cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6p8p0/2
title: CAC.Mimulus.2013.photoperiod.experiment

description: This data file contains flowering data for Mimulus guttatus and Mimulus nasutus from a growthchamber, photoperiod experiment performed in 2013. Individuals from five maternal M. guttatus lines (N=11-12 per line, per treatment) and two M. nasutus lines (N=23 per line, per treatment) were grown under two daylength treatments: 12 or 16 hrs. Whether an individual flowered was recorded as yes or no after eight weeks of growth. Families were originally collected from Catherine Creek in Washington State (USA) in 2010 or 2012. Each row in the data sheet is one individual. See additional information and descriptions of their location of origin in Kenney and Sweigart 2016.
DOI: 10.5061/dryad.6t066/1
title: Origin_struc_resubmission

description: microsatellite markers in genepop2 format, with 10 loci
DOI: 10.5061/dryad.7205r/5
title: Phylogeny alignments

description: Alignments of MYB, HY5, WD40, HD-ZIP genes
DOI: 10.5061/dryad.785sc/1
title: Purple Martin Intratropical Migration Data - Stutchbury et al

description: Timing of migration and location of wintering roosts for Purple Martins tracked by deploying geolocator tracking devices at multiple breeding colonies in North America
DOI: 10.5061/dryad.8c26b/1
title: Probability of eviction data

description: File that contains the relevant data for models that examine the probability of eviction occurring in groups of banded mongooses
DOI: 10.5061/dryad.90p17/1
title: TEAM economic evaluation dataset

description: Clinical and resource use/cost data for economic evaluation. Clinical data variable names in separate document.
DOI: 10.5061/dryad.91bj3/1
title: Raw data
DOI: 10.5061/dryad.9r76h/1
title: orkney_fallofwarness_seabirdenvironment

description: Concurrent information on seabird distributions and environmental variables at 500m and 15min resolution in the Fall Of Warness, Orkney, UK.
DOI: 10.5061/dryad.b952b/1
title: Holman et al DNMT gene expression - DataDryad

description: Raw data for the qPCR experiments. See readme file for a list of the columns' contents.
DOI: 10.5061/dryad.c2p74/1
title: SampleMetadata_and_Summaries

description: Metadata for all fungal community samples, including geographic locations, host species, soil chemical variables, and predicted climate variables. Also includes summaries of fungal communities (richness, rarified richness, and Simpson's diversity) at three levels of taxonomic resolution (operational taxonomic unit, named species, and genus). Data dictionary is available in worksheet 2.
DOI: 10.5061/dryad.c2p74/2
title: CommunityMatrixOTUtranspose

description: Fungal community matrix for all operational taxonomic units delineated at the 97% sequence similarity level. For ease of use in spreadsheet programs, this file is transposed  (OTUs in rows, samples in columns). OTUs are identified to the lowest confident taxonomic level using the RDP naive Bayesian classifier. The first letter in each column heading refers to the functional group as determined by the FUNGuild database. A = arbuscular mycorrhizal fungi, E = ectomycorrhizal fungi, O = "other" fungi, P = plant pathogenic fungi, S = saprotrophic fungi, U = undetermined fungi.
DOI: 10.5061/dryad.c2p74/3
title: CommunityMatrixSpecies

description: Fungal community matrix, with named species in columns and samples in rows. Species are identified to the lowest confident taxonomic level using the RDP naive Bayesian classifier. The first letter in each column heading refers to the functional group as determined by the FUNGuild database. A = arbuscular mycorrhizal fungi, E = ectomycorrhizal fungi, O = "other" fungi, P = plant pathogenic fungi, S = saprotrophic fungi, U = undetermined fungi.
DOI: 10.5061/dryad.c2p74/4
title: CommunityMatrixGenus

description: Fungal Community Matrix, with genera in columns and samples in rows. Genera are identified to the lowest confident taxonomic level using the RDP naive Bayesian classifier. The first letter in each column heading refers to the functional group as determined by the FUNGuild database. A = arbuscular mycorrhizal fungi, E = ectomycorrhizal fungi, O = "other" fungi, P = plant pathogenic fungi, S = saprotrophic fungi, U = undetermined fungi.
DOI: 10.5061/dryad.c2p74/5
title: CommunityMatrixEMFLineage

description: Ectomycorrhizal fungal community matrix, with ectomycorrhizal lineages (following Tedersoo and Smith 2013) in columns and samples in rows.
DOI: 10.5061/dryad.c2p74/6
title: OTU labels and consensus taxonomic assignments

description: OTU labels and consensus taxonomic assignments derived from independent runs of the naive Bayesian Classifer (RDP) using two training sets.
DOI: 10.5061/dryad.kb13m/1
title: European wildcat microsatellites dataset

description: The File contains the raw microsatellites database in GenAlEx format for 1124 cat samples used in the analyses, characterised by 31 loci. For each samples is provided the sampling location, as reported in Tables, Figures and main taxt of the manuscript.This file can be converted to other formats using GenAlEx.
DOI: 10.5061/dryad.kb830/2
title: female productivity at high temperature

description: Female productivity for both heat selection and control population at high temperature. Description for each column in the data sheet can be found in a separate sheet named "Variables" in the file.
DOI: 10.5061/dryad.kb830/3
title: male siring success_generation24

description: Male siring success assayed in generation 24 at high temperature. Description for each column in the data sheet can be found in a separate sheet named "Variables" in the file.
DOI: 10.5061/dryad.kb830/4
title: Supplementary male siring success_generation9

description: Male siring success assayed in generation 9. Description for each column in the data sheet can be found in a separate sheet named "Variables" in the file. The data is not included in the analysis in the main manuscript.
DOI: 10.5061/dryad.np084/1
title: Vital rate data (survival and reproduction)

description: See README
DOI: 10.5061/dryad.np084/2
title: Trait data (first egg laying date synchrony)

description: see README
DOI: 10.5061/dryad.np084/3
title: Pedigree data

description: see README
DOI: 10.5061/dryad.s8r4n/1
title: Brassica_nigra_with_nematodes_and_aphids

description: This file contains data from a greenhouse experiment with nematodes and aphids in a full factorial design on the plant Brassica nigra. There is data  on plant quality (glucosinolates, sugars, amino acids), numbers of herbivores (nematodes, aphids) and results from a simulation model.
DOI: 10.5061/dryad.sv1v1/1
title: Lloret_Garcia_2016_Functional_Ecology

description: N: number of tree
ID: identity of each tree
PLOT: plot where the individual was sample
Lat: Latitude
Lon: Longitude
BA: total basal area (BA) at ground surface, measured individually for each stem and then totalled
dieback:
green.canopy:
fruits:
herbs: % of herbs in the neighbouring vegetation
shrubs: % of shrubs in the neighbouring vegetation
trees: % of tree species in the neighbouring vegetation
eco.pca1: ecological variables were summarised by two Principal Component Axis. These are the scores retained from PCA1.
eco.pca2: ecological variables were summarised by two Principal Component Axis. These are the scores retained from PCA2.
f: mean individual inbreeding estimated based on Jombart et al. (2008)
fij: mean relatedness of each tree with all other trees within its plot. This is the Loiselle's inbreeding estimator according to Loiselle et al. (1995)
DOI: 10.5061/dryad.0643c/1
title: phylogram_bootstrap

description: phylogram of mosses, liverworts, and hornworts with support values based on 500 bootstrap replicates
DOI: 10.5061/dryad.0643c/2
title: moss_chrono

description: chronogram of bryophytes
DOI: 10.5061/dryad.0643c/3
title: control

description: control file for BAMM
DOI: 10.5061/dryad.0643c/4
title: fraction

description: fraction file for BAMM
DOI: 10.5061/dryad.0643c/5
title: alignments

description: 21 gene alignments plus concatenated alignment
DOI: 10.5061/dryad.1p0q9/1
title: FronimosEtAl_Suppl1

description: Reproduction of illustrations from Fick (1890) depicting that author's proposed model for the development of concavo-convex joint polarity.
DOI: 10.5061/dryad.1p0q9/2
title: FronimosEtAl_Suppl2

description: Schematic representation of the experimental setup used to test the hypothesis that proximally-concave joints are more resistant to joint failure by rotation than proximally-convex joints. The setup is depicted for a proximally-concave joint with the maximum load applied to the proximal end of the free element.
DOI: 10.5061/dryad.1p0q9/3
title: FronimosEtAl_SupplTbl1

description: Raw measurements of the weight (in grams) applied to the proximal end of the free element that is necessary to cause joint failure by rotation. The variables are those presented in Text Figure 5. A + symbol denotes the addition of 20 g of weight to the distal end of the free element, representing the presence of additional vertebrae in series.
DOI: 10.5061/dryad.20234/1
title: costData

description: Data from experiment examining host responses (reductions in fitness) as a function of pathogen exposure and/or infection.
DOI: 10.5061/dryad.20234/2
title: costCode pdf

description: R markdown code to reproduce all the analyses from the manuscript. The associated ReadMe file is the compiled pdf containing the code.
DOI: 10.5061/dryad.264j9/1
title: Data_OuedraogoEtAl2016_JEcol

description: We provide a zip file containing three txt files used in the analyses presented in the article showing the alteration of the relationship between forest deciduousness and climate with the geological substrate. The species_trait.txt file contains the species x traits data (767 species, 2 traits). The plot_gen_trait.txt file contains the plot x genera x traits data (62 624 plots, 247 genera). The plot.txt file contains plot location, area, geological substrate, HWSD soil map unit, most common FAO soil type with its proportion in the soil map unit, monthly rainfall, annual rainfall, monthly potential evapotranspiration, annual potential evapotranspiration, and maximum climatological water deficit.
DOI: 10.5061/dryad.2dk3c/1
title: data_packet

description: This is a zipped folder that contains the following files used in analyses for this study: 1) the molecular alignment in NEXUS format with excluded regions, 2) the input file for Bayesian Inference in NEXUS format, 3) the input file for Maximum Likelihood in PHYLIP format, 4) the alignment of only focal group taxa in NEXUS format.
DOI: 10.5061/dryad.3nr2f/1
title: Phenotypic and genotypic data

description: Sheet 1 contains phenotypic (femur length, in millimeters) and genotypic (7 microsatellite loci) data for 352 individuals of the grasshopper Mioscirtus wagneri collected in 12 localities from La Mancha region. Sheet 2 contains phenotypic (femur length, in millimeters) and genotypic (12 microsatellite loci) data for 234 individuals of the grasshopper Ramburiella hispanica collected in 12 localities from La Mancha region. Sheet 3 contains phenotypic (femur length, in millimeters) and genotypic (5 microsatellite loci) data for 204 individuals of the grasshopper Calliptamus barbarus collected in 12 localities from La Mancha region. Sheet 4 contains phenotypic (femur length, in millimeters) and genotypic (6 microsatellite loci) data for 219 individuals of the grasshopper Calliptamus italicus collected in 11 localities from La Mancha region. Sheet 5 contains phenotypic (femur length, in millimeters) and genotypic (8 microsatellite loci) data for 221 individuals of the grasshopper Oedaleus decorus collected in 11 localities from La Mancha region.
DOI: 10.5061/dryad.3nr2f/2
title: Aligned 16S DNA sequences

description: Aligned 16S DNA sequences in FASTA format
DOI: 10.5061/dryad.3nr2f/3
title: Maximum likelihood phylogenetic tree based on 16S DNA sequences

description: Maximum likelihood phylogenetic tree based on 16S DNA sequences and built using the program MEGA
DOI: 10.5061/dryad.3nr2f/4
title: Input files used for STRUCTURE analyses

description: Input files used for Bayesian analyses of genetic structure implemented in the program STRUCTURE. There is one file for each studied species (Mioscirtus wagneri, Ramburiella hispanica, Calliptamus barbarus, Calliptamus italicus, and Oedaleus decorus).
DOI: 10.5061/dryad.3s795/10
title: Hmel1-2.fa.gz

description: Hmel1-1 genome updated to correct all identified misassemblies
DOI: 10.5061/dryad.3s795/11
title: pacbio_falcon_assembly.fa.gz

description: Initial assembly of PacBio reads with FALCON
DOI: 10.5061/dryad.3s795/12
title: pacbio_haploid.fa.gz

description: FALCON PacBio assembly collapsed by HaploMerger
DOI: 10.5061/dryad.3s795/13
title: readdepth_gc_1kb_windows.Hmel2.adjusted.tsv.gz

description: GC content and median read depths unadjusted and adjusted for GC content in 1kb windows for F1 father
DOI: 10.5061/dryad.3s795/14
title: README
DOI: 10.5061/dryad.3s795/8
title: Hmel1-1_haploid.fa.gz

description: Hmel1-2 genome collapsed by HaploMerger
DOI: 10.5061/dryad.3s795/9
title: Hmel1-2_pacbio_merge.fa.gz

description: Hmel1-2_haploid and pacbio_haploid merged by HaploMerger
DOI: 10.5061/dryad.4gn47/2
title: Model Analyses (PDF format)

description: A PDF print-out of the Mathematica 8.0 file.
DOI: 10.5061/dryad.51f00/2
title: OSM File S1. Full 421 character morphological data matrix

description: Morphological data matrix in nexus format with all 421 characters coded for 81 taxa. The file can be opened in the software Mesquite for easy editing, or read directly with any text editor. Data are also available on MorphoBank project # 2167 (www.morphobank.org).
DOI: 10.5061/dryad.51f00/3
title: OSM File S2. Character dissimilarity analysis code

description: R code for running the character dissimilarity analysis described in the text. Comments throughout the code should allow the user to perform the analysis "out-of-the-box". Analysis used to identify characters with 0 dissimilarity, indicating they were possibly not independent.
DOI: 10.5061/dryad.51f00/36
title: Online Supplemental Materials v2

description: Description of online supplementary materials files, figures, tables, methods, results and morphological character descriptions.
DOI: 10.5061/dryad.51f00/4
title: OSM File S3. Reduced 369 character morphological data matrix

description: Reduced morphological data matrix of 369 characters after excluding those characters found to have 0 dissimilarity from the Gower analysis.
DOI: 10.5061/dryad.51f00/5
title: OSM File S4. Morphological data sources GenBank accession numbers and dataset tabulations

description: Sources of morphological and molecular data. Morphological data were either taken from the publication of Seiffert et al. 2015 or scored in this study. GenBank accession numbers are given for each gene used.
DOI: 10.5061/dryad.51f00/6
title: OSM File S5. Concatenated molecular dataset w gene partitions

description: Nexus file of DNA sequence alignments concatenated with the gene partitions indicated
DOI: 10.5061/dryad.51f00/7
title: OSM File S6. Total evidence dataset with reduced morphological data matrix including MrBayes blocks for FBD and TD analyses

description: Nexus file with total evidence dataset (369 morphological characters, 5767 molecular characters) and the MrBayes blocks of code to run the tip-dating and fossilized birth-death process analyses described in the text. The optimal data partitions, including the two molecular partitions identified by PartitionFinder analysis, are specified. The codes for the divergence time analyses are included as comments (enclosed by square brackets []). The first block runs the fossilized birth-death process analysis, remove the [] to run. The second block includes the tip-dating analysis. The individual matrices and codes are also available in the MorphoBank project # 2167.
DOI: 10.5061/dryad.603hs/1
title: GPS coordinates for study populations

description: tab delimited file with GPS coordinates of the six study populations.  US State, County, GPS (Lat/Long) coordinates for each population.
DOI: 10.5061/dryad.603hs/2
title: MHC class IA exon 3 sequences

description: Tympanuchus cupido MHC class IA sequences. Aligned fasta file.
DOI: 10.5061/dryad.603hs/3
title: MHC class II (BLB) exon 2 sequences

description: Tympanuchus cupido MHC class II sequences. Aligned fasta file.
DOI: 10.5061/dryad.603hs/4
title: Data for Fig. 3. genetic and geographic distances between populations

description: Data used in Fig. 3. Pairwise population Jost’s D values for each genetic marker (MHC, mediating and microsatellites) as well as geographic distances and differences in population size between population pairs.  Tab-delimited file.
DOI: 10.5061/dryad.603hs/5
title: Data for Fig1. Genetic variation and population size

description: tab delimited file with data used in Figure 1. Contains Population (state code), genetic marker, alleles per locus (mean-centered), population size, log of population size, squared log of population size, alleles per locus, mean alleles per locus (for each marker) and sample size for each population.
DOI: 10.5061/dryad.603hs/6
title: MHC class I genotypes

description: Number of MHC class I reads from 454 pyrosequencing by individual and sequence.  See MHC class IA exon 3 sequences.fasta for aligned sequences. Tab-delimited file.
DOI: 10.5061/dryad.7q10s/1
title: AFLP data

description: AFLP data
DOI: 10.5061/dryad.7sr33/1
title: All data

description: The file Matassa&&_1-4.zip includes 4 sequentially numbered CSV files containing all the data presented in the manuscript.  The file numbers correspond to the table and figure numbers in the manuscript.
DOI: 10.5061/dryad.82vr4/1
title: Above-ground biomass of Neotropical secondary forests database

description: This database is the product of the 2ndFOR collaborative research network on secondary forests. The database contains aboveground biomass data (in Mg/ha) for 1334 secondary forest plots differing in time since abandonment. The plots belong to different chonosequence studies in the Neotropics. For a description of the database, see Poorter et al. 2016. Biomass resilience of Neotropical secondary forests. Nature doi:10.1038/nature16512.
DOI: 10.5061/dryad.83fb8/1
title: Information of each museum bumble bee specimen screened for Nosema

description: Table showing details of bees screened for Nosema. Details include specimen ID of bees, institution of origin, notes written on museum label associated with each bee, collection date, geographic origin of bee and number of times a bee was screened for Nosema using PCR.
DOI: 10.5061/dryad.83fb8/2
title: Distribution of representative SSUrRNA sequences in various insect samples

description: Table showing how many times each SSU rRNA representative sequence (rows)  is found in each insect sample (columns). Samples were from GenBank, or sequenced with Sanger sequencing or pyrosequencing. Each sample name contains sample ID/GenBank accession no. followed by parasite identification and/or host species identification. See Table S3 for other information associated with each insect sample. See Fig. S4 for phylogenetic network with labeled nodes. Representative DNA sequences can be found in fasta format in the file ssurRNA_rep_sequences.fasta.
DOI: 10.5061/dryad.83fb8/3
title: Alignment of representative SSU rRNA sequences (fasta format)

description: Fasta file of representative SSU rRNA sequences. See file ssurRNA_counts.csv for information on which insect hosts these ssu rRNA sequences are associated with.
DOI: 10.5061/dryad.83fb8/4
title: Nosema genomic loci information

description: Information of six genomic loci used to genotype Nosema from 31 bumbles from North America and Europe. The top BlastX hit of each locus matches a sequence from another Nosema species..
DOI: 10.5061/dryad.9m6n2/1
title: WCT_introgression_data

description: File contains SNP data for all field samples included in the paper.  Additionally, information in table S1 has been included allowing SNPs to be identified by both sequence and source.
DOI: 10.5061/dryad.c2p74/7
title: Representative sequences for each OTU

description: Representative ITS2 sequences for each molecular OTU delineated at the 97% sequence similarity threshold. See "OTU labels and consensus taxonomic assignments" file for taxonomic assignments for each OTU.
DOI: 10.5061/dryad.cm473/1
title: male rep aging data
DOI: 10.5061/dryad.g52j4/1
title: ALPR_SexAllocation

description: 3 data sets of morphological measurements (intensity of infection, host type/mating opportunity, and life history). See README file for more detail.
DOI: 10.5061/dryad.jm6k3/1
title: MIAS DB - File 1

description: The Mammographic Image Analysis Society Digital Mammographic Database * Approval for redistribution provided by J. Suckling (js369@cam.ac.uk)CREDITS: Organiser: J Suckling; Truth-Data: C R M Boggis and I Hutt; Co-Workers: S Astley, D Betal, N Cerneaz, D R Dance, S-L Kok, J Parker, I Ricketts, J Savage, E Stamatakis and P Taylor. Special Thanks: N Karrsemeijer. ========================================================REFERENCE:J Suckling et al (1994) "The Mammographic Image Analysis Society Digital Mammogram Database" Exerpta Medica. International Congress Series 1069 pp 375-378.========================================================
DOI: 10.5061/dryad.jm6k3/2
title: MIAS DB - File 2

description: The Mammographic Image Analysis Society Digital Mammographic Database * Approval for redistribution provided by J. Suckling (js369@cam.ac.uk)CREDITS:Organiser: J Suckling; Truth-Data: C R M Boggis and I Hutt; Co-Workers: S Astley, D Betal, N Cerneaz, D R Dance, S-L Kok, J Parker, I Ricketts, J Savage, E Stamatakis and P Taylor. Special Thanks: N Karrsemeijer. =========================================================REFERENCE:J Suckling et al (1994) "The Mammographic Image Analysis Society Digital Mammogram Database" Exerpta Medica. International Congress Series 1069 pp 375-378.=========================================================
DOI: 10.5061/dryad.jm6k3/3
title: SNUBH-MDB-mCi

description: The Seoul National University Bundang Hospital Digital Mammographic Database - with Individual MC Annotations (SNUBH-MDB-mCi)See also our webpage at http://cv.snu.ac.kr/research/cascade-mc-detector15/index.html for updated information.For questions regarding data, e-mail: syshin@snu.ac.krINFORMATION:1) The size of all images are 1914 pixels x 2294 pixels.2) This zip-file contains 49 mammograms with micro-calcifications (μCs) and corresponding annotations for individual μCs and μC clusters.   - The files named as '****_i.txt' are annotation files for individual μCs and list (x,y) coordinates of each μC.- The files named as '****_c.txt' are annotation files for μC clusters and list bounding boxes of each μC cluster. A bounding box is represented as two (x,y) coordinates, upper left corner and lower right corner.- Coordinate system origin is the upper-left corner.
DOI: 10.5061/dryad.jm6k3/4
title: Annotations of Individual Microcalcification in mini-MIAS DB

description: These files contain image pixel coordinates of individual microcalcifications in the images from the mini-MIAS database, available from http://peipa.essex.ac.uk/info/mias.html. The file name corresponds to the particular image name in the mini-MIAS database. See also our webpage at http://cv.snu.ac.kr/research/cascade-mc-detector15/index.html for updated information.For questions regarding data, e-mail: syshin@snu.ac.kr
DOI: 10.5061/dryad.nf663/1
title: Standardized phenotypic traits and relative fitness in the Anacamptis morio population in 2014

description: Standardized phenotypic traits (plant height, number of flowers, corolla area, spur length, petal brightness, central patch size, petal contrast, proportion dark markings) and relative fitness for 314 individuals of Anacamptis morio (178 open-pollinated controls and 136 supplementally hand-pollinated plants).