cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g7h7n/2
title: Col Coniss

description: Col Pond plot of CONISS model results
DOI: 10.5061/dryad.g7h7n/3
title: Col N2

description: Col Pond Hill's N2 and chlorophyll a output
DOI: 10.5061/dryad.g7h7n/4
title: Col Pond

description: Col Pond diatom raw count data and relative abundances including basionyms and modern taxonomic designations
DOI: 10.5061/dryad.p1v07/5
title: Hirolakillsites_2015

description: Hirola kill sites data contains observed hirola kill sites collected by network of scouts within the hirola's geographic range. Note: due to the sensitive nature of the data, GPS location information for the critically endangered Beatragus hunteri have been removed from the dataset.
DOI: 10.5061/dryad.p8n72/1
title: Example taxonomy for R Code
DOI: 10.5061/dryad.p8n72/2
title: Example chronogram for R code
DOI: 10.5061/dryad.p8n72/3
title: Main R code for Temporal banding method
DOI: 10.5061/dryad.p8n72/4
title: Associated functions for the main R code
DOI: 10.5061/dryad.r19c2/1
title: HIV envelope sequences

description: Aligned HIV subtype B and C envelope sequences for early transmission (Founders) and chronically infected individuals (Chronics). Founders are denoted by FR, Chronics by CR, with B and C in the sequence name denoting the subtype. The reference sequence HXB2 is included.
DOI: 10.5061/dryad.r19c2/2
title: Seroconverter HIV subtype B envelope sequences

description: Pre-seroconverter subtype B envelope sequences for 5 individuals. Separate clones are listed for most individuals.
DOI: 10.5061/dryad.s6f4q/1
title: Raw acoustic data

description: 10 min recording samples of each of the two maerl beds (fished and unfished)
DOI: 10.5061/dryad.t6dg1/1
title: Bird species whose Digital Distribution Maps were examined for comission errors

description: A list of 1,007 bird species that occur in the Amazon, and whose Digital Distribution Maps were examined for comission errors. Digital Distribution Maps are downloaded from http://www.iucnredlist.org/. All species were evaluated in terms of the habitat where they occur, and classified as either occurring in seasonally flooded forest or not occurring in seasonally flooded forests. We then identified the species that had commission errors, i.e., species mapped as occurring throughout the entire Amazon, but that are not reported to occur in seasonally flooded forest.
DOI: 10.5061/dryad.t9m00/1
title: Data matrix of fruit characters used in the phylogenetic analysis of Chinese Heracleum species and related taxa

description: Data matrix of fruit characters used in the phylogenetic analysis of Chinese Heracleum species and related taxa.  Twenty characters and 33 taxa.
DOI: 10.5061/dryad.vs370/1
title: Data package about incompatibilities between adaptive mutations in yeast

description: This package contains files and scripts related to the publication "Widespread Genetic Incompatibilities Between First-Step Mutations During Parallel Adaptation of Saccharomyces
cerevisiae to a Common Environment". Raw data and analyses are included.
DOI: 10.17632/53r87bryfg.1
title: Possible Digraphs Structures Corresponding to Characteristic Polynomial

description: The dataset contains all possible digraphs structures in class K1 corresponding to the one-dimensional characteristic polynomial.
DOI: 10.5061/dryad.2v54j/1
title: Raw microsatellite genotype scores for 6 Blepharoneura species

description: This file contains raw microsatellite genotype data for six species of Blepharoneura fly. The first column of each sheet contains specimen names corresponding to those in mtCOI trees in the supplemental materials of the paper. The second column of each sheet contains plant tissue information (fGA = female Gurania acuminata; mGA = male G. acuminata; fGS = female Gurania spinulosa; mGS = male G. spinulosa). The second column also contains collection site information, the codes for which may be found in the main paper and its supplement. Numbers in the first row refer to microsatellite locus names, with the diploid genotypes for each locus located in the column below each name as well as in the column to the right of the locus name. Genotypes are given as fragment lengths. A score of "-9" indicates missing data.
DOI: 10.5061/dryad.31v01/10
title: Bar plot in Figure 6a

description: Folder containing all files and data needed to plot figure 6a. Text data (pixel averages of the B channel from processed raw images) is obtained using hatchetfishpicanalysis.m.
DOI: 10.5061/dryad.31v01/11
title: Hatchetfish Image analysis

description: Matlab file used to analze raw images of hatchetfish and control objects in different illuminations. Raw image files are contained in 3 folders: Hatchetfish raw camera angle, Hatchetfish raw camera vertical and Control raw camera dng.
DOI: 10.5061/dryad.31v01/12
title: Quantifying Photophore Guide

description: Files needed to quantify light exiting downwelling photophores when entering through fish side.
DOI: 10.5061/dryad.31v01/6
title: BRDF data

description: Mat file to be used with percentisotropic.m for plotting BRDF data from Figure 2a.
DOI: 10.5061/dryad.31v01/7
title: Hatchetfish raw camera angle

description: Folder containing raw images of hatchetfish with angled incoming light and necessary text file used for plotting bar graph in 6a with barplot.m.
DOI: 10.5061/dryad.31v01/8
title: Hatchetfish raw camera vertical

description: Folder containing raw camera images of hatchetfish under vertical illumination. Also includes text files containing data used in bar graph in figure 6a.
DOI: 10.5061/dryad.31v01/9
title: Control raw camera dng

description: Folder containing raw images of control objects (aluminum, mirror, spectralon) for use in bar graph of figure 6a.
DOI: 10.5061/dryad.3k2p7/1
title: model data and nestedness

description: mod.dat.csv: all variables for all sites used for the models that were extracted from individual networks

header of mod.dat.csv:

region				site
functionalgroup			target group of pollinators (icp, hb, rare)
visitspertargetgroup		number of visits	
functionalcomplementarity	functional complementarity of plant community
numberofkeyplantspresent	key plant species richness	
flowerabundancekeyplants	flower abundance of key plant species richness
totalnumberofspecies		total plant species richness
totalflowerabundance		total flower abundance

prop.nestedness.csv. gives the proportional visits for each group to all visited plant species, data used to calculate dissimilarity and nestendess.
DOI: 10.5061/dryad.452b4/1
title: individuals_data

description: Individuals data: Life history traits + presence / absence for each ECE + mean climatic variable
DOI: 10.5061/dryad.452b4/2
title: Rain_data

description: Daily rainfall data (1991-2015)
DOI: 10.5061/dryad.49dn0/5
title: Raw Data (forward)

description: Paired-end Illumina seqeuncing output fastq file with forward
reads.
DOI: 10.5061/dryad.49dn0/6
title: Raw Data (reverse)

description: Paired-end Illumina seqeuncing output fastq file with reverse
reads.
DOI: 10.5061/dryad.49dn0/7
title: Representative Sequences

description: This file contains the representative sequences of the OTUs from this study in fastq format.
DOI: 10.5061/dryad.4f775/3
title: Startle-induced negative geotaxis data

description: Data for Fig 1-3, 6A and 7, and S1C, S2E and S4 (Prism .pzf format)
DOI: 10.5061/dryad.4f775/4
title: Spontaneous locomotor activity data

description: Data for S1D Fig (Prism .pzf format)
DOI: 10.5061/dryad.4f775/5
title: DHE-ROS quantification

description: Data for Fig 4B-D, and S5 (Prism .pzf format)
DOI: 10.5061/dryad.4f775/6
title: Neuronal counts

description: Data for Fig5, 6A, S10 and S11A (Prism .pzf format)
DOI: 10.5061/dryad.6q750/1
title: Complete experimental data

description: [1] Sporulation data for the G_symbiont x G_pathogen experiment. Each line represents one aphid harboring a particular symbiont ("Symbiont_Genotype") infected with the fungal pathogen Pandora neoaphidis ("Fungal_Genotype"). A "0" indicates that the aphid did not produce a sporulating cadaver, a "1" indicates that the aphid sporulated. [2] Survival data from the same experiment (G_symbiont x G_pathogen) (control aphids only). The columns day and survival form the Surv object for survival analysis: status indicates the aphid was alive (0) or dead (1) on a given day. [3] Sporulation data for the G_symbiont x G_host experiment. Aphid genotype ("Host.Genotype") and symbiont genotype ("Symbiont.Genotype") are indicated. As above, each line represents an individual aphid, with a "0" indicating that the aphid did not produce a sporulating cadaver, a "1" indicating that the aphid sporulated.
DOI: 10.5061/dryad.8157n/1
title: AMS 14C dating
DOI: 10.5061/dryad.8157n/2
title: Archaeological strata
DOI: 10.5061/dryad.8157n/3
title: concentration
DOI: 10.5061/dryad.8157n/4
title: Geographical location
DOI: 10.5061/dryad.8157n/5
title: Percentage
DOI: 10.5061/dryad.8157n/6
title: phytoliths
DOI: 10.5061/dryad.8157n/7
title: Record comparison
DOI: 10.5061/dryad.cn642/1
title: 9 traits for 21 datasets
DOI: 10.5061/dryad.f68m0/1
title: Chukchi Sea ice data

description: Sea-ice data are provided in two text files: "Chukchi Sea ice data.txt" and "Southern Beaufort Sea ice data.txt". The data and methods to process them are described in the main text of Regehr et al. (2017) and the Supporting Information Appendix S3. Please see "Sea ice METADATA.txt" for further details.
DOI: 10.5061/dryad.f68m0/2
title: Southern Beaufort Sea ice data

description: Sea-ice data are provided in two text files: "Chukchi Sea ice data.txt" and "Southern Beaufort Sea ice data.txt". The data and methods to process them are described in the main text of Regehr et al. (2017) and the Supporting Information Appendix S3. Please see "Sea ice METADATA.txt" for further details.
DOI: 10.5061/dryad.fh078/1
title: Single visit deposition of pumpkin pollen of three bee species groups in 2015

description: Original source: single visit deposition (SVD) experiments in the field, pollen extracted by acetolysis; Open Office org Calc was used to create the file; abbrevations: "species" = bee species group ("bumble" = Bombus terrestris, B. lucorum; "halictid" = several Halictidae, mainly Lasioglossum malachurum; "honey" = Apis mellifera), "IT.span" = intertegular span.
DOI: 10.5061/dryad.fh078/2
title: R script for the analysis of the single visit deposition data

description: Data analysed "SVD.bee-species_pumpkin_2015.csv"; software R 3.2.2 (2015) used
DOI: 10.5061/dryad.fs8kv/2
title: Matrix II

description: Concatenated matrix of the genes with &gt;75% gene occupancy. See Suppl. Mat. for further information.
DOI: 10.5061/dryad.fs8kv/3
title: Matrix III

description: Concatenated matrix of the genes with &gt;50% gene occupancy. See Suppl. Mat. for further information.
DOI: 10.5061/dryad.fs8kv/4
title: Matrix IV

description: Concatenated matrix of the 100 fastest evolving genes parsed from Matrix I. See Suppl. Mat. for further information.
DOI: 10.5061/dryad.fs8kv/5
title: Matrix V

description: Concatenated matrix of the 100 genes with an evolutionary rate close to the mean parsed from Matrix I. See Suppl. Mat. for further information.
DOI: 10.5061/dryad.fs8kv/6
title: Matrix VI

description: Concatenated matrix of the 100 slowest evolving genes parsed from Matrix I. See Suppl. Mat. for further information.
DOI: 10.5061/dryad.g7h7n/10
title: Proteus broken stick

description: Proteus Lake plot of broken stick model results
DOI: 10.5061/dryad.g7h7n/11
title: SV5 broken stick

description: SV Pond 5 plot of broken stick model results
DOI: 10.5061/dryad.g7h7n/12
title: SV8 broken stick

description: SV Pond 8 plot of broken stick model results
DOI: 10.5061/dryad.g7h7n/13
title: West broken stick

description: West Lake plot of broken stick model results
DOI: 10.5061/dryad.g7h7n/5
title: Elison broken stick

description: Elison Lake plot of broken stick model results
DOI: 10.5061/dryad.g7h7n/6
title: High broken stick

description: High Lake plot of broken stick model results
DOI: 10.5061/dryad.g7h7n/7
title: Moraine broken stick

description: Moraine Pond plot of broken stick model results
DOI: 10.5061/dryad.g7h7n/8
title: Paradise Broken stick

description: Paradise Pond plot of broken stick model results
DOI: 10.5061/dryad.g7h7n/9
title: Plateau Pond 2 broken stick

description: Plateau Pond 2 plot of broken stick model results
DOI: 10.5061/dryad.gk1qk/2
title: Table mapping transcriptome sequence to isogroup ID

description: This file maps the A. millepora sequence name to the isogroup number and also includes the sequence. Generated by Matz lab.
DOI: 10.5061/dryad.gk1qk/3
title: amil.fasta

description: The A. millepora transcriptome used for alignments in this study. This is based on the transcriptome of Moya et al. (PMID 22490231) modified by the Matz lab.
DOI: 10.5061/dryad.m3069/1
title: male courtship rates

description: This file contains data on the number of females courted by a male in one minute.Two types of males: small and large males were sampled in two kinds of habitats: reef slope and reef shelf.
DOI: 10.5061/dryad.m3069/2
title: male and female size distribution

description: File contains point count data taken in slope and shelf habitats at the aggregation site on the distribution of males and females of two size classes : small and large.
DOI: 10.5061/dryad.tf1fm/1
title: Tree mortality and bark-beetle abundance and species richness

description: All data were collected in the field, tree mortality from transects (400 m/site) and bark beetle abundance and species richness from window traps. Sites=our names of the sites, RT90_X/Y=coordinates from RT90-projection, Treat=Treatments (G=gap-cuts, B=Burnes, C=Control), Sp.rich2010=Bark beetle (bb) species richness pre restoration, Abund2010=bb abundance pre restoration, Sp.rich_11_12=Two year bb species richness post restoration, Abund_11_12=Two year bb abundance post restoration, Sp.rich_11=First year bb species richness post restoration, Sp.rich_12=Second year bb species richness post restoration, Abund_pbb_11=First year primary bb abundance post restoration, Abund_pbb_12=Second year primary bb abundance post restoration, Abund_sbb_11=First year secondary bb abundance post restoration, Abund_sbb_12=Second year secondary bb abundance post restoration,
DOI: 10.5061/dryad.v4q0r/1
title: Matrix (Nexus)

description: The matrix in Nexus file format
DOI: 10.5061/dryad.v4q0r/2
title: Matrix TNT

description: The matrix formatted for TNT
DOI: 10.5061/dryad.v4q0r/3
title: Matrix Winclada

description: The Matrix formatted for Winclada
DOI: 10.13020/d6bp4x
title: Filtered Audio Clips from Approximate FIR Filters Designed Using the SABER Algorithm
DOI: 10.17632/mn8r329n6n.1
title: Fluorophores and fluorescence microscopy

description: When utilizing a scanning confocal microscope, better resolution and image contrast is achieved when compared to traditional methods. Thin optical sections of living specimens, 100 micrometers thick can be imaged with such devices, which are capable of examining fluorescence emission between 400nm and 750nm. By using laser light of wavelength 470nm as an excitation source, a root cell sample stained with two different fluorescent dyes was examined. Two distinct peaks were notated at 643.98nm (red) and 537.72nm (green). The fluorophores used were deemed to be monolignol (green) and Peridinin Chlorophyll (red) as they matched the ratio of excitation/emission wavelength de-tected in the experiment.
DOI: 10.17632/mn8r329n6n.2
title: Fluorophores and fluorescence microscopy

description: When utilizing a scanning confocal microscope, better resolution and image contrast is achieved when compared to traditional methods. Thin optical sections of living specimens, 100 micrometers thick can be imaged with such devices, which are capable of examining fluorescence emission between 400nm and 750nm. By using laser light of wavelength 470nm as an excitation source, a root cell sample stained with two different fluorescent dyes was examined. Two distinct peaks were notated at 643.98nm (red) and 537.72nm (green). The fluorophores used were deemed to be monolignol (green) and Peridinin Chlorophyll (red) as they matched the ratio of excitation/emission wavelength de-tected in the experiment.
DOI: 10.5061/dryad.00v09/1
title: Pups.develop.behavior

description: Developmental behavior data for daily testing of mouse pups with GnRHR knock out. Tests for vision, touch, mobility, strength, and righting reflexes. Statistical assessment and figures generated using GraphPad Prism software.  Used to generate Fig 2, 3, 4, & 5.
DOI: 10.5061/dryad.00v09/2
title: Body wt.(tested vs untested mice)

description: Developmental behavior data for daily testing of mouse pups with GnRHR knock out. Tests for body weight of animal tested daily vs animals not tested. Statistical assessment and figures generated using GraphPad Prism software.  Used to generate Fig 6.
DOI: 10.5061/dryad.00v09/4
title: Fat.kidney.liver.thymus % body weight

description: Developmental behavior data for daily testing of mouse pups with GnRHR knock out. Tests for organ weight (% body weight) for inguinal, gonadal, scapular and retro-peritoneal fat pads, kidney, liver and thymus. Statistical assessment and figures generated using GraphPad Prism software. Used to generate Fig 7 & 9.
DOI: 10.5061/dryad.00v09/5
title: Glucose.(tested vs untested mice)

description: Developmental behavior data for daily testing of mouse pups with GnRHR knock out. Tests for blood glucose levels in tested and untested pups. Statistical assessment and figures generated using GraphPad Prism software. Used to generate Fig. 8.
DOI: 10.5061/dryad.00v09/6
title: Body.wt.daily.2-28 - t-tests

description: Developmental behavior data for daily testing of mouse pups with GnRHR knock out. Tests for daily body weights of experimental animals. Statistical assessment and figures generated using GraphPad Prism software. Used to generate Fig 1 T-test statistics.
DOI: 10.5061/dryad.00v09/7
title: Body.wt.daily.2-28 - SNK tests

description: Developmental behavior data for daily testing of mouse pups with GnRHR knock out. Tests for daily body weights of experimental animals. Statistical assessment and figures generated using GraphPad Prism software. Used to generate Fig 1 SNK statistics.
DOI: 10.5061/dryad.2p164/1
title: Supplemental_Data_1

description: Raw data used in the analysis and coefficients of variation calculations.
DOI: 10.5061/dryad.2p164/2
title: Supplemental_Data_2

description: R code used in this analysis
DOI: 10.5061/dryad.3f2j7/1
title: Howison et al 2017 Bioturbation Biocompaction

description: TITLE: Biotically driven vegetation mosaics in grazing ecosystems: the battle between bioturbation and biocompaction
AUTHORS: Ruth A. Howison, Han Olff, Johan van de Koppel, and Christian Smit
Corresponding author: Ruth A. Howison (ruthhowison@gmail.com)

BifurcationModel.zip
Bifurcation model resulting in figures 2 and 3, designed and written by Johan van de Koppel and Ruth Howison, using R.  R Core Team (2015). R: A language and environment for statistical computing. R
Foundation for Statistical Computing, Vienna, Austria. URL  https://www.R-project.org/.
Phase planes depicting the bifurcation analysis of simple plant-herbivore models, showing the more classical A) Herbivore-plant quality feedback, and B) Water-infiltration feedback.
Phase planes depicting the bifurcation analysis of plant-herbivore models with bioturbation, showing that the interplay between bioturbation and biocompaction strongly expands the conditions under which heterogeneity can persist in grazing ecosystems, with A) only bioturbation feedback and B) the consequence of combining bioturbation and biocompaction feedbacks."

GIS_Rainfall_Texture_Analysis.zip
Analysis by Ruth Howison and Han Olff, using ESRI ArcMap 10.3 for Desktop Global prediction of the regions where patchiness generated by bioturbation and biocompaction is possible, eliminating for unsuitable conditions, specifically certain soil characteristics and rainfall. Incompatible soils include; permafrost, sand (&gt; 70% sand fraction and &lt; 15% clay fraction), organic soil (histosols or &gt; 20% organic material dry mass), and rainfall &lt; 400 and &gt; 1200 mm/yr and representing limits to forage quantity and quality required to maintain large herbivores.
Data sources used: 
harmonized world soil database (HWSD) version 1.21, 2) Rainfall parameters were delineated using the global precipitation surface available from BioClim.org (Hijmans et al. 2005)
DOI: 10.5061/dryad.408ht/1
title: Round goby transcript count data

description: This file was generated using Corset software to process BAM files of RNAseq reads mapped to a de novo assembled transcriptome for nine round goby and enumerate counts of reads per transcript as a proxy for transcript abundance.
DOI: 10.5061/dryad.408ht/2
title: Tubenose goby transcript count data

description: This file was generated using Corset software to process BAM files of RNAseq reads mapped to a de novo assembled transcriptome for nine tubenose goby and enumerate counts of reads per transcript as a proxy for transcript abundance.
DOI: 10.5061/dryad.452b4/3
title: Temperatures_data

description: Daily temperature anomalies (1991-2015)
DOI: 10.5061/dryad.4g26c/1
title: Parental_Oviposition_Behavior

description: This folder contains the data for the "oviposition behavior" section of the manuscript. It includes oviposition willingness, oviposition preference, Average number of eggs per needle, preslit presence, and egg spacing for N. lecontei and N. pinetum
DOI: 10.5061/dryad.4g26c/2
title: Host_ Needle_Width

description: This folder contains the data from the "Host needle width" section of the manuscript. It includes both mature and seedling measurements
DOI: 10.5061/dryad.4g26c/3
title: Parental_Ovipositor_Morphology

description: This folder contains the data for the "Ovipositor Morphology" section of the manuscript. It includes the landmark coordinates and ovipositor size measurements for N. lecontei and N. pinetum
DOI: 10.5061/dryad.4g26c/4
title: Interspecific_cross

description: This folder contains the data for the "cross oviposition behavior and success" section of the manuscript. It includes oviposition willingness, oviposition preference, and oviposition success for the interspecific crosses.
DOI: 10.5061/dryad.4js7n/1
title: Sentinel, Refugees, Arabian babbler

description: Excel data set for the manuscript
DOI: 10.5061/dryad.708gr/1
title: IPM-bighorn_archive

description: This .zip file contains two .txt files, one with data for females (IPM-bighornEwes_archive.txt) and another for males (IPM-bighornMales_archive.txt). Both files include a list of individual identifiers for parents and offspring. IPM-bighornEwes_archive.txt also includes variables year, cohort, age and mass (in Kg, adjusted for September 15th).
DOI: 10.5061/dryad.70mt1/1
title: Tamarix "Chorus" Dataset

description: Plant composition (species abundance) following Tamarix control and environmental variables including management, hydrology, soil and climate in 244 treated and 172 reference sites across six U.S. States.
DOI: 10.5061/dryad.7gp59/1
title: Ecology of Avian Influenza Viruses in Wild Dabbling Ducks in Canada
DOI: 10.5061/dryad.b2207/1
title: C code

description: ZIP file containing C code that solves numerically the coupled differential equation system f,g described in the article.
DOI: 10.5061/dryad.bp20k/1
title: Dataset 170331
DOI: 10.5061/dryad.bp20k/2
title: 2017-03-31 List of the variables in the supplementary dataset and explanation of the coding
DOI: 10.5061/dryad.c3c51/1
title: Color span of Oriolus males

description: Color span of male Oriolus, average for a given species. This is a csv file with comma as delimiter. It is an output from spectra processing in R software, package "pavo".
DOI: 10.5061/dryad.c3c51/2
title: LM Hue of Oriolus males

description: LM Hue data for Oriolus males for the 13 plumage patches (see the accompanying publication for the codes). This is a csv file with comma as delimiter.