cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4r267/1
title: tpc130112_SupplementalDS1

description: Supplemental Dataset 1: Morphometric traits for &gt;55,000 leaflets analyzed in this study. For each leaflet, the corresponding file name (“file”), experiment from which it is derived (“experiment”), genotype (“genotype”), leaf number if applicable (“leaf”), leaflet type (“leaflet_type”, where “t” = terminal leaflet, “a” = left distal lateral leaflet, “b” = right distal lateral leaflet, “c” = left proximal lateral leaflet, “d” = right proximal lateral leaflet), proximal-distal position (“prox_dist”), age of the plant sampled (“age”, which is measured as leaf plus flower number for the chamber experiment and leaf number for the wild species experiment), whether the leaflet is on the left or right side of the leaf (“left_right”), light treatment (“trt”, where “l” = low red-to-far red, or simulated foliar shade, and “h” = high red-to-far red, or simulated sun), and trait values for circularity (“circ”), aspect ratio (“ar”), roundness (“round”), solidity (“solid”), allPCs, and asymPCs are given.
DOI: 10.5061/dryad.4r267/2
title: tpc130112_SupplementalDS2

description: Supplemental Dataset 2: Heteroblasty and experimental design information for S. lycopersicum, S. pennellii, and IL leaflets measured in the chamber experiment. For each leaflet is provided the corresponding image file name (“file”), the trait for which hPCs and other information is calculated (“trait”), the mean value of the trait for the plant across the leaflets considered (“mean”), the value of the trait for specific leaflets (terminal leaflet 1, “lft_1t”; mean distal lateral leaflets 2, “lft_2ab”; terminal leaflet 2, “lft_2t”; mean distal lateral leaflets 3, “lft_3ab”; terminal leaflet 3, “lft_3t”; mean distal lateral leaflets 4, “lft_4ab”; terminal leaflet 4, “lft_4t”), hPC values, replicate (“rep”), light treatment (“trt”, where “H” =  simulated foliar shade, “U” = simulated sun), shelf (“shelf”), tray (“tray”), tray position (“position”), IL genotype (“geno”), species or IL information (“species”), the number of leaves and leaf primordia at the time of harvest (“lfn”), the number of flower and floral primordia at the time of harvest (“flwrn”), and the leaf plus flower number (“lf.flow.number”).
DOI: 10.5061/dryad.4r267/3
title: tpc130112_SupplementalDS3

description: Supplemental Dataset 3: hPC variance values. The fraction of shape variance in leaflets across the heteroblastic series explained by hPCs for each shape attribute is provided.
DOI: 10.5061/dryad.6169b.1
title: Data from: Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3
DOI: 10.5061/dryad.6169b.2
title: Data from: Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3
DOI: 10.5061/dryad.6169b.2/1.1
title: SupplementaryFigures1-5
DOI: 10.5061/dryad.6169b.2/2.1
title: onlineAppendices
DOI: 10.5061/dryad.6169b.2/3.1
title: collectedAlignmentsForPosting.tar

description: About 26,000 alignments used in study, in nexus format.
DOI: 10.5061/dryad.6169b.2/4.1
title: annotationGffsForPosting.tar

description: gff formatted files describing gene annotations not available fromother sources. Coordinates correspond to sequence assemblies deposited in Dryad, which may differ from versions in Genbank.
DOI: 10.5061/dryad.6169b.2/5.1
title: SupplementaryTables1-3
DOI: 10.5061/dryad.6169b.2/6
title: seqAssembliesForPosting

description: Sequence assemblies in fasta format for all taxa except O. sativa. Some differ from assemblies deposited in Genbank.
DOI: 10.5061/dryad.6c44q/2
title: Macro_VesselCalibrometry

description: ext of an ImageJ macro used to classify voxels in a binary stack according to the minimal Cartesian surface to which they belong (i.e., the approximated vessel cross-section).
DOI: 10.5061/dryad.6tt66/4
title: DRYAD_Figure4

description: Data for Fig. 4: Glucose stimulates bitter-GRNs in field-collected cockroaches.
DOI: 10.5061/dryad.7341c/1
title: Data for 15 lakes
DOI: 10.5061/dryad.76dc8/4
title: Curlew Caye Shape File

description: This .shp file shows the centroid of the Curlew Caye reef patch, which was our focal study site. Suggested projection: Datum (WGS4); Projection (UTM Zone 16N).
DOI: 10.5061/dryad.76nv3/2
title: SSRData
DOI: 10.5061/dryad.77077/4
title: Focal_node_IBR

description: Regions (focal node locations) defined for isolation by resistance analyses in circuitscape. Regions were defined according to the population definition in Figure 1. Each region consists of the minimum number of demes that contains sampling locations.
DOI: 10.5061/dryad.7r682/2
title: Genotype_data

description: Data on microsatellite genotypes for individual stickleback collected from 12 populations (six lake-stream pairs) on Vancouver Island, British Columbia, Canada.
DOI: 10.5061/dryad.8fc60/1
title: Individual and population level great tit data

description: Comma-separated values data file containing individual level and population level great tit data from the Hoge Veluwe study site, the Netherlands. Explanation of the variables included in the file "parus_maj_MS_code.R"
DOI: 10.5061/dryad.8rv46/1
title: Gene trees generated and used

description: All gene trees generated and used. Includes raw unsmoothed gene trees, and those smoothed using branch smoothing methods. Each of the 16 datasets has up to 30 gene trees (exceptions are explained in the main text). File designation includes the dataset followed by the phylogenetic method followed by the smoothing method. All gene trees are in the NEWICK format.
DOI: 10.5061/dryad.9n8rh/4
title: Bee microbiome paired-end, part D

description: The paired-end deep-sequence data from this paper was generated as a single lane of Illumina data, but was split up into 6 parts (A-F) for Dryad submission.  This is part D.  The file will unzip into two files containing the paired-end reads for the fourth 5.5M sequenced clusters.  Phred+64 quality score encoding.  Library prep details can be found in the Methods of the linked manuscript.
DOI: 10.5061/dryad.bn281/4
title: Table_S1: specimen voucher information

description: specimen voucher information
DOI: 10.5061/dryad.cq376/5
title: Supplementary figure 3

description: The diversity curves produced when taxa of uncertain age are assigned to the full possible stratigraphic range (dashed-dotted lines) compared to the diversity curves produced when each locality of uncertain ages is restricted to two or less time bins (solid line). A, Taxic diversity curves. B, Phylogenetic diversity curves. Timescale representing millions of years ago appears at the bottom
DOI: 10.5061/dryad.cs1k4/1
title: Collection and methodological details - Morphometrics of Cenozoic New Zealand Spissatella and Eucrassatella (Bivalvia, Crassatellidae)

description: Details of collections used for morphometrics, comparisons of morphometric methods, and testing of left/right valve inequality.
DOI: 10.5061/dryad.cv0tr/1
title: Reproductive isolation data

description: Data and formulas used for the calculation of the reproductive isolation indices
DOI: 10.5061/dryad.d865p/1
title: H1genotypes

description: Genotypes of Brachycaudus helichrysi H1 individuals grouped into ten populations. First column: individual's name; following columns: allele score for each locus. This data file is in Genpop format.
DOI: 10.5061/dryad.d865p/2
title: H2 genotypes

description: Genotypes of Brachycaudus helichrysi H2 individuals grouped into 14 populations. Two raws per individuals. First column: individual's name; second column: population indication; following columns: allele score for each locus (first line: first allele; second line: second allele). This data file is in Structure format.
DOI: 10.5061/dryad.dt3k0/1
title: Lamprolepis nexus file for MrBayes

description: Aligned sequences of ND2 gene for all samples with MrBayes blocks to run the different partitioning schemes presented in the paper.
DOI: 10.5061/dryad.g860v/1
title: Aguirre_et_al_ data_ped_output

description: The zip file contains that data and pedigree files for the results presented in the manuscript. Also included are the example output files to be used in the attached .docx tutorial. Last a .r file is attached as an example of a script used to generate the output files.
DOI: 10.5061/dryad.gm201/3
title: Chalcid Workshop Riverside 2005

description: Includes data used at the original workshop. Compiled by Liljeblad, Heraty & Burks.
DOI: 10.5061/dryad.gm201/4
title: Workshop Characters 2006

description: Characters (461 total remaining) after evaluation at workshop, with editorial comments.
DOI: 10.5061/dryad.k9m20/1
title: Wayqecha Peru Bird Community Census Data

description: Bird species presence/absence for 41 species at 72, 0.8 ha, survey points of radius 50 m, arranged 120 m apart on a 6 by 12 point grid across a grassland–forest ecotone (See publication Fig. 1 and Fig. A1). Species were recorded as present at a survey point if detected by either sight or song. Spatial grid references for survey points are also given. Y coordinates are grid rows and X coordinates grid columns. This enables the calculation of species presence/absence at larger spatial scales by grouping together neighboring survey points (e.g. grouping the data for two neighboring survey points creates a survey area of 1.6 ha). Data are in .csv format. Column headings: Site: 0.8 ha survey point names. X: X coordinate on survey grid. Y: Y coordinate on survey grid. Other columns are species names (genus and species separated by an underscore): 1= species presence, 0 = species absence.
DOI: 10.5061/dryad.k9m20/2
title: Wayqecha Peru Bird Community Functional Traits

description: Species average bill, tail, wing and tarsus trait values for 41 primarily insectivorous bird species from a cloudforest–grassland ecotone at Wayqecha Biological Station, Peru. Please refer to main text for additional details on trait collection methods. Data are in .csv format. Column headings: Species: Species name. Taxonomy follows Remsen et al. (2011). Bill.nares: Average length of bill (mm) measured from bill tip to anterior edge of nares. Bill.width: Average bill width (mm) measured at anterior edge of nares. Bill.depth: Average bill depth (mm) measured at anterior edge of nares. Wing.length: Average wing length (mm) measured on unflattened wing. Tail.length: Average tail length (mm) measured from the tip of the longest rectrix to the point at which the two central rectrices protrude from the skin. Tarsus.length: Average tarsus length (mm) measured as the distance from the notch at the knee to the third crease at the ankle. Sample.size: Number of individuals measured. Measured.on.Site: Y = measurements taken on individuals captured within the survey site at Wayqecha. N = measurements taken on museum specimens.
DOI: 10.5061/dryad.mg040/1
title: Scripts for MLreassort and MBreassort
DOI: 10.5061/dryad.q9p4s/1
title: 65_N

description: Non-synonymous polymorphism in 65 accessions
DOI: 10.5061/dryad.q9p4s/3
title: 65_S

description: Synonymous polymorphism in 65 accessions
DOI: 10.5061/dryad.qn1n2/10
title: Clark's Nutcracker 2x reference-guided genome

description: 2x consensus Clark's Nutcracker genome from reference-guided assembly using the Zebra Finch genome as reference. Assembly statistics report is included.
DOI: 10.5061/dryad.qn1n2/11
title: Clark's Nutcracker 5x reference-guided genome

description: 5x consensus Clark's Nutcracker genome from reference-guided assembly using the Zebra Finch genome as reference. Assembly statistics report is included.
DOI: 10.5061/dryad.qn1n2/12
title: Clark's Nutcracker mitochondrial assembly and MITOS annotation

description: Reference-guided assembly of the Clark's Nutcracker mitochondrion using consensus Corvidae mitochondrial sequence as guide. Includes MITOS annotation.
DOI: 10.5061/dryad.qn1n2/5
title: Sage-Grouse 1x reference-guided genome

description: 1x consensus Sage-Grouse genome from reference-guided assembly using the Chicken genome as reference. Assembly statistics report is included.
DOI: 10.5061/dryad.qn1n2/6
title: Sage-Grouse 2x reference-guided genome

description: 2x consensus Sage-Grouse genome from reference-guided assembly using the Chicken genome as reference. Assembly statistics report is included.
DOI: 10.5061/dryad.qn1n2/7
title: Sage-Grouse 5x reference-guided genome

description: 5x consensus Sage-Grouse genome from reference-guided assembly using the Chicken genome as reference. Assembly statistics report is included.
DOI: 10.5061/dryad.qn1n2/8
title: Sage-Grouse mitochondrial assembly and MITOS annotation

description: Reference-guided assembly of the Sage-Grouse mitochondrion using consensus Galliformes mitochondrial sequence as guide. Includes MITOS annotation.
DOI: 10.5061/dryad.qn1n2/9
title: Clark's Nutcracker 1x reference-guided genome

description: 1x consensus Clark's Nutcracker genome from reference-guided assembly using the Zebra Finch genome as reference. Assembly statistics report is included.
DOI: 10.5061/dryad.r759h/1
title: Population data and microsatellite genotype matrix of Disocorea humilis

description: Population data and microsatellite genotype matrix of Disocorea humilis
DOI: 10.5061/dryad.tg7b1/1
title: mouth-licking_observations2012

description: Food sharing observations
DOI: 10.5061/dryad.v2n38/18
title: nt3d outgroups

description: Nexus file for species tree estimates for NT3.
DOI: 10.5061/dryad.v2n38/19
title: sptbn1d outgroups

description: Nexus file for species tree estimates for sptbn1.
DOI: 10.5061/dryad.v2n38/20
title: vim56d outgroup

description: Nexus file for species tree estimates for Vim5-6.
DOI: 10.5061/dryad.v2n38/21
title: wld outgroup

description: Nexus file for species tree for AHR gene.
DOI: 10.5061/dryad.v2n38/22
title: Agk collection master_Burbrink&Guiher

description: Spreadsheet of voucher numbers and collecting localities (georeferenced) for tissues of Agkistrodon contortrix and A. piscivorus used in this study. In the Nexus data files only the numbers prior to the "^"  match up to the TG numbers in this list. For example TG103^9 is TG 103 in this list. Nuclear genes have been phased so there may be two copies in the Nexus files (second copy labeled b).
DOI: 10.7925/drs1.ucdlib_31916
title: Harry Street 5

description: Consists of an orthorectified image of the structure in Adobe PhotoShop (PSD) format. The orthorectified image has been derived from one or more photographic images that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and all other image layers have been extracted and saved in TIFF image files, and JPEG files in various resolutions have been derived from the flattened image layer to facilitate inspection.
description: Stone cladding structure, 5 levels above ground.
description: Funded by an award from the Irish Research Council for Science, Engineering and Technology (IRCSET), Embark Initiative Postgraduate Scholarship, grant identifier RS/2011/435.
DOI: 10.5061/dryad.17bn1/3
title: ASU_Acar_v2.1.gff3 -- The gff3 annotation file.
DOI: 10.5061/dryad.34jb6/18
title: 1998-Stutter

description: Example of a 1998 stutter song (.wav format, 16 bit, 44 kHz)
DOI: 10.5061/dryad.4254b/1
title: This script was used to construct metamodel and to perform scale analysis

description: Software : R;  Packages : lattice, polspline, lhs, ade4, caret, neuralnet, nnet, MASS, Hmisc, Cairo; functions are loaded from the library.R file.
DOI: 10.5061/dryad.4254b/2
title: R library where the functions are described

description: Packages used : lattice, polspline, lhs, ade4, caret, neuralnet, nnet, MASS, Hmisc, Cairo.
DOI: 10.5061/dryad.4254b/3
title: Latin hypercube design simulations

description: Each ".res" file is a one day simulation results of noTG model. There are three design of simulation : construct LHS for the construction of the meta-models; test LHS  for neural network metamodel and polynomial regression spline optimizations; and Valid LHS for intercomparaison of different metamodel techniques. A readme file is attached to describe variables of ".res" files.
DOI: 10.5061/dryad.4254b/4
title: Constructed metamodels

description: A rar file with all constructed meta-models. Meta-model files can be loaded in to R script with the function "load".
DOI: 10.5061/dryad.4254b/5
title: 50 and 100 years simulations with noTG model

description: Data used to provide a multi-scale validation test. Each simulation is stocked in one repertory. The name of the repertory was generated as follow : "meta" or "mod"  for simulation made with or without meta-model; TC is the name of the plot; the number of  the sub-plot; the simulated period. Into each repertory, there are five types of output file:                                                               - "finals_plant.s" : where dimensions, carbon and nitrogen pools of each tree are recorded at the end of the simulation.                                                                                                                                  - "finals_sol.s" : where carbon, nitrogen, ligin and water content of each pixel are recorded at the end of the simulation.                                                                                                                                      - "XXX_TC_X_XXX.Day1D.res" : where species and soil state variables are recorded for each species and for each day.                                                                                                                                                   - "XXX_TC_X_XXXTotal.res" : where cumulated species and soil state variables are recorded for each species and for entire period.                                                                                                                - "XXX_TC_X_XXXTree_X.res" : where tree state variables are recorded for each day.
DOI: 10.5061/dryad.4pf25/1
title: Hornbillmovementsrawdata

description: Tab-delimited raw text data file, with data recovered from satellite transmitters, before filtering for quality of satellite read.
DOI: 10.5061/dryad.4r267/4
title: tpc130112_SupplementalDS4

description: Supplemental Dataset 4: Loading values for cfPCA. Provided are the loading values of different traits for cfPCs. See text for details.
DOI: 10.5061/dryad.6347b/1
title: dryaddata

description: #File 1 - population data on development rate# Populations collected may-aug 2009 by David Berger# Data collected sept 2009 - feb 2010 by David Berger & Richard Walters.Region	Population	Lat:Long	Lines	north	Stockholm	59.34 : 18.07	8	north	Nykoping	58.62 : 16.94	9	central	Bayreuth	49.92 : 11.56	11	central	Vienna		48.21 : 16.35	12	central	Zurich		47.35 : 8.53	13	south	Arezzo		43.52 : 11.57	7	south	Perugia		43.15 : 12.18	11	#Description of coloumns in data file:id = individual.population = population of origin.region = region of origin.latitude = latitude of origin.temperature = experimental temperature in which development rate was measured.food level = flies were raised on either excess (high) or limited (low) food.line = the name of the isofemale line to which each measured fly belonged.replicate = the glas vial containing a subset of flies from an isofemale line in a specific temperature (10-20 flies).development time = the time in days it took for a 24 hour larva to reach the adult stage.development rate = 1/development timedevrateST = temperature-specific mean-standardized development rate.
DOI: 10.5061/dryad.66942/1
title: Trees_UCE_15sp_RAxML

description: Trees estimated from UCEs for all 15 species using RAxML. Results from both unpartitioned and partitioned by GC analyses are included.
DOI: 10.5061/dryad.66942/2
title: Trees_UCE_13sp_RAxML

description: Trees estimated from UCEs of 13 species using RAxML. Results of both unpartitioned and partitioned by GC analyses are included.
DOI: 10.5061/dryad.66942/3
title: Trees_MT_MrBayes_pavonine

description: Trees estimated in MrBayes using the mitochondrial matrix (ND2, CYB, and 12S) from 233 galliforms.
DOI: 10.5061/dryad.66942/4
title: Trees_MT_RAxML_pavonine

description: Trees estimated in RAxML from the mitochondrial matrix (ND2, CYB, and 12S) for 233 galliforms.
DOI: 10.5061/dryad.66942/5
title: Trees_MTandUCE_pavonine

description: Most likely tree estimated tree using the combined mitochondrial plus UCE data. There are two trees. First is the one with original estimated branch lengths. Second is the same tree with branch lengths re-estimated using mitochondrial data.
DOI: 10.5061/dryad.66942/6
title: Tree_UCE_SMRT-ML.bootcons

description: Tree estimated using the SMRT-ML method.
DOI: 10.5061/dryad.6c44q/1
title: 3DFilter

description: Text of an ImageJ macro used to remove small unconnected particles from samples before voxel classification.
DOI: 10.5061/dryad.6c44q/10
title: Graph_2

description: Graph obtained using data archived in file DataForFigures_5&6.txt. Explanation on the meaning of the graph can be found in the readMe associated to that file.
DOI: 10.5061/dryad.6c44q/11
title: Graph_3

description: Graph obtained using data archived in file DataForFigures_5&6.txt. Explanation on the meaning of the graph can be found in the readMe associated to that file.
DOI: 10.5061/dryad.6c44q/12
title: Graph_4

description: Graph obtained using data archived in file DataForFigures_5&6.txt. Explanation on the meaning of the graph can be found in the readMe associated to that file.
DOI: 10.5061/dryad.6c44q/3
title: Spatial_Dispersion plugin

description: Source code for the ImageJ plug-in used in the reference paper to calculate the 3D spatial dispersion of vessels in binary stacks. Expansion was performed by rhombicuboctahedral dilation after volume normalization according to the total number of vessel voxels.
DOI: 10.5061/dryad.6c44q/5
title: OriSect_x_Paper

description: The OriSect.zip file carries a compressed folder containing 32 subfolders each containing 6 stacks representative of vascular maps of vessels showing specific projected cross-sections (values in Table I of the paper).In order to correctly normalize all of the stacks against a common reference, the stack with the highest percent Volume of signal (black pixels) should be added to the other 31 folders.BEWARE ! upon expansion this file will occupy 9.3 GB (gigabytes) of space.
DOI: 10.5061/dryad.6c44q/6
title: DataForFigure_4
DOI: 10.5061/dryad.6c44q/7
title: DataForFigures_5&6
DOI: 10.5061/dryad.6c44q/8
title: FilteredStacks

description: The filteredStacks.zip file carries a compressed folder containing 32 binary stacks representative of vascular trees ready to be splitted in substacks according to vessel caliber.The stacks have already been filtered in order to remove particles less than 1 µm3 but their voxels should still be classified by vessel masking as reported in the paper.BEWARE ! upon expansion this file will occupy 1.45 GB (gigabytes) of space.
DOI: 10.5061/dryad.6c44q/9
title: Graph_1

description: Graph obtained using data archived in file DataForFigures_5&6.txt. Explanation on the meaning of the graph can be found in the readMe associated to that file.
DOI: 10.5061/dryad.6dt17/1
title: Phylip formated data matrices and partition files

description: Data matrices for d327 and d128 analyses with partition files
DOI: 10.5061/dryad.72181/1
title: Bennett&Wernberg_recruit facilitation_JEcol_raw data

description: Net recruitment rates (per 3.14 m2) and standardised net recruitment rates, of Scytothalia dorycarpa and Sargassum spp., into experimental plots of different canopy removal intensity). Collected in the field, at locations in southwestern Australia.
DOI: 10.5061/dryad.7c06s/1
title: data, Collet and Blows, JEB, 2014

description: Pedigree of each animal (sire and dam identity), eye colour of the first male to mate, number of offspring with orange or red eye colour
DOI: 10.5061/dryad.8339m/5
title: Level-5_1Syntopic_per_country

description: Structure data file for level-5 analyis. Syntopic C. arvensis- and U. dioica-associated populations of H. obsoletus from Germany, Switzerland, Italy, and Slovenia and one C. arvensis population from France