cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tn28f/15
title: PacBio CCS Reads

description: Pacbio CCS raw reads, barcode information and primer sequences were used in MLSTEZ for generating consensus sequences.
DOI: 10.5061/dryad.15kb3/1
title: Zinke effect sizes and covariates

description: Dataset used for meta-analysis
DOI: 10.5061/dryad.2q3r2/1
title: Hanley et al Constrained eggshell colors - 2015-1-13-Accompanying Data

description: Reflectance spectra from 636 bird species collected from museum specimens.
DOI: 10.5061/dryad.4tn48/2
title: Experiment 2

description: Data and R code for Fig2_and_S2
DOI: 10.5061/dryad.4tn48/3
title: Experiment 3

description: Data and R code for Fig3_and_S3
DOI: 10.5061/dryad.4tn48/4
title: Experiment 4

description: Data and R code for Fig 4
DOI: 10.5061/dryad.60bd8/3
title: behavioural data for figure 3
DOI: 10.5061/dryad.b20t3/1
title: Latzman_et_al_DTI_DG
DOI: 10.5061/dryad.b56n0/4
title: Calo_Enolase_haplos.trees

description: BEAST v1.8.0 and TreeAnnotator v1.80.0 output files for the nuclear gene cad.
DOI: 10.5061/dryad.b56n0/5
title: Calo_mtDNA_haplos.trees

description: BEAST v1.8.0 and TreeAnnotator v1.80.0 output files for the  concatenated mtDNA.
DOI: 10.5061/dryad.b56n0/6
title: Calo_CAD_haplos.info

description: List of individuals in which each cad haplotype was found.
DOI: 10.5061/dryad.b56n0/7
title: Calo_Enolase_haplos.info

description: List of individuals in which each enolase haplotype was found.
DOI: 10.5061/dryad.d644f/10
title: S. cerevisiae sampled absolute mRNA and protein levels, scaled to (average) molecules per haploid cell, sampled from SCM estimates

description: mRNA and protein levels, scaled to (average) molecules per haploid cell, sampled according to SCM estimates, for haploid budding yeast (S.cerevisiae) growing exponentially in rich medium with glucose
DOI: 10.5061/dryad.d644f/11
title: S. cerevisiae absolute mRNA and protein levels, scaled to (average) molecules per haploid cell, estimated by SCM

description: SCM estimates of absolute mRNA and protein levels, scaled to (average) molecules per haploid cell, for haploid budding yeast (S.cerevisiae) growing exponentially in rich medium with glucose
DOI: 10.5061/dryad.d644f/3
title: S. cerevisiae SCM estimates of mRNA and protein levels, log-transformed and unscaled

description: SCM estimates of mRNA and protein levels, log-transformed and unscaled, for haploid budding yeast (S.cerevisiae) growing exponentially in rich medium with glucose
DOI: 10.5061/dryad.d644f/4
title: S. cerevisiae log-transformed SCM-normalized mRNA and protein measurements, with imputed values

description: SCM-normalized mRNA and protein measurements, with imputed values, for haploid budding yeast (S.cerevisiae) growing exponentially in rich medium with glucose
DOI: 10.5061/dryad.d644f/8
title: S. cerevisiae SCM estimates of mRNA and protein levels, log-transformed and unscaled

description: SCM estimates of mRNA and protein levels, log-transformed and unscaled, for haploid budding yeast (S.cerevisiae) growing exponentially in rich medium with glucose
DOI: 10.5061/dryad.d644f/9
title: Ribosome density, mRNA level, and translational efficiency measurements for haploid budding yeast (S.cerevisiae) growing exponentially in rich medium with glucose

description: Measurements and summary statistics for RNA-seq mRNA levels, ribosome footprint density, and translational efficiency for haploid budding yeast (S.cerevisiae) growing exponentially in rich medium with glucose
DOI: 10.5061/dryad.dr275.2
title: Data from: Disentangling the relative importance of species occurrence, abundance and intraspecific variability in community assembly: a trait-based approach at the whole-plant level in Mediterranean forests
DOI: 10.5061/dryad.dr275.2/1.2
title: Woody plant traits database

description: Functional traits at whole plant level for woody mediterranean plants on three different areas from Córdoba region (Spain)
DOI: 10.5061/dryad.fn2nt/10
title: 26 loci supermatrix

description: Matrix including all loci from this study and Petersen et al. 2011 for one individual per diploid species (data for Fig. S17)
DOI: 10.5061/dryad.fn2nt/11
title: 26 loci supermatrix Tree

description: Tree inferred from all loci from this study and Petersen et al. 2011 with one individual per diploid species (raw tree Fig. S17)
DOI: 10.5061/dryad.fn2nt/12
title: Supplementary Information

description: Supplementary Information containing annotated trees (Figs. S2-S17, S19), figures S1 and S18, tables S1 and S2 and references.
DOI: 10.5061/dryad.fn2nt/5
title: BCA output from BUCKy

description: Concordance file obtained from BUCKy on 12 loci (raw data Fig. S15)
DOI: 10.5061/dryad.fn2nt/6
title: Hordeum diploids Supermatrix

description: 12 loci concatenated matrix, only diploids (data Fig. 1)
DOI: 10.5061/dryad.fn2nt/7
title: Hordeum diploids Supermatrix Tree

description: Bayesian Inference of Hordeum diploids Supermatrix (raw tree Fig. 1)
DOI: 10.5061/dryad.fn2nt/8
title: matK all individuals Matrix

description: Matrix locus matK (data for Fig. S14)
DOI: 10.5061/dryad.fn2nt/9
title: matK all individuals Tree

description: Tree locus matK (raw tree for Fig. S14)
DOI: 10.5061/dryad.g1t1b/1
title: Placustris_AllCOIsequences

description: All COI sequences
DOI: 10.5061/dryad.g1t1b/2
title: Placustris_StructureInput

description: Input file for analyses using Structure software
DOI: 10.5061/dryad.g1t1b/3
title: lacustris_IMa2inputs

description: Ten input files for IMa2 pair-wise analyses
DOI: 10.5061/dryad.g1t1b/4
title: Placutris_MsatGenotypesAndCOInumbers

description: Microsatellite genotypes and COI accession numbers for all analysed Paramysis lacustris individuals
DOI: 10.5061/dryad.g1t1b/5
title: Placustris_MrBayesinput

description: Input file of unique COI sequences for phylogenetic analyses in MrBayes software
DOI: 10.5061/dryad.g1t1b/6
title: lacustris_PCoAinput

description: Matrix of genotypic distances for individual Principal Coordinate analyses
DOI: 10.5061/dryad.gm6mc/1
title: Literature review data for: Translocation tactics: A framework to support the IUCN Guidelines for wildlife translocations and improve the quality of applied methods, Batson, William G., Gordon, Iain J., Fletcher, Donald B., Manning, Adrian D.

description: This data file includes the detection rate of tactics within each publication from the three form of media review during this study. Detection rate is essentially a measure of occurrence within individual publications.
DOI: 10.5061/dryad.hh650/1
title: avida_data

description: TAR archive containing data from Ostrowski et al. (2015). Genetically integrated traits and rugged adaptive landscapes in digital organisms. Archive contains configuration files, a list of run commands, an Excel spreadsheet showing the phenotypes of the evolved organisms, lineages, and organisms.
DOI: 10.5061/dryad.j182q/1
title: crop sizes

description: This file contains data concerning tree location and crop size during 2011, 2012, and 2013.
DOI: 10.5061/dryad.j182q/2
title: fruit initiation

description: This file contains data concerning tree locations and fruit initiation successes during 2012 and 2013.
DOI: 10.5061/dryad.j182q/3
title: fruit development

description: This files contains data concerning tree locations and fruiting development successes during 2011, 2012, and 2013.
DOI: 10.5061/dryad.ms40b/1
title: Appendix 1

description: Raw sclerobiont maps of each of the 150 brachiopod specimens included in the mapping study. Each image is shown to scale. The left-hand column depicts maps of the dorsal view, and the right-hand column depicts maps of the ventral view. Blank cells indicate valves that were unencrusted, and were therefore not mapped. The original photograph of the brachiopod has been removed for clarity. Sclerobionts are colour coded by taxon: Ascodictyon = purple, Hederella = yellow, Microconchus = red, and craniid brachiopods = blue.
DOI: 10.5061/dryad.p0c02/2
title: fecundity
DOI: 10.5061/dryad.p0c02/3
title: Genotypes_adults
DOI: 10.5061/dryad.q1t7v/5
title: tpc00508-SupplementalDS5

description: Transposon Position BED File
DOI: 10.5061/dryad.q1t7v/6
title: tpc00508-SupplementalDS6

description: Allele-Specific PCR Primer Sequences
DOI: 10.5061/dryad.q5h96/1
title: Data_for_dryad

description: Datasets and pedigrees used in the study
DOI: 10.5061/dryad.15kb3/2
title: Bibliographic information

description: List of references included in meta-analysis
DOI: 10.5061/dryad.17hn4/1
title: Hypoxia and parasitic manipulation of geotaxis: datafile

description: one Excel spreadsheet for each experiment - the list of abbreviations is given in the first datasheet
DOI: 10.5061/dryad.2cv1h.1
title: Data from: Evolution of wing shape in hornets: why is the wing venation efficient for species identification?
DOI: 10.5061/dryad.2cv1h.2
title: Data from: Evolution of wing shape in hornets: why is the wing venation efficient for species identification?
DOI: 10.5061/dryad.2cv1h.2/1.2
title: Data-specimens-Perrard-etal-2014-JEB

description: Table of data of the specimens measured for the wing shape. This table mention the name of the specimens, identifications, countries where the specimens have been collected and institutions where the specimens are in collection.
DOI: 10.5061/dryad.2cv1h.2/2.2
title: Wings-coordinates-Perrard-etal-2014-JEB

description: Raw coordinates of the 19 landmarks used to measured the right forewing of the 1025 specimens.
DOI: 10.5061/dryad.2cv1h.2/3.2
title: Script-R-Perrard-etal-2014-JEB

description: Script R used to perform the analyses in Perrard et al. 2014, Evolution of wing shape in hornets: why is the wing venation efficient for species identification?
DOI: 10.5061/dryad.2cv1h.2/4.2
title: Mtree-functions-for-R-phylogenetic-signal

description: R functions to compute the phylogenetic signal according to the method described in Klingenberg & Gidaszewski 2010. The functions include an exact computation of the ancestral states minimizing the squared parsimony (according to the algorithm of McArdle & Rodrigo, 1994), a mapping of the phylogenetic tree in a plot of the morphospace and different methods to test that the phylogeny is significantly shorter than a random tree connecting the terminals in the morphospace.
DOI: 10.5061/dryad.2pb57/1
title: Collection Localities

description: Localities of streams that were surveyed, including those where we collected tailed frogs and those where we found none.
DOI: 10.5061/dryad.2pb57/2
title: Multilocus genotypes

description: Genotypes at 13 microsattelite loci for 2118 Rocky Mountain tailed frogs.
DOI: 10.5061/dryad.4f16h/1
title: Quantitative genetics of plumage color

description: This is an excel file with 5 worksheets containing datasets used for different analyses shown in the paper. 1) Comparing color between sexes and developmental stages, 2) Frequency of extra-pair young (EPY) across years, 3) Comparing color of recruited vs. non-recruited individuals, 4) Within-individual color comparison of recruited individuals, and 5) data used in the animal model analysis. See the ReadMe file for more details.
DOI: 10.5061/dryad.7sk2g/1
title: Irl et al_2015_J Ecol_Dryad

description: Data were collected between 2010 and 2013 on the island of La Palma (Canary Islands). Table giving plot name and coordinates (in UTM 28N). Furthermore all climate variables, all topographic variables as well as all response variables (diversity measures) are given. Abbrevations: Climatic rarity of the Canary Islands = CR_CAN, Climatic rarity of La Palma = CR_LP, INTRA_VAR = Intra-annual precipitation variability, INTER_VAR = Inter-annual preciptation variability, Mean annual temperature = MAT, Mean annual precipitation = MAP, Rainfall seasonality index = RSI, Annual solar radiation = ASR, Geologic Age = Age, Macro-aspect = Macro, Topographic complexity index = TCI. In addition, species richness (SR), number of single island endemics (nSIE), number of archipelago endemics (nAE), percentage of single island endemics (pSIE) and the percentage of archipelago endemics (pAE) are given.
DOI: 10.5061/dryad.dr275.1
title: Data from: Disentangling the relative importance of species occurrence, abundance and intraspecific variability in community assembly: a trait-based approach at the whole-plant level in Mediterranean forests
DOI: 10.5061/dryad.fp94d/2
title: Lima TB Treatment Default Data

description: The attached information is the minimum necessary to reproduce our results.
DOI: 10.5061/dryad.ft36k/1
title: 97% OTUs 454 dataset

description: Following 454 sequencing of the 16s rRNA gene of bacterial communities of 33 samples of attine ants, Megalomyrmex ants and fungus gardens, 923 bacterial OTUs (operational taxonomic units at 97% identity) were identified. The zip file contains an OTU table showing the distribution of sequencing reads for all OTUs across the 33 samples, a taxonomy file with the classification of the OTUs based on the Greengenes reference set (May 2013 release), a fasta file with all 923 representative sequences for these OTUs, and a mapping file containing the barcode sequence for each of the 33 samples that were multiplex sequenced.
DOI: 10.5061/dryad.ft36k/2
title: Unique sequences 454 dataset

description: Following 454 sequencing of the 16s rRNA gene of bacterial communities of 33 samples of attine ants, Megalomyrmex ants and fungus gardens, 4882 unique bacterial sequences were identified. The zip file contains a table showing the distribution of sequencing reads for all unique sequences across the 33 samples, the taxonomic classification of these sequences based on the Greengenes reference set (May 2013 release), and a fasta file with all the 4882 unique sequences.
DOI: 10.5061/dryad.ft36k/3
title: 97% OTUs MiSeq diet experiment dataset

description: Following MiSeq sequencing of the 16s rRNA gene of bacterial communities of 36 samples of attine ants, Megalomyrmex ants and fungus gardens collected after a diet manipulation experiment, 852 bacterial OTUs (operational taxonomic units at 97% identity) were identified. The zip file contains an OTU table showing the distribution of sequencing reads for all OTUs across the 36 samples, a fasta file with all 852 representative sequences for these OTUs and two taxonomy files linking the taxonomic classification of the OTUs based on the Greengenes reference set (May 2013 release) to the OTU IDs found in the OTU table and the sequence identifiers found in the fasta file.
DOI: 10.5061/dryad.ft36k/4
title: Sericomyrmex mtCOI alignment and phylogenetic tree

description: The zip file contains the alignment in fasta format and the maximum likelihood phylogeny in newick format built from the 384 bp of the mitochondrial Cytochrome Oxidase I (mtCOI) gene amplified from 60 colonies of Sericomyrmex fungus-growing ants collected across the Panama Canal Zone.
DOI: 10.5061/dryad.j182q/4
title: seed set 2011

description: This file contains data on tree locations and total seed number per tree during 2011.
DOI: 10.5061/dryad.p0c02/4
title: Genotypes_larvae
DOI: 10.5061/dryad.p0c02/5
title: growth
DOI: 10.5061/dryad.p0c02/6
title: reproductive_success
DOI: 10.5061/dryad.p0c02/7
title: sire_contributions
DOI: 10.5061/dryad.p0c87/1
title: fMRI full experiment 3000 microTesla part 1

description: fMRI full experiment 3000 microTesla part 1-10: MRI and fMRI DICOM images corresponding to the full study conducted with a 3000 microTesla exposure. These DICOM files have been produced by a Siemens 3T Verio (Siemens, Germany) MRI, as described in the paper. DICOM is a standard format for MRI images, and these can be analyzed with software packages such as BrainVoyager (Brain Innovation, The Netherlands), which we have used in the paper; or an open-access software package such as FSL (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/). The analysis procedure for the fMRI data is fully described in the Methods section of the paper. DICOM files are available for each subject pre- and post-exposure, for each of the two tasks presented in the paper (finger tapping and mental rotation). Two tasks were used in this experiment: a mental rotation task and a finger tapping task. The subject who have properly conducted the mental rotation task and have been included in the analysis are: S02, S03, S04, S06, S07, S09, S10, S11, S12, S13, S14, S16, S17, S18, S20, S21, S23, S24, S25, S27, S29. The subject who have properly conducted the finger tapping task and have been included in the analysis are: S03, S04, S06, S07, S08, S09, S10, S12, S13, S14, S16, S17, S20, S22, S23, S24, S25, S26, S27, S29. Please feel free to contact the authors if further guidance is required.
DOI: 10.5061/dryad.p0c87/2
title: fMRI full experiment 3000 microTesla part 2
DOI: 10.5061/dryad.p0c87/3
title: fMRI full experiment 3000 microTesla part 3
DOI: 10.5061/dryad.p0c87/4
title: fMRI full experiment 3000 microTesla part 4
DOI: 10.5061/dryad.p0c87/5
title: fMRI full experiment 3000 microTesla part 5
DOI: 10.5061/dryad.p0c87/6
title: fMRI full experiment 3000 microTesla part 6
DOI: 10.5061/dryad.p0c87/7
title: fMRI full experiment 3000 microTesla part 7
DOI: 10.5061/dryad.p62h7/2
title: Covariates
DOI: 10.5061/dryad.pp6bm/10
title: Dataset_E_Microsat

description: Data consisting of 474 marine iguanas sampled from the island San Cristobal, genotyped at 18 microsatellite loci. The last 20 samples (highlighted in yellow) are individuals identified as hybrids of migrants from other islands.
DOI: 10.5061/dryad.pp6bm/11
title: Dataset_MSVar_Bottleneck

description: Data from marine iguanas sampled on San Cristobal island, genotyped at 18 microsatellite loci and sorted into two populations: Loberia and Punta Pitt. All individuals with &gt;6% missing data and any possible vargrants or migrants from other islands have been removed.
DOI: 10.5061/dryad.pp6bm/12
title: Dataset_B_Mitochondrial

description: 5557 bp from seven mitochondrial genes in a representative selection of the three main haplotype lineages within Amblyrhynchus, and all species of Conolophus.
DOI: 10.5061/dryad.pp6bm/13
title: Morphometry_Amblyrhynchus

description: Measurements and scale counts taken from a microsatellite-genotyped marine iguanas from San Cristóbal to investigate morphological differences between diverged lineages
DOI: 10.5061/dryad.pp6bm/3
title: Dataset_C

description: Complete mitochondrial control region sequences (1181 bp) in 1493 marine iguanas (Amblyrynchus cristatus) sampled across the Galapagos archipelago.
DOI: 10.5061/dryad.pp6bm/7
title: Datasets_F_G_H

description: Data from RAD sequencing for 33 marine iguanas and 8 outgroups.  Described as datasets F, G and H in the manuscript.  More information available in the ReadMe file.
DOI: 10.5061/dryad.pp6bm/8
title: Dataset_A_concatenated_alignment

description: A concatenated alignment of various squamate sequences for nuclear genes: RAG1, BDNF, R35 and NKTR.
DOI: 10.5061/dryad.pp6bm/9
title: Dataset_D_Microsats

description: A dataset of 614 marine iguana samples, genotyped at 12 microsatellite loci and used in analysis to determine population structure across the archipelago.
DOI: 10.5061/dryad.v28f9/1
title: Archive of all annotation and alignment data

description: This file is an archive of all data not publicly archived.  Please see the README.txt file for a detailed description of all contents. The archive can be uncompressed by either double-clicking on the file in most operating systems or using the command:"tar -zxvf file.tar.gz" in a UNIX terminal.
DOI: 10.5061/dryad.18r5f/1
title: Metadata population dynamics in artificial metapopulations

description: The file contains raw data used in the accompanied manuscript. One sheet contains all demographic data (population size, per stage) during the course of the experiment. A second sheet contains dispersal data (counts on quadrants)
DOI: 10.5061/dryad.2rq05/1
title: V12_OTU_biom_table

description: Biom Table for V1-2  16S amplicon
DOI: 10.5061/dryad.2rq05/2
title: V34_OTU_biom_table

description: Biom table for V3-4 16S amplicon
DOI: 10.5061/dryad.2rq05/3
title: V12_OTUs_alignment

description: OTU fasta alignment for V1-2 16S amplicon
DOI: 10.5061/dryad.68686/1
title: Supplemental DataSet 1

description: Processed RNA-Seq Gene Expression Values in FPKM.  Expression data was obtained from six angiosperm plant species, from three root development zones (MZ, EZ, and DZ), and with three biological replicates each.
DOI: 10.5061/dryad.68686/10
title: Supplemental_DataSet10

description: Supergene Expression and Profile Types.  Supergene expression in two development zones (meristematic (M) and overlapping elongation/differentiation (ED)) of seven vascular species and the expression profile types (1 - 5) assigned by EDZ/MZ fold-change for all 18110 GreenPhyl-defined families.
DOI: 10.5061/dryad.68686/2
title: Supplemental DataSet 2

description: GreenPhyl Defined Gene Families.  Genes IDs are included for the seven vascular plants in this study that are present in the 18110 families defined by the GreenPhyl database.
DOI: 10.5061/dryad.68686/3
title: Supplemental DataSet 3

description: Distribution of Root-Expressed Genes by Family.  The number of root-expressed and non-expressed genes from each plant species in each of the 18110 GreenPhyl defined families. Root expressed genes were defined as those exhibiting FPKM ≥ 0.5 in at least one root development zone, with at least 2 of 3 independent biological replicates generating reads.
DOI: 10.5061/dryad.68686/4
title: Supplemental DataSet 4

description: Arabidopsis Genes Preferentially Expressed in Root Developmental Zones. List of Arabidopsis genes preferentially expressed in the meristematic, elongation, and differentiation zones of the primary root.  Differential expression analysis was performed by edgeR tag-wise dispersion with upper quartile normalization method (FC ≥ 2 and FDR ≤ 0.05).
DOI: 10.5061/dryad.68686/5
title: Supplemental DataSet 5

description: Clustering of Root-Expressed Genes.  Temporal gene expression profile types were assigned by fuzzy C-means clustering.
DOI: 10.5061/dryad.68686/6
title: Supplemental DataSet 6

description: Supergene Expression in Three Development Zones.  The expression in the three zones (meristematic (MZ), elongation (EZ), and differentiation (DZ)) of six angiosperm species and the expression profile types (1 - 9) assigned by fuzzy C-Means clustering are presented for all 18110 GreenPhyl-defined families.  Supergene expression was generated by summing all the transcript expressions from the same species within a given family.  Type 0 indicated less than 2 fold-change across development zones.  NA = no gene present or not root-expressed.
DOI: 10.5061/dryad.68686/7
title: Supplemental DataSet 7

description: Supergene Connectivity Values (CNV) for 6161 families possessing root-expressed genes (average FPKM ≥ 0.5 in at least one development zone) from six angiosperm plant species.
DOI: 10.5061/dryad.68686/8
title: Supplemental DataSet 8

description: Processed RNA-Seq Gene Expression Values in FPKM.  Expression data was generated for seven vascular plant species, two root development zones (meristematic (MZ) and overlapping elongation/differentiation (EDZ)) with three biological replicates each.
DOI: 10.5061/dryad.68686/9
title: Supplemental DataSet 9

description: Classification of Genes by Expression Profile.  Gene expression fold-change types were assigned to each root-expressed genes from seven vascular plant species.
DOI: 10.5061/dryad.7s4h1/1
title: Asteraceae-76 genes

description: Sequence alignment of 76 concatenated Asteraceae plastid genes for 29 taxa
DOI: 10.5061/dryad.7s4h1/2
title: Asteraceae-matK-rbcL

description: Sequence alignment of Asteraceae matK + rbcL plastid genes for 29 taxa
DOI: 10.5061/dryad.7s4h1/4
title: Asteraceae-rbcL

description: Sequence alignment of Asteraceae rbcL plastid genes for 29 taxa
DOI: 10.5061/dryad.7s4h1/5
title: Fabaceae-71 genes

description: Sequence alignment of 71 concatenated Fabaceae plastid genes for 20 taxa
DOI: 10.5061/dryad.8c81j/1
title: Part A

description: Part A--use "cat" utility to reassemble into a zipped folder containing the complete code and data files.
DOI: 10.5061/dryad.8c81j/2
title: Part B

description: Part B--use "cat" utility to reassemble into a zipped folder containing the complete code and data files.