cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.14j2m.3/4.3
title: Supplementary Table 3

description: In each sex (Sex) of the time interval in mega-annum (From TimeInterval_start_Ma to TimeInterval_end_Ma), the significant allometry equation consists of the slopes (Slope_b), their standard errors at 1-sigma (Slope_SE), the intercept in common logarithm of micrometer (Intercept_log10(a)), and their standard errors at 1-sigma (Intercept_SE). TimeInterval_mean_Ma and n indicate the mean age of the sediment samples in mega-annum and the number of measurements, respectively.
DOI: 10.5061/dryad.14j2m.3/5.3
title: Supplementary Table 4

description: In the time interval in mega-annum (from TimeInterval_start_Ma to TimeInterval_end_Ma);  depth in m CCSF of the top sample (Sample_top_m)  and of the bottom sample (Sample_bottom_m), geological ages in mega-annum of the top sample (Sample_top_age_Ma) and of the bottom sample (Sample_bottom_age_Ma) and the mean age of the samples (Sample_mean_age_Ma); the number of females (n_females), the mean of female H/L ratio (Female_mean_H/L), the standard deviation of female H/L ratio at 1-sigma (Female_SD_H/L), the mean of female length in micrometer (Female_mean_L), the standard deviation of female length at 1-sigma in micrometer (Female_SD_L); the number of males (n_males), the mean of male H/L ratio (Male_mean_H/L), the standard deviation of female H/L ratio at 1-sigma in micrometer (Male_SD_H/L), the mean of male length in micrometer (Male_mean_L), the standard deviation of male length at 1-sigma in micrometer (Male_SD_L); the proportion of females (Proportion_females); the number of juveniles (n_juveniles), the mean of juvenile H/L ratio (Juvenile_mean_H/L), the standard deviation of juvenile H/L ratio at 1-sigma (Juvenile_SD_H/L).
DOI: 10.5061/dryad.1bj88.1
title: Data from: What North America’s skeleton crew of megafauna tells us about community disassembly
DOI: 10.5061/dryad.1bj88.2
title: Data from: What North America’s skeleton crew of megafauna tells us about community disassembly
DOI: 10.5061/dryad.1bj88.2/1.2
title: Table S1

description: Functional data for large North American mammals used in the analysis.
DOI: 10.5061/dryad.1bj88.2/2.2
title: Table S3

description: Functional data for small, extinct North American mammals used in the analysis simulating total mammal functional diversity.
DOI: 10.5061/dryad.1bj88.2/3.2
title: Appendix S2

description: The folder contains all the R script files and data used in the paper. Two datasets are trimmed .csv versions of Table S1 and S3 and the third is functional data for North American mammals from the EltonTraits 1.0 database. Wilman, H., Belmaker, J., Simpson, J., la Rosa, de, C., Rivadeneira, M. M., & Jetz, W. (2014). EltonTraits 1.0: species-level foraging attributes of the world’s birds and mammals. Ecology, 95(7), 2027.  To recreate all analyses and figures used in the paper, open the script “Davis Disassembly Main Code Open First.R”, highlight all the text and click run.  Make sure that all the script files and data .csv files are in the same folder and that that folder is set as your working directory.
DOI: 10.5061/dryad.1bj88.2/4.2
title: Appendix S1

description: Supplementary methods, results, figures, and tables for the analysis.
DOI: 10.5061/dryad.27114/4
title: pipeline_files.tar

description: Set of files required by the pipeline. Includes: InsectaCoreOrthologs (insect core orthologs processed and in single file); InsMito_sumtrees.procd (example summary tree from the mitogenome analysis, which can be used to constrain a species level tree); H03InsProf.muscle.fas (insect COI barcode profile based on Hebert et al. 2003); 12S_profile (set of 12S sequences); treePL_config_file (configuration file for treePL)
DOI: 10.5061/dryad.2k11f/1
title: dryad_data
DOI: 10.5061/dryad.3c7f6/1
title: Raw data - Parasites and a host’s sense of smell

description: This file includes raw data from a study in which olfactory chamber of fathead minnows was experimentally infected withDactylogyrus olfactorius. The data includes parasite intensity,  olfactory acuity of the host (post-exposure and after treatment with anti-parasite), and density of rodlet and mucous cells on the olfactory chamber of infected animals.
DOI: 10.5061/dryad.45gb4/1
title: Raw radar files from tern colony on Great Gull Island, NY

description: Zipped archive containing 200 raw radar sweeps recorded as NetCDF files on 22 July 2014 on Great Gull Island, NY.  Each file contains a single sweep of the radar's antenna, with three variables.  The variable "amplitude" contains 2-D array of radar reflectivities in polar coordinates.  Amplitudes are recorded as 16-bit signed integer values from the digitizer: to convert them to voltages, divide by the variable's "max_counts" metadata value (which is equal to 32764 for all files in this archive).  The other two variables, "pulse_number" and "range", are the values corresponding to the amplitude array's azimuth and radial axes.  Analysis scripts for these files are found in the article's supplementary online information.
DOI: 10.5061/dryad.4fq25/1
title: Juglans_genotypes_DRYAD

description: Sheet genotypes: Individual-ID, Population-ID, SSR genotypes for 7 loci; sheet quanttraits: Individual-ID, Population-ID, morphometric data for 7 traits
DOI: 10.5061/dryad.4g0vt/1
title: Quantitative data on Linkage to HIV care in Mbeya Tanzania

description: Data collected from newly diagnosed HIV individuals with regards to Linkage to HIV care with in the first six months of HIV testing either at the facility-based or mobile/outreach HIV testing site in the rural settings of  Mbeya region in Tanzania.The interviews were administered during enrollment (round one), then at three months(round two) and last interview at six months( round three)since diagnosis.
DOI: 10.5061/dryad.4nf75/1
title: Vegetation and environmental data from deer exclosures in the Upper Midwest

description: Vegetation data include sapling basal area and proportion of quadrats where each species was found (&gt; 5% abundance) as well as several species groups that were developed by adding together all relevant species frequencies.  Environmental data include soil physical and chemical properties, coarse woody debris, canopy conditions and earthworm invasion levels.
DOI: 10.5061/dryad.6471f/1
title: statistic analyses

description: Complete data: sperm measurements, univariate analyses and multivariate analyses from the study "Using sperm morphometry and multivariate analysis to differentiate species and subspecies of gray Mazama".
DOI: 10.5061/dryad.6g75n/1
title: TLR inferred haplotype sequences

description: Zip archive containing sequence data in fasta format for each TLR gene.  Sequences are the inferred haplotypes as determined using the software PHASE.
DOI: 10.5061/dryad.6pv38/1
title: Ismail et al(2016)-PROS

description: Raw Data files have been organized by unique initials of each observer who participated in the study (eg., 'AM').Some observers participated in more than one test condition.Each Excel file corresponds to one unique observer.Each work-sheet within an Excel file corresponds to data from one test condition (eg., 'same house').Within each work-sheet data for all 3 test blocks (baseline, CW adaptor and CCW adaptor) are given.For a given test block:        Column 1: trial number	Column 2: tilt of the 'pedestal' test stimulus (in degrees)	Column 3: tilt of the 'comparison' test stimulus (in degrees)	Column 4: spatial position of the 'pedestal' test (1 - left of fixation, 2 - right of fixation)	Column 5: observer's response (97 - if the test stimulus to the left of fixation was chosen as appearing more upright or 98 - if the test stimulus to the right of fixation was chosen as appearing more upright)Note: For tilts of the 'pedestal' and 'comparison' test stimuli, positive tilts represent CCW rotations in the fronto-parallel plane and negative tilts represent CW rotations in the fronto-parallel plane.
DOI: 10.5061/dryad.6q4g6/1
title: Fluorescent data (wild-type)

description: Fluorescence measurement data
DOI: 10.5061/dryad.6q4g6/2
title: Fluorescent data (mutants)

description: Fluorescence measurement data
DOI: 10.5061/dryad.85tj6/1
title: Raw XML RFID output

description: Raw XML output from the automated RFID system. Data processed according to the methods described in the publication is available upon request.
DOI: 10.5061/dryad.86jm9/1
title: Rewell - Raw data - PLOS One

description: This Excel file tabulates the raw infarct and behavioural data described in our manuscript.
DOI: 10.5061/dryad.89n87/11
title: All UCE contigs - aligned, untrimmed.

description: All UCE contigs from enriched taxa. Data aligned, but not trimmed or filtered for taxon occupancy. Data also available from GenBank using BioProject accession PRJNA360290.
DOI: 10.5061/dryad.89n87/12
title: UCE contigs from genome-enabled taxa.

description: UCE contigs extracted from genome-enabled taxa and used in some analyses. Files can be used to add genome-enabled taxa to UCE data sets. Contigs include UCE core region and 700 bp of flanking DNA.
DOI: 10.5061/dryad.89n87/4
title: Appendix 2 from study.

description: Appendix 2 from study. Includes supplementary methods, table captions, figures, and references.
DOI: 10.5061/dryad.89n87/5
title: Exon and rDNA alignments (trimmed) - enriched samples only.

description: Exon and rDNA alignments for all enriched samples included in this study. Alignments trimmed to remove introns and excessive flanking DNA.
DOI: 10.5061/dryad.89n87/6
title: Exon and rDNA alignments (untrimmed) - enriched samples only.

description: Exon and rDNA alignments for all enriched samples included in this study. Alignments untrimmed.
DOI: 10.5061/dryad.89n87/7
title: Hym-v2 bait set files.

description: Hymenoptera v2 bait set files. Includes the principal and ant-specific UCE bait set files, and the ant-exon bait set files.
DOI: 10.5061/dryad.89n87/8
title: Phylogenetic trees.

description: All phylogenetic trees from study in PDF and either Newick or Nexus formats. Includes 101-terminal and 1060-terminal trees.
DOI: 10.5061/dryad.8j5s7/1
title: 28S minimum evolution matrix and tree

description: Minimum evolution analyses of Hypothenemus sp. specimens, using the molecular marker 28S. Sequence matrix and resulting tree. Analysis performed in Paup*. Analyses implemented evolutionary models (GTR+G+I) as suggested by MrModelTest.
DOI: 10.5061/dryad.8j5s7/2
title: COI full dataset minimum evolution matrix and tree

description: Minimum evolution analyses of Hypothenemus sp. specimens, using the molecular marker COI (mtDNA). Sequence matrix and resulting tree. Analysis performed in Paup*. Analyses implemented evolutionary models (GTR+G+I) as suggested by MrModelTest.
DOI: 10.5061/dryad.8j5s7/3
title: COI reduced dataset minimum evolution analyses matrix and tree

description: Minimum evolution analyses of Hypothenemus sp. specimens, using the molecular marker COI. Subset of full dataset, using only specimens also sequenced for 28S. Sequence matrix and resulting tree. Analysis performed in Paup*. Analyses implemented evolutionary models (GTR+G+I) as suggested by MrModelTest.
DOI: 10.5061/dryad.8j5s7/4
title: Tree from parsimony analyses of combined COI and 28S data

description: Tree file for parsimony analyses of COI and 28S data combined. Matrix shows included OTUs (one specimen representing each OTU in analysis). Analyzed in PAUP*.
DOI: 10.5061/dryad.8j5s7/5
title: Tree from bayesian analyses of COI and 28S data combined

description: Tree file for bayesian analyses of COI and 28S data combined. Matrix shows included OTUs (one specimen representing each OTU in analysis). Analyzed in MrBayes Version 3.2, implementing evolutionary models (GTR+G+I) as suggested by MrModelTest.
DOI: 10.5061/dryad.8ns60/1
title: Land use data and anuran species richness for North American Amphibian Monitoring Program survey sites

description: Data from 587 NAAMP survey sites.  NAAMP survey locations are organized as "stops" within "routes," each of which has a unique SiteID.  Land use variables were measured within buffers of 300m, 600m, 1000m, 5km, and 10km.  Variables include "wet_prop" (proportion of area covered by wetland), "imperv" (proportion of area covered by impervious surface), "PROP_FOR" (proportion of area covered by forest), "PROP_DEV" (proportion of area covered by developed land uses, and "PROP_AGR" (proportion of area covered by row crop agriculture.  Road-related variables are given as linear lengths (meters) within each buffer.  Variables are T_ROAD_LEN (total road length), P_ROAD_LEN (primary (divided) roads), S_ROAD_LEN (secondary roads), O_ROAD_LEN (other roads, i.e. not P or S), and PS_ROAD_LEN (the sum of primary and secondary road lengths).  Data also show the number of NAAMP surveys of each stop (Num.Surv), the number of years covered (Num.Years), mean car count during surveys (Car.Count), number of surveys with ambient noise (Noise.Num), and proportion of surveys that noted noise (NOISE_LEV = Noise.Num/Num.Surv).  Amphibian presence/absence over all surveys are given for the species ANFO, HYCI, HYSQ, LICA, LICL, LIPA, LIPI, LISP, LISY, HYCV, PSTR (full scientific names are provided in the associated paper).  NAs indicate sites outside the known range of each species.  Richness is shown as the sum of all species detected at each stop, and NPP represents estimated Net Primary Productivity at that set (which provided a geographic expectation of anuran species richness).
DOI: 10.5061/dryad.934fg/1
title: Supplemental_File1_Methods_Results_Figures

description: Detailed description of methods and results including figures S1 and S2.
DOI: 10.5061/dryad.934fg/2
title: Supplemental_File2_Tables

description: This is a summary of results for each species analyzed in our study, including presence of ucp1 annotation, synteny analysis, and blasting of raw reads. This table also includes the ftp links to the sequence data used for each species. Species highlighted in purple had no evidence of ucp1 in Ensembl and were investigated further through synteny analysis and BLAST search of their raw data.
DOI: 10.5061/dryad.934fg/3
title: Supplemental_File3_BlastQUERY_Synteny

description: The exon sequences for ucp1 and six flanking genes used in the BLASTn for synteny analysis.
DOI: 10.5061/dryad.934fg/4
title: Supplemental_File4_Protein_UCP1_Query_for_TBLASTN

description: The UCP1 protein sequences used for tBLASTn against the genomes.
DOI: 10.5061/dryad.93hd6/1
title: Experimental data

description: Data table including protist and bacteria densities, Daphnia magna counts and bioareas of protists for each microcosm and sampling date.
DOI: 10.5061/dryad.9d9s3/2
title: Ambystoma_Genetic Data

description: Compressed file consisting of separate R input files for Ambystoma texanum and unisexual Ambystoma. The data for each group is included as txt input files associated with the included R script and CSV files that include group membership as a separate column.
DOI: 10.5061/dryad.f5vn5/1
title: Data_adults

description: Data on body weight, behaviour and gene expression of adult buttonquails
DOI: 10.5061/dryad.f5vn5/2
title: Data_hatchlings

description: Data on body weight and gene expression of hatchling buttonquails
DOI: 10.5061/dryad.g0hd8/1
title: Lepus granatensis transcriptome

description: De novo transcriptome assembly of the Iberian hare, Lepus granatensis.
DOI: 10.5061/dryad.g0hd8/2
title: SNPs inferred from RNA-sequencing data.

description: SNPs inferred from RNA-sequencing data of the Iberian hare, Lepus granatensis.
DOI: 10.5061/dryad.g0hd8/3
title: Genotyped SNPs

description: SNPs genotyped in Iberian hare, Lepus granatensis, and mountain hare, Lepus timidus.
DOI: 10.5061/dryad.g5v64/1
title: Supplementary material - Szczygielski T

description: supplementary information: extended discussion, character list, character matrix, phylogenetic trees, and lists of synapomorphies
DOI: 10.5061/dryad.g5v64/2
title: Specimen photographs - Szczygielski T

description: Photographs of Proterochersis porebensis (ZPAL V.39/48, ZPAL V.39/49, and ZPAL V.39/72) and Keuperotesta limendorsa (SMSN 17757)
DOI: 10.5061/dryad.h85q3/1
title: TreM_Data.txt

description: Presence/absence of microhabitats on Abies alba, Fagus sylvatica, and diverse species trees in different subnatural forests of the french Pyrenees
DOI: 10.5061/dryad.hj30r/1
title: Body mass and microsatellite genotype data of Maltese reed warblers

description: Sheet 1: Mean and variance of the natural logarithm of body mass (g) from field measurements. Sample size and year. Sheet 2: Genotypes of individuals from 2014 in GenePop format, from microsatellite markers.
DOI: 10.5061/dryad.md712/2
title: McDermott and DeGroote raw data PLOS ONE

description: Data were collected at a bird banding station in Pennsylvania and are summarized by year. Species codes are standard four letter abbreviations (http://www.birdpop.org/docs/misc/Alpha_codes_eng.pdf). Variables beginning with X are temperature means in three week intervals (see manuscript text). The following 3 numbers correspond to the month and day at the beginning of the interval. The other column headings are explained in the Methods section.
DOI: 10.5061/dryad.mm3kr/1
title: Associated data

description: These are the field and colour data used in "Egg discrimination along a gradient of natural variation in eggshell coloration." Data were processed in R. For further details see Materials and Methods.
DOI: 10.5061/dryad.p01f4/1
title: Arthan_etal_2017_SE_Asian_Andropogoneae
DOI: 10.5061/dryad.p7d03/1
title: Phenotype measurements

description: Phenotypic data for each LES isolate, standardised by bacterial density and quantified relative to LESB58 isolate. "Per capita" indicates that value has been standardised by OD of the relevant population.
DOI: 10.5061/dryad.p7d03/2
title: survival analysis

description: Time to death (h) for wax moth larvae infected with each LESB58 isolate. Death =0 indicates that larva was not scored as dead at the final timepoint.
DOI: 10.5061/dryad.v5t1m/1
title: Mathematica code for basic model

description: Develops recursion equations for basic model in standard population genetic notation.
DOI: 10.17632/6rnxjzr8yw.1
title: Supplementary Table S1-Towards Functional Annotation of the Preimplantation Transcriptome: An RNAi Screen in Mammalian Embryos

description: Wei Cui et al. -RNAi Screen in mouse preimplantation embryos-712 screened genes
DOI: 10.17632/8s3fps4vvb.1
title: Supplementary Datasets

description: The shared archived combined in Supplementary Datasets represent the actual databases used in the investigation considered in two papers: 1.GIS and remote sensing investigation of the soaring behavior of the Black vulture (Coragyps atratus, Cathartidae) in the southeast Brazil and its implication for the reduction of bird strike risk. Part I. Dependence on meteorological conditions. 2.GIS and remote sensing investigation of the soaring behavior of the Black vulture (Coragyps atratus, Cathartidae) in the southeast Brazil and its implication for the reduction of bird strike risk. Part II. Dependence on superficial characteristics. The data consist of GIS database, remote sensing data and Microsoft Excel datasets elaborated and used for the study. You can find the description of supplementary files in the Description of Supplementary Dataset.docx. The links on supplementary files and their attribution to the text of articles are considered in the Links on files from the articles.docx. The supplementary files are in the folders Datasets, GIS_others, GIS_Raster, GIS_Shape. For any question please write me on this email: natalieenov@gmail.com
DOI: 10.17632/94252v7873.1
title: Supplementary Table S2-RNAi Screen in mouse preimplantation embryos-59 obvious phenotype genes

description: Wei Cui et al. -RNAi Screen in mouse preimplantation embryos-59 obvious phenotype genes
DOI: 10.17632/wcbh49ybpx.1
title: Supplementary Information-RNAi Screen in mouse embryos-Supplementary Table S3-5 and Supplementary Figure S1-6

description: Supplementary Information-RNAi Screen in mouse embryos-Supplementary Table S3-5 and Supplementary Figure S1-6
DOI: 10.5061/dryad.00v20/1
title: Snijders etal 2016/2017 Ecology and Evolution Data

description: This file includes all the data used for the statistical analyses in the manuscript. The data include information on the experimental stimuli, the subject's individual traits, vocal response, spatial response, and the neighborhood response (3 sheets). An additional sheet provides the legend for the column names.
DOI: 10.5061/dryad.27114/10
title: species_level_tree

description: Species level tree of life for insects, in Newick format. Can be input into high capacity tree viewers and also used in further downstream analysis
DOI: 10.5061/dryad.27114/11
title: species_level_tree.processed

description: Species level tree in Newick format. Processed: has been rerooted and made ultrametric. Can be read with high capacity tree viewing software.
DOI: 10.5061/dryad.27114/12
title: Constraints

description: Set of relational constraints used in species level inference. Human readable in tab delimited text format, with Linux newlines.
DOI: 10.5061/dryad.27114/14
title: Development Commands and Notes

description: Text file containing all commands used during development of this project. For user friendly implementation of the central protocol, see SOPHI documents instead.
DOI: 10.5061/dryad.27114/6
title: transcriptomes_supermatrix.nex

description: supermatrix in nexus format, built from nuclear orthologs taken from 33 transcriptomes, including all insect orders
DOI: 10.5061/dryad.27114/7
title: mitogenome_supermatrix.nex

description: Supermatrix of protein coding genes of 806 mitogenomes
DOI: 10.5061/dryad.27114/8
title: specieslevel_supermatrix.nex

description: Species-level insect supermatrix. In nexus format. 8 genes and 49338 species.
DOI: 10.5061/dryad.33st2/1
title: Bd Fluidigm consensus sequences by amplicon

description: Zip file of cleaned and aligned consensus sequences by amplicom
DOI: 10.5061/dryad.33st2/2
title: Bd Fluidigm Primer Table

description: Table of 192 primer pairs used with relevant information such as amplicon size, chromosome, and marker reference
DOI: 10.5061/dryad.3ft30/1
title: Fst_per_SNP_data

description: Fst per SNP between PA-Microphallus and PE-Microphallus 1) with both sets of reads mapped to the PA-Microphallus set of orthologous transcripts, and 2)with both sets of reads mapped to the PE-Microphallus set of orthologous transcripts.
DOI: 10.5061/dryad.3ft30/2
title: Theta_per_transcript_data

description: We used Popoolation to estimate Watterson's theta for each transcript in our set of orthologous transcript for 1) PA-Microphallus, and 2) PE-Microphallus.
DOI: 10.5061/dryad.3ft30/3
title: Pairwise_distance_data

description: We used Clustal Omega to pairs of orthologous transcripts and calculate Jukes-Cantor-corrected pairwise molecular distance between PA-Microphallus and PE-Microphallus
DOI: 10.5061/dryad.3ft30/4
title: Microsatellites_and_primer_data

description: We used MISA and Primer3 to identify potential microsatellite loci and predict primer sequences for amplification from our set of orthologous transcripts for both PA-Microphallus and PE-Microphallus. This file contains the locus and primer information (Tables S8 and S9 in manuscript).
DOI: 10.5061/dryad.3k15h/1
title: Bayesian consensus tree

description: .tre file from the partitioned Bayesian analysis in MrBayes.
DOI: 10.5061/dryad.3k15h/2
title: Maximum likelihood consensus tree

description: .tre file from the partitioned maximum likelihood analysis in RAxML.
DOI: 10.5061/dryad.3k15h/3
title: Phenotypic TTX resistance data

description: Physiological TTX resistance data of populations assayed for the first time in this study.
DOI: 10.5061/dryad.442r8/1
title: I‘iwi movement locations

description: Date, bird band number, age, sex, location (UTM X,Y), elevation, and distance moved from banding location for radio telemetry tracked I‘iwi
DOI: 10.5061/dryad.53m76/1
title: Online File 1 gplates

description: GPlates Project
DOI: 10.5061/dryad.53m76/2
title: Online File 2 R code geological time

description: R code to transfer stratigraphic position into geological time.