cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9rs5d/2
title: Protonibea diacanthus parasites data

description: This file contains the individual parasites assemblage and abundance used in the paper entitled "Strong population structure deduced from genetics, otolith chemistry and parasite abundances explains vulnerability to localised fishery collapse in a large Sciaenid fish, Protonibea diacanthus"
DOI: 10.5061/dryad.9rs5d/3
title: Protonibea diacanthus otolith microchemistry data

description: This file contains the individual otolith microchemistry data used for the paper entitled "Strong population structure deduced from genetics, otolith chemistry and parasite abundances explains vulnerability to localised fishery collapse in a large Sciaenid fish, Protonibea diacanthus"
DOI: 10.5061/dryad.f51f5/1
title: Spectra and photographs

description: This .zip file contains the spectral measurements taken from the flounders' skin, as well as photographs of the animal against backgrounds of sand, rocks, small gravel, and large gravel. You may find the details of data acquisition and processing in our paper titled:"Changeable camouflage: how well can flounder resemble the colour and spatial scale of substrates in their natural habitats?" Please email the corresponding author for any questions. Code we have used to process these data is also available upon request.
DOI: 10.5061/dryad.g9v24/1
title: Whole mitochondrion consensus sequences

description: Fasta consensus sequences for 24 goat mitochondria published in the study.
DOI: 10.5061/dryad.gc3k5/1
title: Mudskipper image data

description: Original images of the specimens used (n=9 for Boleophthalmus dussumieri; n=10 for Periophthalmus waltoni; n=12 for Scartelaos tenuis).
DOI: 10.5061/dryad.gc3k5/10
title: Mudskipper project R codes II

description: Minor R code for generating the outline of the mudskipper.
DOI: 10.5061/dryad.gc3k5/2
title: Mudskipper TPS data

description: Landmark coordinate data of mudskipper digital images obtained using tpsDig v. 2.16.
DOI: 10.5061/dryad.gc3k5/3
title: Mudskipper maximum likelihood and Bayesian phylogenetic trees

description: RAxML_bipartitions.persian_mudskippers.TRE contains the maximum likelihood phylogenetic tree of 19 fish species. BIpersian_mudskippers.TRE contains the Bayesian phylogenetic tree for the same 19 fish species. mudskipper_three_species_ML_tree.NWK contains the maximum likelihood phylogenetic tree for Boleophthalmus dussumieri, Periophthalmus waltoni, and Scartelaos tenuis inferred from the tree given in RAxML_bipartitions.persian_mudskippers.TRE. All tree data are specified in Newick tree format.
DOI: 10.5061/dryad.gc3k5/4
title: Mudskipper ecological data

description: The ecological data given in Table 1 of the manuscript. Column 1 gives the abbreviated location name of the study plots; Column 2 gives their geographic coordinates. Abbreviations for the ecological variables: B, P, S = number of burrows per square metre of each species; B = B. dussumieri; P = P. waltoni; S = S. tenuis; F = fluvial action; Sc = weight percent fraction of sand; Sd = sediment type; T = tidal action; V = density of the root network; W = wave action.
DOI: 10.5061/dryad.gc3k5/5
title: Mudskipper morphometric data

description: The file contains data of morphometric variables for all 31 mudskipper specimens. Column 1: specimen label identification; Column 2: species name. Abbreviations: BD = body depth; LPD = least depth of caudal peduncle; HD = head depth; PAL = post-anal tail length;	 PDL = predorsal length; INT = internal length; SL = standard length;  Sa = surface area of region a;	 Sb = surface area of region b; Sc = surface area of region c; St = total surface area;	 Va = volume of region a; Vb = volume of region b; Vc = volume of region c; Vt = total volumel;	SAVa = surface area to volume ratio of region a; SAVb = surface area to volume ratio of region b; SAVc = surface area to volume ratio of region c; SAVt = total surface area to volume ratio
DOI: 10.5061/dryad.gc3k5/6
title: Mudskipper Procrustes shape variable matrix

description: The matrix of Procrustes shape variables after application of Generalized Procrustes Analysis as implemented via the gpagen function of the geomorph R package (version 3.0.0). The dimension of the matrix is 31x28 (31 specimens, 14 landmarks).
DOI: 10.5061/dryad.gc3k5/7
title: Mudskipper outline TPS data file

description: The TPS data file containing the coordinates of the 14 landmarks from the mean shape configuration followed by semi-landmarks defining the outlines of the body, the mouth, and the eye.
DOI: 10.5061/dryad.gc3k5/8
title: Mudskipper concatenated multiple sequence alignment

description: Concatenated multiple sequence alignment of cox1-cytb-rag1 DNA sequences from 19 species of fish in Nexus file format.
DOI: 10.5061/dryad.h1157/10
title: Figure S4 and S6

description: Data for figures S4 and S6
DOI: 10.5061/dryad.h1157/11
title: Figure S4

description: Data for figure S4
DOI: 10.5061/dryad.h1157/4
title: Figure 2

description: Data for figure 2
DOI: 10.5061/dryad.h1157/5
title: Figure 3 and 4

description: Data for figures 3 and 4
DOI: 10.5061/dryad.h1157/6
title: Figure 3

description: Data for figure 3
DOI: 10.5061/dryad.h1157/7
title: Figure 5

description: Data for figure 5
DOI: 10.5061/dryad.h1157/8
title: Figure S1

description: Data for figures S1
DOI: 10.5061/dryad.h1157/9
title: Figure S3

description: Data for figure S3
DOI: 10.5061/dryad.h3680/1
title: The data of 100 worms during odor avoidance behavior.

description: The Excel sheets contains x and y positions (mm), the odor concentration at the position (micro-M) and the behavioral states (Run or Pirouette) of 100 animals during 121-720 s of the odor avoidance assay. This dataset was used in Figures 1 and 2.
DOI: 10.5061/dryad.jq87d/1
title: wintering records LK Italy

description: Distribution of wintering records of Falco naumanni in Italy updated to 2014/2015 winter
DOI: 10.5061/dryad.jq87d/2
title: colonies LK Italy

description: Distribution of known colonies of Falco naumanni in Italy between the 2000 and 2015 breeding seasons
DOI: 10.5061/dryad.k9m17/1
title: Iheed poster

description: Poster which outlined the study and was used in conference proceedings
DOI: 10.5061/dryad.k9m17/2
title: Abstraction collation

description: The abstraction information for the 23 included papers in our scoping review
DOI: 10.5061/dryad.rs806/1
title: SNPdata
DOI: 10.5061/dryad.rs806/2
title: Sequence data

description: original sequence data
DOI: 10.5061/dryad.s64sg/1
title: Summary datasets (main and supplementary data).

description: Excel document including three different datasets in separate sheets. The main dataset (dataset1) includes the participants' first looks towards the reward-predictive cue (analyses reported in the results section). The second dataset (dataset2) includes the participants' looking time at pre-test and post-test as well as other additional measures (analyses reported in the electronic supplementary material). Finally, the third dataset (dataset3) includes the ratings of the non-social stimuli, from a group of participants different from the participants taking part in the main experiment (analyses reported in the method section).
DOI: 10.5061/dryad.tq106/2
title: Lung-DAP-February3-2017

description: This file contains data abstracted from medical records including: patient characteristics (age, gender), type of procedure that confirmed the diagnostic result (imaging with computed tomography of the chest; biopsy with fine needle aspiration, bronchoscopy or open biopsy; staging with positron emission tomography or magnetic resonance imaging); and results (positive for cancer, negative for cancer, still suspicious requiring follow-up). Recorded dates included: referral (month and week when referral form received by DAP), confirmatory procedure (month and week when confirmatory diagnostic procedure performed), diagnosis (month and week when finding was recorded in patient record), and consult (month and week of meeting with patient to discuss treatment or follow-up plan)
DOI: 10.5061/dryad.vj12j/1
title: Model_implementation

description: MATCONT model implementation
DOI: 10.5061/dryad.2p57p/1
title: Glycoside Hydrolase Family 63 nucleotide sequences

description: Fasta file with nucleotide sequences of Glycoside Hydrolase Family 63 protein from different fungal strains. In the file the following information of each sequence can be found:
-organism
-mol_type= type of molecule
-tissue_type=origin of the fungal material
-country=country:location
-clone=name of the strain in the fungal collection
The consensus assembling of forward and reverse sequences was made using SeqMan 7v7.0.0
DOI: 10.5061/dryad.31048.1
title: Data from: Combined analysis of extant Rhynchonellida (Brachiopoda) using morphological and molecular data
DOI: 10.5061/dryad.31048.1/20.1
title: README

description: README file describes the file type and contents of all files in this data repository.
DOI: 10.5061/dryad.31048.1/3.1
title: runScripts.zip

description: Zip file containing a necessary directory for recreating analyses
DOI: 10.5061/dryad.31048.1/4.1
title: datafiles.zip

description: Zip file containing a necessary directory for recreating analyses
DOI: 10.5061/dryad.31048.1/5.1
title: make_runI_06-29-15

description: R Script for creating MrBayes script for simulation-based sensitivity analyses
DOI: 10.5061/dryad.31048.2/14.2
title: Appendix_4_05-11-17

description: Table giving the number of taxa having each character state (or coded as missing) for each morphological character in the revised matrix.
DOI: 10.5061/dryad.31048.2/16.2
title: Appendix_5_05-11-17

description: List of the 40 extant rhynchonellide species (modified from Logan 2007; Bitner 2009).
DOI: 10.5061/dryad.31048.2/6.2
title: Appendix_3_05-11-17

description: Information on DNA specimens used in Cohen and Bitner (2013) and their respective Genbank accession numbers, taken from their Table 1.
DOI: 10.5061/dryad.407c5/1
title: Lesser snow goose helminths

description: Parasite counts (by parasite species), sex ('SEX'), age ('AGE') and location of collection ('SAMPL') of each (row) host lesser snow goose bird. Parasite species: HD = Heterakis dispar; TT = Trichostrongylus tenuis; DL = Drepanidotaenia lanceolata; DB = Drepanidotaenia barrowensis; CA = Capillaria anatis; SG = Sobolevicanthus gracilis; ER = Echinostoma revolutum; CL = Cladogyna longivaginata; PC = Platyscolex ciliata.
DOI: 10.5061/dryad.46d37/1
title: Sperm performance and fertilization in jack and hooknose Chinook salmon

description: Data sheet 1: Male metrics: Includes sperm metrics (velocity in water, velocity in ovarian fluid and sperm density) as well as paternity success (water and ovarian fluid) for each male. Data sheet 2: Difference between males: Includes differences between males in a pair (Jack vs. Hooknose) for sperm density, sperm velocity (water and ovarian fluid), paternity, relatedness between mates and amino acid divergence (MHC II B1) between mates. Data sheet 3: Relatedness and AA divergence: Relatedness and amino acid divergence for all male-female combinations used in the study. Data sheet 4: Genotypes: Microsatellite and MHC II B1 genotypes. Data sheet 5: MH sequences: DNA sequence and GenBank reference for six MHC II B1 alleles found in the study.
DOI: 10.5061/dryad.52650/1
title: Database S1 - Database of selection coefficients

description: Database of selection coefficients and associated trait, fitness, and location information. The first two columns describe the columns in the data set.
DOI: 10.5061/dryad.52650/2
title: Database S2 - Database of climatic factors.

description: Database of climatic factors. The first two columns describe the columns in the data set.
DOI: 10.5061/dryad.57917/2
title: Bacterial virulence data

description: Survival (h) of zebra fish (Danio rerio) and rainbow trout (Oncorhynchus mykiss) infected with the high-virulence strain (B185), low-virulence strain (B398) or the high-virulence strain (B067) of F. columnare
DOI: 10.5061/dryad.5t76p/1
title: Dataset_Wang et al. 2017

description: The file contains all the original data including the temperature, relative humidity, litter mass remaining, litter DOC concentrations and cumulative C loss.
DOI: 10.5061/dryad.6806c/1
title: Ratiometric kymographs of growing pollen tubes

description: Kymographs of Arabidopsis pollen tubes growing in vitro, featuring two channels (YFP and CFP) of the genetically encoded ratiometric calcium probe YC3.6.
DOI: 10.5061/dryad.6806c/2
title: MetaMorph tracking of the pollen tube tip

description: Tracking and growth rate series of the of the same growing pollen tubes where the ratiometric kymographs where extracted, performed with the 'Track Object' routine in MetaMorph with 3 different ROI sizes.
DOI: 10.5061/dryad.6806c/3
title: Synchronized oscillations in growth, H+ flux and intracellular Ca2+

description: Growth rate series from a tracking software (MetaMorph) is provided, together with a kymograph with fluorescence of a calcium reporter (Yellow Cameleon 3.6) and extracellular H+ flux measurements at the pollen tube tip from an ion-selective vibrating probe. A video with the tracking trace also used as midline to produce the kymograph is also included.
DOI: 10.5061/dryad.68fn0/5
title: ND2_File

description: ND2_File: Bee hummingbirds sequences of nicotinamide dehydrogenase 9 subunit 2 (mtDNA).
DOI: 10.5061/dryad.68fn0/6
title: ND4_File

description: ND4_File: Bee hummingbirds sequences of nicotinamide dehydrogenase subunit 4 (mtDNA).
DOI: 10.5061/dryad.68n40/1
title: Matrix_Multivariate_Mega

description: The matrix of OTUs (specimens) used in the analysis
DOI: 10.5061/dryad.72v34/1
title: Potency Data

description: See ReadMe file
DOI: 10.5061/dryad.72v34/2
title: Mouse Neutralization Data

description: See ReadMe file
DOI: 10.5061/dryad.74f2r.2/20.2
title: Maximum clade credibility tree of FBDl age range

description: This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the fossilized birth-death analysis using 21 fossils, resulting from the beast2 analysis using the FBDl_ageRange.xml input-file.
DOI: 10.5061/dryad.74f2r.2/21.2
title: Subsample of trees from FBDl "age range" analysis

description: This is a set of 1401 subsampled random trees from the posterior distribution of the fossilized birth-death analysis using 21 fossils (see FBDl_ageRange.xml file for detailed settings of the Bayesian analysis).
DOI: 10.5061/dryad.74f2r.2/22.2
title: Input file for FBDl "age range" analysis

description: This is the XML file which configures all parameters for the beast2 program for the Bayesian MCMC analysis using the fossilized birth-death dating approach including 21 fossils, based on an "age range" dating approach (FBDl_ageRange). The file was generated in BEAUti 2.3.1.
DOI: 10.5061/dryad.74f2r.2/23.2
title: Maximum clade credibility tree of FBDs age range

description: This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the fossilized birth-death analysis using 14 fossils, resulting from the beast2 analysis using the FBDs_ageRange.xml input-file.
DOI: 10.5061/dryad.74f2r.2/24.2
title: Subsample of trees from FBDs "age range" analysis

description: This is a set of 1401 subsampled random trees from the posterior distribution of the fossilized birth-death analysis using 14 fossils (see FBDs_ageRange.xml file for detailed settings of the Bayesian analysis).
DOI: 10.5061/dryad.74f2r.2/25.2
title: Input file for FBDs "age range" analysis

description: This is the XML file which configures all parameters for the beast2 program for the Bayesian MCMC analysis using the fossilized birth-death dating approach including 14 fossils, based on an "age range" dating approach (FBDs_ageRange). The file was generated in BEAUti 2.3.1.
DOI: 10.5061/dryad.74f2r.2/26.2
title: Maximum clade credibility tree of NDus

description: This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the node dating analysis using 12 fossils (based on an uniform density prior), resulting from the beast2 analysis using the NDus.xml input-file.
DOI: 10.5061/dryad.74f2r.2/27.2
title: Subsample of trees from NDus analysis

description: This is a set of 1401 subsampled random trees from the posterior distribution of the node dating analysis using 12 fossils (see NDus.xml file for detailed settings of the Bayesian analysis).
DOI: 10.5061/dryad.78v5j/1
title: README

description: README for all files
DOI: 10.5061/dryad.78v5j/2
title: mammals data

description: All mammal classification data.
DOI: 10.5061/dryad.78v5j/3
title: references

description: List of references used to classify all mammal species. References are cited by number in the mammals_data.csv file.
DOI: 10.5061/dryad.78v5j/4
title: workspace

description: R script that loads data (including some sources listed in the manuscript but not contained here, such as phylogenies and Red Listing data) for subsequent analysis.
DOI: 10.5061/dryad.78v5j/5
title: analyses

description: R script to carry out all analyses as described in the manuscript. Note that the script, as it stands currently, assumes that 24 processors are available on your computer - you may want to change this.
DOI: 10.5061/dryad.78v5j/6
title: processing

description: R script to summarise analyses carried out.
DOI: 10.5061/dryad.9480j/1
title: Raw 454 reads and mapping files for aquatic fungal communities in Scandinavian lakes

description: This zip-file contains: 1) raw reads from 454 Roche sequencing machine (.sff) 2) qual file (.qual) 3) raw reads (.fna) 4) flowgram file (.flow) 5) mapping file for forward reads (.txt) and 6) mapping file for reverse reads (.txt). In forward mapping file forward primer is the linker primer and in reverse mapping file reverse primer is the linker primer to recover all reads from the mixed orientation raw data.
DOI: 10.5061/dryad.f6rc2/1
title: qPCR_hemocytes_evolexp
DOI: 10.5061/dryad.f6rc2/2
title: qPCR_nerve_cord_evolexp
DOI: 10.5061/dryad.f6rc2/3
title: qPCR_ovaries_evolexp
DOI: 10.5061/dryad.f6rc2/4
title: hemocytes_infected_proportion_evolexp
DOI: 10.5061/dryad.f6rc2/5
title: mortalities_histogram_evolexp
DOI: 10.5061/dryad.f6rc2/6
title: survival_curves_evolexp
DOI: 10.5061/dryad.gc3k5/11
title: Raw sediment analysis results

description: The analyses in this file form the bases for subsequent construction of the sediment-related ecological variables Sd = sediment type, and Sc = weight percent fraction of sand, which are ordinal.
DOI: 10.5061/dryad.gc3k5/12
title: Categorisation of sediment-related ecological variables

description: This file explains how the ordinal scales of the sediment-related ecological variables were ascertained for each sampling site, based on the results of the raw sediment analysis.
DOI: 10.5061/dryad.gc3k5/9
title: Mudskipper project R codes I

description: Major R codes for reproducing analyses in the manuscript.
DOI: 10.5061/dryad.h1157/12
title: Figure S5

description: Data for figures S5
DOI: 10.5061/dryad.h3fj0/1
title: APEX 1203

description: APEX model executable, version 1203
DOI: 10.5061/dryad.h3fj0/2
title: APEX1203 prairie simulation-Hays KS

description: The zipped archive contains all of the input files used to run the APEX 1203 model for the various scenarios referenced in the journal article.
DOI: 10.5061/dryad.n1t72
title: Dryad Item 10.5061/DRYAD.N1T72
DOI: 10.5061/dryad.p2c6r/1
title: Demographic data of Cayo Santiago female rhesus

description: Demographic data of Cayo Santiago female rhesus macaques. The data set includes a reference ID, date of birth, date of death and/or date of removal from Cayo Santiago, mom reference ID, and age at delivery of females alive during the period from 1973 to 2013. Original IDs were replaced by dummy codes. The data was collected by staff of the Caribbean Primate Research Center, University of Puerto Rico, and shared to the authors.
DOI: 10.5061/dryad.p2c6r/2
title: Annual projection matrices R

description: Absorbing annual matrices *R* of Cayo Santiago female rhesus macaques. Annual matrices were parameterized with demographic data of female rhesus macaques from 1973 to 2013.
DOI: 10.5061/dryad.sd640/1
title: Maculinea alcon microsatellite data

description: The file Maculinea alcon microsatellite data includes the data from 12 microsatellites for 398 unique genotypes of Maculinea alcon from in total 14 sampling locations located in Belgium and The Netherlands. The data matrix also include the spatial coordinates of each sampled population, given in the two last columns.
DOI: 10.5061/dryad.tn36j/1
title: dryad_dolphin_data

description: Data - dolphins
DOI: 10.5061/dryad.tn36j/2
title: dryad_dolphin_availability

description: Availability file for dolphin model
DOI: 10.5061/dryad.tn36j/3
title: digidolph

description: R code for creation of null model - dolphins
DOI: 10.5061/dryad.tn36j/4
title: digidolph_helper_functions

description: R code - custom functions for use with creation of dolphin model
DOI: 10.5061/dryad.tn36j/5
title: dragon_data_dryad
DOI: 10.5061/dryad.v6q20/1
title: jess's data reanalysis
DOI: 10.5061/dryad.v6q20/3
title: alldata
DOI: 10.5061/dryad.vj12j/2
title: Cannibalistic_preference_estimates

description: Cannibalistic preference estimates from the literature used in generating figure 2.
DOI: 10.5061/dryad.12546/1
title: Phylogenetic matrix (164 species dataset)

description: Phylogenetic matrix containing aligned DNA sequences for 95 nuclear coding loci (88,302 bp) for 164 species of frogs, including details on character partitions and best-fit models of evolution for the partitions.
DOI: 10.5061/dryad.12546/2
title: Phylogenetic matrix (309 species dataset)

description: Phylogenetic matrix containing aligned DNA sequences for 95 nuclear coding loci (88,386 bp) for 309 species of frogs, including details on character partitions and best-fit models of evolution for the partitions.
DOI: 10.5061/dryad.2nd65/1
title: Cowl Female population agonism

description: The CSV file contains all of the data used in the manuscript. All capitalised brain and body values belong to the same dataset. The same for lowercase brain and body values.
DOI: 10.5061/dryad.31048.1/10.1
title: figures_rhynchComb_08-03-16

description: R script for generating all figures in manuscript from provided R workspace file
DOI: 10.5061/dryad.31048.1/11.1
title: figures_for_EvolTalk_06-20-16

description: R script for generating all figures in associated Evolution 2016 from provided R workspace file
DOI: 10.5061/dryad.31048.1/12.1
title: SuppTable1_contraTable

description: Supplemental Table 1 as a PDF, reporting pair-wise CDs between considered summary topologies.
DOI: 10.5061/dryad.31048.1/13.1
title: SuppMat_allTreesPlotted_suppFigures

description: PDF Supplementary Material containing plots of all summary trees considered in this paper, with associated support values.
DOI: 10.5061/dryad.31048.1/17.1
title: write_simple_sumt_01-16-17

description: Revised script for obtaining the simple summary tree files from MrBayes
DOI: 10.5061/dryad.31048.1/7.1
title: rhynchComb_07-25-16

description: Rmarkdown script containing all topological comparison analyses
DOI: 10.5061/dryad.31048.1/8.1
title: rhynchComb_07-25-16

description: PDF generated from knitting Rmarkdown script containing all topological comparison analyses
DOI: 10.5061/dryad.31048.1/9.1
title: rhynchComb_workspace_07-25-2016.Rdata

description: Saved R Workspace from running Rmarkdown script containing all topological comparison analyses
DOI: 10.5061/dryad.350v2/1
title: Supplementary Information

description: Additional information on the methodology and results.
DOI: 10.5061/dryad.350v2/2
title: SD1

description: Taxon scores for measured biomechanical characters, body mass data, and ages.
DOI: 10.5061/dryad.350v2/3
title: SD2

description: Full results from fitting single-rate models of evolution of craniodental and body mass evolution across 1000 dated trees.
DOI: 10.5061/dryad.350v2/4
title: SD3

description: Results from fitting two-rate models of character evolution across 1000 dated trees.