cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.82bg7/1
title: Time to death + Wood frog stage and mass

description: Time to death data + Wood frog stage and mass data
DOI: 10.5061/dryad.c983b/1
title: Field and laboratory measurements of SVL in male and female A. sagrei

description: Field and laboratory measurements of snout-vent length (SVL) of male and female A. sagrei lizards. Field data: Adult males and adult females were captured on six Bahamian islands (Acklins, Andros, Grand Bahamas, Chub Cay, Pidgeon Cay and Staniel Cay). Laboratory data: feeding experiments of juvenile male and female A. sagrei raised under low or high food diets.
DOI: 10.5061/dryad.g6c5q/2
title: Tagged sharks

description: Details of tagged sharks: Date of tagging, ecocean ID number, gender and size (m)
DOI: 10.5061/dryad.g6c5q/3
title: Number of stations

description: Acoustic effort. Number of working acoustic receiver stations per 2-week period
DOI: 10.5061/dryad.g6c5q/4
title: Visual / Photographic identifications

description: Sharks identified on visual surveys
DOI: 10.5061/dryad.g6c5q/5
title: Searching hours

description: Visual effort. Number of searching hours per 2-week period
DOI: 10.5061/dryad.g6c5q/6
title: Individuals' swimming depth and distance from shore

description: Mean swimming depth and distance from shore per individual per 2-week period
DOI: 10.5061/dryad.g6c5q/7
title: R script - presence/absence function
DOI: 10.5061/dryad.h505v/2
title: Elastic constant
DOI: 10.5061/dryad.h77tb/1
title: British Stoat Simulation R code

description: This file contains the annotated R code for the mitochondrial genetic drift simulation for stoats in Britain since 1883.
DOI: 10.5061/dryad.h8n6m/1
title: FieldSurveyData

description: This file contains data collected from Poa secunda grown at a field site in western Montana during the 2013 growing season. The first four columns refer to the plant's location within the field study area (Cell, Plot, Block, and Site). The fifth and sixth columns identify the grass origin (Accession and Source). For the seventh column, Treatment, grasses were either grown with (Challenged) or without (Unchallenged) Bromus tectorum. Plants were monitored over four consecutive surveys (Survey1-Survey4). The remaining columns represent data recorded for Poa secunda variables at each survey. These variables include Germinants (number of germinants out of four seeds planted), Survival (presence/absence), Herbivory (presence/absence), Cover (average Bromus tectorum canopy cover per plot), and Biomass. Microsoft Office Excel software was used to create the data file.
DOI: 10.5061/dryad.jd6m0/1
title: Hoverman & Relyea Oikos 2015 data

description: Pool means for each of the sample dates of the experiment are provided for each experimental unit.  Metadata is provided in the document.
DOI: 10.5061/dryad.k4d0q/1
title: CT scan data - specimen B56629

description: CT scan original files used to reconstruct Osedax boring in specimen B56629. The bone is a plesiosaur humerus from the Cenomanian Cambridge Greensand Member, UK. B56629 is curated at the Sedgwick Museum of Earth Sciences, University of Cambridge, UK
DOI: 10.5061/dryad.k4d0q/2
title: B206000-1

description: CT scan original files used to reconstruct Osedax boring in specimens B206000-1. They are two fragmentary bones (rib and costal plate) belonging to a marine turtle, family Cheloniidae, collected from the Cenomanian Grey Chalk Subgroup (Burham, Kent, UK).  The specimens are curated at the Sedgwick Museum of Earth Sciences, University of Cambridge, UK
DOI: 10.5061/dryad.n21cr/2
title: Python Script

description: This file contains the python scripts used in this study. These scripts can be used to analysis next generation sequence data step by step, including: sorting, assembling, trimming, refining and combining.
DOI: 10.5061/dryad.n21cr/3
title: Total_1435_consensus_seqs

description: This is the final consensus sequences produced by our approach. These data can be used for phylogenetic analysis.
DOI: 10.5061/dryad.n21cr/4
title: Alignment_for_RAxML

description: This alignment is used for ML analysis.
DOI: 10.5061/dryad.n21cr/5
title: Alignment_for_Mrbayes

description: This alignment is used for Mrbayes analysis. The parameters are also included in this file.
DOI: 10.5061/dryad.n21cr/6
title: 16taxa_species_tree

description: This is the species tree result.
DOI: 10.5061/dryad.n21cr/7
title: 16_taxa_raxm_&bayes_tree

description: This tree file contains the results from RAxML and Mrbayes. Both methods result the same topologies and same support values.
DOI: 10.5061/dryad.qd87k/1
title: fig_1.tar

description: Column 1: sigma, Column 2: time (generations), Column 3: histogram of dispersal values, in 1000 bins from 0:1, Column 4: histogram of x values, in 1000 bins from -10:10.            Note that a row of -99s divides each timestep.
DOI: 10.5061/dryad.qd87k/2
title: fig_2.tar

description: Column 1: sigma, Column 2: time (generations), Column 3: histogram of dispersal values, in 1000 bins from 0:1, Column 4: histogram of x values, in 1000 bins from -10:10. Note that a row of -99s divides each timestep.
DOI: 10.5061/dryad.qd87k/3
title: fig_5.tar

description: Column 1: sigma, Column 2: time (generations), Column 3: histogram of dispersal values, in 1000 bins from 0:1, Column 4: histogram of x values, in 1000 bins from -10:10. Note that a row of -99s divides each timestep.
DOI: 10.5061/dryad.r122k/1
title: EVE software release
DOI: 10.5061/dryad.r6m04/10
title: MESO6.1.fastq
DOI: 10.5061/dryad.r6m04/2
title: MESO1.2.fastq
DOI: 10.5061/dryad.r6m04/3
title: MESO2.1.fastq
DOI: 10.5061/dryad.r6m04/4
title: MESO3.1.fastq
DOI: 10.5061/dryad.r6m04/5
title: MESO2.2.fastq
DOI: 10.5061/dryad.r6m04/6
title: MESO4.1.fastq
DOI: 10.5061/dryad.r6m04/7
title: MESO4.2.fastq
DOI: 10.5061/dryad.r6m04/8
title: MESO5.1.fastq
DOI: 10.5061/dryad.r6m04/9
title: MESO5.2.fastq
DOI: 10.5061/dryad.tm8d0/2
title: Data and R code

description: ## snp_D.R -&gt; contains the annotated code for reading and preparing the data, and the custom code for the K-W tests.## prov_inv_snp_D.csv -&gt; contain the raw data for the K-W tests## RDA_SNPxLocationxClimate.R -&gt; Annotated R code for the redundancy analysis (RDA) and for Figure 7## BRsites_bioclim -&gt; climate data for RDA## SNPcommunity_table.csv -&gt; SNP "community"matrix for RDA## sorted_12_pops.csv -&gt;  lositan results. This is the list of loci, with heterozygosity and Fst, ordered by p value.
DOI: 10.5061/dryad.v77cn/1
title: Self-administration, extinction and reinstatement data from all experiments

description: This file contains the self-administration, extinction and reinstatement data collected from all three experiments. It includes active and inactive responses, locomotor activity and rewards obtained.
DOI: 10.5061/dryad.1797v/5
title: Paired-end extended sequences for eulachon
DOI: 10.5061/dryad.1797v/6
title: R code to Impute missing SNP data.

description: This code was developed by Matt Grinnell to impute missing SNPs from the eulachon datasets so it could be used by ONCOR for assignment testing.
DOI: 10.5061/dryad.1797v/7
title: R script to calculate effective population size with an R2 value
DOI: 10.5061/dryad.1797v/8
title: R script to impute missing loci by population
DOI: 10.5061/dryad.1797v/9
title: Thaleichthys pacificus, Osmeridae key file for NCBI SRA database

description: This file contains: sample name, sample number, biosample account, library ID, and barcode.
DOI: 10.5061/dryad.24bg4/1
title: Stationary and tow tests

description: Efficiency, accuracy and precision from stationary and tow tests. Additionally, calculated mean false swimming from stationary tests are included.
DOI: 10.5061/dryad.24bg4/2
title: Lengths of tow tracks

description: Length of tow tracks calculated by the APTs and the true trajectory obtained using DGPS
DOI: 10.5061/dryad.24bg4/3
title: Depth sensor performance

description: True depth measured in field vs depth estimated from pressure sensors in the transmitters
DOI: 10.5061/dryad.27qf3/1
title: Pansu_et_al_SBB_ewDE_sequence_data_alternative_sampling

description: This fasta file contains merged reads assigned to their original sample obtained with the alternative soil sampling scheme covering the entire plot surface. Amplicons were amplified using ewDE primers (ewD: 5’- ATTCGGTTGGGGCGACC-3’ and ewE: 5’- CTGTTATCCCTAAGGTAGCTT-3’) (Bienert et al., 2012). Sequences were obtained by a 2 x 100 bp paired-end sequencing on Illumina HiSeq platform. First filtering steps were performed using the OBITOOLS software (http://metabarcoding.org/obitools) following the data filtering description in supplementary material (Pansu et al., 2015 Soil Biology and Biochemistry). Direct and reverse reads corresponding to the same sequence were aligned and merged thanks to the IlluminaPairEnd program. Only merged sequences with a high alignment quality score were retained (&gt;=40). Then, the ngsfilter program assigned each merged sequence to its original sample using the tags information previously added to primers. Only sequences containing both primers (with a maximum of 3 mismatches per primer) and exact tag sequences were selected. Sequences containing ambiguous nucleotides or shorter than 55 bp were discarded. Strictly identical sequences were merged together while keeping information about the origin of sequences. Strict singletons (i.e. sequences occurring only once in the dataset) were removed.
DOI: 10.5061/dryad.27qf3/2
title: Pansu_et_al_SBB_ewDE_sequence_data_subplots_sampling

description: This fasta file contains merged reads assigned to their original sample obtained with the subplots soil sampling scheme. Amplicons were amplified using ewDE primers (ewD: 5’- ATTCGGTTGGGGCGACC-3’ and ewE: 5’- CTGTTATCCCTAAGGTAGCTT-3’) (Bienert et al., 2012). Sequences were obtained by a 2 x 100 bp paired-end sequencing on Illumina HiSeq platform. First filtering steps were performed using the OBITOOLS software (http://metabarcoding.org/obitools) following the data filtering description in supplementary material (Pansu et al., 2015 Soil Biology and Biochemistry). Direct and reverse reads corresponding to the same sequence were aligned and merged thanks to the IlluminaPairEnd program. Only merged sequences with a high alignment quality score were retained (&gt;=40). Then, the ngsfilter program assigned each merged sequence to its original sample using the tags information previously added to primers. Only sequences containing both primers (with a maximum of 3 mismatches per primer) and exact tag sequences were selected. Sequences containing ambiguous nucleotides or shorter than 55 bp were discarded. Strictly identical sequences were merged together while keeping information about the origin of sequences. Strict singletons (i.e. sequences occurring only once in the dataset) were removed.
DOI: 10.5061/dryad.40jm7/1
title: STEM_probability-of-occurrence

description: Weekly estimates of probability of occurrence for 142 migratory species within 37.5 km radius circles centered on 12 weather surveillance radar stations located in the northeastern USA . Estimates are derived from spatiotemporal exploratory models (STEM) with occurrence information from the eBird citizen science dataset for the combined period 2004 to 2011.
DOI: 10.5061/dryad.40jm7/2
title: WSR_station_reflectivity

description: Daily total effective scattering area (reflectivity) of birds (square centimeters) per unit volume (cubic km) estimated at 12 weather surveillance radar (WSR) stations in the northeastern USA during the autumn of 2010 and 2011 within 37.5 km radius of each WSR station and up to a maximum altitude of 3 km above ground level.
DOI: 10.5061/dryad.43cp5/1
title: Structure input file for Ips typographus

description: Input file for the genetic structure analysis of the European populations of I. typographus by applying the Bayesian procedure implemented in STRUCTURE v2.3.3
DOI: 10.5061/dryad.43cp5/2
title: Aligned sequences

description: Aligned sequences for Ips typographus (COI, EF1a, G6PD, AK, Wg) and for Dendroctonus micans (COI)
DOI: 10.5061/dryad.43cp5/3
title: haplotype composition for individuals of Ips typographus

description: haplotype composition for individuals of Ips typographus (Table S19)
DOI: 10.5061/dryad.573pm/2
title: Alignment of original cpDNA sequences of the Doronicum clusii aggregate (Asteraceae)

description: Alignment (in fasta format) of three concatenated cpDNA regions of the Doronicum clusii aggregate (Asteraceae). The three regions are: ndhF-rpl32 intergenic spacer (positions 1-1099); rpl32-trnL(UAG) intergenic spacer (positions 1100-1959); 3'rps16-5'trnK(UUU) intergenic spacer (positions 1960-2883). Sample names have the following format: Taxon name_population number_individual number.
DOI: 10.5061/dryad.573pm/3
title: Alignment of coded cpDNA sequences of the Doronicum clusii aggregate (Asteraceae)

description: Alignment (in fasta format) of three concatenated cpDNA regions, coded for TCS analysis, of the Doronicum clusii aggregate (Asteraceae). The three regions are: ndhF-rpl32 intergenic spacer (positions 1-1057); rpl32-trnL(UAG) intergenic spacer (positions 1058-1914); 3'rps16-5'trnK(UUU) intergenic spacer (positions 1915-2776). Sample names have the following format: Taxon name_population number_individual number.
DOI: 10.5061/dryad.573pm/4
title: Doronicum_clusii_aggregate_ITS_alignment

description: Alignment (in fasta format) of nuclear ITS sequences of the Doronicum clusii aggregate (Asteraceae). Sample names have the following format: Taxon name_population number_individual number_clone number (clone numbers only for some individuals).
DOI: 10.5061/dryad.6mc8k/1
title: Biomass Density Diversity Ind Biomass main data set

description: Data detailing Biomass, Density, Shannon-Weiner diversity index and Individual Biomass by site, depth and season.
DOI: 10.5061/dryad.6mc8k/2
title: All Sites for calibration

description: Calibration data from four calibration campaigns.
DOI: 10.5061/dryad.6mc8k/3
title: PercentSI

description: Percentage of surface irradiance by site and depth
DOI: 10.5061/dryad.6mc8k/4
title: DailyDose

description: Daily dose of light by site and depth
DOI: 10.5061/dryad.7b5m7/1
title: PerformanceData

description: Performance data from the larval rearing experiments. Each row in the file contains the data for one individual. The columns give the individual number (ind), population (pop), plant treatment (plant), sex, adult weight (weight) whether (1) or not (0) the individual survived (survivorship), and a family number.
DOI: 10.5061/dryad.7b5m7/2
title: Lmelissa1FinalAssembly

description: Draft genome sequence for Lycaeides melissa in fasta format. This assembly was produced by ALLPATHS-LG. It includes 14,029 scaffolds. The assembly report is included as a ReadMe file.
DOI: 10.5061/dryad.7b5m7/3
title: LmelissaAnnotation.tar

description: Compressed directory that contains gff (general feature format) files for each scaffold in the Lycaeides melissa genome assembly. These annotations were generated with the maker pipeline. The maker option file that was used for the annotation is included as a ReadMe file.
DOI: 10.5061/dryad.7b5m7/4
title: filtered_varMelissaAll

description: Compressed vcf (variant call format) file containing the genetic data for the 206,047 single nucleotide variants included in this study. We generated the variant set with samtools and bcftools.
DOI: 10.5061/dryad.7b5m7/6
title: Lmelgenotypes.tar

description: Genotype input files for gemma that were used for polygenic modelling (i.e. association mapping). Genotype files are include for each individual treatment (e.g. GLA by Ms) as well as all of the combined treatments (e.g. GLA regardless of host). Posterior mean genotypes were used.
DOI: 10.5061/dryad.7b5m7/7
title: Lmelphenotypes.tar

description: Phenotype infiles for gemma that were used for polygenic modelling (i.e. association mapping). Adult weight (first column) and survival (second column) are given in each file. Adult weight has been normal quantile transformed.
DOI: 10.5061/dryad.7b5m7/8
title: association (polygenic modelling) results

description: MCMC results from polygenic modelling with gemma for each phenotype and treatment. 10 chains were run for each and all are included (see Ch# in file names). File formats are described in the gemma documentation, which can be found at http://www.xzlab.org/software/GEMMAmanual.pdf.
DOI: 10.5061/dryad.8bf48/1
title: WB_DP_ped

description: ped file with WB and DP individuals
DOI: 10.5061/dryad.8bf48/3
title: WB_DP_structure_infile

description: Structure input file. The four populations correspond to the "Group" column in the file Individuals_info.txt
DOI: 10.5061/dryad.97b50/1
title: BEAST_5k_prune_Trees

description: 5,000 post burn-in trees from the BEAST analysis. Outgroups have been removed.
DOI: 10.5061/dryad.97b50/2
title: BiSSE_unresolved_data

description: Trait data for BiSSE analyses using terminally-unresolved generic-level tree.
DOI: 10.5061/dryad.97b50/3
title: BiSSE_Pruned_BEAST_phylogeny

description: Terminally-unresolved generic-level tree for BiSSE analyses. Outgroups have been removed.
DOI: 10.5061/dryad.97b50/4
title: BayesTraits_3char.data

description: Trait data - 3 character states -for Bayestraits analyses.
DOI: 10.5061/dryad.9fg6p/1
title: camera trap data

description: A dataset of collected by nine below-snow camera traps. See metadata file for detailed description.
DOI: 10.5061/dryad.9fg6p/2
title: snow cover camera traps

description: Records of snow cover at camera trap locations. See metadata file for more detailed description.
DOI: 10.5061/dryad.h77tb/2
title: NZ Stoat Simulation R code

description: This file contains the annotated R code for the mitochondrial genetic drift simulation for the New Zealand stoat population since 1883 - showing the consequences of the founding bottleneck size.
DOI: 10.5061/dryad.h77tb/4
title: Stoat d-loop alignment

description: FASTA file containing the alignment of stoat (Mustela erminea) d-loop sequences from Europe and the haplotypes found in New Zealand (with genbank accession numbers).
DOI: 10.5061/dryad.h77tb/5
title: Sampling location map and coordinates

description: This file contains a map showing the sampling locations and a table providing the coordinates for each location.
DOI: 10.5061/dryad.r6m04/11
title: MESO7.1.fastq
DOI: 10.5061/dryad.r6m04/12
title: MESO6.2.fastq
DOI: 10.5061/dryad.r6m04/13
title: MESO7.2.fastq
DOI: 10.5061/dryad.r6m04/14
title: MESO8.1.fastq
DOI: 10.5061/dryad.r6m04/15
title: MESO9.1.fastq
DOI: 10.5061/dryad.r6m04/16
title: MESO10.1.fastq
DOI: 10.5061/dryad.r6m04/17
title: MESO9.2.fastq
DOI: 10.5061/dryad.r6m04/18
title: MESO11.1.fastq
DOI: 10.5061/dryad.r6m04/19
title: MESO11.2.fastq
DOI: 10.5061/dryad.sd28r/1
title: structure file Genome-wide SNP catalogue in Lagenorhynchus spp

description: Tab Separated Values File in "Structure" format. This file was used to run the software "Admixture". Missing data=0, A=1, C=2, G=3, T=4.
DOI: 10.5061/dryad.sd28r/2
title: vcf file Genome-wide SNP catalogue in Lagenorhynchus spp

description: Variant Call Format (vcf) file containing all the SNPs found within the 113 sampled dolphins (N=40 Lagenorhynchus acutus, white-sided dolphin, and N=73 L.albirostris, white-beaked dolphin).
DOI: 10.5061/dryad.222h3/1
title: Population and Environmental Characteristics

description: The file contains two spreadsheets. The first provides the full dataset of environmental characteristics for all study ponds. The second spreadsheet provides the same data but for the subset of populations included in the common garden experiment. This file also includes the foraging rate of spotted salamanders in the common garden experiment as biomass of zooplankton eaten per day.
DOI: 10.5061/dryad.41m4d/1
title: Visitation network and pollen transport data of the studies used in the analysis

description: Plant-pollinator visitation network data and pollen transport data (including number of pollen grains found on the insects' bodies when swabbed) of the studies used in the analysis. The tabs along the bottom are for each of the 11 studies. Latin names are given. The habitat, sampling design (transect or plot design) and location are given at the top of each spreadsheet.
DOI: 10.5061/dryad.43cp5/4
title: haplotype composition for individuals of Dendroctonus micans

description: haplotype composition for individuals of Dendroctonus micans (Table S20)
DOI: 10.5061/dryad.43cp5/5
title: GenBank accession number associated to each haplotype

description: GenBank accession number associated to each haplotype (Table S18)
DOI: 10.5061/dryad.5rm6d/5
title: Trebouxia clade 'A' ITS alignment

description: Alignment of all Trebouxia ITS sequences belonging to the T. arboricola/gigantea clade
DOI: 10.5061/dryad.5rm6d/6
title: Trebouxia clade 'G' ITS alignment

description: Alignment of all Trebouxia ITS sequences belonging to the T.  galapagensis/usneae clade
DOI: 10.5061/dryad.64687/10
title: LD3_Read2.fastq

description: Raw sequences, Leech diet study, Pool 3, Read 2.
DOI: 10.5061/dryad.64687/5
title: LD1_Read1.fastq

description: Raw sequences, Leech diet study, Pool 1, Read 1.
DOI: 10.5061/dryad.64687/6
title: LD1_Read2.fastq

description: Raw sequences, Leech diet study, Pool 1, Read 2.
DOI: 10.5061/dryad.64687/7
title: LD2_Read1.fastq

description: Raw sequences, Leech diet study, Pool 2, Read 1.
DOI: 10.5061/dryad.64687/8
title: LD2_Read2.fastq

description: Raw sequences, Leech diet study, Pool 2, Read 2.
DOI: 10.5061/dryad.64687/9
title: LD3_Read1.fastq

description: Raw sequences, Leech diet study, Pool 3, Read 1.
DOI: 10.5061/dryad.7b5m7/10
title: scripts.tar

description: Main computer scripts used to analyze the data in this manuscript. This includes the source code for the C++ program used to estimate allele frequencies and genotypes. This compressed directory includes a README file describing each program.
DOI: 10.5061/dryad.7b5m7/9
title: performance data

description: Text file formatted for the phenotypic analyses with R. This file can be read and analyzed the the analyzePheno.R script included with this submission.
DOI: 10.5061/dryad.8bf48/2
title: WB_DP_map

description: map file associated with the ped file
DOI: 10.5061/dryad.8bf48/4
title: Individuals_info

description: Additional information on the individuals analysed
DOI: 10.5061/dryad.8bf48/5
title: README
DOI: 10.5061/dryad.97b50/5
title: BayesTraits_binary.data

description: Trait data - 2 character states -for Bayestraits analyses.
DOI: 10.5061/dryad.97b50/6
title: Diurnality_6gene_data

description: Aligned DNA sequence data in nexus format.
DOI: 10.5061/dryad.97b50/7
title: Diurnality_6gene.part1.Yule

description: Input file for BEAST analyses
DOI: 10.5061/dryad.c030b/1
title: DATA

description: Each row is one sampling point, with its coordinates, and all the associated variables measured. Data file has includes a legend.
DOI: 10.5061/dryad.ct231/1
title: BEAST angio-130

description: MCC tree of the angio-130 analysis with BEAST.
DOI: 10.5061/dryad.ct231/2
title: BEAST angio-140

description: MCC tree of the angio-140 analysis with BEAST.
DOI: 10.5061/dryad.dj6p6/1
title: Female fitness data and D genotype for Iron Mountain M. guttatus (2010-2014)

description: This Excel file includes lifetime female fitness (seedset; 2010-2013), fruit numbers (2010-2013), and flower numbers (2012-2013), as well as LG11 centromere associated drive genotype (D = driver, determined by lb5a marker genotype), for individuals sampled from the Iron Mountain, OR population of Mimulus guttatus. All individuals sampled survived to produce at least 1 fruit, so these data do not include variation in survival to reproduction that may be present in the population.
DOI: 10.5061/dryad.h8972.1
title: Data from: The mating behaviour of the seed shrimp Parapolycope spiralis (Ostracoda: Cladocopina), with insight into the evolution of mating systems in cryptic interstitial habitats
DOI: 10.5061/dryad.h8972.2
title: Data from: The mating behaviour of the seed shrimp Parapolycope spiralis (Ostracoda: Cladocopina), with insight into the evolution of mating systems in cryptic interstitial habitats