cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qt7nr84/2
title: Anther and stigma height

description: Anther and stigma height of the hummingbird-pollinated plant species of the Atlantic forest. Species abbreviations can be found on the supplementary material.
DOI: 10.5061/dryad.rh61t5g/4
title: Normalized read abundance family level

description: Relative read abundance (CSS normalized) at the fungal order level by sample. Data for HMSC analysis.
DOI: 10.5061/dryad.rh61t5g/5
title: Bray Curtis distance matrix

description: Bray Curtis distance matrix for beta diversity analyses by sample
DOI: 10.5061/dryad.rh61t5g/6
title: NMDS coordinates

description: NMDS coordinates by sample for beta diversity analyses (generated from bray curtis distance matrix).
DOI: 10.5061/dryad.28fg251/10
title: Cicurina_238UCEloci_70_BEAST_concat

description: 70% occupancy nuclear UCE BEAST tree
DOI: 10.5061/dryad.28fg251/4
title: Cicurina_COI_RAxML_bipartitions

description: COI RAxML tree
DOI: 10.5061/dryad.28fg251/5
title: Cicurina_399UCEloci_50_RAxML

description: 50% occupancy nuclear UCE RAxML tree
DOI: 10.5061/dryad.28fg251/6
title: Cicurina_238UCEloci_70_RAxML

description: 70% occupancy nuclear UCE RAxML tree
DOI: 10.5061/dryad.28fg251/7
title: Cicurina_399UCEloci_ASTRAL_50

description: 50% occupancy nuclear UCE ASTRAL tree
DOI: 10.5061/dryad.28fg251/8
title: Cicurina_238UCEloci_ASTRAL_70

description: 70% occupancy nuclear UCE ASTRAL tree
DOI: 10.5061/dryad.28fg251/9
title: Cicurina_238UCEloci_70_SVD

description: 70% occupancy nuclear UCE SVDQuartets tree
DOI: 10.5061/dryad.367f16t/10
title: suppfig8_data_triprelexp

description: data for relative expression of mitochondria and wolbachia
DOI: 10.5061/dryad.367f16t/3
title: fig2_data_mitowols

description: data comparing mitochondria and wolbachia titers in wMel genotypes where wolbachia genotype determines wolbachia titer
DOI: 10.5061/dryad.367f16t/4
title: fig3_data_trip

description: mitochondria and wolbachia titers in TRiP knockdown experiments
DOI: 10.5061/dryad.367f16t/5
title: fig3a_data_tripwesterns

description: wolbachia abundance as measured through Western blot in TRiP knockdown experiments
DOI: 10.5061/dryad.367f16t/6
title: fig4a_data_intensitygerm

description: wolbachia abundance from microscopy measured through fluorescence intensity in germaria from TRiP knockdown
DOI: 10.5061/dryad.367f16t/7
title: fig4b_data_intensityearly

description: wolbachia abundance from microscopy measured through fluorescence intensity in early oogenesis from TRiP knockdown
DOI: 10.5061/dryad.367f16t/8
title: fig4c_data_intensitymid

description: wolbachia abundance from microscopy measured through fluorescence intensity in mid oogenesis from TRiP knockdown
DOI: 10.5061/dryad.367f16t/9
title: fig5_data_mitokd

description: wolbachia and mitochondria titers in mito knockdown experiments
DOI: 10.5061/dryad.3gd34v2/2
title: FlowerMorphology

description: Corolla measurements for hummingbird visited flowers.
DOI: 10.5061/dryad.3gd34v2/3
title: FlowerTransectClean
DOI: 10.5061/dryad.3gd34v2/4
title: HummingbirdInteractions
DOI: 10.5061/dryad.3gd34v2/5
title: HummingbirdElevation
DOI: 10.5061/dryad.3gd34v2/6
title: PlantElevation
DOI: 10.5061/dryad.3gd34v2/7
title: HummingbirdMorphology
DOI: 10.5061/dryad.44c5f25/1
title: Table S2

description: List of DEGs Which were Affected by 4-OH-CB107 in Dose-Dependent Manner
DOI: 10.5061/dryad.48t6710/1
title: ZOTUs

description: Denoised, chimera-filtered, and clustered ZOTUs from the sequence data.
DOI: 10.5061/dryad.48t6710/2
title: ZOTUtabs

description: ZOTUtab linking ZOTUs to samples (and replicates).
DOI: 10.5061/dryad.48t6710/3
title: Raw Fastq files

description: Raw fastq files from the first (primers pairs ch, gh, and ITS; all samples pooled and then index-tagged) and second run (primer pairs ch and gh, all reactions and replicates tagged individually) for the study. The file names refer to the sample and replicate as follows:
HA=Arctic hare, PT=ptarmigan, MX=muskox; A=replicate 1; B=replicate 2; E=efterår (late winter); and F=förår (early winter)
DOI: 10.5061/dryad.4r1k05t/1
title: Common garden and greenhouse trait data for 305 H. tuberosus accessions
DOI: 10.5061/dryad.5n7t4/1
title: Figure 1 input files

description: Input files for creation of Figure 1. One input file is not included, but a citation to where to find the data is included in the figure 1 script.
DOI: 10.5061/dryad.5n7t4/8
title: Figure 2, Analysis and Supplementary Materials Inputs

description: inputs to create the analysis, figures and supplementary material associated with Figure 2. Including text files that define the columns and the units.
DOI: 10.5061/dryad.5nt3045/1
title: Winchell_urbansprints_data

description: sprint speed, morphology, and habitat data for Winchell et al. "Linking Locomotor Performance to Morphological Shifts in Urban Lizards"
DOI: 10.5061/dryad.80hs7k1/1
title: elk_surv

description: Adult female elk survival dataset.
DOI: 10.5061/dryad.80hs7k1/2
title: calf_surv

description: mark-resight calf survival data.
DOI: 10.5061/dryad.80hs7k1/3
title: Bayesian_calf_survival_Rscript

description: R code for Bayesian mark-resight calf survival estimation.
DOI: 10.5061/dryad.80hs7k1/4
title: logisticJAGS

description: JAGS model code for Bayesian calf survival analysis.
DOI: 10.5061/dryad.b01k5/10
title: OTU_Table_0.005%_abundnace_Cut-off

description: This file contains OTUs filtered with 0.005% overall abundance cut-off for all the samples included in this study.
DOI: 10.5061/dryad.b01k5/11
title: OTU_Table_even_depth_3000

description: This file contains bacterial OTUs in each sample after rarefying an entire dataset to even depth of 3000 reads
DOI: 10.5061/dryad.b01k5/12
title: Core_OTUs

description: This file contains core bacterial OTUs that occur in &gt;80% of the samples of entire sample set
DOI: 10.5061/dryad.b01k5/13
title: Read_Me

description: This file states few details about the OTU tables and R codes.
DOI: 10.5061/dryad.b01k5/7
title: OTU_Table_Top5_OTUs_for_each_species

description: This OTU table include top 5 abundant OTUs across larvae, pupae and adults of butterfly hosts
DOI: 10.5061/dryad.b01k5/8
title: OTU_Table_minimum_20_reads_Cut-Off

description: This file contains OTUs filtered with minimum 20 reads per OTU per sample cut-off for all the samples included in this study
DOI: 10.5061/dryad.b01k5/9
title: OTU_Table_5%_abundnace_Cut-off

description: This file contains OTUs filtered with 5% abundance cut-off for all the samples included in this study
DOI: 10.5061/dryad.c84f7c4/1
title: Data from: Song performance is a condition-dependent dynamic trait honestly indicating the quality of paternal care in the Bull-headed Shrike
DOI: 10.5061/dryad.dm5p030/1
title: development time data

description: File 1: devtime.xlsx

5 data sheets
Eclose16_LD.txt
Eclose16_LL.txt
Eclose22_LL.txt
Eclose22_LD.txt
Eclose25_LD.txt	

Rows: each row represents a single adult that eclosed on a given date with a particular development time in days (“EcloseDay”)

Columns:
Date — date vial was scored for progeny;
Mito — mtDNA genotype;
Nuc — nuclear genotype;
Temp — rearing temperature;
Light — photoperiod; 12,12 (LD) or 24,0 (LL);
Vial — unique identifier for each vial;
EcloseDay — days until eclosion;
DOI: 10.5061/dryad.dm5p030/2
title: metabolic rate data

description: File 2: metrate.xlsx

4 data sheets
MRdat_Group1616.txt
MRdat_Group2525.txt
MRdat_Group1625.txt
MRdat_Group2516.txt

Rows: each row represents a measure of average VCO2 from a chamber containing 10 adult flies

Columns
date — date of measurement;
run — unique run of the respirometry system;
rep — each chamber was sampled twice during the run;
line — (mtDNA);nuclear genotype;
mtDNA — mtDNA genotype;
nuclear — nuclear genotype;
tdev - development rearing temperature in C;
tmeasure - temperature in C at which metabolic rate was measured;
sex;
CO2 — average rate of CO2 production;
CO2.se — standard error of this average;
mass — mass of 10 flies in chamber;
MassMeasured — the initial mass of 10 flies corrected for any flies lost during the experiment (total mass - mean mass * number of flies lost);
Act1 — the median absolute difference of the squared activity signal;
Act2 — the standard error of the squared activity signal
DOI: 10.5061/dryad.dm5p030/3
title: reproduction data

description: File 3: reproduction.xlsx

datasheet: mitofert.txt

Rows: each row represents a single male’s number of offspring sired across three females

Columns
mtDNA — mtDNA genotype;
nuclear — nuclear genotype;
genotype — mtDNA;nuclear genotype;
male — replicate male ID;
females — number of females who survived and produced offspring;
total — the sum of offspring for each male across the three females;
totalper — total divided by the number of females;
exp — block A or B


datasheet: mitofecund.txt

Rows: each row represents the number of eggs laid by each female (original data are reported in Meiklejohn et al. (2013) PLoS Genet 9:e1003238)

Columns
mtDNA — mtDNA genotype;
nuclear — nuclear genotype;
genotype — mtDNA.nuclear genotype;
female — female ID number;
day1-day10 — egg counts each day;
total — summed egg counts across all days
DOI: 10.5061/dryad.f3j6f8g/1
title: alignment_Scotophilus_cytb_233

description: Nexus file containing 233 unique haplotypes of cytochrome b from African Scotophilus. This alignment was used to generate the gene tree in Fig. 1.
DOI: 10.5061/dryad.f3j6f8g/2
title: Concatenated_alignment_cyt-b_+_6_introns

description: Nexus file containing 31 concatenated sequences of cyt-b, ABHD, ACOX2, ACPT, COPS, ROGDI, and STAT5 from African Scotophilus. This alignment was used to generate the gene tree in Fig. 2A.
DOI: 10.5061/dryad.hm249b5/1
title: 26snp_reference data for analysis of assignment

description: Reference data (individual genetic data (26 SNP's for each ind) for the North sea and coastal component). SNP's are described in paper.The other file contains inds that was genetically assigned to either of the"populations" in this file (North Sea or coastal component)
DOI: 10.5061/dryad.nn514kg/2
title: Greenhouse cage experiment-female moth ovipositon preference

description: Results from greenhouse cage experiments showing oviposition preference of females for undamaged or caterpillar-damaged Bt or non-Bt rice
DOI: 10.5061/dryad.nn514kg/3
title: Feild experiment-female moth oviposition

description: The results from a feild experiment showing egg densities of C. suppressalis on Bt and non-Bt rice under field conditions
DOI: 10.5061/dryad.nn514kg/4
title: Feeding bioassy-caterpillar performance

description: Resusts from a feeding bioasssay showing performance of caterpillars on damaged rice plants in a climate-controlled chamber
DOI: 10.5061/dryad.nn514kg/5
title: GC-MS test-caterpillar induced rice volatiles

description: The results from GC-MS test showing volatiles released by rice plants that have been damaged by caterpilalr or left intact.
DOI: 10.5061/dryad.nn514kg/6
title: Non-choice wind tunnel-response of female males to volatiles

description: The results from non-choice wind tunnel tests showing response of female C. suppressalis to caterpillar-induced nocturnal plant volatiles
DOI: 10.5061/dryad.vb06d3k/1
title: Summary dataset with one value per bumblebee

description: Summary dataset of bumblebee behaviour exposed to 1 ppb imidacloprid in sugar solution and none in pollen. Rawdata is collected via a robotic flower system (Kuusela & Lämsä 2016) and the data is collapsed into a CSV file allowing easy import to statistical software, such as R.
DOI: 10.17632/5r4vhv329k.1
title: Data for: Atomistic and mean-field estimates of effective stiffness tensor of nanocrystalline copper

description: Data for the positions of seeds, orientations and size distribution of grains applied in the molecular statics simulations reported in the paper
DOI: 10.5061/dryad.2b549t4/1
title: Zebra finch gyre number and mid-piece length data

description: Data file containing mid-piece length and gyre number data collected from experimental males in Part 1 of the study using SPIM. Descriptions of variables are included in the R code file “Zebra-finch_mid-piece_analysis.r”
DOI: 10.5061/dryad.2b549t4/2
title: Zebra finch sperm mid-piece cross-section measurement data

description: Data file containing mean mid-piece length and cross-sectional diameter measurement data collected from experimental males in Part 2 of the study using TEM. Descriptions of variables are included in the R code file “Zebra-finch_mid-piece_analysis.r”
DOI: 10.5061/dryad.2b549t4/3
title: Mitochondrial cristae density data

description: Data file containing mean mid-piece length and cristae density measurement data collected from experimental males in part 2 of the study using TEM. Descriptions of variables are included in the R code file “Zebra-finch_mid-piece_analysis.r”
DOI: 10.5061/dryad.2b549t4/4
title: Zebra finch mid-piece analysis R script

description: R script of the analysis reported in the manuscript 'A trade-off between thickness and length in the zebra finch sperm mid-piece'.
DOI: 10.5061/dryad.2b549t4/5
title: README

description: README file for data files associated with the manuscript “A trade-off between thickness and length in the zebra finch sperm mid-piece”
DOI: 10.5061/dryad.2v160c9/1
title: Saarmanetal2018_Gff_RasterLayers

description: This is a zipped folder that contains the connectivity surface and final habitat suitability map in "ascii" raster/ArcGIS format, as well as an R script (see README file) that displays an example of how to load and visualize the included raster files.
DOI: 10.5061/dryad.326b7g3/1
title: Spatial data for 2031 scenarios of the Greater Sydney Basin

description: kmz files (google earth) for supply and demand of phosphorus for two future scenarios for the Greater Sydney Basin
DOI: 10.5061/dryad.3m3k724/1
title: birnbaum_et_al_2018_data

description: raw data file for eight species used in the study
DOI: 10.5061/dryad.3m3k724/2
title: birnbaum_et_al_2018_analysis_Rcode

description: statistical models used to estimate the effects of soil treatment and invasive Bromus diandrus addition to native species performance in microcosms.
DOI: 10.5061/dryad.4b4q7nq/1
title: Caves_etal_ProceedingsB_Apedersoni and client signalling_Dryad data

description: This data file includes behavioral sequences and behavioral dyads (pairs of antecedent-consequent behaviors) for all interactions used during data analysis in Caves et al., Mutual visual signalling between the cleaner Ancylomenes pedersoni and its client fish.
DOI: 10.5061/dryad.4r1k05t/2
title: Data for the field invasiveness experiment
DOI: 10.5061/dryad.4r1k05t/3
title: Rhizome numbers from the greenhouse drought experiment
DOI: 10.5061/dryad.4r1k05t/4
title: Allelopathy estimates for the progenitor species of H. tuberosus
DOI: 10.5061/dryad.4r1k05t/5
title: Soil water content measurements for the invasiveness field experiment
DOI: 10.5061/dryad.5fb633t/1
title: The architecture of an empirical genotype-phenotype map

description: This DRYAD package contains files from:

Aguilar-Rodríguez, J., Peel, L., Stella, M., Wagner, A., and Payne, J. L. The architecture of an empirical genotype-phenotype map. 

This package contains the network files in GML format for the genotype space of transcription factor (TF) binding sites ('genotype_space.gml'), 525 genotype networks of TF binding sites, and 66 genotype networks of DNA binding domains. The genotype networks of TF binding sites are classified in three directories according to their species provenance ('Arabidopsis_thaliana', 'Mus_musculus,' and 'Neurospora_crassa'). Each network file is named with the TF name. More information about these networks can be found in Table S1. The genotype networks of DNA binding domains are within a 'domains' sub-folder that can be found inside each of the three species folders. Each file is named with the DNA binding domain class.

Each network file has the following vertex attributes:
- id: vertex identification number.
- sequence: the nucleotide sequence of the binding site.
- reversecomplement: the reverse complement of 'sequence.'

Genotype network of TF binding sites have the following additional vertex attributes:
- Escore: the enrichment score in protein binding microarrays of the sequence.
- PartitionSBM: Information about the stochastic block model partition group where the vertex is found: '0', '1', or 'None'. 'None' is for vertices not found in the dominant genotype network.
- PartitionBA: Information about the binding affinity partition group where the vertex is found: '0', '1', or 'None'. 'None' is for vertices not found in the dominant genotype network.

For questions regarding these data, contact Joshua Payne at joshua.payne@env.ethz.ch or Andreas Wagner at andreas.wagner@ieu.uzh.ch.
DOI: 10.5061/dryad.5n7t4/2
title: R Scripts for Analysis & Figures

description: R scripts to reproduce the analysis and recreate the figures included in the paper.
DOI: 10.5061/dryad.dg8q0/1
title: Dryad_Repo_for_Submission.tar

description: A compressed archive of nexus alignments, Beast XML files and MCC trees from the analyses performed in this study. The subfolders are clearly labeled to indicate file and analysis type associated with each file.
DOI: 10.5061/dryad.ds543.1
title: Data from: A new phylogeny of Stegosauria (Dinosauria, Ornithischia)
DOI: 10.5061/dryad.ds543.1/1.1
title: Character Taxon Matrix

description: A character-taxon matrix for analysis of stegosaurian dinosaur relationships
DOI: 10.5061/dryad.ds543.2
title: Data from: A new phylogeny of Stegosauria (Dinosauria, Ornithischia)
DOI: 10.5061/dryad.ds543.2/1.2
title: Character Taxon Matrix

description: A character-taxon matrix for analysis of stegosaurian dinosaur relationships
DOI: 10.5061/dryad.ds543.2/2.2
title: Character List

description: A character list to accompany the character-taxon matrix
DOI: 10.5061/dryad.ds543.2/3.2
title: Raven&MaidmentOSI

description: A file containing characters, justifications for changes made to characters, and synapomorphies
DOI: 10.5061/dryad.f2579/1
title: The data of all the figures

description: Keyword: Ceramics; Electroless deposition; H-BN powders; Ionic liquid; Plating nickel times; Deposition mechanism
DOI: 10.5061/dryad.f3j6f8g/10
title: alignment_STAT5_phase

description: Nexus file containing phased alleles from STAT5 sequences of African Scotophilus. This alignment was used to generate the species tree in Fig. 3, individual gene trees in Supplemental Material Fig. 1, and in species delimitation analyses.
DOI: 10.5061/dryad.f3j6f8g/3
title: Concatenated_alignment_6_introns

description: Nexus file containing 31 concatenated sequences of ABHD, ACOX2, ACPT, COPS,  ROGDI, and STAT5 from African Scotophilus. This alignment was used to generate the gene tree in Fig. 2B.
DOI: 10.5061/dryad.f3j6f8g/4
title: alignment_cytb_31

description: Nexus file containing 31 cyt-b sequences of African Scotophilus. This alignment was used to generate the species tree in Fig. 3 and in species delimitation analyses.
DOI: 10.5061/dryad.f3j6f8g/5
title: alignment_ABHD_phase

description: Nexus file containing phased alleles from ABHD sequences of African Scotophilus. This alignment was used to generate the species tree in Fig. 3, individual gene trees in Supplemental Material Fig. 1, and in species delimitation analyses.
DOI: 10.5061/dryad.f3j6f8g/6
title: alignment_ACOX2_phase

description: Nexus file containing phased alleles from ACOX2 sequences of African Scotophilus. This alignment was used to generate the species tree in Fig. 3, individual gene trees in Supplemental Material Fig. 1, and in species delimitation analyses.
DOI: 10.5061/dryad.f3j6f8g/7
title: alignment_ACPT_phase

description: Nexus file containing phased alleles from ACPT sequences of African Scotophilus. This alignment was used to generate the species tree in Fig. 3, individual gene trees in Supplemental Material Fig. 1, and in species delimitation analyses.
DOI: 10.5061/dryad.f3j6f8g/8
title: alignment_COPS_phase

description: Nexus file containing phased alleles from COPS sequences of African Scotophilus. This alignment was used to generate the species tree in Fig. 3, individual gene trees in Supplemental Material Fig. 1, and in species delimitation analyses.
DOI: 10.5061/dryad.f3j6f8g/9
title: alignment_ROGDI_phase

description: Nexus file containing phased alleles from ROGDI sequences of African Scotophilus. This alignment was used to generate the species tree in Fig. 3, individual gene trees in Supplemental Material Fig. 1, and in species delimitation analyses.
DOI: 10.5061/dryad.hm249b5/2
title: BeachSeine_26SNP_all

description: 26 SNP loci for all beach seine data
DOI: 10.5061/dryad.hm249b5/3
title: individual_information

description: Information on all individuals (length position, aso)
DOI: 10.5061/dryad.hq3vq/2
title: assembler_test

description: This zip-archive contains all files related to our testing of different de novo assemblers and their treatment of heterozygous sites. The archive also contains the results of a reference-based assembly of the sequencing reads against reference sequences for all UCE loci.
DOI: 10.5061/dryad.hq3vq/3
title: phylogenetic_analyses

description: This zip-archive contains all input files and results of the Multispecies Coalescent (MSC) analyses from this study. This includes the BEAST analyses of the mitochondrial genome, the STACEY analyses of all sequence data and the SNAPP analyses of all SNP datasets.
DOI: 10.5061/dryad.hq3vq/4
title: summary_coalescent_analyses

description: This zip-archive contains all files related to the MPEST analyses, which are reported in online Appendix 2. This includes gene trees for all loci inferred by PhyML and the MPEST species tree analyses results.
DOI: 10.5061/dryad.hq3vq/5
title: phasing_files

description: This zip-archive contains all files related to the reference based assembly of UCE sequencing reads and the subsequent phasing of these reads into allele haplotype sequences.
DOI: 10.5061/dryad.hq3vq/6
title: simulations

description: This zip-archive contains all files related to the simulation of data generated in this study.
DOI: 10.5061/dryad.hq3vq/8
title: alignments

description: This zip-archive contains all sequence and SNP multiple sequence alignment (MSA) files that were analyzed in this study.
DOI: 10.5061/dryad.hq3vq/9
title: supplemental_material

description: Zip-archive contains online Appendices 1-5, Supplementary Figs. S1-S11 and Supplementary Tables S1 and S2.
DOI: 10.5061/dryad.j3mk157/1
title: Rota_et_al_2018_Oikos_Data_sets
DOI: 10.5061/dryad.m3r3831/1
title: All Data

description: GOX, Body mass and consumption data
DOI: 10.5061/dryad.np7332q/1
title: Simulation data

description: Directories contain the analyses results for replicates in each effective population size (Ne).
DOI: 10.5061/dryad.r0hq0/1
title: Figure5b

description: Phylogeny reconstructed from the Quercus RADseq dataset (Cavender-Bares et al. 2015) using AAF without selection.
DOI: 10.5061/dryad.r0hq0/2
title: Figure5c

description: Phylogeny reconstructed using AAF with SBA reads selection (ks = kp = 21).
DOI: 10.5061/dryad.r0hq0/3
title: Figure5d

description: Phylogeny reconstructed using AAF with pairwise reads selection (ks = kp =21).
DOI: 10.5061/dryad.r0hq0/4
title: Figure S3a

description: Viburnum phylogeny without reads selection (k=15, n=2)
DOI: 10.5061/dryad.r0hq0/5
title: Figure S3b

description: Viburnum phylogeny with SBA reads selection kp=ks=15, n=2
DOI: 10.5061/dryad.r14s8s8/1
title: Marker information
DOI: 10.5061/dryad.r14s8s8/2
title: Sequence Alignment
DOI: 10.5061/dryad.r9k214r/1
title: Annual census-count and demographic data for meerkat social groups

description: Comma separated data, from long-term monitoring of habituated meerkat social groups on and around the Kuruman River Reserve, Northern Cape Province, South Africa (26.978600°S, 21.832300°E).  Columns represent variables of interest for unique group/year combinations (rows); see README file for details.
DOI: 10.5061/dryad.rh67h/1
title: Chemical_physical_soil_properties_colluvial_soils_Germany

description: Lab results of soil samples from the SFB1070 B2 Project.