cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7hb7r.2/1.2
title: TNT Files

description: Edited TNT files partitioned into craniodental and postcranial characters
DOI: 10.5061/dryad.7j1nr/1
title: gorter_et_al._2016_data

description: Resistance/ infectivity of coevolved bacteria and phages from different temperatures and replicate populations assayed at each temperature.
DOI: 10.5061/dryad.7j908/2
title: between group encounters

description: rate of between group encounters during summer
DOI: 10.5061/dryad.7j908/3
title: duration aggression

description: duration of displacements and chasing events (in seconds)
DOI: 10.5061/dryad.7j908/4
title: used microsatellites
DOI: 10.5061/dryad.7j908/5
title: aggression own young crossfostered young

description: aggression of parents towards young crossfostered young during 30 min
DOI: 10.5061/dryad.8507n/1
title: Habitat suitability for Mammals in JCUs and Corridors

description: This file is an Excel database with four worksheets which details the results of an overlap analysis performed in ArcGIS between mammal habitat suitability models and Jaguar Conservation Units and corridors. Worksheets are labeled as "CA_JCU_Analysis", "SA_JCU_Analysis", "CA_Corridor_Analysis" and "SA_Corridor_Analysis". A description of each of these worksheets follows: "CA_JCU_Analysis" details the proportion of high, medium, and low quality habitat of co-occurring mammals that is contained within Jaguar Conservation Units (assuming the total available to be conserved is defined as either the total amount of habitat for each species within Central America, or within the range of the jaguar in Central America). Each row represents the values for a different species, and the columns the different categories of habitat quality. "SA_JCU_Analysis" details the proportion of high, medium, and low quality habitat of co-occurring mammals that is contained within Jaguar Conservation Units (assuming the total available to be conserved is defined as either the total amount of habitat for each species within South America, or within the range of the jaguar in South America). Each row represents the values for a different species, and the columns the different categories of habitat quality. "CA_Corridor_Analysis" shows the proportion of high quality habitat for co-occuring mammals in Central America that is contained within corridors - this value was calculated by summing the amount of high, medium, and low quality habitat contained within corridors and dividing by the total area of the corridor. This analysis was done for the actual modeled jaguar corridors, as well as 10 randomly generated corridors. Each row represents the value for each species, and each column represents the actual corridor or a randomly generated corridor, for each category of habitat quality. SA_Corridor_Analysis shows the proportion of high quality habitat for co-occuring mammals in South  America that is contained within corridors - this value was calculated by summing the amount of high, medium, and low quality habitat contained within corridors and dividing by the total area of the corridor. This analysis was done for the actual modeled jaguar corridors, as well as 10 randomly generated corridors.
DOI: 10.5061/dryad.87k2p.2
title: Data from: Reduced genetic diversity and increased reproductive isolation follow population-level loss of larval dispersal in a marine gastropod
DOI: 10.5061/dryad.87k2p.2/1.2
title: 01, C_ocellifera master COI data

description: Master spreadsheet showing COI haplotype codes, NCBI accession numbers, sampling frequency per location, and specimen identifiers for slugs with a given haplotype
DOI: 10.5061/dryad.87k2p.2/2.2
title: 02, Coce_COI_Evolution2015

description: Nexus file of collapsed COI haplotypes, with BayesPhylogenies command block
DOI: 10.5061/dryad.87k2p.2/3.2
title: 03, Arlequin input file, Coce_13_pops

description: Arlequin input file for COI haplotypic data, each sampling site separated
DOI: 10.5061/dryad.87k2p.2/4.2
title: 04, Coce_COI_CaribP_run1

description: BEAST input files for generating Bayesian skyline plot of pooled Caribbean planktotrophic demes
DOI: 10.5061/dryad.87k2p.2/5.2
title: 05, Coce_LAK_COI_run1

description: BEAST input files for generating Bayesian skyline plot of Lake Surprise population
DOI: 10.5061/dryad.87k2p.2/6.2
title: 06, Coce_GEI_COI_run1

description: BEAST input files for generating Bayesian skyline plot of Geiger Beach population
DOI: 10.5061/dryad.87k2p.2/7.2
title: 07, Coce_LSS_COI_run1

description: BEAST input files for generating Bayesian skyline plot of Little San Salvador population
DOI: 10.5061/dryad.8b416/3
title: Spruce trait data

description: 9 morphometric traits measured for each of the 10 spruce taxa,include:Needle length, Needle width, Cone length, Cone diameter, Seed scale length, Seed scale width,Seed wing length,Seed wing width andSeed length.
DOI: 10.5061/dryad.ks633/1
title: Data Supplement

description: Excel spreadsheet containing wing shape, elevational and geographic range limits, habitat affinity, and foraging stratum for 444 species of Himalayan birds.  Super species designation is indicated. Climate similarity and landscape complexity encountered by each species is also included, and measurements from Field Museum of Natural History specimens are on a separate tab.
DOI: 10.5061/dryad.mf278/1
title: Example of AFLP profiles in .fsa files
DOI: 10.5061/dryad.p4s57/13
title: Additional TreeFam gene duplication data with duplication timing
DOI: 10.5061/dryad.pf4b7/1
title: GENETICS_2015_185553_data

description: Conserved genetic architecture underlying recombination rate variation in a wild population of Soay sheep (Ovis aries).
DOI: 10.5061/dryad.qd73b/1
title: Ungulate movement and range area data for Dryad

description: Movement ecology and range area data for roe deer, chamois and mouflon. These data come originally form GPS loggers but was summarized at different time intervals (from 20 minute intervals to annual range areas) before analyses.
DOI: 10.5061/dryad.rd5rn/3
title: R code for selection analyses

description: MCMCglmm code used in selection meta-analysis and unweighted analysis.
DOI: 10.5061/dryad.rd5rn/4
title: R code for heritability analyses

description: MCMCglmm code used for heritability meta-analysis and unweighted analysis.
DOI: 10.5061/dryad.rd5rn/5
title: R code for Variable hypothesis analysis

description: MCMCglmm code used in Variable hypothesis analysis.
DOI: 10.5061/dryad.rh97t/1
title: A020513

description: Data archive
DOI: 10.5061/dryad.rh97t/2
title: A071014

description: Data archive
DOI: 10.5061/dryad.rh97t/3
title: A090613

description: Data archive
DOI: 10.5061/dryad.rh97t/31
title: Keys

description: Contains information about which data archives go with which experiments.  Download this archive first, untar, and read the ReadMe.txt file within.
DOI: 10.5061/dryad.rh97t/4
title: A120713

description: Data archive
DOI: 10.5061/dryad.rj87v/3
title: Transcriptome assembly of Raineriophrys erinaceoides

description: RNA-seq assembly of Raineriophrys erinaceoides from Genbank SRA accession #SRR2170634. Read quality was assessed with FastQC before and after quality trimming and SMART adaptors removal, which was performed with FastqMcf. Cleaned reads were assembled into contigs with Trinity r20140717 using default parameters.
DOI: 10.5061/dryad.rj87v/4
title: Transcriptome assembly of Choanocystis sp

description: RNA-seq assembly of Choanocystis sp. from Genbank SRA accession #SRR2170626. Read quality was assessed with FastQC before and after quality trimming and SMART adaptors removal, which was performed with FastqMcf. Cleaned reads were assembled into contigs with Trinity r20140717 using default parameters
DOI: 10.5061/dryad.rj87v/5
title: Transcriptome assembly of Acanthocystis sp

description: RNA-seq assembly of Acanthocystis sp. from Genbank SRA accession #SRR2170625. Read quality was assessed with FastQC before and after quality trimming and SMART adaptors removal, which was performed with FastqMcf. Cleaned reads were assembled into contigs with Trinity r20140717 using default parameters
DOI: 10.5061/dryad.rj87v/6
title: Transcriptome assembly of Raphidiophrys heterophryoidea

description: RNA-seq assembly of Raphidiophrys heterophryoidea from Genbank SRA accession #SRR2170621. Read quality was assessed with FastQC before and after quality trimming and SMART adaptors removal, which was performed with FastqMcf. Cleaned reads were assembled into contigs with Trinity r20140717 using default parameters
DOI: 10.5061/dryad.rj87v/7
title: Trimmed alignment

description: Trimmed alignment of all 250 genes. BMGE was used for trimming, following MAFFT-LINSI for automatic alignment.
DOI: 10.5061/dryad.rj87v/8
title: Untrimmed sequences

description: Fasta files of all 250 genes containing untrimmed sequences.
DOI: 10.5061/dryad.rj87v/9
title: Single-gene phylogenetic trees

description: RAxML phylogenetic trees of all 250 genes.
DOI: 10.5061/dryad.v1r34/10
title: Height_Forest_areas
DOI: 10.5061/dryad.v1r34/11
title: Herpeto_Contiguous_forest_areas
DOI: 10.5061/dryad.v1r34/12
title: Herpeto_Forest_areas
DOI: 10.5061/dryad.v1r34/13
title: Invertebrates_Contiguous_forest_areas
DOI: 10.5061/dryad.v1r34/14
title: Invertebrates_Forest_areas
DOI: 10.5061/dryad.v1r34/15
title: Litter_Contiguous_forest_areas
DOI: 10.5061/dryad.v1r34/16
title: Litter_Forest_areas
DOI: 10.5061/dryad.v1r34/8
title: Density_Forest_areas
DOI: 10.5061/dryad.v1r34/9
title: Height_Contiguous_forest_areas
DOI: 10.5061/dryad.25b39/1
title: OTU matrix total fungi Abu and PA data

description: This file contains all the fungal OTUs recovered, including ECM and non ECM, abundance as well as presence-absence data
DOI: 10.5061/dryad.25b39/2
title: OTU matrix ECM fungi Abu and PA data

description: This file contains all the ECM fungal OTUs recovered, abundance as well as presence-absence data
DOI: 10.5061/dryad.25b39/3
title: Environmental data matirx (raw data)

description: This file contains information about raw environmental data associated with each sample.
DOI: 10.5061/dryad.25b39/4
title: Shared species analysis EstimateS

description: OTU Data for shared analysis performed using EstimateS
DOI: 10.5061/dryad.25b39/5
title: Shared species analysis

description: R script for plotting shared species between sampling months
DOI: 10.5061/dryad.2pn59/1
title: Nesting Data Used for Calculating Nest Survival

description: The data file contains nest initiation dates, treatment codes, nest outcome, nest age, nest description for dickcissels, grasshopper sparrows, and eastern meadowlarks.
DOI: 10.5061/dryad.50sg7/1
title: Ligophorus image data

description: Images of ventral and dorsal anchors of 530 specimens from 13 Ligophorus species.
DOI: 10.5061/dryad.50sg7/2
title: Landmark coordinate data of ventral and dorsal anchors of 13 Ligophorus species

description: The file contains landmark coordinate data of ventral and dorsal anchors of 530 specimens from 13 Ligophorus species. Data generated from Ligophorus Image Data using TPSDIG2.
DOI: 10.5061/dryad.50sg7/3
title: R scripts and associated data files

description: This file contains R scripts and associated data files for reproducing the analyses in Khang et al. (2016). Note: The authors of the geomorph package has recently informed me (21 January 2016) that changes to the latest version (3.0.0) have rendered some arguments in the gpagen function obsolete. To ensure smooth running of the script, please install geomorph version 2.1.1. as in Khang et al. (2016). Updates to monogeneaGM are forthcoming and will be announced in the PeerJ reader comment section.
DOI: 10.5061/dryad.50sg7/4
title: Concatenation of MAFFT-aligned DNA sequences for 13 Ligophorus species

description: This file contains concatenated multiple sequence alignments of 18S rRNA, ITS-1 and 28S rRNA sequences (in this order) for 13 Ligophorus species. Multiple sequence alignment was performed using MAFFT (version 7). Alignment parameters: Q-INS-i iterative refinement method; 1PAM/k=2 nucleotide scoring matrix; gap opening penalty = 1.53. The sequences were manually concatenated from trimmed MAFFT-alignments.
DOI: 10.5061/dryad.512s7/1
title: exp_icing_dat

description: Raw data from Cassiope icing experiment in high Arctic Svalbard, 2014. Effects of simulated extreme mid-winter rain-on-snow icing event (treatment) on Cassiope shoot growth, survival and flowering, as compared with plants in control plots.
DOI: 10.5061/dryad.512s7/2
title: AGI_Icing

description: Pre- and post-treatment annual growth increments of Cassiope shoots sampled from experimental treatment and control plots.
DOI: 10.5061/dryad.742fp/3
title: ana_prop_dia.R
DOI: 10.5061/dryad.742fp/4
title: ana_rd.R
DOI: 10.5061/dryad.742fp/5
title: ana_t0.R
DOI: 10.5061/dryad.742fp/6
title: ana_tp.R
DOI: 10.5061/dryad.7hb7r.2/2.2
title: Table1

description: Summary statistics for the 85 vertebrate morphological data sets analysed herein.
DOI: 10.5061/dryad.7j908/10
title: females vs non-breeders data-set

description: ring – non-breeder identity. breeder_ring – breeder identity. obstime – observation bout length: 15min, 30min. year – year of observation. sex – sex of non-breeder. breeder_age – age of breeder. age – age of non-breeder. kinship – kinship breeder vs non-breeder: kin (parent-offspring, non-kin: breeder-immigrant)groupsize – group size. NSI – nesting success index of territory (see Griesser et al. 2008). prop_um – proportion unmanaged forest on territory (see Griesser et al. 2006). displaced – number of displacements received during 30 min. chased - number of chasing events received during 30 min. submissive - number of times submissive behaviour is displayed during 30 min. TrioML - Trio maximum likelihood  r estimator. Ritland - Ritland’s r estimator. DyadML - Dyad maximum likelihood  r estimator. Wang_mb - Wang’s r estimator. LynchLi_mb - Lynch and Li’s r estimator. QuellerGt_mb - Queller and Goodnight’s r estimator. LynchRd - Lynch and Ritland’s r estimator
DOI: 10.5061/dryad.7j908/6
title: microsatellites genepop data

description: used microsatellites for analyses, genepop format
DOI: 10.5061/dryad.7j908/7
title: coancestry relatedness simulations

description: coancestry relatedness simulations year 1999 and 2008-2009, simulation the relatendess of offspring and unrelated individuals
DOI: 10.5061/dryad.7j908/8
title: R_script

description: R-code of the main analyses
DOI: 10.5061/dryad.7j908/9
title: male vs non-breeders data-set

description: ring – non-breeder identity. breeder_ring – breeder identity. obstime – observation bout length: 15min, 30min. year – year of observation. sex – sex of non-breeder. breeder_age – age of breeder. age – age of non-breeder. kinship – kinship breeder vs non-breeder: kin (parent-offspring, non-kin: breeder-immigrant). groupsize – group size. NSI – nesting success index of territory (see Griesser et al. 2008). prop_um – proportion unmanaged forest on territory (see Griesser et al. 2006). displaced – number of displacements received during 30 min. chased - number of chasing events received during 30 min. submissive - number of times submissive behaviour is displayed during 30 min. TrioML - Trio maximum likelihood  r estimator. Ritland - Ritland’s r estimator. DyadML - Dyad maximum likelihood  r estimator. Wang_mb - Wang’s r estimator. LynchLi_mb - Lynch and Li’s r estimator. QuellerGt_mb - Queller and Goodnight’s r estimator. LynchRd - Lynch and Ritland’s r estimator
DOI: 10.5061/dryad.86523/1
title: Morris_2016_Evolution_Carnivora_indices_data

description: Values for all functional indices and geometric means for all specimens used in the analysis.
DOI: 10.5061/dryad.86523/2
title: Morris_2016_Evolution_Carnivora_species_info

description: Body mass and life history trait infomation for all species used in correlational analysis and phylogenetic model selection analysis.
DOI: 10.5061/dryad.8673j/1
title: Henriques et al: microsatellite database

description: Microsatellite allelic scoring for M. capensis and M. paradoxus
DOI: 10.5061/dryad.87k2p.1
title: Data from: Reduced genetic diversity and increased reproductive isolation follow population-level loss of larval dispersal in a marine gastropod
DOI: 10.5061/dryad.87k2p.2/10.2
title: 10, Coce_msats.str

description: Structure input file for microsatellite data
DOI: 10.5061/dryad.87k2p.2/11.2
title: 11, 4runs_Coce_COI_post_burnin.nex

description: Tree file combining post-burnin output from four Bayesian analyses of COI data
DOI: 10.5061/dryad.87k2p.2/8.2
title: 08, Coce_Plana_COI_run1

description: BEAST input files for generating Bayesian skyline plot of Plana Cays population
DOI: 10.5061/dryad.87k2p.2/9.2
title: 09, Coce_msats_14pops

description: Arlequin input file for microsatellite data, each sampling site separated
DOI: 10.5061/dryad.8p1n3/1
title: Raw_data_Gerrits_Dryad

description: See the Dryad_ReadMe_Gerrits word file.
DOI: 10.5061/dryad.c1jr3/1
title: Raw posturographic and MS data

description: This ZIP file contains the center of pressure (CoP) data and the MSSQ and SSQ scores for all subjects included in the study. For details, please see the file README.pdf contained in the ZIP file.
DOI: 10.5061/dryad.f7h13/1
title: Whole-genome alignment of A. arabiensis and A. quadriannulatus pop. samples

description: The data are supplied in the Multisample Variant Format (Pease and Rosenzweig, 2015).  A complete suite of tools for processing MVF files is available on github at https://github.com/jbpease/mvftools.  Each file contains a full-chromosome alignment of computationally phased haplotypes for 23 samples of A. arabiensis, A. quadriannulatus, and A. christyi (outgroup); haplotypes are identified by ".A" or ".B" appended to the sample ID.  The sample key (SampleCode.txt) is also included.
DOI: 10.5061/dryad.fc2vv/1
title: Microsatellite data for lions on small reserves in South Africa

description: Data were prepared in Microsoft Excel. All samples are held at the Veterinary Genetics Laboratory, University of Pretoria, Onderstepoort, South Africa. The ItemID refers to a unique number for each sample on the database. The "Analysis" column refers to the two separate analyses run in the paper: the "Microsatellite cluster analyses" on "pure" populations (Reference Population analysis or RP) and "Assignment testing and levels of mixing" reserve animal dataset (Small Reserves analysis or SR). Some of this data was previously deposited with Dryad (http://dx.doi.org/10.5061/dryad.f61vq) and is indicated in the column "Used in previous publication".
DOI: 10.5061/dryad.mf278/2
title: AFLP in silico size homoplasy

description: The file contains a script for R package that simulate size homoplasy for AFLP fragments.
DOI: 10.5061/dryad.rh97t/10
title: A230713

description: Data archive
DOI: 10.5061/dryad.rh97t/11
title: A230913

description: Data archive
DOI: 10.5061/dryad.rh97t/12
title: A250413

description: Data archive
DOI: 10.5061/dryad.rh97t/5
title: A160413

description: Data archive
DOI: 10.5061/dryad.rh97t/6
title: A190413

description: Data archive
DOI: 10.5061/dryad.rh97t/7
title: A190913

description: Data archive
DOI: 10.5061/dryad.rh97t/8
title: A200613

description: Data archive
DOI: 10.5061/dryad.rh97t/9
title: A220713

description: Data archive
DOI: 10.5061/dryad.t316t/1
title: Weegman et al. 2015 data for Dryad
DOI: 10.5061/dryad.v1r34/17
title: Mammals_Contiguous_forest_areas
DOI: 10.5061/dryad.v1r34/18
title: Mammals_Forest_areas
DOI: 10.5061/dryad.v1r34/19
title: Plants_Contiguous_forest_areas
DOI: 10.5061/dryad.v1r34/20
title: Plants_Forest_areas
DOI: 10.5061/dryad.v1r34/21
title: Script_Contiguous forest areas
DOI: 10.5061/dryad.v1r34/22
title: Script_Forest areas
DOI: 10.5061/dryad.v7h28/1
title: HopV1-trim

description: Aligned and trimmed alignment of putative T3SS effector HopVI found in the E. tracheiphila genome
DOI: 10.5061/dryad.v7h28/2
title: BHKY-assembly

description: E. tracheiphila strain BHKY hybrid mapping + deNovo assembly fasta file
DOI: 10.5061/dryad.v7h28/3
title: MISpSq-assembly

description: E. tracheiphila strain MISpSq hybrid assembly from mapping + deNovo assembly of Illumina short reads
DOI: 10.5061/dryad.v7h28/4
title: NYZuch1-assembly

description: Hybrid mapping and deNovo assembly file for E. tracheiphila strain NYZuch1
DOI: 10.5061/dryad.v7h28/5
title: ppHow2-assembly

description: E. tracheiphila genome assembly for strain ppHow2, from a hybrid mapping + deNovo assembly
DOI: 10.5061/dryad.1525t/1
title: Genotypes_422405SNPs

description: Genotypes for 1033 animals and 422405 SNPs
DOI: 10.5061/dryad.1525t/2
title: Pedigree

description: Pedigree of 1033 animals
DOI: 10.5061/dryad.1525t/3
title: ID_Population

description: Division of the 1033 animals over the three populations
DOI: 10.5061/dryad.1525t/4
title: Phenotypes_QTL_RANDOM

description: Phenotypes for all 1033 animals when QTL are randomly sampled for all seven scenarios and 100 replicates per scenarios. The phenotype files contains: animal number, population number, ID, and phenotype.
DOI: 10.5061/dryad.1525t/5
title: Phenotypes_QTL_LowMAF

description: Phenotypes for all 1033 animals when QTL are sampled with a low Minor Allele Frequency for all seven scenarios and 100 replicates per scenarios. The phenotype files contains: animal number, population number, ID, and phenotype.
DOI: 10.5061/dryad.1pq21/1
title: Contigs sequences analyzed in this study.

description: This file with txt extension, contains the analyzed all contigs in this study.
DOI: 10.5061/dryad.1pq21/2
title: Genotypes, variants and other information from 143 SNPs analyzed

description: 143 SNP name, variants, dataset of the contig (source), annotation, GenBank accession number, external PCR primer sequences (Forward and Reverse), tailed extension primer (showing tails in lower case), extension primer direction and multiplexs are shown. Unfeasible SNPs are indicated in red colour.
DOI: 10.5061/dryad.1pq21/3
title: Information from samples 89 genotype ddRad loci identified.

description: This file contains information from samples 89 genotyped .
DOI: 10.5061/dryad.1pq21/4
title: This file contains the access information in NCBI of 39 samples used of to develop the SNPs.

description: This file contains the access information in NCBI of 39 samples used to develop the SNPs.
DOI: 10.5061/dryad.25b39/6
title: GNMDs ordination analysis

description: R script for GNMDS analysis of ECM fungi
DOI: 10.5061/dryad.25b39/7
title: Illumina sequencing plate1

description: This file contains both forward (t1-UNIS_S1_L001_R1_001.fastq) and reverse (t1-UNIS_S1_L001_R2_001.fastq) Illumina read data and associated barcode mapping files. In Mapfile_T1 forward primer is linker primer and in Mapfile_T1_rev reverse primer is the linker primer to recover all the reads from mix orientation read data files. which is the case in our sequencing.
DOI: 10.5061/dryad.25b39/8
title: Illumina sequencing plate2

description: This file contains both forward (t2-UNIS_S1_L001_R1_001.fastq) and reverse (t2-UNIS_S1_L001_R2_001.fastq) Illumina read data and associated barcode mapping files. In Mapfile_T2 forward primer is linker primer and in Mapfile_T2_rev reverse primer is the linker primer to recover all the reads from mix orientation read data files. which is the case in our sequencing.
DOI: 10.5061/dryad.3c5r9/1
title: Wood_et_al_V niloticus genotypes_GENALEX input file

description: Genotypes used by Wood et al. to analyze the genetic structure of Varanus niloticus populations in Florida. Data is formatted as a GenAlEx input file.
DOI: 10.5061/dryad.46sm5/2
title: ALR et al._Mol Ecol Res_DRYAD_22Feb2016

description: The eDNA concentration (ng/L) per amplification including water temperature, fish abundance, fish biomass, number of the sampled aquarium, types of filters.
DOI: 10.5061/dryad.50sg7/5
title: Trimmed multiple sequence alignments

description: This file contains MAFFT-aligned (Version 7) 28S rRNA, 18S rRNA, and ITS-1 sequences of 13 Ligophorus species which have been manually trimmed at the left and right ends. Alignment parameters: Q-INS-i iterative refinement method; 1PAM/k=2 nucleotide scoring matrix; gap opening penalty = 1.53.