cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sq72d.1/28.1
title: Temperature_Anomolies

description: Provides dates, issues, and resolution when temperature loggers included in the Temperature.csv file were out of water or otherwise malfunctioning. If blocks of data are missing from the Temperature.csv file, check here for dates.
DOI: 10.5061/dryad.ts635/1
title: Swifts-2017-chicks

description: Excel file ocntaining the qPCR telomere measurements made on swift chicks in 2004 and 2006
DOI: 10.5061/dryad.ts635/2
title: Full data set

description: Full data set on offspring and parental telomere length
DOI: 10.5061/dryad.tv854/1
title: DATA BASE

description: This file include information about the three bat species studied  with the number of individuals parasited and no parasited by sampling site. Also include information about landscape characteristics of each sampling site.
DOI: 10.5061/dryad.vv0gg/1
title: 3 real datasets for Colony analysis of mistyping rates

description: This zipped file contains three real datasets in the format of Colony input files. In each input file, the assumed dropout and false allele rates of each marker can be modified manually before running Colony analysis.
DOI: 10.5061/dryad.2875k.1
title: Data from: Core genes evolve rapidly in the long-term evolution experiment with Escherichia coli
DOI: 10.5061/dryad.2875k.1/1.1
title: LTEE-core-genes-project

description: Data, Analysis Scripts, and Results for LTEE-core-genome manuscript
DOI: 10.5061/dryad.2875k.2
title: Data from: Core genes evolve rapidly in the long-term evolution experiment with Escherichia coli
DOI: 10.5061/dryad.2875k.2/1.2
title: LTEE-core-genes-project

description: Data, Analysis Scripts, and Results for LTEE-core-genome manuscript
DOI: 10.5061/dryad.2h3f2.1
title: Data from: Species interactions in occurrence data for a community of tick-transmitted pathogens
DOI: 10.5061/dryad.2h3f2.1/14.1
title: Dataset of records of ticks, hosts, and pathogens (with climate and coordinates) in Western Palearctic

description: This file contains a description of the data package contents for Estrada-Peña and de la Fuente (2016) "Species interactions in occurrence data for a community of tick-transmitted pathogens"
DOI: 10.5061/dryad.2h3f2.1/8.1
title: Environmental variables
DOI: 10.5061/dryad.2h3f2.2/10.2
title: Maps of predicted distribution of ticks
DOI: 10.5061/dryad.2h3f2.2/13.2
title: Maps of predicted distribution of hosts
DOI: 10.5061/dryad.2h3f2.2/3.2
title: Calculating CwHO
DOI: 10.5061/dryad.2h3f2.2/6.2
title: Data for networks
DOI: 10.5061/dryad.2h3f2.2/9.2
title: Fourier coefficients
DOI: 10.5061/dryad.411s8/1
title: Buried bag N concentrations

description: In situ buried bag methodology to measure soil nitrogen availability
DOI: 10.5061/dryad.411s8/2
title: Soil chemistry chronosequence plots

description: Mineral soil and forest floor chemistry from chronosequence plots
DOI: 10.5061/dryad.411s8/3
title: Foliar chemistry Douglas-fir Western hemlock
DOI: 10.5061/dryad.411s8/4
title: tree ring 15N by site and tree

description: Natural 15N abundance of wood samples from increment cores of Douglas-fir over chronosequence plots
DOI: 10.5061/dryad.4m3r4/4
title: FigS2_Treefile

description: Treefile for Figure S2
DOI: 10.5061/dryad.4ps2t/5
title: Lin_etal_2017_praetermissus_FigS2
DOI: 10.5061/dryad.4ps2t/6
title: Lin_etal_2017_praetermissus_FigS3
DOI: 10.5061/dryad.4ps2t/7
title: Lin_etal_2017_praetermissus_FigS4
DOI: 10.5061/dryad.5b1k0/1
title: main.cole

description: Main R script to run first, to load packages, and set up directory structure, along with other housekeeping.
DOI: 10.5061/dryad.5b1k0/2
title: functions.cole

description: Contains functions for analysis. Is sourced by main.cole
DOI: 10.5061/dryad.5b1k0/3
title: figures.cole

description: Contains figure functions. Is sourced by main.R
DOI: 10.5061/dryad.5b1k0/4
title: analyses.cole_MS_161115

description: analysis code, used to generate the statistics, analyses, and output in the manuscript. requires main.cole to be run first.
DOI: 10.5061/dryad.5b1k0/5
title: CalculateKTCode

description: Calculates Kinematic Transmission for the Opercular 4-bar system.
DOI: 10.5061/dryad.5b1k0/6
title: Complexity Simulation

description: Code for the simulation that compares levels of many-to-one mapping across biomechanical systems.
DOI: 10.5061/dryad.5b1k0/7
title: 03.dietCntnt_fromGitHub_161013

description: Gut content data.
DOI: 10.5061/dryad.5b1k0/8
title: Results_all_R_SI_KT_sexSL

description: Biomechanical trait measurements.
DOI: 10.5061/dryad.650fk/1
title: Data_Dyrad_Slade_et_al_Ecology

description: See README file
DOI: 10.5061/dryad.650fk/2
title: SAS code for Slade_Kirwan et al_Ecology

description: SAS code for analyses
DOI: 10.5061/dryad.7h0g6/1
title: Channid_coxI_778

description: Final coxI alignment of 777 chained individuals plus one outgroup
DOI: 10.5061/dryad.835s6/1
title: eDNA detection records_Williams

description: Detection records for methods tested for eDNA capture, inhibitor removal, and amplification techniques.
DOI: 10.5061/dryad.835s6/2
title: eDNA concentrations_Williams

description: DNA concentration measurements for environmental water samples extracted and amplified with optimized method.
DOI: 10.5061/dryad.c3f25/1
title: All data used in the article

description: List of the specimens used in the study with reference to the museum collection, specimen ID, wild or domestic status, country of origin or breed, group of age and raw 3D coordinates
DOI: 10.5061/dryad.cm4nm/1
title: Palm functional traits as used in Onstein et al. NatEcolEvol

description: Trait data for 1774 palm species used in Onstein et al. "Frugivory-related traits promote speciation of tropical palms" published in Nature Ecology and Evolution. These traits include fruit size (binary, 1 = small fruits &lt; 4 cm, 0 = large, megafaunal fruits &gt; 4 cm), understory growth form (binary, 1 = understory growth form, 0 = non understory growth form, i.e. canopy), island distribution (binary, i.e. 1 = species occurs on oceanic or atoll island, 0 = species occurs on mainland or continental island), realm (binary, New World or Old World). These traits can be used to perform Binary State Speciation and Extinction (BiSSE) and Multiple State Speciation and Extinction (MuSSE) analyses as done in this study.
DOI: 10.5061/dryad.cm4nm/2
title: BiSSE_script

description: R script to perform the Binary State Speciation and Extinction (BiSSE) analysis as done in Onstein et al. "Frugivory-related traits promote speciation of tropical palms" published in Nature Ecology and Evolution.
DOI: 10.5061/dryad.cm4nm/3
title: MuSSE_script

description: R script to perform the Multiple State Speciation and Extinction model (MuSSE multistate) analyses as done in Onstein et al. "Frugivory-related traits promote speciation of tropical palms" published in Nature Ecology and Evolution.
DOI: 10.5061/dryad.cm4nm/4
title: Palm MCC phylogenetic tree

description: Palm (Arecaceae) Maximum Clade Credibility (MCC) phylogenetic tree based on data from Faurby, S., Eiserhardt, W. L., Baker, W. J. & Svenning, J.-C. An all-evidence species-level supertree for the palms (Arecaceae). Molecular Phylogenetics and Evolution 100, 57-69, doi:10.1016/j.ympev.2016.03.002 (2016). This tree was used in Onstein et al. "Frugivory-related traits promote speciation of tropical palms" published in Nature Ecology and Evolution and can be used to perform the BiSSE and MuSSE analyses.
DOI: 10.5061/dryad.cm4nm/5
title: Palm 100 phylogenetic trees

description: 100 palm (Arecaceae) trees from Faurby, S., Eiserhardt, W. L., Baker, W. J. & Svenning, J.-C. An all-evidence species-level supertree for the palms (Arecaceae). Molecular Phylogenetics and Evolution 100, 57-69, doi:10.1016/j.ympev.2016.03.002 (2016). These trees were used in Onstein et al. "Frugivory-related traits promote speciation of tropical palms" published in Nature Ecology and Evolution to perform the BiSSE and MuSSE analyses.
DOI: 10.5061/dryad.d11rv/1
title: Data Veen et al_Oikos_10.1111/oik.04158

description: File contains plant, microbial and nematode abundance data + environmental variables (e.g. soil parameters) and a description of methods, plots and species/taxa (READ ME).
DOI: 10.5061/dryad.d76d1/1
title: OTU table after bioinformatics pipeline

description: Table of OTUs (rows) by sample (columns) after bioinformatics pipeline. See "OTUs fasta file" for representative sequences of each OTU. See "metadata file" to match library and tag number of samples to sample names.
DOI: 10.5061/dryad.d76d1/2
title: OTUs fasta file

description: List of representative sequences for each OTU; to be paired with OTU table
DOI: 10.5061/dryad.d76d1/3
title: metadata file

description: List of samples sequenced with library and tag combinations; to be paired to OTU table
DOI: 10.5061/dryad.d76d1/4
title: OTU table for blanks

description: Blanks were run on separate sequencing run. This file is the OTU table for the blanks including their annotation based on the same criteria outlined in the manuscript.
DOI: 10.5061/dryad.f5c50/1
title: Mark_recapture_matrix

description: "Mark_recapture_matrix.csv": A file containing capture records for each individual (by row) for each year of the study (1 is captured in a given year; 0 is not captured). Covariates used in the analysis of annual survival are also provided: Species ID (1 for Ammodramus caudacutus, 0 for Ammodramus nelsoni, NA for unknown species identity), Sex (1 is male), First capture (the date of first capture; 1 is 2010, 2 is 2011, etc.), Site (1-21), and Plot size (standardized by subtracting the mean and dividing by two standard deviations).
DOI: 10.5061/dryad.f5c50/2
title: brood_size_MCMC

description: "brood_size_MCMC.csv": A file containing the posterior estimates of the parameters from a regression of brood size (at fledging) by clutch size. Rows are 1000 draws from the posterior distributions for the regression intercept (intercept) and the effect of clutch size (clutch).
DOI: 10.5061/dryad.f5c50/3
title: nest_failure_MCMC

description: "nest_failure_MCMC.csv": A file containing the posterior estimates of the parameters from a regression of daily nest failure probability by site and date. Rows are 1000 draws from the posterior distributions for each site effect (site[1] through site[21]) and site-specific coefficient for the date effect (one coefficient for each site; date[1] through date[21]).
DOI: 10.5061/dryad.f5c50/4
title: renest_prob_MCMC

description: "renest_prob_MCMC.csv": A file containing the posterior estimates of the parameters from a regression of re-nesting probability by latitude and date. Rows are 1000 draws from the posterior distributions for each coefficient: intercept (intercept of the regression equation), latitude (the effect of latitude on renesting probability), and date (the effect of date on renesting probability).
DOI: 10.5061/dryad.f5c50/5
title: annual_survival_MCMC

description: "annual_survival_MCMC.csv": A file containing posterior estimates of adult annual survival, by site (columns). Rows are 1000 draws from the posterior distributions for the log-odds of survival (survival estimates are back-transformed using the inverse logit in the model code in order to take a value between 0 and 1). Sites are identified by a two-letter code and are provided from low to high latitude.
DOI: 10.5061/dryad.g1g00/1
title: LeeKhanCurley_data

description: Behavioral and Physiological data
DOI: 10.5061/dryad.h297n/1
title: Data File Key

description: Contains descriptors of column headers for both .csv files.
DOI: 10.5061/dryad.h297n/2
title: Great Tit Data File for R

description: Great Tit (Parus major) data file used for statistical analysis in R Statistical Software.
DOI: 10.5061/dryad.r0q02/3
title: VCF for Bothrops moojeni

description: variant data for Bothrops moojeni, including variant and invariant sites; filtered for coverage &gt;=10x and quality &gt;=20 and phased using read-backed phasing
DOI: 10.5061/dryad.r8251/3
title: Animal Genotypes for eQTL analysis at liveweight locus

description: Animal genotypes for the 432 Illumina BovineHD BeadChip markers at the chromosome 14 liveweight locus. Animals were genotyped using this panel directly, apart from 29 animals which were genotyped using the Illumina BovineSNP50 and imputed up to the HDChip density using Beagle. These genotypes were used for association analysis with gene expression phenotypes from the lactating mammary tissue biospies. PLINK was used to recode the genotypes to 0,1,2 to represent the number of alternative allele copies for each marker. anml_id = anonymised animal identification
DOI: 10.5061/dryad.r8251/4
title: Animal Genotypes for milk production analysis at liveweight locus

description: Animal genotypes for the 432 Illumina BovineHD BeadChip markers at the chromosome 14 liveweight locus. Animals were genotyped either using this panel directly, or were genotyped using the Illumina BovineSNP50 and imputed to the HDChip markers using Beagle. These genotypes were used for association analysis with milk production phenotypes generated as part of standard herd test procedures. PLINK was used to recode the genotypes to 0,1,2 to represent the number of alternative allele copies for each marker. anml_id = anonymised animal identification
DOI: 10.5061/dryad.rf7g5.1/1.1
title: final_soap_calo2

description: Assembly of Caloptilia triadicae from Genbank SRA accession #SRR1794032, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Breinholt et al.  (2017) for more details.
DOI: 10.5061/dryad.rf7g5.1/10.1
title: taxa_list

description: List of Sample ID's used in nexus files and corresponding species names in tab-delimited text
DOI: 10.5061/dryad.rf7g5.1/16.1
title: remove_duplicates

description: python script to identify and remove sequences for each taxon that had more than one sequence per locus
DOI: 10.5061/dryad.rf7g5.1/2.1
title: final_soap_GV120010B

description: Assembly of Urbanus proteus from Genbank SRA accession #SRR1794082 , using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Breinholt et al.  (2017) for more details.
DOI: 10.5061/dryad.rf7g5.1/26.1
title: getlist

description: python script to get list of sequences from a fasta file
DOI: 10.5061/dryad.rf7g5.1/3.1
title: final_soap_FG120036B

description: Assembly of Apatelodes pithala from Genbank SRA accession #SRR1794032, using multiple kmers (13,23,33,43,63) with SOAPdenovo-Trans v1.01. Different Kmer assemblies were combined with cd-hit-est and processed with the fastx toolkit. See Breinholt et al.  (2017) for more details.
DOI: 10.5061/dryad.rf7g5.1/39.1
title: contamination_filter

description: python script to process blast results of blasting sequences from each loci against themselves using usearch to identify contamination
DOI: 10.5061/dryad.rf7g5.1/41.1
title: Breinholt_et_al_RAW_DATA.tar.gz

description: compressed file containing the raw Illumina (2X100) AHE data
DOI: 10.5061/dryad.rs449/2
title: Posterior-landPlants.4gene.original.lognormal.constraints

description: BEAST xml file to carry out the posterior analysis of angiosperm divergence times using the original lognormal fossil calibration priors.
DOI: 10.5061/dryad.rs449/3
title: Prior-landPlants.4gene.original.lognormal.constraints

description: BEAST xml file to carry out the prior analysis of angiosperm divergence times using the original lognormal fossil calibration priors.
DOI: 10.5061/dryad.rs449/4
title: Posterior-landPlants.4gene.extreme_exponential_constraints

description: BEAST xml file to carry out the posterior analysis of angiosperm divergence times using the extreme exponential fossil calibration priors.
DOI: 10.5061/dryad.rs449/5
title: Prior-landPlants.4gene_extreme_exponential_constraints

description: BEAST xml file to carry out the prior analysis of angiosperm divergence times using the extreme exponential fossil calibration priors.
DOI: 10.5061/dryad.rs449/6
title: Posterior-landPlants.4gene.uniform_spermatophytes

description: BEAST xml file to carry out the posterior analysis of angiosperm divergence times using the uniform fossil calibration priors.
DOI: 10.5061/dryad.rs449/7
title: Prior-landPlants.4gene.uniform_spermatophytes

description: BEAST xml file to carry out the prior analysis of angiosperm divergence times using the uniform fossil calibration priors.
DOI: 10.5061/dryad.t3gc7/1
title: Coefficients for best survival model

description: Coeeficients and SE for the selected survival model for each of the plant species. The models were selected by forward selection process out of the set of Cox proportional hazard regressions constructed of all combinations of the model explanatory factors.
DOI: 10.5061/dryad.t3gc7/2
title: Coefficients for best abundance model

description: Model Coeefficients and SE for the selected abundance model for each of the plant species. The models were selected by forward selection process out of the GLMM of all combinations of the model explanatory factors.
DOI: 10.5061/dryad.t3gc7/3
title: Coefficients for best pollinator visit models

description: Model coefficients and SE for the selected best model for each of the plant species. The models were selected by forward selection process out of the GLMM of all combinations of the model explanatory factors.
DOI: 10.5061/dryad.t3gc7/4
title: Coefficients for best pollinator choice model

description: Model coefficients and SE for best pollinator choice model. The models were selected by forward selection process out of the GLM of all combinations of the model explanatory factors.
DOI: 10.17632/sxg3xw55fr.1
title: Data for: Efficient isogeometric formulation for vibration analysis of complex spatial beam structures

description: The multi-patch NURBS description for the application examples.
DOI: 10.17632/sxg3xw55fr.2
title: Data for: Efficient isogeometric formulation for vibration analysis of complex spatial beam structures

description: The multi-patch NURBS description for the application examples.
DOI: 10.5061/dryad.0s63q/1
title: Arabis_alpina_data_Evolution

description: Excel file with data in six sheets and including a README.
DOI: 10.5061/dryad.110pk/1
title: Immunological profiles field voles

description: The dataset consists of 248 measurements of immune gene expression levels and parasite prevalence of 60 individuals sampled between 2-7 times, and over a mean time period of 102 days (range = 55-169).
DOI: 10.5061/dryad.1c045/1
title: dryad_submission_ecology
DOI: 10.5061/dryad.23j6t/1
title: R code

description: R code to perform all the analyses
DOI: 10.5061/dryad.23j6t/2
title: Supplementary data file 1

description: Adult body shape data for 166 species. Linear measurements for characterizing the body shape of adult frogs. 1
SVL
From tip of the snout to posterior tip of the urostyle
2
Head_l
From tip of snout to angle of jaw
3
Head_width
Width of head right behind the eyes
4
Eye_naris
From anterior corner of eye to posterior edge of naris 
5
Interorbital
Distance between anterior corners of eyes
6
Internarial

Distance between inner edges of nares
7
Naris_Snout
Distance between anterior edge of naris and tip of the snout 
8
Eye_l
Distance between corners of eye (anterior to posterior) 
9
Mouth_width
Width of the head right between corners of the mouth
10
Humerus_l
Distance between midpart of the pectoral girdle and elbow 
11
Forearm_l
Distance between elbow and wrist
12
Wrist_width
Width of the wrist on its widest point
13
Hand_l
Distance between the midpart of the wrist and the tip of the 3rd finger
14
Thumb
Thumb length
15
Finger_4
4th finger length
16
Femur_l
Distance between the midpart of the urostyle and the knee
17
Femur_width
Maximum width of the femur (midpart)
18
Tibial_l
Knee to heel (tibiofibular)
19
Tibial_width
Maximum width of the tibia (midpart)
20
Foot_l_toe_1
Distance from base of 1st toe to tip of 4th toe
21
Foot_l_total
Distance from heel to tip of 4th toe
22
Toe_1
Length of 1st toe (from tip to join between 1st and 2nd toe)
23
Toe_5
Length of 5th toe (from tip to join between 4th and 5th toe)
DOI: 10.5061/dryad.2h3f2.1/1.1
title: Coordinates of Hosts
DOI: 10.5061/dryad.2h3f2.1/10.1
title: Maps of predicted distribution of ticks
DOI: 10.5061/dryad.2h3f2.1/13.1
title: Maps of predicted distribution of hosts
DOI: 10.5061/dryad.2h3f2.1/3.1
title: Calculating CwHO
DOI: 10.5061/dryad.2h3f2.1/5.1
title: Coordinates of ticks with hosts records
DOI: 10.5061/dryad.2h3f2.1/6.1
title: Data for networks
DOI: 10.5061/dryad.2h3f2.1/9.1
title: Fourier coefficients
DOI: 10.5061/dryad.32q80/1
title: Final filtered SNP data for Saccostrea glomerata

description: SNP data for 90 oysters at 1200 loci, provided in GenAlEx format (0=Missing data, 1=Reference allele, 2=SNP allele) in an Excel file. Population codes match those used in the text of the corresponding published manuscript.
DOI: 10.5061/dryad.55bp8/1
title: mapped_gamma_all_sources_2005

description: Neutral Density (Jackett &  McDougall, 1997) for the year 2005 (with annual and semi-annual harmonics) from 75S to 30S.
DOI: 10.5061/dryad.5ps8j/2
title: Bias correction terms

description: Bias correction terms for each country and year applied to yellow fever vaccination data not derived from post-campaign surveys. These were calculated as ratios of survey-derived Global Burden of Disease Study estimates of mean coverage for third dose of diphtheria-tetanus-pertussis-containing vaccine (DTP3) and WHO/UNICEF Joint Reporting Process administratively reported estimates. Full details are provided in the manuscript.
DOI: 10.5061/dryad.6nj94/1
title: Migration routes of juvenile honey buzzards annotated with wind estimates at 925mb

description: This dataset was processed from the raw tracking data as described in Vansteelant et al. (2017).
DOI: 10.5061/dryad.6rs6q/1
title: COI_alnCAOS

description: COI alignment used to determine diagnostic nucleotides using CAOS software
DOI: 10.5061/dryad.6rs6q/2
title: 28SrRNA_alnCAOS

description: 28S rRNA alignment used to determine diagnostic nucleotides using CAOS software
DOI: 10.5061/dryad.6rs6q/3
title: ITS_alnCAOS

description: Internal Transcribed Spacer (ITS) alignment used to determine diagnostic nucleotides using CAOS software
DOI: 10.5061/dryad.70c9v/1
title: Immature non-conflict intervals

description: 10-minute non-conflict intervals from follows of immatures in a given age bin used to generate bootstrapped means of grooming and play.
DOI: 10.5061/dryad.70c9v/2
title: Maternal non-conflict intervals

description: 10-minute non-conflict intervals from follows of mothers used to generate bootstrapped means of grooming.
DOI: 10.5061/dryad.812rc/2
title: Mapping file (OTUs)

description: Mapping file (OTUs)
DOI: 10.5061/dryad.812rc/4
title: Full_Dataset_CSS_BokuNormalized_F

description: OTU alpha diversity indices, Bd infection load data and abiotic variables for each sample.
DOI: 10.5061/dryad.8jf4q/1
title: ALL DATA ARTHRO

description: Arthropods collected at 3 months
DOI: 10.5061/dryad.8jf4q/2
title: ALL DATA ARTHRO2

description: Arthropods collected at 6 months
DOI: 10.5061/dryad.8jf4q/3
title: Data for R Mesos and Bags

description: Weight of the litter from the mesocosms and the litter bags
DOI: 10.5061/dryad.8jf4q/4
title: COMPLETE MESO DATA_07_01_16_clean

description: Data collected from the mesocosms at 3 and 6 months
DOI: 10.5061/dryad.8jf4q/5
title: ArthroAll2

description: Arthropod data used for the multivarient analysis
DOI: 10.5061/dryad.8m9t1/1
title: JJJ_SSBH_Supplement_new_character_descriptions

description: Description of characters used for the phylogenetic analyses in the study.
DOI: 10.5061/dryad.8m9t1/2
title: JJJ_SSBH_Supplement2_MATRIX

description: Character matrix for the phylogenetic analyses in the study.
DOI: 10.5061/dryad.9jh21/6
title: ReadMe

description: ReadMe describing data files