cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.32j55/1
title: Conservation Genomics Literature Search 2005-2015

description: This text file details the final list of publications fitting ISI Web of Science conservation genomics literature search detailed in Supplement 1 of the publication "Building strong relationships between conservation biology and primary industry leads to mutually-beneficial genomic advances". All final publications included in this literature search are detailed in the following text document by authors, year published, publication title, journal, and (if available) abstract.
DOI: 10.5061/dryad.32j55/2
title: Primary Industry Genomics Literature Search 2005-2015

description: This text file details the final list of publications fitting ISI Web of Science primary industry genomics literature search detailed in Supplement 1 of the publication "Building strong relationships between conservation biology and primary industry leads to mutually-beneficial genomic advances". All final publications included in this literature search are detailed in the following text document by year published, authors, publication title, journal, and (if available) abstract.
DOI: 10.5061/dryad.4544k/1
title: Tree cover change data

description: % woody cover as measured from aerial photographs using Definiens ECognition between 1940 - 2010. Each data point represents cover measured across 4 common land uses  (conservation areas without elephants, conservation areas with elephants, communal rangelands, and cattle ranches) in untransformed savannas sites across north-eastern South Africa.
DOI: 10.5061/dryad.4s1b0/1
title: stats_CoPderivatives

description: Stats of VTC
DOI: 10.5061/dryad.4s1b0/2
title: VTC Anova Graphs

description: Visual VTC Graphs
DOI: 10.5061/dryad.5qf0p/1
title: Book1Data

description: This data file contains the variables used for the analyses reported in our article published in PLOS One. It is a Excel file that contains 22 mainly variables for 753 subjects. Data originate from the Shuyang survey in northern China between 2011-2013.
DOI: 10.5061/dryad.63dr0/2
title: Full dataset 310 SNPs

description: Full dataset of the 310 SNPs using to investigate contemporary hybridization and introgression patterns between two Ciona species (Ciona robusta and Ciona intestinalis). The file contains the genotype of the 451 individuals studied (213 of C. robusta, 236 of C. intestinalis and 2 F1 hybrids from experimental crosses; note that the natural F1 hybrid found in our study is included in the 236 individuals of C. intestinalis). The file contains also informations on the 310 SNPs (chromosome number, exact nucleotide position along chromosomes and category of polymorphism).
DOI: 10.5061/dryad.69f22/1
title: ITS alignment

description: aligned ITS sequences from Elatine and Bergia species
DOI: 10.5061/dryad.69f22/2
title: matK alignment

description: aligned matK sequences from Elatine and Bergia species
DOI: 10.5061/dryad.69f22/3
title: rbcL alignment

description: aligned rbcL sequences from Elatine and Bergia species
DOI: 10.5061/dryad.6fv96.1
title: Data from: Does personality affect the ability of individuals to track and respond to changing conditions?
DOI: 10.5061/dryad.7bh53/1
title: Host and parasite life history Raw Data

description: This data file contains snail growth, prepatent and patent reproduction, and parasite reproduction data collected from snails exposed to drought stress and/or infection as well as control unstressed and uninfected snails.
DOI: 10.5061/dryad.c3v62/1
title: Phylogenetic tree of the Asteraceae species

description: Plant phylogeny was constructed by combining the information from a composite tree of the Asteraceae family (Funk et al. 2009) for most genera, with taxonomy serving as a surrogate for phylogenetic relationships of nodes for which no information was available. When even the taxonomy was unable to provide relationships, unresolved nodes were left as polytomies. Species were also attached as polytomies deriving from each genus.
DOI: 10.5061/dryad.c3v62/2
title: Phylogenetic tree of the endophagous insect species

description: This is an informal tree constructed by taxonomic substitution (sensu Bininda-Edmonds et al. 2001) of the available phylogenetic information for the insect species collected in our study. Starting with a purely taxonomic tree, we added information on the relationships between taxa whenever available (Supplementary material 1 Figure A1).
DOI: 10.5061/dryad.d69r2/1
title: MST data for Figure 3
DOI: 10.5061/dryad.h4k6f/10
title: Partial Least Squares Analyses (R code)

description: R code to conduct all pairwise partial least squares canonical analyses on the corresponding data.
DOI: 10.5061/dryad.h4k6f/11
title: Partial Least Squares Analyses on Independent Contrasts (R workspace)

description: Morphological data and trees required to calculate phylogenetic independent contrasts and run PLS-CA analyses for all possible pairwise comparisons using both reference phylogenies.
DOI: 10.5061/dryad.h4k6f/12
title: Partial Least Squares Analyses on Independent Contrasts (R code)

description: R code required to calculate Phylogenetic Independent Contrasts, merge datasets and run all pairwise PLS-CA analyses on morphological data and trees included in the associated R workspace.
DOI: 10.5061/dryad.h4k6f/13
title: Convergence Analyses (R workspace)

description: Phylogenetic principal component scores and trees used to test for and calculate the strength of convergence using the SURFACE and windex packages in R.
DOI: 10.5061/dryad.h4k6f/14
title: Convergence Analyses (R code)

description: R code used to conduct tests for convergence in R using the SURFACE and windex packages.
DOI: 10.5061/dryad.h4k6f/15
title: Raw and Normalized CIchlid Morphology Data

description: All of the raw data, specimen data, and regression normalized data used in the analyses here. Analysis-specific subsets and associated code are provided as R workspaces.
DOI: 10.5061/dryad.h4k6f/7
title: Disparity Through Time Analyses (R workspace)

description: Data to conduct disparity through time analyses on phylogeny-specific morphological datasets for body, caudal fin, dorsal fin, and anal fin shape.
DOI: 10.5061/dryad.h4k6f/8
title: Disparity Through Time Analyses (R code)

description: R code to conduct disparity through time analyses on corresponding datasets.
DOI: 10.5061/dryad.h4k6f/9
title: Partial Least Squares Analyses (R workspace)

description: Morphological data for all pairwise PLS analyses.
DOI: 10.5061/dryad.jd2s1/1
title: README for Global Grid Dataset
DOI: 10.5061/dryad.jd2s1/2
title: GG_CSV_L2_L13_20160527

description: 7z archive (2.4GB) of text files in CSV format containing the Global Grid for levels 2 thru 13. Please see README file for further information on naming conventions and variables included in the files.
DOI: 10.5061/dryad.jd2s1/3
title: GGe_L14

description: 7z archive (3.8GB) in CSV format containing the Global Grid for eastern hemisphere, level 14.
DOI: 10.5061/dryad.jd2s1/4
title: GGw_L14

description: 7z archive (3.8GB) in CSV format containing the Global Grid for western hemisphere, level 14.
DOI: 10.5061/dryad.jd2s1/5
title: GG_KML_20160603

description: 7z archive (1.3MB) in KML format containing the Global Grid for eastern and western hemispheres at level 10 that represents terrestrial (land) locations stratified across the urban to rural gradient used in Figure 3 of Theobald 2016 paper.
DOI: 10.5061/dryad.kv145/1
title: Tree seedling growth responses to temperature and bryophyte traits

description: tree seedling responses (biomass and N uptake) to growing in 8 bryophyte species at 7.2 and 9.0 °C for 4 months plus data for 6 traits of the 8 bryophyte species. Bryophyte Traits are: water holding capacity, density, height and water extractable NH4+ and dissolved organic N and total phenols
DOI: 10.5061/dryad.n720d/1
title: Veale_Russello_EVA_SNPdata

description: SNP genotypic data in GENEPOP format.
DOI: 10.5061/dryad.p35r2/1
title: Data_for_landscape_of_anthro_mortality

description: GPS positions, random positions, mortality data used in Resource Selection Function analysis to determine the landscape of use, as described in the methods section of Loveridge et al 2016 The landscape of anthropogenic mortality: how African lions respond to spatial variation in risk
DOI: 10.5061/dryad.q10q6/1
title: infile 41 taxa all loci

description: MrBayes input file of 41 taxa, all loci.
DOI: 10.5061/dryad.q10q6/2
title: MrBayes Nuclear 28 taxa (fig2a)

description: MrBayes file for Nuclear dataset with 28 taxa (fig2a)
DOI: 10.5061/dryad.q10q6/3
title: MrBayes mt 41 taxa (Fig2b)

description: MrBayes file used to generate figure 2b using mt data for 41 taxa.
DOI: 10.5061/dryad.rb5s1/1
title: depth_coordinates

description: GPS coordinates and depth of points used to calculate average depth and maximum depth for each loch
DOI: 10.5061/dryad.rb5s1/2
title: Genomic_PCs

description: individual PC scores from the PCA performed on SNPs
DOI: 10.5061/dryad.rb5s1/3
title: NUist_phenotypes

description: Individual phenotypic data
DOI: 10.5061/dryad.rb5s1/4
title: batch_4_fresh.plink

description: Input file for fastStructure (file1 of 3)
DOI: 10.5061/dryad.vf1jj/1
title: Concatenated alignment of CO1, CAD, and EF1a

description: Concatenated alignment of CO1, CAD, and EF1a for Philodoria leaf mining moth species and outgroups
DOI: 10.5061/dryad.vf1jj/2
title: 3GENE Photos

description: Photos of sequenced Philodoria leaf miner tissue
DOI: 10.5061/dryad.11cd0/1
title: EastAltantic_genotypic data_Psaltatrix

description: Microsatellite genotypic data for Pomatomus saltatrix
DOI: 10.5061/dryad.11cd0/2
title: IMa_combined_elf_15loci_1

description: IMa input file, 15 loci (cytochrome b, AM2B1 intron and 13 microsatellite loci)
DOI: 10.5061/dryad.122j7/1
title: Species cover data (%) _2006 to 2009_Figs 1-5
DOI: 10.5061/dryad.20qv5/1
title: Canopy soil trace gas flux in Ecuador

description: Excel CSV file of canopy soil gas flux (CO2, CH4, N2O) measured at 3 elevations (1000 m - Bomb, 2000 m - ECSF, 3000 m - Caja) in forests of southern Ecuador. Fluxes were measured in upper (U) and lower (L) canopy soils from control (C) and treatment (added nitrogen (N), phosphorus (P) and N+P) plots; on each date intact soil cores were incubated in sealed jars and then returned to the tree after measurement.
DOI: 10.5061/dryad.314b2/1
title: Commandlines

description: Biinformatic command lines to obtain final VCF
DOI: 10.5061/dryad.43q71/1
title: BEAST log files for Leave-one-out-cross-validation

description: Example BEAST log files for Leave-one-out-cross-validation analysis and additional files to plot results using the "PlotLOOCV" function using the R-package TipDatingBeast. See tutorial included in package for commands.
DOI: 10.5061/dryad.43q71/3
title: Example BEAST log files for Date-randomized test

description: Example BEAST log files for Date-randomized test to plot results using the "PlotDRT" function using the R-package TipDatingBeast. See tutorial included in package for commands.
DOI: 10.5061/dryad.43q71/4
title: Example datafile for BEAST 1

description: Example datafile for BEAST 1 used to produce the log files deposited here.
DOI: 10.5061/dryad.43q71/5
title: Example datafile for BEAST 2

description: Example datafile for BEAST 2 used to produce the log files deposited here.
DOI: 10.5061/dryad.46n26/1
title: Dataset for Staab et al., Tree phylogenetic diversity...

description: A description of the data is provided in the attached ReadMe document.
DOI: 10.5061/dryad.5331t/1
title: Microsatellite genotypes of Arion vulgaris populations in Europe

description: Length, in base-pairs, of alleles at 15 microsatellite loci in 632 individuals of Arion vulgaris from 32 European populations. Missing data coded as NA.
DOI: 10.5061/dryad.5jn6b/1
title: Charpentier-Cohen_2016_RS_OpenSci

description: Contains raw data for all behavioral experiments and extracellular fluid analyses.
DOI: 10.5061/dryad.5qf0p/2
title: original data to table 4 of text

description: This original data file contains the variables used for the analyses reported in our article published in PLOS One. It is from text in the table 4 (MetS individual components and the risk of SVE in patients with minor ischemic stroke during follow-up, adjusted for age and sex).Sex:1=male,0=female; SVE (subsequent vascular event),1group=yes,2 group =no SVE; MetS (metabolic syndrome),1=with SVE, 0=no SVE; AO(Abdominal obesity):1=with SVE,0=no SVE; HBP(hypertension),1=with SVE,0=no SVE; BG(blood glucose,mmol/l); TG (triglycerides), 1=with SVE, 0=no SVE ; HDL-C(high density lipoprotein cholesterol),1=with SVE,0=no SVE.
DOI: 10.5061/dryad.669qn/1
title: Response to experimental noise

description: Average changes in frequency measure made by black-capped chickadees in response to experimental noise. Mean change is calculated for songs in Hz and for songs which were first log10 transformed ('from log'). Habitat urbanization index and spl (dB(Z)) measures for each male's territory are also provided.
DOI: 10.5061/dryad.669qn/2
title: Average frequency use and local ambient noise

description: Average frequency measures of singing black-capped chickadees. Measures are provided as average Hz and as averages made from songs which were first log10 transformed ('from log'). Habitat urbanization index and spl (dB(Z)) measures for each male's territory are also provided.
DOI: 10.5061/dryad.68h07/1
title: Supporting Data 020916
DOI: 10.5061/dryad.78r91/1
title: Climate grids_GEOTIFF

description: High resolution (50 m) raster maps (format GEOTIFF) of 15 climate variables over Sweden for the time period 2000-2010
DOI: 10.5061/dryad.78r91/2
title: Climate grids_R format

description: High resolution (50 m) raster maps (format: R multi-layer grid)  of 15 climate variables over Sweden for the time period 2000-2010
DOI: 10.5061/dryad.7bh53/2
title: Statistics Information for each Dependent variable

description: This is a table containing specific statistical output for each dependent variable.
DOI: 10.5061/dryad.7bh53/3
title: Aestivation Data R code

description: This file contains the R code used to run our analyses.
DOI: 10.5061/dryad.811h1/1
title: coordinates

description: This file contains the latitude and longitude for each of the 13 sites sampled in this study. Coordinates were obtained from Google Earth. Data columns are as follows: (1) site (n=13); (2) latitude; (3) longitude.
DOI: 10.5061/dryad.811h1/2
title: experimental data

description: This file contains the full results of the inoculation experiment from which susceptibility and the proportion of sexual females were determined for 13 sites in each of three years. Juvenile snails from each were exposed to high doses of parasites from Lake Alexandrina. Following parasite development, snails were evaluated for sex, infection and reproductive mode. Data columns are as follows: (1) year (n=3; 2013, 2014, and 2015); (2) site (n=13); (3) replicate (n=3-6 depending on year); (4) sexual: number of sexual females in the replicate; (5) asexual: the number of asexual females; (6) healthy: the total number of healthy females; (7) infected: the total number of females infected with Microphallus; (8) healthy_sexual: the number of healthy, sexual females; (9) infected_sexual: the number of sexual females infected with Microphallus. Columns 4 and 5 give the proportion of sexual females at a site. Columns 6 and 7 give overall susceptibility, while 8 and 9 give susceptibility of sexual females only. In 2014, the proportion of sexual females was obtained from 6 experimental replicates, and susceptibility from 3.
DOI: 10.5061/dryad.811h1/3
title: temporal change

description: This file contains the change in susceptibility and proportion sexual females at each site through time. The change is calculated as the value in 2015 minus the value in 2013. Data columns are as follows: (1) site (n=13); (2) sex: change in the proportion of sexual females; (3) susceptibility: change in overall susceptibility; (4) sexual_susceptibility: change in susceptibility of sexual females.
DOI: 10.5061/dryad.811h1/4
title: prevalence

description: This file contains the length-corrected estimates of infection prevalence for each site in 2013 through 2015. Length-corrected estimates are given for all females and for sexual females only. The length-corrected estimates of infection prevalence for all females were obtained from Gibson et al. (2016, Am Nat). The raw data for those estimates are associated with that publication – Dryad Digital Repository: http://dx.doi.org/10.5061/dryad.t89hc. The length-corrected estimates of infection prevalence for sexual females only were obtained in the same manner as described in Gibson et al. (2016, Am Nat): they are the estimated marginal means for infection prevalence obtained from a generalized linear model with site, year, their interaction and shell length (mm, covariate) as predictors of the probability of infection of an individual, sexual female. The raw data for those estimates are included in this Dryad data package, with field_data.csv. Infection prevalence of sexual females was only available for 2014-2015. Data columns are as follows: (1) year (n=3); (2) site (n=13); (3) prevalence_lc: length-corrected prevalence for all females; (4) prevalence_sexual_lc: length-corrected prevalence for sexual females.
DOI: 10.5061/dryad.811h1/5
title: field data

description: This file contains data for individual female snails collected from our 13 field sites in 2014 and 2015. These data were used in validating our results for variation in the proportion of sexual females between sites and for estimating the infection prevalence of sexual females. Data columns are as follows: (1) year (n=2); site (n=13); (3) length: shell length in millimeters; (4) infected: 0 for healthy, 1 for castrated with Microphallus; (5) ploidy: 2 for diploid sexual and 3 for triploid asexual.
DOI: 10.5061/dryad.9vs26/1
title: Images and meshes for the BTx623 x IS3620C RIL population part "aa"

description: The file is part "aa" of a set of 7 files (aa-af) corresponding to a compressed archive (.tar.gz) that has been split (using split). These will need to be concatenated (using cat) to restore the original archive (see http://wiki.datadryad.org/Large_File_Transfer). In the archive, each directory represents a timepoint, and each timepoint contains directories with images and a mesh corresponding to RIL lines from the BTx623 x IS3620C population. Each RIL has three replicates, and the suffix indicates the replicate number.
DOI: 10.5061/dryad.9vs26/2
title: Images and meshes for the BTx623 x IS3620C RIL population part "ab"

description: The file is part "ab" of a set of 7 files (aa-af) corresponding to a compressed archive (.tar.gz) that has been split (using split). These will need to be concatenated (using cat) to restore the original archive (see http://wiki.datadryad.org/Large_File_Transfer). In the archive, each directory represents a timepoint, and each timepoint contains directories with images and a mesh corresponding to RIL lines from the BTx623 x IS3620C population. Each RIL has three replicates, and the suffix indicates the replicate number.
DOI: 10.5061/dryad.9vs26/3
title: Images and meshes for the BTx623 x IS3620C RIL population part "ac"

description: The file is part "ac" of a set of 7 files (aa-af) corresponding to a compressed archive (.tar.gz) that has been split (using split). These will need to be concatenated (using cat) to restore the original archive (see http://wiki.datadryad.org/Large_File_Transfer). In the archive, each directory represents a timepoint, and each timepoint contains directories with images and a mesh corresponding to RIL lines from the BTx623 x IS3620C population. Each RIL has three replicates, and the suffix indicates the replicate number.
DOI: 10.5061/dryad.9vs26/4
title: Images and meshes for the BTx623 x IS3620C RIL population part "ad"

description: The file is part "ad" of a set of 7 files (aa-af) corresponding to a compressed archive (.tar.gz) that has been split (using split). These will need to be concatenated (using cat) to restore the original archive (see http://wiki.datadryad.org/Large_File_Transfer). In the archive, each directory represents a timepoint, and each timepoint contains directories with images and a mesh corresponding to RIL lines from the BTx623 x IS3620C population. Each RIL has three replicates, and the suffix indicates the replicate number.
DOI: 10.5061/dryad.9vs26/5
title: Images and meshes for the BTx623 x IS3620C RIL population part "ae"

description: The file is part "ae" of a set of 7 files (aa-af) corresponding to a compressed archive (.tar.gz) that has been split (using split). These will need to be concatenated (using cat) to restore the original archive (see http://wiki.datadryad.org/Large_File_Transfer). In the archive, each directory represents a timepoint, and each timepoint contains directories with images and a mesh corresponding to RIL lines from the BTx623 x IS3620C population. Each RIL has three replicates, and the suffix indicates the replicate number.
DOI: 10.5061/dryad.c3v62/3
title: Asteraceae-Herbivore interaction network

description: Associations between Asteraceae and flower-head endophagous insects were assessed quantitatively in 20 remnants of Cerrado vegetation in southeastern Brazil (Almeida-Neto et al. 2011).The sampled sites were spaced from 0.6 to 41.4 km apart (mean distance = 16.3 km), at elevations ranging from 600 to 950 m. Plants and insects were sampled from April to May 2003. The sampling design consisted of 15 transects of 30m × 5m, randomly allocated in relation to the edge of the areas. We sampled flower heads from at least 20 individuals of each Asteraceae species, collecting about 80 mL of flower-heads per individual plant whenever available. In the laboratory, the flower-head samples were kept in plastic containers covered with a mesh lid. Adult herbivore emergence was checked at least weekly for a period of two months. We spent about four person-hours collecting flower-heads in each period and site. Further information on sampling, vegetation, and studied areas can be found in Almeida-Neto et al. (2010, 2011).
For the purpose of this study, both species and their interactions were integrated into a single regional plant-herbivore network, depicting the presence or absence of interactions between each plant-herbivore pair. We only included in the regional interaction network the plant and insect species that occurred in at least five (25%) of the sampled areas. By constructing the network in this way, we aimed to minimize the effect of spatial mismatch on the structure of plant-herbivore interactions. Among the 1210 plant-herbivore pairs included in our network, only 12 do not co-occur in at least one site.
DOI: 10.5061/dryad.cj38k/1
title: R code

description: R code for estimating the number of pulses in a mass extinction
DOI: 10.5061/dryad.cj38k/2
title: sample dataset

description: Seymour Island ammonite dataset from Macellari 1986
DOI: 10.5061/dryad.dh88c/1
title: IonXpress_009_R_2013_05_26_04_37_58_user_SN2-40-MatthieuSampleA_barcodes7-8-9_Auto_user_SN2-40-MatthieuSampleA_barcodes7-8-9_61

description: Raw amplicon sequence (mtCOI) data obtained on the Ion Torrent platform (Thermo Fisher Scientific).
DOI: 10.5061/dryad.dh88c/2
title: IonXpress_016_R_2013_03_29_20_58_02_user_SN2-4-MarineGeo_J_K_L_Auto_user_SN2-4-MarineGeo_J_K_L_31

description: Raw amplicon sequence (mtCOI) data obtained on the Ion Torrent platform (Thermo Fisher Scientific).
DOI: 10.5061/dryad.dh88c/3
title: Jordan_Metabarcode_OTUtable

description: This table summarize the number of sequences per Operational Taxonomic Units (OTU) and per sample. OTUs were considered matched to a reference barcode when the level of similarity of the Blast search was higher than 97%. In the absence of direct match, the Bayesian phylogenetic approach implemented in the Statistical Assignment Package (Munch et al. 2008) was used for taxonomic assignment. The description of each sample can be found in Table S2 of the manuscript.