cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vj3p9/5
title: tree_data_Figure2

description: Phylogeny tree from Figure 2 in NEXUS multiple alignment format.
DOI: 10.5061/dryad.vj3p9/6
title: tree_data_Figure2

description: Phylogeny tree from Figure 2 in Newick tree format.
DOI: 10.5061/dryad.03768/1
title: Female tissue Sfp detection

description: Values from ELISAs of Large or Small female reproductive tracts   spiked with a consistent amount of SP or OV, to test for interference of female tissue on Sfp detection. See methods: "Test of interference of female tissue with detection of Sfps in ELISAs".
DOI: 10.5061/dryad.1k2k4/1
title: Data Drakeley Lapiedra Kolbe PLOS ONE

description: Field collected behavioral, ecological, morphological and environmental data related to foraging experiments in a lizard.
DOI: 10.5061/dryad.23tp6/10
title: Fig6_ETCenzymes

description: Data for Figure 6
DOI: 10.5061/dryad.23tp6/11
title: Fig7_DF(tank_means)

description: Data for Figure 7 - tank means for all significant variables
DOI: 10.5061/dryad.26th0/2
title: Phenological data

description: Raw data presented in Fig. 4. ('nfem' = total number of females (mated and unmated); 'n unmated fem' = number of unmated females; n tub = number of tuberosus males; n gib = number of gibbosus males; n juv = number of immature individuals)
DOI: 10.5061/dryad.321bv/1
title: phot_alignment_forPhylogeny

description: phototropin alignment trimmed for phylogenetic analyses
DOI: 10.5061/dryad.321bv/2
title: ML_garli

description: maximum likelihood tree reconstructed using Garli
DOI: 10.5061/dryad.321bv/3
title: MLBS_raxml

description: maximum likelihood bootstrap consensus tree reconstructed using RAxML
DOI: 10.5061/dryad.3c2v9/1
title: Seabird and seaice data

description: Breeding success data and sea ice concentration data
DOI: 10.5061/dryad.41356/2
title: Cloud forest tree data

description: The data in this file is at the site level. Each site (AP, SL, and so on) is described in the paper with which this data is associated. Size class is denoted by SE - seedling, SA - sapling, and TR - tree.
DOI: 10.5061/dryad.4st55/1
title: Goatgrass Data

description: Community-level data used in analyses of goatgrass invasion
DOI: 10.5061/dryad.5cc27/1
title: PLOS One data

description: Multiple tabs for nodule analysis.  The Gietema and Veronesi data are calculated values from raw data which I do not have permission to share.
DOI: 10.5061/dryad.6d09b/1
title: MetamorphsR

description: Life-history traits of the seven populations measured at two different temperature treatments.
DOI: 10.5061/dryad.6d09b/2
title: Swimming Performance

description: Excel table with different pages, include: table with tadpole morphological data, table with swimming performance at the different temperatures, table with repeatability for some individuals, extra table with individuals who die at higher temperature.
DOI: 10.5061/dryad.6rj0n.1
title: Data from: A global optimization paradigm based on change of measures
DOI: 10.5061/dryad.6rj0n.2/2.2
title: phase_K

description: The phase data (attached) for the illustrative example in Section 5.2
DOI: 10.5061/dryad.6rj0n.2/3.2
title: phase_K

description: The phase data (attached) for the illustrative example in Section 5.2
DOI: 10.5061/dryad.6rj0n.2/4.2
title: MY_OPTIMIZER

description: The specific optimization algorithm is written here. For solving the global optimization problem with a different algorithm, only this function needs to be modified.
DOI: 10.5061/dryad.6rj0n.2/5.2
title: new_KS_EnKF_gain_matrix

description: This function creates the gain matrix, defined in the main manuscript, which is required in pseudo code 2 for giving the evolving particle proper directionality.
DOI: 10.5061/dryad.74ps0/1
title: Ghanizadeh et al FE all data

description: Excel file of all data used in the manuscript
DOI: 10.5061/dryad.7nr70/1
title: Poisbleau et al. 2015 E&E BDD

description: Original data collected in the field on females and eggs.
DOI: 10.5061/dryad.7qm89/1
title: uncropped and unadjusted Westernblots

description: uncropped and unadjusted Westernblot
DOI: 10.5061/dryad.84c25/2
title: gorter_etal_2015_nickel
DOI: 10.5061/dryad.84c25/3
title: gorter_etal_2015_zinc
DOI: 10.5061/dryad.84c25/4
title: gorter_etal_2015_t100_nickel
DOI: 10.5061/dryad.84c25/5
title: gorter_etal_2015_t100_zinc
DOI: 10.5061/dryad.8np44/1
title: Perea_2015_Oikos_Seed_Recovery_rodents

description: Raw data on the recovery of seeds (acorns of Quercus pyrenaica) by rodents (Apodemus sylvaticus) after having been dispersed by the same rodent species
DOI: 10.5061/dryad.9rs25/3
title: Cynara maximum parsimony tree
DOI: 10.5061/dryad.9rs25/4
title: Cynara neighbor joining tree
DOI: 10.5061/dryad.b0b1c/3
title: Grass nutrient (N and P) data from around termite mounds

description: Nitrogen and Phosphorous content from foliar (grass) samples collected around termite mounds along distance transects in the four cardinal directions. Data come from three savanna sites and were collected during the wet (summer) season.
DOI: 10.5061/dryad.bm29v/1
title: Orchid flower measurements

description: Measurements of Chiloglottis floral traits. L = length, W = width, H = height.
DOI: 10.5061/dryad.bm29v/2
title: Wasp measurements

description: Measurements of thynnine wasp traits. L = length, W = width, H = height
DOI: 10.5061/dryad.bm29v/3
title: Reciprocal pollinator choice tests between orchids

description: Responses of pollinators to morphologically distinct Chiloglottis species that employ the same semiochemical for pollinator attraction. Collected in the field.
DOI: 10.5061/dryad.bm29v/4
title: Labellum manipulation experiments

description: Responses of pollinators to orchids with shortened labella and conspecific control flowers with intact labella. Collected in the field.
DOI: 10.5061/dryad.cb312/10
title: Thur_River_Traits_Staphylinids

description: Traits of Staphylinid beetle species present at the Thur River
DOI: 10.5061/dryad.cb312/8
title: Thur_River_Traits_Plants

description: Traits of Vascular Plant species present at the Thur River
DOI: 10.5061/dryad.cb312/9
title: Thur_River_Traits_Spiders

description: Traits of Spider species present at the Thur River
DOI: 10.5061/dryad.fv8g8/1
title: Processed MEG and Reaction Time Data (Compressed)
DOI: 10.5061/dryad.h838q/1
title: Longterm data

description: Data from laboratory experiment on the sea ice diatom Nitzschia lecointei. Data columns in all data files are explained in more detail in the separate Readme file.
DOI: 10.5061/dryad.h838q/2
title: Cumulative generations clean

description: Clean version of longterm data, i.e. without NA
DOI: 10.5061/dryad.h838q/3
title: Specific BCP clean

description: Clean version of longterm data, i.e. without NA
DOI: 10.5061/dryad.h838q/4
title: Specific PP DOC clean

description: Clean version of longterm data, i.e. without NA
DOI: 10.5061/dryad.h838q/5
title: Specific PP POC clean

description: Clean version of longterm data, i.e. without NA
DOI: 10.5061/dryad.h838q/6
title: Specific PP TOT clean

description: Clean version of longterm data, i.e. without NA
DOI: 10.5061/dryad.h838q/7
title: R Scripts

description: R Scripts (written in R 3.1.1)
DOI: 10.5061/dryad.hk2gc/1
title: Model output of Ideal Free Distribution simulations

description: The data file contains the model output of the Combined Model. Each row represents one simulation. The first four columns are model parameters that were varied in the simulations (see table A1 in the Appendix for parameter descriptions), and the fifth column is the recorded IFD slope of that simulation. All simulations were run in NetLogo.
DOI: 10.5061/dryad.n9r58/1
title: 75 chloroplast coding regions alignments in nexus format

description: This file contains alignments of 75 chloroplast coding regions for orchid taxa plus Mapania (Cyperaceae) generated in this study
DOI: 10.5061/dryad.p15m6/1
title: data-repository
DOI: 10.5061/dryad.p15m6/2
title: Turning-Point

description: The list of turning points in coexpression conservation.
DOI: 10.5061/dryad.p15m6/3
title: Enriched-GO-Terms

description: The list of all enriched GO terms when SCS = 3, 4 and 5
DOI: 10.5061/dryad.ss250/1
title: Pair-wise relatedness values for 2009

description: Pair-wise relatedness values for 2009
DOI: 10.5061/dryad.ss250/2
title: Pairwise relatedness from 2010
DOI: 10.5061/dryad.ss250/3
title: Simple.ratio-2009

description: Social values for 2009
DOI: 10.5061/dryad.03768/2
title: Experiment 1 fly weights

description: Mass of flies from Experiment 1
DOI: 10.5061/dryad.03768/3
title: Experiment 4 fly weights

description: Mass of flies from in Experiment 4
DOI: 10.5061/dryad.03768/4
title: Experiment_1_male_SP and OV production

description: Experiment 1: SP and OV produced by males in their accessory glands.
DOI: 10.5061/dryad.03768/5
title: Experiment_2_rival_male_size

description: Experiment 2: Effects of rival male size on SP production and transfer. Data on latency to mating; mating duration; male SP; female SP; proportion SP transferred.
DOI: 10.5061/dryad.03768/6
title: Experiment 1_Sfp allocation to females

description: Experiment 1: Small and Large males and females. Mating latency and duration; absolute quantity of Sfps transferred to females during mating.
DOI: 10.5061/dryad.03768/7
title: Experiments 3 and 4

description: Experiments 3 and 4: Latency to mating, mating duration and remating data.
DOI: 10.5061/dryad.03768/8
title: Experiment 4_Courtship and Rejection

description: Experiment 4: Courtship and Rejection data
DOI: 10.5061/dryad.1k8kq/1
title: File_S1_Celegans_N2_to_CB4856_lastz_alignment.txt

description: LASTZ alignments between C. elegans N2 (WormBase version WS230) and C. elegans Hawaiian CB4856 (Genbank accession: JZEW00000000)
DOI: 10.5061/dryad.321bv/4
title: BI_mrbayes_con

description: bayesian inference consensus tree reconstructed using MrBayes
DOI: 10.5061/dryad.3c2v9/2
title: script

description: R script for the segmented analyses and Davies tests
DOI: 10.5061/dryad.48643/1
title: S_4 Table
DOI: 10.5061/dryad.4j7jh/1
title: Files for association mapping

description: Genotypes, Phenotypes and Map files for association analysis (PLINK format)
DOI: 10.5061/dryad.6d09b/3
title: CTmax

description: File with the CTmax data of the seven populations
DOI: 10.5061/dryad.7r71q/1
title: GluK2-trans

description: The subdirectory /MD includes five free MD simulation trajectories of GluK2-trans complex described in the manuscript. The subdirectory /isomerization includes five forced switching simulation trajectories from trans-gluazo to cis-gluazo. The subdirectory /umbrella-clamshell includes the files needed to reproduce the umbrella sampling simulation results of LBD clamshell motions of GluK2-trans complex. This data file could be used to reproduce all the results of GluK2-trans complex presented in the manuscript.
DOI: 10.5061/dryad.7r71q/2
title: GluK2-cis

description: The subdirectory /MD includes five free MD simulation trajectories of GluK2-cis complex described in the manuscript. The subdirectory /isomerization includes five forced switching simulation trajectories from cis-gluazo to trans-gluazo. The subdirectory /umbrella-clamshell includes the files needed to reproduce the umbrella sampling simulation results of LBD clamshell motions of GluK2-cis complex. This data file could be used to reproduce all the results of GluK2-cis complex presented in the manuscript.
DOI: 10.5061/dryad.7r71q/3
title: GluK2-glutamate

description: The subdirectory /MD includes five free MD simulation trajectories of GluK2-glutamate complex, which are used as references in the manuscript.
DOI: 10.5061/dryad.7tr41/1
title: PET/MRI
DOI: 10.5061/dryad.f0n35/1
title: Appendix_A_Dryad.DCAP_Dataset

description: Dryad Metadata Application Profile, Version 3.2
DOI: 10.5061/dryad.fm28d/1
title: assembly_carolitertii
DOI: 10.5061/dryad.fm28d/2
title: assembly_torgalensis
DOI: 10.5061/dryad.fm28d/3
title: top_blasthit_torg
DOI: 10.5061/dryad.fm28d/4
title: top_blasthit_carol
DOI: 10.5061/dryad.fm28d/5
title: S.carolitertii annotations
DOI: 10.5061/dryad.fm28d/6
title: S.torgalensis annotations
DOI: 10.5061/dryad.jn14s/1
title: Genototypes of C vestalis females at 98 SNPs

description: SNP genotypes of 139 Cotesia vestalis females collected in Western Taiwan at 98 polymorphic SNPs
DOI: 10.5061/dryad.jn14s/2
title: Reference genome sequence of Cotesia vestalis: scaffolds and contigs

description: No genome information was available for C. vestalis. In order to build a draft reference genome and to develop SNP assays, we sequenced the entire genome of C. vestalis on a single lane of paired-end sequences (2x100 bp) on an Illumina HiSeq 2000 (Illumina Inc., U.S.A.) instrument. The SNP discovery panel consisted of eight C. vestalis females, one from each of eight fields.Before assembly, Illumina reads were trimmed using an in-house Perl script that trims the sequence as soon as two consecutive bases have a quality score lower than 20. Reads that after trimming had a length smaller than 50 bp were removed from the analysis. To obtain C. vestalis sequence contigs to be used as a pseudo-reference genome, we performed a de novo assembly on the 133 million 100 bp reads using SOAPDENOVO version 1.05 [37]. The assembly was done using a k-mer size of 45 and k-mers that were seen only once were removed (option –d). After contig construction, scaffolding was performed using intra-scaffold closure (option –F) and a minimum length for scaffolding of 50 bp. The total size of the assembly was 152 Mb with a contig N50 size of 761 bp and a scaffold N50 size of 2400 bp.
DOI: 10.5061/dryad.jn14s/3
title: Cotesia vestalis SNP information and sequences

description: From our list of putative SNPs across the C. vestalis genome, we selected 100 SNPs for genotyping assay development. We first selected the 200 largest scaffolds; they varied in length from 17-58Kb and contained a total of 7,878 SNPs. We then removed SNPs with a minor allele frequency (MAF) &lt;0.2, SNPs that had another SNP within 50 bp up- or downstream, and SNPs with more than 2 alleles. The remaining SNPs were binned in MAF bins of 0.2-0.3 (1,908 SNPs), 0.3-0.4 (1,605 SNPs) and 0.4-0.5 (1,156 SNPs). Per MAF bin, SNPs were ranked by SNP quality score. We then selected the SNPs with the highest quality scores, picking 20 SNPs with a MAF between 0.2-0.3 and 40 each with a MAF between 0.3-0.4 and 0.4-0.5, all on different scaffolds. All selected SNPs had a quality score of more than 200 (based on SAMTOOLS), and an average read depth of 61. High-throughput genotyping assays based on allele-specific forward primers were developed for these 100 SNP sequences at KBioscience (now LGC Genomics, Hoddesdon, U.K.).
DOI: 10.5061/dryad.jn14s/4
title: Putative SNPs discovered in genome of Cotesia vestalis

description: Individual paired-end reads were aligned against the artificial Cotesia vestalis reference genome obtained from the de novo genome assembly using BWA. The resulting BAM file was then used for the identification of putative SNPs using SAMTOOLS and varFilter from the samtools.pl utility. We only considered nucleotide substitutions and ignored small indels. SNPs were filtered that had a mapping quality higher than 20, a minimum read depth of 3 and a maximum read depth of 90 (3x the average read depth, a strategy to avoid orthologous SNPs, e.g. in multi copy genes.
DOI: 10.5061/dryad.q878c/1
title: LW opsin nucleotide alignment

description: Long-wavelength opsin nucleotide sequence alignment for 38 North American firefly species (FASTA format).
DOI: 10.5061/dryad.q878c/2
title: LW opsin amino acid alignment

description: Long-wavelength opsin amino acid sequence alignment for 38 North American firefly species (FASTA format).
DOI: 10.5061/dryad.q878c/3
title: UV opsin nucleotide alignment

description: Ultraviolet opsin nucleotide sequence alignment for 38 North American firefly taxa (FASTA format).
DOI: 10.5061/dryad.q878c/4
title: UV opsin amino acid alignment

description: Ultraviolet opsin amino acid sequence alignment for 38 North American firefly species (FASTA format).
DOI: 10.5061/dryad.q878c/5
title: Tree 1 (Stanger-Hall and Lloyd taxa + 14 taxa)

description: BEAST phylogeny constructed with taxa from Stanger-Hall and Lloyd (2015) plus 14 additional taxa. The tree has been trimmed to include only species used in this study.
DOI: 10.5061/dryad.q878c/6
title: Tree 2 (Stanger-Hall and Lloyd taxa plus 32 taxa)

description: BEAST phylogeny constructed with taxa from Stanger-Hall and Lloyd (2015) plus 32 additional taxa. The tree has been trimmed to include only species used in this study. Its topology, presented in Text S3, differs slightly from Tree 1, which is presented in the main text.
DOI: 10.5061/dryad.q878c/7
title: Transcriptome_assemblies

description: A zipped folder containing assembled transcriptomes for all 10 species used in this study. After qc, reads were assembled using Trinity with default parameters. These files give the resulting contigs in FASTA format. See README for more details.
DOI: 10.5061/dryad.qh53f/1
title: Fig1A

description: This data file is associated with Fig1A of the accompanied publication.  Survival data of bone marrow only, vehicle treated, and Ibrutinib treated recipients.  Column A is an arbitrary identification number given to each mouse.  Column B indicates the time-point at which a survival (marked as "0') or non-survival event (marked as "1") occurred.  Column C indicates the bone marrow alone group.  Column D indicates  mice treated with vehicle.  Column E indicates mice treated with Ibrutinib 10mg/kg.  Any other relevant information, including experimental conditions and setup is detailed in the accompanied publication.
DOI: 10.5061/dryad.qh53f/2
title: Fig1B

description: This data file is associated with Fig1B of the accompanied publication. Urine protein measurement data of bone marrow only, vehicle treated, and Ibrutinib treated recipients. Column A is an arbitrary identification number given to each mouse. Column B indicates the time-point at which a non-proteinuria event (marked as "0') or a proteinuria event (marked as "1") occurred. Proteinuria event "1" is defined as a mouse showing a &gt;2,000mg/dL score using Albustix urine test strips.Column C indicates the vehicle group, Column D indicates mice treated with Ibrutinib 10mg/kg. Column E indicates mice treated with Ibrutinib 15mg/kg, Column F indicates bone marrow alone mice treated with phosphate buffered saline, Column G indicates bone marrow alone mice treated with vehicle, Column H indicates bone marrow alone mice treated with 10mg/kg Ibrutinib. Any other relevant information, including experimental conditions and setup is detailed in the accompanied publication.
DOI: 10.5061/dryad.qh53f/4
title: Fig1D

description: This data file is associated with Fig1D of the accompanied publication. Urine protein measurement data of bone marrow only, vehicle treated, and Ibrutinib treated recipients. Column A is an arbitrary identification number given to each mouse. Column B indicates the time-point at which a non-proteinuria event (marked as "0') or a proteinuria event (marked as "1") occurred. Proteinuria event "1" is defined as a mouse showing a &gt;2,000mg/dL score using Albustix urine test strips.Column C indicates the BM only group, Column D indicates mice treated with vehicle. Column E indicates mice treated with Ibrutinib 10mg/kg beginning 7 days post-transplant, Column F indicates mice treated with 10mg/kg Ibrutinib beginning 14 days post-transplant.  Any other relevant information, including experimental conditions and setup is detailed in the accompanied publication.
DOI: 10.5061/dryad.qh61d/1
title: Allele count and Allele frequency data at 27 microsatellite marker loci in three breeds of Myanmar goats

description: The file consists of two sheets; First sheet contains allele count data at 27 microsatellite marker loci in three breeds of Myanmar goats, Jade Ni (JNI), Nyaung Oo (NYO) and Waithar Li (WTL). Second sheet contains allele frequency data  at 27 microsatellite marker loci in three breeds of Myanmar goats, Jade Ni (JNI), Nyaung Oo (NYO) and Waithar Li (WTL).
DOI: 10.5061/dryad.r95dh/1
title: Aerial Photographs

description: Aerial photographs taken in the field and used for GIS analysis of vegetation spatial pattern
DOI: 10.5061/dryad.r95dh/2
title: Plant Community Survey

description: Data from plant community surveys used to calculate species diversity metrics and ground-truth aerial photographs for spatial pattern analyses
DOI: 10.5061/dryad.r95dh/3
title: Species Diversity

description: Calculations of plant species diversity metrics
DOI: 10.5061/dryad.r95dh/4
title: Spatial Pattern

description: FRAGSTATS computations of spatial metrics
DOI: 10.5061/dryad.s5h20/1
title: NA-SERS specificity spectra

description: Wavenumber and intensity values for 521 spectra of Mycoplasma pneumoniae, other mycoplasmas, and background controls.
DOI: 10.5061/dryad.ss250/4
title: Simple.ratio-2010

description: Social association values for 2010
DOI: 10.5061/dryad.ss250/5
title: Microsatellite locus alleles

description: Contains alleles information for 14 loci for golden-crowned sparrows. These genetic data were used to estimate pair-wise relatedness
DOI: 10.5061/dryad.v5403/1
title: DATA_Terminated Trials in ClinicalTrialsgov Results Database (19 Feb 2013)

description: CSV data file containing data retrieved from the ClinicalTrials.gov registry and results database on February 19, 2013.  Additional details are available in the ReadMe file.
DOI: 10.5061/dryad.3mf71/1
title: PHACE_Greenness_Dryad
DOI: 10.5061/dryad.3mf71/2
title: PHACE_PlantCover_Dryad
DOI: 10.5061/dryad.3mf71/3
title: PHACEGreennessMatlabCode
DOI: 10.5061/dryad.43md3/1
title: Data from "Very high resolution digital elevation models: are multi-scale derived variables ecologically relevant?"

description: This archive contains the original data from the Digital Elevation Model (DEM) and the measurements of Soil Moisture, Direct Temperature, Ambient Temperature, Ambient Humidity and Landolt Factors used in for the paper. The archive also contains the original R script of the multivariate models.
DOI: 10.5061/dryad.4km38/1
title: Supplementary Information File S1 - Trait divergence under the phenotype matching model

description: Analyses of trait divergence under a continent-island phenotype matching model.  Accompanies Appendices S1 and S2.
DOI: 10.5061/dryad.4km38/2
title: Supplementary Information File S2 - Trait divergence under the preference/trait model

description: Analyses of trait divergence under a continent-island preference/trait model. Accompanies Appendix S4.
DOI: 10.5061/dryad.4km38/3
title: Supplementary Information File S3 - Trait divergence under the prefernece/trait model (continued)

description: Analyses of trait divergence under a continent-island preference/trait model.  Accompanies Appendix S3.
DOI: 10.5061/dryad.4km38/4
title: Supplementary Information File S4 - Evolution of preference strength under the phenotype matching model

description: Analyses of the evolution of preference strength under a continent-island phenotype matching model.  Accompanies Appendix S6.
DOI: 10.5061/dryad.51v2s/1
title: Breeding data from a nestbox population of great tits with individuals identified earlier than standard protocol

description: These data were collected in the field (Wytham Woods, UK, Oxfordshire) as part of a long term study of great tits. RFID technology was used to identify individuals earlier in their breeding attempt than the traditional protocol.
DOI: 10.5061/dryad.574cd/1
title: Data for paternity analyses, female fitness and performance of seedlings from experimental populations of two floral morphs of Narcissus papyraceus in south Spain
DOI: 10.5061/dryad.63pm5/1
title: suppl-data

description: contains the alignments of all the 15 datasets under examination in this study
DOI: 10.5061/dryad.63pm5/2
title: supplement

description: contains supplementary figures referenced in the main text; contains mathematical details as well as additional information on datasets
DOI: 10.5061/dryad.bc578/1
title: Analysis_1_lognormal

description: Input file for BEAST v1.8.1 for Analysis 1
DOI: 10.5061/dryad.bc578/2
title: Analysis_1_lognormal_consensus

description: Analysis 1 consensus tree