cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2601h/5
title: CFD simulation file for Parvancorina minchami from South Australia, original relief, oriented at 90° to the current, MPH format

description: Computational fluid dynamics (CFD) simulations of water flow were performed in COMSOL. A model of Parvancorina minchami from South Australia with original relief was oriented at 90° to the current and was fixed to the lower surface of a half-cylinder. Three-dimensional, incompressible flow of water was simulated with a normal inflow velocity inlet at the upstream end of the half-cylinder and a zero-pressure outlet at the downstream end. Slip boundary conditions were assigned to the top and sides of the half-cylinder, and no-slip boundary conditions were assigned to the Parvancorina model and the lower surface of the half-cylinder. The domain was meshed using free tetrahedral elements and the shear stress transport turbulence model was used to solve the Reynolds-averaged Navier–Stokes equations. A stationary solver was used to compute the steady-state flow patterns. Simulations were performed with an inlet velocity of 0.1, 0.2, and 0.5 m/s.
DOI: 10.5061/dryad.2601h/6
title: CFD simulation file for Parvancorina minchami from South Australia, original relief, oriented at 180° to the current, MPH format

description: Computational fluid dynamics (CFD) simulations of water flow were performed in COMSOL. A model of Parvancorina minchami from South Australia with original relief was oriented at 180° to the current and was fixed to the lower surface of a half-cylinder. Three-dimensional, incompressible flow of water was simulated with a normal inflow velocity inlet at the upstream end of the half-cylinder and a zero-pressure outlet at the downstream end. Slip boundary conditions were assigned to the top and sides of the half-cylinder, and no-slip boundary conditions were assigned to the Parvancorina model and the lower surface of the half-cylinder. The domain was meshed using free tetrahedral elements and the shear stress transport turbulence model was used to solve the Reynolds-averaged Navier–Stokes equations. A stationary solver was used to compute the steady-state flow patterns. Simulations were performed with an inlet velocity of 0.1, 0.2, and 0.5 m/s.
DOI: 10.5061/dryad.2601h/7
title: CFD simulation file for Parvancorina minchami from South Australia, relief increased by 15%, oriented at 0° to the current, MPH format

description: Computational fluid dynamics (CFD) simulations of water flow were performed in COMSOL. A model of Parvancorina minchami from South Australia with relief increased by 15% was oriented at 0° to the current and was fixed to the lower surface of a half-cylinder. Three-dimensional, incompressible flow of water was simulated with a normal inflow velocity inlet at the upstream end of the half-cylinder and a zero-pressure outlet at the downstream end. Slip boundary conditions were assigned to the top and sides of the half-cylinder, and no-slip boundary conditions were assigned to the Parvancorina model and the lower surface of the half-cylinder. The domain was meshed using free tetrahedral elements and the shear stress transport turbulence model was used to solve the Reynolds-averaged Navier–Stokes equations. A stationary solver was used to compute the steady-state flow patterns. Simulations were performed with an inlet velocity of 0.1, 0.2, and 0.5 m/s.
DOI: 10.5061/dryad.2601h/8
title: CFD simulation file for Parvancorina minchami from South Australia, relief increased by 15%, oriented at 90° to the current, MPH format

description: Computational fluid dynamics (CFD) simulations of water flow were performed in COMSOL. A model of Parvancorina minchami from South Australia with relief increased by 15% was oriented at 90° to the current and was fixed to the lower surface of a half-cylinder. Three-dimensional, incompressible flow of water was simulated with a normal inflow velocity inlet at the upstream end of the half-cylinder and a zero-pressure outlet at the downstream end. Slip boundary conditions were assigned to the top and sides of the half-cylinder, and no-slip boundary conditions were assigned to the Parvancorina model and the lower surface of the half-cylinder. The domain was meshed using free tetrahedral elements and the shear stress transport turbulence model was used to solve the Reynolds-averaged Navier–Stokes equations. A stationary solver was used to compute the steady-state flow patterns. Simulations were performed with an inlet velocity of 0.1, 0.2, and 0.5 m/s.
DOI: 10.5061/dryad.2601h/9
title: CFD simulation file for Parvancorina minchami from South Australia, relief increased by 15%, oriented at 180° to the current, MPH format

description: Computational fluid dynamics (CFD) simulations of water flow were performed in COMSOL. A model of Parvancorina minchami from South Australia with relief increased by 15% was oriented at 180° to the current and was fixed to the lower surface of a half-cylinder. Three-dimensional, incompressible flow of water was simulated with a normal inflow velocity inlet at the upstream end of the half-cylinder and a zero-pressure outlet at the downstream end. Slip boundary conditions were assigned to the top and sides of the half-cylinder, and no-slip boundary conditions were assigned to the Parvancorina model and the lower surface of the half-cylinder. The domain was meshed using free tetrahedral elements and the shear stress transport turbulence model was used to solve the Reynolds-averaged Navier–Stokes equations. A stationary solver was used to compute the steady-state flow patterns. Simulations were performed with an inlet velocity of 0.1, 0.2, and 0.5 m/s.
DOI: 10.5061/dryad.2r12j/1
title: Tsuga_in_30iv17

description: needle morphology database
DOI: 10.5061/dryad.2r12j/2
title: Tsuga__4CL_comb_13vi16_Dryad

description: 4CL two loci combined
DOI: 10.5061/dryad.2r12j/3
title: Tsuga__4CL_loci_separate_8vi16_Dryad

description: 4CL two loci separate
DOI: 10.5061/dryad.2r12j/4
title: Tsuga__cpDNA_8vi16_Dryad

description: whole chloroplast genomes
DOI: 10.5061/dryad.41pr0/3
title: Behavior_transition_networks

description: Raw behavior transition matrices used to calculate escalation rate from approach to head-to-head-interaction.
DOI: 10.5061/dryad.5g205/1
title: supFile-all_trees_2017-07-01

description: Final trees from all analyses in nexus format.
DOI: 10.5061/dryad.5g205/2
title: Alignments of individual UCE loci

description: Individual alignments of UCE loci in nexus format.  Loci were aligned using MAFFT and trimmed wtih Gblocks.
DOI: 10.5061/dryad.5g205/3
title: Individual gene trees from UCE loci

description: Individual gene trees per UCE locus were generated using RAxML's GTRGAMMA model of nucleotide evolution and fast bootstrapping options (replicates=1,000).  Individual trees are in Newick format.
DOI: 10.5061/dryad.5g205/4
title: assembled_contigs_from_UCEenriched_reads

description: All loci assembled from baited reads (per taxa).  These sequences were then compared in an all-vs-all manner to identify homologous UCE loci among taxa.  As a results, there are some contigs that may not be present in the final alignments  since they are not UCE loci.
DOI: 10.5061/dryad.5g205/5
title: Sup Fig 1. Phylogenetic content of UCE loci based on length.

description: The length of a UCE locus is correlated with the number of phylogenetically informative characters. UCE loci were sorted by length and ten bins of alignments were created so that the shortest loci were combined into one alignment, the next shortest set of loci were combined … etc. Parsimony informative characters made up a minor part of each alignment.
DOI: 10.5061/dryad.675bg/1
title: README File

description: General introduction to all the data files used in this publication
DOI: 10.5061/dryad.675bg/2
title: Figure 1 ArcGIS files

description: This zipped folder includes contains all the information used to create figure one. It is in ArcGIS format (shape files) and includes both polygons and points. The files included give the locations of the used area, the unused area, and all the palm and soil samples collected.
DOI: 10.5061/dryad.675bg/3
title: Palm biochemical analyses

description: This file includes the biochemical analyses and locations of all the palm samples from both the used and unused areas. The palm species involved include: Attalea butyracea, Attalea phalerata, Euterpes precatoria, Mauritia flexuosa
DOI: 10.5061/dryad.675bg/4
title: Soil analysis data

description: This file includes the physical characteristics, biochemical analyses, and locations of the soil samples from both the used and unused areas.
DOI: 10.5061/dryad.68177/1
title: Alignment in nexus Format of Ipomoea taxa

description: Alignment of Ipomoea taxa relevant to circumscription of new taxa in nexus format.
DOI: 10.5061/dryad.716kr/1
title: repository to reproduce analysis (includes data)

description: Code (Analysis.R) and data (in folder data_) to reproduce a paper about response and effect traits.

Main data is in three files:

specimens.csv: Data on specimens collected per site
gis.csv: Data on landscape characteristics per sites. Can be combined with specimens.csv by site.
traits.csv: Data on ecological traits at species level. Can be combined with specimens by genus and species.
DOI: 10.5061/dryad.7n731/12
title: List of locations of the gathering events 2009

description: List of the locations of all gathering events in 2009. Each entry corresponds to a column in the "individual by gathering event matrix 2009". The values correspond to the rows and columns in the "spatial distance matrix" and the rows in the "eigen vectors of the spatial weighting matrix".
DOI: 10.5061/dryad.7n731/13
title: Spatial distance matrix

description: The spatial distances between all feeding stations (in meters). Rows and columns correspond to the locations of the feeding stations, i.e. the values in the "list of locations of gathering events 2007/2008/2009" files.
DOI: 10.5061/dryad.7n731/14
title: Distance based Moran's Eigenvector Maps

description: The distance based Moran's Eigenvector Maps (db-MEMs) for all feeding stations. Rows correspond to the feeding station locations and columns to the 20 Eigenvectors.
DOI: 10.5061/dryad.7n731/15
title: Asymmetric Eigenvector Maps 2007

description: The Asymmetric Eigenvector Maps for the gathering events in 2007. Rows correspond to the gathering events and columns to the first 500 Eigenvectors.
DOI: 10.5061/dryad.7n731/16
title: Asymmetric Eigenvector Maps 2008

description: The Asymmetric Eigenvector Maps for the gathering events in 2008. Rows correspond to the gathering events and columns to the first 500 Eigenvectors.
DOI: 10.5061/dryad.7n731/17
title: Asymmetric Eigenvector Maps 2009

description: The Asymmetric Eigenvector Maps for the gathering events in 2009. Rows correspond to the gathering events and columns to the first 500 Eigenvectors.
DOI: 10.5061/dryad.7nb8q/1
title: Apis_mellifera_amplicon_bisulfite_sequencing_queen_1

description: Amplicon bisulfite sequencing reads from Apis mellifera newly-emerged queen brains (5 pooled brains). Archive contains four Illumina Miseq libraries (paired end).
DOI: 10.5061/dryad.7nb8q/2
title: Apis_mellifera_amplicon_bisulfite_sequencing_queen_2

description: Amplicon bisulfite sequencing reads from Apis mellifera newly-emerged queen brains (5 pooled brains). Archive contains four Illumina Miseq libraries (paired end).
DOI: 10.5061/dryad.7nb8q/3
title: Apis_mellifera_amplicon_bisulfite_sequencing_queen_3

description: Amplicon bisulfite sequencing reads from Apis mellifera newly-emerged queen brains (5 pooled brains). Archive contains four Illumina Miseq libraries (paired end).
DOI: 10.5061/dryad.7nb8q/4
title: Apis_mellifera_amplicon_bisulfite_sequencing_worker_1

description: Amplicon bisulfite sequencing reads from Apis mellifera newly-emerged worker brains (5 pooled brains). Archive contains four Illumina Miseq libraries (paired end).
DOI: 10.5061/dryad.7nb8q/5
title: Apis_mellifera_amplicon_bisulfite_sequencing_worker_2

description: Amplicon bisulfite sequencing reads from Apis mellifera newly-emerged worker brains (5 pooled brains). Archive contains four Illumina Miseq libraries (paired end).
DOI: 10.5061/dryad.7rr7m/1
title: Summary_Data

description: "Summary_Data.csv" is a comma-separated (.csv) file summarizing population-average (flask-level) measurements.
DOI: 10.5061/dryad.7rr7m/2
title: behavior_data

description: "behavior_data.dat" is a comma-separated file containing behavior data from PIV measurements.
DOI: 10.5061/dryad.8cs37/4
title: Jakobsen's Beach Cichlid Community Matrix
DOI: 10.5061/dryad.8cs37/5
title: Gombe Stream National Park Cichlid Community Matrix
DOI: 10.5061/dryad.8cs37/6
title: Mahale Mountain National Park S1 Cichlid Community Matrix
DOI: 10.5061/dryad.8cs37/7
title: Mahale Mountain National Park S2 Cichlid Community Matrix
DOI: 10.5061/dryad.9k9n0/1
title: README

description: instructions
DOI: 10.5061/dryad.9k9n0/2
title: elab_video.zip

description: the whole pre-elaborated dataset (i.e., whisker shape has been extracted from videos through time). to unzip please note that it is needed the whole file list  in the same folder of unzipData.sh, where the file list is {elab_video.zip elab_video.z01  elab_video.z03  elab_video.z05  elab_video.z07 elab_video.z02  elab_video.z04  elab_video.z06}
DOI: 10.5061/dryad.bj5k0/1
title: protaxscripts

description: Directory containing perl scripts used to run PROTAX
DOI: 10.5061/dryad.bj5k0/2
title: mammal16S_OTU

description: Fasta file containing all mammal 16S OTU sequences
DOI: 10.5061/dryad.bj5k0/3
title: mammal12S_OTU

description: Fasta file containing all mammal 12S OTU sequences
DOI: 10.5061/dryad.bj5k0/4
title: mammal16S_refseqs

description: Fasta file containing mammal 16S reference sequences used in training PROTAX
DOI: 10.5061/dryad.m94f4/8
title: SNPs generated with hyRAD-X aligned against Abies alba transcriptome using VCFtools
DOI: 10.5061/dryad.nj1bp/13
title: Supplementary Table S7
DOI: 10.5061/dryad.nj1bp/14
title: Appendix1_FossilsforBeast
DOI: 10.5061/dryad.nj1bp/15
title: Appendix2_Phylo
DOI: 10.5061/dryad.nj1bp/18
title: SFigS1_SuperTree

description: Supplementary Figure S1. Musteloid supertree using the MRP (matrix representation with parsimony) matrix implemented in Clann.
DOI: 10.5061/dryad.nj1bp/19
title: SFigS2_BEAST_Tree_PA

description: Supplementary Figure S2. Time-calibrated phylogenetic tree (“pruned-after”) of Musteloidea. Mean divergence times estimated using a relaxed molecular clock model on the complete 46 gene dataset with 74 fossil priors. Blue bars across nodes indicate 95% confidence intervals around the mean divergence time estimates. Posterior estimates of mean and 95% HPD of divergence times are presented in Supplementary Table S7. Nodes are numbered (1–74, same as Figure 1). Outgroup taxa were pruned from the tree, and geological time scale is shown below the tree.
DOI: 10.5061/dryad.nj1bp/20
title: SFigS3_DivRate_PA
DOI: 10.5061/dryad.nj1bp/23
title: Appendix3
DOI: 10.5061/dryad.q4b78/1
title: Day 3 003_srgb_1_to_day2 083_srgb_5_human

description: contains the L*a*b* and Gabor filter outputs of all 505 samples of bark, as seen by Human visual systems. Filename+photo= Name of image. rep= number of sample from each image (5 for each image). L= L value of L*a*b*, a= a value of L*a*b*, b= b value of L*a*b*. fxoy= f: the gabor filter’s spatial frequency (1-4 from fine to coarse), o: the gabor filter’s orientation (1-6 from 0 to 150° in 30° increments)
DOI: 10.5061/dryad.q4b78/2
title: Day 3 003_srgb_1_to_day2 083_srgb_5_bird

description: contains the L*a*b* and Gabor filter outputs of all 505 samples of bark, as seen by Bird visual systems. Filename+photo= Name of image. rep= number of sample from each image (5 for each image). L= L value of L*a*b*, a= a value of L*a*b*, b= b value of L*a*b*. fxoy= f: the gabor filter’s spatial frequency (x=1-4 from fine to coarse), o: the gabor filter’s orientation (y=1-6 from 0 to 150° in 30° increments)
DOI: 10.5061/dryad.q4b78/3
title: Survival Experiment

description: contains all the data from the field experiment. Columns: Block= number of block, Treatment: A= treatment with common colours and textures, B: uncommon colours and textures, C: Uncommon colour but common texture, D: Common colour but uncommon texture. Replicate= the number of the sample in each treatment. Time: Hours of survival of each target. Censor= 1: Successful predation by bird, 0: censored data (not taken by bird). Notes= Cause of target’s removal.
DOI: 10.5061/dryad.q4b78/4
title: bark_RGBnTextures (human exp)

description: Contains the RGB and Gabor filter outputs of the backgrounds used in the human experiment. Filename= Name of image file. photo=name of bark, rep= number of sample from each image (5 for each image). R= R value of RGB, G= G value of RGB, B= B value of RGB. fxoy= f: the gabor filter’s spatial frequency (1-4 from fine to coarse), o: the gabor filter’s orientation (1-6 from 0 to 150° in 30° increments)
DOI: 10.5061/dryad.q4b78/5
title: target_RGBnTextures (human exp)

description: Contains the RGB and Gabor filter outputs of the targets extracted from the backgrounds that were used in the human experiment. Filename= Name of image file. photo=name of target, rep= number of sample from each image (5 for each image). R= R value of RGB, G= G value of RGB, B= B value of RGB. fxoy= f: the gabor filter’s spatial frequency (1-4 from fine to coarse), o: the gabor filter’s orientation (1-6 from 0 to 150° in 30° increments)
DOI: 10.5061/dryad.q4b78/6
title: KostasExptAll

description: Contains all the results taken from each participant during the Human experiment. Filename: name of test image. infile: name of background from where the target was extracted. infile2= name background. blank=blank column. filenum= the number of the stimuli+background combination. mothsource= the number of the moth (1-48). barksource= the number of the bark (1-48). cutrow= the row of the image from which the target was taken. cutcol= the column of the image from which the target was taken. pasterow= the row of the background image on which the target was placed. pastcol= the column of the background image on which the target was placed.
DOI: 10.5061/dryad.s402q/1
title: Rydell et al. Age of enlightenment. Supplementary data.

description: Basic data data on churches. Frequency of bat occurrence and information on lights and renovations.
DOI: 10.17632/42snjh2rs6.2
title: Data from: Glue protein production can be triggered by steroid hormone signaling independent of the developmental program in Drosophila melanogaster

description: Glue protein production can be triggered by steroid hormone signaling independent of the developmental program in Drosophila melanogaster
DOI: 10.17632/8dsvswkzft.2
title: Supplementary data

description: Phylogenetic tree
DOI: 10.5061/dryad.12758/7
title: qPCR.Tm.Data

description: qPCR melting curve data per plate, well, and cycle.
DOI: 10.5061/dryad.1f43v/1
title: Hill et al. Oikos

description: Presence-absence macroinvertebrate species list
DOI: 10.5061/dryad.2601h/12
title: CFD simulation file for Parvancorina minchami from South Australia, relief increased by 30%, oriented at 180° to the current, MPH format

description: Computational fluid dynamics (CFD) simulations of water flow were performed in COMSOL. A model of Parvancorina minchami from South Australia with relief increased by 30% was oriented at 180° to the current and was fixed to the lower surface of a half-cylinder. Three-dimensional, incompressible flow of water was simulated with a normal inflow velocity inlet at the upstream end of the half-cylinder and a zero-pressure outlet at the downstream end. Slip boundary conditions were assigned to the top and sides of the half-cylinder, and no-slip boundary conditions were assigned to the Parvancorina model and the lower surface of the half-cylinder. The domain was meshed using free tetrahedral elements and the shear stress transport turbulence model was used to solve the Reynolds-averaged Navier–Stokes equations. A stationary solver was used to compute the steady-state flow patterns. Simulations were performed with an inlet velocity of 0.1, 0.2, and 0.5 m/s.
DOI: 10.5061/dryad.2601h/13
title: CFD simulation file for null model of Parvancorina minchami from South Australia, MPH format

description: Computational fluid dynamics (CFD) simulations of water flow were performed in COMSOL. A null model of Parvancorina minchami from South Australia was fixed to the lower surface of a half-cylinder. Three-dimensional, incompressible flow of water was simulated with a normal inflow velocity inlet at the upstream end of the half-cylinder and a zero-pressure outlet at the downstream end. Slip boundary conditions were assigned to the top and sides of the half-cylinder, and no-slip boundary conditions were assigned to the Parvancorina model and the lower surface of the half-cylinder. The domain was meshed using free tetrahedral elements and the shear stress transport turbulence model was used to solve the Reynolds-averaged Navier–Stokes equations. A stationary solver was used to compute the steady-state flow patterns. Simulations were performed with an inlet velocity of 0.1, 0.2, and 0.5 m/s.
DOI: 10.5061/dryad.2601h/14
title: CFD simulation file for Parvancorina minchami from Russia, original relief, oriented at 0° to the current, MPH format

description: Computational fluid dynamics (CFD) simulations of water flow were performed in COMSOL. A model of Parvancorina minchami from Russia with original relief was oriented at 0° to the current and was fixed to the lower surface of a half-cylinder. Three-dimensional, incompressible flow of water was simulated with a normal inflow velocity inlet at the upstream end of the half-cylinder and a zero-pressure outlet at the downstream end. Slip boundary conditions were assigned to the top and sides of the half-cylinder, and no-slip boundary conditions were assigned to the Parvancorina model and the lower surface of the half-cylinder. The domain was meshed using free tetrahedral elements and the shear stress transport turbulence model was used to solve the Reynolds-averaged Navier–Stokes equations. A stationary solver was used to compute the steady-state flow patterns. Simulations were performed with an inlet velocity of 0.1, 0.2, and 0.5 m/s.
DOI: 10.5061/dryad.2601h/15
title: CFD simulation file for Parvancorina minchami from Russia, original relief, oriented at 90° to the current, MPH format

description: Computational fluid dynamics (CFD) simulations of water flow were performed in COMSOL. A model of Parvancorina minchami from Russia with original relief was oriented at 90° to the current and was fixed to the lower surface of a half-cylinder. Three-dimensional, incompressible flow of water was simulated with a normal inflow velocity inlet at the upstream end of the half-cylinder and a zero-pressure outlet at the downstream end. Slip boundary conditions were assigned to the top and sides of the half-cylinder, and no-slip boundary conditions were assigned to the Parvancorina model and the lower surface of the half-cylinder. The domain was meshed using free tetrahedral elements and the shear stress transport turbulence model was used to solve the Reynolds-averaged Navier–Stokes equations. A stationary solver was used to compute the steady-state flow patterns. Simulations were performed with an inlet velocity of 0.1, 0.2, and 0.5 m/s.