text file allocating individual reads to marine lakes from which they were sampled.
DOI: 10.5061/dryad.1r89hq8/3
title: Brachidontes_Reference

description: Reference file in fasta format to which individual reads were aligned.
DOI: 10.5061/dryad.28660/9
title: Reference A8

description: Sullivan B. 2010. Management plan for midcontinent greater white-fronted geese. Central Flyway Waterfowl Technical Committee, Denver, Colorado, U.S.
DOI: 10.5061/dryad.2fq726m/1
title: Rice canopy spectral data under water stress

description: The data file contains whole 780 canopy spectra and their corresponding soil water potential (kPa) and 72 canopy spectra and their corresponding terminal soil water potential (kPa), relative water content (%) and electrolyte leakage(%).
DOI: 10.5061/dryad.5h6q8/1
title: CONTENT ADHERENCE TO FIDELITY

description: Content adherence of seasonal malaria chemoprevention intervention's activities to implementation fidelity in Kaya health district in 2014 and 2015
DOI: 10.5061/dryad.5h6q8/2
title: SCHEDULE ADHERENCE TO IMPLEMENTATION FIDELITY

description: Schedule adherence of seasonal malaria chemoprevention intervention's activities to implementation fidelity in Kaya health district in 2014 and 2015
DOI: 10.5061/dryad.66rm7/1
title: fungal_occurance_raw_data

description: Data were collected in the field during 2015 in the Flüela and Sertig valley, Davos, Switzerland. Abbreviated headlines are as follows: "soil_sampling_site" = soil sampling site,"distance_to_host" = m of distance to host plant, "elevation" = m a.s.l. of elevation,"soil_moisture" = % of soil moisture, "soil_ph" = pH of soil sample, "read_number" = n of sequencing read number, "region" = valley (D = Flüela, S = Sertig), "season" = sampling season, "MWT" = mean daily temperature (°C ) for the coldest three months (i.e. winter), "MST" = mean daily temperature (°C )for the hottest three months (i.e. summer), "vegetation_cover" = % of vegetation cover, "MMaxST" = mean daily maximum temperature (°C )for the hottest three months, "MMinWT" = mean daily minimum temperature (°C) for the coldest three months, "MHM" = mean daily temperature (°C) for the hottest month (i.e. July), "MCM" = mean daily temperature (°C) for the coldest month (i.e. January), "MMaxHM" = mean daily maximum temperature (°C) for the hottest month, "MMinCM" = mean daily minimum temperature (C°) for the coldest month, "OTU_#" = n of sequencing read number of respective OUT,  "batch" = batch number of soil samples
DOI: 10.5061/dryad.739bs/14
title: SUPPLEMENTARY APPENDIX 14

description: Results of analyses of separate data sets from Scenario V.
DOI: 10.5061/dryad.739bs/15
title: SUPPLEMENTARY APPENDIX 15

description: Inferred species delimitations for Apidae bees.
DOI: 10.5061/dryad.739bs/16
title: SUPPLEMENTARY APPENDIX 16

description: Inferred species delimitations for Osmia bees.
DOI: 10.5061/dryad.bb49h/1
title: Ylanne_etal_2017_FunctEcol_data

description: This file contains the carbon stock, vegetation abundance and soil data that is presented in the article "Consequences of grazer-induced vegetation transitions on ecosystem carbon storage in the tundra". The study sites Raisduoddar (69°31’29 N, 21°19’16 E; altitude 430–570 m asl) and Čearro (69°43’23 N, 21°37’45 E; altitude 540–570 m asl) are located in Northern Norway. In this file, Raisduoddar is referred to as Reisa. Other occuring acronyms are HG, MG and LG that represent the different grazing intensities found at the two sites. LG represents lightly grazed areas that are located 5 meters from the pasture rotation fence on the Winter grazing range. HG represent heavily grazed areas that are located 5 meters from the pasture rotation fence on the summer grazing range. MG represents moderately grazed areas, 100 m away from the fence on the summer grazing range. At each of the sites, we set eight transects perpendicular to the reindeer fence that cross all three grazing intensities.
DOI: 10.5061/dryad.fk41r/10
title: cal_hc_gene_models.rmscaff.cds.fa

description: Coding sequences (CDS) of high-confidence genes in C. gigantea
DOI: 10.5061/dryad.fk41r/11
title: cal_hc_gene_models.rmscaff.pep.fa

description: Protein sequences of high-confidence genes in C. gigantea
DOI: 10.5061/dryad.fk41r/4
title: CAL_genome_asm_v2.2_1000_rmscaff_soft_masked.fasta

description: Final soft masked genome assembly for C. gigantea
DOI: 10.5061/dryad.fk41r/5
title: short_summary_asm_v2.2_1000.txt

description: Table summary of the number and percentage of Embryophyta orthologs for each category
DOI: 10.5061/dryad.fk41r/6
title: full_table_asm_v2.2_1000.tsv

description: Table providing the location in the genome assembly for each Embryophyta ortholog
DOI: 10.5061/dryad.fk41r/7
title: missing_busco_list_asm_v2.2_1000.tsv

description: List of missing Embryophyta orthologs from the genome assembly
DOI: 10.5061/dryad.fk41r/8
title: cal_hc_gene_models.rmscaff.gff3

description: Generic feature format (gff3) of high-confidence genes in C. gigantea
DOI: 10.5061/dryad.fk41r/9
title: cal_hc_gene_models.rmscaff.cdna.fa

description: Transcript sequences (cDNA) of high-confidence genes in C. gigantea
DOI: 10.5061/dryad.g8609/1
title: XML file for BEAST divergence time analysis

description: XML file for BEAST divergence time analysis. Taxon names of some exemplars may differ from those used in the publication due to species names being updated prior to publication after the analyses were completed.
DOI: 10.5061/dryad.g8609/2
title: Species-specific sampling fractions for BAMM

description: File specifying species-specific sampling fractions used in the BAMM diversification rates analysis.  Taxon names of some exemplars may differ from those used in publication due to species names being updated prior to publication after the analyses were completed.
DOI: 10.5061/dryad.g8609/3
title: Phylogenetic tree used for BAMM analysis

description: Phylogenetic tree in newick format used in the BAMM diversification rate analysis. Taxon names of some exemplars may differ from those used in the publication due to species names being updated prior to publication after the analyses were completed.
DOI: 10.5061/dryad.g8609/4
title: Control file for BAMM analysis

description: Control file for BAMM diversification rates analysis.
DOI: 10.5061/dryad.k52g0/1
title: rawdata PC JK

description: Excelfile with all membrane voltages, cell capacitances, current values and time points used for the graphs in the manuscript
DOI: 10.5061/dryad.m5ct8/12
title: Map traits onto phylogeny

description: R script for mapping quantitative or qualitative traits onto the Nepenthes phylogeny.
DOI: 10.5061/dryad.m5ct8/13
title: Conduct PCA

description: R script for conducting principal components analysis (PCA), either a standard PCA or a phylogenetic PCA on continuous trait data to assess differences between altitude classes or pitcher diet (not discussed in manuscript).
DOI: 10.5061/dryad.m5ct8/14
title: Analyze phylogenetic signal in traits

description: R script for conducting tests of phylogenetic signal for both continuous (using Blomberg's K and Pagel's lambda) and binary traits (Fritz and Purvis's D).
DOI: 10.5061/dryad.m5ct8/15
title: my_funcs

description: Supporting functions for R scripts associated with phylogenetic comparative analyses.
DOI: 10.5061/dryad.m5ct8/16
title: my_themes

description: Supporting script used for R scripts associated with phylogenetic comparative analyses.
DOI: 10.5061/dryad.ms2np57/1
title: Lignin Phenols

description: Data file with results from lignin phenol extraction of soil samples, and plant tissue end-members (i.e. shoots, rhizomes and roots of Bahiagrass from inside and outside grazing exclosure). The major families are summarized as v (vannilyl), c (cinnamyl) and s (syringyl). Column 'vsc' represents the sum of v,s, and c, standardized per 100 mg organic carbon, whereas 'vsc.sed' is standardized per 1 g of soil weight. 'adal.v' is the acid-aldehyde ratio of the vanillyl family.
DOI: 10.5061/dryad.ms2np57/2
title: Soils EA/IRMS

description: File with results of elemental analysis and isotope ratio mass spectrometry. Note that plot number needs to be paired with treatment ('trt') to generate a unique ID. 'Back' column identifies whether data is from background survey of exclosures, or from pulse-chase plots.
DOI: 10.5061/dryad.ms2np57/3
title: Pulse Chase Vegetation EA/IRMS

description: Data with results of EA/IRMS analysis on plant samples from pulse chase experiment. Note that plot number and treatment must be combined to generate a unique plot ID. Harvest identifies time post pulse (2 days, 7 days, or 32 days). Pool identifies whether it is shoots ('Ag Veg'), roots or rhizomes ('Rh'). 'Sub' represents replicated harvested swaths ('A' or 'B') per harvest date (for 2 day and 7 day only, hence 32 day is identified as AA). One sample was accidentally combined in the field and is identified with A/B. Biomass is reported only for the t = 0 initial harvests of aboveground material.