cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2601h/16
title: CFD simulation file for Parvancorina minchami from Russia, 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 Russia 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/17
title: CFD simulation file for Parvancorina minchami from Russia, 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 Russia 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/18
title: CFD simulation file for Parvancorina minchami from Russia, 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 Russia 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.36910/1
title: All provisioning and patch visitation data files

description: Data on food availability and patch visitation by individually identified red foxes, derived from camera trap surveys. Data are submitted as they were used for analyses in R, with separate CSV files for the different data types associated with the different analyses in the paper. Refer to the README.txt file for detailed descriptions of the column headings in each CSV file.
DOI: 10.5061/dryad.3d31q/1
title: Complete set of aligned UCE contigs

description: The file includes the complete set of 2448 aligned, untrimmed UCE contigs. The alignments are provided as individual files in FASTA format.
DOI: 10.5061/dryad.3d31q/3
title: Concatenated matrix of aligned UCE loci

description: The primary DNA sequence matrix analyzed in this study. The matrix contains 1672 aligned, filtered, and trimmed UCE loci. Includes by-locus character partitions.
DOI: 10.5061/dryad.3d31q/4
title: Data tables

description: The complete set of data tables included in the main text and supplemental materials of this study. Provided in csv and xlsx formats.
DOI: 10.5061/dryad.3d31q/5
title: BEAST xml data files

description: All BEAST xml data files used in this study. Includes one file for the 29 sample analysis, and two files for the 18 sample analyses (topologies 1 and 2).
DOI: 10.5061/dryad.3d31q/6
title: BioGeoBEARS analysis files

description: BioGeoBEARS analysis files for all of the Pseudomyrmex and Vachellia biogeographic analyses.
DOI: 10.5061/dryad.3d31q/7
title: Tree files

description: Main phylogenetic tree results provided in NEXUS and PDF formats. Includes best RAxML trees with bootstrap scores, ExaBayes consensus trees with posterior probabilities, ASTRAL species trees with bootstrap scores, and BEAST chronograms.
DOI: 10.5061/dryad.3d31q/8
title: Trait reconstruction analysis files

description: R scripts and trait data for inferring habitat and nesting ancestral states.
DOI: 10.5061/dryad.3d31q/9
title: Partition files in RAxML format

description: Partitioning schemes for by-locus, hcluster, and kmeans partitioned analyses. All files in RAxML-style format.
DOI: 10.5061/dryad.3hc80/1
title: RawData

description: Summary table of all colonies genotyped with relevant corresponding data, including microsatellite genotypes at twelve loci and phenotypes.
DOI: 10.5061/dryad.3t2d4/1
title: Jacobsen_Pool1_forward_reads

description: Bzip-compressed fastq-file containing raw sequences (forward reads) from Illumina HiSeq of pooled fungal DNA extracted from 103 samples (Pool1) of wood-inhabiting insects.
DOI: 10.5061/dryad.3t2d4/2
title: Jacobsen_Pool1_backward_reads

description: Bzip-compressed fastq-file containing raw sequences (backward reads) from Illumina HiSeq of pooled fungal DNA extracted from 103 samples (Pool1) of wood-inhabiting insects.
DOI: 10.5061/dryad.3t2d4/3
title: Jacobsen_mapping_file_DNA

description: Excel-file with tag/mid (molecular identifier) sequences, ITS-sequences, sample IDs for tags/mids and lists of repetitions and negatives.
DOI: 10.5061/dryad.3t2d4/4
title: Jacobsen_OTU_table_Fungal_Ecology

description: OTU-table with taxonomic annotation for OTUs and information on insect samples.
DOI: 10.5061/dryad.3t2d4/5
title: Jacobsen_Pool2_forward_reads_part1

description: First half of the bzip-compressed fastq-file containing raw sequences (forward reads) from Illumina HiSeq of pooled fungal DNA extracted from 98 samples (Pool2) of wood-inhabiting insects. Split with HJSplit as recommended by Dryad (http://wiki.datadryad.org/Large_File_Transfer).
DOI: 10.5061/dryad.472s0/1
title: Appendix 1. Complete taxon names, vouchers and Genbank accensions.
DOI: 10.5061/dryad.472s0/2
title: Appendix 2. Extended details of DNA and phylogenetic analyses.
DOI: 10.5061/dryad.472s0/3
title: Appendix 3. Morphological matrices
DOI: 10.5061/dryad.472s0/4
title: Appendix 4. Phylogenetic trees and its topology comparison.
DOI: 10.5061/dryad.4sd8p/1
title: Underlying data to PLOS ONE

description: The data file is in SPSS format (.dat file). It contains all data used for analyses in the manuscript, in addition to explanations of the different data fields and coding, all in English.
DOI: 10.5061/dryad.55636/1
title: Supplementary information_figure data

description: Data for Fig 6,7,8,9,10.
DOI: 10.5061/dryad.55h30/1
title: onlineAppendix1--locus_characteristics

description: Online Appendix 1.     Characteristics of loci used in anchored phylogenomics analyses after masking and trimming of alignments. AVE: average value for all loci, MIN: minimum value for all loci, MAX: maximum value for all loci, Locus#: locus identification number, New#: new number assigned to locus for this analysis (necessary because of paralogs), cov: average coverage across all species, ntax: number of taxa possessing the locus, flank%: percentage of total locus length estimated to be in the "flanking region", aveC: average number of copies of locus across species, before orthology filtering, maxC: maximum number of distinct copies of locus, before orthology filtering, len: alignment length, var: number of variable characters, pi: number of parsimony informative characters, GC%: percentage of GC across all non-gapped bases, amb%: percentage of ambiguous bases, miss%: percentage of missing data.
DOI: 10.5061/dryad.55h30/2
title: onlineAppendix2--saturationPlot

description: Online Appendix 2.     Saturation plot as calculated in DAMBE, showing GTR distance estimated for the ⅓ fastest-evolving sites in relation to the number of transitions and transversions at these sites. Regression lines (forced through the origin) and slope coefficients are shown. Dashed line indicates slope of 1.
DOI: 10.5061/dryad.55h30/3
title: onlineAppendix3--MPtree

description: Online Appendix 3.     Single shortest tree found in PAUP* maximum parsimony searches. Support as MP jackknife, and ACCTRAN branch lengths.
DOI: 10.5061/dryad.55h30/4
title: onlineAppendix4--MLtree

description: Online Appendix 4.     Maximum likelihood tree in RAxML searches. Support as ML bootstrap.
DOI: 10.5061/dryad.55h30/5
title: P0082_Final_NGS_matrix.nex

description: Concatenated sequence matrix.
DOI: 10.5061/dryad.675bg/5
title: Palm use by birds

description: This file contains the data on the numbers of birds feeding on each palm. It includes the raw scans that were done every 2.5 or 5 minutes throughout the study. This information was used to calculate the frequency of use of the palms by each parrot species.
DOI: 10.5061/dryad.675bg/6
title: Parrot count data

description: This file includes the daily summary data showing the number of groups of each species of parrot seen during the afternoon counts. This was used to obtain the relative abundance of each parrot species in the area.
DOI: 10.5061/dryad.675bg/7
title: Palm list and palm fate

description: Includes the breakdown of which palms were alive and which were dead in both 2007 and 2010. It also indicates which trees were alive in 2007 but dead by 2010.
DOI: 10.5061/dryad.7nb8q/6
title: Apis_mellifera_amplicon_bisulfite_sequencing_worker_3

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.8m70g/1
title: Grasshopper mouse acoustics in air and heliox.

description: Data for Figures 2 and 3. Acoustic properties of grasshopper mouse vocalizations produced in air and heliox.
DOI: 10.5061/dryad.9k9n0/10
title: ratto1.zip

description: one video trial shared for a whisker tracking demo, which can produce the data which is shared in elab_video folder. to unzip please note that it is needed the whole file list  in the same folder of unzipData.sh, where the file list is {ratto1.zip ratto1.z01}
DOI: 10.5061/dryad.9k9n0/11
title: ratto1.z01
DOI: 10.5061/dryad.9k9n0/3
title: elab_video.z01
DOI: 10.5061/dryad.9k9n0/4
title: elab_video.z02
DOI: 10.5061/dryad.9k9n0/5
title: elab_video.z03
DOI: 10.5061/dryad.9k9n0/6
title: elab_video.z04
DOI: 10.5061/dryad.9k9n0/7
title: elab_video.z05
DOI: 10.5061/dryad.9k9n0/8
title: elab_video.z06
DOI: 10.5061/dryad.9k9n0/9
title: elab_video.z07
DOI: 10.5061/dryad.bj5k0/10
title: protax_weighted_classify

description: BASH commands used to classify OTU sequences using weighted PROTAX model
DOI: 10.5061/dryad.bj5k0/11
title: BCI_sp_list

description: List of species known to be present on BCI
DOI: 10.5061/dryad.bj5k0/5
title: mammal12S_refseqs

description: Fasta file containing mammal 12S reference sequences used in training PROTAX
DOI: 10.5061/dryad.bj5k0/6
title: Mammalia_taxonomy

description: Full Linnean taxonomy of mammal species
DOI: 10.5061/dryad.bj5k0/7
title: protax_train

description: BASH commands used to train unweighted PROTAX model
DOI: 10.5061/dryad.bj5k0/8
title: protax_classify

description: BASH commands used to classify OTU sequences using unweighted PROTAX model
DOI: 10.5061/dryad.bj5k0/9
title: protax_weighted_train

description: BASH commands used to train weighted PROTAX model
DOI: 10.5061/dryad.bm5b6/1
title: Crossin_Devlin_Dryad_data

description: File presentes biological data for individual fish, experimental treatments, and burst swimming performance data.
DOI: 10.5061/dryad.bm5b6/2
title: Crossin_Devlin_transgenic_swimming

description: Data supporting a manuscript regarding the swimming capabilities of transgenic and non-transgenic rainbow trout.
DOI: 10.5061/dryad.bp462/1
title: alignments of placental mammals
DOI: 10.5061/dryad.bp462/2
title: maximum likelihood gene trees
DOI: 10.5061/dryad.bp462/3
title: mcmctree

description: The 3867 genes are divided into five quintiles according to DVMC values from the lowest to the highest. Then, randomly drew 60, 100 and 200 genes from each quintile, and replicated this procedure three times for each of the three gene-sets. For each of the 60, 100, and 200 gene sets, five different gene partitioning schemes: no partition; five partitions; ten partitions; twenty partitions; and each single gene as a separate partition.
DOI: 10.5061/dryad.c32hr/1
title: Tsuga mertensiana point locations/observations data set

description: Point locations (7480 unique) of Tsuga mertensiana obtained from various databases and references. Meta data including the data base source, collector, date of collection, location, latitude, longitude, and elevations are provided.
DOI: 10.5061/dryad.d4368/1
title: Additional File_M1
DOI: 10.5061/dryad.gn818/1
title: Yahdjian vegetation and litter decomposition data
DOI: 10.5061/dryad.gn818/2
title: Yahdjian vegetation and litter decomposition data
DOI: 10.5061/dryad.jd651/2
title: Sentinel data

description: Time and epoch indexed (rows) classifications of sleep/wake for each individual (columns).
DOI: 10.5061/dryad.jd651/3
title: R-code sentinel5b

description: Simulation R - code.
DOI: 10.5061/dryad.jd651/4
title: Circadian phase measure data

description: The model data used to analyze the drivers of circadian phase measure. Columns include the following variables: age, sex, subject ID.
DOI: 10.5061/dryad.n5q26/1
title: Pischedda & Chippindale 2017 Evolution Data
DOI: 10.5061/dryad.n7v41/1
title: Schnell_et_al_2017_data

description: Schnell_et_al_2017_data contains specific information about and all data described in the manuscript. See the README file for details.
DOI: 10.5061/dryad.nj1bp/21
title: SFigS4_Length_Phylorate_PA

description: Supplementary Figure S4. Phylorate plot of phenotypic (body length) evolution rates through time using the “pruned-after” MCC tree. (a) Phylorate plot of the mean phenotypic evolutionary rate of body length across all shift configurations based the MCC phylogeny. (b–d) Phylorate plots of 4 distinct shift configurations with the highest posterior probability. Rate shifts, shown as red circles with sizes proportional to the marginal probability of the shift, demonstrate significant increase in evolutionary rate. 3 distinct shift configurations account for the majority of the posterior probability of the data but result in conflicting rate configurations. The most frequent shift configuration (f = 0.35) signifies no rate shift (b) whereas the second most frequent shift configuration (f = 0.33) indicates an increase in evolutionary rate at the node leading to the divergence of Ictonychinae, Mustelinae, and Lutrinae (c). Conversely, the third most frequent shift configuration (f = 0.16) reveals a rate shift at the root of Mustelidae (d).
DOI: 10.5061/dryad.nj1bp/22
title: SFigS5_BMrate_PB

description: Supplementary Figure S5. Phylorate plot of phenotypic evolution rates through time based on body mass.
DOI: 10.5061/dryad.q5b10/1
title: Nestling begging responses to familiar versus unfamiliar odour stimuli

description: This data file was used to analyse the likelihood, duration and intensity of nestling begging responses to familiar versus unfamiliar odour stimuli, while controlling for several additional predictor variables.
DOI: 10.5061/dryad.q5b10/2
title: Nestling mass and survival

description: This data file was used to analyse the effect of the olfactory discrimination test trials on nestling mass and survival as observed on day 15 after hatching.
DOI: 10.5061/dryad.q684n/1
title: Data Caching for Where and What

description: Excel file of overlap of cache areas by nut species in different experimental conditions.
DOI: 10.5061/dryad.223tp/1
title: Data contact area Aphrodes platellae

description: Platellae contact area data from high-speed close-up recordings of the hind tarsi for 12 jumps of 5 Aphrodes leafhoppers.
DOI: 10.5061/dryad.223tp/2
title: Data force measurements Philaenus and Aphrodes

description: Friction force data of the hind tarsi of 4 Aphrodes leafhoppers and 5 Philaenus froghoppers on glass.
DOI: 10.5061/dryad.223tp/3
title: Data jump performance Philaenus and Aphrodes

description: Take-off velocity, take-off angle, and spin data for jumps of Aphrodes leafhoppers and Philaenus froghoppers from smooth glass and rough sandpaper surfaces.
DOI: 10.5061/dryad.2601h/19
title: CFD simulation file for Parvancorina minchami from Russia, 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 Russia 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.2601h/20
title: CFD simulation file for Parvancorina minchami from Russia, relief increased by 30%, 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 relief increased by 30% 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/21
title: CFD simulation file for Parvancorina minchami from Russia, relief increased by 30%, 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 relief increased by 30% 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/22
title: CFD simulation file for Parvancorina minchami from Russia, 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 Russia 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/23
title: CFD simulation file for null model of Parvancorina minchami from Russia, MPH format

description: Computational fluid dynamics (CFD) simulations of water flow were performed in COMSOL. A null model of Parvancorina minchami from Russia 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/24
title: CFD simulation file for Parvancorina sagitta 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 sagitta 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.