cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.96qr7n2/2
title: R scripts for phylogenetic comparative analysis

description: This R file contains the complete set of scripts to repeat all analyses that we performed and re-create all figures, plus some additional diagnostic and exploratory plots mentioned in the text. Please consult the README file before executing the script, and be aware that the bayou and mvMORPH anlyses will run for several hours.
DOI: 10.5061/dryad.96qr7n2/3
title: Time-calibrated phylogeny of geckos require for comparative analysis

description: This Newick tree file is from the following source: Zheng Y, Wiens JJ. 2016 Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species. Molecular Phylogenetics and Evolution 94, 537–547. (doi:10.1016/j.ympev.2015.10.009)
DOI: 10.5061/dryad.96qr7n2/4
title: Data on gecko body size, eye size, and diel activity pattern

description: This csv file contains data for 99 species of gecko, specifically: 1) snout-vent length in mm as proxy for body size, 2) antero-posterior diameter of the eye in mm as proxy for eyeball diameter, and 3) discretized information on diel activity pattern (grouped into three categories (cathemeral/crepuscular, diurnal, nocturnal). Please make sure to preserve the file extension when saving the file.
DOI: 10.5061/dryad.c2k7dj5/1
title: Original data used in figures of the paper

description: The data file includes all the experimental and theoretical data shown in Figure 5 to Figure 9.
DOI: 10.5061/dryad.cn0d6h5/1
title: Data
DOI: 10.5061/dryad.d6299fr/2
title: Appendix 2
DOI: 10.5061/dryad.f6v067r/1
title: Hydra behavior dataset

description: This is an annotated Hydra behavior dataset collected from 53 Hydra specimens. The dataset includes both spontaneous behaviors and induced feeding behavior of Hydra, and is annotated with the following 8 labels: silent, elongation, tentacle swaying, body swaying, bending, contraction, somersaulting, and feeding.
DOI: 10.5061/dryad.g32q0h0/1
title: Physiological measurements in the eastern red-backed salamander - corticosterone release rate and thermal performance

description: Data was collected in the laboratory using field-collected salamanders (Plethodon cinereus) from 4 study sites in ME, NY, MD, and VA. The file was created using Microsoft Excel. The column headings are as follows: experiment (indicates which of the physiological studies the data corresponds to); site code (indicates the state of origin); site name (specifies the collection site); site heat value (refers to the mean daily maximum temperature at the collection site as explained in the associated manuscript); salamander ID (a unique code given to each study animal); experimental temp (15 or 25°C as explained in the associated manuscript); sex (m or f); svl (snout-vent length measured to posterior edge of cloaca); tail length (measured from posterior edge of cloaca); total length (svl + tail length); mass (refers to the mass recorded at the time of corticosterone sampling); corticosterone release rate (see associated manuscript for methodology); performance initial mass (refers to the mass recorded at the start of each thermal performance trial); performance final mass (refers to the mass at the end of each performance trial); days between mass (refers to the number of days that passed between initial and final mass events); performance (% change in mass/day); ingestion (total number of flies consumed/day during performance trial).
DOI: 10.5061/dryad.j6f9655/1
title: cpDNA data
DOI: 10.5061/dryad.j6f9655/2
title: GBSSIexons data
DOI: 10.5061/dryad.j6f9655/3
title: GBSSIseqs data
DOI: 10.5061/dryad.n8f2q8g/1
title: Raw bivalve data for PERIL calculation

description: Raw data including valid taxonomy, extinction rate of families, geographic range size, and thermal niche, for the shallow-marine Recent Bivalvia, provided for calculation of PERIL scores.
DOI: 10.5061/dryad.n8f2q8g/2
title: PERIL scores for Pliocene Bivalvia

description: PERIL scores and related data for analysis of PERIL in Pliocene Bivalvia from two regional faunas in California and New Zealand
DOI: 10.5061/dryad.n8f2q8g/3
title: PERIL calculation code

description: R code for the calculation of PERIL from the raw datafile provided for the Recent Bivalvia. Also includes code to build plots from the paper.
DOI: 10.5061/dryad.n8f2q8g/4
title: Code for analysis of Pliocene PERIL

description: Code for analysing Pliocene bivalve PERIL scores using the paleo-PERIL raw data provided
DOI: 10.5061/dryad.r5c64/1
title: Silphidae_Abundance

description: The file Silphidae_Abundance includes abundance data of all captured silphid species per plot and day after piglet cadaver exposition.
DOI: 10.5061/dryad.r5q5v1p/3
title: Data and SAS code for Figure 5

description: First worksheet holds data, 2nd definitions, 3rd SAS code
DOI: 10.5061/dryad.t4p013r/1
title: Estrilid data
DOI: 10.17632/w9k8hxd34t.1
title: Data for: Phase-Space Wavepacket Dynamics of Internal Conversion via Conical Intersection: Multi-State Quantum Fokker-Planck Equation Approach

description: Detailed derivation of equations in "Phase-Space Wavepacket Dynamics of Internal Conversion via Conical Intersection: Multi-State Quantum Fokker-Planck Equation Approach"
DOI: 10.5061/dryad.1759h94/1
title: SSR_data_EAHB_bananas

description: Binary matrix of allele sizes obtained after SSR genotyping in selected diploid and triploid banana species, including East African Highland Bananas.
DOI: 10.5061/dryad.1759h94/2
title: Multiple alignment of ITS1-ITS2 concatenated sequences

description: Multiple alignment of ITS1-ITS2 concatenated sequences of selected diploid and triploid banana accessions, including Ensete ventricosum (used as an outgroup in the study).
DOI: 10.5061/dryad.1h48b38/42
title: SLiM simulation script moderate SOD M3

description: Forward simulation script for the scenario: moderate symmetrical overdominance, selection strength s = 0.05, migration M3 = 2.36E-06. Script run in SLiM v2.5. Example command to run the script: "./slim -d simnum=00000 -d u=1.17e-7 -d locus=0 example_simulation_6_pops_00000_0.txt". example_simulation_6_pops_00000_0.txt - name of the SLiM script with one simulation specification; simnum - simulation number; u - locus mutation rate; locus - locus number.
DOI: 10.5061/dryad.2bj836t/1
title: bydv-viral-ca-data-output-temporal-subset

description: This is the subset of data used for temporal trends in Seabloom et al. (2009) (e.g., Figure 6)
DOI: 10.5061/dryad.2bj836t/2
title: bydv-viral-ca-data-output-spatial-subset

description: This is the subset of data used for cross site comparisons in Seabloom et al. (2009) (e.g., Figures 7 & 8)
DOI: 10.5061/dryad.2bj836t/3
title: bydv-viral-ca-data-output

description: Data used for Seabloom et al. (2009)
DOI: 10.5061/dryad.2bj836t/4
title: bydv-viral-ca-data-metadata

description: File to describe data used in Seabloom et al. (2009)
DOI: 10.5061/dryad.460rp51/1
title: Data
DOI: 10.5061/dryad.587bb57/10
title: DICOM images termite mound Ms1

description: Raw DICOM image files of CT-scanned termite mound Ms1
DOI: 10.5061/dryad.587bb57/11
title: README
DOI: 10.5061/dryad.587bb57/5
title: DICOM images termite mound Mn2

description: Raw DICOM image files of CT-scanned termite mound Mn2
DOI: 10.5061/dryad.587bb57/6
title: DICOM images termite mound Mn4

description: Raw DICOM image files of CT-scanned termite mound Mn4
DOI: 10.5061/dryad.587bb57/7
title: DICOM images termite mound Mn6

description: Raw DICOM image files of CT-scanned termite mound Mn6
DOI: 10.5061/dryad.587bb57/8
title: DICOM images termite mound Mn8

description: Raw DICOM image files of CT-scanned termite mound Mn8
DOI: 10.5061/dryad.587bb57/9
title: DICOM images termite mound Mn9

description: Raw DICOM image files of CT-scanned termite mound Mn9
DOI: 10.5061/dryad.5fj6t/30
title: Cf3
DOI: 10.5061/dryad.5fj6t/31
title: Cf4
DOI: 10.5061/dryad.5fj6t/32
title: Cb_egg2
DOI: 10.5061/dryad.5fj6t/33
title: Cf6
DOI: 10.5061/dryad.5fj6t/34
title: Cf7
DOI: 10.5061/dryad.5fj6t/35
title: Cr2
DOI: 10.5061/dryad.5fj6t/36
title: Cr3
DOI: 10.5061/dryad.5fj6t/37
title: Cr1
DOI: 10.5061/dryad.5fj6t/38
title: Cb_inv2
DOI: 10.5061/dryad.5r2q8t8/4
title: README

description: This file explains all of the variables in each of the datasets required to conduct the analyses used in the article: “Sudden collapse of a mesopredator reveals its complementary role in mediating rocky reef regime shifts." These data files were generated from subtidal SCUBA surveys collected over four years (2013-2016) at 11 rocky reef sites on the central coast of British Columbia led by Jenn M. Burt, Kyle W. Demes, and Anne K. Salomon.
DOI: 10.5061/dryad.5r2q8t8/6
title: Burt_CC-DiveSurveys2013-2016_QuadCounts

description: This data file has information for counts of red urchins (within size categories) and all adult kelp species (Laminariales, stipes &gt;15cm) within 1x1m quadrats (n=18), across 11 survey sites conducted annually over 4 years (2013-2016) on the central coast of BC, Canada.
DOI: 10.5061/dryad.6vn9658/1
title: Produce difference of Gaussians stimulus image

description: Code to generate an image containing an isoluminant visual stimulus derived from a difference of Gaussians.
DOI: 10.5061/dryad.6vn9658/2
title: Spatial resolution MATLAB files

description: MATLAB scripts which can be used to model the spatial resolution required to detect a visual signal of a particular type and arc width.
DOI: 10.5061/dryad.6vn9658/3
title: Urchin model images

description: Micro-tomographic images of the skeleton of Diadema africanum. These images were used to produce 3D reconstructions of the entire skeleton and of a section including tube foot pores.
DOI: 10.5061/dryad.80c3q54/1
title: Recens raw mating data

description: Raw mating data in .csv format of mate trials for D. recens females.  Column 1 has the block (i.e. day), Column 2 has the individual female replicate number, Column 3 has the female line (see Table 1 of the paper for the population abbreviations),  Column 4 has the male type, and Column 5 is whether mating took place with 1=yes and 0=no.
DOI: 10.5061/dryad.80c3q54/2
title: Subquinaria raw mating data

description: Raw mating data in .csv format of mate trials for D. subquinaria females.  Column 1 has the block (i.e. day), Column 2 has the individual female replicate number, Column 3 has the female line (see Table 1 of the paper for the population abbreviations),  Column 4 has the male type, and Column 5 is whether mating took place with 1=yes and 0=no.
DOI: 10.5061/dryad.80c3q54/3
title: Microsatellite data for D. recens and D. subquinaria

description: All microsatellite data with annotations, in structure format.   Column 1 contains the unique label, Column 2 contains the unique fly ID (Species_Population_number), Column 3 indicates the sex of the fly (Female or Male), Column 4 indicates the population (see table 1 of the paper for abbreviations), Column 5 indicates the species (subquinaria or recens), Column 6 indicates the unique population number, and the remaining columns have the microsatellite genotypes.  Loci with an X at the end of the name are on the X-chromosome. Missing data are indicated by a -9.
DOI: 10.5061/dryad.80c3q54/4
title: Hzar clines R code and data

description: This folder contains the data and R code to determine 1) the distance of each population from the crest of the Rockies and 2) the D. subquinaria clines in mating rate, admixture, and species composition.
DOI: 10.5061/dryad.80c3q54/5
title: Structure analyses

description: This folder contains the data, program files, and scripts to run the structure analyses.  Sub-folders are by genome location (all loci, X-linked, autosomal) and by subset of samples (only recens, only subquinaria, both species (i.e., all)). Within the structure data file, each individual is coded by Species_population_individual in the first column and the population number in the second column.
DOI: 10.5061/dryad.80c3q54/6
title: DAPC analyses

description: This folder contains the files to run the DAPC analyses, including the R code and input files.  Analyses were completed by genome location (all loci, X-linked, autosomal) and by subset of samples (only recens, only subquinaria, both species (i.e., all)).
DOI: 10.5061/dryad.8206227/48
title: S15D-Telluraves-Overlap-Split-Concept-Resolution-mir

description: S15D File. Set of Maximally Informative Relations (MIR) inferred for the 2015./2014.Telluraves alignment (higher-level subset), under split-concept resolution. Total = 81 MIR. File format: .csv.
DOI: 10.5061/dryad.8206227/49
title: S16A-Neornithes-Higher-Level-Overlap

description: S16A Text. Reasoner input constraints for the 2015./2014.Neornithes alignment, under whole-concept resolution, ranging from the root to the ordinal level (with exceptions where needed). Includes information on run commands; and 4 instances of "no coverage". File format: .txt.
DOI: 10.5061/dryad.8206227/50
title: S16B-Neornithes-Higher-Level-Overlap

description: S16B Fig. Input visualization for the 2015./2014.Neornithes alignment, under whole-concept resolution, ranging from the root to the ordinal level (with exceptions where needed). File format: .pdf.
DOI: 10.5061/dryad.8206227/51
title: S16C-Neornithes-Higher-Level-Overlap-0-mnpw

description: S16C Fig. Alignment visualization for the 2015./2014.Neornithes alignment, under whole-concept resolution, ranging from the root to the ordinal level (with exceptions where needed). File format: .pdf.
DOI: 10.5061/dryad.8206227/52
title: S16D-Neornithes-Higher-Level-Overlap-mir

description: S16D File. Set of Maximally Informative Relations (MIR) inferred for the 2015./2014.Neornithes alignment, under whole-concept resolution, ranging from the root to the ordinal level (with exceptions where needed). Total = 8,051 MIR. File format: .csv.
DOI: 10.5061/dryad.8206227/53
title: S17A-Neoaves-Conflict-Region-Overlap-Whole-Concept-Resolution

description: S17A Text. Reasoner input constraints for the 2015./2014.Neoaves alignment, under whole-concept resolution, limited to the main conflict region. Includes information on run commands; and 0 instances of "no coverage". File format: .txt.
DOI: 10.5061/dryad.8206227/54
title: S17B-Neoaves-Conflict-Region-Overlap-Whole-Concept-Resolution

description: S17B Fig. Input visualization for the 2015./2014.Neoaves alignment, under whole-concept resolution, limited to the main conflict region. File format: .pdf.
DOI: 10.5061/dryad.8206227/55
title: S17C-Neoaves-Conflict-Region-Overlap-Whole-Concept-Resolution-0-mnpw

description: S17C Fig. Alignment visualization for the 2015./2014.Neoaves alignment, under whole-concept resolution, limited to the main conflict region. File format: .pdf.
DOI: 10.5061/dryad.8206227/56
title: S17D-Neoaves-Conflict-Region-Overlap-Whole-Concept-Resolution-mir

description: S17D File. Set of Maximally Informative Relations (MIR) inferred for the 2015./2014.Neoaves alignment, under whole-concept resolution, limited to the main conflict region. Total = 441 MIR. File format: .csv.
DOI: 10.5061/dryad.96qr7n2/5
title: Extensive dataset on diel activity patterns of geckos

description: This csv file contains data on diel activity pattern for 254 species of gecko. We combined our own data with information from Gamble T, Greenbaum E, Jackman TR, Bauer AM. 2015 Into the light: diurnality has evolved multiple times in geckos. Biological Journal of the Linnean Society 115, 896–910. (doi:10.1111/bij.12536). Please make sure to preserve the file extension when saving the file.
DOI: 10.5061/dryad.dr34q6v/1
title: Code for running simulations

description: This is a .zip file that contains all of the code for running the simulations described in our paper.  The code was run using Matlab 2017.
DOI: 10.5061/dryad.dr34q6v/2
title: Data and code for producing figures

description: This is a .zip file which contains the simulation data used to make the figures in our paper.  It also contains data that was synthesized from two other sources, used to describe the impact of CNDD on species in Panama.  The file also contains code which will produce all of the figures in our paper.
DOI: 10.5061/dryad.f41b11f/1
title: Full dataset Stam, Dicke Poelman

description: This datafile and its folders contain all data presented in the publication. A short read me is included in the file.
DOI: 10.5061/dryad.m151q/1
title: 28S

description: 28S nexus file
DOI: 10.5061/dryad.m151q/2
title: COI

description: COI nexus file
DOI: 10.5061/dryad.m151q/3
title: Puillandre et al. - Supplementary material

description: Supplementary material S1, S2 and S3. Please note: the Tables S1 and S2 are also provided in Excel format as "Sup mat 1 - genetic structure.xls" and "Sup mat 2 - specimens list.xls"
DOI: 10.5061/dryad.m151q/4
title: Sup mat 1 - genetic structure

description: Genetic structure calculated with the COI and 28S genes for respectively eight and five PSH. Fst values are calculated between each pair of stations for which at least six specimens were available. Into parentheses: number of specimens. An AMOVA was also performed for the PSH 67 between two groups (Philippines and Vanuatu) and four populations in the Vanuatu.
DOI: 10.5061/dryad.m151q/5
title: Sup mat 2 - specimens list

description: List of the 1,000 specimens analysed in this study.
DOI: 10.5061/dryad.m2s1735/1
title: Quantitative traits simulated under three-taxon phylogeny

description: R workspace containing simulated quantitative traits (3 species).
DOI: 10.5061/dryad.m2s1735/2
title: Quantitative traits simulated under five-taxon phylogeny

description: R workspace containing simulated quantitative traits (5 species).
DOI: 10.5061/dryad.m2s1735/3
title: Plottable objects

description: R workspace containing objects for producing plots.
DOI: 10.5061/dryad.mr677g8/1
title: Spectra of three strains

description: Spectra of three strains including original data
DOI: 10.5061/dryad.mr677g8/5
title: Ag NPs absorbance

description: The characterization of the Ag nanoparticles
DOI: 10.5061/dryad.mr677g8/6
title: Classification of three pure bacteria after wash
DOI: 10.5061/dryad.mr677g8/7
title: Classification of three bacteria from LB medium
DOI: 10.5061/dryad.mr677g8/8
title: three bacteria from LB medium
DOI: 10.5061/dryad.mr677g8/9
title: three bacteria spectra from artificial urine
DOI: 10.5061/dryad.nv5cr00/1
title: kobayashi_et_al._data.set
DOI: 10.5061/dryad.r5q5v1p/2
title: Data and SAS code for Figure 4

description: First worksheet holds data, 2nd definitions, 3rd SAS code used in paper.
DOI: 10.5061/dryad.rm93865/1
title: source_code
DOI: 10.5061/dryad.t4p013r/2
title: Vidua data
DOI: 10.5061/dryad.t9t0sc4/1
title: LiuEtAl_R1_Data

description: Raw data
DOI: 10.5061/dryad.1qp358p/1
title: Coyote locations from Vertnet

description: Location and date for verified coyote records from Museum specimens (zoology collections) as downloaded from Vertnet
DOI: 10.5061/dryad.1qp358p/2
title: Hody_Kays_coyote_data_Faunmap

description: Fossil coyote locations as downloaded from Faunmap
DOI: 10.5061/dryad.2f5v427/1
title: "All predator" data

description: Raw data behind "All predator" analysis and provides baseline data for R code provided.
DOI: 10.5061/dryad.2f5v427/2
title: Predation data for bird predators only

description: Data compiled and collected in the field for bird predators only.
DOI: 10.5061/dryad.2f5v427/3
title: Predation data for mammals predators only

description: Data collected in the field and compiled for mammal predators only.
DOI: 10.5061/dryad.420b8vn/1
title: Insect data
DOI: 10.5061/dryad.420b8vn/2
title: Plant data
DOI: 10.5061/dryad.4775s65/1
title: Crespi et al Data from: A genetic locus for paranoia

description: These data were originally deposited by Crespi and colleagues (Crespi B, Read S, Salminen I, Hurd P. Data from: A genetic locus for paranoia. Dryad Digital Repository. 2018.) These data were used to test an alternative hypothesis to analyses in Crespi et al (Crespi B, Read S, Salminen I, Hurd P. A genetic locus for paranoia. Biol Lett. 2018;14(1).) Three columns were added to the original data, which reflect basic calculations for the analyses presented in this paper.
DOI: 10.5061/dryad.4f6t3b5/1
title: colony_level_visits_&_feed_time

description: colony_level_visits_&_feed_time.csv
Data for Table S4, proportion of bees visiting each pesticide concentration 
Data for Table S5, count of bees visiting each pesticide concentration
Data for Table S6, average time spent feeding at each pesticide concentration
DOI: 10.5061/dryad.4f6t3b5/2
title: commited_foragers

description: commited_foragers.csv
Data for Table S7, proportion of foraging trips to each concentration made by 31 bees
DOI: 10.5061/dryad.4f6t3b5/3
title: volume_data

description: volume_data.csv
Data for Table S3, average volume of sucrose consumed from each pesticide concentration
DOI: 10.5061/dryad.4f6t3b5/4
title: 01_dryad_colony_level_ consumption

description: 01_dryad_colony_level_ consumption.R
Analysing the volume of sucrose consumed by each colony
Contains code for replicating Fig 1d.
DOI: 10.5061/dryad.4f6t3b5/5
title: 02_dryad_colony_&_individual_level_proportion_of_visits

description: 02_dryad_colony_&_individual_level_proportion_of_visits.R
Analysing the proportion of bees visiting each pesticide concentration 
Contains code for replicating Fig 1e.
Analysing the number of bees visiting each pesticide concentration 
Analysing the average time spent feeding at each pesticide concentration
Analysing the proportion of foraging trips to each concentration made by 31 bees  
Contains code for replicating Fig S4.
DOI: 10.5061/dryad.4f6t3b5/6
title: readme

description: Information about the analysis
DOI: 10.5061/dryad.4tc28
title: Dryad Item 10.5061/DRYAD.4TC28
DOI: 10.5061/dryad.54h75r8/1
title: Experiment 1: Long distance attractiveness of Drakaea livida vs Caledonia pectinata

description: A comparison of (i) how quickly pollinators respond (ii) how many pollinators respond to the floral odour of Drakaea livida and Caladenia pectinata when presented with the same visual stimulus.
DOI: 10.5061/dryad.54h75r8/2
title: Experiment 2: Does the odour of Drakaea livida elicit greater sexual attraction than Caledonia pectinata?

description: When presented with the same visual stimulus, do pollinators land or attempt copulation more frequently in response to the floral odour of Drakaea livida or Caledonia pectinata?
DOI: 10.5061/dryad.54h75r8/3
title: Experiment 3: Does a decrease in floral odour reduce sexual attraction of the pollinator?

description: A comparison of the sexual attraction of pollinators (measured as landing and attempted copulation) with normal or reduced amounts of odour-producing floral tissue
DOI: 10.5061/dryad.587bb57/12
title: metadata

description: Metadata on termite mounds and physical properties analysis
DOI: 10.5061/dryad.587bb57/13
title: Data and scripts for image/data analysis

description: Data and R script on termite mound physical parameters; Matlab script and ImageJ/Fiji macros used for image analysis of termite mound CT scans and cross sections.
DOI: 10.5061/dryad.587bb57/14
title: Ms1DICOM images termite mound Ms3

description: Raw DICOM image files of CT-scanned termite mound Ms3
DOI: 10.5061/dryad.587bb57/15
title: DICOM images termite mound Ms5

description: Raw DICOM image files of CT-scanned termite mound Ms5
DOI: 10.5061/dryad.587bb57/16
title: DICOM images termite mound Ms6

description: Raw DICOM image files of CT-scanned termite mound Ms6
DOI: 10.5061/dryad.587bb57/17
title: DICOM images termite mound Ms7

description: Raw DICOM image files of CT-scanned termite mound Ms7
DOI: 10.5061/dryad.587bb57/18
title: DICOM images termite mound Tp1

description: Raw DICOM image files of CT-scanned termite mound Tp1
DOI: 10.5061/dryad.587bb57/19
title: DICOM images termite mound Tp2

description: Raw DICOM image files of CT-scanned termite mound Tp2
DOI: 10.5061/dryad.587bb57/20
title: DICOM images termite mound Tp3

description: Raw DICOM image files of CT-scanned termite mound Tp3
DOI: 10.5061/dryad.5fj6t/39
title: Cb_inv1
DOI: 10.5061/dryad.5fj6t/40
title: Cb_inv3
DOI: 10.5061/dryad.5fj6t/41
title: Cdor1
DOI: 10.5061/dryad.5fj6t/42
title: Cdil_egg1