cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.23cg1/1
title: xml files for BEAST1.8.0

description: A total of 370 whole mitochondrial genomes (WMGs) corresponding to Native Central and South American populations were collected from published studies. Of note, the large dataset of 215 Mexican WMGs from Kumar et al. 2011 was not used to prevent an over-representation of Mexican samples. We randomly selected three replicate datasets of 87 sequences, all of which contained exclusively the five Native American haplogroups A2, B2, C1, D1, and D4h3a (table S3). We added 20 East Siberian individuals from sister lineages within haplogroups A, B, C and D in order to estimate the time of the split between Siberian and American lineages. We also added the 92 ancient WMGs from the study, as well as the Anzick-1 mitogenome, to obtain three replicate datasets of 200 sequences. The Anzick-1 WMG was included as it added a deep time calibration at 12.6 kya, was the only ancient D4h3a sequence available, and because the Anzick-1 individual can reasonably be considered a descendant of the first wave of colonizers.
DOI: 10.5061/dryad.24610/1
title: Biometric measurements, ptilochronology and fluctuating asymmetry of house sparrows from urban and rural areas in France

description: The database consists of biometric measurements (body mass, tarsus length, wing length, bill height and bill length) and scores of feather moulting stage collected during field sampling and body mass obtained from experiment. Data on ptilochronology were yielded through manual measurement of feather growth bar width. Fluctuating asymmetry data consist of two times measurements of feather length which were used to estimate fluctuating asymmetry.
DOI: 10.5061/dryad.37972/10
title: Vosteen et al. 2016_R Data_Fig. 3 honeydew attractivity

description: file used for statistical analysis in R
DOI: 10.5061/dryad.37972/11
title: Vosteen et al. 2016_R Data_Fig. 4a honeydew quality

description: file used for statistical analysis in R
DOI: 10.5061/dryad.37972/12
title: Vosteen et al. 2016_R Data_Fig. 4b honeydew quantity

description: file used for statistical analysis in R
DOI: 10.5061/dryad.37972/13
title: Vosteen et al. 2016_R Data_Fig. 5 less suitable plant 2014

description: file used for statistical analysis in R
DOI: 10.5061/dryad.37972/14
title: Vosteen et al. 2016_R Data_Fig. 6 less suitable plant 2014_Aug

description: file used for statistical analysis in R
DOI: 10.5061/dryad.37972/8
title: Vosteen et al. 2016_R Data_Fig. 2e quantitative honeydew collection

description: file used for statistical analysis in R
DOI: 10.5061/dryad.37972/9
title: Vosteen et al. 2016_R Data_Fig. 2f quantitative honeydew collection

description: file used for statistical analysis in R
DOI: 10.5061/dryad.42p15/1
title: Dhirsuta1995.2013

description: All measures are for Duroia hirsuta trees in a 50 ha permanent plot at the Yasuni National Park. Diameter at breast height (DBH) (1.30 m) of each tree measuring at least 1 cm DBH. DBH1995= tree DBH in 1995, DBH2013= tree DBH in 2013, Neighbors= number of D. hirsuta trees within 5 m of a focal tree.Habitat= type of habitat where each tree was located, three categories: ridge, slope, valley. Ant.type= ant indicates that the mutualist ant (Myrmelachista schumanni) was recorded in the D. hirsuta tree in 2010, the tree had signs of hosting the tree (ant understory clearings) in 2010, and the ant was recorded in the tree in 2013; no ant= the ant was recorded either in 2010, 2013, or in none of these years.
DOI: 10.5061/dryad.42p15/2
title: Dhirsuta2007.2013

description: All measures are for Duroia hirsuta trees in a 50 ha permanent plot at the Yasuni National Park. Diameter at breast height (DBH) (1.30 m) of each tree measuring at least 1 cm DBH. DBH1995= tree DBH in 1995, DBH2013= tree DBH in 2013, Neighbors= number of D. hirsuta trees within 5 m of a focal tree.Habitat= type of habitat where each tree was located, three categories: ridge, slope, valley. Surv= whether the tree was alive (A) of died (D) in 2013, considering only trees that were alive in 2010. All measures are for Duroia hirsuta trees in a 50 ha permanent plot at the Yasuni National Park. Diameter at breast height (DBH) (1.30 m) of each tree measuring at least 1 cm DBH. DBH1995= tree DBH in 1995, DBH2013= tree DBH in 2013, Neighbors= number of D. hirsuta trees within 5 m of a focal tree.Habitat= type of habitat where each tree was located, three categories: ridge, slope, valley. Ant.type= ant indicates that the mutualist ant (Myrmelachista schumanni) was recorded in the D. hirsuta tree in 2010, the tree had signs of hosting the tree (ant understory clearings) in 2010, and the ant was recorded in the tree in 2013; no ant= the ant was recorded either in 2010, 2013, or in none of these years. Ant.type1= whether M. schumanni was present (1) or absent (0); ant present was in trees that had a record of M. schummani and ant-understory clearing in 2010 and the M. schumanni was present in 2013, or absent was when none of the three conditions were met.
DOI: 10.5061/dryad.61d1m/10
title: treemix_input_30_4

description: Treemix input file.
DOI: 10.5061/dryad.61d1m/11
title: phenotypic_data_analysis

description: This folder contains an R-script with the complete data analysis for the phenotypic traints analized in this paper. Besides the folder contains all phenotpic data and the data logger data from the frost test experiment.
DOI: 10.5061/dryad.61d1m/12
title: temp_logger_high_altitude

description: Temperature logger data from the two high altitude sites. These data were used to produce fig. S9.
DOI: 10.5061/dryad.6p072.2
title: Data from: Spider phylogenomics: untangling the spider tree of life
DOI: 10.5061/dryad.6p072.2/1.2
title: Data Supermatrix

description: Phylogenetic supermatrix data set.
DOI: 10.5061/dryad.7k1g1/1
title: Raw data of field sampling and offspring analysis

description: Raw data of field sampling and offspring analysis
DOI: 10.5061/dryad.7qs68/1
title: Dendrogramma partial transcriptome

description: Trinity assembled Dendrogramma partial transcriptome, zipped fasta format.
DOI: 10.5061/dryad.7qs68/2
title: Pipeline scripts

description: Phylogenomic pipeline: zipped folder containing eight unix shell scripts
DOI: 10.5061/dryad.7qs68/3
title: Read Me file

description: Word document providing contents and information on this DRYAD package.
DOI: 10.5061/dryad.7qs68/4
title: Ancillary files

description: Zipped folder containing ancillary pipeline text files, and excel sample table and newick RAxML tree files.
DOI: 10.5061/dryad.7qs68/5
title: Metazoan phylogenomic data matrix

description: Final 81 taxa, 251 gene fasta format amino acid alignment.
DOI: 10.5061/dryad.8v96r/1
title: Salmonid life history data from published literature

description: This is a compilation of published values of salmonid egg sizes, fecundity, body size, age at maturity, and GSI for 14 species.
DOI: 10.5061/dryad.934qn/1
title: Flies_socioecological_hyena_data

description: The data is a comma separated values spreadsheet with headers in the first row. Headers ending in ".ec" refer to E. coli assays and headers ending in ".pm" refer to P. mirabilis assays. The columns "d.mic.90.bka", "d.igg", and "d.igm" are the primary response variables used in the analyses for the manuscript.
DOI: 10.5061/dryad.9j1cp/1
title: Pasquier_Grüter_Raw_Data

description: The file contains the raw data from the study
DOI: 10.5061/dryad.9k3k5/1
title: microsatellite data by locus and population

description: This file contains microsatellite data (12 loci) for 152 individuals from nine Eurasian lynx populations in Europe (and Russia). The data were used to examine the genetic variability in autochthonous and reintroduced lynx populations. Data is provided by locus and population.
DOI: 10.5061/dryad.d35s0/1
title: Na Wu-corvis primary data
DOI: 10.5061/dryad.dm93h/1
title: Dataset_performance curve Drosophila melanogaster

description: Walking speed of Drosophila melanogaster acclimated to variable and constant temperature. Curve parameters are as follows:  lower optimal limit (X1), upper optimal limit (X2), optimal thermal range (OR), temperature at which performance is maximized (To), maximum performance (Vmax), performance breadth (Tbr), lower and upper thermal limits (LTL and UTL, respectively),
DOI: 10.5061/dryad.f54m5/1
title: Mulloidichthys flavolineatus measurements

description: For each specimen examined we provide Standard Length, Head Length, Head Length in Standard Length, Eye Diameter, Eye Diameter in Standard Length, Barbel Length, and Barbel Length in Standard Length
DOI: 10.5061/dryad.mj0hn/1
title: BEAST XML input files used for the data analysis
DOI: 10.5061/dryad.n193d.1
title: Data from: Effects of fire regime on the population genetics of natural pine stands, in Genetic structure of forest trees in biodiversity hotspots at different spatial scales (Ph.D. thesis).
DOI: 10.5061/dryad.n193d.2
title: Data from: Effects of fire regime on the population genetics of natural pine stands, in Genetic structure of forest trees in biodiversity hotspots at different spatial scales (Ph.D. thesis).
DOI: 10.5061/dryad.n193d.2/1.2
title: Pinus halapensis, 8pops, 369 samples, 251SNPs
DOI: 10.5061/dryad.n193d.2/2.2
title: Pinus halepensis, 8pops, 366 samples, 9 nSSRs
DOI: 10.5061/dryad.pv608/8
title: Home Range Habitat Areas, Salt Valley

description: Inputs for a test of the resource abundance hypothesis. We used the home range data for the mast year (1997) and the first post-mast year (1998) in separate analyses to examine the correlation between home range area and SMPA (seed mass per unit area). We also examined the effect of year on home range size and SMPA using ANOVA. Data were collected at Arches National Park, Grand Co., Utah.
DOI: 10.5061/dryad.v2211/1
title: Raw seed production data for model fitting

description: Numbers of viable seeds of species i-k initially planted (Nt) and produced by plants (Nt1) in the experiment. The id codes of competing species i-k are listed under spi, spj, and spk, and the full species names names that correspond to the id codes are in Table S3. The experiment was replicated in a wet (w) and a dry (d) environment, denoted under 'moisture'.
DOI: 10.5061/dryad.v2211/2
title: Bayesian tree in nexus format

description: Phylogenetic tree used to get estimates of phylogenetic distance, calibrated to millions of years based on the fossil record
DOI: 10.5061/dryad.v63g0/1
title: Microsatsatellite Data

description: The total scored data set for all 17 microsatellite loci for Alticus arnoldorum, including sample site, latitude and Longitude
DOI: 10.5061/dryad.v63g0/2
title: Meta-analysis Data

description: This is the data collected from each study used in the meta-analysis portion of the above publication. For each species data includes; Species, Oder (taxonomy), Spatial Pattern (as identified by authors), Number of populations (per study), Mean population size (calculated from the number of populations), Max Distance (the distance between the two farthest populations), FST for Max distance (the corresponding FST score for the two farthest populations), Min Distance (the distance between the two closest populations), FST for Min Distance (the corresponding, FST score for the two closest populations), FST slope (calculated as the the change in FST divided by the change in distance), IBD Present/Absent (as identified by authors), explanation of spatial pattern (as identified by authors) and reference
DOI: 10.5061/dryad.vc94d/1
title: Raw coordinates for aedeagus
DOI: 10.5061/dryad.vs08j/1
title: Microsatellite genotypes of Hyla orientalis samples

description: The file includes genotypes from 12 microsatellite loci in 521 samples of H. orientalis. For all loci but Ha-T53, genotypes of 150 samples were generated by Dufresnes et al. 2015, BMC Evol Biol and re-analyzed for this study. NA: missing data.
DOI: 10.5061/dryad.vs08j/2
title: Mitochondrial cytochrome-b sequence alignment

description: Sequence alignment of mitochondrial cytochrome-b (cyt-b), from 407 H. orientalis samples.
DOI: 10.5061/dryad.0m068/1
title: Milk transfer to individual cubs

description: main data set for the analysis of milk transfer, nursing bout duration and milk transfer rate to individual cubs
DOI: 10.5061/dryad.0nm8t/1
title: EncHistBuilder_RD

description: This R script contains functions to subset and format the salamander spreadsheet into a multi-catch SCR encounter history for a robust design analysis.
DOI: 10.5061/dryad.0nm8t/10
title: Season3_Closed_Results

description: The results from the autumn 2014 closed-population analysis.
DOI: 10.5061/dryad.0nm8t/2
title: Sal_Data

description: This RData file contains the three seasons of mark-recapture data used for our analyses.
DOI: 10.5061/dryad.0nm8t/3
title: EncHistBuilder_Closed

description: This R script contains functions to subset and format the salamander spreadsheet into a multi-catch SCR encounter history for a closed-population analysis.
DOI: 10.5061/dryad.0nm8t/4
title: Analysis_Closed

description: This R script contains all the steps to load the data, format it, and run the MCMC estimation through program JAGS for the closed-population spatial capture-recapture analysis.
DOI: 10.5061/dryad.0nm8t/5
title: Analysis_RD.R

description: This R script contains all the steps to load the data, format it, and run the MCMC estimation through program JAGS for the robust design spatial capture-recapture analysis.
DOI: 10.5061/dryad.0nm8t/6
title: ClosedPop JAGS Model

description: A model file for program JAGS. Contains the actual closed-population model whose parameters will be estimated in JAGS. Includes a covariate for sex of the individual.
DOI: 10.5061/dryad.0nm8t/7
title: RD JAGS Model

description: A model file for program JAGS. Contains the actual robust design model whose parameters will be estimated in JAGS. Includes a covariate for sex of the individual.
DOI: 10.5061/dryad.0p1f5/1
title: GalliformesCranium

description: Data set of 3D coordinates of 26 landmarks describing cranium shape of Galliformes (Aves, Galloanserae).
DOI: 10.5061/dryad.1n199/1
title: dataset MS female sperm storage

description: raw data
DOI: 10.5061/dryad.1ng8c/1
title: Canadian ACP engagement survey pilot

description: This file contains the responses of 196 patients in acute care, primary care, cancer care and renal care to a 108-item ACP engagement survey.  Process Measures (knowledge, contemplation, self-efficacy, and readiness, 5-point Likertscales) and Action Measures (yes/no whether an ACP behavior was completed) are included.
DOI: 10.5061/dryad.1ng8c/2
title: Summary table of indirect identifier data - Canadian ACP engagement_BMJ Open

description: This file contains descriptive analysis summary tables of indirect identifiers that were removed from the dataset.
DOI: 10.5061/dryad.1ng8c/3
title: README

description: The Readme file includes a list of files in this data package, and a description of the variables that were removed from the dataset to protect participant identity. Please see the "Data dictionary" for a description of the variables that were included in the dataset, and the "Summary table of indirect identifier data" for a summary of values reported at removed variables.
DOI: 10.5061/dryad.1ng8c/4
title: Data Dictionary - Canadian ACP engagement sample BMJ Open

description: This file describes the variables that were included in the dataset, and their allowable values.
DOI: 10.5061/dryad.2t3sn/1
title: Drought history effects on plant and soil microbial C dynamics

description: Data derived from a multi-year drought experiment  testing the effect of drought history on the response of plants and soil microbes and their C turnover during and after a further drought by conducting a 13C pulse-chase labelling study. Data were collected in 2011, the experiments were conducted in the Austrian Central Alps on a extnsively managed meadow. All abbreviations used in the excel file can be found in the ReadMe! tab.
DOI: 10.5061/dryad.5fh08/1
title: Stack of VPD 450 T cells in Lymph node

description: 82 Z slices, 30 time points, with each time point corresponding to a single raster scan of the sample. Created in ImageJ
DOI: 10.5061/dryad.5fh08/2
title: PS-Speck Beads + Signal and noise masks

description: 1000 frame time series of Yellow PS-Speck beads with each frame corresponding to a single raster scan with low excitation power; Also, signal and noise mask images generated from thresholding a gaussian filtered averaged image of all 1000 frames
DOI: 10.5061/dryad.5fh08/3
title: XCR1 Venus Dendritic cell in explanted lymph node

description: 60 frame time series of XCR1 Venus Dendritic Cell imaged within explanted lymph node using Nikon A1R. Each frame corresponds to a single raster scan
DOI: 10.5061/dryad.6226d/1
title: REL606, ancestral genome

description: This files contains the ancestral genome in gff3 format
DOI: 10.5061/dryad.6226d/2
title: REL606 non covered regions

description: This file contains the positons in the ancestral genome that are not covered by the short read sequencing technology used due to repeats.
DOI: 10.5061/dryad.6226d/3
title: LTEE mutator status file

description: This files provides information about the point mutator status of each clone. Clones that have an increased point mutation rate have a value of 1 in column 5.
DOI: 10.5061/dryad.6226d/4
title: LTEE mutation file

description: This file stores all mutations that were identified in the sequenced genomes of the LTEE, expect the ones in masked regions or in the neighbourhood of IS elements. It is used to compute most mutation analysis.
DOI: 10.5061/dryad.6226d/5
title: MAE mutation file

description: This file stores all mutations that were identified in the sequenced genomes of the MAE (Mutation Accumulation Experiment), expect the ones in masked regions or in the neighbourhood of IS elements.
DOI: 10.5061/dryad.6p072.1
title: Data from: Spider phylogenomics: untangling the spider tree of life
DOI: 10.5061/dryad.6p072.2/2.2
title: Data partitions

description: Partitions for accompanying data set.
DOI: 10.5061/dryad.6p072.2/3.2
title: Output from EXAML

description: Output from EXAML run that includes all genes
DOI: 10.5061/dryad.6p072.2/4.2
title: allGenesTree

description: Tree file derived from all genes run
DOI: 10.5061/dryad.6p072.2/5.2
title: pHMM spider core orthologs

description: Archive file containing pHMM spider core orthologs
DOI: 10.5061/dryad.b449r/1
title: Supplementary Information

description: Supplementary results, discussion, references and figures.
DOI: 10.5061/dryad.b449r/2
title: Matrix and character lists

description: Phylogenetic matrix and lists of characters.
DOI: 10.5061/dryad.b449r/3
title: Matrix

description: Phylogenetic matrix as nexus file.
DOI: 10.5061/dryad.bt4vj.2
title: Data from: The role of inhibitory dynamics in the loss and re-emergence of macropodoid tooth traits
DOI: 10.5061/dryad.bt4vj.2/1.2
title: crownH_data

description: Extant macropodoid crown height data based on measurements of museum specimens. "ID" specimen collection number,"Side" = describes if the specimen is a left (L) or right (R) dentary."Source" = collection holding specimen (AM= Australian Museum Sydney, SAM= South Australian Museum Adelaide, WAM= Western Australian Museum Perth, FU= Flinders University Vertebrate Palaeontology Laboratory Adelaide , ANWC= Australian National Wildlife Collection Canberra, NTM= Northern Territory Museum, Alice Springs), "PW"= posterior width, "PHb"=Molar crown height measured at the hypoconid,  "Tooth_identity"= molar position of the tooth.
DOI: 10.5061/dryad.bt4vj.2/2.2
title: FAD

description: Chronostratigraphic data on macropodoid first appearances in the fossil record. Data was compiled in Excel and exported as text file. As described in the papert the "FAD" corresponds to the earliest representative of the lineage while "LAD" refers to the first appearance of the tip taxon associated with that respective branch. All numeric values refer to millions of years before present (Myr). Tip taxa correspond to those in the morphological phylogeny.
DOI: 10.5061/dryad.bt4vj.2/3.2
title: Molecular_tree_states

description: Tree states relating to a pruned version of the molecular phylogeny originally produced by Mitchell et al. (2014; see paper text for full citation). Data was compiled in Excel and exported as text file. "1" = Posthypocrsitid present, "0" = Posthypocrsitid absent.
DOI: 10.5061/dryad.c3k7s/1
title: AlignmentFile

description: Nexus alignment of 257 species of gobies, including deep-reef taxa.
DOI: 10.5061/dryad.c3k7s/2
title: BEAST_Output

description: A posterior distribution of phylogenetic trees resulting from a BEAST2 analysis.
DOI: 10.5061/dryad.c3k7s/3
title: Beast2_Input

description: Input XML file for BEAST2 analysis.
DOI: 10.5061/dryad.gf54q/1
title: Demographic data_Aphis gossypii on melon crops
DOI: 10.5061/dryad.gf54q/2
title: Genetic data_Spring migrants Aphis gossypii on melon crops

description: Aphis gossypii spring migrants- collected during the 3 weeks following transplantation- on melon crops in France. MLG= MultiLocus Genotype based on 8 SSR markers
DOI: 10.5061/dryad.gf54q/3
title: Genetic data_Wingless Aphis gossypii on melon crops
DOI: 10.5061/dryad.gf54q/4
title: MLG Aphis gossypii_Allelic composition at 8 SRR

description: Size of Amplification product  at each locus. 999 = missing data
DOI: 10.5061/dryad.nv783/1
title: Immediate_response

description: Data used for the analysis of the immediate responses to the fecal presentations
DOI: 10.5061/dryad.nv783/2
title: Movement_response

description: Data used for the analysis of movement responses in the hour after encountering the fecal presentation
DOI: 10.5061/dryad.nv783/3
title: Variable_descriptions

description: A table explaining the variable abbreviations used in the two data files
DOI: 10.5061/dryad.q72b7/1
title: Reference sequences

description: Reference sequences in fasta format
DOI: 10.5061/dryad.q72b7/2
title: Details of MIP design

description: This Excel file contains the sequences of MIP probes as well as information about the position of MIPs on contigs from the Lissotriton reference transcriptome available at http://newtbase.eko.uj.edu.pl/
DOI: 10.5061/dryad.q72b7/3
title: scripts_for_MIP_design.tar

description: Gzipped tar archive containing scripts used for MIP design. These scripts were developed by O'Roak et al. (2012) and slightly modified to fit our needs. Please note that there these scripts have been supplanted by the MIPGEN software available et https://github.com/shendurelab/MIPGEN
DOI: 10.5061/dryad.q72b7/4
title: vcf_1st_experiment.tar

description: Gzipped tar archive containing vcf files for samples from the 1st experiment described in the paper.
DOI: 10.5061/dryad.q72b7/5
title: vcf_2nd_experiment.tar

description: Gzipped tar archive containing vcf files for samples from the 2nd experiment described in the paper.
DOI: 10.5061/dryad.t4660/1
title: Dataset- Caregivers' Stigma

description: This file contains the data form the study "Caregivers’ Attitude towards People with Mental Illness and Perceived Stigma: A Cross-Sectional Study in A Tertiary Hospital in Nepal"
DOI: 10.5061/dryad.vc94d/2
title: Raw coordinates for paramere
DOI: 10.5061/dryad.vc94d/3
title: Capture rates of Pterostichus thunbergi and P. habui at the sympatric site (site D)
DOI: 10.5061/dryad.vc94d/4
title: headlength
DOI: 10.5061/dryad.0m068/2
title: Milk transfer to matched siblings

description: the matched twin sibling comparison data set
DOI: 10.5061/dryad.0m068/3
title: Milk transfer to whole litters

description: data on milk transfer to whole litters, combining data from the two other milk transfer files for singletons and the matched twin sibling comparison data set
DOI: 10.5061/dryad.0m068/4
title: Milk composition

description: analysis of the composition of spotted hyena milk
DOI: 10.5061/dryad.0nm8t/11
title: RD_Results

description: The results from the robust design analysis.
DOI: 10.5061/dryad.0nm8t/12
title: Workflow

description: This file gives detailed instructions on how to use all of the scripts found in this repository and provides a step-by-step guide to run the analyses discussed in the manuscript.